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MOPACinst - MOPAC Molecular Orbital Calculations on...

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MOPAC Molecular Orbital Calculations on Diatomics To run a molecular orbital calculation for a diatomic on a Windows or Mac system, use a text editor like Word, SimpleText, or Notepad to create the input file. An example input file for LiH at 1.61Å bond length is given below. The first line contains keywords for the calculation. MNDO specifies the “chemistry” or the Hamiltonian. (AM1 is the most useful Hamiltonian for general organics. PM3 is best for compounds containing P or S. However, MNDO is necessary for compounds containing Be, Li, Na, Mg, and K.) VECTORS is needed to have the program print out the eigenvectors (i.e. the molecular orbital wavefunctions). BONDS has the program print summary calculations on bond orders and valencies. For other keywords and the description of the BONDS calculations, see the keyword list below. The next two lines are for comments. These lines can contain anything you like, but they must be present even if they are blank. The next two lines specify the atoms and the bond length. The atomic symbols should be written in caps. The first atom is specified as lithium. The next line specifies the second atom as hydrogen. The bond length is input as 1.61 in angstrom units. The "0" following the bond length specifies that the bond length is to be kept constant. If a "1" were specified instead, MOPAC would vary the bond length to find the minimum energy. This process is called energy minimization, which corresponds to the same process in molecular mechanics calculations but from a quantum mechanical perspective. A blank line is necessary at the end of the file to signal that no more atoms are to be input. VECTORS BONDS LiH MNDO 1.61A LI H 1.61 0 If you use Word to create the input file, remember to save the file in “text only” or “Plain text” format. The file name should end in “.dat”. You can use the zmatrix application (www.colby.edu/chemistry/PChem/zmatrix.html) to create the input files for more complex molecules. Make sure to close the file in Word before trying to run MOPAC. Running MOPAC for the PC: On the Schupf lab systems, MOPAC is installed in the Shared Documents folder: “C:\Documents and Settings\All Users\Shared Documents”. There should be a shortcut to this folder on the desk top. To run MOPAC just drag your input file onto the mopac entry. If this “drag and drop” method doesn’t work, see the section on Alternate Versions of MOPAC below. When the calculation is complete, you use a text editing program to read the results from output files. The main output file has the “.mno” extension. Running MOPAC for the OS-X version: First, you must install a script to run MOPAC in your Documents directory. Instructions for doing this installation are listed below. Note also the section on “Getting the Correct File Formatting on OS-X,” below. After installation, to run MOPAC open a Terminal window (TV-type icon with the ">" symbol), and change to the mopac directory by typing (if you have already not done so): $ cd Documents/mopac
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Now run MOPAC by typing: $ ./mopac file-name
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MOPACinst - MOPAC Molecular Orbital Calculations on...

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