Chapter 22Chapter 22

Organic and Biochemical Organic and Biochemical MoleculesMolecules

Chapter 22: Organic and Biochemical Molecules

22.1 Alkanes: Saturated Hydrocarbons

22.2 Alkenes and Alkynes

22.3 Aromatic Hydrocarbons

22.4 Hydrocarbon Derivatives

22.5 Polymers

22.6 Natural Polymers

Computer model of a globular protein

The Position of Carbon in the Periodic Table

“I am Carbon and I am Special”

1. I can form strong and short C-C bonds.

2. The C-C bond is short enough to allow sideways overlap of the unused p orbitals, resulting in bonding. I gladly form carbon- carbon double bonds, and I can even form carbon-carbon triple bonds.

3. I have no problem bonding to other elements (H, O, N, S, etc.– I love them all). Given where I am in the periodic table, I typically form four bonds, except in carbon monoxide.

I Am Special -- Try Comparing Me to My Brother, Si

1. The C-C bond is much stronger than the Si-Si bond. (Atomic size increases down the group: bonds between atoms become longer and weaker.)

2. For me BE (C-C) ~ BE (C-O). For Si, BE (Si-O) >> BE (Si-Si). With availability of oxygen in nature, Si will exist mostly with Si-O bonds.

3. I have no d - orbitals to worry about. CH3-CH3 is stable while SiH3-SiH3 is very susceptible to species with a pair of lone pairs of electrons to donate into the vacant d orbitals.

You can spend your whole life learning about me!

Bond Energy and the Stability ofCarbon Chains

I Can Amaze You With Diversity

Consider the number of compounds with the formula C4H8O.

These are called structural isomers–compounds with the same chemical formulas, but different ways of connecting the atoms together to form different functional groups, or different compounds with completely different chemical and physical properties.

Chemical Diversity of Organic Compounds

Reactivity & Polarity of Bonds in Organic CompoundsC C Bonds are nonpolar, no difference in the EN values of the atoms. They are relatively short (200 pm). Result: UnreactiveC H Bonds are nearly nonpolar and short (109 pm) EN (C-H) = 2.5 – 2.1 = 0.4 Result: UnreactiveC O Bonds are highly polar, with the oxygen end very electron rich EN (C-O) = 2.5 – 3.5 = 1.0 Result: ReactiveC Br Bonds are nearly nonpolar: EN (C-Br) = 2.5 – 2.8 = 0.3 Result: Relatively unreactiveC S Bonds are exactly nonpolar: EN (C-S) = 2.5 – 2.5 = 0.0 Result: Relatively unreactiveEven though the EN differences are small for Br & S with carbon, theatoms are so large that their bonds to carbon are long, weak, and reactive.

Certain Parts of Me Make Me Behave in Certain Predictable Ways

Functional Groups – atoms or specific groups of atoms that impart given characteristics.

The secret to learning organic chemistry.

As the periodic table is to inorganic chemistry, functionalgroups are the easy way to learn organic chemistry.

A Polarized Marriage Does Not Last Very Long

“ I am no different. I am quite reactive at the sites (bonds)that have the high polarity.”

Figure 22.1: C-H bonds in methane

Figure 22.2: (a) Lewis structure of ethane ( C2H6 ). (b) molecular structure of ethane

Figure 22.3: Structures of (a) propane (b) butane

Alkanes

• Methane CH4

• Ethane C2H6 CH3CH3

• Propane C3H8 CH3CH2CH3

• Butane C4H10 CH3CH2CH2CH3

• Pentane C5H12 CH3CH2CH2CH2CH3

• Hexane C6H14 CH3CH2CH2CH2CH2CH3

• Heptane C7H16 CH3-(CH2)5-CH3

• Octane C8H18 CH3-(CH2)6-CH3

• Nonane C9H20 CH3-(CH2)7-CH3

• Decane C10H22 CH3-(CH2)8-CH3

Table 22.1 (P1014) Selected properties of the First 10 Normal Alkanes Number of Molar Melting Boiling structuralName Formula Mass Point (oC) Point(oC) isomers

Methane CH4 16 -182 -162 1Ethane C2H6 30 -183 -89 1Propane C3H8 44 -187 -42 1Butane C4H10 58 -138 0 2Pentane C5H12 72 -130 36 3Hexane C6H14 86 -95 68 5Heptane C7H16 100 -91 98 9Octane C8H18 114 -57 126 18Nonane C9H20 128 -54 151 35Decane C10H22 142 -30 174 75

Figure 22.4: (a) normal butane (b) branched isomer

n-Butane

Isobutane

Pentane

n - Pentane

CH3-CH2-CH2-CH2-CH3

Isopentane2-Methyl Butane

CH3-CH-CH2-CH3 CH3

Neopentane

2,2-Dimethyl Propane

CH3

CH3 – C – CH3

CH3

Boiling Points of Hydrocarbons

Rules for Naming Alkanes (P 1016-1017)-I1) The names of the alkanes beyond butane are obtained by adding the suffix –ane to the Greek root for the number of carbon atoms (pent- for five, hex- for six, and so on). For a branched hydrocarbon, the longest continuous chain of carbon atoms determines the root name for the hydrocarbon. For example in the alkane: The longest chain contains 6 carbon atoms. CH3 The compound is named hexane. CH2 CH2 CH3-CH2-CH-CH2-CH3 2) When alkane groups appear as substituents, they are named by droping the –ane and adding –yl. For example, -CH3 is obtained by removing a hydrogen from methane and is called methyl, -C2H5 is called ethyl, -C3H7 is called propyl, and so on. The compound above is therefore an ethylhexane. (see table 22.2)

Longest Chain 6 carbons

Rules for Naming Alkanes (P 1016-1017)-II

3) The positions of aubstituent groups are specified by numbering the longest chain of carbon atoms sequentially, starting at the end closest to the branching. For example, the compound CH3 CH3-CH2-CH-CH2-CH2-CH3 1 2 3 4 5 6 is called 3-methylhexane. Note that the set of numbers is correct since the left end of the molecule is closest to the branching, and this gives the smallest number for the position of the substituent. Note that a hyphen is written between the number and the substituent name. 4) The location and name of each substituent are followed by the root alkane name. The substituents are listed in alphabetical order, and the prefixes di-, tri-, and so on, are used to indicate multiple, identical substituents.

