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Organic Chemistry

L-T-P-C: 3-2-0-4

Dr. Soumendra Rana


IIT Bhubaneswar
Image Credits: Books, Journals, Google
Organic Chemistry?
• Organic chemistry is the study of the structure, properties,
composition, reactions, and preparation of carbon-containing
compounds.

• It not only include hydrocarbons but also compounds with any


number of other elements.

• It was originally limited to compounds produced by living


organisms but has been broadened to include human-made
substances such as plastics.

• The range of application of organic compounds is enormous and


also includes, but is not limited to, pharmaceuticals,
petrochemicals, food, explosives, paints, and cosmetics.
Job Prospect of Organic Chemistry?
• Food & Drug Administration
• Patent & Trademark office
• Pharmaceutical Industry
• Biotechnology & Bioengineering Industry
• Chemical Industry
• Petroleum Industry
• Consumer Product
Chemical Elements in Life & Health
Long Chain Hydrocarbons?
Auto Ignition Temperature
Silicones?
• Silicones are synthetic polymers with a silicon-oxygen backbone
similar to that in silicon dioxide (silica), but with organic groups
attached to the silicon atoms by C-Si bonds.

• The silicone chain exposes organic groups to the outside. Non


biodegradable polymers.

• Thus, despite having a very polar chain, the physical properties of


silicones are similar to those of an alkane. However, the -Si-O-
framework of the silicone gives the polymers thermal stability, as
in silica, and so they can be used where comparable organic
materials would melt or decompose.
Chemistry of Silicones
Classification of Silicones
• Silicones can be sub-divided into four classes:
a) Silicone fluids
b) Silicone gels
c) Silicone elastomers (rubbers)
d) Silicone resins

• Their physical form and uses depend on the


structure of the polymer.
Organic Molecules in Daily Life

Lipids

Sterols
Chemistry of DNA?

Heterocyclic Compounds
Heterocyclic Compounds
• Any of a class of organic compounds whose molecules contain
one or more rings of atoms with at least one atom (the
heteroatom) being an element other than carbon, most
frequently oxygen (oxa), nitrogen (aza), or sulfur (thia).

• Lowest number assigned to the hetero atom with the highest precedence:
O>S>N

NH
S O
thiacyclobutane 1-oxa-3-azacyclopentane
Nitrogenous Heterocyclic Compounds

piperidine purine
Important Purines and Pyrimidines
Basic Reactions Related to Heterocycles
Carbohydrates?
• “Hydrates of carbon” with a common formula Cm(H2O)n. Generally poly-
hydroxy aldehydes or poly-hydroxy ketones or the organic compounds,
which can yield the above compounds on hydrolysis.

• The most abundant organic molecules in nature produced by


photosynthesis.

• 6 CO2 + 6 H2O hn C6H12O6 + 6 O2

• All carbohydrates are “saccharides”. Greek “sakcharon” =


sugar
Aldose vs. Ketose
• Carbohydrate with an aldehyde group: Aldose
• Carbohydrate with a ketone group: Ketose

Glyceraldehyde Dihydroxyacetone
Glyceraldehyde Erythrose Ribose

Glucose Fructose Sedoheptulose Neuraminic acid


Fisher Projections

CHO CHO
CHO
H OH H OH
H C
CH2OH CH2OH
HO CH2OH

(R)-(+)-glyceraldehyde

CHO CHO
CHO
HO H HO H
HO C
CH2OH CH2OH
H CH2OH

(S)-(-)-glyceraldehyde

Representation of a three-dimensional molecule as a flat structure


R and S Configurations
1. Assign priorities to the four substituents according to the Cahn-Ingold-Prelog
rules.
2. Perform the two allowed manipulations of the Fischer projection to place the
lowest priority group at the top or bottom.
3. If the priority of the other groups 1®2®3 is clockwise then assign the carbon
as R, if priority of the other groups 1®2®3 is counterclockwise then assign
the center as S.

