Molecular-orbital calculations deprotonation

Electrons are selectively captured by the pyrimidines and the holes formed on the base stack, or transferred to the base stack, are nearly all trapped by Gua, giving Gua +. This species is in a reversible equilibrium with its deprotonated form Gua(NI-H) (Fig. 2). While initial distributions between the pyrimidines are nearly equal upon annealing, or irradiation to high dose, the excess electron transfers to cytosine as the most stable site as a result of protonation of Cyt at N3 forming Cyt(N3+H) [10]. Molecular orbital calculations show that the major factor that affects the relative yields of DNA base ion radicals is the difference in both the ionization potential and electron affinity ofthe DNA bases [11]. In addition, experimental and theoretical work shows that variations in relative radical yields are also affected by the... 

Figure 8. Theoretical Jcc values for 4-methylimidazole based on a finite perturbation theory self-consistent field molecular orbital calculation, a-c correspond to varied protonation states of the molecule d-f include the effects of hydrogen bonding interactions with the solvent, and with the deprotonated and protonated amino group, respectively. (Based on calculations given in Ref. 40.)...

MO-LCAO-MNDO method allowed calculation of proton affinities and dipole moment <90Mi 8ii-02>. A MINDO/1 calculation on the ylide (13) predicted more ready addition of DMAD to position 6 than to position 2, thus rationalizing the proportion of pyrrolopyrimidines (14) and (15) formed in cycloaddition (Equation (1)) <86H(24)3473> (see also 8.11.9.2.2). In partly reduced systems, Molecular Orbital Package (MOPAC) heats of formation of pyrrolizine derivatives from pyrrolooxazinone (16) and alkynes <92JA593>, and deprotonation preference in pyrrolopyrazinedione (17) were calculated <79JA1885>. 

In addition to charge descriptors, two energy descriptors have been extensively used for QSAR studies. They are the energy difference AE (or enthalpy difference AH) between the protonated and deprotonated forms of the acid, and Ehomo the energy of the highest occupied molecular orbital of the acid. As early as 1979 Catalan and Macias [171] used INDO calculations [226] to establish a relationship between calculated AE values and the gas-phase acidities of meta- and / ara-substituted phenols. In 1985 La Manna, Tschinke, and Paoloni [227] used STO-3G Hartree-Fock calculations to demonstrate a relationship between Ehomo the gas-phase acidities of a series of benzoic acid... 

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