Modelling Instructions: CAChe

Instructions for Use of the CAChe System

The CAChe software can be run on the eMac Computers. There are three licenses for such systems, two of which are fitted to the eMac computers in the Perkin lab, and one is installed on the eMac computer in the main computer room. Although you can log into these machines using your conventional account, unresolved issues (with file permissions) mean the CACHe software does not yet run properly. As a temporary solution, please log in as user cache and password expt9.

At the end of this part of the experiment, you will probably need to transfer files from these systems to a Windows system. To do so, select Go/Connect to Server from the "Finder" window, and enter afp://chnts1.ch.ic.ac.uk/mac-PC. Enter your normal login and password, whereupon a volume will appear on your desktop called Mac-PC. Save your files there (in your own folder) and you can read them again using a Windows computer.

To invoke the CAChe structure "Editor", find this in the "Dock" that appears on the bottom of the Screen.

A new "Window" opens called Untitled - 0 and several new menu items appear on the top of the screen. Select the atom tool;

If there are appropriate templates, you could instead start with one of those;

The default atom using the atom tool is sp³ hybridised carbon. Draw a carbon skeleton as follows;
Click once on the drawing area, when a carbon atom appears.
Locate the cursor over the top of this atom, press the mouse button, and KEEP IT PRESSED. Move ("drag") the mouse while you are doing this to a new position and release the button. A second carbon appears with a bond connecting it to the first.
If you "locate, press, drag and release" between two existing atoms, the single bonds can be changed to a double bonds.
To change carbon to a heteroatom, go to the atom menu, press the mouse button, "drag" to the element you want and release to select as the drawing tool;

Position the cursor on the atom you want to change, hold down the apple key and click the mouse button.
You now have a structure with no hydrogens and the incorrect configurations (ie sp³ etc) for the atoms. The structure can be 'Beautified'

You now have a complete structure which should fill the window. To view this molecule from different angles, the virtual "trackball" can be used.

To rotate your view of objects on the screen, press the Apple key and the SHIFT key at the same time and drag the view with the mouse
To translate your view of objects on the screen, press the Apple key and the OPTION or ALT key at the same time and drag the view with the mouse.
To zoom and pan your view of objects on the screen, press the Apple, OPTION/ALT and the CONTROL keyss at the same time and drag the view with the mouse
To scale objects, press Apple and CONTROL at the same time.

If you want to delete superfluous atoms, first chose the select tool;

Select them by positioning the cursor on the first atom and click the mouse. Now hold the SHIFT key down and keep it down while you click on all the remaining atoms you want to delete. Each will appear highlighted. Press the "Delete" key (often shown with a reverse arrow) on the keyboard to delete these atoms. If you make a mistake, undo from the Edit menu will do just that. Whilst atoms are selected, you can measure distances angles etc between them. Go to the Adjust menu and select e.g. "Dihedral Angle" if you have four atoms selected;

The display will tell you what the current angle is (if you select only two atoms, you can measure a distance, etc).If you type 0 from the keyboard, you will change the current value to 0deg. for the angle. Click on "Apply" and then "Done" to implement the new value.

The next stage is to optimise the geometry. Normally, this would be performed first using Molecular Mechanics but for a molecule as small as this one can use the program MOPAC directly, as selected from Applications menu;

You will be first asked if you want to save your file to disk. Please take care to save the file correctly. It should be saved to the local machine hard drive, ideally in the path Users/cache/Documents, and in this area you should create a New directory for your experiment. Otherwise, there is a possibility that you may overwrite another persons files [this rather awkward requirement is necessitated because the CAChe software does not work correctly when so-called network logins, ie using your own private account, are used. Hence the need to use the communal cache account for this experiment]. After selecting OK, you enter the MOPAC module. All the default parameters should have the following values. If they do not, then reset them to the values shown below;

At this point, MOPAC will start running; the output looks similar to that below. It may take 5 or so minutes to finish. Using the PM3 parameter set, you should get an answer similar to that shown below. If its significantly ( ie 0.5 kcal/mol) different, you probably have a wrongly connected structure, or an entirely different molecule to the requisite. Check your structure again by return to the Editor;

You should inspect the final optimised structure at this stage, not only for any anomalies, but also for any expected (or unexpected) structural features. If you have time, you could repeat with a different parameter set (PM5 is the latest, and may even be better than PM3) and also establish if any unusual structural features persist across different semi-empirical MOPAC methods.

Next comes the Tabulator (from the applications menu), where the required molecular orbitals will be evaluated. Choose only those of interest;

If you have time, you could also compute the molecular electrostatic potential at this stage (it takes about 20 minutes to produce).

Next comes Visualizer+; you will have to select the orbital you want by opening a surface from Visualiser.

Resize the molecule if necessary using the Find command.

You should inspect each orbital in turn. From the nature of the HOMO, can you predict the regiospecificity of molecule 12? In the literature reference, an argument is presented for why the two π HOMO orbitals are different in energy. Can you reproduce this argument by illustrating the relevant orbitals? If you want to inspect the eigenvalues (energy levels) or eigenvalues (coefficients) of the orbitals, proceed as follows. (NOTE: due to a software bug, the orbital numbering starts at 0 (zero), not 1. The HOMO should always have a strongly negative energy, e.g. -8 or more eV. Note also 1 Hartree= 27.2 eV (you may need this conversion factor if using other programs such as Gaussian).

Next you can display the calculated atomic charges. From the View menu;

followed by;

The scale should be set to 2.0 (or greater) from the default value of 0.25. The size of the atom spheres now indicates the charge on the atom (yellow negative, red positive). Comment on these values in relation to the regioselectivity towards an electrophile!

You can copy the orbital window to the clipboard, and paste the contents to a Word processor document to produce a report of your experiment.
To exit from Visualiser (or any of the other programs);

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