The Amino Group in Adenine: MP2 and CCSD(T) Complete Basis Set Limit Calculations of the Planarization Barrier and DFT/B3LYP Study of the Anharmonic Frequencies of Adenine

Abstract

The amino group in adenine plays a key role in formation of hydrogen bonds in nucleic acids and in other molecular systems. Thus, the structure of this group is of fundamental importance in the molecular recognition phenomena. Ab initio MP2 and density functional B3LYP methods with various basis sets have been used to calculate the optimized structure and the infrared spectrum of adenine (the N9-H tautomer). Calculations at the MP2 level with larger basis sets tend to decrease the degree of pyramidalization of the C-NH2 group, whereas the B3LYP method consistently yields the planar or nearly planar structure of adenine. MP2 complete basis set (CBS) limit method with the aug-cc-pVTZ --> aug-cc-pVQZ (aTZ --> aQZ) extrapolation scheme has predicted very small planarization barrier of adenine, 0.015 kcal/mol, which is in very good agreement with the MP2-predicted planarization barrier of 0.020 kcal/mol, reported by S. Wang and H. F. Schaefer III, J. Chem. Phys. 2006, 124, 044303. Similar results were obtained in calculations by the coupled cluster CCSD(T) CBS method. Thus, it can be concluded that the amino group in adenine, in the gas phase, is very flexible with a small degree of nonplanarity. Extremely low planarization barrier implies that adenine requires very little energy to conform the structure of the amino group to formation of the complementary hydrogen bonds with other molecules. This fact is very important for base pairing in nucleic acids or other polymers containing adenine residues. The anharmonic frequencies of adenine have been calculated at the B3LYP/6-311++G(df,pd) level of theory. The theoretical results show excellent agreement with the available experimental data. The revised assignment of the infrared spectrum of adenine in Ar matrix has been made. The predicted anharmonic frequency of the NH2 inversion, 181 cm(-1), is supported by the experimental data. It is demonstrated that the vibrational frequencies and potential energy distribution (PED) obtained from the B3LYP calculations are more reliable than those obtained at the MP2 level.

Fermi resonance in Ne, Ar and Kr-matrix infrared spectra of 5-bromouracil

“…However, both the correlation bases rank below to 6-311++G(df,pd) not only in the nonmonotonous regression but in the least values of ∆ max , δ rms and K (Table 1). This verified the conclusion of the previous works on efficiency of the DFT/B3LYP/6-311++G(df,pd) method for calculations of vibrational spectra [19,20]. Besides, 6-311++G(df,pd) basis requires smaller computational cost than aug-ccpVTZ one.…”

“…4) may also be assigned to the Fermi resonanceenhanced combination bands. Previously, Fermi resonance has been demonstrated in this area for uracil [19] and isocytosine [20]. Besides absorption bands, which do not correspond to the calculated spectra we can see close satellites of fundamental vibrations in the experimental spectra (Figs.…”

“…Splitting of bands due to Fermi resonance can be observed in the vibrational spectra of the pyrimidine bases in the low-temperature matrices [19,21,41,42]. By analogy with these studies, the BrU_0 absorption bands about 1710 см -1 (Figs.…”

“…Therefore, in our work, the vibrational spectra of isolated BrU molecules were obtained not only in the matrices with relatively close lattice parameters (Ar, Kr) but in Ne matrices also. To calculate vibrational spectra by the DFT/B3LYP method, in addition to correlation consistent basis sets, 6-311++G(df, pd) one was used, revealed the best results in some works [19,20]. For the first time, to scale the calculated frequencies, we employed the least square method with the corrective multiplier as the polynomial.…”

Elementary Molecular Mechanisms of the Spontaneous Point Mutations in DNA: A Novel Quantum-Chemical Insight into the Classical Understanding

“…Its interconversion is accomplished via two plane-symmetric transition states with Gibbs free energy of 14.34 and 14.57 kcal/mol and also through the planar transition state with the activation energy of 0.12 kcal/mol 1 (Table 1). MP2 complete basis set limit method with the aug-cc-pVTZ → aug-cc-pVQZ (aTZ → aQZ) extrapolation scheme has predicted very small planarization barrier of the Ade amino group, 0.015 kcal/mol (Zierkiewicz et al, 2008), which is in very good agreement with the MP2-predicted planarization barrier of 0.020 kcal/mol reported by Wang and Schaefer III (S. Wang & Schaefer III, 2006). Similar results were calculated using coupled cluster CCSD(T) complete basis set method -0.125 kcal/mol (Zierkiewicz et al, 2008).…”