Chapter 27 - Organic Chemistry Beyond nomenclature. Much of the discussion that we have had about the nomenclature of organic compounds is either directly in section 27.1 of the textbook or scattered throughout the rest of the chapter (or in the remainder of the first note package which I would recommend reading!). For the remainder of the course, the assumption is that you both know and understand nomenclature and we will not be addressing the topic directly again.
27.3 Alkanes The essential characteristic of alkanes is that they are all saturated - giving the general chemical formula of: C n H 2n+2 All of the members of the series of alkanes have slightly different but closely related chemical and physical properties. For example, intermolecular attractions between the straight-chain molecules are strongest and they have the highest boiling points. (see Table 27.3)
Conformations: The presence of single bonds between the carbon atoms means that alkanes can bend and fold into a variety of conformations. One of the most important considerations is rotation around the C-C bond which leads to two distinct geometries:
Energetically, the eclipsed is less stable than the staggered. This is because the hydrogen atoms are forced together causing repulsion. All things being equal, an alkane will adopt a staggered geometry. Further, it will arrange the bulkiest groups to lie on opposite sides of the single bond.
Ring Structures: With cycloalkanes, different arrangements of the rings are possible for rings with more than five carbons. (A cyclopropane is planar by definition and a cyclobutane has only one geometry possible.)
For cyclohexane, this leads to two conformations called the "boat" and the "chair" conformation:
Preparation of Alkanes: 1) The chief source is petroleum (which ultimately comes from living organisms). The alkanes are separated using "fractional distillation" within a refinery. 2) They can also be made by the hydrogenation of olefins (the addition of H 2 across a double bond in the presence of a catalyst such as platinum metal) and by the combination of smaller alkyl halides such as: 2CH 3 CH 2 Br + 2Na 2NaBr + CH 3 CH 2 CH 2 CH 3
or by the fusion of the salt of a carboxylic acid with an alkali metal hydroxide: Note that this is a chain shortening reaction. That is, the resulting alkane is one atom shorter than the initial acid.
Reactions of Alkanes: Because they are saturated, alkanes are not very reactive. The most obvious reaction, however, is the combustion of alkanes with oxygen: i.e. C 5 H 12 + 8O 2 5CO 2 + 6H 2 O Less common is the reaction with platinum to form alkenes and the light-initiated free radical insertion of a halogen onto the alkane chain.
for example: CH 3 CH 3 CH 2 =CH 2 + H 2 (using a Pt or other metal catalyst) and: CH 3 CH 3 + Cl 2 CH 3 CH 2 Cl + HCl (using heat or light to initiate the reaction) The difficulty with the latter reaction is that it is very nonspecific and can easily lead to other products - such as longer chains and molecules with multiple chlorines.
Alkanes from Petroleum The petrochemical industry is a subset of the petroleum industry as a whole. It is an important source, however, for hydrocarbons. Most of these end up as "fuel":
but some are used for other purposes. However, it is the lack of reactivity of saturated hydrocarbons that make them poor feedstocks for other chemical processes. Invariably, these compound must be subject to some form of transformation to generate a functional group before they can be processed to other useful compounds. Much of the machinery at a petroleum refinery is dedicated to such transformations. One of the most common is the conversion to an alkene.
27.3 Alkenes and Alkynes "Unsaturation" leads to a general chemical formula for alkenes of: C n H 2n for compounds with a single double bond. Further unsaturation reduces the number of hydrogens. For example, consider the chemical formula for coal: C 135 H 96 O 9 NS The low hydrogen-to-carbon ratio implies a great deal of unsaturation which is observed in the structure of coal.
Geometric Isomerism The cis/trans designation of double bonds is an important aspect of the chemistry of alkenes but it is not applicable to alkynes. Geometric isomerization is only one aspect of the whole question of stereoisomerism or stereochemistry. The number and types of atoms and bonds in stereoisomers are the same but the spatial orientation varies. Recall that the consequence is that a number of structures are possible for any given compound.
