Conformational analyses of 9-(3-(3-indolyl)propyl)adenine and 9-(3-(3-indolyl)propyl)-1-methyladeninium by empirical energy calculations, a model study for the intramolecular stacking interaction of indole ring with adenine base and with N(1)-methylated adenine base.

Abstract

In order to elucidate the energetically stable conformations of 9-[3-(3-indolyl) propyl] adenine and 9-[3-(3-indolyl) propyl]-1-methyladeninium, as intramolecular stacking models for the indoleadenine and indole-adeninium interactions, respectively, empirical energy calculations considering nonbonded, electrostatic and torsional energies were carried out. Two or one out of four kinds of stacking modes were considered to be energetically stable for the former or latter molecule, respectively. These stacking modes were significantly stabilized by the orbital interaction between the highest occupied molecular orbital of the indole ring and the lowest unoccupied one of the adenine or the adeninium ring.