Quick Start Guide: Exercise 19

Sketching and Modifying Molecules in 2D

The 2D Sketcher lets you create and modify small molecules in a 2D representation.

Sketching a new molecule

  • From the top menu, choose Workspace > Clear Workspace to exclude all structures
  • Choose Edit > 2D Sketcher...
  • In the 2D Sketcher, draw 4-Aminobenzoic acid:
    • Choose Benzene, then click in the white area to add the ring
    • Choose C, then click on each of the two mid-points of the ring to add a bond at each end
    • Click twice on the terminal carbon of the right-side bond to add two more bonds there
    • Click on the upper of those two bonds to increase the bond order
    • Choose O, then click on the terminal carbons of the double-bond and its neighbor, to change them to O and OH, respectively
    • Choose N, then click on the terminal carbon of the left-side bond, to change it to H2N

Saving the molecule as a 3D project entry

  • Click Save as New… at the bottom of the 2D Sketcher; a small dialog opens
  • In the dialog, change the title to “4-Aminobenzoic acid” and click OK; the structure appears in the 3D Workspace and at the bottom of the Entry List

Modifying an existing structure

With the new 4-Aminobenzoic acid structure included in the Workspace:
  • Right-click the 2D Overlay and choose View in 2D Sketcher... from the menu
  • In the 2D Sketcher, change the structure to sulfanilamide:
    • Choose S, then click the carbon between the two oxygens to change it to sulphur
    • Choose N, then press the mouse down on the S, drag some distance, and release the mouse to add a bonded NH2
    • Click on the single bond between the S and the O to increase the bond order
    • Click Save as New... to create a second new molecule
    • Change the title to sulfanilamide and click OK; the new entry is also added to the project

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