1
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Xu R, Jiang Z, Yang Q, Bloino J, Biczysko M. Harmonic and anharmonic vibrational computations for biomolecular building blocks: Benchmarking DFT and basis sets by theoretical and experimental IR spectrum of glycine conformers. J Comput Chem 2024. [PMID: 38682874 DOI: 10.1002/jcc.27377] [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: 02/12/2024] [Revised: 04/01/2024] [Accepted: 04/02/2024] [Indexed: 05/01/2024]
Abstract
Advanced vibrational spectroscopic experiments have reached a level of sophistication that can only be matched by numerical simulations in order to provide an unequivocal analysis, a crucial step to understand the structure-function relationship of biomolecules. While density functional theory (DFT) has become the standard method when targeting medium-size or larger systems, the problem of its reliability and accuracy are well-known and have been abundantly documented. To establish a reliable computational protocol, especially when accuracy is critical, a tailored benchmark is usually required. This is generally done over a short list of known candidates, with the basis set often fixed a priori. In this work, we present a systematic study of the performance of DFT-based hybrid and double-hybrid functionals in the prediction of vibrational energies and infrared intensities at the harmonic level and beyond, considering anharmonic effects through vibrational perturbation theory at the second order. The study is performed for the six-lowest energy glycine conformers, utilizing available "state-of-the-art" accurate theoretical and experimental data as reference. Focusing on the most intense fundamental vibrations in the mid-infrared range of glycine conformers, the role of the basis sets is also investigated considering the balance between computational cost and accuracy. Targeting larger systems, a broad range of hybrid schemes with different computational costs is also tested.
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Affiliation(s)
- Ruiqin Xu
- Department of Physics, College of Sciences, Shanghai University, Shanghai, China
| | | | - Qin Yang
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Prague, Czechia
| | - Julien Bloino
- Classe di Scienze, Scuola Normale Superiore, Pisa, Italy
| | - Malgorzata Biczysko
- Department of Physics, College of Sciences, Shanghai University, Shanghai, China
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2
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Dymińska L, Hanuza J, Janczak J, Ptak M, Lisiecki R. Spectroscopic and optical properties of 1,2,4-triazolo[4,3-a]pyridin-3(2H)-one as a component of herbicides. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 303:123141. [PMID: 37481842 DOI: 10.1016/j.saa.2023.123141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/03/2023] [Accepted: 07/11/2023] [Indexed: 07/25/2023]
Abstract
The herbicides azafenidin [(2-(2,4-dichloro-5-prop-2-ynoxyphenyl)-5,6,7,8-tetrahydro-[1,2,4]triazolo[4,3-a]pyridin-3-one)] and flumetsulam [(N-(2,6-difluorophenyl)-5-methyl-[1,2,4]triazolo[1,5-a]pyrimidine-2-sulfonamide)] were subjected to IR, Raman, UV-Vis and emission studies. As triazolopyridine is the most prominent and active component of these herbicides, this molecule was characterised by XRD studies, FTIR, Raman, UV-Vis and emission spectra. The experimental data were compared to the results of the DFT quantum chemical calculations carried out for its optimised structure, IR intensities and Raman activities, HOMO-LUMO transitions, and energies of the singlet and triplet states. The characteristics for triazolopyridine quantities were used in the analysis of the studied herbicides.
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Affiliation(s)
- Lucyna Dymińska
- Department of Bioorganic Chemistry, Wroclaw University of Economics and Business, Komandorska 118/120, 53-345 Wrocław, Poland.
