Effect of counterions on the protonation state in a poly(G)-poly(C) radical cation.
The proton transfer process from a guanine to its complementary cytosine in a B-form d[GG] radical cation is investigated theoretically. The d[GG] radical cation is optimized by the ONIOM + PCM method. In this two-layer ONIOM method, the high layer consists of the π-stacked complementary base pairs with a hole charge, which is treated at the B97D/6-31G(d) level. The low layer includes the sugar-phosphate backbone and sodium ions, which is treated with the Amber99SB/Parmbsc0 force field. Our calculations reveal that the stabilization of the deprotonated state in d[GG] oligomers is related to the location of sodium ions. When sodium ions are located near phosphate groups, the proton prefers bonding with the guanine, and 80% of the hole charge is delocalized on the guanine residues. When sodium ions are placed in the major groove, the deprotonated state is favorable, and 70% of the hole charge localizes on the corresponding guanine-cytosine pair. According to the natural bond orbital analysis, the N-H···N hydrogen bond between the guanine-cytosine pair provides an important contribution to the stabilization of the deprotonated state. Stabilization of this hydrogen bond is very sensitive to the d[GG] oligomer configuration. In summary, the proton transfer process in a guanine-cytosine pair of poly(G)-poly(C) radical cations is largely affected by the arrangement of counterions.
Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada.
Jian
J
Wu
Laura
L
Albrecht
Russell J
RJ
Boyd
D002412:Cations / Q000737:chemistry; D006860:Hydrogen Bonding; D008958:Models, Molecular; D011066:Poly C / Q000737:chemistry*; D011068:Poly G / Q000737:chemistry*; D011522:Protons; D012964:Sodium / Q000737:chemistry
D002412:Cations; D011522:Protons; D011068:Poly G; C008961:poly G-poly C; D011066:Poly C; D012964:Sodium