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| Unit 7
Alcohols & Thiols
Synthesis, Structure & Reactions
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Overview
If, as an organic chemist, you
were allowed to choose the ten aliphatic compounds with which to be stranded on
a desert island, you would be strongly advised to pick all alcohols. This
choice would be based on
their wide spectrum of chemical versatility. Using them as precursors, you
could synthesize nearly every other kind of aliphatic compound: alkyl
halides, alkenes, ethers, aldehydes, ketones, acids, esters, as well as many
others.
From the alkyl halides, you could
make Grignard reagents, and from the reaction between these and the aldehydes
and ketones obtain more complicated alcohols, and so on. On your desert island,
you could use your alcohols not only as raw materials, but frequently as the
solvents in which reactions are carried out and from which products are
re-crystallized. Finally, hot and tired after a long day in the tropical
laboratory, you could refresh yourself with an (isopropyl) alcohol rub and
perhaps relax over a cool (ethyl) alcohol drink.
Alcohols are organic compounds
that contain the hydroxyl group (-OH) as their functional group which determines
the properties characteristic of the family. The general
formula for an alcohol is R-OH, where R is any kind of alkyl
group. The group may be primary, secondary or tertiary. It may be open
chain, alicyclic or aromatic. Compounds in which the hydroxyl group is attached
directly to an aromatic ring are not alcohols. Rather, they are phenols, and
differ so markedly from the alcohols in their chemical behavior that we shall
consider them separately.
Nomenclature
Alcohols are named by two
principal systems. For the simpler alcohols, the common names are most often
used. A common name consists simply of the alkyl group followed by the word
alcohol. In the following table, all but eight alcohols are named by their
common names.

According to the IUPAC
system of naming, the basic 3 rules are as follows:
1) Select as the parent
structure the longest continuous carbon chain that contains the OH group. Then
consider the compound to have been derived form this structure by replacement of
hydrogen by various groups. The parent structure is known as ethanol,
propanol, butanol, etc. depending upon the number of carbon atoms. Each name
is derived by replacing the terminal "-e" of the corresponding alkane
name by the suffix "-ol".
2) Indicate by a whole
number the position of the OH group in the parent chain, generally using the
lowest possible number for this purpose.
3) Indicate by numbers the
positions of other groups attached to the parent chain.
Industrial Sources
For alcohols to be such important
starting materials in aliphatic chemistry, they must not only be versatile in
their reactions but also available in large quantities at low prices. There are
three principal ways to get the simple alcohols that re the backbone of
aliphatic organic synthesis. These three methods can utilize all our sources of
organic raw material - petroleum, natural gas, coal, and the biomass. These
methods are:
1) Hydration
of alkenes obtained from cracking
of complex petroleum
(fractions of distilled crude oil) hydrocarbons into simpler molecules. This
method requires a catalyst of phosphoric
acid under high temperature and pressure.
2) By the "oxo"
process from alkenes, carbon monoxide and hydrogen. This involves alkene
precursors (obtained from cracking) engaged in a sulfuric acid-catalyzed
hydration reaction. The reaction typically yields secondary or tertiary alcohols
(e.g. RCHOHCH3)
3) Anaerobic
fermentation of carbohydrates, or the conversion of sugar molecules into
ethanol and carbon dioxide by yeast. E.G. Using glucose produced from sugars
(from the hydrolysis of molasses, sugar cane or starch). The sugar reacts in the
presence of yeast at temperatures below 37 °C in
order to produce ethanol.
...... as well as other methods (see figure) which have more limited
application.

Physical Properties
Structurally, an alcohol is a
composite of an alkane and water. Thus, it contains an alkane-like alkyl
group and a water0like hydroxyl group. It is clearly the OH functional group that
gives alcohol its characteristic physical properties, and the alkyl group that,
depending on its size and shape, modifies these properties.
Alcohols are among the most
polar organic compounds because the hydroxyl OH group is strongly polar and (because the H
atom is bonded to the highly electronegative O atom) can easily
participate in hydrogen bonding. Thus, the simplest alcohols (e.g. methyl
alcohol or methanol, ethyl alcohol or ethanol) are completely miscible in
water.
Ethyl alcohol is sometimes called "grain alcohol" because it is
produced by the fermentation of grain or other organic material. Isopropyl
alcohol is the common name for 2-propanol, used as rubbing alcohol.
Two opposing solubility trends in
alcohols are: the tendency of the polar OH to promote solubility in water, and
of the carbon chain to resist it and thus limit the solubility in
water. Thus, methanol, ethanol, and propanol are
miscible in water because the hydroxyl group wins out over the short carbon
chain. Butanol,
with a four-carbon chain, is moderately soluble because of a balance between the
two trends. Alcohols of five or more carbons (pentanol and higher) are effectively insoluble because of the hydrocarbon chain's
dominance.
Alcohols, like water, are associated
liquids. Thus, due to hydrogen
bonding, alcohols tend to have higher boiling points than comparable
hydrocarbons and ethers.
The boiling point of the ethanol is 80 °C, compared to 70 °C for the n-Hexane
(a common constituents of gasoline),
and 35 °C for Diethyl
ether. The lone pairs of electrons on the oxygen of the hydroxyl group also
makes alcohols medium strength nucleophiles.
Alcohols, like water, can show either acidic or
basic properties at the OH group. Due to potential cleavage of the
O-H bond, alcohols can behave as Lewis acids by losing a proton. With an acid
dissociation constant (pKa) of 16-19, they are generally slightly
less acidic than water. But they are still able to react with strong bases such
as sodium
hydride or reactive metals such as sodium.
The resulting salt is called an alkoxide
(the conjugate
base of an alcohol) with the general formula ROM (Alkyl group R,
Oxygen O, Metal M).
Meanwhile the oxygen O atom has lone
pairs of non-bonding electrons that render it weakly basic in the presence
of strong acids such as sulfuric
acid. For example, with methanol:

