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O
R C
R OH
Combining the names of functional groups with the names of the parent alkanes
generates what is termed a systematic nomenclature for naming organic
compounds. In traditional nomenclature, the first carbon atom after the carbon
that attaches to the functional group is called the alpha carbon; the second, beta
carbon, the third, gamma carbon, etc. If there is another functional group at a
carbon, it may be named with the Greek letter, e.g., the gamma-amine in gamma-
aminobutyric acid is on the third carbon of the carbon chain attached to the
carboxylic acid group. IUPAC conventions call for numeric labeling of the
position, e.g. 4-aminobutanoic acid. In traditional names various qualifiers are
used to label isomers, for example isopropanol (IUPAC name: propan-2-ol) is an
isomer is n-propanol (propan-1-ol). Functional groups are structural units within
organic compounds that are defined by specific bonding arrangements between
specific atoms. The structure of capsaicin, the compound discussed in the
beginning of this chapter, incorporates several functional groups, labeled in the
figure below and explained throughout this section.
Alkanes
Most of the compounds in crude oil are hydrocarbons. This means they
only contain hydrogen and carbon atoms, joined together by covalent bonds.
Remember that a covalent bond is a shared pair of electrons. Alkanes are a type of
hydrocarbon.The number of hydrogen atoms in an alkane is double the number of
carbon atoms, plus two. For example, the molecular formula of methane is CH4.
For ethane, it is C2H6.
Structure of alkanes
molecular
alkane structural formula molecular model
formula
methaneCH4
ethane C2H6
propane C3H8
butane C4H10
Notice that the molecular models on the right show that the bonds are not really at
90.Alkanes are saturated hydrocarbons. This means their carbon atoms are joined
to each other by single covalent bonds.
ethene
propyne
1. Select as the parent structure the longest continuous chain that contains the
carbon-carbon double bond; then consider the compound to have been
derived from this structure by replacement of hydrogen by various alkyl
groups. The parent structure is known as ethane, propene, butene, pentene,
and so on, depending upon the number of carbon atoms . each name is
derived by changing the ending "-ane" of the corresponding alkane name
to "-ene".
propene
1. If the parent chain is longer than three carbons, indicate by a number the
position of the double bond in the parent chain. Although the double bond
involves two carbon atoms designate its position by the number of the first
doubly-bonded carbon encountered when numbering from the end of the
chain nearest the double bond.
1-butene 2-butene
3,3-dimethyl-1-butene 4-methyl-2-pentene
Aromatics
Haloalkanes
In the alcohol functional group, a carbon is single-bonded to an OH group (the
OH group, by itself, is referred to as a hydroxyl). Except for methanol, all
alcohols can be classified as primary, secondary, or tertiary. In a primary alcohol,
the carbon bonded to the OH group is also bonded to only one other carbon. In a
secondary alcohol and tertiary alcohol, the carbon is bonded to two or three other
carbons, respectively. When the hydroxyl group is directly attached to an aromatic
ring, the resulting group is called a phenol. The sulfur analog of an alcohol is
called a thiol (from the Greek thio, for sulfur).
Note that the definition of a phenol states that the hydroxyl oxygen must be
directly attached to one of the carbons of the aromatic ring. The compound below,
therefore, is not a phenol - it is a primary alcohol.
The distinction is important, because as we will see later, there is a
significant difference in the reactivity of alcohols and phenols.
The deprotonated forms of alcohols, phenols, and thiols are called alkoxides,
phenolates, and thiolates, respectively. A protonated alcohol is an oxonium ion.
Ethers can act as Lewis bases. For instance, diethyl ether forms a complex
with boron compounds, such as boron trifluoride diethyl etherate (BF 3.OEt2).
Ethers also coordinate to magnesium in Grignard reagents (RMgBr).
Nomenclature
In the IUPAC nomenclature system, ethers are named using the general
formula "alkoxyalkane", for example CH3-CH2-O-CH3 is methoxyethane. If the
ether is part of a more complex molecule, it is described as an alkoxy substituent,
so -OCH3 would be considered a " methoxy-" group. The simpler alkyl radical is
written in front, so CH3-O-CH2CH3 would be given as
methoxy(CH3)ethane(CH2CH3). The nomenclature of describing the two alkyl
groups and appending "ether", e.g. "ethyl methyl ether" in the example above, is a
trivial usage.
Similar structures
Ethers are not to be confused with the following classes of compounds with the
same general structure R-O-R.
Aromatic compounds like furan where the oxygen is part of the aromatic
system.
o Esters R-C(=O)-O-R
o Acetals R-CH(-O-R)-O-R
o Aminals R-CH(-NH-R)-O-R
o Anhydrides R-C(=O)-O-C(=O)-R
Polyethers
Polyethers are compounds with more than one ether group. While the term
generally refers to polymers like polyethylene glycol and polypropylene glycol,
low molecular compounds such as the crown ethers may sometimes be included.
Organic reactions
Synthesis
Ethers can be prepared in the laboratory in several different ways.
