Step 4. Z-matrix and constraints
This simulation will be a linear transit simulation where the reaction coordinate will be the distance from the Pd center to the midpoint of the complexed ethene molecule. In order to use midpoint of the ethene molecule as the reaction coordinate we must use a dummy atom to define the midpoint and a few constraints to maintain the dummy atom at the midpoint. The dummy atom is atom number 15 and the two carbon atoms of the ethene moiety are atoms 16 and 17. Each of the two carbons of the ethene will be 'bonded' to the midpoint using the same (free) bond distance variable 'B15'. This will ensure that the midpoint dummy atom is always equidistant to each ethene carbon. To ensure that the midpoint dummy atom always lies along the C-C bond vector the dihedral variable 'D14' will be constrained to 180 degrees. Finally, to prevent C-C bond distance of olefinic group used to model the ferrocenyl ligand to revert to its natural bond length of approximately 1.34 Ang, the C-C distance (B8) will be constrained to 1.45 Ang. This is the distance found in the C-C bond distance in the ferrocenyl ligand. One might be concerned about the internal coordinate definition of the cyclopentadienyl rings of the ferrocenyl ligand. Since the ferrocenyl ligand is part of the MM region, the Z-matrix will be used only to construct the initial geometry. From there the molecular mechanics code takes over and where the optimization is done in Cartesian coordinates. For MM atoms it is important that care be taken when defining the connection table.
ATOMS internal Pd 0 0 0 0 0 0 N 1 0 0 B1 0 0 P 1 2 0 B2 A1 0 Si 1 2 3 B3 A2 D1 Cl 4 1 2 B4 A3 D2 Cl 4 1 5 B5 A4 D3 Cl 4 1 5 B6 A5 D4 C 3 1 2 B7 A6 D5 C 8 3 1 B8 A7 D6 C 9 8 3 B9 A8 D7 N 10 9 8 B10 A9 D8 C 11 2 1 B11 A10 D9 C 12 11 2 B12 A11 D10 C 2 1 11 B13 A12 D11 XX 1 2 3 B14 A13 D12 C 15 1 2 B15 A14 D13 C 15 1 16 B15 A15 D14 H 16 15 1 B17 A16 D15 H 16 17 18 B18 A17 D16 H 17 16 18 B19 A18 D17 H 17 16 18 B20 A19 D18 C 3 1 8 B21 A20 D19 C 3 1 8 B22 A21 D20 C 8 3 9 B23 A22 D21 C 9 8 10 B24 A23 D22 H 10 9 8 B25 A24 D23 C 10 9 26 B26 A25 D24 H 12 11 13 B27 A26 D25 H 13 12 11 B28 A27 D26 C 14 2 1 B29 A28 D27 Fe 24 8 3 B30 A29 D28 H 27 10 9 B31 A30 D29 H 27 10 32 B32 A31 D30 H 27 10 32 B33 A32 D31 C 25 9 8 B34 A33 D32 H 25 9 35 B35 A34 D33 H 35 25 9 B36 A35 D34 H 24 8 31 B37 A36 D35 C 31 24 8 B38 A37 D36 C 39 31 24 B39 A38 D37 C 40 39 31 B40 A39 D38 C 41 40 39 B41 A40 D39 C 39 31 40 B42 A41 D40 H 43 39 31 B43 A42 D41 H 39 31 40 B44 A43 D42 H 40 39 41 B45 A44 D43 H 41 40 42 B46 A45 D44 H 42 41 40 B47 A46 D45 C 23 3 1 B48 A47 D46 C 49 23 3 B49 A48 D47 C 50 49 23 B50 A49 D48 C 51 50 49 B51 A50 D49 C 52 51 50 B52 A51 D50 H 49 23 50 B53 A52 D51 H 50 49 51 B54 A53 D52 H 51 50 52 B55 A54 D53 H 52 51 53 B56 A55 D54 H 53 52 51 B57 A56 D55 C 22 3 1 B58 A57 D56 C 59 22 3 B59 A58 D57 C 60 59 22 B60 A59 D58 C 61 60 59 B61 A60 D59 C 62 61 60 B62 A61 D60 H 59 22 60 B63 A62 D61 H 60 59 61 B64 A63 D62 H 61 60 62 B65 A64 D63 H 62 61 63 B66 A65 D64 H 63 62 61 B67 A66 D65 C 30 14 2 B68 A67 D66 C 69 30 14 B69 A68 D67 C 70 69 30 B70 A69 D68 C 71 70 69 B71 A70 D69 C 72 71 70 B72 A71 D70 C 69 30 70 B73 A72 D71 H 70 69 71 B74 A73 D72 C 71 70 72 B75 A74 D73 H 72 71 73 B76 A75 D74 C 73 72 71 B77 A76 D75 H 74 69 30 B78 A77 D76 H 74 69 79 B79 A78 D77 H 74 69 79 B80 A79 D78 H 78 73 72 B81 A80 D79 H 78 73 82 B82 A81 D80 H 78 73 82 