Alcohols can also undergo oxidation
to give aldehydes, ketones
or carboxylic
acids. They can also be dehydrated to alkenes.
In addition, they can react to form ester
compounds, and they can also (if activated first) undergo nucleophilic
substitution reactions.
Reactions
The chemical properties of an alcohol, ROH, are
determined by its functional group, OH. Much of what we learn here about
reactions in alcohols will apply similarly to other OH-bearing hydrocarbon
compounds, such as the hydroxy halides, hydroxy acids, hydroxy aldehydes,
etc.
Reactions of an alcohol can involve the
cleavage of either of two bonds:
1) The R-OH bond, with removal of the OH group
2) The O-H bond, with removal of the H atom.
Either type of reaction can involve:
1) Substitution -- in which a group replaces
the OH group or the H atom
2) Elimination -- in which a double
bond is formed.
Difference in the structure of the alkyl
group R may cause differences in reactivity, and possibly even alter the course
of the reaction.
I. Acid-Base Reactions
Of the varied chemical properties of alcohols,
the most fundamental is their role as an acid or base. Like their
familiar structural relative water, alcohols are weak acids and weak bases.
It is oxygen, with its unshared
electron pairs, that gives an alcohol its basic properties. Like
water, alcohols are basic enough to accept a proton from strong acids (e.g. HCl
and H2SO4)
and thus bring about complete dissociation of these acids. For example:
ROH
+ H2SO4
= (ROH2)+
+ (HSO4)-
In alcohols, the H atom is bonded
to the highly electronegative O atom. The polarity of the O-H bond facilitates
the release of a proton. I.E. the electronegative O atom readily accommodates
the residual negative charge of free or non-bonded electrons.
The acidity of alcohols is
illustrated by their reaction with active metals to form metallic salts and
liberate hydrogen gas. The products are called alkoxides
-- with the general formula: ROM (Alkyl group R, Oxygen O, Metal M).

Relative acidity is measured by
the ability of a compound to displace another from its salt. Thus, when
water is added to the above alkoxide, there is obtained sodium hydroxide and the
parent alcohol. The weaker acid, R-OH, is displaced from its salt by the
stronger acid, HO-H. In other words, the stronger base, RO-, pulls the proton
away form the weaker base, HO-. Thus, if RO- holds the proton more tightly than
OH-, then RO-H must be a weaker acid than HO-H.
Like water and ammonia, alcohols
are much stronger acids than alkanes, and readily displace them from their salts
(e.g. Grignard reagents) as follows:
ROH + R' Mg X
= R'H + Mg (OR) X
We can thus place alcohols
in a sequence of relative acidity values to other familiar hydrocarbon
compounds. This sequence would (naturally) be the same as the order of basicity
for the corresponding conjugate bases.
Relative
acidity:
H2O
> ROH > NH3
> RH
Relative
basicity:
OH- < OR-
< NH2-
< R-
It is certainly worth commenting
here on the influence of the alkyl group R, especially as this is what
distinguishes the alcohol from water. Not only does the alkyl group make
an alcohol less acidic than water, but the bigger the alkyl
group, the less acidic the alcohol. Thus, methanol is the strongest in acidity
and the tertiary
alcohols are the weakest.
Since an alcohol is a weaker acid
than water, an alkoxide is not prepared by the reaction of the alcohol with
sodium hydroxide, but rather by the reaction of the alcohol with the
active
metal itself. Alkoxides are extremely useful as powerful bases (stronger than
hydroxide) and, by varying the alkyl group R, we can vary their degree of
basicity, their steric requirements, and their solubility properties. As
nucleophiles, they can be used to introduce the
alkoxy (RO) group into molecules.
II. Halogenation by SN1
While the acidity of alcohols
clearly involves the cleavage of the O-H bond, other reactions clearly
involve the cleavage of the R-OH bond. One method of making alkyl halides
is by the reaction of alcohols with hydrogen halides via nucleophilic
substitution.

