Nayana Iyer’s notes

CBI2: Biomolecular Bonding

The type of chemical bond formed between two substances is dependent on their
difference in electronegativity.
§ Ionic bonds are formed when the electronegativity difference is greater than 2.
Electrons are transferred.
o Cations are positively charged and are smaller than neutral atoms
o Anions are negatively charged and are larger than neutral atoms
§ Covalent bonds occur when the electronegativity difference is less than 1.7.
Electrons are shared between the atoms.
o Polar covalent bonds form when there is an electronegativity difference
greater than 0.5. The more electronegative atom will draw the electrons
closer to itself, resulting in partial (d- and d+) charges.
o Non-polar covalent bonds form when the electronegativity difference is less
than 0.5. The electrons will therefore be shared more evenly around the
bond.

Covalent bonds have different orbital overlapping patterns and bond lengths:
¨ Single bonds – longest bonds which are s bonds formed from s-s or s-pz or pz-pz
orbital overlap
¨ Double bonds – mid-length bonds formed from one s bond and one p bond (formed
from side-on px-px or py-py orbital overlap)
¨ Triple bonds – shortest bonds formed from one s bond and two p bonds

p bonds make double bonds non-rotational as it is energetically unfavourable to do so. This

means double bonds are planar and groups are in fixed positions relative to one another.

The shapes of molecules changes depending on the repulsion from lone pairs of electrons
and negatively charged regions. This is defined in the Valence Shell Electron Pair Repulsion
(VSEPR) theory:

• Linear – 180° with two bonding pairs (O=C=O)

• Trigonal Planar – 120° with three bonding pairs (BF3)
o Bent – 117.5° with two bonding pair and one lone pair (SO2)
• Tetrahedral – 109.5° with four bonding pairs (CH4)
o Trigonal Pyramidal – 107° with three bonding pairs and one lone pair (NH3)
o Bent – 104.5° with two bonding pairs and two lone pairs (H2O)
• Trigonal Bipyramidal – 120° and 90° with five bonding pairs (PCl5)
• Octahedral – 90° with six bonding pairs (SF6)
Note that lone pairs decrease bond angles as they increase the repulsion between negative
regions.
Nayana Iyer’s notes

Orbitals can also hybridise in order to form bonds in carbon (for example). This is where
electrons from one orbital are ‘promoted’ to the next energy level in order to form
degenerate hybrid orbitals.

§ sp3 – one s-orbital and three p-orbitals become degenerate to form four bonds
§ sp2 – one s-orbital and two p-orbitals become degenerate to form two bonds and
one double bond
§ sp – one s-orbital and one p-orbital become degenerate to form one bonds and one
triple bond

In addition to chemical bonds, molecules also have non-covalent interactions between or

within themselves:

¨ Dipoles – polar covalent bonds can result in an overall dipole moment, allowing
dipole-dipole or dipole-ion interactions to occur.
¨ Van der Waals – non-polar molecules have transient dipoles as a result of electron
shifting. This induces dipoles in neighbouring molecules resulting in weak but
significant bonds when their cumulative effect is considered.
¨ Hydrogen bonds – if H atom is bonded to an electronegative atom (O/F/N) hydrogen
bonding can occur. These are stronger than dipole interactions.