Introduction to organic chemistry

Introduction to organic chemistry

Organic chemistry is the branch of science that deals with compounds of carbon. The name organic implies a connection with living things. This is because in early times it was found out that certain compounds are associated with living systems and it was observed that these compounds generally contain carbon. These compounds were thought to be a consequence of a “vital force” responsible for life process. The term organic was applied to substances isolated from living things by Jons Jacob Berzelius (1779-1848).

It was believed then that organic compounds could only be isolated from living systems. This was called vitalism. However, in 1828 Friedrick Wohler accidentally synthesized urea by heating ammonium cynate, an inorganic compound. From this time interest in the study of organic compounds and their syntheses started. It is estimated that currently 98% of synthetic compounds are organic. Carbon forms so many compounds because of catenation, its ability to form chains and rings with itself.

Organic compounds contain carbon, but contain a wide variety of other elements. The simplest organic compounds are hydrocarbons. These contain only the elements carbon and hydrogen. These simple compounds are divided into two broad classes: aliphatic hydrocarbons and aromatic hydrocarbons. The aliphatic hydrocarbons consist of three hydrocarbon families: alkanes, alkenes and alkynes. Alkanes (paraffin) contain only single bonds. Alkenes (olefins) are hydrocarbons that contain carbon-carbon double bonds; and the alkynes (acetylenes) contain carbon-carbon triple bonds.Having learned some basic concepts about structure, bonding, and acid–base chemistry After these questions are answered, we can understand some important phenomena. Forexample, why do we store some vitamins in the body and readily excrete others? How does soap clean away dirt? We will also use the properties of organic molecules to explain some basic biological phenomena, such as the structure of cell membranes and the transport of species across these membranes.

 Functional Groups

What are the characteristic features of an organic compound? Most organic molecules have C– C and C – H σ bonds. These bonds are strong, nonpolar, and not readily broken. Organic molecules may have the following structural features as well:• Heteroatoms—atoms other than carbon or hydrogen. Common heteroatoms are nitrogen,

oxygen, sulfur, phosphorus, and the halogens.• p Bonds. The most common π bonds occur in C – C and C – O double bonds.These structural features distinguish one organic molecule from another. They determine a molecule’s

geometry, physical properties, and reactivity, and comprise what is called a functional

group.• A functional group is an atom or a group of atoms with characteristic chemical and physical properties. It is the reactive part of the molecule.

Why do heteroatoms and π bonds confer reactivity on a particular molecule?

• Heteroatoms have lone pairs and create electron-defi cient sites on carbon.• π Bonds are easily broken in chemical reactions. A π bond makes a molecule a base and a nucleophile.Don’t think, though, that the C – C and C – H σ bonds are unimportant. They form the carbon backbone or skeleton to which the functional groups are bonded. A functional group usually behaves the same whether it is bonded to a carbon skeleton having as few as two or as many as

20 carbons. For this reason, we often abbreviate the carbon and hydrogen portion of the molecule by a capital letter R, and draw the R bonded to a particular functional group.

R Functional Group

Carbon skeleton... bonded to... a particular functional group.Ethane, for example, has only C – C and C – H σ bonds, so it has no functional group. Ethane has no polar bonds, no lone pairs, and no π bonds, so it has no reactive sites. Because of this, ethane and molecules like it are very unreactive.Ethanol, on the other hand, has two carbons and fi ve hydrogens in its carbon backbone, as well as an OH group, a functional group called a hydroxy group. Ethanol has lone pairs and polar bonds that make it reactive with a variety of reagents, 

HYDROCARBONS

 CYCLOALKANES

Alkanes are hydrocarbons that contain only single bonds. Alkanes are also called saturated hydrocarbons because they contain only C-C and C-H single bonds and thus contain the maximum possible number of hydrogens per carbon. Straight chain alkanes are numbered according to the number of carbon atoms in the chain as shown in Table 1.1. With exception of the first four compounds, methane, ethane, ethane and butane, the alkanes are named based on Greek numbers according to how many carbons the molecule has.

