Syllabus 2

CH2C06 ORGANIC REACTION MECHANISM
Credit: 4 Contact Lecture Hours: 72
Unit 1: Review of Organic Reaction Mechanisms (9 Hrs)

1.1 Review of organic reaction mechanisms with special reference to nucleophilic and
electrophilic substitution at aliphatic carbon (SN1, SN2, SNi, SE1, SE2, addition-
elimination and elimination-addition sequences), elimination (E1 and E2) and
addition reactions (regioselectivity: Markovnikov’s addition-carbocation
mechanism, anti-Markovnikov’s addition-radical mechanism). Elimination vs
substitution.
1.2 A comprehensive study on the effect of substrate, reagent, leaving group, solvent
and neighbouring group on nucleophilic substitution(SN2 and SN1) and
elimination (E1 and E2) reactions.
Unit 2: Chemistry of Carbanions (9 Hrs)

2.1 Formation, structure and stability of carbanions. Reactions of carbanions: C-X
bond (X = C, O, N) formations through the intermediary of carbanions. Chemistry
of enolates and enamines. Kinetic and Thermodynamic enolates- lithium and
boron enolates in aldol and Michael reactions, alkylation and acylation of
enolates.
2.2 Nucleophilic additions to carbonyls groups. Named reactions under carbanion
chemistry-mechanism of Claisen, Dieckmann, Knoevenagel, Stobbe, Darzen and
acyloin condensations, Shapiro reaction and Julia elimination. Favorski
rearrangement.
2.3 Ylids: chemistry of phosphorous and sulphur ylids - Wittig and related reactions,
Peterson olefination.
Unit 3: Chemistry of Carbocations (9 Hrs)

3.1 Formation, structure and stability of carbocations. Classical and non-classical
carbocations.
3.2 C-X bond (X = C, O, N) formations through the intermediary of carbocations.
Molecular rearrangements including Wagner-Meerwein, Pinacol-pinacolone,
semi-pinacol, Dienone-phenol and Benzilic acid rearrangements, Noyori
annulation, Prins reaction.
3.3 C-C bond formation involving carbocations: oxymercuration, halolactonisation.
Unit 4: Carbenes, Carbenoids, Nitrenes and Arynes (9 Hrs)

4.1 Structure of carbenes (singlet and triplet), generation of carbenes, addition and
insertion reactions.
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4.2 Rearrangement reactions of carbenes such as Wolff rearrangement, generation
and reactions of ylids by carbenoid decomposition.
4.3 Structure, generation and reactions of nitrene and related electron deficient nitrene
intermediates.
4.4 Hoffmann, Curtius, Lossen, Schmidt and Beckmann rearrangement reactions.
4.5 Arynes: generation, structure, stability and reactions. Orientation effect-
amination of haloarenes.
Unit 5: Radical Reactions (9 Hrs)

5.1 Generation of radical intermediates and its (a) addition to alkenes, alkynes (inter
and intramolecular) for C-C bond formation - Baldwin’s rules (b) fragmentation
and rearrangements-Hydroperoxide: formation, rearrangement and reactions.
Autooxidation.
5.2 Named reactions involving radical intermediates: Barton deoxygenation and
decarboxylation, McMurry coupling.
Unit 6: Chemistry of Carbonyl Compounds (9 Hrs)

6.1 Reactions of carbonyl compounds: oxidation, reduction (Clemmensen and Wolf-
Kishner), addition (addition of cyanide, ammonia, alcohol) reactions, Cannizzaro
reaction, addition of Grignard reagent. Structure and reactions of α, β- unsaturated
carbonyl compounds involving electrophilic and nucleophilic addition-Michael
addition, Mannich reaction, Robinson annulation.
Unit 7: Concerted reactions (18 Hrs)

7.1 Classification: electrocyclic, sigmatropic, cycloaddition, chelotropic and ene
reactions. Woodward Hoffmann rules-frontier orbital and orbital symmetry
correlation approaches-PMO method.
7.2 Highlighting pericyclic reactions in organic synthesis such as Claisen, Cope,
Wittig, Mislow-Evans and Sommelet-Hauser rearrangements. Diels-Alder and
Ene reactions (with stereochemical aspects), dipolar cycloaddition(introductory).
7.3 Unimolecular pyrolytic elimnination reactions: cheletropic elimination,
decomposition of cyclic azo compounds, β-eliminations involving cyclic
transition states such as N-oxides, acetates and xanthates.
7.4 Problems based on the above topics.
References
01. R. Bruckner, Advanced Organic Chemistry: Reaction Mechanism, Academic
Press, 2002.
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02. F.A. Carey, R.A. Sundberg, Advanced Organic Chemistry, Part B: Reactions and
Synthesis, 5th Edn., Springer, 2007.
03. W. Carruthers, I. Coldham, Modern Methods of Organic Synthesis, Cambridge
University Press, 2005.
04. J. March, M.B. Smith, March's Advanced Organic Chemistry: Reactions,
Mechanisms, and Structure, 6th Edn., Wiley, 2007.
05. A. Fleming, Frontier Orbitals and Organic Chemical Reactions, Wiley, 1976.
06. S. Sankararaman, Pericyclic Reactions-A Text Book, Wiley VCH, 2005.
07. R.T. Morrison, R.N. Boyd, S.K. Bhatacharjee, Organic Chemistry, 7th Edn.,
Pearson, 2011.
08. J. Clayden, N. Greeves, S. Warren, P. Wothers, Organic Chemistry, Oxford
University Press, 2004.
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CH2C07 CHEMICAL BONDING AND COMPUTATIONAL
CHEMISTRY
Credit: 4 Contact Lecture Hours: 72
Unit 1: Approximate Methods in Quantum Mechanics (18 Hrs)

