0 An Advanced
Introduction to Organic Chemistry
Organic chemical history, bonding,
variety and complexity of compounds
Chemistry Advanced Level Pre-University Chemistry Revision Study Notes for UK
KS5 A/AS GCE level organic chemistry students US K12 grade 11 grade 12 organic chemistry
for Part 0
A brief history of organic chemistry
The basis of organic chemistry - variety and complexity
0.3 Bonding theory and examples of
bonds surround a carbon atom
Representation of organic molecular
formulae and structures and
Organic Chemistry Indexes
All Advanced Organic
Index of GCSE/IGCSE Oil - Useful Products
Chemistry Revision Notes
brief history of
organic chemistry (advanced AS/A level chemistry
The word 'organic' historically refers to chemical
materials pertaining to plant or animal or animal organisms. The term organic
was used as a convenient classification for substances derived from plant or
this sense organic substances go back to prehistoric
times e.g. making wines by fermentation of sugary fruit materials (alcohol,
ethanol solution) and the souring of wine to make vinegar (acetic acid/ethanoic
Methods of using vegetable oils and animal fats to make soap
have been known since Roman times,
and methods of applying the vegetable dye
indigo and dyeing with madder root (alizarin) were also developed by both Roman
and Egyptian civilisations. The production of dyed fabrics was an important
commercial venture and some dyes were highly prized and the resulting fabrics
very costly - purple only for very high status citizens! From these humble
origins from the late 19th century to the present day the development and
production of synthetic dyes shows no sign of slowing down!
By AD 900 the Islamic civilisation had developed a crude
distillation process to increase the concentration of alcohol and produce oil of
terpentine from pine resin. The words alchemy and chemistry are derived from
Arabic words such as Al-Kimiya (which effectively means chemistry in Arabic
today). The word alkaline is derived from the Arabic word Al-Qali which referred
to substances derived from calcined ashes of the glass-wort plant that the Arabs
used to make soap and glass. In medieval English it became 'alkali'. The names
of substances like benzoin and benzene are derived from the Arabic phrase 'Luban
Jawi' meaning substances derived from a natural 'aromatic' resin Arabic traders
brought from Indonesia. Later benzoic acid was derived from benzoin resin and in
turn benzene was synthesised from benzoic acid in the 19th century. In Victorian
times dyes were made from aniline (phenylamine, aminobenzene), the Arabic word
for dyes from indigo was annil. The word 'alcohol' is derived from the Arabic 'Al-khul'
which mean body eating fluid! (it may also be the origin of the word ghoul!),
but we are getting ahead of ourselves in the development of organic chemistry.
In the 16th and 17th century other products
were made by pyrolysis e.g. the dry distillation of wood that yielded a
variety-mixture of organic liquids including acetone (propanone). In the 18th century the technique of solvent
extraction was used to obtain substances from plant and animal materials. In the
years 1769-1785 the great Swedish chemist Scheele did many investigations that
effectively prepared the way for the chemistry of studying biological products
e.g. he isolated tartaric acid (2,3-dihydroxybutanedioic
acid) as the sour taste of the grape, citric acid (2-hydroxypropane-1,2,3-tricarboxylic
acid) from lemon, malic acid (2-hydroxybutanedioic acid) from apples,
lactic acid (2-hydroxypropanoic acid) from sour milk, uric acid from urine and
oxalic acid (ethanedioic acid) from wood sorrel, and he also prepared the latter by
oxidation of sugar with concentrated nitric acid (a powerful oxidising agent).
This was impressive work, but he had no idea what the molecular structure of
these compounds was, but YOU can now work them out from the IUPAC
systematic names in brackets.
Back to the late 18th century and early
19th century; from 1772-1777 the French chemist Lavoisier conducted some
combustion analysis of organic compounds by measuring the amounts of water and
carbon dioxide formed and was able to deduce the percentage of carbon and
hydrogen in organic compounds. He produced the best results of his time, but
they far from accurate, but it was recognised that organic compounds seemed to
consist of carbon, hydrogen only, or these two elements combined with oxygen or
nitrogen or both. unfortunately atomic theory and accurate atomic masses
('atomic weights') were still a few decades in the future.
The term 'organic' as a branch of the
study of chemistry, was used by the Swedish chemist Berzelius in 1807, and it
was believed that these substance derived from once living material had some
kind of 'vital force' associated with them. Organic compounds seemed more
'reactive', 'sensitive' or 'less stable' and so different from inorganic
compounds e.g. they were combustible or readily transformed into different
materials, especially by the application of heat and most organic compounds were
liquids and low melting solids, compared to most inorganic compounds like salts
which seemed so stable and high melting.
