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Master of Science in Applied Organic Chemistry
Detailed syllabus – 2010
MOC 5001: Advanced Organic Chemistry (45L) - 3 credits
Mechanistic & stereochemical approach to organic reactions (11 L)
Reactions of organic compounds as acids and bases, Reaction pathways,
Conformational analysis, Overview of stereochemistry, Nucleophilic substitution
and elimination reactions, Nucleophilic addition to carbonyls, Nucleophilic
substitution of carboxylic acid derivatives, Enols and enolate anions as
nucleophiles, Electrophilic substitution of aromatic compounds, Chemistry of
amines, Oxidation and reductions.
Organic synthesis (12 L)
Retrosynthetic analysis, Simple examples of retrosynthetic analysis with C-C
bond disconnections, Synthesis of alkenes, Two-group disconnections: 1,3Dioxygenated skeletons, 1,5-Dicarbonyl compounds, “Illogical” two group
disconnections: 1,2-Dioxygenation pattern, 1,4-Dioxygenation pattern, Analysis
of 1,6-Dicarbonyl compounds, Disconnections of heterocyclic compounds,
Synthesis of 3- and 4-membered rings, Use of protecting groups in organic
synthesis, Examples of total synthesis & asymmetric synthesis.
Heterocyclic chemistry (06 L)
Nomenclature, Aromatic heterocyclic compounds, Reactions of heterocycles as
acids and bases, Synthesis of heterocycles by reaction of nucleophiles with
carbonyls compounds, Substitution reactions of heterocyclic compounds:
Pyrimidines, purines, pyridines and five membered heterocycles and their
biological significance.
Concerted reactions (06 L)
Overview of concerted reactions, Cycloaddition reactions of carbons compounds:
Electrocyclic reactions, 1,3-dipolar additions and sigmatropic rearrangements,
Reactions of carbenes.
Industrial organic synthesis (06 L)
Introduction to organometallic chemistry, Basic products of industrial synthesis:
Synthesis gas: Generation, purification and applications, Pure synthesis gas
components: Generation, purification and applications, C1 units: Manufacture and
applications of methanol, formaldehyde etc.
Synthesis and fabrication of organic nanomaterials (04 L)
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Introduction to organic nanomaterials, synthesis, characterization using Scanning
Electron Microscopy (SEM)/Transmission Electron Microscopy (TEM)/ Atomic
Force Microscopy (AFM).
MOC 5002: Separation and Characterization Techniques (30L) - 2
credits
Separation methods (10 L)
Chromatogrpahic separation mechanisms, Chromatographic retention, Normal and
reverse phase liquid chromatography: Capacity factor, selectivity, resolution, column
efficiency, temperature programming and gradient elution, Qualitative and
quantitative analytical methods, GC instrumentation and troubleshooting, HPLC
instrumentation and troubleshooting, Chromatographic detectors.
Molecular spectroscopy – absorption (12 L)
Ultraviolet and visible spectroscopy, Infrared spectroscopy, Advanced 1H and 13C
NMR spectroscopy: Chemically and magnetically equivalent nuclei, long range
coupling, first order versus complex spectra, introduction to 2D NMR (COSY,
Hetcorr), uses of HMQC and HMBC, Mass spectrometry: Fragmentation patterns of
the common classes of compounds in electron ionization, different soft ionization
methods (FAB, electrospray and MALDI), GC-MS, LC-MS and MS/MS techniques
and their use in structure elucidation.
Molecular spectroscopy - emission (04 L)
Molecular fluorescence, phosphorescence and chemiluminescence, Theory of
fluorescence and phosphorescence, Applications and photoluminescence methods:
Steady state and time resolved methods, fluorescence quenching and enhancing
reagents, fluorescence probes.
Atomic spectroscopy - absorption and emission (04 L)
Absorption of radiation by free atoms, Difficulties of the use of a continuous source
of radiation, Hollow Cathode Lamp (HCL), Nebulizers. Flame and non-flame
atomizers, Interferences in AAS and methods to eliminate them, Solvent effects,
Matrix effect. Atomic emission spectroscopy, Precautions in using flame photometry.
