Chapter 23: Organic Chemistry, Polymers, and Biochemicals Chemistry: The Molecular Nature of Matter,...

Chapter 23: Organic Chemistry,

Polymers, and Biochemicals

Chemistry: The Molecular Nature of Matter, 6E

Jespersen/Brady/Hyslop1

Jespersen/Brady/Hyslop Chemistry: The Molecular Nature of Matter, 6E

Carbon ChemistryBonding

Strong covalent bonding to itself and to other non-metal elements

Capable of forming extremely long carbon-carbon chains

Multiple arrangements of

identical molecular formulas

lead to numerous isomers.

Structural Formula RepresentationsLewis Structure of Pentane

Condensed Structural Formula CH3CH2CH2CH2CH3 pentane

Structural Formula Representations Lewis Structure of Pentan-1-ol

Condensed Structural FormulaCH3CH2CH2CH2CH2OH 1-pentanol

Chiral Isomers of CarbonChirality exists when carbon has four unique constituents bond to itself

Non-superimposable mirror images

Chiral Isomers of Butan-2-ol

Abbreviated or Bond-Line Structure

Carbon atoms occur at intersection but no symbol used

CH3–CH2–CH3 would appear as:

Non-carbon atoms would appear as symbols

CH3–CH2–CH2–OH would appear as:

Abbreviated or Bond-Line Structure

Open-Chain CompoundsExamples

butane-1-ol

butane

Abbreviated or Bond-Line Structure of Ring Compounds

Benzene

Chair Form of CylcohexaneCyclohexane

Cyclopropane

Abbreviated or Bond-Line Structure Heterocyclic Compounds

Piperazine Pyridine Pyrazole

Tetrahydropyran Furan

Learning Check1. Draw at least two geometric isomers of

C4H10 using abbreviated structures.

1. Draw the four carbon chain first2. Now rearrange CH3 groups

Your Turn!When a chemical formula is written in the following form, CH3CH2CH2COOH, the representation is known as

A. an abbreviated structure

B. a Lewis dot structure

C. a condensed formula

D. an optical isomer

Functional Groups in Organic Organic families can be defined by

functional groups. Frequently use “R” as a place holder for

alkane-like hydrocarbon groups

R–OH alcohol

R–COOH organic acid

R–O–R’ ether

Functional Groups in Organic

Learning Check

1. Write the abbreviated structure for benzoic acid.

2. What family does C6H5NH2 belong to?

1. 2. amine family

Your Turn!Which of the following is an example of an ester?

A.CH3CH2CH2OH

Hydrocarbons Hydrocarbon compounds only contain C and

Alkanes CnH2n+2 CH3CH2CH3 propane

Alkenes CnH2n CH3CHCH2 propene

Alkynes CnH2n-2 CH3CCH propyne

Aromatic C6H6 benzene Characterized by cyclic delocalized π bonding

Hydrocarbons Alkanes are defined as saturated

compounds. All singles bond to carbon Cannot add more hydrogen atoms

Alkenes and alkynes are unsaturated compounds. Alkenes have double bonds and H atoms

can be added to the double bond to create a saturated compound.

Alkynes have triple bonds and H atoms can be added to create a saturated compound.

CH2=CHCH3 + H2 CH3CH2CH318

Aromaticity- Characterized by conjugated bonds in a ring

such as benzene.

- π electrons are delocalized over the ring

- Leads to greater stability than expected

- Properties are different than those of other hydrocarbon families

- Polycyclic examples:

napthalene anthracene

Hydrocarbon NomenclatureRules for naming alkanes

Established by IUPAC

1. Name ends in “-ane”2. Complete name uses that of parent compound with constituent groups added.

3. Parent is longest continuous carbon chain.

4. Name of longest chain based on the number of carbons.

5. Carbon atoms are numbered starting at the end that gives the lowest number for the

first branch.20

Straight Chained Alkanes

Alkyl GroupsAlkane type groups added to parent chain are known as alkyl groups. Consist of alkane, minus one H atom. Name always ends in –yl

Example

CH4 : now remove one H which yields –CH3

Naming of –CH3

Start with parent name, which is methane

Drop –ane and add –yl So methane becomes methyl group

Alkyl Groups CH3CH2CH3 yields –CH2CH2CH3 when one H

atom is removed from the end carbon. The name of the aryl group is propyl. Note, you can have another isomer of propyl.

