M. Sc. Syllabus Semester – 4

CH 640 Principles and Applications of Luminescence Spectroscopy

Luminescence, a brief history, different kinds of luminescence, electronic transition, transition probability, fluorescence and other de-excitation process, phosphorescence versus non-radiative de-excitation, delayed fluorescence, basic instrumentation of steady-state and time-resolved fluorometer, characteristics of fluorescence emission, solvent and environmental effects, red-edge effects, effects of intermolecular photophysical processes on emission, static and dynamic quenching, Stern-Volmer kinetics, emission anisotropy, intrinsic and extrinsic probes, chemical sensing probes, probes of analyte recognition, electron transfer probes, energy transfer, energy transfer to multiple acceptor, biochemical applications, pH and CO2 sensors, protein fluorescence and protein sensors, glucose sensors, novel fluorophores: semiconductor nano particles, lanthanides, metal-ligand complexes, long-wavelenth and long-lifetime fluorophores, advanced techniques in fluorescence spectroscopy.

Text Books:
1. J. R. Lakowicz, Principles of Fluorescence Spectroscopy, Springer, 3rd Ed. 2006.
2. B. Valuer, Molecular Fluorescence, Wiley-VCH, 2002.
3. N. J. Turro, Modern Molecular Photochemistry, University Science Books, 1991.

References:
1. J. R. Lakowicz, Topics in Fluorescence Spectroscopy, Vol. 1: Techniques, Plenum Press, 1991.
2. J. R. Lakowicz, Topics in Fluorescence Spectroscopy, Vol. 4: Probe Design and Chemical Sensing, Kluwer Academic Press, 1994.
3. B. Valuer and J. C. Brochon, New Trends in Fluorescence Spectroscopy: Applications to Chemical and Life Sciences, Springer, 2001.

CH 501: Computers in Chemistry

Computer programming in FORTRAN. Computer application in Chemistry: Development of small computer codes involving simple formulae in chemistry, such as van der Waals equation, pH titration, kinetics, radioactive decay. Evaluation of lattice energy and ionic radii from experimental data. Linear simultaneous equations to solve secular equations within the Hückel theory. Elementary structural features such as bond lengths, bond angles, dihedral angles etc., of molecules extracted from a database such as Cambridge database.

Use of computer programmes: Execution of linear regression, X-Y plot, numerical integration and differentiation as well as differential equation solution programmes. Monte Carlo and Molecular dynamics. Programmes with data preferably from physical chemistry laboratory.

Text Books:

  1. Computational Chemistry by A. C. Norris, John Wiley
  2. Numerical Recipes in FORTRAN/C by W. H. Press, S. A. Teukolsky, W. T. Vetterling and B. P. Flannery, Cambridge University Press, 2nd Ed. 1996.
  3. Fortran 77 and Numerical Methods by C. Xavier, New Age International, 2002

Reference:

  1. Inside the IBM PC by Peter Norton

CH 615 Advanced Organometallic Chemistry

Definition, classifications and bonding in organometallic compounds. Isolobal analogies. Structural methods of Organometallics. Preparative methods.

Spectroscopic techniques in Organometallic chemistry. Electronic and magnetic properties of Organometallic compounds. Stoichiometric and catalytic reactions. Fundamental processes in reactions of organo-transition metal complexes. Applications of transition metal complexes to catalysis, organometallics directed towards organicsynthesis.

Bio-organometallics, Organometallics in environmental chemistry. Metal clusters and models for heterogeneous catalysis. Application of Organometallics in Industry.

Text Books:

  1. Organotransition metal chemistry, Fundamental concept and applications, A. Yamamoto, John Wiley, 1986.
  2. The organometallic Chemistry of transition metals, R.H. Crabtree, John Wiley, 1994.

CH 637: Advance Quantum Chemistry

Introduction: Vector Interpretation of Wavefunction, Hermitian Operator, The Generalized Uncertainty principle, The quantum Mechanical Virial Theorem, Solution of harmonic oscillator (Operator approach), Second quantization (Boson and Fermion), Quantum theory of angular momentum, One electorn Atom, Spin angular momentum.

Approximate solutions to the Schroedinger equation: The Variation method (Time independent and Time Dependent), Time independent perturbation theory (non – degenerate and degenetrate), Time dependent perturbation theory.

Electron Spin and Many – Electron Systems: The Antisymmetry Principle, Spin angular momenta and their Operators, The Orbital Approximation (Slaterdeterminant, Pauli exclusion principle), Two electron wavefunctions.

The Hartree-Fock Self-Consistent Field Method: The generation of Optimized orbitals, Koopman’s Theorem (The Physical Significance of Orbital Energies), The electron correlation energy, Density matrix analysis of the Hartree-Fock Approximation, Natural orbitals, The matrix solution of the Hartree- Fock Equations (Roothaan’s equations).

Introduction to Molecular Structure: The Born – Oppenheimer Approximation, Solution of the Nuclear Equation, Molecular Hartree- Fock Calculations.

Electronic Structure of Linear Molecule: The MO – LCAO Approximation, The Hydrogen Molecule Ion, H+ 2 , The Hydrogen molecule, Molecular Configuration – Interactions, The Valence Bond Method, Molecular Perturbation Calculations.

Electronic Structure of Non-linear Molecule: The AHn molecule: Methane, Ammonia and Water, Hybrid Orbitals: The Ethylene and Benzene Molecules.

Semiempirical Molecular Orbital Methods I – PI Electron Systems: The H¨uckel Approximation for Conjugated Hydrocarbons, The Pariser-Parr-Pople Method.Semiempirical Molecular Orbital Methods II – All valence – Electron systems: The Extended H¨uckel Method, The CNDO Method.

Text Books:

  1. Elementary Quantum Chemistry by Frank L. Pilar, 2nd Edition, McGraw – Hill Publishing Company, 1990.
  2. Molecular Quantum Mechanics by P. W. Atkins and R. S. Friedman, 3rd Edition, Oxford Univ. Press, 1997.

References:

  1. Quantum Chemistry by D. A. McQuarrie, Oxford Univ. Press, 1983.
  2. Quantum Chemistry by I. N. Levine, Allyn and Bacon Inc., 3rd Edition.

CH 628 Advances in Nucleic Acid and Lipid Chemistry

Nucleic acids: Definition, structure and properties, base pairing, double helices, DNA replication, genetic information storage, transmission and gene expression, chemical synthesis of oligonucleotides, hybridization with synthetic oligonucleotides, characterization and purification techniques, nucleic acids as molecular probes. DNA damages, mutations and repair.

Modified nucleic acids: Peptide nucleic acids (PNAs), LNAs, synthesis of PNAs, doubly labeled PNAs as probes for the detection of point mutations. Lipids, fatty acids, bilayer, liposome, lipidation of proteins and peptides, farnesylation of the Ras protein. Synthesis of lipids. Role of lipids in drug delivery and gene delivery. Lipid probes. Biophysical properties of lipid-protein, lipid-peptide interactions. Transport across membranes. Lipidated proteins and peptidesin model membranes. Basic concepts of fluorescence and lipid markers. synthesis of fluorescence quencher and lipidated peptides.

Text books:

  1. C.M. Dobson, J.A. Gerrard and A.J. Pratt., Foundations of Chemical biology, Oxford University Press. 2002.
  2. A. Miller and J. Tanner, Essentials of Chemical Biology, Willey & Sons Ltd. 2008.

References:

  1. S. L. Schreiber, T. Kapoor and G. Wess, Chemical Biology: from small molecules to systems biology and drug design, Wiley – VCH Verlag GmbH & Co. 2007.