Chapter 4. Tutorials

PCMODEL is designed to be easy to use. In this chapter the basics of using the program, along with many of its options, will be covered through example. Before beginning the specific examples, there are some general points about structure entry to be considered.

The screen is two dimensional. Initial input occurs at 0 on the z-axis. The screen itself is the xy-plane. Thus, a hexagon drawn to represent cyclohexane using the DRAW Command is initially flat. To obtain three-dimensional structures you need to move atoms behind or in front of the z plane with the IN and OUT commands on the TOOLS menu. Once some three-dimensional information is available, further structural input can be done by rotating the structure. If you pick an atom and draw a bond to a new atom, the new atom will lie parallel to the picked atom along the coordinate that is perpendicular to the screen.

Complex structures are easier to build using the substructure ADD, ROTATE and MOVE commands. You can use the built-in substructure templates, or build a library of your own by creating structures and saving the minimized coordinates in an MMX or PCM file.

Options are selected by pointing to the desired option and clicking (move the cursor until it is over the desired option and click the left mouse button). If the wrong option is chosen, simply choose the correct one and continue. Likewise, atoms are input or selected by pointing to the appropriate spot in the drawing box. When the cursor is over an atom the atom will be highlighted (a box will be drawn around the atom) so you may tell which atom is closest to the cursor.

On the PC the right mouse button may always be used to rotate the current structure. Holding the right mouse button down and dragging the mouse will cause the structure to rotate. Moving the mouse to the left or right will rotate about the y-axis, while up and down movement rotates about the x-axis. Holding down the shift key while dragging the mouse will rotate the structure about the Z-axis. On the Macintosh simply hold down the mouse button and drag. More complete control of rotation, translation and scaling is had using the Control panel in the View Menu.

The following examples will illustrate a few of the options available for structural input, minimization and display using PCMODEL. A few mistakes will be purposely made along the way to illustrate how they may be corrected.

4.1 Methylcyclohexane

Structures are drawn on the screen in essentially the same way as they would be represented as 3-D structures on paper. For example, a hexagon could be drawn. Initially this would be in the XY plane with all Z coordinates equal to zero. Three-dimensional information could be entered by using IN to push one atom in to the screen and OUT to place the opposite atom in front of the screen. Alternatively, OUT could be used to place 3 alternating carbons in front of the screen to provide a chair shape. In this tutorial, however, we will begin by drawing a side-on view of the chair form.

4.1.1 Drawing the Structure

Begin by selecting the DRAW button on the TOOLS menu with the mouse. A dotted outline will indicate that you are in Draw mode. Move the cursor off the TOOLS menu and into the drawing box, somewhere in the upper right hand corner. (We will be drawing cyclohexane as in Figure 4.1.) Click the mouse button once then move the cursor down ~ 3 cm and left another 3 cm, and click again. A line indicating a bond between the first atom and the one just placed will be drawn. Continue drawing in this manner, placing atoms 3, 4 and 5.

Figure 4.1 Completed cyclohexane structure with atom numbers displayed.

The atom numbers can be displayed on the screen by choosing LABELS from the VIEW menu, then clicking in the circle next to "atom numbers" and clicking on "okay". They can be removed by again choosing LABELS from the VIEW menu, then clicking in the circle next to "Hydrogens and Lone Pairs"

At this point, we will purposely make a mistake, by connecting atom 2 to atom 5. To get back into the drawing mode, select DRAW from the TOOLS menu. Then, click on atom 5, then on atom 2. This will create a bond between atoms 2 and 5. (If the cursor is within about 1/4 inch or 0.5 cm or an atom, then that atom will be picked by the program instead of creating a new one.) To correct the mistake, move the cursor to the DEL button on the TOOLS menu and click on it. Now click on the middle of the bond between atoms 2 and 5 (the incorrect bond). The structure will be redrawn with the deleted bond removed.

To continue drawing, again click on the DRAW button on the TOOLS menu, then click on atom 5 and continue to draw atom 6 and the bond back to atom 1. At this point the structure should resemble a chair cyclohexane as in Figure 4.1. However, remember that all the atoms are still in the plane of the screen, that is, no 3-D information has been included. To fix the structure, choose OUT from the TOOLS menu, and then click on atom 2 twice. Each click moves the atom 0.33 Å out of the plane of the screen. Next, point to atom 3 and click 2 times. Now select IN from the TOOLS menu and click on atom 5 twice and atom 6 once (another mistake which we will shortly correct). Rotation of the structure by dragging the mouse will reveal the changes in the structure.

