Intermolecular bonds

To understand how enzymes and substrates interact at the molecular level, it is also important to understand what types of bonds can form between molecules. These bonds are called intermolecular bonds.

Intermolecular bonds determine the physical properties of a molecule when it interacts with other molecules. The bonds are important for the boiling and melting point of substances as well as polarity. In a glass of water, it is the intermolecular bonds between_H2Omolecules that prevent the water from evaporating at room temperature. There are 4 types of intermolecular bonds; ionic bonds, dipole-dipole interactions, hydrogen bonds, and London bonds.

See the video below about intermolecular bonds. DISCLAIMER: In the video it is said that H-bonds are weaker than dipole-dipole bonds, which is wrong!

Ionic bonds are the strongest of the intermolecular bonds and are formed between charged atoms or molecules – better known as ions. The ions are created by an atom or molecule either giving up or absorbing an electron from another atom or molecule. This forms two ions with opposite charges, which are now attracted to each other and form a bond.

Positively charged ions such as Na⁺ (sodium ion) and NH₄⁺ (ammonium ion) are called cations, and negatively charged ions such as Cl^– (chloride) and COO^– (carboxylate) are called anions.

Figure 1: Ionic bond between magnesium and oxygen that forms magnesium oxide together.

Dipole-dipole interactions occur in molecules with permanent dipoles. In a polar bond, the atom that is more electronegative will attract the electrons in the bond. Electronegativity is an expression of an atom’s ability to pull on the electrons in a chemical bond; The higher the electronegativity, the better the atom’s ability to attract electrons. This creates a negative dipole, denoted δ⁺, and positive dipole, denoted δ^–. Dipole-dipole interaction in a molecule makes a molecule polar.

Figure 2: Water molecule shown with polarity.

If you have a mixture of molecules with permanent dipoles, the negative and positive poles in the molecules will attract each other. Dipole-dipole interaction makes the molecules stick together better, and thus they also have a higher boiling and melting point, as it requires more energy to break the dipole-dipole interaction. It is precisely because of dipole-dipole interactions that water is liquid at room temperature.

Hydrogen bonds are a type of dipole-dipole interactions. These bonds occur between a hydrogen atom in one molecule and a highly electronegative atom in another molecule, which is either oxygen (O), nitrogen (N), or fluorine (F). Hydrogen is slightly electropositive. Therefore, it is attracted to free electron pairs in an electronegative atom. Hydrogen bonds have a significant role in the physical properties of water, and so are hydrogen bonds that form between base pairs in DNA. These types of bonds are drawn with dotted lines when illustrating.

Figure 3: Adenine and thymine from DNA shown by the two hydrogen bonds they form.

Since electrons are always in motion, they will sometimes be unevenly distributed in a molecule. The uneven distribution creates a short-term dipole moment. Then the electrons move again, and the dipole arises elsewhere in the molecule. Bonds between short-term dipole moments in two molecules are called London bonds. It is the weakest bond, and it takes place in all molecules, as all molecules contain electrons. London bonds are essential for nonpolar molecules to stick together, as there must be a positive and negative pole that can attract each other for the molecules to stick together.

In biochemistry, we often talk about hydrophobic effects, which are also called hydrophobic interactions. These effects are important as they play a significant role in the folding of proteins, among other things. Hydrophobic effects are not bonds, but a phenomenon used to describe how nonpolar molecules or side groups tend to aggregate, i.e. cluster together. It is due to hydrophobic effects that globular proteins have hydrophobic inner and hydrophilic exteriors, making them water-soluble. In a water solution, nonpolar molecules will gather together and exclude the water. This also explains why you have 2 phases if you mix water and oil – as polar and non-polar liquids will not mix.