Theoretical study of hyperfine coupling constants of uracil, cytosine and their halogenated derivatives in triplet state

New Insights into the Structure and Reactivity of Uracil Derivatives in Different Solvents-A Computational Study

Ab initio calculations were carried out to understand the reactivity and stability of some uracil derivatives, cytosine, 1-methyl cytosine, and cytidine in solvents, water, dimethyl sulfoxide (DMSO), n-octanol, and chloroform. Geometries were fully optimized at MP2 and B3LYP using the 6-31+G(d,p) basis set by applying the Solvation Model on Density (SMD) in solvent systems. The syn conformer of cytidine (cytidine II) is the most stable conformer in the gas phase, while the anticonformer (cytidine IV) is most stable in all of the solvents. Solvation free energy and polarizability values in different solvents decrease in the order water > DMSO > n-octanol > chloroform, while dipole moment, first-order hyperpolarizability, and HOMO-LUMO energy gap values follow the order of polar protic solvent (water and n-octanol) > polar aprotic solvent (DMSO) > nonpolar solvent (chloroform). The solvation free energy, dipole moment, polarizability, and first-order hyperpolarizability values also follow the order of cytosine > 1-methyl cytosine > cytidine. To illustrate that the molecular properties correlate well with the reactivity of the molecules, ab initio calculations were carried out for the reaction of uracil derivatives with Br2 in the gas phase, water, DMSO, n-octanol, and chloroform. All ground and transition state geometries were fully optimized at B3LYP/6-31+G(d,p), and energies were also calculated at G3MP2 for cytosine and 1-methyl cytosine. For cytosine and 1-methyl cytosine, Gibbs energies of activation decrease with the polarity of the solvent that is chloroform > n-octanol > DMSO > water, while the Gibbs energies of activation for the reaction with cytidine decrease in the order of water > DMSO > n-octanol > chloroform. These results suggest that solvent polarity is very important for the stability and reactivity of uracil derivatives. Hydrogen bonding may also play an important role mainly for cytidine. Free energies of activation decrease with the size of the molecule, i.e., cytosine > 1-methyl cytosine > cytidine.

Simulation of a tetramer form of 5-chlorouracil: the vibrational spectra and molecular structure in the isolated and in the solid state by using DFT calculations

A Raman and FT-IR study of the biomolecule 5-chlorouracil in the solid state was carried out. The unit cell found in the crystal was simulated as a tetramer form by density functional calculations. They were performed to clarify the assignments of the experimentally observed bands in the spectra. Calculations in the monomer form and comparisons with the experimental data in Ar matrix were also carried out. The error in the calculated frequencies was analyzed and reduced by using scaling equations and scaling factors deduced from the uracil molecule. The calculations with the B3LYP method and with the 6-31G(d,p) and 6-311+G(2d,p) basis set, appear in general to be useful, when combining with a scaling equation procedure or with the specific scale factors, for interpretation of the general features of the IR and Raman spectra. The scaled values were used in the reassignment of the IR and Raman experimental bands. Comparison of the results with those determined in uracil and 5-halogenated derivatives were performed. The substitution at 5-position of the uracil ring by a chlorine atom has a little effect on the geometric parameters.

TDDFT STUDY OF NUCLEOBASE THIOANALOGUES AND OXO-DERIVATIVES EXCITED STATES

Thioanalogues of nucleic-acid bases have been shown to be the place of preferential charge or energy localization when incorporated in the system of respective regular bases. Most evidence of such behavior is based on experiments using γ-ray or other ionizing radiation. Here time dependent density functional theory (TDDFT) has been applied to investigate singlet and triplet excited state spectra of thioanalogues and some oxo-derivatives of nucleic-acid bases and compare the spectra to the calculated spectra of the regular bases as well as to the existing experimental data. It has been shown that thioanalogues have lower excitation singlet and triplet energies than are the respective energies in the regular bases. Energy localization on thioanalogues and their spectroscopic properties are related to the effect of sulfur substitution in such systems.

DFT Calculations of EPR Parameters in an Ionic Lattice of [M(CN)4]3-(M = Ni, Pd, Fe, Ru, Os) Complexes

The electronic g-tensor and hyperfine coupling constants were calculated for cyanide coordination complexes [M(CN)4]3- (M = Ni, Pd, Fe, Ru, Os) in KCl or NaCl host lattices through an embedded calculation approach using the Density Functional Theory and compared with previous experiments. For all tested complexes, the B3LYP functional is in good agreement with the experiments for the hyperfine coupling constants. For the electronic g-tensor calculations, performed using the coupled perturbed SCF theory, some discrepancies were found, and the best agreements with the experimental values were achieved by the B3LYP functional.