Ab initio periodic modelling of the vibrational spectra of molecular crystals: the case of uracil

被引:11
作者
De la Pierre, Marco [1 ]
Pouchan, Claude [2 ]
机构
[1] Curtin Univ, Sch Mol & Life Sci, Curtin Inst Computat, GPO Box U1987, Perth, WA 6845, Australia
[2] Univ Pau & Pays Adour, Inst Sci Analyt & Physicochim Environm & Mat, CNRS, UMR5254, F-64000 Pau, France
关键词
IR spectrum; Raman spectrum; Nucleobases; Quantum-mechanical simulation; CRYSTAL code; DENSITY-FUNCTIONAL COMPUTATIONS; NUCLEIC-ACID CONSTITUENTS; HARTREE-FOCK GRADIENTS; RAMAN-SPECTRA; INFRARED-SPECTRA; MATRIX-ISOLATION; WATER COMPLEXES; ATOMIC CHARGES; FREQUENCIES; IMPLEMENTATION;
D O I
10.1007/s00214-017-2191-y
中图分类号
O64 [物理化学(理论化学)、化学物理学];
学科分类号
070304 ; 081704 ;
摘要
The structure and vibrational spectra of solid uracil have been simulated in the framework of Density Functional Theory (DFT) using a periodic unit cell model. Structural parameters are reproduced reasonably well by using the dispersion corrected, global hybrid Hartree-Fock/DFT functional B3LYP-D* and an all-electron, Gaussian type, triple zeta basis set with polarisation. The periodic calculation provides the full set of fundamental harmonic vibrational modes, whose nature can be investigated by inspecting the corresponding eigenvectors. Accounting for dispersive interactions indirectly affects the spectra, through the impact on the cell parameters. Marked differences are found between the gas and solid phase spectra, that can be related to either mode coupling or direct alteration of the potential energy via neighbour-neighbour molecular interactions. Anharmonicity needs to be considered for a meaningful comparison with experiments; a single scaling factor provides a significantly improved agreement for most of the frequencies, except for the NH stretchings, which require a larger downscaling. This rescaling strategy yields results of comparable quality with respect to previously reported calculations with a cluster model and a perturbative treatment of anharmonicity.
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页数:15
相关论文
共 59 条
[1]   Effect of silver nanowires on the surface-enhanced Raman spectra (SERS) of the RNA bases [J].
Badr, Y ;
Mahmoud, MA .
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY, 2006, 63 (03) :639-645
[2]   Accurate vibrational spectra of large molecules by density functional computations beyond the harmonic approximation: the case of uracil and 2-thiouracil [J].
Barone, V ;
Festa, G ;
Grandi, A ;
Rega, N ;
Sanna, N .
CHEMICAL PHYSICS LETTERS, 2004, 388 (4-6) :279-283
[3]   Development and validation of the B3LYP/N07D computational model for structural parameter and magnetic tensors of large free radicals [J].
Barone, Vincenzo ;
Cimino, Paola ;
Stendardo, Emiliano .
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2008, 4 (05) :751-764
[4]   Toward anharmonic computations of vibrational spectra for large molecular systems [J].
Barone, Vincenzo ;
Biczysko, Malgorzata ;
Bloino, Julien ;
Borkowska-Panek, Monika ;
Carnimeo, Ivan ;
Panek, Pawel .
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 2012, 112 (09) :2185-2200
[5]   DENSITY-FUNCTIONAL THERMOCHEMISTRY .3. THE ROLE OF EXACT EXCHANGE [J].
BECKE, AD .
JOURNAL OF CHEMICAL PHYSICS, 1993, 98 (07) :5648-5652
[6]  
Broyden C.G., 1970, IMA J APPL MATH, V6, P76, DOI [10.1093/IMAMAT/6.1.76, DOI 10.1093/IMAMAT/6.1.76, 10.1093/imamat/6.1.76]
[7]   MATRIX-ISOLATION STUDIES OF NUCLEIC-ACID CONSTITUENTS .2. QUANTITATIVE ABINITIO PREDICTION OF THE INFRARED-SPECTRUM OF INPLANE MODES OF URACIL [J].
CHIN, S ;
SCOTT, I ;
SZCZEPANIAK, K ;
PERSON, WB .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1984, 106 (12) :3415-3422
[8]   Multiple isomers of uracil-water complexes: infrared spectroscopy in helium nanodroplets [J].
Choi, MY ;
Miller, RE .
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 2005, 7 (20) :3565-3573
[9]   Hartree-Fock geometry optimisation of periodic systems with the CRYSTAL code [J].
Civalleri, B ;
D'Arco, P ;
Orlando, R ;
Saunders, VR ;
Dovesi, R .
CHEMICAL PHYSICS LETTERS, 2001, 348 (1-2) :131-138
[10]   B3LYP augmented with an empirical dispersion term (B3LYP-D*) as applied to molecular crystals [J].
Civalleri, Bartolomeo ;
Zicovich-Wilson, Claudio M. ;
Valenzano, Loredana ;
Ugliengo, Piero .
CRYSTENGCOMM, 2008, 10 (04) :405-410