Preparations of Alkenes/Alkynes: Predominantly, this is achieved by elimination reactions. These fall into two broad classes: The first is the catalytic removal of hydrogen which we have already discussed for the reactivity of alkanes. The second is the elimination of functional groups such as the dehydration of alcohols: CH 3 CH 2 CH 2 OH CH 3 CH=CH 2 + H 2 O Addition of conc. H 2 SO 4 is sufficient to remove water.
Alkynes are mostly derived by either further elimination of hydrogen from an alkene: CH 3 CH=CH 2 CH 3 C CH + H 2 or by addition of acetylene which is produced through the carbide reaction: CaCO 3 CaO + CO 2 CaO + 3C CaC 2 + CO and: CaC 2 + 2H 2 O HC CH + Ca(OH) 2 further reactions take advantage of the acidic protons
That is, HC CH can be readily transformed to HC C - and reacted: HC C - + CH 3 CH 2 Br HC CCH 2 CH 3 + Br - further, the remaining proton is still sufficiently acidic that the triple bond can be positioned at any point in any chain: CH 3 CH 2 C CH + NaNH 2 CH 3 CH 2 C C - Na + + NH 3 CH 3 CH 2 C C - Na + + CH 3 CH 2 Br CH 3 CH 2 C CCH 2 CH 3 + NaBr
Reactions of Alkenes and Alkynes: Two reactions dominate the use of alkenes and of alkynes. The first is the polymerization of ethylene (proper name is "ethene") to make polyethylene. CH 2 =CH 2 + CH 2 =CH 2 "-CH 2 -CH 2 -CH 2 -CH 2 -" The second is the conversion of acetylene to 1,2- dichloroacetylene (proper name: 1,2-dichloroethene) which is then polymerized to give PVC or polyvinyl chloride.
Addition Reactions: Alkenes and Alkynes can also react by addition reactions in which two new groups are added "across the double bond": CH 2 =CH 2 + Br 2 Br-CH 2 CH 2 -Br or: CH 2 =CH 2 + HCl H-CH 2 CH 2 -Cl
When an unsymmetical reactant (HX, HOH, HOSO 3 H) is added to an unsymmetrical alkene or alkyne, the more positive fragment (usually the H + ) adds to the carbon atom with the greatest number of attached H atoms under normal conditions. This is called "Markovnikov's Rule". It is generally true except under exceptional circumstances. Hence,
Addition to alkynes also follows Markovnikov's Rule: Br CH 3 C CH + HBr CH 3 C=CH 2 Note that, in the absence of a suitable catalyst, the addition reaction will lead to both the "cis" and the "trans" products (where possible). But with a suitable catalyst, the hydrogenation of an alkyne to an alkene can be made "stereospecific": Lindlar's catalyst ö cis-product Sodium in liquid ammonia catalyst ö trans-product
27.4 Aromatic Hydrocarbons Characteristic features of Aromatic Hydrocarbons: - they are all planar (flat), cyclic molecules - they all have a conjugated π-bonding system The first is a consequence of the second. The odd number of double bonds in the ring ensure a conjugated and planar π-bonding system. All have (4n+2)πelectrons. To be aromatic, the molecules must be cyclic.
Naming Aromatic Hydrocarbons: One additional note on the nomenclature. Although aromatic compounds can be named with the conventional numbering scheme, the terms "ortho", "para", and "meta" are also used: where the symbols "o","m", and "p" stand for ortho, meta, and para, respectively.
Aromatic Substitution Reactions: Unlike the alkenes and alkynes, aromatic substitution does not lead to addition of groups across a double bond. Rather, there is substitution of the functional group for one of the hydrogens in the compound. For benzene, this results in the formation of a substituted benzene compound. But the presence of a substituent on the ring controls the position of subsequent substitutions.
There is a great deal of chemistry here that we will not explore further. Suffice it to say that it is covered in more advance courses in much greater detail.
