suppmat282.doc 59KB Jun 05 2011 09:30:54 PM

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/
(rad2). 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

bond3
bond3

204
114

114
114

32.2907
44.0344

2.2546
1.4550

bond
bond
bond
bond
bond
bond

2
204
8
204
204
114

204
7
204
1
9
113

24.1979
15.0944
36.5999
17.3396
28.7738
15.6715

2.0958
1.7405
1.9210
2.0806
1.7668
0.9600

bond5
bond5

204
204

8
6

12.1294
2.8314

1.9200
1.9403

0

angle3
angle3

114
204

204
114

114
114

12.931
24.718

37.877
73.621

0.000
0.000

0.000
0.000

angle5
angle5
angle5
angle5

204
114
114
114

114

114
204
204

1
1
1
8

43.232
47.358
41.676
27.216

125.415
129.699
103.342
103.664

0.000

0.000
0.000
0.000

0.000
0.000
0.000
0.000

S1

angle5
angle5
angle5
angle5

114
8
204
204

204
204
8
6

6
6
1
1

40.049
50.000
18.198
22.492

101.057
80.178
122.231
119.195

0.000
0.000
0.000
0.000

0.000
0.000
0.000
0.000

angle
angle
angle
angle
angle
angle
angle
angle
angle

angle
angle
angle
angle
angle
angle
angle
angle
angle
angle
angle
angle
angle
angle
angle
angle

2
2
7
2
2
7
114
2
2
8
1
1
204
204
7
204
9
9
204
1
204
114
2
204
114

2
204
204
204
204
204
1
8
8
204
204
204
1
1
204
8
204
204
9
1
114
114
204
9
1

204
7
7
2
114
114
5
2
204
7
7
1
2
5
6
1
9
1
2
204
113
113
9
1
1

6.740
6.561
28.594
42.869
28.005
17.008
4.073
23.664
0.463
32.906
21.657
41.249
25.755
32.036
10.556
12.947
37.012
26.255
16.318
17.741
38.996
45.357
20.471
12.358
32.045

130.408
103.409
112.839
91.698
106.584
108.273
109.249
123.296
121.598
104.790
93.847
86.013
115.347
96.613
109.294
123.761
120.394
101.537
170.068
123.928
121.254
131.000
112.309
163.275
113.753

0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000

0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000

angle4
angle4

114
114

204
114

114
114

40.835
25.926

61.950
115.214

0.000
0.000

0.000
0.000

torsion5
torsion5
torsion5
torsion5
torsion5
torsion5
torsion5
torsion5
torsion5

114
2
1
1
6
8
204
8
1

204
204
114
114
204
204
8
1
1

114
114
114
204
8
6
1
1
6

114
114
204
114
1
1
1
6
204

-14.092
-12.686
-20.000
1.750
18.731
-0.826
20.000
-12.659
-12.550

0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000

1
1
1
1
1
1
1
1
1

-19.319
-3.490
14.914
-9.708
-14.795
19.309
-6.490
2.832
14.581

180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000

2
2
2
2
2
2
2
2
2

4.921
16.202
-10.620
13.722
-4.352
10.007
18.383
18.916
8.502

0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000

3
3
3
3
3
3
3
3
3

torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion

2
1
2
5
2
2
2
7
7
114
204
204
114
2
2
2
114
1
114
114
7
7
1
1
204
114
114
1
1

2
2
2
2
2
2
204
204
204
204
114
114
114
2
2
8
114
114
204
204
204
204
204
204
1
114
114
114
114

2
2
204
2
204
204
114
114
114
114
114
1
1
8
8
204
204
204
1
1
1
1
1
1
2
204
204
204
204

204
204
7
204
2
114
1
114
1
1
1
5
5
2
204
7
1
1
2
5
2
5
2
5
2
8
6
8
6

16.066
-6.756
-20.000
-17.749
20.000
-2.308
-3.022
12.722
-17.534
18.438
-11.940
-19.904
-12.368
5.030
1.973
-13.345
-3.889
2.798
0.384
10.499
-14.580
16.971
11.024
-3.858
1.404
5.678
-16.062
-8.856
8.109

0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000

1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1

0.007
12.503
-18.229
11.742
17.632
9.394
12.278
19.577
-9.167
-11.354
7.354
10.504
8.301
6.134
-19.271
-2.218
17.714
-14.543
-20.000
12.845
-11.471
-13.856
-0.504
16.963
13.165
0.067
9.238
-5.744
17.754

