Formation of hydrogen-bonded dimers of uracil and amino acids: Cysteine, lysine and phenylalanine. A density functional theory study

Abstract

Hydrogen-bonded dimers of uracil, N1-methyluracil, cysteine, lysine and phenylalanine have been studied by density functional theory (DFT), at the B3LYP/6-311++G** level, with counterpoise correction. In self-association, the most stable hydrogen-bonded dimers involved NH and CO groups in uracil and N1-methyluracil, and the carboxylic groups in amino acids. Hydrogen bond energies were found to be between −33.8 and −21.8 kJ mol −1 for uracil and between −33.7 and −32.1 kJ mol −1 for the amino acids, indicating that relatively strong hydrogen bonds may be formed in both systems. Hetero-association between uracils and amino acids was studied at the same level of calculations used for self-association. Hydrogen-bonded heterodimers involving those groups which are active in self-associations were found. Dimer formation energies between uracil and the three amino acids were similar, showing that a preferential interaction of uracil with a particular partner is not evident at this level of structural complexity. The nature of the uracil donor group regulates the processes of association as observed from a comparison of the respective energies. Self-association of uracil is favoured over hetero-association with amino acids when N1H is the donor group, but hetero-association is predominant when N3H is the donor group.