Spectra and structure of uracil and its 5-haloderivatives: a review (original) (raw)
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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.
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.
Infrared Spectra and Thermodynamic Functions of 5-Iodo-Uracil
The infrared (4000-600 cm KBr matrix of title compound has been analyzed for the purpose of vibrational assignments. The tautomeric forms of the title compound have also been shown and discussed. Probable assignments to observe bands have been discussed. The thermodynamic functions have been computed, plotted and discussed.
Journal of Molecular Structure-theochem, 2009
The molecular structure and vibrational spectra of uracil have been investigated by Hartree-Fock and density functional (B3LYP) methods with the 6-31G(d,p) basis set. The optimized geometric bond lengths and bond angles obtained by computations show good agreement with experimental data. Comparison of the experimental spectra with anharmonic vibrational frequencies indicates that B3LYP results are more accurate than the HF approach for the molecule.
The effect of C5 substitution on the photochemistry of uracil
Phys. Chem. Chem. …, 2010
A combined experimental and theoretical study on the excited-state behavior of the uracil analogues, 5-OH-Ura and 5-NH 2 -Ura is reported. Two-photon ionization and IR/UV double-resonant spectra show that there is only one tautomer present for each with an excited state lifetime of 1.8 ns for 5-OH-Ura and 12.0 ns for 5-NH 2 -Ura as determined from pump-probe experiments. The nature of the excited states of both species is investigated by means of multi-reference ab initio methods. Vertical excitation energies, excited state minima, minima on the crossing seam and reaction paths towards them are determined. Sizeable barriers on these paths are found that provide an explanation for the lifetimes of several nanoseconds observed in the experiment.
Journal of Molecular Structure: THEOCHEM, 2010
Density functional calculations (DFT) by various methods were performed to clarify wavenumber assignments of the experimental observed bands. A comparison with the molecule of uracil was made, and specific scale factors were deduced and employed in the predicted wavenumbers of 5-IU. Comparisons were also performed with other halo-uracil derivatives. The scaled wavenumbers were compared with IR and Raman experimental data. Good reproduction of the experimental wavenumbers is obtained and the % error is very small in the majority of cases. The equilibrium geometry of 5-IU was also calculated at several levels, as well as the atomic charges and several thermodynamic parameters. All the tautomer forms of 5-iodouracil were determined and optimized. Several general conclusions were underlined.
Theoretical structural and vibrational study of 5-trifluoromethyluracil. A comparison with uracil
2014
A theoretical study on the ionization of tetrachloroethylene with analysis of vibrational structure of the photoelectron spectra A theoretical study on the ionization of pyrrole with analysis of vibrational structure of the photoelectron spectra A theoretical study on ionization of ethylene with analysis of vibrational structure of the photoelectron spectra Abstract. In the present work, a comparative study on the structural and vibrational properties of the 5trifluoromethyluracil (TFMU) derivative with those corresponding to uracil in gas and aqueous solution phases was performed combining the available H 1 -NMR, C 13 -NMR, F 19 -NMR and FTIR spectra with Density Functional Theory (DFT) calculations. Three stable conformers were theoretically determined in both media by using the hybrid B3LYP/6-31G* method. The solvent effects were simulated by means of the self-consistent reaction field (SCRF) method employing the integral equation formalism variant (IEFPCM). Complete assignments of the vibrational spectra in both phases were performed combining the internal coordinates analysis and the DFT calculations with the Scaled Quantum Mechanics Force Field (SQMFF) methodology. The atomic charges, bond orders, solvation energies, dipole moments, molecular electrostatic potentials and force constants parameters were calculated for the three conformers of TFMU in gas phase and aqueous solution.
Role of different 5‐substituents on the mass spectrometric behaviour of uracil
The influence of different 5-substituents on the mass spectrometric behaviour of uracil was systematically studied by means of mass-analysed ion kinetic energy spectrometry. By applying this technique to the molecular ions and the major primary product ions formed by loss of HNCO, the electron impact-induced fragmentation patterns of a series of substituted uracils could be elucidated. In addition to the common decomposition processes, distinctive fragmentation routes were identified for some compounds, and a rationale for the observed behaviour is given based on the electronic properties of the substituents.
Density functional calculations (DFT) by various methods were performed to clarify wavenumber assignments of the experimental observed bands. A comparison with the molecule of uracil was made, and specific scale factors were deduced and employed in the predicted wavenumbers of 5-IU. Comparisons were also performed with other halo-uracil derivatives. The scaled wavenumbers were compared with IR and Raman experimental data. Good reproduction of the experimental wavenumbers is obtained and the % error is very small in the majority of cases. The equilibrium geometry of 5-IU was also calculated at several levels, as well as the atomic charges and several thermodynamic parameters. All the tautomer forms of 5-iodouracil were determined and optimized. Several general conclusions were underlined.