Effects of ionization and proton-transfer on bond length alternation in favored and rare isomers of isocytosine

Abstract

For favored and rare prototropic tautomers of isocytosine (iC), geometric consequences of ionization, one-electron loss (iC − e → iC+) and one-electron gain (iC + e → iC−), have been studied. Effects of protonation and deprotonation on geometry of neutral isocytosine (iC + H+ → iCH+ and iC − H+ → iC−H−) as well as of its charged radicals (iC− + H+ → iCH and (iC+ − H+ → iC−H) have also been examined for selected isomers. Bond length alternation for the ground states of individual isomers, investigated in two extreme environments at the B3LYP/6-311+G(d,p) and PCM(water)//B3LYP/6-311+G(d,p) levels, have been quantitatively described using the geometry-based HOMED (harmonic oscillator model of electron delocalization) index. Generally, one-electron loss, one-electron gain, and proton-transfer reactions change electron delocalization in isocytosine isomers, and consequently the HOMED values. However, the HOMED indices calculated for structures optimized at the DFT level vary analogously to those optimized with PCM. When compared to other pyrimidine bases, cytosine (C) and uracil (U), exhibiting analogous tautomeric equilibria, rotational and/or geometric isomerism of exo groups (NH2/NH and/or OH/O), linear trends can be distinguished between the HOMED values of negatively ionized isomers (iC−, C−, and U−). For positively ionized isomers (iC+, C+, and U+), relations between the HOMED indices seem to be more complex. This indicates some similarities in mechanisms of one-electron gain and some differences in mechanisms of one-electron loss for isomers of pyrimidine bases. Hence, the HOMED descriptor can be considered as some kind of ‘marker index’ for ionization mechanism in analogous series of tautomeric π-electron systems.