Displaying Nonbonded Interactions

hydrogen bond, H-bond, halogen bond, pi-pi stacking, pi-cation, steric clash

If you want to display nonbonded interactions or unfavorable steric interactions, you can do so by using the Interactions Toolbox. To open this toolbox, move the pointer to the Interactions button on the Workspace Configuration toolbar, and click the … button that appears above it.

The interactions are divided into three groups:

• Noncovalent bonds—hydrogen bonds, halogen bonds, aromatic halogen bonds, and salt bridges
• Pi interactions—pi-cation and pi-pi stacking
• Contacts/clashes—good (favorable), bad (poor), and ugly (too close).

You can turn on or off the display of individual interactions and the groups of interactions, and also set the color for the interaction markers. Interactions are shown as dashed lines between the interacting groups. For hydrogen bonds, if the hydrogen is hidden, the dotted line is drawn to the donor heavy atom instead of the hydrogen. Bad or ugly contacts are not shown if there are noncovalent bonds between the same atoms.

Interactions are defined in terms of a set of distances and angles. The definitions can be changed in the Preferences Panel, in the Nonbonded Interactions Preferences. You can also define the width and color of the lines in this group.

To quickly show or hide all displayed interactions, click the Interactions button on the Workspace Configuration toolbar.