Download Introduction to the Names and Structure of Organic Molecules

Introduction to the Names and Structure of Organic Molecules
Homologous series
The diversity of life owes much to the diverse chemistry of one element - carbon. Over 90% of
known compounds contain carbon. Carbon’s ability to form this vast range of compounds has led to
an equally vast range of living things composed of carbon-based molecules. Because the major
source of carbon compounds is living or once-living material, it was originally thought that only
living things had an ‘organic vital force’ needed to produce carbon-based compounds. The synthesis
of urea ((NH2)2CO) in 1828 by Friedrich Wöhler (1800–1882) showed this to be untrue, but the
name ‘organic’ is still applied to the branch of chemistry dealing with the study of carbon-based
compounds (excluding such compounds as CO, CO2 and the carbonates).
Several factors contribute to the vast range of carbon compounds:
• Carbon has four outer-shell electrons allowing each carbon atom to form up to four covalent
bonds.
• Carbon can form single, double or triple bonds.
• Carbon can bond to itself, forming long chains and cyclic (ring) molecules.
• Carbon can bond to a range of other elements, including hydrogen, oxygen, nitrogen, sulfur
and chlorine.
The study of organic chemistry is central to understanding the chemistry (and biology) of living
systems. Knowledge of organic chemistry is used in the manufacture of drugs, foods, pesticides,
fertilisers and other chemicals used by humans in agriculture, nutrition and medicines. Production
of other materials of huge importance in society, such as fuels, solvents and polymers, also requires
a sound knowledge of organic chemistry.
Features of a homologous series
To classify such a vast range of compounds, chemists look at various ‘families’ of carbon
compounds that have common characteristics. The usual starting point is hydrocarbons, as they
contain only two elements: hydrogen and carbon. A ‘family’ of carbon compounds with common
characteristics is called a homologous series. A homologous series is a group of carbon compounds
with the same general formula. Each member of a homologous series differs from the previous
member by one CH2 group.
Questions
1
(M06/S/2) State two characteristics of a homologous series.
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Alkanes
The most basic non-cyclic (straight chained) hydrocarbons are those where only single bonds occur.
The simplest of these is methane (CH4), which is the first in a series of compounds called the
alkanes. The term ‘saturated’ is also applied to alkanes. Saturated hydrocarbons have only single
carbon–carbon bonds and therefore have the maximum number of hydrogen atoms; that is, they
are saturated with hydrogen.
The general formula for the homologous series of alkanes is CnH2n + 2. For example, if a molecule has
five carbon atoms (n = 5), the alkane formed is C5H12 (2 × 5 + 2 = 12).
Table 1 shows the first six straight chain alkanes. The naming of carbon compounds is very
systematic. Both the prefix and suffix provide information. The prefix indicates the number of
carbon atoms and the suffix ‘–ane’ indicates an alkane.
Table 1: Complete the table first six members of the alkane homologous series.
Molecular Empirical
Name
Structural formula
Properties
formula
Formula
Uses
CH4
non-polar,
gas, boiling
point
Bpt –164ºC
cooking,
Bunsen
burners, gas
heating
ethane
C2H6
non-polar,
gas,
Bpt –87ºC
Producing
ethene
propane
C3 H 8
non-polar,
gas,
Bpt –42ºC
liquid
petroleum
gas (LPG)
C4H10
Non-polar,
gas,
Bpt –0.5ºC
LPG,
cigarette
lighters,
camp stoves
Non-polar,
liquid,
Bpt 36.1 ºC
Present in
natural gas,
cigarette
lighters and
aerosol
propellants
methane
butane
Pentane
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C5H12
Hexane
C6H14
Non-polar,
liquid,
Bpt 68.7 ºC
Present in
petrol and
many
solvents
The molecular formula shows the actual numbers of all the atoms in a molecule of the compound,
but gives no information about the way the atoms are arranged, whereas the structural formula
shows the way in which the atoms are bonded to each other and the shape of the molecule. A
structural formula is much more useful when you need to visualise the molecule. The empirical
formula is the lowest whole number ratio of elements in a compound, so the empirical formula of
ethane would be CH3 and for butane would be C2H5.
