1. Chemistry 2100 Fall 2011

2. Bloom’s Taxonomy Richard C. Overbaugh, Lynn Schultz Old Dominion University

3. Student Objectives for this course Analyze and explain chemical differences among the various classes of organic compounds Evaluate carbohydrate structure and reactivity Compare and contrast the four main classes of key biomolecules Explain the processes of protein folding and enzymatic catalysis Use knowledge of replication, transcription, and translation to predict the outcome of genetic diseases Relate biochemical concepts to digestion, metabolism, and nutrition

4. Organic & Biological Chemistry

6. General Chemistry H 1 0 C 4 0 N 3 1 O 2 2 X 1 3 element covalent bonds lone pairs ~109.5°

7. Valence Shell Electron Pair Repulsion Theory 4tetrahedral 109.5° 3 trigonal planar 120° 2 linear 180° regions of predicted predicted electron density geometry bond angles ~109.5° 120° 180° 120°

8. Meet the Elements http://www.youtube.com/watch?v=Uy0m7jnyv6U

9. English Language Cursive Print Shorthand Type

10. The language of Chemistry Molecular Formula C2H6OC2H6O Structural Formula Condensed Structural Formula CH 3 CH 2 OH 3D Structural Formula Molecular Representation Skeletal, line-angle Formula or

11. Alkanes Simplest hydrocarbons Composed of only single bonds Often referred to as aliphatic hydrocarbons –From Greek aleiphar (fat or oil) Also called Paraffins –From Latin parum affinis (barely reactive) General formula: C n H 2n+2

12. Methane & Ethane

13. Propane & Butane

14. Butane & Constitutional Isomers n-butane isobutane C 4 H 10

15. How many constitutional isomers? C 5 H 12 3 C 6 H 14 5 C 10 H 22 75 C 20 H 42 366,319 C 30 H 62 > 4 billion C 40 H 82 > 65 trillion C 20 H 42 366,319 C 30 H 62 > 4 billion C 40 H 82 > 65 trillion constitutional (structural) isomers

16. Naming Conventions: IUPAC Nomenclature International Union of Pure and Applied Chemistry Gives a set of unambiguous names Despite this, common names are still used

17. Naming Alkanes #C Prefix + -ane C 3 "prop" Gr., protos pion (first fat)* C 4 "but" L., butyrum (butter) C 5 "pent" Gr., pente (five) C 6 "hex" Gr., hex (six) C 7 "hept" Gr., hepta (seven) C 8 "oct" L., octo (eight) C 9 "non" L., nona (nine) C 10 "dec" L., deca (ten) C 1 "meth" Gr., methy (wine)* C 2 "eth" Gr., aithein (blaze)

18. Alkyl groups

19. Naming Algorithm (a) parent C-chain (b) substituents (c) numbers (d) alphabetical listing Parent —Suffix IUPAC Rules Substituents—

20. Dreadful Details! 1. The name for an alkane with an unbranched chain of carbon atoms consists of a prefix showing the number of carbon atoms and the ending -ane. 2. For branched-chain alkanes, the longest chain of carbon atoms is the parent chain and its name is the root name. 3. Name and number each substituent on the parent chain and use a hyphen to connect the number to the name. 4. If there is one substituent, number the parent chain from the end that gives the substituent the lower number.

21. Dreadful details (part 2)! 5. If the same substituent occurs more than once: –Number the parent chain from the end that gives the lower number to the substituent encountered first. –Indicate the number of times the substituent occurs by a prefix di-, tri-, tetra-, penta-, hexa-, and so forth. –Use a comma to separate position numbers. 6. If there are two or more different substituents –List them in alphabetical order. –Number the chain from the end that gives the lower number to the substituent encountered first. –If there are different substituents at equivalent positions on opposite ends of the parent chain, give the substituent of lower alphabetical order the lower number. 7. Do not include the prefixes di-, tri-, tetra-, and so forth or the hyphenated prefixes sec- and tert- in alphabetizing; –Alphabetize the names of substituents first, and then insert these prefixes.

22. Alkane Origins

23. Physical Properties of Alkanes

24. Isomers and Physical Properties pentane bp 36°C; mp -130°C d 0.626 neopentane bp 9°C; mp -16°C d 0.606 isopentane bp 28°C; mp -160°C d 0.620

25. Alkane Origins

26. Gasoline, Combustion, & Octane Ratings C6-C12 mixture CH 4 + 2O 2  CO 2 + 2H 2 O + 212 kcal/mol CH 3 CH 2 CH 3 + 5 O 2  3 CO 2 + 4H 2 O + 530 kcal/mol but… 2 CH 3 CH 2 CH 3 + 7 O 2  2 CO 2 + 2 CO + 2 C + 8H 2 O + < 530 kcal/mol Octane Rating – Controlled Explosions 2,2,4-trimethylpentane (iso-octane) Octane rating 100 Heptane Octane rating 0 Ethanol Octane rating 105 Octane Octane Rating -20

27. Halogenation Perfluorodecalin polytetrafluoroethylene (PTFE) Teflon dichlorodifluoromethane Freon dichlorodiphenyltrichloroethane DDT

28. Cycloalkanes C n H 2n 60° 90° 108° 120° 128° 135° 60° 88° 105° 109° 109° 109°

29. Interesting Cycloalkane Derivatives Testosterone Cholesterol Estradiol Muskone

30. Cyclohexane

31. Cyclohexane – the Chair 1 2 3 5 6 4 "chair"

32. Cyclohexane Substituents H H CH 3 H H H H 1 6 5 4 3 (3) (3') (1) 2 3 2 1 6 5 4 (3) (3') (1) 95% 5% 1,3-diaxial interactions H H CH 3 H H H H 1 6 5 4 3 (3) (3') (1) 2 3 2 1 6 5 4 (3) (3') (1)

44. Geometric Isomers, a.k.a. cis-trans isomers perspective Haworth Cl H H H H cis-1,2-dichlorocyclopentane perspective Haworth Cl H H H H trans-1,2-dichlorocyclopentane