25.5 Alcohols, Phenols, and Ethers Alcohols and Phenols are all characterized by the presence of the hydroxy functional group - by "-OH":
Compounds with more than one alcohol group are referred to as "diols" or "triols": In all cases, the physical and chemical properties of the compounds are strongly influenced or controlled by the presence of the hydroxy group - which bears a strong resemblance to "water". The larger the organic portion, though, the less like water the compound becomes. The more hydroxy's, the more soluble a compound is.
Preparation of Alcohols: Three methods are generally used: Fermentation - biologically controlled conversion of sugar compounds to simpler alcohols. Hydration of alkenes: OH CH 3 CH=CH 2 + H 2 O CH 3 CH-CH 3 Hydrolysis of alkyl halides: CH 3 CH 2 CH 2 Cl + H 2 O CH 3 CH 2 CH 2 OH + HCl
Ethers are compounds with an R-O-R' group and are structurally similar to the alcohols. That is, an alcohol can be thought of as just a "special" case of an ether where R' = H. Ethers can be "symmetric" or "unsymmetric":
Preparation and Reactivity of Ethers: Preparation of symmetrical ethers can be achieved through the use of a simple dehydrating agent (i.e. conc. H 2 SO 4 ) and the corresponding alcohol: CH 3 CH 2 OH + HOCH 2 CH 3 CH 3 CH 2 OCH 2 CH 3 + H 2 O Unsymmetrical ethers require making the "alkoxide" first and then reacting that with an alkyl halide: CH 3 CH 2 OH + Na CH 3 CH 2 O - Na + + ½H 2 (g) CH 3 CH 2 O - Na + + CH 3 Br CH 3 CH 2 OCH 3 + NaBr
Ethers are very unreactive compounds. They do not react with most oxidizing or reducing agents nor with dilute acids or bases. It is this "inertness" that allows diethyl ether to be used as an "anesthetic" as the compound displaces air in the lungs (causing the patient to lapse into unconsciousness) but does not react with any of the constituents found there.
27.6 Aldehydes and Ketones Aldehydes and ketones all contain the carbonyl functional group: If one of the R-groups is "H", then it is an aldehyde, otherwise it is a ketone.
Preparation of Aldehydes and Ketones: Aldehydes and ketones can generally be generated by the oxidation of the corresponding alcohol: Oxidation of a primary alcohol: CH 3 CH 2 CH 2 OH O CH 3 CH 2 CH 1-propanol propanal Oxidation of a secondary alcohol:
However, in the case of aldehydes, the oxidation will continue to the corresponding carboxylic acid if a strong oxidizing agent is used (i.e. KMnO 4 or Cr 2 O 7 2- ) A number of milder oxidizing agents have been discovered/formulated that "stop" at the formation of the aldehyde. For example, PCC or pyridinium chlorochromate will result in only the aldehyde: PCC CH 3 (CH 2 ) 6 CH 2 OH CH 3 (CH 2 ) 6 CHO
Ketones and Aldehydes occur in a number of natural compounds: But probably some of the most important are the simple sugars (which also contain alcohol groups):
Addition Reactions of the Carbonyl Groups in Ketones and Aldehydes: Like the double bond in an alkene, the double bond of the carbonyl group is susceptible to attack through an addition reaction. That is, any HX,HOH, or HOSO 3 H type species can add across the double bond with the hydrogen bonding to the oxygen. In addition, ketones can be reduced to a secondary alcohol by sodium borohydride (NaBH 4 ) or other reagents.
The big difference between a "double bond" and a "carbonyl" is that C=O is "polarized" with a slight positive charge on the carbon and a slight negative charge on the oxygen. These are designated "δ+" and "δ-", respectively, and they orient incoming groups such that the negative ion will attack the carbon: This molecule is called a "cyanohydrin" and it increases the length of the organic chain by one carbon.
