Organic Chemistry
Prof Amanda Rousseau (A-diagonal)
Dr Maya Makatini (B-diagonal)
Dr Kennedy Ngwira (E-diagonal)
First Year Organic Chemistry:
• 19/20 lectures (end of block 2 and beginning of block 3)
• Prescribed textbook: Chemistry the Central Science - Brown (Chapter 24)—
not good for organic chemistry
• Background notes – green booklet
• Extra reading: Organic Chemistry – McMurry (any edition)
In 2021 for this section we will provide online audio PowerPoint lectures,
recorded by Professor de Koning, Dr Ngwira and Dr Makatini
In the absence of face to face lectures, we would like to invite you to address
any queries by email to Kennedy. [email protected], Maya.
[email protected] or [email protected]
Introduction - Organic chemistry
• The study of carbon compounds, their reactions
and structure
• Often with C-H bonds
• These compounds are known as ORGANIC
COMPOUNDS
• Known as hydrocarbons if only C & H are
present
• Can also contain O, N, S, P (heteroatoms) and
almost always H
Organic chemistry
• Organic compounds form the basis of life
• Biology at a molecular level = organic chemistry
• Also important in: food, dyes, paints,
pharmaceuticals, agrochemicals, fuel, glue,
flavourings, perfumes, cosmeceuticals, plastics
Organic chemistry
Photo taken from “Breakthroughs in
Bioscience” FASEB
O1: Ways of representing organic molecules
1. Molecular formula
• Indicates composition
• Gives no indication of how the atoms are bonded
or connected
E.g. C3H8 ; C2H4; C5H9NO2
O1: Ways of representing organic molecules
2. Condensed structural formula
• Shows groupings of atoms in a condensed or
compact manner
E.g. CH3CH2CH3; H2CCH2;
HCOCH2CH2NHCOCH3
O1: Ways of representing organic molecules
3. 2-D projection formula / expanded formula
• Shows connectivity between atoms
• Geometry may be unrealistic – gives no indication
of 3-D shape
O1: Ways of representing organic molecules
4. 3-D structural formula / perspective drawing
• Best representation – gives indication of geometry
• But, cumbersome for large molecules
H H H
H In the plane of
the paper
Out of the page –
towards you C C
H C H
~109.3°
H H Into the page –
away from you
O1: Ways of representing organic molecules
5. Line drawing
Short-hand “stick formulae”
CH2 CH3
=
H3C CH2
CH CH3
= H3C CH
OH
OH
CH CH3
= H3C C
O
O
O1: Ways of representing organic molecules
Compare:
H bonded to End of the line
any atom other 3 bonds to C are shown, represents a carbon.
than C is shown only 1 H is implied It also has 2 H atoms
Terminal C All 4 bonds to C shown,
Must carry 2 H atoms,
carries 3 H atoms therefore no H
as only 2 bonds are shown
O2: Trivial and IUPAC nomenclature
1. Trivial names
• Common names
• Often based on historical origins
• Non-systematic
O Acetic acid
C – found in vinegar
H3C OH
O2: Trivial and IUPAC nomenclature
2. Systematic name
• Follows IUPAC rules
• International Union of Pure and Applied
Chemistry
O Ethanoic acid
C
H3C OH
Why we use trivial names.......
A chemist walks into a pharmacy and asks the
pharmacist, "Do you have any acetylsalicylic
acid?“
"You mean aspirin?" asked the pharmacist.
"That's it, I can never remember that word."
O2: Trivial and IUPAC nomenclature
IUPAC rules:
Prefix Parent Suffix
Where are the How many carbons What family?
substituents? in the chain?
O2: Trivial and IUPAC nomenclature
How many carbons
IUPAC rules: Parent in the longest chain?
CH4 Methane 1 + CH2
CH3CH3 Ethane 2
+ CH2
CH3CH2CH3 Propane 3
CH3CH2CH2CH3 Butane 4
Homologous series
C5 Pent- 5 • Consistent difference
C6 Hex- 6 of CH2 between family
C7 Hept- 7 members
C8 Oct- 8 • Similar chemical
properties (3rd block)
C9 Non- 9
• Related physical
C10 LEARN! Dec- 10 properties
O2: Trivial and IUPAC nomenclature
IUPAC rules: Suffix What family?