1.1 Many-body problem and the need of approximation methods, independent particle
model. Variation method, variation theorem with proof, illustration of variation
theorem using the trial function x(a-x) for particle in a 1D-box and using the trial
function e-ar for the hydrogen atom, variation treatment for the ground state of
helium atom.
1.2 Perturbation method, time-independent perturbation method (non-degenerate case
only), first order correction to energy and wave function, illustration by
application to particle in a 1D-box with slanted bottom, perturbation treatment of
the ground state of the helium atom. Qualitative idea of Hellmann-Feynman
theorem.
1.3 Hartree Self-Consistent Field method. Spin orbitals for many electron atoms-
symmetric and antisymmetric wave functions. Pauli's exclusion principle. Slater
determinants. Qualitative treatment of Hartree-Fock Self-Consistent Field
(HFSCF) method. Roothan's concept of basis functions, Slater type orbitals (STO)
and Gaussian type orbitals (GTO), sketches of STO and GTO.
Unit 2: Chemical Bonding (18 Hrs)

2.1 Schrödinger equation for molecules. Born-Oppenheimer approximation. Valence
Bond (VB) theory, VB theory of H2 molecule, singlet and triplet state functions
(spin orbitals) of H2.
2.2 Molecular Orbital (MO) theory, MO theory of H2+ ion, MO theory of H2
molecule, MO treatment of homonuclear diatomic molecules Li2, Be2, N2, O2
and F2 and hetero nuclear diatomic molecules LiH, CO, NO and HF. Bond order.
Correlation diagrams, non-crossing rule. Spectroscopic term symbols for diatomic
molecules. Comparison of MO and VB theories.
2.3 Hybridization, quantum mechanical treatment of sp, sp2 and sp3 hybridisation.
Semiempirical MO treatment of planar conjugated molecules, Hückel Molecular
Orbital (HMO) theory of ethene, allyl systems, butadiene and benzene.
Calculation of charge distributions, bond orders and free valency.
Unit 3: Applications of Group Theory in Chemical Bonding (9 Hrs)

3.1 Applications in chemical bonding, construction of hybrid orbitals with BF3, CH4,
PCl5 as examples. Transformation properties of atomic orbitals. Symmetry
adapted linear combinations (SALC) of C2v, C2h, C3, C3v and D3h point groups.
MO diagram for water and ammonia.
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Unit 4: Computational Chemistry (18 Hrs)
(The units 4 and 5 have been designed to expose the students to the field of
computational chemistry, which has emerged as a powerful tool in chemistry
capable of supplementing and complementing experimental research. The
quantities which can be calculated using computational methods, how to prepare
the input to get these results and the different methods that are widely used to
arrive at the results are introduced here. Detailed mathematical derivations are
not expected. Though computer simulations form an important part of
computational chemistry, they are not covered in this syllabus.)
4.1 Introduction: computational chemistry as a tool and its scope.
4.2 Potential energy surface: stationary point, transition state or saddle point, local
and global minima.
4.3 Molecular mechanics methods: force fields-bond stretching, angle bending,
torsional terms, non-bonded interactions, electrostatic interactions. Mathematical
expressions. Parameterisation from experiments or quantum chemistry. Important
features of commonly used force fields like MM3, MMFF, AMBER and
CHARMM.
4.4 Ab initio methods: A review of Hartee-Fock method. Basis set approximation.
Slater and Gaussian functions. Classification of basis sets - minimal, double zeta,
triple zeta, split valence, polarization and diffuse basis sets, contracted basis sets,
Pople style basis sets and their nomenclature, correlation consistent basis sets.
4.5 Hartree-Fock limit. Electron correlation. Qualitative ideas on post Hartree-Fock
methods-variational method, basic principles of Configuration Inetraction(CI).
Perturbational methods-basic principles of Møller Plesset Perturbation Theory.
4.6 General introduction to semiempirical methods: basic principles and terminology.
4.7 Introduction to Density Functional Theory (DFT) methods: Hohenberg-Kohn
theorems. Kohn-Sham orbitals. Exchange correlation functional. Local density
approximation. Generalized gradient approximation. Hybrid functionals (only the
basic principles and terms need to be introduced).
4.8 Model Chemistry-notation, effect on calculation time (cost).
4.9 Comparison of molecular mechanics, ab initio, semiempirical and DFT methods.
Unit 5: Computational Chemistry Calculations (9 Hrs)

