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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.

1. General discussion about oxidation and reduction, electron transfer vs atom transfer, oxidation no. 2. 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, How to construct a voltaic cell? 3. Electrical dimensions and unit, Mechanism of electrolysis (Grotthuss vs Faraday), Theory of electrolytic dissociation, Ostwald dilution law, Faraday’s laws of electrolysis, Significance of  faraday’s laws, Specific Conductance, Equivalent conductance, Equivalent conductance at infinite dilution, Application of ion conductance, Kohlrausch law, Outline of Debye Huckel theory,  Nernst equation and Concept of free energy. 4. Definition: Electrode potential, Std. potential and Formal potential; Physical significance of electrode potential. 5. 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?   6. 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. 7. Application of electrode potential; Periodic trend of the reduction potential; Pourbaix diagram. 8. Electroanalytical techniques: Potentiometry, Coulometry, Voltammetry and Amperometry. 9. How to measure 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.  10. Bulk electrolysis.

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.  

Applied Chemistry COURSE DESCRIPTION: 1: Atomic structure, Periodic table, Quantum Chemistry, Spectroscopy 2: Thermodynamics, Energy, Chemical Kinetics, Photosystems 3: Nano materials, Organic Chemistry, Polymers 4: Water Corrosion and Biochemistry" ASSESSMENT SCHEME : Grading in the lecture will be based on a mid-term and a final examination with 10% of the lecture grade based on class participation. The student needs to achieve 40% in both the theory and lab separately to pass the course. To pass the course you will have to pass the lab and lecture portion separately and achieve 40% independently in each part. These parts will be weighted as 40% for lab and 60% for lecture.

Transition metals in the synthesis of complex organic molecules

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.

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).

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).

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.

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).

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.

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).

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).

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).

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.

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.

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

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).

General Introduction: Biomolecules: Carbohydrates, Proteins, Nucleic Acids, Lipids, Enzymes and Vitamins Carbohydrates: Structure and Functions Carbohydrates metabolism, Kreb’s Cycle and Glycolysis. Proteins: Properties, Structure and Functions Protein Sequencing Edman degradation Sanger’s reagent and Dansyl chloride Sequence by Mass Spectrometry (MALDI, ESI-MS, Tandem MS). Nucleic Acids: Introduction of Nucleic acids Gene expression, Genetic Code DNA Sequencing Sanger dideoxy method Maxam Gilbert Bisulfite Functions of nucleic acids DNA replication Repair and recombination DNA chemistry DNA damage Methylation and demethylation Oxidative DNA damage DNA-DNA crosslinks DNA-Protein crosslinks Mutagenesis Diseases and carcinogenesis 4.9. Gene Sequence, 4.10. PCR, RT-PCR techniques, 4.11. DNA Finger printing (Agarose gel electrophoresis) 4.11.1. Forensics, 4.11.2. Relationships, 4.11.3. Medical Diagnostics Lipids: Fats: Properties and functions Fatty Acids, Classes of Lipids Nomenclature of fatty acids Examples of diff. Lipids Phospholipids, Steroids Beta Oxidation mechanism Enzymes: Co-factors, Co-enzymes, Apo-enzyme, Halo enzymes Factors effecting Enzymes (Con., pH, T) Nomenclature, Mechanism of Enzymes Biosynthesis of cofactors NAD+-NADPH Biosynthesis of Niacin (Vitamin B3) FAD-FADH-FADH2 Thiamine pyrophosphate TPP Enzyme assay in Diagnostic Medicine   Hormones and Vitamins Classifications of Hormones, Examples and Function of Hormones Classifications of Vitamins Examples and Function of Vitamins

Course description not available.

Course description not available.

Course description not available.

Course description not available.

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.

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.

Organometallic Chemistry

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.

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

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

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.

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.

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.