M. Sc. Syllabus Semester – 3

CH 511: Principles of Bioinorganic Chemistry

Role of alkali and alkaline earth metal ions in biology; Na -K Pump, ionophores and crown ethers. Metal site structure, function. Metal ion transport and storage: Ferritin, Transferrin, Siderophores and metallothionein. Electron Transfer: Cytochromes, Iron-Sulfur Proteins and Copper Proteins. Oxygen transport and storage: Hemoglobin, myoglobin, hemerythrin, hemocyanin Oxygen activation: Cytochrome P450, Cytochrome c oxidase. Other metal containing enzymes: Catalase, peroxidase, superoxide dismutase, alcohol dehydrogenase, carbonic anhydrase, carboxypeptidase, xanthine oxidase, nitrogenase, vitamin B12 coenzyme, photosystem I and II, oxygen evolving center. Various spectroscopic methods used in bioinorganic chemistry: electronic spectra, EPR (emphasis on firstrow transition metal ions and their spectra), brief description of CD / MCD and multinuclear NMR. Applications of newer methods like EXAFS, XANES and ENDOR in characterization of biological molecules. Use of coordination complexes as models for various enzymes, metalloproteins. Role of hazardous materials such as nitric oxide, cyanide and methyl isocyanate etc. in biological systems.

Text Books:

  1. S. J. Lippard and J. M. Berg, Principle of Bioinorganic Chemistry , University Science Books (1994).
  2. Lawrence Que, Jr, Physical Methods in Bioinorganic Chemistry: Spectroscopy and Magnetism, University Science Books (2000).

References:

  1. F. A. Cotton and G. W. Wilkinson, Advanced Inorganic Chemistry, John-Wiley & Sons, (1988). 5th Ed.,
  2. 2 D. Banerjea, Coordination Chemistry, 2nd Ed, Asian Books Pvt. Ltd. (2007).
  3. J. E. Huheey, E. A. Keiter and R. L. Keiter, Inorganic Chemistry: Principles of Structure and Reactivity , 4th Ed. Harper Collins (1993).

CH 520: Concepts in Organic Synthesis

Pericyclic Reactions: Molecular orbital symmetry, Frontier orbitals of ethylene, 1,3- butadiene, 1,3,5-hexatriene and allyl system. Classification of pericyclic reactions. Woodward-Hoffmann correlation diagrams. FMO and PMO approach. Electrocyclic reaction; conrotatory and disrotatory motions 4n, 4n+2 and allyl systems. Cycloaddition; antrafacial and suprafacial addition, 4n and 4n+2 systems, 2+2 addition of ketenes, 1,3 dipolar cycloadditions and cheleotropic reactions. Sigmatropic Rearrangements; suprafacial and antrafacial shifts of H, sigmatropic shifts involving carbon moieties, 3,3- and 5,5- sigmatropic rearrangements, Claisen, Cope and Aza-Cope rearrangements. Ene reaction. Photochemistry: Quantum yields, intersystem crossing, photosensitization and energy transfer reactions. Photochemistry of olefins and carbonyl compounds, photo oxygenation and photo fragmentation, Photochemistry of aromatic compounds: isomerisation, additions and substitutions. Singlet molecular oxygen reactions. Patterno-Buchi reaction, Dipimethane rearrangement, Bartons reaction and Photo-Fries rearrangement. Reagents in Organic Synthesis: Use of the following reagents in organic synthesis and functional group transformations; complex metal hydrides, Gilman’s reagent, lithium dimethylcuprate, lithium diisopropylamide (LDA), dicyclohexylcarbodiimide, 1,3-dithiane (reactivity Umpoloung), trimethylsilyl iodide, tri-n-butyltin hydride, Woodward and pervost hydroxylation, osmium tetroxide, DDQ, selenium dioxide, Phase transfer catalysts, crown ethers and Merrifield resin, Peterson’s synthesis, Wilkinson’s catalyst, Baker yeast. Heterocyclic Chemistry: Synthesis and reactivity of furan, thiophene, pyrrole,
pyridine, quinoline, isoquinoline and indole; Skraup synthesis, Fisher indole synthesis. Chemistry of Natural Products: Structure elucidation and biosynthesis of Alkaliods, Terpenoids, Steroids.

Text Books:

  1. Frontier Orbital and Organic Chemical Reactions by I. Fleming, John Wiley, 1976.
  2. Some modern Methods of Organic Synthesis by W. Carruthers, Cambridge University Press, 1990.
  3. Protective Groups in Organic Synthesis by T.W. Greene, Wiley-VCH, 1999.

Reference:

  1. Modern Heterocyclic Chemistry by L. A. Paquette, W.A. Benjamin, Inc.,1968.
  2. Organic Chemistry by I. L. Finar, Vol II, ELBS, 1968.
  3. Heterocyclic Chemistry by T. R. Gilchrist, Longman,1989.
  4. Selectivity in Organic Synthesis by Ward, Wiley-VCH, 1999.

CH 521: Modern Techniques and Scope of Chemical Biology

Chemical biology: definition, history. Peptide and Protein: amino acids, peptides, primary, secondary, tertiary, and quaternary structure of proteins, protein folding.

