Organic Chemistry

Shapes of Organic Molecules

Carbon will almost always form four bonds.
If it has four single bonds it will be tetrahedral - sp3 hybridized
H
C H
H
H

If it has one double bond it will be trigonal planar - sp2 hybridized.

H H
C C
H H
If it has a triple bond it will be linear - sp hybridized.
H C C H
Solubility and Acid-Base Properties
C–C and C–H bonds have low polarity and are soluble in non-polar solvents.

If a molecule is soluble in water and other polar solvents it must have polar groups
in it.
O O
C O H
C
O H
carbonyl carboxyl hydroxy
Soaps and Detergents have both polar (water soluble; hydrophilic) parts and non-
polar (fat soluble; hydrophobic) parts.
O
C
O–

Organic and Biological Chemistry 1

Carboxylic acids
O
R C
O H sp2

Amines organic bases -NH2, –NHR, –NR2

H3 C NH2 (CH3 )2 NH (CH3 )3 N

Amino acids contain both groups

O O
H2N CH C OH H2N CH C OH
CH3 H2C CH CH3
CH3
Alanine Leucine

In solution they exist as dipolar ions or zwitterions.

O
+
H3N CH C O–
CH3

Organic and Biological Chemistry 2

Hydrocarbons
Contain only carbon and hydrogen
Four classes
Alkanes - only single bonds - saturated CnH2n+2
Alkenes - at least on double bond -CnH2n
Alkynes - at least one triple bond - CnH2n-2
Aromatics - carbon atoms in a planar ring linked by single and double bonds.
H
H C H
C C
C C
H C H
H

Benzene

Alkanes, CnH2n+2
Name depends on the number of carbon atoms.
Differ by CH2
End in -ane
Number of carbons name
1 methane
2 ethane
3 propane
4 butane
5 pentane
6 hexane
7 heptane
8 octane
9 nonane
10 decane

Intermolecular forces are mostly London dispersion forces

1-4 carbons gases (methane, propane, butane)
5-12 carbons liquid (gasoline)
20 or more solid (paraffin, wax)

Organic and Biological Chemistry 3

Condensed structural formula
H H H H
H C C C C H
H H H H CH3CH2CH2CH3

CH3
H H H
CH3
H C C C C H
CH3CHCH2 CH3
H H H H
3
All carbons are sp - tetrahedral
C–C bond rotation is easy.

Isomers
Straight chain - carbon bonded to no more than two carbons.

H H H H
H H
C C
C C C

H H H H H H

Branched chains: Four or more carbons.

H2 CH3
C CH3
H3 C C CH
H2 H3 C CH3

CH3
H2 H2 CH3
C C C
H3 C C CH3 CH CH3
H2 H3 C CH3
H3 C C
H2 CH3

Organic and Biological Chemistry 4

Nomenclature of Alkanes
There are two general types of nomenclature:
trivial names (acetone, acetic acid)
IUPAC System (propanone, ethanoic acid)

IUPAC or Systematic Names

The systematic way to name all organic compounds.

For alkanes:
(1) Find the longest continuous chain of carbon atoms. This is the base name
of the compound.
(2) Number the longest chain beginning with the end nearest a substituent.
(3) Name the substituent groups attached to the longest chain as alkyl
groups. Also state the location of each alkyl group according to its
numbered carbon on the main chain.
(4) When two or more substituents are present, list them in alphabetical
order. If two or more of the same alkyl groups are present, use the
prefixes di-, tri- etc to avoid repetition.
Examples:
CH2 CH3

CH3 CH2 CH2 CH2 CH3

3-methylhexane
If there are two chains of equal length, choose the chain that has the highest
number of substituents.

CH3 CH3

CH3 CH CH2 CH3 CH CH2

CH CH CH3 CH CH CH3

CH3 CH CH3 CH3 CH CH3

CH3 CH3

Organic and Biological Chemistry 5

Numbering starts at the end nearest a substituent so that the alkyl substituents have
as low numbers as possible.
CH3 CH3

CH3 CH CH2 CH3 CH CH2

CH CH CH3 CH CH CH3

CH3 CH CH3 CH3 CH CH3

CH3 CH3

Alkyl groups are named by replacing the –ane suffix of the alkane name with –yl.