The initial view of the molecule is in the XY plane. The Z+ axis comes out towards the user. To view the structure from a different orientation, select CONTROL_PANEL from the VIEW menu. A new window entitled "Dials" will appear. Within this window will be continuous sliders that allow you to change the orientation of the structure. By clicking on the arrow at either end of a slider once, the view will move slightly. Holding down on one of the arrows will provide continuous movement in that direction. Alternatively, you may click on the box in the middle of the slider bar, and drag it while holding down with the mouse button. This will also provide continuous movement of the view until the mouse button is released. The RESET_VIEW button will return the structure to its original orientation. If you rotate the structure in the Y direction, you can see how atoms 2 and 3 line up, but atoms 5 and 6 do not (because atom 6 was purposely moved only once). This could be corrected by returning to the original view, then using IN on atom 6 one more time. However, we will correct this using the MOVE command from the TOOLS menu. After selecting MOVE from the TOOLS menu, click on atom 6, then near atom 5 (the position to which atom 6 should be moved). The structure will be redrawn with the correction.

Hydrogens may be automatically added by selecting the H/AD command from the TOOLS menu. However, once you have done this, there is no free valence at which to add the methyl group. This can be corrected in one of two ways. The first alternative is to delete the hydrogens by clicking on H/AD again, then select DRAW and click on atom 1 then on a blank space to the right of atom 1 to add the extra methyl group. (If the structure is too large, there will not be room on the screen to add the methyl group. If this is the case, use the SCALE option, accessed through the CONTROL_PANEL option of the VIEW menu, to shrink the structure to a more manageable size.) The structure would them be completed by re-selecting H/AD to add the hydrogens. A second alternative is to change the equatorial hydrogen into a carbon. Select PT (Periodic Table) from the Tools menu. Select C from the list of available atom types, and click on the equatorial hydrogen. Select H/AD to delete hydrogens (but the equatorial carbon will stay), then H/AD again to add hydrogens. The PERIODIC_TABLE window may be removed be selecting CANCEL (the last option in this window). This method of replacing specific hydrogens is very useful for controlling the stereochemistry when building large and complicated structures. A third alternative is to use the Build command from the Tools. In Build mode clicking on a hydrogen replaces that hydrogen with a carbon and then does a hydrogen delete/add sequence so the methyl group is added with only one click of the mouse.

It is not important if the structure does not look perfect at this point. Only a crude approximation of the structure is needed for minimization. However, the closer to correct the structure is, the faster the minimization will proceed. Methyl groups pointing in to the middle of a cyclohexane ring will obviously cause problems. Also, if three carbons are attached to a central carbon such that all 4 are in a plane, the program will have difficulty in adding a hydrogen in the correct position. You can check for such errors by using the rotation and translation sliders in the DIALS box to get different views of the molecule. Use IN, OUT and MOVE from the TOOLS menu to correct these problems.

Before starting a minimization, it is a good idea to store the structure with a descriptive filename. Select SAVE from the FILE menu. Select the appropriate file type from the list provided by clicking on it with the left mouse button. (The default file type of PCM is preferable.) The "File Name:" box will change to indicate the default extension for that type of file. The "*" in the file name should be changed to a descriptive name for this structure, for example, etcyclo. The path indicating where the file is to be saved may also be changed at this time. When the correct path and filename have been entered, click on "OK" or press return on the keyboard to save the structure in the indicated location.

At the beginning, every five iterations during, and at the end of the minimization process a backup file of the structure, called PCMOD.BAK will be written (the format is PCM). If anything should go wrong or should you need to stop the program, you may restart the minimization by reading in this file and continuing from the last saved point.

4.1.2 Building the Structure

A structure may also be constructed by using the BUILD command of the DRAW TOOLS. Begin by selecting BUILD. An ethane will appear (Figure 4.2). Click on the upper right hydrogen to produce propane as shown in Figure 4.3. Next click on hydrogen 10 to provide butane as shown in Figure 4.4. It may be easier to see the 3-dimensional nature of the structure if you turn on Tubular Bonds from the View Menu as in Figure 4.5. However it is usually easier to click on atoms using the stick figure. You can rotate the structure at any time by holding down the mouse button (right button on the PC) and dragging.

Figure 4.2. Figure 4.3 Figure 4.4

Continue the build by clicking on the next hydrogen in the sequence to obtain Figure 4.6 and then to obtain Figure 4.7. Again it may be helpful to turn on Tubular Bonds to see the 3-d structure.

