Organic Chemistry I

Introduction  -  Why is Carbon Special?

·        carbon has a very unusual ability --- it is capable of bonding strongly to itself to form long chains or complicated rings of carbon atoms or even buckyballs! Why is this? Carbon’s 2.5 electronegativity is too weak to pull electrons from other atoms and too strong to relinquish its own. The result is strong covalent bonds.

                                                                                                             



                                                                                                           Buckyball C-60

·        additionally, carbon can form strong bonds to other non-metallic elements like oxygen, hydrogen, sulfur, nitrogen and the halogens.

·        of the 11 million compounds known to man, approximately 10 million of them contain carbon.

·        carbon forms the basis for most biomolecules, the molecules responsible for maintaining and reproducing life.

·        the study of carbon compounds and their properties is called Organic Chemistry (some carbon compounds, like the carbon oxides and carbonates are considered to be inorganic molecules).

·        organic molecules typically contain chains or rings of carbon atoms and can become quite complex.

Viagra

·        initially, the distinction between organic and inorganic compounds was that organic compounds were created by living organisms and inorganic compounds were not --- this idea was rejected after Friedrich Wöhler who prepared urea crystals (a carbon based, organic compound found in urine) by heating ammonium cyanate.

The increasingly large number of organic compounds identified with each passing day, together with the fact that many of these compounds are isomers of other compounds, requires that a systematic nomenclature system be developed. Just as each distinct compound has a unique molecular structure which can be designated by a structural formula, each compound must be given a characteristic and unique name.

A rational nomenclature system should do at least two things. First, it should indicate how the carbon atoms of a given compound are bonded together in a characteristic lattice of chains and rings. Second, it should identify and locate any functional groups present in the compound. Since hydrogen is such a common component of organic compounds, its amount and locations can be assumed from the tetravalency of carbon, and need not be specified in most cases.

The IUPAC nomenclature system is a set of logical rules devised and used by organic chemists to circumvent problems caused by arbitrary nomenclature. Knowing these rules and given a structural formula, one should be able to write a unique name for every distinct compound. Likewise, given a IUPAC name, one should be able to write a structural formula. In general, an IUPAC name will have three essential features:

•  A root or base indicating a major chain or ring of carbon atoms found in the molecular structure.
•  A suffix or other element(s) designating functional groups that may be present in the compound.
•  Names of substituent groups, other than hydrogen, that complete the molecular structure.

As an introduction to the IUPAC nomenclature system, we shall first consider compounds that have no specific functional groups. Such compounds are composed only of carbon and hydrogen atoms bonded together by sigma bonds (all carbons are sp³ hybridized).

Hydrocarbons having no double or triple bond functional groups are classified as alkanes or cycloalkanes, depending on whether the carbon atoms of the molecule are arranged only in chains or also in rings. Although these hydrocarbons have no functional groups, they constitute the framework on which functional groups are located in other classes of compounds, and provide an ideal starting point for studying and naming organic compounds

The following table lists the IUPAC names assigned to simple continuous-chain alkanes from C-1 to C-10. A common "ane" suffix identifies these compounds as alkanes. Longer chain alkanes are well known, and their names may be found in many reference and text books. The names methane through decane should be memorized, since they constitute the root of many IUPAC names. Fortunately, common numerical prefixes are used in naming chains of five or more carbon atoms.

Some important behavior trends and terminologies:

  (i)   The formulas and structures of these alkanes increase uniformally by a CH₂ increment.
 (ii)   A uniform variation of this kind in a series of compounds is called homologous.
(iii)   These formulas all fit the C_nH_2n+2 rule. This is also the highest possible H/C ratio for a stable hydrocarbon.
(iv)   Since the H/C ratio in these compounds is at a maximum, we call them saturated (with hydrogen) or with the maximum number of single bonds.

Beginning with butane (C₄H₁₀), and becoming more numerous with larger alkanes, we note the existence of alkane isomers. For example, there are five C₆H₁₄ isomers, shown below as line formulas (A through E):

Although these distinct compounds all have the same molecular formula, only one (A) can be called hexane. How then are we to name the others?

The IUPAC system requires first that we have names for simple unbranched chains, as noted above, and second that we have names for simple alkyl (C&H) groups that may be attached to the chains. Examples of some common alkyl groups are given in the following table. Note that the "ane" suffix is replaced by "yl" in naming groups. The symbol R is used to designate a generic (unspecified) alkyl group.

