Molecular Modeling Lab

CHEM 211

Dr. Leong

 

 

Objectives: To use PCMODEL, a molecular modeling software, to learn conformations of alkanes & cycloalkanes and study their properties such as energies, bond angles, bond length & dipole moments; and to learn a powerful tool in modern chemistry.

 

To start:

 

  1. You need to copy the folders “Module” and “pcmod75” from the network “Profshar” drive, “aleong” folder to your local “c:” drive.  From “pcmod75” folder, double click on “pcm7.exe” to open the modeling program window.  Whenever a file needs to be loaded, find it from the “Module” folder.
  2. The lab material is at my web site.  So open the Internet Explorer window and log on to my web site at the following address: http://www.ehcweb.ehc.edu/faculty/ALEONG/module/GreenLabframeset2.htm
  3. Size the two screens such that both are visible.  Size the IE window such that about 4 lines of text at full width can be seen.  Put this at the bottom of the screen.  The modeling window can then be made as big as possible without covering up the IE texts.  Alternatively, put the two windows side-by-side, PCMODEL on the left and web site on the right.
  4. Click on “Introductions” to read general procedures.  Click “Activities” to go through the exercises and record data obtained in the report sheet handout and spreadsheet.
  5. The whole purpose of this lab is to learn the important concepts of conformation in a hands-on manner.  So make sure that the material makes sense before moving on.  Refer to links for dihedral angles and Newman projections when appropriate.
  6. You should also use your molecular model set as you go through these exercises.  Solid models are rigid and not very informative but they give you a 3-dimensional feel in your hands.
  7. As lab report, turn in the Report sheet handout, graphs and spreadsheet.
  8. Some of you may feel a little overwhelmed with juggling a modeling program, web technologies, spreadsheet and others to learn molecular conformations, energies and properties.  The positives are that you are learning some very important concepts in organic chemistry and state-of-the-art modeling tools in chemical and biological sciences.

 

 

Please ask if you have any questions during lab.  Happy modeling.

 

 

 

 

Report sheet for Molecular Modeling Lab

 

 

A.  1,2-dichloroethene

 

 

 

Cis

Trans

Heat of formation

 

 

 

Dipole Moment

 

 

 

Bond lengths

C=C

 

 

 

C-H

 

 

 

C-Cl

 

 

Bond Angles

C-C-Cl

 

 

 

H-C-Cl

 

 

 

H-C-C

 

 

Dihedral angles

Cl-C=C-Cl

 

 

 

Cl-C=C-H

 

 

 

H-C=C-H

 

 

 

 

Conclusions:

 

Which is more stable, cis or trans?   ___________

Which is polar?  ________   Which is nonpolar?  _______

Are the bond angles exactly 120 degrees?  If not, why not? ________________________________________________________________________.

From the dihedral angles, is the cis or the trans compound flat? ________________________________________________________________________.

 

 

B. 1.  Ethane

 

 

MMX (kcal/mol)

HF (kcal/mol)

Distance between H’s (Angstroms)

Percentage

Staggered ethane

 

 

 

 

Eclipsed ethane

 

 

 

 

 

Conclusion: From HF energies, the _____________ conformation is more stable than the ____________ conformation by _________ kcal/mol.

 

B. 2.  1,2-Dichloroethane

 

 

MMX energy (kcal/mol) from graph

Percentage at 25 C

Anti

 

 

Gauche

 

 

Difference

 

---------------

 

 

B. 3.  Butane

 

Compared to 1,2-dichloroethane, what do you expect to see for the energy versus rotation graph of butane?  (hint: think of methyl group as a large group just like Chlorine.) _____________________.

 

 

MMX energy (kcal/mol) from graph

Percentage at 25 C

Anti

 

 

Gauche

 

 

Difference

 

---------------

 

 

C. 1.  Cycloalkanes

 

Conclusion: The cycloalkanes all resemble the ____________________  butane conformation.  This is the _________  energy of the butane.

