1. 1 Organic and Biological Molecules Chapter 22

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

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

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

5. 5 22.1 Alkanes: Saturated hydrocarbons Saturated hydrocarbons, C n H 2n+2 Saturated hydrocarbons, C n H 2n+2 “Saturated” because they can’t take any more hydrogen atoms “Saturated” because they can’t take any more hydrogen atoms Normal straight chains (unbranched hydrocarbons) Normal straight chains (unbranched hydrocarbons) H 3 C–(CH 2 ) n–2 –CH 3 H 3 C–(CH 2 ) n–2 –CH 3 Waxes, oils, & fuel gases as n decreases. Waxes, oils, & fuel gases as n decreases.

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

7. 7 The Lewis structure of ethane.

8. 8 Propane

9. 9 Butane

10. 10 The First 10 “Normal” Alkanes NameFormulaM.P.B.P.# Structural Isomers MethaneCH 4 -183-1621 MethaneCH 4 -183-1621 EthaneC 2 H 6 -172-891 EthaneC 2 H 6 -172-891 PropaneC 3 H 8 -187-421 PropaneC 3 H 8 -187-421 ButaneC 4 H 10 -138 02 ButaneC 4 H 10 -138 02 PentaneC 5 H 12 -130 363 PentaneC 5 H 12 -130 363 HexaneC 6 H 14 -95 685 HexaneC 6 H 14 -95 685 HeptaneC 7 H 16 -91 989 HeptaneC 7 H 16 -91 989 OctaneC 8 H 18 -5712618 OctaneC 8 H 18 -5712618 NonaneC 9 H 20 -5415135 NonaneC 9 H 20 -5415135 DecaneC 10 H 22 -3017475 DecaneC 10 H 22 -3017475 C1 - C4 are Gases at Room Temperature C5 - C16 are Liquids at Room Temperature

11. 11 IUPAC Rules for Naming Branched Alkanes Find and name the parent chain in the hydrocarbon - this forms the root of the hydrocarbon name 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 Number the carbon atoms in the parent chain starting at the end closest to the branching Name alkane 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… Name alkane 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 When there are more than one type of branch (ethyl and methyl, for example), they are named alphabetically Finally, to indicate multiple branches Finally, use prefixes to indicate multiple branches

12. 12 Rules for Naming Alkanes 1. For alkanes beyond butane, add -ane to the Greek root for the number of carbons. C-C-C-C-C-C : hexane C-C-C-C-C-C : hexane 2. Alkyl substituents: drop the -ane and add -yl -C 2 H 5 is ethyl

13. 13

14. 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 C-C-C-C-C-C3-methylhexane Start numbering at the end closest to the branching 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. 15 Normal vs Branched Alkanes Normal alkanes consist of continuous chains 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. 16 Structural Isomerism Structural isomers are molecules with the same chemical formulas but different molecular structures - different “connectivity”. 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. They arise because of the many ways to create branched hydrocarbons. n-pentane, C 5 H 12 2-methlbutane, C 5 H 12

17. 17 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. The parent chain is indicated by the ROOT of the name - “pentane”. This means there are 5 carbons in the parent chain. dimethyl “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 “2,2-” tell us that BOTH methyl branches are on the second carbon atom in the parent chain. 1 2 3 4 5

18. 18 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. 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 “2,4-dimethyl” tells us there are TWO methyl branches on the parent chain, at carbons #2 and #4. 3-ethyl “3-ethyl-” tell us there is an ethyl branch (2-carbon branch) on carbon #3 of the parent chain. 1 2 3 4 5 7 6

19. 19 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. 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“2,3,3-trimethyl” tells us there are THREE methyl branches - one on carbon #2 and two on carbon #3. 4-propyl“4-propyl-” tell us there is a propyl branch (3-carbon branch) on carbon #4 of the parent chain. 1 2 3 4 5 7 6 8 1 2 3 4 5 7 6 8

