MULTIFUNCTIONAL GROUP COMPOUND

O
R C
R OH

In organic chemistry, functional groups are specific groups (moieties) of

atoms or bonds within molecules that are responsible for the characteristic
chemical reactions of those molecules. The same functional group will undergo
the same or similar chemical reaction(s) regardless of the size of the molecule it is
a part of.[1][2] However, its relative reactivity can be modified by other functional
groups nearby. The atoms of functional groups are linked to each other and to the
rest of the molecule by covalent bonds. Any subgroup of atoms of a compound
also may be called a radical, and if a covalent bond is broken homolytically, the
resulting fragment radicals are referred as free radicals. Functional groups can
also be charged, e.g. in carboxylate salts (-COO ), which turns the molecule into a
polyatomic ion or a complex ion.

Complexation and solvation is also caused by specific interactions of functional

groups. In the common rule of thumb "like dissolves like", it is the shared or
mutually well-interacting functional groups which give rise to solubility. For
example, sugar dissolves in water because both share the hydroxyl functional
group (-OH) and hydroxyls interact strongly with each other.

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.

As we progress in our study of organic chemistry, it will become

extremely important to be able to quickly recognize the most common functional
groups, because they are the key structural elements that define how organic
molecules react. For now, we will only worry about drawing and recognizing
each functional group, as depicted by Lewis and line structures. Much of the
remainder of your study of organic chemistry will be taken up with learning about
how the different functional groups behave in organic reactions.

The 'default' in organic chemistry (essentially, the lack of any functional

groups) is given the term alkane, characterized by single bonds between carbon
and carbon, or between carbon and hydrogen. Methane, CH4, is the natural gas
you may burn in your furnace. Octane, C8H18, is a component of gasoline.

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.

Alkane molecules can be represented by displayed formulas in which each

atom is shown as its symbol (C or H), and the covalent bonds between them by a
straight line. The table shows four alkanes.

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.

Alkenes (sometimes called olefins) have carbon-carbon double bonds, and

alkynes have carbon-carbon triple bonds. Ethene, the simplest alkene example, is
a gas that serves as a cellular signal in fruits to stimulate ripening. (If you want
bananas to ripen quickly, put them in a paper bag along with an apple - the apple
emits ethene gas, setting off the ripening process in the bananas). Ethyne,
commonly called acetylene, is used as a fuel in welding blow torches.
Alkenes and alkynes

Introduction to Alkenes and Alkynes

There are two other types of basic hydrocarbons: alkenes and alkynes.
Alkenes contain less hydrogen, carbon for carbon, than the alkanes. To account
for this difference, the carbon atoms are joined by a double bond. The carbon-
carbon double bond is the distinguishing feature of the alkene structure.

ethene

Alkynes contain an even smaller proportion of hydrogen than the alkenes. To

account for this difference, the carbon atoms share three pairs of electrons . that is,
they are joined by a triple bond. The carbon-carbon triple bond is the
distinguishing feature of the alkyne structure.

propyne

Rules for Naming Alkenes

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

1. Indicate by numbers the positions of the alkyl groups attached to the

parent chain.

3,3-dimethyl-1-butene 4-methyl-2-pentene

Rules for Naming Alkynes

The alkynes can also be named by the IUPAC system. The rules are exactly the
same as for the naming of alkenes except that the ending "-yne" replaces "-ene".
The parent structure is the longest continuous chain that contains the triple bond,
and the positions both of the substituents and of the triple bond are indicated by
numbers. The triple bond is given the number of the first triply-bonded carbon
encountered, starting from the end of the chain nearest the triple bond.
 2-butyne 4-methyl-2-pentyne
1-butyne

The bonding in alkenes is trigonal planar in in alkynes is linear.

Furthermore, many alkenes can take two geometric forms: cis or trans. The cis
and trans forms of a given alkene are different molecules with different physical
properties because, as we will learn in chapter 2, there is a very high energy
barrier to rotation about a double bond. In the example below, the difference
between cis and trans alkenes is readily apparent.

Alkanes, alkenes, and alkynes are all classified as hydrocarbons, because

they are composed solely of carbon and hydrogen atoms. Alkanes are said to be
saturated hydrocarbons, because the carbons are bonded to the maximum possible
number of hydrogens - in other words, they are saturated with hydrogen atoms.
The double and triple-bonded carbons in alkenes and alkynes have fewer
hydrogen atoms bonded to them - they are thus referred to as unsaturated
hydrocarbons. As we will see in chapter 15, hydrogen can be added to double and
triple bonds, in a type of reaction called 'hydrogenation'.

