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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 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 LengthsBond Angles

Bond / Distance Å / Expected Å / Angle / Angle  / Expected
C-C (Methyl) / 1.53 / C-C-C (1)
C-C / 1.53 / C-C-C (2)
C-C / 1.53 / 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 bondangle 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% (qEG – qMCH )/qMCH]?

Problem 3.6: PEOE Charges

Contribution / ethylene glycol
MMFF charges
(kcal/mol) / ethylene glycol
PEOE charges
(kcal/mol) / difference
(kcal/mol)
bond str energy
angle energy
torsional energy
Van der Waals
electrostatic
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)]?