Molecular Modeling for Educators (MMEd) is fully capable of creating optimized 3-D chemical structures of great complexity containing up to 20,000 atoms, 1000 rings and 50 simultaneously displayed molecules. Molecular construction follows the chemical literature automatically (especially for organic molecules), but you can change the geometry any way you wish.

This Help page assumes you have MMEd installed and running. Note that there is a blue message area that will often appear near the top of the screen which will help you draw and modify molecules.

Select background color for the drawing. The default black background is not to everyone's taste. If you would like to change the background color go to the Format menu and choose "Set Background Color". Click on the color you desire. You can also use the Format menu to change the atom colors.

To start drawing a molecule select the atom type from the buttons at the left (e.g. C for carbon, N for nitrogen etc.) and click anywhere on the screen. The atomic symbol will appear in the center of the screen. Carbon is the default.

Select a bond type and an atom type for the second atom from the buttons at the left (e.g "1" for a single bond, "2" for a double bond or "3" for a triple bond). Click on the atomic symbol at the center of the screen and diatomic molecule will be drawn with a bond length obtained in most cases from the chemical literature. The default bond type is "1". If you select a "2", then subsequent atoms will be added with a double bond until you click on the 1 or 3 button. Similarily, the last atom type you selected will remain in memory until you change it. In other words, the defaults are "C" (carbon) and "1" (single bond). If you wish to build an unsaturated hydrocarbon, you never have to click on the buttons at the left, you just keep clicking on the atoms displayed on the screen until your molecule is built.

To add more atoms simply change the bond and atom types as needed and click on the atom where the addition is to be made. The program will not allow you to add atoms past the maximum valence unless you click on the "+" or "-" buttons to add charge to the atom being added to. Bond angles are usually obtained from a table of "correct" literature values. The program also determines if centers are SP, SP2 or SP3 and adjusts torsional angles accordingly.

Atom types other than C, H, N, O, F, Cl, Br, I , P or S are selected by clicking the "Other" button. This brings up the Periodic Table. Right clicking on the Periodic Table brings up a number of useful atomic properties including, the atomic symbol, number, weight, valences, van der Waal's radius, covalent radius, electronegativity and the number of electrons per orbital. Left clicking on the Periodic Table selects that atom type and returns you to the drawing screen.

If you wish to have the atomic symbols for heteratoms displayed select "Labels" from the Display menu (this is the default). If you want carbons and hydrogens to be lableled select "Label Carbons" or "Label Hydrogens" from the Display menu.

Rotating and scaling the molecule: As you build the 3-D molecule, atoms may be hidden under other atoms, requiring molecule rotation to draw the molecule. Holding the right mouse button down on the left or right side of the drawing screen will rotate the molecule around the Y axis, and holding the right mouse button down near the top or bottom of the screen will cause X axis rotations. Letting up on the button will stop the rotation.

The program usually scales the molecule by the length along the X axis. As you draw a molecule it may increase along the Y axis faster than the X axis causing part of the molecule to disappear off the screen. You can rotate the molecule as above to view the molecule or you can Scale the molecule smaller by clicking on the "Scale" button near the top of the screen and using the Scaling tool that appears.

Deleting atoms: Select the delete button at the left and click on an atom to delete it. Note that by clicking twice on the Delete button you can delete whole molecules or all hydrogens from a molecule. Click on the "Add" button when you are ready to start adding atoms again (else the program will remain in "Delete mode").

Changing atom types of drawn atoms. Click on the Change button (screen left) and select the Atom type from the buttons at the left. Then click on the atom you wish to change. Click on the Add button when you are ready to start adding atoms again.

Changing bond types and deleting bonds: Click on the Change button, then select the bond type by clicking on the "0", "1", "2" or "3". Click on the two atoms whose bond is to be affected. Selecting bond type "0" causes the bond to be deleted. Hit the "Add" button when you are done making the changes.

Adding Rings: There are three ways to add rings - (1) use one of the 141 pre-built rings, (2) use the generic ring builer or (3) draw a ring with the mouse.

(1) For most cases the best and easiest method is to use a pre-built ring (these rings are already minimized). Click on the "Rings" button on the left and simply select a ring from the menu. If there is a structure already drawn to which the ring is to be connected then you can select an atom in the ring and on the existing structure where a connection is to be drawn.

(2) If your ring is not on the list then the second option is to again click on the "Rings" button, but click on the "2-D Generic" button that appears instead. An option panel will appear where you will need to supply the number of atoms in the ring and whether the ring is aromatic. A ring will be drawn containing all carbon atoms and either all single bonds or alternating double bonds if you checked the aromatic option. You will then have to change atom and bond types using the mouse and the buttons at the left of the screen. Select the "Change" button, then select the atom type or bond type that needs to be changed. If you have not already connected the ring to any existing structures and wish to do so then you may click on the "Connect" button near the top right of the screen and then click on the two atoms to be connected.

Adding Hydrogens: You can add hydrogens to all the atoms at once by clicking on the "H" button twice. All unfilled valences will be filled.

Changing bond lengths, angle and torsional angles. You can change the bond lengths, angles and torsional angles to any desired value from the Geometry menu. Select "Reference bonds and angles from this list". In most cases the bond lengths and angles chosen by the program will be nearly correct as they are taken from the scientific literature. Minimizing the molecule will change these lengths and angles too.

Changing an atom's hybridization: You can also change the hybridization of an atom by selecting "Hybridization" from the Geometry menu and choosing the hybridization type from the submenu. In most cases the default hybridization chosen by the program will be correct. Minimization will likely reset the molecule back to the default hybridization schemes.

Drawing more than one molecule: To start a second molecule, hit the "New Mol" button near the top of the screen and click anywhere on the drawing surface to start a new molecule. You can then add more atoms to any existing molecule as before.

Proteins and polymers can be automatically generated from the Tools menu.

From the Tools menu "Add Amino Acid" would be selected to create proteins. Check the Build polypeptide box to add an amino acid to the end of the polypeptide chain. Clicking on an amino acid will then add it to the existing polypeptide. Do not add all the hydrogens until you are done. Clicking on the "Alpha", "Beta" or "Turn" buttons will cause MMEd to choose a different optimized amino acid connection table file and cause it to use a different torsional angle in adding the amino acid to the protein chain.

From the Tools menu select "Add Monomer..." to build a polymer. Make sure the Build Polymer box is checked and then click on a monomer in the list and the Run button to add it to the end of the polymer chain. You can add many monomers at once by typing in the number to add in the "Number of monomers to add" text box. You can also specify the torsional angles for addition of the monomer - the default is a straight chain.