Hydrogen bonding functional groups

Similarly to peroxycarboxylic acids, DMDO is subject to cis or syn stereoselectivity by hydroxy and other hydrogen-bonding functional groups.93 However a study of several substituted cyclohexenes in CH3CN —H20 suggested a dominance by steric effects. In particular, the hydroxy groups in cyclohex-2-enol and... 

Table 2.1. Hydrogen bond functional groups in biological molecules...

In protein neutron crystal structure analyses, complete H/D exchange is rarely obtained and the partial deuterium substitution has become a standard method of exploring the relative accessibility of hydrogen-bonding functional groups to solvent exposure. 

It is apparent from these examples that extreme caution is necessary when assessing the predictive power of the theory for complex molecules with many and varied hydrogen-bonding functional groups. Tb be convincing, the results must be supported by direct experimental evidence from X-ray crystallography or NMR spectroscopy. 

This appears not to be the case. On average, the crystal field forces have a distortion effect. This was realized from some of the earliest analyses of hydrogen-bond lengths [52]. It arises from two factors one is the influence of many-atom effects, such as cooperativity. The second is the fact that all other atom-pair interactions are striving toward the equilibrium minimum. Since hydrogen-bonded functional groups tend to protrude from molecules, this results in an overall distortion. The most obvious example of this difference is that between the values for the H 0 distances of 1.7 to 1.8 A observed in the ices and 2.0 A for the water dimer (see Thble 4.3). Similarly, the distribution for two-center OwH O bonds in the hydrates of small molecules, discussed in Part IV, has a mean value of 1.80 A, in agreement with the ices. 

The urea trihydrogen phosphate crystal structure [405] shown in Fig. 7.1, for example, possesses one very short, almost symmetrical C-OH 0 = P bond and one normal N(H)H 0=P bond. The latter hydrogen-bonding functional group is likely to be present in protein-nucleic acid interactions. 

Box 14.1. Hydrogen-bonding functional groups in amino acids and their salts... 

In the homopolymers formed by uridine or 2-thiouridine, base pairs with twofold symmetry are feasible, as described in Part II, Chapter 16 [529, 699]. The situation is more complex, however, because the homopolymer folds back on itself, giving rise to a hairpin-like structure where the polynucleotide strands are necessarily antiparallel and the base pairs are of the form shown in Fig. 20.10. Not surprisingly, a comparable double helix is also observed for polyxanthylic acid poly (X) [700]. The purine base of xanthosine displays the same hydrogen-bonding functional groups as uracil and therefore, the same base pair can be formed, but the purine-purine pair requires a larger separation between the glycosidic links and consequently a wider helix radius. 

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