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Different conformations of 2?-deoxycytidine in the gas and solid phases: competition between intra- and intermolecular hydrogen bonds

Ling, Sanliang; Gutowski, Maciej


Maciej Gutowski


Computational results have been reported for 2′-deoxycytidine (dC), its gas phase isomers, tautomers, and their conformers, as well as for the crystalline phase. In addition to the neutral gas phase molecules, we have also considered associated radical anions and cations. The structural calculations were performed at the density functional and MP2 levels of theory. Vertical electron ionization energies and excess electron binding energies were determined using electron propagator theory. The α-anomer proved to be more stable by a fraction of kcal/mol than the biologically relevant canonical β-anomer. The conformational space of canonical dC has been systematically probed. dC in the crystalline phase or DNA structures favors canonical anti conformations. These structures were used in past computational studies to model gas phase characteristics of dC. Our findings indicate, however, that the gas phase dC favors syn conformations. It has repercussions for earlier interpretations of gas phase experimental results based on these computational results. The thermodynamic dominance of syn conformations results from the formation of an intramolecular O5′-H13···O2 hydrogen bond. The IR spectra of the most stable syn and anti canonical conformers differ markedly in the region of frequencies corresponding to NH/OH stretching modes. The MP2 value of deprotonation enthalpy of dC of 1411.7 kJ/mol is in very good agreement with the experimental value of 1409 ± 2.5 kJ/mol. The most stable valence anions are characterized by electron vertical detachment energies (VDE) in the 0.8–1.0 eV range, in good agreement with the experimental VDE of 0.87 eV. The barrier for the glycosidic bond cleavage is significant in the neutral canonical dC, 40.0 kcal/mol, and it is reduced to 22 and 16 kcal/mol for the anionic and cationic radicals of dC, respectively. The cleavage reaction is exothermic by 4 kcal/mol for dC– and endothermic by 7 and 9 kcal/mol for dC+ and dC, respectively. We decomposed the crystal cohesive energy into repulsive one-body terms associated with the syn–anti conformational changes, and the attractive intermolecular interaction term. We exposed that the syn–anti conformational changes are very favorable for intermolecular interactions; in particular they make the imino-amino side of the cytosine residue accessible to intermolecular interactions.

Journal Article Type Article
Acceptance Date Sep 29, 2016
Online Publication Date Sep 29, 2016
Publication Date Oct 20, 2016
Deposit Date Nov 20, 2018
Journal The Journal of Physical Chemistry A
Print ISSN 1089-5639
Electronic ISSN 1520-5215
Publisher American Chemical Society
Peer Reviewed Peer Reviewed
Volume 120
Issue 41
Pages 8199-8210
Public URL
Publisher URL