Courses for M.Sc. in Chemistry | Welcome to Jawaharlal Nehru University

Course Structure for M.Sc. in Chemistry

Semester I (Total Credits: 21)	Semester II (Total Credits: 22)
Organic Chemistry-I (4)	Organic Chemistry-II (4)
Inorganic Chemistry-I (4)	Inorganic Chemistry-II (4)
Introductory Quantum Chemistry (4)	Introductory Molecular spectroscopy (4)
Mathematical Methods and Group Theory (3)	Basic Physical Chemistry (4)
Laboratory - I (6)	Laboratory - II (6)
Total Credits at the end of first year = 43
Semester III (Total Credits: 23)	Semester IV (Total Credits: 18)
Advanced Organic Chemistry (4)	Elective I (3)
Advanced Inorganic Chemistry (4)	Elective II (3)
Fundamental Analytical Techniques in Chemistry (4)	Elective III (3)
Advanced Physical Chemistry (4)	Seminar Course (1)
Chemistry Research Project-I (7)	Chemistry Research Project-II (8)
Total Credits at the end of second year = 43 + 41 = 84

List of Elective Courses (3 Credits):

PS 468C	Solid State Chemistry	PS 616C	Molecular Materials
PS 469C	Biophysical Chemistry	PS 622C	Medicinal Inorganic Chemistry
PS 470C	Physical Organic Chemistry	PS 473C	Bioorganic Chemistry and Drug Discovery
PS 471C	Natural Products and Medicinal Chemistry	PS 623C	Chemistry and Biology of Glycoconjugates
PS 472C	Group Theory and its Application	PS 614C	Advanced Spectroscopy and its Application
PS 613C	Computational Chemistry Applications	PS 615C	Supramolecular Chemistry

Syllabus for Courses in M.Sc. in Chemistry/Post-graduate Diploma in Chemistry:

Organic Chemistry-I (PS4XXC) 4 Credits

Introduction: Basic principles of structure and bonding, acidity and basicity in organic molecules, HSAB theory and applications, tautomerism, Hückel’s rule, aromaticity, antiaromaticity and homo-aromaticity.

Reactive Intermediates: Generation, structure, stability and reactivity of following reactive intermediates: carbocations, carbanions, free radicals, carbenes, nitrenes and benzynes.

Organic Stereochemistry: Linear and circularly polarized light and chiroptical properties, Stereoisomerism: definitions and classifications, absolute configuration and nomenclature, racemic modification, Axial and planar chirality and helicity (P & M). Prochiral centers and topicity, Racemizations and methods for resolution, Conformations of acyclic compounds and cyclic compounds, Stereospecific and stereoselective reactions.

Organic Reaction Mechanisms: Nucleophilic substitution reactions in aliphatic and aromatic systems, Electrophilic substitution reactions, Addition reactions, Elimination reactions, Nucleophilic addition to unsaturated systems, Rearrangement reactions. Pericyclic reaction: Introduction and classification, Theory of pericyclic reactions: correlation diagrams, FMO, and PMO methods, Electrocyclic reactions, Cycloadditions reactions, Sigmatropic rearrangements. Group transfer reactions. Molecular rearrangements (pericyclic and non-pericyclic), Photochemistry: basics and mechanistic principles.

Tutorials: Problems and their solutions related to above topics will be discussed in the tutorial class.

Recommended Texts:

Michael B. Smith, March's Advanced Organic Chemistry: Reactions, Mechanisms, and Structure, Wiley, 7^th Edition, 2013.
I. L. Finar and A. L. Finar. Organic Chemistry Vol. 1 and Vol. 2. Pearson Education India, 6th edition, 2002.
J. Clayden, N. Greeves, S. Warren. Organic Chemistry, 2nd Edn, Oxford University Press, 2014.
C.B. Fryhle, S. A. Snyder, G. Solomons. Organic Chemistry-ISV, John Wiley & Sons, 2015.
F. A. Carey and R. J. Sundberg. Advanced Organic Chemistry, Parts A & B, Springer; 5th Corrected ed. 2007. Corr. 2nd printing 2008 edition.
P. Sykes. A Guidebook to Mechanism in Organic Chemistry. Pearson Education; 6 edition (2003).
Samuel H. Wilen, Ernest L. Eliel, Stereochemistry of Organic Compounds, Wiley, 2008.
D. N. Nasipuri. Stereochemistry of Organic Compounds: Principles & Applications, New Age; Third edition, 2011.
Subrata Sen Gupta, Basic Stereochemistry of Organic Molecules, Oxford University Press; First edition 2014.

Inorganic Chemistry-I (PS4XXC) 4 Credits

Structure and Bonding: The basic concepts of VBT, hybridization, VSEPR theory, Bent’s rule, introduction to MOT, homonuclear diatomic molecules, heteronuclear diatomic molecules, polyatomic molecules, isomers of coordination compounds: geometrical and optical isomers.

Acids and Bases: Bronsted acids and bases, properties of Lewis acids and bases, Solvent system concept, theory of hard and soft acids and bases (HSAB), strength of acids and bases, gas phase versus solution acidity, superacids, Hammet acidity function, surface acidity.

Oxidation and Reduction: Redox reactions and EMF, standard reduction potential, Nernst equation, factors affecting the EMF, the effect of complex formation, pH, precipitation, concentration, electrochemical series, over potential, disproportionation/comproportionation reactions, redox stability in water, redox potential diagrams, Frost, Latimer, Pourbaix, Ellingham diagrams.

Coordination Chemistry: Crystal field theory (CFT) and its applications, d-Orbital splitting in various fields, determination of CFSE, factors affecting the magnitude of CFSE, spinels, Jahn-Teller effect, spectroscopic states and term symbols, hole formalism, electronic spectra, Orgel and Tanabe-Sugano diagrams, Nephlauxetic effect, molecular orbital theory (MOT), ligand field theory, bonding involving pi-donor ligands, back-bonding, magnetic properties, orbital contribution, spin-orbit coupling, f-orbital splitting, spectral and magnetic properties of f-block elements, the chemistry of actinides and lanthanides.

Inorganic Reaction Mechanisms: Substitution reactions, kinetics of octahedral substitution, trans-effect, associative and dissociative interchange, molecular rearrangements, kinetics consequences of reaction pathway, experimental evidences in octahedral substitution, electron transfer reactions: inner sphere and outer sphere reactions - Photo-dissociation and photo-redox reactions of metal complexes.

Tutorials: Problems and their solutions related to above topics will be discussed in the tutorial class.

Recommended Texts:

P. Atkins, T. Overton, J. Rourke, M. Weller, F. Armstrong: Shriver and Atkins, Inorganic Chemistry, 6th Edn, 2014.
J. D. Lee, Concise Inorganic Chemistry, 5th Edn, John Wiley & Sons, 2008.
Housecroft and A. G. Sharpe, Inorganic Chemistry, 4th Edn, Pearson, 2012.
F. A. Cotton and G. Wilkinson, Advanced Inorganic Chemistry, 5th Edn, John Wiley, 1999 (or F. A. Cotton, C. A. Murillo, M. Bochmann and R. N. Grimes, Advanced Inorganic Chemistry, 6th Edn, Wiley, 1999).
J. E. Huheey, E. A. Keiter, R. L. Keiter, Inorganic Chemistry: Principles of Structure and Reactivity, 4th Edn, Prentice Hall, 2006 (or a previous edition).
G. L. Miessler and D. A. Tarr, Inorganic Chemistry, 5th Edn, Pearson Education, 2014.
G. Wulfsberg, Inorganic Chemistry, University Science Books, 2000.

Introductory Quantum Chemistry (PS 4XXC) 4 Credits

Introduction: Black body radiation, review of classical mechanics, electron diffraction, measurements in quantum theory, hydrogen atom spectrum, Bohr Sommerfeld theory, uncertainty principle, wave-particle duality.

Quantum Mechanics: Postulates of quantum mechanics, Schrodinger equation, Born approximation, operators, eigenvalue problem, commutators.

Applications of Quantum Mechanics: Particle motion in one-dimension, wave packets, bound motion of particles in square well, tunneling, perturbation theory, simple harmonic oscillator and rigid rotors, charged particle in a uniform magnetic field, angular momentum algebra - Hydrogen atom, atomic orbitals, many electron atoms.

Variation method, Slater determinants, self-consistent field, atomic orbitals, Slater type orbitals and LCAO-MO, VSEPR theory, molecular orbital and valence bond approaches, Hückel orbitals, Born-Oppenheimer approximation, Introduction to approximate theory, Hartree-Fock method, Kopmann’s theorem, Roothan’s equation, introduction to electron correlation calculation.