180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000

2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2

-13.916
5.917
4.338
8.938
12.163
13.177
-18.863
-4.298
-11.760
-1.259
-5.538
0.343
11.379
-14.875
0.216
16.162
7.280
-8.800
-19.185
-8.784
7.612
17.588
-19.600
-17.855
11.305
-12.578
15.136
18.582
3.807

0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000

3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3

S2

torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion

114
7
6
114
7
204
5
9
1
9
204
9
204
1
1
7
114
204
114
1
113
2
2
9
204
204
114
114

204
204
204
204
204
8
1
204
204
204
9
2
1
1
1
204
204
114
114
114
114
2
204
204
9
114
114
1

8
8
8
6
6
1
6
9
9
1
2
2
1
204
204
114
114
114
114
114
114
204
9
9
1
1
1
1

1
1
1
1
1
5
204
2
2
5
2
1
1
1
7
113
113
113
113
113
113
9
1
1
1
1
1
5

2.996
-17.230
12.364
12.573
4.733
-1.940
8.798
-15.014
18.374
-8.925
-17.196
-1.368
10.936
-14.305
12.866
17.535
11.127
-10.299
-13.185
-10.797
0.100
-18.033
2.284
-1.587
-20.000
0.921
4.809
-12.037

0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000

1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1

-20.000
10.064
-0.077
1.556
15.320
-18.967
-0.562
7.396
4.301
-7.248
-0.594
-10.340
-8.020
1.128
-12.428
1.969
5.352
-7.915
-13.401
7.758
5.165
-9.800
-7.042
-0.101
-13.897
-13.017
2.965
10.593

180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000

2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2

10.160
-11.232
19.170
-10.632
16.536
1.253
-0.404
10.955
1.809
-14.017
14.654
-5.246
-0.957
-1.161
19.886
19.649
-9.635
4.260
-20.000
0.505
-3.543
9.671
-15.960
-13.407
-14.806
-2.396
-12.244
-15.340

0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000

torsion4
torsion4

114
204

204
114

114
114

114
114

-15.253
-11.199

0.000 1
0.000 1

-16.767
-2.024

180.000 2
180.000 2

-11.262
-16.452

0.000 3
0.000 3

opbend

2

204

1.609845

Parameters for five coordinated Rhenium
atom
atom

202
205

N
Re

"N for Re 5 KOORD"
"RHENIUM 5 KOORD"

7
75

14.003
186.207

bond
bond
bond
bond
bond
bond
bond
bond
bond

205
205
205
202
25
205
205
205
15

7
1
2
1
205
10
74
15
2

38.2301
26.4803
13.4452
26.2423
5.5964
38.3202
12.4368
47.0143
6.1897

1.6531
2.1319
2.1500
1.4904
2.4007
1.6300
2.1100
2.3200
1.7921

bond5
bond5
bond5
bond5

205
205
205
205

6
202
1
1

39.8486
49.9927
24.1684
31.5803

1.9411
2.4000
2.1132
1.4503

0
0

angle5
angle5
angle5
angle5
angle5
angle5

6
202
205
205
202
205

205
205
202
1
1
6

6
1
1
1
1
1

30.192
43.519
43.534
38.859
29.182
45.067

77.892
79.562
107.557
118.635
106.608
122.344

0.000
0.000
0.000
0.000
0.000
0.000

0.000
0.000
0.000
0.000
0.000
0.000

angle
angle
angle
angle
angle
angle
angle

6
7
7
1
7
1
205

205
205
205
205
205
205
1

6
7
1
1
2
2
1

0.389
21.049
13.439
14.897
22.930
26.772
41.083

99.174
108.265
95.633
129.322
115.884
73.728
113.980

0.000
0.000
0.000
0.000
0.000
0.000
0.000

0.000
0.000
0.000
0.000
0.000
0.000
0.000

S3

3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3

angle
angle
angle
angle
angle
angle
angle
angle
angle
angle
angle
angle
angle
angle
angle
angle
angle
angle
angle
angle
angle
angle
angle

