Chemistry and Biochemistry Courses

Chemistry and Biochemistry MSc and PhD Courses

Specific course offerings in subject areas listed under Topics will generally vary from year to year, depending on the availability of faculty and the requirements of graduate students in the program.

Over the next few years, the department will offer a selection of courses from those listed below. Additional Selected Topics courses may be offered in a given year, and these will be identified by different subtitles. Further information on Selected Topics courses will be available from the department at the beginning of each academic year.

Topics in Analytical & Bioanalytical Chemistry

Description: This course explores themes within the area of Analytical Chemistry.

Component(s): Lecture

Notes:
  • This course may be repeated for credit, provided that the subject matter is different each time.

Prerequisite/Corequisite: The following courses must be completed previously: CHEM 218; CHEM 312, or equivalent.

Description: High performance liquid separations on an analytical (non-preparative) scale are surveyed. Fundamental separation mechanisms and application of the techniques are discussed. Emphasis is placed on separations of biologically relevant analytes which include peptides, proteins and nucleic acids.

Component(s): Lecture

Prerequisite/Corequisite: The following course must be completed previously or concurrently: CHEM 494 or equivalent.

Description: Theoretical and operational aspects of modern mass spectrometry are discussed in a number of formal lectures and training sessions. All students must carry out an independent mass spectrometry project on their molecules of choice. Projects can be selected from all areas of chemistry, biochemistry or biology including the “omics” sciences (e.g., proteomics, metabolomics).

Component(s): Lecture

Notes:
  • Students who have received credit for this topic under a CHEM 630 number may not take this course for credit.

Topics in Bioorganic and Organic Chemistry

Description: This course explores themes within the area of Organic Chemistry.

Component(s): Lecture

Notes:
  • This course may be repeated for credit, provided that the subject matter is different each time.

Prerequisite/Corequisite: The following courses must be completed previously: CHEM 222 ; CHEM 235; CHEM 324 or CHEM 325; or equivalent.

Description: Determination of organic reaction mechanisms using kinetics, activation parameters, acid-base catalysis, Bronsted catalysis law, solvent effects, medium effects, isotope effects, substitutent effects, and linear free energy relationships.

Component(s): Lecture

Prerequisite/Corequisite: The following courses must be completed previously: CHEM 222; CHEM 235; CHEM 324; or equivalent.

Description: This course is concerned with synthetic strategy and design. It provides an introduction to advanced synthetic methods and reagents, involving heteroatoms such as sulphur, phosphorus, tin and selenium, as well as an overview of the uses of protecting groups in organic chemistry. The concept of retrosynthesis and a few asymmetric reactions are discussed using syntheses of natural products from the literature as examples.

Component(s): Lecture

Notes:
  • Students who have received credit for CHEM 623 may not take this course for credit

Prerequisite/Corequisite: The following courses must be completed previously: CHEM 222, CHEM 235, CHEM 324, or equivalent.

Description: This course is concerned with synthetic strategy and design. It provides an introduction to advanced synthetic methods and reagents, involving heteroatoms such as sulphur, phosphorus, tin and selenium, as well as an overview of the uses of protecting groups in organic chemistry. The concept of retrosynthesis and a few asymmetric reactions are discussed using syntheses of natural products from the literature as examples.

Component(s): Lecture

Prerequisite/Corequisite: The following courses must be completed previously: CHEM 221; CHEM 222; CHEM 271; or equivalent.

Description: This course introduces students to various topics in nucleic acid chemistry. The topics include nomenclature, structure and function of RNA and DNA; techniques and methods to investigate nucleic acid structure; DNA damage and repair; interaction of small molecules and proteins with nucleic acid; oligonucleotide-based therapeutics (antisense, antigene, RNAi); synthesis of purines, pyrimidines and nucleosides; and solid-phase oligonucleotide synthesis.

Component(s): Lecture

Notes:
  • Students who have received credit for this topic under a CHEM 620 number may not take this course for credit.

