Department of Chemistry University of Manitoba

Undergraduate Course Booklet

(not including "topics" courses)

2011-2012

Chemistry Courses - Prerequisite Structure (note: most non-chemistry prerequisites are not shown)
Gr 12 Chem or CHEM 0900 CHEM 1300 or MATH 0900 Gr 12 Math (Pre-calculus or Applied) CHEM 1000

CHEM 2560

CHEM 1310

CHEM 1320

CHEM 2770

CHEM 1030

CHEM 2550

CHEM 2400

CHEM 2210

CHEM 2290

CHEM 2280

CHEM 2360 CHEM 2860

CHEM 2470

CHEM 2780

CHEM 3400

CHEM 2220

CHEM 3360

CHEM 3370

CHEM 2370

CHEM 3570

CHEM 3590

or CHEM 4570 CHEM 4680 CHEM 3390 CHEM 3580 CHEM 3490 CHEM 4660 CHEM 4640 CHEM 4360 CHEM 4370 or CHEM 4690 CHEM 4580 or or CHEM 4600 CHEM 4630 CHEM 4620 or CHEM 4700 CHEM 4550 CHEM 4590

permission & in 4th year of program

CHEM 4710

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Table of Contents
CHEM 0900 Preparatory Chemistry....................................................................................................................... 1 CHEM 1300 (L) University I Chemistry: Structure and Modelling...................................................................... 2 CHEM 1310 (L) University I Chemistry: Introduction to Physical Chemistry...................................................... 3 CHEM 1320 (L) University I Chemistry: Introduction to Organic Chemistry ..................................................... 4 CHEM 2210 (L) Introductory Organic Chemistry I: Structure and Function ........................................................ 5 CHEM 2220 (L) Introductory Organic Chemistry II: Reactivity and Synthesis .................................................... 6 CHEM 2280 (L) Physical Chemistry: Microscopic Descriptions of Matter .......................................................... 7 CHEM 2290 (L) Chemical Energetics and Dynamics: Macroscopic Descriptions................................................ 8 CHEM/MBIO 2360 (L) Biochemistry 1: Biomolecules and an Introduction to Metabolic Energy ...................... 9 CHEM/MBIO 2370 (L) Biochemistry 2: Catabolism, Synthesis, and Information Pathways............................. 10 CHEM 2400 (L) Inorganic Chemistry: Structure and Applications..................................................................... 11 CHEM 2470 (L) Introductory Analytical Chemistry............................................................................................ 12 CHEM 2550 (L)/ENVR 2550 (L) Environmental Chemistry .............................................................................. 13 CHEM 2560 (L) Water Quality Analysis ............................................................................................................. 14 CHEM/MBIO 2770 (L) Elements of Biochemistry I ........................................................................................... 15 CHEM/MBIO 2780 (L) Elements of Biochemistry II.......................................................................................... 16 CHEM 2860 (L) Chemistry of Biomolecules....................................................................................................... 17 CHEM 3360 (L) Elementary Quantum Chemistry and Molecular Bonding........................................................ 18 CHEM 3370 (L) Symmetry, Spectroscopy and Structure .................................................................................... 19 CHEM 3400 (L) Inorganic Chemistry: Transition Metals ................................................................................... 20 CHEM 3390 (L) Structural Transformations in Organic Chemistry .................................................................... 21 CHEM 3490 Introduction to Polymer Chemistry................................................................................................. 22 CHEM 3570 Biophysical Chemistry .................................................................................................................... 23 CHEM 3580 (L) Methods in Physical Organic Chemistry................................................................................... 24 CHEM 3590 (L) Instrumental Analysis................................................................................................................ 25 CHEM 4360 Signalling and Regulation of Gene Expression............................................................................... 26 CHEM 4370 Glycobiology and Protein Activation.............................................................................................. 27 CHEM/ENVR 4550 Aquatic Chemistry............................................................................................................... 28 CHEM 4580 Topics in Organic Chemistry: Design of Organic Syntheses.......................................................... 29 CHEM 4590 Bioanalytical Methods..................................................................................................................... 30 CHEM 4600 (L) Advanced Chemical Techniques............................................................................................... 31 CHEM 4620 Biochemistry of Nucleic Acids ....................................................................................................... 32 CHEM 4630 Biochemistry of Proteins ................................................................................................................. 33 CHEM 4660 Computational Chemistry................................................................................................................ 34 CHEM 4670 Drug Design and Drug Discovery ................................................................................................... 35 CHEM 4680 Organometallic Chemistry .............................................................................................................. 36 CHEM 4690 Specific Methods in Organic Synthesis........................................................................................... 37 CHEM 4700 (L) Advanced Biochemistry Laboratory ......................................................................................... 38 CHEM 4710 (L; 6 cr hrs) Research Project in Chemistry and Biochemistry....................................................... 39

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CHEM 0900 Preparatory Chemistry Jacqueline Ching

Required Textbook Package: John Olmsted III, Greg Williams, and Robert C. Burk; Chemistry: Canadian Edition; John Wiley & Sons Canada, Ltd. For CHEM 0900 students, the textbook package includes (1) an access to the electronic Student Solutions Manual and to WileyPlus/Catalyst online assignment system, and (2) a copy of the Wiley Canada customized Course Material for CHEM 0900 Preparatory Chemistry document (provided separately to students). Subscription to Late Nite Labs REACTOR system: This system is an online Laboratory Simulation Website (cf. Laboratory Work below) (MANDATORY; subscription cost is paid through course registration fee). This course is offered on campus (Fall and Spring terms) and online (Fall, Winter, and Summer terms). General Outline: This course is designed for students with little or no background in chemistry and who wish to achieve the prerequisites for the first-year chemistry course CHEM 1300, or for students who require a refresher course in basic chemistry. The course material is covered within five (5) modules. Fundamental scientific concepts (Scientific Method, Measurements, SI Units and Conversions, Experimental Errors, Significant Figures, Precision and Accuracy) are covered and consolidated in the first module. This material is then followed by: (a) the Structure of Matter (Matter and its States, Mixtures and Pure Substances, Elements and Compounds, Atoms and Molecules), (b) the Properties of Matter (Chemical and Physical Properties, Atomic and Molecular Masses, Molar Masses, etc.), and (c) Chemical Reactivity (Types of Chemical Reactions, Chemical Equations, Stoichiometry, Reactions in Solutions, Reactions in Gas Phase, etc.). The concepts of Language of Chemistry (Chemical Nomenclature) are integrated within Modules 2, 3, and 4 of course material. Module 1: Lets Start from the Beginning! (Basic Concepts of Science): Discussion about the Scientific Method, the Three Levels of Chemistry, The Systme International of Units and Units Conversion, Uncertainty in Measurements, Significant Figures, Errors, and Precision versus Accuracy. Module 2: Whats the Matter? (Composition, Structure, and Properties): Pure Substances, the Three States of Matter, Chemical and Physical Properties, Mixtures, Early Atomic Theory, Introduction to the Periodic Table, Atomic Particles, Compounds (covalent and ionic, organic and inorganic), Introduction to Lewis Structures. Module 3: How Much or How Many? (Amounts of Matter): Atomic Mass Units, Isotopes, Isotopic Abundance, Atomic and Molecular Masses, Moles and Molar Masses, Number of Particles, Chemical Formulas of Compounds (percent composition, empirical formulas, molecular formulas). Module 4: Lets Not Overreact! (Description of Chemical Reactivity): Chemical Reactions, Chemical Equations and Balancing, Types of Reactions (oxidation-reduction, acid-base, & precipitation), Stoichiometry (Limiting Reactant and Reaction Yield), Chemistry in Solution (solubility and solubility rules, solution composition, preparation and dilution), Applications. Module 5: The Third State of Matter: Its a Gas! Gas Properties, Pressure (definition and units), Gas Laws, Absolute Temperature Scale, State Changes of Gases, State Function of Gases, Standard Conditions, Applications, Daltons Law of Partial Pressures, Ideal versus Real gases. Laboratory Work: Three virtual laboratory experiments are performed online by students using Late Nite Labs REACTOR system (www.latenitelabs.com). The themes of these experiments are consolidating the topics that are covered in the course: Experiment 1: Identification of an Unknown Metal by Density Measurements. Experiment 2: Identification on an Unknown Hydrate Compound by Dehydration Mass Measurements. Experiment 3: Standardization of a Sodium Hydroxide (NaOH) Solution by Acid-Base Titration.

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CHEM 1300 (L) University I Chemistry: Structure and Modelling Debbie Armstrong, Peter Budzelaar, Krystyna Koczanski, Elena Smirnova, Sarrah Vakili, James Xidos
Required Textbook Package: John Olmsted III, Greg Williams, and Robert C. Burk; Chemistry: Canadian Edition; John Wiley & Sons Canada, Ltd. The textbook package includes an access to the electronic Student Solutions Manual and to WileyPlus/Catalyst online assignment system. CHEM 1300 Lab Manual (2010 2011 Edition) which includes a subscription to Late Nite Labs REACTOR system (an online Laboratory Simulation Website). General Outline: In this course we introduce models of atomic and molecular structure that allow us to explain the properties of materials that we encounter in our daily lives. 1. Models of atomic structure: nuclear structure; wave and particle properties of light and matter; quantum mechanical model of the atom; electron configurations and valence; periodic trends in physical and chemical properties of atoms. Models of chemical structure: Lewis model of chemical bonding; VSEPR model of molecular shapes; bond and molecular polarity; localized, delocalized, and composite models of electronic structure in molecules; band theory of solids; semiconductors. Condensed phases and organic chemistry: Interparticle forces and how they affect the physical properties of liquids and solids; Structure of crystalline and amorphous solids; classes of organic molecules; organic reactions.

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Laboratory Work: Laboratory Supervisors: James Xidos and Krystyna Koczanski The CHEM 1300 Laboratory Program combines wet-lab work, virtual lab activities, and molecular modeling task: Exp. 1 WET-LAB: Density &d Boiling Point Measurements: Unknown Volatile Liquid Exp. 2 WET-LAB: Solution Stoichiometry: Copper Cycle Reactions Exp. 3 WET-LAB: Volumetric Techniques: Analysis of Polyprotic Acid Solutions Exp. 4 VIRTUAL LAB: Alcohol Content of Vodka by Dichromate Titration Exp. 5 WET-LAB: Heating Techniques: Hydrate and Oxide Compounds Exp. 6 WET-LAB: Crystallization and Filtration Techniques: Synthesis of Alum Exp. 7 MOLECULAR MODELLING: Computational Modelling of Molecular Properties

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CHEM 1310 (L) University I Chemistry: Introduction to Physical Chemistry (commonly described as: Chemical Reactivity) Debbie Armstrong, Carl Bartels, John Cullen, Kathy Gough, Krystyna Koczanski, Sarrah Vakili, James Xidos
Required Textbook Package: John Olmsted III, Greg Williams, and Robert C. Burk; Chemistry: Canadian Edition; John Wiley & Sons Canada, Ltd. The textbook package includes an access to the electronic Student Solutions Manual and to WileyPlus/Catalyst online assignment system. CHEM 1310 Lab Manual (2010 2011 Edition) which includes a subscription to Late Nite Labs REACTOR system (an online Laboratory Simulation Website). General Outline: In this course we examine chemical reaction processes: the energy absorbed or released (thermochemistry), the sponteneity of reactions (thermodynamics), how reactions proceed (kinetics), and the extent of chemical reactions (chemical equilibrium); we examine many types of equilibrium, most notably those of acids and bases. 1. 2. 3. 4. 5. Thermochemistry: energy types and transformations; state functions; heat and work; heat capacity; bond energies; enthalpy; standard states; Hesss Law; enthalpies of formation and phase changes Thermodynamics: entropy; free energy; spontaneity; applications. Chemical Kinetics: elementary reactions and reaction mechanism; rates of chemical reaction; rate laws; experimental kinetics; temperature and rate; catalysis Chemical Equilibrium: characteristics and properties of equilibria; equilibrium constants; Le Chatelier principle and its applications; types of equilibria (e.g. acid-base, solubility, complexation) Acids and Bases: Brnsted-Lowry theory; pH scale; Ka, Kb, and Kw; recognition of acids and bases and how molecular structure affects their strength; Lewis theory; buffer solutions; acid-base titrations

Laboratory Work: Laboratory Supervisors: James Xidos and Krystyna Koczanski The CHEM 1310 Laboratory Program combines wet-lab work, virtual lab activities, and molecular modeling task: Exp. 1 WET-LAB Experiment: Synthesis and Analysis of Acetylsalicylic Acid Exp. 2 VIRTUAL LAB Experiment: Specific Heat of Metals Exp. 3 WET-LAB Experiment: Heat of Reaction, Hesss Law, and Heat of Dissolution Exp. 4 WET-LAB Experiment: Chemical Kinetics Initial Rate Method Exp. 5 WET-LAB Experiment: Titration of Strong and Weak Acids (Titration Curves) Exp. 6 WET-LAB Experiment: Qualitative Solubility and Ksp of Calcium Hydroxide Exp. 7 MOLECULAR MODELLING: Computational Modelling of Chemical Reactions

