Course Catalog | Department of Chemistry

Course Catalog

To graduate with a B.Tech in Chemical Engineering the Department of Chemical Engineering each student must have 121 credits in Chemical Engineering (out of a minimum total of 163 credits) obtained over the course of the undergraduate programme. The remaining 42 credits will fulfill SNU’s requirements for University-Wide Electives (UWEs) / a minor in another discipline (24 credits) and minimum 18 credits towards Common Core Curriculum (CCC) courses.

CHY324
Medicinal Chemistry
3.00
Undergraduate
CHY 324, Spring 2019 Instructor: Dr. Goutam Chowdhury 3 Credits In this course we will address various issues regarding drugs and its role inside a cell. We will learn what are drugs and their different types? How do drugs work? What causes side effects? How do drugs become resistance? These and other questions will be considered in this course. We will learn the chemistry and biochemistry necessary to understand the mechanism of drug action and the process of drug discovery and development. Students will investigate what is known about active ingredients in natural remedies. Social, ethical and economic issues related to drugs will be addressed. Instruction will be through a combination of group discussions, reading assignments, projects, video presentations and lectures. Students are expected to do library research, read papers, and present discussion in class. Course Evaluation 2 Take Home Quizzes: 10% 1 Assignment & 1 Presentation: 10% each. Content: Drugs and the body What are drugs? What are the common drug targets? Why do they work? How are drugs transported? Types of Drugs Drug Targets DNA Damaging agents Enzymes, mechanism based inhibitors, covalent inhibitors Receptors Drug Discovery and optimization Generation of lead compounds Lead Optimization Preclinical studies Clinical trials Drug Metabolism Phase I Cytochrome P450 Aldehyde dehydrogenase Monoamine oxidase Phase II GST UGT Transporters Drug toxicity Reactive intermediate Adverse effects Drug-drug interaction Polymorphism and its effect on drug action/toxicity Structure-activity relationships Mechanism of action Painkillers and opioids (e.g. morphine) Antidiabetic Antibiotics Anticancer NSAIDS Statins Blood Thinners Antacids/Proton pump inhibitors Antivirals Antidepressant/antipsychotic Synthesis and biosynthesis of drugs Combinatorial chemistry
CHY343
Advanced Inorganic Chemistry
3.00
Undergraduate
Advanced Inorganic Chemistry PART A: COURSE IDENTIFIERS   School SNS   Department Chemistry   Course Code CHY343   Course Title Advanced Inorganic Chemistry   Credits (L:T:P) 2:1:0 Contact Hours (L:T:P) 2:1:0 Prerequisites CHY111/CHY112 Course Type Major Elective for B.Sc. (R) Chemistry Instructor’s Name Dr. Gouriprasanna Roy (R block, Room # 118) Visiting Time Monday and Friday (4 pm – 5 pm)   Curriculum Content Ionic equilibrium A. General principle of equilibrium, equilibrium in solutions of acids and bases – strong acids and strong bases – weak acids and weak bases – polyprotic acids and bases, the equilibrium constant - Strength of acids and bases in aqueous solution in terms of Ka, Kb; OH the pH scale, pKw, pKa, pKb, etc., numerical problems, aqueous solutions of salts – hydrolysis salts – equilibrium in hydrolysis of salts – salts derives from weak acids and strong bases - salts derives from strong acids and weak bases - salts derives from weak acids and weak bases, numerical problems on hydrolysis of salts, buffer solutions – pH of a buffer solution – Henderson equations – Numerical problems, acid-base titrations – choice of indicator – neutralization of a strong acid by a strong base - neutralization of a weak acid with a strong base - neutralization of a weak base with a strong acid - neutralization of a weak acid by a weak base - neutralization of a weak acid with a strong base - neutralization of a weak base with a strong acid - neutralization of polyprotic acids with strong base.         B. Solid – solution equilibrium, the solubility and solubility product (Ksp), common ion effect, effect of H/OH– and complexing agents. Application of the concept in qualitative analysis; calculation on pH condition and precipitation. Acid-Base i) Theories of acids – bases : Bronsted – Lowry theory, conjugate acid – base pairs, solvent system definition, periodic trends in aqua acid strength, oxoacids, anhydrous oxides, amphoterism, Lux concept, factors affecting strength of acids and bases, proton affinities, Lewis theory of acids – bases, examples of Lewis acids and bases – group characteristics of Lewis acids – reactions and properties of Lewis acids and bases – the fundamental types of reaction,complex formation as acid – base reaction; levelling effect;general strength of acid and base; the concept of Hard and Soft Acids and Bases (HSAB).   Chemistry in nonaqueous solvents/Molecular structure and bonding/The s–block and p–block elements. Teaching and Learning Strategy Teaching and Learning Strategy Description of Work Class Hours Out-of-Class Hours Teaching Problem solving, Quizzes,  presentations 40 hours     Learning   8 hours 8 hours   PART C: ASSSESSMENT. Assessment Strategy           Formative Assessment: Assignments/Quizzes/presentation (seminars) Summary Assessment Final Exam Mapping of Learning Outcomes to Assessment Strategy Assessment Scheme Type of Assessment Percentage Continuous assessment from assignments/quizzes/performance on presentation 60 Final Examination 40 Total 100% Bibliography Shriver and Atkin’s INORGANIC CHEMISTRY. Inorganic Chemistry: Principles of Structure and Reactivity by James E. Huheey, Ellen A. Keiter and Richard L. Keiter. Inorganic Chemistry: Catherine Housecroft, Alan G. Sharpe. Atkins' Physical Chemistry, Peter W. Atkins, Julio de Paula. Advanced Inorganic Chemistry by F. A. Cotton and G. Wilkinson Inorganic Chemistry, A. G. Sharpe Concise Inorganic Chemistry, J. D. Lee Douglas, B.; McDaniel, D.H.; Alexander, J.J. Concepts and Models of Inorganic Chemistry General Inorganic Chemistry by R Sarkar. General Chemistry – Principles and modern application by Ralph H. Petrucci, F. Geoferey Herring, J D Madura, Carey Bissonnette. Greenwood, Norman, and A. Earnshaw. Chemistry of Elements. Other reading materials will be assigned as and when required.
CHY402
Green Chemistry and Sustainability
3.00
Undergraduate
Green Chemistry and Sustainability
CHY316
Electrochemistry
3.00
Undergraduate
Electrochemistry
CHY451
Bioinorganic Chemistry
2.00
Undergraduate
Bioinorganic Chemistry
CHY411
Applications of Group Theory
3.00
Undergraduate
Advanced Chemical Applications of Group Theory Topics Learning Objectives Introduction Importance of Group Theory in Chemistry Symmetry elements And symmetry operations Use molecular models to identify symmetry elements of different molecules. Understanding of the interrelation of different symmetry elements present in a molecule, product of symmetry operations Point Group Concepts and properties of a group, group multiplication Tables, Similarity transformation, Class, Determination of symmetry point group of molecules, Matrix representations and Character Table Matrix representation of groups, reducible and irreducible representations, Great orthogonality theorem, character tables SALC, direct product, Molecular vibration Direct Product and Spectroscopic selection rule, Molecular Vibrations, Normal coordinates, Symmetry of normal mode vibrations, Symmetry Adapted Linear Combination, Infrared and Raman active vibrations, Molecular orbital Theory, Hybrid orbital Molecular orbitals, LCAO MO approach, HMO method, Hybrid orbitals,  Terms and states, Transition metal chemistry Free ion configuration, terms and states, splitting of levels and terms in a chemical environment, correlation diagrams, spectral and magnetic properties of the transition metal complexes.  
CHY244
The Nature of Materials
3.00
Undergraduate
The Nature of Materials
CHY112
Structure and Bonding
5.00
Undergraduate
Structure and Bonding
CHY101
Applied Chemistry
5.00
Undergraduate
Applied Chemistry
CHY453
Forensic Chemistry
2.00
Undergraduate
Chemistry for Forensic Scientists, Skills for Forensic Scientists, Crime Scene Science, Aspects of Forensic Science, Application of Forensic Science, Forensic Science Dissertation, Advances in Forensic Chemistry, Forensic Toxicology. BOOKS: Forensics : The Anatomy of Crime by McDermid, Val. Publisher: London : Profile Books : Wellcome Collection, 2014 Written in Blood by Mike Silverman,Tony Thompson  Publisher: Transworld Publishers (August 1, 2015) ISBN: 9780552169318 Further readings will be assigned from multiple sources.
CHY417
Theoretical Chemistry Seminar
2.00
Undergraduate
This advanced course will cover special topics in quantum chemistry and statistical mechanics. Chemical concepts such as atoms, molecular structure, electron density, equilibrium, reaction path, etc. will also be discussed from a historical and philosophical context. Students will examine in-depth selected articles from the current scientific literature, and develop a viable research proposal in the chosen area. REFERENCES: Readings will be assigned from the current literature.
CHY421
Organic Synthesis
4.00
Undergraduate
Students will gain expertise in the techniques of organic synthesis. A major project will be the development of a research proposal based on the student's own question. Background from the literature will motivate the proposal and initial experiments will be proposed.