Tutorials: Problems and their solutions related to above topics will be discussed in the tutorial class.

Recommended Texts:

D. A. McQuarrie, Quantum Chemistry, Viva Books, 2011.
F. L. Pilar, Elementary Quantum Chemistry, 2nd Edition, Dover Books, 2003.
I. R. Levine, Quantum Chemistry, Pearson Education India; Seventh edition, 2016.
P. W. Atkins and R. S. Friedman, Molecular Quantum Mechanics, Fifth Edition, Oxford University Press.
R.P. Feynman, Feynman Lectures (Volume 3).

Mathematical Methods and Group Theory (PS477C) 3 Credits

Numbers: Real and Complex numbers, vector algebra – vector multiplication, gradient, divergence, curl.

Differential Calculus: Differential calculus, evaluation of minimum and maximum, partial differentiations, exact and inexact differentials, gamma and delta functions, Fourier and Laplace transformation.

Integral Calculus: Indefinite and definite integrals, improper integrals. Line, surface and volume integrals, Stokes and Gauss theorem.

Differential Equations: Ordinary first- and second-order differential equations, partial differential equations.

Matrices and Determinants: Vector spaces, eigenvalues and eigenvectors, matrix diagonalization, rank and inverse of matrix, determinants.

Curve fittings: Introduction to Curve fitting and data analysis, introduction to least square fitting analysis, goodness of fit.

Fundamental Concepts: Symmetry Operations and Elements, Defining the Coordinate System, Cartesian Coordinate systems and Symmetry Elements, Combining Symmetry Operations, Symmetry multiplication Table, Mathematical requirement for a point group. Similarity transformation and conjugate classes.

Molecular Point Groups: Points Groups, Identification of Molecular Point Groups, Stereographic projection of point group, Molecules of Low Symmetry, Molecules of High Symmetry, Molecules of Special Symmetry, Systematic Assignment of point groups to Molecules, Symmetry criteria for Optical Activity, Symmetry Restrictions on dipole moments.

Representation of Groups: Group Multiplication Table, Group Generating Elements, Isomorphic Groups, Subgroup, Classes, Irreducible representation & its Properties, Unit Vector Transformations, Reducible representation, characters of symmetry operators in a representation, invariance of character under similarity transformation, Construction of Character Tables.

Recommended Texts:

Mathematics for Physical Chemistry. R. G. Mortimer, Academic Press.
Mathematics for Engineers and Scientists, A. Jeffrey, Sixth Edition, CRC Press.
Vector Analysis. M. R. Spiegel, Schaum’s Outline.
Numerical Analysis: A Practical Approach. Melvin J. Maron, Macmillan Publishing Co.
F. Albert Cotton, 3^rd Edition, Chemical Application of Group Theory, Tata McGraw-Hill Publishing, 1990.
David M. Bishop, Group Theory and Chemistry, Dover Publications.
Robert L. Carter, Molecular Symmetry and Group Theory, John Wiley & Sons Inc, 2005.
Alan Vincent, 2^nd Edition, Molecular Symmetry and Group Theory, John Wiley & Sons Ltd, 2001.
Roy McWeeny, Symmetry: An Introduction to Group Theory and Its Applications, Dover Publications Inc., New York 2002.
K V Raman, Group Theory and its Applications to Chemistry, Tata McGraw-Hill, New Delhi, 10^th Reprint, 2003.
A. K. Mukherjee and B. C. Ghosh, Group Theory in Chemistry: Bonding and Molecular Spectroscopy, University Press (India) Pvt. Ltd.

Laboratory-1 (PS475C) 6 Credits

Note: Selected experiments from the list below will be carried out.

Determination of composition of binary liquid mixtures from surface tension measurement.
Determination of viscosity of liquid mixtures (e.g., glycerol/water mixture) using viscometer.
Determination of molecular weight of polymers (e.g., polystyrene, polyethylene oxide, polyvinylpyrrolidone) using viscometer.
Determination of fluorescence quantum yield of unknown dye in solution using standard fluorophore.
Estimation of critical micellar concentration (CMC) of micelle (e.g. sodium dodecyl sulphate) and critical association concentration (CAC) of polymer-surfactant aggregate (e.g. sodium dodecyl sulphate/polyvinylpyrrolidone) using fluorescence spectroscopy.
Micellization and determination of critical micellar concentration (CMC) of ionic micelles (e.g. sodium dodecyl sulphate, cetyltrimethylammonium bromide) using conductmeter and comparison with fluorescence results.
Estimation of Oscillator Strength of dye molecule (e.g. rhodamine, comarin) using

spectrophotometry.

Separation and qualitative analysis of mixture of organic compounds. Spectroscopic characterizations and precise identification of the individual compounds.
Purification techniques: Recrystallization, distillation, vacuum distillation, Column chromatography, Thinlayer chromatography techniques.
Quantitative estimation of aniline, ascorbic acid, glucose, methylethyl ketone and phenol.
Quantitative estimation of the following functional groups: (a) –OCH₃, -OH, -COOH and -NH₂ groups.
Analysis of ores and minerals (Qualitative analysis).
Ion exchange: separation of Zn²⁺ and Mg²⁺ on an ion exchanger.
Estimation of metal ions (Ca²⁺ and Mg²⁺) using EDTA titrations.
Gravimetric analysis of Nickel (Preparation of hexamminenickel (II) chloride: estimation of ammonia and nickel by titrimetric and gravimetric methods).
Analysis of hydrogen peroxide.
Spectrochemical determination of different anions in aerated drinks.
Acid-base and redox titration of tablets containing vitamin C.
Group separation of cations.

Recommended Texts:

A. I. Vogel. Textbook of Practical Organic Chemistry, 5th Edn.
F. G. Mann and B. C. Saunders. Practical Organic Chemistry, 1979.
A. I. Vogel. Textbook of Macro and Semi-micro Qualitative Inorganic Analysis, 5th Edn, Orient Longman, 1982.
J. Mendham. Vogel's Textbook of Quantitative Chemical Analysis, 5th Edn, 2009.
Anil J. Elias. A Collection of Interesting General Chemistry Experiments, University Press, 2007.
Lab Manual.

Organic Chemistry-II (PS4XXC) 4 Credits

Oxidation Reactions and Reagents: Alcohol oxidation (chromium (VI) oxidants, DMSO based oxidation, hypervalent iodine compounds, oxammonium salts, oxidations with Silver and other metals), Oxidation of alkenes (peroxide based epoxidations and asymmetric epoxidation reactions, dihydroxylation reactions), Oxidative cleavage of C=C/C-C bonds (KMnO₄, osmium reagents, ruthenium reagents, chromium reagents, ozonolysis, lead tetraacetate, sodium periodate), Oxidation of alkyl/alkenyl groups (SeO₂ oxidation, DDQ oxidation, photochemical oxidations). Miscellaneous oxidizing reagents like IBX, DMP, CAN etc.

Reductions: Metal hydride based reduction (LAH reduction of carbonyl compounds, epoxides, nitriles, azides, nitro compounds, sulfonamide, alkyl halides etc), Use of different reducing agents in organic transformations (alkoxyaluminate reducing agents, sodium/lithium/zinc borohydride, acyloxy-borohydride, super hydride, Selectrides, sodium cyanoborohydride, boranes, aluminum hydride, DIBAL, etc.), Stereoselectivity in reduction chemistry, Catalytic hydrogenation (hydrogenation of alkenes, alkynes, carbonyl compounds, other heteroatom functional groups, aromatic and heteroaromatic compounds, asymmetric catalytic hydrogenation), Dissolving metal reductions (reduction of carbonyls, alkene and alkynes), Reduction with non-metallic reagents (reduction with silanes, diimide, hydrazine and photochemical reductions).

Methods in Organic Synthesis: Preparation and applications of diazomethane and phosphorus/sulphur/nitrogen ylides in organic synthesis, principles and applications of phase transfer catalysis (PTC) and crown ethers in organic synthesis, umpolung transformations.

Organometallic Chemistry: Preparation and applications of organosilicon compounds, organolithium and organocuparate, organomagnesium in organic synthesis. Some aspects of commonly used ligands in homogeneous catalysis, such as, CO, amines, phosphines, NHCs, alkenes, alkynes, carbenes, carbynes, etc. Coupling and C-H activation: Applications of Pd(0) and Pd(II) complexes in Stille, Suzuki, Sonogashira, Heck, Negishi and Buchwald-Hartwig coupling reactions.

Tutorials: Textual problems referred to above topics will be discussed.

