Stereochemistry
Stereochemistry is the relative spatial arrangement of the atoms within the molecule. The real molecule is 3-dimensional and this can be extremely important in its chemistry (and hence biochemistry and medicinal chemistry). The 'wedged' and 'dashed' bonds are used to represent this by indicating bonds that are coming out of and going out of the paper respectively.
Stereochemistry
Stereochemistry is the relative spatial arrangement of the atoms within the molecule. The real molecule is 3-dimensional and this can be extremely important in its chemistry (and hence biochemistry and medicinal chemistry). The 'wedged' and 'dashed' bonds are used to represent this by indicating bonds that are coming out of and going out of the paper respectively.
The alcohol which some people drink is called ethanol and has the molecular formula C2H6O. Its actual structure can be represented in a number of different ways, each of which has a particular level of sophistication and usefulness.
Use the mouse to rotate the structure and the buttons below to change the model
Ethanol is a very simple molecule, but as soon as any complexity is introduced, it is very difficult to comprehend a molecule's structure if all the H atoms are included. So in practice, the stick representation is always used for all but the simplest molecules.
In a stick structure:
Lines represent bonds - 1, 2 or 3 lines for single, double or triple bonds respectively.
Carbon atoms are not shown - they are assumed to be at intersections and ends of lines (bonds).
C–H bonds are omitted - the number of hydrogens bonded to each carbon can be calculated, as carbon always has a valence of 4.
All heteroatoms are shown and so are the hydrogens bonded to them.
When drawing neutral molecules:
C always has valence of 4 (4 bonds, 0 lone pairs)
N always has valence of 3 (3 bonds, 1 lone pair)
O always has valence of 2 (2 bonds, 2 lone pairs)
F, Cl, Br, I always have valence of 1 (1 bond, 3 lone pairs).
The bond angles around carbons, nitrogens and oxygens are usually drawn as 120° or 90°, though the actual bond angle is closer to 109.5° unless double or triple bonds are involved. Otherwise, bond angles are drawn to be as realistic as possible.
Some aspects of stereochemistry may be shown if relevant to the discussion at hand.
Roll the mouse over the molecule below, vitamin A, to change between the full and stick structures. Even for this relatively simple molecule, isn't the stick structure much tidier and comprehensible?
Use the mouse to rotate the structure and the buttons below to change the model
Click on the atoms in the tool below to further practice switching between the different representations used in organic chemistry, and then proceed to the next section using the link below.
