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.