20. 20 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 ” parent chain has 8 carbons - “ octane ” two methyl branches - start counting from the left - #3 and #4 two methyl branches - start counting from the left - #3 and #4 one ethyl branch - #5 one ethyl branch - #5 name branches alphabetically name branches alphabetically 3,4-dimethyl 4 3 octane 5 5-ethyl-

21. 21 Reactions of alkanes Combustion reactions Combustion reactions 2C 4 H 10 + 13 O 2 8CO 2 + 10 H 2 O(g) Substitution Reactions Substitution Reactions CH 4 + Cl 2 CH 3 Cl + HCl CH 3 Cl + Cl 2 CH 2 Cl 2 + HCl CH 2 Cl 2 + Cl 2 CH Cl 3 + HCl CHCl 3 + Cl 2 C Cl 4

22. 22 Dehydrogenation Reactions CH 3 CH 3 CH 2 CH 2 Ethylene

23. 23 Cyclic alkanes C n H 2n A cycloalkane is made of a hydrocarbon chain that has been joined to make a “ring”. 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. 24 Ring Structures

25. 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. 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 The BOAT and CHAIR (99%) are two conformations Boat chair

26. 26 22.2 Alkenes and Alkynes Alkenes: hydrocarbons that contain a carbon-carbon double bond. Alkenes: hydrocarbons that contain a carbon-carbon double bond. [C n H 2n ] C=CEthene CC=Cpropene : hydrocarbons containing a carbon-carbon triple bond. Alkynes: hydrocarbons containing a carbon-carbon triple bond. [C n H 2n-2 ] C ΞCEthyne C ΞCEthyne CCC Ξ CC 2-pentyne

27. 27 Alkenes & Alkynes Alkenes are hydrocarbons that contain at least one carbon-carbon double bond Alkenes are hydrocarbons that contain at least one carbon-carbon double bond Alkynes are hydrocarbons that contain at least one carbon-carbon triple bond 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

28. 28 Alkenes, C n H 2n Cycle formation isn’t the only possible result of dehydrogenation. Cycle formation isn’t the only possible result of dehydrogenation. Adjacent C’s can double bond, C=C, making an (unsaturated) alkene. Adjacent C’s can double bond, C=C, making an (unsaturated) alkene. Sp 2

29. 29 Nomenclature for Alkenes 1. Parent hydrocarbon name ends in -ene C 2 H 4; CH 2 =CH 2 is ethene C 2 H 4; CH 2 =CH 2 is 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 C=C-C-C is 1-butene

30. 30 Nomenclature alkenes and alkynes

31. 31 Cis and Trans Isomers  Double bond is fixed (rotation around the double bond is restricted)  Cis/trans Isomers are possible CH 3 CH 3 CH 3 CH = CH CH = CH CH = CH CH = CH cis trans CH 3 cis trans CH 3

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

33. 33 Hydrogenation reaction Adds a hydrogen atom to each carbon atom of a double bond Adds a hydrogen atom to each carbon atom of a double bond H H H H H H H H catalyst catalyst H – C=C – H + H 2 H – C – C – H H H H H Ethene Ethane Ethene Ethane CH 3 -CH 3

34. 34 Halogenation reaction Adds a halogen atom to each carbon atom of a double bond Adds a halogen atom to each carbon atom of a double bond H H H H H H H H catalyst catalyst H – C=C – H + Cl 2 H – C – C – H Cl Cl Cl Cl Ethene Dichloro ethane Ethene Dichloro ethane

35. 35 Halogenation Reactions CH 2 CHCH 2 CH 2 CH 2 + Br 2 CH 2 Br CHBrCH 2 CH 2 CH 2 1,2-dibromopentane

36. 36 Alkynes, C n H 2n–2  Carbon-carbon triple bonds  Names end in -yne HC  CHethyne(acetylene) HC  C-CH 3 propyne sp triple bonding makes a rigid 180° segment in a hydrocarbon.