This doctrine of an essential
vital force remained unchallenged until the German chemist Wohler, by chance
discovery in 1828, that an inorganic salt (of non-plant/non-animal origin) was
converted into a well known organic compound urea
All you do is evaporate
ammonium cyanate solution ===> urea crystals; NH4OCN
This is actually an (the
first known?) example of an isomerisation reaction, in this case based on
the formula CH4N2O
Clearly the inorganic salt
had no 'vital force', and as Wohler said in a letter to Berzelius "I must
tell you that I can prepare urea without requiring a kidney of an animal,
either man or dog". Nearly the end of 'vital force' theory, but still no
molecular structures known!
However, the term organic
chemistry, has been universally accepted as the chemistry of carbon
compounds bar carbon oxides and inorganic carbonates.
Further syntheses e.g.
Kolbe's synthesis of ethanoic acid (acetic acid) from its elements in
1845, further proved that no vital force was needed to make vinegar,
identical to that formed by the souring of fermented sugar solution!
The pioneering work of Lavoisier was
continued by the German chemist Liebig (of condenser fame) who improved
combustion analysis apparatus so that the technique of burning organic
compounds was producing quite accurate data by 1838. It actually took until 1911
via the work of the chemists like the Austrian Pregl to perfect the technique of
semi-micro analysis on small samples of highly purified samples of organic
compounds to give % composition to at least 3 significant figures. During the
same period techniques for determining the percentage of nitrogen were also
developed (by the French chemist Dumas 1830 and more accurately by the Danish
chemist Kjeldahl in 1883 (a technique I was taught to do in the 1960s). This
meant by the end of the 19th century the majority of organic compounds could now
be analysed accurately, and from patterns in formula the idea of 'valency' or
'combining power' was beginning to shape (see work of Kekule below). Atomic
masses e.g. of carbon, hydrogen, oxygen and nitrogen were now accurately known.
By the mid 19th century different substances
with the same empirical formula were being recognised
(ethanol) and dimethylether (methoxymethane), both having an
empirical formula C2H6O, but at that time, all they
really knew that these compounds contained the same % of carbon, hydrogen
and oxygen but were obviously different chemicals but of unknown structure.
From the increasing accurate and widening
analysis of organic compounds, the idea of 'valency' ('combing power') of
carbon, hydrogen, oxygen and nitrogen atoms was beginning to emerge and thanks
to the brilliance of chemists like the German chemist Kekule, a solution to
explaining the different formulae began to emerge.
Remarkably, as early as
1859 Kekule proposed that that carbon could form four bonds in a variety of
ways, and added a similar idea for oxygen and hydrogen and came up with the
following 'bonding' situations:
(4 single), =C= (two double),
(single plus triple), -O- (two
single), =O (one double) and
-H (one single)
Recognise this lot, not
bad for a graphical representations of 1859, and it meant that Kekule could
write out simple structures like
carbon dioxide O=C=O,
hydrogen cyanide (methanenitrile) H-CN
and the structures of
hydrocarbons like ethane
fitted the analytical data.
Therefore organic chemists
now had a way of writing out formula and explore possible structures based
on empirical formula analysis and of course be able to explain isomerism
(different molecular structures with the same molecular formula).
We of course now take
these structures to another level and draw electronic dot and cross
diagrams, but they only emerged in the 1920s via the electron octet theory
of compound structure!
So, it was only by the late 19th century
the concept of 'homologous series' and 'functional group' were beginning to
BUT, although structural formulae could now
be correctly written down, the actual 3D shape of molecules was still a
Stereochemistry, 'three dimensional
chemistry', didn't begin with organic
molecules, but from 1812 to 1820 it was noticed that hemihedral quartz crystals
seem to occur in two forms that were mirror images of each other. It was also
demonstrated that each crystal form rotated plane polarised light in opposite
directions. This occurs when molecular structures exhibit a centre of asymmetry.
From 1820 to 1854 via the work of scientists like Louis Pasteur and Biot ,
crystals of some organic acid salts like ammonium tartrate could be separated
into two forms with the same chemical formula, that were chemically and
physically identical except that the solution of each form rotated plane
polarised light in equal but opposite directions.
