CH EL1 : Departmental Elective I


List of Electives

  • CH 510 Heterocyclic Chemistry
  • CH 546 Introduction to Biomolecules
  • CH 582 Inorganic Photochemistry
  • CH 584 Biophysical Chemistry
  • CH 518 Macromolecular Crystallography


Syllabi and Textbooks for Electives

CH 510: Heterocyclic Chemistry

  1. Introduction to heterocyclics and their importance.
  2. Nomenclature of ring systems: (a) Trivial System (b) Replacement system (c) Fusion system, (d) Hantzsch-Widman nomenclature.
  3. Structure, reactivity and synthesis of reduced three membered Heterocycles: (a) Oxirane: Sharpless method, Shi epoxidation, Jacobsen epoxidation, etc, (b) Thiirane (c) Aziridine.
  4. Structure, reactivity and synthesis of reduced four membered Heterocycles: (b) Oxetane (b) Thietane (c) Azetine.
  5. Structure, reactivity and synthesis of reduced five membered Heterocycles: (a) Pyrrole: Paal Knorr, Hantzsch Methods, etc, (b)Thiophene: Paal Knorr, Hinsberg method, etc. (c) Furan: Paal Knorr, Fiest-Benary, Industrial Method, etc.; (d) Pyrazole, Imidazole, Oxazole, Thiazole, (e) Synthesis using modern methods.
  6. Structure, reactivity and synthesis of reduced Six membered Heterocycles: (a) Pyridine: Synthesis, heterynes, pyridones, N-oxides.
  7. Aromatic heterocyclics: a) Indole: Fischer indole synthesis, Bischler synthesis, Madelung synthesis, Domino and cascade methods of indole synthesis, (b) Quinoline and Isoquinoline, (c) Coumarins and Chromones.
  8. Polyhetero ring systems: Click chemistry in heterocycle synthesis.
  9. Synthesis of selected heterocylic natural products.
  10. Some modern methods of heterocycle synthesis with emphasis on organometallic reagents.


  1. Topics in Heterocycles Chemistry. G. W. Gribble. Spinger-Verlag Berlin Heidelberg, 2010.
  2. Modern Heterocyclic Chemistry. 4 Volume Set. Julio Alvarez-Builla, Juan Jose Vaquero, José Barluenga. Wiley. 2011.
  3. L.A. Paquette, Principles of Modern Heterocyclic Chemistry, W.B. Benjamin, Inc., 1978.
  4. Handbook of Heterocyclic Chemistry. Alan R. Katritzky and A. F. Pozharskii, Elservier 2000.
  5. The Chemistry of Heterocycles. T. Eicher, S. Hauptmann, Wiley-VCH 2003 R. K. Bansal, Heterocyclic Chemistry, Synthesis, Reactions and Mechanisms, Wiley Eastern Ltd., 1990.
  6. J.A.J. Joule and G.F. Smith, Heterocyclic Chemistry, ELBS, 2nd Ed., 1982.
  7. F.G. Riddell, The Conformational Analysis of Heterocyclic Compounds, Academic Press, 1980.
  8. B.M. Acheson, An Introduction to the Chemistry of Heterocyclic Compounds, Interscience, 2nd Ed., 1975.


CH 546: Introduction to Biomolecules

Aminoacids, peptides and proteins: Amino acids: structure, acid-base chemistry, and chemical synthesis; peptide bond formation and coupling reagents-carbodiimides and phosphonium reagents; orthogonal protecting groups; solid-phase peptide synthesis: (Fmoc/Boc strategies); native peptide ligation; cyclic peptides; amino acid analysis and peptide sequencing; brief introduction to ribosomal protein synthesis; combinatorial chemistry; enzyme chemistry: proteases and phosphotases; proteins as drug targets.

Carbohydrates: Introduction to carbohydrates; structure, configuration and conformation; common protecting groups and protecting group strategies; glycosylation: general concepts, various methods of glycoside bond formation; strategies in oligosaccharide synthesis: automated and enzymatic approaches; glycoconjugates: glycolipids and glycoproteins; fundamentals of glycobiology; tools for glycomics; carbohydrate based drug discovery.

Nucleosides, nucleotides and nucleic acids: Introduction to nucleic acids: biological importance, discovery, structure; chemical synthesis of nucleosides and protecting groups for nucleobase, sugar and phosophates; solution and solid phase synthesis of oligonucleotides: phosphotriester, H-phosphonate and phosphoramidite strategies; DNA Processing Enzymes: DNA polymerases, ligases, restriction endonucleases, PCR; enzymatic synthesis of nucleic acids; principle behind sequencing; nucleic acid as drug targets; quadruplex nucleic acids; nucleic acids based enzymes: ribozymes, DNA enzymes and riboswitches; nucleic acid based therapeutic strategies: antisense, RNA interference and aptamers; DNA damage and repair.