As the length and complexity of molecules increase, drawing full structural formulas becomes
laborious. In those cases, more useful representations are semi-structural formulas, also known as
condensed structural formulas, in which each carbon atom is listed alongside its attached
hydrogen atoms. Condensed Structural formulas of pentane is: CH3CH2CH3CH2CH3.
Question
2.
Draw the structural and condensed formulas of heptane, C7H16
Drawing in 2d or 3d
It is difficult to draw molecules to accurately represent their three-dimensional structure. Using
pentane as an example, each carbon atom has four bonds. The expected tetrahedral arrangement
exists around each of these carbon atoms. However, for simplicity, as the size and complexity of the
molecules increases, many molecules are simply drawn in two dimensions. Three dimensional
structures are drawn for simple inorganic and organic molecules wherever possible.
3d structural formula for a tetrahedral molecule
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Question
3. Draw the Lewis structure for the methane and ethane molecule in their 2d shape. Give a reason
for shape using VSEPR theory.
The standard way of naming compounds (nomenclature) was developed by the International Union
of Pure and Applied Chemistry; and is referred to as the IUPAC system. The IUPAC organization was
formed in 1919 by chemists around the world with the goal of fostering a common language for
communicating chemistry using of clear, concise and unambiguous terminology. The advantage of
this system is that the name gives clues as to the structure of the molecule. Using this IUPAC
system, it is possible to write the structural formula of any organic compound from its name. It is
gradually replacing the older, less systematic way of naming organic compounds. For example, the
chemical used to preservative animal samples is called ‘methanal’. Like methane, this compound
has one carbon atom. It is an aldehyde (see later) and so has the ending ‘-al’. The name methanal is
a more useful and informative name than the older name, ‘formalyn’.
Table 2: Prefixes used for carbon compounds in IUPAC system
Number of
carbon atoms
1
2
3
4
5
6
7
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Prefix
MethEthProButPentHexHept-
8
9
10
OctNonDec-
Structural Isomers
The structural formulas shown in table 1 show only one possible arrangement of the atoms in the
molecular formula. Molecules with the same molecular formula and different structural formulas
are called isomers or structural isomers.
The first member of the alkane homologous series to exhibit structural isomerism is butane.
Methane, ethane and propane can each only take on one structure. Butane has two isomers called
butane and 2-methylpropane.
Structural isomers of butane:
Butane
2-methylpropane
Using the IUPAC system, branched alkanes are named by considering them as straight-chain alkanes
with side groups attached. Side groups are named using the prefix for the appropriate number of
carbon atoms, and the suffix ‘–yl’. Thus a CH3– side group is a methyl group; a CH3CH2– side group is
an ethyl group and so on.
Question
4. Draw the three structural isomers of pentane and their condensed structural formula.
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Table 2 Naming hydrocarbons
Steps
CH3CH2CH2CH2CH2 CH3


CH3 CH3
Name this alkane
Identify the longest carbon chain.
Number the carbon of the
longest chain so as to give the
carbon atoms attached to the
side group or the branch the
lowest sum.
CH3CH2CH2CH2CH2 CH3


CH3 CH3
1
2
3
4
5
6
CH3CH2CH2CH2CH2 CH3


CH3 CH3
Name the side branches and
main chain.
2, 3 - dimethyl
Combine to write the full name.
2, 3-dimethylhexane
In cases where identical side groups are present on the hydrocarbon stem, they are given numbers,
and the prefix ‘di-’, ‘tri-’, ‘tetra-’ and so on, is added to the hydrocarbon stem name. When
numbering the carbon chain, numbering is such that the side groups or branch have the lowest
possible numbers.
It is important to inspect a formula carefully, because the most ‘obvious’ carbon chain is not always
the longest one.
The name is written as a single word, using hyphens to separate the different prefixes and using
commas to separate numbers. If two or more different substituents are present, they are cited in
alphabetical order. Prefixes like ‘di’, ‘tri’ etc are not used for alphabetising purposes.
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Question
5. Draw and name the five structural isomers of hexane.
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Cycloalkanes
In cycloalkanes the carbon atoms are joined up in a ring. The smallest cycloalkane is cyclopropane.
If you count the carbons and hydrogens, you will see that they no longer fit the general formula
CnH2n+2. By joining the carbon atoms in a ring, you have had to lose two hydrogen atoms. All the
cycloalkanes from cyclopentane upwards exist as "puckered rings".
