Guanine electrostatic potentials

Amine bases in nucleic acids can react with alkylating agents in typical Sjsj2 reactions. Look at the following electrostatic potential maps, and tell which is the better nucleophile, guanine or adenine. The reactive positions in each are indicated. 

Figures 3.1 and 3.2 show calculated electrostatic potentials for guanine (1), in the plane of the molecule and on the molecular surface, respectively. Looking at Figures 3.1 and 3,2, it can be seen that there are negative potentials associated with N3, N7 and the carbonyl oxygen, with the latter two overlapping to form a strong and extensive negative region on one side of the molecule. Both Figs. 3.1 and 3.2 allow us to rank N as the site most suscepti-...

Fig. 3.1 Calculated electrostatic potential of guanine (1), in kcal/mole, in the plane of the molecular framework. Dashed contours correspond to negative potentials. The positions of the most negative potentials are indicated the values are —92.6 A —72.6 0 —69.2.

Fig. 3.2 Calculated electrostatic potential on the molecular surface of guanine (1). Three ranges of V(r) are depicted, in kcal/mole. These are white for V(r) < 0 light gray for F(r) from 0 to 10 dark gray for V(r) >10.

Bonaccorsi, R., E. Scrocco, J. Tomasi, and A. Pullman. 1975. Ab Initio Molecular Electrostatic Potentials, Guanine Compared to Adenine. Theor. Chim. Acta 36, 339. 

With aquated Pt(II) compounds, numerous studies have revealed the kinetic preference of the 6-oxopurine N7 site [15,35]. In addition to the favorable electrostatic potential mentioned above [23] also steric factors seem to favor coordination to the guanine N7 site, in particular [36]. Estimated relative steric parameters (in parenthesis) suggest that the guanine N7 (1.00) and hypoxanthine N7 (1.03) atoms are the least sterically hindered binding sites in alkylated nucleobases, followed by the adenine N7 (1.17) and deprotonated hypoxanthine N1 (1.17) sites and the deprotonated N3 atoms of the different pyrimidine bases (1.39 for U, 1.44 for T, and 1.56 for C), while the adenine N1 (1.58) and... 

Maxam-Gilbert DNA sequencing relies on mcthylation of guanosine and adenosine nitrogens. Use SpartanView to examine electrostatic potential maps of 9-methyl-guanine and 9-methyladenine, and compare the electrostatic potentials at positions 7 on guanine and 3 on adenine. Which molecule is the better nucleophile, and why ... 

For illustrative purposes, Fig. 1 shows our computed electrostatic potentials on the surfaces of cytosine (1) and guanine (2). Only three ranges of values are given however, this could of course be increased by using various colors. 

Figure 1 Electrostatic potentials on the molecular surfaces of (a) cytosine, 1, and (b) guanine, 2, computed at the Hartree-Fock 6-31G level. Color ranges, in kcal/mol red, more positive than 17 blue, more negative than —20 (see legend). The relative positions of the molecules are such that the portions that hydrogen bond are facing each other, showing how the extended positive and negative regions will interact. (See color plate at end of chapter.)...

The electrostatic potentials of the nucleic acid bases [adenine (9), guanine (10), cytosine (1), and thymine (11)] were first studied in the early 1970s. Each of these molecules has several likely sites for electrophilic attack V(r)... 

Electrostatic potential maps illustrating hydrogen bonding between thymine and adenine (a) and cytosine and guanine (b). The oxygens are red, and the nitrogens are blue. 

Compare its formula with those of adenine and guanine. Do you expect caffeine to form N-glycosides with sugars such as 2-deoxy-D-ribose Use the electrostatic potential map of caffeine to determine which nitrogen is most basic. Why is this in accord with expectations ... 

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