B83 A82 D81 H 76 71 70 B84 A83 D82 H 76 71 85 B85 A84 D83 H 76 71 85 B86 A85 D84 XX 24 8 31 B87 A86 D85 XX 41 40 42 B88 A87 D86 END GEOVAR B1=2.18381 B2=2.33889 B3=2.25474 B4=2.11579 B5=2.13955 B6=2.11791 B7=1.81730 B8=1.45807 F B9=1.50544 B10=1.47768 B11=1.36193 B12=1.38405 B13=1.34409 B14=2.50000 5.000 B15=0.66631 B17=1.08903 B18=1.09082 B19=1.09092 B20=1.08943 B21=1.86801 B22=1.85275 B23=1.43426 B24=1.42814 B25=1.10060 B26=1.52360 B27=1.08226 B28=1.08182 B29=1.50380 B30=2.00032 B31=1.09827 B32=1.10198 B33=1.09896 B34=1.43456 B35=1.08513 B36=1.08532 B37=1.08347 B38=2.03122 B39=1.43448 B40=1.43413 B41=1.43347 B42=1.43383 B43=1.08361 B44=1.08347 B45=1.08341 B46=1.08540 B47=1.08451 B48=1.39867 B49=1.39691 B50=1.39740 B51=1.39722 B52=1.39822 B53=1.08455 B54=1.08520 B55=1.08569 B56=1.08594 B57=1.08280 B58=1.39816 B59=1.39740 B60=1.39734 B61=1.39754 B62=1.39750 B63=1.08166 B64=1.08484 B65=1.08604 B66=1.08530 B67=1.08396 B68=1.40109 B69=1.40042 B70=1.39823 B71=1.39824 B72=1.39818 B73=1.53667 B74=1.08452 B75=1.53315 B76=1.08501 B77=1.53287 B78=1.09990 B79=1.10064 B80=1.10001 B81=1.09746 B82=1.10018 B83=1.09915 B84=1.10005 B85=1.10036 B86=1.10053 B87=1.20119 B88=1.21941 A1=94.7463 A2=158.2223 A3=117.0192 A4=115.6423 A5=115.0054 A6=120.3960 A7=128.6001 A8=124.4982 A9=113.0381 A10=110.6944 A11=107.5291 A12=123.1566 A13=72.5934 A14=90.0001 A15=90.0001 A16=121.4060 A17=121.7463 A18=121.7273 A19=121.2990 A20=113.4758 A21=117.0770 A22=124.4140 A23=107.1936 A24=108.2564 A25=114.7923 A26=122.2418 A27=126.8321 A28=119.5733 A29=70.7204 A30=111.7865 A31=109.8825 A32=110.4946 A33=110.3514 A34=125.5260 A35=127.2980 A36=125.4579 A37=133.3349 A38=68.8766 A39=107.9605 A40=108.0463 A41=69.7028 A42=125.7664 A43=129.5676 A44=126.2672 A45=125.9595 A46=126.0404 A47=117.3031 A48=120.5489 A49=119.8703 A50=119.8287 A51=120.1922 A52=119.7123 A53=120.0017 A54=120.0478 A55=119.9075 A56=118.9447 A57=120.7197 A58=120.6090 A59=119.9563 A60=119.7586 A61=120.0640 A62=120.1660 A63=120.0615 A64=120.1253 A65=119.9602 A66=119.0914 A67=119.1156 A68=119.5849 A69=120.7057 A70=119.1275 A71=120.7701 A72=120.6568 A73=119.8697 A74=121.2330 A75=119.5074 A76=118.2033 A77=109.0914 A78=110.4834 A79=111.6228 A80=111.7639 A81=109.9169 A82=109.0716 A83=109.9009 A84=111.6715 A85=108.9122 A86=55.1829 A87=54.0180 D1=-150.6568 D2=-100.8347 D3=-119.5809 D4=123.4778 D5=35.1598 D6=-2.9958 D7=7.2171 D8=-72.9107 D9=164.5027 D10=0.9220 D11=163.0063 D12=135.2677 D13=65.6662 D14=180.0000 F D15=90.0000 D16=179.5031 D17=-179.9904 D18=-0.4168 D19=-117.3520 D20=124.7005 D21=-169.6021 D22=-179.2713 D23=-3.3919 D24=119.3500 D25=179.9891 D26=-179.9514 D27=17.4102 D28=-129.2972 D29=60.6432 D30=120.3390 D31=-120.3043 D32=1.2969 D33=179.4155 D34=179.5397 D35=123.6746 D36=68.3005 D37=62.0893 D38=58.4426 D39=0.0736 D40=119.7199 D41=127.1496 D42=-120.1862 D43=178.4186 D44=-179.8093 D45=179.5019 D46=-30.2454 D47=-178.8402 D48=-0.0598 D49=0.3012 D50=-0.1575 D51=-179.8476 D52=-179.9824 D53=179.8951 D54=-179.8926 D55=179.8489 D56=-81.7949 D57=179.3002 D58=-0.2287 D59=-0.6445 D60=0.0510 D61=-179.9960 D62=179.9913 D63=-179.8879 D64=-179.8700 D65=-178.0390 D66=114.6178 D67=-177.7647 D68=1.7082 D69=-3.4460 D70=1.3564 D71=179.4189 D72=179.8505 D73=-179.9397 D74=-179.8352 D75=-176.6101 D76=76.9134 D77=-120.1615 D78=119.9038 D79=165.3767 D80=-119.6911 D81=121.2928 D82=-135.8162 D83=120.3122 D84=-119.4211 D85=-58.7928 D86=0.0762 END
