The correlation between hydration of Nucleic Acid Bases (NABs) and their conformational flexibili... more The correlation between hydration of Nucleic Acid Bases (NABs) and their conformational flexibility was analyzed based on the results of Car-Parrinello Molecular Dynamics (CPMD) simulations of NABs in bulk water environment. Correlations with quantum chemical results were drawn whenever it was possible. Statistical analysis confirmed that hydration causes bond length alteration in NABs and formation of zwitter-ionic resonance structures. In contrast to the gas phase, bulk hydration results in restricted mobility of amino group and increase in population of its planar-like conformations. At the same time, rings of all NABs become almost equally flexible in the dynamic aqueous environment. Therefore, each NAB possesses a non-planar effective conformation of pyrimidine ring despite the fact that planar geometry corresponds to minimum on the potential energy surface.
Page 1. Morphology and Optical Response of Carbon Nanotubes Functionalized by Conjugated Polymers... more Page 1. Morphology and Optical Response of Carbon Nanotubes Functionalized by Conjugated Polymers Al'ona Furmanchuk § , Jerzy Leszczynski § , Sergei Tretiak † , Svetlana V. Kilina ‡∗ § Department of Chemistry and Biochemistry, ...
Cleavage of the O-P bond in 8-bromo-2&amp... more Cleavage of the O-P bond in 8-bromo-2'-deoxyguanosine-3',5'-diphosphate (BrdGDP), considered as a model of single strand break (SSB) in labelled double-stranded DNA (ds DNA), is investigated at the B3LYP/6-31++G(d,p) level. The thermodynamic and kinetic characteristics of the formation of SSB are compared to those related to the 5',8-cycloguanosine lesion. The first reaction step, common to both damage types, which is the formation of the reactive guanyl radical, proceeds with a barrier-free or low-barrier release of the bromide anion. The guanyl radical is then stabilized by hydrogen atom transfer from the C3' or C5' sites of the 2'-deoxyribose moiety to its C8 center. The C3' path, via the O-P bond cleavage, leads to a ketone derivative (the SSB model), while the C5' path is more likely to yield 5',8-cycloguanosine.
High level ab initio studies demonstrate substantial conformational flexibility of amino groups o... more High level ab initio studies demonstrate substantial conformational flexibility of amino groups of nucleic acid bases. This flexibility is important for biological functions of DNA. Existing force field models of molecular mechanics do not describe this phenomenon due to a lack of quantitative experimental data necessary for an adjustment of empirical parameters. We have performed extensive calculations of nucleic acid bases at the MP2/6-31G(d,p) level of ab initio theory for broad set of amino group configurations. Twodimensional maps of energy and geometrical characteristics as functions of two amino hydrogen torsions have been constructed. We approximate the maps by polynomial expressions, which can be used in molecular mechanics calculations. Detailed considerations of these maps enable us to propose a method for determination of numerical coefficients in the developed formulae using restricted sets of points obtained via higher-level calculations.
Recently proposed protocol for accurate (errors within about 1kcal/mol of experimental data) pred... more Recently proposed protocol for accurate (errors within about 1kcal/mol of experimental data) prediction of the thermodynamic parameters of intermolecular interactions have been tested against other DFT, MP2 and CCSD(T) based methods for complexes including GC and AT DNA base pairs. Newly optimized procedure comprising of two steps proved itself as good compromise between computational demand and chemical accuracy. The first step of proposed protocol involves the counterpoise corrected optimization and calculation of harmonic frequencies at B3LYP/cc-pVTZ level. The second step consists of single point MP2 (cc-pVDZ and cc-pVTZ) calculations and extrapolation to the complete basis set limit.
Oxo-hydroxy tautomerism and phototautomerism of 2-quinolinone, 1-isoquinolinone, 3-hydroxyisoquin... more Oxo-hydroxy tautomerism and phototautomerism of 2-quinolinone, 1-isoquinolinone, 3-hydroxyisoquinoline, 2-quinoxalinone, and 4-quinazolinone were studied using the matrix-isolation technique. These compounds contain a benzene ring fused with a heterocyclic ring of 2-pyridinone, 2-pyrazinone, or 4-pyrimidinone. It turned out that direct attachment of a benzene ring to a heterocycle leads to a very pronounced increase of the relative stability of oxo tautomers (in comparison with the tautomerism of the parent compounds 2-pyridinone, 2-pyrazinone, and 4-pyrimidinone). The only exception concerns 3-hydroxyisoquinoline, where fusion with a benzene ring enforces rearrangement of the double-and single-bond system in the oxo tautomer. This destabilizes substantially the oxo form with respect to the hydroxy tautomer. The ratios of population of the oxo and hydroxy tautomers observed in Ar matrixes correspond to the tautomeric equilibria of the compounds in the gas phase. These equilibria were well reproduced by theoretical calculations carried out at the QCISD and QCISD(T) levels. The combined experimental and theoretical results reveal links between aromaticity and tautomerism. Moreover, a UV-induced phototautomeric reaction transforming the oxo forms into the hydroxy tautomers was observed for all (except 3-hydroxyisoquinoline) studied compounds. This photoeffect allowed separation of the IR spectra of the tautomers in question.