37. 37 The Bonding in Acetylene

38. 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 1 2 3 4 CH 2 =CHCH 2 CH 3 1-butene CH 3 CH=CHCH 3 2-butene CH 3 CH  CHCH 3 2-butyne CH 3 CH  CHCH 3 2-butyne

39. 39 Question Write the IUPAC name for each of the following unsaturated compounds: A.CH 3 CH 2 C  CCH 3 CH 3 CH 3 B. CH 3 C=CHCH 3 C. 2-pentyne 2-methyl-2-butene 3-methylcyclopentene

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

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

42. 42 22.3 Aromatic hydrocarbons Unsaturated Cyclic hydrocarbons Alternating single/double bond Alternating single/double bond cycles occur in many organic molecules cycles occur in many organic molecules This class is called “aromatic” (by virtue of their aroma). 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. 43 Benzene C 6 H 6 sp 2 The  structure is often preserved in benzene chemical reactions The  structure is often preserved in benzene chemical reactions Aromatic rings do not add, they substitute instead Aromatic rings do not add, they substitute instead

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

45. 45 Aromatic Hydrocarbons Substitution reaction + Cl 2 + HCl +H 2 O +HCl benzene Chlorobenzene HNO3HNO3 HNO 3 CH 3 Cl -NO 2 -CH3 Nitroobenzene Toluene

46. 46

47. 47 Nomenclature of benzene derivatives

48. 48 More Complex Aromatic Systems

49. 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. 50 The Common Functional Groups ClassGeneral Formula HalohydrocarbonsR  X HalohydrocarbonsR  X AlcoholsR  OH AlcoholsR  OH EthersR  O  R EthersR  O  R Aldehydes

51. 51 ClassGeneral Formula Ketones Carboxylic Acids EstersAmines

52. 52 Some Types of Functional Groups Haloalkane-F, -Cl, -Br CH 3 Cl Alcohol-OH CH 3 OH Ether-O- CH 3 -O-CH 3 AldehydeKetone

53. 53 More Functional Groups Carboxylic acid -COOH CH 3 COOH Ester -COO- CH 3 COOCH 3 Amine -NH 2 CH 3 NH 2 Amide -CONH 2 CH 3 CONH 2

54. 54

55. 55 Haloahydrocarbons An alkane in which one or more H atoms is replaced with a halogen (F, Cl, Br, or I) CH 3 Brbromomethane Br (methyl bromide) CH 3 CH 2 CHCH 3 2-bromobutane Cl chlorocyclobutane

56. 56 Name the following: bromocyclopentane1,3-dichlorocyclohexane 1 2 3

57. 57 Substituents List other attached atoms or groups in alphabetical order Br = bromo, Cl = chloro Cl Br Cl Br CH 3 CHCH 2 CHCH 2 CH 2 CH 3 4-bromo-2-chloroheptane 4-bromo-2-chloroheptane 1 2 3 4 5

58. 58 Nomenclature The name of this compound is: Cl CH 3 CH 3 CH 2 CHCH 2 CHCH 3 CH 3 CH 2 CHCH 2 CHCH 3 4-chloro-2-methylhexane 4-chloro-2-methylhexane

59. 59 Alcohols: R–OH The – OH makes alcohol polar enough to hydrogen bonding The – OH makes alcohol polar enough to hydrogen bonding Thus, they are water soluble Thus, they are water soluble Ethanol is produced by the fermentation of glucose Ethanol is produced by the fermentation of glucose yeast C 6 H 12 O 6 Glucose 2CH 3 CH 2 OH Ethanol + 2 CO 2 CO + 2H 2 O CH 3 OH Methanol Methanol is produced industrially by hydrogenation of carbon monoxide

60. 60 Uses of alcohols Methanol is used to synthesize adhesives, fibers, plastics and recently as motor fuel Methanol is used to synthesize adhesives, fibers, plastics and recently as motor fuel It is toxic to human and can lead to blindness and death It is toxic to human and can lead to blindness and death Ethanol can be added to gasoline to form gasohol and used in industry as solvent Ethanol can be added to gasoline to form gasohol and used in industry as solvent Commercial production of ethanol: Commercial production of ethanol: CH 2 =CH 2 + H 2 O CH 3 CH 2 OH CH 2 =CH 2 + H 2 O CH 3 CH 2 OH

