Molecular models are tools used for classroom or research to visualize better and interpret three-dimensional structures of organic molecules. The toolkit can be made of wood, plastic, metal, or other materials.
These models are digitally represented using computer graphics covered under molecular modelling, a branch of chemistry that uses computational and theoretical methods to model and mimic the molecule's behaviour in chemical and biological environments.
Framework or Stick models
The framework model studies the pattern of bonds in a molecule while disregarding the atom's size. Therefore, the atoms are not visible, and only the bonds connecting the atoms are seen.
The framework model of propenamide (CH3CH2CONH2) would look like this-
The framework model does not allow the viewer to envision the space-filling properties of a molecule.
Ball and stick model/Tinker toy Model
The ball and stick model use balls for the atom representation and sticks for the bonds.
The ball and stick graphical representation of 2-aminoethanol (H2N-CH2-CH2-OH) is-
Unsaturated compounds containing C=C and C ≡ C or strained rings are represented using flexible connectors or springs, not sticks.
The model provides a good description of the bond angles and molecular structure. However, the space-filling feature of the molecule needs to be captured accurately.
Space filling models
Space-filling models reveal the information related to an atom’s size without laying any emphasis on the bond. The relative size of each atom, depending on their Vander Waals’ radii, is shown, conveying the volume occupied by each atom in the molecule.
The space-filing model of propenamide (CH3CH2CONH2) is-
CPK Colour Scheme for the elements
The common elements in organic chemistry are- Carbon, Hydrogen, Oxygen, and Sulphur. In the CPK colour scheme named after their creators for Corey–Pauling–Koltun, carbon is Gray or black, oxygen is red, nitrogen is blue, sulphur is yellow, and hydrogen is white.
Complete list of the CPK colours for all the elements-
hydrogen (H) | white |
carbon (C) | black |
nitrogen (N) | blue |
oxygen (O) | red |
fluorine (F), chlorine (Cl) | green |
bromine (Br) | dark red |
iodine (I) | dark violet |
noble gases (He, Ne, Ar, Kr, Xe) | cyan |
phosphorus (P) | orange |
sulfur (S) | yellow |
boron (B), most transition metals | beige |
alkali metals (Li, Na, K, Rb, Cs, Fr) | violet |
alkaline earth metals (Be, Mg, Ca, Sr, Ba, Ra) | dark green |
titanium (Ti) | grey |
iron (Fe) | dark orange |
other elements | pink |
Several of the CPK colours refer to the pure element's colour as observed on the earth.
For example, hydrogen is a colourless gas. Carbon found in nature as charcoal, graphite, or coke is black, the sulphur powder is yellow, chlorine is a greenish gas, bromine is a dark red liquid, iodine crystals are deep violet, amorphous phosphorus is red, Iron rust is dark orange red, etc. Oxygen is assigned red, perhaps due to the red colour of the blood carrying oxygen in the human body. Nitrogen's abundance in the earth's atmosphere scatters sunlight, due to which the sky appears blue maybe the reason for Nitrogen's blue colour in the CPK colour scheme.
Still, computer models may have their default settings; for example, the carbon is cyan in ACD lab's ChemSketch default setting.