Organic & Biochemistry
CY 711 - Applied and Environmental Microbial Chemistry
The beginnings of microbiology - contributions of Antonie Van Leeuwenhoek, Pasteur, Koch, Ehrlich, Fleming, Wakaman, Winogradsky etc. in three centuries,and microbiology in the twentieth century.
The methods of microbiology - pure culture techniques, microbial nutrition principles, construction of culture media, isolation and environment.
The relationship between structure and function in bacteria, fungi and viruses.
The principles of bacterial classification and phylogeny.
Microbial growth and effect of physical and chemical agents in environment viz.
pH, temperature, pressure, electromatgnetic radiations, solutes, phenols, alcohols and oxygen relations.
The Archaebacteria and their significance.
Microbial metabolism - fuelling ractions, biosynthesis, polymerization and assembly.
Microbial genetics - transformation, conjugation, transdution, protoplast fusion, genetic recombination.
Microorganisms as geochemical agents in mineral transformation, cycles of matter through geological time, biofertilizers, bioleaching of metals.
Microbes in industry - fermentation processes for the production of alcohols, organic acids, amino acids, enzymes, vitamins, antibiotics and steroid transformations - “primary and secondary metabolites”.
Ouline of roles of microbes in air, soil, water, food, dairy, diseases, waste disposal and recycling.
CY 712 - Bioanalytical Techniques
pH and buffers used in biochemical experiements, pKa values and titration curves.
Determination of biomolecules by absorption photometry, fluorimetry, biochemical applications of mass spectrometry.
Manometry and respiration measurement, oxygen polarography, BOD estimation, resting cells prepastion.
Principles of microscopy - light, darkfield, phase contrast, fluorescence and eletron microscope, fixing and preparation of samples.
Breaking of cells by chemical and physical methods, ultrasonication, pressure cell disintegrators, detection of cell-free and cell-bound proteins.
Principles of centrifugation - calculation of r.c.f. values, ultracentrifuges, density gradients.
Biomolecules separation by chromatography, paper, thin layer and column chromatrography, ion exchangers, molecular sieves, affinity columns, Gas chromatography and HPLC.
Electrophoresis - theory and practice, mobility, buffers, agarose and polyacrylamide matrices, gel apparatuses, native and SDS -PAGE gels, Isoelectric focussing, Zymograms.
Immunochemical methods - immunoassays, immunodiffusion, rocket immunoelectrophoresis.
Use of radioisotope tracer techniques in biochemical experiments and their detection.
CY 713 - Trace Element Biochemistry
Metalloproteins and metal containing biological molecules, Metal activated enzymes in hydrolysis. Transition metals in biological redox reactions.
Nitrogen fixation and nitrogen cycle, Oxygen carriers, storage and transport or iron, alkali metal and alkalene earth metal cations in biology. Role of chelating agents in medicine and metals in medicine.
Non metals as trace elements and newer knowledge on trace elements Absorption, Transport and Tissue storage.
Suggested as Text
Other references materials:
In addition, relevant literature will be included from Annual Review of Biochemistry, Nature, Biochemistry etc. on Special Topics.
CY 732 - Advanced Spectroscopic Techniques in organic Chemistry and Biochemistry
UV-visible spectroscopy - advancements in experimental methods, analysis of mixtures, dissociation constants of acids and bases, study of enzyme catalysis, applications of ORD and CD.
IR spectroscopy - intra and intermolecular hydrogen bonding, effect of concentration and temperature, Fourier transform IR, applications of UV, VISIBLE AND IR in the structural elucidation of complex natural products.
NMR spectroscopy - experimental aspects, FT NMR, factors influencing sensitivity and resolution,applications of chemical shift and spin-spin coupling, Karplus equation and conformational analysis; NMR of carbon-13, fluorinee-19, phosphorous-31, Nitrogen- 14 and 15 and oxygen 17. Multiple-pulse experiments - gated decoupling and NOE, measurement of T1 and T2, polarisation transfer, INEPT, DEPT, two - dimensional NMR, J-resolved spectra, shift correlated spectra including COSY, HETCOR, INADEQUATE, NOE correlted spectroscopy, applications of 2D-NMR in the structural analysis of complex natural products and biopolymers, applications of solid state NMR.