Cyclohexane, for example, has a ring structure which looks like this:
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Alkenes
Another homologous series of hydrocarbons is the alkenes, formed when the molecule contains one
carbon–carbon double bond. Because at least two carbon atoms are required for a carbon-carbon
double bond to be present, the simplest is ethene, C2H4. The alkenes have the general formula
CnH2n.
Alkenes are an example of an unsaturated hydrocarbon. Unsaturated hydrocarbons contain at
least one carbon-carbon double bond, so also contain less than the maximum number of hydrogen
atoms.
Table 3:
Number
carbon
atoms
2
Complete the table for the first six alkenes
Molecular
formula
Name
C2H4
Ethene
3
4
C4H8
5
C5H10
6
Structural formula
CH2=CH2
Boiling
point (°°C)
–104
Propene
–47
Butene
–6
30
Hexene
CH2=CHCH2CH2CH2 CH3
64
Alkenes also exhibit structural isomerism, the double bond may occur in different places along the
chain, or branching may occur. There are two straight chain isomers of butene called but-1-ene and
but-2-ene. The number indicates the position of the double bond in the chain. But-1-ene has its
double bond in the first position along the chain – between carbons 1 and 2, whereas but-2-ene has
its double bond in the second position – between carbons 2 and 3. When naming branched alkenes
the carbon atoms of the double bond are given the lowest number.
Questions
6. Draw and name the two straight chain structural isomers of butene.
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7. Draw and name the two branched chain isomer of butene.
8.
a)
Classify each of the following as alkanes or alkenes.
C12H24
b)
C16H32
c)
C15H32
d)
C72H146
9.
a)
Name the hydrocarbon molecules whose semi-structural (condensed structural) formulas
are given below.
CH3CH(CH3)CH2CH2CH3
b)
CH2CHCHCH3
c)
CH3CH2C(CH3)CH3
d)
CH3C(CH3)2CHCHCH2CH3
i)
ethene, C2H4
ii)
ethane, C2H6
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Functional Groups
Alkanes and alkenes only carbon and hydrogen. Introducing other types of atoms into a
hydrocarbon allow a vast range of compounds to be formed. Atoms or groups of atoms attached to
a hydrocarbon chain are called functional groups. These functional groups are significant because
they change the reactivity of the molecule and can change the chemical properties of the
compound.
When we are focussing on the presence of a functional group in a hydrocarbon, it is common to
write the general formula with the symbols of the functional group written as they appear in the
structure of the molecule and a single letter R to represent the alkyl group (the rest of the
hydrocarbon). If there is more than one alkyl group, then R′′ represents the second alkyl group and
R′′′ may represent a third alkyl group.
The structural formula of the important homologous series containing functional groups
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Alcohols
The alcohol functional group is made up of an oxygen atom bonded to a hydrogen atom. This –OH
group is known as a hydroxyl group and replaces one hydrogen in the structure of an alkane. The
prefixes that are used to indicate the number of carbon atoms still apply to alcohols, however the
suffix (ending) of the name of an alcohol is always –ol. The general formula of the alcohol
homologous series is CnH2n+1OH or R-OH.
Table 1 The first six members of the alcohol series.
Condensed
Name
structural
Structural formula
formula
Boiling
Point (ºC)
Solubility in
water
methanol
CH3OH
65
Soluble
ethanol
C2H5OH
78
Soluble
propanol
C3H7OH
97
Slightly
soluble
butanol
C4H9OH
118
Insoluble
pentanol
C5H11OH
138
Insoluble
hexanol
C6H13OH
156
Insoluble
The position of the hydroxyl group is indicated by a number corresponding to the position in the
carbon chain of the carbon atom to which the hydroxyl group is bonded. As with all isomers, the
carbon atoms are counted from the end closest to the hydroxyl group.
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10. Draw structural formulas and state the names of all the alcohols with the molecular
formula C5H12O.
11. Draw the structural formulas for ethanol and hexan-1-ol. Explain why it is necessary to write
the ‘1’ in hexan-1-ol, but no number is given with ethanol.
12. Draw the Lewis dot diagram for methanol and deduce the shape and bond angle with respect
to the carbon and oxygen atoms.