| | - Jerzy Hanuza
- Institute of Low Temperature and Structure Research, Polish Academy of Sciences, Okólna 2, 50-422 Wrocław, Poland
| | - Jan Janczak
- Institute of Low Temperature and Structure Research, Polish Academy of Sciences, Okólna 2, 50-422 Wrocław, Poland
| | - Maciej Ptak
- Institute of Low Temperature and Structure Research, Polish Academy of Sciences, Okólna 2, 50-422 Wrocław, Poland
| | - Radosław Lisiecki
- Institute of Low Temperature and Structure Research, Polish Academy of Sciences, Okólna 2, 50-422 Wrocław, Poland
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3
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Dalagnol LV, Bettega MHF, Jones NC, Hoffmann SV, Souza Barbosa A, Limão-Vieira P. Electronic State Spectroscopy of Nitromethane and Nitroethane. J Phys Chem A 2023; 127:1445-1457. [PMID: 36730450 PMCID: PMC9940216 DOI: 10.1021/acs.jpca.2c08023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
High-resolution photoabsorption cross-sections in the 3.7-10.8 eV energy range are reinvestigated for nitromethane (CH3NO2), while for nitroethane (C2H5NO2), they are reported for the first time. New absorption features are observed for both molecules which have been assigned to vibronic excitations of valence, Rydberg, and mixed valence-Rydberg characters. In comparison with nitromethane, nitroethane shows mainly broad absorption bands with diffuse structures, which can be interpreted as a result of the side-chain effect contributing to an increased number of internal degrees of freedom. New theoretical quantum chemical calculations performed at the time-dependent density functional theory (TD-DFT) level were used to qualitatively help interpret the recorded photoabsorption spectra. From the photoabsorption cross-sections, photolysis lifetimes in the terrestrial atmosphere have been obtained for both compounds. Relevant internal conversion from Rydberg to valence character is noted for both molecules, while the nuclear dynamics of CH3NO2 and C2H5NO2 along the C-N reaction coordinate have been evaluated through potential energy curves at the TD-DFT level of theory, showing that the pre-dissociative character is more prevalent in nitromethane than in nitroethane.
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Affiliation(s)
- Luiz V.
S. Dalagnol
- Departamento
de Física, Universidade Federal do
Paraná, Caixa
Postal 19044, 81531-980Curitiba, Paraná, Brazil
| | - Márcio H. F. Bettega
- Departamento
de Física, Universidade Federal do
Paraná, Caixa
Postal 19044, 81531-980Curitiba, Paraná, Brazil
| | - Nykola C. Jones
- ISA,
Department of Physics and Astronomy, Aarhus
University, Ny Munkegade
120, DK-8000Aarhus
C, Denmark
| | - Søren V. Hoffmann
- ISA,
Department of Physics and Astronomy, Aarhus
University, Ny Munkegade
120, DK-8000Aarhus
C, Denmark
| | - Alessandra Souza Barbosa
- Departamento
de Física, Universidade Federal do
Paraná, Caixa
Postal 19044, 81531-980Curitiba, Paraná, Brazil,
| | - Paulo Limão-Vieira
- Departamento
de Física, Universidade Federal do
Paraná, Caixa
Postal 19044, 81531-980Curitiba, Paraná, Brazil,Atomic
and Molecular Collisions Laboratory, CEFITEC, Department of Physics,
NOVA School of Science and Technology, Universidade
NOVA de Lisboa, 2829-516Caparica, Portugal,
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4
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Carvalho JR, Vidal LN. Calculation of absolute Raman scattering cross-sections using vibrational self-consistent field/vibrational configuration interaction wave functions. J Comput Chem 2022; 43:1484-1494. [PMID: 35731622 DOI: 10.1002/jcc.26951] [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: 04/18/2022] [Revised: 05/21/2022] [Accepted: 06/02/2022] [Indexed: 11/12/2022]
Abstract
In the present study, the differential scattering cross-sections, depolarization ratios and Raman shifts of small molecular systems are obtained from configuration iteration wave functions of vibrational self-consistent field (VSCF) states. The transition polarizabilities were modeled using the Placzek approximation, neglecting those contributions not arising from the electric dipole mechanism. This theoretical approach is considered a good approximation for samples that absorb in the UV range if the excitation radiation falls in the visible region, as is the case of the molecules selected for the present study, namely: water, methane, and acetylene. Potential energy and electronic polarizability surfaces are calculated by the CCSD(T) and CC3 methods with aug-cc-p(C)V(T,Q,5)Z basis sets. The vibrational Hamiltonian includes the vibrational angular momentum contribution of the Watson kinetic energy operator. As expected, due to the variational nature of the VSCF and vibrational configuration interaction (VCI) methods, the Raman transition wavenumbers are substantially improved over the harmonic predictions. Surprisingly, the scattering cross-sections obtained using the harmonic approximation or the VSCF method better agrees with the experimental values than those cross-sections predicted using VCI wave functions. The more significant deviations of the VCI results from the experimental reference may be related to the significant uncertainties of the measured cross-sections. Still, it may also indicate that the VCI Raman transition moments may require a more accurate description of the electronic polarizability surface. Finally, the depolarization ratios calculated for H2 O and C2 D2 using harmonic and VCI wave functions have similar accuracy, whereas, for C2 H2 and C2 HD, the VCI results are more accurate.
