MO Orbital Plots

Moilin can draw MO plots from Mopac, Iconc, Firefly and Orca.

In all cases Chimera can be used to produce MO surface plots from CUB files.

Plotting Benzene MOs using Mopac

Start Moilin and in build mode click purge, if any molecule is present, click the empty window, select Phenyl on the dialog and click OK



Click the Mo button or press m/M to go to Mopac.



Click Newinput



on the dialog click Run Mopac



Click Properties and select Plot MO /Spin Density



On dialog 11 the HOMO (no. 15) is the default. Click OK and an outline MO plot is produced.
 


The files jobname_mo.pdb and mo_015.cub are also written and can be used to obtain an MO surface plot using Chimera

 

When Chimera is used to open the pdb and cub files the default surface colours are shown. In the volume viewer the left limit bar is for the negative side and it is selected. To change its colour to blue type "blue" into the colour name and hit return.

The darker surfaces should now be blue. Selecting the right +ve limit bar and setting its colour to red gives the picture above. mo_011.cub is also shown with surface transparency set to 40% using Actions/Surface/Transparency.


Check that Data type is set to Organic click apply and OK.
In MCE Zoom using Shift + left click mouse move up/down. Move within the window using shift + cursors.

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