Exercises 20&21 - HyperChem 8.04 Molecular Modeling.

Molecular-Mechanic (MM) Calculations

Optimizing the Geometry of the Molecule via MM+ Parameterization
Theoretical Organic Chemistry, 2013
Anastazija Ristovska
Below is the hydrocarbon molecule weve been working with in most exercises displayed in several
different ways, using the Molecular Mechanics MM+ method of Geometry Optimization through the
Newton-Raphson Algorithm in HyperChem 8.04. Below in order are given the balls, balls and cylinders,
overlapping spheres, and tubes atom-rendering models of display. The numeration of the molecule as
projected by HyperChem 8.04 is given on a sticks atom-rendering model. Bond lengths, atomic distances,
and angles between atoms are given as well.

Bond distance from atom 10 to atom 9 is 1.276.

Bond distance from atom 9 to atom 4 is 0.5265.
The angle of atoms 10-9-4 is 61.16.
Bond distance from atom 4 to atom 3 is 2.195.
The angle of atoms 9-4-3 is 110.241.
The torsion angle of atoms 10-9-4-3 is 180.
Bond distance from atom 3 to atom 2 is 2.684.
The angle of atoms 4-3-2 is 169.5.
The torsion angle of atom 9-4-3-2 is 0.
The distance from atom 1 to atom 7 is 5.134.
The improper angle of atoms 7-4-1 is 51.50.
The distance from atom 7 to atom 4 is 3.084.
The angle of atoms 3-2-1 is 158.0.
The torsion angle of atoms 1-2-3-4 is 180.
The distance from atom 8 to atom 1 is 8.998.
The improper angle of atoms 7-9-10 is 174.9.
The improper angle of atoms 9-4-7 is 57.31.
The improper angle of atoms 1-7-10 is 107.9.
The angle of atoms 8-5-4 is 164.7.
The angle of atoms 6-5-4 is 82.10.
The angle of atoms 8-5-6 is 113.2.
The improper angle of atoms 8-5-6-7 is 180.
The angle of atoms 7-6-5 is 146.8.
The angle of atoms 5-4-9 is 21.34.
The improper angle of atoms 5-4-9-10 is 0.
The improper angle of atoms 8-5-4-9 is 180.
The distance between atoms 8 and 10 is 2.882.
Bond distance between atoms 2 and 1 is 1.649.
Bond distance between atoms 5 and 4 is 1.773.
Bond distance from atom 8 to atom 5 is 1.393.
Bond distance from atom 5 to atom 6 is 2.031.
Bond distance between atoms 6 and 7 is 1.341.

Distances of atoms that do not have covalent bonds formed between each other are given in bold:
1
2
3
4
5
6
7
8
9
10

1
0
1.649
4.258
6.452
7.712
6.358
5.134
8.998
6.640
7.494

2
1.649
0
2.684
4.868
6.066
4.740
3.568
7.349
5.016
5.930

3
4.258
2.684
0
2.195
3.621
2.970
2.484
4.993
2.428
3.247

4
6.452
4.868
2.195
0
1.773
2.505
3.084
3.138
0.527
1.121

5
7.712
6.066
3.621
1.773
0
2.031
3.238
1.393
1.296
1.805

6
6.358
4.740
2.970
2.505
2.031
0
1.341
2.879
2.079
3.301

7
5.134
3.568
2.484
3.084
3.238
1.341
0
4.214
2.835
4.107

8
8.998
7.349
4.993
3.138
1.393
2.879
4.214
0
2.684
2.882

9
6.640
5.016
2.428
0.527
1.296
2.079
2.835
2.684
0
1.276

10
7.494
5.930
3.247
1.121
1.805
3.301
4.107
2.882
1.276
0

The distance between atoms 3 and 1 is 4.258.

The distance between atoms 2 and 4 is 4.868.
The distance between atoms 1 and 4 is 6.452.
The distance between atoms 1 and 5 is 7.712,
and so on, all the distances between non-bonded atoms in this molecule are given in bold in the table
above, whereas the bond lengths of the bonded atoms are given in non-bolded characters.

2-Ethenylpyrrole

All the distances between non-bonded atoms in 2-ethenylpyrrole are given in bold in the table below,
whereas the bond lengths of the bonded atoms are given in non-bolded characters.
1
2
3
4
5
6
7

1
0
1.417
2.274
1.346
2.283
3.683
4.717

2
1.417
0
1.411
2.243
2.254
2.535
3755

3
2.274
1.411
0
2.258
1.344
1.460
2.455

4
1.346
2.243
2.258
0
1.471
3.688
4.392

5
2.283
2.254
1.344
1.471
0
2.502
2.973

6
3.683
2.535
1.460
3.688
2.502
0
1.341

7
4.717
3755
2.455
4.392
2.973
1.341
0

The angles between atoms are:

atoms
1-2-3
1-4-5
4-1-2
3-5-4
2-3-5
6-3-5
3-6-7

angle
107.0
108.2
108.4
106.6
109.8
126.3
122.3