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CHEM 1320 (L) University I Chemistry: Introduction to Organic Chemistry Horace Luong
Required Textbook: Introduction to Organic Chemistry (4th Edition) by W.H Brown and T. Poon (Wiley) CHEM 1320 Lab Manual (2011 Edition) Recommended Supplement: Students are strongly encouraged to obtain a molecular model kit which may be used in examinations to aid in the understanding of stereochemistry. Students may also purchase the Study guide and Problems Book (Erickson).
The course content will consist of an introduction to the reactions and properties of the main types of organic functional groups. The understanding of organic reactions will be aided by the discussion of mechanistic features. All material covered will be examinable. The instructor will suggest practice questions from the text and students are encouraged to do as many others as possible. It is expected students will be familiar with material covered in the prerequisite CHEM 1300 course. The present 1320 course will cover the properties of the main families of organic compounds, their syntheses and reactions. 1. Covalent Bonds and Shapes of Molecules Although the main parts of this Chapter have been covered in CHEM 1300, the contents of this chapter are essential to this course. Students should review the chapter on their own if they are unfamiliar with its contents. 2. Alkanes and Cycloalkanes Structures, isomers, IUPAC naming, conformations, Newman projections. Cycloalkanes, cyclohexane, chair and boat conformations, axial and equatorial substituents. Cis and trans will respect to disubstituted cycloalkanes, properties of alkanes, bp, solubility. Reactions-oxidation; primary, secondary, tertiary types of carbons and hydrogens. Petroleum and oil refining. 3. Alkenes and Alkynes Structures, unsaturation, cis and trans isomers, E and Z designation, priority rules. Some examples of terpenes. Some comments on alkynes will also be included. 4. Reactions of Alkenes General characteristics of reactions, addition reactions of HX, H2, H2O, X2,. Electrophiles, carbocations, Markownikow orientation of products. Reaction with OsO4, reduction. Alkyne reactions Addition of H2, X2, HX. 5. Stereochemistry Types of isomers, stereoisomers, stereocentres, chirality, R, S, designation, Newman representations. Stereochemistry of disubstituted cycloalkanes. Comments on polarimetry, d and l designations, optical rotations. Comment on significance of chirality. 6. Acids and Bases Bronsted-Lowry and Lewis acids and bases. Qualitative and quantitative treatment of acid and base strengths. 7. Alcohols, Ethers, and Thiols Structures, naming, types, properties, solubility. Acidity of alcohols, reaction with metals, basicity of alcohols. Reactions with thionyl chlorides. Explanations of SN1 and SN2 type reactions. Dehydration to alkenes with introduction of E1 and E2, oxidation to aldehydes, ketones, and acids. Brief discussion of thiols. 8. Alkyl Halides Types, naming. Nucleophilic substitution. Examples and synthetic utility. More discussion of SN1 and SN2 rate expressions. Elimination, E1 and E2 types. 9. Benzene and its Derivatives Structure, representation, resonance, other aromatic systems, naming of some aromatic compounds. Examples of electrophilic aromatic substitution, halogen, NO2, SO3H, R, RCO, NO2 reduced to NH2. List of o, p and m directors, Phenols and reactions. 10. Amines Types, naming, classification, primary, secondary, tertiary. Basicity will not be covered, other than protonation to form ammonium salts. .11. Aldehydes and Ketones Structure, types, naming, polarity of C=O bond, addition of C, O nucleophiles. Acidity of alpha-hydrogens and tautomerism. Oxidation and reduction. 12. Carbohydrates Monosaccharides and their cyclic nature particularly glucose (ring structure) and simple glucosides. Fischer Projections. 13. Carboxylic acidsStructures, naming, properties, solubility, H bonding. Acidity, reduction, conversion to alkyl halides, esterification (no mechanism). Soap.14. Functional Derivitives of Carboxylic Acids Omit lactones and lactams. Types, structures, names. Nucleophilic substitution and interconversations, hydrolyses. Polyesters and polyamides. Laboratory Work: Laboratory Supervisor: Horace Luong

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CHEM 2210 (L) Introductory Organic Chemistry I: Structure and Function John Sorensen
Required Textbook(s): David Klein, Organic Chemistry, (John Wiley & Sons) CHEM 2210 Lab Manual (2011 Edition) I>Clicker Handset Recommended Supplements: David Klien , Organic Chemistry, Student Study Guide & Solutions Manual molecular model kit
General Outline: The course consists of an introduction to the structure, bonding and functional groups of organic molecules. An introduction to the use of spectroscopic tools to determine molecular structure will cover, 1H and 13C nuclear magnetic resonance spectroscopy, mass spectrometry infrared and visible/ultraviolet spectroscopy. This material will be followed by a discussion of stereochemistry, organic reaction mechanisms, and a number of common organic reaction types. 1. Structure and Bonding in Alkanes: a review of many aspects of bonding and structure of alkanes from the CHEM 1300 course and an introduction to nomenclature 2. Alkenes, Aromatic Hydrocarbons, and Alkynes: hybridization (sp2 and sp), sigma {} and pi {} bonding, molecular orbitals; resonance structures and aromatic stability; more on nomenclature 3. Functional Groups Containing Heteroatoms: compounds containing sp3, sp2, sp hybridized nitrogen; compounds containing sp3, sp2, sp hybridized oxygen; bond cleavage and formation; aldehydes, ketones, carboxylic acids, alkyl halides; nomenclature of functional groups 4. Spectroscopy: Determination of structure using spectroscopic methods. Emphasis will be placed on the use of 1H and 13 C NMR spectroscopy to determine the idenity of unknown organic molecules. 5. Stereochemistry: geometric isomerism of bonds in alkenes: rotation about and bonds; conformational analysis of ethane, butane, and cyclohexane; chirality, designation of absolute configuration; optical activity and purity via polarimetry 6. Understanding Organic Reactions: reaction profiles/energy diagrams: thermodynamic factors (enthalpy and entropy); characterization of transition states (Hammond postulate); reactive intermediates (carbocations; radicals; carbanions; carbenes; radical ions); kinetics; kinetic and thermodynamic control; chemical equilibria and acidity; reaction rates 7. Mechanisms of Organic Reactions: classification of organic reactions (addition; elimination; substitution; condensation; rearrangement; isomerization; oxidation - reduction); thermodynamics of bond making and breaking; mechanisms of selected reactions (SN2 and SN1 reactions; free-radical halogenation); review and competition between SN2 and SN1 pathways 8. Substitution by Nucleophiles at sp3-Hybridized Carbon: functional group interconversion via SN2 and SN1 reactions; preparation and use of carbon nucleophiles; synthetic methods involving functional group interconversion Laboratory Work: Laboratory Instructor: Horace Luong The laboratory is a mandatory component of the overall course, and a minimum grade of 60% is required to pass the lab. A passing grade in the laboratory is required to pass the overall course. The laboratory provides an introduction to the basic techniques and tools of experimental organic chemistry: measuring by weight and volume, common glassware and the use of ground-glass joints, handling solvents and reagents safely, heating and cooling, running reactions and isolating products by liquid-liquid extraction, purification by distillation or recrystallization. It also includes the determination of melting points, and the use of classical wet chemistry tests along with IR, NMR and MS to identify unknown organic materials. The experiments planned for Fall 2011: Experiment 1: Purification of an Unknown Organic Solid Experiment 2: Separation of Liquids Experiment 3: Spectroscopic Analysis of an Unknown Experiment 4: Gas Chromatography Experiment 5: Separation of Compounds by Extraction Experiment 6: Substitution Reactions Experiment 7: Synthesis of t-Butyl Chloride

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CHEM 2220 (L) Introductory Organic Chemistry II: Reactivity and Synthesis Phil Hultin
Required Textbook(s): (a) David Klein, Organic Chemistry, (John Wiley & Sons) (same book as for CHEM 2210), (b) CHEM 2220 Laboratory Manual (Winter 2012 Edition). Recommended Supplements: (a) David Klien , Organic Chemistry, Student Study Guide & Solutions Manual (b) William C. Groutas Organic Reaction Mechanisms: Selected Problems and Solutions. General Outline: CHEM 2220 presents the underlying principles of organic reactivity. The course provides a sound basis of both fact and principle in organic chemistry, and uses this to teach logical analysis and problem solving. 1. 2. Elimination Reactions: E1, E2 and E1cb mechanisms, competition between substitution and elimination, regioselectivity (Zaitsev vs. Hofmann), oxidation reactions that employ elimination mechanisms. Addition to Carbon-Carbon Multiple Bonds: hydration, hydrohalogenation and dihalogenation, Markovnikovs rule, conjugated dienes, rearrangements, oxymercuration-demercuration, addition of carbenes, epoxidation, hydroboration, oxidations, ozonolysis, Diels-Alder reaction, hydrogenation. Electrophilic Aromatic Substitution: aromaticity, mechanism (-complex, Wheland complex), halogenation, sulfonation, nitration, Friedel-Crafts alkylation and acylation, aromatic amines and diazotization, azo-coupling and Sandmeyer reaction, substituents effects (activating and deactivating substituents, single and multiple substituents), polycyclic aromatic compounds. Nucleophilic Addition and Substitution at Carbonyl Groups: general reactivity, complex metal hydride reduction, reactions with oxygen nucleophiles (hydrate formation, Cannizzaro reaction, formation of hemiacetals and hemiketals as well as acetals and ketals), reactions with nitrogen nucleophiles (amines, reductive amination, imines, enamines, hydrazones, oximes and semicarbazones), reactivity of carboxylic acids and acid derivatives (esters, acid chlorides, anhydrides, reactions with carbon nucleophiles (cyanides, Grignards, organolithium reagents), Wittig reaction. Substitution to Carbonyl Groups: Enolate Anions and Enols as Nucleophiles: general reactivity, formation and reactions (re-visiting pKa values), haloform reactions, Hell-Volhard-Zelinski reaction, kinetics and thermodynamics of enolate formation (kinetic vs. thermodynamic enolate), alkylation of esters, acids and ketones to C=O, aldol reaction, ,-unsaturated C=O groups (conjugate addition, 1,2 vs. 1,4 addition, Michael addition, Robinson annulation), Claisen condensation, Dieckmann condensation, alkylation of dicarbonyl compounds (malonate ester syntheses, Knoevenagel reaction). Skeletal Rearrangement Reactions: cationic rearrangements (Wagner-Meerwein rearrangement, Hofmann vs. Zaitsev product, Pinacol rearrangement, benzilic acid rearrangement), pericyclic rearrangements ([3,3]sigmatropic rearrangement - Cope rearrangement, [1,5]-sigmatropic hydrogen shift), Beckmann rearrangement, Hofmann rearrangement, Baeyer-Villiger rearrangement, Claisen rearrangement. Multistep Synthesis: grouping chemical reactions, retrosynthetic analysis, evaluating synthetic efficiency (linear vs. convergent synthesis), protecting groups, practical examples.

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Laboratory Work: Laboratory Instructor: Horace Luong The laboratory is a mandatory component of CHEM 2220, and a minimum grade of 60% is required to pass the lab. A passing grade in the laboratory is required to pass the overall course. The laboratory utilizes the laboratory techniques taught in CHEM 2210 to help synthesize and isolate organic compounds. The experiments primarily involve reactions covered in the lecture portion of the course.

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CHEM 2280 (L) Physical Chemistry: Microscopic Descriptions of Matter Carl Bartels
Textbook: Physical Chemistry, by Thomas Engel and Philip Reid (Pearson Education, 2010, 2nd edition).

In this course, our goal is to build a better understanding of macroscopic behavior of matter through an understanding of its microscopic properties. We follow the development of models for the description of matter: electrons as waveparticles, associated wave functions and use this knowledge to study simple idealized systems such as the effects of quantum confinement and molecular motion. The harmonic oscillator model is introduced, followed by a look at the various ways of storing energy in a molecule: rotation, vibration, electronic, etc. Models for atomic structure and the chemical bond are discussed as a way of understanding molecular properties such as bond lengths and bond strengths. Examples from the field of spectroscopy are used throughout the course to provide practical experience with the various quantum mechanical models. The lectures will follow the text but some topics are omitted and others are expanded on. Topics 1) Bridging the gap between microscopic properties and the macroscopic world 5-6 lectures Kinetic theory of gases, Equipartition of energy, Maxwell distribution of molecular speeds, Boltzmann distribution of energies 2) Introduction to quantum theory 4-5 lectures Failures of classical physics, Quantization, Wave-particle duality of light and matter, Schrdinger equation, operators, wavefunctions, Heisenbergs uncertainty principle 3) Quantum chemical models of motion Translation (Free particle, Particle in a box, Tunnelling) Vibration (Harmonic and anharmonic oscillator, IR/Raman spectroscopy) Rotation (Rigid rotor, microwave spectroscopy, rovibrational spectroscopy) 4) Electronic structure and spectra of atoms Hydrogen atom, Helium and multielectron atoms, atomic term symbols Atomic spectroscopy 5) Electronic structure and spectra of molecules Born Oppenheimer approximation, H2+ molecule, Molecular orbitals, Hybridization, Electronic spectroscopy 3-4 lectures 3-4 lectures 2-3 lectures 7-8 lectures 7-8 lectures

Laboratory Work: Laboratory Instructor: Carl Bartels The laboratory is a mandatory component of the overall course, and a minimum grade of 60% is required to pass the lab. A passing grade in the laboratory is required to pass the overall course.

