organic molecules

Experiment 1: Molecular Models Modeling the shape of small organic molecules

Previously we have considered molecules and ions for which one chemical formula corresponded to one chemical compound only. Not all chemical compounds are like that. For example, consider the formula C2H6O. It turns out that there is more than one compound with that chemical formula:


Ethanol Dimethyl ether

These two molecules have completely different chemical and physical properties. They are called structural isomers. They have the same chemical formula with different bonding between atoms. Another example would be the compounds that correspond to butane, with the chemical formula C4H10. There are two structural isomers of butane.


1. Explain why the two structures above are NOT considered structural isomers.

2. Construct two structural isomers of C4H10. Draw them below using expanded structural or line formulas. When you are finished, compare them with the results of other students.

Geometric Isomerism:

An example of a different kind of isomerism occurs when the molecules have the same bonding between the atoms but their arrangement in space is different. We say that these compounds are geometric isomers. A classic example involves molecules that contain double bonds.


Circle the structure named cis-2-butene. The double bond between the carbon atoms does not allow the free rotation of the methyl (CH3) groups with respect to one another, preventing the interconversion between the trans and cis isomers. Geometric isomers have different physical properties but almost identical chemical properties

3. What do you think is the meaning of the prefix “cis-” vs “trans-”?

Here’s another example of geometric isomers.

Construct cyclopentane, C5H10, which does not contain any double bonds.


(the blue lines show these atoms are on the other side of the ring)

Replace one of the hydrogens with chlorine to obtain trans-1,3dichloropcyclopentane (as in the drawing below). Build the trans-isomer of this molecule (based on what you learned above) and draw your structure in the empty box.

There is no free rotation around the C-C bonds that connect the carbons where the chlorine atoms are bound because of the rigidity of the cyclopentane molecule. Therefore, there is no interconversion between the cis and trans forms.

Thus, cis- and trans- prefixes refer to geometrical isomers!

We have briefly introduced the concepts of structural and geometric isomers. There is yet a third type of isomerism that we will leave out of this discussion: it is the so-called optical isomerism that will be covered in the organic chemistry courses.

Follow-up Questions

1. In the first few pages you learned about structural isomers and geometric isomers. Define these terms below:

Structural isomer


Geometric isomer


2. Identify whether the following pairs of compounds are structural isomers, geometric isomers, or identical molecules.



b. (CH3)2CHCH2CH3 CH3(CH2)3CH3



3. Convert the following into an expanded structural formula:

a) (CH3)2CHCH2CH3 b) CH3CH(OH)CH2CH3 c) Br(CH2)3CH3

In organic chemistry, functional groups are specific substituents or moieties within molecules that are responsible for the characteristic chemical reactions of those molecules. The same functional group will undergo the same or similar chemical reaction(s) regardless of the size of the molecule it is a part of.[1] HYPERLINK “” \l “cite_note-2” [2] This allows for systematic prediction of chemical reactions and behavior of chemical compounds and design of chemical syntheses. Furthermore, the reactivity of a functional group can be modified by other functional groups nearby. In organic synthesisfunctional group interconversion is one of the basic types of transformations.

Functional groups are groups of one or more atoms of distinctive chemical properties no matter what they are attached to. The atoms of functional groups are linked to each other and to the rest of the molecule by covalent bonds. For repeating units of polymers, functional groups attach to their nonpolar core of carbon atoms and thus add chemical character to carbon chains. Functional groups can also be charged, e.g. in carboxylate salts (–COO−), which turns the molecule into a polyatomic ion or a complex ion. Functional groups binding to a central atom in a coordination complex are called  ligands Complexation and solvation are also caused by specific interactions of functional groups. In the common rule of thumb “like dissolves like”, it is the shared or mutually well-interacting functional groups which give rise to solubility. For example, sugar dissolves in water because both share the hydroxyl functional group (–OH) and hydroxyls interact strongly with each other. Plus, when functional groups are more electronegative than atoms they attach to, the functional groups will become polar, and the otherwise nonpolar molecules containing these functional groups become polar and so become soluble in some aqueous environment.1,2

4. Identify the functional groups in the following structures.1




















Hydrocarbons are a class of molecule that is defined by functional groups called hydrocarbyls that contain only carbon and hydrogen, but vary in the number and order of double bonds. Each one differs in type (and scope) of reactivity.2,3

5. Draw the structures for the following hydrocarbons.

 a. 3-methylpentane

b. 3-hexene

c. 4-methyl-1-pentene

d. 3-heptyne

e. 4-methyl-2-pentyne

6. Give the complete name for each of the following compounds.


a. ____________________________


b.  ______________________________

c. CH3CH2CH=CHCH3 __________________________________________________



e. (CH3)3CCl _____________________________________

1. 2. 3.

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