Hydrogen bond potentials

Gavezzotti A and Filippini G 1994 Geometry of the intermolecular XH.. . Y (X,Y = N,0) hydrogen bond and the calibration of empirical hydrogen-bond potentials J. Phys. Chem. 98 4831... 

The representation of molecules by molecular surface properties was introduced in Section 2.10. Different properties such as the electrostatic potential, hydrogen bonding potential, or hydrophobicity potential can be mapped to this surface and seiwe for shape analysis [44] or the calculation of surface autocorrelation vectors (refer to Section 8.4.2). 

The AMBER force field replaces the van der Waals by a 10-12 potential for pairs of atoms that can participate in hydrogen bonding (equation 12). The hydrogen bond potential does not contribute significantly to the hydrogen bonding attraction between two atoms rather, it is implemented to fine-tune the distances between these atoms. 

Rey, S., Caron, G., Ermondi, G., Gaillard, P., Pagliara, A., Carrupt, P. A., Testa, B. Development of molecular hydrogen bonding potentials (MHBPs) and their application to structure-permeation... 

Fig. 37), suggesting that desolvation of the polar bonds in the molecule is a major determinant of permeability. Consistent with this, good correlations were found between the permeabilities of these peptides and their partition coefficients between heptane-ethylene glycol (r2 = 0.87) or the differences in partition coefficients between n-octanol-buffer and isooctane-buffer (r2 = 0.82) both these buffer systems provide experimental estimates of hydrogen-bonding potential. These results are qualitatively identical with those described earlier for the permeability of these peptides across Caco-2 cell monolayers. 

CHEMLAB can provide information such as energetic feasibility, hydrogen bonding potential, etc. These can be used to explain observed behavior or to predict the properties of proposed compounds. Hypothesis testing is the greatest utility of molecular modeling. 

N. F. Ho, and P. S. Burton. Physicochemical determinants of passive membrane permeability role of solute hydrogen-bonding potential and volume, J. Med. Chem. 2001, 44, 3721-3729... 

Figure 2. Hydrogen bond potential of dUMP vs. dCMP with the side-chain amide of Asn229.

Apart from the hydrogen bond potential at the bottom of the pTyr pocket, the phenol ring of pTyr makes a number of hydrophobic contacts with the SH2... 

TABLE 11. Conformational energies (kcalmol1) of ethylenediamine as calculated ab initio (6-31G ), by the original MM3 force field (MM3) and by MM3 augmented with a directional hydrogen bonding potential function (MM 3-94 Reproduced by permission of John Wiley Sons Ltd... 

Alveolar macrophages Viscosity Hydrogen bonding potential... 

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