Quantum Mechanical Studies for Structures and Energetic of Double Proton Transfer in Biologically Important Hydrogen-bonded Complexes

Abstract

We have performed quantum mechanical calculations to study the geometries and binding energies of biologically important, cyclic hydrogen-bonded complexes, such as formic acid + H 2 O, formamidine + H 2 O, formamide + H 2 O, formic acid dimer, formamidine dimer, formamide dimer, formic acid + formamide, formic acid + formamidine, formamide + formamidine, and barrier heights for the double proton transfer in these complexes. Various ab initio, density functional theory, multilevel methods have been used. Geometries and energies depend very much on the level of theory. In particular, the transition state symmetry of the proton transfer in formamidine dimer varies greatly depending on the level of theory, so very high level of theory must be used to get any reasonable results.

Effects of Positive and Negative Ionization on Prototropy in Pyrimidine Bases: An Unusual Case of Isocytosine

“…As it could be expected, acidity and basicity parameters of charged radicals strongly increase in the gas phase in comparison to neutral isocytosine. Analogous increase effects have also been observed for acid–base properties of charged radicals of nucleobases, their derivatives, and other molecules in the gas phase as well as in solution. − ,,,,− …”

“…For the favored radical anions, the labile proton can be transferred from the exo N7 atom to endo N3 atom and vice versa in the amidine group. The Gibbs energy barriers for neutral and ionized forms of isocytosine are typical for tautomeric conversions in the amide and amidine groups (>140 kJ mol –1 ). ,− Positive ionization slightly increases the energy barrier for proton-transfer in comparison to the neutral forms. Other prototropic molecules present in environment usually participate in the intramolecular proton-transfer of tautomeric system and reduce the energy barrier. ,− …”

The Role of Proton Transfer on Mutations

“…The protonation of NABs also contributes to the stabilization of triple helix, which is stabilized at acidic pH. The PT reaction is also seen in the molecular identification of cytosine–acidic nucleobase derivatives (Park et al, 2011). The DPT in prototropic tautomerisms for many amidine systems and porphyrins was studied experimentally, and the rates and the kinetic isotope effects for both types of DPT were reported.…”

Synthesis, microwave spectra, x-ray structure, and high-level theoretical calculations for formamidinium formate

“…9 Tropolone -formic acid has the C2v(m) symmetry but splittings were not observed due to the high barrier. 10 There are theoretical calculations of double proton transfers in the formamidine formic acid dimer by Kim, Lim and Kim, 11 Lim, Lee and Kim, 12 Park, Kim, Kim and Kim, 13 Radom, 14 et al, and Simperler, Mikenda, and Schwarz. 15 From the latter two references it was proposed that the double proton transfer could be asynchronous (nonconcerted).…”

“…The two ions present in the x-ray structure showing numbering system used.Bond lengths and angles: C(1)-O(1) 1.2464(9), C(1)-H(1) 0.950, C(2)-N(2) Non-decoupled13 C NMR spectrum (75.458 MHz) Bond lengths and angles for formamidine in the inertial axis frame. The atomic numbering is the same as those of the dimer inFigure 1.…”