HYPERCHEM 6.0 Exercise:
Using molecular modeling to visualize the 3-D shape of molecules is extremely powerful. In this exercise, you
will use Hyperchem 7.5 to visualize the H-bonds holding together some important biological molecules.
Hyperchem also indicates hydrogen bonding. In this assignment, you may build a small protein (Polyglycine)
and take a look at how hydrogen bonds help determine the shape of this large molecule.
First answer the following questions:
O
1
2
H2N
CH
C
OH
3
4
This is glycine, the world’s simplest amino acid. Amino acids are the building blocks
(monomer units) of proteins. Glycine has the potential to form H-bonds:
H
1. Draw the structure of glycine & clearly indicate the H’s on glycine that can
H-bond.
2. On your glycine structure, clearly indicate the atoms on glycine that also
participate in H bonds
(circle all correct ones) N C O
3. Which of the following are H-bonds (Covalent bonds are represented by -; H
bonds by ---) (Circle all correct ones )
A.
B.
C.
D.
E.
F.
N-H --- O
O-H --- N
C-H --- O
C-H --- N
O-H --- O
N-H ---C
This is 5 glycines polymerized together:
3
1
O
H2N
4
2
CH
H
C
N
CH
H
H
O
H
C
N
O
CH
H
C
N
CH
H
H
5
O
H
C
N
O
CH
C
OH
H
This is a long, flexible chain, and intramolecular H-bonding is possible. The dotted line indicates one such
possible H-bond, between O one glycine 1 and N-H on glycine 5.
4. Draw pentaglycine and clearly draw another possible intramolecular H bond.
Now use Hyperchem, which is available on the computers in SCIENCE 211, to visualize what a polyglycine
made up of 10 glycime monomers looks like, and what intramolecular H-bonds contribute to its shape:
Click on Start
Click on Programs
Click on Course applications
Click on Hyperchem 7.5
Click on Hyperchem 7.5 Professional edition
Click on File
Click on New
Click on Databases
To make a Polyglycine:
Click on Amino Acids
In the Conformation box, click on -helix.
For clarity, work with a simple amino acid, eg glycine H2N-CH2-COOH.1
Click the gly tab 1 times.
Click the blue bar on the dialog box to move it out of the way& look at your monomer (Greek for 1 thing, 1
amino acid).
Note that H is white, O is red, N is blue and C is cyan.
(You can change that by clicking on display and then element color)
Click on Display
Click on Rendering
Click on Balls and cylinders
Click OK
Click on Display
Click on show Hydrogen bonds if there is no check ( ) by it.
Click on Recompute Hydrogen bonds. H bonds show up as white dotted lines.
5.  See any H bonds in 1 glycine? If not:
Click the gly tab again, and, and see what happens. Two monomers have liked together and made a dimer
(Greek for “two things”). The dimer is H2N-CH2-CO-NH-CH2-COOH. Click on Recompute Hydrogen
bonds. H bonds show up as white dotted lines.
6.  See any H bonds in 2 glycines? If not:
Click the gly tab once more times and make a trimer (Greek for “three things”).
Keep adding gly until you finally see H-bands. Remember to click on Recompute Hydrogen bonds every
time you add a gly.
7.  How many glycines do you need to finally get an H-bond?
Keep adding gly until you have a polymer of 10 glycines.
Note the SHAPE of the molecule. To make this easier to see, click on display and then element color. Click
on carbon and red, Nitrogen and red, oxygen and black, and hydrogen and black.) Now describe your
protein’s shape. Now , click on display and then element color, and then revert to get the original colors back.
To visualize H-bonds holding the molecule in its shape:
Click on Display
Click on show Hydrogen bonds if there is no check ( ) by it.
Click on Recompute Hydrogen bonds.
To rotate the molecule around, click on the 3rd box from the left.
Rotate the molecule in all directions,
See where the H-bonds are holding it
together. Especially, rotate the
molecule so that it is end on
8. Clearly describe the shape of
the molecule.
1
polyglycine actually has been shown to fold into a type II left-handed helix if left to its own devises.
FOR EXTRA CREDIT, IF YOU WANT YOU CAN DO THE SAME THING WITH A PIECE OF DNA:
Click on Nucleic Acids
In the Conformation box, click on B-form and double stranded.
For clarity, work with just adenine and thymine (AT) base pairs..
Click the dA tab 1 time. Hyperchem will automatically add the complementary dT.
Click the blue bar on the dialog box to move it out of the way & look at your monomer (Greek for 1 thing, 1
base pair).
Note that H is white, O is red, N is blue and C is cyan.
(You can change that by clicking on display and then element color)
Click on Display
Click on Rendering
Click on Balls and cylinders
Click OK
Click on Display
Click on show Hydrogen bonds if there is no check ( ) by it.
Click on Recompute Hydrogen bonds.
Locate the H bonds holding the dA and dT together (They are white dotted lines).
Click the gly tab again, and, and see what happens. Two monomers have liked together and made a dimer
(Greek for “two things”). The dimer is H2N-CH2-CO-NH-CH2-COOH. Click the gly tab again 8 more times
and make a polymer (Greek for “Many things”). Note the SHAPE of the molecule. To make this easier to see,
click on display and then element color. Click on carbon and red, Nitrogen and red, oxygen and black, and
hydrogen and black.) Now describe your protein’s shape. Now , click on display and then element color, and
then revert to get the original colors back.
Click the dA tab 10 times. This will generate 10 AT base pairs
Click the x in the upper right corner of the dialog box to close it, and see your DNA starnd.
Note that H is white, O is red, N is blue and C is aqua.
(You can change that by clicking on display and then element color)
Click on Display
Click on Rendering
Click on Balls and cylinders
Click OK
Note that H is white, O is red, N is blue and C is cyan.
(You can change that by clicking on display and then element color)
To visualize H-bonds holding the molecule in its helical shape:
Click on Display
Click on show Hydrogen bonds if there is no check ( ) by it.
Click on Recompute Hydrogen bonds.
To rotate the molecule around, click on the 3rd box from the left.
Rotate the molecule in all directions, See
where the H-bonds are holding it
together. Especially, rotate the molecule
so that it is end on.
 9. Clearly describe the shape of the
molecule