1
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Dall’Osto G, Corni S. Time Resolved Raman Scattering of Molecules: A Quantum Mechanics Approach with Stochastic Schroedinger Equation. J Phys Chem A 2022; 126:8088-8100. [PMID: 36278928 PMCID: PMC9639147 DOI: 10.1021/acs.jpca.2c05245] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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Raman scattering is a very powerful tool employed to
characterize
molecular systems. Here we propose a novel theoretical strategy to
calculate the Raman cross-section in time domain, by computing the
cumulative Raman signal emitted during the molecular evolution in
time. Our model is based on a numerical propagation of the vibronic
wave function under the effect of a light pulse of arbitrary shape.
This approach can therefore tackle a variety of experimental setups.
Both resonance and nonresonance Raman scattering can be retrieved,
and also the time-dependent fluorescence emission is computed. The
model has been applied to porphyrin considering both resonance and
nonresonance conditions and varying the incident field duration. Moreover
the effect of the vibrational relaxation, which should be taken into
account when its time scale is similar to that of the Raman emission,
has been included through the stochastic Schroedinger equation approach.
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Affiliation(s)
- Giulia Dall’Osto
- Department of Chemical Sciences, University of Padova, via Marzolo 1, Padova, 35131, Italy
| | - Stefano Corni
- Department of Chemical Sciences, University of Padova, via Marzolo 1, Padova, 35131, Italy
- CNR Institute of Nanoscience, via Campi 213/A, Modena, 41125, Italy
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2
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Hanson-Heine MWD. Static Electron Correlation in Anharmonic Molecular Vibrations: A Hybrid TAO-DFT Study. J Phys Chem A 2022; 126:7273-7282. [PMID: 36164938 PMCID: PMC9574917 DOI: 10.1021/acs.jpca.2c05881] [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: 01/07/2023]
Abstract
Hybrid thermally-assisted-occupation density functional theory is used to examine the effects of static electron correlation on the prediction of a benchmark set of experimentally observed molecular vibrational frequencies. The B3LYP and B97-1 thermally-assisted-occupation measure of static electron correlation is important for describing the vibrations of many of the molecules that make up several popular test sets of experimental data. Shifts are seen for known multireference systems and for many molecules containing atoms from the second row of the periodic table of elements. Several molecules only show significant shifts in select vibrational modes, and significant improvements are seen for the prediction of hydrogen stretching frequencies throughout the test set.
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3
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Effects of non-local exchange functionals in the density functional theories for the description of molecular vibrations. J CHEM SCI 2022. [DOI: 10.1007/s12039-022-02061-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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4
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Ravichandran L, Banik S. Investigation of the Failure of the MP2 Method to Describe the Out-of-Plane Bending Motions of Carbon-Carbon Double-Bonded Molecules: The Role of Atomic Orbitals. J Phys Chem A 2021; 125:9298-9317. [PMID: 34666490 DOI: 10.1021/acs.jpca.1c06336] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a detailed study on the role of atomic orbitals in the unphysical description of the out-of-plane bending (OOPB) vibrations with the MP2 method. The anharmonicities of the OOPB vibrations are found to be unphysically large for several basis sets with the MP2 method. We find that the inclusion of additional valence s and p orbitals to the basis set leads to the lowering of π* orbitals' energies along with the generation of several spurious low-energy virtual molecular orbitals (VMOs). Such erroneous VMOs create a disbalance between the σ and π correlations for the planar structure of the molecules. Since the OOPB vibrations distort the π* orbitals, the disbalance in the σ and π correlations leads to errors in the derivatives of the correlation energy with respect to the displacement along with OOPB modes. The diffuse functions in the basis set enhance the unphysical anharmonicities of the OOPB modes since these functions are of s- and p-type atomic orbitals. The polarization atomic orbitals of higher angular momentum improve the description of the π* orbitals and thereby reduce the disbalance between the σ and π correlations in the MP2 calculations. We find that the unphysical frequencies for the OOPB modes are significantly eliminated with the d and f orbitals on the C atoms in the basis set.
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Affiliation(s)
| | - Subrata Banik
- Department of Chemistry, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, Tamil Nadu 613401, India
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5
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Yadav S, Banik S, Prasad MD. Understanding of the C-H stretch region of infra-red spectroscopy: an analysis of the final state wavefunctions. Phys Chem Chem Phys 2021; 23:9176-9188. [PMID: 33885051 DOI: 10.1039/d0cp01157f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The nature of the wavefunctions associated with the final states in the CH stretching region of several medium sized molecules is analysed. The number of optically bright transitions is much larger than the number of CH oscillators present in the molecule, and they are spread over a range of about 300 cm-1. Several of them are clustered together within about 5 cm-1 with near equal intensities. The final states of all these transitions are superpositions of multiple zeroth order states. In almost all of such superpositions, no single zeroth order state has more than 50% weight. Several multiquantum states, with three to four quanta of excitation dominate the final states, with the CH chromophore contributing only a small weightage. Thus the band structure of the CH stretch region is due to several optically bright transitions whose final states are superpositions of low frequency multiquantum states with the CH chromophore contributing only a small weight to make them spectroscopically active.
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Affiliation(s)
- Swati Yadav
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India.