E.g. CH3CH3 Ethane CH3CH2- Ethyl group

CH3CH2CH3 Propane CH3CH2CH2- Propyl group

Cycloalkanes

cyclopropane cyclobutane cyclopentane cyclohexane

cycloheptane cyclooctane
H2
C
H2C CH2

H2C CH2

Alkanes are relatively unreactive (good to use as solvents)

Combustion produces CO2 and H2O

Organic and Biological Chemistry 6

Unsaturated Hydrocarbons

Alkenes have at least one double bond

H H H H
C C C C
H H H3 C H

ethene propene

Location of double bond is indicated by numbers.

H2C CH CH2 CH3 H3C CH CH CH3

1-butene 2-butene
H3 C H
C C
H3 C H

2-methylpropene

There is no free rotation about double bonds.

H H
H CH3
C C
C C
H3 C CH3
H3 C H

cis-2-butene trans-2-butene

Alkynes one or more C≡C

One sigma, σ, and two pi, π, bonds.

Ethyne (acetylene) HC≡CH

Propyne, CH3C≡CH
H C C CH2 CH3 CH3 C C CH3

1-butyne 2-butyne
Replace -ane with -yne

Organic and Biological Chemistry 7

Saturated hydrocarbons undergo addition reactions.

Br2, H2 (Hi T and cat.)

H2 C CH2 + Br2 BrH2 C CH2 Br

Polar molecules: HX and H2O

H H H H
H Br H3 C CH3
+
H3 C CH3 H
Br –

H H

H3 C CH3

Br H

Aromatics

NO2
H2 SO4
+ HNO3 + H2 O

CH3

Naphthalene Anthracene Toluene

Organic and Biological Chemistry 8

Functional Groups

Simplest C=C, C≡C

R, R', R" Represent alkyl groups (–CH3, –CH2CH3, …)

Alkyl Halides (R–X)

H3 C Cl CH2 Cl2 CHCl3 CCl4

Chlormethane Dichloromethane Trichlormethane Tetrachloromethane

Methyl chloride Methylene chloride Chloroform Carbon tetrachloride

Alcohols (R–OH)
Replace -ane with -ol

ethane ethanol CH3CH2OH

-OH group makes alcohols more soluble in water.

Polyols more than one OH group

HOCH2CH2OH ethylene glycol.

Ethers (R–O–R')

Synthesized by condensation reactions

CH3CH2–OH + H–OCH 2CH3 CH3CH2–OCH2CH3 + H2O

O
CH3–O CH3 CH3–O CH2CH3 H2 C CH2

H2 C CH2
dimethyl ether ethyl methyl ether
methoxy methane methoxy ethane tetrahydrofuran (THF)

Organic and Biological Chemistry 9

Carbonyl Group ( C=O)
!+ !"
C O

Aldehydes and Ketones

Aldehydes: H bonded to carbonyl carbon

H H
C O C O
R H
aldehyde formaldehyde

Ketone: Two carbons bonded to carbonyl carbon

R' H3 C
C O C O
R H3 C
ketone acetone
propanone

Carboxylic Acids: –OH attached to carbonyl carbon

O
C H
O
Carboxyl Group

O O

C H C H
H O H3 C O

Formic Acid Acetic Acid

Methanoic Acid Ethanoic Acid

–5
Weak acids: Acetic acid Ka = 1.8 x 10

Organic and Biological Chemistry 10

Amines and Amides
Amines are organic bases

Amides RCONR2
O
C R"
R N
R'

Esters RCOOR'
O
C R'
R O
Formed by the condensation of a carboxylic acid with an alcohol.
Name the alcohol part, then the acid part

O O

C CH2 CH3 C CH3

H3 C O CH3 CH2 O

Ethyl acetate Methyl Propanoate

Ethyl ethanoate

Chirality in Organic Chemistry

chiral
nonsuperimposable mirror images - enantiomers
50/50 mixture of enantiomers is a racemic mixture.

Organic and Biological Chemistry 11

Proteins - composed of amino acids
amino acids
H O H O
+
H2 N C C OH or H3 N C C O–

R R

peptides
In proteins amino acids are linked together by peptide bonds.
O O
H2N CH C OH H N CH C OH
+ H
CH3 H2C CH CH3
CH3
Alanine Leucine

O O
H
H2N CH C N CH C OH
+ H 2O
CH3 H2C CH CH3
CH3
polypeptides
O O O
H
H2 N CH C N CH C N C C OH
H
CH3 H2 C CH CH3 H

CH3

Ala Leu Gly

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