Chapter 22 organic and biological molecules
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Chapter 22 Organic and Biological Molecules. 22.1 – Alkanes: saturated hydrocarbons. Uses of organic chemistry: Biochemistry Medicinal chemistry Molecular biology Synthetics Industry (petroleum) And more!. 22.1 – Alkanes: saturated hydrocarbons.

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Chapter 22 Organic and Biological Molecules

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Chapter 22 organic and biological molecules

Chapter 22Organic and Biological Molecules


22 1 alkanes saturated hydrocarbons

22.1 – Alkanes: saturated hydrocarbons

  • Uses of organic chemistry:

    • Biochemistry

    • Medicinal chemistry

    • Molecular biology

    • Synthetics

    • Industry (petroleum)

    • And more!


22 1 alkanes saturated hydrocarbons1

22.1 – Alkanes: saturated hydrocarbons

  • Hydrocarbons: compounds containing carbon and hydrogen

  • Saturated: hydrocarbons where each carbon is bound to four atoms

  • Unsaturated: hydrocarbons that contain carbon-carbon multiple bonds (double or triple)


22 1 alkanes saturated hydrocarbons2

22.1 – Alkanes: saturated hydrocarbons

  • The simplest saturated hydrocarbon is methane (CH4)


22 1 alkanes saturated hydrocarbons3

22.1 – Alkanes: saturated hydrocarbons

Number of carbonsIUPAC prefix

1meth-

2eth-

3prop-

4but-

5pent-

6hex-

7hept-

8oct-

9non-

10dec-


22 1 alkanes saturated hydrocarbons4

22.1 – Alkanes: saturated hydrocarbons

  • If you add the suffix –ane, to any of those prefixes, you have generated their alkanes.

  • If that is all you add, they are called straight-chained alkanes, or unbranchedalkanes

  • For all alkanes, the general formula is given by:

    CnH2n+2


22 1 alkanes saturated hydrocarbons5

22.1 – Alkanes: saturated hydrocarbons


22 1 alkanes saturated hydrocarbons6

22.1 – Alkanes: saturated hydrocarbons

  • Isomerism:

    • In organic chemistry, isomers are chemical compounds with the same molecular formula, but a different structural formula


22 1 alkanes saturated hydrocarbons7

22.1 – Alkanes: saturated hydrocarbons

  • Isomerism:


22 1 alkanes saturated hydrocarbons8

22.1 – Alkanes: saturated hydrocarbons

  • Isomerism:

    • C4H10 and up all exhibit structural isomerism, also known as constitutional isomerism. In this form of isomerism, the molecules have the same number of atoms, but different bonds


22 1 alkanes saturated hydrocarbons9

22.1 – Alkanes: saturated hydrocarbons

  • Nomenclature

    1. Find the longest uninterrupted carbon chain. Depending on how many carbons there are, this determines the prefix (here, it is ______hexane)


22 1 alkanes saturated hydrocarbons10

22.1 – Alkanes: saturated hydrocarbons

  • Nomenclature

    2. Branches are named by dropping the -ane suffix and adding an -yl suffix


22 1 alkanes saturated hydrocarbons11

22.1 – Alkanes: saturated hydrocarbons

  • Nomenclature

    3. The position of the branch must be indicated by finding its position on the main carbon chain. The goal is to always have the lowest numbering possible


22 1 alkanes saturated hydrocarbons12

22.1 – Alkanes: saturated hydrocarbons

  • Nomenclature

    We could call this 3-ethylhexane or 4-ethylhexane. Since the numbering is smaller in 3-ethylhexane, it is the suitable name


22 1 alkanes saturated hydrocarbons13

22.1 – Alkanes: saturated hydrocarbons

  • Nomenclature

    4. The naming goes alphabetically. If there are more than one of a substituent (branch), the prefixes –di and –tri are used. They do not count when alphabetizing.


22 1 alkanes saturated hydrocarbons14

22.1 – Alkanes: saturated hydrocarbons

  • Nomenclature


22 1 alkanes saturated hydrocarbons15

22.1 – Alkanes: saturated hydrocarbons

  • Nomenclature


22 1 alkanes saturated hydrocarbons16

22.1 – Alkanes: saturated hydrocarbons

  • Nomenclature


22 1 alkanes saturated hydrocarbons17

22.1 – Alkanes: saturated hydrocarbons

  • Reactions

    • Combustion

      • Common in the petroleum industry (methane, propane, butane, octane, etc…)

      • In a perfect world, the products are CO2 and H2O

        (incomplete combustion leads to CO and others)


22 1 alkanes saturated hydrocarbons18

22.1 – Alkanes: saturated hydrocarbons

  • Reactions

    • Substitution

      • Primarily seen when halogens (F, Cl, Br, I) replace hydrogen atoms in an alkane

      • Example, the free radical halogenation of CH4 with Cl2


22 1 alkanes saturated hydrocarbons19

22.1 – Alkanes: saturated hydrocarbons

  • Reactions

    • Dehydrogenation

      • Is the creation of double bonds in an alkane (turning it into an alkene)


22 1 alkanes saturated hydrocarbons20

22.1 – Alkanes: saturated hydrocarbons

  • Cyclic alkanes

    • Simplest cyclic alkane is cyclopropane, C3H6.