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Aldehydes and Ketones
Aldehydes and ketones are both homologous series containing the carbonyl functional group (C=O).
The general formula of aldehydes is CnH2nO or RCHO. To avoid confusion with alcohols, the
aldehyde functional group is written as -CHO in a formula indicating that the H is not directly
bonded to the O, whereas the alcohols functional group is written as -OH.
Ketones are similar to aldehydes in that they have a single carbonyl group (C=O), however the
difference is that in an aldehyde, the carbonyl group is bonded to a carbon that is on the end of the
carbon chain, whereas in a ketone, the carbonyl group is bonded to a carbon atom that is not on
either end of the carbon chain. The general formula of ketones is RCOR′′ where R and R′′ may or may
not be the same alkyl group. The consequence of this structure is that the smallest ketone,
propanone, has three carbon atoms in its chain.
The names of aldehydes and ketones follow the same pattern as other hydrocarbons. The number
of carbon atoms in the chain including that in the carbonyl group is indicated by the prefix methan-,
ethan-, propan- and the presence of the aldehyde or ketone functional group is indicated by the
suffix. The names of aldehydes finish with the suffix –al and those of ketones finish with the suffix –
one. The position of the carbonyl group in a ketone is indicated by a number just before the suffix (one). This number indicates which carbon atom is part of the carbonyl group.
Table 2 Complete the table for aldehydes with up to 6 carbon atoms.
Boiling
Point
(°C)
Solubility in
water
Name
Molecular
formula
Methanal
HCHO
-21
soluble
Ethanal
CH3CHO
21
soluble
46
Slightly
soluble
C2H5CHO
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Structural formula
75
Very slightly
soluble
Pentanal
103
insoluble
Hexanal
119
insoluble
Butanal
C3H7CHO
Table 3 Complete the table with Ketones with up to 6 carbon atoms.
Condensed
Name
structural
Structural formula
formula
Boiling
Point
(°C)
Solubility
in water
Propanone
CH3COCH3
56
soluble
Butanone
C2H5COCH3
80
Slightly
soluble
Pentan-2-one
C3H7COCH3
102
insoluble
Pentan-3-one
C2H5COC2H5
100-102
insoluble
Hexan-2-one
C4H9COCH3
127
insoluble
Hexan-3-one
C3H7CO C2H5
123
insoluble
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Questions
13. (N05/S/1) Which compound is a member of the aldehyde homologous series?
A. CH3COCH3
B. CH3CH2CH2OH
C. CH3CH2COOH
D. CH3CH2CHO
14. (M07/H/2/9) Draw the functional group isomers of C3H6O. (2 marks)
Carboxylic Acids
Carboxylic acids are organic acids. The carboxylic acid functional group is called the carboxyl group,
has the formula –COOH and is made up of a carbonyl group (C=O) and a hydroxyl (-OH) group.
Naming of carboxylic acids follows the same pattern as other hydrocarbons. The number of carbons
in the carbon chain, including the carbon in the functional group is indicated by the prefix: methan-,
ethan-, propan- and the presence of the carboxyl functional group is indicated by the suffix –oic
acid.
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Table 4 Complete the table for Carboxylic acids with up to 6 carbon atoms.
Boiling
Point
(°C)
Solubility
in water
HCOOH
101
Soluble
CH3COOH
118
Soluble
141
Soluble
C3H7COOH
164
Soluble
C4H9COOH
186
Slightly
soluble
202
Slightly
soluble
Name
Molecular
formula
Methanoic
acid
Propanoic
acid
Butanoic
acid
Hexanoic
acid
Structural formula
Works Cited
Clark, Jim. Chem Guide. 2008. 5 January 2008 <http://www.chemguide.co.uk/>.
Derry, Lanna, Maria Connor and Carol Jordan. Chemistry for use with the IB Diploma Standard
Level. Melbourne: Pearson Education, 2008.
Clugston, Michael and Rosalind Flemming. Advanced Chemistry. Oxford: Oxford University Press,
2000.
Organisation, International Baccalaureate. Online Curriculum Centre.
<http://occ.ibo.org/ibis/occ/guest/home.cfm>.
—. "Chemistry Data Booklet." International Baccalaureate Organisation, March 2007.
—. "Chemistry Guide." International Baccalaureate Organisation, March 2007.
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