Example B: Pd⁺-Ethene pi-complexation Linear Transit

This example is more complex to demonstrate some problems that one might encounter in a more advanced problem. For instance, the simulation will involve the customization of the standard Tripos force field, the use of dummy atoms in the MM region and QM region and the use of constraints. Figure 5-3a depicts the system that we intend to simulate. More specifically we wish to determine the reaction profile of removing the olefinic substrate from the metal center of Pd⁺-phosphino-ferrocenyl-pyrazole complex. For this purpose we wish to perform a linear transit run with ADF, whereby the distance between the metal center and the midpoint of the olefinic carbons is used as a reaction coordinate. The linear transit geometry optimization will be done in internal coordinates. This reaction coordinate is shown as the arrow line in Figure 5-3. This example originates from our research on similar neutral bis-trichlorosilyl compounds. The system has been changed slightly to introduce additional technical considerations when using dummy atoms and linear transit calculations. The QM/MM calculations of these related compounds reveal that the approximations introduced in this system are quite reasonable. Also, in terms of predicting the geometry of this class of complexes, the QM/MM method performs exceptionally well.

a b

Figure 5-3 Example system Pd⁺-ethene pi-complex. a) Full system, with linear transit coordinate indicated by the arrow line. The QM/MM boundary is shown as the dotted polygon with the QM region residing inside. The 'LI' atoms are denoted with the asterisks. b) The QM model system with the capping hydrogen atoms depicted in bold.