Naming Saturated Hydrocarbons

Based on the longest chain of carbon atoms

Prefix + root + suffix

Location and nature of substituents on chain

Indicator of the # of C’s in the longest chain

Class of organic compound -ane for alkanes

Numerical Roots for Carbon Chains and Branches

Root Number of Carbon Atoms

meth- 1eth- 2prop- 3but- 4pent- 5hex- 6hepta- 7oct- 8non- 9dec- 10

Like Example 22.2 (P 1017-18)-I

Draw the structural isomers for the saturated hydrocarbon heptane C7H16 .name each of the isomers.

Solution: Straight chain: CH3-CH2-CH2-CH2-CH2-CH2-CH3 n-Heptane

One methyl group: CH3-CH-CH2-CH2-CH2-CH3 2-Methylhexane CH3 3-Methylhexane CH3-CH2-CH-CH2-CH2-CH3

CH3 Two methyl groups: CH3-CH-CH2-CH-CH3 CH3 CH3 2,4-dimethyl pentane

CH3 CH3-CH-CH-CH2-CH3 CH3-C-CH2-CH2-CH3 CH3 CH3 CH3 2,2-dimethylpentane 2,3-dimethylpentane

Like Example 22.2 (P 1017-18)-IITwo methyl groups cont. CH3 CH3-CH2-C-CH2-CH3 CH3

CH3CH2-CH-CH2-CH3 3,3-dimethylpentane CH2 3-ethylpentane CH3 CH3

2,2,3-trimethylbutane CH3-CH-C-CH3 CH3 CH3

Reactions of Alkanes - Chlorination

The Stepwise Chlorination of Methane by Chlorine:

CH4 (g) + Cl2 (g) CH3Cl(g) + HCl(g)

CH3Cl(g) + Cl2 (g) CH2Cl2 (g) + HCl(g)

CH2Cl2 (g) + Cl2 (g) CHCl3 (g) + HCl(g)

CHCl3 (g) + Cl2 (g) CCl4 (g) + HCl(g)

CH4 (g) + 4 Cl2 (g) CCl4 (g) + 4 HCl(g)

Figure 22.5: (a) molecular structure of cyclopropane (b) overlap of sp3 orbitals

Figure 22.6: (a) chair (b) boat forms

Figure 22.7: Bonding in ethylene

Figure 22.8: Bonding in ethane

Figure 22.9: The two stereoisomers of 2-butene

Figure 22.10: Bonding in acetylene

Hydrocarbons C + H

Compounds containing only carbon and hydrogen with only single bonds and no multiple bonds - Saturated hydrocarbons - Alkanes CnH2n+2

Compounds containing only carbon and hydrogen with only single bonds and no multiple bonds, but a ring structure - Saturated hydrocarbons - Cycloalkanes CnH2n

Compounds containing only carbon and hydrogen with double bonds - Unsaturated hydrocarbons - Alkenes CnH2n

Compounds containing only carbon and hydrogen with triple bonds - Unsaturated hydrocarbons - Alkynes CnH2n–2

Conformations from rotation of single bonds–isomers exist as a resultof rearrangements of the atoms in different structural formulas.

Drawing Hydrocarbons–I Problem: Draw structures for hydrocarbons that have different structures with: a) seven C atoms, no multiple bonds, and no rings. b) five C atoms, one double bond, and no rings. c) five C atoms, no multiple bonds, and one ring.Plan: In each case, we draw the longest carbon chain and then work down to smaller chains with branches at different points along them. The process typically involves trial and error. Then we add H atoms to give each C atom a total of four bonds.Solution: (only the carbon backbone will be shown here) a) compounds with seven C atoms: (9) [C7H16]

C-C-C-C-C-C-C C-C-C-C-C-C C

C-C-C-C-C-C C

CC-C-C-C-C C

C-C-C-C-C C C

C-C-C-C-C C C

CC-C-C-C-C C

C-C-C-C-C C C

CC-C-C-C C C

Drawing Hydrocarbons–II

b) compounds with 5 C atoms and one double bond: (5) [C5H10]

C=C-C-C-C C=C-C-C C=C-C-C

C-C=C-C-C

C-C=C-C

c) compounds with 5 C atoms and one ring: (5) [C5H10]

C-C-C-C C

C-C-C-C C

CC-C-C C

C-C-CC-C

C-CC C C

C CC

Naming and Drawing Alkanes, Alkenes, and Alkynes–I

Problem: Give the systematic name for each of the following, indicate the chiral center in part (d), and draw two geometric isomers for part (e).(a) CH3 (b) CH2-CH3

CH3 - CH - CH-CH3 CH3-CH2-CH2-CH-CH-CH3

CH3 CH2

CH3

(c) CH3 CH3

(d) CH3-CH2-CH-C-CH3

CH3 CH3

(e) CH3-CH2-CH=C-CH-CH3

CH3

Plan: For (a) to (c), we refer to Table 15.2. We first name the longest chain (root- + -ane). Then we find the lowest branch numbers by counting C atoms from the end closer to a branch. Finally, we name each branch (root- + -yl) and put them alphabetically before the chain name.