To explain the two
different forms, which we now know as optical isomers (enantiomers),
Kekule's valency theory offered a solution by presenting his 2D structures
in a 3D way. The brilliant Dutch scientist van't Hoff proposed in 1874 that the four
valencies of the 'central carbon' (we know call this the asymmetric or
chiral carbon), pointed to the corners of a tetrahedron. Therefore
with a molecule Cabcd, where a, b, c and d
are different atoms or groups of atoms, it is possible to construct
two models of the compound which are non-superimposable mirror image forms.
These forms cannot have a plane of symmetry, whereas Ca4, Ca3b,
Ca2b2, and Ca2bc all have a plane of
symmetry . Unknown to van't Hoff, the French chemist Le Bel had come to the
same theoretical proposition (hypothesis). We now know that from x-ray
diffraction studies of optically active organic compounds, that both of
these great scientists were absolutely correct, but that was about 40 years
later in the early 20th century!
Now we can confidently
draw structures such as
for alpha amino acids, and deduce bond angles from electron pair
repulsion theory, no problem!
So, by the end of the 19th century the basic
structure of thousands of organic molecules was understood and ideas on the 3D
structure of them too. Atomic masses were accurately known and methods of
molecular mass determination were also developed so that the relationship
between empirical formula and molecular formula were now clearly understood.
1899 full commercial production of the sedative aspirin (acetylsalicylic
acid, 2-ethanoylhydroxybenzoic acid), a medication used to treat pain,
fever, or inflammation, was in full commercial production but the original
molecules with these medicinal properties were obtained from plants such as
willow and had been known in ancient Greece as early as 400 BC from the
writings of Hippocrates, who describes the preparation of willow herb tea!
This was one of many developments that 2300 years on from the ancient Greeks that
contributed to the development of the pharmaceutical industry.
The pain killer codeine is derived from
morphine, the chief alkaloid molecule in opium. There are many instances where a
whole series of drugs are developed from a starter molecule from a plant
resource including analgesics, blood pressure controls, Statins to control
cholesterol levels in the blood etc. etc. The skill of organic chemists is such
that very complicated naturally occurring molecules can be synthesised in the
laboratory by amazing multi-stage preparations from indigo like dyes to
However, the spatial arrangement of atoms in
organic molecules was not clear, so the idea of bond angles and 3D shape was
still very much in its infancy and the propositions of van't Hoff and Le Bel,
although correct, were not proven. The development of X-ray
crystallography to get to the 3D molecular structure of organic molecules began
in 1912-1914 with the work of Bragg (Cambridge, England) and the German Max von
Laue. Initially they worked with inorganic crystals but as the x-ray diffraction
analysis techniques improved, crystals of organic compounds were analysed. At
the same time the electronic theory of atomic and molecular structure was
developing and bond angles measured and compared with bonding theory
X-ray crystallography of biological
molecules progressed e.g. with the remarkable and pioneering work of the
English woman Professor Dorothy Hodgkin, who solved the structures of
cholesterol (1937), penicillin (1946) and vitamin B12 (1956), for which she
was awarded the Nobel Prize in Chemistry in 1964 (apart from mother Marie and
daughter Irene, the Curies were the only other women to get a Nobel prize in chemistry). In
1969, she succeeded in solving the structure of insulin, on which she had
worked for over thirty years!
In 1952 Rosalind Franklin and others
working at Kings College, London and Cambridge, obtained crucial x-ray diffraction
photographs (crystallographic data) that would help lead to the recognition
of the double helix structure of DNA. Her work was not fully recognised at
the time and she should have got a Nobel Prize in 1962 with the likes of
Crick, Watson and Wilkins (who also used x-ray diffraction), but she
tragically died of cancer in 1958 at the age of 37.
One of the problems was the complex
mathematics needed to analyse x-ray diffraction data. What might take months
in the 1950s can be done in minutes today with modern high speed computers.
IT is now a powerful too in the development of chemistry.
The structure of many essential molecules
such as vitamins are known and many can be synthesised in the laboratory.
Synthetic proteins can be made and manipulation of DNA genetic material is
nothing short of amazing.
