Dr Sirirat Kumarn Feb 2014

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Chemistry of Life

Dr Sirirat Kumarn

Institute of Molecular Biosciences, Mahidol University
E-mail: sirirat.kum@mahidol.ac.th

Sirindhorn International Institute of Technology
February 2014
TU130 Integrate Sciences and
Technology

Dr Sirirat Kumarn

Institute of Molecular Biosciences, Mahidol University
E-mail: sirirat.kum@mahidol.ac.th

Sirindhorn International Institute of Technology
February 2014
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Stories like Dr Jekyll and Mr Hyde project a vision of chemistry as a grim tool
whereas the reality is that without the work of chemical scientists every man,
woman and child in the country would suffer
The Royal Society of Chemistry, May 2006
Actor Neal Upton and Kathryn Lees with Victorian chemical equipment and modern products
http://www.rsc.org/AboutUs/News/PressReleases/2006/JekyllandHyde.asp
Everyday, chemistry is everywhere!
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Dr Sirirat Kumarn Feb 2014
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You are already a highly skilled chemist.

As you read these words, your eyes are using an organic compound
(retinal) to convert visible light into nerve impulses
When you picked up a pen, your muscles were doing chemical
reactions on sugars to give you the energy you needed
As you understand, gaps between your brain cells are being bridged by
simple organic molecules (neurotransmitter amines) so that nerve
impulses can be passed around your brain

And you did all that without consciously thinking about it!
Organic Chemistry and You
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Do not worry if you do not understand the diagrams. Explanation is on its way!
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Like all sciences, chemistry has a unique place in our pattern of
understanding the universe
Chemistry is the science of molecules
But organic chemistry is something more!
Organic Chemistry and You
Organic chemistry began as a tentative attempt to understand the
chemistry of life
It has grown into the confident basis of vast multinational industries
that feed (foodstuff), clothe (textile) and cure millions of people
(medicines)
Chemists cooperate with physicists and mathematicians to understand
how molecules behave and with biologists to understand how
molecules determine life processes
You do not yet understand these processes in your mind as well as you can
carry them out in your brain and body
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Organic Chemistry and You
Organic chemistry literally creates itself as it grows
We need to study the molecules of nature both because they are
interesting in their own right and because their functions are important
to our lives
Organic chemistry often studies life by making new molecules that give
information not available from the molecules actually present in living
things
The creation of new molecules has given us new materials such as
plastics, new dyes to colour our clothes, new perfumes to wear, new
drugs to cure diseases
Some people think that these activities are unnatural and their products
are dangerous and unhealthy
These new molecules are built by humans from other molecules found on
earth using the skills inherent in our natural brains. Birds build nests; man
makes houses. Which is unnatural?
There are toxic compounds and nutritious ones both in nature and man-
made
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Organic Compounds
Organic chemistry started as the chemistry of life
Then it became the chemistry of carbon compounds
Now it is both!
It is the chemistry of the compounds of carbon along with other elements
such as those found in living things and elsewhere
A flavouring compound
from the essential oil of
spearmint
An example of a
perfume distilled from
jasmine flowers
Extracted from the bark of
the South American
cinchona tree and used to
treat fever, especially
malaria
Dr Sirirat Kumarn Feb 2014
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Organic Compounds
What do organic compounds look like?
They may be crystalline solids, oils, waxes, plastics, elastics, volatile
liquids or gases
Familiar ones are white crystalline sugar and petrol
Sucrose ordinary sugar
isolated from sugar cane or
sugar beet as hard, white
crystals when pure
Isooctane (2,2,5-trimethylpentane) a
major constitute of petrol is a volatile
inflammable liquid
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Organic Compounds
Organic compounds can be deeply coloured even though they are not
dyestuffs
Dr Sirirat Kumarn Feb 2014
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Organic Compounds: Dyestuffs
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Indigo
the colour of
blue jeans
ICIs Dispersol benzodifuranone
red dye for polyester
Ciba Geigys Pigment Red 254
deep DPP pigment
ICIs Monastral Green GNA
for plastic objects
Fast Green FCF
Used in foods
and cosmetics
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Organic Compounds
Colour is not the only characteristic by which we recognise compounds
Often it is their odour that lets us know they are around
Skunk spray contains:
The smell of the skunk is a mixture of 2 thiols (compounds containing the
SH group)
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Organic Compounds
There are also 2 candidates for the worst smell in the world that nobody
wants to find the winner!
Compounds that have delightful odours:
S S
the divine smell of the
black truf f le comes
f rom this compound
O
damascenone - the smell of roses
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Organic Compounds: Products in Modern Life
Dr Sirirat Kumarn Feb 2014
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Organic Compounds: Toxins
Tetrodotoxin the deadly poison that
must be removed from Japanese fugu
(puffer fish) before it is eaten
Okadaic acid a toxin that accumulates in
bivalves and causes diarrheal shellfish poisoning
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Organic Compounds
The pharmaceutical businesses produce drugs and medicinal products of many kinds
The most successful drug ever is ranitidine (Zantac), the Glaxo-Wellcome ulcer
treatment
One of the fastest-growing drugs is Pfizers sildenafil (Viagra)
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The Organic Chemistry Language