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CHEM 2290 (L) Chemical Energetics and Dynamics: Macroscopic Descriptions Georg Schreckenbach
Textbook(s): Physical Chemistry, by Thomas Engel and Philip Reid (Pearson Education, 2010, 2nd edition).

Course Description General Outline: This course covers the fundamentals of chemical thermodynamics with applications to topics such as chemical potential, solution chemistry and phase diagrams, as well as an introduction to electrochemistry. The course consists of three components, (i) lecture, (ii) laboratory, and (iii) problem solving (covered by assignments and suggested problems.) Brief Course Outline: 1. Equations of state (Engel, chapters 1 and 7) - mathematical tools, definitions, ideal gases, van der Waals equation 2. Fundamental concepts of thermodynamics (Engel, chapters 2 to 6) - work, heat, internal energy, First Law of thermodynamics, heat capacity, enthalpy, entropy, Second Law, Third Law, Gibbs and Helmholtz energies, Maxwell relations 3. Phase equilibria (chapter 8) - phase boundaries, phase diagrams, Clapeyron equation, Clausius-Clapeyron equation 4. Chemical equilibira (chapter 6) - equilibrium constant, le Chateliers principle, vant Hoff equation 5. Solutions (chapters 9 and 10) - ideal and non-ideal solutions, Gibbs-Dunhem equation, Raoults Law, Henrys Law, colligative properties, solvent and solute activity 6. Electrochemistry (chapter 11) - electrochemical cells, Nernst equation, batteries (Chapter references refer to Engel and Reid, Physical Chemistry, 2nd edition.) Remark on Mathematical Tools: Physical Chemistry is, in general, the application of the principles of physics to chemistry. In order to describe the physics (and thus the physical chemistry) appropriately, a good command of the language and tools of mathematics is necessary! In this course, we will, specifically, make frequent use of (i) integrals, (ii) differentiation, and (iii) partial derivatives, as well as, to a lesser degree, of differential equations. These mathematical tools will be reviewed briefly in class. Reviews are also available in the textbooks. Laboratory Work: Laboratory Instructor: Carl Bartels The laboratory is a mandatory component of the overall course, and a minimum grade of 60% is required to pass the lab. A passing grade in the laboratory is required to pass the overall course.

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CHEM/MBIO 2360 (L) Biochemistry 1: Biomolecules and an Introduction to Metabolic Energy Sean McKenna, Brian Mark
Required Textbook(s): Lehningers Principles of Biochemistry, 4th Edition, by D. L. Nelson and M. M. Cox (Freeman) CHEM 2360 Lab Manual (2010 Edition) Recommended Supplements: none Course Description General Outline: An introductory course dealing with kinds of molecules encountered in biochemistry, and the concept of metabolic energy as a product of catabolism and a requirement for biosynthesis.
1. 2. Introduction: the molecules of biochemistry; review of bonding and polarity. Water and pH: structure of liquid water; hydrogen bonding; electrostatic and van der Waals interactions; the hydrophobic effect; detergents. Ionization of water; strong and weak acids and bases; ionization constants; calculation of pH, and understanding titration curves; Henderson-Hasselbalch equation; buffers. Amino Acids: structures of the 20 common amino acids found in proteins; properties and classification of the R-groups; stereochemistry; ionization properties, titration curves, and calculation of pH. Protein Structure: the peptide bond; amino acid sequence (primary structure); secondary structure and H-bonding: alpha-helix, beta-sheets and polyproline helix; disulfide bonds; tertiary structure and the hydrophobic effect; quaternary structure; folding and denaturation of proteins; prosthetic groups; methods of protein purification. Enzymes: catalysis; the enzyme-substrate complex; transition state theory; how enzymes lower the transition state; chiral specificity of enzymes; fundamentals of enzyme kinetics, and the Michaelis-Menten equation; inhibitors and their effects on kinetics; allosteric enzymes. Carbohydrates: structures of simple sugars: aldoses and ketoses; naming, stereochemistry, and Fischer structures; hemiacetal and acetal chemistry; cyclic forms of monosaccharides, Haworth structures, mutarotation and reducing sugars; sugar derivatives; glycosidic bonds; oligosaccharides; polysaccharides, including their physical properties. Nucleic Acids: purines and pyrimidines; structures and naming of nucleosides and nucleotides; the nucleic acids; DNA structure, including the double helix, Watson-Crick base pairs, denaturation; RNA and secondary structure; messenger, transfer and ribosomal RNA; mutations and oxidative damage to DNA. Lipids and Membranes: properties of lipids; fatty acids and fats derived from them; storage and membrane lipids; phospholipids; glycolipids, including sphingolipids and gangliosides; steroids and terpenoids; beta-carotene and vision; cholesterol and other steroids; composition of biomembranes; facilitated diffusion and active transport mechanisms. Bioenergetics: brief review of thermodynamic concepts; free energy as a means of understanding metabolism; standard free energy change and its measurement from equilibrium constants or cell potentials; redox reactions; biochemical electron carriers; ATP and its central role as storage form and source of free energy.

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10. Glucose metabolism: glucose oxidation by cells as a source of ATP; detailed description of glycolysis and the tricarboxylic acid cycle; fate of pyruvate under anaerobic conditions; the electron transport chain; mechanism of oxidative phosphorylation; calculations of ATP yield.

Laboratory Work: Supervisor: TBD There is a weekly three-hour laboratory session in which some of the basic analytical methods of biochemistry are used together with methods for separating and purifying biomolecules. The following is a list of specific experiments. 1. Identification of an unknown amino acid by pH titration and paper chromatography; the Ninhydrin reaction. 2. Analytical spectrophotometry of phenol red and the biuret assay for protein measurement. 3. Properties and kinetics of enzymes. 4. Identification of an unknown carbohydrate; paper chromatography and chemical analysis. 5. Isolation of salmon sperm DNA and measurement of viscosity changes; heat denaturation. Formal lab reports are required. The laboratory work is worth 15% of the course grade; also, part of the final examination covers the laboratory material.

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CHEM/MBIO 2370 (L) Biochemistry 2: Catabolism, Synthesis, and Information Pathways Peter Loewen
Textbook: Lehningers Principles of Biochemistry, 4th Edition, by D. L. Nelson and M. M. Cox (Freeman) CHEM/MBIO 2370 Lab Manual (2009 Edition) Recommended Supplements: none
General Outline: An introductory course dealing with the basic metabolic processes that occur in living cells, including the production and use of metabolic energy, the breakdown and synthesis of biomolecules; the synthesis of DNA, RNA and proteins; and the regulation of these processes. GLYCOLYSIS AND PENTOSE PHOSPHATE PATHWAYS: Detailed description of pathways. Alcoholic fermentation. PPP as an alternate pathway for glucose oxidation. TRICARBOXYLIC ACID CYCLE: Detailed description of pyruvate dehydrogenase and the production of acetyl-S-CoA. Details of cycle, including structures and enzymes. ELECTRON TRANSPORT AND OXIDATIVE PHOSPHORYLATION: Description of the intermediates and structure with an emphasis on electron flow and energy release. ATP synthesis. Chemiosmotic mechanism. BALANCING REACTIONS AND REGULATION: Anaplerotic or balancing reactions. Regulation of glycolysis and TCA cycle. FATTY ACID OXIDATION: Role of lipases and phospholipases. Transport and the carnitine cycle. Beta-oxidation of saturated, straight chain, even #C atoms. Fate of propionyl-S-CoA derived from odd #C atoms. AMINO ACID OXIDATION AND UREA PRODUCTION: Transamination, significance and mechanism. Oxidative deamination. Production of gln and its use as N-transporter in mammalian blood. Urea cycle. Amino acid degradation including asp, ala, glu and gln. Three examples of degradation pathways: thr/gly/ser, tyr/phe and val. CARBOHYDRATE SYNTHESIS: Overall reactions of photosynthesis. Light reactions and generation of ATP and NADPH. Dark reactions in both C-3 and C-4 plants. Gluconeogenesis. Life on acetate (glyoxylate cycle). Glycogen synthesis and regulation. LIPID SYNTHESIS: Fatty acid synthesis of palmitic acid. Introduction of unsaturation. Triacylglycerol and membrane phospholipid synthesis. Cholesterol metabolism. N-FIXATION, AMINO ACID AND NUCLEOTIDE SYNTHESIS: N-cycle and N-fixation. N-assimilation involving glu and gln. Three examples of amino acid synthesis: ser/gly, val, asp/thr/ile. Purine nucleotide synthesis by the de novo and salvage pathways. Pyrimidine nucleotide synthesis. Nucleotide kinases, pyrophosphorylases, CTP synthesis. Deoxynucleotide synthesis including dTMP. NUCLEIC ACID METABOLISM: DNA replication including the semi-conservative model and enzymology. Transcription and RNA polymerase C. PROTEIN SYNTHESIS: Mechanism of translation including initiation, elongation, termination. Genetic code and the Wobble Hypothesis. REGULATION: Control of enzyme activity including branched pathways. Control in catabolic operons using the lac operon as an example. Control in biosynthetic operons including the trp operon. Final overview and summary. Laboratory Work: Laboratory Supervisor: TBA There is a weekly three-hour laboratory session in which methods for separating and purifying biomolecules are used together with some of the basic analytical methods of biochemistry. The following is a list of specific experiments. 1. Isoenzyme separation by electrophoresis using the enzyme activity as the basis of a stain. 2. Plant pigment isolation and separation by adsorption chromatography and paper chromatography. The purity of bands seen in the latter is assessed by extracting bands and doing visible spectra. 3. Separation of lysozyme from egg white using gel chromatography and ion exchange chromatography. Collected fractions are assayed for both protein and enzyme activity. 4. Isolation and assay of DNA, RNA and protein from liver. 5. Glucose tolerance test. Formal lab reports are required. The laboratory work is worth 15% of the course grade; also, part of the final examination covers the laboratory work.

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CHEM 2400 (L) Inorganic Chemistry: Structure and Applications Scott Kroeker
Required Textbook(s): Inorganic Chemistry, Shriver & Atkins, W.H. Freeman and Company, New York (2010), 5th Edition CHEM 2400 Online Laboratory Manual (2011 Edition)

Course Description General Outline: This is a foundational course in inorganic chemistry which covers key structural aspects of inorganic compounds and their applications. It provides models and concepts required for understanding connections between structure and properties in a wide variety of inorganic systems.
1.

Overview of the Periodic Table: Trends and characteristics of the periodic table, with examples of specific compounds and applications. Coordination Chemistry: Introduction to coordination chemistry, including naming and drawing complexes, typical ligands, coordination numbers, geometry and isomerism. Crystal-field theory of idealized geometries will be presented, along with examples drawn from biochemistry and materials science. Oxidation and Reduction: Balancing redox reactions, standard reduction potentials, electrochemical series and the Nernst equation. Latimer and Frost diagrams are presented as convenient ways to represent potentials. Theories of Chemical Bonding: Brief review of Lewis structures, the VSEPR model for the prediction of molecular geometries, the octet rule and its limitations. Valence bond theory is presented to introduce valuable concepts in molecular bonding. Molecular orbital theory and electron spectroscopy provide theoretical and experimental approaches to understanding orbital energy levels. The Structures of Solids: Unit cells and crystal systems, fractional atomic coordinates and determination of composition. Structures of metals, including close packing of spheres (cubic close-packed and hexagonal close-packed structures) and non-close-packed structures, including hole-filling in close-packed structures. Ionic structures rationalized within the ionic model, energetics of ionic bonding, lattice enthalpies, BornHaber cycle and Born-Mayer calculations, defects and non-stoichiometry. The use of diffraction-based methods to determine structures is introduced. Applications and Uses of Inorganic Compounds: Selected examples of applications of inorganic compounds from across the periodic table.

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Laboratory Component: This course has a compulsory laboratory component consisting of weekly three-hour laboratory experiments. Experiments include the preparation of compounds such as barium peroxide, zeolite A, tellurium dioxide and potassium nitrososulfonate, and their characterization by methods including x-ray diffraction and chemical techniques.

