PSMA Organic Chemistry (PT 2)

isomers

these are compounds with the same molecular formula and same molecular weight but different structural formula, this differ in physical and chemical properties

1. Structural isomers

2. Constitutional isomers

3. Stereoisomerism

2 types of isomers

1. chain isomers

2. positional isomers

3. functional isomers

3 types of structural isomers:

chain isomers

• Same molecular formula, but different arrangements of the carbon ‘skeleton’.

• The positions of the carbon atoms can be rearranged to give ‘branched’ carbon chains coming off the main chain.

• The name of the molecule changes to reflect this, but the molecular formula is still the same.

1. n-butane

2. 2-methylpropane

example of chain isomers:

positional isomers

• same molecule formula; same functional group, but its position in the molecule changes.

• the name of the molecule changes to reflect the new position of the functional group

1. but-1-ene

2. but-2-ene

example of positional isomers:

functional isomers

• same molecular formula but the atoms are rearranged to give different functional group.

• the name of the molecule changes to reflect the new functional group.

1. ethanol

2. methoymethane

example of functional isomers:

constitutional isomers / structural

• same atoms but linked together differently

• same MF different connectivity

1. dimethyl ether C2H6O

2. ethanol C2H6O

example of constitutional isomers:

stereoisomerism

positioning the different functional groups in their site of action

1. optical isomer

2. geometric isomers

3. conformational isomers

three main groups of stereoisomerism:

Optical Isomer

• Enantiomer - D and L forms

• Diastereomer ex. Epimers

Conformational Isomers

Boat and Chair

optical isomer

• ENANTIOMER - D and L forms

• DIASTEROMER - ex. epimers

• contain at least one asymmetric, or chiral carbon atom

• each asymmetric carbon atom can exist in one of two non-superimposable isometric forms

  • chiral center or stereogenic center

• differ by the placement of different substituents around one or more atoms in a molecule

• different arrangements of these substituents can be impossible to superimpose.

chiral

carbons that have four non-identical substituents around it (chiral center or stereogenic center)

chiral

non-chiral

non-chiral

chiral

1. enantiomers

2. diasteriomers

2 types of stereoisomers:

Enantiomers

are mirror images of each other and non-superimposable

Diasteromers

are not mirror images of each other and non-superimposable

1. D-erythrose

2. D-threose

example of diastereomers:

Epimers

isomers differing as a result of variations in configuration of the -OH and -H on carbon atoms 2,3 and 4 of glucose are known as this

• D-Galactose

• D-Glucose

• D-Mannose

examples of epimers:

Sinister

What does the “S” in (S)-enantiomer mean?

Rectus

What does the “R” in (R)-enantiomer mean?

clockwise

rotation of (+) dextrorotatory

counter clockwise

rotation of (-) levorotatory

geometric isomers

• Cis and Trans

• commonly exhibited by alkenes, the presence of two different substituents on both carbon atoms at either end of the double bond.

• two different non-superimposable isomers due to the restricted rotation of the bond.

1. (E)- 1,2-Dichloroethene

2. (Z)- 1,2-Dichloroethene

E- opposite side (left)

Z- same side(right)

example of geometric isomers:

For morning sickness

(R)-thalidomide

Teratogenic

(S)-thalidomide

bioisosteres

groups that are spatially and electronically equivalent and, thus, interchangeable without significantly altering the molecules’ physicochemical properties.

• enhance desired biological or physical properties

• increased potency

• decreased side-effects

• increase duration of action

purpose of bioisosteres

1. B. Positional Isomers

2. C. Functional Isomers

3. C. Functional Isomers

hydrocarbons

chemical compounds composed only of hydrogen and carbon atoms

alicyclic hydrocarbons

• this group includes saturated and unsaturated cyclic hydrocarbons which resemble with the aliphatic hydrocarbons in properties.

1. pyridine

2. pyrimidine

3. purine

4. furan

5. imidazole

example of “Heterocyclic” in Alicyclic hydrocarbons

Aliphatic hydrocarbons

• hydrocarbon compounds joined together in straight chains, branched chains or non-aromatic rings

alkanes

• paraffins

• sp3 hybrid

• suffix ane

alkenes

• olefins

• sp2 hybrid

• suffix - ene

alkynes

• acetylenes

• sp hybrid

• suffix - yne

cyclic

prefix - cyclo

Aromatic Hydrocarbons

• carbocylic compounds containing conjugated double bonds

Benzene

Simplest aromatic hydrocarbon

August Kekule (1865)

benzene ring as a flat molecule, having alternating single and double bonds between carbon atoms

• p orbital overlap

Kathleen Lonsdale (1929)

used x-ray crystallography to show carbon-carbon bonds in a benzene ring are the same length.

• delocalised electrons

• Fluorobenzene

• Chlorobenzene

• Bromobenzene

• Iodobenzene

Examples of “Halogen-Containing” Benzene Derivatives

• Toluene

• Cumene

• Ethylbenzene

• Styrene

• Ortho-xylene

• Meta-xylene

• Para-xylene

Examples of “Hydrocarbon Derivatives” Benzene Derivatives

• Phenol

• Benzoic acid

• Benzaldehyde

• Acetophenone

• Methyl benzoate

• Anisole

Examples of “Oxygen-containing” Benzene Derivatives

• Aniline

• Nitrobenzene

• Benzonitrile

• Benzamide

Examples of “Nitrogen-containing” Benzene Derivatives

• Benzenesulfonic Acid

Examples of “Sulfur-containing” Benzene Derivatives

• Naphthalene

• Anthracene

Examples of “Polyaromatics” Benzene Derivatives

aromatic compounds

it can form three disubstituted compounds namely 1,2 (ortho-) 1,3 (meta-) and 1,4 (para-) derivatives.

