2Types of interactions: H-BondPi StakingDipole StackingSteric BulkInclusion Complex
31- H-BondThe hydrogen bond is the attractive force between the hydrogen attached to an electronegative atom of one molecule and an electronegative atom of a different molecule.Usually the electronegative atom is oxygen, nitrogen, or fluorine, which has a partial negative charge. The hydrogen then has the partial positive charge.It is responsible for many of the properties of water.
4H-Bond Essential requirements for formation of hydrogen bond: 1- A hydrogen atom must be directly bonded to a highly electronegative atom (e.g. F, O and N)2- An un-bonded pair of electrons (lone pair electrons) is presented on the electronegative atom
5H-Bond Two types of H-bond: 1- Intermolecular hydrogen bond: Hydrogen bond formed between two molecules2- Intra molecular hydrogen bond: Hydrogen bond formed between two different atoms in the same molecule
6H-Bond Examples: water molecules: water has a very high boiling point, melting point, and viscosity compared to otherwise similar liquids not conjoined by hydrogen bonds.water molecule can potentially form four hydrogen bonds
7H-BondHuman DNA:the hydrogen bonding that occurs between base pairs in a strand of DNA results in DNA’s familiar double helix shape. This hydrogen bond enables the replication of DNA strands.Proteins:result in "protein folding.”. The intra-molecular hydrogen bond is necessary for these proteins to hold their shape and remain stable once they have folded.
82- Pi stacking pi stacking (also called π–π stacking): - It is noncovalent interactions between aromatic rings.These interactions are important in:- Nucleobase stacking within DNA and RNA molecules, protein folding, and molecular recognition.
9Pi stackingThe ability to alter pi stacking interactions would be useful in numerous synthetic efforts.One example would be to increase the binding affinity of a small-molecule inhibitor to an enzyme pocket containing aromatic.
10Pi stacking Applications of pi stacking: Pi stacking is common in the structure of the protein.Also contributes to the interactions between small- molecules and proteins.As a result, pi-pi interactions important in rational drug design.
11Pi stackingOne example is the FDA-approved acetylcholinesterase (AChE) inhibitor Tacrine.which is used in the treatment of Alzheimer's disease.Tacrine is suggest to have a pi stacking interaction with the indolic ring of Triptophan-84.
123- Dipole StackingA dipole is a separation of electrical charges. In chemistry, a dipole refers to the separation of charges within a molecule between two covalently bonded atoms.It is a force between the positive of one polar molecule and the negative of another molecule.They are much weaker than the ionic or covalent bond.Examples: Iodine monochloride , Magnetic
134- Steric BulkThe effect seen in molecule that comes from the fact that atoms occupy space, when atoms are put close to each other, this costs energy, the electron near the atoms want to stay away from each other.This can change the way molecules want to reactIt can also change the shape of molecule.The amount of space that a group of atoms takes place is called steric bulk
14Steric BulkSteric effects arise from the fact that each atom within a molecule occupies a certain amount of space.If atoms are brought too close together, there is an associated cost in energy due to overlapping electron clouds , and this may affect the molecule's preferred shape (conformation) and reactivity.Understanding steric effects is critical to chemistry, biochemistry and pharmacology.
155- Inclusion ComplexIt is any chemical complex in which one component (the host molecule) forms a crystal lattice containing tunnel- or channel-shaped spaces in which molecular entities of a second species (the guest molecule) are located.There is no bonding between the host and the guest molecules.Example: Cyclodextrin forms inclusion compounds