The other isomer’s aryl group is 1-methylethyl, or isopropyl, and is created when the H atom is removed from the non-terminal carbon.

Nomenclature6. Aryl groups names are prefixed to parent name.

7. Multiple aryl groups on a parent are numbered and named alphabetically.

8. When there are multiple identical groups add di, tri, tetra to the aryl name.

9. If multiple, identical aryl groups are attached to the same carbon repeat the carbon number.

ExamplesWhat is the name of the compound

shown?

1. The longest carbon chain (parent) is four. Parent name is butane.

2. Start numbering from the left to get the smallest number for the attached group.

Examples3. The attached alkyl group is a methyl

group. Thus, the correct name is:

2-methylbutane

What is the name of the following compound?

Examples The parent chain contains five carbons. Thus, the parent name is pentane. Number from the left to obtain the smallest

number for the first alkyl group.

The alkyl groups are at the 2 and 3 positions. The 2 and 3 positions each contain a methyl

group.27

Examples Thus, the correct name is: 2,3-dimethylpentane

Let’s consider an alkane with two substituents on the same carbon.

Examples The parent chain is six carbons long. The lowest correct numbering of positions

is shown below.

There are methyl and ethyl groups attached to carbon 3.

Examples The correct name is:

3-ethyl-3-methylhexane

Your Turn!What is the correct name for the molecule

below?

A. 3-butylpentane

B. 1,1-diethylpentane

C. 3-ethylheptane

D. 5-ethylheptane

Your Turn!What is the name of the compound shown

below?

A. 3-methyl-3-methyloctane

B. 3,3-dimethyloctane

C. 2-ethyl-2-methylheptane

D. 6,6-dimethyloctane

Chemical Properties of Alkanes Alkanes are relatively unreactive

Not reactive in conc. NaOH or H2SO4 at room temperature.

React with hot HNO3

Will react with Cl2 and Br2 to form halogenated hydrocarbons.

Examples are CH3Cl, CH2Cl2 and CHCl3

Can crack molecules like ethane under controlled conditions to form CH2CH2

Will react with O2 to form CO2, CO, and H2O33

Alkenes and Alkynes Alkenes contain one or more double bonds

General form: CnH2n

Alkynes contain one or more triple bonds General form: CnH2n-2

Non-polar compounds are not water soluble

Examples:

Ethene or ethylene Ethyne or acetylene

Alkenes and Alkynes Nomenclature

The parent chain must contain the multiple bond even if it is a smaller chain length than one without a multiple bond

Number from end that gives the lowest number to the first carbon of the multiple bond

The number is given as -x- and placed just before the –ene or –yne of the parent name.

For example, but-2-ene. The double bond starts on carbon 2 of the chain.

Alkene Examples

Start numbering from the left to get the lowest number for the first carbon with the double bond

The parent is heptene and the correct naming including the double bond location would be hep-2-ene

Alkene Example

The parent chain is four carbons 2,3-dimethylbut-2-ene

We would not name this 2-methyl-3-methylbut-2-ene

Naming Polyenes How do we name compounds such as the

following?

This compound contains two double bonds and is known as a diene

We want the lowest number for the first carbon of each of the double bonds

Start numbering from the right

Naming Polyenes The correct name would be hex-1,3-diene

Three double bonds would be a triene

hex-1,3,5-triene

Cyclic Alkenes

Number ring to obtain lowest number for first carbon of the double bond

Cyclic Alkenes Correct name is 1,6-dimethylcyclohex-1-

Other ring examples

Cyclopentene Cyclooctene

Your Turn!What is the correct name for the compound

below?

A. 1,4-dimethylcyclopent-1-ene

B. 1,3-dimethylcyclopent-1-ene

C. 1-methyl-4-methylcyclopent-1-ene

D. 1,3-dimethylcyclo-1-pentene

Your Turn!What is the correct structure for 3,3-dimethylpro-

1-ene?

