Handling of Abbreviated Groups

    Marvin Pro can handle common chemical abbreviations that are connected with one bond to the scaffold.

    Adding Abbreviated Groups to the Canvas

    There are two ways to add the abbreviated groups to the canvas. In both cases, you need to modify an atom already present. You can either hover the cursor over this atom and start typing (in this case, a drop-down menu appears with possible group names) or use the Text tool to rewrite an atom with a group’s name (no drop-down menu appears to guide you in this case).

    {info} While you can apply any label on the atom with the Text tool, you can only pick from the pre-set list of common chemical abbreviations from the drop-down.

    The figure below shows the drop-down menu suggestions. As you can see, it is not case-sensitive.

    Abbreviated Groups Drop-down

    Transforming Abbreviated Groups

    Once an abbreviated group is on the canvas, you can right-click it to invoke its context menu. From there, you can expand the group to show the underlying structure. The Expand command also cleans and selects the structure.

    Abbreviated Groups Context Menu

    The figure below shows an expanded Boc group.

    Abbreviated Groups Boc Expanded

    If you hover over it, the group is highlighted in pink to make it easier to distinguish from other structures on the canvas. A pink dot also indicates the group’s attachment point, which, in this case, is occupied by a single bond.

    While the group’s structure is unchanged, you can contract it. Simply select Contract from the context menu. On the other hand, if you made changes to the structure, for example, overwritten one of its atoms or added a bond, the group automatically ungroups. In this case, it is no longer possible to contract the group. It is also possible to manually ungroup an abbreviated group through its context menu by using Ungroup. This command also cleans and selects the structure.

    The figure below shows an expanded Boc group and an ungrouped Phenyl group.

    {info} You can also expand or ungroup the Methyl group.

    Abbreviated Groups Boc Expanded