C-H/O interactions of nucleic bases with a water molecule: a crystallographic and quantum chemical study

Abstract

The C-H/O interactions of nucleic bases with a water molecule were studied by analyzing data in the Cambridge Structural Database (CSD) and by ab initio calculations. The analysis of the C-H/O interactions in the crystal structures from the CSD indicates that nucleic base-water C-H/O interactions do not show preference for linear contacts. The results of the ab initio calculations are in accord with the CSD data and show that the bifurcated C-H/N-H interactions are stronger than linear interactions for all nucleic bases. The bifurcated C-H/N-H interactions are also stronger than the bifurcated C-H/C-H interactions. The strongest interaction is the bifurcated C6-H/N1-H interaction of uracil with an energy of -5.46 kcal mol(-1) calculated at the MP2/cc-pVTZ level. All linear C-H/O interactions, except one with adenine, are stronger than -2.0 kcal mol(-1). The strongest linear interaction is with uracil, -3.59 kcal mol(-1). The calculated electrostatic potential maps for nucleic base molecules can explain the results we obtained for interaction energies. The results show that C-H/O interactions of nucleic bases with a water molecule are substantially stronger than C-H/O interactions of benzene (-1.28 kcal mol(-1)) and pyridine (-1.97 kcal mol(-1)). The investigation of C-H/O interactions of nucleic bases with water could shed light on the intermolecular interactions of DNA or RNA bases with other molecules.