The R-X cannot be used to react with the alcohol. However, phenols can
be used to replace the alcohol, while maintaining the alkyl halide. Since
phenols are acidic, they readily react with a strong base like sodium
hydroxide to form phenoxide ions. The phenoxide ion will then substitute
the -X group in the alkyl halide, forming an ether with an aryl group
attached to it in a reaction with an SN2 mechanism.
Reactions
Structure of the polymeric diethyl ether peroxide
Ethers in general are of very low chemical reactivity. Organic reactions are:
Hydrolysis.
Ethers are hydrolyzed only under drastic conditions like heating with
boron tribromide or boiling in hydrobromic acid. Lower mineral acids
containing a halogen, such as hydrochloric acid will cleave ethers, but
very slowly. Hydrobromic acid and hydroiodic acid are the only two that
do so at an appreciable rate. Certain aryl ethers can be cleaved by
aluminium chloride.
Nucleophilic displacement.
Peroxide formation.
Primary and secondary ethers with a CH group next to the ether oxygen
easily form highly explosive organic peroxides (e.g. diethyl ether
peroxide) in the presence of oxygen, light, and metal and aldehyde
impurities. For this reason ethers like diethyl ether and THF are usually
avoided as solvents in industrial processes
Important ethers
Amines are characterized by nitrogen atoms with single bonds to hydrogen and
carbon. Just as there are primary, secondary, and tertiary alcohols, there are
primary, secondary, and tertiary amines. Ammonia is a special case with no carbon
atoms.
One of the most important properties of amines is that they are basic, and are
readily protonated to form ammonium cations. In the case where a nitrogen has
four bonds to carbon (which is somewhat unusual in biomolecules), it is called a
quaternary ammonium ion.
Amines
Note: Do not be confused by how the terms 'primary', 'secondary', and 'tertiary'
are applied to alcohols and amines - the definitions are different. In alcohols,
what matters is how many other carbons the alcohol carbon is bonded to, while in
amines, what matters is how many carbons the nitrogen is bonded to.
Organic phosphates
When a carbonyl carbon is bonded on one side to a carbon (or hydrogen) and on
the other side to an oxygen, nitrogen, or sulfur, the functional group is considered
to be one of the carboxylic acid derivatives, a designation that describes a set
of related functional groups. The eponymous member of this family is the
carboxylic acid functional group, in which the carbonyl is bonded to a hydroxyl
group. The conjugate base of a carboxylic acid is a carboxylate. Other
derivatives are carboxylic esters (usually just called 'esters'), thioesters, amides,
acyl phosphates, acid chlorides, and acid anhydrides. With the exception of
acid chlorides and acid anhydrides, the carboxylic acid derivatives are very
common in biological molecules and/or metabolic pathways, and their structure
and reactivity will be discussed in detail in chapter 11.
Nitriles
The hormone testosterone, the amino acid phenylalanine, and the glycolysis
metabolite dihydroxyacetone phosphate all contain multiple functional groups, as
labeled below.
While not in any way a complete list, this section has covered most of the
important functional groups that we will encounter in biological organic
chemistry. Table 9 in the tables section at the back of this book provides a
summary of all of the groups listed in this section, plus a few more that will be
introduced later in the text.
Exercise 1.12: Identify the functional groups (other than alkanes) in the following
organic compounds. State whether alcohols and amines are primary, secondary, or
tertiary.
Naming organic compounds
A system has been devised by the International Union of Pure and Applied
Chemistry (IUPAC, usually pronounced eye-you-pack) for naming organic
compounds. While the IUPAC system is convenient for naming relatively small,
simple organic compounds, it is not generally used in the naming of biomolecules,
which tend to be quite large and complex. It is, however, a good idea (even for
biologists) to become familiar with the basic structure of the IUPAC system, and
be able to draw simple structures based on their IUPAC names.
2 carbons: ethane
3 carbons: propane
4 carbons: butane
5 carbons: pentane
6 carbons: hexane
7 carbons: heptane
8 carbons: octane
9 carbons: nonane
10 carbons: decane
Substituents branching from the main parent chain are located by a carbon
number, with the lowest possible numbers being used (for example, notice in the
example below that the compound on the left is named 1-chlorobutane, not 4-
chlorobutane). When the substituents are small alkyl groups, the terms methyl,
ethyl, and propyl are used.
Other common names for hydrocarbon substituent groups isopropyl, tert-butyl
and phenyl.
Notice in the example below, an ethyl group (in blue) is not treated as a
substituent, rather it is included as part of the parent chain, and the methyl group
is treated as a substituent. The IUPAC name for straight-chain hydrocarbons is
always based on the longest possible parent chain, which in this case is four
carbons, not three.
Alkenes are designated with an 'ene' ending, and when necessary the location and
geometry of the double bond are indicated. Compounds with multiple double
bonds are called dienes, trienes, etc.
Some groups can only be present on a terminal carbon, and thus a locating
number is not necessary: aldehydes end in al, carboxylic acids in oic acid, and
carboxylates in oate.