Halogen substituents are easily accomodated, using the names: fluoro (F-), chloro (Cl-), bromo (Br-) and iodo (I-). For example, (CH₃)₂CHCH₂CH₂Br would be named 1-bromo-3-methylbutane. If the halogen is bonded to a simple alkyl group an alternative "alkyl halide" name may be used. Thus, C₂H₅Cl may be named chloroethane (no locator number is needed for a two carbon chain) or ethyl chloride.

Illustration 1.

CH₃(CH₂)₂CH(CH₃)CH₂CH₃

When viewing a condensed formula of this kind, one must recognize that parentheses are used both to identify repeating units, such as the two methylene groups on the left side, and substituents, such as the methyl group on the right side. This formula is elaborated and named as follows:

The condensed formula is expanded on the left. By inspection, the longest chain is seen to consist of six carbons, so the root name of this compound will be hexane. A single methyl substituent (colored red) is present, so this compound is a methylhexane. The location of the methyl group must be specified, since there are two possible isomers of this kind. Note that if the methyl group were located at the end of the chain, the longest chain would have seven carbons and the root name would be heptane not hexane. To locate the substituent the hexane chain must be numbered consecutively, starting from the end nearest a substituent. In this case it is the right end of the chain, and the methyl group is located on carbon #3. The IUPAC name is thus: 3-methylhexane

Illustration 2.

(CH₃)₂C(C₂H₅)₂

Again, the condensed formula is expanded on the left, the longest chain is identified (five carbons) and substituents are located and named. Because of the symmetrical substitution pattern, it does not matter at which end of the chain the numbering begins.

When two or more identical substituents are present in a molecule, a numerical prefix (di, tri, tetra etc.) is used to designate their number. However, each substituent must be given an identifying location number. Thus, the above compound is correctly named: 3,3-dimethylpentane.
Note that the isomer (CH₃)₂CHCH₂CH(CH₃)₂ would be named 2,4-dimethylpentane.

Illustration 3.

(CH₃)₂CHCH₂CH(C₂H₅)C(CH₃)₃

This example illustrates some sub-rules of the IUPAC system that must be used in complex cases. The expanded and line formulas are shown below.

In this case several six-carbon chains can be identified. Some (colored blue) are identical in that they have the same number, kind and location of substituents. The IUPAC name derived from these chains will not change. Some (colored magenta) differ in the number, kind and location of substituents, and will result in a different name. From rule 1 above the blue chain is chosen, and it will be numbered from the right hand end by application of rule (i). Remembering the alphabetical priority, we assign the following IUPAC name: 3-ethyl-2,2,5-trimethylhexane.

Illustration 4.

Write a structural formula for the compound 3,4-dichloro-4-ethyl-5-methylheptane.
First, we draw a chain of seven carbon atoms to represent the root name "heptane". This chain can be numbered from either end, since no substituents are yet attached. From the IUPAC name we know there are two chlorine, one ethyl and one methyl substituents. The numbers tell us where the substituents are located on the chain, so they can be attached, as shown in the middle structure below. Finally, hydrogen atoms are introduced to satisfy the tetravalency of carbon. The structural formula on the right can then be written in condensed form as: CH₃CH₂CHClCCl(C₂H₅)CH(CH₃)CH₂CH₃ or C₂H₅CHClCCl(C₂H₅)CH(CH₃)C₂H₅

In naming this compound it should be noted that the seven carbon chain is numbered from the end nearest the chlorine by applying rule (ii) above.

      Cycloalkanes have one or more rings of carbon atoms. The simplest examples of this class consist of a single, unsubstituted carbon ring, and these form a homologous series similar to the unbranched alkanes. The IUPAC names of the first five members of this series are given in the following table. The last (yellow shaded) column gives the general formula for a cycloalkane of any size. If a simple unbranched alkane is converted to a cycloalkane two hydrogen atoms, one from each end of the chain, must be lost. Hence the general formula for a cycloalkane composed of n carbons is C_nH_2n.

Examples of Simple Cycloalkanes

Name	Cyclopropane	Cyclobutane	Cyclopentane	Cyclohexane	Cycloheptane	Cycloalkane
Molecular Formula	C3H6	C4H8	C5H10	C6H12	C7H14	CnH2n
Structural Formula
Line Formula

Substituted cycloalkanes are named in a fashion very similar to that used for naming branched alkanes. The chief difference in the rules and procedures occurs in the numbering system. Since all the carbons of a ring are equivalent (a ring has no ends like a chain does), the numbering starts at a substituted ring atom.

Small rings, such as three and four membered rings, have significant angle strain resulting from the distortion of the sp³ carbon bond angles from the ideal 109.5º to 60º and 90º respectively. This angle strain often enhances the chemical reactivity of such compounds, leading to ring cleavage products. It is also important to recognize that, with the exception of cyclopropane, cycloalkyl rings are not planar (flat).