Geometric Isomers Groups cannot freely rotate about a double

bond Therefore, it is possible to have geometric

isomers

Examples:

trans-1,2-dibromoethene

cis-1,2-dibromoethene

Reactions of Alkene Alkenes readily add across the double

bond Examples of an addition reaction:

CH2CH2 + H2 CH3CH3 hydrogenation

CH2CH2 + HCl → CH3CH2Cl

CH2CH2 + H2O → CH3CH2OH

CH2CH2 + Cl2 → CH2ClCH2Cl

Aromatic Hydrocarbons The most common aromatic compound is

benzene and its derivatives Representation of bonding

Delocalized π bonds create unique stability, called resonance stabilization. The circle in the ring represents delocalization.

Reactions Substitution reactions maintain benzene’s

resonance structure. Addition reactions, like those of alkenes,

destroy resonance structure

Substitution reaction:

Addition Reaction

Notice that you have reduced the double bonding in the ring and altered the resonance stabilization of the ring

Learning Check:What product would form if benzene

reacted with

nitric acid using an appropriate catalyst?

Sulfuric acid is the catalyst A substitution reaction occurs

Which product is most likely formed when sulfuric

acid reacts with benzene?

Your Turn!

Organic Compounds Containing OxygenImportant functional groups:

Alcohol Ether Aldehyde

Ketone Carboxylic acid Ester

Alcohols and Ethers Common alcohols: names end in –ol

CH3OH methanol

CH3CH2OH ethanol

CH3CH2CH2OH propan-1-ol If the –OH group was attached to the central

carbon then the alcohol would be propan-2-ol

Alcohols form hydrogen bonds, causing their boiling points to be higher than predicted.

Alcohols and Ethers Primary alcohols:

Secondary alcohols:

Tertiary alcohols:

Alcohols and Ethers Common ethers:

CH3OCH3 dimethyl ether

CH3CH2OCH2CH3 diethyl ether

CH3OCH2CH3 methyl ethyl ether

No hydrogen bonding occurs, thus, boiling points are lower than corresponding alcohols

Like alkanes, ethers are not very reactive

Reactions of Alcohols Alcohols can undergo oxidation to form a

variety of products. Oxidation removes an H atom from the alcoholic carbon as well as the H on the –OH group.

Primary alcohols can be oxidized to aldehydes and carboxylic acids

Reactions of Alcohols Aldehydes are more readily oxidized than

alcohols

Secondary alcohols can be oxidized to ketones

Reactions of Alcohols Ketones are not further oxidized Tertiary alcohols have no H atom on the

alcoholic carbon and thus, do not undergo oxidation

Alcohols undergo elimination reactions in the presence of concentrated H2SO4 forming water and alkenes

–OH group readily accepts a proton from sulfuric acid

Elimination Reaction Dehydration of an alcohol

During the reaction a very unstable carbocation is formed. This ion eliminates a proton to form the alkene.

Substitution Reactions of Alcohols Using heat and concentrated HBr, HI, or

HCl, a halogen will replace the –OH group

A proton adds to the –OH forming –OH2+

Water leaves and the halogen ion attaches to the carbon site where the –OH was attached

2-bromo-2-methylpropane

Aldehydes and Ketones

Naming aldehydes Parent name ends in –al, replacing –e in the

alkane name The aldehyde group is always at the end of a

chain and numbering starts with that end of the chain

Aldehyde group Keto group

Naming Aldehydes

Number from the aldehyde end Do not use -1- for aldehyde: 3-methylpropan-1-al, or 3-methyl-1-

propanal would be wrong

3-methylpentanal

Learning CheckWhat is the name of the following

aldehyde?

4-ethylhexanal

Naming Ketones Parent name ends in –one Parent chain must contain carbonyl group Numbering so carbonyl carbon has lowest

possible number

4-ethylheptan-3-one

NOT: 4-ethylheptan-5-one63

Your Turn!What is the correct name for the aldehyde

below?

A. 2,4-dimethylpentanal

B. 2,4-dimethyl-1-pentanal

C. 2-methyl-4-methylpropanal

D. 2,4-dimethyl-5-pentanal64

Your Turn! - Solution Aldehydes are numbered from the

aldehyde end of the molecule

There are two identical groups, (methyl) so we use –di in the naming

2,4-dimethylpentanal

Your Turn!What is the correct name for the ketone

below?