2
place at
CO2H the top 4
H
1 H2N H 4 2 HO2C NH2 1
hold steady CH3
CH3
rotate other 3 3
three groups
counterclockwise
1-2-3 counterclockwise = S
2
4 2
CO2H
H CO2H
4 H 1 2
NH2 1 H2N
H2N CO2H CH3
CH3 1 3
CH3 H
3 4
3

1-2-3 clockwise = R
Assigning R and S Configurations
Epimers
CHO CHO
H OH HO H
HO H HO H
H OH H OH
H OH H OH
CH2OH CH2OH
D-glucose D-mannose

epimers

Stereoisomers that differ only in configuration about one chiral center.


Chain Degradation
Aldose chain is shortened by oxidizing the aldehyde to -COOH, then
decarboxylation (Ruff degradation)
Ribose Sugar
Ribose in Solution
Anomeric Carbon in Ribose
Mechanism
Keto—Enol Tautomerism
Ribonucleosides
β-N-glycosidic bond

Found in RNA
Anti vs. Syn
Nucleotides
• Nucleotides are phosphoric acid esters of nucleosides.
• The –OH groups of monosaccharides can behave as alcohols and react with acids
(especially phosphoric acid) to form esters.
Adenosine Tri Phosphate

Cyclic AMP
Adenosine 3'-5'-Cyclic Monophosphate (cAMP)

• Cyclic AMP is an important regulator of many biological


processes.
Hydrogen Bonding Between Nucleobases

A T
2-deoxyribose

2-deoxyribose

G
C
2-deoxyribose

2-deoxyribose
Amino Acids?
Types of Amino acids
Small Amino acids

Non-polar aliphatic R-groups


Hydrophobic Amino acids

Non-polar aliphatic R-groups


Nucleophilic Amino acids

Polar uncharged R-groups


Amino acids with Amides

Polar uncharged R-groups


Basic Amino acids

Positively charged R-groups


Acidic Amino acids

Negatively charged R-groups


Aromatic Amino acids

Aromatic R-groups
Isoelectric Point

Anionic Form Cationic Form


Reaction With Amino acids
Reaction with Amino acids
Idea
Redox Example
Sulfur Oxidation States
Condensation of Amino acids

Peptide Bond
The Chemistry of Vision
The Chemistry of Vision
The Chemistry of Vision
The Chemistry of Colors
The Chemistry of Taste
The Chemistry of Taste

Freshness of Mint leaves

Spiciness of Chilli peppers


The Chemistry of Smell
Chemistry in Health & Medicine
Lipids?
• Lipids (Greek: lipos, means fat or lard)

• Lipid is the collective name for fats, oils, waxes


and fat-like molecules (such as steroids) found in
the body.

• Heterogeneous class of naturally occurring


organic substances.

• Insoluble in water, thus different from other


bioorganic molecules.
Type of Lipids
Fatty Acids

• Fatty acids are long chain carboxylic acids


containing up to 24 carbon atoms.
• Common fatty acids in plants and animals
have C16 and C18 chain, such as palmitate and
stearate.
• Found in both saturated and unsaturated
forms.
Unsaturated Fatty Acids
Cis and Trans Oleic acids
Triglycerides
Lipid Aggregation in Water
Phospholipids
Phospholipids: They are esters of phosphoric acids.
There are two main types of phospholipids in cellular
membranes:

Phosphoglecerides: They are also known as Phosphaitdyl


choline (lecithin). They are built from long chain fatty acid,
glycerol and phosphoric acids.

sphingomyelins: They do not contain glycerol. Instead, they


contain sphingosine, a long-chain unsaturated amino
alcohol. Only one fatty acid is attached to the sphingisine.
Sphingomylins are found in brain and nervous tissue and in
the myelin sheath, the protective coat of nerves.
General Structure of
Glycerophospholipid
Phosphatidylcholine (POPC)
Physiological Sterols
Cholesterol
Sex Steroids
Chemistry in Life
Chemistry in Life
Oxytocin

8 3
Vasopressin

8
Dopamine, Serotonin & Norepinephrine