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CHEM 2470 (L) Introductory Analytical Chemistry Elena Smirnova

Textbook: Fundamentals of Analytical Chemistry, Eighth edition by Douglas A. Skoog, Donald M. West, F. James Holler; Stanley R. Crouch. A number of supplemental text books are listed in the laboratory manual.
The objectives of introductory analytical chemistry: 1. Teaching the principles and methods of practical analytical chemistry; 2. Teaching self-discipline and good technique in laboratory work. The material covered in the course intends to prepare a chemist, who: a) understands the theory and principles of analysis, which can be applied or modified (if necessary) to solve a particular problem, and b) is able to interpret the results of quantitative analysis and develop completely new methods thereof.. Introduction. The scope of quantitative chemical analysis. Steps in a chemical analysis. Sampling, standardization, calibration. Treatment of analytical data. Errors in chemical analysis. Systematic errors. Random errors. Reliability of results. Statistical aids to hypothesis testing: Q-test, G-test t-test, F-test. Equilibrium and activity. Types of equilibria encountered in analytical chemistry (overview). The Debye-Huckel equation. Activity and activity coefficients. Thermodynamic, concentration and conditional equilibrium constants. The rule of electroneutrality. Mass-balance equation. Chemical Equilibria in Homogeneous Solutions Acid-Base Equilibria. Aqueous solutions and chemical equilibria. Acid-Base equilibria in aqueous and nonaqueous solvents. Calculations of pH of strong and weak acids and bases, ampholites and buffers. Concentration calculations of species present at a given pH. Principles of neutralization titration.Titration curves. Acid-base indicators. Volumetric analysis: application of neutralization titration. Reagents for neutralization titration. Standardization of acids (bases). Determination of inorganic and organic substances. Complexation Equilibria. Calculations of complexation equilibria. Addition of one or more ligands. Calculations in pHdependent equilibria. Organic complexing reagents. EDTA. Other chelating reagents. Aminocarboxylic acid titration. EDTA titration curves. Metal ion indicators. Analytical applications of complex formation. Titration methods employing EDTA. Determination of calcium or /and magnesium. Hardness of water. Oxidation-Reduction Equilibria. Electrical potential. Electromotive force of a cell. Electrode potential. Electrochemical (galvanic) and electrolysis cells. Nernst equation. Standard and formal potentials. Equilibrium constants of cell reactions. Effect of complex formation on electrode potential. Dependence of potential on pH. Construction redox titration curves. Theoretical properties of redox titration curves. Theory of redox indicators. Oxidation-reduction methods using potassium permanganate and iodine. Chemical Equilibria in Heterogeneous Solutions Solid-Liquid Equilibria. Theory of solid- liquid equilibria. Solubility and solubility product. Factor affecting the formation of precipitates. Factors affecting the solubility of precipitates: common-ion effect, complex formation with excess of precipitant, effect of hydrogen ion. Experimental studies of precipitate formation. The growth of precipitate particles. Conditions of analytical precipitation. Colloidal properties of precipitates. Aging of precipitates. Contamination of precipitates. Precipitation titration. Gravimetric analysis. Determination of chlorine as chloride. Determination of sulfur as barium sulfate. Determination of nickel with dimethylglyoxime. LABORATORY: Five experiments will be performed by the students in the laboratory: four assigned by the instructor and one chosen by a student. All twelve experiments given in the laboratory manual are divided into two sets. The students will do either set I or set II. The choice is established by drawing the corresponding set during the first day of laboratory.

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CHEM 2550 (L)/ENVR 2550 (L) Environmental Chemistry Feiyue Wang

Textbook(s): VanLoon, G.W. and S.J. Duffy. 2005. Environmental Chemistry: A Global Perspective. Second Edition. Oxford University Press, Oxford, UK Recommended Supplements: Handouts, lecture slides Learning Outcomes / Key Objectives This course examines the chemistry of the environment, emphasizing on the composition of the natural environment and the processes of natural and anthropogenic chemicals in the environment. The purpose is to provide students with the chemical basis for understanding the environment and environmental problems. Learning outcomes from the lecture session: 1. 2. 3. 4. Atmospheric Chemistry: Temperature, pressure, radiation, and chemical profiles of the atmosphere; major types of chemical processes in the atmosphere; chemistry of ozone depletion, smog, acid rain, and climate change; aerosols in the atmosphere. Aquatic Chemistry: Composition and speciation of chemicals in the aquatic environment; major types of chemical processes in the aquatic environment; pC-pe diagram; organic matter, metals, organic contaminants in the aquatic environment; water pollution and waste water treatment plants. Terrestrial Chemistry: Soil formation; biological processes in the terrestrial environment; nutrients, pesticides, and solid wastes in the terrestrial environment. Global Biogeochemical Cycles: Introduction to global biogeochemical cycles of elements.

Learning outcomes from the Laboratory session: 1. 2. 3. 4. Classical chemical analytical techniques: gravimetry; titrimetry; chemical equilibrium calculations; Introductory UV-visible spectroscopy Basic field sampling skills Consolidate topics covered in the lectures

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CHEM 2560 (L) Water Quality Analysis Shaune McFarlane

Textbook: Chemistry for Environmental Engineering and Science by Clair Sawyer, Perry McCartny and Gene Parkin, fifth edition (McGraw-Hill Higher Education) Optional textbooks: Chemistry, a Molecular Approach by Nivaldo Tro (Pearson). A Survival Kit for Stoichiometry by E.Smirnova and N. Hunter (U of M)

The objectives of the course: The course introduces a number of basic concepts in various branches of Chemistry (General, Physical, Organic, Biological, Colloid, Analytical, and Electrochemistry) to the Civil Engineering students. The course offers basic education in the Science of Chemistry, which helps to solve environmental problems, such as those that pertain to water analysis. (This course is currently being redesigned, and the list of topics below is preliminary). Basic Concepts from General Chemistry. Review (Chemical equations. Valency, oxidation state, and bonding. Oxidation-Reduction Equations . Nomenclature. Stoichiometry). The Gas Laws. Solutions. Activity and activity coefficients. Variations of the equilibrium relationship. Basic concepts of acid-base, complex formation, oxidation-reduction and solubility equilibria. Basic concepts from Physical Chemistry. Thermodynamics. Kinetics. Membrane processes. Osmosis and dialysis. Principles of solvent extraction. Basic concepts from Organic Chemistry. Features and properties of different classes of organic compounds from the viewpoint of their importance for the environment. Basic concepts from Colloidal Chemistry. Adsorption and adsorption isotherms. Colloidal dispersion in liquids and air. Basic concepts from Statistical Analysis. Definitions. Distribution of Experimental data. Errors. Hypothesis testing. Detection limits. Quality assurance and Quality control. Basic concepts from Analytical Chemistry. Principles of classical and selected instrumental methods. Standard solutions preparation. Theory and application of acidity, alkalinity, hardness of water. Theory of measurement and interpretation of pH. Water and wastewater analysis. Dissolved oxygen. Biochemical Oxygen demand. Chemical Oxygen demand. Determination of solids. Residual chlorine and chlorine demand. Laboratories: Weekly 2-hour laboratories provide essential training in basic laboratory techniques as well as some classical and instrumental analysis of environmental objects. These skills are transferrable to other areas of environmental science.

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CHEM/MBIO 2770 (L) Elements of Biochemistry I TBA

Required Textbook(s): H. R. Horton et al., Principles of Biochemistry, 4thEd. (Pearson) CHEM/MBIO 2770 Laboratory Manual (2009 Edition) Recommended Supplements: Hiram F. Gilbert, Basic Concepts in Biochemistry: A Student's Survival Guide, 2nd Ed. (McGraw-Hill) General Outline: Basic concepts of biochemistry including the properties of biomolecules (amino acids and proteins, enzymes, carbohydrates, lipids, and nucleic acids) and aspects of biomolecule metabolism in cells. For students in Agricultural and Food Sciences, Human Ecology, and Botany, Ecology or Zoology programs in Science.
1. INTRODUCTION AND TYPES OF BIOLOGICAL MOLECULES Students should read the first textbook chapter as a review of material covered in first-year courses in chemistry and biology. Topics include: entropy, enthalpy, free energy, and equilibrium constants. WATER -- ITS EFFECT ON BIOMOLECULES Buffers. Ionization of H2O, pH, weak and strong acids and bases. Titration curves and pKa values. Calculations of pH. Use of Henderson-Hasselbalch Equation in calculations and making buffer solutions. Carbonic acid/bicarbonate buffer in blood. AMINO ACIDS Structure and classification according to R group. Selected chemical properties. Stereochemistry, chirality, D- and L-forms, biological importance of chirality. Ionic properties and titration curves. Isoelectric pH (pI). PEPTIDES & PROTEINS Introduction to peptide & protein structure. Working with proteins. Covalent (Primary) Structure -- sequence determination. Three-dimensional structure. The peptide bond; secondary structure and the forces maintaining; alpha-helix and beta-sheet. Tertiary & quaternary structures; globular and fibrous proteins. Denaturation. ENZYMES General properties and classification. Enzymes as catalysts -- the active or catalytic site, activation energy and reaction rates. Enzyme kinetics: reaction rates, effects of enzyme concentration, pH, temperature, and substrate concentration. Michaelis-Menten equation, significance of Km and Vmax. Lineweaver-Burk (reciprocal) plots. Enzyme specificity. How enzymes increase reaction rates: proximity and orientation effects, bond-stress, catalytic. R-groups and role of metal ions. Enzyme inhibition: competitive and non-competitive inhibition. Irreversible inhibition. Enzyme regulation: allosteric effects, feed-back inhibitors, activators. Sigmoidal kinetics. Regulation via covalent modification. CARBOHYDRATES Monosaccharides: Aldose and ketose nomenclature, stereochemistry, D- and L-classification, enantiomers and epimers. Intramolecular hemiacetal and hemiketal formations. Anomers. Mutarotation. Sugar derivatives, glycosides. Disaccharides: maltose, isomaltose, lactose, sucrose. Reducing and non-reducing sugars. Polysaccharides: Starch, glycogen, chitin and cellulose. LIPIDS AND MEMBRANES Classification of lipids. Structure & properties of fatty acids. Structure & properties of triacylglycerols (fats and oils), waxes. Membrane lipids: glycerophospholipids, sphingolipids. Sterols and steroids, e.g. Cholesterol. Amphipathic nature of membrane lipids. Composition of membranes, the Fluid-Mosaic model, bilayers, integral and peripheral proteins, control of membrane fluidity through changes in fatty acid composition. Selected functions of membranes. Transport. NUCLEOTIDES and NUCLEIC ACIDS Purines and pyrimidines. Nucleosides, nucleotides. Ribo- and deoxyribonucleotides. Polynucleotides and nucleic acids. RNA and DNA. Structure of DNA: Chargaffs rules, base pairing, the right-handed double-helical DNA and the forces stabilizing it. Some properties of DNA. BIOENERGETICS Spontaneous and non-spontaneous processes. Endergonic and exergonic processes. Standard free energy changes and equilibrium constants. Oxidation-reduction reactions and reduction potential. Biological electron carriers. ATP structure and properties as a "high-energy" phosphate. Low-energy phosphates. Free energies of hydrolysis as measure of phosphate transfer potentials. Use of ATP in driving unfavorable reactions.

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10. DNA METABOLISM Replication, Meselson-Stahl experiment, molecular mechanism. 11. RNA METABOLISM RNA Polymerase, promoters, RNA processing, RNA replicase, reverse transcriptase 12. PROTEIN METABOLISM Introduction to the problem, coding, bilingual tRNA, genetic code, mechanism of translation initiation, elongation, termination, post-translational modification.

Laboratory Work: Supervisor: TBA There is a weekly three-hour laboratory session in which some of the basic analytical methods of biochemistry are used together with methods for separating and purifying biomolecules. The following is a list of specific experiments. 1. Identification of an unknown amino acid by pH titration and paper chromatography; the Ninhydrin reaction. 2. Analytical spectrophotometry of phenol red and the biuret assay for protein measurement. 3. Properties and kinetics of enzymes. 4. Identification of an unknown carbohydrate; paper chromatography and chemical analysis. 5. Isolation of salmon sperm DNA and measurement of viscosity changes; heat denaturation. Formal lab reports are required. The laboratory work is worth 15% of the course grade; also, part of the final examination covers the laboratory material.

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CHEM/MBIO 2780 (L) Elements of Biochemistry II TBA

Required Textbook(s): R.H. Garrett & C.M. Grisham, Biochemistry, 3rd Ed. (Thomson Brooks/Cole) CHEM/MBIO 2780 Laboratory Manual (2009 Edition) 1. Pentose Phosphate Pathway (PPP): Uses in fat & steroid synthesis, cell protection, photosynthesis. 2. Anaplerotic Mechanisms. 3. Gluconeogenesis: Synthesis of sugars from non-sugar sources: lactate, amino acids, glycerol, fatty acids (only in plants & microorganismsthe Glyoxylate Cycle) 4. Glycogen Metabolism: Breakdown for energy, synthesis & regulation. Role of epinephrine. 5. Photosynthesis: Light & Dark Stages. Excitation of electrons, electron carriers, Calvin Cycle. 6. Fatty Acid Metabolism: 1) Degradation: Saturated & unsaturated, -oxidation, Krebs Cycles, ATP yields. Odd Number of Carbons: Role of vitamin B12. Ketone Bodies. 2) Synthesis. 3) Synthesis of Triacyl Glycerols. 7. Steroids & Terpenes: 1) Biosynthesis of Cholesterol. All 32 reactions revealed. Regulation & drug control of cholesterol levels. Lipoproteins. 2) Bile acids, Sex hormones, Anabolic Steroids in Sports. 3) UV-Induced Vitamin D Synthesis. 4) Terpenoids: Overview of molecules in plant & animal kingdoms. 8. Inorganic N Metabolism: Nitrogen Fixation, Haber-Bosch process. N-Fixing microorganisms. Nitrification, nitrate respiration, denitrification. Nitrogen assimilation. Amino Acid (AA) Metabolism 1. Focus on the Amino Group: Transamination, vitamin B6. Deamination, oxidative & non-oxidative. 2. Focus on the C-Skeleton: 1) Synthesis: Source of Carbon: PPP, glycolytic pathway, Krebs & Glyoxylate cycle. Illustrations from the 6 families; essential & non-essential AAs. Monsanto's glyphosate herbicide. Serine/Glycine Family: Folic acid vitamin & 1-C atom metabolism. Integration of AA metabolism. 2) Uses of AAs as Synthetic Precursors: Lipids (bile acids). Vitamins (niacin, folate). Hormones (epinephrine, thyroxine). Neurotransmitters (serotonin). Heme. 3) Degradation: Phenylalanine, tyrosine. Phenylketonuria. 4) Urea Cycle. Nucleic Acid Metabolism 1. Purine & Pyrimidine Nucleotide Synthesis 2. DNA Replication 3. Genetic Code 4. DNA Transcription 5. Protein Synthesis
Laboratory Work: Laboratory Supervisor: TBA There is a weekly three-hour laboratory session in which methods for separating and purifying biomolecules are used together with some of the basic analytical methods of biochemistry. The following is a list of specific experiments. 1. Isoenzyme separation by electrophoresis using the enzyme activity as the basis of a stain. 2. Plant pigment isolation and separation by adsorption chromatography and paper chromatography. The purity of bands seen in the latter is assessed by extracting bands and doing visible spectra. 3. Separation of lysozyme from egg white using gel chromatography and ion exchange chromatography. Collected fractions are assayed for both protein and enzyme activity. 4. Isolation and assay of DNA, RNA and protein from liver. 5. Glucose tolerance test. Formal lab reports are required. The laboratory work is worth 15% of the course grade; also, part of the final examination covers the laboratory work.

