H-bonding parameters

One can start building up a list of MM3 parameters by use of the TINKER analyze command. Don t expect to build up the entire set, which occupies about 100 pages in the MM3 user s manual, but do obtain a few representative examples to get an idea of how a parameter set is constr ucted. From previous exercises and projects, you should have input and output geometries for an alkene, an alkane, and water. From these, the object is to determine the stretching and bending parameters for the C—C, C=C, C—H, and O—H bonds. The C—H bond parameters are not the same... 

Short description of 3D H-bonding parameters and descriptors is included in... 

Three-dimensional H-bond Descriptors 135 Tab. 6.3 Three-dimensional H-bonding parameters and descriptors. 

I 6 H-bonding Parameterization in Quantitative Structure-Activity Relationships ef Drug Design Tab. 6.4 X-ray data, H-bond parameters and optimum energies and distances for few ideal complexes [48]. 

H-bonding is an important, but not the sole, interatomic interaction. Thus, total energy is usually calculated as the sum of steric, electrostatic, H-bonding and other components of interatomic interactions. A similar situation holds with QSAR studies of any property (activity) where H-bond parameters are used in combination with other descriptors. For example, five molecular descriptors are applied in the solvation equation of Kamlet-Taft-Abraham excess of molecular refraction (Rj), which models dispersion force interactions arising from the polarizability of n- and n-electrons the solute polarity/polarizability (ir ) due to solute-solvent interactions between bond dipoles and induced dipoles overall or summation H-bond acidity (2a ) overall or summation H-bond basicity (2(3 ) and McGowan volume (VJ [53] ... 

Calculated molecular descriptors including H-bond parameters were used for QSAR studies on different types of permeabiUty. For example, the new H-bond descriptor characterizing the total H-bond ability of a compound, was successfully appUed to model Caco-2 cell permeability of 17 drugs [30]. A similar study on human jejunal in vivo permeabiUty of 22 structurally diverse compounds is described in Ref. [62]. An exceUent one-parameter correlation of human red ceU basal permeabiUty (BP) was obtained using the H-bond donor strength [63] ... 

Pi is the reference solvent and HBj is an H-bonding parameter. Leahy et al. suggested that a more sophisticated approach incorporating four model systems would be needed to adequately address issues of solute partitioning in membranes (121). Thus, four distinct solvent types were chosen— apolar, amphiprotic, proton... 

Chen implied that was the enthalpy contribution to the Flory-Huggins parameter and plotted the solubility data in a 5 -%jj diagram where 4 was the H-bond parameter in the Hansen approach. In these diagrams sphere-like volumes of Hansen s solubility have degenerated to circles. 

Figure 12.13 Utilization of H-bonding parameters and conformational analysis in HtL (ligand-...

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