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6
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Mitra H, Roy TK. Comprehensive Benchmark Results for the Accuracy of Basis Sets for Anharmonic Molecular Vibrations. J Phys Chem A 2020; 124:9203-9221. [DOI: 10.1021/acs.jpca.0c06634] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hrishit Mitra
- Department of Chemistry and Chemical Sciences, Central University of Jammu, Rahya-Suchani (Bagla), Jammu, Jammu and Kashmir 181143, India
| | - Tapta Kanchan Roy
- Department of Chemistry and Chemical Sciences, Central University of Jammu, Rahya-Suchani (Bagla), Jammu, Jammu and Kashmir 181143, India
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7
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Erfort S, Tschöpe M, Rauhut G. Toward a fully automated calculation of rovibrational infrared intensities for semi-rigid polyatomic molecules. J Chem Phys 2020; 152:244104. [DOI: 10.1063/5.0011832] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Sebastian Erfort
- Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Martin Tschöpe
- Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Guntram Rauhut
- Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
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8
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Hope M, Šebestík J, Kapitán J, Bouř P. Understanding CH-Stretching Raman Optical Activity in Ala–Ala Dipeptides. J Phys Chem A 2020; 124:674-683. [DOI: 10.1021/acs.jpca.9b10557] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marius Hope
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610 Prague, Czech Republic
- Norwegian University of Science and Technology NO-7491 Trondheim, Norway
| | - Jaroslav Šebestík
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610 Prague, Czech Republic
| | - Josef Kapitán
- Department of Optics, Palacký University, 17. listopadu 12, 77146 Olomouc, Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610 Prague, Czech Republic
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9
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Sibert EL. Modeling vibrational anharmonicity in infrared spectra of high frequency vibrations of polyatomic molecules. J Chem Phys 2019; 150:090901. [DOI: 10.1063/1.5079626] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Edwin L. Sibert
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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10
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Roy TK, Kopysov V, Pereverzev A, Šebek J, Gerber RB, Boyarkin OV. Intrinsic structure of pentapeptide Leu-enkephalin: geometry optimization and validation by comparison of VSCF-PT2 calculations with cold ion spectroscopy. Phys Chem Chem Phys 2018; 20:24894-24901. [PMID: 30234204 DOI: 10.1039/c8cp03989e] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The intrinsic structure of an opioid peptide [Ala2, Leu5]-leucine enkephalin (ALE) has been investigated using first-principles based vibrational self-consistent field (VSCF) theory and cold ion spectroscopy. IR-UV double resonance spectroscopy revealed the presence of only one highly abundant conformer of the singly protonated ALE, isolated and cryogenically cooled in the gas phase. High-level quantum mechanical calculations of electronic structures in conjunction with a systematic conformational search allowed for finding a few low-energy candidate structures. In order to identify the observed structure, we computed vibrational spectra of the candidate structures and employed the theory at the semi-empirically scaled harmonic level and at the first-principles based anharmonic VSCF levels. The best match between the calculated "anharmonic" and the measured spectra appeared, indeed, for the most stable candidate. An average of two spectra calculated with different quantum mechanical potentials is proposed for the best match with experiment. The match thus validates the calculated intrinsic structure of ALE and demonstrates the predictive power of first-principles theory for solving structures of such large molecules.
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Affiliation(s)
- Tapta Kanchan Roy
- Department of Chemistry and Chemical Sciences, Central University of Jammu, Rahya-Suchani (Bagla), Jammu 181143, India
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11
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Hanson-Heine MW, Calladine JA, Yang J, Towrie M, Horvath R, Besley NA, George MW. A combined time-resolved infrared and density functional theory study of the lowest excited states of 9-fluorenone and 2-naphthaldehyde. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2018.04.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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12
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Morzan UN, Alonso de Armiño DJ, Foglia NO, Ramírez F, González Lebrero MC, Scherlis DA, Estrin DA. Spectroscopy in Complex Environments from QM–MM Simulations. Chem Rev 2018; 118:4071-4113. [DOI: 10.1021/acs.chemrev.8b00026] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Uriel N. Morzan
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Diego J. Alonso de Armiño
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Nicolás O. Foglia
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Francisco Ramírez
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Mariano C. González Lebrero
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Damián A. Scherlis
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Darío A. Estrin
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
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13
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Ravichandran L, Banik S. Performance of different density functionals for the calculation of vibrational frequencies with vibrational coupled cluster method in bosonic representation. Theor Chem Acc 2017. [DOI: 10.1007/s00214-017-2177-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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14
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Spectroscopic Characterization of Key Aromatic and Heterocyclic Molecules: A Route toward the Origin of Life. ACTA ACUST UNITED AC 2017; 154. [DOI: 10.3847/1538-3881/aa7d54] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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15
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Wang J. Ultrafast two-dimensional infrared spectroscopy for molecular structures and dynamics with expanding wavelength range and increasing sensitivities: from experimental and computational perspectives. INT REV PHYS CHEM 2017. [DOI: 10.1080/0144235x.2017.1321856] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Jianping Wang
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, The Chinese Academy of Sciences, Beijing, P.R. China
- College of Chemistry, University of Chinese Academy of Sciences, Beijing, P.R. China
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16
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Shiekh BA, Kaur D, Seth B, Mahajan S. The theoretical-cum-statistical approach for the investigation of reaction NO2+ O(3P) → NO + O2 using SCTST and a full anharmonic VPT2 model. Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2016.08.058] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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17
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On the choice electronic structure method to calculate the quartic potential energy surface for the vibrational calculation of polyatomic molecules. Theor Chem Acc 2016. [DOI: 10.1007/s00214-016-1962-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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18
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The role of torsional motion on the properties of propiolic acid and its H/D isotopic analogs: A density functional study using SCTST and a full anharmonic VPT2 model. Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2016.01.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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19
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Barone V, Cimino P, Stendardo E. Development and Validation of the B3LYP/N07D Computational Model for Structural Parameter and Magnetic Tensors of Large Free Radicals. J Chem Theory Comput 2015; 4:751-64. [PMID: 26621090 DOI: 10.1021/ct800034c] [Citation(s) in RCA: 213] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Extensive calculations on a large set of free radicals containing atoms of the second and third row show that the B3LYP/N07D computational model provides remarkably accurate structural parameters and magnetic tensors at reasonable computational costs. The key of this success is the optimization of core-valence s functions for hyperfine coupling constants, while retaining (and even improving) the good performances of the parent 6-31+G(d,p) basis set for valence properties through reoptimization of polarization and diffuse p functions.