Recommended Texts:

J. March. Advanced Organic Chemistry, John Wiley & Sons, 1992.
M. B. Smith. Organic Synthesis, 3rd Edn, Elsevier, 2011.
W. Carruthers. Modern Methods of Organic Synthesis, Cambridge University Press, 1971.
F. A. Carey and R. J. Sundberg. Advanced Organic Chemistry, Parts A & B, Plenum: U.S, 2004.
R. B. Grossman. The Art of Writing Reasonable Organic Reaction Mechanism, 2nd Edn, Springer, 2003.
A. Meijere and F. Diederich. Metal-Catalyzed Cross-Coupling Reactions, Vol. 1 and Vol. 2. Willey-VCH, 2004.
J. Clayden, N. Greeves, S. Warren. Organic Chemistry, 2nd Edn, Oxford University Press, 2014.
B. D. Gupta & Anil J. Elias. Basic Organometallic Chemistry (Concept, Synthesis & Application), 2nd Edn, University Press, 2013.

Inorganic Chemistry-II (PS4XXC) 4 Credits

Hydrogen: Position in the periodic table, hydrides of elements, hydrogen storage, hydrogen as renewable fuel and hydrogen-based fuel cells, the chemistry of green hydrogen.

Group 1 and 2: Reaction with water, s-block elements compounds: hydrides, halides, oxides, peroxides, superoxides, hyroxides and oxyacids, complexation with acyclic and macrocyclic ligands (e.g., crown ethers and cryptands).

Group 13 elements: Structure of crystalline boron, metal borides, boranes: bonding and topology, Wades and mno rules, carboranes and metallocarboranes, borates, boron-nitrogen compounds, borylene and boron-based Lewis bases, trialkyl aluminium compounds, organoaluminum compounds, organo-gallium, indium, and thallium compounds.

Group 14 elements: Allotropes of carbon, intercalation compounds of graphite, fullerenes, synthesis and properties of carbon nanotubes, synthesis of pure elemental silicon, silica and silicates, organosilicon compounds and silicones, low valent silicon compounds, brief survey of Ge, Sn, and Pb chemistry.

Group 15 elements: Hydrides of nitrogen, oxides of nitrogen, oxoacids of nitrogen, allotropes of phosphorus, phosphides, phosphorus oxides and sulfides, phosphorus oxoacids and salts, phosphorus nitrogen compounds.

Group 16 elements: Allotropes of sulfur, metal sulfides, polysulfides, oxides and oxyacids of sulfur, sulfur-nitrogen compounds.

Group 17 elements: Charge-transfer complexes of halogens, interhalogen compounds and polyhalogen ions, oxides of chlorine, bromine and iodine, oxoacids and oxygen fluorides.

Group 18 elements: Noble gas clathrates, compounds of xenon halides, xenon oxides, xenon oxyhalides, compounds of other noble gases.

Tutorials: Problems and their solutions related to above topics will be discussed in the tutorial class.

Recommended Texts:

A. J. Elias, The chemistry of the p-block elements: Syntheses, reactions and applications Universities Press, Hyderabad, 2018.
A. G. Massey, Main group chemistry, 2nd Edn, Wiley, 2000.
N. N. Greenwood and A. Earnshaw, Chemistry of the Elements, 2nd Edn, Butterworth-Heinemann, 1997.
P. Atkins, T. Overton, J. Rourke, M. Weller and F. Armstrong: Shriver and Atkins, Inorganic Chemistry, 6th Edn, 2014.
C. Housecroft and A. G. Sharpe, Inorganic Chemistry, 4th Edn, Pearson, 2012.
F. A. Cotton and G. Wilkinson, Advanced Inorganic Chemistry, 5th Edn, John Wiley, 1999 (or F. A. Cotton, C. A. Murillo, M. Bochmann and R. N. Grimes, Advanced Inorganic Chemistry, 6th Edn, Wiley, 1999).
J. E. Huheey, E. A. Keiter and R. L. Keiter, Inorganic Chemistry: Principle of Structure and Reactivity, 4th Edn, Pearson Education, 2006.

Introductory Molecular Spectroscopy (PS4XXC) 4 Credits

Introduction: Electromagnetic radiation, Maxwell’s equations, spectral measurement procedures, dispersive and Fourier transform spectrometers, concepts of signal to noise ratio.

Interaction radiation with Matter: Interaction of EM-radiation with matter. Origin of spectral line-shapes and population of states, selection rules. Time-dependent perturbation theory, transition dipole moment, Fermi's Golden rule, Einstein’s coefficients. Lasers – population inversion, examples of lasers, laser cavity modes.

Rotational and Vibrational Spectroscopy of Molecules: Rotational, vibrational and rotational-vibrational spectroscopy of molecules, selection rules. Analysis of local and normal modes, symmetry of normal modes. Infrared spectroscopy, selection rules, matrix formulation of vibration of polyatomic molecules. Raman effect and Raman spectroscopy, Rotational and vibrational Raman Spectroscopy, selection rules.

Electronic Spectroscopy of Molecules: Electronic spectroscopy, Fortrat diagram, Franck-Condon principle, selection rules. Vibrational progressions and geometry of excited states. Radiative and nonradiative processes-internal conversion and intersystem crossing, fluorescence and phosphorescence. Resonance Energy Transfer, Förster theory, Overlap integral. Solvent effect on absorption and emission spectroscopy.

Spin Resonance Spectroscopy: Magnetic resonance spectroscopy-origin of chemical shift and spin-spin coupling, Paramagnetic shifts. classical treatment of relaxation. Introduction to EPR spectroscopy.

Tutorials: Textual problems referred to above topics will be discussed.

Recommended Texts:

C. N. Banwell and E. M. McCash, Fundamentals of Molecular Spectroscopy, Tata McGraw-Hill publishing.
R. Kakkar, Atomic and Molecular Spectroscopy: Basic Concepts and Applications, Cambridge, 2015.
I. N. Levine, Molecular Spectroscopy, Wiley Interscience Publication.
J. M. Hollas, Modern Spectroscopy, Wiley India Exclusive, 2015.
G. M. Barrow, Introduction to Molecular Spectroscopy, McGraw-Hill.
William T. Silvast, Laser Fundamentals, Cambridge University Press.

Basic Physical Chemistry (PS4XXC) 4 Credits

Chemical Thermodynamics

Review of laws of thermodynamics, thermodynamics of ideal and non-ideal gases, and ideal and non-ideal solution, partial molar quantities and their significances. Thermodynamic description of various types of processes, Maxwell’s relations, Chemical potential, Gibbs-Duhem equation, interaction parameters; Regular solution model, concepts of positive and negative deviation.

The thermodynamics of mixing – the Gibbs function of mixing after thermodynamics mixing functions. Raoultian and Henrian solutions.

Physical Transformation of pure materials; Phase equilibria and phase rule, Representative examples, Thermodynamic aspects of phase transitions, Representative phase diagrams, Application of phase rule to three component systems; second order phase transitions.

Limitations of classical (equilibrium) thermodynamics, entropy production in some simple irreversible processes, concept of forces and fluxes, linear phenomenological relations; stationary states: variation of entropy production with time, Prigogine’s criterion for establishment of stationary state, applicability of Le Chateliar’s principle on stationary states.

Kinetics

Methods for determining reaction mechanism and rate laws. Composite reactions - rate equation, steady state treatment, Fast reactions, Chain reactions, Oscillatory reactions. Collision Theory, Transition State Theory, Theory of unimolecular reactions, Lindemann mechanism, Hinshelwood-treatment, RRKM model, Enzyme kinetics, Dielectric effect on ion- ion reaction, electrostriction, volume of activation, effect of pressure on reaction rate, classification of reactions on the basis of volume of activation, Curtin-Hammett principle, linear free energy relationship, Hammett and Taft equation; study of fast reactions ⎯ flow process and relaxation techniques.

Electrochemistry

Basic concepts of electrochemistry, Derivation of the Debye-Huckel theory of activity coefficients. Genesis of double layer, polarizable and non-polarizable interfaces. Electrocapillary thermodynamics. Structure of the double layer: HB, GC, Stern and BDM models, overpotential, corrosion. Cyclic voltametry, Characteristics of irreversible & reversible CV. Ion-solvent interaction: Born model and Born equation, enthalpy of ion-solvent interaction and its calculation.

Tutorials: Problems and their solutions related to above topics will be discussed in the tutorial class.

