Department of Chemistry Presidency University Ph.D. Course Work syllabus 1. Research Methodology (4 credits, compulsory) 1.1 Concept of Research, Scientific Approach to Research, Types of Research. 1.2 Research Process and Planning for Research. Review of Literature. 1.3 Defining Research Problem. 1.4 Methods of data collection 1.5 Quantitative Techniques of Data Analysis: Application of mean, mode, median; coefficient of correlation, standard deviation; least squares fitting methods (both linear and non-linear regression analyses); usage of software packages for data analysis including CHEMDRAW and ORIGIN; Fourier transformations and applications in spectroscopy. Use of molecular geometry optimization software (Gaussian 09); construction of z-matrix and concept of force field. Classical Molecular Dynamics (MD) simulation and application to simple systems like Lennard-Jones fluids; writing computer programs. 1.6 Computer Application in Research: Knowledge of MS office application; knowledge of internet application, and knowledge of application of data-bases of research publications. 1.7 Syllabus for Spectroscopy in Research Methodology: Recording and analysis of UV-Vis absorption spectrum and emission spectrum of organic fluorophores. Study of Fluorescence quenching, interaction of different fluorophores with biomolecules / nano materials using Fluorescence spectrophotometer.
2. Elective Courses (Two subject courses, 8 credits) Any two of the following to be chosen by the students 2.1 Application of spectroscopic studies in chemical research [Odd Sem] Unit 1: Spectroscopy (M = 30) Details of UV and IR spectroscopy, principle and application in interpretation of organic functional groups, Woodward-Hoffman rule. 1 H NMR Spectroscopy: Basic theory – phenomenon of energy absorptions (resonance) and relaxation, chemical shift, shielding and deshielding mechanisms, equivalence and nonequivalence of protons, spin-spin coupling – notation for spin systems, coupling constant and
its variation with stereochemistry-Karplus equation. Structural application of 1H NMR, aromaticity, antiaromaticity and homoaromaticity of organic molecules and related problems. 13 C NMR Spectroscopy: Principles; broad band decoupling, DEPT; structural applications of 13C NMR. Mass Spectrometry: Types of ionization techniques, basic principles of EI.Fragmentation processes and structural analysis; ESI, GC/MS, LC/MS and MS/MS techniques,fragmentation pattern of small molecules and interpretation of spectroscopic (NMR, IR and mass) data, as applied to organic, inorganic and biological systems Problems incorporating spectroscopic data.
Unit 2: FT NMR, FT IR, 2D NMR, Mass spectrometry (M = 20) Fourier transformations, time domain versus frequency domain. Principles of FT NMR, instrumentation, the rotating frame of reference, simple 1D experiment. FT IR – principles and instrumentation. Introduction to 2D NMR: NOESY, COSY, HETCOR, HOMCOR, INADEQUATE, INDOR, INEPT for simple compounds and problems. Applications of multinuclear NMR in inorganic compounds – Examples from 1H, 11B, 13C, 19F, 31P. NMR of paramagnetic molecules – Lanthanide shift.
2.2 Advanced quantum mechanics (M=50) [Even Sem] Degenerate and non-degenerate states perturbation method with some simple applications, like expression for polarizability, ground state of helium atom, Stark effect, lifting of degeneracy by application of a magnetic field (e.g. , the 1P1 state of helium atom). Variation method – Euler variation, principle and Rayleigh-Ritz variation theorem, applications. Concept of vector space, matrix representation of operators, Hermitian operators and matrices, solutions of eigenvalue equation. Comparison between Schrodinger and Heisenberg pictures. Born-Oppenheimer approximation, theories of valence, the MO and VB methods for H2 molecule – their relative merits, dissociation curve, excited state, configuration interaction. Many electron systems – its charectaristics, independent particle model (IPM), Hartree and HartreeFock methods for closed shell (elementary ideas).
2.3 Physical chemistry of polymer [Odd Sem] Unit 1 (M=30) Classification of polymers, kinetics of two dimensional polymerization, condensation and addition polymerizations; initiation, propagation and termination; chain transfer, copolymerization; molecular weights of polymers and polydispersity index; determination of molecular weights. Kinetic chain length.
Unit 2 (M=20) Glass Transition temperature of polymers. Thermodynamics of polymerization. Polymer surfactant interactions. Introduction to different controlled polymerization techniques and synthesis of block copolymers and their properties.
2.4 Advanced electrochemistry: Electrolyte to polyelectrolytes [Even Sem] Unit 1 Electrolytes (M=25) The extension of Debye-Hückel limiting law; Pitzer ion-interaction approach for osmotic and activity coefficients of electrolyte solutions; Debye-Hückel-Onsager theory for electrical conduction in electrolyte solutions; limitation of Debye-Hückel-Onsager theory; Shedlovsky equation; Fuoss conductance-concentration relationship. Unit 2 Polyelectrolytes (M=25) Poisson-Boltzmann cell model of polyelectrolyte solutions; osmotic and activity coefficients of polyelectrolytes; vapor pressure osmometry; electrical conductivity of polyelectrolyte solutions; Manning model; scaling theory for the configuration of polyions in solutions; model for semidilute polyelectrolyte conductivity.
