Chemists use models to envision molecules, to explore complex systems and to predict chemical reactions.
The whole idea of modeling is to get a sense of how something should look, such as an architect building a small scale model of a future building, or how something works, such as flying a model airplane. Chemists use models for both purposes.
Because chemists frequently deal with phenomena that are too small to be viewed even with a microscope, they rely on models to help envision how molecules and atoms look. At the first level, models represent different characteristics of molecules. A simple formula such as CH4 to a young scientist does not invoke a picture of a molecule, so a ball and stick model is used to illustrate the three-dimensional skeleton of the molecule, and a space filling model helps the young scientist understand that in a molecule, the electron clouds of atoms actually overlap, rather than bonds being sticks holding two balls at a distance. Each model can be chosen to optimize the visualization of a particular principle.
Chemists also use models to explore how systems work, especially when dealing with large molecules such as proteins or DNA fragments, which are challenging to isolate, purify, and structurally characterize. In these cases, chemists may try to synthesize “model compounds” to display the significant structural and chemical properties of the macromolecule. For example, the active site in hemoglobin, the oxygen transport protein found in red blood cells, is the iron-containing heme. Exploring iron complexes with porphyrins, which are similar to the heme, allows chemists to envision possible reaction paths without the complexity of the surrounding protein.
Scientists also use molecular models as aids in theoretical and computational methods. Models help scientists understand the behavior of molecules by focusing on the behavior of individual atoms or groups of atoms. One such application is in the pharmaceutical field where the known X-ray crystal structure of a protein can be used to explore interactions with potential drugs. Molecular simulations can be used to “dock” candidate drug molecules with the target active site of a macromolecule to see if spatial and electronic interactions are favorable, suggesting that a certain drug might be used to produce a particular effect.
Between exploring how molecules look and how molecules work, modeling in its many forms is a powerful tool across the field of chemistry and beyond.
The Center for Molecular Modeling at the National Institutes of Health explores many applications of modeling at http://cmm.cit.nih.gov/
This topic was suggested by Laura Slocum of University High School of Indiana in Carmel, Ind.