Correlated ab initio study of nucleic acid bases and their tautomers in the gas phase, in a microhydrated environment and in aqueous solution. Part 4. Uracil and thymine.
Altogether 13 keto and enol tautomers of uracil and 13 keto and enol tautomers of thymine were studied theoretically in the gas phase, in a microhydrated environment (1 and 2 water molecules) and in a water environment. Bulk water was described using the thermodynamic integration method, Conductor-like polarizable continuum model (C-PCM, COSMO) and hybrid model (C-PCM + 1-2 explicit water molecules). The structures of various tautomers were determined at the RI-MP2 level using the TZVPP basis set while relative energies were determined at the CCSD(T) level. The relative free energies at 298 K were based on the relative energies mentioned above and zero-point vibration energies, and temperature dependent enthalpy terms and entropies evaluated at the MP2/6-31G** level. The effect of bulk solvent on the relative stability of uracil and thymine tautomers was studied using molecular dynamics free energy calculations by means of the thermodynamic integration method and self-consistent reaction field. Despite the completely different nature of these methods they provide comparable solvation free energies. Besides theoretical investigation, experimental detection of uracil and thymine tautomers was performed by means of steady-state fluorescence. We conclude that it is impossible to utilize the method used by Suwaiyan and Morsy (M. A. Morsy, A. M. Al-Somali and A. Suwaiyan, J. Phys. Chem. B, 1999, 103(50), 11205) for tautomer detection, even if a very sensitive fluorimeter is used. Theoretical relative energies and free energies for isolated uracil and thymine tautomers support the existence of the canonical form only. The microhydrated environment and bulk solvent stabilize enol forms more than the canonical keto one, but gas phase destabilization of these enol forms is too high. Population of rare enol forms of uracil and thymine in bulk water will thus be very low and canonical structure will also be dominant in this phase.
Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, 166 10 Prague 6, Czech Republic.
Jaroslav
J
Rejnek
Michal
M
Hanus
Martin
M
Kabelác
Filip
F
Ryjácek
Pavel
P
Hobza
D001703:Biophysics / Q000379:methods; D005470:Fluorometry / Q000379:methods; D005740:Gases; D008956:Models, Chemical; D009690:Nucleic Acid Conformation; D009696:Nucleic Acids / Q000737:chemistry*; D012997:Solvents / Q000737:chemistry; D013050:Spectrometry, Fluorescence / Q000379:methods; D013816:Thermodynamics; D013941:Thymine / Q000737:chemistry*; D014498:Uracil / Q000737:chemistry*; D014867:Water / Q000737:chemistry*
D005740:Gases; D009696:Nucleic Acids; D012997:Solvents; D014867:Water; D014498:Uracil; D013941:Thymine