Organic and Biological Molecules

1. Organic and Biological Molecules Chapter 22

2. Organic Chemistry and Biochemistry • The study of carbon-containing compounds and their properties. • The vast majority of organic compounds contain chains or rings of carbon atoms. • The study of the chemistry of living matter

3. Hydrocarbons • compounds composed of carbon and hydrogen. • Saturated compounds (alkanes) have the maximum number of hydrogen atoms attached to each carbon atom

4. Unsaturatedcompounds have fewer hydrogen atoms attached to the carbon chain than alkanes • Unsaturated: They contain carbon-carbon multiple bonds (double or triple)

5. 22.1 Alkanes: Saturated hydrocarbons • Saturated hydrocarbons, CnH2n+2 • “Saturated” because they can’t take any more hydrogen atoms • Normal straight chains (unbranched hydrocarbons) H3C–(CH2)n–2–CH3 • Waxes, oils, & fuel gases as n decreases.

6. Alkanes: Saturated Hydrocarbons The C-H Bonds in Methane

7. The Lewis structure of ethane.

8. Propane

9. Butane

10. The First 10 “Normal” Alkanes C1 - C4 are Gases at Room Temperature Name Formula M.P. B.P. # Structural Isomers • Methane CH4 -183 -162 1 • Ethane C2H6 -172 -89 1 • Propane C3H8 -187 -42 1 • Butane C4H10 -138 0 2 • Pentane C5H12 -130 36 3 • Hexane C6H14 -95 68 5 • Heptane C7H16 -91 98 9 • Octane C8H18 -57 126 18 • Nonane C9H20 -54 151 35 • Decane C10H22 -30 174 75 C5 - C16 are Liquids at Room Temperature

11. IUPAC Rules for Naming Branched Alkanes • Find and name the parent chain in the hydrocarbon - this forms the root of the hydrocarbon name • Number the carbon atoms in the parent chain starting at the end closest to the branching • Namealkane branches by dropping the “ane” from the names and adding “yl”. A one-carbon branch is called “methyl”, a two-carbon branch is “ethyl”, etc… • When there are more than one type of branch (ethyl and methyl, for example), they are named alphabetically • Finally, use prefixes to indicate multiple branches

12. Rules for Naming Alkanes 1. For alkanes beyond butane, add -aneto the Greek root for the number of carbons. C-C-C-C-C-C : hexane 2. Alkyl substituents: drop the -aneand add -yl -C2H5 is ethyl

14. Rules for Naming Alkanes 3. Positions of substituent groups are specified by numbering the longest chain sequentially. C  C-C-C-C-C-C 3-methylhexane • Start numbering at the end closest to the branching 4. Location and name are followed by root alkane name. Substituents are given in alphabetical order and use di-, tri-, etc.

15. Normal vs Branched Alkanes • Normal alkanes consist of continuouschains of carbon atoms • Alkanes that are NOT continuous chains of carbon atoms contain branches • The longest continuous chain of carbons is called the parent chain

16. Structural Isomerism • Structural isomers are molecules with the same chemical formulas but different molecular structures - different “connectivity”. • They arise because of the many ways to create branched hydrocarbons. n-pentane, C5H12 2-methlbutane, C5H12

17. 2 4 1 3 5 Example : Show the structural formula of 2,2-dimethylpentane • The parent chain is indicated by the ROOT of the name - “pentane”. This means there are 5 carbons in the parent chain. • “dimethyl” tells us that there are TWO methyl branches on the parent chain. A methyl branch is made of a single carbon atom. • “2,2-” tell us that BOTH methyl branches are on the second carbon atom in the parent chain.

18. 2 4 1 3 5 6 7 Example: Structural formula of 3-ethyl-2,4-dimethylheptane? • The parent chain is indicated by the ROOT of the name - “heptane”. This means there are 7 carbons in the parent chain. • “2,4-dimethyl” tells us there are TWO methyl branches on the parent chain, at carbons #2 and #4. • “3-ethyl-” tell us there is an ethyl branch (2-carbon branch) on carbon #3 of the parent chain.

19. 3 5 4 6 2 7 1 8 5 3 2 4 6 7 1 8 Example: 2,3,3-trimethyl-4-propyloctane • The parent chain is indicated by the ROOT of the name - “octane”. This means there are 8 carbons in the parent chain. • “2,3,3-trimethyl” tells us there are THREE methyl branches - one on carbon #2 and two on carbon #3. • “4-propyl-” tell us there is a propyl branch (3-carbon branch) on carbon #4 of the parent chain.

