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Organisation
Chemistry for
Health Sciences
Michaelmas term
¾ Organic Chemistry
• Me! Dr. Thorfinnur Gunnlaugsson
– 5 weeks (almost!)
2003
¾
Physical Chemistry
• Prof. John Corish
• Dr. Dónall Macdónaill
– 4 weeks
Organisation
Organic Chemistry
Introduction
Bonding
Simple Hydrocarbons
Stereochemistry
Lecturer:
• Dr. Thorfinnur Gunnlaugsson.
– Room: 2.4
– E-mail: [email protected]
– Phone: 608 3459
Textbooks:
• Organic Chemistry: A Short Course
– by H. Hart (Houghton Mifflin, Boston)
• Organic Chemistry. 7th Ed
– by T. W. Solomons
• Organic Chemistry
– by Clayden, Greeves, Warren and Wothers
Organisation
Department of Chemistry
Overview
¾ Introduction
• Simple functional groups
• Drawing organic structures
• Nomenclature of Organic chemistry
¾
Bonding
• Intramolecular
– ionic bonds, covalent bonds (hybridisation)
• Intermolecular
– Hydrogen bonding, Dipole-dipole interactions
1
Organisation
Introduction
Overview
¾ Alkanes, Alkenes, Alkynes and Benzene
¾
What is Organic Chemistry?
• Chemistry:
– Small or large assembly of covalently liked
atoms where carbon and hydrogen dominate!
Eg. Alcohols, small drugs etc.
Halogen Compounds, Alcohols,
• Stereochemistry
• Isomers, chirality
¾
• Biology:
– living organisms
Eg. Cells, plants and animals
Phenols, Ethers, Amines
• Biochemistry:
Duration
¾
– The chemistry of life
Eg. Enzymes and their role, DNA ,
Carbohyhdrates etc.
5 weeks; 20 lectures (more like 18!!)
Introduction
Introduction
Deals with compounds in which
carbon (C) is the principle element
¾ Not whole periodic table
¾
Organic Chemistry
¾ May/may not involve natural process
A
H
Li
B
Na Mg
Cr Mn
Cu Zn
Pd
• Organic chemists use REAGENTS /
CATALYSTS in SYNTHESIS, employing
solvents, heat, pressure, etc.
• Nature uses ENZYME, cofactors etc.
Se Br
Sn
I
Hg
Os
Introduction
OH
HH
Ethanol
H
Introduction
¾
H
H H
H
C
HH
B
F
Al Si P S Cl
Ti
K
C N O
O
Even enzymes are
organic!
Ethanal
(acetaldehyde)
Nature uses ADH
¾ Organic chemist
uses:
O
¾
C
C
N
H
H H
C
C
O
H
N
O
C
H H
C
N
H
C
• Oxidising agent
- H2O2, HNO3, etc.
2
Introduction
Introduction
Organic Chemistry
¾ Many branches
Organic substances are everywhere
plants
animals
industry
•
•
•
•
•
•
•
research
labs
Medicinal and pharmaceutical chemistry
Perfume and Food chemistry
Synthesis
Mechanistic
natural product chemistry
Polymers
Supramolecular!
Introduction
Introduction
Pharmaceuticals
Eg. Ranitidine: sales > £1,000,000,000
per annum for Glaxo-Wellcome
~ 12 million organic substances
• increases by 10,000 per week!
¾
NO2
N
S
Number
O
¾
N
H
Eg. Viagra: Rapidly expanding market!
EtO
N
N
N
NH
N
1900
1920
1940
1960
1980
N
H
2000
O
S
N
O
O
Aims of Course
O
Cl
Me O H O
O
N
MeO
Me
N
Me
Me
OH
OMe
To understand ….
¾ Structures and shapes
Me
Me O
Me
O
O
OH
OH
OH
N
MAYTANSINE
A very potent anti-tumour agent
E. J. Corey et. al. 1978-1980
O
• BONDING
O
O
?
?
¾
Basic reaction mechanisms
• HOW SHAPES ARE CREATED
3
The Basics
Drawing Chemicals
Molecular Formula
Drawing Chemicals
•
•
•
•
•
• Actual number and type of atoms
eg. Ethanol = C2H6O
eg. Dimethyl Ether = C2H6O
Molecular Formula
Condensed Structural Formula
Lewis Forms
Kekule Structure
Skeletal Structure
Condensed Structural Formula
• Shows which way atoms are
bonded/connected, but doesn’t require all
bonds to be drawn
eg. Ethanol = CH3CH2OH
eg. Dimethyl Ether = CH3OCH3
Nomenclature
• Functional Groups
• Examples
Drawing Chemicals
Drawing Chemicals
Valence shell!
