Formulas, Structures and Projections
There are different ways to represent molecules. The best method to use depends on the situation. In this article we will shortly describe the most commonly used ways.
Chemical formula
The most basic representation of a molecule is the so-called chemical formula (or molecular formula). This is simply a listing of all chemical symbols and their amounts. Water is for example H2O (two hydrogens and one oxygen), methane is CH4 (one carbon and four hydrogens) and (S)-alanine is C3H7NO2 (three carbons, seven hydrogens, one nitrogen and two oxygens). Typically for chemical formulas is that the symbols for carbon and hydrogen are put in front, followed by the remainders in alphabetical order.
One disadvantage of chemical formulas is that they don't say anything about the 3D-structure of the molecule.
Lewis structure
A lewis structure displays every atom, every bond, every lone pair and their positions relative to each other. Bonds are indicated using lines where double and triple bonds are represented by two and three stacked lines respectively. Lone pairs of electrons are represented as dots. See for example the lewis structure of water below, where the hydrogen atoms are connected to the central oxygen atom through single bonds. The central oxygen atom has two lone pairs of electrons.
Lewis structure of water, or H2O. Image from Wikipedia.
Make sure that all atoms of the lewis structure comply with the octet rule. It states that every atom must be surrounded by eight valence electrons (see previous lesson), except for hydrogen that must be surrounded by two. This can simply be checked by adding the amount of lone pair electrons to the amount of shared electrons. In the water example, oxygen has four free electrons (two lone pairs) and four shared electrons (two single bonds), making eight in total.
Formal charge
Once all atoms and bonds are in position, the next step is to determine the formal charge of every atom in the structure. The formal charge of an atom is the difference between the amount of valence electrons of the unbound atom and the amount of bound electrons, which can be represented as a formula as follows:
Formal charge = Valence electrons - (free electrons + ½ × bound electrons)
Lewis structure of oxonium (protonated water), or H3O+. Image from Wikipedia.
Let's calculate the formal charge of the central oxygen atom in oxonium. Note that in the image above the single bonds between oxygen and hydrogen are drawn in a way to bring attention to the 3-dimensional structure.
- Unbound oxygen has six valence electrons
- The oxygen atom has one lone pair (two electrons)
- The oxygen atom has three single bonds (six shared electrons)
- The formal charge = 6 - (2 + ½ × 6) = +1 (see formula above)
Kekulé structure
A kekulé structure (named after the chemist August Kekulé) is a simplified variant of a lewis structure where lone pairs are left out as much as possible.
Original drawing of the structure of benzene by Kekulé. Image from Wikipedia.
Skeletal formula
The skeletal formula (also known as line-angle formula or bond-line formula) is a futher simplified representation of a molecular structure that is commonly used in organic chemistry. In a skeletal formula, sequential carbon atoms are reduced to a single line where each angle represents a carbon atom. Hydrogens and lone pairs are left out unless they are used to bring attention to a specific group or situation.
Skeletal formula of (S)-citalopram. Image from Wikipedia.
Condensed structure
A condensed structure is an extremely simplified representation of a molecule where both lone pairs and single bonds are left out and all atoms are simply listed in order of the carbon chain. Atoms other than carbon are written next to the carbon atom they are bonded to. For example, hexane becomes CH3CH2CH2CH2CH2CH3 and 2-bromo-5-chlorohexane becomes CH3CHBrCH2CH2CHClCH3.
Projections
Sometimes it is necessary to view a molecule from a specific perspective to explain certain chemical properties. In closing we will discuss three commonly used projections.
Newman projection
A newman projection is a way to view the spatial structure of a molecule. For this a single bond is viewed from a right angle where the back atom is represented by a circle. Multiple conformations can be represented this way due to the rotation of single bonds. The situation where all groups are aligned is called eclipsed, the situation where all groups are spaced apart as far as possible is called staggered. As a general rule groups try to avoid each other as much as possible.
A newman projection of butane. Left is eclipsed, right is staggered. Image from Wikipedia.
Fischer projection
A fischer projection is used to represent molecules with a lot of stereocenters, such as sugars or amino acids, without having to explicitly draw the 3-dimensional direction of each individual bond. In a fischer projection, vertical lines indicate bonds that lie behind the plane and horizontal lines indicate bonds that lie in front of the plane. More about chirality in later lessons.
Schematic for creating a fischer projection. Image from Wikipedia.
Haworth projection
A haworth projection is used to show the 3-dimensional structure of cyclical monosaccharides. A think line is used to show the part of the molecule that is closer to the viewer. Every carbon atom (all numbered in the image below) is also connected to a hydrogen atom that is positioned opposite to the OH-group, but these hydrogens are often left out.
A haworth projection of α-D-glucopyranose. Image from Wikipedia.