H2H2

H2

H2

CH3

CH2-CH3

Naming and Drawing Alkanes, Alkenes, and Alkynes–II

Plan:Cont. For (e), the longest chain that includes the multiple bond is numbered from the end closer to it. For (d), the chiral center is the C atom bonded to four different groups. In (e), the cis isomer has larger groups on the same side of the double bond, and the trans isomer hasthem on opposite sides.Solution:

(a) CH3

CH3

CH3 - CH - CH - CH3

1 2 3 4

2,3-Dimethylbutane

CH2 - CH3

H(b) CH3

CH3 - CH2 - CH2 - C - C -

CH2

CH31

234567

3-Methyl-4-ethylheptane

Naming and Drawing Alkanes, Alkenes, and Alkynes–III

(c)

CH3

H2

H2

H2

H2

CH2 - CH3

1

2

3

1-Ethyl-3-methylcyclohexane

(d) CH3 CH3

CH3 - CH2 - C - C - CH3

H CH3

12345

2,2,3-Trimethylpentane

chiral center

(e)

CH3 - CH2 - C = C - CH - CH3

H CH3

CH3

CH3 - CH2 - C = C - CH - CH3

H

CH3

CH3

cis-2,3-Dimethyl-3-hexene trans-2,3-Dimethyl-3-hexene

Alkenes

Alkenes–Carbon compounds that contain at least one C=C double bond. Alkenes have the general formula: CnH2n

Alkenes are called unsaturated hydrocarbons The names of alkenes differ from those of alkanes in two respects: 1) The root chain must contain both C atoms of the double bond, even if it is not the longest chain. The chain is numbered from the end closer to the C=C bond, and the position of the bond is indicated by the number of the first C atom in it. 2) The suffix for alkenes is -ene. Examples: Ethylene, C2H4; Propene, C3H6; Butene, C4H8

H2C=CH2

EthyleneH2C=CH-CH3

Propylene =

H2C=CH-CH2-CH3

1-ButeneH3C-CH=CH-CH3

2-Butene

H3C-CH2-CH=CH2

1-ButeneH3C-CH=CH2

Propene

H2C=C-CH3

2-Methyl propene CH3

Alkenes

C2H4 Ethylene H2C=CH2

C3H6 Propylene H2C=CH–CH3

C4H8 Butene H2C=CH–CH2–CH3

C5H10 Pentene H2C=CH–CH2–CH2–CH3

C6H12 Hexene H2C=CH–CH2–CH2–CH2–CH3

C7H14 Heptene H2C=CH–( CH2)4–CH3

C8H16 Octene H2C=CH–( CH2)5–CH3

The Initial Chemical Event in Vision

Alkynes

Alkynes –Hydrocarbons that contain at least one C C bond Alkynes have the general formula: CnH2n–2

Alkynes are named the same way as alkenes, except that the suffix is -yne. Examples:

HC CHAcetylene

HC C-CH3

PropyneH3C-C CH Propyne

HC C- CH2-CH3

1-ButyneH3C-C C-CH3

2-ButyneH3C-CH2-C CH 1-Butyne

HC C-CH2-CH2-CH3

1-PentyneH3C-C C-CH2-CH3

2-Pentyne

R-Group Names and Chemical Formulas

methyl - CH3

ethyl - CH2 - CH3 or - C2H5

n-propyl - CH2 - CH2 - CH3 or - C3H7

isopropyl - CH - CH3

CH3

n-butyl - CH2 - CH2 - CH2 - CH3 or - C4H9

isobutyl - CH2 - CH - CH3

CH3

CH3

tert-butyl - C - CH3 CH3

H2 H2

H2

H2H2

Hcyclohexyl

H2 H2

H2

H2

cyclopentyl H

H2

H2

H2

cyclobutylH

H2

H2H

cyclopropyl

Figure 22.11: The structure of benzene

Figure 22.12: Some selected substituted benzenes and their names

Compounds containing aromatic rings are often used in dyes, such as these for

sale in a market in Nepal

Source: Getty Images

Some Reactions of Alcohols–I

1) The reaction of an alcohol with an alkali metal to form an alkoxide ion:

As with water: 2 Na(s) + 2 H2O(l) 2 NaOH(aq) + H2 (g)

With alcohols a similar reaction occurs, forming an alkoxide ion:

2 Na(s) + 2 CH3-CH2-OH(l) 2 CH3-CH2-O-(aq) +2 Na+

(aq) + H2 (g)

2 Li(s) + 2 CH3-OH(l) H2 (g) + 2 CH3-O-(aq) + 2 Li+

(aq)

2) Dehydration of alcohols yields an unsaturated compound–an alkene or an ether (R-O-R). An example of the formation of an alkene:

OH

+ H2OH2SO4

Phenol Cyclohexene

Some Reactions of Alcohols–II2) cont., Formation of an ether:

2 CH3-OH(l) CH3-O-CH3 (g) + H2O(l)

H2SO4

CH3-CH2-OH(l) + HO-CH2-CH3 (l) H2O(l) + CH3-CH2-O-CH2-CH3

Dimethyl ether

H + HO-Diethyl ether

H2SO4

OHCH3-CH2-CH2-CH2-CH2-CH2-OH(l) + CH3-CH-CH2-CH3 (l)

H2SO4

CH3

H-C-O-CH2-CH2-CH2-CH2-CH2-CH3 (l) CH2

CH3

2-Butyl n-hexyl ether

n-Hexanol 2-Butanol

Ethyl alcohol Ethanol

Methanol

Some Reactions of Alcohols–III

3) Oxidation - Yields an aldehyde, acid or, for some alcohols, a ketone.

Primary alcohols Aldehyde Organic Acid

Secondary alcohols Ketone

Tertiary alcohols no oxidation

O OCH3-CH2-OH(l) CH3-C-H CH3-C-OH

K2Cr2O7

H2SO4

= [O] = “Oxidation”

[O][O]

Ethanol Ethanal Acetic acid

OH OCH3-CH-CH2-CH3 (l) CH3-C-CH2-CH3 (l)

2-Butanol Ethyl methyl ketone

[O]

-H2O -H2O

-H2O

Ethanol is being tested in selected areas as a fuel for automobiles

Source: AP/Wide World Photos

Some Molecules with Alcohol Functional Group

Cinnamaldehyde produces the characteristic odor of cinnamon

Source: Visuals Unlimited

Aldehydes

Formaldehyde Methanal

H C H

O

Acetaldehyde Ethanal

H3C C H

O

Benzaldehyde

CH

CCH

CHCH

CH

C H

O

Dimethyl ketoneH3C C CH3

O

Acetone

Ethyl methyl ketone

H3C CH2 C CH3

O

Diethyl ketone

H3C CH2 C CH2 CH3

O

Ketones

Some Common Aldehydes and Ketones

Figure 22.13: Some common ketones and akdehydes

The CarbonylGroup

Carboxylic Acids

Formic acidH C O H

O

Acetic acid

H3C C O H

O

Propionic acid

H3C CH2 C O H

O

Butanoic acid

H3C CH2 CH2 C O H

O

Figure 22.14: Some carboxylic acids

Some Molecules with the Carboxylic Acid Functional Group

Which Reactant Contributes Which Group to the Ester?

