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Hydrogen Bonding-I: An overview in Pictures

Hydrogen bonding is one of the most important forces responsible for binding interactions between a drug molecule and a receptor. It is also an important factor which determines the secondary structures of macromolecules like proteins or nucleic acids.
Hydrogen bond (H-bond) is a type of electrostatic bond, significantly weaker than covalent and ionic bonds. H-bond has an energy range of 2.4 to 24 Kcal/mol. Figure 1 shows the H-bond formation between two dipoles. Hydrogen is attached to an electronegative element X. Due to X, the X-H bonding electrons shift towards X resulting in partial negative charge on X and a corresponding partial positive charge on H. H is then attracted by another electronegative element “A” causing the H-bonding between the two dipoles.
H-bonding is essential for 3D structures of macromolecules like proteins and nucleic acids.
H-bond energies are within the range of thermal motion of molecules at physiological temperature. This facilitates the formation and breakage of H-bond frequently to maintain the structural integrity of biological molecules.H-bond
Figure 1: H-bond formation.
The weaker attraction of H-bonds is easily overcome by their number and additive effect. A large macromolecule keeps its structure intact by "several" H-bonds. Since the H-bonds are highly directional, their presence imparts unique geometric arrangement of atoms in a molecule.

The stronger the electro-negativity of the atom to which the H is attached, the stronger the H-bond.
The electronegative atom X with a hydrogen attached to it via a covalent bond is said to be an H-bond donor atom. Similarly, another electronegative atom A which forms a bond to this X-H pair is called as H-bond acceptor atom.

Some common H-bond donor groups in biological systems
Figure 2: H-bond donor groups
Some common H-bond acceptor groups in biological systems
Figure 3: H-bond acceptor groups
Some H-bonds in biological systems: Common H-bonding patterns in biological systems.
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Figure 4: H-bonding between donor and acceptor groups.
H-bonding in DNA
Three H-bonds between G and C; two H-bonds between A and T
H-bond in DNA
Figure 4: H-bonding between GC and AT base pairs in duplex DNA.


Figure 6: Showing hydrogen bonding in 3D.
Figure 7: Showing top view of figure 6.


Anonymous said…
Interesting article with iice pictures.

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