A. 4-methyl-3-ethylhexan-2-one

B. 4-ethyl-3-methylhexan-5-one

C. 3-ethyl-4-methylhexan-2-one

D. 3,4-diethylpentan-2-one66

Your Turn! - Solution Number to give lowest number to keto

group so you start from the right

Alkyl groups are ordered alphabetically so ethyl comes before methyl

Reactions of Aldehydes and Ketones Aldehydes and ketones add hydrogen

across the C=O bond Process is hydrogenation or reduction

Carboxylic Acids and Esters

Naming Carboxlic Acids Name ends in –oic, replacing –e in the

parent name Numbering begins with carboxyl group –COOH or –CO2H is the condensed form

CH3COOH is ethanoic acid (acetic acid)

Naming Carboxylic Acids Benzoic acid

Propanoic acid

Naming Esters Name begins with alkyl group attached to

the –O Name of parent acid is separate from the

alkyl group name and –oic is replaced with –ate

Ethyl propanate72

Learning Check What is the name of the following ester?

Alkyl group is propyl Number, starting with

the ester carbon Propyl 4-methylpentanate

Your Turn!What is the correct name for the product

when 3-

methylbutan-1-ol is completely oxidized?

A. 3-methylbutanoic acid

B. 2-methyl-1-butanoic acid

C. 2-methlybutan-1-oic acid

D. 3-methylbutan-1-oic acid

Reactions of Carboxylic Acids The –COOH is weakly acidic and therefore

reacts with base

RCOOH + OH– → RCOO– + H2O

Formation of Esters Esters give fruits their characteristic odor

Saponification Strong base reacts with an ester to form

alcohol and the ester’s anion forms

pentanoate ion

Your Turn!Name the ester formed when methanol

reacts with

hexanoic acid.

A. 1-methyl hexanoate

B. methylhexanoate

C. methyl hexanoate

D. methyl hexan-1-oate

Organic Derivatives of Ammonia Amines are derived from ammonia with

one or more H atoms replaced with organic groups

Like ammonia, amines are weakly basic

Amines react with acids

Acid Property of Protonated Amines Ethylmethylammonium ion is the

conjugate acid of ethylmethylamine

pKa = 10.76 pKb= 3.24

Amides General form

Where (H)R indicates either an H atom or an R group attached

Naming The name of the parent acid is amended

dropping the –oic ending and replacing it with –amide

Example Names of Amides Propanamide

4-ethylhexamide

These are examples

of simple amides

Synthesis of Simple Amides An organic acid reacts with aqueous NH3 to

form an amide

2-methylpropanoic acid yields 2-methylpropanamide

Amide Reactions Amides can be hydrolyzed back to their

acid form producing ammonia in the process

Amide Reactions Urea, an amide, ultimately hydrolyzes to

NH3, CO2 and water

Carbonic acid is formed, which then decomposes to carbon dioxide and water

The overall reaction is:

Basicity of Amides Amides are not basic like amines The lone pair on the N atom is delocalized

and thus not readily available for donation to a proton

Amides are neutral in an acid-base sense

Your Turn!What is the correct name for the molecule

below?

A. 4,5-dimethylhexanamide

B. 2,3-dimethyl-6-hexanamide

C. 4-methyl-5-methylhexanamide

D. 4-isopropyl-4-methylpropanamide87

Organic Polymers Macromolecule made up of small,

repeating units Example, polypropylene

Starting material

Polymers Repeating unit is called a monomer The reaction to create a polymer is known

as polymerization

Chain Growth Polymers Polymers created by the addition of one

monomer to another monomer Polypropylene is an example of a chain

growth polymer

Common Polymers

General Repeat Unit for Polyvinyl Chloride

This unit is repeated n times to create the polymer

Step-Growth Polymers Condensation reaction A small molecule such as water is eliminated

when the monomers are joined: Nylon 6,6, for example

Nylon is a copolymer, two different molecules combined

Dacron-A Polyester Another example of a condensation

copolymer

Physical Properties Dependent on how polymers pack Branching polymers create non-crystalline,

amorphous solids

Physical Properties Amorphous polymer of polyethylene is

known as low density polyethelene or LDPE Low molecular mass and low structural

strength Used to make plastic grocery bags

Non-branching polyethylene forms high density polyethylene or HDPE

Strong London forces between chains Strong fibers are formed

Physical Properties HDPE is lightweight, water repellent,

resists tears Common uses

Strong mailing envelopes Tyvek

Ultrahigh molecular weight polyethlene 3 to 6 million molar mass UHMWPE Used to make very strong polymers Sails, bullet proof vests, bike helmets