Isotopic labeling shows that the oxygen atom in the ester comes from the alcohol, not the acid, and that the oxygen found in thewater formed as a byproduct comes from the acid.

Alcohol + Organic Acids Esters–I

Ethyl alcohol + Acetic acid = Ethyl acetate

H3C CH2 OH + H3C C O H

H3C CH2 O C CH3 + H2O

O

O

Ethanol Acetic acid

Ethyl acetate Water

Methyl alcohol + Formic acid = Methyl formate

H3C O H + H O C H H3C O C H + H2O

O O

Methyl alcohol + Butyric acid = Methyl butyrate

H3C O H + H3C CH2 CH2 C O H

O

H3C CH2 CH2 C O CH3H2O +

O

Alcohol + Organic acid Esters–II

Methyl formate H C O CH3

O

Methyl acetateH3C C O CH3

O

Ethyl acetate H3C C O CH2 CH3

O

Ethyl butyrateH3C CH2 CH2 C O CH2 CH3

O

Pineapples

Alcohol + Organic acid Esters–III

Some Lipid Molecules with the Ester Functional Group

Esters are the Flavoring in Fruits–IBenzyl acetate C9H10O2 –oil of jasmine O

CH3-C-O-CH2-Isoamyl acetate C7H14O2–ripe apples

O CH3

CH3-C-O-CH2-CH2-CH-CH3

Ethyl 2-methylbutanoate C7H14O2–ripe apples

CH3 OCH3-CH2-CH-C-O-CH2-CH3Isoamyl acetate C7H14O2–bananas

Ethyl butyrate C6H12O2–pineapple

Ethyl formate C3H6O2–rum

O CH3

CH3-C-O-CH2-CH2-CH-CH3

OCH3-CH2-CH2-C-O-CH2-CH3

OH-C-O-CH2-CH3

Esters are the Flavoring in Fruits–II

Amyl butyrate C9H18O2–apricot

Methyl salicylate C8H8O3–oil of wintergreen

Ethyl formate C3H6O2–lemonade

n-Octyl acetate C10H20O2–oranges

OCH3-CH2-CH2-C-O-CH2-CH2-CH2-CH2-CH3

OH-C-CH2-CH3

OCH3-C-O-CH2-CH2-CH2-CH2-CH2-CH2-CH2-CH3

OC-O-CH3

OH

Computer-generated space-filling model of acetylsalicylic acid (aspirin)

Source: Photo Researchers, Inc.

Amines–I

NH3 Ammonia

CH3NH2 Methyl amine

(CH3)2NH Dimethyl amine

(CH3)3N Trimethyl amine

N

CH3

CH3

CH3

N

H

. .. .

CH3

CH3

. .N

HH

H

. .N

H

H CH3

Figure 22.15: The general formulas for primary, secondary, and tertiary amines:

Amines–II

CH3-CH2-NH2 Ethyl amine

CH3-CH2-CH2-NH2 n-Propyl amine

CH3-CH2-CH2-CH2-NH2 n-Butyl amine

CH

CCH

CHCH

CH

NH2

Phenyl amine

Soybeans

Source: AP/Wide World Photos

Benzoyl Peroxide

O

O

O

OO

O

.2

Heat

A “free radical” is a molecule with an unpaired electron.

Polymerization of Ethylene–IO

O . + H2C CH2

O

O

CH2

CH2

.

EthyleneBenzoyl peroxideradical

Adduct

Polymerization of Ethylene–II

O

O CH2

CH2

.

+ H2C CH2

O

O

CH2

CH2 CH2

CH2 CH2

CH2

.

2

Structures and Applications of Some Major Addition Polymers (Based upon the Ethylene Molecule)–I

Monomer Polymer ApplicationsH H C CH H

F F C CF F

H H C CH CH3

H H C CH Cl

Polyethylene Plastic bags, bottles, toys

Polytetrafluoroethylene Cooking utensils (e.g. Teflon)

Polypropylene Carpeting (indoor-outdoor), bottles

Poly(vinyl chloride) Plastic wrap, garden hose, indoor plumbing

Structures and Applications of Some Major Addition Polymers (Based upon the Ethylene Molecule)–II

Monomer Polymer ApplicationsH H C CH Phenyl

H H C CH C N

H H C C OH O C CH

H Cl C CH Cl

H CH3

C CH C O CH3

O..

Polystyrene Insulation, furniture

Polyacrylonitrile Yarns, fabrics, wigs, (e.g. Orlon, Acrilon)

Poly(vinyl acetate) Adhesives, paints, textile coatings, computer disks

Poly(vinylidene chloride) Food wrap (e.g. Saran)

Poly(methyl methacrylate) Glass substitute (e.g. Lucite, Plexiglas), bowling balls, paint

Poly(Vinyl Chloride) (PVC) and Teflon

H Cl

C C

H H

C C C C C C C C

H H H H H H H H

H Cl H Cl H Cl H Cl n

Vinyl chloride PVC

C C

F F

F F

Tetrafluoroethylene

C C C C C C C C

F F F F F F F F

F F F F F F F F

Teflon

n

Polystyrene

C C

H

H

H

H

H

HHH

H

C C C C C C C C C

H H

H H

H

H HH

n

Styrene

Figure 22.17: Major use of HDPE is for blow-molded objects such as bottle for soft

drinks, shampoos, bleaches, and so on

Important Polymer Linkage Groups

• Linkage -COO- -CONH- -C-O-C-

• Name Ester Amide Ether

• Precursors Acid + Acid + Alcohol +

• Alcohol Amine Alcohol

• Polymer

• Type

• Polyesters Polyamides Cellulose

• Proteins Starch

Nylon netting magnified 62 times

Source: Corbis

Colored water drops are shown beading onKevlar fabric treated with a non-scale

water-resistant coating.

