Hydrogen bonding molecular surfaces

A theoretical analysis of the reaction kinetics was given in the study by Jodkowski et a/.31 A hydrogen-bonded molecular complex was found for the hydroxymethyl reaction channel. The formation of this complex may be a ratedetermining process in the two-step reaction mechanism of the H-abstraction from methyl group. On the other hand, the reaction channel which produces methoxy radicals is a simple metathesis reaction. The profile of the potential energy surface obtained by Jodkowski et al at the G2 level is shown in Fig. 14. 

Hill, H. A. O., Page, D. J., Walton, N. J., Intra-Molecular Hydrogen Bonding in Surface-Modified Gold Electrodes and the Effect of Specific Anions on the Electrochemistry of Cytochrome C , J. Electroanal. Chem. 208 (1986) 395-400. 

The representation of molecular properties on molecular surfaces is only possible with values based on scalar fields. If vector fields, such as the electric fields of molecules, or potential directions of hydrogen bridge bonding, need to be visualized, other methods of representation must be applied. Generally, directed properties are displayed by spatially oriented cones or by field lines. 

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). 

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