JME Molecular Editor Tutorial

The JME Molecular Editor is a structural drawing program created by Peter Ertl at Novartis Pharma AG. This applet can convert structural drawings into text strings called "SMILES". Learning how to use the editor requires only a few minutes. This tutorial is designed to help you develop the skills you will need to submit answers to questions that involve drawing chemical structures. When you click on the Load the JME Editor link below, a new page will open. Position that page near the top right of your computer screen so that you can see most of this page as well as the editor page at the same time. As you work your way through the tutorial, you will have to alternate between these two windows repeatedly.

The Editor

Figure 1 presents an image of the JME Molecular Editor. As you can see, it has two rows of "tools" or buttons aligned across the top of the drawing area and a column of "atom label tools" along the left edge. You activate a tool by clicking on it. Once you have activated a tool, you use it by clicking or click-dragging in the drawing window.

The buttons along the top row perform the following functions:

  • CLR erases everything in the drawing area.
  • NEW allows you to draw more than one structure in the drawing window.
  • DEL deletes a selected atom or bond.
  • 1-2-3 allows you to number the atoms in a structure.
  • D-R deletes a group of atoms in a chain. The atoms to be deleted are highlighted with red boxes.
  • +/- assigns charges to anions and cations.
  • UDO undoes your last action

Figure 1

The JME Molecular Editor

The buttons in the second row are, for the most part, self-explanatory. The tools under the CLR, NEW, and DEL buttons are for drawing single, double, and triple bonds, respectively. The tool beneath the 123 button is called the "chain tool". It is useful for drawing long, unbranched chains of carbon atoms. The remaining seven tools are for drawing cyclic structures. The wedge-shaped tool beneath the smiley face is called the "steroechemical bond tool". It is used to indicate the stereochemistry at stereogenic centers.

The tools in the column beneath the stereochemical bond tool are called "atom label tools". After activating one of these tools, clicking on an atom in a structure replaces that atom with the atom you have chosen. The atom label tool X allows you to insert atoms other C,N,O,S,F,Cl,Br,I, or P. To do so, click on the X atom label tool and enter the symbol of the atom you wish to insert into the text field of the window that opens. Close the window. Click on the atom in the drawing window that you want to change to the desired atom. The atom that you specify remains the active value of X until you change it or quit the program.

Okay, now Load the JME Editor and try the following exercises.

Simple Examples

Method 1

  1. Activate the single bond tool, then click the mouse within the drawing window. The program will draw an horizontal line like this ____ . This is bond-line notation for the structure of ethane CH3CH3.
  2. Clear the drawing window.
  3. Repeat Step 1, but hold the mouse down when you click within the drawing window. While holding the mouse down, move it in a circular motion and note how the orientation of the line changes. Release the mouse when you find an orientation that you like.
  4. Position the cursor on one end of the line you drew in Step 3. When a square appears, click the mouse. That's all there is to it.
  5. Click the Structure to SMILES button. The string CCC should appear in the SMILES Text Field.

Method 2

  1. Clear the drawing window and activate the chain tool.
  2. Click and drag the mouse until the number 3 appears in the lower left corner, just below the drawing area. The number signifies the number of atoms in the chain.
  3. Release the mouse. That's it.
  4. Click the Structure to SMILES button. The string CCC should appear in the SMILES Text Field.

Method 1

  1. Clear the drawing area. Activate the phenyl ring-the 4th cyclic structure- and place the ring in the drawing area.
  2. Activate the single bond tool and click on one of the atoms in the phenyl ring. This generates the structure of toluene, C6H5CH3. Click the Structure to SMILES button. The SMILES should be Cc1ccccc1.
  3. Click on the carbon atom of the CH3 This creates ethylbenzene, C6H5CH2CH3. Click the Structure to SMILES button. The SMILES should be CCc1ccccc1.
  4. Click on the carbon atom of the CH2 group. This creates cumene, C6H5CH(CH3)2. Click the Structure to SMILES button. The SMILES should be CC(C)c1ccccc1.
  5. Click on either of the CH3 groups. That's it. Click the Structure to SMILES button. The SMILES should be CCC(C)c1ccccc1.

Method 2

  1. Clear the drawing area. Activate the chain tool and draw a 4-carbon chain.
  2. Activate the phenyl ring tool and click the mouse on the second carbon in the chain. That's it!
  3. Click the Structure to SMILES button. The SMILES should be CCC(C)c1ccccc1.

  1. Use the chain tool to draw a 4-carbon chain.
  2. Use the single bond too to draw a bond to the second carbon atom in the chain. You can count from either end.
  3. Select the O atom label tool and click on the end of the bond you drew in Step 2. That's it.
  4. The SMILES of this structure is CCC(C)O.