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Affiliation(s)
- Jhonatas R Carvalho
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Luciano N Vidal
- Departamento Acadêmico de Química e Biologia, Universidade Tecnológica Federal do Paraná, Curitiba, Paraná, Brazil
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5
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Raj A, Chao YB, Witek HA. Testing the limitations of harmonic approximation in the determination of Raman intensities. Mol Phys 2022. [DOI: 10.1080/00268976.2022.2069613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Ankit Raj
- Department of Applied Chemistry and Institute of Molecular Science, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Yen-Bang Chao
- Department of Applied Chemistry and Institute of Molecular Science, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Henryk A. Witek
- Department of Applied Chemistry and Institute of Molecular Science, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
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6
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Noble BB, Todorova N, Yarovsky I. Electromagnetic bioeffects: a multiscale molecular simulation perspective. Phys Chem Chem Phys 2022; 24:6327-6348. [PMID: 35245928 DOI: 10.1039/d1cp05510k] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Electromagnetic bioeffects remain an enigma from both the experimental and theoretical perspectives despite the ubiquitous presence of related technologies in contemporary life. Multiscale computational modelling can provide valuable insights into biochemical systems and predict how they will be perturbed by external stimuli. At a microscopic level, it can be used to determine what (sub)molecular scale reactions various stimuli might induce; at a macroscopic level, it can be used to examine how these changes affect dynamic behaviour of essential molecules within the crowded biomolecular milieu in living tissues. In this review, we summarise and evaluate recent computational studies that examined the impact of externally applied electric and electromagnetic fields on biologically relevant molecular systems. First, we briefly outline the various methodological approaches that have been employed to study static and oscillating field effects across different time and length scales. The practical value of such modelling is then illustrated through representative case-studies that showcase the diverse effects of electric and electromagnetic field on the main physiological solvent - water, and the essential biomolecules - DNA, proteins, lipids, as well as some novel biomedically relevant nanomaterials. The implications and relevance of the theoretical multiscale modelling to practical applications in therapeutic medicine are also discussed. Finally, we summarise ongoing challenges and potential opportunities for theoretical modelling to advance the current understanding of electromagnetic bioeffects for their modulation and/or beneficial exploitation in biomedicine and industry.
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Affiliation(s)
- Benjamin B Noble
- School of Engineering, RMIT University, GPO Box 2476, Melbourne, Australia. .,Australian Centre for Electromagnetic Bioeffects Research, Australia
| | - Nevena Todorova
- School of Engineering, RMIT University, GPO Box 2476, Melbourne, Australia. .,Australian Centre for Electromagnetic Bioeffects Research, Australia
| | - Irene Yarovsky
- School of Engineering, RMIT University, GPO Box 2476, Melbourne, Australia. .,Australian Centre for Electromagnetic Bioeffects Research, Australia
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7
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Crișan G, Macea AM, Andrieș G, Chiș V. Experimental and computational Raman spectroscopies applied to 2-methoxy-2-methylpropylisonitrile (MIBI) ligand of the 99mTc-sestamibi radiopharmaceutical. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.131159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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8
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Dundas KHM, Beerepoot MTP, Ringholm M, Reine S, Bast R, List NH, Kongsted J, Ruud K, Olsen JMH. Harmonic Infrared and Raman Spectra in Molecular Environments Using the Polarizable Embedding Model. J Chem Theory Comput 2021; 17:3599-3617. [PMID: 34009969 PMCID: PMC8278393 DOI: 10.1021/acs.jctc.0c01323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Indexed: 12/14/2022]
Abstract
We present a fully analytic approach to calculate infrared (IR) and Raman spectra of molecules embedded in complex molecular environments modeled using the fragment-based polarizable embedding (PE) model. We provide the theory for the calculation of analytic second-order geometric derivatives of molecular energies and first-order geometric derivatives of electric dipole moments and dipole-dipole polarizabilities within the PE model. The derivatives are implemented using a general open-ended response theory framework, thus allowing for an extension to higher-order derivatives. The embedding-potential parameters used to describe the environment in the PE model are derived through first-principles calculations, thus allowing a wide variety of systems to be modeled, including solvents, proteins, and other large and complex molecular environments. Here, we present proof-of-principle calculations of IR and Raman spectra of acetone in different solvents. This work is an important step toward calculating accurate vibrational spectra of molecules embedded in realistic environments.
