160
T. A. Zubatiuk et al.
of calculations by the AM1 method that the N7 atom has the highest PA value for
GMP [77]. Other anionic nucleotides have the same preferable sites of protonation
as molecules with a neutral phosphate group. In the case of anionic AMP, the highest stability of tautomer with the proton located at the N3 atom was also confirmed
by calculations using DFT methods [78]. However, contrary to AM1 data, it was
found that the N7 atom of adenine is the most preferable site for protonation of a
molecule with a neutral phosphate group. It should be noted that analysis of the
molecular structure of protonated DNTs represents a considerably more complex
task as compared to nucleobases. As it was discussed above, the nucleotides can
adopt several stable conformations differing in geometrical parameters and energy
[19, 20, 52]. Moreover, the presence of negative charge on the phosphate group
significantly influences the relative stability and geometry of molecules. Protonation of such molecules may lead to significant changes in their conformations and
energetics. For example, investigation of protonated AMP indicated [78] that attachment of a proton to the N3 atom results in switching of the base orientation from
anti to syn because of the formation of strong intramolecular hydrogen bond. A
significant increase of strength of usually weak C-H...O hydrogen bonds was found
in protonated AMP due to electrostatic attraction between the negatively charged
phosphate group and protonated adenine. Taking into account these data, it is possible to assume that each tautomer of protonated nucleotide can exist in several
stable conformations characterized by different energy. Therefore, comprehensive
evaluation of PAs requires careful consideration of the population of conformers of
non-protonated anionic DNTs and each tautomer of protonated molecules.
Before starting an analysis of the influence of a protonation on the molecular
structure and relative stability of conformers of protonated molecules, it is necessary to summarize conformational characteristics of non-protonated nucleotides,
discussed above. Despite the high conformational flexibility of nucleotides, they
adopt only four conformational states, being incorporated into DNA macromolecules. These states are characterized by the conformation of a SU belonging to the
south or north region of a pseudo rotation cycle and by the syn or anti orientation of
BU. Therefore, only these conformations are considered usually for DNTs as related
to DNA. Earlier, [52, 53] it was found that conformers with a syn orientation of
base are absent in pyrimidine nucleotides as well as in AMP. However, in the case
of CMP and AMP, it was found that minima on the potential energy surface correspond to conformers with an almost orthogonal orientation of base with respect
to the C1′−H bond and geometry of the furanose ring belonging to the north region
of the pseudo rotation cycle. Thus, non-protonated DNTs contain two (mTMP),
three (mCMP, mAMP), or four (mGMP) stable conformers. On the basis of the
relative Gibbs energy of these conformers, it is possible to conclude that for every
nucleotide only one of conformers dominates in the gas phase state (Table 5.15).
There is an S/anti conformer in mTMP, mCMP, and mAMP and an S/syn conformer
in mGMP. The latter conformer is stabilized by a strong intramolecular N–H...O
hydrogen bond between the amino and phosphate groups.
The relative stability of tautomers was calculated as the difference in average
Gibbs free energies as compared to the most stable tautomer. Average Gibbs free energies were calculated using population of conformers of tautomers with Eq. (5.1):
T. A. Zubatiuk et al.
of calculations by the AM1 method that the N7 atom has the highest PA value for
GMP [77]. Other anionic nucleotides have the same preferable sites of protonation
as molecules with a neutral phosphate group. In the case of anionic AMP, the highest stability of tautomer with the proton located at the N3 atom was also confirmed
by calculations using DFT methods [78]. However, contrary to AM1 data, it was
found that the N7 atom of adenine is the most preferable site for protonation of a
molecule with a neutral phosphate group. It should be noted that analysis of the
molecular structure of protonated DNTs represents a considerably more complex
task as compared to nucleobases. As it was discussed above, the nucleotides can
adopt several stable conformations differing in geometrical parameters and energy
[19, 20, 52]. Moreover, the presence of negative charge on the phosphate group
significantly influences the relative stability and geometry of molecules. Protonation of such molecules may lead to significant changes in their conformations and
energetics. For example, investigation of protonated AMP indicated [78] that attachment of a proton to the N3 atom results in switching of the base orientation from
anti to syn because of the formation of strong intramolecular hydrogen bond. A
significant increase of strength of usually weak C-H...O hydrogen bonds was found
in protonated AMP due to electrostatic attraction between the negatively charged
phosphate group and protonated adenine. Taking into account these data, it is possible to assume that each tautomer of protonated nucleotide can exist in several
stable conformations characterized by different energy. Therefore, comprehensive
evaluation of PAs requires careful consideration of the population of conformers of
non-protonated anionic DNTs and each tautomer of protonated molecules.
Before starting an analysis of the influence of a protonation on the molecular
structure and relative stability of conformers of protonated molecules, it is necessary to summarize conformational characteristics of non-protonated nucleotides,
discussed above. Despite the high conformational flexibility of nucleotides, they
adopt only four conformational states, being incorporated into DNA macromolecules. These states are characterized by the conformation of a SU belonging to the
south or north region of a pseudo rotation cycle and by the syn or anti orientation of
BU. Therefore, only these conformations are considered usually for DNTs as related
to DNA. Earlier, [52, 53] it was found that conformers with a syn orientation of
base are absent in pyrimidine nucleotides as well as in AMP. However, in the case
of CMP and AMP, it was found that minima on the potential energy surface correspond to conformers with an almost orthogonal orientation of base with respect
to the C1′−H bond and geometry of the furanose ring belonging to the north region
of the pseudo rotation cycle. Thus, non-protonated DNTs contain two (mTMP),
three (mCMP, mAMP), or four (mGMP) stable conformers. On the basis of the
relative Gibbs energy of these conformers, it is possible to conclude that for every
nucleotide only one of conformers dominates in the gas phase state (Table 5.15).
There is an S/anti conformer in mTMP, mCMP, and mAMP and an S/syn conformer
in mGMP. The latter conformer is stabilized by a strong intramolecular N–H...O
hydrogen bond between the amino and phosphate groups.
The relative stability of tautomers was calculated as the difference in average
Gibbs free energies as compared to the most stable tautomer. Average Gibbs free energies were calculated using population of conformers of tautomers with Eq. (5.1):