The aromatic group is exemplified by benzene (which used to be a

commonly used solvent on the organic lab, but which was shown to be
carcinogenic), and naphthalene, a compound with a distinctive 'mothball' smell.
Aromatic groups are planar (flat) ring structures, and are widespread in nature.
We will learn more about the structure and reactions of aromatic groups in
chapters 2 and 14.

Aromatics

When the carbon of an alkane is bonded to one or more halogens, the

group is referred to as a alkyl halide or haloalkane. Chloroform is a useful solvent
in the laboratory, and was one of the earlier anesthetic drugs used in surgery.
Chlorodifluoromethane was used as a refrigerant and in aerosol sprays until the
late twentieth century, but its use was discontinued after it was found to have
harmful effects on the ozone layer. Bromoethane is a simple alkyl halide often
used in organic synthesis. Alkyl halides groups are quite rare in biomolecules.

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).

Alcohols, phenols, and thiols

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.

In an ether functional group, a central oxygen is bonded to two carbons.

Below is the structure of diethyl ether, a common laboratory solvent and also one
of the first compounds to be used as an anesthetic during operations. The sulfur
analog of an ether is called a thioether or sulfide.

Ethers and sulfides

Ether is a class of chemical compounds which contain an ether group

an oxygen atom connected to two (substituted) alkyl or aryl groups of general
formula ROR'. A typical example is the solvent and anesthetic diethyl ether,
commonly referred to simply as "ether" (ethoxyethane, CH3-CH2-O-CH2-CH3).
Physical properties
Ether molecules cannot form hydrogen bonds among each other, resulting
in a relatively low boiling point comparable to that of the analogous alcohols.
However, the differences in the boiling points of the ethers and their isometric
alcohols become smaller as the carbon chains become longer, as the hydrophobic
nature of the carbon chain becomes more predominant over the presence of
hydrogen bonding.

Ethers are slightly polar as the R - C - O - C - Z bond angle in the functional

group is about 110 degrees, and the C - O dipole does cancel out. Ethers are less
polar than alkenes but not as polar as alcohols, esters or amides of comparable
structure. However, the presence of two lone pairs of electrons on the oxygen
atoms makes hydrogen bonding with water molecules possible, causing the
solubility of alcohols (for instance, butan-1-ol) and ethers (ethoxyethane) to be
quite dissimilar.

Cyclic ethers such as tetrahydrofuran and 1,4-dioxane are totally miscible

in water because of the more exposed oxygen atom for hydrogen bonding as
compared to aliphatic ethers.

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

Not all compounds of the formula R-O-R are ethers.

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.

Compounds where one of the carbon atoms next to the oxygen is

connected to oxygen, nitrogen, or sulfur:

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

Primary, secondary, and tertiary ethers

The terms "primary ether", "secondary ether", and "tertiary ether" are occasionally
used and refer to the carbon atom next to the ether oxygen. In a primary ether this
carbon is connected to only one other carbon as in diethyl ether CH 3-CH2-O-CH2-
CH3. An example of a secondary ether is diisopropyl ether (CH 3)2CH-O-CH(CH3)2
and that of a tertiary ether is di-tert-butyl ether (CH3)3C-O-C(CH3)3.

Dimethyl ether, a primary, a secondary, and a tertiary ether.

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.

Intermolecular Dehydration of alcohols:

R-OH + R-OH R-O-R + H2O

This direct reaction requires drastic conditions (heating to 140 degrees

Celsius and an acid catalyst, usually concentrated sulfuric acid). Effective
for making symmetrical ethers, but not as useful for synthesising
asymmetrical ethers because the reaction will yield a mixture of ethers,
making it usually not applicable:

3R-OH + 3R'-OH R-O-R + R'-O-R + R'-O-R' + 3H2O

Conditions must also be controlled to avoid overheating to 170 degrees

which will cause intramolecular dehydration,a reaction that yields alkenes.
In addition, the alcohol must be in excess.

R-CH2-CH2(OH) R-CH=CH2 + H2O

Such conditions can destroy the delicate structures of some functional

groups. There exist several milder methods to produce ethers.

Nucleophilic displacement of alkyl halides by alkoxides

R-O- + R-X R-O-R + X-

This reaction is called the Williamson ether synthesis. It involves treatment

of a parent alcohol with a strong base to form the alkoxide anion followed
by addition of an appropriate aliphatic compound bearing a suitable
leaving group (R-X). Suitable leaving groups (X) include iodide, bromide,
or sulfonates. This method does not work if R is aromatic like in
bromobenzene (Br-C6H5), however, if the leaving group is separated by at
least one carbon from the benzene, the reaction should proceed (as in Br-
CH2-C6H5). Likewise, this method only gives the best yields for primary
carbons, as secondary and tertiary carbons will undergo E2 elimination on
 exposure to the basic alkoxide anion used in the reaction due to steric
hindrance from the large alkyl groups. Aryl ethers can be prepared in the
Ullmann condensation.