  1. Use the chain tool to draw a 4-carbon chain.
  2. Activate the Cl atom label tool and click on one end of the chain.
  3. Activate the X atom label tool.
  4. Enter Si into the text field and close the window.
  5. Click on the atom adjacent to the Cl atom. Note-If you are using Netscape as your browser, the JME Editor may insert something other than Si in this step, e.g. SiH or S. In that case make sure that the atomic symbol in the text field is Si and then click on the specified carbon atom until the desired atom appears.
  6. Activate the single bond tool and click twice on the carbon adjacent to the silicon atom.
  7. The SMILES for this structure is CC(C)(C)[Si]Cl.

  1. Select the double bond tool and click in the drawing area.
  2. Select the single bond tool and click on the left end of the bond.
  3. Click on the right end. Note-By default the program will orient the bond it attaches to the right-hand carbon on the opposite side of the double bond as shown in the structure at the top right of the diagram above. If you click and drag, you can change the orientation so the structure looks like the one shown in the lower right -hand corner of the diagram.
  4. The SMILES for this structure is CC=CC.

Stereochemical examples

  1. Follow the directions given in the previous example to draw the structure of the Z-isomer.
  2. Select the stereochemical bond tool and click on the double bond. The double bond should become highlighted in color.
  3. The SMILES of this structure is C/C=C\C.

  1. The SMILES of this structure is C/C=C/C.

Note-Until you have developed the ability to visualize chiral centers and to draw stereochemical projection formulas, it is a good idea to make a molecular model of a molecule that contains a stereogenic center. Then you can use the JME Molecular Editor to draw a projection of the model. Also, you should be certain to draw all four bonds to the stereogenic center.

  1. Draw the structure of 2-butanol.
  2. Activate the stereochemical bond tool and click on the C-O bond.
  3. Click on the C-2 to add another wedged bond, then click that wedged bond to convert it to a hashed bond.
  4. Activate the X atom label tool. The default value is H. If the default value is not in the text field, change the value that is there to H and click the Close button.
  5. Click on the end of the hashed bond.
  6. The SMILES for this compound is [H][C@](C)(O)CC.

  1. Draw the structure of 2-butanol.
  2. Repeat Steps 2-5 from the directions for drawing R-2-butanol, but interchange the positions of the H and OH groups.
  3. The SMILES for this compound is [H][C@@](C)(O)CC.

  1. Draw the structure of R-2-butanol.
  2. Follow the approach described in the previous two examples, entering H and Cl at one chiral center and H and OH at the other.
  3. The SMILES for this compound is [H][C@](C)(O)[C@@]([H])(C)Cl.

Ions

Without Counter Ions

  1. Draw the structure of ethylbenzene.
  2. Select the +/- tool.
  3. Click on the carbon adjeacent to the phenyl ring. Click a second time. Note that clicking this tool toggles between a - charge and a + charge.
  4. The SMILES for this structure is C[CH+]c1ccccc1.

  1. Draw the structure of acetic acid, .
  2. Click the +/- tool on the OH group.
  3. The SMILES for this ion is CC(=O)[O-].

With Counter Ions

  1. Draw the structure of triethylamine, .
  2. Activate the +/- tool and click on the N atom. This should produce .
  3. Activate the NEW button.
  4. Activate the Cl atom label tool and click it in the drawing window. Thiswill create the structure ClH .
  5. Activate the +/- tool and click on the Cl atom.
  6. The SMILES for this ion is CC[NH+](CC)CC.[Cl-]. Note that this is really two SMILES, one for the cation and one for the anion.

The Nitro Group

The Hard Way

  1. Draw .
  2. Activate the N atom label tool and click on the carbon attached to the aromatic ring.
  3. Activate the O atom label tool and click on the two carbons above the nitrogen atom.
  4. Activate the +/- tool and click on the OH group.
  5. Click the Structure to SMILES button. The drawing will change from the one shown above where the N and O atoms bear charges to the one where the N atom has 5 bonds.

The Easy Way

  1. Draw benzene.
  2. Press the Y key (lower case).
  3. Click on one of the carbon atoms of the ring.

Either way, the SMILES for this structure is O=N(=O)c1ccccc1.

Practice Exercises

Draw the structures of the following compounds. Generate the SMILES for your structure. Copy the SMILES and paste it into the text field next to the appropriate structure. Then click the mouse anywhere outside the text field. A message will appear in the bottom frame indicating whether or not y ou are correct.

Note-In order to minimize the possibility of errors, you should check any SMILES you wish to submit to see that it generates the structure you expect. To do this, you can use a program called DEPICT, which converts SMILES back to structural drawings. Simply paste your SMILES into the text field in the DEPICT window and click the Submit button. You may want to set a bookmark to the DEPICT page.
3-ethylcyclopentane:

Lauric acid, a saturated fatty acid:

Methyl tert-butylether, MTBE, a gasoline additive:

L-alanine, an amino acid:

E-stilbene:

cyclopentadienyl anion:

a phosphorous ylide:

O=CHem Directory