MOC 5003: Medicinal Chemistry (45L) - 3 credits
Drug design and development (05 L)
History, Pharmacokinetics: The dynamics of drug absorption, distribution,
metabolism and elimination, Pharmacodynamics, Membrane transporters and
drug response, Discovery and development of drugs, Strategies in drug design,
Molecular modeling.
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Therapy of infectious diseases (06 L)
General principles, Antibacterial drugs (sulfonamides, beta-lactam antibiotics,
aminoglycosides, tetracyclines, macrolides etc), Drugs used in the chemotherapy
of protozoal infections and antiprotozoal drugs, Drugs used in the treatment of
cestoda, trematoda and nematoda (helminthiasis), Antifungal compounds.
Drugs acting on the central nervous system (08 L)
Neurotransmission and the central nervous system, Volatile anesthetics, Local
anesthetics, Central nervous system depressants: Sedative hypnotics,
anticonvulsants, neurtolepics, anxiolytics, antidepressants, mood stabilizers,
Stimulants and hallucinogens, Drugs used to treat neuromuscular disorders:
Antiparkinsonism agent and skeletal muscle relaxants, Opioid receptors and
analgesics.
Drugs affecting renal, blood and cardiovascular function (08 L)
Cardiac agents: Cardiac inotropes (cardiac glycosides), antianginals and
antiarrhythmic drugs, anticoagulants (thrombolytic and antiplatelet), coagulants
and plasma extenders, anti-hypertensive agents, Diuretics, Hyperlipidemia and the
mechanism of lipid transport, Antilipidemic drugs: Statins.
Drugs used in controlling allergies and inflammation (06 L)
Histamines, Antiallergenic agents such as antihistamine and leukotreine receptor
modulators, Chemical mediators in hypersensitivity reactions, Drugs acting on the
respiratory system: Bronchodilators and mast-cell stabilizing agents,
Adrenocorticoids, Structure-activity relationship of steroidal anti-inflammatory
compounds, Non-steroidal anti-inflammatory drugs, Disease-modifying
antirheumatic drugs, Drugs used in SLE and inflammatory bowel disease.
Hormones and hormone antagonists (05 L)
Pituitary hormones and their hypothalamic releasing hormones, Thyroid function,
Thyroid and antithyroid drugs, Estrogens and progesterone and their therapeutic
use, Drugs affecting sugar metabolism: Insulin and oral hypoglycemic agents.
Drugs used in the chemotherapy of neoplastic diseases (05 L)
Antiviral agents and their development in chemotherapy of AIDS, Drugs for
neoplastic diseases: Alkylating agents, antimetabolites, antimitotic drugs and
topoisomerase inhibitors.
Drugs acting on the gastrointestinal system and drugs acting on bone (02 L)
Pharmacotherapy of gastric acidity: Antacids, H2 receptor blockers, proton pump
inhibitors, Prokinetic agents, Anti-spasmodics, Treatment of disorders of bowel
motility and water flux: Anti-motility agents, anti-emetics and anti-resorption
agents.
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MOC 5004: Natural Product Chemistry (30 L) - 2 credits
Introduction to secondary metabolism (04 L)
The building blocks in primary and secondary metabolism, Construction
mechanisms in biological systems such as alkylation, Wagner-Meerwein
rearrangement, Aldol and Claisen condensations, Schiff base formation, Mannich
reaction, Transamination, Decarboxylation, Phenolic oxidative coupling and
Glycosidation, Vitamins and cofactors, Elucidation of biosynthetic pathways.
The acetate pathway (05 L)
Saturated fatty acids, Unsaturated fatty acids, Prostaglandins, Thromboxanes,
Leukotrienes, Aromatic polyketides, Oxidative cleavage of aromatic rings, Starter
groups other than acetate, Macrolides and polyethers, Cyclization through DielsAlder reactions.
The shikimate pathway (04 L)
Aromatic amino acids and simple benzoic acids, Lignans and lignin,
Phenylpropanes, Benzoic acids from C6C3 compounds, Coumarins, Flavonoids
and stilbenes, Isoflavonoids, Vitamin K.
The mevalonate and deoxyxylulose phosphate pathways (06 L)
Isoprene repeating unit, Monoterpenes, Essential oils and their importance,
Biosynthesis, Important reactions and stereochemical aspects of monoterpenoids,
Sesquiterpenoids, Diterpenoids, Sesterterpenoids, Triterpenoids, Carotenoids,
Main types of steroids, their stereochemistry and biological functions, Important
reactions and synthesis/partial synthesis of steroids.