From the mid 19th century to the early 20th century,
particularly in the USA, the commercial usefulness of crude oil was recognised
and so the petrochemical industry was born from which, to this day, we derive a
variety of hydrocarbon products ranging from fuels to polymers (the latter via
alkenes from cracking) and a host of other organic molecules including the
synthesis of many pharmaceutical products once derived from natural plant and
In the late 19th century plastics were produced by modifying
natural polymers e.g. celluloid by reacting cellulose from plants with nitric
acid. The first truly synthetic plastic was the hard brown material known as
Bakelite, patented in 1910. All the well known plastics like nylon, Terylene,
poly(ethene) - discovered by accident in 1933, poly(propene), PVC, polystyrene,
Perspex and polyurethanes were developed through 1930s to the 1960s. Crude
oil has become the
largest source of organic chemicals and we are very much dependent on its
World War II lead to many technological developments in radar
and electronics. This in turn lead to major advances in spectroscopic techniques
for investigating the structure of organic molecules. Techniques like infra-red
spectroscopy and mass spectroscopy are quite limited but nuclear magnetic resonance spectroscopy
(proton NMR and C-13 NMR) is the most powerful molecular technique apart from
x-ray diffraction analysis.
1H proton NMR is so
sophisticated now, you can deduce the whole structure of quite complex
organic molecules from the NMR spectra alone, it is an amazing technique. I
presume you still need x-ray diffraction analysis to get the full 3D
Some of the most advanced chemical advances are
now being made using computer databases of highly accurate 3D images of organic
molecules. Even complex protein molecules like enzymes are being modelled and
drugs can be designed to fit into the active site to inhibit their action, the
basis of many medical treatments.
TOP OF PAGE
0.2 An advanced introduction to organic chemistry - VARIETY and
chemistry revision notes)
More on WHY is there such a range of organic molecules and hence why
discipline of organic chemistry?
AND more on homologous series and functional groups.
There are many possible series
of organic molecules, so why such variety?
belong to different
families, though all organic compounds are based on carbon C, usually hydrogen H, and
elements such as oxygen, nitrogen, phosphorous and sulfur.
Most food is chemically
organic in nature, apart from some minerals, and many drugs and plastic
materials are composed of organic molecules, consequently, organic compounds
and organic chemistry is rather important to us!
organic compound comes from the fact that most of the original organic compounds studied
by scientists-chemists came from plants or animals, i.e. of natural origin and
contained the 'vital force' of mother nature!
Historically, for thousands of
years, many organic compounds have been used indirectly in herbal
preparations for healing and alleviating symptoms and in food materials such
Many natural products have proved
precursors for the development of synthetic 'man-made' drugs manufactured by
the pharmaceutical industry.
These days most organic compounds are
produced and synthesised from raw materials, in
particular the physical separation and chemical manipulation of the products
of fractionally distilling crude petroleum oil.
However, this description of
organic chemistry and its historical origins does NOT explain the vast range
of organic molecules and their complex chemistry.
The principal reason why the range
of organic molecules is primarily due to the fact that carbon atoms have the ability to
link together by strong covalent bonds to form linear chains, branched chains and
cyclic chains and with considerable numbers of rearrangements to make
different molecules of the same formula (isomers).
Carbon is in Group 4 of the
periodic Table with four outer electrons (2.4 or 1s22s22p2)
which readily pair with electrons from an atom like oxygen or nitrogen
to give four stable covalent bonds (maybe 4 single bonds, 2 single and a
double bond, two double bonds or a triple and a single bond), either
way, the normal valency (combining power) of carbon in organic compounds
The property of forming
chains is called catenation and the C-C bonds are generally
strong giving rise to whole groups (homologous series) of stable organic
To add to the complexity
and variety of organic molecules, carbon can also form stable
bonds with other elements, especially ...
oxygen as in alcohols
like ethanol which is used in fuels, as a solvent and combined
with organic acids to make esters used in flavourings and perfumes.
nitrogen as in amines
like ethylamine are
organic bases and form alkaline solutions when dissolved in water.
nitrogen and oxygen
in amino acids like aminoethanoic acid
is found combined with other amino acids in polypeptides - proteins.
as in bromoethane
an 'intermediate' compound and used in the organic synthesis of more complex
& phosphorus etc. by substituting a hydrogen atom with another element
or group of atoms compared to hydrocarbon alkanes like butane which
only consists of carbon and hydrogen atoms.
So, this leads to even more
possible 'families' of organic compounds and many more individual
There is no limit to the
number of different organic molecules that can be made, though only a
small percentage of them would be useful (others maybe unstable or
very difficult to synthesise).
The molecular formula
represents a summary of all the atoms in the molecule and a general formula
sums up the formulae a series of compounds e.g. a homologous series
of chemically similar compounds.