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Affiliation(s)
- Vincenzo Barone
- LSDM and INSTM-Village, Dipartimento di Chimica 'Paolo Corradini', Complesso Universitario Monte S. Angelo, via Cintia, I-80126 Napoli, Italy
| | - Paola Cimino
- LSDM and INSTM-Village, Dipartimento di Chimica 'Paolo Corradini', Complesso Universitario Monte S. Angelo, via Cintia, I-80126 Napoli, Italy
| | - Emiliano Stendardo
- LSDM and INSTM-Village, Dipartimento di Chimica 'Paolo Corradini', Complesso Universitario Monte S. Angelo, via Cintia, I-80126 Napoli, Italy
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20
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Cappelli C, Monti S, Scalmani G, Barone V. On the Calculation of Vibrational Frequencies for Molecules in Solution Beyond the Harmonic Approximation. J Chem Theory Comput 2015; 6:1660-9. [PMID: 26615698 DOI: 10.1021/ct100048g] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report some results on the calculation of vibrational spectra of molecules in condensed phase with accounting simultaneously for anharmonicity and solute-solvent interactions, the latter being described by means of the polarizable continuum model (PCM). Density functional theory force fields are employed as well as a new implementation of the PCM cavity and its derivatives. The results obtained for formaldehyde and simple peptide prototypes show that our approach is able to yield a quantitative agreement with experiments for vacuo-to-solvent harmonic and anharmonic frequency shifts.
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Affiliation(s)
- Chiara Cappelli
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Risorgimento 35, I-56126 Pisa, Italy, Istituto per i Processi Chimico-Fisici del Consiglio Nazionale delle Ricerche, via Moruzzi,1 I-56124 Pisa, Italy, Gaussian, Inc., 340 Quinnipiac Street, Building 40, Wallingford, Connecticut 06492, and Scuola Normale Superiore, Piazza dei Cavalieri, 7 I-56126 Pisa, Italy
| | - Susanna Monti
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Risorgimento 35, I-56126 Pisa, Italy, Istituto per i Processi Chimico-Fisici del Consiglio Nazionale delle Ricerche, via Moruzzi,1 I-56124 Pisa, Italy, Gaussian, Inc., 340 Quinnipiac Street, Building 40, Wallingford, Connecticut 06492, and Scuola Normale Superiore, Piazza dei Cavalieri, 7 I-56126 Pisa, Italy
| | - Giovanni Scalmani
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Risorgimento 35, I-56126 Pisa, Italy, Istituto per i Processi Chimico-Fisici del Consiglio Nazionale delle Ricerche, via Moruzzi,1 I-56124 Pisa, Italy, Gaussian, Inc., 340 Quinnipiac Street, Building 40, Wallingford, Connecticut 06492, and Scuola Normale Superiore, Piazza dei Cavalieri, 7 I-56126 Pisa, Italy
| | - Vincenzo Barone
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Risorgimento 35, I-56126 Pisa, Italy, Istituto per i Processi Chimico-Fisici del Consiglio Nazionale delle Ricerche, via Moruzzi,1 I-56124 Pisa, Italy, Gaussian, Inc., 340 Quinnipiac Street, Building 40, Wallingford, Connecticut 06492, and Scuola Normale Superiore, Piazza dei Cavalieri, 7 I-56126 Pisa, Italy
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21
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Quantum chemical calculations and analysis of FTIR, FT–Raman and UV–Vis spectra of temozolomide molecule. J Mol Struct 2015. [DOI: 10.1016/j.molstruc.2015.07.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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22
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Krasnoshchekov SV, Craig NC, Boopalachandran P, Laane J, Stepanov NF. Anharmonic Vibrational Analysis of the Infrared and Raman Gas-Phase Spectra of s-trans- and s-gauche-1,3-Butadiene. J Phys Chem A 2015; 119:10706-23. [DOI: 10.1021/acs.jpca.5b07650] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Norman C. Craig
- Department of Chemistry and Biochemistry, Oberlin College, Oberlin, Ohio 44074, United States
| | | | - Jaan Laane
- Department of Chemistry, Texas A&M University, College Station, Texas 77843-3255, United States
| | - Nikolay F. Stepanov
- Lomonosov Moscow State University, Leninskiye Gory, 119991, Moscow, Russian Federation
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23
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Krasnoshchekov SV, Vogt N, Stepanov NF. Ab Initio Anharmonic Analysis of Vibrational Spectra of Uracil Using the Numerical-Analytic Implementation of Operator Van Vleck Perturbation Theory. J Phys Chem A 2015; 119:6723-37. [DOI: 10.1021/acs.jpca.5b03241] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sergey V. Krasnoshchekov
- Lomonosov Moscow State University, Leninskiye Gory, 119991, Moscow, Russian Federation
- Chemieinformationssysteme, Universität Ulm, Albert Einstein Allee 47, D-89069 Ulm, Germany
| | - Natalja Vogt
- Lomonosov Moscow State University, Leninskiye Gory, 119991, Moscow, Russian Federation
- Chemieinformationssysteme, Universität Ulm, Albert Einstein Allee 47, D-89069 Ulm, Germany
| | - Nikolay F. Stepanov
- Lomonosov Moscow State University, Leninskiye Gory, 119991, Moscow, Russian Federation
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24
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Oschetzki D, Rauhut G. Pushing the limits in accurate vibrational structure calculations: anharmonic frequencies of lithium fluoride clusters (LiF)n, n = 2-10. Phys Chem Chem Phys 2015; 16:16426-35. [PMID: 24981078 DOI: 10.1039/c4cp02264e] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The vibrational spectra of a series of small lithium fluoride clusters, i.e. (LiF)n, n = 2-10, were studied by vibrational configuration interaction (VCI) calculations relying on potential energy surfaces including three-mode coupling terms and being obtained from explicitly correlated local coupled cluster calculations. Due to the account for anharmonicity effects, the simulated spectra allow for a direct comparison with experimental data and may thus help to identify clusters in the experiments. Even structurally closely related clusters can clearly be distinguished by infrared spectroscopy. The largest system in this study required more than 1000 basis functions in the electronic structure calculations and more than 10(7) configurations in the vibrational structure calculations and became computationally feasible only due to a combination of different approximations and highly parallelized algorithms.
