Accurate vibrational spectra of large molecules by density functional computations beyond the harmonic approximation: the case of uracil and 2-thiouracil

Barone, Vincenzo; Festa, Gaetano; Grandi, A.; Rega, Nadia; Sanna, Nico

doi:10.1016/j.cplett.2004.03.024

Cited by 106 publications

(101 citation statements)

References 23 publications

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“…Similar results have also been observed in studies of azabenzenes [29,30,31], pyrrole and furan [32], uracil [33] or, more recently, monofluoroanilines [26]. The anharmonic frequencies  anh obtained for DBMH are in very good agreement with the experimental values, and this agreement is even better than that observed for  hsc , whose values were obtained semiempirically using the scaled quantum mechanical method.…”

Section: Comparison Of "Harmonic" "Harmonic Scaled" and "Anharmonic"supporting

confidence: 78%

Vibrational spectroscopy and DFT calculations of 1,3-dibromo-2,4,6-trimethylbenzene: Anharmonicity, coupling and methyl group tunneling

Zeroual

Meinnel

Łapiński

et al. 2013

Vibrational Spectroscopy

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Abstract-The Raman, IR and INS spectra of 1,3-dibromo-2,4,6-trimethylbenzene (DBMH) were recorded in the 80-3200 cm -1 range. The molecular conformation and vibrational spectra of DBMH were computed at the MPW1PW91/LANL2DZ level. Except for the methyl 2 environment, the agreement between the DFT calculations and the neutron diffraction structure is almost perfect (deviations < 0.01 Å for bond lengths, < 0.2° for angles). The frequencies of the internal modes of vibration were calculated with the harmonic and anharmonic approximations; the later method yields results that are in remarkable agreement with the spectroscopic data, resulting in a confident assignment of the vibrational bands. Thus, no scaling is necessary. The coupling, in phase or antiphase, of the motions of symmetrical C-Br and C-Me bonds is highlighted. Our DFT calculations suggest that the torsion of methyl groups 4 and 6 is hindered in deep wells, whereas methyl group 2 is a quasi-free rotor. The failure of the calculations to determine the frequencies of the methyl torsional modes is explained as follows: DFT does not consider the methyl spins and assumes localization of the protons, whereas the methyl groups must be treated as quantum rotors.Keywords: Raman spectroscopy; IR spectroscopy; Inelastic neutron scattering; DFT calculations; 1,3-dibromo-2,4,6-trimethylbenzene 1-IntroductionA tremendous amount of work has been devoted to the spectroscopy of polysubstituted benzenes.Among those relative to penta-and hexa-substituted compounds, two extensive papers were published in 1985: one paper compared eleven polymethyl-benzenes (pMeB) [1] and the second described six chloromethyl-benzenes C 6 (CH 3 ,Cl) 6 (ClMeB) [2]. In these studies, the experimental spectra were assigned using normal coordinate calculations to determine a common multi-parameter force field. Because the molecular conformations were not accurately known the authors assumed that the aromatic ring in all molecules was a regular hexagon, that the bond angles were 120°, and the bond lengths were 1.396 Å for the carbon-carbon aromatic bond, 1.509 Å for the methyl carbonaromatic carbon bond, 1.083 Å for the aromatic carbon-hydrogen bond and 1.096 Å for the methylcarbon hydrogen bond. For the pMeB species, the Raman and infra-red measurements were performed with samples in the gaseous phase at approximately 550 K. A 46-parameter valence force field had been proposed, and the average error between the 736 observed and calculated wavenumbers was 6.4 cm -1 . This agreement suggests that the use of an excessive number of off-diagonal constants (interactions terms) allows us to compensate for the large errors done in the geometrical parameters. According to the authors in these previous studies: "there is a great stability of the internal methyl modes, in a limit of ± 5 cm -1 they are located at: 2930 cm -1 for the C-H stretching, 1445 cm -1 for the asymmetric C-H bending, 1380 cm -1 for the C-H symmetric bending, 1000 and 1060 cm -1 for the C-H rocking". For the "torsion mode" of the meth...

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Section: Comparison Of "Harmonic" "Harmonic Scaled" and "Anharmonic"supporting

confidence: 78%

Vibrational spectroscopy and DFT calculations of 1,3-dibromo-2,4,6-trimethylbenzene: Anharmonicity, coupling and methyl group tunneling

Zeroual

Meinnel

Łapiński

et al. 2013

Vibrational Spectroscopy

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“…Vibrational wavenumbers have been computed within the generalized VPT2 model (GVPT2), where nearly-resonant contributions are removed from the perturbative treatment (leading to the deperturbed model, DVPT2) and treated in a second step variationally 61,66,68 . This model, as implemented in the GAUSSIAN package 86 , provided accurate vibrational wavenumbers for several semi-rigid systems 31,32,90,[97][98][99]103,104,117,129,130,132,134,135 . Such an approach relies on semi-empirical thresholds for Fermi and Darling-Denninson resonances.…”

Section: Computational Detailsmentioning

confidence: 99%

Dispersion corrected DFT approaches for anharmonic vibrational frequency calculations: nucleobases and their dimers

Fornaro

Biczysko

Monti

et al. 2014

Phys. Chem. Chem. Phys.

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101

113

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Computational spectroscopy techniques have become in the last years effective means to analyze and assign infrared (IR) spectra for molecular systems of increasing dimensions and in different environments. However, transition from compilations of harmonic data to full anharmonic simulations of spectra is still under way. 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 to a quantitative reproduction of the spectra of nucleic acid bases 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 interaction, 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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“…1) The present work focuses on the vibrational properties of FA. It was recently shown that the combination of harmonic and anharmonic frequency calculations using Density Functional Theory (DFT) provides unambiguous assignments of vibrational bands with <10 cm -1 average prediction error for reported cases [10][11][12] . Each frequency is obtained -without use of a scaling procedure -as the sum of a harmonic large basis set frequency and an anharmonic small basis set frequency correction (obtained by a perturbative treatment [13] ), henceforth referred to as a hybrid calculation.…”

Section: Introductionmentioning

confidence: 99%

Combined Raman Spectroscopic and Theoretical Investigation of Fundamental Vibrational Bands of Furfuryl Alcohol (2-furanmethanol)

Barsberg

Berg

2006

J. Phys. Chem. A

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Furfuryl alcohol (FA) is a promising reactive precursor for new materials. FA reaction mechanisms, e.g., self-reactions or cross reactions with other substances, can be studied by vibrational spectroscopy. We present a Raman spectroscopic and theoretical study of vibrational properties of FA based on density functional theory (DFT/B3LYP), and a recently proposed hybrid approach to the calculation of fundamental frequencies. Excluding one frequency the remaining ones are predicted to a best RMS error of 8 cm -1 , and are qualitatively assigned. A CH stretching mode is underestimated by 65 cm -1 . This may be due to deficiencies of DFT to model dispersion forces.

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Accurate vibrational spectra of large molecules by density functional computations beyond the harmonic approximation: the case of uracil and 2-thiouracil

Cited by 106 publications

References 23 publications

Vibrational spectroscopy and DFT calculations of 1,3-dibromo-2,4,6-trimethylbenzene: Anharmonicity, coupling and methyl group tunneling

Vibrational spectroscopy and DFT calculations of 1,3-dibromo-2,4,6-trimethylbenzene: Anharmonicity, coupling and methyl group tunneling

Dispersion corrected DFT approaches for anharmonic vibrational frequency calculations: nucleobases and their dimers

Combined Raman Spectroscopic and Theoretical Investigation of Fundamental Vibrational Bands of Furfuryl Alcohol (2-furanmethanol)

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