Just to give you an idea
of the limitlessness of organic chemistry, using some simple
molecular formulae and general formulae, consider the table below of
the number of molecules which can theoretically exist for a given
The different structures with
the same molecular formula are called isomers (see
types of isomerism).
Isomers have the same
molecular formula, but differ in the way the atoms are
connected or how the atoms are spatially arranged.
Examples are shown in
the diagram below, but don't worry about the details here, just
appreciate what we mean by the concept of isomers and how it
makes organic chemistry much more interesting!
You will appreciate more about
the structures after studying section 0.4
Representation of organic molecules
The easiest example to
appreciate is the two isomers of
two completely different molecules from the same 9 atoms of the
same molecular formula, you will understand the rest in time!
The following table really brings home
the possibilities and sheer huge variety of organic molecules.
n = 5 for
the number of carbon atoms in the molecular formula you get ...
alkanes of molecular
of molecular formula C5H10
and amines of
Some of these
numbers of these isomers
(highlighted in blue) have been worked out using a computer program i.e.
an algorithm is used to compute possible numbers of molecules of a
given general formula given a set of rules based on
|Number of carbon
atoms n in the general formula below
||examples of homologous series with this general formula
The number of possible isomers
? a lot !
the number of carbon atoms increases the number of possible arrangement
of the atoms increases dramatically even for molecules just containing
carbon and hydrogen.
Once you substitute a hydrogen atom for another element
or group of atoms, there is a bewildering number of possible
The fact that life, as far as
we know it, is based on carbon chemistry, and we do not know of another
element from which the same huge variety of stable molecules can be me
Even unstable organic
molecules can be synthesised and manipulated in the laboratory and
biochemistry is based on the thousands of molecules that exist in
living systems e.g. sugars, proteins (tissue, enzymes etc.), RNA,
DNA, fats like lipids etc. etc. etc.!!!.
In one of the simplest
living cells like an E coli cell, there may be 5000 different
compounds, most of them organic molecules! (e.g. as many as 3000
proteins and 1000 nucleic acids i.e. RNA/DNA molecules)
The compounds in each family have a similar chemical structure and a similar chemical
formula and each family of organic compounds forms what is called a homologous
As pointed out, different families arise because carbon atoms readily join together in
chains (catenation) and strongly bond with other atoms such as hydrogen,
oxygen and nitrogen.
The result is a huge variety of 'organic compounds'
which can be classified into groups of similar compounds i.e. these different
A homologous series is a family of
compounds which have a general formula and have similar
physical and chemical
properties because they have the same functional group of atoms i.e.
a significant similarity in molecular structure, but with an increasing
number of carbon atoms (usually in a chain).
C=C alkene, C-OH alcohol or -COOH carboxylic acid etc.
Usually, the addition of a -CH2- group
gives the next member in the homologous series.
functional group is an atom or combination of atoms which gives an organic molecule its
particular chemistry - a characteristic set of reactions..
In effect a functional group is an atom
or group of atoms, when part of different molecules, gives those molecules
similar and distinctive chemical properties.
This applies to all homologous series except alkanes which do not have a
defined functional group.
The term 'functional' group is linked to the concept of a homologous
homologous series is a group of molecules with the
same general formula and the same
They have similar physical and chemical properties
such as similar characteristic chemical reactions, appearance, melting/boiling points, solubility etc. albeit with trends
in physical properties
e.g. increasing boiling point with increasing carbon chain
length i.e. increase in molecular mass due to increasing intermolecular
The terms higher/lower refer to a
longer/shorter carbon chains e.g.. the higher or lower number of CH2
groups in the carbon chain.
You should notice as you move from one
member of a homologous series to the next, you add on an extra -CH2- unit.
molecular formula represents a summary
of all the atoms in the molecule e.g. butane is C4H10
and can be derived from a general formula - which is explained more in
section 9.1.1 onwards.
TOP OF PAGE
Bonding theory and examples of ways bonds surround a carbon might be represented
An advanced introduction to organic
You might not have encountered all the
types of molecular/ionic bonding situations mentioned here, but that shouldn't matter
too much if you have started
studying molecules with different functional groups.
Reminder of s
and p orbitals
quantum level rules,
carbon's electron configuration is
In terms of the separate orbitals you can express it as
2px1, 2py1, 2pz0
This can be further expressed as an electron box diagram:
with two unpaired electrons.
However, as you should know by now, carbon usually forms
four bonds (valency of 4) rather than two.
