Outline

1. Outline • 4.1 Alkanes: The Simplest Organic Compounds • 4.2 Representing Structures of Organic Compounds • 4.3 Families of Compounds—Functional Groups • 4.4 Nomenclature of Simple Alkanes • 4.5 Isomerism in Organic Compounds

2. Organic Chemistry The chemistry of the compounds of carbon Pure carbon exists in nature in multiple forms Graphite C?? Diamond C?? Buckeyballs C60

3. Hydrocarbons Chemical compounds containing only C and H Alkanes A class of linear hydrocarbons with no double bonds Formula: CnH(2n+2) Alkanes are nonpolar compounds C & H are close in electronegativity (2.5 vs. 2.1) bonds are nonpolar covalent small or no dipole moment insoluble in water (like dissolves like)

4. Naming Alkanes – hydrocarbons with CnH(2n+2) Methane CH4 Ethane C2H6 Propane C3H8 Butane C4H10 Pentane C5H12 Hexane C6H14 Heptane C7H16 Octane C8H18 Nonane C9H20 Decane C10H22

5. Cyclic alkanes have ring structures Use cyclo prefix CnH2n

6. Representing hydrocarbon structures – e.g. propane C3H8 Draw the Lewis Structure for Propane Is the chain (3 carbons) for propane …. a) straight (180º) b) bent at ~ 109º b) bent at ~ 90º

7. Naming alkanes that have branched chains and/or substituents Name of alkane corresponding to longest chain Alkanes as substituents – replace ‘ane’ with yl - CH3 methyl - CH2 - CH3 ethyl - CH2 - CH2- CH3proply - CH2 - CH2- CH2 - CH3butyl etc. Other substituents halides: - F (fluoro) - Cl(chloro) etc. - OH (hydroxy) etc.

8. Naming alkanes that have branched chains and/or substituents Rules CH3 – CH2 – CH2 – CH – CH3 | Cl 1. Identify the parent (longest) chain 2. Identify the substituent(s) 3. Assign a number to each substituent based on where it is located on the parent chain. Proceed in the direction that gives the lowest number 2-chloropentane

9. Naming alkanes that have branched chains and/or substituents Rules CH3 – CH2 – CH2 – CH – CH3 | | ClCl CH3 – CH2 – CH2 – CH – CH2 | CH3 2,3-dichloropentane 2-methylpentane 2,3 –dimethylpentane 2-metylhexane 3-methylhexane CH3 – CH2 – CH2 – CH – CH2 | | CH3 CH3

10. Naming alkanes that have branched chains and/or substituents Rules CH3 – CH2 – CH2 – CH – CH3 | CH2 – CH2 - CH3 2-propylpentane 4-methylheptane CH3 – CH2 – CH2 – CH – CH2– CH3 | | Cl CH3 2-chloro-4-methylhexane 3-methyl-5-chlorohexane

11. Isomers Sets of molecules with the same molecular formula …. that are not identical Structural isomers – Have different atom connectivity (or arrangement) Cis-trans isomers – Have the same connectivity but differ in 2D orientation typically in molecules with double bonds or rings Optical isomers – Have the same connectivity but differ in 3D orientation optical isomers have “chiral” carbon – bonded to 4 distinct groups

12. Isomers Sets of molecules with the same molecular formula …. that are not identical Structural isomers – Have different atom connectivity (or arrangement) Butane - C4H10

13. Hydrocarbons Chemical compounds containing only C and H Alkenes A class of hydrocarbons with a double bond Formula: CnH(2n) Ethene (or ethylene) CH2 = CH2 Draw the Lewis dot structure for ethylene Describe the molecular geometry around each C Draw the structure with as accurate a geometry as possible. H H C = C H H

14. Propene CH2 = CH – CH3 1-butene CH2 = CH – CH2 – CH3 2-butene CH3 - CH = CH – CH3 Structural isomers – Have different atom connectivity (or arrangement) Are 1-butene and 2-butene structural isomers? Cis-trans isomers – Have the same connectivity but differ in 2D orientation typically in molecules with double bonds or rings Draw the Lewis dot structure for 2-butene Describe the molecular geometry around the C = C carbons. Draw the structure with as accurate a geometry as possible.

15. 4.5 Isomerism in Organic Compounds

16. Hydrocarbons Chemical compounds containing only C and H Alkynes A class of hydrocarbons with a triple bond Ethyne (or acetylene) CH ≡ CH Draw the Lewis dot structure for acetylene Describe the molecular geometry around each C Draw the structure with as accurate a geometry as possible. H - C ≡ C - H Can you have cis-trans isomerism around a triple bond? a) Yes b) No

17. Benzene and aromatic hydrocarbons Toluene or methylbenzene 2,4,6 – trinitrotoluene TNT

18. Hydrocarbons Alkanes Alkene contain C=C double bond Alkynes contain C≡C triple bond Aromatic contains ring with multiple double bonds - delocalized Functional Groups Organic Molecules often contain atoms other than C and H. Most common are bonds to O and N. Specific arrangements atoms are referred to as Functional groups. This is because they give molecules various functions. Most cellular molecules are organic molecules containing one or more functional groups.