20. 4 3 5 5-ethyl- 3,4-dimethyl octane Example : Name the molecules shown • parent chain has 5 carbons - “pentane” • two methyl branches - start counting from the right - #2 and #3 • 2,3-dimethylpentane • parent chain has 8 carbons - “octane” • two methyl branches - start counting from the left - #3 and #4 • one ethyl branch - #5 • name branches alphabetically

21. Reactions of alkanes • Combustion reactions 2C4H10 + 13 O2 8CO2 + 10 H2O(g) • Substitution Reactions CH4 + Cl2 CH3Cl + HCl CH3Cl+ Cl2 CH2Cl2 + HCl CH2Cl2 + Cl2 CHCl3 + HCl CHCl3 + Cl2 CCl4

22. Dehydrogenation Reactions CH3CH3 CH2CH2 Ethylene

23. Cyclic alkanesCnH2n • A cycloalkane is made of a hydrocarbon chain that has been joined to make a “ring”. • Note that two hydrogen atoms were lost in forming the ring

24. Ring Structures

25. Cyclohexane - Boat & Chair Conformations • Cyclohexane is NOT a planar molecule. To achieve its 109.5° bond angles and reduce angle strain, it adopts several different conformations. • The BOAT and CHAIR (99%) are two conformations Boat chair

26. 22.2 Alkenes and Alkynes Alkenes: hydrocarbons that contain a carbon-carbon double bond. [CnH2n] C=C Ethene CC=C propene Alkynes: hydrocarbons containing a carbon-carbon triple bond. [CnH2n-2] C ΞC Ethyne CCC Ξ CC 2-pentyne

27. Alkenes are hydrocarbons that contain at least one carbon-carbon doublebond Alkynes are hydrocarbons that contain at least one carbon-carbon triple bond The suffix for the parent alkane chains are changed from “ane” to “ene” and “yne” e.g. ethene, ethyne Where it is ambiguous, the BONDS are numbered like branches so that the location of the multiple bond may be indicated Alkenes & Alkynes

28. Alkenes, CnH2n • Cycle formation isn’t the only possible result of dehydrogenation. • Adjacent C’s can double bond, C=C, making an (unsaturated) alkene. Sp2

29. Nomenclature for Alkenes 1.Parent hydrocarbon name ends in -ene C2H4; CH2=CH2is ethene 2. With more than 3 carbons, double bond is indicated by the lowest numbered carbon atom in the bond. C=C-C-C is 1-butene

30. Nomenclature alkenes and alkynes

31. Cis and Trans Isomers • Double bond is fixed (rotation around the double bond is restricted) • Cis/trans Isomers are possible CH3 CH3 CH3 CH = CH CH = CH cistrans CH3

32. Reactions of alkenes and alkynes • in which (weaker)  bonds are broken and new (stronger)  bonds are formed to atoms being added. 1. Addition Reactions

33. Hydrogenation reaction • Adds a hydrogen atom to each carbon atom of a double bond H H H H catalyst H–C=C–H + H2 H–C–C–H H H Ethene Ethane CH3-CH3

34. Halogenation reaction • Adds a halogen atom to each carbon atom of a double bond H H H H catalyst H–C=C–H + Cl2 H–C–C–H Cl Cl Ethene Dichloro ethane

35. Halogenation Reactions CH2 CHCH2CH2CH2 + Br2 CH2Br CHBrCH2CH2CH2 1,2-dibromopentane

36. Alkynes, CnH2n–2 • Carbon-carbon triple bonds • Names end in -yne HCCH ethyne(acetylene) HCC-CH3 propyne • sp triple bonding makes a rigid 180° segment in a hydrocarbon.

37. The Bonding in Acetylene

38. Naming Alkenes and Alkynes When the carbon chain has 4 or more C atoms, number the chain to give the lowest number to the double or triple bond. 1 2 3 4 CH2=CHCH2CH3 1-butene CH3CH=CHCH3 2-butene CH3CHCHCH3 2-butyne

39. Question Write the IUPAC name for each of the following unsaturated compounds: A. CH3CH2CCCH3 CH3 B. CH3C=CHCH3 C. 2-pentyne 2-methyl-2-butene 3-methylcyclopentene

40. Question • Name the following compound 5-ethyl-3-heptyne

41. Additions reactions:Hydrogenation and Halogenation Hydrogens and halogens also add to the triple bond of an alkyne.

42. 22.3 Aromatic hydrocarbonsUnsaturated Cyclic hydrocarbons • Alternating single/double bond cycles occur in many organic molecules • This class is called “aromatic” (by virtue of their aroma). • Delocalized  bonds • possess a great stability • thus benzene does not • react like unsaturated • hydrocarbons

43. sp2 sp2 sp2 Benzene C6H6 • The  structure is often preserved in benzene chemical reactions • Aromatic rings do not add, they substitute instead

44. Shorthand notation for benzene rings The bonding in the benzene ring is a combination of different Lewis structures

45. Aromatic Hydrocarbons Substitution reaction Nitroobenzene Chlorobenzene -NO2 -CH3 + Cl2 Toluene HNO3 HNO3 benzene CH3Cl + HCl +H2O +HCl

47. Nomenclature of benzene derivatives

48. More Complex Aromatic Systems

49. 22.4 Hydrocarbon Derivatives(Functional Groups) • Molecules that are fundamentally hydrocarbons but have additional atoms or group of atoms called functional groups • Part of an organic molecule where chemical reactions take place • Replace an H in the corresponding alkane • Provide a way to classify organic compounds

50. The Common Functional Groups ClassGeneral Formula Halohydrocarbons RX Alcohols ROH Ethers ROR Aldehydes