This is because it is energetically favourable to promote
one electron from the 2s orbital into the third empty 2pz
orbital, the energy required for this 'promotion' is far less than that
released when the carbon atom forms four bonds rather than two..
This gives a theoretical electron configuration of
2px1, 2py1, 2pz1
This gives four unpaired electrons, all of which can pair up with an
electron from another atom to form four covalent bonds, but they may be of
two varieties if a double or triple bond is involved in the carbon based
molecule - read on ...
Reminders (if needed): The diagrams below show the bonding situation in alkenes, that
conveniently involve two of the most important types of covalent bond
between atoms, including carbon.
Sigma and pi
covalent bonds in alkenes
A single bond (sigma bond,
is formed by the overlap of two orbitals which can be either an s orbital or
a p orbital (illustrated above).
Two electrons (an electron pair) are mutually attracted to the
positive nuclei on either side.
A molecular orbital is formed and the
axis of the bond lies on a central line between the two nuclei.
In this case. the pi
bond (π bond) is formed by the overlap of
two p orbitals, but, due to repulsion with the bonded pairs of the sigma
bond electrons, they cannot form another sigma
bond molecular orbital along the same central axis.
Instead, a pi orbital
(containing one electron), is formed above and below the planar arrangement
of the bonds linking the two carbon, and other atoms together (>C=C<
planar bond arrangement).
Incidentally, the presence of the pi
orbitals inhibits rotation around the double bond in unsaturated
alkenes, because it requires a lot of energy to twist the orbitals
around and break the pi bond. However, in alkanes everything is free to
rotate around the sigma bonds of the C-C bonds in saturated alkane
Note 1. to 7. apply to the above
Four single bonds (four sigma bonds
σ): You find this tetrahedral bonding arrangement
around the carbon atom in methane (CH4)
or methanol (CH3OH).
VSEPR theory - predicting molecule/ion shapes
Two single bonds and one double bond
(three sigma bonds
and one pi bond π):
You find this trigonal planar bonding situation in alkenes like ethene (H2C=CH2)
or propene and also in ketones like propanone (CH3)2C=O).
One single bond and one triple bond
(two sigma bonds
and two pi bonds π):
You find this linear triple/single bonding arrangement in alkyne
hydrocarbons like ethyne
See VSEPR theory - predicting molecule/ion shapes
Three single bonds (three sigma bonds
σ): The unpaired electron means this is a free radical
fragment of a molecule e.g. the ethyl free radical
The trigonal pyramidal arrangement of the bonds arises from there being
four groups of electrons around the carbon atom
See VSEPR theory - predicting molecule/ion shapes
Three single bonds (three sigma bonds
σ): You find this trigonal planar arrangement of bonds
in carbocations e.g. the ethyl carbocation would be written as
There are three groups of electrons around the carbon atom (highlighted)
carrying the positive charge, hence the trigonal planar arrangement of
See predicting molecule shapes
One single bond and a double bond
(two sigma bonds σ and one pi bond π):
You might not come across one of these, but its called an acylium
cation, a positive ions based on an acyl group e.g.
the positive ion based on the ethanoyl group. There are two groups of
electrons around the carbon atom (highlighted)
carrying the positive charge, hence the linear arrangement of
Three single bonds (three sigma bonds
σ): The lone pair of electrons means that this carbon
species is a negative ion, known as a carbanion e.g. the ethyl carbanion
There are four groups of electrons around the carbon atom (highlighted)
carrying the negative charge, hence the trigonal pyramidal arrangement of the
8 You can also have, but not shown in
the diagram above, another version of two sigma bonds and two pi bonds about a
carbon atom, but this time involving two double bonds
Notice for 4., 5. and 7., I've
deliberately used structures based on the ethyl (CH3CH2)
group to highlight their essential
OF PAGE - INDEX
0.4 Representation of organic molecular formulae and structures and
gives a summary of all the atoms in the molecule, but gives no information
e.g. the above molecular formula three atoms of carbon combined with
six atoms of hydrogen and two atoms of oxygen.
However, there may be more than one
structure with that molecular formula and you can't tell which is which from
the molecular formula.
You have no idea about the arrangement of atoms i.e.
their structural arrangement, positions of bonds and atoms and not a clue
about what its shape may be!
formula is the simplest whole number ratio of the atoms in a
compound as found by experiment i.e. chemical analysis.
It gives no
structural information and may or may not be the same as the molecular
formula e.g. CH4 is both the empirical formula and the
molecular formula of methane. You can't simplify CH4 into a
simple integer ratio formula.