CHY111
Chemical Principles
5.00
Undergraduate
This course will focus on introductory chemical principles, including periodicity, chemical bonding, molecular structure, equilibrium and the relationship between structure and properties. Students will explore stoichiometric relationships in solution and gas systems which are the basis for quantifying the results of chemical reactions. Understanding chemical reactivity leads directly into discussion of equilibrium and thermodynamics, two of the most important ideas in chemistry. Equilibrium, especially acid/base applications, explores the extent of reactions while thermodynamics helps us understand if a reaction will happen. The aim of the laboratory will be to develop your experimental skills, especially your ability to perform meaningful experiments, analyze data, and interpret observations. This is a required course for Chemistry majors, but also satisfies UWE requirements for non-majors. COURSE CONTENT: Atomic structure, Periodic table, VSEPR, Molecular Orbital theory, and biochemistry: Introduction: why chemistry in engineering? Concept of atom, molecules, Rutherford’s atomic model, Bohr’s model of an atom, wave model, classical and quantum mechanics, wave particle duality of electrons, Heisenberg’s uncertainty principle, Quantum-Mechanical Model of Atom, Double Slit Experiment for Electrons, The Bohr Theory of the Hydrogen atoms, de Broglie wavelength, Periodic Table. Schrodinger equation (origin of quantization), Concept of Atomic Orbitals, representation of electrons move in three-dimensional space, wave function (Y), Radial and angular part of wave function, radial and angular nodes, Shape of orbitals, the principal (n), angular (l), and magnetic (m) quantum numbers, Pauli exclusion principle. Orbital Angular Momentum (l), Spin Angular Momentum (s), spin-orbit coupling, HUND’s Rule, The aufbau principle, Penetration, Shielding Effect, Effective Nuclear Charge, Slater’s rule. Periodic properties, Ionization Energies of Elements, Electron affinities of elements, Periodic Variation of Physical Properties such as metallic character of the elements, melting point of an atom, ionic and covalent nature of a molecule, reactivity of hydrides, oxides and halides of the elements. Lewis structures, Valence shell electron pair repulsion (VSEPR), Valence-Bond theory (VB), Orbital Overlap, Hybridization, Molecular Orbital Theory (MO) of homo-nuclear and hetero-nuclear diatomic molecules, bonding and anti-bonding orbitals. Biochemistry: Importance of metals in biological systems, Fe in biological systems, Hemoglobin, Iron Storage protein - Ferritin] 2. Introduction to various analytical techniques: UV-Visible Spectroscopy, IR Spectroscopy, NMR spectroscopy, X-Ray crystallography Spectroscopy: Regions of Electromagnetic Radiation, Infra-Red (IR) Spectroscopy or Vibrational Spectroscopy of Harmonic oscillators, degree of freedom, Stretching and Bending, Infrared Spectra of different functional groups such as OH, NH2, CO2H etc., UV-Vis Spectroscopy of organic molecules, Electronic Transitions, Beer-Lambert Law, Chromophores, principles of NMR spectroscopy, 1H and 13C-NMR, chemical shift, integration, multiplicity, X-ray crystallography: X-ray diffraction, Bragg’s Law, Crystal systems and Bravais Lattices The Principles of Chemical Equilibrium, kinetics and intermolecular forces: Heat & Work; State Functions Laws of thermodynamics Probability and Entropy Thermodynamic and Kinetic Stability Determination of rate, order and rate laws Free Energy, Chemical Potential, Electronegativity Phase Rule/Equilibrium Activation Energy; Arrhenius equation Catalysis: types; kinetics and mechanisms Electrochemistry Inter-molecular forces  4. Introduction to organic chemistry, functional group and physical properties of organic compounds, substitution and elimination reaction, name reactions and stereochemistry Texts & References: Chemical Principles - Richard E. Dickerson, Harry B. Gray, Jr. Gilbert P. Haight Valence - Charles A. Coulson [ELBS /Oxford Univ. Press] Valence Theory - J. N. Murrell, S. F. A. Kettle, J. M. Tedder [ELBS/Wiley] Physical Chemistry - P. W. Atkins [3rd Ed. ELBS] Physical Chemistry - Gilbert W. Castellan [Addison Wesley, 1983] Physical Chemistry: A Molecular Approach -Donald A. McQuarrie, J.D . Simon Inorganic Chemistry:  Duward Shriver and Peter Atkins. Inorganic Chemistry: Principles of Structure and Reactivity by James E. Huheey, Ellen A. Keiter and Richard L. Keiter. Inorganic Chemistry: Catherine Housecroft, Alan G. Sharpe. Atkins' Physical Chemistry, Peter W. Atkins, Julio de Paula. Strategic Applications of Named Reactions in Organic Synthesis, Author: Kurti Laszlo et.al Classics in Stereoselective Synthesis, Author: Carreira Erick M & Kvaerno Lisbet Molecular Orbitals and Organic Chemical Reactions Student Edition, Author: Fleming Ian Logic of Chemical Synthesis, Author: Corey E. J. & Xue-Min Cheng Art of Writing Reasonable Organic Reaction Mechanisms /2nd Edn., Author: Grossman Robert B. Organic Synthesis: The Disconnection Approach/ 2nd Edn., Author: Warrer Stuart & Wyatt Paul Other reading materials will be assigned as and when required. Prerequisite: None.
CHY120
Molecules and Medicine
3.00
Undergraduate
Since the time of Hippocrates until modern days, human being has explored several means of alleviating pain and curing disease. There have been pathbreaking discoveries resulting in the development of medicines of immense benefit. Present day research of inventing novel molecules constantly adds to the repertoire of drugs available to counter ill-health. We will begin with a short introduction (which discusses fundamental organic chemistry followed by development and testing of drugs). Next we will explore the discovery and development of a range of drugs and medicines that relieve pain, effect cures and reduce the symptoms of ill-health. We will discuss how drugs interact with and affect their target areas in the human body. There are online videos to help you to understand the three-dimensional structures and shapes of the molecules concerned and to develop an understanding of how the drugs work. Books: Scientific journals will be provided Prerequisite: None.
CHY122
Basic Organic Chemistry I
4.00
Undergraduate
Intermolecular forces of attraction: van der Waals forces, ion-dipole, dipole-dipole and hydrogen bonding Homolytic and heterolytic bond fission. Hybridization- Bonding Electron displacements: Inductive, electromeric, resonance, hyperconjugation effect Reaction intermediate- their shape and stability a. carbocations, b. carbanions, c. free radicals, d. carbenes, e. benzynes Acidity and basicity of organic molecules: Alkanes/Alkenes, Alcohols/Phenols/Carboxylic acids, Amines pKa, pKb. Electrophiles and nucleophiles. Nucleophilicity and Basicity Aromaticity and Tautomerism Molecular chirality and Isomerism a. Cycloalkanes (C3 to C8): Relative stability, Baeyer strain theory and Sachse Mohr theory. b. Conformations and Conformational analysis: Ethane, n-butane, ethane derivatives, cyclohexane, monosubstituted and disubstituted cyclohexanes and their relative stabilities. Stereochemistry (Structural- and Stereo-isomerism) Molecular representations: Newman, Sawhorse, Wedge & Dash, Fischer projections and their inter conversions. Geometrical isomerism in unsaturated and cyclic systems: cis–trans and, syn-anti isomerism, E/Z notations. Geometrical isomerism in dienes- Isolated and conjugated systems, determination of configurations. Chirality and optical isomerism: Configurational isomers. Molecules with one or two chiral centres- constitutionally symmetrical and unsymmetrical molecules; Enantiomers and diastereomers. Optical activity, disymmetry, meso compounds, racemic modifications and methods of their resolution; stereochemical nomenclature: erythro/threo, D/L and R/S nomenclature in acyclic systems. Measurement of optical activity: specific rotation. Books: Morrison, Robert Thornton & Boyd, Robert Neilson Organic Chemistry, Dorling Kindersley (India) Pvt. Ltd. (Pearson Education), Seventh Edition, 2005. Finar, I. L. Organic Chemistry (Volume 1), Dorling Kindersley (India) Pvt. Ltd. (Pearson Education), Sixth Edition, 2003. Finar, I. L. Organic Chemistry (Volume 2: Stereochemistry and the Chemistry of Natural Products), Dorling Kindersley (India) Pvt. Ltd. (Pearson Education). Fifth Edition, 1975. Graham Solomons, T.W., Craig B. Fryhle Organic Chemistry, Ninth edition Eliel, E. L. & Wilen, S. H. Stereochemistry of Organic Compounds; First Edition, Wiley: London, 1994. Clayden, Greeves Warren and Wothers, Organic Chemistry, Oxford University Press. Oxford Chemistry Primers, Introduction to Organic Chemistry, Oxford University Press. Prerequisite: Chemical Principles (CHY111).
CHY140
Chemistry of Colour and Art
3.00
Undergraduate
This inter-disciplinary course will introduce students to the basic principles of optics, colour theory and the chemical principles behind the colours of gemstones, pigments and nanomaterials. Absorption, scattering and emission of light, changes associated with chemical reactions, thermal radiation, colour vision, colours of bulk materials and at the nanoscale will be discussed and demonstrated. Topics covered include spectroscopy, art forensics, colour theory in art, colour spaces, colour in culture, introduction to photography, drawing and painting. Students will also explore how artists through the ages have used and exploited colour, and will have the opportunity to discover for themselves the fundamentals of colour photography, painting and art. Lab and studio sessions will be conducted during alternate weeks. Field trips to natural locations, art galleries and museums will be included to provide opportunities for creating individual works of art. RECOMMENDED BOOK(S): Colour Chemistry by Robert M. Christie, RSC Publishing, Cambridge, 2015. BRAIN AND ART, Editors: Idan Segev, Luis M. Martinez, Robert J. Zatorre, Frontiers in Human Neuroscience, December 2014 http://journal.frontiersin.org/researchtopic/104/brain-and-art The Dimensions of Colour, by Dr David. J.C. Briggs, Julian Ashton Art School and National Art School, Sydney, Australia: http://www.huevaluechroma.com/index.php Additional reading assignments will be given from multiple sources.
CHY142
Main Group Chemistry
3.00
Undergraduate
The s–block elements and the noble gases: The s–block elements of Gr – I, Gr – II, their general electronic configuration, trends in I. P., ionic radii; reaction with H, O, N, C, and hydrolytic behaviour of the products. General metallurgical consideration of these elements. Differences of Li and Be from other members of their groups (the diagonal relationship). Isotopes of H, industrial preparation of deuterium, its properties, reactions and uses; ortho–para – hydrogen. Separation and uses of the noble gases; compounds of Kr and Xe – preparation, properties, structures. The p–block elements: Gr. III. (a) The general group properties * (b) Boron Chemistry – preparation, properties of boranes; Structure and bonding of diborane, Boranine Boron nitrides; electron deficient nature of hydrides, halides and their polymerisation. Gr. IV (a) The general group properties * (b) Aspects of C and Si chemistry the difference of C and P from the rest of the group elements. Preparation, properties, u ses of the fluoroecarbons, the silanes and the silicones. Gr. IV (a) The general group properties * (b) N and P – Chemistry: The presence of lone pair and basicity of trivalent compounds; trends in bond angles of hydrides, halides, preparation, properties, structures and bonding of hydrazine, hydroxylamine, hydrazoic acids, the oxides and oxyacids of N, P; d – orbital participation in P–compounds. Gr. VI (a) The general group properties * (b) S–Chemistry – Preparation, properties, structures and bonding of the oxides, oxyacids (including the thionous, thionic and per–acids), halides, oxy–halides and poly sulphides; d–orbital participation in S–Compounds. Gr. VII (a) The general group properties * (b) The halogen hydrides, their acidity; Preparation, properties, structures and bonding of the oxides and oxy acids; the inter halogen compounds including polyhalides, the pseudohalides – including their preparation, properties, structures. The cationic compounds of iodine. * Note : General group properties : – For each group this includes discussion, on a comparative basis, of major physical and chemical properties, e.g. – i) Physical properties – the electronic configuration; ionisation potential / electron affinity; m.p. – b.p. ; ionic/covalent radii etc. ii) Chemical properties – Various oxidation states and their relative stability (redox behaviour in solution, wherever applicable), higher stability of the higher oxidation states for the heavier members; gradual changes of the ionic/covalent character of the compounds from lighter to heavier members; the relative acidity, amphoteric, basic characteristics of the oxides and formation of oxocations (wherever applicable); examples of compounds in all the oxidation states, in particular, the unusual (rare) oxidation states being stabilised through coordination; hydrides, halides (including the halo complexes) and their hydrolytic behaviour; dimerization and/or polymerization through halogen bridges (wherever applicable) etc. iii) Common natural sources of the elements. Acid-Base / Ionic Equilibrium / Non-aqueous solvents, reduction. BOOKS: Inorganic Chemistry:  Duward Shriver and Peter Atkins. Inorganic Chemistry: Principles of Structure and Reactivity by James E. Huheey, Ellen A. Keiter and Richard L. Keiter. Inorganic Chemistry: Catherine Housecroft, Alan G. Sharpe. Atkins' Physical Chemistry, Peter W. Atkins, Julio de Paula. Cotton F.A. and Wilkinson, G. Advanced Inorganic Chemistry Sharpe, A.G. Inorganic Chemistry Douglas, B.; McDaniel, D.H.; Alexander, J.J. Concepts and Models of Inorganic Chemistry Greenwood, Norman, and A. Earnshaw. Chemistry of Elements. Oxford, UK: Elsevier Science, 1997. ISBN: 9780750633659 Other reading materials will be assigned as and when required. Prerequisite: Chemical Principles (CHY111).