2.5 X-ray crystallography for chemists (M=50) [Odd Sem] The geometry of the crystalline state: the general features of crystals, the external and internal symmetries of crystals, crystal systems, Bravais lattices, crystal classes, Miller indices, space groups. The generation and nature of X-rays: production of monochromatic X-rays. The scattering of X-Rays: scattering from a general distribution of point scatterers. Diffraction of X-Rays: diffraction from one-, two- and three-dimensional arrays of atoms, the reciprocal lattice, diffraction from a crystal, atomic scattering factor, structure factor. The determination of space groups and crystal structures: the optical properties of crystals, systematic absences and information obtained therefrom; the heavy-atom method, Fourier transform.
2.6 Advanced synthetic organic chemistry: Asymmetric synthesis and catalysis (M=50) [Even Sem] The course is designed for chemistry Ph.D. students and aims to enhance their broad understanding of chemistry about the importance of synthesizing enantiomerically pure organic
compounds and strategies available for this purpose. The students can expect to reach frontiers of knowledge in key aspects of this subject through series of specialized advanced lecture courses, problem solving class and home assignment. It will include basic understanding of stereochemistry, biological relevance of isomers, importance of asymmetric synthesis, resolution, asymmetric synthesis using chiral pool material, chiral auxiliary, asymmetric catalysis, chiral-ligand designing featuring Sharpless and Noyori’s work and organocatalysis. Introduction-Scope of Study Chirality in nature - molecular and supramolecular chirality – utility of chiral organic molecules – forms of chirality – asymmetric carbon – axial chirality – analytical methods for optical isomer separation and identification – determination of optical purity – resolution of optical antipodes – chiral HPLC Chiral induction – Diastereoselective synthesis Stereoselectivity and stereospecificity – Nucleophilic addition to a-chiral carbonyl compounds – 1,2-induction and 1,3-induction – Cram’s rule and beyond – chelation control and non-chelation control directed functionalization – direct biomimetic polyene cyclization (Johnson) Chiral auxiliary - Diastereoselective synthesis Basic requirements of chiral auxiliary – ‘chiral pool’ sources – polular and generally adaptable chiral auxiliaries (Oppolzer, Evans, Enders, Davies, 8-phenylmenthol, BINOL etc.) – kinetic resolution by chiral auxiliary – boronic ester mediated homologation – disadventages of ‘auxiliary’ approach Asymmetric aldol condensation and alkylation Equilibrium-controlled condensation reaction has its own disadvantage – transition state – enolate of lithium, boron, zinc etc. – configuration of enolate and stereochemistry of aldehyde addition – product assignment and extent of stereocontrol – transition state model – ‘double stereo differentiation’ concept – Masamune’s sugar synthesis – macrolide antibiotics as target – alkylation of chiral nucleophiles – Meyer’s oxazoline based enolate - ‘memory of chirality’ – Evan’s oxazolidinone derived enolates – polyanions in peptide backbone (Seebach) Chirality modified reagents Reducing agents like boron/aluminium hydrides – allylation and crotylation – oxazaboralidines – TADDOL – chiral lithium amides – chiral Lewis acids in enolate reaction, cycloadditions and sigmatropic rearrangements – enantioselective deprotonation and protonation – ‘chiral cavity’ for enantioselection Asymmetric catalysis Metal mediated catalysis – asymmetric hydrogenation; early advances DIPAMP, DIOP and Noyori’s BINAP – Sharpless epoxidation, dihydroxylation, aminohydroxylation of alkenes – metal biocatalysis – organocatalysis – Proline mediated aldol reaction and further expansion in the field of organocatalysis, ‘non-linear effects’ – ‘ligand accelerated catalysis’ and ‘chiral amplification’.
2.7 Advanced heterocyclic chemistry (M=50) [Even Sem] Systematic nomenclature (Hantzsch – Widman system) for monocycle and fused heterocycles. General approach to heterocyclic synthesis – cyclisation and cycloaddition routes. Heterocycles in organic synthesis – masked functionalities, umpolung, Stork annulation reaction and applications (synthesis of testosterone, estrone, progesterone, ranitidine, lansoprazole and/or recently discovered molecules etc. Rearrangement and ring transformation involving 5- and 6membered heterocycles with one heteroatom. Synthesis and reactivity of 5,6-membered rings containing two heteroatoms, pyrimidines and purines. Introduction to chemistry of azepins, oxepins, thiepins and their analogues; phosphorous and selenium containing heterocycles with the use of modern reagents. ANRORC and Vicarious nucleophilic substitutions in heterocycles. Synthesis of few heterocyclic novel natural products.
