Thymine parameters

Addition and elimination reactions of RS radicals derived from cysteamine and 2-mercaptoethanol involving C5-C6 double bond in various pyrimidines (thymine, uracil, and cytosine) were studied by the pulse radiolysis technique in aqueous solutions.For this purpose the kinetic parameters, i.e. the rate constants of the addition and elimination reactions, were determined using two chemical-monitoring systems. 

No experimental results are available for the nucleic acids, with or without methyl substitution, to test the theories, but we can compare the results for thymine to three theoretical estimates based on the linearized Poisson-Boltzmann equation. The AM1-SM2 and PM3-SM3 values are —16.5 and -20.1 kcal/mol, respectively. Using charges and force field parameters from the AMBER,347 CHARMM, and OPLS molecular mechanics force fields and a solute dielectric constant of 1, Mohan et al.i calculated solvation energies of -19.1, -10.4, and -8.4 kcal/mol. The wide variation is disconcerting. In light of such wide variations with off-the-shelf parameters, the SMx approach based on parameters specifically adjusted to solvation energies appears to be more reliable. 

Spin Resonance Spin Hamiltonian Parameters for Thymine ... 

Figure 12.9 Morse potential energy curves for thymine in the N—H dimension calculated from E and data in Figure 12.5 [7, 28]. The molecular anion formed at 0.2 eV comes from the vertical transition to the A curve, while those at 0.8 eV come from the B and C curves and the one at 6 eV comes from the D curve. There is no peak at 1.5 eV, as occurs in cytosine. The parameters are given in Table 12.8.

The slopes of these plots are a measure of the parameter [3, which is a function of the intervening bases between the G and 2AP(-H) residues. We found that in the case of intervening thymines, the parameter 3 = 0.4 A-1 while in the case of intervening adenines 3 = 0.12 A-1 in double-stranded DNA [28, 56]. 

Adsorption Parameters of Adenine, Thymine, and Their Derivatives in the Negative Potential Region on Au... 

Table V Hyperfine Coupling Parameters for Thymine Oxidation Products ...

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