In this inherently sluggish reaction, the
OH
makes a very poor leaving group without heating the alcohol in the presence of
concentrated aqueous acid, thus protonating the OH group to OH2+.
The least reactive of the hydrogen halides, HCl, generally requires the presence
of zinc chloride for reaction with primary and secondary alcohols.
Alternatively, the highly reactive tert-butyl alcohol is converted to the
chloride by simple mechanical agitation with concentrated HCl at room
temperature.
The facts about this reaction include 1) acid
catalysis, 2) rearrangement of alkyl groups, and 3) order of reactivity
of
alcohols (as listed above). These facts lead us to speculate on the mechanism
of reaction as that of a typical nucleophilic SN1
type reaction -- with the protonated alcohol as the substrate and the
halide ion as the nucleophile.

Primary alcohols do not undergo
rearrangement, and therefore do not react by this mechanism. Instead, they react
by the alternative SN2
mechanism.

SN1 vs. SN2
Let us review what is likely happening here.
The methyl substrate is least capable of heterolysis
and most open to nucleophilic attack. It thus reacts by a full-fledged SN2
reaction. Due to greater steric hindrance, primary substrates react less rapidly
than the methyl substrate by the same SN2 mechanism. Secondary substrates give
even more steric hindrance, but are more capable of forming carbo-cations. For
them heterolysis is faster than nucleophilic attack by a halide ion, and the
mechanism changes here to SN1. Accompanying the change in mechanism is a rise in
reaction rate. Tertiary substrates, too, react by an SN1 mechanism. They react
faster than secondary substrates because of the greater dispersal of charge in
the incipient hydrocarbons.
III. Dehydration
An alcohol is converted into an alkane by the
process of dehydration -- or elimination of a molecule of water. Dehydration
requires the presence of an acid and the application of heat.

For dehydration of secondary and tertiary
alcohols, the following reaction mechanism is generally accepted. Step
(1) is a fast acid-base reaction between the alcohol and the acid catalyst,
which yields the protonated alcohol and the conjugate base of the acid. In step
(2) the protonated alcohol undergoes heterolysis in order to form the
carbo-cation and water. In step (3) the carbo-cation loses a proton to the base
to yield the alkene.



The fact the the dehydration reaction must be acid-catalyzed
supports the reaction mechanism proposed in step (1). Thus, acid is necessary
ion order to convert the alcohol into the protonated alcohol, which can then
undergo heterolysis in order to lose the weakly basic water molecule. I.E. the
acid transforms the very poor OH leaving group into the very good OH2+ leaving
group.
It is worth noting here that this dehydration
is a completely reversible reaction. On this basis, dehydration of
alcohols must involve precisely the same steps (in reverse order) that are
involved in the hydration of alkenes. Indeed, the experimental evidence supports
this conclusion.
Regarding the order of reactivity (or
ease of dehydration), there is evidence that the rate of reaction depends both
upon step (2), formatio0n of a carbocation, and step (3), its loss of a proton.
Tertiary alcohols undergo dehydration the most rapidly because they form the
most stable carbocations. Once formed, those cations yield the most stable
alkenes.
IV. Oxidation
The oxidation of an alcohol involves the loss
of one or more (alpha) hydrogens from the carbon-bearing OH group. The type
product formed depends upon how many of these (alpha) hydrogens the alcohol
contains -- that is, whether the alcohol is primary, secondary, or tertiary.
A primary alcohol contains two (alpha)
hydrogens, and can lose one of them to form an aldehyde
or both of them to form a carboxylic
acid. A secondary alcohol can lose its only (alpha) hydrogen
to form a ketone. A tertiary
alcohol contains no (alpha) hydrogens and is not oxidized.

