Supplementary Material Strassner et. al.
Modifications to TINKER
As described by the authors of TINKER, the file
sizes.i
needs to be modified
before compilation:
The line "parameter (maxval=4)" has to be replaced by "parameter (maxval=10)"
Usage of
MOLDEN
To enable MOLDEN to create a TINKER file with the right connectivity it was
necessary to substitute the rhenium in the CSD mol2 file. Two problems may
arise depending on the structure used. One problem might be that the hydrogen
atoms have not been localized in the Xray structure. MOLDEN allows to add
hydrogen atoms which have to be added prior to the generation of the TINKER
file. The other problem might arise while writing the TINKER file. Molden can
only write six connections of any atom. Therefore sometimes (like for the
cyclopentadienyl systems) it is necessary to add the connectivity of atoms
with more than six neighboring atoms manually in the file. Finally in the
TINKER xyz file the force field type number for rhenium needs to be added.
Range for optimized bonds, angles, torsions
The bond lengths were allowed to refine in an interval that was 0.05 Å larger
than the maximum values of all occurences of the respective bond, the bond
stretching force constants were restricted to an interval of 0 - 50 mdyn/Å.
The angles were allowed to refine in an interval that was on each side 5°
larger than the the maximum values of all occurences of the respective angle,
the angle bending force constants were set to an interval of 0 - 50 mdyn/
(rad
2). The torsional force constants were set between -20 kcal/mol and 20
kcal/mol.
Parameters for four coordinated Rhenium
atom 204 Re "RHENIUM 4 KOORD" 75 186.207 0
bond3 204 114 32.2907 2.2546 bond3 114 114 44.0344 1.4550
bond 2 204 24.1979 2.0958 bond 204 7 15.0944 1.7405 bond 8 204 36.5999 1.9210 bond 204 1 17.3396 2.0806 bond 204 9 28.7738 1.7668 bond 114 113 15.6715 0.9600
bond5 204 8 12.1294 1.9200 bond5 204 6 2.8314 1.9403
angle3 114 204 114 12.931 37.877 0.000 0.000 angle3 204 114 114 24.718 73.621 0.000 0.000
torsion 114 204 8 1 2.996 0.000 1 -20.000 180.000 2 10.160 0.000 3 torsion 7 204 8 1 -17.230 0.000 1 10.064 180.000 2 -11.232 0.000 3 torsion 6 204 8 1 12.364 0.000 1 -0.077 180.000 2 19.170 0.000 3 torsion 114 204 6 1 12.573 0.000 1 1.556 180.000 2 -10.632 0.000 3 torsion 7 204 6 1 4.733 0.000 1 15.320 180.000 2 16.536 0.000 3 torsion 204 8 1 5 -1.940 0.000 1 -18.967 180.000 2 1.253 0.000 3 torsion 5 1 6 204 8.798 0.000 1 -0.562 180.000 2 -0.404 0.000 3 torsion 9 204 9 2 -15.014 0.000 1 7.396 180.000 2 10.955 0.000 3 torsion 1 204 9 2 18.374 0.000 1 4.301 180.000 2 1.809 0.000 3 torsion 9 204 1 5 -8.925 0.000 1 -7.248 180.000 2 -14.017 0.000 3 torsion 204 9 2 2 -17.196 0.000 1 -0.594 180.000 2 14.654 0.000 3 torsion 9 2 2 1 -1.368 0.000 1 -10.340 180.000 2 -5.246 0.000 3 torsion 204 1 1 1 10.936 0.000 1 -8.020 180.000 2 -0.957 0.000 3 torsion 1 1 204 1 -14.305 0.000 1 1.128 180.000 2 -1.161 0.000 3 torsion 1 1 204 7 12.866 0.000 1 -12.428 180.000 2 19.886 0.000 3 torsion 7 204 114 113 17.535 0.000 1 1.969 180.000 2 19.649 0.000 3 torsion 114 204 114 113 11.127 0.000 1 5.352 180.000 2 -9.635 0.000 3 torsion 204 114 114 113 -10.299 0.000 1 -7.915 180.000 2 4.260 0.000 3 torsion 114 114 114 113 -13.185 0.000 1 -13.401 180.000 2 -20.000 0.000 3 torsion 1 114 114 113 -10.797 0.000 1 7.758 180.000 2 0.505 0.000 3 torsion 113 114 114 113 0.100 0.000 1 5.165 180.000 2 -3.543 0.000 3 torsion 2 2 204 9 -18.033 0.000 1 -9.800 180.000 2 9.671 0.000 3 torsion 2 204 9 1 2.284 0.000 1 -7.042 180.000 2 -15.960 0.000 3 torsion 9 204 9 1 -1.587 0.000 1 -0.101 180.000 2 -13.407 0.000 3 torsion 204 9 1 1 -20.000 0.000 1 -13.897 180.000 2 -14.806 0.000 3 torsion 204 114 1 1 0.921 0.000 1 -13.017 180.000 2 -2.396 0.000 3 torsion 114 114 1 1 4.809 0.000 1 2.965 180.000 2 -12.244 0.000 3 torsion 114 1 1 5 -12.037 0.000 1 10.593 180.000 2 -15.340 0.000 3
torsion4 114 204 114 114 -15.253 0.000 1 -16.767 180.000 2 -11.262 0.000 3 torsion4 204 114 114 114 -11.199 0.000 1 -2.024 180.000 2 -16.452 0.000 3
opbend 2 204 1.609845
Parameters for five coordinated Rhenium
atom 202 N "N for Re 5 KOORD" 7 14.003 0 atom 205 Re "RHENIUM 5 KOORD" 75 186.207 0
bond 205 7 38.2301 1.6531 bond 205 1 26.4803 2.1319 bond 205 2 13.4452 2.1500 bond 202 1 26.2423 1.4904 bond 25 205 5.5964 2.4007 bond 205 10 38.3202 1.6300 bond 205 74 12.4368 2.1100 bond 205 15 47.0143 2.3200 bond 15 2 6.1897 1.7921
bond5 205 6 39.8486 1.9411 bond5 205 202 49.9927 2.4000 bond5 205 1 24.1684 2.1132 bond5 205 1 31.5803 1.4503
angle5 6 205 6 30.192 77.892 0.000 0.000 angle5 202 205 1 43.519 79.562 0.000 0.000 angle5 205 202 1 43.534 107.557 0.000 0.000 angle5 205 1 1 38.859 118.635 0.000 0.000 angle5 202 1 1 29.182 106.608 0.000 0.000 angle5 205 6 1 45.067 122.344 0.000 0.000
torsion 25 205 15 2 19.112 0.000 1 -8.092 180.000 2 2.795 0.000 3 torsion 74 205 15 2 -2.761 0.000 1 2.848 180.000 2 -8.278 0.000 3 torsion 1 205 15 2 14.362 0.000 1 7.837 180.000 2 -17.464 0.000 3 torsion 15 205 15 2 -5.557 0.000 1 -8.052 180.000 2 -15.950 0.000 3 torsion 205 15 1 5 -8.385 0.000 1 -7.076 180.000 2 3.427 0.000 3 torsion 205 15 1 2 12.846 0.000 1 -5.279 180.000 2 17.938 0.000 3 torsion 205 15 2 2 -1.604 0.000 1 -5.042 180.000 2 -5.855 0.000 3 torsion 1 2 2 15 -11.799 0.000 1 15.943 180.000 2 -1.691 0.000 3 torsion 2 2 2 15 18.480 0.000 1 16.340 180.000 2 12.009 0.000 3 torsion 15 2 2 5 4.078 0.000 1 7.142 180.000 2 -2.321 0.000 3