Nucleophilic Displacement of Alkyl halides by phenoxides

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.

HO-C6H5 + OH- O--C6H5

O--C6H5 + R-X R-O-C6H5

Electrophilic addition of alcohols to alkenes.

R2C=CR2 + R-OH R2CH-C(-O-R)-R2

Acid catalysis is required for this reaction. Often, Mercury trifluoroacetate

(Hg(OCOCF3)2 is used as a catalyst for the reaction, creating an ether with
Markovnikov regiochemistry. Tetrahydropyranyl ethers are used as
protective groups for alcohols.

Cyclic ethers which are also known as epoxides can be prepared:

By the oxidation of alkenes with a peroxyacid such as m-CPBA.

By the base intramolecular nuclephilic substitution of a halohydrin.

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.

Epoxides, or cyclic ethers in three-membered rings, are highly susceptible

to nucleophilic attack and are reactive in this fashion.

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

Ethylene oxide The smallest cyclic ether.

Dimethyl ether An aerosol spray propellant.

A common low boiling

Diethyl ether
solvent (b.p. 34.6C).
Dimethoxyethane A high boiling solvent (b.p.
(DME) 85C):

A cyclic ether and high

Dioxane
boiling solvent (b.p. 101.1C).

A cyclic ether, one of the most

Tetrahydrofuran
polar simple ethers that is
(THF)
used as a solvent.

An aryl ether and a major

Anisole
constituent of the essential oil
(methoxybenzene)
of anise seed.

Cyclic polyethers that are

Crown ethers used as phase transfer
catalysts.

Polyethylene glycol A linear polyether, e.g. used in

(PEG) cosmetics:
Amines

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.

Phosphate and its derivative functional groups are ubiquitous in biomolecules.

Phosphate linked to a single organic group is called a phosphate ester; when it
has two links to organic groups it is called a phosphate diester. A linkage
between two phosphates creates a phosphate anhydride.

Organic phosphates

There are a number of functional groups that contain a carbon-oxygen double

bond, which is commonly referred to as a carbonyl. Ketones and aldehydes are
two closely related carbonyl-based functional groups that react in very similar
ways. In a ketone, the carbon atom of a carbonyl is bonded to two other carbons.
In an aldehyde, the carbonyl carbon is bonded on one side to a hydrogen, and on
the other side to a carbon. The exception to this definition is formaldehyde, in
which the carbonyl carbon has bonds to two hydrogens.
A group with a carbon-nitrogen double bond is called an imine, or sometimes a
Schiff base (in this book we will use the term 'imine'). The chemistry of
aldehydes, ketones, and imines will be covered in chapter 10.

Aldehydes, ketones, and imines

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.

Carboxylic acid derivatives

Finally, a nitrile group is characterized by a carbon triple-bonded to a nitrogen.

Nitriles

A single compound often contains several functional groups, particularly in

biological organic chemistry. The six-carbon sugar molecules glucose and
fructose, for example, contain aldehyde and ketone groups, respectively, and both
contain five alcohol groups (a compound with several alcohol groups is often
referred to as a polyol).

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.

Naming an organic compound usually begins with identify what is referred to as

the 'parent chain', which is the longest straight chain of carbon atoms. Well
start with the simplest straight chain alkane structures. CH4 is called methane,
and C2H6 ethane. The table below continues with the names of longer straight-
chain alkanes: be sure to commit these to memory, as they are the basis for the rest
of the IUPAC nomenclature system (and are widely used in naming biomolecules
as well).

Names for straight-chain alkanes:

1 carbon: methane

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.

Cyclic alkanes are called cyclopropane, cyclobutane, cyclopentane, cyclohexane,

and so on:
In the case of multiple substituents, the prefixes di, tri, and tetra are used.

Functional groups have characteristic suffixes. Alcohols, for example, have ol

appended to the parent chain name, along with a number designating the location
of the hydroxyl group. Ketones are designated by one.

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.

If an amide has an unsubstituted NH 2 group, the suffix is simply amide. In the

case of a substituted amide, the group attached to the amide nitrogen is named
first, along with the letter N to clarify where this group is located. Note that the
structures below are both based on a three-carbon (propan) parent chain.