Saturated
Single bond - σ bond – Alkane
hydrocarbon
“Ethane”
Double bond - 1σ & 1π bond – Alkene
“Ethene” Unsaturated
hydrocarbon
Triple bond - 1σ & 2π bonds - Alkyne
“Ethyne”
O2&3: Trivial and IUPAC nomenclature &
structural features
IUPAC rules:
Prefix Where are the
substituents?
• Branches containing C and H only
• Substituents containing other kinds of atoms
OH
H2
CH C
H 3C C CH3
Cl Cl
O2&3: Trivial and IUPAC nomenclature &
structural features
Examples: Use the IUPAC rules to name the following:
CH3CH2CH(CH3)CH2CH2CH3
H2 H2
C C CH3
1) Draw the molecule H
H3C C C
H2
CH3
2) Count the carbons in the longest chain
H2 H2 H2 H2
C C CH3 C C CH3
H3C CH C H3C CH C
H2 H2
CH3 CH3
6 = hex 5 = pent
O2&3: Trivial and IUPAC nomenclature &
structural features
3) Identify and name the substituent
H2 H2
C C CH3 -CH3 = methane – H =
H3C CH C
H2 methyl
CH3
Similarly: CH2CH3 – ethyl
CH2CH2CH3 – propyl
IN GENERAL: ALKYL
O2&3: Trivial and IUPAC nomenclature &
structural features
4) Identify position of substituent by a number
Number the carbons so that the carbon with the branch is nearest C1
5 3
2 4 H2 H2
H2 H2 C C CH3 1
6 4
C 3
C CH3
6 H3C CH C
1 H3C CH C H2
H2 2
5 CH3
CH3
5) Name the compound
H2 H2
C C CH3
H3C CH C = 3-methylhexane
H2
CH3
O2&3: Trivial and IUPAC nomenclature &
structural features
Note: If there is more than one substituent:
• Each must have its own number – you may have to
repeat a number
• Number the longest chain from the end that gives the
lowest numbers TOTAL for the substituents
• TWO methyl groups = dimethyl
THREE propyl groups = tripropyl
FOUR ethyl groups = tetraethyl
O2&3: Trivial and IUPAC nomenclature &
structural features
Note: If there is more than one substituent:
• Substituents are listed alphabetically, BUT, ignore di-; tri-;
tetra etc
• Other substituents – called heteroatoms:
F – Fluoro
Cl – Chloro
These will be known as haloalkanes
Br – Bromo
I – Iodo
NO2 – Nitro
NH2 - Amino
O2&3: Trivial and IUPAC nomenclature &
structural features
Examples: Use the IUPAC rules to name the following:
methyl
methyl
ethyl
methyl
chloro
4-chloro-6-ethyl-3,3,5-trimethyloctane
O2&3: Trivial and IUPAC nomenclature &
structural features
Examples: Use the IUPAC rules to name the following:
What about this? There are 2
H3C double bonds. What will this
CH2 CH3 be called?
