Every atom can be represented by a
symbol. These symbols are usually the first letter in the name. For example, the symbol
for hydrogen is H, the symbol for carbon is C, the symbol for oxygen is O, the symbol for
nitrogen is N, and the symbol for sulfur is S.
Using symbols, a molecule of water is represented by H2O
where the subscript indicates that there are two hydrogen atoms in every water molecule.
Figures 6.1A and 6.1B show how chemicals can be represented by names, symbols, balls and
sticks, and spheres. The lines connecting the atoms are chemical bonds. Chemical bonds are
the glue that hold molecules together.
In figure 6.1A, three chemicals are represented, oxygen, water and
methane. The chemical formulas for each are O2, H2O and CH4.
The ball and stick models make it easy to see what chemical looks like, but the ball and
stick models do not show the electron orbitals. Atoms are really much bigger as shown in
the space filling models of figure 6.1A.
The book will also generate many images using a molecular visualization
tool called Rasmol. The images of chemicals are more accurate with this tool. Figure 6.1B
shows the amino acid, valine. Because the atoms are no longer labeled, the color must be
used as an indication of atom type. In figure 6.1B, black is oxygen, white is hydrogen,
light gray is carbon, and dark gray is nitrogen. Rasmol can generate a space fill image, a
ball and stick image, and a stick image as shown in figure 6.1B. Rasmol also allows the
image to be rotated by the user. While the space fill model in figure 6.1B is the only
accurate representation of valine, it is too difficult to see how the atoms are connected
using this model. So the stick and ball and stick are often preferred. In complex
molecules, the cartoon view generated by Rasmol is often preferable (figures 3.13 and
3.14).
Figure 6.1A: Ball and Stick and Space Filling Model
Figure 6.1B: Rasmol Images of Valine
next: chemical bonds
home: Intelligent Design and the origin of life
|