61. 61 Classes of alcohols number of hydrocarbon fragments bonded to the carbon Alcohols can be classified according to the number of hydrocarbon fragments bonded to the carbon where the –OH group is attached

62. 62 Naming Alcohols In IUPAC name, the -e in alkane name is replaced with -ol. In IUPAC name, the -e in alkane name is replaced with -ol. CH 4 methane CH 3 OH methanol (methyl alcohol) CH 3 CH 3 ethane CH 3 CH 2 OH ethanol (ethyl alcohol )

63. 63 Phenol (Aromatic alcohol)

64. 64 Some Typical Alcohols OH OH “ Rubbing alcohol ” CH 3 CHCH 3 2-propanol (isopropyl alcohol) Antifreeze HO-CH 2 -CH 2 -OH 1,2-ethanediol (ethylene glycol)

65. 65 Naming Alcohols IUPAC names for longer chains number the chain from the end nearest the -OH group. IUPAC names for longer chains number the chain from the end nearest the -OH group. CH 3 CH 2 CH 2 OH1-propanol OH OH CH 3 CHCH 3 2-propanol CH 3 OH CH 3 OH CH 3 CHCH 2 CH 2 CHCH 3 5-methyl-2-hexanol 5 2

66. 66 Name the following alcohols: OH OH CH 3 CHCHCH 2 CH 3 CH 3 CH 3 Example 3-methyl-2-pentanol

67. 67 Aldehydes and Ketones In an aldehyde, an H atom is attached to a carbonyl group In an aldehyde, an H atom is attached to a carbonyl group Ocarbonyl group Ocarbonyl group  CH 3 -C-H CH 3 -C-H In a ketone, two carbon groups are attached to a carbonyl group In a ketone, two carbon groups are attached to a carbonyl group Ocarbonyl group Ocarbonyl group   CH 3 -C-CH 3 CH 3 -C-CH 3

68. 68 Naming Aldehydes IUPAC name: Replace the -e in the alkane name by -al IUPAC name: Replace the -e in the alkane name by -al Common Add aldehyde to the prefixes form (1C), acet (2C), propion(3), and butry(4C) Common Add aldehyde to the prefixes form (1C), acet (2C), propion(3), and butry(4C) O O O O O O       H-C-H CH 3 -C-HCH 3 CH 2 C-H methanal ethanal propanal methanal ethanal propanal (formaldehyde) (acetaldehyde) (propionaldehyde) methane ethane propane

69. 69 Aldehydes as Flavorings

70. 70 Naming Ketones IUPAC name: the -e in the alkane name is replaced with – one and a number to indicate the position of carbonyl group when needed. IUPAC name: the -e in the alkane name is replaced with – one and a number to indicate the position of carbonyl group when needed. In the common name, add the word ketone In the common name, add the word ketone after naming the alkyl groups attached to the after naming the alkyl groups attached to the carbonyl group O O O O     CH 3 -C-CH 3 CH 3 -C-CH 2 -CH 3 2-Propanone 2-Butanone 2-Propanone 2-Butanone (Dimethyl ketone) (Ethyl methyl ketone) (Dimethyl ketone) (Ethyl methyl ketone) Acetone propane butane cyclohexane

71. 71 Name the following compounds O  A. CH 3 CH 2 CCH 3 B. 2-butanone (ethyl methyl ketone) CH 3 O CH 3 O   C. CH 3 -C-CH 2 CH cyclohexanone cyclohexanone CH 3 CH 33,3-dimethylbutanal

72. 72 Draw the structural formulas for each of the following compounds CH 3 O  CH 3 O  A. 3-MethylpentanalCH 3 CH 2 CHCH 2 CH Br O Br O  B. 2,3-Dibromopropanal Br-CH 2 CHCH O   C. 3-Methyl-2-butanoneCH 3 CHCCH 3 CH 3 CH 3

