Anharmonic vibrational analysis of uracil by ab initio Hartree–Fock and density functional theory calculations (original) (raw)
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Journal of Molecular Structure, 2001
Interaction of water molecules (up to seven) with uracil (RNA base) through the ®rst hydration shell has been analysed by means of density functional theory (DFT) calculations at the B3LYP/6-31G p level. Water molecules in uracil 1 2H 2 O and uracil 1 4H 2 O complexes interact with adjacent N±H and CyO chemical groups of the base. In addition to these groups, water molecules are also H-bonded to the uracil C±H groups in the uracil 1 7H 2 O complex. It has been shown that the formation of water dimer and water trimer around uracil is necessary to complete its ®rst hydration shell. Harmonic vibrational calculations have been performed after full geometry optimisation of each compound. A discussion has then been undertaken on the vibrational analysis of uracil in going from gas phase to solution state on the basis of available observed vibrational spectra and those calculated for isolated uracil and uracil 1 nH 2 O complexes. q
Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 2010
Radical cations of uracil and thio-uracils a b s t r a c t DFT calculations at the B3LYP/6-311++G** level have been carried out to study the vibrational characteristics of the neutral molecules, anionic and cationic radicals of uracil, 2-thiouracil and 4-thiouracil. In the U molecule, C C bond loses its double bond character and magnitude of the C C stretching frequency decreases significantly as a result of radicalization. Frequency for the in-plane deformation mode of C O increases when a sulfur atom is substituted for the oxygen atom at the site C 2 in the uracil molecule but decreases when a sulfur atom is substituted for the oxygen atom at the site C 4 . The magnitude of both the N-H stretching frequencies decreases in all the radical cations as compared to their neutral molecules. Radicalization leads to significant changes in the magnitudes and intensities corresponding to some of the normal modes for all the three cases. Removal of an electron leads to decrease in the electronic charge mainly from the sulfur atom in the case of 2-TU and 4-TU, whereas it is distributed over the sites N 1 , C 5 , O 8 and O 10 in case of the U molecule.
Relationships observed in the structure and spectra of uracil and its 5-substituted derivatives
… Acta Part A: Molecular …, 2010
The effects on the geometry structure, atomic charges and vibrational wavenumbers of the main different substituents in the 5th position of the uracil ring were analysed, and relationships were established. The 5-monosubstituted derivatives studied were 5-XU (X = F, Cl, Br, I, CH 3 , NH 2 , NO 2 ). The geometry and vibrational wavenumbers were determined in these molecules. The FT-IR and Raman spectra were studied with the support of B3LYP calculations using several basis sets. Several general conclusions were underlined.
Ab initio periodic modelling of the vibrational spectra of molecular crystals: the case of uracil
Theoretical Chemistry Accounts, 2018
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.
Journal of Chemical Theory and Computation, 2011
The vibrational spectrum (frequencies as well as intensities) of uracil has been investigated at a high level of theory. The harmonic force field has been evaluated at the coupled-cluster (CC) level in conjunction with a triple-ζ basis set. Extrapolation to the basis set limit as well as inclusion of core-correlation and diffuse-function corrections have been considered by means of the second-order MøllerÀPlesset perturbation theory. To go beyond the harmonic approximation, a hybrid CC/DFT approach has been employed, which will be proved to provide state-of-the-art results. As the spectroscopic investigation of uracil is hampered by numerous Fermi resonances, models for explicitly taking them into account have been implemented and applied. On general grounds, the computational procedure presented is able to provide the proper accuracy to support experimental investigations of large molecules of biological interest.
This work describes the different scaling procedures used to correct the quantum-chemical theoretical predictions of the IR and Raman vibrational wavenumbers. Examples of each case are shown, with special attention to the uracil molecule and some derivatives. The results obtained with different semiempirical and ab initio methods, and basis sets, are compared and discussed. A comprehensive compendium of the main scale factors and scaling equations available to obtain the scaled wavenumbers is also shown.
The Journal of Physical Chemistry A, 2015
The numerical-analytic implementation of the operator version of the canonical Van Vleck second-order vibrational perturbation theory (CVPT2) is employed for a purely ab initio prediction and interpretation of the infrared (IR) and Raman anharmonic spectra of a medium-size molecule of the diketo tautomer of uracil (2,4(1H,3H)-pyrimidinedione), which has high biological importance as one of the four RNA nucleobases. A nonempirical, semidiagonal quartic potential energy surface (PES) expressed in normal coordinates was evaluated at the MP2/cc-pVTZ level of theory. The quality of the PES was improved by replacing the harmonic frequencies with the "best" estimated CCSD(T)-based values taken from the literature. The theoretical method is enhanced by an accurate treatment of multiple Fermi and Darling−Dennison resonances with evaluation of the corresponding resonance constants W and K (CVPT2+WK method). A prediction of the anharmonic frequencies as well as IR and Raman intensities was used for a detailed interpretation of the experimental spectra of uracil. Very good agreement between predicted and observed vibrational frequencies has been achieved (RMSD ∼4.5 cm −1 ). The model employed gave a theoretically robust treatment of the multiple resonances in the 1680−1790 cm −1 region. Our new analysis gives the most reliable reassignments of IR and Raman spectra of uracil available to date. a IR intensities are presented in units of km/mol; RS absolute normalized cross sections are presented in units of 10 −48 cm 6 /sr. b According to eq 3.1
Spectra and structure of uracil and its 5-haloderivatives: a review
The effects on the geometry structure, atomic charges and vibrational wavenumbers due to different substituents in the 5 th position of the uracil ring were analysed. The 5-monosubstituted derivatives studied were 5-XU (X = F, Cl, Br, I). The FT-IR and Raman spectra were studied with the support of B3LYP calculations using several basis set. Several general conclusions were underlined.
Feasible and comprehensive computational protocols for simulating the spectroscopic properties of large and complex molecular systems are very sought after. Indeed, due to the great variety of intra-and inter-molecular interactions which may take place, the interpretation of experimental data becomes more and more difficult as the system under study increases in size and/or is placed in a complex environment, such as condensed phases. 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, with increasing complexity towards condensed phases and monolayers of biomolecules on solid supports. We have resorted to fully anharmonic quantum mechanical computations within the generalized second order vibrational perturbation theory (GVPT2) approach, combined with the cost-effective B3LYP-D3 method, in conjunction with basis sets of double-ζ plus polarization quality. Such approach has been validated in a previous work (PCCP 2014, 16, 10112-10128) for simulating the IR spectra of the monomers of nucleobases and some of their dimers. In the present contribution we have extended such computational protocol to simulate spectroscopic properties of a molecular solid, namely poly-crystalline uracil. Firstly we have selected a realistic molecular model for representing the spectroscopic properties of uracil in the solid state, the uracil heptamer, and then we have computed the relative anharmonic frequencies combining less demanding approaches such as the hybrid B3LYP-D3/DFTBA one, in which the harmonic frequencies are computed at a higher level of theory (B3LYP-D3/N07D) while the anharmonic shifts are evaluated at a lower level of theory (DFTBA), and the reduced dimensionality VPT2 (RD-VPT2) approach, where only selected vibrational modes are computed anharmonically along with the couplings with other modes.