2.8 Chemistry of medically important compounds [Even Sem] Unit 1 Chemistry of Medicinally important compounds (M = 30) (a) Bacterial and animal cells, antibiotics and antibacterial agents; β-lactam antibiotics: penicillins and cephallosporins; General method of synthesis of β-lactam ring,Structure of penicillin,mechanism of action of β-lactam antibiotics with reference topenicillin,structure-activity relationship of penicillin, synthesis and modification of penicillinfor newer antibacterial agents with improved activity, synthesis of 6-APA, cephalosporin, 7-ACA; Morin – Jackson rearrangement and it’s application in conversion of penam to cepham derivative, prodrug and co-drug. (b) New generation antibiotics/antibacterial agents: Synthesis and mechanism of action of (i) fluoroquinolones – norfloxacin, ciprofloxacin, O-floxacin, levofloxacin (ii) anti AIDS drugs – AZT, lamivadine (iii) antihypertensive agent – captopril (iv) calcium channel blocker – amlodipine (v) gastric secretion inhibitor – omeprazole and it’s mechanism of action (vi) drug for impotency – sildenafil and it,s mechanism of action., (c) Tetracyclin antibiotics, synthesis and activity. Unit 2 The molecules of life (M = 20) Introduction: The molecules of life – nucleic acids, proteins and enzymes, Protein structure – Protein folding; building blocks, peptide bond, Chemical synthesis of peptides and proteins;Biomolecular complexes: protein-ligand, enzyme-substrate levels of structure;Techniques for study of biomolecular structure and function- optical techniques: CD, ORD: Cotton effect.Fluorescence anisotropy for biomolecular structure determination; Carbohydrates, lipids. Mechanism in biological chemistry: (i) Mechanism of enzyme action, examples of enzyme mechanisms for chymotrypsin, ribonuclease, lysozyme and carboxypeptidase A (ii) Enzyme catalysed reactions – examples of nucleophilic displacement on
a phosphorus atom, coupling of ATP cleavage to endergonic processes, proton transfer reactions to and from carbon (iii) Mechanism of reactions catalysed by cofactors including coenzyme A, NAD+, NADH, FAD and thiamine pyrophosphate;
2.9 Magneto-chemistry (M=50) [Odd Sem] Definition of magnetic properties, types of magnetic bodies, Curie equation, Curie’s law and Curie-Weiss law. Anisotropy in magnetic susceptibility, diamagnetism in atoms and polyatomic system, Pascal’s constants, two sources of paramagnetism, spin and orbital effects, spin-orbit coupling, Lande interval rule, energies of J levels, first order and second order Zeeman effects, temperature independent paramagnetism, simplification and application of van Vleck susceptibility equation, quenching of orbital moment, magnetic properties of transition metal complexes, low spin, high-spin crossover, magnetic behavior of lanthanides and actinides, magnetic exchange interactions. Molecular magnets, Single Molecule Magnets (SMMs), 3d, 4f and 3d-4f based SMMs. Experimental arrangements for determination of magnetic susceptibility: SQUID.
2.10 Advanced organometalic chemistry (M=50) [Even Sem] Preliminary idea and applications of 16 and 18 electrons rule for organometallic compounds. 18 and 16 electron rule exceptions. Reaction of organometallic complexes: substitution, oxidative addition, reductive elimination, insertion and elimination, electrophilic and nucleophilic reactions of coordinated ligands. Stereochemical non-rigidity and fluxional behaviour of organometallic compounds. Metallocenes: η5 Cyclopentadienyl – complexes, η6 arene Metal complexes, Half sandwich complexes and Reactivity changes in coordinated ligands Applications of Organometallic Chemistry: (i) catalysis by organometallic compounds: Wilkinson’s catalyst, Tolman’s catalytic loops; synthesis gas, water gas shift reaction, synthesis of methanol, hydroformylation (oxo process), hydrogenation of unsaturated compounds, Masanto acetic acid process, Waker process, synthetic gasoline, Fischer-Tropsch process and mobil process; Polymerisation, oligomerisation and metathesis reactions of alkenes and alkynes; Zieglar-Natta catalysis. (ii) Medicinal applications of organometallic complexes.
2.11 Non-equlibrium statistical mechanics (M=50) [Odd Sem] Brownian motion : Einstein’s theory, Diffusion and mobility, experimental confirmation of Einstein's theory, observations on Brownian motion and the existence of a random force, Langevin description of Brownian motion, relation between random and viscous force : The fluctuation-dissipation theorem, Brownian motion in velocity space : Fokker-Planck equation, Fokker-Planck, Brownian motion in phase space (motion in a force field), Kramers’ equation, Kramers equation as a generalization of Liouville equation and connection to equilibrium
statistical, theory of activated processes, a simple connection to Transition State Theory, Overdamped motion : Smoluchowski equation and diffusion over a barrier, Smoluchowski equation, Diffusion of particles over the barrier, The master equation and applications Unidirectional random walk, quantized harmonic oscillator interacting with a radiation field.
2.12 Techniques used in biophysical chemistry (M=50) [Odd Sem] Absorption of protein and other biomolecules, fluorescence of biomolecules, Structure of Biomolecules: Protein structure – building blocks, peptide bond, levels of structure; Biomolecular complexes: protein-ligand, enzyme-substrate. Laser flash photolysis technique and information from it, precautions to be implemented.
3. Review of research work (4 credits, compulsory) Extensive survey of published literature relevant to the chosen topic of research which appeared in referred research journals of national and international repute, edited books, reference books, monographs, survey / study reports, dissertations / theses published in book form, and books / reports containing proceedings of national and international conferences / seminars / symposia.