H
C C C
H3C C CH CH2
CH3
Cl H2C
CH3
5-chloro-3-ethyl-4,6,6-trimethylocta-1,4-diene
5-chloro-3-ethyl-4,6,6-trimethyl-1,4-octadiene
O2&3: Trivial and IUPAC nomenclature &
structural features
Examples: Use the IUPAC rules to name the following:
H3C
CH2 CH3
CH
C C C
H3C C CH
CH3
Cl H2C
CH3
5-chloro-3-ethyl-4,6,6-trimethyloct-4-ene-1-yne
O3: Structural features of organic molecules
Molecules with rings
Add “cyclo” to name of parent system:
H2
H2 C
C
H2C H 2C CH2 H2C H2C CH2
CH2 CH2
H2C H 2C CH2 H2C H2C CH2
C C
H2 H2
cyclopropane cyclobutane cyclopentane cyclohexane
O3: Structural features of organic molecules
Molecules with rings
ethylcyclooctane
1-ethyl-2-methylcyclopent-1-ene
4-propylcyclohex-1-ene
O3: Structural features of organic molecules
1. Acyclic
2. Cyclic
3. Polycyclic
4. Straight Chain
All single bonds
5. Branched Chain
6. Saturated
Double or triple
7. Unsaturated bonds present
O3: Structural features of organic molecules
8. Heteroatom Ethanoic acid
ethanol
9. Heterocycle pyrrolidine
H
N
10. Aromatics with heteroatom pyrrole
(heteroaromatic)
benzene
11. Aromatic hydrocarbon
Delocalised
electrons
Summary
• Ways of representing molecules:
CH3CHCH2
• Nomenclature of hydrocarbons:
• Longest chain
• Family (alkane/ene/yne)
• Number chain to give branches the lowest number
• List substituents alphabetically
O5: Isomerism
• Isomers are compounds which have the same:
• Atomic composition
• Molecular formulae
but differ in:
• The way in which the atoms are
arranged
• Chemical reactivity and physical
properties – 3rd block
• Leads to structural diversity and a vast
number of compounds
O5: Isomerism
• There are two classes of isomers:
1. Structural Isomers
2. Stereoisomers
O6: Isomerism
1. Structural isomers
• Different “connectivity” between atoms:
sequence of bonds between atoms is different
• Different physical properties (and possibly,
different chemical properties)
C4H10
Butane 2-methylpropane
B.P. -0.5°C B.P. -10°C
O6: Isomerism
1. Structural isomers
C2H6O
Ethanol Methoxymethane
B.P. 79°C B.P. -24°C
Chemical and physical properties completely different.
A consequence of this is structural diversity and a vast number
of possible compounds!
O6: Isomerism
1. Structural isomers
e.g. How many structural isomers of C6H14 can you
find? Can you name them?
hexane 2-methylpentane
3-methylpentane 2,2-dimethylbutane
2,3-dimethylbutane
O7: Isomerism
2. Stereoisomers
Same bonding sequence of atoms BUT:
• Different orientation of atoms in space
Shape is important! We often need to use 3-D
projection formulae
3 different classes of stereoisomers
– Conformational isomers
– Geometric isomers
– Enantiomers
O7: Isomerism
2a. Conformational Isomers
• Require: σ bonds
free rotation about these bonds
• No bond is broken, energy barrier is low
• For example, C2H6 has two conformers
(use model kits to check for yourself)
Staggered Eclipsed
Sawhorse
Newman
Lower energy Higher energy
O7: Isomerism
2a. Conformational Isomers
eg: Cyclohexane
Chair
Not a flat ring - puckered Boat
Low energy 109°
High energy
Ring flip (rapid at RT)
3
Steric strain
2
1
All C-H bonds are C-H’s eclipsed –
staggered torsional strain
O7: Isomerism
2b. Geometric Isomers
• Require: a rigid unit about which rotation is
NOT possible
• For example: a π bond or a ring
• Interconversion of isomers requires bond
breaking → lots of energy!
O7: Isomerism
2b. Geometric Isomers
Alkane
• All single or σ bond
• Fully saturated
• Rotation about C-C bond is possible
• No geometric isomers possible
Alkene
• C=C bond – one σ bond and one π bond
• Unsaturated
• Rotation about C=C bond is not possible
• Geometric isomers possible
O7: Isomerism
2b. Geometric Isomers
• Two types of isomers
• Cis – on the same side (also called Z)
• Trans – on opposite sides (also called E)
• Different physical properties (similar chemical properties)
But-2-ene
cis-but-2-ene trans-but-2-ene
BP ~ 4°C BP ~ 1°C
O7: Isomerism
2b. Geometric Isomers
1,2-dimethylcyclobutane
cis-1,2-dimethylcyclobutane trans-1,2-dimethylcyclobutane
CH3
H
H
CH3
O7: Isomerism
2b. Geometric Isomers
Example: How many isomers of C4H8 are there? Can
you name them?
cyclobutane 1-methylcyclopropane but-1-ene
cis-but-2-ene trans-but-2-ene 2-methylprop-1-ene
O7: Isomerism
2b. Geometric Isomers
Hint: General formula for alkanes: CnH2n+2
i.e. a relationship between the number of carbons and
hydrogens
Does C4H8 fit this formula?
If YES, compound is an alkane
If NO, then compound either contains double or triple
bonds, or is cyclic.