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CHEM 2860 (L) Chemistry of Biomolecules Sean McKenna, Brian Mark

Required Textbook(s): Lehningers Principles of Biochemistry, 4th Edition, by D. L. Nelson and M. M. Cox (Freeman) CHEM/MBIO 2360 Lab Manual (2008 Edition) Recommended Supplements: none Course Description General Outline: The chemistry of molecules encountered in biochemistry, including their structures, reactions and physical properties. The concept of metabolic energy in biochemistry. This course is available only to students registered in the Chemistry Honours or Four Year Major program.
1. 2. Introduction: the molecules of biochemistry; review of bonding and polarity. Water and pH: structure of liquid water; hydrogen bonding; electrostatic and van der Waals interactions; the hydrophobic effect; detergents. Ionization of water; strong and weak acids and bases; ionization constants; calculation of pH, and understanding titration curves; Henderson-Hasselbalch equation; buffers. Amino Acids: structures of the 20 common amino acids found in proteins; properties and classification of the R-groups; stereochemistry; ionization properties, titration curves, and calculation of pH. Protein Structure: the peptide bond; amino acid sequence (primary structure); secondary structure and H-bonding: alpha-helix, beta-sheets and polyproline helix; disulfide bonds; tertiary structure and the hydrophobic effect; quaternary structure; folding and denaturation of proteins; prosthetic groups; methods of protein purification. Enzymes: catalysis; the enzyme-substrate complex; transition state theory; how enzymes lower the transition state; chiral specificity of enzymes; fundamentals of enzyme kinetics, and the Michaelis-Menten equation; inhibitors and their effects on kinetics; allosteric enzymes. Carbohydrates: structures of simple sugars: aldoses and ketoses; naming, stereochemistry, and Fischer structures; hemiacetal and acetal chemistry; cyclic forms of monosaccharides, Haworth structures, mutarotation and reducing sugars; sugar derivatives; glycosidic bonds; oligosaccharides; polysaccharides, including their physical properties. Nucleic Acids: purines and pyrimidines; structures and naming of nucleosides and nucleotides; the nucleic acids; DNA structure, including the double helix, Watson-Crick base pairs, denaturation; RNA and secondary structure; messenger, transfer and ribosomal RNA; mutations and oxidative damage to DNA. Lipids and Membranes: properties of lipids; fatty acids and fats derived from them; storage and membrane lipids; phospholipids; glycolipids, including sphingolipids and gangliosides; steroids and terpenoids; beta-carotene and vision; cholesterol and other steroids; composition of biomembranes; facilitated diffusion and active transport mechanisms. Bioenergetics: brief review of thermodynamic concepts; free energy as a means of understanding metabolism; standard free energy change and its measurement from equilibrium constants or cell potentials; redox reactions; biochemical electron carriers; ATP and its central role as storage form and source of free energy.

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10. Glucose metabolism: glucose oxidation by cells as a source of ATP; detailed description of glycolysis and the tricarboxylic acid cycle; fate of pyruvate under anaerobic conditions; the electron transport chain; mechanism of oxidative phosphorylation; calculations of ATP yield.

Laboratory Work: Laboratory Supervisor: TBA There is a weekly laboratory (3-hour session), in which basic analytical methods used in biochemistry, and methods for separating and purifying biomolecules, are demonstrated. Formal lab reports are required. The laboratory work is worth 15% of the course grade; also, part of the final examination covers the laboratory work. NOTE: The lectures and laboratories in this course are taken together with course CHEM 2360, but there will be an extra assignment to reflect the requirements of the Chemistry programs. Students are asked to contact Dr. Duckworth during the first full week of term to arrange the details of the assignment.

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CHEM 3360 (L) Elementary Quantum Chemistry and Molecular Bonding John Cullen
Textbook(s): Ira N. Levine, Quantum Chemistry, 5th ed., Prentice Hall, 2000 Recommended Supplements: C. J. Cramer, Essentials of Computational Chemistry: Theories and Models, 2nd ed., Wiley (particularly useful for the computational chemistry parts of the course; available in the library) General Outline: This course covers the fundamentals of quantum chemistry, starting from the postulates of quantum mechanics. We will discuss various systems including the particle in a box, harmonic oscillator and hydrogen atom. A second, complementary topic (mostly covered in the lab portion of the course) is an introduction to modern computational chemistry. Scope: We take a quantum-chemistry approach (as opposed to a more general quantum-mechanics approach). This means that, while we will introduce the fundamentals of quantum mechanics, we will do so in a limited fashion, with a focus on systems that are relevant to chemistry. Lecture outline: Subject Weeks (Approx.) a 1 Historical Background of Quantum Mechanics: 0.5 2 Review of Classical Mechanics 1 3 Postulates of Quantum Mechanics 1.5 4 Simple One-Dimensional Systems 2.5 5 Formalism of Quantum Mechanics (Introduction) 1 6 Three-Dimensional Systems 0.5 7 Hydrogen Atom 1.5 8 Harmonic Oscillator 1 9 Many-particle systems 0.5 10 Computational Chemistry (Introduction)b 2 Molecular Hamiltonian; Born-Oppenheimer approximation Hartree-Fock (HF) and correlated methods (introduction) Variational principle, basis sets Density functional theory (DFT) Property calculation 11 Angular Momentum 1; time permitting (a) Please note that these are approximate times only. (b) This section is really only an introduction, and most subjects will barely be touched. Remark on Mathematical Tools: Physical Chemistry is, in general, the application of the principles of physics to chemistry. In order to describe the physics (and thus the physical chemistry) appropriately, a good command of the language and tools of mathematics is necessary! As in all parts of physical chemistry, we make frequent use of these tools provided by mathematics. In particular, quantum mechanics relies heavily on the calculus of differential equations. Other mathematical tools include partial differentiation, vector algebra and integration. Laboratory Work: Laboratory Instructor: James Xidos The laboratory is a mandatory component of CHEM 3360, and a minimum grade of 60% is required to pass the lab. A passing grade in the laboratory is required to pass the overall course. Three-hour laboratory sessions are held throughout the term. The laboratory is a practical introduction to computational chemistry. Students will learn how to set up, run, and analyze the results of quantum mechanics calculations using Gaussian on Linux computers. Topics covered include molecular input using Z-matrix, wave functions, basis sets, SCF and geometry optimization procedures, thermodynamic properties, vibrational frequencies, potential energy surfaces, visualization of electronic structure, spectroscopic properties, solvent effects, and the accuracy and reliability of results. All laboratory exercises will require a formal lab report. Students will be required to prepare and deliver one short presentation during the last laboratory session.

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CHEM 3370 (L) Symmetry, Spectroscopy and Structure Kathy Gough

Textbook: Molecular Symmetry and Group theory, by Robert L. Carter (John Wiley and Sons, 1998) paperback Modern Spectroscopy, by J. Michael Hollas 4th edition (John Wiley and Sons, 2004) paperback Lab text: Experiments in Physical Chemistry, by Shoemaker, Garland and Seinfeld. No purchase necessary, copies available in laboratory and on reserve Topics include: Group theory, crystal and ligand field theories, rotational, vibrational (IR, Near IR, Raman) and electronic spectroscopies (atomic and molecular, both excitation and relaxation, as well as several photoelectron techniques). In this course, we examine the relationships between molecular structure and the various means we have for probing and exploiting properties of matter to learn more about energetics and structure of individual molecules and systems. The theoretical models used to describe energy states and the transitions between them will be studied more formally and in much greater depth than in Chem 2280 (formerly 002.228). Where symmetry exists, certain well-defined relationships must also exist. Students learn the basics of group theory and how to apply it in many situations, including the determination of symmetry adapted orbitals and the rules that necessarily apply in each of the atomic and molecular spectroscopies. It is equally important to recognize that most molecules have little if any degree of symmetry. Both labs and lectures will address this reality. Current applications of spectroscopy to realworld problems will be made an integral part of the course. Laboratory Work: Laboratory Instructor: Carl Bartels The laboratory is a mandatory component of the overall course, and a minimum grade of 60% is required to pass the lab. A passing grade in the laboratory is required to pass the overall course.

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CHEM 3400 (L) Inorganic Chemistry: Transition Metals Mario Bieringer

Textbook(s): Shriver and Atkins, Inorganic Chemistry, 5th Ed. (W.H. Freeman and Co.: 2010) CHEM 3400 Laboratory Manual (current edition supplied online via Aurora)

General Overview: This course is intended to serve as an introduction to inorganic chemistry, with an emphasis on transition metals. Students will be exposed to basic concepts in coordination chemistry such as naming, structure, symmetry, bonding, electronic structure and properties, spectroscopy, and reaction mechanisms. Recent topics from the literature include applications in materials science and bioinorganic chemistry. 1. Structure and Symmetry: coordination numbers; nomenclature; ligands (bridging, multidentate, linkage isomerism); isomerism (constitutional, stereoisomers); 18-electron rule; symmetry elements and point groups; chirality (preparation and separation) 2. Ligand-Field Theory: crystal-field theory (octahedral, tetrahedral, square planar); symmetry labels; spectrochemical series; ligand-field stablization energy; high/low spin; magnetic measurements; tetragonal distortion; Jahn-Teller effect; symmetry-adapted linear combination of molecular orbitals; sigma- and pi-bonding; character tables 3. Electronic Spectroscopy: Russell-Saunders coupling; Hunds rules; molecular term symbols; correlation diagrams; Tanabe-Sugano diagrams; nephelauxetic parameter; charge-transfer bands; selection rules 4. Reactions and Mechanisms: stepwise formation constants; chelate effect; water exchange rates; ligand substitution mechanisms (association, dissociation, interchange); nucleophilicity; trans-effect; steric effects; ligand-field activation energy; volume of activation; linear free-energy relations; cone angle; electron transfer mechanisms (outer sphere, inner sphere); Marcus cross-relation Laboratory Component: The laboratory is an essential part of this course and must be satisfactorily completed to obtain credit. All compounds will be characterized by modern analytical methods which will provide insights into the characteristics of those molecular and extended structures and their respective electronic behavior. 1. Ligand-field transitions in K3[Cr(C2O4)3]3H2O 2. Synthesis and measurement of paramagnetic susceptibility by 1H NMR of tris(acetylacetonato)manganese(III) 3. Synthesis and characterization of Co-complexes 4. Preparation and characterization of a ferrofluid 5. Synthesis and evaluation of a high temperature superconductor 6. Preparation of a Cr-(II) complex under inert conditions 7. Preparation and equilibria of nickel(II) ethylenediamine complexes

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CHEM 3390 (L) Structural Transformations in Organic Chemistry Phil Hultin

Textbook(s): Structure and Selectivity: An Introduction to Selective Organic Transformations, P.G. Hultin (CDROM) Recommended Supplements: reserve reading in the Science library includes: Electron Flow in Organic Chemistry (P. Scudder); Advanced Organic Chemistry (A and B) (Carey and Sundberg); Spectrometric Identification of Organic Compounds (Silverstein et al.). Course Description Organic reactions must be selective to be useful that is, the chemist must be able to rely on a given set of reagents and reaction conditions to provide a readily predictable product when applied to a range of organic substrates. CHEM 3390 takes the fundamental concepts introduced in earlier courses and shows how they provide the foundation for a sophisticated understanding of selective organic transformations. The course reviews and elaborates on the concepts of stereochemistry and conformation first encountered in CHEM 2210, along with some elements of thermodynamics and kinetics. 1. General physical concepts: reaction thermodynamics; simple transition state theory; activation barriers; kinetic and thermodynamic control of reaction outcomes; bond formation; qualitative valence bond and MO models; acidity and basicity and their relationship to ion stability; reaction coordinates and reaction intermediates; arrow-pushing mechanisms their use and misuse; connecting simple models to more fundamental ideas. Stereochemistry: stereoisomerism defined; chirality; enantiomers; the CIP priority rules and stereochemical nomenclature; diastereomers; meso compounds; heterotopicity. Conformational analysis: torsional barriers; van der Waals contacts; dipolar effects; acyclic compounds; simple cyclic systems; the A-value for substituents; multiple substituents; effects of heteroatoms; the anomeric effect; conformational locking and biasing; alkenes and carbonyl compounds.

