Hydrogen bonds

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A hydrogen bond is an attraction between a hydrogen atom and an electronegative atom, with only nitrogen (N), oxygen (O) or fluorine (F)[1]. Hydrogen bonds appear frequently within biological molecules and exist in polar compounds. A common example of this is water, where the attractive interaction exists between the oxygen and hydrogen atoms. Hydrogen bonding is a type of intermolecular force, where the Hydrogen bond is found between different molecules, or intramolecular, where the bond exists between different parts of the same molecule[2].

A hydrogen bond is a non-covalent bond; they have much stronger attractions than van der Waals forces and permanent dipole-permanent dipole interactions, but are weaker than ionic bonding or covalent bonding. Evidence for hydrogen bonding can be found when comparing the boiling points of hydrogen molecules across groups 5, 6 and 7 of the periodic table. The compounds where hydrogen bonding is present produce a much higher boiling point as hydrogen bonds require more energy to be broken than van der Waals forces[3].

The distance between two parts of the same molecule, or different molecules, can vary and this has an effect on the strength of the hydrogen bond. This why the hydrogen bonds are said to be "elastic," the greater the distance between the hydrogen atom and the electronegative atom the longer the hydrogen bond will be and this results in a weaker hydrogen bond.

A hydrogen bond can be defined as the polar interaction between an electronegative atom (Nitrogen, oxygen or fluorine) and a hydrogen atom which is covalently bonded to another electronegative atom that is on the same molecule, or on a different molecule. The bond is strongest when all three of these atoms are arranged in such a way that their bond angles are at a value of 180 degrees.

Hydrogen bonding is extremely prevalent throughout nature and can be found in water, DNA base-pair interactions, protein folding, protein structure and protein-ligand binding.

Hydrogen bond formation is due to the attraction of different elements which has variety of electron. The electronegativity series is O > N > C = H.


A water molecule consists of one oxygen atom attached to two hydrogen atoms. A hydrogen bond can be formed between two molecules of water due to the 'unequal distribution of electrons within a water molecule'[4]. The oxygen has a strong attraction for the electrons and has a negative charge, whereas the hydrogen only has a weak attraction and therefore has a slight positive charge. When these two oppositely-charged regions come close to each other, the result is a hydrogen bond[5].

Although water has a low molecular mass, it has an unusually high boiling point. This property can be attributed to the large number of hydrogen bonds that exists within water. Since these bonds are difficult to break, water’s melting and boiling points are relatively high in comparison to other liquids that are similar but lack the hydrogen bonding.

Another unusual property of water is it has a higher density than it's solid counterpart - ice. This is due to the unique formation of the hydrogen bonds forming a lattice structure whereby the strength and relative rigidity of the bonds allow for greater separation between molecules than in its liquid form where the molecules interact at a greater velocity.


In the DNA helix, the bases: adenine, cytosine, thymine and guanine are each linked with their complementary base by hydrogen bonding. Adenine pairs with thymine with 2 hydrogen bonds. Guanine pairs with cytosine with 3 hydrogen bonds[6].This creates a difference in strength between the two sets of Watson and Crick bases. Guanine and cytosine bonded base pairs are stronger then thymine and adenine bonded base pairs in DNA. This difference in strength is because of the difference in the number of hydrogen bonds. This allows researchers to figure out the base content of DNA by observing at what temperature it denatures. The higher the temperature at which DNA denatures the more guanine and cytosine base pairs are present. this variation in the number of hydrogen bonds a nucleic base can make in a Watson Crick base pair is also pertinent for the designing of primers for PCR. To ensure both primers anneal proportionally to their binding sites they must be designed such that they produce hydrogen bonds of similar affinity. The greater strength of hydrogen bonding between guanine and cytosine is also utilised during PCR primer design to ensure that primers is thoroughly bound to the target DNA at it's 3' end so that the polymerase can begin reading in the 3' to 5' direction. The inclusion of guanine or cytosine at the 3' end of a primer is known as a GC clamp.



  1. https://www.chemguide.co.uk/atoms/bonding/hbond.html
  2. http://www.chemguide.co.uk/atoms/bonding/hbond.html
  3. http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/H/HydrogenBonds.html
  4. Alberts, B et al. (2008). Molecular Biology of the Cell. 5th ed. US: Garland Science. 1268. p55
  5. Alberts, B et al. (2008). Molecular Biology of the Cell. 5th ed. US: Garland Science. 1268. p55
  6. J.M.Berg, J.L.Tymoczko, L.Stryer,(2007) Biochemistry, 6th edition, New York: W.H.Freeman and company p112
  7. Alberts, B et al. (2008). Molecular Biology of the Cell. 5th ed. US: Garland Science. 1268. p137
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