Figure 4.5 Figure 4.6 Figure 4.7

Complete the ring by removing the hydrogens (H/AD) and then use Draw to create a bond between carbon 1 and 6. It does not matter if you draw the bond first or remove hydrogens first. You will arrive at Figure 8 either way.

Figure 4.8 Figure 4.9. Figure 4.10

Complete the structure by adding the hydrogens (H/AD) to give Figure 4.9 and then using Build to add the methyl group (Figure 4.10).

The easiest method for constructing methylcyclohexane is to read C6 from the RINGS template of the Draw Tools or under Template on the Menu Bar then add the methyl group using BUILD.

4.1.3 Minimizing and Adjusting the Structure

The structure may now be minimized. Select MINIMIZE from the ANALYZE menu, and the calculation will automatically start. Once the minimization process has started, pointing to the Stop Job button may stop it. The cursor will change into an hourglass shape while the minimization is in progress, and will return to the arrow shape when it is completed. The final energy should be around 6.89 kcal. Save this structure, as it will be used later.

We now want to compare the energy of the equatorial isomer to that of the axial isomer. We could start from scratch by clearing the current structure by selecting ERASE from the DRAW menu, and drawing in a new chair cyclohexane with an axial methyl group. However, it is usually simpler to modify the present structure. This can be done in several ways. Some choices are:

Use MOVE: Select H/AD to remove the hydrogens. Then select MOVE from the TOOLS menu, and click on the equatorial carbon. Next point to a new position above atom 1 where the axial group is to be located. Use H/AD again to add the hydrogens back on to the structure. Check that you have in fact obtained the axial isomer. If not, remove the hydrogens again and move the carbon atom further.

Use DEL and the Periodic Table: Bring up the Periodic Table by selecting PT from the TOOLS menu. Choose the C atom, and click on the axial hydrogen to change it into a carbon. Then select DEL from the TOOLS menu and click on the carbon of the equatorial methyl group. It, along with the attached hydrogens, will be automatically deleted. Then click on H/AD twice to remove then replace the hydrogen atoms.

Use DEL and BUILD: Select DEL from the TOOLS menu and click on the carbon of the equatorial methyl group. It, along with the attached hydrogens, will be automatically deleted. Then select BUILD and click on the axial hydrogen.

Use EPIMER: Click on Sel-Atm on the TOOLS menu. Then click on carbon 1, then to the axial hydrogen and equatorial carbon. Small filled circles will indicate that the atoms have indeed been selected. If hydrogens obscure any of the atoms, use the DIALS box to rotate the structure to a better orientation, or SCALE it up to zoom in on the area of interest. Then select EPIMER from the EDIT menu, and the two attached groups will be switched.

Now select MINIMIZE from the ANALYZE menu to find the energy of this structure. It should be about 8.67 kcal or 1.78 kcal higher than the equatorial isomer. Save this file with a different filename from that used for the equatorial isomer.

4.2 Trans-Decalin

We will next illustrate how to build up a simple structure by converting axial methyl cyclohexane into 1-methyl- trans-decalin. Begin by reading in the minimized axial methyl cyclohexane structure previously saved by choosing OPEN from the FILE menu. Use H/AD to remove the hydrogens. Turn on atom numbering (LABELS under VIEW menu), bring up the DIALS box by choosing CONTROL_PANEL from the VIEW menu, and rotate the structure along the X-axis until it has an orientation similar to that in Figure 4.11. Using DRAW from the TOOLS menu, click on atom 1, then continue to place atoms 8, 9, 10 and 11, and the final bond back to atom 2.

Figure 4.11 Completed 1-methyl-trans-decalin structure with atom numbers displayed.

Carbons 8 through 11 will have the same Z coordinate as atom 1, the last atom selected prior to drawing them. If we had chosen atom 2 as the starting point, then carbons 8 through 11 would have the same Z coordinate as atom 2. Use OUT to push atom 9 out 2 clicks, and IN to move atoms 10 and 11 each in 4 clicks. Use the rotation and translation sliders to check placement of the atoms and MOVE to correct any mistakes. Add the hydrogens back with H/AD and proceed with the minimization.

