Several molecules (and some crystals) are listed below. The structures of most of the molecules
are given in "Protein DataBank" format and the data files have
a ".PDB" extension. You can view these molecules with a program
that reads files which are in PDB format. If you do not have such a program
you can download one from the Internet. Instructions for downloading a
molecular viewing program named RasMol are given on the Molecular
Viewing Information page.
You can download the RasMol program and the PDB files for the molecules
you want to see, or you can download the RasMol program and set it up as
a "helper application" in your web browser. In the latter case,
when you select one of the molecules below, your browser will automatically
launch RasMol and load the PDB file for the molecule you selected. (At present
the general access computer labs on the UofA campus have not installed RasMol
as a helper application for Netscape - they may eventually do so. However, they
do have the program loaded on the servers in each of the labs.
You can download the PDB files to a floppy disk and then run the program
from the server using your floppy as the data file source.)
Once you have the molecule showing on your screen you can rotate it by moving
the mouse with the left mouse button held down. (Or
you can use the slide bars at the right and bottom of your screen.) You can
make the molecule larger or smaller by moving the mouse with the left mouse
button and the shift key held down. You can move the
image around on the screen by moving the mouse with the right mouse button held
down. (You can get another rotation angle by moving the mouse with the
right button and the shift key held down.)
H2 is the smallest
stable molecule. Its shape is not very interesting, but we have placed his model
here to emphaize the point that it is not two dots with a line drawn between them.
the H2 molecule has volume and that volume is due to the electrons. On the scale
of this model the nuclei would not even be visable so all of the spatial extent
of the molecule must be due to the elecrons. In the same manner
N2 is not two dots
connected by three lines.
C2H2 is acetylene
(or "ethyne" if you want to get picky). It is a four-atom linear molecule.
C2H4 is ethylene
(or ethene). It is a planar molecule with 120 degree bond angles.
C2H6 is ethane.
The ethane bond angles are 109 degrees.
a planar ring molecule of six carbons (with six hydrogens attached).
Cyclohexane (chair form) is a puckered six-member ring of carbon atoms. Each carbon has two hydrogen atoms attached.
Ammonia is a
trigonal pyramidal molecule. Why is this molecule not trigonal planar like
CHBr3 is called
a "substituted methane." Three of the hydrogens of methane have been replaced
by bromine atoms.
oxirane is a
molecule that has a "small ring" structure. The three-membered ring distorts
the bond angles around the two carbon atoms so that the bond angles do not
have the values you would expect from VSEPR.
C60 is the newly
discovered allotropic form of carbon. It is the famous buckminsterfullerene,
a carbon molecule in the shape of a soccer ball. This is the molecule which
got Smalley, Curl, and Kroto the 1996 Nobel prize (and for which the University
of Arizona's Dr. Don Huffman should
have shared the prize). The molecule is hollow, but in spacefill mode you can't tell
it. There is a cutaway version
of this molecule which allows you to see the the inside of the
S8 is one of the
allotropic forms of sulfur. It has the so-called crown structure.
P4 is one of the
allotropic forms of phosphorus. As you can see, the P4 bond angles do not
fit the VSEPR model.
The following molecules fit the VSEPR model for five and six sigma-bonded
pairs of electrons. In Chemistry 101A we did not cover the "expanded
ocet" molecules where there can be more than four pairs of valence electrons
around the central atom. The expanded octet is covered in Chemistry 103A. The nonmetals below the first row can have an
"expanded octet," which means that under the right conditions they can have
ten, or even twelve electrons in their valence shell.
PCl5, phosphorus pentachloride, has a
trigonal bipyramid structure. It has the structure you would expect if
five pairs of electrons were trying to get as far away from each other as
possible. There is a whole series of molecules based on this shape where bonded electron
pairs are replaced by lone pairs (nonbonded pairs). We have models for:
XeF2. In each case we can't see the lone pairs, but their presence
forces the bonded pairs into the configuration you see.
SF6 is sulfur hexaflouride.
It has the structure you would expect if six sigma-bonded pairs were trying to get as far away from each other as possible.
Making all the bonds requires an expanded octet of twelve electrons. Sulfur
can do this, but oxygen - for example - can't.
The molecules we show are variations on SF6 where the bonded pairs are
replaced by lone pairs. We have models for:
In the expanded octet molecules the structures with lone pairs are probably not completely accurate. We expect that
a lone pair would "take up more space" than a bonded pair. The resultant crowding probably forces the bonded
pairs together resulting in a small distortion of the idealized structures we have shown.