CHY211
Chemical Equilibrium
5.00
Undergraduate
In this course, we adopt a case studies approach to understanding thermodynamic principles already familiar to students from earlier courses. In class we will explore real chemical questions involving equilibrium, acid base chemistry, electrochemistry, surface phenomena and solution chemistry by reading and discussing research papers. COURSE CONTENT: Entropy and Information Absolute temperature Shannon Entropy Thermodynamics & Thermochemistry First, second and third laws of thermodynamics and their applications in chemistry Enthalpy change and its impact on material science and biology Enthalpies of formation and reaction enthalpies Internal energy, entropy, Gibbs free energy Ideal Gas Law Kinetic Theory of Gases Design of an air bag Maxwell-Boltzmann Distribution Phase Equilibria Phase diagrams and impact on material sciences Phase transitions Chemical equilibrium and its impact on technology and biochemistry Changes in equilibria with temperature and pressure Colligative properties Raoult's Law Ideal and non-ideal mixtures Acid-base equilibria Open systems Soil Equilibria & Acid Rain Chemical Kinetics Determination of rate, order and rate laws Impact of Chemical Kinetics on Biochemistry Oxidation of glucose in biological systems Catalysis Activation energy Arrhenius equation Kinetics; Mechanisms; Enzymes Reducing Air Pollution from Automobiles Diffusion across membranes Osmosis and reverse osmosis Design of a water filter Adsorption and Chromatography Ion Exchange columns and water purification Electrochemistry in biology Nernst Equilibrium Potential Voltage-gated ion channels Photosynthesis and solar cells Protein-ligand binding Binding free energy Force fields Empirical potentials Conformational freedom Docking & scoring computer lab Statistical Thermodynamics Microcanonical, Canonical and Grand Canonical Ensembles Partition function Molecular Dynamics computer lab Monte Carlo simulations computer lab Membrane Protein Simulations computer lab Molecular Reaction Dynamics Transition State Effect of translational and vibrational kinetic energy RECOMMENDED BOOK(S): Physical chemistry by Peter Atkins, Julio De Paula. Edition: 9th ed. South Asia Edition. Publisher: UK Oxford University Press 2011 Physical chemistry by Gilbert W. Castellan, Edition: 3rd ed. Publisher: New Delhi. : Narosa Publishing House, 1985, 2004  Basic Physical Chemistry: The Route to Understanding by E. Brian Smith      ISBN:978-1-78826-293-9 Publisher: World Scientific Elements of Classical Thermodynamics for Advanced Students of Physics by A. B. Pippard [Paperback] ISBN:9780521091015 A Farewell to Entropy: Statistical Thermodynamics Based on Information by Arieh Ben-Naim   ISBN:978-1-270-706-2 Publisher: World Scientific Physical Chemistry by Thomas Engel, Philip Reid. Publisher: New Delhi Pearson 2006 Other reading materials will be assigned as and when required. Prerequisites: Chemical Principles (CHY111).
CHY212
Chemical Applications of Group Theory
2.00
Undergraduate
Symmetry operations and symmetry elements, Concepts and properties of a group, group multiplication Tables, Similarity transformation, Class, Determination of symmetry point group of molecules, Matrix representation of groups, reducible and irreducible representations, Great orthogonality theorem, Character tables, Direct Product and Spectroscopic selection rule, Molecular Vibrations, Normal coordinates, Symmetry of normal mode vibrations, Symmetry Adapted Linear Combination, Infrared and Raman active vibrations, Molecular orbitals, LCAO MO approach, HMO method, Hybrid orbitals, Free ion configuration, terms and states, splitting of levels and terms in a chemical environment, correlation diagrams, spectral and magnetic properties of the transition metal complexes. Course outline: Introduction: Importance of Group Theory in Chemistry Symmetry elements and symmetry operations: Use molecular models to identify symmetry elements of different molecules. Understanding of the interrelation of different symmetry elements present in a molecule, product of symmetry operations. Point Groups: Concepts and properties of a group, group multiplication Tables, Similarity transformation, Class, Determination of symmetry point group of molecules. Matrix representations and Character Tables: Matrix representation of groups, reducible and irreducible representations, Great orthogonality theorem, character tables. SALC, direct product, Molecular vibrations: Direct Product and Spectroscopic selection rule, Molecular Vibrations, Normal coordinates, Symmetry of normal mode vibrations, Symmetry Adapted Linear Combination, Infrared and Raman active vibrations. Molecular orbital Theory, Hybrid orbitals: Molecular orbitals, LCAO MO approach, HMO method, Hybrid orbitals. Terms and states, Transition metals chemistry: Free ion configuration, terms and states, splitting of levels and terms in a chemical environment, correlation diagrams, spectral and magnetic properties of the transition metal complexes.
CHY213
Physical Methods in Chemistry
4.00
Undergraduate
Analyses of compounds are an integral aspect of chemistry. We get to know the structure, spatial orientation and purity of compounds we synthesize through analysis which helps us to advance in our investigation. To address this purpose a bevy of instruments ranging from UV spectroscopy, IR spectroscopy to High Pressure Liquid Chromatography are available. However accurately understanding the output from these instruments is an essential attribute for a successful chemist. The purpose of this course is to familiarize the students with the basic principles of spectroscopic and diffraction methods that are instrumental to the analysis of molecules and structures in the day-to-day life of a chemist. In this course, we will learn to interpret and understand working of various types of analytical instruments commonly used for analysis in a chemistry lab. COURSE CONTENT: UV-visible spectroscopy: Beer–Lambert law, types of electronic transitions, effect of conjugation. Concept of chromophore and auxochrome. Bathochromic, hypsochromic, hyperchromic and hypochromic shifts, Woodward–Fieser rules, Woodward rules, introduction to fluorescence. Vibrational spectroscopy: Molecular vibrations, Hooke’s law, Modes of vibration, Factors influencing vibrational frequencies: coupling of vibrational frequencies, hydrogen bonding, electronic effects, The Fourier Transform Infrared Spectrometer, Calibration of the Frequency Scale, Absorbance and Transmittance scale, intensity and position of IR bands, fingerprint region, characteristic absorptions of various functional groups and interpretation of IR spectra of simple organic molecules, basic mention of Raman Spectroscopy including the mutual exclusion principle, Raman and IR active modes of CO2. Nuclear Magnetic Resonance (NMR) spectroscopy: Spinning nucleus, effect of an external magnetic field, precessional motion and precessional frequency, precessional frequency and the field strength, chemical shift and its measurement, factors influencing chemical shift and anisotropic effect, proton NMR spectrum, influence of restricted rotation, solvents used in NMR, solvent shift and concentration and temperature effect and hydrogen bonding, spin-spin splitting and coupling constants, chemical and magnetic equivalence in NMR, Lanthanide shift reagents, factors influencing the coupling constant, germinal coupling, vicinal coupling, heteronuclear coupling, deuterium exchange, proton exchange reactions. Electron Spin Resonance Spectroscopy: Derivative curves, g values, Hyperfine splitting X-ray Diffraction: X-ray and diffraction of X-rays by atoms, Bragg’s law, lattice, crystal systems, planes and Miller indices, reciprocal lattice, crystal growth and mounting, diffractometer operation, recording diffraction pattern, reflection analysis and preliminary structure determination. , Mass spectrometry: Basic principles, basic instrumentation, electron impact ionization, separation of ions in the analyzer, isotope abundances, molecular ions and metastable ions, basic fragmentation rules, factors influencing fragmentation, McLafferty rearrangements, chemical ionization. Data Analysis: Uncertainties, errors, mean, standard deviation, least square fit. Books: Spectroscopy of organic compounds, 6th Edition by P. S. KALSI, New Age International Publishers. Spectrometric Identification of Organic Compounds, 6th Edition by R. M. Silverstein and F. X. Webster, Wiley Student Edition. Molecular Fluorescence: Principles and Applications. Bernard Valeur, Wiley-VCH X-ray structure determination: A Practical Guide (2nd Ed.) by George H. Stout and Lyle H Jensen, Wiley-Interscience, New York, 1989. Prerequisites: Chemical Principles (CHY111), Basic Organic Chemistry-I (CHY122).
CHY221
Basic Organic Chemistry II
4.00
Undergraduate
Organic reactions; nucleophilic substitution, elimination, addition and electrophilic aromatic substitution reactions with examples will be studied. COURSE CONTENT: A. Substitution reactions: Free radical halogenation, relative reactivity and selectivity, allylic and benzylic bromination Nucleophilic Subsititution (SN1, SN2, SN1′, SN2′,SNi) Electrophilic Substitution (SNAr, Addition Elimination vs. Elimination addition) Electrophilic aromatic substitution will be studied in detail B. Elimination reactions: Formation of alkenes and alkynes by elimination reactions, Mechanism of E1, E2, E1cB reactions. Saytzeff and Hofmann eliminations. C. Addition reactions: a. Alkanes sigma bonds Chemistry of alkanes: Formation of alkanes, Organometallic reagents, Wurtz reaction, Wurtz-Fittig reactions. b. Alkenes and alkynes pi bonds Electrophilic additions their mechanisms (Markownikoff/ Anti-Markownikoff addition), mechanism of oxymercuration-demercuration, hydroboration oxidation, ozonolysis, reduction (catalytic and chemical), syn and anti-hydroxylation(oxidation). 1,2-and 1,4-addition reactions in conjugated dienes and Diels-Alder reaction; electrophilic and nucleophilic additions. Hydration to form carbonyl compounds, alkylation of terminal alkynes. RECOMMENDED BOOK(S): Morrison, Robert Thornton & Boyd, Robert Neilson Organic Chemistry, Dorling Kindersley (India) Pvt. Ltd. (Pearson Education), Seventh Edition, 2005. Finar, I. L. Organic Chemistry (Volume 1), Dorling Kindersley (India) Pvt. Ltd. (Pearson Education), Sixth Edition, 2003. Clayden, Greeves, Warren and Wothers, Organic Chemistry, Oxford University Press (2001). Peter Sykes, Mechanism in Organic Chemistry, (Pearson Education), Sixth Edition. Paula Yurkains Bruice Organic Chemistry, Prentice Hall; 7th  edition (2013) Prerequisites: Chemical Principles (CHY111), Basic Organic Chemistry-I (CHY122).
CHY222
Chemistry of Carbonyl Compounds
4.00
Undergraduate
Nucleophilic Addition: (a) Reactivity of carbonyl groups (b) Cyanide as nucleophile- cyanohydrin formation (c) Oxygen/sulfur as nucleophile - Acetals, Ketals and Hydrates (d) Hydride as the nucleophile - Reduction reactions (e) Carbon as nucleophile - Organometallics (Grignard and alkyl lithiums) (f) Nitrogen as nucleophile - Imine and hydrazones. (g) Nucleophilic addition to carbonyl analogs Nucleophilic Substitution: (a) Reactivity of carboxylic acid family (b) Oxygen/sulfur as nucleophile – Esters and carboxylic acids (c) Nitrogen as nucleophile – Amides (d) Acyl halides and anhydrides (e) Hydride as the nucleophile - Reduction reactions (f) Carbon as nucleophile - Organometallics (Grignard and alkyl lithium) (g) Enantiomer resolution (h) Nucleophilic Substitution at sulfuric and phosphoric acids The alpha carbanion – nucleophilic-electrophilic reactivity of carbonyls (a) Enols and enolate anions (b) Addition-dehydration – The aldol reaction (c) Ester condensation (d) Fragmentation of Beta-dicarbonyl compounds (e) Alkylation of enolate anions (f) Other stabilized carbanions and carbon nucleophiles Nucleophilic additions and substitutions in Synthesis (a) Available reactions (b) Experimental considerations (c) The strategy of synthesis (d) Synthesis examples Prerequisites: Basic Organic Chemistry-I (CHY122), Basic Organic Chemistry-II (CHY221).
