Adding Groups

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Adding Groups

Several substituents can be selected from the palette and added directly to a structure in a single step. These include amino, hydroxyl, keto, nitro, the halogens, methyl groups and hydrogen or deuterium. All are available as individual selections on the palette. The difference between these groups and the corresponding individual atoms grouped below them is that these groups are added directly as bonded groups (i.e. as substituents) whereas the atoms are generally used simply to replace another atom without creating an additional bond.

To add any of these bonded objects to a structure, first select the desired object then click on the attachment atom. Clicking directly on the attachment site in this manner will generate the bond automatically with a pre-defined angle and length. However, if the location of the resulting group is not what you want, then Undo the addition and repeat by clicking near the attachment site and drawing the bond manually to the desired final location. When drawing a group manually, a dotted line will track the movement of the mouse pointer until the button is released. On release, the substituent will be added at that location, and a bond from the attachment atom to the substituent will be created. It is also possible to simply click once at the desired final position and the group will be added at that spot and bonded to the nearest atom (which may or may not be the one you intended).

Note that you can add methyl groups in this same manner by selecting one of the bond tools and then clicking on the attachment atom. Alkyl Chains of variable length also can by added by using the Alkyl Chain tool.

One exception is the R-group option. R-groups cannot be added by just clicking on an attachment atom; with this item you should press the left mouse button on the attachment atom and hold the button while drawing a bond out to the desired location of the new R-group.