CHEM 760/7600 - Carbohydrate Chemistry

Semester: Fall 2024

Professor: F.I. Auzanneau | Discipline: Organic | Campus: Guelph

Description

Chemistry CHEM 760/7600 is a one-semester reading course covering the chemistry and biological chemistry of carbohydrates. This course will apply concepts learned in Chem*2700 and Chem*3750 to carbohydrate molecules.

Specific Learning Objectives:

  1. To learn about the structural fundamentals of carbohydrates.
  2. To learn the basic biological importance of oligo-and polysaccharides.
  3. To learn fundamentals concepts of synthetic carbohydrate chemistry and to be able to design syntheses of organic molecules of moderate complexity.
  4. To learn then be able to use one dimension and two dimension NMR experiments to characterize synthetic molecules.
  5. To be able to survey the literature and identify a question that has yet to be answered in the area of glycobiology.
  6. To design a sound research proposal that would allow answering the question identified
  7. To learn the basic skills required to write a Grant proposal in the NSERC format.
  8. To concisely present the proposed research orally to a mixed audience.

Materials

  • Textbook required:

Essentials of Carbohydrate Chemistry and Biochemistry, 3rd Completely Revised and Enlarged Edition, Thisbe K. Lindhorst, Wiley-VCH, ISBN: 978-3-527-31528-4

Recommended additional readings will be selected from:

Organic synthesis with carbohydrates
Author: Boons, Geert-Jan. Hale, Karl.
Publisher: Malden, MA: Blackwell Science, 2000

Bioorganic Chemistry: Carbohydrates.
Editor: S. Hecht.
Publisher: Oxford University Press

Glycochemistry: Principles, Synthesis and Applications
Editors: P.G. Wang and C.R Bertozzi
Publisher: Marcel Dekker, Inc., New York. Basel

Modern Methods in Carbohydrate Synthesis.
Editors: S. H. Khan and R.A. O’Neill
Publisher: Harwood Academic Publishers

Spectrometric Identification of organic Compounds, 6th or 7th Edition
Authors: R.M. Silverstein, F.X. Webster, D.J. Kiemle
Publisher: Wiley&Sons

  • Additional resources are:

Title: Preparative carbohydrate chemistry
Author: Hanessian, Stephen.
Publisher: New York : Marcel Dekker, c1997.

Carbohydrates in chemistry and biology
Authors: Ernst, Beat Hart, Gerald W, Sinaÿ, Pierre
Publisher: Weinheim ; New York : Wiley-VCH, c2000.

  • REQUIRED: TOPSPIN software– I will give you a set of data to print and analyze.
  • Other resources such as pdf files of literature articles as well as lecture material will be sent to you by email.

Evaluation

You will be assessed on the following:

  • 1 take home NMR analysis (you will need to process and print the data)
  • 1 in person test to be scheduled (may be combined with the NMR test below)
  • 1 in person test NMR analysis to be scheduled
  • 1 NSERC-style research proposal

Grades will be calculated as follow:

Exam: 40%
Research Proposal: 20%
NMR Test: 20%
NMR practice: 20%

NMR practice and test: This will be based on “real” set of NMR data.

Research Proposal:

Each student will search the glycobiology literature and design an original research project. Such project could be aimed towards the synthesis of molecules relevant to glycobiology, method development for synthetic carbohydrate chemistry etc… You will write up this research proposal in an NSERC format, including Background/Relevance, descriptive short-term goals, long-term goals and impact. You will also be asked to provide an appropriate budget. We will have one meeting to discuss grant proposal writing.

Lab/Project

This is a reading course that will not have “official” class time. You can meet me online (or in person) by appointment only. Below is the schedule of reading. It is highly recommended that you follow it and not fall behind as you will be tested on all aspects covered in these readings.

 Week 1:

Structure of monosaccharides

Objectives

  • Learn about carbohydrates, their CONFIGURATION, nomenclature.
  • Be able to name/draw the most important sugars (Glc, Gal, Man, Fuc, Rha and their derivatives) in various representations (Fischer, Haworth, chair)
  • Understand and be able to name the CONFORMATION of monosaccharides in their 6-membered ring form.
  • Understand mutarotation, the anomeric effect, understand the NOMENCLATURE of the anomeric position (α is not necessarily axial…)

Readings and Activities

  • Read pdf file “1. Structure of monosaccharides-F24”
  • Read Chapter 2 in our textbook
  • Practice all questions in textbook chapter 2 as well as Problem set 1.