• We know that eight electrons in –an electron
octet- in the outermost shell, or valence shell,
impart special stability to the noble-gas
elements: Neon 2+8, Argon (2+8+8) etc.
• These valence electrons are the one that
participate in bonding.
• Methane is one of these molecules that forms
an octet. Carbon has 1s2 2s2 2p3 electrons and
needs 4 more to form the octate. Hydrogen has
1s1, i.e. we need four of these:
CH4 is methane!
Drawing Structures
¾
• Dots are used to represent all valence
electrons
Kekule Structure
• Dots represent nonbonding valence
electrons (not used e-), or lone-pair
electrons! e.g. NH3!!
• Lines represent bonding valence
electrons
Example: CH3Cl (Chloromethane)
H
H C
H
H
H C
H
H
C O H
H
H
O C H
H
H H
H C C O H
H H
H
H
H C O C H
H
H
Drawing Chemicals
Skeletal Structure
Structures in Reality!
HH
HH
HH
C
H
Structural Formula
Lewis Structure
8 max!!
C
C
HH
C
C
HH
H
• The carbon backbone is represented by a zigzag line (reflects reality)
• All hydrogens attached to the carbon backbone
are neglected (convenient and fast)
• Carbon atoms are the corners and ends
• Important for drawing larger chemicals and
highlighting functional groups
OH
O
4
Drawing Chemicals
Functional Groups
Guidelines
• Realistic
• Economical!
• Clear
Introduced
bond angles
HH
H
H C C O H
Definition
¾ An atom or group of atoms that is part
of a larger molecule and that has a
characteristic reactivity
eg. alcohol
=
HH
C
H
OH
H
Ethanol, Ethan-2-ol
C
H
C
H
C
H
Alkanes
C
C
C
H
H
Alkenes
H
C
C
C
C
HH
Ethanol
• R is chemists shorthand for ‘alkyl’
H
HH
C
H
eg. R = ethyl =
Alkynes
R
H
H
C
C
C
HH
Cl
Alkyl Halides
H
H
eg. H
C
H
Aromatic Hydrocarbons
H
H
Cl
C
HH
Functional Groups
Functional Groups
Hydrocarbon Derivatives cont.
Hydrocarbon Derivatives cont.
cont.
¾
¾
Alcohols R—OH
Ethers
¾
Amines
¾
Phenols
H
Hydrocarbon Derivatives
H
HH
HH
O
C
Functional Groups
Hydrocarbons
H
C
Ethane
Functional Groups
HH
HH
C
H
H
O
R—O —R
Carbonyl group
R
C
O
H
R
Aldehyde
R—NH2
O
OH
R
C
C
R
Ketone
O
OH
Carboxylic acids
R
C
O
OR
Esters
R
C
NH2
Amides
5
Functional Groups
Naming Chemicals
Importance
¾ Determine chemical behaviour
Overview (IUPAC system)
¾ Names of chemicals have 4 main parts:
OH CH2OH O
O2N
C
H
C
H
N
H
C
CHCl2
chlorampenicol: an antibiotic
O
F
C
OH
C C C N
H2 H2 H2
haloperidol: an anaesthetic and antipsychotic
Cl
• Parent name: describes the main carbon
section of the molecule.
• Suffix: identifies the principle functional
group
• Prefix: identifies the substituents on the main
chain or ring
• Locants: shows where the substituents are
located
Naming Chemicals
Naming Chemicals
Common Parent and Substituent Names
Overview
¾ Names of chemicals have 4 main parts:
Number of Carbons
1
2
3
4
5
6
7
8
9
10
Parent Name
methane
ethane
propane
butane
pentane
hexane
heptane
octane
nonane
decane
Substituent Name
methyl
ethyl
propyl
butyl
pentyl
hexyl
heptyl
octyl
nonyl
decyl
Naming Chemicals
Rules
1. Name the Parent
• Identify the longest carbon chain containing the
most important functional group
2. Add the Suffix
• Identify the most important functional group
and add the appropriate suffix
Locant
Prefix
2
Methyl
Parent
Suffix
hex
ane
eg. 2-Methylhexane
locant:
prefix:
parent:
suffix:
2methyl
hex
ane
2
1
4
3
6
5
Naming Chemicals
3. Add the Prefix
¾ Name any substituents
• Substituents are arranged in alphabetical order
• If more than one group is present use ‘di’, ‘tri’,
‘tetra’, ‘penta’, ‘hexa’, ‘hepta’, ‘octa’, ‘nona’ or
‘deca’ before the group
Note: these additional prefixes do not count
when alphabetising the substituents
eg. Alkanes = ‘ane’
6
Naming Chemicals
4. Include the Locants
¾ Specify substituent location
• Number the parent chain from the end closest
to the functional group
• Different substituents can have the same
number if they are attached to the same carbon
• Use hyphens to separate no. and letters
• Use commas to separate no. form no.