    • These alkanes follow CnH2n


22 1 alkanes saturated hydrocarbons21

22.1 – Alkanes: saturated hydrocarbons

  • Naming Cyclic alkanes

    • Just add the prefix –cycloto the alkane

    • If there is only one substituent coming off of the cyclic hydrocarbon, you do not need to number it


22 1 alkanes saturated hydrocarbons22

22.1 – Alkanes: saturated hydrocarbons

  • Stability of cyclic alkanes

    • Cyclohexane


22 2 alkenes and alkynes

22.2 – Alkenes and Alkynes

  • Alkenes

    • The carbons involved have sp2 hybridization, and adopt a trigonal planar shape (flat!)


22 2 alkenes and alkynes1

22.2 – Alkenes and Alkynes

  • Alkenes

    • Recall from chapter 9 that a C=C has a sigma bond (from overlapping sp2 orbitals) and a pi bond (from overlapping pi orbitals).


22 2 alkenes and alkynes2

22.2 – Alkenes and Alkynes

  • Alkenes

    • Naming alkenes:

      • Instead of an –ane suffix, use a –enesuffix

      • IUPAC name for the simplest alkene is:

        ethene (although it is often called acetylene)


22 2 alkenes and alkynes3

22.2 – Alkenes and Alkynes

  • Alkenes

    • Naming alkenes:

      • In longer alkenes, you must number the parent chain to figure out the location of the double bond. Since it exists in two carbons, put the lower number carbon in the name


22 2 alkenes and alkynes4

22.2 – Alkenes and Alkynes

  • Alkenes

    • Cis-trans (Z/E) isomerism:

      • Only occurs if both carbons involved in double-bonding have two different substituents coming off of them

Cannot have isomers


22 2 alkenes and alkynes5

22.2 – Alkenes and Alkynes

  • Alkenes

    • Cis-trans (Z/E) isomerism:

      • Example, 2-pentene

cis-2-pentene trans-2-pentene

(Z)-2-pentene(E)-2-pentene


22 2 alkenes and alkynes6

22.2 – Alkenes and Alkynes

  • Alkenes

    • Cis-trans (Z/E) isomerism

      • Cahn-Ingold-Prelog rules for assigning E/Z:

        1. The higher priority goes to the higher atomic number


22 2 alkenes and alkynes7

22.2 – Alkenes and Alkynes

  • Alkenes

    • Cis-trans (Z/E) isomerism

      • Cahn-Ingold-Prelog rules for assigning E/Z:

        2. If there is a tie, you go to the next atom in the line (count double bonds as two single bonds to the same atom )


22 2 alkenes and alkynes8

22.2 – Alkenes and Alkynes

  • Alkenes

    • Properties:

      • More reactive than alkanes

      • Usually have a strong odor


22 2 alkenes and alkynes9

22.2 – Alkenes and Alkynes

  • Alkenes

    • Reactions:

      • Alkenes are synthesized through elimination reactions (because two atoms are eliminated)


22 2 alkenes and alkynes10

22.2 – Alkenes and Alkynes

  • Alkenes

    • Reactions:

      • Addition reaction


22 2 alkenes and alkynes11

22.2 – Alkenes and Alkynes

  • Alkenes

    • Reactions:

      • Hydrogenation


22 2 alkenes and alkynes12

22.2 – Alkenes and Alkynes

  • Alkynes

    • Have sphybridization (linear)


22 2 alkenes and alkynes13

22.2 – Alkenes and Alkynes

  • Comparing properties of alkanes, alkenes, and alkynes

    Alkanes

    Alkenes

    Alkynes

Low BP

Less acidic

Less energy in bonds

High BP

More energy in bonds

More acidic


22 3 aromatic hydrocarbons

22.3 – Aromatic Hydrocarbons

  • Aromatic hydrocarbons are extremely stable (unreactive) cyclic hydrocarbons

  • They are planar molecules (all atoms in the cyclic structure are sp2 hybrids)

  • They have delocalized pi electrons


22 3 aromatic hydrocarbons1

22.3 – Aromatic Hydrocarbons

  • Examples


22 3 aromatic hydrocarbons2

22.3 – Aromatic Hydrocarbons

  • Benzene is a commonly studied aromatic compound.


22 3 aromatic hydrocarbons3

22.3 – Aromatic Hydrocarbons

  • Naming the positions

    • Ortho-, meta-, para-


22 3 aromatic hydrocarbons4

22.3 – Aromatic Hydrocarbons

  • As a substituent, benzene is called a phenyl group


22 3 aromatic hydrocarbons5

22.3 – Aromatic Hydrocarbons

  • Some notable benzene derivatives:

Hydroxybenzene

(phenol)


22 3 aromatic hydrocarbons6

22.3 – Aromatic Hydrocarbons

  • Reactions:

    • Substitution


22 4 hydrocarbon derivatives

22.4 – Hydrocarbon Derivatives


22 4 hydrocarbon derivatives1

22.4 – Hydrocarbon Derivatives

  • Alcohols and ethers

    • Alcohols have an -OH group

    • Has hydrogen bonding, therefore

      has a higher boiling point

    • Methanol boils at 65oC

    • Ethane boils at -89oC

      Same molar mass, difference in BP’s

      come from the H-bonding!


