Dimers of and tautomerism between 2-pyrimidinethiol and 2(1H)-pyrimidinethione: a density functional theory (DFT) study.
Density functional theory (BLYP, B3LYP, B3P86, B3PW91) with the 6-31+G(d,p), 6-311+G(d,p), and cc-pVTZ basis sets has been used to calculate structural parameters, relative energies, and vibrational spectra of 2-pyrimidinethiol (1) and 2(1H)-pyrimidinethione (2) and their hydrogen-bonded homodimers (C(2) 3, C(2h) [4](double dagger), C(2h) 5), monohydrates, and dihydrates and a heterodimer (6). Several transition state structures proposed for the tautomerization process have also been examined. At the B3PW91/6-311+G(d,p)//B3PW91/6-31+G(d,p) level of theory 2-pyrimidinethiol (1) is predicted to be 3.41 kcal/mol more stable (E(rel)) than 2(1H)-pyrimidinethione (2) in the gas phase and 2 is predicted to be 6.47 kcal/mol more stable than 1 in aqueous medium. An unfavorable planar intramolecular strained four center transition state (TS1) for the tautomerization of 1 and 2 in the gas-phase lies 29.07 kcal/mol higher in energy than 2-pyrimidinethiol (1). The C(2) 2-pyrimidinethiol dimer (3) is 6.84 kcal/mol lower in energy than the C(2) homodimer transition state structure ([11](double dagger)) that connects dimers 3 and 4. Transition state [11](double dagger) provides a facile pathway for tautomerization between 1 and 2 in the gas phase (monomer-dimer promoted tautomerization). The hydrogen bonded 2-pyrimidinethiol- - -H(2)O and 2-pyrimidinethiol- - -2H(2)O structures are predicted to be 1.27 and 1.55 kcal/mol, respectively, higher in energy than 2(1H)-pyrimidinethione- - -H(2)O and 2(1H)-pyrimidinethione- - -2H(2)O. Water promoted tautomerization via cyclic transition states involving one water molecule (TS- - -H(2)O, [12](double dagger)) and two water molecules (TS- - -2H(2)O, [13](double dagger)) lie 11.42 and 11.44 kcal/mol, respectively, higher in energy than 2-pyrimidinethiol- - -H(2)O and 2-pyrimidinethiol- - -2H(2)O. Thus, the hydrated transition states [12](double dagger) and [13](double dagger) are involved in the tautomerism between 1 and 2 in aqueous medium.
Freeman
Fillmore
F
Department of Chemistry, University of California, Irvine, 92697-2025, USA.
Po
Henry N
HN
D019281:Dimerization; D006860:Hydrogen Bonding; D008956:Models, Chemical; D015394:Molecular Structure; D011743:Pyrimidines / Q000737:chemistry*; D011789:Quantum Theory; D013237:Stereoisomerism; D013438:Sulfhydryl Compounds / Q000737:chemistry*; D013871:Thiones / Q000737:chemistry*
C521859:2-pyrimidinethiol; C520795:3,4-dihydro-2(1H)-pyrimidinethione; D011743:Pyrimidines; D013438:Sulfhydryl Compounds; D013871:Thiones