Prerequisite/Corequisite: The following courses must be completed previously: CHEM 324; CHEM 325; or equivalent.

Description: This course offers an introduction to reactive intermediates with an emphasis on structure and stability as found in modern (physical) organic chemistry. While the focus is on radicals and carbenes, carbocations are discussed near the end of the term. The material covered is relevant to chemistry and biochemistry.

Component(s): Lecture

Notes:
  • Students who have received credit for this topic under a CHEM 621 number may not take this course for credit.

Prerequisite/Corequisite: The following courses must be completed previously: CHEM 324 or CHEM 325; CHEM 335; or equivalent. If prerequisites are not satisfied, permission of the Department is required.

Description: This course reviews some fundamental aspects of synthetic and biological supramolecular chemistry and nanotechnology. Topics covered may include supramolecular forces, ion binding and ion channels, molecular recognition, self-assembly (meso-scale and molecular-scale), organometallic supramolecular chemistry, dynamic combinatorial chemistry (DCC), and foldamers.

Component(s): Lecture

Notes:
  • Students who have received credit for this topic under a CHEM 620 number may not take this course for credit.

Prerequisite/Corequisite: The following courses must be completed previously: CHEM 293, CHEM 324.

Description: This course provides an introduction to the small molecule drug discovery process, addressing early target identification, hit discovery, lead optimization and preclinical considerations. The course focuses primarily on the rational design and synthesis of drugs that employ multidisciplinary approaches to satisfy a multitude of specificity and safety requirements. The emphasis is on organic synthesis within the special context of medicinal chemistry that illustrates the challenges involved in leveraging the opportunities presented by high throughput, parallel and/or combinatorial synthesis in light of physical limitations imposed by processing large numbers of compounds. Case studies from the current literature are used to highlight how new technologies and strategies have overcome some of those limitations and are used to highlight recent innovations in the field. The course also charts the evolution of powerful techniques from structural research (NMR, X-ray crystallography, and computational modeling) as fully integrated medicinal chemistry tools for modern drug-discovery to highlight key advances.

Component(s): Lecture

Topics in Physical Chemistry

Description: This course explores themes within the area of Physical Chemistry.

Component(s): Lecture

Notes:
  • This course may be repeated for credit, provided that the subject matter is different each time.

Prerequisite/Corequisite: The following courses must be completed previously: CHEM 234; CHEM 241; CHEM 333; or equivalent. If prerequisites are not satisfied, permission of the Department is required.

Description: This course presents the concepts, tools, and techniques of modern computational chemistry, and provides a very broad overview of the various fields of application across chemistry and biochemistry. The course is divided into two parts: 1) Molecular structure, which covers molecular mechanics and elementary electronic structure theory of atoms and molecules; and 2) Chemical reactivity, which covers applications of quantum chemistry and molecular dynamics techniques to studies of chemical reactions. The applications discussed include organic molecules and their reactions, peptides and proteins, drug design, DNA, polymers, inorganics, and materials. The course includes a practical component where students acquire hands-on experience with commonly used computational chemistry computer software. Lectures and laboratory.

Component(s): Lecture

Prerequisite/Corequisite: The following course must be completed previously: CHEM 234 or equivalent.

Description: In this course, the basic concepts of classical (equilibrium) thermodynamics are first reviewed, followed by an introduction to statistical thermodynamics which gives a unified method of treating transport processes. At this point, the Boltzmann distribution function is derived, which leads to the statistical interpretation of entropy. Other important thermodynamic functions such as the partition function, the partition function for large ensembles and the Sackur-Tetrode equation are examined. The course also addresses non-equilibrium thermodynamics in the linear domain. The relations describing the production of entropy in irreversible processes due to heat transfer, charge transfer, change of volume, and chemical reactions are examined. The establishment of flux equations and the use of the Onsager reciprocal relations are then applied to the description of a variety of open systems.