Functional groups are atoms or small groups of atoms (two to four) that exhibit a characteristic reactivity when treated with certain reagents. A particular functional group will almost always display its characteristic chemical behavior when it is present in a compound. Because of their importance in understanding organic chemistry, functional groups have characteristic names that often carry over in the naming of individual compounds incorporating specific groups. In the following table the atoms of each functional group are colored red and the characteristic IUPAC nomenclature suffix that denotes some (but not all) functional groups is also colored.

Group Formula	Class Name	Specific Example	IUPAC Name	Common Name
	Alkene	H2C=CH2	Ethene	Ethylene
	Alkyne	HC≡CH	Ethyne	Acetylene
	Arene	C6H6	Benzene	Benzene

Group Formula	Class Name	Specific Example	IUPAC Name	Common Name
	Halide	H3C-I	Iodomethane	Methyl iodide
	Alcohol	CH3CH2OH	Ethanol	Ethyl alcohol
	Ether	CH3CH2OCH2CH3	Diethyl ether	Ether
	Amine	H3C-NH2	Aminomethane	Methylamine
	Nitro Compound	H3C-NO2	Nitromethane
	Thiol	H3C-SH	Methanethiol	Methyl mercaptan
	Sulfide	H3C-S-CH3	Dimethyl sulfide

Group Formula	Class Name	Specific Example	IUPAC Name	Common Name
	Nitrile	H3C-CN	Ethanenitrile	Acetonitrile
	Aldehyde	H3CCHO	Ethanal	Acetaldehyde
	Ketone	H3CCOCH3	Propanone	Acetone
	Carboxylic Acid	H3CCO2H	Ethanoic Acid	Acetic acid
	Ester	H3CCO2CH2CH3	Ethyl ethanoate	Ethyl acetate
	Acid Halide	H3CCOCl	Ethanoyl chloride	Acetyl chloride
	Amide	H3CCON(CH3)2	N,N-Dimethylethanamide	N,N-Dimethylacetamide
	Acid Anhydride	(H3CCO)2O	Ethanoic anhydride	Acetic anhydride

Distinguishing Carbon Atoms
When discussing structural formulas, it is often useful to distinguish different groups of carbon atoms by their structural characteristics. A primary carbon (1º) is one that is bonded to no more than one other carbon atom. A secondary carbon (2º) is bonded to two other carbon atoms, and tertiary (3º) and quaternary (4º) carbon atoms are bonded respectively to three and four other carbons. The three C₅H₁₂ isomers shown below illustrate these terms.

Alkenes and alkynes are hydrocarbons which respectively have carbon-carbon double bond and carbon-carbon triple bond functional groups. The molecular formulas of these unsaturated hydrocarbons reflect the multiple bonding of the functional groups:

Expanding these formulas we have:

Both these compounds have double bonds, making them alkenes. In example (1) the longest chain consists of six carbons, so the root name of this compound will be hexene. Three methyl substituents (colored red) are present. Numbering the six-carbon chain begins at the end nearest the double bond (the left end), so the methyl groups are located on carbons 2 & 5. The IUPAC name is therefore: 2,5,5-trimethyl-2-hexene.
In example (2) the longest chain incorporating both carbon atoms of the double bond has a length of five. There is a seven-carbon chain, but it contains only one of the double bond carbon atoms. Consequently, the root name of this compound will be pentene. There is a propyl substituent on the inside double bond carbon atom (#2), so the IUPAC name is: 2-propyl-1-pentene.
 

The next two examples illustrate additional features of chain numbering. As customary, the root chain is colored blue and substituents are red.

The double bond in example (3) is located in the center of a six-carbon chain. The double bond would therefore have a locator number of 3 regardless of the end chosen to begin numbering. The right hand end is selected because it gives the lowest first-substituent number (2 for the methyl as compared with 3 for the ethyl if numbering were started from the left). The IUPAC name is assigned as shown.
Example (4) is a diene (two double bonds). Both double bonds must be contained in the longest chain, which is therefore five- rather than six-carbons in length. The second and fourth carbons of this 1,4-pentadiene are both substituted, so the numbering begins at the end nearest the alphabetically first-cited substituent (the ethyl group).