27.7 Carboxylic Acids and Their Derivatives The carboxylic group is the organic acid group that we have touched on in acid/base chemistry. It results from the almost complete oxidation of a carbon atom. All carboxylic acids have the general formula "R-COOH":
Because the carboxylic acid is the most important functional group in naming a compound, it is always numbered "1". In addition, another system for designating the carbon chain has been developed for substituents attached to acids:
Oxidation of a primary alcohol with a strong oxidizing agent (such MnO 4- or Cr 2 O 7 2- ) will result in the formation of the acid: MnO 4- /OH - H + CH 3 CH 2 OH CH 3 COO - K + CH 3 COOH Cr 2 O 7 2- /H + CH 3 CH 2 CH 2 OH CH 3 CH 2 COOH
One minor nomenclature note: The group: is a common substituent and is called the "acetyl" group. It can take the place of the hydrogen in any number of hydroxy compounds - for example, salicylic acid:
The carboxylic acid group displays both the chemistry of the carbonyl group and the hydroxy group. There are a number of compounds or derivatives that can be readily formed from this functional group. But the carboxylic acids themselves have a rich chemistry. In particular, the "fatty acids" show up in a number of areas. For example, soap is typically a sodium or potassium salt of a long chain fatty acid. It is made by cleaving naturally occurring esters.
Formation of Esters (Reactions of carboxylic acids): The reaction of an alcohol with a carboxylic acid is an ester: The reaction is called a "condensation" reaction because it results from condensing water from between the two molecules. This reaction can be driven by any dehydrating agent, such as conc. H 2 SO 4 or P 4 O 10.
The reaction is reversible. That is, in the presence of aqueous base, the ester is cleaved to regenerate the alcohol and the acid (as its salt). This is the reaction is called "saponification" and is used to make soap from fat:
Formation of amides (Reactions of carboxylic acids): The addition of nitrogen to a carboxylic acid can result in the replacement of the -OH group giving an "amide": Like esters, amides can be hydrolyzed back to the carboxylic acid. Note that the -NH 2 might be -NR 2.
Reduction of Carboxylic Acids, Esters, and Amides: Just as the acids are the product of oxidation of alcohols, they can be reduced by a strong reducing agent such as Lithium Aluminum Hydride (LAH) back to simpler groups:
27.8 Amines The amines are a class of organic compounds that are similar to the alcohols - but with "-NH 2 " instead of "-OH". They have similar physical properties being generally soluble in water. They also have distinctive odours. Like alcohols, amines can be classified:
Preparation of Amines: One method that we have just seen is from the amide but the "best" method is from the reduction of the corresponding nitro compound: An alternative method involves the reaction of ammonia with an alkyl halide: CH 3 Br + NH 3 CH 3 NH 3 + Br -
The resulting salt can react with any excess ammonia to give the amine and ammonium bromide: CH 3 NH 3+ Br - + NH 3 CH 3 NH 2 + NH 4+ Br - but this is complicated by the possibility of a further reaction of the resulting amine with the alkyl halide: to give more complicated and unwanted products. The reaction needs to be carefully controlled to make just the primary amine.
Amines can be used to make amides - and in the case of amino acids, this provides the backbone or peptide linkages that result in the formation of proteins. But there are any number of other important organic amine compounds in the body - particularly in the brain. Two examples: Ephedrine
27.10 Nomenclature of Stereoisomers in Organic compounds Cis/trans isomerism is one example of stereoisomerism but there are other possibilities. One of the most important is the concept of "chirality" or handedness. Two non-superimposable mirror images are possible with some organic compounds. That is, some compounds occur in a "left handed" and "right handed" version. Whether or not a compound is "chiral" depends upon whether or not it contains at least one "chiral carbon".
A "chiral carbon" is a carbon with four different groups attached to it. For example: In the above compounds, only those with four unique groups are chiral carbons. This does not mean that the four groups must be substituents other than carbon!