However, the molecular formula of the
butane molecule is C4H10 but its empirical formula
is C2H5 (≡
C4H10 ÷ 2)
The molecular formula of a glucose sugar
molecule is C6H12O6 but its empirical
formula is only CH2O (≡
The molecular formula will be a simple
integer multiple of the empirical formula ... (atomic masses H = 1, C =
12, O =16)
e.g. 2 x C2H5
gives C4H10 (since molecular
mass of butane is 58 and the empirical formula mass is 29)
6 x CH2O gives C6H12O6
(since molecular mass of the sugar is 180 and the empirical
formula mass is 30)
In order to decide what the real
molecular formula is, you need more information - need to know the relative molecular
For calculations of empirical formula
and molecular formula from chemical analysis and molecular mass ...
moles to calculate empirical formula and deduce molecular formula of
formula - may be minimal, abbreviated or shortened e.g. ethanol or cyclohexene,
a 'limited' molecular structure view of a molecule but
unambiguous if you know how to interpret the representation.
Therefore, however abbreviated, a
structural formula shows the unique arrangement of atoms in a molecule, but
does not show all the individual bonds.
Some individual bonds
may be shown (in cyclohexene) or non at all (ethanol).
need to be able to translate the structural formula into the full
formula showing the position of every atom and bond e.g. ethanol (right
diagram and below). Lots more on displayed formula in the
formulae: The full graphical formula or full
structural formula, usually described these days as the full
displayed formula shows
all the individual atoms and bonds.
e.g. ethanol above right and 1-bromo-1-chlorobutane, shown
here on the
right (but don't worry about the naming at the moment).
However, it can be acceptable
to show some side-chain groups in an abbreviated form e.g. methylpropane
side-chain methyl group may be written in the abbreviated 'structural' form, but take care in
exams, if unsure, clearly show ALL the atoms and bonds if the displayed formula
In displayed formula many bond angles look as
if they are 900, when they are actually 109o or 120o.
Therefore you can go one stage further and give a
3D representation of the molecule e.g. to show the tetrahedral arrangement
of the bonds emanating from a carbon atom.
structural displayed formula with full
3D spatial representation e.g. which
shows the shape of the molecule methanol and implies bond angles (in this case all
are 109o). The 'dotted line' bond is behind the plane of the
screen/paper/page and the 'wedge' bond is towards you. The other two
thin line bonds are in the plane of the screen/paper/page etc. This
a good impression of the real shape of the molecule in terms of the
directional covalent bonds and all bond angles here are ~109o.
The dotted line bond is now usually shown as a wedge pointing down away
from the carbon atom.
Footnote on bond representation in structural-displayed formulae
represents a single bond between carbon atoms,
a single bond between a carbon and oxygen atom.
single bond consists of a single sigma bond (σ).
represents a double bond between carbon atoms,
a double bond between a carbon and oxygen atom.
double bond consists of a sigma bond (σ)
and a pi bond (π),
more details in appropriate sections.
represents a triple bond between carbon atoms,
a triple bond between a carbon and nitrogen atom.
triple bond consists of a single sigma bond (σ)
and a two pi bonds (π).
Skeletal formula - something a
bit different than all the other molecular representations so far!
A skeletal formula e.g.
is one in which,
(in most cases),
of the H atoms bonded
to carbon atoms are shown, and none of the carbon atoms
of the chain either!
This is actually 3-ethylpent-1-ene, CH3CH2CH(CH2CH3)CH=CH2,
(don't worry about the name if you
haven't done the nomenclature of alkenes).
of some kind of structural or displayed formula, lines represent carbon-carbon bonds
(single, double or triple), but other lines are needed to show bonds from
the carbon chain to
other atoms which are NOT carbon or hydrogen e.g. like C-Cl in
C-OH in alcohols like propan-1-ol
(its acceptable to show the hydroxy group as OH rather than O-H, but you should
put O-H in displayed formulae and make sure the bond line goes to the O of the
-OH and the C of the -Cl.
The bond lines should indicate the underlying
shape of the molecule e.g. the zig-zag chain of carbon atoms.
As already pointed out, where hydrogen is part of a functional
group involving non-carbon atoms attached to a carbon atom, then you will show
the H atoms involved.
e.g. –OH in alcohols (above),
–OH in carboxylic acids e.g. the -COOH in propanoic acid
and –NH2 in amines
(-NH2 functional group in ethylamine)
and in acid amides
e.g. the CONH2 functional group in propanamide
To sum up molecular representations using
ethanol in all its various guises!
