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MOE Exercises Answers Chapt. 1 and 2
Problem 1.1: What is the barrier height for rotation around the methyl group C-C bond?
Could you get the methyl group to stay in the eclipsed conformation?
Problem 1.2:
Contribution Methyl cyclohexane
(kcal/mol)
2-methylhexane
(kcal/mol) difference
(kcal/mol) favored stucture bond str energy angle energy torsional energy
Van der Waals electrostatic total*
*
The total should include all force field terms, as listed by the Potential Energy listing.
(a). Which contribution dominates the preference?
(b). Which changes most, the ring strain (as measured by the sum of the bond stretch, bond angle, and dihedral torsion terms) or the through-space Van der Waals term?
Problem 2.1
Contribution equatorial
(kcal/mol) axial
(kcal/mol) difference
(kcal/mol) favored conformer bond str energy angle energy torsional energy
Van der Waals electrostatic total
(a). Which force field contribution dominates the preference?
(b). Which changes most, the ring strain (as measured by the sum of the bond stretch, bond angle, and dihedral torsion terms) or the through-space Van der Waals term?
Problem 3.1
(a). The shortest distance between a methyl hydrogen and a ring hydrogen in axial- methylcyclohexane _________________ Å
The shortest distance between a methyl hydrogen and a ring hydrogen in equatorial- methylcyclohexane_________________ Å
(b). Do these shortest distances in the axial and equatorial conformers correlate with the change in Van der Waals energy that you found in Problem 2.1? The MMFF94 Van der Waals radius for

2
H is about 1.485Å. Explain your reasoning (don’t just answer yes or no)(Hint: at what distance does the H-H Van der Waals interaction become repulsive?):
Problem 3.2:
Bond Lengths
Bond
C-C (Methyl)
Distance Å Expected Å
Bond Angles
Angle Angle

1.53 C-C-C (1)
Expected
C-C
C-C
1.53
1.53
C-C-C (2)
C-C-C (3)
C-C 1.53 H-C-C-H
C-H 1.10 C-C-C-C
(a). Do the C-C or C-H bond distances vary much from the expected values?
Which C-C bond angle differs most from the normal values or do they all have about the same difference?
(b). Do the bond lengths or bond angles deviate more from the normal values?
Problem 3.3: MMFF Forcefield Charges
Compare the electrostatic and Van der Waals terms; does the electrostatic term exceed the Van der Waals term in this molecule?
Problem 3.4: MMFF Forcefield Charges
MMFF methylene H charges: ethylene glycol ___________ methylcyclohexane ___________
H in –OH ___________ O in –OH ___________
Problem 3.5: PEOE Charges
PEOE methylene H charges: ethylene glycol ___________ methylcyclohexane ___________
H in –OH ___________ O in –OH ___________
By what percentage difference does the PEOE charge on the methylene H’s in ethylene glycol exceed the PEOE charge on the methyl H’s in methylcyclohexane [100% (q
EG
– q
MCH
)/q
MCH
]?

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Problem 3.6: PEOE Charges
Contribution ethylene glycol
MMFF charges
(kcal/mol) bond str energy angle energy torsional energy
Van der Waals electrostatic ethylene glycol
PEOE charges
(kcal/mol) difference
(kcal/mol) total
(a). Does the partial charge method make a significant difference in the overall steric energy?
(b). Does minimization with PEOE charges make significant changes in the individual forcefield energy terms? Which changes most?
(c). Compare the potential energy changes, are they in the same direction [e.g. all greater, all smaller, or all increase in magnitude (positives get more positive and negatives get more negative)]?