Ab Initio Molecular Dynamics Studies of Stacked Adenine–Thymine and Guanine–Cytosine Nucleic Acid Base Pairs in Aqueous Solution

Ab initio MD studies have been performed on stacked adenine–thymine (A–T) and guanine–cytosine (G–C) nucleobase pairs solvated in water using Born–Oppenheimer molecular dynamics. These two systems have been analyzed using RDF, SDF, angle-distance CDF (combined distribution functions), plane projection analysis, hydrogen bond analysis, and non-covalent interaction (NCI) plots. The stacking property studies have shown that the molecular orientation of the A–T pair is completely opposite to that of the G–C pair though the center of mass distance between the two molecules is similar. The G–C pair shows significantly more stability in water than the A–T system does. RDF analyses show that the –NH– group and carbonyl groups show predominant interaction with water molecules. Water molecules are found to be most in numbers around the cytosine molecule and least around the adenine molecule. Hydrogen bonding studies show that the guanine molecule forms the highest number of hydrogen bonds with water molecules. On the other hand, the hydrogen atom attached to the –NH– group of adenine molecule shows the longest mean H-bond lifetime with water oxygen atoms. NCI interactions calculated through the ab initio method help us to visualize the [Formula: see text]-electron stacking and H-bonding between aromatic nucleobases and water molecules. A great shift in bond polarity and interaction intensity in different functional groups is observed for the nucleobases going from individually solvated molecules to paired states.