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CHEMISTRY 2120: Chemistry for the Life Sciences II Dr CHEMISTRY 2120: Chemistry for the Life Sciences II Dr. Ying Zheng 1 Written and compiled by Keith Aiken, under the supervision of Dr. Ying Zheng. This OER project has been funded by the Teaching Centre at the University of Lethbridge. Project Leader: Dr. Ying Zheng Project Assistant: Keith Aiken This work is licensed under a Creative Commons Attribution- NonCommercial-ShareAlike 4.0 International License. 2 Contributors and Online Resources Organic Chemistry With a Biological Emphasis by Tim Soderberg (University of Minnesota, Morris) Jonathan Mooney (McGill University) Chemistry: The Central Science by Brown, LeMay, Busten, Murphy, and Woodward William Reusch, Professor Emeritus (Michigan State U.) Paul Flowers (University of North Carolina - Pembroke), Klaus Theopold (University of Delaware) and Richard Langley (Stephen F. Austin State University.) Dr. Dietmar Kennepohl FCIC (Professor of Chemistry, Athabasca University) Richard Banks (Boise State University) Organic Chemistry by John McMurry Ekta Patel (UCD), Ifemayowa Aworanti (University of Maryland Baltimore County) Stephen Lower, Professor Emeritus (Simon Fraser U.) Contributed by Elizabeth Gordon, Lecturer (Chemistry) at Furman University CK-12 Foundation by Sharon Bewick, Richard Parsons, Therese Forsythe, Shonna Robinson, and Jean Dupon. Gamini Gunawardena from the OChemPal site (Utah Valley University) Charles Ophardt, Professor Emeritus, Elmhurst College; Virtual Chembook Tiffany Lui, University of California, Davis. Simarjit Batth (UCD) Jim Clark (Chemguide.co.uk) Former Head of Chemistry and Head of Science at Truro School in Cornwall Prof. Steven Farmer (Sonoma State University) Satish Balasubramanian Prof. R Balaji Rao (Dept of Chemistry, Banaras Hindu University, Varanasi) as part of Information and Communication Technology Chris P Schaller, Ph.D., (College of Saint Benedict / Saint John's University) Other References • John D. Robert and Marjorie C. Caserio (1977) Basic Principles of Organic Chemistry, second edition. W. A. Benjamin, Inc., Menlo Park, CA. ISBN 0-8053-8329-8. • Vollhardt, K. Peter C., and Neil E. Schore. Organic Chemistry Structure and Function. New York: W. H. Freeman, 2007. • Fox, Mary Ann, and James K. Whitesell. Organic Chemistry. 3rd Ed. Burlington: Jones & Bartlett Learning, 2005. • Schore and Vollhardt. Organic Chemistry Structure and Function. New York: W.H. Freeman and Company, 2007. • McMurry, John and Simanek, Eric. Fundamentals of Organic Chemistry. 6th Ed. Brooks Cole, 2006. • Dehestani, Ahmad et al. “Ligand-assisted reduction of osmium tetroxide with molecular hydrogen via a [3+2] mechanism.” Journal of the American Chemical Society, 2005, 127 (10), 3423-3432. • Sorrell, Thomas, N. Organic Chemistry. New York: University Science Books, 2006. • Vollhardt, Peter, and Neil E. Schore. Organic Chemistry: Structure and Function. 5th Ed. New York: W. H. Freeman & Company, 2007. 3 TOPIC 1: REPRESENTATIVE HYDROCARBONS ............................................................................................ 8 SATURATED HYDROCARBONS ........................................................................................................................... 8 Structural Formula (SF), Condensed SF, and Molecular Formula (MF) .................................................................................. 8 Equivalent Dash Formulas ...................................................................................................................................................... 9 Dash Formulas that are Not Equivalent ................................................................................................................................. 9 Constitutional Isomers ........................................................................................................................................................... 9 Line-Angle (Bond-Line) Formulas ......................................................................................................................................... 10 Nomenclature ...................................................................................................................................................................... 10 Nomenclature: Alkanes ........................................................................................................................................................ 11 IUPAC Rules for Alkane Nomenclature ................................................................................................................................ 13 More on Constitutional Isomers .......................................................................................................................................... 13 Classifying Carbons and Their Hydrogens ............................................................................................................................ 14 How to Recognize an Alkyl Group ........................................................................................................................................ 14 Haloakanes ........................................................................................................................................................................... 15 Unsaturated Hydrocarbons: Alkenes & Alkynes ............................................................................................... 15 Alkenes ................................................................................................................................................................................. 15 Alkynes ................................................................................................................................................................................. 16 Three-Dimensional Structural Formulas ........................................................................................................... 16 Nomenclature ...................................................................................................................................................................... 17 Additional Naming Adjustments .......................................................................................................................................... 17 Terpenes, Cyclic Alkanes, and Aromatic Compounds ........................................................................................ 18 Terpenes .............................................................................................................................................................................. 18 Unsaturated Hydrocarbons: Cyclic Alkanes ...................................................................................................... 18 Naming Cycloalkanes ........................................................................................................................................................... 18 Unsaturated Hydrocarbons: Aromatic Compounds .......................................................................................... 19 TOPIC 2: STEREOCHEMISTRY I ................................................................................................................ 21 Conformations and Conformers ...................................................................................................................... 21 Newman Projection ........................................................................................................................................ 21 Dihedral Angle and Torsional Strain ................................................................................................................ 22 Ring Strain ...................................................................................................................................................... 24 Two Kinds of Hydrogen of Cyclohexane ............................................................................................................................... 27 Substituents Prefer Equatorial Position in Cyclohexane ...................................................................................................... 27 Disubstituted Cycloalkanes ............................................................................................................................. 28 Conformational Preference of Disubstituted Cyclohexanes ................................................................................................ 29 TOPIC 3: FAMILIES OF ORGANIC COMPOUNDS ....................................................................................... 31 What is Functional Group? .............................................................................................................................. 31 Nomenclature................................................................................................................................................. 31 Naming Priorities ................................................................................................................................................................. 32 Alcohols ......................................................................................................................................................... 32 Primary alcohols ................................................................................................................................................................... 32 Secondary alcohols .............................................................................................................................................................
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