Source: AP/Wide World Photos

Condensation Polymers Polyamides–Nylon-66

HOOH

O

OH2N

NH2

+Adipic acid

Hexamethylenediamine

NN

H

HO

O n

The formationof nylon - 66

Figure 22.16: The reaction to form nylon can be carried out at the interface of two immiscible liquid layers in a beaker

Wallace H. Carothers

Source: Dupont - Wilmington, Delaware

Two Molecules with the Same Functional Group at Both Ends of Each Molecule–

Two Different Monomers

Nylon-66 Adipic acid and Hexamethylenediamine

Kevlar Terephthalic acid and Phenylenediamine

Polyesters Terephthalic acid and Ethylene glycol

Kevlar

C

C

O

O

HO

OH

H2N

NH2Terphthalic Acid Phenylenediamine

+

HO C

C

O

O

N

H

NH2

+ H2O

E TC

Polyesters ( PET )

Polyethylene Terphthalate

C

C

O

O

HO

HO

CH2

O

OH C C OH

H H

Ethylene GlycolTerphthalic acid

+

C

C

O

O

O

CH2

n

H H

+ H2O

Polyurethane

NC

O

H3C N C O

C O H

C O H

C O H

H

H

H

H

H

+

NC

O

H3C N C O C C C O H

H H

H HO

H

O

H

Toluene diisocyanateGlycerol

Polymer

Plastic Recycling–I

1) PET Polyethyleneterephthalate Soft drink bottles, blister packs, photographic film, oven proof trays,

fiberfill (Dacron)

2) HDPE High density polyethylene Milk jugs, many types of containers (food, liquid detergent, shampoos, etc.)

3) PVC Poly(vinyl chloride) “Synthetic leather” upholstery, water pipes, house siding, flooring, bottles for cooking oils, shrink wrap, meat & poultry wrap, garden hoses, phonographic records, laboratory tubing

4) LDPE Low density polyethylene Films (food wrappings, plastic bags, etc.), flexible containers such as squeeze bottles for mustard, etc.

Plastic Recycling–II

5) PP Polypropylene Appliances, autos, pipe, drinking straws, bottle caps, luggage, bread and cheese wrap, cereal box liners,

wrap for clothing

6) PS Polystyrene Styrofoam, hot-drink cups, plastic plates & silverware, egg cartons, food trays, and fast food containers

7) Other plastics–addition polymers Teflon Lucite, plexiglass Poly(vinyl acetate) Natural rubber Neoprene rubber Styrene butadiene rubber

A scanning electron microscope image showing the fractured plane of a self-healing

material with a ruptured microcapsule in a thermosetting matrix

Source: University of Illinois Urbana-Champaign

Macromolecules in Living Organisms

Nucleic Acids

Carbohydrates

Proteins - The molecular machinery of the cell

* Polyamides made from the condensation reactions of amino acids. Each amino acid contains a carboxyl group at one end and an amino group at the other end.

* Nine amino acids have nonpolar character and are found inside of proteins.

* Eleven amino acids have polar side chains, are more polar, and found on the outside of a protein where they may be in contact with water.

Figure 22.18: The 20 α-amino acids found in most proteins. [ Nonpolar R Groups ]

Figure 22.18: The 20 α-amino acids found in most proteins. [ Nonpolar R Groups ] (cont’d)

Figure 22.18: The 20 α-amino acids found in most proteins. [ Polar R Groups ]

Figure 22.18: The 20 α-amino acids found in most proteins. [ Polar R Groups ]

Figure 22.18: The 20 α-amino acids found in most proteins. [ Polar R Groups ]

Figure 22.18: Alpha-amino acids, Polar R groups (continued).

Amino Acids–The Building Blocks of Proteins

R OIn general, amino acids have the form: H2N - C - C - O - H H

Amino acids are normally charged, because the carboxyl grouptransfers an H+ ion to H2O to form H3O+, which transfers the H+

to the amine group.

R OH2N - C - C - O - H H

R OH3N+- C - C - O -

H

H3O+

+ H2O- H2O

Polypeptides

• A macromolecule made up of amino acids;• All proteins are polypeptides;• A small protein (polypeptide) consists of 50-100

amino acids;• A large protein may contain up to thousands;

myosin, a muscle protein, has approximately 1750 amino acids.

Tripeptide containing glycine, cysteine, and alanine

Source: Photo Researchers, Inc.

Figure 22.19: The amino acid sequences in (a) oxytocin and (b) vasopressin

Figure 22.20: Hydrogen bonding within a

protein chain

Figure 22.21: Ball-and-stick

model of a portion of a protein chain

Figure 22.22: Hydrogen bonding

Figure 22.23: (a) collagen (b) pleated sheet arrangement of many proteins bound together to from

the elongated protein found in silk fibers

Figure 22.24: Protein myoglobin

Figure 22.25: Summary of the various types of interactions that stabilize the tertiary

structure of protein

Figure 22.26: Permanent waving of hair

Figure 22.27: Schematic representation of the thermal denaturation of a protein

Carbohydrates

• General formula = Cx(H2O)y

• Carbohydrates are an important food source for organisms.