Aspirin is not
exactly a small molecule, but it fits the VSEPR rules. You should be able to tell
all of the bond angels in this molecule. (Aspirin is in Alchemy (.alc) format, but
RasMol will read molecules in .alc format. If you are using RasMol as a helper application, RasMol
will probably not view Aspirin. You will have to download the Asprin.alc file and the RasMol program
and run the program on your computer separate from your web browser.)
We have included some large molecules so that you can get an idea of what
kinds of structures really large molecules can have. In most cases you would be able to predict the
individual bond angles using VSEPR, but the molecules are so large that they can flop around
and fold. The exact way the molecules fold is much harder to predict from theory and
in most cases there is no perfectly satisfactory way to make this prediction.
The DNA molecule is too large to show
so only a portion of the molecule is shown here.
. DNA is the molecule which carries the genetic information
in living things. This fragment of a DNA molecule contains twelve "base pairs"
(see if you can identify them). The human DNA molecule contains about THREE
BILLION base pairs. That means that an actual human DNA molecule would be
250 million times bigger than the fragment shown on your screen. (You might be
interested in calculating how big your screen would have to be to see a complete
human DNA molecule. Also, the file that contains this data is about 74 kbytes long,
how big a file would it take to hold the structure of a human DNA molecule?)
The DNA molecule will complex with
proteins in the process of transmitting genetic information.
Hemoglobin is the protein molecule in red blood cells that carries oxygen. The
following are portions of hemoglobin molecules with
no bound molecules, with oxygen bound,
with carbon monoxide bound, and with
is a relatively small enzyme (protein molecule) which catalyses the breakdown
of molecules related to sugar. It is famous for having a "pocket" into which the
molecule being acted upon (the substrate) fits. Sometimes another molecule occupies
the "pocket" preventing the lysozyme from doing its job. This other molecule
is called an inhibitor.
Perhaps you can pick out the inhibitor in the pocket.
We have included some .pdb files of crystals and we will add more as they
become available. You will have to view most of these in either "Space Fill" mode
or "Ball and Stick" mode. Don't be surprised when your RasMol screen comes up
blank when you load the file. Just change the Display mode to "Space Fill"
or "Ball and Stick."
(The relative sizes of the ions in these ionic crystal structures are not
exactly correct, but they are close. Raswin
does not "do" ions so we have had to improvise by selecting
neutral atoms whose relative sizes are approximately correct.)
NaCl is an ionic
crystal. It consists of a regular cubic array of alternating sodium and
chloride ions. The chlorine ions are larger than the sodium ions. This
is a "six-coordinate" crystal because each ion is surrounded by six ions
of the opposite charge. The six-coordination is easier to see in the
version of this model.
CsCl is an eight-coordinate
crystal because each ion is surrounded by eight ions of the opposite charge.
Compare this crystal to the NaCl structure. The eight coordination is hard to see
on this model. It is easier to see in the small CsCl
ZnS is an example
of a four-coordinate crystal. Since the charges on the zinc ions and the
sulfide ions are +2 and -2, respectively, there is one zinc ion for each
sulfide ion. Nevertheless, the ions still pack in such a way that each ion
has four nearest neighbor ions of opposite charge. The coordination is easier
to see in a smaller
fragment of this crystal.
the mineral flourite. It is an example of an ionic crystal in which one ion, the calcium ion, has
two positive charges and the negative ion, the fluoride ion, has only one negative charge. In order
for the crystal to be electrically neutral there must be twice as many
fluoride ions as calcium ions. There is no way a simple cubic arrangement
of ions could satisfy this condition. However, in one view this crystal
appears cubic. See if you can find that view. (It's easier to see the
relative arrangement of the ions in a
fragment of the crystal. In this one you can see that each calcium ion is surrounded
by eight fluoride ions.)
Diamond is a
molecular crystal in which each carbon is bound to four nearest neighbor carbon
atoms. (The crystal is really one giant molecule!) The bonds around each
carbon atom are tetrahedrally arranged. This
structure will show up in the "Wire frame" mode in RasMol, but is probably
best viewed in "Sticks" mode. If you rotate the
model around you will see a number of interesting structures. The
actual bonding is somewhat easier to see in a smaller
fragment of this crystal. Looking at the crystal in the space fill mode
should convince you that the crystal is not mostly empty space.
Graphite is another (allotropic) form
of carbon. Planes of hexagonally bonded carbon atoms are stacked on top
of each other with adjacent planes slightly offset from each other.
The bonding within a plane is covalent, but the bonding
between planes is much weaker - which is why graphite has a slippery feel
and is sometimes used as a lubricant. There is also a
small version of the graphite crystal.
These structures are easiest to comprehend by viewing them
in "Sticks" mode.
Last updated 27 Jan 1998
W. R. Salzman
Department of Chemistry
University of Arizona, Tucson