Alkaloids (06 L)
Chemical structure, Isolation and purification methods, and general methods
employed for determining the structure of alkaloids, Biosynthesis of alkaloids
derived from ornithine, lysine, nicotinic acid, tyrosine, tryptophan, anthranilic
acid, and histidine, Purine alkaloids.
Carbohydrates (05 L)
Configurational relationships, conformational analysis, mutarotation, Reactions of
anomeric and non-anomeric carbon atoms, Reactions of the hydroxyl groups,
Aminosugars, Reducing and non-reducing sugars, Nature of di-, tri-, and
polysacaccharides, Structures of streptomycin, starch, glycogen, cellulose, chitin,
pectic substances, carrageenan, glycoproteins and glycolipids.
MOC 5005 Proteins in industry (45 L) - 3 credits
Protein function (14 L)
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Active site residues of different enzymes and positioning, Functions of
coenzymes, Mechanism of enzyme catalysis, Enzyme catalysis in organic media,
Primary and secondary isotope effects on enzyme catalyzed reactions, Enzyme
catalysis group transfer reactions: Peptidases, esterases and lipases, Amination,
Phosphorylation reactions catalyzed by enzymes; Phosphatases and
phosphodiesterases, kinases, Redox reactions that require coenzymes; Oxidases
and reductases, Monooxygenation and dioxygenation, Carboxylases and
decarboxylases; Pyridoxyl dependent decarboxylases, Amino acid racemases,
epimerases, aldose-ketose isomerases, cis-trans isomerases, Enzyme catalyzed
elimination and addition reactions, Rearrangement reactions. Methods of
improving enzyme stability.
Tools in recombinant DNA technology (10 L)
Nucleic acid structure and function, Chemical synthesis of DNA, Enzymes used
in recombinant DNA technology and their applications, Vector systems, Cloning
strategies, Analysis of cloned/recombinant DNA molecules.
Applications in recombinant DNA technology (08 L)
Application of recombinant DNA technology in medicine, forensic science and
industry, Genetically modified organisms and foods.
Fermentation process (05 L)
Fermentation principle, Enzymatic reactions involved in fermentation, Microbial
growth curve and kinetics, Basic functions of a fermenter, Application of
fermentation in industries and carrying out fermentation in large scale processes,
Purification and characterization of fermented products, Usage of fermentation
end products.
Microbial products (08 L)
Commonly used microbes in industry, Metabolic pathways for the biosynthesis of
microbial products (enzymes, antibiotics, organic acids, alkaloids etc), Over
production of microbial products, Applications of microbes in industry, medicine,
food, milk & milk products and beverages.
MOC 5006: Optional Topics (conducted by experts from Industry) (45L)
-3 credits
These optional topics will be taught by persons well acquainted in the relevant areas
and working in industrial environments. Having specialists from industry will bring
in the aspects of industrial economics, industrial business and management sciences
in to these special topics. Aspects of marketing such as the product pricing, quality
and supply chain management can also be addressed by these experts within the
stipulated time frame if it is relevant to the topic. Topics will be offered depending
on the availability of the lecturers and the demand from the candidates registered in
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the M.Sc. program. At least 6 topics will be covered each year and 6-8 lecture hours
will be allocated for each topic.
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Plastics
Rubber and rubber products
Brewing technology and chemistry of fermentation processes
The chemistry of cosmetics
Persistent Organic Pollutants (POP)
Paints and surface coating techniques
Industrial detergents
Oil and fat technology
Chemistry of food
Tea, coffee and Sri Lankan beverages
Dyes and dyeing
Quality management and assurance
Plastics
Introduction to types of plastics, Structure property relationships, Glass transition
temperature of polymers & how polymers are classified as plastics. Types of
plastics: Thermosets & Thermoplastics & main types of plastics such as (low
density, High density, linear low density), Polypropylene, Polyvinyl Chloride,
Fluorocarbon Polymers, Polyethers, Polyesters, Polycarbonates, Polyamides,
Polystyrene, Acrylic Polymers. Plastics in packaging. Permeability properties of
different plastics and the suitability of different plastics for different packaging
applications. Polyurethanes: Major areas of application, chemistry of
polyurethanes – reactions of polyisocyanates with polyols. Applications of
polyurethane in the garment industry. Types of materials used in polyurethane
industry and structure/strength properties relationship.