Suggested reading:

Physical Chemistry. P. W. Atkins and J. de Paula, Oxford University Press.
Physical Chemistry. I. N. Levine, McGraw Hill.
Physical Chemistry. R. G. Mortimer, Academic Press.
Electrochemistry by Carl H. Hamann, Andrew Hamnett and Wolf Vielstich, Wiley VCH, 1998.
M. R. Wright, Fundamental Chemical Kinetics, Horwood Publishing, 1999.
R. A. McQuarrie and J. D. Simons, Physical Chemistry 1st Edn, Viva Books Private Limited, New Delhi, 1998.
J. O’M. Bockris and A. K. N. Reddy, Modern Electrochemistry, Vol. I, Plenum Press, New York, 1970.
Electrochemistry by Carl H. Hamann, Andrew Hamnett and Wolf Vielstich, Wiley VCH, 1998.

Laboratory-2 (PS476C) 6 Credits

Note. Selected experiments from the list below will be carried out.

Basic laboratory techniques to synthesize, purify, and characterize small organic molecules by analytical and spectroscopic methods.

Aldol condensation
Friedel Craft Alkylation and Acylation reaction
Photochemical reaction
Diazotization reaction
Coupling reactions
Schiff base formation
Acetylation of Salicylic acid (Aspirin)
Synthesis of Benzanilide/ Hippuric acid

Elucidation of Synthesized product under conceotual name reactions-Mannich Reaction, Beckmann rearrangement, Claisen condensation, Perkin reaction.

Synthesis of Saccharin, Dichloramine-T, Isatin, Indole.
Isolation and characterization of natural products: lycopene, Carotene, Caffeine, Limunine.
Estimation of thermodynamic parameters of protein denaturation (e.g. serum albumin, lysozyme) using UV-vis spectrophotometry and fluorescence spectroscopy.
Determination of Kinetic constant of the reaction between ferric and iodide ions.
Kinetic study of hydrolysis of ester.
Determination of composition of component in a mixture (e.g. KCl+KBr+KI) using potentiometric titration.
Estimation of the pKa of amino acid and organic molecule using pH meter.
Estimation of thermodynamic parameters for protein-ligand interaction using absorption and fluorescence spectroscopy.
Determination of spectroscopic and molecular constants of HCl using Fourier-Transform infrared spectrometer.
Preparation of tris-acetylacetonatoIron(III).
Acetylation of ferrocene.
Potassium tris-oxalatoferrate(III): synthesis, analysis and photochemistry.
Preparation of [M(Salen] (M= Fe, Ni, Cu).
Preparation of tetra(p-tolyl)porphyrinatozinc(II), [Zn(TTP)].
Synthesis of a cobalt(III) complex of an encapsulating ligand.
Preparation of cis- and trans-bis(glycinato)copper(II) monohydrate.
Preparation of ethylenediamine coordination complexes (M=Co, Ni).
Preparation of biguanide.

Recommended Texts:

A. I. Vogel. Textbook of Practical Organic Chemistry, 5th Edn,
F. G. Mann and B. C. Saunders. Practical Organic Chemistry, 1979.
A. I. Vogel. Textbook of Macro and Semi-micro Qualitative Inorganic Analysis, 5th Edn, Orient Longman, 1982.
J. Mendham. Vogel's Textbook of Quantitative Chemical Analysis, 5th Edn, 2009.
Anil J. Elias. A Collection of Interesting General Chemistry Experiments, University Press, 2007.
Lab Manual.

Advanced Organic Chemistry (PS4XXC) 4 Credits

Retrosynthetic Analysis: Selectivity in organic synthesis: chemo-, regio-, stereo- and enantioselectivity. Target-oriented synthesis: Designing organic synthesis, Retrosynthesis, disconnection approach, linear and convergent synthesis. Retrosynthesis of different organic compounds and applications in natural product synthesis.

Heterocyclic Chemistry: Nomenclature, reactivity, synthesis and reactions of three-, four-,five- and six-membered heterocycles, benzo-fused and other fused heterocycles. Tandem, domino and multi-component reactions in the synthesis of heterocycles.

Organic Spectroscopy: Applications of UV, IR, NMR, and mass spectral methods in structure determination of organic compounds.

Chemistry of Biomolecules: Carbohydrates: Introduction and general aspects, anomeric effect, glycosylation reactions, sugars in different natural products and biomolecules. Amino acids: Introduction, types of amino acids and structures, peptides and proteins, primary, secondary, tertiary and quaternary structure of proteins. Nucleic acids: Introduction, purine and pyrimidine bases, structure of DNA and RNA.

Tutorials: Problems and their solutions related to above topics will be discussed in the tutorial class.

Recommended Texts:

F. A. Carey and R. J. Sundberg. Advanced Organic Chemistry, Parts A & B, Plenum: U.S, 2004.
R. M. Acheson. Introduction to the Chemistry of Heterocyclic Compounds, John Wiley & Sons, 1976.
J. A. Joule and K. Mills. Heterocyclic Chemistry, 5th Edn. Wiley-Blackwell, 2010.
S. Warren. Organic Synthesis: The Disconnection Approach, Wiley, 2007.
D. L. Nelson and M. M. Cox. Lehninger Principles of Biochemistry, 6th Edn, Macmillan Learning, 2013.
T.K. Lindhorst. Essentials of Carbohydrate Chemistry and Biochemistry, 3rd Edn, Wiley-VCH, 2007.

Advanced Inorganic Chemistry (PS4XXC) 4 Credits

Organometallic Chemistry: Ligands in organometallic chemistry: sigma-donor and pi-acceptor ligands, 18 and 16 electron rules, metal carbonyls, metal carbonylate, metal hydrides, metal hydrido carbonyl, metal nitrosyls, metal phosphines, Tolman cone angle, organometallic complexes of alkyls, alkenes, alkynes, allyl, carbenes, carbynes, arene. Synthesis and properties of cyclopentadienyl complexes, agostic interaction, isolobal analogy, oxidative addition and reductive elimination, migratory insertion and elimination reactions, metathesis reactions, metallocenes, fluxional molecules.

Metal Clusters: Structure and bonding, metal-metal bonds, carbonyl and non-carbonyl clusters, dinuclear and multinuclear clusters.

Homogeneous and Heterogeneous Catalysis: Hydrogenation of alkenes, hydroformylation, Wacker process, Monsanto acetic acid process, olefin metathesis, Ziegler-Natta olefin polymerization, Palladium-catalyzed coupling reactions.

Bioinorganic Chemistry: Structure and function of hemoglobin, myoglobin, hemocyanin and hemerythrin, Transport and storage of dioxygen, Biochemistry of iron: transport, storage and function, Electron transport proteins: cytochromes and Fe-S proteins, Copper containing enzymes: blue and non-blue copper enzymes, tyrosinase, galactose oxidase, superoxide dismutase and ascorbate oxidase, Zinc containing enzymes: carbonic anhydrase, carboxy peptidase A and alcohol dehydrogenase, Iron containing enzymes, cytochrome P-450, peroxidase and catalase, photosynthesis and nitrogen fixation, bioinorganic chemistry of alkali and alkaline earth metal cations.

Metals in biology: Diagnostic (Gd, ^99mTc, etc.) and therapeutic (Pt, Au, Ag, etc.) metallodrugs, toxicity of metals (e.g., Hg, Pb, etc.).

Tutorials: Textual problems referred to above topics will be discussed.

Recommended Texts:

J. E. Huheey, E. A. Keiter and R. L. Keiter, Inorganic Chemistry: Principle of Structure and Reactivity, 4th Ed, Pearson Education, 2006.
C. Housecroft and A. G. Sharpe, Inorganic Chemistry, 4th Ed, Pearson, 2012.
B. D. Gupta and A. J. Elias, Basic Organometallic Chemistry, 2nd Ed, University Press, 2013.
S. J. Lippard and J. M. Berg, Principles of Bioinorganic Chemistry, University Science Books, 1994.
G. L. Miessler and D. A. Tarr, Inorganic Chemistry, 5th Ed, Pearson Education, 2014.
I. Bertini, H. B. Gray, S. J. Lippard and J.S. Valentine, Bioinorganic Chemistry, University Science Books, 1998.
D. Rehder, Bioinorganic Chemistry, 1st Ed., Oxford University Press, 2014.

Fundamental Analytical Techniques in Chemistry (PS4XXC) 4 Credits

Molecular Spectroscopy: Infra-red spectroscopy- Theory; instrumentation; sample handling; interpretation of spectra; characteristic group absorptions of molecules. Mass spectroscopy- Instrumentation; mass spectrum; determination of molecular formula; recognition of molecular ion peak; ionization techniques; fragmentation and rearrangements; quantitative applications of mass spectrometry. EPR: Principle and application. Fundamentals of FT NMR spectroscopy, relation between structure and NMR properties, one-dimensional spectroscopy (1H, 13C, DEPT, steady state NOE, saturation transfer) and an introduction to two-dimensional NMR (COSY, NOESY, and HSQC) and their use in structure elucidation.

