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Draw Chemical Structures in JME Molecular Editor

The following table describes how to draw and edit chemical structures in the JME Molecular Editor.

Note
  • Java™, version 1.6.0 through 1.7.35 is required. See Browser Plugins.
  • Whenever you add an atom in JME, the implied hydrogen atoms are listed based on the valence. For example, adding N displays NH3. The hydrogen atoms are implied, but are not explicitly drawn. This is the way most questions expect you to draw structures.

    If a question specifically asks you to show hydrogen atoms, then add the hydrogen atoms explicitly.

Task

Steps

Add a new structure to the drawing

By default, the JME tools add or change items in existing structures. To create a new structure in the drawing:

  1. Click NEW.
  2. Add an atom, bond, ring, or carbon chain anywhere in the drawing area.

Add an atom of one of the following elements — C, N, O, S, F, Cl, Br, I, P — as a new structure
  1. Click NEW.
  2. Click the element's symbol.
  3. Click in the drawing area.

Add any atom as a new structure
  1. Click NEW.
  2. Click X.
  3. In the popup window that is displayed, type the symbol of the atom you want to add.
  4. Click in the drawing area.

Add an atom and its bond to an existing structure
  1. Click a single bond Single bond, double bond Double bond, or triple bond Triple bond.
  2. Click the atom in the structure where the bond should be added.
  3. Click the symbol of the atom that you want to add to the end of the bond, or click X and type the symbol of the atom you want to add.
  4. Click the end of the bond where the atom should be added.
Note When you add a bond to a structure in this way, a Carbon atom is always added to the end of the bond. When you "add" a different atom to the end of the bond, you are really replacing the Carbon.

Add a bond between existing atoms
  1. Click a single bond Single bond, double bond Double bond, or triple bond Triple bond.
  2. Drag from one atom to another.

Change a bond type
  1. Click a single bond Single bond, double bond Double bond, or triple bond Triple bond.
  2. Click the bond to be changed.

Replace an atom
  1. Click the symbol of the new atom that you want to use, or click X and type the symbol of the atom you want to use.
  2. Click the atom to be replaced.

Set the charge for an atom

  1. Click +/-.
  2. Click the atom to be changed. If needed, click the atom multiple times to see the possible charges suggested by the JME Editor.
Note To set a different charge than those suggested, use the X tool and type a SMILES string without brackets, for example, Si, Fe++, or NH3+.

Add a chain of carbon atoms
  1. Click Carbon chain.
  2. Starting from the atom to which the carbon chain attaches, drag in the drawing area until the number of carbon atoms you want to insert is displayed.

Add a carbon ring
  1. Click the button that displays the kind of ring you want to add.
    ring buttons
  2. Click the atom to which the ring should be attached.

Add wedge bonds
  1. Click Wedge bond.
  2. Click the atom in the structure where the bond should be added.
  3. If needed, click the wedge bond in the structure to change its type.

Delete a bond or atom
  1. Click Delete.
  2. Click the item you want to delete.

Delete a structure
  1. Move the pointer over the structure to be deleted until a portion of the structure displays a blue selection outline.
  2. Click Clear. The structure is deleted.

Delete a functional group
  1. Click Delete Functional Group.
  2. Click the bond connecting the group with the main skeleton.

Move a structure

  1. Move the pointer over the structure to be moved until a portion of the structure displays a blue selection outline.
  2. Move the pointer over an empty part of the drawing area.
  3. Drag the pointer to move the structure.

Rotate a structure
  1. Move the pointer over the structure to be moved until a portion of the structure displays a blue selection outline.
  2. Move the pointer over an empty part of the drawing area.
  3. Hold down the Shift key and drag the pointer to rotate the structure.

Undo your last change

Click Undo. You can undo only one change.

View the SMILES string for your drawing

Click smile button. The SMILES string is displayed in a popup window.