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Monday, 29 April 2013

Three-Dimensional Representation of Organic Molecules

The three-dimensional (3-D) structure of organic molecules can be represented on paper by using certain conventions. For example, by using solid and dashed wedge formula, the 3-D image of a molecule from a two-dimensional picture can be perceived. In these formulas the solid-wedge is used to indicate a bond projecting out of the plane of paper, towards the observer. The dashed-wedge is used to depict the bond projecting out of the plane of the paper and away from the observer. Wedges are shown in such a way that the broad end of the wedge is towards the observer. The bonds lying in plane of the paper are depicted by using a normal line (-). 3-D representation of methane molecule on paper has been shown in Fig. 12.1.


Molecular Models
Molecular models are physical devices that are used for a better visualisation and perception of three-dimensional shapes of organic molecules. These are made of wood, plastic or metal and are commercially available. Commonly three types of molecular models are used: (1) Framework model, (2) Ball-and-stick model, and (3) Space filling model. In the framework model only the bonds connecting the atoms of a molecule and not the atoms themselves are shown. This model emphasizes the pattern of bonds of a molecule while ignoring the size of atoms. In the ball-and-stick model, both the atoms and the bonds are shown. Balls represent atoms and the stick denotes a bond. Compounds containing C=C (e.g., ethene) canbest be represented by using springs in place of sticks. These models are referred to as balland- spring model. The space-filling model emphasises the relative size of each atom based on its van der Waals radius. Bonds are not shown in this model. It conveys the volume occupied by each atom in the molecule. In addition to these models, computer graphics can also be used for molecular modelling.
12.4 CLASSIFICATION OF ORGANIC COMPOUNDS
The existing large number of organic compounds and their ever-increasing numbers has made it necessary to classify them on the basis of their structures. Organic compounds are broadly classified as follows:

I. Acyclic or open chain compounds
These compounds are also called as aliphatic compounds and consist of straight or branched chain compounds, for example:

II Acyclic or closed chain or ring compounds
Acyclic (aliphatic cyclic) compounds contain carbon atoms joined in the form of a ring homocyclic). Sometimes atoms other than carbon are also present in the ring (heterocylic). Some examples of this type of compounds are:

These exhibit some of the properties similar to those of aliphatic compounds.
Aromatic compounds
Aromatic compounds are special types of compounds. You will learn about these compounds in detail in Unit 13. These include benzene and other related ring compounds (benzenoid). Like alicyclic compounds, aromatic comounds may also have hetero atom in the ring. Such compounds are called hetrocyclic aromatic compounds. Some of the examples of various types of aromatic compounds are:



