Hydrogen bonding donors

The flic presented contains 11 data items. The header lines arc property names as used by CACTVS [64, 65], and arc sufficiently self-descriptive. For example, E NHDONORS is the number of hydrogen bond donor.s, E SM1LES" is the SMILES string representing the structure of sulfamidc, and E LOGP is the logP value (octanol/water partition coefficient) for this substance. 

A fuzzier atom type participating in these descriptors has been defined that is pharmacologically relevant - the physicochemical type at near-neutral pH [24], which is one of the following seven binding property classes 1 = cation 2 = anion 3 = neutral hydrogen-bond donor 4 = neutral H-bond acceptor ... 

Many phenomena ask for local, site-specific properties of a molecule such as the partial charge on a specific atom in a molecule or the hydrogen bond donor ability of a certain OH group. It would be highly desirable to have methods as simple as an additivity model to estimate such site-specific molecular properties. 

Interactions between hydrogen-bond donor and acceptor groups in different molecules play a pivotal role in many chemical and biological problems. Hydrogen bonds can be studied with quantum chemical calculations and empirical methods. 

Two ligands may be able to position a hydrogen-bond acceptor in different locations in space yet still vith the same hydrogen-bond donor. 

The solvent effect on the diastereofacial selectivity in the reactions between cyclopentadiene and (lR,2S,5R)-mentyl acrylate is dominated by the hydrogen bond donor characteristics of the solvent... 

Table 1.2. Relative rate constants of some selected Diels-Alder reactions in water compared to organic solvents of different hydrogen bond donor capacities.

In conclusion, the special influence of water on the endo-exo selectivity seems to be a result of the fact that this solvent combines in it three characteristics that all favour formation of the endo adduct (1) water is a strong hydrogen bond donor, (2) water is polar and (3) water induces hydrophobic interactions. 

Table 1,5, Donor scales (Dg, DN and DNbulk) of some selected solvents, as well as acceptor number (AN) and hydrogen bond donor capacities (a).

The second important influence of the solvent on Lewis acid - Lewis base equilibria concerns the interactions with the Lewis base. Consequently the Lewis addity and, for hard Lewis bases, especially the hydrogen bond donor capacity of tire solvent are important parameters. The electron pair acceptor capacities, quantified by the acceptor number AN, together with the hydrogen bond donor addities. O, of some selected solvents are listed in Table 1.5. Water is among the solvents with the highest AN and, accordingly, interacts strongly witli Lewis bases. This seriously hampers die efficiency of Lewis-acid catalysis in water. 

Fig. 9. Sweetener receptor binding sites postulated by Tinti and Nofre, where 5 is an anionic group, eg, CO 2y or CN a hydrogen bond donor...

Variations on the a helix in which the chain is either more loosely or more tightly coiled, with hydrogen bonds to residues n + 5 or n + 3 instead of n + 4 are called the n helix and 3io helix, respectively. The 3io helix has 3 residues per turn and contains 10 atoms between the hydrogen bond donor and acceptor, hence its name. Both the n helix and the 3to helix occur rarely and usually only at the ends of a helices or as single-turn helices. They are not energetically favorable, since the backbone atoms are too tightly packed in the 3io helix and so loosely packed in the n helix that there is a hole through the middle. Only in the a helix are the backbone atoms properly packed to provide a stable structure. 

Figure 7.4 The edges of the base pairs in DNA that ate in the major groove are wider than those in the minor groove, due to the asymmetric-attachment of the base pairs to the sugar-phosphate backbone (a). These edges contain different hydrogen bond donors and acceptors for potentially specific interactions with proteins (b).

Figure 7.7 Color codes for the recognition patterns at the edges of the base pairs in the major (a) and minor (b) grooves of B-DNA. Hydrogen-bond acceptors are red hydrogen-bond donors are blue. The methyl group of thymine is yellow, while the corresponding H atom of cytosine is white.

Under these circumstances, a distinct contribution to the overall rate will be seen for each potential hydrogen-bond donor D—H. General acid catalysis is also observed when a ratedetermining proton transfer occurs fiom acids other than the solvated proton ... 

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