Argus lab - a freeware PC program for modelling
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The document outlines steps for performing molecular orbital calculations using ArgusLab, including constructing molecules, optimizing geometry, and calculating HOMO and LUMO surfaces. It emphasizes using the PM3 method over AM1 for particular molecules like O2 due to diradical character and provides instructions for visualizing results and interactions. Additionally, it discusses the binding and orientation of imine with respect to a Zn-O bond during ligand docking.
Argus lab - a freeware PC program for modelling
- 1. MO Calculations on PC Dr. Christoph UP, April 2015
- 2. http://www.arguslab.com/ arguslab.com/ArgusLab.html Step 1: Construct a molecule by dropping atoms on the screen (“Builder Tool”)
- 3. Step 2: Define atoms by right-click on them Step 3: Optimize geometry
- 4. Step 4: Calculate HOMO and LUMO surface Step 5: Calculate MO energies
- 5. Exercises Construct the O2 molecule and get HOMO and LUMO We should use PM3 as method, not AM1 Because of the diradical character most QM methods do not work here ! Only EHT as very crude method.
- 6. H2O Here it is enough just to put an sp3 O atom and then choose “add Hydrogens” Mark 2 atoms: left click and ctrl-left click Then display the distance:
- 7. HOMO and LUMO “Quick Plot” The LUMO looks very confusing in standard view Right Click on the surface around the Hydrogens Modify surface -> choose Mesh display We see now that the LUMO is actually a lone pair !
- 8. Interaction between Imine and ZnO Mark all atoms of one group (CTRL-left click) and select: Make a group… Group 1: Binding Site Group 2: Ligand
- 9. “Docking” Ligand to binding site Calculation suggests that the imine double bond is perpendicular to the Zn-O axis, actually like “inserted” into the Zn-O bond