CHY241
Electrochemistry
3.00
Undergraduate
Electrical dimensions and unit, Faraday’s laws of electrolysis, Theory of electrolytic dissociation, van’t Hoff factor and degree of dissociation, Specific Conductance, Equivalent conductance, Equivalent conductance at infinite dilution, Variation of equivalent conductance with concentration for strong and weak electrolytes, Conductance ratio and degree of dissociation, Equivalent conductance minima, Influence of dielectric constant on conductance, Kohlrausch’s law, Application of ion conductance, Ionic mobility, Influence of temperature on ionic conductance, Ion conductance and viscosity, Drift Speed, Variation of ionic mobility with ionic size and hydrodynamic radius, factors affecting the ionic mobility for strong electrolytes, Ionic Atmosphere, relaxation effect or asymmetry effect, Electrophoretic effect, partial molar quantities (briefly), partial molar free energy and chemical potential, Electrolytes as a non-ideal solution, activity coefficient, mean ionic activity, mean ionic molality, mean ionic activity coefficient, Outline of Debye-Hückel theory, Debye-Hückel’s limiting law, variation of activity coefficient with ionic strength, Nernst equation. General discussion about oxidation and reduction, electron transfer vs atom transfer, oxidation no. Concept of electrochemistry, Definition: Electrochemical cell, electrodes, salt bridge and its function etc. Battery; types of cell: Electrolytic cell vs Galvanic cell; concentration cell vs chemical cell, construction of a voltaic cell. Definition: Electrode potential, Std. potential and Formal potential; Physical significance of electrode potential. Types of electrodes: (i) metal electrode, advantage of amalgam electrode; (ii) non-metal electrode, e.g. hydrogen gas electrode, glassy carbon electrode. What is glassy carbon electrode? What is the difference between glassy carbon and graphite electrode?  Factors affecting the electrode potential: (i) effect of concentration, (ii) effect of pH e.g. formation of insoluble hydroxide and (iii) effect of precipitation and complexation. Application of electrode potential; Periodic trend of the reduction potential; Pourbaix diagram. Electroanalytical techniques: Potentiometry, Coulometry, Voltammetry and Amperometry. Measurement of electrode potential; 3 electrode system: working electrode, reference electrode and counter electrode; comparison between three and two electrode system; linear sweep voltammetry, Cyclic voltammetry (CV), Differential pulse voltammetry (DPV) etc. Bulk electrolysis. Prerequisite: Chemical Principles (CHY111) Co-requisites: Chemical Equilibrium (CHY211).
CHY242
Coordination Chemistry
4.00
Undergraduate
Metals ions play important role in producing colour in coordination complexes. Understanding of the coordination complexes lies at the heart of coordination chemistry. This course will focus on the basic concept of coordination chemistry and their quantification in photophysical and magnetic properties. Students will synthesize interesting colour compounds and perform reactions to promote the understanding of common reactions. Intensive use of analytical and spectroscopic techniques to interpret extent of reaction, purity of product and photophysical property particularly colour of the coordination complexes will be involved. COURSE CONTENT: Introduction and structures of complexes: Meaning of metal coordination and use of metal coordination in formation of color complex. Coordination number, bonding of organic ligands to transition metals, coordination number, linkage isomerism, electronic effects, steric effects, the chelate effect, fluxional molecules. Crystal field theory: application and limitation Molecular orbital theory: Application in pi-bonding, electronic spectra including MLCT, LMCT d-d transition, and magnetic properties of complexes. Inorganic substitution reaction; Types; Base catalyzed hydrolysis; Linear free energy relationship. Reaction and kinetics: Nucleophilic substitution reactions, rate law, mechanism of reactions, trans effect, ligand field effect, inner sphere and outer sphere reactions. Text Books: Inorganic Chemistry; Principles of Structures and Reactivity: James E. Huheey; Allen A. Keiter;Richard L. Keiter, Pearson Edition.                             Inorganic Chemistry by Shriver & Atkins, 5th edition. Inorganic chemistry by Miessler, Gary L. Tarr, Donald A . Concise Inorganic Chemistry by J. D. Lee Application of physical methods to inorganic and bio-inorganic chemistry     by scot Robert A.; Lukehart, Charles M. Prerequisites: Chemical Principles (CHY111) and Chemical equilibrium (CHY211). .
CHY252
Biochemistry
3.00
Undergraduate
Course description not available.
CHY311
Chemical Binding
4.00
Undergraduate
Quantum mechanics provides the microscopic basis for a fundamental understanding of chemistry, molecular structure, bonding, and reactivity. This course and the associated computer lab provide a comprehensive treatment of valence bond and molecular orbital theories, post Hartree-Fock wave function and density functional methods. Students will learn to compute molecular structures, spectra, and thermochemical parameters for molecules in the gas-phase and for condensed-phase systems. COURSE CONTENT: Postulates of Quantum Mechanics Atomic Orbitals and Basis Sets The Born-Oppenheimer approximation and the molecular Hamiltonian The Concept of the Potential Energy Surface Geometry Optimization and Frequency Analysis Semi-empirical and ab initio Quantum Mechanics Variation and Perturbation Theory Valence Bond and Molecular Orbital theories Independent-Particle Models: the Hartree method Spin, statistics and the Pauli principle The Hartree-Fock Self-Consistent Field equations Electron Correlation, Density Matrices and Natural Orbitals Density Functional Theory Periodic systems Implicit and explicit solvent methods QM/MM and ONIOM RECOMMENDED BOOK(S): Frank Jensen: Introduction to Computational Chemistry (Wiley) Henry Eyring, John Walter and George E. Kimball: Elementary Quantum Chemistry (John Wiley) J. N. Murrell, S. F. A. Kettle, J. M. Tedder: Valence Theory  [ELBS & John Wiley] Richard P. Feynman, Robert B. Leighton & Matthew Sands: The Feynman Lectures on Physics, Vol.III (Addison Wesley Longman) James B. Foresman, AEleen Frisch, Exploring Chemistry With Electronic Structure Methods: A Guide to Using Gaussian (Gaussian, Inc.) Errol G. Lewars, Computational Chemistry: Introduction to the Theory and Applications of Molecular and Quantum Mechanics (Kluwer Academic Publishers, 2003) N. Sukumar, ed. A Matter of Density: Exploring the Electron Density Concept in the Chemical, Biological, and Materials Sciences (John Wiley, Hoboken, NJ, 2013) Prerequisites: Chemical Principles, Calculus, Linear Algebra, physics, CS. Co-requisite: Molecular Spectroscopy.
CHY313
Molecular Spectroscopy
3.00
Undergraduate
Blackbody radiation, Einstein A and B coefficients, absorption and emission of radiation, lineshape functions, natural Lifetime broadening, pressure broadening, Doppler broadening. Rotational Spectroscopy: Rotation and rigid bodies, moment of inertia tensor and principal axis, diatomic and linear molecule: selection rule, centrifugal distortion, rotational line intensities for diatomic and linear molecule, symmetric tops. Vibrational Spectroscopy: Diatomic molecules, wave function for harmonic and anharmonic oscillator, , selection rule, spectrum for harmonic and anharmonic oscillator, Fundamental, overtone, diatomic vibrating rotator and vibration-rotation spectrum: P, Q, R branches, vibrations of polyatomic molecules, Normal mode coordinates and their symmetry, Determining Infrared active vibrations from character table. Light scattering and the Raman effect, classical model of Raman effect, Polarizability tensor, Stokes scattering and Anti stokes scattering, Depolarization ration in Raman, Rotational Raman spectrum for diatomic and linear molecules and symmetric tops, Rule of Mutual exclusion, vibrational Raman spectrum, Raman activity of vibrations from character table. Electronic Spectroscopy: Electronic wave function, hydrogen atom spectrum, orbital angular momentum, electron spin angular momentum, total electronic angular momentum, fine structure of hydrogen atom spectrum, many electron atoms, term symbols, Zeeman effect, electronic spectra of diatomic molecules, vibrational progressions, Frank-Condon principle, Rotational Fine structure, Fortrat diagram, electronic angular momentum for diatomic molecules, spectrum of molecular hydrogen, photoelectron spectroscopy; Fluorescence spectroscopy. NMR: relaxation, 2-D NMR, Bloch equation, factors influencing the coupling constant, germinal coupling, vicinal coupling, heteronuclear coupling, deuterium exchange, simplification of complex spectra in NMR: spin decoupling and Lanthanide shift reagents, Nuclear Overhauser effect (NOE), resonance of other nuclei. 13C NMR: Chemical shift, 13C coupling constants, two-dimensional NMR spectroscopy, NOESY, DEPT, INEPT terminology. Recommended Books: Fundamentals of Molecular Spectroscopy by Banwell, C. N. Modern Infrared spectroscopy analytical chemistry by open learning, by Molecular Fluorescence: Principles and applications by Valeur, Bernard, Berberan-Santos, Mario, N. (available in library). NMR spectroscopy Basic Principles, Concepts and applications in chemistry Organic spectroscopy by William Kemp. Spectroscopy of organic compounds by Kalsi, P. S. Prerequisites: Physical Methods in Chemistry (CHY213); Chemical Applications of Group Theory (CHY212). Co-requisite: Chemical Binding (CHY311).
CHY321
Named Organic Reactions and Mechanism
3.00
Undergraduate
C-C bond forming reactions and their mechanism focusing on Carbanion alkylation, Carbonyl addition and carbonyl substitution reactions, Conjugate addition reactions (1,2-addition & 1,4- addition), Reactions of alkene, alkynes and aromatics. C-N and C-O bond forming reactions and their mechanism. Glycosylation reactions. Oxidation and reduction reactions, Rearrangement reactions, Free radical reactions. Photochemical reactions and mechanism, Norrish type I and II reactions, Electrophilic substitution reactions. These types of reactions will be taught under following name reactions. C-C Bond forming reactions and Mechanism - Grignard Reaction, Aldol Condensation, Diels Alder Reaction, Ring Closing Metathesis, Heck Reaction, Negishi Reaction, Suzuki Reaction, Benzoin condensation, Reformatsky reaction, Ugi reaction, Wittig reaction, Morita-Baylis-Hillmann Reaction. C-N Bond forming reactions and Mechanism - Ullmann reaction, Buchwald and Hartwig reaction, Metal free C-N bond formation reactions, Fisher Peptide synthesis, Hetero Diels Alder reaction, Click reaction. C-O Bond forming reactions and Mechanism - Allan-Robinson Reaction, Baeyer-Villiger Reaction, Fisher Oxazole synthesis, Ferrier Reaction, Glycosidation reaction, Sharpless asymmetric Epoxidation. Oxidation, Reduction reactions and Mechanism - Bayer-Villeger oxidation, Dess-Martin periodinane oxidation, Swern Oxidation, Corey–Kim oxidation, Jones Oxidation, Luche reduction, Birch reduction, Gribble reduction. Rearrangement Reactions and Mechanism - Benzilbenzilic acid rearrangement, Pinacol Pinacolone rearrangement, Fries rearrangement, Amadori rearrangement, Beckmann rearrangement, Demzanov rearrangement, Payne rearrangement, Wallach rearrangement, Ferrier rearrangement Conjugate addition reactions and Mechanism - 1,2-addition reaction, 1,4-addition reaction, Reformatsky reaction, Prins reaction, Michael reaction Photochemical reactions and Mechanism - Norish type I reaction, Norish type II reaction Prerequisites: Basic Organic Chemistry-II (CHY221).
