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.
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.
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
Figure 4: H-bonding between GC and AT base pairs in duplex DNA.
Preliminary examination of blood stains do not confirm the presence of blood. It merely indicates that the positive stain might be due to blood.
In order to confirm the identity of blood, there are certain crystal and spectroscopic tests that are regularly employed in the forensic science laboratories.
1. Takayama Test: Reagent Preparation:
Standard Glucose Solution (100g/100ml) 3 ml
10% Sodium hydroxide (NaOH) 3 ml
Pyridine 3 ml
Distilled Water 7 ml
Reagents should be made fresh daily.
1. Place material to be tested on a microscopic slide and cover with a cover slip.
2. Add a drop of Takayama Reagentand allow to flow under the cover slip.
3. Warm slide gently at 65oC for 10-20 seconds
4. Allow to cool and observe under microscope at 100X magnification.
The appearance of pink needle shaped crystals of pyridine hemochromogen (Pyridine ferroprotoprophyrin) is positive reaction for heme.
2. Teichmann’s Test: Reagent Preparation:
Potassium Chloride or 0.1 g
It is often necessary in various scientific disciplines to prepare sketches of molecules for project reports, research papers and teaching assignments, etc. Drawing a sketch also helps in developing the concepts in science, for example, the bonding patter in organic molecules, their valencies, etc. Educators and researchers regularly use sketches in their daily work. With the development of computing computer based sketching has become more common and more and more people are using computers for everything for drug design, manufacturing and publications of results. Several tools are available for sketching. Here, we will see how small molecules can be drawn using an exciting and free software ‘ACDChem Sketch’ from ACD Labs. Lets begin by drawing a simple molecule ‘Indole’. The pictures below are self explaining.
You can build a larger molecule by adding side chains at the desired positions on the main Indole ring. The method is shown below.