Recommended Additional readings:

    • Chapter 1 Organic synthesis with carbohydrates (Boons, G-J; Hale, K Publisher: Malden, MA: Blackwell Science, 2000)

Weeks 2 and 3:

Biological Relevance of carbohydrates

Objectives

  • Realize the variety of carbohydrate-based molecules and their importance in Biology.
  • Be able to cite/describe biologically relevant oligo- or polysaccharides and their occurrence.

Readings and Activities

  • Read pdf file “2. Biological relevance of carbohydrates_2024”
  • Read Chapter 6 in textbook
  • Answer questions 6.1, 6.3, 6.9, 6.13, 6.17 in textbook, as well as Problem set 2.

Recommended Additional readings:

  • Read Chapters 8 and 10 from Bioorganic Chemistry: Carbohydrates. Editor: S. Hecht.

 Week 4 and 5:

Synthetic carbohydrate chemistry: Protecting Groups

Objectives

  • Have a basic understanding of the major protecting groups class.
  • Know mechanisms to “put them on” and “take them off.”
  • Understand regiochemical reactions, kinetic vs thermodynamic products.
  • Be able to design a synthetic strategy to prepare a given monosaccharide building block.

Readings and Activities

  • Read pdf file “3. Protecting Groups 2024”
  • Read Chapter 3 in textbook
  • Practice on textbook problems 3.1–3.17 and Problem set 3: 1A, 1B, 3, 5.

Recommended Additional readings:

  • Read Chapter 2 in Organic synthesis with carbohydrates Author: Boons, Geert-Jan. Hale, Karl.

Week 6 and 7:

Synthetic Carbohydrate Chemistry: The Glycosylation Chemistry

Objectives

  • Understand the glycosylation reaction and the factors that impact stereochemistry of the products.
  • Know mechanism of glycosylation reactions, the expected products depending on the structures of the donor and acceptor.
  • Know mechanisms for the formation of the major types of glycosyl donors and their activation in glycosylation reaction.
  • Understand stereochemical outcomes: kinetic vs thermodynamic products.
  • Understand participation and intramolecular aglycon delivery.
  • Be able to design a synthetic strategy to prepare an oligosaccharide of defined stereochemistry.

Readings and Activities

  • Read pdf file “4. The Glycosylation Reaction 2024”
  • Read Chapter 5 in textbook
  • Practice on textbook questions 5.2–5.19, 5.24, 5.30 (1, 4) and Problem set 3: 1C, 1D, 2, 4.

Recommended Additional readings:

  • Read Chapter 4 in Organic synthesis with carbohydrates Author: Boons, Geert-Jan. Hale, Karl.
  • Also read the selected chapters mentioned in the pdf file.

 Week 8 and 9:

NMR of Carbohydrates and Oligosaccharides

Objectives

  • Be able to assign hydrogens’ and carbons’ chemical shifts using 1D and 2D experiments.
  • Be able to distinguish between the main sugar units.
  • Be able to assign protecting group signals.
  • Understand the importance of NMR data to confidently assign structures and assess mono- and oligosaccharides’ conformations.

Readings and Activities

  • Read pdf file “5. NMR and Conformation 2024”
  • Read textbook Chapter 8: 8.2.
  • Practice assigning the data for spectra 1 – 8.

Recommended Additional readings:

  • Read Chapter 7 from Bioorganic Chemistry: Carbohydrates. Editor: S. Hecht.
  • Read the relevant Chapters in Spectrometric Identification of organic Compounds, 6th or 7th Edition Authors: R.M. Silverstein, F.X. Webster, D.J. Kiemle (6th Edition: Chapters 4,5 and 6; 7th edition: Chapters 3, 4 and 5)

Week 10-12:

Prepare NSERC-type research proposal

Schedule

  • Thu: 9:30 am - 10:30 am in Remote (by appointment)

Office Hours

Email: [email protected]. Last minute information may be sent to you by email, make sure that you retrieve your mail regularly.