H-bonding directionality

The two properties of H-bonds, directionality and enthalpies of formation of about 10 kT at room temperatures for weak H-bonds, are thus fundamental and explain the central role they play in molecular biology. We shall, however see, in Ch. 6 and the following ones, that they have a third property that makes them even more crucial they allow transfer of protons or of H-atoms between the two molecules they link. This third property of H-bonds is at the origin of the reactivity of aqueous media, particularly biomedia. 

The H-bond directionality is important in topology optimization. Keeping track of both the existence and direction of the H-bonds in a cluster can be accomplished by using a digraph. The latter can be represented by a directed adjacency matrix D. As with the adjacency matrix, the absence of a bond between monomers i and j is indicated by Dy = 0 and so all diagonal elements vanish, D = 0. If there is a bond in the direction then Dy = 1 and Dy = 0. The D matrix contains, for example, information about the number of donor (don) and acceptor (acc) H-bonds for each molecule = Y,j Dju A cc = S ij- Note that the summation index depends on the definition of the H-bond direction. In a computer program, the sparsity of A and D can be exploited by storing them as linked lists of non-zero elements. 

The H-bonding in the anhydrous 1 Im (Table 24) has topologic properties (Fig. 46) similar to those in the alcohol coordinatoclathrates of 1 with 1 2 host guest stoichiometry (cf. Fig. 17 a). Assuming a perfectly ordered crystal lattice, the resulting central loop of H-bonds should appear to have homodromic directionality with the donor/acceptor functions separated in space. This contrasts to the behavior in the dihydrated l Im where no such characteristic loops are formed. Involvement of the C—H hydrogen atoms of the imidazole molecule, however, is similar in both cases. 

Both species exhibit the expected linear geometry that maximizes the dominant n- - a interaction. However, these isomers are rather perplexing from a dipole-dipole viewpoint. The dipole moment of CO is known to be rather small (calculated Fco = 0.072 D), with relative polarity C- 0+. 40 While the linear equilibrium struc-ture(s) may appear to suggest a dipole-dipole complex, robust H-bonds are formed regardless of which end of the CO dipole moment points toward HF This isomeric indifference to dipole directionality shows clearly that classical dipole-dipole interactions have at most a secondary influence on the formation of a hydrogen bond. 

The elimination step itself is the reverse of Cossee-type insertion into an Al—H bond. This insertion is much easier than in the Al—C bond, presumably because of the lack of directionality of the hydride Is orbital involved in the reaction (compared to the sp hybrid of an alkyl group). Nevertheless, -elimination has a rather high activation energy because the initial product, a terminal aluminium hydride, is very unfavourable. This initial product can... 

Figure 2.4 shows the distributions of anions about cations for [CjCjImJCl as determined from EPSR at two different probabilities. The directionality of the interactions is clear, with the highest probability regions of anions located along the vectors of the aromatic C-H bonds of the ring and... 

Similarly to other software packages such as DISCO and Catalyst, Phase uses chemical features (hydrophobic, H-bond acceptors, H-bond donors, negative charge, positive charge, aromatic ring) to define the pharmacophore points called sites. These features are encoded in SMARTS and can be edited. H-bond-ing features are vectorized features (their directionality is considered). 

Vedani, A., Dunitz, J.D. Lone-pair Directionality of H-bond Potential Functions for Molecular Mechanics Calculations the Inhibition of Human Carbonic Anhydrase II by Sulfonamides. 

The results cast doubts as to whether a true H-bond exists between the acetylene molecules. The T-shape is precisely what one would expect based solely upon electrostatic con-siderations i-. The symmetry of HCCH yields a zero dipole moment, so the moment of lowest order is a quadrupole. A T-arrangement would best allow the approach of the two quadrupole moments. The interaction, probably less than 2 kcal/mol, is less than normally expected for a H-bond. Finally, the ease of rotation of one molecule around the other contrasts with the directionality of most H-bonds. 

Some authors have postulated the existence, beside ordinary H-bonds, of bifurcated H-bonds or three-centre H-bonds that can be occasionally encountered and consist of a single X-H donor group that simultaneously interacts with two acceptor groups Y and Y. These multicentred H-bonds lose the properties of directionality of ordinary H-bonds. These authors are mainly crystallographers (2 pp. 136-146) who measured, by X-ray or neutron diffraction, distances X- Y and X- -Y that are nearly the same in an appreciable number of systems. The existence of such H-bonds has never been experimentally put into evidence by other techniques, particularly IR spectroscopy, the most sensitive method to observe H-bonds (Chs. 4 and 5). It has been occasionally used as an ad hoc explanation of some... 

We have seen above that the conjugation of structural and thermodynamic properties of weak H-bonds, namely their directionality combined with their enthalpies of about 5-lOkr at room temperature, allows building well-defined molecular structures that combine stability with flexibility and adaptability or evolution. Snch structures are most important in the organization of macromolecules, especially biomacromolecules for which the appearance or disappearance of such supramolecular organization may completely change their properties, making for instance a living protein irreversibly becomes a bio-inert polypeptide. 

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