Basic Instructions for Using Vega ZZ Modeling Software (For PCs only) Open Vega ZZ. To build a molecule: The steps below show how you can select molecule fragments and piece them together to construct a larger molecule. 1. To select the first fragment of your desired molecule, go to Edit → Add → Fragments Select Group (e.g. rings) and Fragment (e.g. cyclohexane) Click Finish If done click Close Or, to continue adding to your molecule, click Next Repeat steps 1 and 2. Click Next (You will not see the original fragment, or molecule, at this point) “Pick a fragment H” is highlighted in red. Click the H on part of the new fragment that will attach to the original molecule. 9. Click Next (Screen now goes back to the original molecule.) 10. “Pick a molecule H” is highlighted in red. Click the H on the part of the original molecule that will attach to the new fragment. 11. Click Next (you will now see the two fragments combined). 12. Then Close 13. To continue adding groups repeat steps 6 to 12. 2.
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There are other ways to build molecules, for example, for a small molecule it is relatively straightforward to pick a molecule from the templates that is close to the desired molecule (steps 1 to 4 above) and then use the Change menu to modify it. You may also discover your own shortcuts as you become familiar with the software. To change an atom/residue/chain 1. Go to Edit → Change → atom/residue/chain 2. Click on the atom to change on the structure -­‐ (a list of boxes shows up to the left) select the atom listed in the Element box, e.g. H, and type the atom to replace it with. 3. Click Apply 4. To continue changing atoms, repeat steps 2 and 3 (Note, to get a clearer picture of what you have changed, click on View →Display →Ball and stick solid or CPK Solid) Calculations: Now that you have built your molecule, you are ready to do calculations. You will need to set up to do the AM1 calculations that will give you the heat of formation value (Hf). 1. AM1 Calculations: Go to Calculate → Mopac →AM1 (select GEO-­‐OK) → Run Make sure that you have assigned the correct charge to your molecule. Data are shown in the window below the drawing window. Scroll up for HEAT OF FORMATION. Make sure you note the sign (+ or -­‐) and units of Hf (kcal/mol). Note: If you download Vega ZZ to your own computer, you will also need to download Mopac to do the AM1 calculations. To measure bond length, angles, etc. Right click on the drawing area and select Measure, pick the type of measurement (e.g. distance, angle, torsion), then click on the atoms that define the measurement (two for distance, three for angle, four for torsion). Note, torsion = dihedral. The measurement is shown in the data window below drawing window. To change, angle, torsion etc. Go to Edit → Change → Bond/Angle/Torsion “Change bond/angle/torsion” box appears, select Edit. A second box appears (Selection tool). In this box select what to change (torsion, distance etc.) from the drop down menu under Selections, then click Add. Click on the defining atoms on the molecule. In the example above, the 4 atoms defining the torsion, or dihedral angle, between the Cl and F atoms (ClC1C2F = pink, green, green, blue) have been selected, and they show up under “Selected Atoms”. The defined measurement value now shows up in the first box (179.715 deg in this example). Type in a new value to change the measurement.