73. 73 Preparation of aldehydes and Ketones They are produced by oxidation of alcohols: CH 3 CH 2 OH Oxidation acetaldehyde acetone Primary alcohol Secondary alcohol ethanal propanone

74. 74 Carboxylic Acids and Esters Carboxylic acids contain the carboxyl group as carbon 1. O R  R  CH 3 — C — OH CH 3 — COOH carboxyl group General formula R — COOH

75. 75 Nomenclature of Carboxylic Acids Formula IUPAC Common alkan -oic acid prefix – ic acid alkan -oic acid prefix – ic acid HCOOH methanoic acid formic acid CH 3 COOH ethanoic acid acetic acid CH 3 CH 2 COOH propanoic acid propionic acid CH 3 CH 2 CH 2 COOH butanoic acid butyric acid

76. 76 IUPAC nomenclature for Carboxylic acids Identify longest chain Identify longest chain Number carboxyl carbon as 1 Number carboxyl carbon as 1 CH 3 CH 3 | | CH 3 — CH — CH 2 — COOH 3-methylbutanoic acid 3-methylbutanoic acid 1 2 3 4

77. 77 CH 3 CH 3 | CH 3 CHCOOH CH 3 CHCOOH 2-methylpropanoic acid; 2-methylpropanoic acid;

78. 78 Reaction of carboxylic acid with alcohol Ester Carboxylic acid Alcohol Esterification

79. 79 Esters In ester, the H in the carboxyl group is replaced with an alkyl group O   CH 3 — C — O — CH 3 CH 3 — COO — CH 3 ester group Esters give fruity odors

80. 80 Naming Esters The parent alcohol is named first with a –yl ending Change the –oic ending of the parent acid to –ate acidalcohol O  methyl CH 3 — C—O —CH 3 Ethanoate methyl ethanoate (IUPAC) (acetate)methyl acetate (common)

81. 81 Amines Organic compounds of nitrogen N; derivatives of ammonia Organic compounds of nitrogen N; derivatives of ammonia Classified as primary, secondary, tertiary Classified as primary, secondary, tertiary CH 3 CH 3 CH 3 CH 3     CH 3 — NH 2 CH 3 — NH CH 3 — N — CH 3 Primary Secondary Tertiary one N-C two N-C three N-C bond bonds bonds

82. 82 Naming Amines IUPAC aminoalkane Common alkylamine CH 3 CH 2 NH 2 aminoethane(ethylamine) NH 2 NH 2 | CH 3 CHCH 3 2-aminopropane Aniline (isopropylamine)

83. 83 22.5 Polymers Poly= many; mers=parts Polymers are large, usually chainlike molecules that are built from small molecules called monomers joined by covalent bonds Polymers are large, usually chainlike molecules that are built from small molecules called monomers joined by covalent bonds MonomerPolymer EthylenePolyethylene Vinyl chloridePolyvinyl chloride TetrafluoroethyleneTeflon

84. 84 Some common synthetic polymers, their monomers and applications

85. 85 Types of Polymerization Addition Polymerization: monomers “ add together ” to form the polymer, with no other products. ( Polyethylene and Teflon) Condensation Polymerization: A small molecule, such as water, is formed for each extension of the polymer chain. (Nylon)

86. 86 Addition Polymerization The polymerization process Is initiated by a free radical A species with an unpaired electron such as hydroxyl free radical Free radical attacks and break The  bond of ethylene molecule To form a new free radical Repetition of the process thousands of times creates a long chain polymer The process is terminated when two radicals react to form a bond; thus there will be no free radical is available for further repetitions.

87. 87 Condensation Polymerization Formation of Nylon Small molecule such as H 2 O is formed from each extension of the polymer chain both ends are free to react Dimer Diamine Dicarboxylic acid

88. 88 Nylon