Protein Synthesis: biosynthesis, chemical synthesis, solid phase peptide synthesis, strategy of combinatorial synthesis, combinatorial solid phase synthesis of antibiotics.

Lipids: fatty acids, bilayer, lipidation of proteins and peptides, farnesylation of the Ras protein.

Insertion of lipidated peptides into model membrane: biological membranes, transport across membranes, model membrane, biophysical properties of lipidated peptides in model membranes, basic concepts of fluorescence and fluorescence markers, synthesis of vesicles containing fluorescence
quencher and lipidated peptides.

Nucleic acids: base pairing, double helices, DNA replication, genetic information storage, transmission and gene expression, chemical synthesis of oligonucleotides, hybridization with synthetic oligonucleotides. Peptide nuclic acids (PNAs), synthesis of PNAs, doubly labeled PNAs as probes for the detection of point mutations. Use of small molecules to link a protein target to a cellular phenotype and as probes for biological processes.

Text Books:

  1. Chemical Biology: A practical course, edited by H. Waldmann and P. Janning. Wiley – VCH Verlag GmbH & Co. 2004
  2. Foundations of Chemical biology, by C.M. Dobson, J.A. Gerrard and A.J. Pratt. Oxford Univ. Press. 2002
  3. Biochemistry by J. M. Berg, J. L. Tymoczko and L. Stryer. W. H. Freeman and Company, New York

References:

  1. Chemical Biology: from small molecules to systems biology and drug design, Vol.-1, edited by S. L. Schreiber, T. Kapoor and G. Wess. Wiley – VCH Verlag GmbH & Co. 2007
  2. Chemical Biology: Application and Techniques, edited by Banafshe Larijani, Colin A. Rosser and Rudiger Woscholski, John Wiley & Sons Ltd. England, 2006
  3. Principles of Biochemistry by Lehninger, Nelson and Cox, CBS Publishers, 1993.

CH-530: Classical and Statistical Thermodynamics

Classical Thermodynamics: Review of the laws of thermodynamics, free energy, chemical potential and entropies. Partial molar quantities and their significances. Determination of these quantities, concept and determination of fugacity.

Non- ideal systems: Excess function for non-ideal solutions. Activity, activity coefficient, Debye-Hückel theory for activity coefficient of electrolytic solutions; determination of activity and activity coefficients; ionic strength. Application of phase rule to three component systems; second order phase transitions.

Statistical Thermodynamics: Statistical concepts and examples. Simple random walk problemin one dimension. General discussion of mean values and its use for the random walk problem. Specification of the state. Statistical ensembles. Basic postulates. Probability calculations. Behaviour of the density of states. Exact and inexact differentials. Equilibrium conditions and constraints. Reversible and irreversible processes. Distribution of energy between systems in equilibrium. Isolated system. System in contact with heat reservoir. Canonical distribution and its simple applications. Ensembles used as approximation. Calculation of thermodynamicquantities, Gibbs paradox, Validity of the classical approximation, Equipartition theorem and its applications: Specific heats of solids, Maxwell velocity distribution. Quantum Statistics of ideal gases. Identical particles and symmetry requirements. Quantum distribution functions. Maxwell-Boltzman, Photon, Bose- Einstein, and Fermi-Dirac statistics. Quantum statistics in the classical limit. Electromagnetic radiation in thermal equilibrium inside an enclosure. Consequences of Fermi-Dirac equation. Lattice vibration and normal modes. Debye approximation.

Text Books:

  1. Physical Chemistry by R. S. Berry, S. A. Rice and J. Ross, Oxford University Press, 2nd Ed. 2000.
  2. Fundamental of Statistical and Thermal Physics by F. Reif, McGraw Hill, International edition 1985.

Reference:

  1. Physical Chemistry: A Molecular Approach by D. A. McQuarrie and J. D. Simon, University Science Books, 3rd Ed. 2001.
  2. Statistical Mechanics by R. K. Pathria, Butterworth-Heinemann, 2nd Ed. 1999.

CH-535: Physical Chemistry Laboratory

Introduction to Computers and Computing: Basic structure and functioning of computers with a PC as an illustrative example. Memory, I/O devices. Secondary storage. Computer languages. Operating systems with DOS as an example.
Introduction to UNIX and WINDOWS. Data processing, principles of programming. Algorithms and flow-charts.
Experiments based on
UV – Visible spectroscopy with application
Fluorescence Spectroscopy with application
Infrared Spectroscopy
Solvents effects in spectra
Differential Scanning Calorimetry
High Pressure Liquid Chromatography
Spectroscopy Instrumentation
Cyclic voltametry
Temperature dependence of reaction rates
Enzymetic reaction
LB films / Liposomes
Ion selective electrodes
Semiconductor materials
Optical materials

Text Books:

  1. A Handbook of Instrumental techniques for analytical chemistry, Ed F. A Settle, 1997, Prentice hall PTR
  2. Introduction to Instrumental Analysis by R. D. Braun, 1987, McGraw-Hill Int. Ed.
  3. Journal of Chemical Education, ACS: some selected readings and experiments will be offered from this journal.