EPR Spectroscopy - epr spectra of solutions, frozen solution, especially organic molecules.
Mass spectrometry - high resolution mass spectrometry, linked scans, MIKES, HV scan, negative ion mass spectrometry, applications of field desorption, plasma desorption, fast atom bombardment, electrospray and tandem mass spectrometry and FTMS.
Also included are topics from current literature on the applications of modern spectroscopic techniques.
CY 733 - Chemistry of Bioactive Carbohydrates
Definition and classification of sugars, nomenclature, aldoses and ketoses, configuation of (+)- glucose: the Fischer proof, ring structures and conformation, mutarotation, anomericity, naturally occurring monosaccharides, oligosaccharides and polysaccharides, three-dimensional structure of macromolecular carbohydrates.
Methods for isolation, purification and structural analysis, complete and partial hydrolysis, methylation analysis, Smith degradation, chromatographic and electrophoretic techniques, advanced spectroscopic techniques including fast atom bombardment mass spectrometry and two-dimensional NMR.
Chemical ractions of carbohydrates, oxidation, reduction, formation of derivatives, glycosides, ethers, esters and cyclic acetals, modern chemical transformations, methods for the formation and cleavage of O-glycosidic bond, use of protecting groups, chemical and enzymatic synthesis of oligosaccharides, carbohydrates as chiral synthons for natural products synthesis.
Carbohydrate biopolymers, animal glycoproteins, blood-group substances, plant and algal glycoproteins, proteoglycans and glycosaminoglycans, glycolipids, structural basis for the biological functions of glycan chains in glycoconjugates, carbohydrates and biological molcular recognition, carbohydrate componets of nucleic acids and antibiotics.
CY 734 - Modern Concepts in Organic Synthesis
Additions to C-X bonds
Organometallic reagents of Al, Cu, Ti, Zr, C, Zn, Cd, Hg and Ce metals. Nucelophilic addition to imines, imine derivatives and carboxylic acid derivates; Carbanions stabilized by N,B, S, Si and Se, containing groups; epoxidation and skeletal reorganization; allyl organometallics, transition metal enolates, homoeneolates, metalloenamines, enol ethers, asymmetric synthesis with enol ethers; Eschenmoser coupling reactions; Passserini and Ugi reaction.
Carbon-carbon o-bond formation
Alkylation of enols,enolates; stabilized and non-stabilized carbanions; cyclization reactions; coupling reactions and rearrangements. Additions to and substitutiion at C-C ? bonds Organocuprates and conjugate reactins; nucleophiles with cationic pentadienyl- metal complexes; kroganopalladium reagents; carbometallation.
Combining C-C ? bonds
Ene reactions; oxa-di-?-metals photoisomerisation, transition metal mediated cycloadditions; retrogade Diels-Alder reactions; Nazarov cationic cylization; charge-transfer accelerated cyclization.
Synthesis of glycosides, sulphides, sulphoxides, phosphonium ylides and related compounds, Ritter type eaction; protecting groups; Nef reaction; reductive elimination; vicinal deoxygenation and vicinal desilylation.
Oxidation by remote functionalisation, microbial methods; epoxidation and asymmetric epoxidation; glycol formation; electrochemical oxidation; oxidative rearrangements; solid-support oxidants and electron transfer reactions.
Reduction by metal hydrides; asymmetric hydrogenation; enzymatic reduction; hydro-zirconation, - boration, - aluminatin and - silylation reaction.
Transition metals in organic synthesis; Birch-Pearson, Dotz, Heck-Stille, Hegedus, Mcmurray, Noyori, Pauson-Khand, Sharpless, Tebbe-Grubbs and Vollhardt reactions; asymmetric synthesis; chiral auxiliaries; catalytic enantioselective reactions; chemzymes. Antibody catalysis; biological-chemical transformations. Structural elucidation and reaction dynamics by multi-dimensional NMR spectroscopy and crystal diffraction methods; novel separation methods.
