Organic Functional Groups Jmols

Organic Functional Groups



This tutorial focuses on organic functional groups found on biochemical and organic molecules. It will also include the types of intermolecular forces that these organic molecules have. These functional groups are what give the molecules their unique characteristics and determine some types of reactions that they undergo.

This first section is a review of electronegativity and polarity, two concepts that are essential when determining properties of functional groups.

All the small molecules used in this tutorial have had their structures determined using X-ray crystallography or diffraction. These structures are deposited in the Cambridge Structural Database (CSD) for use by researchers, educators and students. The CSD accession numbers are provided for each small molecule in this tutorial, in case you want to explore the molecules further.

Throughout the tutorial, clicking on the buttons will launch a Jmol image of the small molecule on the screen at the right. You must have Java installed on your computer to see these images. You may access a free Java download here. Note that in some operating systems and/or web browsers, you may have to click a button to allow Java to run on the web page.

Once a molecule appears in the Jmol window, wait until the image stops flashing before pushing a button to execute another script. You may spin the protein (left mouse button click and drag), or, if you wish, you may use Jmol commands to explore the molecule further. A Jmol Quick Reference Sheet and Jmol Training Guide are available if you want to play with the images. (WARNING: This can be a lot of fun!)

If you hover over an atom in Jmol, a popup window will identify the atom in the format:

[UNK].1 C1 #4


[UNK].1 is the code of the small molecule. [UNK].1 stands for "unknown". Because these small molecules are originally saved in format different than .pdb, the name of the molecule is changed in the transfer process.

C1 is the type of atom.

#4 identifies the atom number in the pdb file.

As you work through the tutorial, an icon Pencil will remind you to answer questions on your worksheet.

The most common elements in living things are listed below. Complete the table.

OFG Table 1


The most electronegative atoms are at the upper right hand side of the Periodic Table. electronegativity

Electronegativity is a measure of how tightly an element holds its electrons (and how much they pull on other atoms' electrons). The more tightly the valence electrons are held the more electronegative the element (atom). An electronegative atom can also remove electrons from other atoms. Fluorine is the most electronegative atom. Oxygen and nitrogen are also electronegative. In biochemistry and organic chemistry we focus on oxygen and nitrogen because fluorine is not commonly found.

PencilGo back to the previous table and choose which of the elements is most electronegative.

Polar and Nonpolar

Polar molecules have electronegative atoms. These atoms "pull" the electrons in the covalent bond closer to themselves, resulting in a partial negative charge on those atoms. The atoms on the other side of the bond have a slightly positive charge, as electrons are further away. In water molecules, hydrogen has a partial positive change and oxygen has a partial negative charge due to their differences in electronegativity. Notice that ethane is nonpolar because the carbon and hydrogen have similar electronegativities.


In covalent molecules when one of the atoms is more electronegative than the other(s), the molecule is termed "polar". This describes the fact that the electrons spend more time around one element than the other(s).

pencilIn each compound below, circle the electronegative elements and write polar or nonpolar next to each.

OFG Table 2

Intermolecular Forces

Intermolecular forces are noncovalent and non-ionic attractions between molecules. These forces are responsible for the structure of your DNA and proteins along with boiling points and melting points of all compounds. When these forces are weak, for example, the melting and boiling points are low. When the forces are strong, the melting and boiling points are high. There are three intermolecular forces that we will be studying this semester: hydrogen bonds, dipole-dipole interactions, and (London dispersion forces or induced dipole-induced dipole forces). The last one has multiple names; they are not all exactly the same, but are often used interchangeably. (The term van der Waals is used as a blanket term for these forces in biology, but in chemistry we will be more correct).

London Dispersion Forces or Induced Dipole-Induced Dipole Forces

The London dispersion or induced dipole-induced dipole forces occur in all molecules and are very weak (the weakest of all the intermolecular forces). They are the ONLY ones that occur between nonpolar molecules. They occur between ALL atoms and molecules – ALWAYS. They occur when the electrons in one of the molecules, for an instant, are around one of the elements more than another and are attracted to another element in another molecule that is the same. Below is an example.

London Dispersion

pencilAre these molecules polar or nonpolar?

pencilWould both polar and nonpolar molecules have London dispersion, induced dipole-induced dipole forces or not?

Dipole-Dipole Forces

Polar molecules always have London dispersion forces (induced dipole-induced dipole forces) AND can have dipole-dipole forces or attractions occur. These happen when the positively charged end of one molecule is attracted to the negative end of another molecule. These are stronger than the induced dipole-induced dipole (London dispersion forces). (H is not involved in dipole-dipole interactions). Remember that the δ (delta) symbol is used to designate partial charge. Below is an example.


pencilAre these molecules polar or nonpolar?

pencilWould London dispersion or induced dipole-induced dipole forces also occur? If so why?

Hydrogen Bonding

Hydrogen bonds are very common and important in all living things. They are a special type of dipole-dipole attractions -- BUT don't occur in all polar molecules. Molecules that Hydrogen bond also have induced dipole-induced dipole (London dispersion forces).

In order for hydrogen bonds to occur, there must be a hydrogen directly attached to an electronegative atom (O, N, halogens). This hydrogen would then hydrogen bond with another electronegative atom (often O or N in living things). They are stronger than either of the other two attractions and are designated with a series of dashed or dotted lines.

Below are examples:

hbond example

pencilAre these molecules polar or nonpolar?

pencilWould London dispersion or induced dipole-induced dipole forces also occur? If so why?

In the following molecules circle any polar hydrogens.

hbond practice 1

In the following molecules draw any hydrogen bonds that could form.

hbond practice 2


In the following molecules, label the intermolecular attractions: dipole-dipole, hydrogen bonds, and London dispersion or induced dipole-induced dipole.


hbond question 1


hbond question 2


hbond question 3


hbond question 4









3-dimensional Jmol Display