Procedure 4.5 Semi-empirical Calculations for AA Ligands

To start a new project, go to File, New. On the right-hand side screen are various palates from which you may construct the four iron complexes (see Fig. 4.7) and the two free amino acid ligands (see Fig. 4.8). Iron is under the Exp. pallet and the Gly and Met are under the Pep. pallet. To place the central iron on the worksheet, simply select Fe and octahedral geometry and click anywhere on the workspace. Ligands may be added by clicking any of the yellow active sites around the iron atom. After each structure is completed, save under File. 

Run similar calculations for all six structures (the four iron complexes and the two free amino acid ligands). 

When all the calculations are finished, look at the HOMO and LUMO of the four iron complexes. To do this you must again go to Setup, and this time select Surfaces. In the Surfaces window click the Add button. Choose HOMO under Surface. Leave the Resolution at the default Medium. Click OK. To add the LUMO orbital, again click Add in the Surface window. Select LUMO under Surface and click OK. Under Setup, choose Submit. 

TABLE 4.5 The Iron Atomic Orbital Contributions Towards the First 

Now go to Display, Vibrations. By clicking the box next to a listed frequency in the vibration window, you can see how the molecule vibrates at that frequency. View the CN- and carbonyl vibrations for the [Fe(CN)5AA] - complexes and free met and gly. (Hint met carbonyl vibrations are at approximately 560, 1550, and 1850 Hz. Gly carbonyl vibrations are at approximately 600, 1560, and 1850 Hz.) Look for any shifts in frequency for a given vibration when the AA ligand is bound as opposed to when the ligand is free. 

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