205
205
7
205
1
202
202
2
25
25
25
1
6
6
25
74
25
74
1
15
205
205
15

1
2
205
202
202
1
1
25
205
205
205
205
205
205
205
205
205
205
205
205
15
15
2

5
2
202
1
1
5
1
205
1
25
10
10
7
1
74
1
15
15
15
15
1
2
2

0.699
37.815
3.340
44.956
29.150
20.915
23.497
11.495
44.361
29.683
10.347
45.102
13.277
5.768
30.997
40.128
2.712
17.306
4.473
29.964
22.387
10.589
40.379

torsion5
torsion5
torsion5
torsion5
torsion5
torsion5
torsion5

6
1
202
205
205
1
205

205
205
205
202
1
1
6

6
202
1
1
1
1
1

1
1
1
1
1
202
1

-13.814
-4.002
-19.094
-5.936
8.163
-4.078
-4.643

0.000
0.000
0.000
0.000
0.000
0.000
0.000

1
1
1
1
1
1
1

-14.334
5.822
8.188
-11.288
-13.384
-2.407
-3.914

180.000
180.000
180.000
180.000
180.000
180.000
180.000

2
2
2
2
2
2
2

-1.861
-3.727
3.526
16.840
-15.848
11.480
5.468

0.000
0.000
0.000
0.000
0.000
0.000
0.000

3
3
3
3
3
3
3

torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion

6
7
7
1
1
2
2
7
1
205
205
205
7
1
202
205
1
1
205
205
5
202
2
2
2
2
25
10
7
1
6
205
2
2
74
15
25
74
1
15

205
205
205
205
205
205
205
205
205
1
2
2
205
205
205
202
202
202
202
1
1
1
2
25
25
25
205
205
205
205
205
6
25
25
205
205
205
205
205
205

6
1
1
1
1
1
1
2
2
1
2
2
202
202
1
1
1
1
1
1
1
1
25
205
205
205
1
1
6
6
1
1
205
205
1
1
15
15
15
15

1
1
5
1
5
1
5
2
2
1
2
5
1
1
5
5
1
5
1
5
202
1
205
1
25
10
5
5
1
1
5
1
74
15
5
5
1
1
1
1

17.253
9.226
8.391
-17.990
-9.587
-0.821
-10.339
-1.976
4.796
6.942
-13.397
19.876
-19.994
17.846
18.797
-14.992
7.235
17.097
2.380
19.483
-5.492
11.289
8.983
0.473
2.391
1.053
-17.659
18.054
-18.140
-1.179
-8.304
4.156
19.562
0.666
2.121
-10.517
12.845
15.340
-9.831
-15.677

0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000

1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1

-0.249
-19.342
18.509
-0.840
-7.732
-6.761
-16.884
-17.466
-20.000
-7.277
2.251
-17.324
18.389
1.260
15.411
14.895
-15.929
19.916
-20.000
-7.757
-19.550
14.677
11.430
-14.099
-15.589
-2.051
6.722
11.704
-7.173
-15.150
12.672
-18.412
9.433
-3.426
18.606
3.475
12.008
12.702
-10.375
5.670

180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000

2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2

11.511
0.018
16.316
1.791
18.183
15.148
11.972
-1.153
-7.799
-16.244
-5.832
-15.031
11.739
6.020
12.884
18.792
-1.392
7.177
13.701
7.293
-13.489
-3.806
15.760
-6.232
-9.327
-8.893
2.917
-16.822
-15.143
-7.727
12.784
0.950
1.848
-9.583
13.304
19.589
-1.111
18.375
13.797
-18.589

0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000

3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3

S4

111.489
125.309
105.319
109.273
108.010
109.373
113.346
113.640
83.987
159.000
101.381
106.000
107.583
98.395
94.138
117.524
103.017
111.800
93.685
88.690
114.012
104.550
123.454

0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000

0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000

torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
torsion
opbend
opbend

25
74
1
15
205
205
205
1
2
15
2
2

205
205
205
205
15
15
15
2
2
2
15
205

15
15
15
15
1
1
2
2
2
2

2
2
2
2
5
2
2
15
15
5

19.112
-2.761
14.362
-5.557
-8.385
12.846
-1.604
-11.799
18.480
4.078

0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000

13.865889
12.499404

S5

1
1
1
1
1
1
1
1
1
1

-8.092
2.848
7.837
-8.052
-7.076
-5.279
-5.042
15.943
16.340
7.142

180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000
180.000

2
2
2
2
2
2
2
2
2
2

2.795
-8.278
-17.464
-15.950
3.427
17.938
-5.855
-1.691
12.009
-2.321

0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000

3
3
3
3
3
3
3
3
3
3