CHY322
Organic Reaction and Synthesis
3.00
Undergraduate
COURSE CONTENT: Electrophilic addition to carbons Electrophilic aromatic substitution Common heterocycles and their reactions Electrophilic addition to carbon-carbon multiple bonds. Rearrangement reactions Migration to C, N, O and B Free radical rearrangements Anion rearrangement Sigmatropic rearrangements Oxidation and Reduction reactions Oxidation/Reduction of carbonyls Reductive elimination and fragmentation Olefin reduction Reductive deoxygenation of carbonyl groups Chemoselective oxidation and reduction reactions of functional groups Cycloaddition, unimolecular rearrangement and thermal eliminations Name reactions and mechanism Applications and limitations of the major reactions in organic synthesis Application in natural product synthesis Literature review Reaction involving transition metals Name reactions and mechanism, Applications and limitations of the major reactions in organic synthesis. Application in natural product synthesis Literature review Each topic will end with a discussion section, where student participation is important. Prerequisites: Basic Organic Chemistry-II (CHY221).
CHY323
Organometallic Chemistry
3.00
Undergraduate
The course will discuss various organometallic compounds involving Pd, Pt, Cr, Mo, Mn, their various complexes with several organic ligands and their application in the synthesis of heterocycles and natural products. The course will also cover all the name reactions involving organometallics. Since the advent of Pd as a suitable metal for C-C bond formation along with Ru-in Grubbs Metathesis the present pharmaceutical industry relies heavily on organometallics. Nearly 40% of the reactions in the lab involve organometallics. The intricacies of the reactions, the subtlety of the condition in the reactions involving organometallic compounds requires utmost understand of the mechanism of the reactions. Hence this course will provide an in-depth understanding of organometallic reactions and their applications. Reference Books: The Organometallic Chemistry of the Transition Metals (6th Edition) by Robert H. Crabtree. Organotransition Metal Chemistry: From Bonding to Catalysis; 1st edition (10 February 2010) by John F. Hartwig. Basic Organometallic Chemistry: Concepts, Syntheses and Applications (Paperback) 2nd edition by B.D. Gupta, Anil J. Elias.
CHY332
Informatics & Molecular Modelling
3.00
Undergraduate
This course and the associated computer lab deal with Molecular Modelling and Cheminformatics, applied to the search for new drugs or materials with specific properties or specific physiological effects (in silico Drug Discovery). Students will learn the general principles of structure-activity relationship modelling, docking & scoring, homology modelling, statistical learning methods and advanced data analysis. They will gain familiarity with software for structure-based and ligand-based drug discovery. Some coding and scripting will be required. COURSE CONTENT: Introduction: Drug Discovery in the Information-rich age Introduction to Pattern recognition and Machine Learning Supervised and unsupervised learning paradigms and examples Applications potential of Machine learning in Cheminformatics & Bioinformatics Introduction to Classification and Regression methods Representation of Chemical Structure and Similarity: Sequence Descriptors Text mining Representations of 2D Molecular Structures: SMILES Chemical File Formats, 3D Structure Descriptors and Molecular Fingerprints Graph Theory and Topological Indices Progressive incorporation of chemically relevant information into molecular graphs Substructural Descriptors Physicochemical Descriptors Descriptors from Biological Assays Representation and characterization of 3D Molecular Structures Pharmacophores Molecular Interaction Field Based Models Local Molecular Surface Property Descriptors Quantum Chemical Descriptors Shape Descriptors Protein Shape Comparisons, Motif Models Molecular Similarity Measures Chemical Space and Network graphs Semantic technologies and Linked Data Mapping Structure to Response: Predictive Modelling: Linear Free Energy Relationships Quantitative Structure-Activity/Property Relationships (QSAR/QSPR) Modeling Ligand-Based and Structure-Based Virtual High Throughput Screening 3D Methods - Pharmacophore Modeling and alignment ADMET Models Activity Cliffs Structure Based Methods, docking and scoring Model Domain of Applicability Data Mining and Statistical Methods: Linear and Non-Linear Models Data preprocessing and performance measures in Classification & Regression Feature selection Principal Component analysis Partial Least-Squares Regression kNN, Classification trees and Random forests Cluster and Diversity analysis Introduction to kernel methods Support vector machines classification and regression Introduction to Neural Nets Self-Organized Maps Deep Neural Networks Introduction to evolutionary computing Genetic Algorithms Data Fusion Model Validation Best Practices in Predictive Cheminformatics RECOMMENDED BOOK(S): Johann Gasteiger, Thomas Engel,Chemoinformatics: A Textbook (Wiley-VCH, 2003) Jürgen Bajorath (Editor), Chemoinformatics and Computational Chemical Biology (Methods in Molecular Biology) (Humana Press, 2004) Leach & Gillet, An Introduction to Chemoinformatics Prerequisites: Basic Organic chemistry/Biochemistry, Basic Statistics, Computer Programming.
CHY334
Environmental Chemistry
2.00
Undergraduate
Environmental chemistry is an interdisciplinary science that includes atmospheric, aquatic and soil chemistry. During this course chemistry of the air, water, and soil, and how anthropogenic activities affect this chemistry on planet Earth will be covered. Specifically, sources, reactions, transport, effects, and fates of chemical species in air, water, and soil environments, and the effects of technology thereon will be examined. This course is divided into 5 major parts that reflect the most pressing issues in Environmental Chemistry today. 1.Fundamental concepts;  2.Introduction to Environmental Chemistry: Chemistry and the atmosphere, hydrosphere and soil, the role of chemistry in environmental studies;  3.The Hydrosphere: Fundamentals of aquatic chemistry, speciation and redox equilibria in natural waters, gases in water, organic matter in water, metals in water, environmental colloids, water pollution and waste water treatment,  microplastics chemical aspects of the nitrogen and phosphorus cycles;  4.The Atmosphere: Introduction to the nature and composition of the atmosphere, the greenhouse effect and global warming, the case against global warming, Energy production and global warming, Climate Change and Energy. 5. The Biosphere: Nitrogen and food production, pest control
CHY342
Chemistry of Solids and Surfaces
3.00
Undergraduate
In this course the students will get to know the chemistry behind the formation of solids and on their surfaces, the kind of bonding involved and the available techniques to characterize them. Through this course students will also learn how to interpret various chemical structures of solids and their surfaces. Students will further understand crystallographic terminology, selected diffraction theory, nomenclature at surfaces, reconstruction and relaxations at surfaces and how to determine the surface structure. They will also realize the wide range of chemical information available from diffraction based techniques. Further the students will learn about different surface phenomena such as adsorption, catalysis, work function, and basics of the electronic, magnetic, and optical properties, and their relevance to nanomaterials. This is a required course for Chemistry majors, but also satisfies UWE requirements for non-majors. COURSE CONTENT: INTRODUCTION TO SOLID STATE CHEMISTRY CRYSTAL CHEMISTRY Introduction to Crystallography Unit cells and Crystal Systems Symmetry, Lattice, Lattice spacing Crystal Densities and Packing Crystallographic Notations BONDING IN SOLIDS Overview on Bonding Ionic, Covalent, Metallic, van der Waals and Hydrogen Bonding Born-Haber Cycle The Shapes of Molecules Intermolecular Forces CRYSTALLINE MATERIALS Properties of X-Rays X-Ray Emission & Absorption X-Ray Diffraction Techniques Point, Line, Interface & Bulk Defects AMORPHOUS MATERIALS Introduction to Glasses Glass Properties INTRODUCTION TO THE CHEMISTRY of SURFACES Surface structure                Nomenclature                Surface unit cell                Relaxation and reconstruction at surfaces and its relevance to nanomaterials                How to characterize atomic structure at surfaces Basics of different phenomena at surfaces Surface energy Electronic structure, 2D Brillouin zone, photoemission Work function Magnetic properties and relevance to nanomaterials Optical properties Adsorption and catalysis Two dimensional structures Recommended reading: 1. P. Atkins and J. dePaula, Atkins' Physical Chemistry A. R. West, Basic Solid State Chemistry.L. Smart and E. Moore, Solid State Chemistry An Introduction J. P. Glusker, K. N. Trueblood, Crystal Structure Analysis W. Clegg, Crystal Structure Determination J.M. Blakely, Introduction to the properties of Crystal Surfaces, New York, Plenum Press 1973. G A Somarjai, Chemistry in Two Dimensions: Surfaces, Ithaca, New York, Cornell University Press 1981. A. Zangwill, Physics at Surfaces, New York: Cambridge University Press 1988. Surface Science, An Introduction, John B. Hudson, 1992, Butterworth-Heinemann. Solid Surfaces, Interfaces and Thin Films – Springer, by H Lüth. Modern Techniques of surface Science, Second Edition D.P. Woodruff and T A Delchar, Cambridge University Press 1994. Prerequisites: Chemical Principles (CHY111), Physics (PHY101/102 or PHY103/104).
CHY344
Topics In Nanotechnology
3.00
Undergraduate
The next few years will see dramatic advances in atomic-scale technology. Molecular machines, nanocircuits, and the like will transform all aspects of modern life - medicine, energy, computing, electronics and defense are all areas that will be radically reshaped by nanotechnology. These technologies all involve the manipulation of structures at the atomic level - what used to be the stuff of fantasy is now reality. The economics impact of these developments has been estimated to be in the trillions of dollars. But, as with all new technologies, ethical and legal challenges will arise in their implementation and further development. This course will examine the science of nanotechnology and place it in the larger social context of how this technology may be, and already is, applied. Underlying physical science principles will be covered in lecture sessions and students will read articles from current news sources and the scientific literature. There will be presentations on scientific literature on topics of student interests, to examine the science and applications of a well-defined aspect of nanotechnology of their choosing. Lecture material will focus on the principles behind modern materials such as semi-conductors (organic, inorganic) and novel nanostructures. COURSE CONTENT: Introduction Bulk Vs. Nano Quantum confinement effect Surface area to volume ratio Effect on Properties: Material (electrical, magnetic, mechanical etc.) and structural properties Carbon nano-architectures: Fullerene, SWNT, MWNT, Graphite etc., Classification of structure Q-Dots • Bonding parameters Methods of preparation Nanomaterial’s synthesis: Top down and Bottom up approach, Physical and chemical methods Applications (Nano-machines, solar cells, coatings, MEMS, nano-medicine, sensors, miscellaneous) Characterization Techniques and Instruments: Microscopy SEM, TEM, AFM, X-Ray diffraction, UV-vis, Photoluminescence, Raman, FTIR, ESR, XPS, BET, DLS, Zeta potential
CHY346
Bio-inorganic chemistry
3.00
Undergraduate
General discussion about bioinorganic chemistry Biological important elements, Biological ligands Alkali and alkaline earth metal in biology: Role of Na, K (Na-K pump, chelate chemistry, SHAB theory); Mg (ATP hydrolysis and chlorophyll) and Ca Importance of Oxygen, Great oxygenation event Iron based chemistry in nature; Iron metabolism: Iron transport, Iron storage; Iron cycle. Oxygen utilization: (i) Oxygen transport and storage (ii) Oxidases enzyme: Cytochrome c oxidase, Electron transport chain, Cytochrome c oxidase vs. Cytochrome in respiratory cycle; electron transfer reaction in biology Oxygenase: Cyt P450: Reaction mechanism (iv) Peroxidase: HRP. Fe-S protein, Hydrogenase enzyme. Toxicity: Superoxide dismutase and Catalase Mo- containing enzyme: Nitrogenase, nitrogen cycle. Co, V containing enzymes. Zn containing enzymes. Photosynthesis: O-H bond activation, role of Mn in OEC f-orbitals and oxidation states; atoms and ion sizes (lanthanoid contractions); coordination no. Spectroscopic and magnetic properties of lanthanoids and actinoids. Lanthanoids metals: Complexes of Ln(III), Organometallic complexes. Actinoids metals: Inorganic and Organometallic complexes of Th and U. Nuclear Property: Mass defect and binding energy; Nuclear emissions (alpha and beta particles, gamma radiations); Nuclear transformations, the kinetics of radioactivity decay, units of radioactivity, Nuclear fission vs. fusion. Applications of isotopes: Kinetic isotope effects, Radiocarbon dating. Books: Inorganic Chemistry; Principles of Structures and Reactivity: James E. Huheey; Allen A. Keiter;Richard L. Keiter, Pearson Edition. Principles of Bioinorganic Chemistry: Stephen J. Lippard, Jeremy M. Berg, University Science Books, 1994. Physical Methods in Bioinorganic Chemistry: Spectroscopy and Magnetism: Lawrence Que, University Science Books, 1999. Reference Materials: Other reading materials will be assigned as and when required.