• Some important ones are:– Glucose C6H12O6

– Fructose C6H12O6

– Sucrose C12H22O11

• Oligosaccharides - Disaccharides– Two simple sugars (monosaccharides) linked together

• Polysaccharides–biopolymers– Starch–cellulose

Figure 22.28: Tetrahedral carbon atom has four different substituents

Self-tanning products

Figure 22.29: The mirror image optical isomers of glyceraldehyde

Figure 22.30: The cyclization of D-fructose

Figure 22.31: The cyclization of glucose

Figure 22.32: Sucrose is a disaccharide formed from α-D-glucose and fructose

Polysaccharides

• Glycogen–produced in the livers of animals– ~1000 Monomers

– Many branches on the main chain, but their average length is less than 30 monomer units

– Branches are fairly frequent with them occurring every 8-12 monmer units

• Starch–produced in plants– Glucose polymers: amylose and amylopectin

• Cellulose–produced in plants– ~ 2000-3000 Glucose units long, but glucose units are

combined as cellobiose units which have a beta linkage

Figure 22.33: Polymers amylose and cellulose

Amylose -

Cellulose -

A Portion of the Structure of Glycogen, the Major Storage Polysaccharide in Animals

3 Important Building Blocks of Nucleic Acids

• 1) A pentose sugar–In RNA the sugar is ribose, and in DNA it is deoxyribose, in which one hydroxy group has been replaced by a hydrogen.

• 2) A nitrogen containing organic base:– Adenine– Guanine– Thymine– Cytosine– Uracil

• 3) A phosphate linkage derived from phosphoric acid

Figure 22.34: Pentoses

DNA

RNA

Figure 22.35:

The organic bases found inDNA/RNA

Figure 22.36: Adenosine reaction

Figure 22.37: Nucleic acid chain

Figure 22.38: DNA double helix

Prize-Winning Work on Nucleic Acids and DNA

• 1940’s British chemist Alexander Todd– (Nobel Prize)– Discovered the basic composition of DNA.

• 1950’s Edwin Chargaff (Columbia Univ.)– Found that different species had different numbers of bases.

– Found that the molar ratio of guanine to cytosine and adenine to thymine was always very close to 1.0, suggesting that somehow, adenine and thymine are paired in DNA and so are guanine and cytosine.

• 1953 James D. Watson , Francis Crick and Maurice Wilkins–Nobel Prize– Found the double helix structure of DNA.

Figure 22.39: Cell division of DNA

Figure 22.40: mRNA molecule

Four of the Functional Groups

C O H

Alcohol

Alcohol group - Hydroxyl group

..

..Ether group

C O C....

Ether

Carboxylic acid group Ester group

.. ..

C O C

O

..

..

.. ..

C O H

O

Carboxyl

..

..

....

Ester

More Functional Groups

Alkenes

Alkynes

Thiols and Disulfides

Amines (primary, secondary, tertiary)

Aldehydes

Ketones

Amides

Suggested “Must Learn Items”

Functional Group Compound Type Suffix or Prefix ofname

Example Systematic Name(Common Name)

alkene -ene ethene(ethelene)

alkyne -yne ethyne(acetylene)

alcohol -ol methanol(methyl alcohol)

ether ether dimethyl ether

haloalkane halo- chloromethane(methyl chloride)

amine -amine ethylamine

C C C C

HH

HH

C C C C HH

C O H....

Important Functional Groups in Organic Compounds-I

H

H C O H

H

..

..

C O C

H H

H C O C H

H HC X

....

......

H

H C Cl

HC N

H H

H C C N H

H H H

Functional Group Compound Type Suffix or Prefix ofName

Example Systematic Name(Common Name)

aldehyde -al ethanal(acetaldehyde)

ketone -one 2-propane(acetone)

carboxylic acid -oic acid ethanoic acid(acedic acid)

ester -oate methyl ethanoate(methyl acetate

amide -amide ethanamide(acetamide)

nitrile -nitrile ethanenitrile(acetonitrile,methyl cyanide)

Important Functional Groups in Organic Compounds - II

O

C H

H O

H C C H

H O

C C C

H O H

H C C C H

H H O

C O H

H O

H C C O H

H O

C O C

H O H

H C C O C H

H HO

C N

H O

H C C N H

H HC N H

H C C N

H

....

....

..

..

..

....

......

.. ........

.. ......

.. ..

....

..

..

.... ..

....

Some Five-Carbon Skeletonsone double bond one simple ringsaturated carbon cpds.

Adding the H-Atom Skin to the C-Atom Skeleton

Xylenes–The Three Isomers of C8H10

CH3

CH3

CH3CH3

CH3

CH3

1,2-Dimethylbenzene (o-xylene) bp = 144.4°C

1,3-Dimethylbenzene (m-xylene) bp = 139.1°C

1,4-Dimethylbenzene (p-xylene) bp = 138.3°C

TNT and its Decomposition (Explosion!)

CH3

NO2

NO2

O2N

2,4,6-Trinitromethylbenzene (trinitrotoluene, TNT) C7H5N3O6

4 C7H5N3O6 (s) + 33 O2 (g)

28 CO2 (g) + 10 H2O(g) + 12 NO2 (g) + Energy

Naphthalene and Benzo[a]pyrene Aromatic Carcinogens

Napthelene C10H8

Benzo[a]pyrene C20H12

(P 621)

Isomers

Structural Stereoisomers

Geometric Optical

Optical Isomerism and Chiral Molecules

Stereoisomerism: Molecules with the same sequence of atoms, but different orientations of groups in space.

Optical isomerism: A type of stereoiosmerism that occurs when an object and its mirror image cannot be superimposed on each other.

Chiral: An asymmetric organic molecule that contains at least one carbon atom that is bonded to four different groups.

An Analogy for

Optical Isomers

Consider carbon bonded to A, B, C, and D. There are two possible structures.

Optical Isomers

A

D

B

C

A

D

C

B

B a

nd C

do

not s

uper

impo

se The two structures are mirrorimages of each other. Theyare optical isomers of each other.

Each of the two forms is asymmetric - noplane of symmetry. An organic molecule ischiral if it has a carbon atom that is bondedto four different groups.

