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 Hartree-
Fock 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, co-
polymerization; 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 6-
membered 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.