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Affiliation(s)
- Karen
Oda Hjorth Minde Dundas
- Hylleraas
Centre for Quantum Molecular Sciences, Department of Chemistry, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Maarten T. P. Beerepoot
- Hylleraas
Centre for Quantum Molecular Sciences, Department of Chemistry, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Magnus Ringholm
- Hylleraas
Centre for Quantum Molecular Sciences, Department of Chemistry, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Simen Reine
- Hylleraas
Centre for Quantum Molecular Sciences, Department of Chemistry, University of Oslo, N-0315 Oslo, Norway
| | - Radovan Bast
- Department
of Information Technology, UiT The Arctic
University of Norway, N-9037 Tromsø, Norway
| | - Nanna Holmgaard List
- Department
of Chemistry and the PULSE Institute, Stanford
University, 94305 Stanford, California, United States
- SLAC
National Accelerator Laboratory, 94025 Menlo Park, California, United States
| | - Jacob Kongsted
- Department
of Physics, Chemistry and Pharmacy, University
of Southern Denmark, DK-5230 Odense M, Denmark
| | - Kenneth Ruud
- Hylleraas
Centre for Quantum Molecular Sciences, Department of Chemistry, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Jógvan Magnus Haugaard Olsen
- Hylleraas
Centre for Quantum Molecular Sciences, Department of Chemistry, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
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9
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Barone V, Alessandrini S, Biczysko M, Cheeseman JR, Clary DC, McCoy AB, DiRisio RJ, Neese F, Melosso M, Puzzarini C. Computational molecular spectroscopy. ACTA ACUST UNITED AC 2021. [DOI: 10.1038/s43586-021-00034-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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10
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Richter WE, Duarte LJ, Vidal LN, Bruns RE. AC/DC Analysis: Broad and Comprehensive Approach to Analyze Infrared Intensities at the Atomic Level. J Phys Chem A 2021; 125:3219-3229. [PMID: 33847496 DOI: 10.1021/acs.jpca.1c01314] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
We present a complete theoretical protocol to partition infrared intensities into terms owing to individual atoms by two different but related approaches: the atomic contributions (ACs) show how the entire molecular vibrational motion affects the electronic structure of a single atom and the total infrared intensity. On the other hand, the dynamic contributions (DCs) show how the displacement of a single atom alters the electronic structure of the entire molecule and the total intensity. The two analyses are complementary ways of partitioning the same total intensity and conserve most of the features of the total intensity itself. Combined, they are called the AC/DC analysis. These can be further partitioned following the CCTDP (or CCT) models according to the population analysis chosen by the researcher. The main conceptual features of the equations are highlighted, and representative numerical results are shown to support the interpretation of the equations. The results are invariant to rotation and translation and can readily be extended to molecules of any size, shape, or symmetry. Although the AC/DC analysis requires the choice of a charge model, all charge models that correctly reproduce the total molecular dipole moment can be used. A fully automated protocol managed by the Placzek program is made available, free of charge and with input examples.