4.3 Special Options

4.3.1 Compare

The COMPARE option is used to calculate the differences in two structures and to produce an overlaid view of two structures. Begin with axial methyl cyclohexane as the active structure. Select COMPARE from the VIEW menu. Select NEXT_STRUCTURE from the COMPARE menu, and enter the name of the equatorial cyclohexane structure. We will want to see how the axial and equatorial atoms change positions if the remainder of the ring is held constant. Use the Sel-Atm button from the TOOLS menu to mark carbons 3,4 and 5 on the left (axial) isomer, then carbons 3,4 and 5 on the right (equatorial) isomer. The comparison will pair the first atom selected on the first structure with the first atom selected in the second structure, etcetera, so it is important to select the atoms in the same order on the two structures. Once the atoms have been selected, choose CALCULATE from the COMPARE window. PCMODEL will now find the best least squares fit for these three atoms, and will give the rms differences between all corresponding atoms in the Compare Output window, and the structures will be redrawn overlapped, with red lines connecting the atoms that are being compared. If the structures overlap well, the red lines may not be visible. The structures may be rotated in mono or stereo to get a better view of the comparison.

Select MOVE from the SUBSTR menu, and choose the substructure "untitled". Use the DIALS box to translate this substructure away from the other one. A new set of atoms for comparison can now be marked on each substructure (using the Sel-Atm option), and the calculation re-done. Click on CANCEL to dismiss the COMPARE window.

4.3.2 Rotational Energy Barriers

PCMODEL can calculate rotational barriers using the DIHEDRAL_DRIVER option in the ANALYZE menu. However, there is a quick way to explore rotational minima using ROT_E from the ANALYZE option. Read in the equatorial methyl cyclohexane structure and convert one of the methyl hydrogens to a carbon using the BUILD option from the Draw Tools menu.

After minimization, we will explore the rotational minima of the ethyl group. We will need to Sel-Atm carbon 1 and the first carbon of the attached methyl group (carbon 7). If hydrogens obscure these, rotate the structure until they are not hidden.

Choose Sel-Atm from the tools menu, and click on the carbon of the ring where the ethyl group is attached and the first connected carbon atom. One may also use Sel-Bnd and click on the bond to be rotated. Then select ROT_E from the ANALYZE menu. Enter an increment of 10 and an extent of 360. Click on okay (or hit return). The program will then produce a plot and of energy vs. angle (this may take a few seconds to appear) similar to that shown. The energy scale is relative to the energy of the starting conformation and the angles are in degrees. The plot can be printed. To return to the structure window: In the Windows version pull down the File menu and choose Exit (the plot window has it's own menu bar and under the File menu there will be two choices, Print and Exit); In the Macintosh version choose Stick Figure from the View Menu.

4.4 Benzene and a Pi Calculation

Select DRAW from the TOOLS menu and draw a hexagon. Next select ADD_B from the TOOLS menu to change every other bond in the ring to a double bond, by clicking in the middle of the bonds. Finally, use H/AD to add the hydrogens to create benzene. Although the structure now looks like benzene, it is not ready to be minimized because PCMODEL does not have any information about the pi system. Choose PIATOMS from the MARK menu, and the structure will be redrawn with small ~ symbols near each of the pi atoms. (PCMODEL automatically determines which atoms are pi atoms, once it has been told to look for them.) Minimize the molecule using MINIMIZE from the ANALYZE menu, then save it to disk using the SAVE command from the FILE menu.

4.5 Biphenyl and a Pi Calculation

Begin with the benzene structure studied above as the active structure. Select READ from the SUBSTR menu, and read the benzene file back into the program. There will now be 2 benzene rings on the screen, side by side and several inches apart. Sel-Atm one hydrogen from each substructure, then choose CONNECT from the SUBSTR menu. The screen will be redrawn with the two hydrogens removed and a carbon-carbon bond in their place. Use Sel-Atm from the TOOLS menu to highlight 4 carbons involved in the biphenyl dihedral, then select ROTATE_BOND from the TOOLS menu. Change the dihedral angle to plus or minus 5 degrees, then click on EXIT to return to the main window. Finally, select PIATOMS from the MARK menu since the atoms in the substructure may not be labeled as pi atoms at this time.

Now minimize the system by choosing MINIMIZE from the ANALYZE menu. This time all the pi atoms will not lie in one plane. The structure should minimize to a dihedral angle of about 39 degrees with a shallow potential energy surface.

4.6 Ferrocene - Using Metals and Coordination

The sandwich complex of iron and two cyclopentadiene rings can easily be modeled with PCMODEL. There are two ways to represent the cyclopentadiene rings: as aromatic rings with two double bonds and a carbon anion, or as a ring of aromatic carbons. Since the first option would require a pi calculation, the second option will be used. This atom type is designed to reproduce the bond lengths and angles of aromatic rings without requiring a special pi calculation.