2. 3.

A relatively small repertoire of reaction types is then studied in depth, to illustrate how an understanding of reaction mechanism can be used to predict reaction outcomes. The laboratory illustrates reactions from the lectures, and introduces new but related processes. 1. Electrophile-promoted addition to alkenes: acid-catalyzed addition of halides, water, alcohols, carboxylic acids; discrete carbonium ions and bridged cationic intermediates; Wagner-Meerwein rearrangements; additions via mercuration/reduction and the use of organomercury intermediates as sources of carboncentred radicals; stereoelectronic influences on the opening of bridged ion intermediates; hydroboration/oxidation and the origins of anti-Markovnikov selectivity; diastereofacial preferences. Oxidative additions to alkenes: addition of elemental halogens; preparation of halohydrins and their conversion to epoxides; halolactonization and related reactions; epoxidation by peracid reagents; osmylation; the Prvost and Woodward-Prvost reactions and the role of anchimeric effects. Oxidation of oxygen functional groups: chromium (VI) oxidants; chemoselective oxidation of primary alcohols to aldehydes or carboxylic acids; the DMSO/electrophile oxidations (Swern, Moffatt etc); MnO2 and free-radical oxidation of benzylic and allylic alcohols; the Baeyer-Villiger oxidation/rearrangement; chemoselective oxidative cleavages of diols, hydroxycarbonyl and dicarbonyl compounds using periodate and Pb(OAc)4. Reduction reactions: free-radical reduction of halides; Barton deoxygenation; radical-mediated C-C bond formation; dissolving-metal reductions of enones, alkynes and aromatic systems; regioselectivity in the Birch reduction; catalytic hydrogenation and hydrogenolysis reactions; diastereofacial selectivity in hydrogenations; Lindlar catalysts and reduction of alkynes to alkenes; the haptophilic effect; hydrogenation using diimide; reduction of carbonyl compounds using hydride-donor reagents borohydrides and boranes, alanes and aluminohydrides; electrophilicity/reactivity trends in carbonyl compounds and the choice of appropriate reagents; preparation of bulky reducing agents; electronic effects on reducing power; NaBH3CN and reductive amination; 1,2- and 1,4-reduction of enones; chemoselective reductions of carboxylic acids using borane; reduction of esters and lactones using DIBAL; reduction of amides to amines or aldehydes; diastereoselective reduction of ketones; Crams rule and the Felkin-Anh model; chelation-controlled reductions.

2. 3.

4.

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CHEM 3490 Introduction to Polymer Chemistry Carl Bartels

Textbook(s): Contemporary Polymer Chemistry, by H. R. Allcock, F. W. Lampe, and J. E. Mark (Pearson Education, 2003, 3rd edition).

Course Description General Outline: This course explores basic aspects of polymer chemistry from a physical chemistry perspective. The behaviour of polymer based materials can be quite different from that of other materials. A detailed understanding of these materials is based on an investigation of their chemical structure and the unique physical chemistry that their structure causes. Brief Course Outline: Topic 1. Introduction, terminology and nomenclature 2. Classification and structure of polymers and polymer materials 3. Synthetic strategies 4. Thermodynamics of polymerization 5. Kinetics of step growth polymerization 6. Kinetics of free radical polymerization 7. Kinetics of living polymerization 8. Molecular weight determination, primary methods 9. Molecular weight determination, secondary methods 10. Chain statistics and solution behaviour 11. Glass transition and mechanical properties Approximate time 1 week 1 week 1 week 1 week 1 week 2 weeks 1 week 2 weeks 1 week 1 week 1 week

If time permits, other subjects such as structure-property relationships and speciality polymers will be explored. The course contains many synthetic organic aspects, but is also firmly grounded in physical chemistry. A strong background in thermodynamics and mathematical skills will be required. The grading scheme is as follows: Five assignments, worth 4% each (20% total) Midterm 1 worth 15% Midterm 2 worth 20% Final Exam worth 45%

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CHEM 3570 Biophysical Chemistry Mazdak Khajehpour

Recommended Textbook: Gordon G. Hammes, Physical Chemistry for the Biological Sciences, (Wiley 2007) Recommended Supplement:
rd

Robert G. Mortimer, Mathematics for Physical Chemistry, 3 Ed. (Elsevier, 2005). General Outline: Biophysical chemistry applies the principles of solution thermodynamics, chemical kinetics and spectroscopy to discuss experimental data and analysis of the thermodynamics (driving forces, coupled conformational changes etc.) and mechanisms of biochemical processes involving proteins, lipids, and nucleic acids in solution. Applications include protein folding, nucleic acid helix formation, micelle formation; ligand binding, cooperative binding and other assembly processes; effects of water, salts, other solutes, temperature and pressure on biochemical processes and enzyme catalysis. Weekly problem sets develop these applications. This course will be required for biochemistry Honours and Majors students and is highly recommended for students in microbiology and biology. Prerequisites: CHEM 2360 and MATH 1500. Part I: Energetics of Bio-processes: a) Review of Thermodynamic Principles b) Applications of Thermodynamics to Biological Systems: Calorimetry of bio-molecules (batch and differential scanning); free energy from a biological standpoint; equilibrium processes in living organisms; the effects of temperature and pressure upon bioprocesses; phase changes in biology; thermo-chemistry of biochemical reactions; thermodynamics of metabolic cycles; direct synthesis of ATP; thermodynamics of transport across biological membranes; protein structure; the protein folding problem; protein melting and denaturation; nucleic acid structures (e.g. base pair associations); DNA melting and RNA structure. c) Ligand Binding to Macromolecules: Binding of small molecules to multiple identical binding sites, microscopic and macroscopic equilibrium constants, statistical effects in ligand binding to macromolecules, cooperativity in ligand binding, models for cooperativity, allosterism. Part II: Transport Processes, Kinetics and Enzymology: a) Transport Phenomena in Biology: Diffusion in the cell (motion of small molecules and ions in aqueous media, movement of macromolecules in aqueous media, transport of species across bio-membranes; diffusion of molecules in biological membranes and lipid bilayers); molecular volume and hydrodynamic radii of biomolecules in solution; centrifugation (velocity, equilibrium and density); dynamic light scattering; electrophoresis and chromatography. b) Review of Chemical Kinetics c) Application of Kinetics to Biological Systems: The transition state and enzyme catalysis; the MichaelisMenten formalism; enzyme inhibition; case studies for a few enzyme systems (chymotypsin and protein tyrosine phosphatase), Ribozymes, DNA melting and renaturation kinetics, protein folding kinetics; application of kinetic relaxation methods to ligand binding processes; kinetic studies of cooperative binding. Part III: Biospectroscopy: a) Review of Spectroscopic Principles b) UV Spectra of Biomolecules (Proteins, Nucleic Acids and Prosthetic Groups); probing active sites of proteins using UV spectra; monitoring ligand binding to heme proteins using UV spectroscopy. c) Fluorescence and Phosphorescence of Biomolecules; emission properties of tryptophan; enzyme activity monitored by fluorescence, protein folding monitored by fluorescence; fluorescence resonance energy transfer (FRET) and its applications to biological systems. d) Circular Dichroism, Optical Rotary Dispersion and Fluorescence Polarization: Optical rotary dispersion; circular dichroism; optical rotary dispersion and circular dichroism of proteins; optical rotary dispersion and circular dichroism of nucleic acids; small molecule binding to DNA; protein folding monitored by CD; interaction of DNA with zinc finger proteins; fluorescence polarization; applications of fluorescence polarization (e.g. integration of HIV genome into the host genome, measuring domain motion). e) Vibrations in Macromolecules: protein structure determination with vibrational spectroscopy, monitoring protein conformation using vibrational spectroscopy; probing the structure of enzyme-substrate complexes using vibrational spectroscopy.

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CHEM 3580 (L) Methods in Physical Organic Chemistry Frank Schweizer

Recommended Textbook(s): Perspectives on Structure and Mechanism in Organic Chemistry Felix A. Carroll, Brooks/Cole The following reference textbooks will be useful.
Advanced Organic Chemistry, Fourth Edition, Jerry March Advanced Organic Chemistry, Third Edition, Part A: Structure and Mechanisms, F.A. Carey and R.J. Sundberg.

1. Methods of studying organic reactions: Identification of reaction products, intermediates, trapping of intermediates, crossover experiments, isotopic labeling, solvent effects, solvent polarity, Kossower scale, review of kinetics, energetics, Arrhenius theory, Eyring transition state theory, kinetic/thermodynamic control, kinetic isotope effect, Hammett plots, free energy relationships 2. Reactive intermedates: Structure, stability of carbocations, carbanions, radicals, carbene/carbenoids, generation of intermediates, reaction of intermedates, rearrangement reactions of intermediates, anchimeric assistance, nonclassical carbocations, intimate ion pairs, internal return, salt effects 3. Acid-base catalyzed reactions: Acidity in solution and in the gas phase, pKa and pKb values, general acid/base catalysis, enzymatic hydrolysis of glycosides, Aldol reactions, ester hydrolysis (AAc2, AAc1, AAl1 reactions), acetal hydrolysis, stereoelectronic effects, amide hydrolysis 4. Pericyclic Reactions: Electrocyclic reactions (Woodward-Hoffmann rules, Frontier-Orbital Theory, correlation diagrams), thermal cycloaddition reactions (correlation diagrams, secondary orbital effects, photochemical cycloaddition reactions) 5. Supramolecular Chemistry and Molecular Recognition: Thermodynamic analysis of binding phenomena, binding isotherm, molecular recognition (crowns, cryptands, spherands, tweezers, clefts, ion paring, hydrogen bonding in organic solvents and water, hydrophobic recognition (cyclodextrins, cyclophanes) cation interactions, polar - interactions, self assembly. Laboratory Work: Evaluation of this session consists of two parts: 75% will be assigned to laboratory reports and 25% will be determined by the demonstrator and supervisor based on laboratory performance. You will be assigned an F in the course if you fail to attend 2 or more laboratory sessions. Time for catch-up will be provided. Laboratory reports must be handed in by the second Friday following the termination of a laboratory project. The penalty for late submission of the laboratory reports is 20% for each day late.

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CHEM 3590 (L) Instrumental Analysis Michael Freund

Textbook(s): D. A. Skoog, F. J. Holler and S. R. Crouch, Principles of Instrumental Analysis, 6th Edition (ISBN-10: 0495012017) Recommended Supplements: Handouts, lecture slides Learning Outcomes / Key Objectives This course introduces instrumental techniques for the analysis of chemical substances and the interpretation of data obtained from such analyses. The objective is to provide the students with fundamental knowledge and hands-on experiences for chemical analysis, which is essential in almost all the areas of chemistry. Learning outcomes from the lecture session: 1. 2. 3. 4. 5. 6. 7. 8. QA/QC: Basic statistics, QA/QC (using environmental analysis as an example). Sampling and Sample Preservation: Basic sampling techniques for air, water, sediment, soil, and biological samples; sample preservation techniques. Sample preparation: Physical separation (e.g., filtration, sieving) of samples; chemical digestion and extraction of analytes from the samples. Electroanalytical techniques: potentiometry; voltammetry. Spectroscopy: Principles and applications of spectroscopy in general; atomic absorption spectroscopy; atomic emission spectroscopy; atomic fluorescence spectroscopy; molecular UV-Vis spectroscopy; synchrtron-based x-ray absorption spectroscopy. Chromatography: GC, LC, Electropheresis. Mass Spectrometry: Introdcutory atomic mass spectrometry (ICP-MS) and molecular mass spectrometry (ESI-MS) Data Interpretation: Statistics on outlier detection and population comparisons.

Learning outcomes from the lab session: 1. 2. 3. Hands-on experience with most instrumental analytical techniques in chemical analysis; Sample preparation techniques and calibration; Consolidate topics covered in the lectures

Laboratory Instructor: Tom Ward

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CHEM 4360 Signalling and Regulation of Gene Expression Jrg Stetefeld

Required Textbook(s): None. All lecture notes used in class will be posted on Angel, and available for download by registered members of the class. General Outline: The biochemistry of cell response to external stimuli, with emphasis on animals. Cell surface receptors and ligands; signalling to the nucleus; phosphorylation and proteolysis; transcription; gradients in cell patterning. 1. 2. 3. Introduction: what signalling is; oncogenes and developmental mutants as starting points for understanding signalling at the molecular level. G-protein coupled receptors and related processes: ligands that use this signalling pathway; the receptors and heterotrimeric G proteins; second messages; protein kinases; signalling in perception of taste and smell. The growth factor signalling pathway: growth factors and their receptors; tyrosine protein kinases; SH2 and SH3 domains; small (Ras-type) G proteins; the mitogen-activated protein kinase cascade; other small G proteins. The cytokine (JAK/Stat) pathway: cytokines; their receptors; JAK kinases; the Stat proteins. Transcription in eukaryotes: gene structure; chromatin structure and chromatin remodelling; the transcription initiation complex; role of specific transcription factors; structure of sequence-specific DNA binding domains; direct signalling to the nucleus via nuclear receptor proteins; chromatin silencing; microRNAs and siRNAs. The TGF-beta signalling pathway: ligands and receptors; Smad proteins. The NF-kappaB signalling pathway and related processes: TNF-alpha signalling; choice between survival and apoptosis; death domains; ubiquitination and the 26S proteasome; other NF-kappaB dependent pathways, including the role of Toll-like receptors in innate immunity. Apoptosis (programmed cell death): intrinsic and extrinsic pathways, including roles of p53, caspases, Bcl-2 family proteins, and permeabilization of mitochondria. Anterior-posterior patterning in Drosophila: the hierarchy of segmentation genes; discovery of transcription factor motifs (Zn fingers, Hox proteins) and their use in identifying orthologous proteins in vertebrates.