CHY351
Macromolecules
3.00
Undergraduate
In this course we will learn about cellular macromolecules namely nucleic acids, proteins, carbohydrates and lipids. The chemistry and biochemistry associated with these macromolecules will be discussed. The goal is to learn about important natural molecules, not only from a structural but from a chemical point of view as well. We will talk about the chemistry associated with these molecules, their importance and how we can interfere with it.Classes will be through a combination of group discussions, reading assignments, projects, presentations and lectures. Students are expected to do library research, write papers, and present discussion in class. Review articles and papers used in this course will be provided. COURSE CONTENT:  Introduction Nucleic Acid (DNA and RNA) Background Function and importance Structure Biosynthesis/replication Chemical synthesis Sequencing Maxam Gilbert Sanger dideoxy Bisulfite sequencing Mass spectrometry NGS DNA chemistry DNA damage Spontaneous depurination deamination Alkylation Oxidative DNA damage DNA-DNA crosslinks DNA-Protein crosslinks DNA methylation and demethylation Mutagenesis Repair Epigenetics RNA editing Ribozymes Diseases and carcinogenesis Proteins What are proteins Functions Amino acids Structure (primary, secondary, tertiary, quaternary) Sequencing Chemical and proteomics Peptide synthesis Enzymatic reactions Diseases Lipids Functions and importance Fatty acids Phospholipids Steroids Diseases Carbohydrates Introduction Function and importance in chemistry and biology Glycoconjugates Structural features Biosynthesis Chemical synthesis Industrial preparation Prerequisites: CHY221, CHY112, Biochemistry.
CHY352
Advanced Biochemistry
3.00
Undergraduate
Students in this course will apply principles from general and organic chemistry, as well as general biology, to understand the molecular processes that characterize life. The goal of this class will be to give students a solid background with which they can appreciate the chemistry of life. Beginning with fundamental principles, the course will then delve into a detailed look at metabolism - the specific means by which organisms use chemical energy to drive cell functions and how they convert simple molecules to complex biological molecules. Students will have the opportunity for independent work, and will apply the principles of biochemistry to a research project that they will design, execute, and present.
CHY354
Biochemical Toxicology
3.00
Undergraduate
COURSE CONTENT: 1. General Principals of toxicology 2. Classes of toxicants 3. Metabolism 4. P450 and P450 catalyzed reactions 5. Other phase 1 reactions 6. Phase II/Conjugation reactions 7. Bioactivation and Reactive intermediates 8. Reaction of Chemicals with DNA 9. DNA adducts and its consequences (Mutagenesis, DNA repair and Translesion DNA synthesis) 10. Protein adducts 11. Genetic toxicology (polymorphism) 12. Molecular basis of toxicology 13. Biomarkers 14. Natural Products 15. Cellular Oncogenesis 16. Metals 17. Drug induced liver damage 18. Mass spectrometry and other analytical methods
CHY400
Chemistry Colloquium
1.00
Undergraduate
Eminent speakers from around the world (and possibly from the department) present seminars about current topics at the forefront of chemical research. Students are expected to participate actively in these seminars by asking questions. This course serves to introduce undergraduate students to the range of research opportunities in chemistry.
CHY413
Applications of Analytical Techniques
3.00
Undergraduate
Applications of UV, IR, NMR, and mass spectral methods in structure elucidation /determination of organic compounds.
CHY415
Advanced Kinetics and Thermodynamics
3.00
Undergraduate
Course description not available.
CHY422
Transition metals in the synthesis of complex organic molecules
3.00
Undergraduate
Course description not available.
CHY452
Introduction to Bio-organic Chemistry
2.00
Undergraduate
Basic structure of nucleic acids, proteins, lipids and carbohydrates; biological functions and biosynthesis of precursors.
CHY498
Senior Project
6.00
Undergraduate
Individual faculty mentor(s) assigned to each student. Undergraduate research allows students to integrate and reinforce chemistry knowledge from their formal course work, develop their scientific and professional skills, and create new scientific knowledge. Original research culminating in a comprehensive written report provides an effective means for integrating undergraduate learning experiences, and allows students to participate directly in the process of science. Students enrolled in this course carry out an individual hands-on project over the full academic year, on a topic chosen from any area of Chemistry, and are assigned to a faculty mentor for their supervision. Course Evaluation: This course will be evaluated based on: an Oral Presentation and Examination before the Department, at the end of the first semester of research, dealing with the formulation of the research problem and survey of existing literature in the field. The student will be expected to demonstrate sufficient mastery of the background in the subject necessary to carry out research. a comprehensive written Project Report and Oral Presentation / Examination before the Department, at the completion of the project. The Project Report should contain a comprehensive account of the student’s research, and should demonstrate the student’s understanding of the research area, familiarity with the techniques used, and ability to report research data in a clear manner and to draw logical conclusions from the results. This course carries an S/U grade.
CHY499
Senior Project
6.00
Undergraduate
Individual faculty mentor(s) assigned to each student. Undergraduate research allows students to integrate and reinforce chemistry knowledge from their formal course work, develop their scientific and professional skills, and create new scientific knowledge. Original research culminating in a comprehensive written report provides an effective means for integrating undergraduate learning experiences, and allows students to participate directly in the process of science. Students enrolled in this course carry out an individual hands-on project over the full academic year, on a topic chosen from any area of Chemistry, and are assigned to a faculty mentor for their supervision. Course Evaluation: This course will be evaluated based on: an Oral Presentation and Examination before the Department, at the end of the first semester of research, dealing with the formulation of the research problem and survey of existing literature in the field. The student will be expected to demonstrate sufficient mastery of the background in the subject necessary to carry out research. a comprehensive written Project Report and Oral Presentation / Examination before the Department, at the completion of the project. The Project Report should contain a comprehensive account of the student’s research, and should demonstrate the student’s understanding of the research area, familiarity with the techniques used, and ability to report research data in a clear manner and to draw logical conclusions from the results. This course carries an S/U grade.
CHY412
Dynamics of Chemical Reactions
3.00
Undergraduate
The principles of chemical kinetics, as well as equilibrium and non-equilibrium statistical .mechanics will be covered in this advanced course. The associated computer lab will introduce the student to classical and ab initio quantum molecular dynamics and Monte Carlo simulations of liquids and proteins. The techniques learned in this course will applied to substantive research projects that the students will design, execute, and present. Students will be encouraged to seek avenues for publication of their most significant results BOOKS: Readings will be assigned from multiple sources.
CHY533
Coordination and Bio-Inorganic Chemistry
2.00
Graduate
Coordination and Bio-Inorganic Chemistry
CHY501
Medicinal Chemistry
3.00
Graduate
The objectives of the course are to give synthetic chemists, biochemists and pharmacologists a broad and balanced introduction to the background, general principle, concepts and tools of medicinal chemistry. The course will also highlight the new understanding of the factors governing modern drug discovery. Case histories of drug discovery will be explained with particular examples along with their biochemistry, pharmacology and toxicology, drug metabolism and disposition. Modern preclinical drug research is thus the focus of the course, which combines lectures, tutorials and practical work. This course will cover the following main topics: Introduction to Medicinal Chemistry Biological Mechanisms Pharmacokinetics and Drug Metabolism Screening of New Compounds Molecular Biology in Medicinal Chemistry Exploiting a Chemical Lead Combinatorial Chemistry and Molecular Diversity Case Histories of Drug Discovery Toxicology in Drug Discovery Pharmaceutical Considerations in Drug Development Structure-guided Drug Design Diversity oriented synthesis (DOS) Fragment based drug design (FBDD) Physical Properties and Quantitative Structure-Activity Relationships Hints and Tips in Medicinal Chemistry RECOMMENDED READING(S): An Introduction to Medicinal Chemistry (4th Ed, 2009) by Graham L. Patrick, Oxford University Press,.ISBN 978-0-19-923447-9. Fundamentals of Medicinal Chemistry (1st Ed, 2003) by Gareth Thomas, John Wiley & Sons Inc. ISBN 0-470-84307-1. The Organic Chemistry of Drug Design and Drug Action (2nd Ed, 2004) by Richard Silverman Academic Press. ISBN 0-12-643732-7. Analogue-Based Drug Discovery (1st Ed, 2006) by J. Fischer and C. R. Ganellin, Wiley-VCH. ISBN 3-527-31257-9. Contemporary Drug Synthesis (1st Ed, 2004) by J. Jack Li, Douglas S. Johnson, Drago R. Sliskovic and Bruce D. Roth. Wiley-Interscience.ISBN 0-471-21480-9.
CHY502
Synthetic Organic Chemistry
3.00
Graduate
1) Organic Synthesis and Structure a. Mechanism, b. Applicability and limitations of the major reactions in organic synthesis. c. Stereochemical control in synthesis. 2) New Synthetic Reactions and Catalysts a. Recent highlights of new synthetic reactions and catalysts for efficient organic synthesis. b. Mechanistic details as well as future possibilities will be discussed. 3) Tactics of Organic Synthesis a. A dissection of the most important syntheses of complex natural and unnatural products. b. Synthesis, planning and methodology. c. The logic of synthesis. d. Biogenesis.
CHY503
Chemistry and Biology of Glycoconjugates
3.00
Graduate
Introduction of glycocongugates, Structure and function of Glycoproteins, proteoglycans and glycosaminoglycans; Glycopeptides. glyco-amino-acids and glycosyl-amino-acids and Peptidoglycans. Inter- and intra-cellular communication and “Glycocode”, The need for homogeneity and pure, welldefined conjugates. Glycocongugate assembly and vaccine development.
CHY504
Applications of Analytical Techniques
3.00
Graduate
Course description not available.
CHY512
Advanced Molecular Spectroscopy
4.00
Graduate
Group theory: Theorems of linear algebra Time-independent and time-dependent perturbation theory Discrete and Continuous Groups, Group multiplication tables, Generators Symmetry Elements, Symmetry Operations and Point Groups Reducible and Irreducible Representations, the Great Orthogonality Theorem and Character Tables Projection Operators and symmetry-adapted linear combinations Selection Rules for Molecular Spectroscopy Electron Density, Structure Factor, Density Matrix, Density Operator and Bloch equations Molecular Spectroscopy:   Microwave spectroscopy IR spectroscopy of organic molecules Raman Spectroscopy Atomic and molecular spectroscopy UV-Vis spectroscopy of organic molecules Detection of functional groups of organic molecules by IR spectroscopy (labs) UV-Vis Spectroscopy of various Organic Molecules (labs). NMR spectroscopy Mass spectrometry Moessbauer spectroscopy Textbooks:   F. A. Cotton, Chemical Applications of Group Theory (Wiley Eastern, New Delhi, 1976) B. S. Garg, Chemical Applications of Molecular Symmetry and Group Theory (MacMillan India, 2012) E. B. Wilson, J. C. Decius and P. C. Cross, Molecular Vibrations: The Theory of Infrared and Raman Vibrational Spectra (Dover, New York, 1955) J. I. Steinfeld, Molecules and Radiation: An Introduction to Modern Molecular Spectroscopy (MIT Press, Cambridge, MA, 1979) H. Weyl, The Theory of Groups and Quantum Mechanics (Dover, New York, 1950) C. N. Banwell, Fundamentals of Molecular Spectroscopy (Tata McGraw-Hill, New Delhi, 1987) N. Sukumar, ed. A Matter of Density: Exploring the Electron Density Concept in the Chemical, Biological, and Materials Sciences (John Wiley, Hoboken, NJ, 2013) S.K. Dewan, Organic Spectroscopy (CBS Publishers).
