Step 5. Connection Table, MM force field atom-types and Force Field Modification

In order to construct a molecular mechanics potential, the program needs to know the connectivity of the molecular system and the molecular mechanics force field atom-type designations. In this example we are using the Tripos or Sybyl force field. The Tripos force field does not support either Pd or ferrocenyl ligands, so we need to modify the standard force field file to handle these groups. Modification of a molecular mechanics force field without re-parameterization of the force field may not always be appropriate. However, in this case sort of 'ad hoc' additions to the Tripos force field can be justified. For Pd, all of the principle interactions will be contained within the QM region and only weak non-bonded interactions involving Pd will be approximated by the molecular mechanics potential. The ferrocenyl ligand is assumed to act as a spectator ligand and therefore it is adequate to simply attain the approximate structure of the complex with the molecular mechanics potential.

In the Tripos force field, the nitrogen atoms of the pyrazole ring should be assigned the 'N_2' atom-type; the P atom of the phosphine should be assigned the 'P_3' atom-type. The Cl, H and Si atoms are given the 'Cl', 'H', and 'Si' atom types respectively. The carbon atoms of the phenyl substituents are given the 'C_ar' atom-type, while the sp³ hybridized carbon atoms are given the 'C_3' atom-type.

Connections involving the dummy atom defining the midpoint of the ethene molecule are really not needed since this atom is contained within the QM region.

For the ferrocenyl ligand the ferrocene force field of Bosnich and coworkers will be used. Four new MM atom types will be introduced, C_cp, H_cp and CEN, representing the carbon, hydrogen and centroid of the cyclopentadienyl rings, respectively and Fe. In the connection table, the C_cp atoms will be bonded to the centroid and not the Fe center. The only two bonds made to the Fe center will be to the (two) central dummy atoms of the Cp rings. In making a connection between the C_cp atom and the centroid, a direct bond will is made to a QM atom and a MM atom. A warning will be issued during the run but as long as the 'WARNING_LEVEL' flag is set to 1 the job will continue. In this case the link bond between the C_cp atom and the centroid does not need to be mediated by a capping atom. This bond is used only for the construction of the MM potential for the ferrocenyl ligand. Special bond stretching, bending, torsion and out-of-plane potentials need to be added to the force field file. For the most part these parameters are taken from the Bosnich Ferrocene force field. For example for the bond stretches, the following potentials need to be added to the force field.

The force field file is simply a text file and so the above section needs to be added to the 'BONDS' key block between the two '=======' separator lines. Bond potentials need to be defined between the centroid of the Cp rings with the Fe center and the carbon atoms.

For the angle and torsion terms, the additions are somewhat more complex. The following angle potential terms need to be introduced.

Any angle potentials involving the Cp centroid and any atoms outside of the ferrocenyl ligand have been set to zero since the centroid was only a construct for the optimization of the ferrocenyl ligand. For the torsions, the following potentials have been added to the standard Tripos force field.

Here any torsional potentials involving the Centroid atom of the ferrocenyl ligand were set to zero. Torsional potentials involving atoms outside of the ferrocenyl ligand and having the C_cp-C_cp atoms central atom pair, these potentials were equated with those of the Tripos ' *-C_ar C_ar - * ' torsional potentials. Again, these somewhat arbitrary choices for the MM potentials involving the ferrocenyl ligand are justified by the fact that the ferrocenyl ligand acts only as a spectator group.

The van der Waals parameters used for the five new atoms types, Pd, Fe, CEN, C_cp and H_cp were taken from either existing Tripos van der Waals parameters of similar atom-types or they were taken from Rappe's UFF (Universal Force Field). They are given below with their origins provided in the 'NOTES' column.

Now that the addition of the new MM potentials and atom-types has been discussed, the 'MM_CONNECTION_TABLE' subkey block is given below. In practice, one typically constructs the input first, and then runs the program to see what force field potentials/parameters are missing. If any force field parameters are missing in the force field file, the ADF QM/MM program will print all missing potentials that need to be defined in the force field and then stop.