O7: Isomerism
2c. Enantiomers
• Require: saturated sp3 hybridised carbon
(tetrahedral) with 4 different
substituents
• These molecules are non-superimposable – but
are mirror images of one another.
* *
A star indicates a
stereogenic (chiral)
centre
O7: Isomerism
2c. Enantiomers
• Enantiomers are known as chiral (handed)
compounds
Bergman, J. Why the Miller–Urey research argues against abiogenesis;
http://www.answersingenesis.org/tj/v18/i2/abiogenesis.asp
O7: Isomerism
2c. Enantiomers
• Have virtually identical chemical properties
• Physical properties are identical EXCEPT: they interact
with plane polarised light differently. One enantiomer
will rotate the polarised light x° and the other will rotate
the light –x°
• They have optical activity and are known as optical
isomers
• Optical activity measured using a polarimeter
O7: Isomerism
2c. Enantiomers
• Enantiomers rotate plane polarised light to the:
Right – Dextrorotatory (+)
Left – Laevorotatory (-)
• This was discovered in 1849 by Pasteur.
• A mixture of 50% (+) and 50% (-) = Racemic mixture
and the mixture is optically INACTIVE, but the
individual molecules are still optically active
O8: Chirality
A molecule that exists as a pair of nonsuperimposable
mirror images (enantiomers) is called chiral.
A carbon atom attached to four different atoms or
groups is called a: stereogenic centre, a chiral carbon
or an asymmetric carbon.
O8: Chirality
Remember:
Molecules with one stereogenic centre exist as a pair
of enantiomers.
The enantiomers are nonsuperimposable mirror
images.
If two enantiomers are placed in a solution in equal
amounts, then the mixture is optically inactive and is
called racemic.
Many pharmaceuticals are chiral molecules.
O8: Examples of Chirality
Ibuprofen Stereogenic centre – can you draw the 3-D
structural formulae for the two enantiomers?
*
COOH
active pain reliever inactive!!
O8: Chirality
Examples: Do these molecules contain a stereogenic
centre? If so, identify the asymmetric carbon & draw
both enantiomers
* *
O8: Chirality
Examples: Are these molecules chiral? If so, identify
the chiral centre & draw the other enantiomer
Draw mirror image
OR:
O8: Chirality
Example
Pentan-2-ol is chiral but pentan-3-ol is not.
Explain.
O8: Chirality
Stereoisomerism is very important in biology
Anon. Fundamentals of Drugs I, Chapter 4; http://tigger.uic.edu/~kbruzik/text/chapter4.htm
O8: Chirality
Thalidomide
One enantiomer -Sedative, painkiller, antiemetic, antidepressant
Other enantiomer - Teratogen – intercalates DNA & affects limb &
H ear development
O N O
O
*
N Sold as a racemate (1957-62)
Caused 10,000 birth defects
O
Stereogenic carbon
O8: Chirality
Thalidomide
O8: Chirality
• Example of compounds with more than one stereogenic
centre
Ephedrine Pseudoephedrine
Stimulant, appetite Nasal/sinus decongestant
suppressant, decongestant
O8: Chirality
Maitotoxin – one of the causative toxins of ciguatera, a
poisoning caused by ingestion of coral reef fish (95
stereogenic centres!)
O9: Structural vs stereoisomers
Isomers
Structural
Stereoisomers
isomers
Different connectivity between atoms Same connectivity between
eg: C5H10 atoms but different orientation
of atoms in space
O10: Stereoisomers
Stereoisomers
Conformational
Geometric isomers Enantiomers
isomers
σ bonds, free rotation C=C; rings; cis - trans Stereogenic centre
Low E = staggered High E barrier Optical activity
High E = eclipsed Non superimposable
mirror images
O10: Comparison of stereoisomer
properties
• Conformational
Sigma (σ)bonds
free rotation
• Geometric
Pi (π) bond or ring
no free rotation
• Enantiomers
Carbon with 4 different substituents
Optically active
O11: Classification of organic molecules
Organic
compounds
C and H C and H plus
Hydrocarbon Heteroatoms
Saturated Unsaturated Saturated Unsaturated
• C & H ONLY • C & H ONLY • C, H & other • C, H & other atoms
• σ / single • Multiple (π & σ) atoms such as such as O, N, S, P etc
bonds only bonds present O, N, S, P etc • Multiple (π & σ)
C=C, CΞC • σ / single bonds present –
bonds only C=C, CΞC, C=O, C=N,
CΞN etc
O11: Classification of organic molecules
• To which broad class do the following belong?