- Chemists need to be able to communicate with other chemists about the
work they do

- There are many different systems for drawing and naming compounds
invented/used over the years

- How to draw structures is more or less settled but naming is more
complicated

- Systematic rules of naming are often put to one side in favour of names
that are easier to handle

- We need to learn the language before we can study the chemistry
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The Organic Chemistry Language

There are many different ways to depict molecules:
- For example, butane could be written C
4
H
10
, CH
3
(CH
2
)
2
CH
3
,
CH
3
CH
2
CH
2
CH
3
or in a pictorial manner
Which way we choose depends on what we are trying to show
- The formula C
4
H
10
only tells us the elemental composition
- It does not tell us which isomer we are referring to
- The displayed formulae indicate which isomer we are referring to, but not
the shape of the molecule
This structure shows the connectivity of all the atoms but is rather
misleading about the 3D shape of the molecule
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The Organic Chemistry Language
The structure of a tetra-valent carbon atom is based on a tetrahedron

- For example, methane could be drawn:

C
H
H
H
H
These bonds are in the
plane of the paper
This bond goes back into
the paper
This bond comes out of
the paper
- A more informative drawing of butane would be:

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The Organic Chemistry Language
- The drawing shows the tetrahedral structure but is rather cluttered
- With larger molecules, it gets even harder to see what is important
and what is not
- What we need is a way of representing structures in an informative
yet clear way
Most chemists would draw butane like this:
This represents
a CH
3
group
This represents
a CH
2
group
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The Organic Chemistry Language
Guidelines for drawing organic structures

1) Draw chains of atoms as zigzags with 120 angles to show their shape
2) Miss out the capital Cs representing carbon atoms
3) Miss out the Hs attached to carbon atoms, along with the CH bonds
4) Draw in all other atoms, together with their bonds and all the atoms
attached to them
5) If a carbon atom is drawn in, include all the other atoms attached to it
Examples
- propanol - isopropyl alcohol
(propan-1-ol) (propan-2-ol)
- 3-hexene - 3-hexyne
- cyclohexane - benzene
- propionitrile - propylamine
(CH
3
CH
2
CN) (CH
3
CH
2
CH
2
NH
2
)
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The Organic Chemistry Language

Some frequently used groups have their own abbreviations to save time
writing them out fully
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The Organic Chemistry Language