hydrocarbon derivatives

one or more hydrogen atoms in the molecules is replaced by certain group of atoms

1. Hydroxy Derivatives - Compounds containing a hydroxyl group (-OH), such as alcohols and phenols)

2. Ethers - Compounds featuring an oxygen atom connected to two alkyl or aryl groups (R-O-R’)

3. Carbonyl Compounds (Molecules containing a carbon double-bonded to an oxygen (C=O) primarily aldehydes and ketones.

4. Carboxylic Acids Compounds containing a carboxyl group (-COOH)

5. Amides - Derivatives of carboxylic acids where the -OH group is replaced by an amine derivative (-C(=O)NH2, -C(=O)NHR, or -C(=O)NR2)

6. Esters - Derivatives of carboxylic acids where the hydrogen of the carboxyl group is replaced by an alkyl group (-COOR)

7. Nitrogen Containing Compound - A broad class containing nitrogen atoms, such as amines (-NH2), nitriles (-CN), or nitro compounds (-NO2)

8. Alkyl Halides - (Haloalkanes): Hydrocarbons where one or more hydrogen atoms are replaced by a halogen (F, Cl, Br or I)

8 Functional Groups

carbonyl compounds

• aldehydes

• ketones

carboxylic acids

• monocarboxylic acids

• dicarboxylic acids

nitrogen containing compounds

• amine

• nitriles/cyanides

-ane

saturated (all C-C bonds)

-ene

unsaturated: one C=C

-diene

unsaturated: two C=C

-yne

unsaturated: one C≡C

-diyne

unsaturated: two C≡C

-enyne

unsaturated: one C=C and C≡C

-COOH

-oic acid

-carboxylic acid (NOT part)

carboxy-

representation of Carboxylic acid

-COOR

alkyl -oate

alkyl -carboxylate (NOT part)

alkoxycarbonyl-

representation of Ester

-COX

-oyl halide

-carbonyl halide (NOT part)

halocarbonyl-

representation of Acid halide

-CONH2

-amide

-carboxamide (NOT part)

carbamoyl-

representation of Acid amide

-CN

-nitrile

-carbonitrile (NOT part)

cyano-

representation of Nitrile

-CHO

-al

-carbaldehyde (NOT part)

oxo-

representation of Aldehyde

-CO-

-one

oxo-

representation of Ketone

-OH

-ol

-hydroxy

representation of Alcohol

-SH

-thiol

mercapto

representation of Thiol

-NH2

-amine

amino-

representation of Amine

=NH

-imine

imino-

representation of Imine

C=C

-ene

representation of Alkene

C☰C

-yne

representation of Alkyne

alcohols

• with hydroxy (-OH) functional group

• prefix - hydroxy

• suffix - ol

• R-OH

1. primary

2. secondary

3. tertiary

according to the number of alkyl groups attached to the hydroxyl-bearing carbon

1. monohydric

2. dihydric

3. trihydric

according to the number of hydroxyl groups

methanol

“wood alcohol”

ethanol

“grain alcohol”

phenol

“carbolic acid”

Phenols

With hydroxyl (-OH) functional group attached to a carbon atom that is a part of an aromatic ring, Ar-OH

• Catechol

• Resorcinol

• Quinol

• Pyrogallol

• Hydroxyquinol

• Phloroglucinol

examples of Phenols:

Ethers

• Alkoxy-substituted alkanes

• R-O-R

• Formed by the bimolecular dehydration of alcohols with sulfuric acid

• methyl alcohol → dimethyl ether

• ethyl alcohol → diethyl ether

examples of Ethers:

Aldehydes

• Contains at least 1 hydrogen atom attached to the carbonyl carbon

• RC=OH

• Formed by oxidation of primary alcohols

• Prefix – oxo

• • Suffix – al

• Methanal (Formaldehyde)

• Ethanal (Acetaldehyde)

• Propanal (Propionaldehyde)

examples of Aldehydes:

Ketones

• Contains two carbon groups bonded to the carbonyl carbon

• RC=OR

• Formed by oxidation of secondary alcohols

• Prefix – oxo

• Suffix – one

• Propanone (Acetone)

• 2-butanone (Ethyl methyl ketone)

• 3-pentanone (Diethylketone)

examples of Ketones:

Carboxylic Acids

• Produced by oxidation of aldehydes

• Contains the carboxyl functional group

• RC=OOH

• Suffix – oic acid

• formic acid (methanoic acid)

• acetic acid (ethanoic acid)

• propionic acid (propanoic acid)

• butyric acid (butanoic acid)

• valeric acid (pentanoic acid)

• caproic acid (hexanoic acid)

• enanthic acid (heptanoic acid)

• caprylic acid (octanoic acid)

• pelargonic acid (nonanoic acid)

• capric acid (decanoic acid)

• Oxalic acid (ethanedioic acid)

• malonic acid (propanedioic acid)

• succinic acid (butanedioic acid)

• glutaric acid (pentanedioic acid)

• adipic acid (hexanedioic acid)

• pimelic acid (heptanedioic acid)

examples of Carboxylic Acids:

Amides

• Formed by the reactions of organic acids with ammonia or with amides

• the least reactive of the common carboxylic acid derivatives

• RC=ONH2

• Suffix – amide

• Primary amide

• Secondary amide

• Tertiary amide

Esters

• Formed by the reactions of acids and alcohols with acid catalysts

• derived from acids by replacing the -OH group by an -OR group and have the general formula RCOOR

• Alkyl alkanoate, RC=OOR

• Suffix – oate