The Rotation of Plane-Polarized Light by an Optically Active Substance

Some Reactions of Alcohols–IV

4) Substitution reaction of an alcohol with hydrohalic acids to form haloalkanes and water:

CH3-OH(l) + HCl(aq) CH3-Cl(g) + H2O(l)

CH3-CH2-CH2-OH(l) + HI(aq) CH3-CH2-CH2-I(l) + H2O(l)

General formula: R-OH + HX R-X + H2O

Examples:

5) Esterification: Alcohol + Organic Acid = Ester + Water

O OCH3-OH(l) + HC-OH H-C-O-CH3 (l)

[H+]

Methanol Formic acid Methyl formate

O OCH3-CH2-OH(l) + CH3-C-OH(l) CH3- C-O-CH2-CH3 (l)

Ethanol Ethanoic acid Ethyl ethanoate

[H+]

Optical Isomerism

How different are optical isomers? They have the exact same chemical formula, chemical and physical properties, but they are different in two ways:

1) They rotate the plane of polarized light (Fig 15.11): rotation to the right detrorotatory ( d or + ) rotation to the left levorotatory ( l or - ) 2) In their chemical properties, optical isomers differ only in a chiral environment. dform of A + dform of B product. dform of A + lform of B no reaction.

Example: Of d-glucose and l-glucose, only d-glucose is metabolizedin humans–a good example of the important selectivity of life forms.

The Binding Site of an Enzyme

The Basis of Proton Spin Resonance

Fig. 15.B (p. 622)

The 1H-NMR Spectrum of Acetone

Fig. 15.C (p. 623)

1H-NMR Spectrum of Dimethoxymethane

Fig. 15.D (p. 623)

Fig 15.EMRI ofthe HumanBrain(P 623)

R-Group Names and Chemical Formulas

methyl - CH3

ethyl - CH2 - CH3 or - C2H5

n-propyl - CH2 - CH2 - CH3 or - C3H7

isopropyl - CH - CH3

CH3

n-butyl - CH2 - CH2 - CH2 - CH3 or - C4H9

isobutyl - CH2 - CH - CH3

CH3

CH3

tert-butyl - C - CH3 CH3

H2 H2

H2

H2H2

Hcyclohexyl

H2 H2

H2

H2

cyclopentyl H

H2

H2

H2

cyclobutylH

H2

H2H

cyclopropyl

Types of Organic Reactions–I

1) Addition Reactions: These reactions occur when an unsaturated compound containing a double or triple bond becomes saturated by adding a compound. This reaction occurs for C=O, C=C and C=C bonds. X YGeneral form: R-CH=CH-R + X-Y R-C-C-R H H

Examples:

CH3-CH=CH-CH3 + H2 CH3-CH2-CH2-CH3

Br BrH-CH=CH-CH2-CH3 + Br2 H-C-C-CH2-CH3

H H

H ClH2C=CH2 + HCl H-C-C-H H H

A Color Test for the C=C Bonds

Fig. 15.14 (P 624)

Types of Organic Reactions–II

2) Elimination Reactions: These are the opposite of addition reactions. A saturated reactant becomes an unsaturated compound, and another molecule is formed.

X YGeneral form: R-CH-CH2 R-CH=CH2 + X-Y

Examples: OH H H2SO4

CH3-CH-CH2 CH3-CH=CH2 + H2O

OH Cr2O72- O

CH3-CH2-CH-CH3 CH3-CH2-C-CH3 + H2O H2SO4

Cl HCH3-CH-CH-CH2-CH3 CH3-CH=CH-CH2-CH3 + HCl

Types of Organic Reactions–III

3) Substitution Reactions: These reaction occur when an atom (or group) from an added reagent substitutes for one in the organic reactant.

General form: R-C-X + Y R-C-Y + X

Examples: CH3-OH + HBr CH3-Br + H2O

O CH3 CH3-C-Cl + CH3-CH-CH2-CH2-OH HCl + O CH3

CH3-C-O-CH2-CH2-CH-CH3

CH3-CH2-CH2-Br + CH3-CH2-ONa NaBr + CH3-CH2-CH2-O-CH2-CH3

CH3-CH2-CH2-Br + NaOH CH3-CH2-CH2-OH + NaBr

Recognizing the Type of Organic ReactionProblem: State whether each of the following reactions is an addition, elimination, or substitution reaction: a) CH3-CH2-OH + CH3-OH CH3-CH2-O-CH3 + H2O b) CH3-CH2-CH=CH-CH3 + H2 CH3-CH2-CH2-CH2-CH3

c) CH3-CH2-CH2-CH2-Cl CH3-CH2-CH=CH2 + HClPlan: We determine the type of reaction by examining the change in the number of atoms bonded to carbon. a) More atoms bonded to carbon is an addition. b) Fewer atoms bonded to carbon is an elimination. c) Same number of atoms bonded to carbon is a substitution.Solution: a) Substitution–the C-OH in both reactant molecules is converted into C-O bonds in the product molecule, so the same number of atoms are bonded to carbon.b) Addition–two C-H bonds form in the product, so more atoms are bonded to carbon.c) Elimination–two bonds in the reactant (C-H,C-Cl) are not in the product, so fewer atoms are bonded to carbon in the product.

The Redox Process in Organic Reactions

Oxidation numbers are not relied upon as much in organic reactions.

Instead, organic chemists note the movement of electron density around the carbon atom by counting the number of bonds to more electronegative atoms (normally oxygen) or to less electronegative atoms (normally H).

An oxidation-reduction (redox) reaction involves both oxidation and reduction, but organic chemists normally focus on the organic reactant only. Therefore:

When a C atom in the organic reactant forms more bonds to O or fewer bonds to H, the reactant is oxidized and the reaction is anoxidation.When a C atom in the organic reactant forms fewer bonds to O ormore bonds to H, the reactant is reduced and the reaction is a reduction.

Organic Oxidation and Reduction Reactions

An example of an organic reaction that involves oxidation-reductionis the reaction that occurs with ethanol and acidic potassium dichromateto yield acetic acid: O

CH3-CH2-OH CH3-C-OHK2Cr2O7 (acid)

In ethanol the C-2 has 2 bonds to hydrogen, and 1 bond to oxygen, whereas in the product (acetic acid) C-2 has three bonds to oxygen and no bonds to hydrogen. Thus, in this reaction the ethanol is oxidized toform acetic acid, so this reaction is an oxidation.