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Affiliation(s)
- Wagner E Richter
- Department of Chemical Engineering, Federal University of Technology-Paraná, Ponta Grossa, Paraná 81280-340, Brazil
| | - Leonardo J Duarte
- Institute of Chemistry, State University of Campinas, Campinas, São Paulo 13081-970, Brazil
| | - Luciano N Vidal
- Department of Chemistry and Biology, Federal University of Technology-Paraná, Ponta Grossa, Paraná 81280-340, Brazil
| | - Roy E Bruns
- Institute of Chemistry, State University of Campinas, Campinas, São Paulo 13081-970, Brazil
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11
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Mattiat J, Luber S. Time Domain Simulation of (Resonance) Raman Spectra of Liquids in the Short Time Approximation. J Chem Theory Comput 2020; 17:344-356. [DOI: 10.1021/acs.jctc.0c00755] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Johann Mattiat
- Department of Chemistry, University of Zurich, Zurich 8057, Switzerland
| | - Sandra Luber
- Department of Chemistry, University of Zurich, Zurich 8057, Switzerland
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12
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Lam J, Abdul-Al S, Allouche AR. Combining Quantum Mechanics and Machine-Learning Calculations for Anharmonic Corrections to Vibrational Frequencies. J Chem Theory Comput 2020; 16:1681-1689. [DOI: 10.1021/acs.jctc.9b00964] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Julien Lam
- Center for Nonlinear Phenomena and Complex Systems, Code Postal 231, Université Libre de Bruxelles, Boulevard du Triomphe, 1050 Brussels, Belgium
| | - Saleh Abdul-Al
- Lebanese International University, Bekaa, Lebanon and International University of Beirut, Beirut, Lebanon
| | - Abdul-Rahman Allouche
- Institut Lumière Matière, UMR5306 Université Lyon 1-CNRS, Université de Lyon, 69622 Villeurbanne Cedex, France
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13
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Walter M, Moseler M. Ab Initio Wavelength-Dependent Raman Spectra: Placzek Approximation and Beyond. J Chem Theory Comput 2019; 16:576-586. [DOI: 10.1021/acs.jctc.9b00584] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Michael Walter
- Fraunhofer IWM, MikroTribologie Centrum μTC, Wöhlerstrasse 11, D-79108 Freiburg, Germany
- FIT Freiburg Centre for Interactive Materials and Bioinspired Technologies, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
- Cluster of Excellence livMatS @ FIT − Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, D-79110 Freiburg, Germany
| | - Michael Moseler
- Fraunhofer IWM, MikroTribologie Centrum μTC, Wöhlerstrasse 11, D-79108 Freiburg, Germany
- Cluster of Excellence livMatS @ FIT − Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, D-79110 Freiburg, Germany
- Physikalisches Institut, Universität Freiburg, Herrmann-Herder-Straße 3, D-79104 Freiburg, Germany
- Freiburger Materialforschungszentrum, Universität Freiburg, Stefan-Meier-Straße 21, D-79104 Freiburg, Germany
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14
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Pietropolli Charmet A, Cornaton Y. Benchmarking fully analytic DFT force fields for vibrational spectroscopy: A study on halogenated compounds. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2018.01.089] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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15
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Cornaton Y, Ringholm M, Ruud K. Complete analytic anharmonic hyper-Raman scattering spectra. Phys Chem Chem Phys 2018; 18:22331-42. [PMID: 27459194 DOI: 10.1039/c6cp03463b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present the first computational treatment of the complete second-order vibrational perturbation theory applied to hyper-Raman scattering spectroscopy. The required molecular properties are calculated in a fully analytic manner using a recently developed program [Ringholm, Jonsson and Ruud, J. Comp. Chem., 2014, 35, 622] that utilizes recursive routines. For some of the properties, these calculations are the first analytic calculations of their kind at their respective levels of theory. We apply this approach to the calculation of the hyper-Raman spectra of methane, ethane and ethylene and compare these to available experimental data. We show that the anharmonic corrections have a larger effect on the vibrational frequencies than on the spectral intensities, but that the inclusion of combination and overtone bands in the anharmonic treatment can improve the agreement with the experimental data, although the quality of available experimental data limits a detailed comparison.
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Affiliation(s)
- Yann Cornaton
- Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Tromsø-The Arctic University of Norway, N-9037 Tromsø, Norway.
| | - Magnus Ringholm
- Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Tromsø-The Arctic University of Norway, N-9037 Tromsø, Norway.
| | - Kenneth Ruud
- Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Tromsø-The Arctic University of Norway, N-9037 Tromsø, Norway.