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Affiliation(s)
- Dominik Oschetzki
- Institute of Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, Stuttgart D-70569, Germany.
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25
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Fornaro T, Burini D, Biczysko M, Barone V. Hydrogen-Bonding Effects on Infrared Spectra from Anharmonic Computations: Uracil–Water Complexes and Uracil Dimers. J Phys Chem A 2015; 119:4224-36. [DOI: 10.1021/acs.jpca.5b01561] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Teresa Fornaro
- Scuola Normale Superiore, Piazza
dei Cavalieri 7, I-56126 Pisa, Italy
| | - Diletta Burini
- Dipartimento
di Matematica e Informatica, Università di Perugia, INFN Sezione
Perugia Via Vanvitelli, I-106123 Perugia, Italy
| | - Malgorzata Biczysko
- Physics
Department, and International Centre for Quantum and Molecular Structures, Shanghai University, 99 Shangda Road, Shanghai, 200444 China
- Consiglio
Nazionale delle Ricerche, Istituto di Chimica dei Composti OrganoMetallici
(ICCOM-CNR), UOS di Pisa, Area della Ricerca CNR, Via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza
dei Cavalieri 7, I-56126 Pisa, Italy
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26
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Ramakrishnan R, Rauhut G. Semi-quartic force fields retrieved from multi-mode expansions: Accuracy, scaling behavior, and approximations. J Chem Phys 2015; 142:154118. [DOI: 10.1063/1.4918587] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Raghunathan Ramakrishnan
- Institute of Physical Chemistry and National Center for Computational Design and Discovery of Novel Materials (MARVEL), Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Guntram Rauhut
- Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Germany
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27
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Cai K, Du F, Liu J, Su T. Solvent induced conformational fluctuation of alanine dipeptide studied by using vibrational probes. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 137:701-710. [PMID: 25260065 DOI: 10.1016/j.saa.2014.08.126] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 08/05/2014] [Accepted: 08/24/2014] [Indexed: 06/03/2023]
Abstract
The solvation effect on the three dimensional structure and the vibrational feature of alanine dipeptide (ALAD) was evaluated by applying the implicit solvents from polarizable continuum solvent model (PCM) through ab initio calculations, by using molecular dynamic (MD) simulations with explicit solvents, and by combining these two approaches. The implicit solvent induced potential energy fluctuations of ALAD in CHCl3, DMSO and H2O are revealed by means of ab initio calculations, and a global view of conformational and solvation environmental dependence of amide I frequencies is achieved. The results from MD simulations with explicit solvents show that ALAD trends to form PPII, αL, αR, and C5 in water, PPII and C5 in DMSO, and C5 in CHCl3, ordered by population, and the demonstration of the solvated structure, the solute-solvent interaction and hydrogen bonding is therefore enhanced. Representative ALAD-solvent clusters were sampled from MD trajectories and undergone ab initio calculations. The explicit solvents reveal the hydrogen bonding between ALAD and solvents, and the correlation between amide I frequencies and the CO bond length is built. The implicit solvents applied to the ALAD-solvent clusters further compensate the solvation effect from the bulk, and thus enlarge the degree of structural distortion and the amide I frequency red shift. The combination of explicit solvent in the first hydration shell and implicit solvent in the bulk is helpful for our understanding about the conformational fluctuation of solvated polypeptides through vibrational probes.
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Affiliation(s)
- Kaicong Cai
- College of Chemistry and Chemical Engineering, Fujian Normal University, Fuzhou 350007, Fujian, PR China.
| | - Fenfen Du
- College of Chemistry and Chemical Engineering, Fujian Normal University, Fuzhou 350007, Fujian, PR China
| | - Jia Liu
- College of Chemistry and Chemical Engineering, Fujian Normal University, Fuzhou 350007, Fujian, PR China
| | - Tingting Su
- College of Chemistry and Chemical Engineering, Fujian Normal University, Fuzhou 350007, Fujian, PR China
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28
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Licari D, Baiardi A, Biczysko M, Egidi F, Latouche C, Barone V. Implementation of a graphical user interface for the virtual multifrequency spectrometer: The VMS-Draw tool. J Comput Chem 2014; 36:321-34. [DOI: 10.1002/jcc.23785] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 10/12/2014] [Indexed: 11/09/2022]
Affiliation(s)
- Daniele Licari
- Scuola Normale Superiore; piazza dei Cavalieri 7 I-56126 Pisa Italy
| | - Alberto Baiardi
- Scuola Normale Superiore; piazza dei Cavalieri 7 I-56126 Pisa Italy
| | - Malgorzata Biczysko
- Scuola Normale Superiore; piazza dei Cavalieri 7 I-56126 Pisa Italy
- Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR), UOS di Pisa, Area della Ricerca CNR; Via G. Moruzzi 1 I-56124 Pisa Italy
| | - Franco Egidi
- Scuola Normale Superiore; piazza dei Cavalieri 7 I-56126 Pisa Italy
| | - Camille Latouche
- Scuola Normale Superiore; piazza dei Cavalieri 7 I-56126 Pisa Italy
| | - Vincenzo Barone
- Scuola Normale Superiore; piazza dei Cavalieri 7 I-56126 Pisa Italy
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29
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Barone V, Biczysko M, Bloino J, Puzzarini C. Accurate molecular structures and infrared spectra of trans-2,3-dideuterooxirane, methyloxirane, and trans-2,3-dimethyloxirane. J Chem Phys 2014; 141:034107. [PMID: 25053301 PMCID: PMC4612369 DOI: 10.1063/1.4887357] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Oxirane derivatives are the most used benchmarks for chiroptical spectroscopies in view of their small size and relative rigidity. The molecular structure, vibrational harmonic and anharmonic frequencies, and infrared intensities of the ground electronic states are analyzed in this paper. Equilibrium structure and harmonic force fields have been evaluated by means of high-level quantum-chemical calculations at the coupled-cluster level including single and double excitations together with a perturbative treatment of triples (CCSD(T)). Extrapolation to the complete basis-set limit as well as core-correlation effects have also been taken into account. Anharmonic contributions have been computed at the CCSD(T)/cc-pVTZ level for trans-2,3-dideuterooxirane. These data can serve as references to evaluate the accuracy of less expensive computational approaches rooted in the density functional theory (DFT). The latter have been used within hybrid CC/DFT approaches, which have been applied to simulate fully anharmonic infrared (IR) spectra. Finally, the best theoretical estimates of the equilibrium structures and vibrational wavenumbers are compared to the most accurate experimental data and show in all cases very good agreement, i.e., within 0.001 Å, 0.1 deg, 10 cm(-1), and 0.5 km mol(-1), for bond lengths, angles, wavenumbers, and IR intensities, respectively.
