Geometry for Large/Organic Molecules

[noob3n]

Hi all,

 

firstly I should say that I am not a chemistry student and I have virtually no education in chemistry. However I am a Computer Science student and I decided to build software for an assignment that would take a bunch of elements from the periodic table, and connect/bond them together in the correct geometrical form using Lewis Structures and VSEPR.

 

So far my software correctly predicts the geometry of any simple molecule and displays it in 3D. But when looking into creating larger moleculular structures using the rules for Lewis Structures I cannot find any reasoning as to why they are connected the way they are and thus cannot predict the molecular geometry.

 

As an example take Tyrosine, there is no 'central atom' and therefore no way to bond the elements together using Lewis Structure rules. And VSEPR theory can only deal with terminal atoms bonded to a central atom.

 

The formula for Tyrosine is : C20 H32 F2 O5

 

Can somebody please tell me what steps I could take to try to predict the structure of Tyrosine or some other arbitrary compound/molecule using only the formula? Is it even possible? Please try to keep the answer simple or point me to some good reading because as I said, I am not a chemistry student.

 

I really appreciate the help, this has been driving me nuts.

 

James

[John Cuthber]

I'm not sure if you will be pleased to hear this but the reason you are having problems is that the question is impossible.

 

Tyrosine is quite complicated so I will try to illustrate the point with something simple.

Alcohol has 2 carbons, an oxygen and 6 hydrogens in it.

If you connect two of the carbons together then hang the oxygen on one of them and fill up all the leftover bonds with hydrogens you will get the structure of alcohol.

But if you start with the oxygen atom and put a carbon on each side of it, then (as before) fill up the rest of the molecule with hydrogens you get dimethyl ether

 

CH3 CH2 O H

 

vs

 

CH3 O CH3

 

Since there are two perfectly reasonable compounds made from the same collection of atoms it would be impossible for your program to "know" which one to generate.

 

In general these molecules with the same molecular formula, but different structures are called isomers.

There are often a lot of them for any given formula.

 

Incidentally, you have completely the wrong formula for tyrosine

http://en.wikipedia.org/wiki/Tyrosine