22 4 hydrocarbon derivatives2

22.4 – Hydrocarbon Derivatives

  • Alcohols and ethers

    • Naming alcohols:

      • Uses the suffix –ol

      • This can be named as either 2-butanol or butan-2-ol

      • This is a secondary alcohol


22 4 hydrocarbon derivatives3

22.4 – Hydrocarbon Derivatives

  • Alcohols and ethers

    • Naming alcohols:

      • Uses the suffix –ol

      • This name is 6-bromo-2-methyl-2-hexanol

        or

        6-bromo-2-methylhexan-2-ol


22 4 hydrocarbon derivatives4

22.4 – Hydrocarbon Derivatives

  • Alcohols and ethers

    • Ethers are two organic compounds joined by an oxygen atom

    • They generally do not experience hydrogen bonding (low BP’s)


22 4 hydrocarbon derivatives5

22.4 – Hydrocarbon Derivatives

  • Alcohols and ethers

    • Naming ethers

      • Uses the suffix –oxy for the short chain, followed by the regular alkane name for the long chain

      • This ether is called methoxyethaneor ethyl methyl ether


22 4 hydrocarbon derivatives6

22.4 – Hydrocarbon Derivatives

  • Aldehydes and Ketones

    • Carbonyl groups are C=O

    • Aldehydes have a C=O at the final carbon (or 1st C)

    • Ketones have a C=O in the middle of the parent chain


22 4 hydrocarbon derivatives7

22.4 – Hydrocarbon Derivatives

  • Aldehydes and Ketones

    • Naming

    • For aldehydes, add the suffix –al

    • This is the simplest aldehyde, methanal(aka formaldehyde)


22 4 hydrocarbon derivatives8

22.4 – Hydrocarbon Derivatives

  • Aldehydes and Ketones

    • Naming

    • For aldehydes, add the suffix –al

    • This one is called propanal


22 4 hydrocarbon derivatives9

22.4 – Hydrocarbon Derivatives

  • Aldehydes and Ketones

    • Naming

    • For a ketone, add the suffix –one

    • This is the simplest ketone, 2-propanone (acetone)


22 4 hydrocarbon derivatives10

22.4 – Hydrocarbon Derivatives

  • Aldehydes and Ketones

    • Creating aldehydes/ketones from alcohols

      • Oxidation of a 1o alcohol:


22 4 hydrocarbon derivatives11

22.4 – Hydrocarbon Derivatives

  • Aldehydes and Ketones

    • Creating aldehydes/ketones from alcohols

      • Oxidation of a 2o alcohol:


22 4 hydrocarbon derivatives12

22.4 – Hydrocarbon Derivatives

  • Aldehydes and Ketones


22 4 hydrocarbon derivatives13

22.4 – Hydrocarbon Derivatives

  • Carboxylic acids and esters

    • Carboxylic acids have a carboxyl group:


22 4 hydrocarbon derivatives14

22.4 – Hydrocarbon Derivatives

  • Carboxylic acids and esters

    • Naming carboxylic acids

      • Uses the suffix –oic acid

      • The simplest carboxylic acid is methanoic acid (also known as formic acid)


22 4 hydrocarbon derivatives15

22.4 – Hydrocarbon Derivatives

  • Carboxylic acids and esters

    • Esters are formed by reacting a carboxylic acid with an alcohol (as you will do to make acetylsalicylic acid)


22 4 hydrocarbon derivatives16

22.4 – Hydrocarbon Derivatives

  • Carboxylic acids and esters

    • Name the R’ side first with an –yl suffix

    • Then name the R side with the –oate suffix


22 4 hydrocarbon derivatives17

22.4 – Hydrocarbon Derivatives

  • Carboxylic acids and esters


22 4 hydrocarbon derivatives18

22.4 – Hydrocarbon Derivatives

  • Amines and amides

    • Amines are organic compounds containing nitrogen. They look live derivatives of NH3

    • They are basic (can accept a H+)


22 4 hydrocarbon derivatives19

22.4 – Hydrocarbon Derivatives

  • Amines and amides

    • They are named by adding the –amine suffix


22 4 hydrocarbon derivatives20

22.4 – Hydrocarbon Derivatives

  • Amines and amides

    • Amides are a combination of a carboxylic acid and amine:

    • Amides are the bonds found in proteins, between the amino acids (called polypeptide bond in bio)


22 4 hydrocarbon derivatives21

22.4 – Hydrocarbon Derivatives

  • Amines and amides

    • To name amides, simply add the –amide suffix


22 4 hydrocarbon derivatives22

22.4 – Hydrocarbon Derivatives

  • Amines and amides

    • Similar to esters, if there is a group coming off of the N, it gets named first.


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