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Affiliation(s)
- Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | | | - Julien Bloino
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Cristina Puzzarini
- Dipartimento di Chimica "Giacomo Ciamician," Università di Bologna, Via F. Selmi 2, I-40126 Bologna, Italy
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30
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Fornaro T, Biczysko M, Monti S, Barone V. Dispersion corrected DFT approaches for anharmonic vibrational frequency calculations: nucleobases and their dimers. Phys Chem Chem Phys 2014; 16:10112-28. [PMID: 24531740 PMCID: PMC4612423 DOI: 10.1039/c3cp54724h] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Computational spectroscopy techniques have become in the last few years an effective means to analyze and assign infrared (IR) spectra of molecular systems of increasing dimensions and in different environments. However, transition from compilation of harmonic data to fully anharmonic simulations of spectra is still underway. The most promising results for large systems have been obtained, in our opinion, by perturbative vibrational approaches based on potential energy surfaces computed by hybrid (especially B3LYP) density functionals and medium size (e.g. SNSD) basis sets. In this framework, we are actively developing a comprehensive and robust computational protocol aimed at quantitative reproduction of the spectra of nucleic acid base complexes and their adsorption on solid supports (organic/inorganic). In this contribution we report the essential results of the first step devoted to isolated monomers and dimers. It is well known that in order to model the vibrational spectra of weakly bound molecular complexes dispersion interactions should be taken into proper account. In this work we have chosen two popular and inexpensive approaches to model dispersion interactions, namely the semi-empirical dispersion correction (D3) and pseudopotential based (DCP) methodologies both in conjunction with the B3LYP functional. These have been used for simulating fully anharmonic IR spectra of nucleobases and their dimers through generalized second order vibrational perturbation theory (GVPT2). We have studied, in particular, isolated adenine, hypoxanthine, uracil, thymine and cytosine, the hydrogen-bonded and stacked adenine and uracil dimers, and the stacked adenine-naphthalene heterodimer. Anharmonic frequencies are compared with standard B3LYP results and experimental findings, while the computed interaction energies and structures of complexes are compared to the best available theoretical estimates.
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Affiliation(s)
- Teresa Fornaro
- Scuola Normale Superiore, piazza dei Cavalieri 7, I-56126 Pisa, Italy.
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31
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Egidi F, Giovannini T, Piccardo M, Bloino J, Cappelli C, Barone V. Stereo-electronic, vibrational, and environmental contributions to polarizabilities of large molecular systems: a feasible anharmonic protocol. J Chem Theory Comput 2014; 10:2456-2464. [PMID: 26550004 DOI: 10.1021/ct500210z] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Reliable computations of linear and non-linear optical properties of molecular systems in condensed phases require a proper account of stereo-electronic, vibrational, and environmental effects. In the framework of density functional theory, these effects can be accurately introduced using second-order vibrational perturbation theory in conjunction with polarizable continuum models. We illustrate the combination of an anharmonic description of the ground-state potential energy surface with solvation effects treated with the polarizable continuum model (PCM) in the calculation of the electronic, zero-point, and pure vibrational polarizabilities of selected systems. The description of the solvation environment is enriched by taking into account the dynamical aspects of the solute-solvent interactions through the inclusion of both electronic and vibrational non-equilbrium effects, as well as the direct effect of the solvent on the electric field that generates the molecular response (local field effect). This treatment yields accurate results which can be directly compared with experimental findings without the need of empirical corrections.
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Affiliation(s)
- Franco Egidi
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | | | - Matteo Piccardo
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Julien Bloino
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy ; Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organometallici, UOS di Pisa, Via G. Moruzzi 1, 56124 Pisa, Italy
| | - Chiara Cappelli
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Risorgimento 35, 56126 Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
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Barone V, Biczysko M, Bloino J. Fully anharmonic IR and Raman spectra of medium-size molecular systems: accuracy and interpretation. Phys Chem Chem Phys 2014; 16:1759-87. [PMID: 24346191 PMCID: PMC4604664 DOI: 10.1039/c3cp53413h] [Citation(s) in RCA: 295] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Computation of full infrared (IR) and Raman spectra (including absolute intensities and transition energies) for medium- and large-sized molecular systems beyond the harmonic approximation is one of the most interesting challenges of contemporary computational chemistry. Contrary to common beliefs, low-order perturbation theory is able to deliver results of high accuracy (actually often better than those issuing from current direct dynamics approaches) provided that anharmonic resonances are properly managed. This perspective sketches the recent developments in our research group toward the development of a robust and user-friendly virtual spectrometer rooted in second-order vibrational perturbation theory (VPT2) and usable also by non-specialists essentially as a black-box procedure. Several examples are explicitly worked out in order to illustrate the features of our computational tool together with the most important ongoing developments.