To begin, draw a five-membered ring. Double bonds may be added, but this is not necessary when the aromatic carbon type is used. Use the PT (Periodic Table) option from the TOOLS menu and replace all the ring atoms with atom type Ca (aromatic Carbon). Use H/AD to add hydrogens, then rotate the ring onto its side using the DIALS box (accessed via the CONTROL_PANEL option on the VIEW menu). Save the ring to a file, then read it back in as a new substructure using the READ option in the SUBSTR menu. If the two rings are too close together, Sel-Atm an atom in one and use SUBSTR MOVE to separate them. Select DRAW and place an atom between the two rings. To make this the iron atom select METALS, click on Fe and click on the isolated atom. Select UPDATE to clean up the structure. There should only be one hydrogen on each of the aromatic carbons, whether or not you have drawn in the double bonds in the cyclopentadiene rings.

At this time PCMODEL does not know anything about the interaction of the cyclopentadiene rings with the iron atom. Use Sel-Atm to mark the iron atom and all 10 of the Ca atoms, then select METAL_COORD from the MARK menu. A dialog box will appear asking for information about the metal. Since this is an 18 electron complex select "saturated_18_e" for the electron count. Clicking on OK causes the screen to be redrawn with the metal coordination bonds shown in red. The structure can now be minimized. If the structure had been minimized without coordinating the iron to the rings, the iron atom would not have been bonded to anything and would have wandered out of the picture.

4.7 The Methanol dimer - Hydrogen Bonding and Docking

This calculation will demonstrate the hydrogen bonding and docking capabilities of PCMODEL. To begin, draw and minimizing methanol. Select DRAW from the TOOLS menu and draw a 3-carbon skeleton. Next select PT and change the central atom to an oxygen (O) and one of the terminal carbons to a hydrogen (H). Now use H/AD to add the remaining hydrogens and lone pairs. If you repeat the H/AD command you will note that the hydroxyl hydrogen is not removed. Hydrogens attached to heteroatoms are not removed by H/AD and must be removed explicitly using the DEL command. (This is to ensure that particular hydrogen bonding orientations drawn by the user will not be disturbed by the normal H/AD function.) Minimize this structure (MINIMIZE on the ANALYZE menu) and then save it in to file (SAVE under the FILE menu). Since there are no other heteroatoms present, hydrogen bonding was not important during this step.

Next, read the methanol structure back in as a substructure using the READ command under the SUBST menu. A red line will appear between one lone pair and one hydroxyl hydrogen, indicating a potential hydrogen bond. Use the MOVE command under SUBST to move the second methanol molecule around so that the O-H-O system is linear, and is within bonding distance. (By default Hydrogen bonding is now turned on, use the REST option in the Mark Menu to turn it off). MINIMIZE (ANALYZE menu) the dimer. If the linear dimer is obtained, the energy should be -3 to -4 kcal. Next select DOCK from the ANALYZE menu to begin a simulated annealing calculation. The default settings are adequate for this system. Click on OK, and then enter a filename to store the results of the calculation. If the calculation is successful, the dimer energy will be between -4 and -5 kcal, and a linear hydrogen bond will be present. The calculation may be stopped at any point by hitting the ESC key.

4.8 Substructures - Creation and Manipulation

In this example, we will create, move, rotate, hide and reset substructures. First, sketch two separate structures - a hexane and a pentane. To make the pentane into a substructure, choose Sel-Atm from the TOOLS menu and click on any atom in pentane. Select CREATE from the SUBST menu. A dialog box will appear asking for the name of this substructure, type "pentane" and select OK or hit return. Select LABELS from the VIEW menu and click on "Substructure Numbers". The atoms will now be labeled with numbers, according to the substructure to which they belong.

Select MOVE from the SUBST menu, and the DIALS box will appear. Since an atom in the pentane substructure was still selected when SUBSTR MOVE was selected, the DIALS box will only move the pentane substructure. Click on EXIT to dismiss the DIALS box, then click on Sel-Atm on the TOOLS menu to de-select all atoms. Now select MOVE from the SUBSTR menu, and a dialog box will appear with a list of all currently defined substructures. Select a substructure from this list, and a new DIALS box will appear which will move only that substructure. To move a different substructure select click on one atom in a different substructure. As long as no other Draw Tools options have been used, the Sel-Atm option will still be active. This substructure now becomes the active structure and will be translated or rotated by the DIALS box.

