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COMPUTATIONAL CHEMISTRY

Chemistry 2311 – Spring 2023

75 pts

Report output data to .001 ONLY

Introduction and Practice

Cyclohexane Conformations –  see Mohrig, pp. 110-112 for directions

Record the MM2 steric energy value (Total) for each conformation of cyclohexane below:

a.     chair  = __6.5564____kcal/mol  

b.     boat   =      _13.0166_____kcal/mol               

c.     twist-boat   =  _11.4172______kcal/mol  

Problem 1:  Monosubstituted Cyclohexane

sec-butylcyclohexane Conformations – be sure to run the Dihedral Driver.

 Record the MM2 steric energy value (Total) for each conformation of sec-butylcyclohexane below:

a.   chair, sec-butyl axial    =     _14.6488______kcal/mol  

b.     chair, sec-butyl equatorial    =  __15.0368_____kcal/mol

Problem 2:  1,4-Disubstituted Cyclohexane. Record the MM2 Total steric energy values for each conformation and the corresponding Parameter Values for the trans compounds. (may need to cursor up in the output box to see) for each conformation below:

cis-1-tert-butyl-4-methylcyclohexane. Run a dihedral driver to find global minimums.

     cis-equatorial-1-tert-butyl-axial-4-methylcyclohexane (A) =  __13.5912__________kcal/mol

       cis-axial-1-tert-butyl-equatorial-4-methylcyclohexane  (B) =  _18.4880__________kcal/mol

trans-1-tert-butyl-4-methylcyclohexane

trans-diequatorial-1-tert-butyl-4-methylcyclohexane (C) =  __13.5904_________kcal/mol

Stretch: 1.4682 Bend:2.0972 Stretch-Bend: 0.3043

Torsion:3.7214 Non VW:-1.6809 VDW: 7.6803

trans-diaxial-1-tert-butyl-4-methylcyclohexane (D) =  _ 20.4301__________kcal/mol

Stretch: 1.6569 Bend: 4.9145 Stretch-Bend: 0.432

Torsion: 6.4906 Non VW: -1.5872 VDW: 8.5224

Problem 3:  Dihedral Driver, Newman Projections, and Elimination Reaction

Consider the 2-bromo-3-methylpentanenitrile structures below.

Label each chiral carbon (stereocenter) as R or S in Compound A and B.   

What is their relationship?  Constitutional isomers, enantiomers, or diastereomers?  _________________

Determine a MM2 steric energy value for each compound. Be sure to run Dihedral Driver rotations on the necessary substituents to avoid local minimums. Start with Compound A and continue with the instructions below before moving on to Compound B.

                                     __________ kcal/mol  (Compound A)

                                      __________ kcal/mol  (Compound B)  

Newman Projection and Elimination Reaction.

Compound A.   Once you have a minimized structure for Compound A rotate the structure so you are looking down Carbon 2 to Carbon 3 as in a Newman projection.  Then rotate slightly to the side so you can highlight the C2-C3 bond.  Run the Dihedral Driver to obtain the chart output which represents a 360 degree rotation around this bond.  Sketch the plot below and label:   a)  a local minimum; b) energy maximum; and c) global minimum.

 

 

 

Use the 3D structure and Dihedral driver plot to rotate the C2-C3 bond to the proper orientation required for an E2 elimination reaction that would occur when Compound A is treated with a strong, sterically hindered base.  Hint: recall the necessary positioning of the H on carbon 3 to the Br on carbon 2.   Circle the alkene below which would be the MAJOR product.   

  

Compound B:  

Repeat the instructions above using Compound B.  Run the Dihedral Driver looking down carbon 2 to carbon 3 and chart the output below.  Observe whether it is identical to the dihedral driver plot of Compound A.  Label:   a)  a local minimum; b) energy maximum; and c) global minimum.    

 

 

Use the 3D structure and Dihedral driver plot to rotate the C2-C3 bond to the proper orientation required for an E2 elimination reaction that would occur when Compound B is treated with a strong, sterically hindered base.   Circle the alkene below which would be the MAJOR product.

 

 

Problem 4:

MOPAC Heat of Formation of 1-pentene, (E)-2-pentene, and (Z)-2-pentene 

Draw the structure for each compound on the left and determine its MOPAC Δ H_f energy value (PM3, Mullikan): 

1-pentene  = ___________     = kcal/mol

(E)-2-pentene _________  =  kcal/mol

(Z)-2-pentene  =  __________    =   kcal/mol

Problem 5:

Partial Charges and Resonance Structures (use the structures below, NOT what is in the manual)

 

a. MOPAC (Method PM3, Mullikan) ) DH_f energy value for allylic cation (1) = __________kcal/mol

 

b. MOPAC (Method PM3, Mullikan) ) DH_f energy value for allylic anion (2) =

        

__________kcal/mol

Record the minimized charge values for each structure: 

                                                                                        

Problem 6: Creative Exploration: Partners should come up with an ORIGNIAL problem not related to questions on this worksheet that could be addressed through computational chemistry using either molecular mechanics or quantum mechanics. State the question/problem you are investigating below, outline how you approached the problem through computational chemistry, and summarize your conclusions based on calculated output (or attach a separate piece of paper). Attach all appropriate printouts. Extra space provided on the last page.

Additional Questions:

Problem 1:  Monosubstituted Cyclohexane

sec-butylcyclohexane Conformations

Calculate the difference in steric energy for conversion of the sec-butyl group from the axial to equatorial position using values a & b below (remember product – reactant).   

Δ Steric Energy  =

As described on page 113 of Mohrig, this difference can approximate the free energy change, ΔG, and is related to the K_eq value by the formula, DG = -RTlnK_eq.  Calculate an equilibrium constant, K_eq, for the conversion of axial to equatorial sec-butylcyclohexane.  Think about whether the value should be greater or less than one based on the equations below.  Be careful of the sign and units.

 

Using K_eq, determine the percentage of the equatorial chair conformation compared to axial overall at room temperature.  Discuss this outcome.  

Problem 2:  1,4-Disubstituted Cyclohexane

cis and trans-1-tert-butyl-4-methylcyclohexane 

 

Draw the four different chair conformations (using letters given) of the cis and trans isomers studied with their lowest steric energy conformation values given. Be sure proper angles are used for axial and equatorial substituents.   

A        B C D

Steric Energy:

What two energy parameters were affected MOST by moving the substituents from the equatorial to axial positions?

Which substituent, the methyl group or tert-butyl group, has a greater effect on total energy in the axial position? Discuss TWO specific steric interactions that cause an axial substituent to be higher in energy than equatorial one.

Hint:  look at the each structure from the side view chair perspective and then a Newman projection looking from “front to back” as illustrated in Wissinger lecture slides.

Problem 4:

MOPAC Heat of Formation of 1-pentene, (E)-2-pentene, and (Z)-2-pentene

Discuss the output results of the alkenes by ordering the compounds from most stable to least stable based on the heat of formation values.  Do the results correlate with known stabilities of double bonds? Discuss.

Problem 5:

Partial Charges and Resonance Structures

What conclusion can be drawn from the charge distributions?   Do the calculations correlate with predicted resonance structures?  Explain.  

Problem 6: repeated from p. 4.

Problem 6: Creative Exploration: Partners should come up with an ORIGNIAL problem not related to questions on this worksheet that could be addressed through computational chemistry using either molecular mechanics or quantum mechanics. State the question/problem you are investigating below, outline how you approached the problem through computational chemistry, and summarize your conclusions based on calculated output (or attach a separate piece of paper). Attach all appropriate printouts. Extra space provided on the last page.