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Affiliation(s)
- Vincenzo Barone
- Scuola Normale Superiore, piazza dei Cavalieri 7, I-56126 Pisa, Italy.
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34
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Egidi F, Bloino J, Cappelli C, Barone V. A robust and effective time-independent route to the calculation of Resonance Raman spectra of large molecules in condensed phases with the inclusion of Duschinsky, Herzberg-Teller, anharmonic, and environmental effects. J Chem Theory Comput 2013; 10:346-363. [PMID: 26550003 DOI: 10.1021/ct400932e] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
We present an effective time-independent implementation to model vibrational resonance Raman (RR) spectra of medium-large molecular systems with the inclusion of Franck-Condon (FC) and Herzberg-Teller (HT) effects and a full account of the possible differences between the harmonic potential energy surfaces of the ground and resonant electronic states. Thanks to a number of algorithmic improvements and very effective parallelization, the full computations of fundamentals, overtones, and combination bands can be routinely performed for large systems possibly involving more than two electronic states. In order to improve the accuracy of the results, an effective inclusion of the leading anharmonic effects is also possible, together with environmental contributions under different solvation regimes. Reduced-dimensionality approaches can further enlarge the range of applications of this new tool. Applications to imidazole, pyrene, and chlorophyll a1 in solution are reported, as well as comparisons with available experimental data.
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Affiliation(s)
- Franco Egidi
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Julien Bloino
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy ; Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organometallici, UOS di Pisa, Via G. Moruzzi 1, 56124 Pisa, Italy
| | - Chiara Cappelli
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Risorgimento 35, 56126 Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
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35
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EGIDI FRANCO, BLOINO JULIEN, CAPPELLI CHIARA, BARONE VINCENZO. Development of a virtual spectrometer for chiroptical spectroscopies: the case of nicotine. Chirality 2013; 25:701-8. [PMID: 23857879 PMCID: PMC4604657 DOI: 10.1002/chir.22200] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Accepted: 05/07/2013] [Indexed: 02/03/2023]
Abstract
The impressive advances of computational spectroscopy in most recent years are providing robust and user-friendly multifrequency virtual spectrometers, which can also be used by nonspecialists to complement experimental studies. At the heart of these developments there are latest-generation models based on Density Functional Theory for the proper treatment of stereo-electronic effects, coupled to the polarizable continuum model to deal with bulk solvent effects, and low-order perturbative treatments of anharmonic effects. Continuing our efforts to increase the range of application of virtual spectrometers, we report here about chiroptical spectroscopies with special reference to optical rotation and vibrational circular dichroism. The capabilities and possible limitations of our latest tool will be analyzed for the specific case of (S)-nicotine in vacuo and in different solvents.
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Affiliation(s)
- FRANCO EGIDI
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - JULIEN BLOINO
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
- Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti OrganoMetallici, UOS di Pisa, Via G. Moruzzi 1, 56124 Pisa, Italy
| | - CHIARA CAPPELLI
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Risorgimento 35, 56126 Pisa, Italy
| | - VINCENZO BARONE
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
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36
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Charmet AP, Quartarone G, Ronchin L, Tortato C, Vavasori A. Quantum Chemical Investigation on Indole: Vibrational Force Field and Theoretical Determination of Its Aqueous pKa Value. J Phys Chem A 2013; 117:6846-58. [DOI: 10.1021/jp4049692] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Andrea Pietropolli Charmet
- Dipartimento
di Scienze Molecolari e Nanosistemi, Università Ca’ Foscari Venezia, Calle
Larga Santa Marta 2137, I-30123, Venezia, Italy
| | - Giuseppe Quartarone
- Dipartimento
di Scienze Molecolari e Nanosistemi, Università Ca’ Foscari Venezia, Calle
Larga Santa Marta 2137, I-30123, Venezia, Italy
| | - Lucio Ronchin
- Dipartimento
di Scienze Molecolari e Nanosistemi, Università Ca’ Foscari Venezia, Calle
Larga Santa Marta 2137, I-30123, Venezia, Italy
| | - Claudio Tortato
- Dipartimento
di Scienze Molecolari e Nanosistemi, Università Ca’ Foscari Venezia, Calle
Larga Santa Marta 2137, I-30123, Venezia, Italy
| | - Andrea Vavasori
- Dipartimento
di Scienze Molecolari e Nanosistemi, Università Ca’ Foscari Venezia, Calle
Larga Santa Marta 2137, I-30123, Venezia, Italy
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37
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Egidi F, Bloino J, Cappelli C, Barone V, Tomasi J. Tuning of NMR and EPR parameters by vibrational averaging and environmental effects: an integrated computational approach. Mol Phys 2013. [DOI: 10.1080/00268976.2013.796413] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Franco Egidi
- a Scuola Normale Superiore , Piazza dei Cavalieri , Pisa , Italy
| | - Julien Bloino
- a Scuola Normale Superiore , Piazza dei Cavalieri , Pisa , Italy
- b CNR, Consiglio Nazionale delle Ricerche , Istituto di Chimica dei Composti Organometallici , UOS di Pisa, Via G. Moruzzi, Pisa , Italy
| | - Chiara Cappelli
- a Scuola Normale Superiore , Piazza dei Cavalieri , Pisa , Italy
- c Dipartimento di Chimica e Chimica Industriale , Università di Pisa , via Risorgimento, Pisa , Italy
| | - Vincenzo Barone
- a Scuola Normale Superiore , Piazza dei Cavalieri , Pisa , Italy
| | - Jacopo Tomasi
- c Dipartimento di Chimica e Chimica Industriale , Università di Pisa , via Risorgimento, Pisa , Italy
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38
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Abstract
IR and Raman spectra of selenophene and of its perdeuterated isotopomer have been obtained in gas phase through density-functional theory (DFT) computations. Vibrational wavenumbers have been calculated using harmonic and anharmonic second-order perturbation theory (PT2) procedures with the B3LYP method and the 6-311 basis set. Anharmonic overtones have been determined by means of the PT2 method. The introduction of anharmonic terms decreases the harmonic wavenumbers, giving a significantly better agreement with the experimental data. The most significant anharmonic effects occur for the C–H and C–D stretching modes, the observed H/D isotopic wavenumber redshifts being satisfactorily reproduced by the PT2 computations within 6–20 cm−1(1–3%). In the spectral region between 500 cm−1and 1500 cm−1, the IR spectra are dominated by the out-of-plane C–H (C–D) bending transition, whereas the Raman spectra are mainly characterized by a strong peak mainly attributed to the C=C + C–C bonds stretching vibration with the contribution of the in-plane C–H (C–D) bending deformation. The current results confirm that the PT2 approach combined with the B3LYP/6-311 level of calculation is a satisfactory choice for predicting vibrational spectra of cyclic molecules.