Separation Methods: An introduction to chromatographic separations; Gas chromatography; Gas chromatographic columns and stationary phases; principles and applications of gas-liquid chromatography; High-Performance Liquid Chromatography (HPLC); Thin layer and column chromatography; Ion-Exchange chromatography; Size- exclusion chromatography.

Electroanalytical Chemistry: Principles, instrumentation and applications; Potentiometry, Coulometry and Voltammetry.

Microscopy Techniques: AFM, STM, SEM, TEM, Confocal Fluorescence.

X-ray Diffraction: Fundamental, Principles and analysis of powder and single crystal x-ray data.

Thermal Methods: Thermogravimetric methods; Differential Thermal Analysis; Differential Scanning Calorimetry.

Tutorials: Problems and their solutions related to above topics will be discussed in the tutorial class.

Recommended Texts:

Principles of Instrumental Analysis by Douglas A. Skoog, F. James Holler, Timothy A. Nieman; SaundersGolden Sunburst Series.
Modern Analytical Chemistry by David T Harvey; McGraw-Hill Science.
Spectrometric Identification of Organic Compounds by R. M. Silverstein, F. X. Webster; John Wiley and sons.
Analytical Chemistry by Gary D. Christian; John Wiley and sons.
200 and More NMR Experiments: A Practical Course by Stefan Berger, Siegmar Braun; Wiley.
Nuclear Magnetic Resonance spectroscopy: Introduction to principle and applications and experimental methods by J. B. Lambert and E. P. Mazzola: Pearson Education Inc.
Organic Spectroscopy by William Kemp: Palgrave.
Mass Spectrometry: Principles and Applications by Edmond de Hoffmann and Vincent Stroobant: Wiley.
Mass Spectrometry: Instrument, Interpretation and Applications by R. Ekman, J. Silberring, A. Westman-Brinkmalm and A. Kraj: Wiley.
Mossbauer Spectroscopy and Transition Metal Chemistry: Fundamentals and Applications by P. Gutlich, E. Bill and A. X. Trautwein: Springer

Advanced Physical Chemistry (PS4XXC) 4 Credits

Statistical Mechanics

Concepts of statistical thermodynamics. Thermodynamic probability and most probable distribution, Micro canonical, canonical and grand canonical ensembles. Ensemble averages. Undetermined multipliers. Stirling’s approximation

Types of Statistics; Boltzmann statistics, Fermi-Dirac statistics and Bose-Einstein statistics.

Molecular Partition functions and its importance, Evaluation of translational, vibrational and rotational partition functions for monoatomic, diatomic and polyatomic gases, the electronic and nuclear partition function, Statistical mechanics of ionic solutions. Calculation of various thermodynamic properties, internal energy, entropy, heat capacity and equilibrium constant in terms of partition function. Statistical definition of entropy

Electromagnetic radiation in thermal equilibrium inside an enclosure. Consequences of Fermi-Dirac equation. Lattice vibration and normal modes. Einstein theory and Debye theory of heat capacities of monoatomic solids.

Quantum statistics in the classical limit.

Surface Chemistry

Surface free energy and surface tension, contact angles and wetting, work of adhesion and cohesion, curved interface, Young's equation, capillary action, surfactants and surface pressure, surface excess, Gibbs isotherm, surface double layer and potential.

Adsorption and desorption of molecules, physisorption and chemisorption, Langmuir Isotherm, BET and other isotherms, dissociative adsorption, temperature dependence of adsorption, sticking probability. Surface analytical techniques, spectroscopies (Auger, photoelectron, vibrational) temperature programmed techniques. Surface imaging electron microscopy.

Heterogeneous catalysis, Langmuir-Hinshelwood and Eley-Rideal mechanisms, activation energy. Structure of adsorbed species. Supported catalysts and metal-support interaction. Catalyst deactivation and regeneration, acid-base catalysis.

Tutorials: Problems and their solutions related to above topics will be discussed in the tutorial class.

Suggested reading:

Physical Chemistry. P. W. Atkins and J. de Paula, Oxford University Press.
Statistical Mechanics. D. A. McQuarrie, University Science Books.
Physical Chemistry. I. N. Levine, McGraw Hill.
Physical Chemistry. R. G. Mortimer, Academic Press.
Physical Chemistry by R. S. Berry, S. A. Rice and J. Ross, Oxford University Press, 2^nd Ed. 2000.
Fundamental of Statistical and Thermal Physics by F. Reif, McGraw Hill, International edition 1985.
Elements of Statistical Thermodynamics: Second Edition by L. K Nash

Chem. Research Project-I (PS4xxC) 7 Credits

The students will carry out research project with the respective assigned supervisor. At the end of the semester, the students would present their research work in front of the chemistry faculty, and submit a detailed thesis report to the M.Sc. Advisor.

Chem. Research Project-II (PS4xxC) 8 Credits

Seminar Course (XXX) 1 Credit

The students will attend the departmental and Journal Club seminars.

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Elective Courses (3 Credits)

Note: Any three elective courses from the following courses have to be chosen by the student.

Supramolecular Chemistry (PS615C)

Principles of molecular recognition: Quantification of non-covalent forces and medium effects; Host design; preorganization; enthalpy and entropic contributions; cooperativity and allosteric effects; Induced fit; complexation selectivity.

Cation Binding Hosts: Lariat ethers and podands, crown ethers, cryptands, calyx[n]arenes, cucurbit[n]urils, spherands; selectivity of cation complexation; macrocyclic, macrobicyclic and template effects.

Anion Binding Hosts: Concepts in anion host design; guanidinium-based receptors; organometallic receptors; Neutral receptors; Hydride sponge; anticrowns; biological anion receptors.

Binding of neutral molecules: Binding by cavitands, cyclodextrins, cucurbit[n]urils, dendrimers, molecular clefts and tweezers, cyclophane hosts.

The Supramolecular Chemistry of Life: Biological inspiration for supramolecular Chemistry, alkali metal cations in biochemistry, porphyrins and tetrapyrrole macrocycles, supramolecular features of plant photosynthesis, uptake and transport of oxygen by hemoglobin, enzymes and coenzymes, neurotransmitters and hormones.

Solid-State Inclusion Compounds: Solid-State Host-Guest compounds, clathrate hydrates, urea and thiourea clathrates, other channel clathrates, hydroquinone, phenol, dianin’s compound and the hexahost strategy, tri-o-thymotide, cyclotriveratrylene, inclusion compounds of the calixarenes, solid-gas and solid-liquid reactions in molecular crystals.

Self-Assembly: Introduction, proteins and foldamers: Single molecule self-assembly, biochemical self-assembly, self-assembly in synthetic systems; kinetic and thermodynamic considerations, self-assembling coordination compounds, self-assembly of closed complexes by hydrogen bonding, catenanes and rotaxanes, helicates and helical assemblies, molecular knots.

Recommended Texts:

J. W. Steed and J. L. Atwood, Supramolecular Chemistry, John Wiley and Sons, Ltd.
Jean –Marie Lehn, Supramolecular Chemistry-Concepts and Perspectives, VCH.
Hans-Jorg Schnider and Anatoly K. Yatsimirsky, Principles and Methods in Supramolecular Chemistry, John Wiley and Sons, Ltd.
A. Bianchi, K. B. James and E. Garcia-Espana, Supramolecular Chemistry of Anions, Wiley-VCH.

Solid State Chemistry (PS468C)

Solid state Chemistry: Basic Principles and applications

Solid State Reactions: General Principles, Experimental procedure, Kinetics of solid-state reactions, Crystallization of solutions, melts, glasses and gels. Growth of single crystals:Czochralski method, Bridgman and Stockbarger methods. Zone Melting. Reactions at solid surfaces.

Phase transitions, electronic and magnetic properties:

Phase Transitions: Thermodynamic and Burger’s classification of phase transition, Kinetics of phase transition- nucleation and growth, T-T-T diagrams, Factors that influence kinetics of phase transition, Martensitic and order-disorder transitions.

Electronic Properties and Band Theory: Electronic structure of solids- band theory, Refinement to simple band theory- k-space and Brillouin Zones, Band structure of metals, insulators and semiconductors, Intrinsic and extrinsic semiconductors, Doped semiconductors, p-n junctions.