Another reaction is the addition of hydrogen to the double bond in propylene to form propane:

CH3-CH=CH2 + H2 CH3-CH2-CH3

Pd

Note that the C-2 and C-3 have more bonds to hydrogen than in the reactant propylene, so this the reactant is reduced , and the reaction isa reduction.

Alcohols

CH3OH Methyl alcohol-Methanol

C2H5OH Ethyl alcohol-Ethanol CH3CH2OH

C3H7OH Propyl alcohol-Propanol

H3C CH2 CH2 OH H3C CH OH

n-Propyl alcoholCH3

2-Propyl alcoholH3C CH2 CH2 CH2 OH

n-Butyl alcohol

Ethers

Dimethyl ether H3C–O–CH3

Ethyl methyl ether H3C–O–CH2–CH3

Diethyl ether H3C–CH2–O–CH2–CH3

Diphenyl etherC

CH CH

CH

CH

C CH

CH CH

CH

CH

CH O

Reactions of Alkyl Halides with Anions

CH3-CH2-CH2Cl + NaCN CH3-CH2-CH2CN + NaCl

CH3-CH2-Br + NaSH CH3-CH2-S-H + NaBr

CH3-CH2I + NaO-CH3 CH3-CH2-O-CH3

1-Chloropropane 1-Cyanopropane

1-Iodoethane Methylethyl ether

Bromoethane Ethylmercapton

CH3-CH2-Cl + NaNH2 CH3-CH2-NH2 + NaCl

Chloroethane Ethylamine

CH3-CH2-CH2-CH2-Br + NaOH CH3-CH2-CH2-CH2-OH + NaBr

1 - Bromobutane 1-Butanol1-Butyl alcohol

Polychlorinated Biphenyls (PCBs)

.. Cl.... ..Cl..

..

..Cl...... Cl..

..

Until recently, halogenated aromatics were used as insulating fluidsin electrical transformers and were discharged in waste water. Because of their low solubility, they accumulated for decades in river and lakesediment and were eaten by microbes and invertebrates. Fish ate the invertebrates, and birds and mammals, including humans, ate the fish. PCBs become increasingly concentrated in body fat at each stage. As a result of their health risks, PCBs in natural waters present a real problem.

PCBs

Some Biomolecules with the Amine Functional Group

General Structures of Amines

Reactions of Alcohols, Alkyl Halides and Amines

Problem: Determine the reaction type and predict the products of the following chemical reactions: ( a) CH3-CH2-CH2-OH

(b) CH3-CH2-Br + KOH

(c) CH3-CH2-OH + CH3-OHPlan: We examine the reactant(s) and other reagent(s) to decide on thepossibilities for each functional group, keeping in mind that, in general,one functional group changes into another.Solution:

Cr2O7-2

H2SO4

H2SO4

(a) Elimination (oxidation):

(b) Substitution:

(c) Elimination:

OCH3-CH2-C-OH Propanoic acid

CH3-CH2-OH + KBr Ethyl alcohol

CH3-CH2-O-CH3 Methylethyl ether

Hydrolysis-SaponificationThe Reverse Reaction of Ester Formation

Animal fats and/or vegetable fats which are “triglycerides” were broken down using a strong base such as lye (NaOH) to produce a “soap”.

OR- C-O-CH2

OR’-C-O-CH OR”-C-O-CH2

A triglyceride

+ 3 NaOH

OR-C-O- Na+

OR-C-O- Na+

OR-C-O- Na+

+

HO-CH2

HO-CH

HO-CH2

3 Soapmolecules

Glycerol

Amides

Formation of amides: Amides may be formed by the reaction between an organic acid or ester and amine in a dehydration-condensation reaction.

General formation: O H O H R-C-OH + H-N-R’ R-C-N-R’ + H2O

Examples:

O O HCH3-C-O-CH3 + H2N-CH2-CH3 CH3-C-N-CH2-CH3 + CH3-OH

Methyl ethanoate + Ethylamine N-Ethylethanamide + Methanol

O H O HCH3-CH2-C-OH + H-N-CH3 CH3-CH2-C-N-CH3 + H2O

Propionic acid Methyl amine N-Methylpropylamide

O CH3 O CH3

CH3-CH2-CH2-C-OH + H-N-CH2-CH3 CH3-CH2-CH2-C-N-CH2-CH3Butanoic acid Methylethylamine N-Ethyl-N-methylbutanamide

Some Molecules with the Amide Functional Group

The Formation of Anhydrides

Image to come.

Rules for Naming an Organic Compound–I

1. Naming the longest chain (root) (a) Find the longest continuous chain of carbon atoms. (b) Select the root that corresponds to the number of carbon atoms in this chain.2. Naming the compound type (suffix) (a) For alkanes, add the suffix -ane to the chain root. (Other suffixes appear in Table 15.5 with their functional group and compound type.) (b) If the chain forms a ring, the name is preceded by cyclo-.3. Naming the branches (prefix) (a) Each branch name consists of a subroot (number of C atoms) and the ending -yl to signify that it is not part of the main chain. (b) Branch names precede the chain name. When two or more branches are present, name them in alphabetical order.

Rules for Naming an Organic Compound-II

3. continued: (c) To specify where the branch occurs along the chain, number the main-chain C atoms consecutively, starting at the end closer to a branch, to achieve the lowest numbers for the branches. Precede each branch name with the number of the chain C atom to which that branch is attached. (d) If the compound has no branches, the name consists of the root and suffix. 6 carbons hex-

hex- + -ane = hexane CH3

CH3 CH CH CH2 CH3 CH3

CH2 CH3

methyl

ethyl

1 2 3 4 5

ethylmethylhexane

3-ethyl-2-methylhexane

6

Condensed vs. Expanded Formulas

Look at the formulas of 3-ethyl-2-methylpentane:

H

H C H H H H H

H C C C C C H

H H H H H C H

H C H

H

CH3

CH3 CH CH CH2 CH3

CH2

CH3

ExpandedFormula

Condensed Formula

Structure of a Cationic Detergent