The correlation between hydration of Nucleic Acid Bases (NABs) and their conformational flexibili... more The correlation between hydration of Nucleic Acid Bases (NABs) and their conformational flexibility was analyzed based on the results of Car-Parrinello Molecular Dynamics (CPMD) simulations of NABs in bulk water environment. Correlations with quantum chemical results were drawn whenever it was possible. Statistical analysis confirmed that hydration causes bond length alteration in NABs and formation of zwitter-ionic resonance structures. In contrast to the gas phase, bulk hydration results in restricted mobility of amino group and increase in population of its planar-like conformations. At the same time, rings of all NABs become almost equally flexible in the dynamic aqueous environment. Therefore, each NAB possesses a non-planar effective conformation of pyrimidine ring despite the fact that planar geometry corresponds to minimum on the potential energy surface.
Page 1. Morphology and Optical Response of Carbon Nanotubes Functionalized by Conjugated Polymers... more Page 1. Morphology and Optical Response of Carbon Nanotubes Functionalized by Conjugated Polymers Al'ona Furmanchuk § , Jerzy Leszczynski § , Sergei Tretiak † , Svetlana V. Kilina ‡∗ § Department of Chemistry and Biochemistry, ...
Cleavage of the O-P bond in 8-bromo-2&amp... more Cleavage of the O-P bond in 8-bromo-2'-deoxyguanosine-3',5'-diphosphate (BrdGDP), considered as a model of single strand break (SSB) in labelled double-stranded DNA (ds DNA), is investigated at the B3LYP/6-31++G(d,p) level. The thermodynamic and kinetic characteristics of the formation of SSB are compared to those related to the 5',8-cycloguanosine lesion. The first reaction step, common to both damage types, which is the formation of the reactive guanyl radical, proceeds with a barrier-free or low-barrier release of the bromide anion. The guanyl radical is then stabilized by hydrogen atom transfer from the C3' or C5' sites of the 2'-deoxyribose moiety to its C8 center. The C3' path, via the O-P bond cleavage, leads to a ketone derivative (the SSB model), while the C5' path is more likely to yield 5',8-cycloguanosine.
High level ab initio studies demonstrate substantial conformational flexibility of amino groups o... more High level ab initio studies demonstrate substantial conformational flexibility of amino groups of nucleic acid bases. This flexibility is important for biological functions of DNA. Existing force field models of molecular mechanics do not describe this phenomenon due to a lack of quantitative experimental data necessary for an adjustment of empirical parameters. We have performed extensive calculations of nucleic acid bases at the MP2/6-31G(d,p) level of ab initio theory for broad set of amino group configurations. Twodimensional maps of energy and geometrical characteristics as functions of two amino hydrogen torsions have been constructed. We approximate the maps by polynomial expressions, which can be used in molecular mechanics calculations. Detailed considerations of these maps enable us to propose a method for determination of numerical coefficients in the developed formulae using restricted sets of points obtained via higher-level calculations.
Recently proposed protocol for accurate (errors within about 1kcal/mol of experimental data) pred... more Recently proposed protocol for accurate (errors within about 1kcal/mol of experimental data) prediction of the thermodynamic parameters of intermolecular interactions have been tested against other DFT, MP2 and CCSD(T) based methods for complexes including GC and AT DNA base pairs. Newly optimized procedure comprising of two steps proved itself as good compromise between computational demand and chemical accuracy. The first step of proposed protocol involves the counterpoise corrected optimization and calculation of harmonic frequencies at B3LYP/cc-pVTZ level. The second step consists of single point MP2 (cc-pVDZ and cc-pVTZ) calculations and extrapolation to the complete basis set limit.
Oxo-hydroxy tautomerism and phototautomerism of 2-quinolinone, 1-isoquinolinone, 3-hydroxyisoquin... more Oxo-hydroxy tautomerism and phototautomerism of 2-quinolinone, 1-isoquinolinone, 3-hydroxyisoquinoline, 2-quinoxalinone, and 4-quinazolinone were studied using the matrix-isolation technique. These compounds contain a benzene ring fused with a heterocyclic ring of 2-pyridinone, 2-pyrazinone, or 4-pyrimidinone. It turned out that direct attachment of a benzene ring to a heterocycle leads to a very pronounced increase of the relative stability of oxo tautomers (in comparison with the tautomerism of the parent compounds 2-pyridinone, 2-pyrazinone, and 4-pyrimidinone). The only exception concerns 3-hydroxyisoquinoline, where fusion with a benzene ring enforces rearrangement of the double-and single-bond system in the oxo tautomer. This destabilizes substantially the oxo form with respect to the hydroxy tautomer. The ratios of population of the oxo and hydroxy tautomers observed in Ar matrixes correspond to the tautomeric equilibria of the compounds in the gas phase. These equilibria were well reproduced by theoretical calculations carried out at the QCISD and QCISD(T) levels. The combined experimental and theoretical results reveal links between aromaticity and tautomerism. Moreover, a UV-induced phototautomeric reaction transforming the oxo forms into the hydroxy tautomers was observed for all (except 3-hydroxyisoquinoline) studied compounds. This photoeffect allowed separation of the IR spectra of the tautomers in question.
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