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Both internal and external hydrogen bonds can be displayed. Hydrogen bonds are determined by typing all of the atoms as either acceptors, donors, both, or neither. Then the hydrogen bond energy is calculated between all acceptors and donors based on the ChemScore scoring function which takes into account both interatomic distance as well as the geometry. This function provides a relative score between 0 and 1.0 for the energy of the hydrogen bond. For all hydrogen bonds with an energy greater than 0, the bond is drawn as a dotted green line. The thickness of the line as well as the spacing between the dots correlates to the bond energy. Therefore, thicker more solid lines have higher energy than thinner more dotted lines. An example of both internal and external hydrogen bonds can be seen in Figure 5.10.
[Internal Hydrogen Bonds]
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The Hydrogen Bonds section of the Molecules page of the Style Window (see Figure 5.3) provides the mechanisms to control the display of hydrogen bonds in the 3D display.
The first button in this section adds all of the molecules in the specified scope to the list of molecules to be considered when calculating hydrogen bonds. It is important to note that this operation will add hydrogens to the molecule if hydrogens are not already present. These new hydrogen atoms will be written out with the molecule if the molecule is subsequently saved. However, while hydrogens are necessary for the calculation, they need not be visible to show hydrogen bonds.
The second button removes the molecules in specified scope from the list of molecules to be considered when calculating hydrogen bonds. The third buttons toggles whether or not internal hydrogen bonds should be displayed. The fourth button toggles whether or not external hydrogen bonds (those between two separate molecules) should be displayed.
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