Consider 3-methylhexane: CH 3 CH 3 CH 2 CHCH 2 CH 2 CH 3 although it contains nothing but carbon, it exists in two chiral or "stereochemically inequivalent" forms:
A pair of compounds that are mirror images are called "enantiomers". (Compounds that are stereoisomers but not mirror images are called "diastereomers".) Enantiomeric pairs of compounds are designated with either a "+/-" system or an "R/S" system (and sometimes both!):
The R/S system requires that we rank the groups in order of priority and then determine either a "clockwise" (R) or "counterclockwise" (S) rotation for the groups:
Rule #1. A substituent atom of higher atomic number takes precedence over one of lower atomic number. Hence, in 1-chloro-1-iodoethane:
Rule #2. If two substituent atoms attached to the chiral carbon have the same atomic number, then the more substituted substituent has higher priority. Note that this may require following a chain of carbon atoms away from the chiral carbon until we reach the "point of difference" and then determining which has higher priority. Rule #3. Double and triple bonds lead to high priority as the atoms attached are counted "twice" or "thrice", respectively.
The rules read as a little more complicated than actually determining the chirality. The best practice is to try the examples in the textbook (Example 27-6 and problems 81 to 84.) We will not pursue the "E" and "Z" nomenclature for alkenes - which is a way to describe alkenes with multiple substituents attached to the double bond using a similar system of giving groups priority.
27.11 An Introduction to Substitution Reactions at sp 3 -Hybridized Carbon Atoms An sp 3 -hybridized carbon is a standard tetrahedral carbon centre (see your Chem 100 notes from Chap. 12 or the other note package for a more full explanation).
In the section on the reaction of alkanes, we saw that we could replace a hydrogen in methane by chlorine using "photolysis": hν CH 4 + Cl 2 CH 3 Cl + HCl This is a "substitution" as the chlorine atom replaces the hydrogen atom. It is a special kind of substitution called "photolytic substitution" and we shall not dwell upon it here except to note that it produces an alkyl halide.
More generally, an example of a replacement reaction is the substitution of -OH for -Cl: CH 3 Cl + OH - CH 3 OH + Cl - This type of reaction is called a "nucleophilic substitution reaction" where the term "nucleophile" means "nucleus loving" and is applied to a group that seeks a positively charged carbon atom. This goes back to the "Lewis Acid/Base" definitions!! Any compound that we can describe as a "Lewis base" is a "nucleophile". In acid/base chemistry, the nucleus that the base seeks is the proton, H +.
This is also tied to the information in Chapter 12 about "bond polarity". Atoms that are electronegative draw electron density to themselves. Chlorine and oxygen, when attached to carbon, create polar bonds. We can designate this bond polarity with our "δ+" and "δ-" terms which imply only partial bond polarization. Hence, a nucleophile is a group with either a negative charge or a partial negative charge ("δ-") that is looking for a positively charged or partially positively charged ("δ+") centre. And vice versa for an "electrophile".
Substitution occurs when one nucleophile "pushes" out another:
The S N2 and S N1 Mechanisms of Nucleophilic Substitution Reactions: Kinetics can be used to show that the substitution reaction of a nucleophile into an organic compound can proceed by two different pathways. (The rate laws for these pathways are different.) The first mechanism (S N2 ) is an example of a concerted mechanism in which substitution by one group forces the leaving group to fall off. The second mechanism (S N1 ) results from an initial reaction in which the leaving group departs prior to the addition of the incoming nucleophile.
S N2 :
S N1 :
One of the most important differences between these two reactions is that S N2 results in the retention of chirality at the chiral carbon. That is, since the leaving group does not leave until the nucleophile attacks, there is only one place where that attack can occur. This means that the resulting compound will be only one of the possible stereoisomers:
For an S N1 reaction, the intermediate is a carbon with only three bonds and the incoming nucleophile is free to pick which side it will attack. This will result in the formation of a racemic mixture - an equal mixture of both stereoisomers or of R and S:
27.12 Synthesis of Organic Compounds Originally, all organic compounds were derived from living matter - from plants, trees, and animals. However, in 1828, Friedrich Wöhler was able to show that urea could be synthesized from Ammonium cyanate: AgOCN (s) + NH 4 Cl (aq) AgCl (s) + (NH 2 ) 2 C=O Since then, the transformation of organic compounds or, more accurately, functional groups, into one another has been a huge part of chemistry. We have barely scratched the surface! But Figure 27-16 tries to sum it all up:
and that is a good place to stop!