Rubber and rubber products
Natural rubber & synthetic rubbers, Structure property relationships,
Vulcanization of rubbers, Vulcanizing agents and vulcanization mechanisms,
Other chemicals used in the process, Degradation and stabilization, Thermoplastic
elastomers, Rubber processing techniques, Dry rubber and latex based industries.
Brewing technology and chemistry of fermentation processes
Raw Materials: Water, malt, hops and other important materials, Chemistry and
its impact on processing, Malting & Mashing: Chemical composition of barley,
nitrogen/protein, enzymes, starch, Polysaccharides & impact on brewing,
Chemistry & Biochemistry of Malting, Brew house procedures: Milling, mashing,
boiling, filtration, equipment & machinery in brewing, Chemistry & Biochemistry
of Fermentation: Yeast characteristics, yeast Biochemistry, metabolism of sugars,
nitrogen metabolism, post fermentation techniques, Other industrial fermentation
processes other than beer fermentation.
The chemistry of cosmetics
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Raw material (Rheology of cosmetic systems, thickeners and gums, oil, fats and
waxes) Safety and Legislation, Surface Chemistry, Decorative cosmetics,
Personal care, Packaging, Perfumery manufacturing & marketing, Natural
products as cosmetics.
Persistent Organic Pollutants (POPs)
What they are? Characteristics of POPs, Why they are important? Policies,
Categories of POPs: PCBs, PAHs, PCDDs, PCDFs, PBDEs and organochlorine
pesticides; structures, sources, adverse effects and mode of action. How their
physico-chemical properties govern their environmental fate and behaviour,
Source inventories, Source apportionment, Methods of detection.
Paints and surface coating techniques
Introduction to paints: Composition of a paint, ingredients used in paints, types of
paints such as varnish, enamel paint, lacquer, emulsion paint, filler paints, primers,
sealers, surfacers or undercoats, top coats etc., Dry film properties: Adhesion to
substrate, hardness, flexibility, surface appearance, scratch resistance, solvent
resistance etc., Drying of paint: drying with and without chemical reactions.
Ingredients used in the paint industry: Pigments (key properties & functions of
pigments, selection of pigments and incorporation of pigments into a paint), types
of pigments (natural or synthetic pigments, inorganic or organic pigments),
Colour matching, Liquids used in making paints and their properties, Additives
used to make paints, Types of paints: Lacquers, emulsion paints & non aqueous
dispersions, oils & alkyd paints, thermosetting alkyd, polyester and acrylic paints
based on nitrogen resins, epoxy coatings, polyurethanes, unsaturated polyesters
and acrylics.
Industrial detergents
Types of detergents, Preparation of detergents: synthetic detergents, Additives in
detergents, The effectiveness of detergents as cleansing agents, Anionic, cationic,
nonionic and amphoteric detergents, Properties of soaps versus detergents.
Oil and fat technology
Oils & fats (Structure, Composition and Classification), Oil Extraction
Technologies (Pulp oils, Seed oils, & Animal fats), Crude Oil Processing
(Purification & Refinery Process), Fats & Oils Modification (Fractionation &
Transestertification), Lipid oxidation & its control.
Quality management
ISO 9000 QMS, Lab Quality Management, Documentation of QMS.
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MOC 5007: Practical Component - 6 credits
The number given in the following list indicates the number of 5 hr time slots. A
total of 36, five hour times slots give the required 180 hrs.
Simple and muti-step synthesis of organic compounds
Isolation of natural products
Biochemical applications
Analytical chemistry
Recombinant technology and fermentation processes
Molecular modeling and drug design
Statistical analysis
Presentation (15 min)
Presentation is based on a paper (less than 10 pages) prepared
Evaluation: There will be at least one practical examination and
are subjected to a continuous assessment.
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by the student.
all experiments
MOC 5008: Research Project - 8 credits
Full-time students will spend approximately 8 months for the completion of the
research project. The dissertation written on the research work will be evaluated
by a viva voce examination.