Organic Nomenclature Naming organic compounds is an important ...

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Organic Nomenclature. Naming organic compounds is an important skill to acquire for anyone who is interested in being informed in today's society. Many of the ...
Organic Nomenclature Naming organic compounds is an important skill to acquire for anyone who is interested in being informed in today’s society. Many of the hot political issues of the day center around orgnaic compounds and their role as pesticides, pollutants, pharmaceuticals, preservatives, nutrients, and manufacturing materials. The CFC’s, (chlorofluorocarbons), recently the topic of an major international atmospheric emissions treaty are one important example. The compounds daminozide (ALAR) and EDB (ethylene dibromide), responsible for major media hype and exageration concerning the safety of foodstuffs and the need for regulation by the federal government are another. We must try, as members of a democratic society to be as knowledgeable as possible concerning these types of issues and that requires that we learn to recognize the chemical structures that are asssociated with the names of chemical compounds so we are able to understand the chemical properties and reactivity that is to be expected from them. One of the most fundamental tenants of chemistry is that chemical behavior, i.e. The chemical and physcial properties of a compound, are determined by the structure. Knowing the three-dimensional arrangement of atoms within a molecule and how they are connected one to another, in fact, should tell us all there is to know about a molecule. In practice we find that this is true to a significant extent but we still lack the sophistication in our theoretical understanding of the way molecular interactions occur between molecules. We are forced by the constraints placed on us by the speed of performing calculations on digital computers to perform experiments to determine the exact reactivity of many important chemical systems. Further, there are aspects of the theory of molecules which are not developed to anywhere near the level of predictive power necessary to eliminate the need for experimentation. There are an astronomical number of carbon containing, organic molecules. Carbon is exceptional in its ability to form several types of covalent bonds with itself and with other elements. Today there are over three million unique orgnaic compounds which have been described in the literature and that number is growing at an increasing rate each year. This number corresponds to an average rate of discovery and description of 5 new organic comonds every two hours for the last one hundred and fifty years. The synthesis of the first organic compound occurred in 1834 by Frederick Wohler. In order to name each of these compounds so that all chemists would understand what structure was being referred to necessitated the establishment of uniform rules for naming. For this purpose the IUPAC (International Union of Pure and Applied Chemistry) was formed and the rules it formulates are used by chemists (most of the time) in naming of new compounds. Virtually all carbon comounds are characterized by the fact that there is more than a single carbon within each molecule. The first means of differentiating between different carbon comounds is therefore based upon the number of carbons per molecule. The existence of multiple bonds, three-dimensional connectivity of those atoms and the presence of other elements in the molecule can be viewed as refinements on this basic naming system.

The most common organic compounds are hydrocarbons of which the alkanes, (also called aliphatics or saturated hydrocarbons) are the least compolicated. Hydrocarbons as a class of organics contain only the elements carbon and hydrogen. Alkanes are those hydrocarbons which have only carbon-carbon single bonds and carbon-hydrogen single bonds. Each carbon atom, in order to achieve an octet, must form four covalent bonds with its neighbors. In alkanes these must be either another carbon atom or a hydrogen atom. The simplest group of alkanes are the unbranched acyclic alkanes, that is those in which the carbon atoms are attached one to the other as beads upon a string. These are named based upon the number of carbons present in molecule. Straight chain alkanes are also referred to as normal alkanes. Table I. Straight chain alkanes, saturated hydrocarbons or paraffins Carbon number 1 2 3 4 5 6 7 8 9 10 11 12 13 15 18 20

formula CH4 CH3CH3 CH3CH2CH3 CH3CH2CH2CH3 CH3CH2CH2CH2CH3 CH3(CH2)4CH3 CH3(CH2)5CH3 CH3(CH2)6CH3 CH3(CH2)7CH3 CH3(CH2)8CH3 CH3(CH2)9CH3 CH3(CH2)10CH3 CH3(CH2)11CH3 CH3(CH2)13CH3 CH3(CH2)16CH3 CH3(CH2)18CH3

name Methane Ethane Propane Butane Pentane Hexane Heptane Octane Nonane Decane Undecane Dodecane Tridecane Pentadecane Octadecane Eicosane

Note the consequences of the octet rule for carbon are that it always has four covalent bonds. When carbon is found in an alkane where only single bonds exist this means that carbons at the end of a chain will always have three hydrogen atoms. Another useful fact about acyclic alkanes is that they always have the formula CnH2n+2. Chemists often draw the carbon chain in different ways not always horizontally. Remember that drawing the same molecule on the page in differen orientations will not change the identity of the molecule, it must always have the same name (a Volkswagen is still a Volkswagon when you look at the back in stead of the front!) Branched alkanes also exist. These compounds differ from those above in that one or more of the carbons has three carbon atoms attached to it. Alkanes with branches are named based upon the number of carbons in the longest single chain, end-to-end within the molecule. (In some cases more than one choice of ending carbons is possible. Then we choose the longest chain with the greatest number of branches.) It is also necessary to

name the branches and their positions on that longest chain. To understand this it is easiest to illustrate with an example: Table II. Side chains -CH3 methyl

-CH2CH3

ethyl

-CH2CH2CH3

propyl

-CH(CH3) 2

isopropyl

-CH2CH2CH2CH3

butyl

-CH2CH(CH3) 2

-CH(CH3)CH2CH3

sec-butyl

-C(CH3) 3

-CH2CH2CH2CH3

pentyl

-CH2CH2CH(CH3) 2 isopentyl (also isoamyl)

