On the Nature of Intermolecular Interactions in Nucleic Acid Base−Amino Acid Side-Chain Complexes

Abstract

Twenty hydrogen-bonded complexes composed of nucleic acid base and amino acid side chain have been analyzed using ab initio quantum chemistry methods with the aim of gaining insights into the nature of molecular interactions in these systems. The intermolecular interaction energies were estimated using the second-order Møller-Plesset perturbation theory and coupled clusters approach with single and double excitations, while their components have been determined by means of a hybrid variational-perturbational decomposition scheme. Additionally, the topological analysis of an electron density distribution of the studied complexes has been performed. In the case of all of the studied neutral complexes, the main source of stabilization is the delocalizaction energy associated with the electron density deformation upon the interaction which contributes almost half of the total interaction energy. Furthermore, analysis of the interaction induced difference density maps of complexes containing neutral amino acid side chains reveals that the delocalization component involves the electron density changes localized in the double-hydrogen-bonded ring structures. A relatively good correlation between the sum of densities at hydrogen-bond critical points and the Hartree-Fock intermolecular interaction energy components (electrostatic, delocalization, and exchange) has been observed for the two independently considered sets of complexes, containing positively charged and neutral amino acid side chains.

Signature motifs of GDP polyribonucleotidyltransferase, a non-segmented negative strand RNA viral mRNA capping enzyme, domain in the L protein are required for covalent enzyme–pRNA intermediate formation

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