Helical Structures

Helical or coiled structures are very common in many biological materials, such as proteins and nucleic acids.  Here is the protein myoglobin - the left structure is the wireframe chemical structure, while on the right is the structure in cartoon display showing the backbone (side chains removed).  Can you find the helical parts of myoglobin?

                   

Now it is a little complicated to deal with a protein at this stage, so let's examine some simpler molecules.  Compare and contrast the two relatively straight chain structures given below.  Decane is C10H24, while the peptide is a short chain of four glycine molecules.  Long chains of a variety of different amino acids are what form proteins.

            decane, a hydrocarbon chain            peptide, an amino acid chain of glycine

                   

Make a list of similarities and differences.

Now compare the helical or coiled structures of the same two substances.  You may want to change the display to "stick" to help view the helix composed of carbon atoms in decane and carbon and nitrogen in the peptide.

helical decane                                  helical peptide

                   

Chains of amino acids are common in the form of a helix, while hydrocarbons do not exist in the helical form.  Explain this observation based on intramolecular interactions.

Here is an unusual structure of fused benzene rings, the six-member planar carbon ring compound (C6H6).  Look at the two structures of octahelicene given below displayed in the tube mode for ease of viewing.  How would you describe octahelicene's structure?

What is the difference in them?

         

Source of animated molecule - http://www.cmbi.kun.nl/~borkent/ohrac.html

Peptides can be helical or straight chains, does the octahelicene molecule have a choice?  Explain why or why not.

Right click on the octahelicene image on the left above, select animation, and observe what happens to the molecule.  The two images show a clockwise and counterclockwise helical molecule!  The animation shows the molecule converting from one to the other.  These two molecules are optical isomers or mirror images of each other.  Isn't molecular motion grand!

Let's examine whether the helical nature of helicences is voluntary or forced due to intramolecular interactions.  Given below are the structures of phenanthrene ("trihelicene") and tetrahelicene.  

         

phenanthrene                             tetrahelicene

What do you notice about them?  

Measure some hydrogen-to-hydrogen distances (these are non-bonded distances) in both molecules.   Why is tetrahelicene helical and phenanthrene flat?

 

Back to the CHM 103 webpage.

Some structures generated using Spartan '02 and AM1 minimization calculations.

Scott A. Sinex        Department of Physical Sciences         Prince George's Community College            3/2002