5.1 Molecular geometry input-cartesian coordinates and internal coordinates, Z-
matrix. Z-matrix of: single atom, diatomic molecule, non-linear triatomic
molecule, linear triatomic molecule, polyatomic molecules like ammonia,
methane, ethane and butane. General format of GAMESS / Firefly input file.
GAMESS / Firefly key word for: basis set selection, method selection, charge,
multiplicity, single point energy calculation, geometry optimization, constrained
optimization and frequency calculation.
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5.2 Identifying a successful GAMESS/ Firefly calculation-locating local minima and
saddle points, characterizing transition states, calculation of ionization energies,
Koopmans’ theorem, electron affinities and atomic charges.
5.3 Identifying HOMO and LUMO-visualization of molecular orbitals and normal
modes of vibrations using suitable graphics packages.
References
01. I.N. Levine, Quantum Chemistry, 6th Edn., Pearson Education, 2009.
02. D.A. McQuarrie, Quantum Chemistry, University Science Books, 2008.
03. R.K. Prasad, Quantum Chemistry, 3rd Edn., New Age International, 2006.
04. F.A. Cotton, Chemical Applications of Group Theory, 3rd Edn., Wiley Eastern,
1990.
05. V. Ramakrishnan, M.S. Gopinathan, Group Theory in Chemistry, Vishal
Publications, 1992.
06. A.S. Kunju, G. Krishnan, Group Theory and its Applications in Chemistry, PHI
Learning, 2010
07. E.G. Lewars, Computational Chemistry: Introduction to the Theory and
Applications of Molecular and Quantum Mechanics, 2nd Edn., Springer, 2011.
08. J.H. Jensen, Molecular Modeling Basics, CRC Press, 2010.
09. F. Jensen, Introduction to computational chemistry, 2 nd Edn., John Wiley & Sons,
2007.
10. A. Leach, Molecular Modelling: Principles and Applications, 2nd Edn., Longman,
2001.
11. J.P. Fackler Jr., L.R. Falvello (Eds.), Techniques in Inorganic Chemistry: Chapter
4, CRC Press, 2011.
12. K.I. Ramachandran, G. Deepa, K. Namboori, Computational Chemistry and
Molecular Modeling: Principles and Applications, Springer, 2008.
13. A. Hinchliffe, Molecular Modelling for Beginners, 2nd Edn., John Wiley & Sons,
2008.
14. C.J. Cramer, Essentials of Computational Chemistry: Theories and Models, 2nd
Edn., John Wiley & Sons, 2004.
15. D.C. Young, Computational Chemistry: A Practical Guide for Applying
Techniques to Real-World Problems, John Wiley & Sons, 2001.
Softwares
Molecular Mechanics:
1. Arguslab available from www.arguslab.com/
2. Tinker available from www.dasher.wustl.edu/ffe/
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Ab initio, semiempirical and dft:
1. Firefly / PC GAMESS available from http://classic.chem.msu.su/gran/gamess/
2. WINGAMESS available from http://www.msg.ameslab.gov/gamess/
Graphical User Interface (GUI):
1. Gabedit available from http://gabedit.sourceforge.net/
2. wxMacMolPlt available from http://www.scl.ameslab.gov/MacMolPlt/
3. Avogadro from http://avogadro.openmolecules.net/wiki/Get_Avogadro
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CH2C06 ORGANIC REACTION MECHANISM

Credit: 4 Contact Lecture Hours: 72

Unit 1: Review of Organic Reaction Mechanisms (9 Hrs)

Unit 2: Chemistry of Carbanions (9 Hrs)

Unit 3: Chemistry of Carbocations (9 Hrs)

Unit 4: Carbenes, Carbenoids, Nitrenes and Arynes (9 Hrs)

Unit 5: Radical Reactions (9 Hrs)

Unit 6: Chemistry of Carbonyl Compounds (9 Hrs)

Unit 7: Concerted reactions (18 Hrs)

Unit 1: Approximate Methods in Quantum Mechanics (18 Hrs)

Unit 2: Chemical Bonding (18 Hrs)

Unit 3: Applications of Group Theory in Chemical Bonding (9 Hrs)

Unit 5: Computational Chemistry Calculations (9 Hrs)

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