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   practical five: viewing orbitals and normal modes

Practical Five: Viewing Orbitals and Normal Modes

(1) Orbitals

The Diels Alder reaction of methoxybutadiene with acrolein preferentially gives the ortho adduct. In this practical, molecular orbital calculations will be used to rationalise this result.

(a) Build the two reactants as separate molecules using MacroModel and optimise them using the MM2 force field. MM2 will put lone pairs on the methoxy oxygen, which are not needed for the molecular orbital calculation. They must be deleted before the minimised structures are written to files. Write each structure to a different file. Stop MacroModel running.

(b) Type 'xed' to run the Xed molecular modelling package. In this practical, you will use only a small part of this program's capabilities. The relevant page of the manual is available. Read in the file. Xed can read MacroModel files. Move the mouse to the INPUT/OUTPUT area, and select 'R/W macromodel'. Note that Xed will expect the file to be in your home directory, and not the current directory.

Once the structure has been read in, move the mouse to the PROCEDURE/MULTIFILES area. Click on 'Mopac-Run & Look'. Type 'R' for Run, and the choose the default option (No Optimisation). Your structure has already been optimised by MacroModel, and this does not need to happen again. You will be asked for a filename, and you must choose one that you have not used before. It may be a good idea to put '_mo' and the end of the filename, to remind you that it is a molecular orbital calculation.

When the calculation is complete, click on 'Mopac-Run & Look' again, but this time choose 'D' for display. You will be asked for a filename, and you must type the name of the original macromodel file, including the '.dat' You will be asked for a second filename containing the eigenresults. This will be the name that you used for the MOPAC calculation (probably ending '_mo'). Type this name, followed by '.mov'. For example, if your MacroModel structure was called acrolein.dat and the MOPAC calculation filename was acrolein_mo, then you should type first 'acrolein.dat' and then 'acrolein_mo.mov'

(c) Examine the results. This will draw your molecule, and let you add the molecular orbitals to it. The left hand side of the screen shows the energies of the orbitals graphically. Clicking on an orbital will add it to the molecule displayed in the centre of the screen. The Highest Occupied Molecular Orbital (HOMO) and the Lowest Unoccupied Molecular Orbital (LUMO) are the most important ones. The energies of these orbitals will be displayed when you select them. Occupied molecular orbitals are represented as full lines, and unoccupied orbitals as dotted lines.

(d) You can rotate the molecule while the orbitals are displayed. To get back to the menus, move the mouse into the text window at the top of the screen. If this does not work, try pressing 'Esc' or the right hand mouse button. 'Clear display' will remove the orbitals from the molecule, but continues to display the molecule itself.

The mouse buttons for rotation are slightly different to that for MacroModel. Moving the mouse whilst holding down the left mouse button makes the molecule rotate. Holding the right mouse button translates the molecule. The middle button rotates around an axis coming out of the screen.

(e) Will HOMO of the butadiene react with LUMO of the dienophile- or the other way round? Look at the energy differences. Which way round will the molecules prefer to react? (Look for the best orbital overlap.)

(f) Build the two combined structures (acrolein up and acrolein down) with the two reactants within roughly the distance shown (not too close!) and repeat the calculation using MOPAC. Now see where HOMO and LUMO appear and display the coefficients (orbital sizes). You can move the molecules relative to each other by clicking on TRMol then selecting one of the molecules. A small cross will appear, and you can move this molecule by clicking on the cross with the middle mouse button and holding the button down. Moving the mouse will move just the selected molecule. If you hold down the shift key, you will rotate just this molecule.

(g) Can you also explain the relative stereochemistry of the product?

(2) Normal Modes

A minimum energy conformation of a molecule will not be still, even at absolute zero of temperature, but will wobble around. These movements can be separated into a series of simple motions, called the normal modes, each of which corresponds to a particular frequency. Analysis of the normal modes allows us to see which motions have low energy, and which are less accessible.

Some examples are in the directory /usr/local/examples/NMA To see them, use the program Eadfrith. From your home directory, type 'render /usr/local/examples/NMA/filename' where filename is one of the files. Make sure that NMA (option G) is switched on. When the molecule appears, you can see its normal vibrational modes by moving the mouse around with no buttons pressed. Pressing the mouse buttons manipulates the molecules in the normal way.

Normal mode analyses are given for water, methane, and a formaldehyde H2BCl complex. They were all calculated using ab initio molecular orbital theory. One example is available on line, if your browser will display multiframe gif images.




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department of chemistry University of Cambridge