Table 1.1              Unbranched alkanes

All non-cyclic alkanes (alkanes without rings) have the general formula C_nH_2n+2 in which n is the number of carbon atoms. The structural formula of a molecule is its Lewis structure, which shows the connectivity of its atoms. For example, a structural formula for hexane is the following:

Hexane

Notice that this type of formula does not portray the molecular geometry. A condensed structural formula is another simpler way of representation that gives the same information.

The structural formula can be further abbreviated to CH₃CH₂CH₂CH₂CH₂CH₃ or CH₃(CH₂)₄CH₃

The family of alkanes forms a series in which successive members differ from one another by one CH₂ group (methylene group) in the carbon chain. A series of compounds that differ by addition of methylene groups is called a homologous series. Generally, physical properties within a homologous series vary in a regular way. Table 1.2 shows the regular variation of boiling points melting points and densities. This variation can be useful for quickly estimating the properties of a member of the series whose properties are not known.

 

Table 1.2:             Variation of physical properties of alkanes

There are two general trends in the variation of boiling point with structure:

1. Boling points increase with increasing molecular weight within a homologous series. This increase is due to the greater van der Waals attractions between larger molecules.
2. Boiling points tend to be lower for highly branched molecules that approach spherical proportions because they have less molecular surface available for van der Waals attractions.

Melting points tend to show the following general trends:

1. Melting points tend to increase with increasing molecular mass within a series
2. Many highly symmetrical molecules have usually high melting points (neopentane Vs pentane)

Isomers

When a carbon atom in a molecule is bound to more that two other carbon atoms, a branch in the carbon chain occurs at that position. The smallest branched alkane has four carbon atoms. As a result, there are two four-carbon akanes; one is butane, and the other is isobutene. These are different compounds with different properties for example, boiling points. Yet both have the molecular formula C₄H₁₀. Different compounds that have the same molecular formula are said to be isomers.

butane

isobutane

There are different types of isomers. Isomers such as butane and isobutane that differ in the connectivity of their atoms are termed constitutional isomers. In earlier literature they were called structural isomers. There are only two constitutional isomers with the formula C₄H₁₀. However, more constitutional isomers are possible for alkanes with more carbon atoms. There are nine constitutional isomers of the heptanes (C₇H₁₆), 75 constitutional isomers of the decanes (C₁₀H₂₂) and 366,319 constitutional isomers of the eicosanes (C₂₀H₄₂)! The large number of isomers that are possible for organic compounds of even modest size creates a problem of nomenclature. There is therefore a need to have a systematic way to construct a unique name for each of many possible isomers.

Substitutive Nomenclature of Alkanes

The system we will use is substitutive nomenclature proposed by the Union of Pure and Applied Chemistry (IUPAC). The IUPAC rules for nomeclature of alkanes form the basis for substitutive nomenclature of most other organic compound classes.

A chemical name has three parts in IUPAC system: prefix, parent and suffix. The parent selects a main part of the molecule and tells how many carbon atoms are in that part; the suffix identifies the functional group family the molecule belongs to; and the prefix gives the location(s) of the functional groups and other substitutents on the main part.

Alkanes are named by applying the following 5 rules:

1.         Determine the parent chain.

(a) The parent chain is the longest continuous carbon chain in the molecule. Use the name of that chain as the parent name.

(b) If two or more different chains of equal length are present, choose one with the larger number of branch points as the parent.

2.         Number the atoms in the main chain:

(a) Begin at the end nearer the first branch point and number each atom in the parent chain

(b) If there is branching an equal distance away from both ends of the parent chain, begin numbering at the end nearer the second branch point.

(c) If all the branches are an equal distance from both ends, the first-cited group (alphabeticaly) receives the lowest number.

3.         Identify and number the substituents. These are called alkyls:

(a) Assign a number to each substituent according to its point of attachment to the main chain. Substituents on the same carbon are assigned the same number.

