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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.