CHY522
Informatics and Drug Discovery
3.00
Graduate
This course and the associated computer lab deal with Bioinformatics and Cheminformatics, applied to the search for new drugs with specific physiological effects (in silico Drug Discovery). Students will learn the general principles of structure-activity relationship modeling, docking & scoring, homology modeling, statistical learning methods and advanced data analysis. They will gain familiarity with software for structure-based and ligand-based drug discovery. Some coding and scripting will be required. At the end of the course, students will be expected to present a completed piece of software of significant utility and/or an analysis of experimental data from the published literature. Students will be encouraged to seek avenues for publication of their most significant results. Syllabus: Introduction Drug Discovery in the Information-rich age Introduction to Pattern recognition and Machine Learning Supervised and unsupervised learning paradigms and examples Applications potential of Machine learning in Chem- & Bioinformatics Introduction to Classification and Regression methods, and types of classification and regression: KNN and Linear Discriminant analysis Representation of Chemical and Biochemical Structures Drug Discovery in the Information-rich age Sequence Descriptors Text mining Representations of Molecular Structures Characterizing 2D structures with Descriptors and Fingerprints Searching 2D Chemical Databases Chemical File Formats and SMARTS Topological Indices Substructural Descriptors Molecular Fingerprints Physicochemical Descriptors Descriptors from Biological Assays Representation and characterization of 3D Molecular Structures Calculation of Structure Descriptors Pharmacophores Molecular Interaction Field Based Models Local Molecular Surface Property Descriptors Quantum Chemical Descriptors Shape Descriptors Protein Shape Comparisons 3D Motif Models Representation of Chemical Reactions and Databases Analysis and Visualization Molecular Similarity Analysis Molecular Quantum Similarity Measures Cluster and Diversity analysis Network graphs from Molecular Similarity 3D visualization tools Self-Organized Maps Semantic technologies and Linked Data Mapping Structure to Response: Predictive Modeling Linear Free Energy Relationships Quantitative Structure-Activity Relationships (QSAR) Modeling Ligand-Based and Structure-Based Virtual High Throughput Screening 3D Methods - Pharmacophore Modeling and alignment ADMET Models Activity Cliffs Structure Based Methods, docking and scoring Site Similarity Approaches and Chemogenomics Model Domain of Applicability assessment 5. Data Mining and Statistical Methods Linear and Non-Linear Models Feature selection Partial Least-Squares Regression Introduction to Neural Nets, Bayesian Methods and Kernel Methods Support vector machines classification and regression and application to chemo & bioinformatics Random forest Principal Component analysis and SVD Data preprocessing and different performance measures in Classification & Regression Introduction to evolutionary computing Deep Learning and Convolutional Neural Nets Data Fusion Model Validation Interpretation of Statistical Models Best Practices in Predictive Cheminformatics Textbooks: Johann Gasteiger, Thomas Engel,Chemoinformatics: A Textbook (Wiley-VCH, 2003) Jürgen Bajorath (Editor), Chemoinformatics and Computational Chemical Biology (Methods in Molecular Biology) (Humana Press, 2004) An Introduction to Chemoinformatics by Leach & Gillet
CHY542
Nano and Supramolecular Chemistry
3.00
Graduate
This course will help to understand the basic concept of supramolecular chemistry (non-covalent interactions) and their quantification in molecular recognition process. It will cover the area of non-covalent interaction, multiple hydrogen bonding (H-B) stems, self-assembly,  acyclic receptors for neutral and charged guests, macrocycles and macrobicycle,  cryptands and macropolycycles, cyclodextrin. The chemistry of nanomaterials will deal with the basic understanding of the atomic and electronic structures of different nanomaterials such as clusters and nanoparticles of inorganic materials (metals and semiconductors), fullerenes, nanotubes, nanowires, and two dimensional systems such as graphene. Aspects related to optical, magnetic and vibrational properties of nanomaterials as well as the development of nanomaterials will be covered. Text Book: Supramolecular Chemistry Concept and Perspective: Jean-Marie Lehn, VCH, Weinheim, 1995 Reference Book: Supramolecular Chemistry: J. W. Steed and J. L. Atwood, John Wiley and Sons, 2009 The references to nanomaterials will be original journal papers and review articles in journals and edited volumes. Other reading materials will be assigned as and when required.
CHY545
Fundamentals of Crystallography
3.00
Graduate
Crystallography in combination with X-ray or neutron diffraction yields a wealth of three-dimensional structural information unobtainable through other methods. The course has been designed to give an overview of crystallography, in general. This basic course will cover the topics such as symmetry in crystallography, crystals systems, Bravais lattices, crystal symmetry, crystallographic point groups and space groups, Miller indices, theory of X-ray diffraction, data collection, data reduction, structure factors and Fourier syntheses, electron density, phase problem, direct methods, Patterson method, crystal structure refinement etc. The course will also highlight the application of single crystal and powder X-ray diffraction techniques and will include hands on training on crystal growth, mounting, structure solution, refinement and analysis. Further, training on the use of database for structural search will also be provided. Introduction - Introduction on Crystallography and discussion on course structure Crystallographic Symmetry - Concept of 1D and 2D symmetry and lattices, notations of symmetry elements, space groups in 2D, 3D lattices, 32 point groups and their notations, stereographic projections, Laue symmetry; glide planes, screw axes and their notations, space groups, equivalent points, space group symmetry diagrams etc. Miller Indices, crystallographic planes and directions, close pack structures, linear density, planar density, Miller-Bravais indices for hexagonal systems. Theory of X-ray diffraction - What is X-ray, generation and classification of X-ray, X-ray sources, diffraction of X-rays, Bragg’s law, the reciprocal lattice, reciprocal relationship, Bragg’s law in reciprocal space, Ewald’s sphere, Laue Method, Oscillation, rotation and precession methods. Data reduction - L-P corrections, structure factor, scaling, interpretation of intensity data, temperature factor, symmetry from intensity statistics, structure factor and Fourier synthesis, Friedel’s law; exponential, vector and general forms of structure factor, determination of systematic absences for various symmetry or lattice centering, FFT, Anomalous scattering. The Phase Problem - Definition, Direct Methods, structure invariants and semi invariants, probability methods, Phase determination in practice, Patterson Methods, Patterson Symmetry, completion of structure solution, F synthesis. Refinement of Crystal Structures - Refinement by Fourier synthesis, refinement by F synthesis, Refinement by least squares method, weighting functions, Goodness-Of-Fit (GOF) parameter, treatment of non-hydrogen atoms, and treatment of hydrogen atoms. Powder X-ray diffraction (PXRD) - Methodology, geometrical basis of powder X-ray diffraction, applications of PXRD (determination of accurate lattice parameters, identification of new/unknown phases, applications in pharmaceutical industry, structure solution from PXRD etc.), Reitveld method for structure refinement, indexing of PXRD, handling of PXRD using DASH. Neutron and Electron Diffraction - Basics of neutron, synchrotron and electron diffraction and their applications. Practical - Crystal growth, selection, indexing of crystals, data collection, data reduction, space group determination and structure refinement using SHELXS97, SIR and SHELXL97, introduction to International Tables for Crystallography and crystallographic packages (e.g. WinGx, PLATON, OLEX-2), IUCr validation of the structure and use of Cambridge Structural Database for structural search. Text Book: X-ray structure determination: A Practical Guide (2nd Ed.) by George H. Stout and Lyle H Jensen, Wiley-Interscience, New York, 1989. Reference Books: Fundamentals of Crystallography (2nd Ed.) by C. Giacovazzo, Oxford University Press, USA, 2002. X-ray analysis and The Structure of Organic Molecules (2nd Ed.) by Jack D. Dunitz, Wiley-VCH, New York, 1996. Chemical Applications of Group Theory (3rd Ed.) by F. A. Cotton, Wiley-India Edition, India, 2009. International Table of Crystallography.
CHY552
Polymer Chemistry and Its Scope
3.00
Graduate
How do changing demands in society lead to polymer invention? How are monomers bonded in nature to form our body’s building blocks? How do scientists mimic nature in labs? How does the several-fold change in molecular weight from monomer to polymer result in different sets of properties? Most of the polymeric materials around us are synthesized in different ways, depending upon end usage. This course will help the students to understand the need and importance of polymers in today’s world. Interesting chemical aspects of synthesis of polymeric architectures from small molecules will be explored. Course Outline: 1. Introduction to Polymers Nomenclature, Classification, Molecular weight, Physical state, Applications 2. Step Growth Polymerization Polyamide, Polyesters, Polycarbonates, Phenolic polymers, Epoxy resins, Polyethers, Polyurea, Polyurethanes, Carother’s equation 3. Chain Growth Polymerization Free Radical polymerization: Initiators, Inhibitors and retarders, Mechanism, Kinetics and Thermodynamics, Polymerization processes (Bulk, Solution, Suspension, Emulsion), Copolymers Ionic polymerization Cationic and Anionic Polymerization: Mechanism, Ring Opening Polymerization (ROP) Controlled/Living polymerizations: ATRP (Atom Transfer Radical Polymerization), RAFT (Reversible Addition Fragmentation Chain Transfer), GTP (Group Transfer Polymerization), Ziegler Natta Polymerization, Metathesis 4. Specialty Polymers Conducting Polymers, Liquid Crystal Polymers, Organometallic Polymers, Green Polymers and their applications 5. Polymer Characterization (Molecular weight determination) Number average molar mass, End group assay, Colligative Properties of Solutions, Osmometry, Light scattering (Dynamic Light Scattering), Viscometry, Gel Permeation Chromatography, MALDI (Matrix Assisted Laser Desorption/Ionization) 6. Polymers in Life Proteins: Synthesis of amino acids and their reactions, Test reactions, Zwitter ion, Isoelectric point and Electrophoresis. Overview of Primary, Secondary, Tertiary and Quaternary Structure of proteins. Determination of Primary structure of Peptides by N-terminal and C–terminal analysis. Synthesis of peptides by N-protection & C-activating groups, Merrifield solid-phase synthesis. Nucleic acids: Nucleosides and Nucleotides, ATP (energy storage and release), Mechanism of Phosphoryl Transfer Reactions, Composition of nucleic acids. Different types of DNA and RNA, Biosynthesis of DNA, m-RNA and proteins, Determining base sequence of DNA, Lab synthesis of DNA fragments, Polymerase Chain Reaction (PCR). Textbooks:       Principles of Polymerization, George Odian, John Wiley & Sons, Inc., 3rd Ed., 1991. Introduction to Polymer Science and Chemistry: A Problem Solving Approach, Manas Chandra, CRC press, Taylor & Francis, 1st Ed., 2006. Malcolm P. Stevens, Polymer Chemistry: An Introduction, 3rd Edition, Oxford University Press Polymer Characterization: Physical techniques, D. Campbell and J. R. White, Chapman and Hall. London- New York. Organic Chemistry, Paula Yurkanis Bruice, Pearson, 3rd Ed., 2011. Biology, N. A. Campbell, and J. B. Reece, 8th Ed., Pearson Benjamin Cummings, San Francisco. Biochemistry, J. M. Berg, J. L. Tymoczko, and L. Stryer, W. H. Freeman & Co Ltd, 6th Ed., 2002.