These oxidation products - aldehydes, ketones
and carboxylic acids - are extremely important to us, and at this point we need
only to learn to recognize their structures. Their preparation by the
oxidation of alcohols is an essential part of organic synthesis.
The number of oxidizing
agents available to the organic chemist is growing at a tremendous rate. As
with all synthetic methods, emphasis is on the development of highly selective
reagents which will operate on only one functional group at a time in a complex
molecule, and leave the other functional groups untouched.
Traditionally, strong oxidants such as the
anions present in potassium
dichromate K2Cr2O7, or potassium
permanganate KMnO4
are used, under acidic conditions. These are the most common sources of
the strongly oxidizing Mn (VII) and Cr (VI) ions.
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Thiols
A thiol is a compound that
contains the functional group composed of a sulfur atom and a
hydrogen atom (-SH). This functional group is
referred to either as a thiol group or a
sulfhydryl group. More traditionally, thiols are often
referred to as mercaptans. In general, the
deprotonated form RS− (called a
thiolate) is more chemically reactive than the
protonated thiol form RSH.
The thiol group is the sulfur
analog of the
hydroxyl group (-OH) found in alcohols. Since sulfur and
oxygen belong to the same periodic table group, they share some
similar chemical bonding properties. The chemistry of thiols is
thus related to the chemistry of alcohols. Thiols form
thioethers,
thioacetals and
thioesters, which are analogous to
ethers,
acetals, and
esters. Furthermore, a thiol group can react with an alkene
to create a thioether. (In fact, biochemically, thiol groups may
react with
vinyl groups to form a
thioether linkage.)
Chemical & Physical Properties
The sulfur atom of a thiol is
quite nucleophilic, rather more so than the oxygen atom of an
alcohol. The thiol group is fairly acidic with a usual pKa
around 10 to 11. In the presence of a base, a thiolate anion is
formed which is a very powerful nucleophile. The group and its
corresponding anion are readily oxidized by reagents such as
bromine to give an organic
disulfide (R-S-S-R), or by more powerful reagents such as
sodium hypochlorite to yield
sulfonic acids (RSO3H).
Because of the small
electronegativity difference between sulfur and hydrogen, an S-H
bond is practically non-polar covalent. Thiols show little
association by
hydrogen bonding. They have lower boiling points and are
less soluble in water and other polar solvents than alcohols of
similar molecular weight.
Many thiols are colorless
liquids having an odor resembling that of garlic. The odor of
thiols is often strong and repulsive, particularly for those of
low molecular weight. Thiols bind strongly to skin
proteins, and are responsible for the intolerable,
persistent odor produced by feces, rotting flesh and the
spraying of skunks.
Natural gas distributors began adding various forms of
pungent thiols, usually
ethanethiol, to natural gas, which is naturally odorless,
after the deadly 1937 New London School explosion in New London,
Texas. Thiols are also responsible for a class of wine faults
caused by an unintended reaction between sulfur and
yeast. However, not all thiols have unpleasant odors. For
example, grapefruit mercaptan, a
monoterpenoid thiol, is responsible for the characteristic
scent of grapefruit.
A major difference
between alcohols and thiols concerns their oxidation.
We have seen now that oxidation of alcohols produces carbonyl
compounds. Analogous oxidation of thiols to compounds with C=S
functions does not occur. In thiols, only sulfur is oxidized --
not carbon. Thus, compounds containing sulfur in various
oxidation states are possible. These include a series of
acids classified as
sulfenic (-SOH),
sulfinic (-SOOH), and
sulfonic (-SO2OH)
according to the number of oxygen atoms attached to the sulfur
atom.
Biochemistry of Thiols
As the functional group of
cysteine (a naturally occurring amino acid found in most
proteins) the thiol group plays an important role in
biological systems. When the thiol groups of two cysteine
residues (as in monomers or constituent units) are brought near
each other in the course of
protein folding, an
oxidation reaction can create a
cystine unit with a
disulfide bond (-S-S-). Disulfide bonds can contribute to a
protein's
tertiary structure if the cystines are part of the same
peptide chain, or contribute to the
quaternary structure of multi-unit proteins by forming
fairly strong covalent bonds between different peptide chains.
The
heavy and
light chains of
antibodies are held together by disulfide bridges. Also, the
kinks in curly
hair
are a product of
cysteine formation.
Hair 'permanents' make use of
the oxidizability of cystine residues. The chemicals used for straightening
hair are
reductants that reduce cysteine disulfide bridges to free
cysteine sulfhydryl groups. Alternatively, the chemicals used
for curling
hair are
oxidants that oxidize cysteine sulfhydryl groups to form cysteine disulfide bridges. Sulfhydryl groups in the
active site of an
enzyme can form
non-covalent bonds with the enzyme's
substrate as well, contributing to
catalytic activity. Active site cysteine residues are the
functional unit in
cysteine proteases.
In many receptors
GPCR,
there may exist one or more free thiol groups that modulate the
receptor's activity toward drugs and endogenous ligands. These
free thiols may be in a redox equilibrium with their
surroundings so that they undergo
Thiol-disulfide exchange.
Nomenclature
When a thiol group is a
substituent on an
alkane, there are several ways of naming the resulting
thiol:
- The preferred method (used
by the
IUPAC) is to add the suffix -thiol to the name of
the alkane. E.G. CH3SH would be
methanethiol.
- An older method, the word
mercaptan replaces alcohol in the name of the
equivalent alcohol compound. E.G. CH3SH would
be methyl mercaptan.
- As a prefix, the term
mercapto- is used. Example:
mercaptopurine.
- It is also referred to
generically as a sulfhydryl group.