 

 

 

C. 2-5.  Cyclopropane, Cyclobutane, Cyclopentane, Cyclohexane

 

 

Geometry

HF

DHF

HF per CH2

CCC Angles

D angle strain

D torsional strain

D steric strain

Cyclopropane

Flat

 

-------

 

 

-------

-------

------

 

---------

------

-------

-------

-------

-------

-------

------

Cyclobutane

Flat

 

-------

-------

 

-------

-------

------

 

Puckered

 

 

 

 

 

 

 

Cyclopentane

Flat

 

-------

-------

 

-------

-------

------

 

Puckered

 

 

 

 

 

 

 

Cyclohexane

Flat

 

-------

-------

 

-------

-------

------

 

Puckered

 

 

 

 

 

 

 

 

 

Notes:

 

  1. HF are values computed by PCMODEL
  2. DHF = (HF of Puckered) – (HF of Flat)
  3. HF per CH2 = (HF)/(number of CH2’s in ring)
  4. CCC Angles are measured from experiment
  5. For the changes in angle strain, torsional strain and steric strain, use “I” for increase and “D” for decrease.

 

Conclusion:  Except for _______________, the cycloalkanes become more ____________ by puckering.  The cycloalkane that gains the most in stability is ___________________.  For alkanes, each CH2 contributes –4.9 kcal/mol in stability, which cycloalkane comes closest to this gain in stability? ________________.

 

 

 

D.  Cyclohexane conformations

 

 

Cyclohexane

HF

No. of butane eclipsed methyls conformations

No. of butane gauche conformations

No. of butane anti conformations

1,4 nonbonding steric interaction

Percentage at 25 C

Flat

 

 

 

 

-----------

--------

Half chair

 

 

 

 

-----------

--------

Boat

 

 

 

 

 

--------

Twist boat

 

 

 

 

 

 

Chair

 

 

 

 

-----------

 

 

Conclusion: The most stable conformation for cyclohexane is the ____________ conformation with bond angles of about _____ degrees.

 

 

 

E.  Cyclohexane – Axial & Equatorial Positions

 

 

Axial positions occupied by

Equatorial positions occupied by

Original chair

H’s

D’s

New chair

 

 

 

Conclusion: Ring flip from one chair to the other causes all the axial groups to become ______________ and all the equatorial groups to become _______________.

 

 

 

F.  Monosubstituted Cyclohexanes

 

Cyclohexane

HF of axial, kcal/mol

HF of equatorial, kcal/mol

% Equatorial

% Axial

Fluoro

 

 

 

 

Chloro

 

 

 

 

Bromo

 

 

 

 

Iodo

 

 

 

 

Hydroxy

 

 

 

 

Methyl

 

 

 

 

Ethyl

 

 

 

 

t-Butyl

 

 

 

 

 

 

Conclusion:  In general, for a monosubstituted cycloalkane, the conformation with group at ______________ is more stable.

 

 

 

G.  Disubstituted cyclohexanes

 

Dimethylcyclohexane

Positions of the 2 methyls

HF

Percent at 25C

1,2-cis

 

 

 

 

 

 

 

1,2-trans

 

 

 

 

 

 

 

1,3-cis

 

 

 

 

 

 

 

1,3-trans

 

 

 

 

 

 

 

1,4-cis

 

 

 

 

 

 

 

1,4-trans

 

 

 

 

 

 

 

 

 

Conclusions: 

 

For 1,2-dimethylcyclohexane, the most stable conformation is _____ with methyls at _____ positions.

For 1,3-dimethylcyclohexane, the most stable conformation is _____ with methyls at _____ positions.

For 1,4-dimethylcyclohexane, the most stable conformation is _____ with methyls at _____ positions.

 

So, in general, for disubstituted cyclohexanes, conformations (in terms of ee, ea, aa) in decreasing order of stability is:

____ > ____ > ____ .

 

Therefore, to say that trans is always more stable than cis (as in alkenes) is inaccurate and imprecise.

 

 

H.  Local and Global Minima

 

What is the global minimum conformation for cyclohexane?  _________________.

 

 

I.  Biomolecules

 

What do you see? _________.