CY 721 - Advanced Solid State Chemistry
Introduction, detailed description of structures of complex oxides and related compounds, Phillips ionicity and crystal chemistry; Structural interrelations .
Origin of defects; Types of defects - equilibrium, nonequilibrium, point, line, planar, nonstoichiometry, Wadsley defect; Experimental methods of investigating defects in solids; Dislocations, grain boundaries etc. Defects and physical properties.
Bonding and electron transport:
Atoms to molecules to crystals; Orbitals - bond - bands: Electronic structure of solids, band theory, non metals, metals, metal- nonmetal transitions; Transport properties, techniques, electrical conductivity, thermopower and Hall effect measurements; Chemical approach to bonding in solids; Case studies - Oxides.
Dia, para, ferro, antiferro and ferromagnetism; Magnetism of free electrons; Measurements; Magnetically ordered solids, soft and hard magnetic materials; Case studies - Oxides.
Dielectric and optical properties: Principle and theory;
Standard examples like BaTiO3; Applications.
Classification; Landau’s Theory; Nucleationgrowth,
Solid state synthesis:
Conventional and novel methods; Specific examples;
Characterization by diffraction
Superconductivity of oxide materials, C60; Intercalation chemistry etc.
CY 723 - Structural Methods in Inorganic Chemistry
Structural aspects of inorganic compounds, structural methods and their classification.
Principles, experimentation and illustration of the scope of different methods viz., NMR, ESR, NQR, MW, IR RAMAN, UV-VIS, UPS, XPS, Mossbauer and Mass spectral techniques, A variety of case studies will be dealt with in each case.
X-ray, neutron and electron diffraction techniques (Principles, instrumentation and applications).
ORD, CD and MCD techniques - principles, experimentation and scope with specific examples.
TGA, DTA and DSC techniques - principles, instrumentation and uses (applications to polymers and explosives will also be considered).
Principles, determination, scope and uses of i) Magnetic ii) dipole moment iii) refractive index and iv) conductance properties of inorganic compounds for structural elucidation.
Physical Organic Chemistry
CY 731 - Advanced Physical Organic Chemistry
Kinetics and thermodynamics - chemical equilibrium - activation - transition state model - potential energy surface for substitution and elimination reactions - the rate limiting step - Hammond postulate - the principle of microscopic reversibility - the principle of least motion - isokinetic relationship - kinetic and thermodynamic control of products - isotope effects - primary, secondary and solvent isotope effects.
Correlation of structure with reactivity - linear free energy relationships Hammett equation - interpretation of substitutent and reaction constants - ?, ?+, ? -, polar and steric substitutent constants - the Taft model - deviation from Hammett equation - acidity functions - determination of solvent polarity and solvent polarity scales.
Determination of reaction mechanism, reactions and mechanistic classifications - kinetics as an aid - detection and trapping of reactive intermediates - stereochemical probe - isotope effects - solvent effect - salt effect - ion pairs in solvolysis raction - intra- and intermolecular reactions - anchimeric assistance - stereoelectronic effects on rates and course.
Catalysis - homogeneous - acids and bases and their strengths - specific and general acid base catalysis - Bronsted catalysis law - intepretation of Bronsted coefficient - nucleophilic and electrophilic catalysis - mechanisms of some acid- base catalysed reactions in carbonyl and olefin chemistry.
Reactive intermediats - carbenes - nitrenes - arynes - free radicals - carbonium ions and carbanions - their generation, detection, characterization, structure and reactivity.
Recent topics in mechanistic organic chemistry - electron transfer reactions - electron transfer catalysed reactions - substitution via free radicals - free radical cyclization - Baldwin;s rules - Lewis acid catalysis of some common organic reactions.
CY 722 - Chemistry of Novel Materials
Chemistry today, an overview-molecular materials, functional materials, nanomaterials, new techniques for microscopic investigation.
