TDDFT investigation on nucleic acid bases: Comparison with experiments and standard approach

Abstract

A comprehensive theoretical study of electronic transitions of canonical nucleic acid bases, namely guanine, adenine, cytosine, uracil, and thymine, was performed. Ground state geometries were optimized at the MP2/6-311G(d,p) level. The nature of respective potential energy surfaces was determined using the harmonic vibrational frequency analysis. The MP2 optimized geometries were used to compute electronic vertical singlet transition energies at the time-dependent density functional theory (TDDFT) level using the B3LYP functional. The 6-311++G(d,p), 6-311(2+,2+)G(d,p), 6-311(3+,3+)G(df,pd), and 6-311(5+,5+)G(df,pd) basis sets were used for the transition energy calculations. Computed transition energies were found in good agreement with the corresponding experimental data. However, in higher transitions, the Rydberg contaminations were also obtained. The existence of pisigma* type Rydberg transition was found near the lowest singlet pipi* state of all bases, which may be responsible for the ultrafast deactivation process in nucleic acid bases.

UV degradation of deoxyribonucleic acid

“…The peak at 161.8 nm (7.66 eV) arises from strong thymine absorption as determined by Shlukla and Leszczynsky [22]. The peaks at 177.4 nm (6.99 eV), 188.3 nm (6.59 eV) and 201.5 nm (6.15 eV) are due to the strong transitions located at 6.28 (4 1 A'), 6.38 (6 1 A') and 6.81 (8 1 A') calculated by Borin et al [23] for purine N(7)H and N(9)H. The peak 209.9nm (5.91 eV) may be due to n π* guanine transition and a π π* transition in thymine [22] and the peak at 263.4 (4.708 eV) is generally assigned to all bases, see for example the recent work of So and Alavi [24], with assignments of vertical excitation energies displayed in [25]. In addition, the DNA molecule spectra should have contributions of deoxyribose and phosphate groups as will be discussed later.…”

Photoexcitation of Dinucleoside Radical Cations: A Time-Dependent Density Functional Study

“…In recent years, the TD-DFT method has been found suitable to compute vertical transition energies of both gas phase and solvated molecules, with results that are comparable to experimental results. [15][16][17][18][19] In this study, we calculated the transition energies of all the systems in aqueous media (ε = 78.4) using self-consistent reaction field (SCRF) calculations and the polarized continuum model (PCM). The transition energies in aqueous media were calculated using the gas phase optimized geometries.…”

“…In the S 12 transition, the hole is localized on the thymine, with a very small part on the connected sugar ring. Transitions S 18 , and S 20 occur at 3.40 and 3.58 eV, respectively, with the hole localized on both sugar rings, a phosphate and the guanine ring.…”

Vertical excitation energies for ribose and deoxyribose nucleosides

“…The vertical excitation energies of the bases have been calculated at different levels of theory and for the low-lying vertical excitation energies, the TDDFT method at the B3LYP level has been shown to give correct experimental vertical ordering of the states. 1,2 Ref. 1 gives a review of experimental measurements and calculations of vertical excitation energies up to 2004.…”