4.         Write the name as a single word, using hyphens to separate the different prefixes (words from numbers) and commas to separate numbers. If two or more different substituents are present, cite them in alphabetical order. If two or more identical sustitutents are present, use one of the prefixes di-, tri-, tetra-, and so forth. Don’t use the prefixes for alphabetizing purposes. The name for the compound in rule 3 will therefore be;

4-ethyl-2,4-dimethylhexane

5.         A complex substituent is named by applying the first four steps above, just as though the substituent were itself a compound. For the compound shown below the compex substitutent is a substituted propyl group:

We begin numbering at the point of attachment to the main chain and find that the complex substituent is a 2-methylpropyl group. To avoid confusion, this substituent is put in parentheses when naming the complete molecule

For historical reasons some of the simpler branched alkyl groups also have non systematic, or common names.

Table: 1.3: Nomenclature of some short branched-chain alkyl groups

Classification of Carbon Substitution

Before studying chemical reactions, it will be important to recognize different types of carbon substitution in branched compounds. A carbon is said to be primary, secondary, tertiary or quaternary when it is bonded to one, two, three or four other carbons, respectively.

Likewise, the hydrogens bonded to each type of carbon are called primary, secondary, or tertiary hydrogens, respectively.

Cycloalkanes and skeletal structures

Alkanes that contain carbon chains in closed loops, or rings, are called cycloalkanes. These compounds are named by adding the prefix cyclo to the name of the alkane. Thus, the six-membered cycloalkane is called cyclohexane
Since cycloalkanes consist of rings of CH₂ units, they have the general formula C_nH_2n. Because of the tetrahedral configuration of carbon in the cycloalkanes, the carbon skeletons of the cycloalkanes (except for cyclopropane) are not planar.

An important convention for drawing cyclic molecules involves skeletal structures, which are structures that show only the carbon-carbon bonds. In a skeletal structure it is understood that a carbon is located at each vertex of the figure, and that enough hydrogens are present on each carbon to fulfill its tetravalency. Thus, the skeletal structure of cyclohexane is drawn as follows:

Skeletal structures may also be drawn for open-chain alkanes. For example, hexane can be indicated in this way:

When drawing a skeletal structure for an open-chain compound, remember that carbons are not only at each vertex, but also at the ends of the structure. Thus, the six carbons of hexane are indicated by the four vertices and the two ends of the skeletal structure. Here are two examples of skeletal structures:

Nomenclature of cycloalkanes

The nomenclature of cycloalkanes follows essentially the same rules used for open-chain alkanes. For most compounds, there are only two rules:

1.     Count the number of carbon atoms in the ring and the number in the largest substitutent. If the number of carbon atoms in the ring is equal to, or greater than, the number in the largest substituent, the compound is named as an alkyl-substituted cycloalkane. If the number of carbon atoms in largest substituent is greater than the number in the ring, the compound is named as a cycloalkyl-substituted alkane.

2.     For alkyl-substituted cycloalkanes, start at a point of attachment and number the substituents on the ring so as to arrive at the lowest sum:

(a) When two or more different alkyl groups are present and there is no lowest sum, number them by alphabetical priority. (Halogens if present are treated exactly like alkyl groups.)

Physical properties of cylcloalkanes

The physical properties of some cycloalkanes are given in table 1.4.

Table 1.4:             Physical properties of some cycloalkanes

The variation in boiling points is like with the non cyclic alkanes. However, the melting points are higher for symmetrical molecules. This is because of effective packing in a crystal structure.

REFERENCES

Crocker,Ernest C (1992).Application of the Octet Theory To Single-Ring Aromatic Compounds

Macmurry,John(2007).Organic Chemistry(7th edition).Brooks-Cole

  Organic Chemistry. Marc Loudon, 3^rd edition The Benjamin/Cummings Publishing Company,Inc., California, 1995.

  Organic Chemistry. John MucMurry. 3^rd edition. Brooks/Cole Publishing Company, 1992