Four bases score a run: Ab initio calculations quantify a cooperative effect of h-bonding and pi-stacking on ionization energy of adenine in the AATT tetramer

K.B. Bravaya, E. Epifanovsky, and A.I. Krylov
J. Phys. Chem. Lett. 3, 2726 – 2732 (2012)

Benchmark calculations of the lowest ionized state of the (A:T)₂ (mixed adenine-thymine) cluster at the geometry taken from the DNA X-ray structure are presented. Vertical ionization energies (IEs) computed by the equation-of-motion coupled-cluster method with single and double substitutions are reported and analyzed. The shift in IE relative to the monomer (A) is -0.7 eV. The performance of widely used B3LYP as well as long-range and dispersion corrected wB97X-D and meta-GGA M06-2X functionals with respect to their ability to describe energetics and the character (localization versus delocalization) of the ionized states is also investigated. The shifts in IEs and changes in charge distributions caused by H-bonding and stacking interactions are analyzed in terms of additive versus cooperative effects. It is found that the cooperative effect accounts for more than 20% of the shift in IE relative to the monomer. The shifts are analyzed in terms of electrostatic interactions revealing that the cooperative effect is dominated by electrostatic interactions between adenine and thymine that are not hydrogen-bonded, i.e., cross-interactions in the duplex. Since the hole is primarily localized on adenines, QM/MM (quantum mechanics/molecular mechanics) models may be employed to describe the electronic structure of such a system, with the QM part comprising at least two adenines. The cooperative effect and, consequently, the magnitude of the shift are well reproduced by the QM/MM scheme in which neutral thymine bases are represented by point charges.

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