Organic compounds can also be classified on the basis of functional groups, into families or homologous series.
Functional Group
The functional group may be defined as an atom or group of atoms joined in a specific manner which is responsible for the characteristic chemical properties of the organic compounds. The examples are hydroxyl group (-OH), aldehyde group (-CHO) and carboxylic acid group (-COOH) etc.
Homologous Series
A group or a series of organic compounds each containing a characteristic functional group forms a homologous series and the members of the series are called homologues. The members of a homologous series can be represented by general molecular formula and the successive members differ from each other in molecular formula by a -CH2 unit. There are a number of homologous series of organic compounds. Some of these are alkanes, alkenes, alkynes, haloalkanes, alkanols, alkanals, alkanones, alkanoic acids, amines etc.
12.5 NOMENCLATURE OF ORGANIC COMPOUNDS
Organic chemistry deals with millions of compounds. In order to clearly identify them, a systematic method of naming has been developed and is known as the IUPAC (International Union of Pure and Applied Chemistry) system of nomenclature. In this systematic nomenclature, the names are correlated with the structure such that the reader or listener can deduce the structure from the name.
Before the IUPAC system of nomenclature, however, organic compounds were assigned names based on their origin or certain properties. For instance, citric acid is named so because it is found in citrus fruits and the acid found in red ant is named formic acid since the Latin word for ant is formica. These names are traditional and are considered as trivial or common names. Some common names are followed even today. For example, Buckminsterfullerene is a common name given to the newly discovered C60 cluster (a form of carbon) noting its structural similarity to the geodesic domes popularised by the famous architect R. Buckminster Fuller. Common names are useful and in many cases indispensable, particularly when the alternative systematic names are lengthy and complicated. Common names of some organic compounds are given in Table 12.1.
Table 12.1 Common or Trivial Names of Some Organic compounds
Compound Common name
CH4
Methane
H3CCH2CH2CH3
n-Butane
(H3C)2CHCH3
Isobutane
(H3C)4C
Neopentane
H3CCH2CH2OH
n-Propyl alcohol
HCHO
Formaldehyde
(H3C)2CO
Acetone
CHCl3
Chloroform
CH3COOH
Acetic acid
C6H6
Benzene
C6H5OCH3
Anisole
C6H5NH2
Aniline
C6H5COCH3
Acetophenone
CH3OCH2CH3
Ethyl methyl ether
12.5.1 The IUPAC System of Nomenclature
A systematic name of an organic compound is generally derived by identifying the parent hydrocarbon and the functional group(s) attached to it. See the example given below.By further using prefixes and suffixes, the parent name can be modified to obtain the actual name. Compounds containing carbon and hydrogen only are called hydrocarbons. A hydrocarbon is termed saturated if it contains only carbon-carbon single bonds. The IUPAC name for a homologous series of such compounds is alkane. Paraffin (Latin: little affinity) was the earlier name given to these compounds. Unsaturated hydrocarbons are those, which contain at least one carboncarbon double or triple bond.

12.5.2 IUPAC Nomenclature of Alkanes
Straight chain hydrocarbons: The names of such compounds are based on their chain structure, and end with suffix ‘-ane’ and carry a prefix indicating the number of carbon atoms present in the chain (except from CH4 to C4H10, where the prefixes are derived from trivial names). The IUPAC names of some straight chain saturated hydrocarbons are given in Table 12.2. The alkanes in Table 12.2 differ from each other by merely the number of -CH2 groups in the chain. They are homologues of alkane series.
Table 12.2 IUPAC Names of Some Unbranched Saturated Hydrocarbons
Name Molecular formula Name Molecular formula
Methane
CH4
Heptane
C2H6
Ethane
C2H8
Octane
C8H18
Propane
C3H8
Nonane
C9H20
Butane
C4H10
Decane
C10H22
Pentane
C5H12
Icosane
C20H42
Hexane
C6H14
Triacontane
C30H62
Branched chain hydrocarbons: In a branched chain compound small chains of carbon atoms are attached at one or more carbon atoms of the parent chain. The small carbon chains (branches) are called alkyl groups. For example:

In order to name such compounds, the names of alkyl groups are prefixed to the name of parent alkane. An alkyl group is derived from a saturated hydrocarbon by removing a hydrogen atom from carbon. Thus, CH4 becomes -CH3 and is called methyl group. An alkyl group is named by substituting ‘yl’ for ‘ane’ in the corresponding alkane. Some alkyl groups are listed in Table 12.3.
Table 12.3 Some Alkyl Groups
Alkanes Alkyl group
Molecular formula
Name of alkane
Structural formula
Name of alkyl group
CH4
Methane
CH3
Methyl
C2H6
Ethane
-CH2CH3
Ethyl
C3H8
Propane
-CH2CH2CH3
Propyl
C4H10
Butane
-CH2CH2CH2CH3
Butyl
C10H22
Decane
-CH2(CH2)8CH3
Decyl
Abbreviations are used for some alkyl groups. For example, methyl is abbreviated as Me, ethyl as Et, propyl as Pr and butyl as Bu. The alkyl groups can be branched also. Thus, propyl and butyl groups can have branched structures as shown below.

Common branched groups have specific trivial names. For example, the propyl groups can either be n-propyl group or isopropyl group. The branched butyl groups are called sec-butyl, isobutyl and tert-butyl group. We also encounter the structural unit, -CH2C(CH3)3, which is called neopentyl group

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