Visualizing Molecules

 

Using GABEDIT to visualize MOPAC lanthanide complexes output files:

  1. Insert the keyword AUX in your MOPAC2012 .mop file.
     
  2. Run your MOPAC2012 calculation. An .aux file will be also produced, along with the .out and .arc files.
     
  3. Open GABEDIT and fix the maximum bond valencies of the lanthanide and of the coordinating atoms (see below).
     
  4. Open the .out or .aux file of your complex in GABEDIT.
     
  5. Check the bond connections and make sure that they are correct.
     

How to fix the Maximum Bond Valencies

First step: Study your complex.

  1. Determine the coordination number of your lanthanide ion in your complex of interest, e.g, 8, 9, 10, 11, 12, etc.
     
  2. Determine which atoms are directly coordinated to the lanthanide ion.
     
  3. For each type of atom direcly coordinated to the lanthanide ion, determine the maximum number of bonds in your complex. Ex. if water is coordinated to a lanthanide ion, the oxygen has a maximum bond valency of 3.
     

Second step: fix GABEDIT.

  1. Open GABEDIT.
     
  2. Go to the toolbar, click on GEOMETRY and then choose DRAW.
     
  3. The GABEDIT "Draw Geometry" window appears.
     
  4. Right-click anywhere on this window, and then choose SET on the menu.
     
  5. Click on PROPERTIES OF ATOMS. A periodic table appears.
     
  6. Click the lanthanide atom of your complex, a new window called "Set properties of Ln atom" appears.
     
  7. Change its maximum Bond Valence to exactly the number you determined in item 1 of the First Step above (no more no less).
     
  8. Click on OK. This windows closes and you are back to the periodic table.
     
  9. Now, click on each of the coordinating atoms, eg. O and N, and change their maximum bond valencies to the numbers deermined in item 3 of the First Step (above).
     

Third Step:

  1. Open the .out or .aux file of your complex im GABEDIT, and check the bond connections and make sure that they are correct.
     
  2. Please, right click on the black screen of the "Gabedit: Draw Geometry" window, go to "Read" > "Mopac" > "Last geometry from a Mopac output file".
     
  3. Find your .out MOPAC output file and click on "Open".
     

You can measure atom-atom distance, angles and torsion angles. For this, click to the  icon and select from two to four atoms of the molecule.

The bond connection algorithm of GABEDIT may not always work efficiently with some high coordination number lanthanide complexes. Every now and then, some coordinating bonds may not appear, while sometimes some other spurious bond connections may also appear. However, the positions of the atoms are always correct.

You can erase the spurious bonds and/or draw the missing bonds as described in the Draw your lanthanide complex in GABEDIT section of the Drawing complexes tutorial.