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39
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Hanson-Heine MWD, George MW, Besley NA. Rapid anharmonic vibrational corrections derived from partial Hessian analysis. J Chem Phys 2012; 136:224102. [DOI: 10.1063/1.4727853] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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40
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Hanson-Heine MWD, George MW, Besley NA. Investigating the Calculation of Anharmonic Vibrational Frequencies Using Force Fields Derived from Density Functional Theory. J Phys Chem A 2012; 116:4417-25. [DOI: 10.1021/jp301670f] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
| | - Michael W. George
- School of Chemistry, University of Nottingham, University Park, Nottingham
NG7 2RD, U.K
| | - Nicholas A. Besley
- School of Chemistry, University of Nottingham, University Park, Nottingham
NG7 2RD, U.K
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41
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Biczysko M, Bloino J, Brancato G, Cacelli I, Cappelli C, Ferretti A, Lami A, Monti S, Pedone A, Prampolini G, Puzzarini C, Santoro F, Trani F, Villani G. Integrated computational approaches for spectroscopic studies of molecular systems in the gas phase and in solution: pyrimidine as a test case. Theor Chem Acc 2012. [DOI: 10.1007/s00214-012-1201-3] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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42
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Krasnoshchekov SV, Isayeva EV, Stepanov NF. Numerical-analytic implementation of the higher-order canonical Van Vleck perturbation theory for the interpretation of medium-sized molecule vibrational spectra. J Phys Chem A 2012; 116:3691-709. [PMID: 22369280 DOI: 10.1021/jp211400w] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Anharmonic vibrational states of semirigid polyatomic molecules are often studied using the second-order vibrational perturbation theory (VPT2). For efficient higher-order analysis, an approach based on the canonical Van Vleck perturbation theory (CVPT), the Watson Hamiltonian and operators of creation and annihilation of vibrational quanta is employed. This method allows analysis of the convergence of perturbation theory and solves a number of theoretical problems of VPT2, e.g., yields anharmonic constants y(ijk), z(ijkl), and allows the reliable evaluation of vibrational IR and Raman anharmonic intensities in the presence of resonances. Darling-Dennison and higher-order resonance coupling coefficients can be reliably evaluated as well. The method is illustrated on classic molecules: water and formaldehyde. A number of theoretical conclusions results, including the necessity of using sextic force field in the fourth order (CVPT4) and the nearly vanishing CVPT4 contributions for bending and wagging modes. The coefficients of perturbative Dunham-type Hamiltonians in high-orders of CVPT are found to conform to the rules of equality at different orders as earlier proven analytically for diatomic molecules. The method can serve as a good substitution of the more traditional VPT2.
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43
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Bloino J, Biczysko M, Barone V. General Perturbative Approach for Spectroscopy, Thermodynamics, and Kinetics: Methodological Background and Benchmark Studies. J Chem Theory Comput 2012; 8:1015-36. [DOI: 10.1021/ct200814m] [Citation(s) in RCA: 213] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Julien Bloino
- Scuola Normale Superiore, piazza
dei Cavalieri 7, I-56126 Pisa, Italy
- Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organometallici (CNR-ICCOM), UOS di Pisa, Via G. Moruzzi, 1 I-56124 Italy
| | - Malgorzata Biczysko
- Center for Nanotechnology Innovation
@NEST, Istituto Italiano di Tecnologia, Piazza San Silvestro 12, I-56127
Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, piazza
dei Cavalieri 7, I-56126 Pisa, Italy
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44
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Dračínský M, Bouř P. Vibrational averaging of the chemical shift in crystalline α-glycine. J Comput Chem 2012; 33:1080-9. [PMID: 22410968 DOI: 10.1002/jcc.22940] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Revised: 01/04/2012] [Accepted: 01/04/2012] [Indexed: 11/06/2022]
Abstract
Averaging of the chemical shift over the molecular motion improves the simulated data and provides additional information about the temperature dependence and system dynamics. However, crystal modeling is difficult due to the limited precision of the plane-wave density functional theory (DFT) methods and approximate vibrational schemes. On the glycine example, we investigate how the averaging can be achieved within the periodic boundary conditions at the DFT level. The nuclear motion is modeled with the vibrational configuration interaction, with other simplified quantum anharmonic schemes, and the classical Born-Oppenheimer molecular dynamics (BOMD). The results confirm a large vibrational contribution to the isotropic shielding values. Both the first and second derivatives of the shielding were found important for the quantum averaging. The first derivatives influence the shielding mostly due to the anharmonic character of the CH and NH stretching modes, whereas second derivatives produce most vibrational corrections associated with the lower-frequency vibrational modes. Temperature excitations of the lowest-frequency vibrational states and the expansion of the crystal cell both determine the temperature dependence of nuclear magnetic resonance parameters. The vibrational quantum approach as well as classical BOMD schemes provided temperature dependencies of the chemical shifts that are consistent with the previous experimental data.
