*3.1.1. Analysis of the electron and geometric structures of hydrogen bonds in complementary pairs of NA by the PM3 method*

As a control, computations were performed for the interactions of bases in classical complementary pairs AT and CG, which are DNA components. Selection of computation models showed that substitution of methyl groups for the sugar-phosphate backbone has no effect on the parameters of hydrogen bonds, but considerably reduces the computation time. It was found that the PM3 method adequately describes the geometric and electron structures of hydrogen bonds in AT and CG pairs. The two interacting molecules are lying approximately in the same plane.

In the AT pair, the bases form two hydrogen bonds, one between the amino and keto groups and the other between nitrogen atoms of the purine and the pyrimidine. The mean length of the bonds is about 1.8 Å, and their total energy is –5.55 kcal/mol (Fig. 2). In the CG pair, three hydrogen bonds are formed, including two between the amino and keto groups of the bases and one between nitrogen atoms. The mean length of the hydrogen bonds is also about 1.8 Å (Fig. 2), similar to that reported in (Singer M., Berg P., 1998). The total energy of the three hydrogen bonds is –11.73 kcal/mol (Fig. 2). Thus, the РМ3 method can be used to study other types of hydrogen bonds formed by nucleotide bases.

The results of computations performed by the РМ3 methods for pairs of noncomplementary nucleotides are shown in Table 4.

ΔЕ= –5.55 kcal/mol ΔЕ= –11.73 kcal/mol

**Figure 2.** Hydrogen bonding in the AT and CG pairs of complementary nucleotides. Quantum chemical analysis by the PM3 method. Here and below, carbon atoms are shown green or black; oxygen atoms, red; nitrogen atoms, blue; and hydrogen atoms, gray.


Note: Energy (kcal/mol) was computed by the РМ3 method.

**Table 4.** Energy of hydrogen bonds in all possible pairs of thymine (T), adenine (A), cytosine (C), and guanine

Е = -7.08 kcal/mol

**Figure 3.** Hydrogen bonding in the noncomplementary pairs AA, GA, and CA. Quantum chemical computations by the PM3 method.

As follows from Table 4, A is theoretically capable of forming pairs with a total energy of - 2.71 (А), -5.55 (Т), -6.07 (C), and -7.08 (G) kcal/mol. Based on the energy, the preferential partner of A is G or at least C, but it is actually T. Let us consider in more detail the results of computations performed for the interactions of A with A and G with C (Fig. 3).

As Fig. 3 demonstrates, hydrogen bonding between noncomplementary nucleotides is possible, but the pairs are formed so that the angle between the interacting nucleotides is distorted in the case of AA and GA (Fig. 4) or the necessary distance between two strands in the NA double helix is not maintained in the case of CA (Fig. 4). The distance is higher in CA (Singer M., Berg P., 1998).

**Figure 4.** Geometric structure of hydrogen bonds in the complementary pairs AT and CG.

The above data allow the following conclusions.

270 The Complex World of Polysaccharides

red; nitrogen atoms, blue; and hydrogen atoms, gray.

Note: Energy (kcal/mol) was computed by the РМ3 method.

computations by the PM3 method.

Е = -7.08 kcal/mol

guanine

А -5.55 -2.71

Т -2.79

**Figure 2.** Hydrogen bonding in the AT and CG pairs of complementary nucleotides. Quantum chemical analysis by the PM3 method. Here and below, carbon atoms are shown green or black; oxygen atoms,

ΔЕ= –5.55 kcal/mol ΔЕ= –11.73 kcal/mol

Thymine (T) Adenine (A) Cytosine (C) Guanine (G)

T A C G

G -6.12 -7.08 -11.73 -10.57

**Table 4.** Energy of hydrogen bonds in all possible pairs of thymine (T), adenine (A), cytosine (C), and

А-А C-А

**Figure 3.** Hydrogen bonding in the noncomplementary pairs AA, GA, and CA. Quantum chemical

Е = -2.71 kcal/mol Е = -6.07 kcal/mol

**G-А**

C -4.46 -6.07 -9.24