CHY553
Coordination and Bio-inorganic Chemistry
3.00
Graduate
Metals ions play important role in many biological processes. Their function can range from simple structural roles in which they hold a protein in a specific conformation, to more complex roles in which they are involve in multiple electron transfer processes and in bond cleavage and formation. Understanding of the biological functions of metal ions lies at the heart of bio-inorganic chemistry. This course will focus on the biologically important metal ions and their binding sites, and the techniques used to probe these sites (e.g.IR, UV-VIS, NMR, EPR, Mossbauer and CV). A more in-depth look at several key metalloenzymes and the functional role of the metal ions therein will also be taken. Text Books: Inorganic Chemistry; Principles of Structures and Reactivity: James E. Huheey; Allen A. Keiter;Richard L. Keiter, Pearson Edition.  Principles of Bioinorganic Chemistry: Stephen J. Lippard, Jeremy M. Berg, University Science Books, 1994.  Physical Methods in Bioinorganic Chemistry: Spectroscopy and Magnetism: Lawrence Que, University Science Books, 1999. Reference Materials: Other reading materials will be assigned as and when required.
CHY554
Green Chemistry and Sustainability
3.00
Graduate
Since a decade, scientific community especially chemistry has been mobilized to develop new chemistries that are less hazardous to human health and the environment. Several steps were taken to protect both the nature and maintain ecological balance. But still such an effort is in nascent stage. Are we really protecting earth? Are we utilizing nature’s sources wisely? What are the hazards associated with one wrong step…and with several such steps? We are surrounded by chemistry since we wake up in morning till we sleep in night such as toothpaste, soap, cloth, perfume, medicine, plastic furniture, shoes etc. For those of us who have been given the capacity to understand chemistry and practice it as our day to day life, it is and should be expected that we should use it in a sustainable manner. With knowledge comes the burden of responsibility. We should not enjoy this luxury with ignorance and cannot turn a blind eye to the effects of the science in which we are engaged. We have to work hard and put brain waves together to develop new chemistries that are more benign, and safer to mother earth!! Green chemistry Lessons from past for a better future: Need, Limitations and Opportunities. Principles of Green Chemistry and their illustrations with examples: Scales of measurement such as Atom efficiency, E factors etc., homo vs. heterocatalysis, reaction efficiency, toxicity reduction etc. Green reactions: Green alternatives of starting materials, non-risky reagents, benign solvents (Aqueous medium, Ionic liquids, Supercritical fluids, Solvent free reactions, Flourous phase reactions), and reaction conditions (Nonconventional energy sources: Microwave assisted reaction, Ultrasound assisted reactions, Photochemical reactions), catalysis (heterogeneous catalysis, biocatalysis, phase-transfer catalysis), Replacement of Non-Green reactions with Green reactions (Real/Award cases) Safety for sustainable environment: Hazards assessment and mitigation in chemical industry Future trends in Green Chemistry: Green analytical methods, Redox reagents, Green catalysts; Green nano-synthesis, Green polymer chemistry, Exploring nature, Biomimetic, multifunctional reagents; Combinatorial green chemistry; Proliferation of solvent-less reactions; Non-covalent derivatization, Biomass conversion, emission control. Reference Books: Green Chemistry: Theory and Practice. P.T. Anastas and J.C. Warner. Oxford University Press. Green Chemistry: Introductory Text. M. Lancaster Royal Society of Chemistry (London). Introduction to Green Chemistry. M.A. Ryan and M.Tinnesand, American Chemical Society (Washington). Real world cases in Green Chemistry, M.C. Cann and M.E. Connelly. American Chemical Society (Washington). Real world cases in Green Chemistry (Vol 2) M.C. Cann and T.P.Umile. American Chemical Society (Washington) Alternative Solvents for Green Chemistry. F.M. Kerton. Royal Society of Chemistry (London). Handbook of Green Chemistry & Technology. J. Clark and D. Macquarrie. Blackwell Publishing. Solid-Phase Organic Synthesis. K. Burgess. Wiley-Interscience. Eco-Friendly Synthesis of Fine Chemicals. R. Ballini. Royal Society of Chemistry (London) Green Polymer Chemistry: Biocatalysis and Biomaterials; Cheng, H., et al.; ACS Symposium Series; American Chemical Society: Washington, DC, 2010.
CHY556
Inorganic Reaction Mechanism
3.00
Graduate
General discussion about reaction kinetics, how to derive rate law and the ambiguity of mechanistic interpretations of rate laws Inorganic substitution Reaction for octahedral geometry vs square planar geometry, Trans effect, Redox reactions: Outer sphere ET vs. Inner sphere ET vs. Proton coupled ET (PCET) Organometallic reactions, mechanism and catalysis: Insertion, Oxidative addition, Reductive elimination C-H activation: Introduction, C-H functionalization vs. C-H activation, Importance, Classification, Organometallic C-H activation vs. biological C-H activation, Present research status C-C coupling reactions, mechanism, Present research status
CHY557
Intelligent Materials for Medicine
3.00
Graduate
Recent advances in field of medicine have resulted in designing and development of large number of novel synthetic architectures for target drug delivery in order to revolutionize the treatment and prevention of disease. Advanced drug delivery and targeting can offer significant advantages to conventional drugs, such as increased efficiency, safety for drug delivery, convenience. However, such potential is severely compromised by significant obstacles to delivery of these drugs in vivo. These obstacles are often so great that effective drug delivery and targeting is now recognized as the key to effective development of many therapeutics. This course will provide a comprehensive introduction to the vehicles for drug delivery, principles of advanced drug delivery and targeting, their current applications and potential future developments. Books: Principles of Polymerization, George Odian, John Wiley & Sons, Inc., 3rd Ed., 1991. Chemistry of Nanocarbons, T. Akasaka, F. Wudl, S. Nagase, John Wiley & Sons, Inc.,1 st Ed., 2010. Contemporary Polymer Chemistry, Harry R Allcock, F W Lampe, J. E Mark, Pearson Publication Chemistry and Applications of Polyphosphazenes, Harry R. Allcock, John Wiley & Sons, Inc., 2003. Stem Cells: A Very Short Introduction, Jonathan Slack (Mar 24, 2012) Stem Cells for Dummies, Lawrence S.B. Goldstein and Meg Schneider (Feb 2, 2010) Essentials of Stem Cell Biology (2nd Edition, July 2009) by Robert Lanza, John Gearhart, Brigid Hogan and Douglas Melton. Scientific journals will be provided
CHY558
Organometallic Chemistry
3.00
Graduate
Course description not available.
CHY600
Research Methodology
3.00
Graduate
1. Quantitative Methods: This module will deal with Data handling and Data Analysis, the elements of Quantitative Logic, including Hypothesis testing, Weight of Evidence, and Domain of Applicability estimation. 2. Research Literature and Seminar: This part of the course will be conducted as a Journal Club. Each week one student will be expected to read and summarize a research paper from the recent literature in an area outside their immediate domain of research. The student will familiarize himself/herself with the background necessary to understand the research paper, and will be expected to critically analyze the work and to answer questions from other students and from the faculty moderator(s). Also covered: the research process - meaning of research, objectives, motivation, types; method vs. methodology, scientific and research method, and detailed description of the research process. 3. Grantsmanship: This module will deal with identification of a research problem, formulation of a testable hypothesis and design of experiments to address the question. Strategies for writing a fundable research proposal will be discussed, with particular emphasis on the Specific Aims, and succinctly conveying the significance of the problem to both technical and non-technical readership. Students will refine both writing and presentation skills during this module. Experts will be invited from funding agencies like DBT, DST, ICMR and Wellcome Trust/DBT Alliance to provide recent updates and guidelines for grant submission (as part of an yearly mini-symposium). [Core course required of all Ph.D. students]
CHY601
Quantitative Methods
1.00
Graduate
This course will deal with Data handling and Data Analysis, Elements of Qualitative and Quantitative Logic, including Hypothesis testing, Weight of Evidence, and Domain of Applicability estimation.
CHY602
Transition Metals in the Synthesis of Complex Organic Molecules
3.00
Graduate
Formalisms, Electron Counting, Bonding (How Things Work) Organometallic Reaction Mechanisms Synthetic Applications of Complexes Containing Metal-Carbon Sigma-Bonds Synthetic Applications of Transition Metal Carbonyl Complexes Synthetic Applications of Transition Metal Carbene Complexes Synthetic Applications of Transition Metal Alkene, Diene, and Dienyl Complexes Synthetic Applications of Transition Metal Alkyne Complexes Note: Each topic will end with a discussion section, where student participation is important and will have direct implication on their grade
CHY615
Graduate Seminar
1.00
Graduate
Faculty members from the department (and possibly beyond) present seminars about their areas of interest, the proposed research in their respective groups and the experimental (or computational) techniques used in their field. Students will be expected to participate actively in these seminars by asking questions. This module serves to introduce new students to the possibilities for research, preparatory to selection of their research advisors.
CHY622
Computational Chemistry
3.00
Graduate
Classical Force Field Methods; Molecular Mechanics Postulates of Quantum Mechanics and measurement The Born-Oppenheimer approximation and the Molecular Hamiltonian The Concept of the Potential Energy Surface Semiempirical and ab initio Quantum Mechanics Variation and Perturbation Theory Independent-Particle Models: the Hartree method Spin and statistics in non-relativistic quantum mechanics The Hartree-Fock Self-Consistent Field equations Basis Sets and Relativistic Pseudopotentials Geometry Optimization Techniques and Frequency Analysis Valence Bond Methods Electron Correlation and Configuration Interaction Density Functional Theory - Hohenberg-Kohn theorems, v- and N-representability DFT - Fremi hole, Exchange-Correlation potential and Kohn-Sham method Conceptual DFT Density Matrices and Natural Orbitals Multi-configuration methods: MCSCF and CASSCF Diagrammatic Methods: Coupled Cluster Theory Wave Function Analysis Computation of Molecular Properties Periodic systems and theory of Insulators Basis Set Superposition Error and the Counterpoise method Introduction to Classical Statistical Mechanics Continuum (Implicit) solvent and Explicit solvent methods Protein Simulations QM/MM and ONIOM methods Introduction to TDDFT Carr-Parinello molecular dynamics Textbooks: Frank Jensen: Introduction to Computational Chemistry (Wiley) Frank L. Pilar: Elementary Quantum Chemistry (McGraw Hill) Errol G. Lewars, Computational Chemistry: Introduction to the Theory and Applications of Molecular and Quantum Mechanics (Kluwer Academic Publishers, 2003) James B. Foresman, AEleen Frisch, Exploring Chemistry With Electronic Structure Methods: A Guide to Using Gaussian (Gaussian, Inc.) P. A. M. Dirac: The Principles of Quantum Mechanics (Clarendon Press; Oxford,1981) J. N. Murrell, S. F. A. Kettle, J. M. Tedder: Valence Theory [ELBS & John Wiley] Richard P. Feynman, Robert B. Leighton & Matthew Sands: The Feynman Lectures on Physics, Vol.III (Addison Wesley Longman) N. Sukumar, ed. A Matter of Density: Exploring the Electron Density Concept in the Chemical, Biological, and Materials Sciences (John Wiley, Hoboken, NJ, 2013)
CHY899
Litterature Seminar
1.00
Graduate
Graduate students from the department present seminars based on current literature in their areas of interest. Other students will be expected to participate actively in these seminars by asking questions. Communicating research findings before an audience of peers is an integral component of a scientist’s career training. This module serves to introduce new students to the art of delivering presentations and hone their verbal communication skills. The course will be conducted during 1hr each week with input from faculty so that real improvements may be effected.