- In organic structures, a line joining 2 atoms represents a bond
- But this is not necessarily the case in inorganic structures
- In inorganic structures, the lines indicate the atoms are in some way
connected but in some cases they are often no more than a guide to
the eye to indicate the geometry of the structure
S
F
F F
F
F
F
SF
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: S has 6 bonds NaCl: would not say each
Na and Cl has 6 bonds
- What about this?
- Should the boron (B)
atoms be joined?
- Does H have 2 bonds?
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The Organic Chemistry Language
Structure 1 emphasises that all of the 4 groups on the chiral
centre are different by drawing in the H atom we missed out
Structure 2 shows that one of the groups points out of the plane
of the paper towards us and one into the plane of the paper
away from us
Structure 3 misses out the H atom, which can be assumed to be
behind the plane of the paper
Leucine
Chirality and mirror images:
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Importance of Controlling Stereochemistry
Nature has a left and a right and can tell the difference between them

We take our lead from Nature: all life is chiral
All living systems are chiral environments

Enantiomers are chemically identical until being placed in a chiral
environment







Just as you can distinguish the smell of oranges from that of lemons.
The smells of orange and lemon differ in being the left- and right-handed
versions of the same molecule, limonene
One carvone gives the smell of spearmint and the other that of caraway
seeds
(R)-(+)-limonene
smells of oranges
(S)-(-)-limonene
smells of lemons
(R)-(-)-carvone
smells of caraway seeds
O
(S)-(+)-carvone
smells of spearmint
O
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Importance of Controlling Stereochemistry
Enantiomers = mirror images of the same compound
One isomer is the active ingredient of drugs, the other inactive
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Importance of Controlling Stereochemistry
R-Thalidomide
sleep-inducing (effective isomer)
S-Thalidomide
Teratogenic (causing birth defects)
Thalidomide: a drug to treat morning sickness
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The Organic Chemistry Language

- Names for carbon chains











- Prefixes: primary, secondary, tertiary
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- Alkanes contain no functional groups (-ane)
- Alkenes (sometimes called olefins) contain C=C double bonds (-ene)
- Alkynes contain CC triple bonds (-yne)
- Alcohols (R-OH) contain a hydroxyl (OH) group (-ol)
- Ethers (R
1
-O-R
2
) contain an alkoxy (-OR) group (-ether)
- Amines (R-NH
2
) contain the amino (NH
2
) group (-amine)
- Aldehydes (R-CHO) and ketones (R
1
-CO-R
2
) contain the carbonyl group
(C=O) (-al/-one)
- Carboxylic acids (R-CO
2
H) contain the carboxyl group (CO
2
H) (-ic acid)
- Amides (R-CONH
2
, R
1
-CONHR
2
, or R
1
-CONR
2
R
3
) (-amide)
The Organic Chemistry Language
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The Organic Chemistry Language

- Systematic nomenclature:
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The Organic Chemistry Language
Numbers are used to locate functional groups:
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The Organic Chemistry Language
Nonetheless, chemists still need to talk about the chemicals they use
There are books of rules and even computer programs which enable any
compound to be given a systematic name
But these names are rarely used in the laboratory or even in scientific papers
In the previous example, N-iodosuccinamide was used. This is not a
systematic name but a trivial name
Trivial names are preferred, mainly because they are often considerably
shorter
The names of the very common reagents will simply have to be learnt
Examples
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The Organic Chemistry Language

- Often the simplest way of referring to a compound is to draw its
structure
- In scientific papers, structures are given and referred to by numbers
For example, 16 was obtained in good overall yield and converted
smoothly to the cyclic ether 17 by treatment with N-iodosuccinimide,
followed by tri-n-butylstannane reduction.









Taken from one of the chemical journals, Tetrahedron Letters
MeO
O
MeO
OMe
HO
H
H
MeO
O
MeO
OMe
O
H
H
H
1. N-iodosuccinamide
2. nBu
3
SnH
(71% yield)
16 17
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The Organic Chemistry Language
Systematic name?
Palytoxin was isolated in 1971 in Hawaii from Limu make o Hane (deadly seaweed of
Hana) which had been used to poison spear points
One of the most toxic compounds requiring only about 0.15 microgram per kilogram
for death by injection
The complicated structure was determined a few years later