Hydrogen-Bonded Pairs of Bases

The difficulties (in particular, length of the calculations) have curtailed the execution of extensive calculations of these systems. But it must be pointed out that the basic difficulty is due to the nature of the hydrogen 

In general one would not expect the 71-approximation to be appropriate for this problem. The c-electrons should be included in the calculations, but it is difficult to judge the influence of this modification as very few results are available. 

Comparison of other values, such as energies, is rather difficult. It must be mentioned, however, that a characteristic of the results is the existence of multiple potential wells. One of the difficulties in the evaluation of potential energy curves lies in the assumptions to be made for the repulsion energy. This is particularly so when the -electrons are not explicitly included in the calculation. 

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Table 21. Summary of calculations for hydrogen-bonded pairs of bases...

The electronic structure of hydrogen-bonded pairs of bases guanine-cytosine... 

Base pair (Section 23.5) A hydrogen-bonded pair of bases, always adenine-thymine (A-T) in DNA or adenine-uracU (A-U) in RNA, and cytosine-guanine (C-G) in both DNA and RNA. 

We now turn to substituent-sensitive tautomerism. Johnson and Rumon studied a series of solids derived by cocrystallizing substituted benzoic acids and substituted pyridines (108). Their IR evidence indicated, as expected, that when the benzoic acid is a strong acid and the pyridine a strong base, salts 50a are formed. For a weak acid and a weak base, hydrogen-bonded pairs of neutral molecules,... 

FIGURE 24.18 The coil of the sugar-phosphate backbone is visible on the outside of the DNA double helix in this computer-generated structure, while the hydrogen-bonded pairs of amine bases lie flat on the inside. 

C-4 -C-5 bond is gauche (42.3°, -75.7°), Adjacent bases are linked together by pairs of N-6-H---N-7 and N-6-H-"N-l hydrogen-bonds. In both types of hydrogen-bonded pairs, the base planes make dihedral angles of 37°. Base stacking was not observed. The coordinates published correspond to the wrong enantiomorph. 

Perhaps the prototypical examples of organic heterodimeric co-crystals involve the hydrogen-bond pairing of purine and pyrimidine base pairs, postulated in 1953 by Watson and Crick for adenine thymine (uracil) 60 and guanine cytosine 61 to unravel the structure of DNA [204], and since confirmed by numerous crystal structure analyses, as recently reviewed by Jeffrey and Saenger [10]. 

Fig. 4.5 a Box-shaped platinum host 7. b The stabihzation of the hydrogen-bonding pairs of mononucleotides and dinucleotides within the different host complexes, c X-ray crystal structiure of a hydrogen-bonded A-U base pair within host 7... 

Studies of small chloride ion water clusters indicate that the intermolecular nuclear quantum effects stabilize the ionic hydrogen bonds in the single-shell structures, while they are destabilized through the competition with intramolecular nuclear quantum effects in the multishell structures [231]. Nuclear quantum effects on the hydrogen-bonded structure of base pairs were recently studied in Ref. [232] and in the out-of-plane ring deformation of hydrogen maleate anion in Ref. [233]. 

Double helix (Section 28.8) The form in which DNA normally occurs in living systems. Two complementary strands of DNA are associated with each other by hydrogen bonds between their base pairs, and each DNA strand adopts a helical shape. 

The DNA isolated from different cells and viruses characteristically consists of two polynucleotide strands wound together to form a long, slender, helical molecule, the DNA double helix. The strands run in opposite directions that is, they are antiparallel and are held together in the double helical structure through interchain hydrogen bonds (Eigure 11.19). These H bonds pair the bases of nucleotides in one chain to complementary bases in the other, a phenomenon called base pairing. 

The two strands which make up DNA are held together by hydrogen bonds between complementary pairs of bases adenine paired with thymine and guanine paired with cytosine. The integrity of the genetic code (and of life as we know it) depends on error-free transmission of base-pairing information. 

The DNA double heUx illustrates the contribution of multiple forces to the structure of biomolecules. While each individual DNA strand is held together by covalent bonds, the two strands of the helix are held together exclusively by noncovalent interactions. These noncovalent interactions include hydrogen bonds between nucleotide bases (Watson-Crick base pairing) and van der Waals interactions between the stacked purine and pyrimidine bases. The hehx presents the charged phosphate groups and polar ribose sugars of... 

Figure 35-11. Typical aminoacyl tRNA in which the amino acid (aa) is attached to the 3 CCA terminal. The anticodon, "PPC, and dihydrouracil (D) arms are indicated, as are the positions of the intramolecular hydrogen bonding between these base pairs. (From Watson JD Molecular Biology of the Gene, 3rd ed. Copyright ...

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