Clusters, gas phase spectroscopy, metallic clusters, tools for their study.
Fullerenes, discovery electronic structure spectroscopy, chemistry, derivatives, novel properties, superconductivity, orientational ordering associated properties, carbon nanotubes, onions, new forms of carbon.
Organic monolayers, L-B films, self assembly, techniques to study thickness, molecular properties , chemistry with LB and SAM film. Novel polymeric materials, conducting polymers.
Metal-carbon clusters, metallocarbohedrenes, gas phase chemistry.
Semiconductor nanocrystals, quantum dots, electronic structure, spectroscopy.
Mesoporous solids, new materials for catalysis.
CY 741 - Developments in Catalytic and Surface Science
Ceramics rare earth oxides, vanadia-based materials, micro-and mesoporous oxides, zeolites, sulphated-ZrO2 and layered materials - Architecture, synthetic methods, structure - property correlation and characterization, ion exchange, acidic and basic nature of these materials.
Type and clays, kaolinites, hydrotalcites, clay polymers, clay colloids, and pillared clays. Structure, ion exchange and acidic properties of clays. Clays as supports and catalysts. Clay-mediated organic reactions.
Automotive emission catalysis:
Air pollution, development of three-way catalysts, principles and operation of exhaust catalysts, surface chemistry, use of zeolites in exhaust emission control.
Preparation, characterization and special catalytic properties.
Surface science view of catalysis:
Methods of surface science studies, chemical transformations related to catalysis on oxides, mono- and bimetal surfaces, monitoring surface reactions by in-situ spectroscopic methods. Structure sensitive and insensitive reactions, oscillations in catalytic reactions, structure and bonding modifications, measuring heat of adsorption, single crystal adsorption calorimetry - a new development.
Active site - interpretation, surface frontier molecular orbitals, reaction kinetics, modeling of heterogeneous catalytic reactions. Catalytic reactors.
CY 742 - Ion-Beam Techniques and Nuclear Energy
Nuclear potential, Nuclear forces, charge symmetry and charge independence, Fermi gas model, Shell model, Spin-orbit coupling, Collective model, rotational and vibrational states in Odd-A nuclei.
Pulse Processing and shaping, Linear and Logic pulse functions, Pulse height analysis, Timing spectroscopic modules with pulse timing, Computerized spectrum analysis.
Radiation spectroscopy with scientilators, semiconductor diode detectors, Germanium and solid state detectors, Neutron detection and Spectroscopy, Perturbed angular correlation measurements with coincidence counting positron annihilation and life time measurements.
Particle Sources and Ion-Beam analysis:
Van-de-Graaff generators, charged particle and Tandem accelerator, Linear Accelerators (electron and proton LINACS), Synchrotrons as Photon sources.
Ion-Solid interaction, Range and damage profiles, Nuclear and electronic Stopping powers, Secondary ion mass spectroscopy\Ion neutralisation spectroscopy, Rutherford back scattering and resonant scattering, Particle induced x-ray emission, Nuclear Reaction analysis.
Nuclear Reactors and Nuclear Energy:
Chain reacting systems, conversion of mass to energy and transmutation of elements, Reactors, Fuel refining and reprocessing (PUREX process), Nuclear safety and radioactive waste disposal, controller thermonuclear reactions and fusion energy.
CY 743 - Ion Chemistry
Mass spectrometry in 90’s and beyond, mass spectrometer as laboratory-tandem mass spectrometers-MS/MS with electric, magnetic, quadrupole, time of flight, FT- ICR and ion traps-hybrid instruments.
Collisional activation and reaction-kinematics-dynamics-collision energy and target gas effects-MS/MS in ion structures-reaction mechanism - thermochemistry.
Analytical applications-attomole chemistry. SIMS and analysis of surfaces.
Ion/molecule scattering-surface induced dissociation and reaction surface transformation ultrathin films.
Ion chromatography-state selction in MS/MS spectrometry neutralization reionization mass spectrometry.