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.

In biochemistry, nonsystematic names (like 'cocaine', 'capsaicin', 'pyruvate' or

'ascorbic acid') are usually used, and when systematic nomenclature is employed it
is often specific to the class of molecule in question: different systems have
evolved, for example, for fats and for carbohydrates. We will not focus very
intensively in this text on IUPAC nomenclature or any other nomenclature system,
but if you undertake a more advanced study in organic or biological chemistry you
may be expected to learn one or more naming systems in some detail.
Drawing abbreviated organic structures

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.

Finally, 'R' groups can be used to concisely illustrate a series of related

compounds, such as the family of penicillin-based antibiotics.

Using abbreviations appropriately is a very important skill to develop when

studying organic chemistry in a biological context, because although many
biomolecules are very large and complex (and take forever to draw!), usually we
are focusing on just one small part of the molecule where a change is taking
place.

As a rule, you should never abbreviate any atom involved in a bond-breaking or

bond-forming eventthat is being illustrated: only abbreviate that part of the
molecule which is not involved in the reaction of interest.
For example, carbon #2 in the reactant/product below most definitely is involved
in bonding changes, and therefore should not be included in the 'R' group.

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.

Table of Functional Group Priorities for Nomenclature

We need some kind of priority system for nomenclature. And so, IUPAC has
developed one. If you have a molecule with, say, a carboxylic acid and a ketone
you consult the table. The functional group with the highest priority will be the
one which gives its suffix to the name of the molecule. So in example #1 above,
the suffix of the molecule will be -oic acid , not -one, because carboxylic
acids are given higher priority. However, if a ketone is present with an alcohol
(example 3) then we will use the suffix, -one because ketones have a higher
priority for nomenclature than alcohols.

[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

Chemical synthesis is concerned with the construction of complex chemical

compounds from simpler ones. A synthesis usually is undertaken for one of three
reasons. The first reason is to meet an industrial demand for a product. For
example, ammonia is synthesized from nitrogen and hydrogen and is used to
make, among other things, ammonium sulfate, employed as a fertilizer; vinyl
 chloride is made from ethylene and is used in the production of polyvinyl
chloride (PVC) plastic. In general, a vast range of chemical compounds are
synthesized for applications as fibres
and plastics, pharmaceuticals, dyestuffs, herbicides, insecticides, and other
products.

Industrial polymers are synthesized from simple compounds joined together to

form long chains. For

Encyclopdia Britannica, Inc.

Second, an enormous number of compounds of

considerable molecular complexity occur naturally, in both living organisms and
their degradation products; examples are proteins (in animals)
and alkaloids (alkaline materials found in plants). The syntheses of these natural
products have usually been undertaken in the context of the determination of the
structures of the compounds; if a material is deduced to have a particular structure
on the basis of its chemical reactions and physical properties, then the discovery
that a compound synthesized by an unambiguous method for this structure is
identical to the natural product provides confirmation of the validity of the
assigned structure.
Third, a synthesis may be carried out to obtain a compound of specific structure
that does not occur naturally and has not previously been made. This type of
synthesis is performed in order to examine the properties of the compound and
thereby test theories of chemical structure and reactivity.

Approach to synthesis

The range of compounds that are capable of being synthesized is essentially

limitless. In practice, the synthesis of a preselected compound is made possible by
particular functional groups undergoing transformations that, while they are
dependent on the conditions applied to the compound, are largely independent of
the structure of the remaining part of the molecule. Thus, the combination of
knowledge of the structure of the compound to be synthesized and knowledge of
the general types of transformation that compounds undergo enables a synthesis to
be planned. The general approach, cut to its barest essentials, is to examine the
structure of the desired end productfor example, Zand to deduce the structure
of some (slightly simpler) compoundfor example, Ythat should be capable of
transformation into Z by a reaction of known type. A possible precursor of Y is
sought in similar manner, and in this way the chain of compounds is extended
until a compound, A, is reached that is available for the work; the necessary
transformations, beginning with A and ending with Z, are then carried out. Most
individual steps in the sequence result in a change in only one bond; some result
in changes in two bonds at a time, but it is unusual for more extensive changes to
occur.
Evaluation of a synthetic method

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

The product of a synthesis is normally contaminated with reagents used in the

synthesis, by-products, and possibly some unchanged starting material; these
contaminants must be removed in order for a pure product to be obtained. In a
multistep synthesis, it is normally desirable to purify the product from each step
before proceeding to the next. For more information about the various techniques
for isolation and purification, see separation and purification.