19. Functional Groups Alcohols - OH (hydroxyl group) R – OH R represents any hydrocarbon chain CH3 - OH methanol or methyl alcohol CH3 – CH2 – OH ethanol or ethyl alcohol OH 2-hydroxypropane or isopropanol or isopropyl alcohol a secondary alcohol rubbing alcohol is typically a 70% solution of IPA in water

20. Functional Groups O || CH3 - C - H O || - C - Aldehydes and Ketones Formaldehyde acetaldehydeacetone O || CH3 - C – CH3 O || R - C - H O || R - C - R' O || H - C - H The combination of alcohols with aldehydes or ketones is found in sugar molecules (with a little twist!)

21. Functional Groups Amines -NH2 (amino group) R – NH2R represents any hydrocarbon chain CH3 – NH2methyl amine CH3 – CH2 – NH2ethyl amine CH3 – CH2 – CH2 – CH – CH3 | NH2 2-aminopentane Fish oils contain amines, so amines are said to smell fishy!

22. Carboxylic acids COOH (carboxyl group) O || R - C - OH Functional Groups Acetic acid - vinegar is a 5% acetic acid solution O || CH3 - C - OH Benzoic acid Fatty acids – Carboxylic acids with long chains saturated – no C=C bonds unsaturated – one or more C=C bonds

23. Fatty acids – Carboxylic acids with long chains saturated – no C=C bonds unsaturated – one or more C=C bonds stearic acid 18 C – saturated oleic acid 18 C – 1 C=C monounsaturated Bent structure (cis only) linolenic acid 18 C – 3 C=C polyunsaturated Ω – 3 fatty acid

24. 4.3 Families of Compounds—Functional Groups

25. Functional Groups ethers - C – O – C - Functional Group combinations O O || || R - C – OH + HO - R' → R - C – O - R' + H - OH Carboxylic acid + alcohol → ester + water O H O H || | || | R - C – OH + H - N - R' → R - C – N - R' + H - OH Carboxylic acid + amine → amide + water

26. 4.5 Isomerism in Organic Compounds • A right-handed and a left-handed baseball glove are nonsuperimposable mirror images. • Objects such as these are termed chiral (from the Greek cheir, meaning “the hand”). • Most enantiomers contain a chiral center—a tetrahedral carbon atom bonded to four different atoms or groups of atoms.

27. 4.5 Isomerism in Organic Compounds • On paper, a chiral carbon is represented with an asterisk.

28. 4.5 Isomerism in Organic Compounds Identifying Chiral Carbons in a Molecule • Step 1: Locate the tetrahedral carbons (carbons with four atoms bonded to them). • Step 2:Inspect the tetrahedral carbons. Determine if the four groups attached to the tetrahedral carbons are different. • Step 3:Assign the chiral centers. Typically, an asterisk is drawn next to the chiral carbon.

29. 4.5 Isomerism in Organic Compounds

30. Thalidomide Story 1954: synthesized West Germany 1957: approved as sedative/soporific 1960: application to FDA denied 1961: peripheral neuritis noted  birth defects noted 1962: drug withdrawn in Europe Kelsey awarded medal

31. Distinguishing Properties of Enantiomers optical isomers that are mirror images of each other 1.They can’t be superimposed 2. They rotate plane polarized light in different directions 3. They react differently in a chiral environment!

32. Protein Surface binding points D L

33. Protein Surface correct ligand incorrect ligand D L

34. 4.5 Isomerism in Organic Compounds r-thalidomide s-thalidomide L teratogen sedative & soporific D

35. Chapter Four Summary (continued) • 4.3 Families of Compounds—Functional Groups • Organic compounds are grouped into families based on the identity of the functional group(s) present. • A functional group is a common grouping of atoms bonded in a particular way. • Functional groups have specific properties and reactivity. Compounds with the same functional group behave similarly. • Since the functional group is the part of the molecule that is of interest, we typically represent the hydrocarbon portion as R (the Rest of the molecule). • The hydrocarbon families the alkenes, alkynes, and aromatics are highlighted in this section. • Fatty acids are alkane-like biomolecules that are the primary components of dietary fats. Fatty acids with a carbon–carbon double bond in their structure are referred to as unsaturated, while those without a double bond are referred to as saturated.

36. 4.5 Isomerism in Organic Compounds