These
lab exercises are designed to allow the students to learn some important
organic chemistry concepts in a hands-on interactive manner. The concepts of structural isomers,
molecular properties, energies, conformations of ethane, butane, cycloalkanes,
especially cyclohexane, substituted cyclohexanes, and biomolecules are
explored. In fact, modules in these lab
exercises may take the place of several lectures in organic chemistry in the
classroom. At the discretion of the
instructor, these exercises may be used as classroom demonstrations, lab
exercises, take-home assignments or combinations of these activities. These lab exercises can easily take two lab
periods and it is important for the students not to rush through the work. They need to see, feel, experience at their
own pace. Work can be done individually
or in pairs to alleviate limited computers in a computer lab. Although learning how to use modeling
software is not the goal primary goal here, students will have learned about
the very important tools in molecular modeling while learning basic organic
chemistry concepts. While many modeling
software packages are available, PCMODEL is chosen because of its general ease
of use, suitability to the teaching and learning tasks at hand, and costs. Special rates for ACA schools have been
arranged with Dr. Kevin Gilbert of SerenaSoft
and Indiana University. For pricing,
contact: gilbert@indiana.edu. The software will run on PC’s and Mac’s
and in various operating systems.
Students will need help to find equilibrium ratios and percentages of
the conformations. They will need
review in writing equilibrium equations, equilibrium constants, free energy
equations and converting ratio to percentages.
From these results, the importance of energy and conformations can be
emphasized. The basic theory is included
as a web page. To facilitate
determining percentages without going through individual calculations and
detail theories, an Excel spreadsheet is available to use as a calculator or it
can be collected as part of the student report.
A
report sheet handout is available to print and give to students. You may want to modify the first page on
general instructions. If you would like
to have a copy of the report sheet with typical results from this modeling lab,
send me an email and please indicate your official position.
Materials
needed to use this module are:
(1) PC or MacIntosh computers. PC’s should be Pentium II or later with
Windows 95, 98, or 2000.
(2) "PCMODEL" from SerenaSoft installed.
(3) Internet connection to web site Molecular
modeling E&H .
(4) Support files installed on your local
drive. To download these files, click Support files to
access ftp site. When connected, right
click on the "Support files" folder, choose "Copy To
Folder" and select your local drive, directory to download. Go to this
folder when files are asked for in the exercises.
The
goal here is to introduce the student to the software with a molecule that is easy
to draw and study.
As
the lab progresses, you may want to
-
Explain
dihedral angles when this term comes up
-
Emphasize
MMX energies are generated by the modeling program and are comparable only to other
MMX energies
-
Emphasize
number of data points and appearance of resulting graphs
-
Explain
steric and torsional energies on conformations.
The
concept of Newman projections on paper can be conveniently introduced at the
end of this exercise. A web page on Newman
projection is available. The percentages
of each conformer can be estimated.
For convenience, a link to a spreadsheet is provided so the
student can just enter the values to see the estimated percentages. This spreadsheet is used throughout the rest
of these exercises. If it is desirable
for the students to learn the theory, this is also available as a
separate link.
2. !,2-dichloroethane
The
rotation around the C-C bond here is clearer to students than in the case of
butane. Having studied the
conformations of 1,2-dichloroethane, the student can easily extrapolate that
butane should have the similar shape of Energy versus Rotation plot.
3. Butane
By
observing the process of rotations and calculations, students should have a
good idea of where the minima and maxima are with respect to rotation. They can always see this again by repeating
this and keep the step size small. An
understanding of butane conformations is used to study cycloalkanes.
By
examining the adjacent carbons of flat cycloalkanes, the student will see that
each pair of carbons is in a conformation similar to that of the highest energy
conformation of butane, the one with eclipsed methyls.
2
- 5. Cyclopropane, Cyclobutane, Cyclopentane, Cyclohexane
Cyclopropane
and the other theoretically flat cycloalkanes can be studied conveniently in
molecular modeling. By comparing the
properties and energies of the flat and puckered conformations, the student can
gain a better appreciation for the angle, torsion and steric strains involved.
The
important cyclohexane conformations – flat, half chair, boat, twist boat, chair
- are studied in more detail here.
The
relationships of groups on “top or bottom” and “axial or equatorial” of the
ring is examined. Students will have a
good understanding of how they are related.
Students
will gain an understanding that, in general, equatorial groups are more stable
than axial groups on cyclohexane.
Students may be assigned to do only certain ones to save time. The instructor may want to make the part of
finding equilibrium distributions optional.
The
misconception that trans is always more stable than cis for dialkylcyclohexanes
is dispelled here. The student will see
that, as in part F, it is equatorial versus axial that is important.
Finding the lowest energy conformation, Global minimum, is often a difficult task. When software finds a local minimum, it may not look any more as incremental small changes lead to higher energies. For example, minimizing the boat cyclohexane only gives the twist boat as low energy conformation. Many strategies are used including making large Cartesian changes in atom coordinates and rotations. A global search will give the chair conformation for cyclohexane as the global minimum.
By
looking at a protein segment, student will gain an appreciation of the
three-dimensional shape of large molecules.
In this case a spiral with a hole in the middle when viewed from the top
or bottom. Viewing real molecules,
“myoglobin” and a “HIV DNA strand” from the protein data bank further
emphasizes the real world applications of molecular modeling.
Other
viewers and explorers are available over Internet for biomolecules. Protein Explorer is available at http://www.umass.edu/microbio/chime/explorer/index.htm. Protein Explorer runs online from its web
site and requires Netscape Navigator and Chime to work. Another viewer, Rasmol, is available at http://www.umass.edu/microbio/rasmol/. Rasmol allows you to download pdb files and
view them later on your computer.
Students
often have trouble recognizing that “different looking” drawings of the same molecule
are possible. This creates various
problems such as writing isomers of a given molecular formula. Students who do not learn this basic concept
early will encounter much difficulty throughout the two semesters of organic
chemistry. This module hopefully will
give students a good sense of the three dimensional nature of molecules. And by actually manipulating the molecules
themselves, it’s a lesson they won’t easily forget. Further work on this can involve additional assignment (to be
added) and have students determine if they are or are not the same by bond and
molecule rotations. Alternatively, the
instructor as introduction to the module can use this exercise as a
demonstration. The advantage of this
exercise over holding up large models is that everyone can see the same
perspective with molecular modeling.