Molecular structure and properties of protonated and methylated derivatives of cytosine.
Ab initio techniques were used to determine the effects of protonation and methylation on cytosine's molecular geometry, molecular affinities, relative stability, and structural rigidity. The geometries of local minima were fully optimized by the gradient procedure at DFT and MP2 levels of theory with the medium size 6-31G(d,p) basis set. The results of energetic analysis indicate that N(3)-methyl-cytosine and C(5)-methyl-cytosine are the most stable derivatives for monocationic and neutral species, respectively. The structural rigidity of each species was assessed by an analysis of normal out-of-plane frequencies, the amplitudes, and by the contribution of internal coordinates to the potential energy distributions. The obtained evidence suggests that methylation increases the overall structural flexibility of cytosine and that all molecules in this study populate a non-planar conformation 50% of the time.
Forde
Gareth
G
Computational Center for Molecular Structures and Interactions, Jackson State University, Jackson, MS 39217, USA. gforde@ccmsi.us
Gorb
Leonid
L
Shiskin
Oleg
O
Flood
Aviane
A
Hubbard
Curinetha
C
Hill
Glake
G
Leszczynski
Jerzy
J
D003596:Cytosine / Q000031:analogs & derivatives* / Q000737:chemistry*; D019175:DNA Methylation; D015394:Molecular Structure; D011522:Protons; D013816:Thermodynamics
D011522:Protons; D003596:Cytosine