Y. Podolyan - Academia.edu (original) (raw)

Papers by Y. Podolyan

Journal of Molecular Structure: THEOCHEM, 1999

The results of an ab initio post Hartree±Fock study of the relative stabilities and mechanism of ... more The results of an ab initio post Hartree±Fock study of the relative stabilities and mechanism of intramolecular proton transfer in isolated and monohydrated thiocytosine are reported. The geometries of local minima and transition states were optimized without symmetry restrictions by the gradient procedure at the HF and MP2 levels of theory and were veri®ed by energy second derivative calculations. The standard 6-31G(d) basis set was used. The single point calculations have been performed at the MP4(SDQ)/6-31 1 G(d,p)//MP2/6-31G(d) and MP2/6-31111G(d,p)//MP2/6-31G(d) approximations. The post Hartree±Fock ab initio theory predicts different distributions of the tautomers for cytosine and thiocytosine both in the gas phase and in polar media (PCM solvation model). Interaction of thiocytosine tautomers with one water molecule decreases the difference in the energies of the two most stable tautomers signi®cantly but does not change the order of the stability of tautomers. However, ®ve water molecules forming a ®rst solvation shell change the stability pattern. The heights of the barriers of sulfur-involved proton transfers in thiocytosine are much smaller than analogous barriers in cytosine. In contrast, corresponding barriers for the complexes with one water molecule are higher in thiocytosine. q

International Journal of Molecular Sciences, 2003

The Journal of Physical Chemistry A, 2002

... The values of Gibbs free energy of formation have been calculated by the standard formula ΔG ... more ... The values of Gibbs free energy of formation have been calculated by the standard formula ΔG = ΔH − TΔS at room temperature (298.15 K). The ΔS values have been calculated at the same levels of theory as the optimizations. ...

The Journal of Physical Chemistry A, 2000

ABSTRACT The post-Hartree−Fock ab initio studies were performed to predict the properties of eigh... more ABSTRACT The post-Hartree−Fock ab initio studies were performed to predict the properties of eight tautomers of 5-azacytosine. All geometries were optimized without symmetry restrictions by the gradient procedure at the MP2 level of theory using the standard 6-31G(d,p) basis set. Single-point calculations have been performed at the MP2/6-311++G(d,p), MP2/6-31++G(2df,2pd), MP4(SDTQ)/6-31G(d,p), and CCSD(T)/6-31G(d,p) levels for all eight tautomers. The calculations of the stabilities of the tautomers in a polar medium have been performed using explicitly water molecules which form a first solvation shell, and PCM solvation model. The results are compared to the corresponding data for cytosine tautomers. Ab initio calculations predict a different order of tautomers in cytosine and 5-azacytosine; however, the relative stabilities of the two lowest energy tautomers are the same for both bases. The molecular geometries of guanine−5-azacytosine and guanine−cytosine base pairs have been optimized using the MP2/6-31G(d,p) and B3LYP/6-31G(d,p) levels of theory. The interaction energies have been calculated at the MP2/6-31G(d,p), MP2/6-311++G(d,p), MP4(SDQ)/6-31G(d,p), and B3LYP/6-31G(d,p) levels and corrected for the basis set superposition error. The interaction and solvation energies of base pair complexes with water have been estimated using first solvation shell of water molecules and PCM solvation model. The study has shown the similar geometrical parameters for fragments of both bases associated with the formation of hydrogen bonds with guanine and different molecular parameters associated with the moieties involved in the interactions with cytosine-5-methyltransferase.

Chemical Physics Letters, 2003

The double proton transfer reaction in model formamide-formamidine dimer mimicking adenine-thymin... more The double proton transfer reaction in model formamide-formamidine dimer mimicking adenine-thymine base pair was investigated. The physical nature of the catalytic activity of the first hydration shell has been analyzed using hybrid variation-perturbation decomposition of intermolecular interaction energy. The differential transition state stabilization energy is dominated by long range electrostatic multipole term, whereas electrostatic penetration, exchange and delocalization terms are negligible or partly cancel each other. This allowed to derive (within electrostatic approximation) the generalized static and dynamic properties of the molecular environment exerting optimal catalytic activity towards canonic ! rare and rare ! canonic tautomeric rearrangement.

Biopolymers, 2001

High-level quantum-chemical and quantum-dynamics calculations are reported on the tautomerization... more High-level quantum-chemical and quantum-dynamics calculations are reported on the tautomerization equilibrium and rate constants of guanine and its complexes with one and two water molecules. The results are used to estimate the fraction of guanine present in the cell during DNA synthesis as the unwanted tautomer that forms an irregular base pair with thymine, thus giving rise to a spontaneous GC --&amp;gt; AT point mutation. A comparison of the estimated mutation frequency with the observed frequency in Escherichia coli is used to analyze two proposed mechanisms, differing in the extent of equilibration reached in the tautomerization reaction. In the absence of water, the equilibrium concentration of tautomeric forms is relatively large, but the barrier to their formation is high. If water is present, tautomeric forms are less favored, but water molecules may serve as efficient proton conduits causing rapid tautomerization. It is tentatively concluded that the mechanism in which a high tautomerization barrier keeps the tautomeric transformation far from a state of equilibrium is more likely than a mechanism in which water and/or polymerases produce a low equilibrium concentration of the tautomeric forms.