4. 5.

6. 7.

8. 9.

10. Pathways discovered through segment polarity genes: the wnt and hedgehog pathways.

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CHEM 4370 Glycobiology and Protein Activation Gro Thorne-Tjomsland

Textbook(s): none (lecture notes posted online).
For take-home assignments, the following textbook - available free online - may serve as a useful reference text: "Essentials of Glycobiology" by Varki et al, 1st ed (1999) or 2nd ed (2009) Cold Spring Harbor Laboratory Press

Outline: This course covers the structure and biosynthesis of glycans that are covalently attached to proteins or lipids. Glycan function will be discussed relative to and independent of the backbone structures. Also discussed are Glycanbinding proteins (GBPs) that bind to glycan epitopes to code for specific biochemical events within an organism, or at the interface between organisms. Topics: 1. 2. 3. Monosaccharides as building blocks for glycans: Chemical features of monosaccharides, and glycosidic linkages that contribute to the diversity of glycan structures will be identified. Glycan structure: The conserved and variant structures of glycans. attached to either protein- or lipidbackbones in mammalian systems, will be presented. Biosynthesis of Glycans: The glycan biosynthetic pathways will be explained in context of evolution and the generation of bio-active intermediates. Structure-function relationships of the glycosylation enzymes and donor sugars will be discussed. The relationship between non- template driven biosynthesis pathways and the potential coding capacity of glycans is introduced. Glycan function: The overall function of glycans relative to and independent of the backbone structures will be discussed. The concept of glycan epitopes within glycans, that collectively form the "glycan code" and code for biological events, will be discussed. Principles of interactions between glycan epitopes and glycan-binding proteins: Examples will be provided of glycan epitopes interacting with glycan-binding proteins (GBP) located in the same organism or in a different organism to produce biological outcomes. Clinical importance of glycans: Genetic defects relating to the biosynthesis or turn-over of glycans will be discussed, as will be the role of glycans and their binding partners in cancer and microbial infections. Methods for analyzing glycans and glycan-binding proteins: Time permitting, methods including emerging high-throughput adaptations to analyze glycans/GBP will be introduced.

4.

5.

6. 7.

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CHEM/ENVR 4550 Aquatic Chemistry Feiyue Wang

Textbook(s): J. J. Jensen, 2003. A Problem-Solving Approach to Aquatic Chemistry. Wiley. Recommended Supplements: Handouts, lecture slides Learning Outcomes / Key Objectives This course deals with chemical reactions and processes affecting the distribution, speciation and bioavailability of chemical species in natural waters. The objective is to develop a theoretical basis for the chemical behavior of natural water systems, as well as for the description of processes involved in wastewater treatment. The course draws primarily on the principles of chemistry; however, a fundamental understanding of geology and biology will be very helpful. Learning outcomes: 1. 2. 3. Chemical speciation modeling in the aquatic environment: Theoretically modelling the distribution of a chemical across different interfaces in the aquatic environment (air overlying water, sediment, biota), based on equilibrium calculations of dissolution/precipitation, sorption/desorption, and redox reactions. Kinetic constrains: Introductory level of kinetic calculations of chemical species in the aquatic environment. Chemical Bioavailability: Relating chemical speciation to bioavailability of chemicals in the aquatic environment.

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CHEM 4580 Topics in Organic Chemistry: Design of Organic Syntheses Phil Hultin
Textbook(s): Organic Synthesis: the Disconnection Approach (S. Warren).

Recommended Supplements: on reserve in the science library: Organic Synthesis (2nd ed) (M.B. Smith); Marchs Advanced Organic Chemistry (J. March and M.B. Smith); Classics in Total Synthesis (K.C. Nicolaou, E.J. Sorensen); The Logic of Chemical Synthesis (E.J. Corey). Course Description The construction of a complex target molecule must be planned carefully if it is to be successful. Retrosynthetic analysis is a proven strategy for such planning, based on conceptually dismantling the target step-by-step until a suitable starting compound is obtained. This course, taught in a discussion/seminar format, provides a general introduction to the design of multistep organic syntheses. The textbook by Stuart Warren provides the basis for the course, and students are expected to read approximately 40 pages of the book per week. This material serves as the starting point for in-class discussion. Additional material that updates Warrens book is provided in handouts. In addition, chapters from Nicolaou and Sorensen are used to illustrate the application of the general concepts. Students are expected to participate in class discussions. As well, there are three problem sets in which students may be asked to suggest short syntheses of relatively simple compounds, identify errors in proposed routes, discuss the use of selected reagents or protecting groups, compare and contrast published syntheses. The problem sets may also include predict-the-product and reaction mechanism questions. Towards the end of the course, each student will be assigned a published synthesis and asked to present a critical analysis of this paper. The analysis is presented as a 30-minute seminar to the class, and should cover not only the step-by-step chemistry but also the reasons behind the synthesis, the general strategy, comparisons with other syntheses, and a critical evaluation of the chemistry. The class is expected to participate in the discussion of the critique and the synthesis. There are no tests or exams in this course. The final assignment is to develop a detailed proposal for the total synthesis of a new compound. Target compounds are chosen from the natural products literature published during that year. They will never have been synthesized but are usually members of structural families that have received some synthetic attention. The proposal must be an essay-style document, providing a complete justification for the synthesis, an explanation of the strategy employed, and specific reagents proposed to execute each step. Full referencing to the primary literature as well as to secondary sources is mandatory. During the course, students are also given experience using online database searching using SciFinder Scholar, as well as an introduction to the standard texts of synthetic methodology Fieser and Fieser, Larock, Organic Syntheses, Organic Reactions, Greenes Protecting Groups among others. NOTES: 1. Design of Organic Syntheses is usually offered every second year unless there is strong demand. 2. This course is intended for students having a very strong background and interest in organic chemistry. Students planning to take Design of Organic Syntheses should consult with Dr. Hultin before registering.

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CHEM 4590 Bioanalytical Methods (Hlne Perreault)

Textbook(s): Principles of Instrumental Analysis, fifth edition, Skoog, Holler and Nieman, Harcourt Publishing, New York, (ISBN 0-03-002078-6). Recommended Supplements: Handouts will be presented in class.

Outline: This course will cover most analytical techniques of importance in the analysis of biomolecules. Altough some of the techniques discussed were developed for the characterization of inorganic materials, applications will focus on novel methods of determining structures, compositions, molecular weights, and especially concentrations of bio-organic molecules. More specifically, the course will start with a section on FTIR and Raman spectroscopy, then quantitative NMR experiments will be discussed. These topics will be followed by a section on surface characterization techniques such as scanning electron microscopy, atomic force microscopy and secondary ion mass spectrometry (SIMS). Following SIMS, techniques used in biological mass spectrometry will be explored, along with a section on high throughput methods for analyzing bio-organic compounds, where high throughput proteomics will be emphasized. As thermal analytical methods are useful for characterizing biopolymers, thermogravimetric analysis, differential thermal analysis and differential scanning calorimetry will be described before the last segment of the course, which will focus on forensic analysis (e.g. drug testing and DNA fingerprinting). Also, before the midterm break, each student will be asked to give a 15-min talk on a selected topic in bioanalytical chemistry. Grading will be based on five pre-announced one-hour tests (taking place during class slots), on the laboratory portion of the course and on the 15-min talk. Participation during student talk sessions will be evaluated based on a very low percentage of the final grade. Laboratory: Instructor: Dr. Tom Ward In the laboratory section, students will be guided through three experiments that focus on one type of analyte but that may require more than one analytical method to be used. For a fourth experiment, students will be asked to decide on their own analysis based on equipment available in the 4590 laboratory. Each these last experiments has to be approved by the lab instructor before students can proceed. Each student will accomplish a total of four experiments during the term.

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CHEM 4600 (L) Advanced Chemical Techniques Various Instructors (Peter Budzelaar, coordinator)
Textbook:
Robert M. Silverstein, Francis X. Webster, David J. Kiemle, "Spectrometric Identification of Organic Compounds", 7th edition, Wiley, 2005

This course covers a number of advanced analytical techniques that many students will encounter as soon as they start doing research (in a research project, e.g. CHEM 4710, in summer research or as a graduate student). The course consist of 4 sections each representing about 0.75 cr hrs, and each worth 25% of the final grade. Section 1: Organic Spectroscopy H. Luong

General overview in spectroscopy; Combustion analysis; UV spectroscopy Infrared spectroscopy; Mass spectrometry
1 13

H-NMR spectroscopy;

C-NMR spectroscopy; further NMR topics

Integration of spectral methods for structure elucidation - (solving an unknown structure) Section 2: Advanced Magnetic Resonance Spectroscopy - K. Marat Introduction: Why bother with pulses and Fourier transform? Basic NMR theory: the origins of the NMR phenomenon, chemical shifts and couplings. The NMR Hamiltonian (simplified) The vector description of pulse NMR; the rotating reference frame; the Bloch equations in the rotating frame; introduction of a second frequency dimension Polarization transfer (INEPT and DEPT) and the nuclear Overhauser effect (nOe). Hands-on: Practical aspects of recording spectra on a modern NMR spectrometer Description and applications of the commonly used 2D NMR techniques: H-H correlation (COSY and TOCSY), C-H correlation (HETCOR/HMAC/HSQC), long-range correlation (COLOC/HMBC), internuclear distances (NOESY and ROESY), INADEQUATE Hands-on: The recording and processing of 2D NMR spectra: COSY, HMQC and HMBC Section 3: X-ray diffraction - M. Bieringer An overview of powder and single-crystal X-ray diffraction methods and their use for the determination of solid-state structures. Diffraction is a very versatile method for structure determination of crystalline solids used in all fields of chemistry, material sciences, pharmacy, life sciences, mechanical and electrical engineering and is often used as a tool in archaeology as well. This section will introduce the basic concept of diffraction theory with examples of single crystal diffraction and powder diffraction. Students will conduct powder X-ray diffraction experiments as part of the teaching module. Section 4: Spectromicroscopy K. Gough Technological advances have lead to the development of many new forms of microscopy, with light from X-ray to IR and terahertz. With IR, any material can be imaged based on molecular vibrations of the chemical components; with visible lasers, Raman imaging is possible; soft and hard-X-ray instruments enable many imaging modalities: PEEM, STXM, XAS, XRF, etc. Each wavelength range necessitates a completely different type of instrument and analysis and provides different types of chemical information on a different spatial scale. We will examine several of these.

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CHEM 4620 Biochemistry of Nucleic Acids Sean McKenna

Textbook(s): None required. Occasional journal articles will be required reading. All course material, including lecture material, will be available online to students. Course Description This course will cover the basic principles of nucleic acid biochemistry, with an emphasis on the important role that protein-nucleic acid interactions play in governing cellular systems. The central goal of the course is to relate the chemical characteristics of nucleic acids to their ultimate biochemical function. A brief description of the topics to be covered follows: 1. Origins of Nucleic Acids Research: A brief historical perspective on the chemical and biological discoveries central to nucleic acid research will be presented, concluding with a discussion of where the research field is currently focusing its efforts. 2. Nucleosides and Nucleotides: Chemical features of the building blocks of nucleic acids with be discussed, including their cellular biosynthesis. 3. Nucleic Acid Structure: Idealized and physiological strucutres of both DNA and RNA oligonucleotides will be presented. Lectures on the dynamic nature of nucleic acid structures, higher order structures (histones, chromatin, etc.), and the sysnthesis of oligonucleatides (both in vivo and in vitro) will be discussed. 4. Methods for Studying Nucleic Acids: Current strucutral biology, spectroscopic, and bicohemical approaches specific to the study of both nucleic acids in isolation and in complex with protein binding partners will be introduced, and referenced throughout the remainder of the course. 5. Principles of Protein-DNA Interactions: The physical chemistry of protein-nucleic acid interactions will be introduced in order to understand the key concepts of recognition and specificity in these complexes. Biological consequences of these interactions will also be emphasized. 6. RNA Structure and Function: The unique role that RNA plays in cellular systems will be explored, starting with a discussion of the RNA World hypothesis. An introduction to the unique catalytic capabilties of both ribozymes and riboswitches will be presented. Lectures investigating RNA-protein interactions will follow, with an emphasis on the chemical basis of complex formation. A discussion of RNA silencing, RNA processing, and protein translation will also be presented, with an focus on the RNA-protein interactions that govern these processes. 7. Drug-DNA Interactions: An introduction to pharmaceuticals that directly target nucleic acids will be presented.