  1. P. Lloyd-Williams, F. Albericio, E. Giralt, Chemical Approaches to the Synthesis of Peptides and Proteins, 1st Edition, CRC Press, Boca Raton,1997.
  2. S. Doonan, Peptides and Proteins, 1st Edition, RSC Publishing House, London, 2002.
  3. T. Bugg, An Introduction to Enzyme and Coenzyme Chemistry, 2nd Edition, Blackwell Science, Oxford, 2004.
  4. B. G. Davis & A.J. Farbanks, Carbohydrate Chemistry, 1st Edition, Oxford University Press, 2002.
  5. R. V. Stick., Carbohydrates: The Essential Molecules of Life, 2nd Edition, Academic Press, 2009.
  6. D. E. Levy and P. Fugedi, The Organic Chemistry of Sugars, CRC Press, 2006.
  7. G. M. Blackburn, M. J. Gait, D. Loakes, D. M. Williams, Nucleic Acids in Chemistry and Biology, 3rd Edition, RSC Publishing, London, 2006.
  8. S. Doonan, Nucleic Acids, 1st Edition, RSC Publishing House, London, 2004.
  9. A. Lehninger, D. L. Nelson, Cox, M. M. Principles of Biochemistry, 5th Edition, W.H Freeman, 2008.


CH 582: Inorganic Photochemistry

Introduction to inorganic photochemistry. Photochemical laws and photochemical kinetics. Photophysical processes. The electronic absorption spectra of inorganic compounds. Characteristics of the electronically excited states of inorganic compounds. Photoelectochemistry of excicted state redox reactions. Photosensitization. Photochemical reactions; substitution, decomposition and fragmentation, rearrangement, and redox reactions. Selective inorganic photochemistry using laser beams. Inorganic photochemistry in biological processes and their model studies.


  1. G. L.Geoffrey and M. S. Wrighton, Organometallic Photochemistry, Academic Press, 1979.
  2. K. K. Rohatagi-Mukherjee, Fundamentals of Photochemistry, Wiley Eastern, 1978.
  3. M. S. Wrighton, Inorganic and Organometallic Photochemistry, ACS Pub.,1978.
  4. V. Balzani and V. Carasiti, Photochemistry of Co-ordination compounds, Academic Press, 1970.


CH 584: Biophysical Chemistry

Structure of water. Biological relevance of chemical potential. Hydrophobic and hydrophilic interactions in biological systems. Protein-Solvent Interactions - preferential binding, hydration and exclusion. Protein structure, stability, folding, unfolding and their studies with spectroscopic and calorimetric methods. Protein-Ligand Binding. Structure-Function relationships. Equilibria across membranes.


  1. R. B. Gregory, ed., Protein-Solvent Interactions, Marcel Dekker,Inc., 1995.
  2. B. T. Nall and K. A. Dill, ed., Conformations and Forces in Protein Folding, American Association for the Advancement of Science, 1991.
  3. C. Branden and J. Tooze, Introduction to Protein Structure, Garland Publishing, Inc., 1991.
  4. J. Wyman and S. J. Gill, Binding and Linkage : Functional Chemistry of Biological Macromolecules, University Sciences Books, 1990.
  5. C. R. Cantor and P. R. Schimmel, Biophysical Chemistry, Part III, W.H.Freeman and Co., 1980.


CH 518: Macromolecular Crystallography

Basic Diffraction Theory, Bragg’s law, Miller Indices, Laue Equations, Protein and Nucleic acid Structure, X-ray major sources and production, Xray detectors, Crystallization techniques and principles, symmetry and space groups, reciprocal space, Fourier transform, structure factor equation, phase problem, data collection and processing, methods of structure determination, heavy atom solutions like direct methods, patterson methods, Multiple Anomalous diffraction, Single Anomalous diffraction, sulpur phasing, Isomorphous replacement, Molecular replacement, structure refinement and validation, structure deposition, elucidation of mechanism from structure, biological crystallography examples of virus, ribosomes, membrane proteins, macromolecular assemblies.


  1. Principles of protein x-ray crystallography Jan Drenth
  2. Crystallography Made Crystal Clear , Gale Rodes
  3. Structure determination by X-ray crystallography M. Ladd and R Palmer