Exploring Our Fluid Earth

Chemistry can be a difficult subject to understand, partly because the structure and shape of atoms and molecules can be hard to imagine. Over time the way in which molecules are modeled has changed. Each molecular representation has advantages and disadvantages, but each contributes to scientists’ ability to understand chemistry. SF Table 2.2 shows four different models used for showing the molecule for butane (C₄H₁₀).

Lewis dot structures are two-dimensional representations of molecules that illustrate each atom as its chemical symbol. Lines indicate bonds to other atoms, and non-bonding electrons are represented as small dots next to the chemical symbols.

Bond-line notation shows selected atoms as their chemical symbols while depicting some carbon atoms as corners between lines and omitting hydrogen atoms that are assumed to be in the structure. Bond-line notation is predominantly used in organic chemistry (chemistry associated with living things).

Ball and stick models are three-dimensional models where atoms are represented by spheres of different colors and bonds are represented by sticks between the spheres. Particular atoms are associated with different colors, for example, black is usually used to represent carbon and white to represent hydrogen.

Space fill models are similar to ball and stick models in that they are three-dimensional models that represent atoms as colored spheres. The difference between them is that instead of sticks representing bonds, as in the ball and stick model, the spheres that represent atoms are fused together and the size of the sphere represents the size of the actual atom.

SF Table 2.2. Four common molecular models of butane (C₄H₁₀)

Model	Representation	Advantages	Disadvantages
Lewis Dot	Image Image copyright and source Image courtesy of Benjah-bmm27 from Wikipedia	Shows bonding and non-bonding electrons.	Larger molecules can become crowded and confusing.
Bond-Line Notation	Image Image copyright and source Image created by Jmol: an open-source Java viewer for chemical structure in 3D.	Simplifies large structures to highlight important atoms, bonds, and groups.	Atoms can sometimes be forgotten in structures when assumed to be there.
Ball and Stick	Image Image copyright and source Image created by Jmol: an open-source Java viewer for chemical structure in 3D.	Shows three-dimensional arrangement of atoms and bonds.	Identification of atoms requires a key of color representations.
Space Fill	Image Image copyright and source Image created by Jmol: an open-source Java viewer for chemical structure in 3D.	Shows three-dimensional arrangement as well as size relationships between atoms.	Bonding between atoms can sometimes be difficult to distinguish.

These four models represent some of the most common models used to represent molecules, but they are not the only models used by scientists. Some models are highly specialized and are used by certain types of scientists. For example, biochemists and biologists use a modeling system called ribbon protein modeling to represent large and complex molecules called proteins.