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CHEM 4630 Biochemistry of Proteins Mazdak Khajehpour

Required Textbook(s): None Recommended Supplements: Thomas E. Creighton, Proteins: Structures and Molecular Properties, 1st or 2nd ed. (W.H. Freeman & Co.) 1984, 1989, QP551.C737. C. Branden & J. Tooze, Introduction to Protein Structure, 1st or 2nd ed. (Garland Publishing, Inc.) 1991 QP551.B7635. Jack Kyte, Structure in Protein Chemistry (Garland Publishing, Inc.) 1995 QP551.K98. C.R. Cantor and & P.R. Schimmel, Biophysical Chemistry Part 2 (Freeman & Co.) QH345.C36. General Outline: The structure and function of proteins, their physical and chemical properties, and methods for studying them. 1. 2. 3. 4. 5. 6. 7. 8. 9. Introduction: current state of protein science; summary of tractable research problems; areas of application of protein biochemistry. Amino Acid, Peptide, and Protein Purification: HPLC chromatography, capillary electrophoresis, immobilized metal chelate chromatography. Amino Acid Analysis: acid and base hydrolysis; difficult sequences; sensitive side-chains; pre- and postcolumn detection; quantification with Ninhydrin. Protein Sequencing: details of the Edman degradation; liquid- and gas-phase technologies. Mass Spectrometry and Proteomics: methods of ionization; instrumentation; molecular weight determination; protein and peptide sequencing; introduction to proteomics; isoelectric focusing. Solid Phase Peptide Synthesis: details of the Merrifield (BOC) method; comparison to FMOC chemistry; limitations of the technology. Applications of Peptide Methods: total synthesis of D- and L-HIV-1 protease; introduction to Circular Dichroism of proteins; examples from the current literature. Protein Secondary and Tertiary Structure: -helix, -sheet, turns, and others; motifs and domains. Major Protein Structure Families: All -proteins, myoglobin dynamics; all -proteins, green fluorescent protein; + proteins; / proteins; spherical viruses; membrane proteins; photosynthetic reaction centre; porins.

10. The Protein Folding Problem: introduction to the problem; timescale of folding; free-energy landscape; forces that determine the folded states of proteins; in vitro folding; in vivo folding; chaperonin structure and function; introduction to X-ray diffraction. 11. Natively-unfolded Proteins structural classes, functions

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CHEM 4660 Computational Chemistry James Xidos

Required Textbook: Cramer, Essentials of Computational Chemistry 2nd Edition

The field of computational chemistry encompasses the development and application of numerical methods for the study of chemical systems. The successful investigation of problems in chemistry using computational chemistry requires both an understanding of the nature of the chemistry being studied and an understanding of the computational methods employed. The theoretical framework of computational chemistry methods will be presented, with an emphasis on practical understanding of their strengths, weaknesses, and ranges of applicability. This knowledge will allow for the critical evaluation of the validity and accuracy of results and of the conclusions derived from the computational chemistry modelling of particular chemical problems. The following topics will be discussed: Empirical force field models and their use in chemical and biochemical studies, including molecular dynamics simulations. Potential energy surfaces and the exploration tools available for the location of local and global minima and transition states. Electronic structure models for the prediction of energies, thermodynamic quantities, geometries, and electronic and spectral properties. The solvation process and the incorporation of its effects in molecular modelling. Considerations, strategies, and goals in setting up computational chemistry studies.

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CHEM 4670 Drug Design and Drug Discovery Frank Schweizer

Recommended Textbooks: The Organic Chemistry of Drug Design and Drug Action, 2nd Edition by Richard. B. Silverman, Elsevier Academic Press. In addition, instructor will provide relevant reading material such as review articles and research papers. Course Objective: Upon completion of the course, the student should be able to demonstrate an understanding of the concepts involved in drug design and drug interaction, drug synthesis and biological evaluation. General Outline: 1. (a) (b) (c) 2. (a) (b) (c) (d) (e) (f) 3. (a) (b) (c) 4. (a) (b) (c) (d) (e) 5. (a) (b) (c) 6. Drug Discovery, Design and Development Drug Discovery Lead Modification: Drug Design and Development Quantitative Structure-Activity Relationships Receptors Introduction Drug-Receptor Interactions Interactions involved in the Drug-Receptor Complex Determination of Drug Receptor Interactions Theories for Drug-Receptor Interactions Topographical and Stereochemical Considerations Enzymes Enzymes as catalysts Mechanisms of Enzyme catalysis Coenzyme Catalysis Enzyme Inhibition and Inactivation Introduction Drug Resistance Drug Synergism Reversible Enzyme Inhibition Irreversible Enzyme Inhibition DNA-Interactive Agents Introduction DNA Structure and Properties Classes of Drugs That interact with DNA Drug Metabolism/Prodrugs/Drug Delivery Systems (if time permits)

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CHEM 4680 Organometallic Chemistry Peter Budzelaar

Textbook(s): Robert H. Crabtree, The Organometallic Chemistry of the Transition Metals, 4th Ed. (Wiley, 2005) Recommended Supplements: Christoph Elschenbroich, Albrecht Salzer, Organometallics, 2nd Ed. (VCH, 1992), p 15-56 (groups 1 and 2) and 75-146 (Al-Tl, Si-Pb)

Course Description General outline: The course covers the organometallic chemistry of main-group and transition metals, and their relevance to organic synthesis and homogeneous catalysis. Topics include: 1. 2. 3. 4. 5. 6. 7. 8. 9. Electron counting. The 8/18-electron "rule" and its exceptions. Relation to reactivity and stability. Multicenter (2e-3c and 2e-4c) bonding. Formal oxidation states. Main-group metal chemistry: electropositive elements. Synthesis, use as intermediates in organic synthesis. Reactivity as nucleophile, base and reductant. Main-group metal chemistry: less electropositive elements (mainly silicon). Synthesis and applications. NMR of organometallic compounds. Symmetry and fluxionality. Transition-metal organometallic chemistry: metal-ligand bonding, standard synthesis and decomposition routes. Ligand substitution and activation. Insertion and elimination reactions, including olefin polymerization and -bond metathesis. Oxidative addition and reductive elimination. Olefin metathesis.

10. Electrocyclic reactions. Optional special topics: 11. Hot topics and hypes in organometallic chemistry 12. Separation of steric and electronic effects (Tolman , ; QALE) 13. Chiral catalysis. 14. C-H activation. 15. Modelling of organometallic reactions. Ca 3/4 into the course, students are expected to present a recent paper (to be selected during the course). At the end of the course, students should be able to draw "reasonable" mechanisms for most reactions of homogeneous catalysis (and provide alternatives), should be able to understand the effects of ligand variation and should have an overview of organometallic reactions commonly used in organic synthesis. There is no laboratory work in this course. Final grading: Assignments Presentation Mid-term Final 10% 20% 20% 50%

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CHEM 4690 Specific Methods in Organic Synthesis Torsten Hegmann

Textbook(s): Organic Chemistry, J. Clayden, N. Greeves, S. Warren, P. Wothers, Oxford University Press, 2001, (ISBN: 0-19-850346-6). Recommended Supplements: (a) Organic Synthesis, M. B. Smith, McGraw-Hill Publishing, (b) Advanced Organic Synthesis Part B, F. A. Carey, R. J. Sundberg, Kluwer Academic/Plenum Publishers. (c) Organic Chemistry Solutions Manual, J. Clayden, N. Greeves, S. Warren, P. Wothers, Oxford University Press, 2001 General Outline: This course is primarily concerned with the applications of CC bond formation to the synthesis of complex molecules, stereochemistry, modern organic transformations, and heterocyclic chemistry. Emphasis will also be put on natural products and products for high-tech applications (OLEDs, displays, etc.). 1. 2. Protecting groups in organic synthesis: principles, examples, amino acids, peptide syntheses. CC bond forming reactions of enols and enolates: application of the general principles, use of carbanions, stabilized carbanions and organometallics in alkylation, enols and enolates in reactions with alkylating agents, aldehydes and ketones. Aldol reactions: crossed aldol reaction, intramolecular aldol reactions, syn-aldol (Evans aldol), anti-aldol. Acylation reactions: Claisen condensation and related reactions. Conjugate addition: conjugate addition of enolates, Michael addition, Robinson annelation. Retrosynthetic analysis: disconnection-synthon approach; including selected synthesis from the literature. Controlling the geometry of double bonds: focusing on Wittig, Wittig-Horner-Emmons reactions. Stereoselective reactions of cyclic compounds: 4 to 6-membered ring systems, bicyclic, spirocyclic and fused bicyclic systems as well as cyclic reactive intermediates. Diastereoselectivity: single diastereomers, prochirality, chelation.

3. 4. 5. 6. 7. 8. 9.

10. Pericyclic reactions: ring closure/ring opening; Baldwins rule closure rules; preparation of small rings; methods for synthesis of medium to large ring systems; cycloaddition (primarily [4+2] and [2+2]); electrocyclic reactions; metathesis reactions, Diels-Alder reaction, [2+2] cycloaddition, 1,3-dipolar cycloaddition, Claisen rearrangement, Cope rearrangement, [3,3], [2,3], [1,5] sigmatropic rearrangements. 11. Asymmetric synthesis: resolution, chiral auxiliaries, asymmetric hydrogenation, asymmetric epoxidation, asymmetric dihydroxylation. 12. Organo-main-group chemistry: focusing on sulfur or boron. 13. Heterocycles: 3 to 7-membered rings, IUPAC nomenclature, reactivity. 14. Modern cross-coupling reactions for C-C bond formation: Suzuki, Kumada, Stille, Heck, Ullmann coupling, etc. 15. Organic Materials in High-Tech Applications: selected examples for the use of organic compounds in OLEDs (organic light emitting diodes), displays, and conductors.

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CHEM 4700 (L) Advanced Biochemistry Laboratory Coordinator: Sean McKenna

Required Textbook(s): A PDF format Laboratory Manual is provided. Recommended Supplements: Alan Cooper, Biophysical Chemistry, (University of Glasgow UK) QD 476.2 C66 2004; ISBN 0 85404 480 9. Cantor & P. R. Schimmel, Biophysical Chemistry Part 2 (R. Freeman & Co.) QH345.C36; ISBN: 07167-1188-5. H. Willard et al. Instrumental Methods of Analysis any ed. (Wadsworth Inc.) 1988 QD79.I5I52. General Outline: A laboratory and workshop consisting of lectures, problem solving, and advanced instrumental techniques such as magnetic resonance spectroscopy, mass spectrometry, circular dichroism, x-ray crystallography, fluorescence spectroscopy, and computer analysis of protein sequences and structure. 1. 2. 3. 4. 5. 6. 7. 8. 9. Course Introduction & Protein Purification Workshop. Introduction to the concepts involved in the molecular biology, expression, and purification techniques required to produce protein. S. McKenna Purification of Green Fluorescent Protein-Calmodulin: DNA shearing; heat-denaturation precipitation; hydrophobic interaction chromatography; UV spectrophotometry; dialysis, freeze-drying: TBA Circular Dichroism of Nucleic Acids: introduction to the instrumentation; spectra of 5'AMP and APA; effects of temperature and viscosity: TBA Circular Dichroism of Proteins: protein secondary structure analysis; protein thermal denaturation; protein denaturation by urea; data analysis using Mathematica: TBA Mass Spectrometry Workshop and Demonstration: principles of mass spectrometry; introduction to the instrumentation; analysis of calmodulin: H. Perreault Protein/Nucleic Acid Structure Workshop: An introduction to protein and nucleic acid databases, with a focus on software for sequence analysis and three-dimensional structure visualization/manipulation: TBA Workshop on NMR Spectroscopy of Proteins: the NMR phenomenon; chemical shift; scalar coupling, the nuclear Overhauser effect; multidimensional NMR; protein structure determination: S. McKenna. Monitoring Protein Ligand Interactions with Fluorescence and UV Spectroscopies: M. Khajehpour X-ray Diffraction of Proteins: crystallization of lysozyme; microscopic inspection of crystals; introduction to diffraction theory and protein structure determination: B. Mark

10. Research Proposal: students are given a research paper and asked to use it as the basis of a brief research proposal.

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CHEM 4710 (L; 6 cr hrs) Research Project in Chemistry and Biochemistry Various Research Supervisors (Peter Budzelaar, coordinator)
Textbook: None Expectations: CHEM 4710 is an independent research project course which extends over both the fall and winter terms. Students arrange to work with a particular professor on a mutually agreeable research problem. Students in CHEM 4710 are expected to begin work on the research project at the beginning of September and to maintain a steady level of work during the entire academic year. Students must consult regularly with their supervising professors to ensure that their work stays on track. Every student in CHEM 4710 is expected to conform to University of Manitoba standards of laboratory safety at all times. Students should also meet the standards of the research group that they are working in with regard to experimental procedures, notebook keeping, and general laboratory behavior. Students will be required to submit an interim report in early December and a final report by mid-April. In addition, students will give a 15 minute presentation to the Department of Chemistry on their research near the end of second term.

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