Proton and hydrogen atom adducts to cytosine. An experimental and computational study

Tautomerism of cytosine probed by gas phase IR spectroscopy

“…Two structures that are formed upon protonation of the most stable tautomer of neutral cytosine compete as the lowest energy structure. In previous high level ab initio calculations it was found that protonation of the oxygen C(2) O oxo group is slightly more favorable than protonation of the ring N(3) and a calculated value for G at 298 K at the CCSD(T)/augcc-pVTZ level of 6.4 kJ/mol was found [19]. Also, it was reported that a correct energy ordering can be obtained using the B3LYP method provided that a sufficiently large basis set, including diffuse function is used, but that the energy difference is significantly underestimated [19].…”

“…In previous high level ab initio calculations it was found that protonation of the oxygen C(2) O oxo group is slightly more favorable than protonation of the ring N(3) and a calculated value for G at 298 K at the CCSD(T)/augcc-pVTZ level of 6.4 kJ/mol was found [19]. Also, it was reported that a correct energy ordering can be obtained using the B3LYP method provided that a sufficiently large basis set, including diffuse function is used, but that the energy difference is significantly underestimated [19]. This is indeed found in the present calculations at the B3LYP/6-311++G(3df,2p) level, where the Cyt(O + H) is only slightly lower in energy than the Cyt(N + H) tautomer and the G value at 298 K is only 0.6 kJ/mol.…”

“…An activation energy value of 157 kJ/mol has been calculated at a high ab initio level (DH(0K) at the CCSD(T)/6-311++G(3df,2p) level) [19]. Upon addition of a base, however, such 1,3 proton transfer can be efficiently catalyzed.…”

“…Although several MS [14][15][16][17] studies have characterized the gas-phase basicity and proton affinity of the nucleobases, structural information from MS can only be derived using theory [18][19][20][21][22][23][24][25][26][27]. In the case of protonated cytosine, for instance, the transition state associated with tautomerization lies well below the fragmentation threshold, and it is thus difficult to distinguish the tautomers through collision induced dissociation [19]. It is therefore clear that direct information on the protonation sites of nucleic bases and on the presence of tautomers in the gas phase is of fundamental importance.…”

Infrared Spectra of Protonated Uracil, Thymine and Cytosine

“…[99] Finally, it should be recalled that the orientation of the hydroxyl group in C1_hc is quite important. Indeed, the C1_hc and C1_hd structures only differ by the rotation (1808) of the hydroxyl group, but the energy difference between these two forms is rather important.…”