Molecules in 3D

A. Molecular Models

Atoms and molecules are so small that we are unable to see them with our naked eyes. To view the three-dimensional structures of molecules we use models. Molecular models generated by computer programs or physical models rely on accurate data derived from experiments on bond lengths, bond angles and atomic radii. To distinguish atoms colors have been assigned. (Take a quick look at the colors. Keep the web page open for future reference.)

Different molecular models emphasize certain features of three dimensional arrangement. For example, the ball-and-stick model helps visualize accurate bond angles. Figure A below shows the ball-and-stick model of the hydrogen molecule. The hydrogen atoms, shown in white, are connected to each other by a short piece of plastic which represents the bond between the two atoms. Figure B shows the same ball-and-stick model for water. As you can see the oxygen atom in the center is connected to two hydrogen atoms. The angle between the two hydrogen atoms is accurate.

Figure A Figure B

Identify each of the following diatomic molecules. Write their names and chemical formulas on your data sheet.

Notice that these molecules are shown in spacefill model. It shows atom sizes in the molecule. This type of model gives us an idea of molecular size.

B. Molecular Shapes

Atoms arrange themselves in three-dimensional aggregates with specific molecular shapes. Factors which influence the shape of a molecule are: the number of bonds, non-bonding electrons, atomic radii, bond length among others. The first two factors are the result of electron-electron repulsion. Bonds are made up of two electrons. If a molecule has 3 atoms it is likely that the bonds between the atoms be as far apart as possible, thus reducing repulsion.

Let's consider an example. The water molecule has 3 atoms. From its Lewis dot structure (shown left) notice that there are two bonds and two pairs of non-bonding electrons (electrons not used in bonding). These non-bonding electrons in addition to occupying space they repel other non-bonding and bonding electrons. (What would the shape of the water molecule be if it did not have non-bonding electrons? Move your mouse over the figure to find out.) The end result is that the molecule's shape is bent.

There are some other molecular shapes shown below. On your data sheet write the chemical formula, the name and the molecular shape of each.

Linear Bent Trigonal Planar

Trigonal Pyramidal Tetrahedral


On your data sheet write the chemical formulas, names and molecular shapes of the molecules listed below.

C. Alkanes

Compounds made solely of carbon and hydrogen in a chain with all single bonds are called alkanes. Below are the three-dimensional shapes of the first eight alkanes.


D. Other Molecules

There are some other molecules which we will encounter in the course. It is a good idea to get acquainted with their shapes. On your data sheet draw their chemical structures (do not forget double bonds) along with their names.

Benzene Ethene or Ethylene

Methylamine Acetic acid or Ethanoic acid


Stanitski, C.L., Eubanks, L.P., Middlecamp, C.H. and Stratton, W.J. Chemistry in Context Applying Chemistry to Society American Chemical Society, 2006.