Effect of AU(111) on hydrogen bonds in PNA and DNA base pairs

Abstract

The structures of DNA and peptide nucleic acid (PNA) base pairs were affected in the electron density toward the geometry change by Au(111), which were investigated using the 6-311++G(d,p) basis set for nucleic acid structures and LANL2DZ basis set for Au(111) at B3LYP level to generate the wave functions for analysis in the atoms in molecules theory (AIM). The results indicated that the hydrogen bond interactions within the PNA structures experience stronger effects than DNA except N・ ・ ・H of guanine and cytosine (GC) base pairs. PNA has the same tendency of the structure change in every conformer while DNA has a high variability. For the effect of electric field on base pair structures combined with Au(111), the results manifest four categories of the tendency: depending on the electric field intensity and direction, depending on the intensity of electric field in one direction, depending on the electric field intensity but independent of the electric field direction, and a trend that cannot be classified.