Biochemical molecules Carbohydrates

Structures of glucose, a monosaccharide

Building unit for cellulose and starch

Disaccharide Sucrose

Disaccharide Reactions Disaccharide molecules split into

monosaccharides Gal-O-Glu + H2O → galactose + glucose

Polysaccharides Starch is a large polymeric sugar molecule Can be broken down into glucose, which is

used for energy in biochemical reactions Amylose is the structurally simpler glucose

polymer portion of starch

Disaccharide Reactions Amylose

Amylose +n H2O → n glucose

Polysaccharides The majority of starch is made up of a

more complex polysaccharide known as amylopectin

Cellulose A polymer of glucose with different oxygen

bridge orientations We lack an enzyme to digest cellulose

Lipids Water insoluble natural products Dissolve in non-polar solvents Relatively non-polar with large segments

that are hydrocarbon-like Cholesterol

Lipids Fats and oils

Triacylglycerols-esters of glycerol and long chain carboxylic acids (fatty acids)

Fatty Acids

Triacylglycerols Triacylglycerol example

Reactions of Triacylclycerols Digestion

Breaks down the triacylclycerol into its three component fatty acids and glycerol. Takes place in base so in fact the fatty acids are in their anion form

Hydrogenation The addition of hydrogen to the double bonds Turns oils into solids

Soap Castile soap is made from olive oil Olive oil has many different fatty acids

Two major fatty acid constituents are oleic acid, 50-85%, and linoleic acid, 4-20%

Saponification of triacylglcerols using NaOH or other base, and heat, results in salts of the fatty acid components plus glycerol Sodium oleate and sodium linoleate, for example

This product mixture, soap, is thus the result of saponification of triacylglcerols

Cell Membranes Glycerophospholipids

Diacylclcerols with phosphate unit which is attached to a amino alcohol unit

Contain a hydrophobic, water avoiding, unit and a hydrophilic, water loving, unit

Aggregate together to form lipid bilayers with hydrophilic layers oriented to the outside and inside layers of the membrane

Cell Membranes

Cell Membranes Membrane also contains protein units,

some which act as ion channels to move select ions in and out of cells

Other proteins act as molecular recognition sites for hormones and neurotransmitters

Proteins Polypeptides made up of α-amino acids Serve as hormones, neurotransmitters,

and enzymes Essential amino acids are those the

body does not synthesize Basic amino acid

structure:

Amino Acids

Lysine

Cysteine

Amino Acids Isoleucine

Alanine

Polypeptides Formation of peptide bond

PolypeptidesCombining two amino acids forms a dipeptide

Often the amino acids are abbreviated Glycine – Gly Alanine – Ala

A dipeptide of these would then be shown as: Gly-Ala

A few amino acids can be arranged in a very large number of orders leading to many different proteins Gly-Ala-Arg Gly-Arg-Ala Ala-Gly-Arg Plus three more

Polypeptides and Proteins How many ways can you arrange n

different objects? n ! Therefore 3 amino acids have 6

arrangements

You can also use the same amino acid more than once in a polypeptide

Proteins Consist of polypeptides and usually small

organic molecules They may also incorporate metal ions into

their structure

Structure of Hemoglobin

Nucleic Acids RNA – ribonucleic acid DNA – deoxyribonucleic acid

The chemical of a gene Chemical basis of inherited characteristics

Nucleic Acid Sugars

Basic Nucleic Acid Structure

Where G is a placeholder for a unique nucleic acid side chain

The sugars are ribose for RNA and deoxyribose for DNA

The groups, G, are: adenine (A), thymine (T), uracil (U), guanine

(G), and cytosine(C)

DNA - Double Helix Structure A unique arrangement of amino acids

maximized hydrogen bonding resulting in a pairing of strands to form a double helix Base Pairing A only with T

C only with G

DNA Replication Enzyme catalyzed process unzips the two

strands Arrangement of base pairs dictates

replication pattern

Polypetide Synthesis Controlled formation of peptide bonds to make

a polypeptide Repeated many times to form polypeptides and

proteins Genetic information is transcribed from DNA in

the nucleus onto RNA (m RNA) This messenger RNA moves outside the

nucleus and through a complex process, using other RNA types, synthesizes a specific protein

The order of amino acid synthesis is coded so that the correct amino acids are made available in the proper sequence

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