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Affiliation(s)
- Martin Dračínský
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, Prague 166 10, Czech Republic.
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45
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Egidi F, Barone V, Bloino J, Cappelli C. Toward an Accurate Modeling of Optical Rotation for Solvated Systems: Anharmonic Vibrational Contributions Coupled to the Polarizable Continuum Model. J Chem Theory Comput 2012; 8:585-97. [DOI: 10.1021/ct2008473] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Franco Egidi
- Scuola Normale Superiore, Piazza
dei Cavalieri, 7 I-56126
Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza
dei Cavalieri, 7 I-56126
Pisa, Italy
| | - Julien Bloino
- CNR, Consiglio
Nazionale delle Ricerche, Istituto di
Chimica dei Composti Organometallici, UOS di Pisa, Via G. Moruzzi,
1 I-56124, Italy
| | - Chiara Cappelli
- Scuola Normale Superiore,
Piazza dei Cavalieri, 7 I-56126
Pisa, Italy and Dipartimento di Chimica e Chimica Industriale, Università
di Pisa, via Risorgimento, 35 I-56126 Pisa, Italy
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46
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Barone V, Baiardi A, Biczysko M, Bloino J, Cappelli C, Lipparini F. Implementation and validation of a multi-purpose virtual spectrometer for large systems in complex environments. Phys Chem Chem Phys 2012; 14:12404-22. [DOI: 10.1039/c2cp41006k] [Citation(s) in RCA: 122] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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47
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Hudecová J, Hopmann KH, Bouř P. Correction of Vibrational Broadening in Molecular Dynamics Clusters with the Normal Mode Optimization Method. J Phys Chem B 2011; 116:336-42. [DOI: 10.1021/jp208785a] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Jana Hudecová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo nám. 2, 166 10 Prague, Czech Republic
- Institute of Physics, Charles University, Ke Karlovu 5, 12116 Prague 2, Czech Republic
| | - Kathrin H. Hopmann
- Department of Chemistry, Centre for Theoretical and Computational Chemistry, University of Tromsø, N-9037 Tromsø, Norway
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo nám. 2, 166 10 Prague, Czech Republic
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48
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Howard JC, Hammer NI, Tschumper GS. Structures, energetics and vibrational frequency shifts of hydrated pyrimidine. Chemphyschem 2011; 12:3262-73. [PMID: 21994177 DOI: 10.1002/cphc.201100457] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Indexed: 11/11/2022]
Abstract
More than 70 unique micro-hydrated structures of pyrimidine, ranging in size from 1 to 7 water molecules, have been characterized with the B3LYP density functional and the 6-311++G(2df,2pd) triple-ζ split-valence basis set. Explicitly correlated MP2-F12 single-point computations were performed on each structure with a correlation consistent triple-ζ basis set to estimate the relative and dissociation energies at the MP2 complete basis set (CBS) limit. Many of these new structures have significantly lower energies than those previously reported (by as much as 12.66 kcal mol(-1)). For clusters with 1 and 2 water molecules, the MP2-F12 relative and dissociation energies are virtually identical to the corresponding CCSD(T)-F12 values. As the number of hydrating waters increases, the structures in which the water molecules are clustered together at one of the N atoms have lower energies than those where the water molecules are more distributed around the pyrimidine ring. Micro-hydrated structures that effectively extend the low-energy hydrogen-bonding motifs to both sides of the ring, as would be expected in the bulk phase, reproduce the experimentally observed vibrational frequency shifts of ν(1) and ν(8b) in very dilute aqueous pyrimidine solutions to within 1 cm(-1) . Micro-hydrated structures of pyrimidine in which water molecules are clustered together have lower energies than structures in which the water molecules are more evenly spread around the pyrimidine ring.
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Affiliation(s)
- J Coleman Howard
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS 38655-1848, USA
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49
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Puzzarini C, Biczysko M, Barone V. Accurate Anharmonic Vibrational Frequencies for Uracil: The Performance of Composite Schemes and Hybrid CC/DFT Model. J Chem Theory Comput 2011; 7:3702-10. [DOI: 10.1021/ct200552m] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Cristina Puzzarini
- Dipartimento di Chimica “G. Ciamician”, Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy
| | - Malgorzata Biczysko
- Center for Nanotechnology Innovation @NEST, Istituto Italiano di Tecnologia, Piazza San Silvestro, 12 - 56127 Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
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50
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Zhao B, Wang YY, Zhang YH, Dai L, Zhou ZY. Structure and vibrational spectroscopy investigation of 2-(4-chlorophenyliminomethyl)-8-hydroxyquinoline. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2011; 81:251-256. [PMID: 21802352 DOI: 10.1016/j.saa.2011.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2010] [Revised: 06/05/2011] [Accepted: 06/13/2011] [Indexed: 05/31/2023]
Abstract
2-(4-Chlorophenyliminomethyl)-8-hydroxyquinoline was synthesized and crystal data was obtained in the orthorhombic space group P-1, with Z=4. Unit cell parameters a=4.744(7) Å, b=9.981(15) Å, c=27.27(4) Å and V=12915(3) Å(3). In this paper the structural properties and vibrational frequencies of 8-hydroxyquinoline derivative, 2CP8HQ, are studied with the B3LYP and HF methods. Two stable conformers are obtained. The calculated frequencies are in good agreement with the experiment results. It is indicated that both of theoretical calculations were suitable for molecular vibrational frequencies study and the scaled B3LYP method was superior to the scaled HF methods.
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Affiliation(s)
- Bin Zhao
- College of Chemistry, Qufu Normal University, Shandong, Qufu 273165, PR China
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