Molecular Representations and
Tables of Common Polyatomic Ions
Graphical computer modeling has greatly improved our ability to represent three-dimensional structures. One of the goals of graphical computer modeling is to create a computer-generated model that appears to be three-dimensional. By replicating the effect of light on three-dimensional objects, computers can give the impression of depth to simulate a three-dimensional appearance. The use of interactive molecular viewing ( e.g., using the Jmol program) has enhanced our understanding of molecular structure, especially in the biochemical area. By interactively rotating the molecules, a clear picture of the three-dimensional structure emerges. In addition, this increases our chemical intuition because it teaches us to look at two-dimensional images and visualize their three-dimensional structure in our brains.
This course uses different types of structural representations, such as 2D-ChemDraw, stick, CPK, and ribbon, to illustrate the structure of molecules and macromolecules. PDB files are also available for viewing the molecules interactively. Figure 1 is a segment of an alpha helix polypeptide string shown in four different types of computer-generated molecular representations. Although all four representations depict the same molecule, each has a distinct appearance and offers different information about the molecule’s structure.
By examining the four representations in Figure 1, you can see that each picture tells us something different about the structure of the molecule. For instance, if we wanted to know how the atoms in an alpha helix are connected to one another, we would use 2D-ChemDraw or stick representation. To see the relative sizes of the atoms in an alpha helix, we would use the CPK representation. Descriptions of the four types of representations, their major strengths, and their drawbacks are given in the table below.
Tables of Common Polyatomic Ions
The tables below list common polyatomic ions that you will be using throughout this General-Chemistry laboratory series (Chem 151-152). These ions are separated by charge on the ion into four (4) different tables and listed alphabetically within each table. For each polyatomic ion, the name, chemical formula, two-dimensional drawing, and three-dimensional representation are given.
The three-dimensional structures are drawn as CPK models. CPK structures represent the atoms as spheres, where the radius of the sphere is equal to the Van der Waals radius of the atom; these structures give an approximate volume of the polyatomic ion. In these tables, the three-dimensional structures have all been drawn to the same scale; therefore you can compare their relative sizes. In addition, the atoms in the CPK structures have been color-coded to match the two-dimensional drawings for easier comparison. Table 5 explores molecular representations that are commonly seen in biological and chemical fields. To view the ions interactively, please use Jmol. For viewing and rotating the ions listed in the tables below, please click on the appropriate three-dimensional structure.
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© 2011, Washington University.
Materials and Information present may be reproduced for educational purposes only.
Revised: 7/11/2011 (G Noelken)