-CH2C(CH3)3

neopentyl

-C6H5 phenyl -CH=CH2

-CH2C6H5 ethenyl (vinyl)

-CH2CH=CH2

isobutyl

tert-butyl

benzyl allyl

Example 1. 1

CH3 CH3 CH2 CH2 CH CH2 CH2 CH CH3

C

C

C

CH2 H 2C

C

5

C

C

C

C

4

3

2

6 C

CH3

C

C

7

8

C

The following alkane is to be named by the IUPAC system of nomenclature. To do so we nust first determine the longest single chain of carbons atoms within th molecule. By rewriting the structure without showing the hydrogen atoms it is a little clearer and the longest chain can be identified by counting from end to end. Notice that chemists don’t always place the longest chain in a single horizontal line. The longest chain of carbon atoms in this molecule contains eight atoms. The compound will therefore be named as an octane.

Locant numbers for side chains 2,5 not 4,7! 8

1

CH3

5

4

CH3 CH2 CH2 CH CH2 CH2 CH CH3 6 CH2

H 2C 7

4

3

5

6

CH3

CH3 CH2 CH2 CH CH2 CH2 CH CH3

2

3

H2C

CH3

CH3

2

8

7

CH2

1

In the structure shown below the longest chain has been drawn to be horizontal with the branches coming off vertically. This illustrates how different an organic molecule can appear when drawn in a different orientation. Never-the-less, it must have a single unique name.

C C

C

C

C

C

C

C

C

C

C

C

In orger to completely name this compound we need to identify the length of each sidebranch from the main chain and where it attaches. The attach-points are identified by numbering the major or root chain (see bold-faced atoms below) from one end to the

other. Since the major chain has two ends it is possible to number the chain in either direction. Only one of these can be correct if we are to be able to give a single unique name to the compound, see below.

2-methyl-5-propyloctane CH3 CH3 CH2 CH2 CH CH2 CH2 CH CH3 CH2 H2C

CH3

The correct number system is the one which results in the series of locant numbers having the smallest numerical value when they are all written together. In this case we have branching side groups at only two points in the molecule. The positions of the branlches are either 2,5 or 4,7 (it is conventional to list them in increasing numerical order). Since 25 is less than 47 the 2,5 numbering for the branch points or locats is the correct one. We have still to address the problem of naming the side-chains that are found at the 2 and 5 positions along the main chain. These are named based upon the number of carbons in each. To indicate that we are referring to a side-chain within a molecule we change the suffix of the side-chain group dropping the –ane present in the alkane name and replace it with –yl. At the 2 posistion we find a 1 carbon side chain whose root name would be methane, droping the –ane and adding –yl gives us the side-chain name methyl. Silmilarly, at the 5 position we find a 3 carbon side-chain which we name propyl according to the same rules. The last problem to be solved is what order do we present all these pieces of information when writing down the name. It is conventional to name the side-chains first followed by the root name of the longest chain. The order to be used when there is more than a single-chain is alphabetical. The complete name for this compound is therefore 2-methyl-5-propyloctane. The locants (number of the carbon atoms along the main chain) are always separated from the sidechain name by a hyphen, the name is incorrect without them.

Example 2. Step 1: find the longest single chain in the compound and the root name. Octane CH3 CH3 H3C

CH CH2 CH2 CH2 C CH2

CH

CH3

CH3

C

7 C

C

8C

6

C 5

C 4

C

C

C 3 C

C

C

2

1

9C

CH3

Step 2: Number the carbon atoms so that the side-chain locants when listed in order give the lowest number. In this case there are two side-chains on the same carbon, each of them is given its own locant number to avoid ambiguity.

Locant numbers are 2,3,3,6 not 3,6,6,7

Step 3: Name the side-chain at each locant position 2,3,3,6-tetramethyl Step 4: Write the entire, correct name for the alkane (remembering to alphabetize sidechains in the name!) 2,3,3,6-tetramethyloctane This example points out two important featres. (1) When two side-chains are attached at a single carbon atom each has its own locant number within the name. (2) When there is more than one of a given side-chain present within the molecule not matter where it is found, all locants for that type of side-chain are listed together separated by commas from each other and by a hyphen from the side-chain name.. Further, the side-chain name is preceded by the greek prefix to indicate thenumber of times the side-chain appears within the molecule. Table III. Greeek prefixes for multiples 2 3 4 5

ditritetrapenta-

6 7 8 9 10

hexa hepta octa nona deca

Cyclic Alkanes In addition to straight-chain and branded chain alkanes the possiblity exists for carbon compounds to form loops or rings. These are referred to as cyclic alkanes. These ring compounds can be thought of as closed two-dimensional regular polygons. Since the smallest polygon is the triangle, the smallest possible cyclic alkane must be the three membered ring system. Since three carbons in a straight chain are referred to as a propane it is only reasonable that when they form a ring they are referred to as cyclopropane. The table below shows the most common small ring systems.

cyclopentane

cyclopropane

cyclobutane cyclohexane

cycloheptane

cyclooctane

Numbering side-chain on cyclic alkanes As with acyclic alkanes side chain locations are given by numbering the ring carbons in a way that gives the lowest number sequence when the locants are listed as a group.