Modelling Instructions: CHem3D

Instructions for Use of the Chem3D System

The Chem3D software can be run on the Windows Computers. There are two licenses for such systems in the Perkin Laboratory, in the Start/Programs//Chemoffice 2006 directory. Two further licences have been installed on the systems in the study area (CHSTUDY 1 and 2) which can be used out of normal laboratory times. If you get a message that the software is unlicensed, please report this to Nick Davies in room 134.

Before starting, go to File/Model Settings/Model Building. If you will be using the program for Mechanics calculation, leave the first three buttons checked (Correct atom types, rectify and apply standard measurements). If you intend "importing" a file from another program as e.g. a PDB or Molfile, then deselect all these options (otherwise you may find the program eg adding hydrogens when you dont want it to). You may also find it useful to deselect these options if you are trying to rearrange the geometry of a model (the "apply standard measurements" option in particular may prevent you from moving atoms around). If in doubt, deselect all the options. Remember to "Set as default" if you want these settings to persist. Also at this stage, check the toolbars you might wish to use are displayed.
Draw the molecule using the appropriate single double or triple bonds in the drawing toolbar. To add perspective, rotate the molecule occasionally. You could also draw the molecule in ChemDraw (using stereochemical hashes and wedges), copy this 2D structure to the clipboard, and paste it into Chem3D. The 3D characteristics of such structurs may be unreliable however. When finished, make sure the structure is "rectified", which is babble for "add hydrogens". First Edit/Select all, then Structure/Rectify.
To tidy the structure up use Calculations/MM2/MinimiseEnergy then Run. When complete, the sub-division of the Mechanics energy components will be seen in the status pane at the bottom. Record the total energy (in the example below, 1.5025) and if relevant to the experiment, the components of that energy.
You can also rotate the molecule using the rotation trackball tool, and move selected atoms or molecules around using the move tool at the top. To rotate around a bond, select the two atoms involved (click at the bond centre) and move the mouse in the vertical rotation strip at the left hand side of the molecule window.
You can select the whole molecule, and Copy/as bitmap for pasting into eg Word.
MOPAC calculations are done in a similar manner as Mechanics. You will have to select the appropriate run time options (say PM3 instead of AM1).
You can also compute properties such as Molecular surface. To display the result, select Surfaces/Choose Surface/Molecular Orbital and then to change the displayed orbital, Surfaces/Molecular Orbital and select the one you want.
Ab initio Gaussian calculations are done in a similar manner. You will have to select the appropriate run time options of B3LYP, 6-31G Basis set and Heavy atom d Polarisation functions (RB3LYP/6-31G(d) is the shorthand for these options as shown below and is a "standard" combination often used for research-level calculations). For a molecule typical of the size in this experiment, this combination will take about 5-6 minutes to complete. The time scales more or less as the third power of the number of atoms! Record the final total energy (in units of Hartree; 1 Hartree= 627.5 kcal/mol, in this example -119.14425).
If you dont want to wait for the Program to do the calculation in real time, you can instead submit the calculation to the SCAN. Instead of selecting Minimise energy from the menu shown below, instead select Create input file, and save the file with the extension .gjf. Submit this file to the SCAN following the instructions on that web page.
BUG: There is currently a hanging bug in this program which we are trying to get fixed. If you Go to the General tab as shown below you will see the Results path as on the left below. Change it to look like the one on the right below by browsing to the C:\temp\ or C:\tmp\ directories. If you try this AFTER doing a calculation, even setting C:\temp\ will not work. The bug only relates to the output log file, and does not mean that the calculation itself has not worked.

If you don't make this change, the following error will occur;
As noted above for MOPAC, do a calculation to compute a property such as Molecular surface. This is an additional calculation to the geometry minimisation just done. Select the same parameters as before for the calculation.

Note: if you don't do this second calculation, you will by default get a Huckel calculation performed for you. This gives the wrong answers in this case, so take care. To display the result, select Surfaces/Choose Surface/Molecular Orbital. By default, the HOMO will now be displayed. To change the displayed orbital, Surfaces/Select Molecular Orbital and select the one you want. To capture the orbital for your report, Edit/Copy and then in Word Edit/paste. You can also try computing the surfaces with something other than PM3, ie a density functional/ab initio method.
When your calculation is complete, you should save the final coordinate file, via

The MDL Molfile or Chemical Markup Language (CML) are the two best options. These files can then be used (e.g. with the Jmol applet) to incorporate into a Web page, or "supporting information" for journal publication.
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