Component(s): Lecture

Prerequisite/Corequisite: The following courses must be completed previously: CHEM 333; CHEM 431 or CHEM 631; or equivalent.

Description: This course includes a thorough review of basic quantum mechanics in both the Schroedinger and Heisenberg representations, electronic structure theory, symmetry and group theory, interaction of matter with light, quantum scattering, the path integral formalism, quantum theories of chemical reaction rates, time-dependent approaches to spectroscopy, wave packet propagation, correlation functions and dynamics processes, and density matrices.

Component(s): Lecture

Prerequisite/Corequisite: The following courses must be completed previously: CHEM 234; CHEM 235; or equivalent.

Description: This course examines the physical chemistry of interfaces including surface and interfacial tensions, the absorption of surface active substances/surface excess properties, and surfactant self-assembly. Topics covered may include Gibbs and Langmuir monolayers, micelle formation, emulsions, foams, surfactant liquid crystals, layer-by-layer polymer self-assembly, and biological membranes. Techniques for characterization and applications (biological and industrial) of these systems are addressed.

Component(s): Lecture

Notes:
  • Students who have received credit for this topic under a CHEM 630 number may not take this course for credit.

Prerequisite/Corequisite: The following courses must be completed previously: CHEM 234; CHEM 333; or equivalent.

Description: This course essentially explores how electrical conductivity is influenced by the nature of the chemical bonding in these solid-state materials. The course provides an introduction to solid-state structures and then goes on to explore band theory, the central model used to describe electrical conductivity in the following three categories of electronic materials: conductors, semiconductors, and insulators. Finally, the course explores the extension of the band model to interpret electrical conductivity in molecular semiconductors and charge-transfer complexes.

Component(s): Lecture

Topics in Bioinorganic & Inorganic Chemistry

Description: This course explores themes within the area of Inorganic Chemistry.

Component(s): Lecture

Notes:
  • This course may be repeated for credit, provided that the subject matter is different each time.

Prerequisite/Corequisite: The following courses must be completed previously: CHEM 324; CHEM 341; or equivalent.

Description: This course covers the structure and properties of organometallic compounds, their main reactions and their application in catalysis and organic chemistry.

Component(s): Lecture

Description: This course provides an in-depth evaluation of the different methods used in modern physical chemistry such as laser, microwave, FT-IR, electron spin resonance, nuclear magnetic resonance, x-ray photoelectron, x-ray diffraction and fluorescence, Auger electron, Mössbauer, and gamma-ray spectroscopic analysis, as well as scanning probe microscopy and mass spectrometry.

Component(s): Lecture; Laboratory

Prerequisite/Corequisite: The following courses must be completed previously: CHEM 241; CHEM 271; or equivalent.

Description: This course covers the role of metals in biochemical systems. Specifically, it focuses on essential trace elements, zinc enzymes, oxygen transport and storage, metalloproteins and biological electron transfer, structure-function relationships in heme enzymes, nitrogen fixation; model compounds for metalloproteins and metalloenzymes.

Component(s): Lecture

Prerequisite/Corequisite: The following courses must be completed previously: CHEM 234; CHEM 235; or equivalent.

Description: This course covers basic and recent concepts in catalysis are described with particular emphasis on heterogenous catalysis. The technical, economic and environmental aspects of industrial catalysis are covered. The processes to be studied are chosen from the petroleum industry, the natural gas and coal processing industry, and the production of thermoplastics and synthetic fibres. The course ends with a rapid survey of problems associated with the treatment of industrial pollutants and with catalytic converters.

Component(s): Lecture

Topics in Multidisciplinary Chemistry

Description: This course explores themes within the area of Multidisciplinary Chemistry.

Component(s): Reading

Notes:
  • This course may be repeated for credit, provided that the subject matter is different each time.

Prerequisite/Corequisite: The following courses must be completed previously: CHEM 217; CHEM 218; CHEM 221; CHEM 222; CHEM 234; CHEM 235; CHEM 241; or equivalent.