Now click on H/AD to add the hydrogen atoms. Use Sel-Atm to mark one hydrogen in each substructure, and select CONNECT from the SUBSTR menu. A bond connecting the two substructures will replace the hydrogens. Select MOVE from the SUBSTR menu, translate one structure, and notice that the central bond of the hexane is stretched. This will be the case whenever two separate substructures, which are directly bonded, are moved.

Choose HIDE from the SUBST menu, if no atoms are selected a substructure list window will appear again. However, each substructure will have a lowercase "v" next to it, indicating that it is currently visible on the screen. Select pentane and say okay. The pentane structure will disappear from the display. Select HIDE from the SUBST menu again, and this time pentane will have an "i" next to it, indicating that it is invisible. Select pentane again and click on OK, and pentane will re-appear on the screen.

Select ERASE from the SUBSTR menu, and select "Str 0" from the list. Note that the entire complex is erased. This is because pentane is still part of "Str 0", the initial structure, as well as being its own substructure ("pentane").

4.8.1 Building Polystryene using Dummy Atoms

Read in benzene from the Rings Templates and then select BUILD from the DrawTools. Select one of the hydrogen atoms on the ring to replace it with a methyl group. Next select one of the hydrogens of the methyl group and you should now have ethyl benzene. Minimize the structure to obtain a reasonable geometry. Bring up the Periodic Table from the DrawTools menu and select the dummy atom type, DU, from the dialog box. Next point to one of the hydrogens of the CH2 group and then the hydrogen anti to the first hydrogen on the CH3 group. Do an HAD sequence and notice that the hydrogens that were converted to dummy atoms are not removed by the hydrogen delete. Once the hydrogens are readded do a Minimization. Next , using SUBSTR READ, read in the pcmod.bak file. Highlight the Dummy atoms by using the Show Dummy command from the SUBSTR menu. There should be four dummy atoms showing on the screen. Next select the Connect command from the SUBSTR menu. This will bring up the Connect dialog box with the dummy atoms boxes filled. Selecting Connect will connect the two structures from the second dummy atom of structure 1 to the first dummy atom of structure 2. Selecting Next Structure brings up a File Open dialog box and a new structure can be read. Reread pcmod.bak and note that the Substructure Connect dialog box will be updated with new atom numbers for the dummy atoms. Selecting Connect adds the new structure to the old structure. Repetition of this procedure makes it easy to build oliogmers. You are not limited to single monomers since any structure can be read using the Next Structure button. As long as the new structure has two atoms marked as Dummy Atoms, the substructure connect function will work.

4.9 Diels-Alder Transition State

To model the Diels-Alder transition state for the reaction of butadiene and ethylene, begin by drawing a hexagon of atoms (a flat cyclohexane). Use PT from the TOOLS menu to replace atoms 1 and 2 by C* and atoms 3 and 4 by C# and atoms 5 and 6 by C·. Use H/AD to add hydrogens and select MINIMIZE from the ANALYZE menu to optimize the structure. A dialog box will appear inquiring about what bond orders to use. The C*-C* bond represents a sigma bond being formed between one terminus of butadiene and one terminus of ethylene. Enter 0.3 for this bond order. The C#-C# bond represents the other sigma bond being formed. Enter 0.3 for this bond also, and then click on OK. This will start the minimization. The resulting structure should be very similar to that calculated by Houk et al. (Houk, K. N., Paddon-Row, M. N., Rondan, N. G., Wu, Y. D., Brown, F. K., Spellmaeyer, D. C., Metz, J. T., Li, Y., and Loncharich, R. J. Science, 1986, 231, 1108 and references therein.)

It should be noted that the bond length between the two C· carbons is 1.4 Å. (You can check this by selecting QUERY from the TOOLS menu, then clicking on each of the C atoms, then on a blank space on the screen. The distance between the two atoms will be displayed on the screen. To remove the distance from the screen, click on UPDATE twice.) If a normal double bond were drawn between these two atoms, the resulting minimized structure would have a 1.34 Å bond between these two carbons, which will ultimately give a double bond in the product.

If other bond orders are chosen, the distances between the C* or C# carbon pairs will respond, as will the 1,3 angles at C* and C#. The calculated MMX energy is the potential energy of the system relative to the potential functions for the transition state, NOT relative to the ground state. As usual, the potential energy of a minimized structure can only be compared to a conformational isomer or a diastereomer. The potential energy of a transition state with one set of bond orders might be compared to the potential energy of another transition state with different bond orders, but only the difference in steric energy can be determined, not the actual free energy difference between the two structures. That is, the electronic energy difference is not considered in the MMX calculation. See the chapter on the MMX force field for more information.