Empirical formula C2H6O,
molecular formula C2H6O but you can't distinguish
it from the isomer methoxymethane CH3-O-CH3
Isomers are molecules with
different molecular structures, but have the same molecular formula
Structural formula , ,
All of which clearly distinguish ethanol
and a 3D version of the displayed formula
In the 3D version of the displayed
formula the dots mean bonds to atoms behind the plane of the paper/screen,
wedges towards you mean bonds coming out from the plane of the paper/screen
and you can consider the atoms of the H-C-C-O-H sequence to be all in the
plane of the paper/screen. You also get a good impression of the bond angles
of the molecule, all of which are ~109o and NOT 90o!
for H-C-H, H-C-C, C-C-H and C-O-H.
and finally the skeletal formula is
There are lots more examples on the pages
(links further down) covering the individual classes of organic compounds.
sums up the formulae a series of compounds e.g. a
homologous series of
chemically similar compounds with closely related formulae e.g. the only
difference may be more/less -CH2- groups in the longest
carbon chain of the molecule.
There are many examples quoted throughout the rest of this page in the
style CxHyOz etc. where x, y and z are
integer variables like 1 (never shown), 2, 3 etc. which must be shown, but they are related for a particular homologous series
e.g. for saturated non-cyclo alkanes by a general formula e.g.
so that n = 1 generates the formula for methane CH4 and
n = 5 generates the formula for pentane C5H12 etc.
is the general formula for monocarboxylic acids,
so that n = 0 generates the
formula for methanoic acid HCOOH, the first aliphatic carboxylic acid
and n = 4 generates the formula for pentanoic
acid CH3CH2CH2CH2COOH, the 5th acid
in the series.
NOTE: Do not
assume n always indicates the total carbon atoms in a molecule!
However in all cases, the
IUPAC systematic name is derived from the longest possible carbon chain in the
molecule, so both meth...
(for one carbon) and pent... (for five carbons) occur in the names of the
examples and details of functional groups and homologous series
- A homologous series is a family of
compounds which have the same general formula (*) and have
a similar molecular structure and similar chemical
properties because they have the same functional group of atoms (e.g.
C=C alkene, C-OH alcohol or -COOH carboxylic acid).
examples of general formula and the functional group for four
homologous series of organic molecules
- These examples are based on a linear chain of 2 to 8
carbons atoms, but the amply illustrate the four homologous series
Homologous series of alkanes
where n = 1, 2, 3 etc. number of carbon atoms in the molecule
- The diagram shows ethane, the 2nd in the
series, n = 2.
- Alkanes don't really have a functional group
like most other homologous series.
n = 8 and is 8th in the homologous series of linear alkanes.
Homologous series of alkenes
where n = 2, 3, 4 etc. number of carbon atoms in the molecule
- Here the functional group is the carbon -
carbon double bond, >C=C<
- The diagram shows ethene, the 1st in the
series, n = 2.
n = 5 and is 4th in the homologous series of linear 1-ene alkenes.
Homologous series of
where n = 1, 2, 3 etc. number of carbon atoms in the molecule
- Here the functional group is the hydroxy
group attached to a carbon atom, C-O-H
- The diagram shows ethanol, the 2nd in the
series, n = 2.
n = 5 and is 5th in this homologous series of linear 1-ol aliphatic
Homologous series of carboxylic acids
where n = 0, 1, 2 etc. number of carbon atoms in the molecule minus 1
- Here the functional group is, COOH, a
combination of one carbon, two oxygen and one hydrogen atom.
- The diagram shows ethanoic acid, the 2nd in
the series, n = 2.
hexanoic acid C5H11COOH,
n = 5 and is 6th in this homologous series of linear aliphatic
usefulness of skeletal formulae!
Skeletal formula are particular useful
for depicting large complicated 'biological' molecules e.g. fats or opiate
Triglyceride fats are pretty big
molecules and best represented using skeletal formula
The molecular formula of three well known
opiate molecules - can you see all the functional groups present? (clockwise)
functional groups: secondary alcohol, ether, (benzene ring), phenol,
tertiary amine, alkene
functional groups: secondary alcohol, ether, (benzene ring), ether, tertiary
functional groups: ester, ether, (benzene ring), ester, tertiary amine,
(Let me know if haven't spotted
another functional group, and they all described below.)
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