Laser vapourization-cluster chemistry with mass spectrometers-clusters- fullerenes metallocarbohedrenes-modern tools and novel applications. Ion scattering methods - ISS and RBS.
CY 744 - Luminescence Spectroscopy
Characteristics of fluorescence and phosphorescence emission, Time scale of excited state molecular processes in solution, Life times and quantum yields.
Steady state Fluorescence:
Basic instrumentation, Effects of solvents on fluorescence spectra (general and specific), The Lippert equation Biochemical applications of solvent effects: localization of membrane-bound and protein- bound fluorophores, Polarization of emission, Measurements of fluorescence Polarization, Extrinsic causes of fluorescence depolarization. Effect of rotational diffusion on fluorescence anisotropies: the perrin equation. Chemical and biochemical applications of anisotropy measurements.
Time-resolved Fluorescence Spectroscopy:
Measurement of fluorescence lifetimes, instrumentation. mechanism and dynamics of solvent induced relaxation. Theories of fluorescence quenching. Radiative and nonradiative energy transfer. Applications. Phase-sensitive detection of fluorescence; Analysis of heterogeneous resonance by phase-sensitive detection. Time dependent decays of fluorescence anisotropy. Applications of Phosphorescence Spectroscopy: Fluorescence Line Narrowing Spectroscopy, Matrix Isolation Fluorescence Spectroscopy. Interactions and Kinetics of single molecules as observed by fluorescence correlation spectroscopy. Multidimensional Luminescence Spectroscopy and its applications in Analytical Chemistry.
CY 745 - Structure and Dynamics of Electrochemical Interfaces
Equilibrium properties of charged interfaces; Metal/Electrolyte interface: Models for interfacial organisation of ions and dipoles; Solvent structure at interface; Phenomenological and microscopic models for dipolar polarization; Recent theories and their limitations; Cooper - Harrison catastrophe; Unified description of electrical double layer; Jellium models and their refinements; Influence of metal surface on differential capacitance.
Statistical mechanics of adsorption; Ising models; Variation of work function with surface coverages; ionic and dipolar adsorption isotherms; partial charge transfer; electrosorption valency and chemisorption.
Chemically modified electrodes: Nature of modifications of electrode surfaces - Applications in batteries, biosensors etc charge transfer through film covered electrodes - elucidation of mechanism of electrocatalysis - Saveiant zone diagram - electron hopping and diffusion coefficient - Redox capacity.
Non steady state electrochemical techniques: Need for transient analysis; Different types of diffusion; planar; cylindrical etc; Mathematical formalism; diffusion equations; choice of initial and boundary conditions; Laplace transform method of solutions; potential step perturbation; chronopotentiometry, Linear Sweep Voltammetry; Reversible and irreversible charge transfer schemes.
CY 746 - Surface Structure and Properties of Polymeric Materials
Importance of polymer surface structure; Differences between polymer and other material surfaces; Theoretical models. Thermodynamics of polymer surfaces; Surface energy and methods of determination.
Methods of characterization of polymer surfaces
Liquid contact angle, reflectivity methods (neutron, x-ray, visible-SPO, XPS, forward recoil elastic scattering, (FRES), secondary ion mass spectrometry (SIMS), TOF-FRES, TOF-SIMS, Rutherford backscattering, ATR-IR, AFM, STM and inteterference microscopies, surface-force apparatus.
Methods of polymer surface modification - plasma, ion etch, chemical etching, organic transformations, surface restructuring, vapour deposition (chemical and physical), photochemical transformations, super critical carbon dioxide processing and entrapment functionalization.
Applications - Adhesion/printing, growth of organisms on surfaces, wetting, friction, lubrication, corrosion prevention, interfacial mechanical properties, low surface energy coatings for anti-vandalism, flocculation, polymer composities and bio-compatibility
CY 7001 - Photoinduced Electron and Energy Transfer Processes
Basic concepts: Introduction to photoinduced electron transfer reactions-enhanced reactivity of photo-excited state compared to the ground state-photosynthesis-history of electron transfer reactions.
