Atoms and Molecules

Organic Chemistry for Biochemistry

Methane and the Alkanes

Each carbon is surrounded by four equally-spaced electron pairs so the shapes are regular tetrahedra with bond angles 109° 28´. The electrons are sp³ hybridised with all the bonds having very nearly the same length and the same strength.

The general formula of alkanes is C_nH_2n+2. Methane is the smallest alkane (n = 1)
The molecular formula of methane is CH₄

Structural formula      a 2D representation      of a 3D structure      actual structure

Alkanes may have branched chains

e.g. 2-methylpropane (Isobutane)

The alkanes form an homologous series, with n (in C_nH_2n+2) increasing. In an homologous series, the physical properties show gradual trends.

Combustion of alkanes

Alkanes burn in air with formation of H₂O and CO₂.

C_nH_2n+2 + (3n+1)/2 O₂ CO₂ + (n+1) H₂O

Alkenes

Alkenes are alkanes which have lost pairs of hydrogen atoms from neighbouring carbon atoms. These carbon atoms are surrounded by three equally-spaced electron pairs so the shapes are flat (planar) triangular with bond angles 120°. The electrons are sp² hybridised with the bond between the carbon atoms consisting of two bonds (a sigma bond as is found in alkanes and a pi bond with high electron density above and below the plane of the bond). These double bonds make alkenes more reactive than alkanes.
Alkenes are attacked by electrophilic (electron-loving) reagents. These contain molecules with reactive groups that are attracted to the extra electrons in the pi bond part of the double bond; e.g. the decolourisation of Br₂/water (bromine water) where the two bromine atoms add to both ends of the double bond, 

Examples of alkenes:

Structural Isomerism

Structural isomers have the same molecular formula but different structural formula.

There are three types of structural isomers.

1. Skeletal isomers where the carbon skeleton is different.
2. Position isomers where the functional group is attached to a different position in the carbon skeleton.
3. Functional group isomers where the functional group is different.

Skeletal isomers
e.g. molecular formula, C₅H₁₂

                        pentane                  2-methylbutane       2,2-dimethylpropane

Position isomers
e.g. molecular formula, C₅H₁₁F

1-fluoropentane                 2-fluoropentane             3-fluoropentane

Note that '4-fluoropentane' is correctly named 2-fluoropentane and '5-fluoropentane' is correctly named 1-fluoropentane.

Functional group isomers

e.g. (a) molecular formula, C₂H₆O

CH₃-O-CH₃             CH₃-CH₂-O-H
dimethylether                 ethanol        

e.g. (b) molecular formula, C₃H₆O₂

CH₃-CH₂-CO₂H                     CH₃-CO₂-CH₃
                    propionic acid         methyl ethanoate (methyl acetate)

Stereoisomers

Stereoisomers have the same atoms and groups but different positions in space.

There are two types of stereoisomers, geometrical isomers and optical isomers.

Geometrical isomers

Consider CHCl=CHCl

There are two distinctly different structures:

cis-dichloroethene     trans-dichloroethene

Note that is also cis-dichloroethene (the drawing is just flipped over)

Note that are both the same molecule (1,1-dichloroethene) where the drawing is simply flipped over.

These are all chloroethene   

Test for geometrical isomers

There must be two different atoms or groups at the left hand end of the C=C double bond AND two different atoms or groups at the right hand end also.

Geometrical isomers such as these occur as there is no free rotation about a C=C double bond.

Chiral isomers

These have a requirement that they must possess a tetrahedral carbon atom to which four different atoms or groups are attached. These isomeric structures form two non-superimposable mirror images. This is called chirality or handedness, and is also known as optical isomerism. N.B. Mittens will fit either hand but gloves won't; gloves are 'handed' but mittens are not.

* a chiral centre         R-isomer             S-isomer
chiral isomers form non-superimposable mirror images

Properties of optical isomers

Optical isomers rotate the plane of polarised light. The extent of the rotation is proportional to the concentration of the solution. i.e. One isomer might rotate plane of polarised light 10° to the left (laevorotatory) and the other might rotate plane of polarised light10° to the right (dextrorotatory). For most biochemical molecules the isomers are distinguished as the D- or L- structures, e.g. D-glucose is the optical isomer of L-glucose. Only one chiral isomer is generally found in Biochemistry, thus the amino acids that form the structure of proteins are L-amino acids, and the sugars found in our diet are D-sugars.

N.B. Consider the molecule:
Is it chiral?

It is chiral with four different groups (H, Cl, Cl-(CH₂)₁₀ and Br-(CH₂)₁₀) around the carbon.

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This page was last updated by Martin Chaplin
on 10 February, 2005