Calculations and Characterization of the Electronic Spectra of DNA Bases Based on ab Initio MP2 Geometries of Different Tautomeric Forms

Abstract

The absorption spectra and transition moment directions of the four DNA bases and uracil were calculated, utilizing the semiempirical INDO/S-CI method and the ab initio CIS/6-31G* method. A linear scaling of the CIS/6-31G* transition energies was necessary to get good agreement with the observed energies. CASPT2 π → π* transition energies and polarizations of adenine were also calculated. Fully MP2/6-31G*-optimized geometries were used in the calculations of the electronic spectra. The effect of possible tautomerism was investigated by calculation of the spectrum of several tautomers of guanine and cytosine. Specific and nonspecific solvent effects were considered in the calculations. Nonspecific solvent effects were modeled by a continuum model. Specific solvent interactions were modeled by inclusion of one water molecule in “supermolecule” calculations of the geometry and the spectrum of cytosine and guanine. Experimental transition energies were reproduced with an average error of less than 0.3 eV, and in most cases even better. Transition moment directions were calculated in good agreement with observations and other theoretical results in most cases. In some cases directions do not agree with observations. In these cases we have shown that the observed directions might be affected by the presence of more than one tautomeric form or by solvent or crystal effects. We propose a new interpretation of the π → π* absorption spectrum of cytosine and guanine due to solvent effects and tautomerism. A simple model, based on symmetry and geometry arguments, was used to rationalize the computed transition moment directions.

The fluorescence transition of 2‐aminopurine in double‐ and single‐stranded DNA

“…Table I shows the computed wavelengths and oscillator strengths for the lowest energy vertical transitions of the single-stranded (three base) and doubled-stranded (six base) structures studied. As the method used, CIS, is known to systematically over-estimate transition energies, mainly due to its neglect of electron correlation, the computed energies have been scaled by a constant factor of 0.72, as recommended by Broo and Holmén [9]. It should be noted that the absolute values of the oscillator strengths will also be lower than those predicted by the CIS method.…”

Theoretical Analysis of the Excited State Properties of Wybutine: A Natural Probe for Transfer RNA Dynamics

“…As a rule, excitation energies are substantially overestimated in the CIS calculations, since it fails to properly account for differences in dynamical electron correlation in the ground and the excited states. Broo and Holmén have suggested that this difference is comparable in all the nucleobases and have used a scaling factor of 0.72 for the excitation energies of π − π * transitions [22].…”

QM/MM calculation of solvent effects on absorption spectra of guanine

“…Guanine has been the subject of many theoretical [15][16][17][18][19][20][21][22][23][24][25][26][27][28][29] and experimental investigations. [30][31][32][33][34][35][36][37][38] Over the years a wealth of information about its ground and electronically electronic states has been gathered.…”