Description: This modular course covers the areas of production, characterization and applications of nanoscale structures and materials. Each module is taught by a different professor as well as guest lecturers. Topics may include (but are not limited to): size dependent properties, synthesis of organic and inorganic nanostructures, self-assembled structures, chemical patterning and functional nanopatterns, biomaterials. Nanometer scale fabrication techniques such as lithographic methods, nano-stamping and patterned self-assembly are discussed. Modern analysis techniques such as atomic force microscopy and electron microscopy, which are used to map and measure at the single molecule level are introduced. Applications such as photonics, optical properties, biodetection and biosensors, micro- and nano-fluidics, nanoelectronics and nanomachines are presented. The course includes a term project carried out using the nanoscience facilities held in the department research labs.

Component(s): Lecture

Prerequisite/Corequisite: Students must complete 30 credits of CHEM courses including CHEM 293 or CHEM 335; or NANO 610.

Description: This course covers state-of-the-art nanomaterials physical characterization techniquesincluding but not limited to: dynamic light scattering, transmission and scanning electronicmicroscopies (size and morphology), X-ray powder and electron diffraction (crystallinityand phase identification), Fourier transform/attenuated total reflectance infrared, Ramanand X-ray photoelectron spectroscopies (surface chemical state and chemicalcomposition), differential scanning calorimetry and thermogravimetric analysis(polymorphism, moisture content and weight loss), Brunauer–Emmett–Teller analysis(surface area), nuclear magnetic resonance (chemical bonding and nuclei interactions).Content is delivered through lectures and laboratory demonstrations.

Prerequisite/Corequisite: The following courses must be completed previously: CHEM 217; CHEM 218; CHEM 312; or equivalent.

Description: The major aim of this course is to present a quantitative treatment of the variables that determine the composition of natural waters. Chemical equilibrium is the central theme of the course, but consideration is also given to kinetics, steady-state and dynamic models. Related themes include global chemical cycles, air and water pollution, as well as current research topics in water chemistry and chemical oceanography. Lectures only.

Component(s): Lecture

Notes:
  • Students who have received credit for CHEM 618 or for this topic under a CHEM 610 number may not take this course for credit.

Topics in Biochemistry

Description: This course explores themes within the area of Biochemistry and Biophysics.

Component(s): Lecture

Notes:
  • This course may be repeated for credit, provided that the subject matter is different each time.

Prerequisite/Corequisite: The following courses must be completed previously: BIOL 266; CHEM 375; or equivalent.

Description: Examples from the current literature are used to discuss what is known about how the membranes of biological organisms are assembled and the roles that these membranes play in a number of important processes. Emphasis is placed on the transport of proteins to and through biomembranes and the roles that membranes play in metabolite and ion transport. Where applicable, the significance of these processes is illustrated by examining the roles of membranes in health and disease.

Component(s): Lecture

Notes:
  • Students who have received credit for CHEM 671 may not take this course for credit.

Prerequisite/Corequisite: The following courses must be completed previously: CHEM 271; CHEM 375; or equivalent.

Description: This course explores steady-state kinetics, including such topics as the use of initial velocity studies and product inhibition to establish a kinetic mechanism; nonsteady-state kinetics, isotope effects, energy of activation, and the detailed mechanisms of selected enzymes.

Component(s): Lecture

Prerequisite/Corequisite: The following courses must be completed previously: CHEM 271; CHEM 375; or equivalent.

Description: This course examines the principles behind protein design, how techniques of protein engineering are used, and the methods used to assess protein properties. Examples include studies of protein stability, structure-function relationships, and applications to drug design.

Component(s): Lecture

Topics in Instrumentation

Description: This course explores themes within the area of Instrumentation.

Component(s): Lecture

Notes:
  • This course may be repeated for credit, provided that the subject matter is different each time.