Ethers and sulfides are designated by naming the two groups on either side of the
oxygen or sulfur.
For esters, the suffix is 'oate'. The group attached to the oxygen is named first.
All of the examples we have seen so far have been simple in the sense that only
one functional group was present on each molecule. There are of course many
more rules in the IUPAC system, and as you can imagine, the IUPAC naming of
larger molecules with multiple functional groups, ring structures, and substituents
can get very unwieldy very quickly. The illicit drug cocaine, for example, has the
IUPAC name 'methyl (1R,2R,3S,5S)-3-(benzoyloxy)-8-methyl-8-azabicyclo[3.2.1]
octane-2-carboxylate' (this name includes designations for stereochemistry, which
is a structural issue that we will not tackle until chapter 3).
You can see why the IUPAC system is not used very much in biological organic
chemistry - the molecules are just too big and complex. A further complication is
that, even outside of a biological context, many simple organic molecules are
known almost universally by their common, rather than IUPAC names. The
compounds acetic acid, chloroform, and acetone are only a few examples.
Often when drawing organic structures, chemists find it convenient to use the
letter 'R' to designate part of a molecule outside of the region of interest. If we
just want to refer in general to a functional group without drawing a specific
molecule, for example, we can use 'R groups' to focus attention on the group of
interest:
The 'R' group is a convenient way to abbreviate the structures of large biological
molecules, especially when we are interested in something that is occurring
specifically at one location on the molecule. For example, in chapter 15 when we
look at biochemical oxidation-reduction reactions involving the flavin molecule,
we will abbreviate a large part of the flavin structure which does not change at all
in the reactions of interest:
As an alternative, we can use a 'break' symbol to indicate that we are looking at a
small piece or section of a larger molecule. This is used commonly in the context
of drawing groups on large polymers such as proteins or DNA.
If you are unsure whether to draw out part of a structure or abbreviate it, the safest
thing to do is to draw it out.
[You might ask: what is this based on? Its an arbitrary agreement by IUPAC
[source], although note that there is some correlation between the oxidation state
of the carbon and the priority (more oxidized groups tend to be higher priority).
However this really is an example of something you have to either look up ,
memorize, or have a computer do for you. Its not conceptual.
Here are some examples of applying the order of functional group priorities to
solve nomenclature problems. The highest ranked functional group becomes the
suffix its highlighted in red.
Polyfunctional compounds
Although each of the functional groups introduced above has a characteristic set
of favoured reactions, it is not always possible to predict the properties of organic
compounds that contain several different functional groups. In polyfunctional
organic compounds, the functional groups often interact with one another to
impart unique reactivity patterns to the compounds. As chemistry evolves as a
science, it becomes possible to understand more of the behaviour of complex
molecules, and chemists are able to design laboratory syntheses of increasingly
complicated molecules, basing the synthetic plan upon the reactivity trends of
functional groups.
Melvyn C. Usselman
Chemical synthesis
Approach to synthesis
Three factors must be borne in mind when evaluating a particular synthetic plan.
The first is costof far greater importance in industrial, large-scale synthesis than
in laboratory work in which a particular synthesis may be carried out only once, as
in the total synthesis of a naturally occurring compound, and which in any case is
likely to be on a relatively small scale. The environmental impact of chemical
syntheses has become an important consideration. Syntheses or processes that
have a benignenvironmental impact, whether by use of safe and commonly
available reagents or by minimization of environmentally harmful waste products,
have become an essential feature of so-called green chemistry.
Second, the yield in each step must be considered. A step in a synthesis may give
a very low yield of the desired product. For example, a proportion of the reactant
may be converted into a different product by an alternative process that competes
with the desired one; some of the product may undergo a subsequent reaction; or
some of the product may be lost in the separation processes required for its
isolation in a pure state. The yield is usually defined, on a percentage basis, as the
number of molecules of product obtained when 100 could in principle have been
formed. A yield of about 80 percent or more is generally considered good, but
some transformations can prove so difficult to achieve that even a yield of 10 or
20 percent may have to be accepted. The ultimate synthetic goal in a perfect
synthesis is to achieve 100 percent atom efficiency, in which all atoms of all
reagents are incorporated into the synthesized product without the formation of
any by-products.
Naturally, the yield of a process affects the cost of the product, because the
shortfall from a 100 percent yield represents wasted material. In addition, yield
can be of the utmost importance in determining whether a synthesis is a
practicable possibility, because the overall yield of a synthesis is the product of
the yields of the individual steps. If these intermediate yields are mostly low, the
ultimate product may not be obtainable in the necessary amount from the
available starting material.
Finally, consideration must be given to the rate at which each step in the planned
sequence occurs. In many instances, a desired reaction is possible in principle but
in practice takes place so slowly as to be ineffective. It is then necessary to
investigate whether the rate can be increased to a practicable level by altering the
conditions of the reactionfor example, by raising the temperature or by adding
an extra species, called a catalyst, that increases the rate without altering the
course of the reaction.
Isolation and purification of products