Anab initio molecular orbital study of hydrogen bonding and ion-molecule association in model systems for DNA bases

Abstract

Ab initio calculations have been performed to investigate hydrogen bonding and ion-molecule association in complexes of H2O with the neutral, protonated, and Li+ complexes of N-formylformaldehyde and N-formylformamidine. In the complexes with the neutral bases, H2O assumes an in-plane bridging position in the amide and amidine regions. The most stable complex is the bridging N-formylformamidine–H2O complex in the amidine region, which has an MP2/6–31 + G(d,p) binding energy of −9 kcal/mol. Hydrogen bonded complexes of H2O with the oxygen-protonated bases have open structures with the protonated bases as proton donors, and binding energies ranging from −16 to −24 kcal/mol. Nitrogen protonation of N-formylformamidine leads to an equilibrium chelated hydrogen bonded structure with a stabilization energy of –21 kcal/mol. When Li+ associates with these bases at a carbonyl oxygen, hydrogen-bonded bridging structures with H2O reappear, and wobble complexes exist in the amide and amidine regions of N-formylformaldehyde and N-formylformamidine. These complexes have binding energies of –13 to –14 kcal/mol. However, the most stable comples has H2O directly bonded to Li+, with an MP2 binding energy of –30 kcal/mol. No hydrogen bonded structures of H2O with N-formylformamidine exist in the amide region when Li+ associates with this base at the CN group. Hydrogen bond energies computed at the single-determinant Hartree–Fock level with the 6−31G(d) basis set approximate correlated MP2/6–31 + G(d, p) energies to within 1 kcal/mol for all of the neutral and charged complexes. However, when H2O is bonded to Li+, HF6–31G(d) association energies overestimate MP2/6–31 + G(d, p) energies by 3 kcal/mol.