Prerequisite/Corequisite: The following courses must be completed previously: CHEM 222; CHEM 393; or equivalent.

Description: This course is designed to provide the background in magnetic resonance theory necessary to understand modern high-resolution NMR experiments and instrumentation. The basic theory in the introductory section also applies to electron spin resonance (ESR). Relaxation and through-bond and through-space interactions, and experiments to investigate them are considered. Spin manipulations and behaviour in multiple-pulse, Fourier transform NMR techniques used for common spectral editing and two-dimensional experiments are discussed.

Component(s): Lecture

Prerequisite/Corequisite: The following course must be completed previously: CHEM 477 or equivalent. If prerequisites are not satisfied, permission of the Department of Chemistry and Biochemistry is required.

Description: This “hands on” course introduces students to the common techniques used to study the structure and function of proteins and other macromolecules. Techniques covered include circular dichroism spectroscopy, fluorescence, UV/Vis spectroscopy, Fourier transform infrared spectroscopy, isothermal titration microcalorimetry, analytical ultracentrifugation, and protein crystallization/X-ray crystallography. The course includes theory, applications of the technique to the study of protein structure and function, and basic practice experiments to become familiar with the instrument and data analysis. For some of the techniques covered hands-on use will be limited. Each student is required to carry out a project on his/her own protein of interest. Each participant asks a specific question about a protein and then uses the techniques covered in the course to address the question.

Component(s): Lecture; Laboratory

Notes:
  • Students who have received credit for this topic under a CHEM 690 number may not take this course for credit.

Chemistry and Biochemistry Theses, Seminars, Comprehensive Exam and Special Courses

Description: Students will work on a research topic under the direction of a faculty member and present an acceptable thesis at the conclusion. The thesis will be examined by the student's supervisory committee before being accepted by the department. In addition, an oral examination will be conducted before a committee of the department to test the student’s ability to defend the thesis.

Component(s): Thesis Research

Notes:
  • Students may submit a manuscript-based thesis following the guidelines outlined in the section on Thesis regulations in this calendar. In addition, an oral examination will be conducted before a committee of the department to test the student’s ability to defend the thesis.

Description: This course is designed to develop students' scientific communication skills in a professional forum via presenting a seminar on their MSc research topic. Students write an abstract, prepare presentation materials, give a seminar and defend their research to a broad and critical audience of chemistry and biochemistry faculty and peers, and critique the seminars of their peers.

Component(s): Seminar

Description: This course is designed to develop students' scientific communication skills in a professional forum via presenting a seminar on a current project/problem in their PhD research. Emphasis is placed on pedagogical approaches to broad-audience seminars with strong emphasis on critical analysis of data and clarity of interpretation. Students critique the seminars of their peers, write an abstract/advertisement for their seminar, prepare presentation materials, give a seminar and defend their research to a broad and critical audience of chemistry and biochemistry faculty and peers.

Component(s): Seminar

Description: Students will work on a research topic under the direction of a faculty member and present an acceptable thesis at the conclusion. In addition, a public oral examination will be conducted to test the student's ability to defend the thesis.

Component(s): Thesis Research

Notes:
  • Students may submit a manuscript-based thesis following the guidelines outlined in the section on Thesis regulations in this calendar.

Description: A student in the doctoral program is required to present a progress report on his/her research and on future research plans. The presentation should reflect the student's awareness of current research in his/her field and demonstrate an ability to carry out a significant research problem and provide a rational approach to its solution. The student's knowledge and understanding of fundamental chemical and biochemical principles will also be examined.

Component(s): Research

Notes:
  • The Examining Committee assigns one of the following two grades: (a) PASS - the student is admitted to candidacy for a PhD degree in Chemistry; (b) FAIL - the student must withdraw from the program.
  • The student is expected to complete this course within 18 months of admission directly into the PhD program, or within 28 months of admission via the MSc stream. In exceptional circumstances the department may permit an extension of time for completion of this course.

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