Learn to Smile

The

Java Molecular Editor (JME) drawing applet is included below. The applet is used in the tutorial questions in this web site, as well as in the online testing package, Carmen. The applet will generate a "smiles" string (a text-based representation of the molecule) from your line-drawing, which will then be used to correct your answer. Remember, in a line drawing the ends of a line are assumed to be carbon atoms unless otherwise indicated by changing the atom type. Hydrogen atoms attached to carbons are NOT indicated in this type of drawing, only those attached to heteroatoms (i.e. O, N, S)

To use the editor, the second horizontal row of buttons is used for drawing the molecule. It is easiest to draw in the entire structure as carbon atoms first, and then change existing C atoms into other atom types (O, N, S...).

Drawing a Structure

Button	Function	Button	Function
	Draws in a single bond. Note: you can generate a double or triple bond from a single bond by clicking on an existing single bond with the single bond button activated.		Draws in a double bond.
	Draws in a triple bond.		Draws in a continuous chain of C atoms as long as the left mouse button is held down and dragged across the applet.
	Draws in a ring (i.e. a cyclopropane ring).		The wedge button is used to indicate the 3-D location (or stereochemistry) of atoms, a solid wedge is above the plane of the page, a dashed wedge is behind the plane of the page. Clicking on an existing bond will change it to a wedge. Clicking on an existing wedge will change between the two wedge configurations.
	This will change an existing C atom into an O atom. Note: do NOT use the X button. This is used to add ANY atom or group in place of a C atom. If you use it, the smiles string will likely be incorrect!		This will change the formal charge on an atom, and adds / subtracts H atoms as needed. Note: this works for any of the atoms on the left side menu. For atoms not in the menu use the X button and add the charge (as +/- or +2/-2 or +3/-3 ..., i.e. Na+, Ca+2, N-3).
	Use the "X" button for atoms not on the atom menu, like the K+ in KOH. Note: you should indicate formal charges in the structures. When using the X button enter inorganic reagents as Na+.		Additional molecules can be added to the dispaly using the "NEW" button.

Fixing Errors

	The clear button will delete the entire structure.
	The delete button will remove atoms or bonds one at a time.
	The undo button will undo the last change to the structure.	smiles