Magnetic Properties: Classification of materials. Magnetism: Types, determination of magnetic susceptibility. Quantum theory of paramagnetism. Cooperative phenomena. Magnetic domains. Hysteresis.

Diffractions Techniques:

X-ray Diffraction: Diffraction of X-rays by crystals: The Laue equations and Bragg’s law, Definitions related to crystal structure. X-ray diffraction experiments: The powder method and the single crystal method. Reciprocal lattice. Structure factor. Structure factor and intensity. Electron density maps.

Electron diffraction: Scattering intensity versus scattering angle, Wierl equation, measurement technique, elucidation of structure of simple gas phase molecules. Low energy electron diffraction and structure of surfaces.

Neutron diffraction: Scattering of neutrons by solids and liquids, magnetic scattering, measurement techniques. Elucidation of structure of magnetically ordered unit cells.

High-Tc Oxide Superconductors: Structural features of cuprate superconductors. 1-2-3 and 2-1-4 cuprates; structure. Normal state properties: anisotropy and temperature dependence of electrical resistance. Superconducting state: heat capacity, coherence length, relation between Tc and holeconcentration in cuprates; mechanism of superconductivity in cuprates. Applications of high Tc- cuprates.

Non-linear materials: Second and third order non-linear effects; molecular rectifiers and frequency doublers; unimolecular electronic devices. Photochromic materials; optical data storage, memory and switches.

Recommended Texts:

A. R. West, Solid State Chemistry and its Applications, John Wiley and Sons, Singapore (2003).
L. V. Azaroff, Introduction to Solids, Tata McGraw-Hill, New Delhi (1977).
Massa, W. Crystal Structure Determination, 2nd Ed. Springer (2004).
Warren, B. E., X-Ray Diffraction, 1st Ed. Dover Publications (1990).
Sands, D. E. Introduction to Crystallography, Reprint Dover Publications (1994).
Michael Tinkham, Introduction to Superconductivity, 2nd Edn, Courier Dover Publications, 2004.
T. V. Rammakrishnan, C.N.R. Rao, Superconductivity Today, Orient Blackswan, 1999.
Neil W. Ashcroft, N. David Mermin, Solid State Physics, Brooks Cole; 1st edition (January 2, 1976).
H. V. Keer, Principles of the Solid State, New Age International, 1993.
N. B. Hannay, Solid State Chemistry, Prentice-Hall, Englewood Cliffs, 1967.
D. K. Chakrabarty, Solid State Chemistry, New Age Science ltd; 2nd Revised edition (2010).
Michael Tinkham, Introduction to superconductivity, 2nd Edition, Courier Dover Publications, 2004.

Biophysical Chemistry (PS469C)

Fundamentals of biological macromolecules:

Protein Structure and Function: Amino acids and Peptide bond; Primary Structure; Secondary Structure-Alpha Helix, the Beta Sheet, and Turns and Loops; Tertiary Structure; Quaternary Structure; Protein-ligand interaction.

DNA: Composition; Minor groove and Major groove of DNA; Role of DNA in Transcription, DNA- ligand interaction.

Lipids and carbohydrates: Fatty Acids; Phospholipids and Glycolipids; Monosaccharides; Complex carbohydrates; Glycoproteins, Lectins.

Chemical bonds in biological systems: Properties of water; enzyme kinetics and Michaelis-Menten mechanism, thermodynamic principles in biological systems-case studies from literature, specificity and cooperativity, binding equilibrium, Hill equation and Scatchard plot, Debye-Huckel theory, screening length in electrostatic interactions.

Biophysical Methods: Stopped-flow, Gel Electrophoresis UV-vis, Circular dichroism, Differential Scanning Calorimetry, Isothermal Titration Calorimetry, Surface Plasmon Resonance, Computational docking, Implications in drug design.

Recommended Texts:

Tinoco, Sauer, Wang, and Puglisi. (2003) Physical Chemistry: Principles and Applications in the Biological Sciences. Prentice Hall, Inc.

Cantor and Schimmel (1980) Biophysical Chemistry. (Parts I, II, and III) W. H. Freeman and Company.
Principles of Biochemistry by Lehninger.
James P. Allen, Biophysical Chemistry (2008) Wiley-Blackwell.
Berg, Tymoczko, and Stryer. (2010) Biochemistry. W. H. Freeman and Company.
Atkins and de Paula. (2009) Physical Chemistry. W. H. Freeman and Company.

Physical Organic Chemistry (PS470C)

Chemical Equilibria, Reactivity of Organic Compounds: Correlation of equilibrium and reactivity with structure, Hammond’s postulate, Curtin Hammett principle and thermodynamic and kinetic control of reactions. Hammett equation, substituent constants and reaction constants.

Chemical Kinetics and Isotope Effects: Various types of catalysis and isotope effects. Importance in the elucidation of organic reaction mechanisms.

Pericyclic Reactions: Conservation of orbital symmetry, and Woodward and Hoffmann rules. cycloadditions, electrocyclizations, sigmatropic rearrangements, and chelotropic reactions. Orbital overlap effects in chemical processes. Diels-Alder reactions in constrained medium.

Electron-Transfer Reactions: Theoretical basis, Examples of photo-induced and chemically-induced electron transfer reactions (PET and CET), photocatalytic oxidation and reduction reactions, Electron transfer reactions in aliphatic, aromatic, hetero-aromatic, carbonyl and amine-based molecules.

Radicals and Radical Ions: A unifying picture of radical anion and radical cation transformation, Stability of radicals and radical ions. Triarylmethyl radicals, phenalenyl and cyclopentadienyl radicals, verdazyl and thiazyl based radicals. TCNQ, TCNE and aromatic amine- based radical ions.

Organic Photochemistry: Energy and electronic spin states, Spectroscopic transitions, photophysical processes, fluorescence and phosphorescence, energy transfer and electron transfer, and properties of excited states, Representative photochemical reactions of carbonyl compounds, olefins, and aromatic compounds.

Recommended Texts:

Isaacs, N. S., Physical Organic Chemistry.
Richardson, L. Mechanism and Theory in Organic Chemistry.
Deslongchamps, P., Stereolectronic Effects in Organic Chemistry.
Balzani, V. Electron Transfer in Chemistry.
Hicks, R. G. Stable Radicals: Fundamentals and Applied Aspects of Odd-Electron Compounds.

Natural Products and Medicinal Chemistry (PS471C)

Natural Products and Medicinal Chemistry

Natural Products Synthesis: Isolation, structure elucidation and synthesis of selected natural products of biological importance. Detailed discussion of synthetic methods and strategies of natural products. Biosynthesis of selected alkaloids. Shikimic acid pathway for biogenesis of aromatic ring. Synthesis and application of flavonoids and related polyphenols. Isoprene rule, mevalonic acid from acetyl Co-enzyme A.

Bioorganic and Medicinal Chemistry:

Introduction to the history of medicinal chemistry. General mechanism of drug action on lipids, carbohydrates, proteins and nucleic acids.
Drug metabolism and inactivation. Receptor structure and sites.
Drug discovery, development, design and delivery systems.
General introduction to antibiotics, Mechanism of action of lactam antibiotics, non-lactam antibiotics and quinilones; antiviral and anti-AIDS.
Neurotransmitters, classes of neurotransmitters, drugs affecting collingeric and adrenergic mechanisms.
Anti-histamines, anti-inflammatory, anti-analgesics, anticancer and anti-hypertensive drugs.
New developments, e.g., gene therapy and drug resistance.
Clinical trials

Recommended Texts:

Finar, I. L. & Finar, A. L. Organic Chemistry, Vol. 2, Addison-Wesley (1998).
Finar, I. L. Organic Chemistry, Vol. 1, Longman (1998).
Warren, S. Organic Synthesis: The Disconnection Approach, John Wiley & Sons (1984).
Lehn, J-M, Supramolecular Chemistry: Concepts & Perspectives. A Personal Account, Vch Verlagsgesellschaft Mbh (1995).
Nicolaou, K. C., and S. A. Snyder. Classics in Total Synthesis II: More Targets, Strategies, Methods. Wiley-VCH, 2003.
Nicolaou, K. C., and E. J. Sorensen. Classics in Total Synthesis: Targets, Strategies, Methods. VCH, 1996.
Corey, E. J., and Xue-Min Cheng. Logic of Chemical Synthesis. New ed., Wiley, 1995.
Silverman, Richard B., and Mark W. Holladay. The Organic Chemistry of Drug Design and Drug Action. 3^rd Edn, Elsevier, 2014.