Dynamics: Rate of electron transfer- activation controlled and diffusion controlled electron transfer rates-reorganization energy- rate dependency on free energy change of electron transfer-Marcus and Rhem-Weller approaches-Marcus Inverted Region-Theoretical prediction and experimental verification-reasons for not observing Marcus Inverted Region- Recent examples of experimental verifications.
Photoinduced Electron Transfer in Donor-Acceptor Systems: Covalently and non-covalently connected donor-acceptor pairs- examples- rate dependency on distance between donor-acceptor pairs in the normal and inverted regions -charge separation and long lived charge separated states- back electron transfer.
Photoinduced Energy Transfer: Characteristics of resonance energy transfer (RET)-theories of energy transfer- Dexter and Förster type resonance energy transfer -rate and efficiency of energy transfer-steady state and time resolved experiments-fluorescence anisotropic experiments- calculation of the distance between donor-acceptor pairs-spectroscopic ruler concept- Förster RET studies in proteins and nucleic acids.
CY 751 - Advanced Magnetic Resonance Spectroscopy
The concept of spin density operator and the dynamics-time evolution of the density operator and the interaction picture-Magnus expansion and average Hamiltonians.
Theory of spin lattice relaxation-Bloch-Wangsness and Redfield relaxation theories, correlation times and relaxation times from first principles.
The Nuclear Overhauser Effect.
Introduction to various operator bases used in pulse dynamics calculations in magnetic resonance-product operators, single spin multiplet operators, fictitious spin 1/2 operators and irreducible spherical tensor operators.
Multiple quantum NMR-basic ideas of time domain multiple quantum NMR spectroscopy.
The theory of two dimensional Fourier transformation in NMR-coherence transfer pathways-concepts and observables-a few selective examples from COSY, TOCSY and NOESY spectra.
CY 752 - Non Linear in Chemistry and Biology
Introduction to dynamical systems. Autonomous equations, critical points, periodic solutions and theory of stability.
Mappings, theory of bifurcation, chaos and self-organization, Quantification of chaos.
Thermodynamical and kinetic aspects of structure formation in systems far from equilibrium. Kinetic interpretation of living systems, spatial and temporal self- organization in biochemical and biological systems.
Order and chaos in chemical and physiological systems.
Self-organizing systems of macromolecules and interpretation of biological evolution.
Chaos and experimental time series analysis.
Control of chaos.
CY 753 -Theoretical Methods for Calculation of Electronic Structure of Molecules and Clusters
Inrtroduction to the LCAO method.
The Hartree-Fock (HF) method, derivation and interpretation of HF equations. Roothan equations. Abinitio calculations using various types of basis functions.
Open shell HF equations, Configuration Interaction, MCSCF method. Density functional theory. The X-alpha method for atoms, molecules and Clusters.
Methods of calculation of various one-electron and two-electron properties of atoms, molecules and clusters.
Application of MO theory to Photoelectron Spectroscopy.
CY 754 -Theoretical Rotational-Vibrational Spectroscopy
The Born-Oppenheimer approximation and the concept of potential energy surfaces for polyatomic molecules.
Rotational-vibrational Hamiltonians with emphasis on coupling terms for diatomic molecules-semiclassical WKBJ approximation.
Polyatomic rotational-vibrational Hamiltonian- the Wilson-Howard-Darling- Dennison form and perturbation theory. The Watson Hamiltonian and contact transformation method for obtaining effective Hamiltonians. Coriolis and centrifugal coupling effects, vibrational anharmonicity.
Numerical methods for solving the vibrational Hamiltonian for small polyatomics. Introduction to the variational method-Discrete variable and Finite Basis Representations.
Theory of line intensities for infra-red and Raman spectra. Introduction to modern laser spectroscopic techniques.
Introduction to the theory of ro-vibrational spectra of non-rigid molecules and van der Waals complexes.
Prerequisite: (M. Sc. Elective Course in Advanced Molecular and Magnetic Resonance Spectroscopy).