Ethers are compounds having two alkyl or aryl groups bonded to an oxygen atom, as in the formula R¹–O–R². The ether functional group does not have a characteristic IUPAC nomenclature suffix, so it is necessary to designate it as a substituent. To do so the common alkoxy substituents are given names derived from their alkyl component, as shown in the table on the right below. Examples of ether nomenclature are provided on the left. Simple ethers are given common names in which the alkyl groups bonded to the oxygen are named in alphabetical order followed by the word "ether". The top left example shows the common name in blue under the IUPAC name. Many simple ethers are symmetrical, in that the two alkyl substituents are the same. These are named as "dialkyl ethers". Examples are: CH₃CH₂OCH₂CH₃, diethyl ether (sometimes referred to as ether), and CH₃OCH₂CH₂OCH₃, ethylene glycol dimethyl ether (glyme).

Aldehydes and ketones are organic compounds which incorporate a carbonyl functional group, C=O. The carbon atom of this group has two remaining bonds that may be occupied by hydrogen or alkyl or aryl substituents. If at least one of these substituents is hydrogen, the compound is an aldehyde. If neither is hydrogen, the compound is a ketone.

The IUPAC system of nomenclature assigns a characteristic suffix to these classes, al to aldehydes and one to ketones. For example, H₂C=O is methanal, more commonly called formaldehyde. Since an aldehyde carbonyl group must always lie at the end of a carbon chain, it is by default position #1, and therefore defines the numbering direction. A ketone carbonyl function may be located anywhere within a chain or ring, and its position is given by a locator number. Chain numbering normally starts from the end nearest the carbonyl group. In cyclic ketones the carbonyl group is assigned position #1, and this number is not cited in the name, unless more than one carbonyl group is present.
Examples of IUPAC names are provided (in blue) in the following diagram. Common names are in red, and derived names in black. In common names carbon atoms near the carbonyl group are often designated by Greek letters. The atom adjacent to the function is alpha, the next removed is beta and so on. Since ketones have two sets of neighboring atoms, one set is labled α, β etc., and the other α', β' etc.

The carboxyl functional group that characterizes the carboxylic acids is unusual in that it is composed of two functional groups. As may be seen in the formula on the right, the carboxyl group is made up of a hydroxyl group bonded to a carbonyl group. It is often written in condensed form as –CO₂H or –COOH.

The carboxyl group must be located at the end of a carbon chain. In the IUPAC system of nomenclature the carboxyl carbon is designated #1, and other substituents are located and named accordingly. The characteristic IUPAC suffix for a carboxyl group is "oic acid", and care must be taken not to confuse this systematic nomenclature with the similar common system. These two nomenclatures are illustrated in the following table, along with their melting and boiling points.

Substituted carboxylic acids are named either by the IUPAC system or by common names.

In the IUPAC system of nomenclature, functional groups are normally designated in one of two ways. The presence of the function may be indicated by a characteristic suffix and a location number. This is common for the carbon-carbon double and triple bonds which have the respective suffixes ene and yne. Halogens, on the other hand, do not have a suffix and are named as substituents, for example: (CH₃)₂C=CHCHClCH₃ is 4-chloro-2-methyl-2-pentene.

Amines are derivatives of ammonia in which one or more of the hydrogens has been replaced by an alkyl group. The nomenclature of amines is complicated by the fact that several different nomenclature systems exist, and there is no clear preference for one over the others. Furthermore, the terms primary (1º), secondary (2º) & tertiary (3º) are used to classify amines in a completely different manner than they were used for alcohols or alkyl halides. When applied to amines these terms refer to the number of alkyl substituents bonded to the nitrogen atom, whereas in other cases they refer to the nature of an alkyl group. The four compounds shown in the top row of the following diagram are all C₄H₁₁N isomers. The first two are classified as 1º-amines, since only one alkyl group is bonded to the nitrogen; however, the alkyl group is primary in the first example and tertiary in the second. The third and fourth compounds in the row are 2º and 3º-amines respectively.

The IUPAC names are listed first and colored blue. This system names amine functions as substituents on the largest alkyl group. The simple -NH₂ substituent found in 1º-amines is called an amino group. For 2º and 3º-amines a compound prefix (e.g. dimethylamino in the fourth example) includes the names of all but the root alkyl group.
The Chemical Abstract Service has adopted a nomenclature system in which the suffix -amine is attached to the root alkyl name. For 1º-amines such as butanamine (first example) this is analogous to IUPAC alcohol nomenclature (-ol suffix). The additional nitrogen substituents in 2º and 3º-amines are designated by the prefix N- before the group name. These CA names are colored magenta in the diagram.
Finally, a common system for simple amines names each alkyl substituent on nitrogen in alphabetical order, followed by the suffix -amine. These are the names given in the last row (colored black).