OH
O
O12: Functional groups
• Definition: An atom, or group of atoms, that imparts
characteristic chemical properties to an organic
compound
• Functional Groups (FGs) include hetero-atoms (not H
or C) & multiple bonds
• FGs are the most reactive sites in a molecule
Hydrocarbon Functional
backbone group
O12: Functional groups
•YOU NEED TO
LEARN THE FGs!!!
•GREEN BOOKLET!!!
O12: Functional groups
Alkene
Alkyne
Haloalkane
Alcohol
Thiol
O12: Functional groups
Ether
Thioether
Amine
Nitrile
H
C
Aromatic ring HC CH
eg. Benzene
HC CH
C
H
O12: Functional groups
Carboxylic acid Carboxylic acid chloride
Carboxylic ester
Carboxylic amide
Aldehyde
R not equal H
Ketone
O12: Functional groups
• Identify the functional groups in lopinavir
O12: Functional groups
• Identify the functional groups in Candarel
O12: Functional groups
• Identify the functional groups in methotrexate
O12: Trivial and IUPAC nomenclature
• Trivial names
• Historical
• Can be ambiguous
• IUPAC
• Follows a set of internationally accepted rules
• Unambiguous
Acetic acid Ethyl alcohol Acetone Acetylene
Ethanoic acid Ethanol Propanone Ethyne
O12: Trivial and IUPAC nomenclature
• Trivial names
• Historical
• Can be ambiguous
• IUPAC
• Follows a set of internationally accepted rules
• Unambiguous
Acetic acid Ethyl alcohol Acetone Acetylene
Ethanoic acid Ethanol Propanone Ethyne
O12: A few trivial names
O12: Trivial and IUPAC nomenclature
Alcohols
• Name the hydrocarbon
• Suffix = – anol not –ane
• Number the carbons and note the position of the
OH
Pentanol Propan-2-ol Pentan-2-ol 2,4-Hexadiol
or or
2-Propanol 2-Pentanol
O12: Trivial and IUPAC nomenclature
• What about these alcohols?
Primary alcohol Secondary alcohol Tertiary alcohol
1° alcohol 2° alcohol 3° alcohol
Carbon atom Carbon atom Carbon atom
carrying carrying carrying
the OH is attached the OH is attached the OH is attached
to one to two to three
other carbon atom other carbon atoms other carbon atoms
O12: Trivial and IUPAC nomenclature
Carboxylic acids
• Contain a –COOH group
• Name the hydrocarbon
• Suffix = – anoic acid, not –ane
Butanoic acid
Methanoic acid Hexanoic acid
O12: Trivial and IUPAC nomenclature
Carboxylic esters
• Derived from a carboxylic acid & an alcohol
• Contain a –COOR group
• Responsible for many flavours and fragrances
Ethyl ethanoate
Trivial name: Ethyl acetate
O12: Trivial and IUPAC nomenclature
Carboxylic esters: other examples
Ethyl methanoate Ethyl propanoate
Propyl propanoate
O12: Trivial and IUPAC nomenclature
Amines
• Contain N
• 1°, 2°, 3° amines
Ethylamine Diethylamine Triethylamine
1° amine 2° amine 3° amine
O12: Trivial and IUPAC nomenclature
• You will need to know how to name simple
organic molecules with no more than 2 FGs
• Use the following table and the green booklet
to guide you
O12: Trivial and IUPAC nomenclature
• Name the following organic molecules
2,2-dichloropentane Pentyl ethanoate butanoic acid
2-butylcyclopentanamine
6,7-dimethyloct-6-en-4-ol
Useful websites
• http://chemistry.about.com/od/organicchemis
tryglossary/a/organic-chemistry-glossary.htm
• http://knowledgebin.org/kb/entry/TOP_75_V
ERY_IMPORTANT_ORDER_AND_FACTS_OF_OR
GANIC_CHEMISTRY_-_Must_Have_514.html
