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Exercises 20&21 - HyperChem 8.04 Molecular Modeling. Molecular-Mechanic (MM) Calculations Optimizing the Geometry of the Molecule via MM+ Parameterization
Below is the hydrocarbon molecule we’ve 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.
1
2
Bond distance from atom 10 to atom 9 is 1.276 Å. Bond distance from atom 9 to atom 4 is 0.5265 Å. The angle of atoms atoms 10-9-4 is 61.16 61.16°. Bond distance from atom 4 to atom 3 is 2.195 Å. The angle of atoms atoms 9-4-3 is 110.241°. The torsion angle angle of atoms 10-9-410-9-4-3 is 180°. Bond distance from atom 3 to atom 2 is 2.684 Å. The angle of atoms atoms 4-3-2 is 169.5 169.5°. The torsion angle of atom 9-4-3-2 is 0°. The distance from atom 1 to atom atom 7 is 5.134 Å. The improper angle angle of atoms 7-4-1 is 51.50°. The distance from atom 7 to atom atom 4 is 3.084 Å. The angle of atoms atoms 3-2-1 is 158.0°. The torsion angle angle of atoms 1-2-31-2-3-4 is 180°. The distance from atom 8 to atom atom 1 is 8.998 Å. The improper angle angle of atoms 7-9-10 is 174.9°. The improper angle angle of atoms 9-4-7 is 57.31°. The improper angle angle of atoms 1-7-10 is 107.9°. The angle of atoms atoms 8-5-4 is 164.7°. The angle of atoms atoms 6-5-4 is 82.10°. The angle of atoms atoms 8-5-6 is 113.2°. The improper angle of atoms 8-5-68-5-6-7 is 180°. The angle of atoms atoms 7-6-5 is 146.8°. The angle of atoms atoms 5-4-9 is 21.34°. The improper angle of atoms 5-4-95-4-9-10 is 0°. The improper angle of atoms 8-5-48-5-4-9 is 180°. The distance between between atoms 8 and and 10 is 2.882 Å. Bond distance between atoms 2 and 1 is 1.649 Å. Bond distance between atoms 5 and 4 is 1.773 Å. Bond distance from atom 8 to atom 5 is 1.393 Å. Bond distance from atom 5 to atom 6 is 2.031 Å. Bond distance between atoms 6 and 7 is 1.341 Å.
3
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 Å 4.258 Å
2 1.649 Å 0 2.684 Å
6.452 Å
4.868 Å
7.712 Å
6.066Å 4.740Å 3.568Å 7.349Å 5.016Å 5.930Å
6.358 Å 5.134 Å 8.998 Å
6.640Å 7.494Å
3
4
5
6
7
8
9
10
4.258 Å
6.452 Å
7.712 Å
6.358 Å
5.134 Å
8.998 Å
2.684 Å 0 2.195 Å 3.621Å
4.868 Å
6.066Å 3.621Å
4.740Å 2.970Å 2.505Å
3.568Å 2.484Å 3.084 Å 3.238Å
7.349Å 4.993Å 3.138Å
6.640Å 5.016Å 2.428Å
1.393 Å
1.341 Å 0
2.879Å 4.214Å
4.214Å 2.835 Å 4.107 Å
0
1.296Å 2.079Å 2.835Å 2.684Å
7.494Å 5.930Å 3.247Å 1.121Å 1.805Å 3.301Å 4.107Å 2.882 Å
0 1.276 Å
1.276 Å 0
2.970Å 2.484Å 4.993Å 2.428Å 3.247Å
2.195 Å 0 1.773 Å 2.505Å 3.084 Å
3.138Å
0.527 Å 1.121Å
1.773 Å 0 2.031 Å 3.238Å 1.393 Å 1.296Å 1.805Å
2.031 Å 0 1.341 Å 2.879Å 2.079Å 3.301Å
2.684 Å 2.882 Å
0.527 Å
The distance between between atoms 3 and and 1 is 4.258 Å. The distance between between atoms 2 and and 4 is 4.868 Å. The distance between between atoms 1 and and 4 is 6.452 Å. The distance between between atoms 1 and and 5 is 7.712 Å, and so on, all the distances between non-bonded 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.
4
2-Ethenylpyrrole
5
6
All the distances between between non-bonded atoms atoms in 2-ethenylpyrrole 2-ethenylpyrrole are given in bold in the table table below, whereas the bond lengths of the the bonded atoms are are given in non-bolded characters. 1 0
2 1.417 Å
3
4
5
6
7
2.274 Å
1.346Å
2.283 Å
3.683 Å
4.717 Å
1.417 Å
1.411 Å 0
2.243 Å
2.254Å
2.535Å
3755Å
2.274 Å
0 1.411 Å
2.258 Å
1.344 Å
1.460Å
2.455Å
1.346 Å
2.243 Å
2.258 Å
4.392 Å
2.254 Å
2.502 Å
2.973Å
3.683 Å
2.535 Å
1.344Å 1.460 Å
1.471 Å 0
3.688Å
2.283 Å
0 1.471 Å 3.688 Å
2.502 Å
4.717 Å
3755 Å
2.455 Å
4.392 Å
2.973 Å
0 1.341 Å
1.341 Å 0
1 2 3 4 5 6 7
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