Computational Chemistry and its Applications (PS613C)

This course is intended for the incoming Ph.D. students to provide the basic knowledge about computational chemistry methods and its use in connection to the experimental research. The aim of this course is to provide students with basic background on computational methods and molecular modeling, including some hands-on experiences to get started in modeling the physicochemical properties of molecules. The basic theoretical background will be provided in this course, and the emphasis will be given on hand-on application of the computational methods to model molecular properties. The topics to be covered will be selected from the list presented below depending on the availability of recourses and time.

Molecular Mechanics: Fundamentals; Potential energy functions; Force fields; Electrostatic interactions; van der Waals interactions; Geometry optimization; Energy minimization methods.

Simulation Methods: An introduction; Overview of Molecular Dynamics and Monte Carlo simulations; Introduction to application of simulation methods to explore bio-macromolecules; Brief on conformational analysis.

Semiempirical Implementation of MO Theory: Extended Hückel theory; CNDO, INDO and NDDO formalisms, Computation of electronic structures.

Ab Initio Hartree-Fock Theory: Review of Hartree-Fock equation and variational principle; Basis sets; Practical issues; Electron correlation techniques; Configuration Integration.

Overview of Density Functional Theory (DFT): Introduction; Hohenberg-Kohn theorem; Kohn-Sham theory; Exchange-correlation functionals.

Recommended Texts:

Frank Jensen, Introduction to Computational Chemistry, 2nd edition, John Wiley & Sons Ltd., England.
Ira. N. Levine, Quantum Chemistry, 5th ed., Prentice Hall, NJ.
Donald A. McQuarrie, Quantum Chemistry, University Science Books, Mill Valley, CA.
Christopher J Cramer, Essentials of Computational Chemistry, 2nd edition, John Wiley & Sons Ltd., England.
Andrew R. Leach, Molecular Modelling: Principles and Applications, 2nd edition, Longman Group, United Kingdom.
Attila Szabo and Neil S. Ostlund, Modern Quantum Chemistry, Introduction to Advanced Electronic Structure Theory, 1st ed., revised, Dover.

Advanced Spectroscopy and its Application (PS614C)

This course is designed as a refresher course for incoming Ph.D. students with Physics or Chemistry background. It reviews some materials that may have been taught in the M.Sc. courses and also includes material designed to familiarize students with some of the advanced spectroscopic techniques and their applications. This course will be beneficial also for students of Biophysics or Biochemistry who want to gain further knowledge about the application of some advanced spectroscopic techniques to study biological macromolecules. The topics to be covered will be selected from the list presented below

Fundamentals of Photochemistry:

Overview: Laws of photochemistry; Interaction of radiation with matter; Transition between states; dipole approximation and two-photon transitions.

Radiative Transitions– Absorption and Emission of Light: Types of photophysical processes;

Absorption of light: Frank-Condon principle; Emission spectra; Fluorescence and phosphorescence; Excited state dipole moments.

Non-radiative Transitions: Internal conversion; Intersystem crossing; Energy gap law; Isotope effect; Temperature effect.

Various Photophysical Processes: Fluorescence Resonance Energy Transfer (FRET); Förster theory; Overlap integral; Solvent effect on absorption and emission; Lippert equation; Solvent relaxation dynamics; Fluorescence anisotropy; Excited state proton and electron transfer.

Spectroscopic Techniques and Applications

Laser Fundamentals: Introduction to Lasers; Coherence; Laser cavity modes; Pulsed laser operations; Q-switching and mode-locking.

Some Spectroscopic Techniques: UV-vis spectrophotometer; Fluorescence spectrometer; Absorption, emission and excitation spectra; Time-resolved techniques; Time-correlated Single Photon Counting (TCSPC); Single molecule spectroscopy.

Applications: Application of fluorescence spectroscopy techniques to study FRET, Solvent relaxation dynamics, charge transfers.

Recommended Texts:

Nicholas J. Turro, Modern Molecular Photochemistry, The Benjamin/Cummings Publishing Co., Inc.
K. K. Rohatgi-Mukherjee, Fundamentals of Photochemistry, New Age International (P) Limited.
J. R. Lakowicz, Principles of Fluorescence Spectroscopy, 3rd edition, Kluwer Academic, New York.
Colin N. Banwell, Elaine M. McCash, Fundamentals of Molecular Spectroscopy, Tata McGraw-Hill.
William T. Silvast, Laser Fundamentals, Cambridge University Press.
D. V. O’Connor and D. Phillips, Time Correlated Single Photon Counting, Academic Press, New York.
Robert M. Silverstein, Francis X. Websterand, David J. Kiemle, Spectrometric Identification of Organic Compounds.

Molecular Materials (PS616C)

Self-Assembled Materials: How can we design giant structures using weak interactions? Self- assembling systems: Carboxylic acid dimers, alcohol-amine, amides etc. Designing molecular squares and boxes, giant self-assembling capsules, molecular tennis-balls, rosettes, self-assembly of metal arrays etc.

Soft Materials: Design and Synthesis of amphiphiles and their self-assembly to Micelles, Vesicles, Hydrogels, Organogels, Metallogels. Application of soft materials towards drug delivery and controlled release. Liquid crystals: Designing principles and classifications. Thermotropic and lyotropic liquid crystals. Nematic, smectic, cholesteric and discotic phases. Liquid crystalline polymers, Metallo-organic liquid crystals. Application towards liquid crystal displays.

Molecular sensors and switches: Design and principles of photochemical sensors, PET (Photo induced electron transfer) systems, ON-OFF molecular switches, Molecular logic gates (AND, NOT, OR, NAND etc.); Electrochemical sensors.

Organic Semiconductors, Organic Superconductors and Organic Light Emitting Diodes (OLED’s): n/p-type organic semiconductors, charge mobility and designing principles, Definition of electroluminescence and electroluminescence quantum efficiency, power efficiency. Design and characterization, examples of OLEDS: conjugated oligomers and polymers, low molecular weight materials. Application, commercialization and optimization of OLED’s.

Electrochromic materials: Definition and designing principles, conducting polymers, metallo polymers, metallophthalocyanines, visible and infrared electrochromism. Applications to practical materials.

Nonlnear Optical (NLO) materials: Definition of First-order and Second-order hyperpolarizabilities, Experimental techniques (Electric field induced second harmonic generation, Hyper Rayleigh Scattering) to determine b and c. Molecular designing principles and characterization of dipolar, multipolar and octupolar molecules. Imparting tunability in NLO molecules. Designing SHG active molecules (Influence of chirality, H-bonding, steric effects).

Recommended Texts:

The design of organic solids by G. R. Desiraju, Elsevier: Amsterdam.
The weak hydrogen bond in structural chemistry and biology by Gautam Desiraju and Thomas Steiner, Oxford University Press.
Supramolecular Chemistry by J. W. Steed and J. L. Atwood, John Wiley and Sons Ltd.
Molecular Fluorescence: Principles and Applications by B. Valeur, Wiley-VCH.
Organic electroluminescent materials and devices, by S. Miyata and H. S. Nalwa, Gordon and Breach Publishers, Amsterdam.
Non-Linear Optical properties of organic molecules and crystals, by D. S. Chemla and J. Zyss, Academic Press, Inc.

Medicinal Inorganic Chemistry (PS622C)

Structures and Functions of Metalloenzymes: The structures of common motifs in the active sites of metalloenzymes and their functions, viz. hemoglobin, myoglobin, hemerythrin, hemocyanin, cytochrome P-450, cytochrome c oxidase, ferritin, transferrin, siderophores, iron-sulfur proteins, copper proteins, superoxide dismutase, alcohol dehydrogenase, carbonic anhydrase, carboxypeptidase, xanthine oxidase, nitrogenase, vitamin B12 coenzyme.

Role of Alkali and Alkaline Earth Metal Ions in Biology: Na⁺-K⁺ Pump, ionophores and crown ethers, Catalysis of phosphate transfer by Mg²⁺ ion, Ubiquitous regulatory role of Ca²⁺ in muscle contraction.

Models of Metalloenzymes: Some selected examples of synthetic metal complexes that mimic the active sites of metalloenzymes and can carry out biologically and environmentally important chemical reactions will be discussed. For example, the modelling of metalloenzymes, such as hemoglobin, myoglobin, hemerythrin, hemocyanin, cytochrome c oxidase, ferritin, transferrin, siderophores, iron-sulfur proteins, copper proteins, superoxide dismutase, carbonic anhydrase, nitrogenase.

Metals in Medicine: The biological essential elements and their roles in life processes and diseases. The diseases caused by deficiency and overload of biologically essential metal ions. Therapeutic applications of metal complexes (Pt, Ru, Rh and Au etc.) as drugs; Interactions of metal complexes with DNA, RNA and proteins.