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16
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Viana RB. On the structure of the simplest triselenide compound model and the stabilizing effect of water molecules. Polyhedron 2017. [DOI: 10.1016/j.poly.2017.03.029] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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17
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Banik S, Ravichandran L, Durga Prasad M. Raman spectral calculation by vibrational coupled-cluster method in bosonic representation. Mol Phys 2017. [DOI: 10.1080/00268976.2017.1321153] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Subrata Banik
- Advanced Center for Research in High Energy Materials, University of Hyderabad, Hyderabad, India
| | | | - M. Durga Prasad
- Advanced Center for Research in High Energy Materials, University of Hyderabad, Hyderabad, India
- School of Chemistry, University of Hyderabad, Hyderabad, India
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18
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Szczepaniak M, Moc J. Cyanoform and Its Isomers. Relative Stabilities, Spectroscopic Features, and Rearrangements by Coupled Cluster and MCSCF-Based Methods. J Phys Chem A 2017; 121:1319-1327. [PMID: 28094531 DOI: 10.1021/acs.jpca.6b10951] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Although an isolation of elusive tricyanomethane HC(CN)3 was recently reported, the existence of other HC4N3 species has yet to be confirmed. In this work, the relative stabilities, spectroscopic features, and rearrangements of tricyanomethane and its four isomers are examined using single- (CCSD(T), CCSD(T)-F12) and multireference (MCSCF, MRPT2) methods. Tricyanomethane and dicyanoketenimine (NC)2CCNH, which are found to be the two most stable HC4N3 isomers lying within 9 kcal/mol, can be discriminated by their spectroscopic parameters. The predicted stepwise interconversion path relating HC(CN)3 and (NC)2CCNH features the HC4N3 species comprising the C-C-N ring moiety, with the largest barrier being associated with the initial H migration to one of the CN carbons. Adding a water molecule reduces the H migration barrier strongly and makes it possible to interconvert tricyanomethane to dicyanoketenimine in a "concerted" way.
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Affiliation(s)
- Marek Szczepaniak
- Faculty of Chemistry, Wroclaw University , F. Joliot-Curie 14, 50-383 Wroclaw, Poland
| | - Jerzy Moc
- Faculty of Chemistry, Wroclaw University , F. Joliot-Curie 14, 50-383 Wroclaw, Poland
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19
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Panek PT, Jacob CR. On the benefits of localized modes in anharmonic vibrational calculations for small molecules. J Chem Phys 2017; 144:164111. [PMID: 27131535 DOI: 10.1063/1.4947213] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Anharmonic vibrational calculations can already be computationally demanding for relatively small molecules. The main bottlenecks lie in the construction of the potential energy surface and in the size of the excitation space in the vibrational configuration interaction (VCI) calculations. To address these challenges, we use localized-mode coordinates to construct potential energy surfaces and perform vibrational self-consistent field and L-VCI calculations [P. T. Panek and C. R. Jacob, ChemPhysChem 15, 3365 (2014)] for all vibrational modes of two prototypical test cases, the ethene and furan molecules. We find that the mutual coupling between modes is reduced when switching from normal-mode coordinates to localized-mode coordinates. When using such localized-mode coordinates, we observe a faster convergence of the n-mode expansion of the potential energy surface. This makes it possible to neglect higher-order contributions in the n-mode expansion of the potential energy surface or to approximate higher-order contributions in hybrid potential energy surfaces, which reduced the computational effort for the construction of the anharmonic potential energy surface significantly. Moreover, we find that when using localized-mode coordinates, the convergence with respect to the VCI excitation space proceeds more smoothly and that the error at low orders is reduced significantly. This makes it possible to devise low-cost models for obtaining a first approximation of anharmonic corrections. This demonstrates that the use of localized-mode coordinates can be beneficial already in anharmonic vibrational calculations of small molecules and provides a possible avenue for enabling such accurate calculations also for larger molecules.
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Affiliation(s)
- Paweł T Panek
- TU Braunschweig, Institute of Physical and Theoretical Chemistry, Hans-Sommer-Str. 10, 38106 Braunschweig, Germany
| | - Christoph R Jacob
- TU Braunschweig, Institute of Physical and Theoretical Chemistry, Hans-Sommer-Str. 10, 38106 Braunschweig, Germany
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Anelli M, Ringholm M, Ruud K. Gauge-origin independent calculations of electric-field-induced second-harmonic generation circular intensity difference using London atomic orbitals. Mol Phys 2016. [DOI: 10.1080/00268976.2016.1249979] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Marco Anelli
- Center for Theoretical and Computational Chemistry (CTCC), Department of Chemistry, University of Tromsø, Tromsø, Norway
| | - Magnus Ringholm
- Center for Theoretical and Computational Chemistry (CTCC), Department of Chemistry, University of Tromsø, Tromsø, Norway
| | - Kenneth Ruud
- Center for Theoretical and Computational Chemistry (CTCC), Department of Chemistry, University of Tromsø, Tromsø, Norway
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