Naming Chemicals
Alkanes
¾ name the following alkane:
CH 2CH3
CH3
C
CH 3
Naming Chemicals
Alkanes
Step 1: Name the Parent Chain
¾ find the longest continuous chain
CH2CH3
CH3
C
Naming Chemicals
Alkanes
Step 2: Add the Suffix
¾ The chemical is an alkane
➠ heptane
CH 2CH2CH 2CH3
CH3
¾
assign appropriate parent name
➠ hept
Step 3: Add the Prefix
¾ Describe any substituents attached to
the parent chain
➠ Dimethylheptane
Naming Chemicals
Alkanes
Step 4: Include the Locants
¾ Include the position of attachment
• use the lowest possible option
¾
CH 2CH 2CH 2CH 3
3,3-Dimethylheptane
• Not 5,5-Dimethylheptane
Naming Chemicals
Alkanes
1. Name the Parent Chain
• oct
Example 2:
2. Add the Suffix
• octane
3. Add the Prefix
• Ethylmethyloctane
4. Include the Locant
• 4-Ethyl-3-methyloctane
7
Naming Cyclic Chemicals
Alkenes and Alkynes
Cycloalkanes
1. Name the Parent Chain (must include functional
group)
1. Name the Parent
•
cyclohex
• hept
2. Add the Suffix
•
cyclohexane
6
5
4 5
1
3
3
2
1
4
3. Add the Prefixes
propylcyclohexane
• methylpropylheptene
4. Include the Locants
• 6-methyl-3-propylhept-2-ene
1-propylcyclohexane
Naming Chemicals
Naming Chemicals
Aromatic Hydrocarbons
¾ ‘Substituent name’ followed by
‘Benzene’
eg.
7
2
• heptene
4. Include the Locant
•
6
2. Add the Suffix
3. Add the Prefix
•
Naming Chemicals
NO2
Cl
CH3
Aromatic Hydrocarbons
¾ A large number of aromatic
hydrocarbons have non-systematic
(common) names
OH
NH2
eg.
Benzene
Chlorobenzene
Methylbenzene
Nitrobenzene
Naming Chemicals
Naming Chemicals
Aromatic Hydrocarbons
• When there is >1 substituent, locants are used
to specify their relative position
• ortho-, meta- and para- maybe used in place of
numerical locants
Halogen Compounds
¾ As for alkanes
¾ The halogen is named as a substituent with
an ‘o’ (eg. bromine becomes bromo)
Cl
Cl
Cl
Aniline
Toluene
Phenol
(Methylbenzene) (Hydroxybenzene) (Aminobenzene)
Cl
Br
Cl
1,2-dichlorobenzene
(ortho-dichlorobenzene)
1,3-dichlorobenzene
(meta-dichlorobenzene)
Cl
1,4-dichlorobenzene
(para-dichlorobenzene)
➠ 3-Bromo-3-methylheptane
8
Naming Chemicals
Naming Chemicals
Alcohols
Ethers
¾ substituents are listed alphabetically
followed by the word ‘ether’
eg.
1. Name the Parent Chain
• octane
HO
2. Remove ‘e’ and add the Suffix ‘ol’
to alkane name
OH
• octanol
O
3. Add the Prefix
• Dimethyloctanol
4. Include the Locants
• 3,5-Dimethyloctan-4-ol
OH
You try these!