Metals in Diagnosis: Metal-based MRI contrast agents and radioactive metals in positron emission tomography (PET) imaging.

Nanomedicine: Metal-based nanoparticles in diagnostic and therapeutic applications.

Toxicity of Metals: Toxicity of metals, such as As, Cd, Hg and Cr etc. with specific examples. Detection of toxic metals contamination in drinking water. Detoxification of metal ions by chelation therapy.

Recommended Texts:

I. Bertini, H. B. Gray, S. J. Lippard, J.S. Valentine, Bioinorganic Chemistry, VLSE with Univ. Sci. Books, 1998.
“Metals in Medicine” 1st Edition. James C. Dabrowiak, WILEY, ISBN: 978-0-470-68196-1.
W. Kaim and B. Schwederski, Bioinorganic Chemistry: Inorganic Elements in the Chemistry of Life (An introduction and Guide), John Wiley & Sons, 1994.

Bioorganic Chemistry and Drug Discovery (PS473C)

Scope and Objective of the Course:

This new course covers the basics of Bioorganic chemistry, process of drug-design and development, and basic concepts of pharmaceutical chemistry relevant to the requirements of pharmaceutical industry. For an organic chemist it's very important to understand the chemistry of life processes in order to design, synthesize and develop new effective, non-toxic, tolerable and acceptable molecules against selective validated target macromolecules of physiological disorders. A chemist must also have understanding of the modern tools and techniques of drug discovery and the process through which a new molecule passes through before we actually call it a drug. Therefore, I hope this course would prove to be a truly interdisciplinary course enabling the chemistry students to acquire the knowledge of Biochemistry, Organic chemistry, Medicinal chemistry, process of drug-design and steps of drug-development.

Unit 1:

Introduction to Bioorganic Chemistry: Overview of Bioorganic Chemistry; Weak Interactions in Organic and Biological molecules; Proximity Effect in Organic Chemistry; Molecular Recognition; Chemistry of the Living Cells; Analogy Between Biochemical and Organic Reaction. Biosynthesis of biomolecules.

Unit 2:

Bioorganic Chemistry of Amino Acids, Peptides and Proteins: Chemistry and classification of Amino Acids; Chemistry of Peptide Bonds; Peptide Secondary Structures; Synthesis and Application of Unnatural Amino acids; Protection and deprotection of carboxyl, amine and side chain functionality; Principle and methods of solution and solid phase peptide synthesis, purification. Structure and function of Proteins; Protein sequencing.

Unit 3:

Bioorganic Chemistry of Enzymes: Introduction to Enzyme Catalysis and Kinetics; Co-enzymes and cofactors; Factors affecting enzyme activity; The Catalytic Triad; Examples of enzymes in organic chemistry; Rational design of enzyme inhibitors: Enzyme inhibitors; design and therapeutic applications of peptidomimetics.

Unit 4:

Bioorganic Chemistry of Nucleic Acids and Carbohydrates: Basics of DNA and RNA, Structure and functions of DNA and RNA; DNA Replication and repair; Transcription, Protein Biosynthesis; DNA intercalators; Basics of Peptide Nucleic Acids (PNA); Antisense and antigene properties of DNA and PNA; Basics of carbohydrate chemistry; Sialic acid and iminosugars

Unit 5

Drug discovery: Diversity of drug targets; Draggability and toxicity of molecules; Stages of drug discovery, lead discovery, identification, validation. Examples of some novel molecular targets along with their pharmacodynamic agents; Basics of drug action: Pharmacodynamic, pharmacokinetic (drug adsorption, metabolism, distribution, and elimination) and toxicological aspects of the drug discovery process. Drug resistance: Causes for drug resistance, strategies to combat drug resistance. Design of small molecule library for drug discovery, Various approaches for drug delivery. (10 lectures)

Unit 6

Online Tools For Drug-Design: Structure drawing tools, conversion of structures from of 2D to 3D formats, PubChem, Protein Data Bank (PDB), Sequence search and alignment, Similarity search softwares, Virtual screening techniques: Similarity based, QSAR based, pharmacophore based and target based in-silico virtual screening (6 lectures)

Recommended Text and Reference Books:

1. Bioorganic Chemistry-A chemical Approach to Enzyme Action. Hermann Dugas, ISBN 978-1-4612-2426-6

2. Organic Chemistry of Drug Design and Action. Richard B. Silverman and Mark W. Holladay, The Academic Press Inc., San Diego, 2000

3. Amino acids, peptides and proteins, J. S. Davies Royal Society of Chemistry, UK, Vol. 35, 2006.

4. Chemistry of Biomolecules, S. P. Bhutani, ISBN 9780367208554 (2019), CRC Press.

5. Biochemistry, Lubert Stryer, Jeremy M. Berg and John L. Tymoczko, New York: W H Freeman; 2002.

6. Burger’s Medicinal Chemistry and Drug Discovery, Abraham D. J., John Wiley and Sons Inc., New York.

7. An Introduction to Medicinal Chemistry, Patrick G.L., Oxford University Press, New York.

8. Peptidomimetics in Organic and Medicinal Chemistry, Guarna A. and Trabocchi A., Wiley Publication.

9. Gisvold’s Textbook of Organic Medicinal and Pharmaceutical Chemistry, Block J.H. and Beale J.M., Wilson, Lippincott Williams and Wilkins, Philadelphia.

Chemistry and Biology of Glycoconjugates (PS623C)

Scope and Objective of the Course:

The objectives of the course are to give MSc and PhD students a broad and balanced introduction to the background, general principle, concepts and tools of carbohydrate chemistry and glycoconjugates. The course will highlight basic principles of structures and conformations of monosaccharides and polysaccharides; factors governing glycobiology and glycoconjugates in vaccine development. Modern research in this area will be the focus of this course, which combines lectures, tutorials and research paper discussion.

Introduction: Structures and conformations of monosaccharides and polysaccharides; Introduction of glycoconjugates, Types and importance of glycoconjugates, chemical synthesis of oligosaccharides, glycoproteins and glycolipids challenges and solutions.

Structure and function of glycoconjugates: Structure of glycoproteins, glycolipids, Role of glycolipids in signal transduction, Inter- and intra-cellular communication and “Glycocode”: The need for homogeneity and pure, well-defined conjugates. The importance of multivalency and functions of multivalent conjugates.

Proteoglycans and glycosaminoglycans: Detailed structure of proteoglycans and glycosaminoglycans. The importance of proteoglycans. Difference between proteoglycans and glycoproteins. Role of proteoglycans in developmental signalling pathwyas. Heparins and the drug action.

Glycopeptides: Structure and function of glycopeptides. Glycopeptide antibiotics action and resistance, vancomycin and teicoplanin, Glyco-amino-acids and glycosyl-amino-acids and their uses. Synthesis of pure and well-defined glycopeptides, The importance of glycopeptide in immunology.

Peptidoglycans: Peptidoglycans structure and architecture, the role of peptidoglycans in pathogen survival. Chemical synthesis of peptidoglycans, how this is an important target for developing novel antibiotics, e.g. M. Tuberculosis.

Glycoconjugates and proteins in membrane systems: Structure and function of membrane bound glycoconjugates. The importance of membrane bound glycoconjugates in cell-cell recognition and host-pathogen interactions.

Glycoconjugate assembly and vaccine development: Current developments of recombinant glycoconjugate vaccines, Interaction of glycoconjugates with T-cells. Successful stories for vaccine developments including Covid-19, semisynthetic vaccine. The H1N1 virus and its mode of infection and discovery of Tamiflu.

Recommended Text and Reference Books:

The Introduction to Glycobiology (3^rd Ed, 2011) by M. E. Taylor and K Drickamer, Oxford University Press.
Glycoconjugates: Composition: Structure, and Function (1^st Ed, 1992) by Howard J. Allen, Edward C. Kisailus, CRC Press. Taylor and Francis group
Modern Synthetic Methods in Carbohydrate Chemistry (1^st Ed 2013) edited by Daniel B. Werz, Sébastien Vidal, Wiley-VCH Verlag GmbH & Co Germany.
The Organic Chemistry of Sugars (1^st Ed, 2006) by Daniel E. Levy and P. Fugedi, CRC Press. Taylor and Francis group.
Chemical Glycobiology (1^st Ed, 2008) by Randall L Halcomb, Peng George Wang, American Chemical Society, USA.
Monosaccharides: Their Chemistry and Their Roles in Natural Products, P. Collins, R. Ferrier, John Wiley & Sons, Chicester, 1998.