MM_CONNECTION_TABLE
 1 Pd QM 2 3 4 0 0 0
 2 N_2 QM 1 11 14 0 0 0
 3 P_3 QM 1 8 22 23 0 0
 4 Si QM 1 5 6 7 0 0
 5 Cl QM 4 0 0 0 0 0
 6 Cl QM 4 0 0 0 0 0
 7 Cl QM 4 0 0 0 0 0
 8 C_cp QM 3 9 24 88 0 0
 9 C_cp QM 8 10 25 88 0 0
 10 C_3 QM 9 11 26 27 0 0
 11 N_2 QM 2 10 12 0 0 0
 12 C_ar QM 11 13 28 0 0 0
 13 C_ar QM 12 14 29 0 0 0
 14 C_ar QM 2 13 30 0 0 0
 15 XX QM 16 17 1 0 0 0
 16 C_2 QM 15 17 18 19 0 0
 17 C_2 QM 15 16 20 21 0 0
 18 H QM 16 0 0 0 0 0
 19 H QM 16 0 0 0 0 0
 20 H QM 17 0 0 0 0 0
 21 H QM 17 0 0 0 0 0
 22 C_ar LI 3 59 63 0 0 0
 23 C_ar LI 3 49 53 0 0 0
 24 C_cp LI 8 35 38 88 0 0
 25 C_cp LI 9 35 36 88 0 0
 26 H QM 10 0 0 0 0 0
 27 C_3 LI 10 32 33 34 0 0
 28 H QM 12 0 0 0 0 0
 29 H QM 13 0 0 0 0 0
 30 C_ar LI 14 69 73 0 0 0
 31 Fe MM 88 89 0 0 0 0
 32 H MM 27 0 0 0 0 0
 33 H MM 27 0 0 0 0 0
 34 H MM 27 0 0 0 0 0
 35 C_cp MM 24 25 37 88 0 0
 36 H_cp MM 25 0 0 0 0 0
 37 H_cp MM 35 0 0 0 0 0
 38 H_cp MM 24 0 0 0 0 0
 39 C_cp MM 40 43 45 89 0 0
 40 C_cp MM 39 41 46 89 0 0
 41 C_cp MM 40 42 47 89 0 0
 42 C_cp MM 41 43 48 89 0 0
 43 C_cp MM 39 42 44 89 0 0
 44 H_cp MM 43 0 0 0 0 0
 45 H_cp MM 39 0 0 0 0 0
 46 H_cp MM 40 0 0 0 0 0
 47 H_cp MM 41 0 0 0 0 0
 48 H_cp MM 42 0 0 0 0 0
 49 C_ar MM 23 50 54 0 0 0
 50 C_ar MM 49 51 55 0 0 0
 51 C_ar MM 50 52 56 0 0 0
 52 C_ar MM 51 53 57 0 0 0
 53 C_ar MM 23 52 58 0 0 0
 54 H MM 49 0 0 0 0 0
 55 H MM 50 0 0 0 0 0
 56 H MM 51 0 0 0 0 0
 57 H MM 52 0 0 0 0 0
 58 H MM 53 0 0 0 0 0
 59 C_ar MM 22 60 64 0 0 0
 60 C_ar MM 59 61 65 0 0 0
 61 C_ar MM 60 62 66 0 0 0
 62 C_ar MM 61 63 67 0 0 0
 63 C_ar MM 22 62 68 0 0 0
 64 H MM 59 0 0 0 0 0
 65 H MM 60 0 0 0 0 0
 66 H MM 61 0 0 0 0 0
 67 H MM 62 0 0 0 0 0
 68 H MM 63 0 0 0 0 0
 69 C_ar MM 30 70 74 0 0 0
 70 C_ar MM 69 71 75 0 0 0
 71 C_ar MM 70 72 76 0 0 0
 72 C_ar MM 71 73 77 0 0 0
 73 C_ar MM 30 72 78 0 0 0
 74 C_3 MM 69 79 80 81 0 0
 75 H MM 70 0 0 0 0 0
 76 C_3 MM 71 85 86 87 0 0
 77 H MM 72 0 0 0 0 0
 78 C_3 MM 73 82 83 84 0 0
 79 H MM 74 0 0 0 0 0
 80 H MM 74 0 0 0 0 0
 81 H MM 74 0 0 0 0 0
 82 H MM 78 0 0 0 0 0
 83 H MM 78 0 0 0 0 0
 84 H MM 78 0 0 0 0 0
 85 H MM 76 0 0 0 0 0
 86 H MM 76 0 0 0 0 0
 87 H MM 76 0 0 0 0 0
 88 CEN MM 8 9 24 25 35 31
 89 CEN MM 39 40 41 42 43 31
SUBEND