Electron-Correlated Calculations of Electric Properties of Nucleic Acid Bases

Abstract

Full geometry optimizations have been performed at the MP2 level of theory using the 6-31G(d,p) basis set for the five common nucleic acid bases (uracil, thymine, cytosine, adenine, and guanine) and three related bases (fluorouracil, 5-methylcytosine, and hypoxanthine). Several electric properties were subsequently calculated using the optimized geometries and the larger polarized basis sets of Sadlej. Including electron correlation decreases the magnitude of the dipole moments by 10-15% for every base except adenine. In all cases, inclusion of electron correlation increases the mean polarizability by 8-12% and also increases the polarizability anisotropy by as much as 14-20%. Results for structurally similar bases were compared in order to qualitatively study the effects of functional group substitution on geometries and electric properties.

Basis set convergence of electric properties in HF and DFT calculations of nucleic acid bases

“…From the fully optimized geometries for benzene and pyridine (at the B3LYP/DZP level) and for the nucleic acid bases and three related bases [17] (at the MP2/6-31G** level), using noncorrelated (HF) and correlated (B3LYP and BP86) methods and the hierarchical sequence of AXZP (X ϭ D, T, Q) basis sets generated by Jorge et al, [8,12] electric properties were calculated and compared with theoretical and experimental results reported in the literature. Table I shows the convergence of the calculated components of the dipole moments and polarizabilities with the basis set quality in benzene, pyridine, uracil, cytosine, thymine, guanine, adenine, fluorouracil, 5-methylcytosine, and hypoxanthine at the HF and DFT levels of theory.…”

“…This conclusion is important, since experiences in electric property calculations of small molecules [12, 28 -32] have shown that reliable indications of the convergence of the HF results to the respective HF limits are slower, i.e., it is necessary to use larger basis sets to obtain it. Thus, from here on, the ADZP results will be used to compare with a selection of theoretical [17] and experimental [4,[21][22][23] , ␣ , and ⌬␣ values reported in the literature. For adenine, guanine, and hypoxanthine (two ring compounds), electrical property calculations using the AQZP basis set were not carried out (cf., Table I) because the computational time spent in these cases increase significantly.…”

“…Initially, the B3LYP/DZP model was used to determine the equilibrium geometries of benzene and pyridine and for the nucleic acid bases and the three related bases the fully optimized MP2 geometries from Ref. [17] were taken. Then, from these optimized geometric parameters, electric properties were evaluated.…”

“…Johnson et al [17] fully reoptimized the geometries of all bases, fluorouracil, 5-methylcytosine, and hypoxanthine with the MP2/6-31G ** model. Several electric properties were subsequently calculated using the optimized geometries and the polarized [5s3p2d]/[3s2p] basis set of Sadlej [18].…”

“…The latter two -conjugated molecules are important because the number of experimental data of electric properties available in the literature is larger and, then, we can better evaluate the accuracy that can be achieved with the models used in this work. Full geometry optimization for benzene and pyridine as well as calculated static values of the dipole moment magnitude () and dipole polarizability (␣ ) are presented and compared with previous theoretical [17] and experimental [4,[21][22][23] results. The effects of basis set enlargements and correlation corrections on the dipole moment and dipole polarizability were examined in this work.…”