Naming Chemicals
➠ Ethyl methyl ether
Naming Chemicals
Amines
Aldehydes
1. Name the Parent Chain as
1. Name the Parent Chain
substituent
• heptane
• propyl
2. Remove ‘e’ and add Suffix
‘al’ to alkane
2. Add the Suffix
• propylamine
N
3. Add the Prefix
H
• heptanal
• Ethylheptanal
4. Include the Locant
4. Include the Locant
• N-Methylpropylamine
• 4-Ethylheptanal
Naming Chemicals
Naming Chemicals
Ketones
Carboxylic Acids
1. Name the Parent Chain
1. Name the Parent Chain
• heptane
• heptane
2. Remove ‘e’ and add Suffix
‘one’ to alkane
3. Add the Prefix
• Ethylheptanone
4. Include the Locants
• 4-Ethylheptan-2-one
H
3. Add the Prefix
• Methylpropylamine
• heptanone
O
2. Remove ‘e’ and add Suffix
‘oic acid’ to alkane
O
• heptanoic acid
3. Add the Prefix
O
OH
• Ethylheptanoic acid
4. Include the Locant
• 4-Ethylheptanoic acid
9
Naming Chemicals
Naming Chemicals
Esters
1. Parent:
• Hexane
2. Remove ‘e’ and add ‘ate’:
• Hexanate
3. Prefix: the other alkyl segment with a space:
• propyl Hexanoate
4. Locants: Not required for this example
Acid Chlorides
O
• replace ‘ic acid’ with ‘yl chloride’
Anhydrides
R
C
• replace ‘acid’ with ‘anhydride’
Amides
R
C
O
O
C
R
O
• replace ‘ic acid’ with ‘amide’
R
C
Nitriles
O
Cl
O
• replace ‘ic acid’ with ‘nitrile’
R
C
NH2
N
O
Naming Chemicals
>1 Functional Group
Priority List
1. Carboxylic acids 5.
2. Aldehydes
6.
3. Ketones
7.
4. Alcohols
8.
Naming Chemicals
>1 Functional Group
1.
Amines
Alkenes
Alkynes
Alkanes
Identify Priority gp.
Carboxylic acid, alcohol
2.
Name parent and suffix as usual
3.
prefix for alcohol substituent
OH
octanoic acid
CO2H
hydroxyoctanoic acid
4.
Locants
6-hydroxyoctanoic acid
Naming Chemicals
Suffix and Prefix
Naming Chemicals
Suffix and Prefix
¾ Alkenes and alkynes
Group
suffix
prefix
aldehyde
-al
formyl-
ketone
-one
oxo-
alcohol
-ol
hydroxy-
amine
-amine
amino-
• Specify location ‘within’ parent
• Essentially as before!
CO2H
But-2-yne
But-2-ynoic acid
10
Naming Chemicals
Further Example
1.
Priority
alcohol aldehyde and alkene
2.
Parent + suffix
oct, ene and al = octenal
3.
Substituents
hydroxy
4.
Locants
5-hydroxyoct-3-enal
Bonding
¾
Intramolecular (within molecules)
• Ionic
• Covalent
• Polar covalent
¾
Intermolecular (between molecules)
•
•
•
•
OH
O
H
Atomic Structure
Ionic
Hydrogen bonding
Dipole-dipole
Van der Waals interactions
Atomic Structure
Shells
Electron Configuration
2e-
+
8e-
18e-
+
3d
E
Orbitals
¾
¾
3rd SHELL
3p
3s
Each shell contains orbitals
most probable location of an electron
s
p
2nd SHELL
d
1st SHELL
2p
x
y
z
2s
1s
Blame Schrödinger and Einstein
Atomic Structure
Atomic Structure
Ground State Configuration
Lowest energy orbitals fill first
Electron Configuration
z
z
z
x
x
y
y
¾
(Aufbau principle)
x
y
2py
2px
¾
2pz
z
2nd SHELL
2p
x
y
Each orbital can contain up to two
electrons
• electrons have opposite spins
z
(Pauli exclusion principle)
2s
x
y
¾
2s
Orbitals of equal energy fill evenly
(Hunds rule)
11
Atomic Structure
Intramolecular Bonding
Ground State Configuration
¾
Eg. Sodium. 11 electrons
3s
E
atoms join together to obtain a more
stable configuration
most stable configuration =
octet in the valence shell
2px,y,z
2s
¾
1s
This desire determines an atoms type
of bonding (ionic or covalent)
Na: 1s2 2s2 2p6 3s1
Ionic Bonding
¾
donation of electrons
Example
Na (1s2 2s2 2p6 3s1)
+
Cl (1s2 2s2 2p6 3s23p5)
↓
Na+ (1s2 2s2 2p6 )
Cl- (1s2 2s2 2p6 3s2 3s6)
Na
Cl
+ –
Na
Cl
12