Organic Chemistry And The Process Of Synthesis Biology Essay


One of the most rapidly developing sciences is organic chemistry. Every year, new applications of organic compounds are used in various fields, for example, in medicine, in agriculture and in industrial processes.1

Organic synthesis is one area of organic chemistry where interest has been focussed. The purposes for studying and carrying on a synthesis are varied. The synthesis of any compound such as a natural product gives absolute confirmation of its structure. Many syntheses are undertaken to study the properties of the compound (physical, chemical and biological). While, there are other purpose of organic synthesis, for example, examining the metabolism of a compound.2

There are two main and important pillars which organic synthesis based on:

Synthesis strategy: is the path which organic chemists planning on paper how to go from starting materials to the target molecule.

Synthetic methodology: which is the way to realize practically in the laboratory the synthesis strategy designed.3

1.1 Synthesis of cyclic compounds:

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Cyclic compounds are assorted as belonging to the carbocyclic or heterocyclic series. Both types of rings can be branched into an alicyclic and an aromatic series.

Alicyclic compounds which are non-benzenoid systems. They are the least prevalent of the cyclic organic molecules. Nevertheless, these compounds are useful in plant and animal products such as terpenes and the steroids, and some beneficial pharmaceuticals, including the prostaglandins. There are some alicylic compounds with 6-membered rings which are prepared from incomplete or complete hydrogenation of benzene rings, but the majority of alicyclic compounds are constructed by ring-forming reactions.

Aromatic compounds are those compounds which have at least one aromatic ring as a structure component. For example, benzene rings exist in natural compounds and synthetic compounds. In addition, benzene rings are part of widespread compounds such as in bicyclic heterocyclic systems.

Heterocyclic compounds are those compounds which have a cyclic structure include atoms of one or more in elements others than carbon within the ring. 4

1.2 Aromaticity and the HÈ•ckel (4n +2):

When any compound is called aromatic this mean there is some special properties correlate with the ring system. Aromatic species is typified by planar ring with a delocalized π system. There is specific rule to decide if the compound is aromatic or not which HÈ•ckel rule. This rule can be applied on ring compounds by using this equation (4n +2) where n is an integer. This rule states that, there must be (4n +2) π electrons, if the compound is aromatic. For example, benzene has six π-electrons and by applying that equation (4n+ 2):

4n +2 = 6 n = 1 (aromatic).

While by applying that equation to cyclobutadiene which has 4 π-electrons

4n +2 = 4 n = 0.5 which is not integer (cyclobutadiene is not aromatic).

Cycloctatetraene has 8 π-electrons, but it is not aromatic compound because when applying the equation it does not obey the (4n +2) rule.


4n +2 = 8 3/2 (not aromatic).

''Cycloheptatriene is a compound with 6 π-electrons and it obeys (4n +2), but it is not aromatic because there cannot continuous delocalized of the π-electrons around the ring as long as one of the carbon atoms is an sp3-hybridized carbon atom with no unhybridized p orbitals on the other carbon atoms''.


Naphthalene has 10 π-electrons and it obeys (4n +2) rule. Also there can be continuous delocalization of the π-electrons around the two rings. So naphthalene is an aromatic compound.5

1.3 Some examples of ring compounds:-

1.3.1 Phenylhydrazine:

Phenylhydrazine (PHZ) is widely used as a chemical intermediate in pharmaceutical, agrochemical and chemical industrial. PHZ has this formula (C6H8N2) and molecular weight 108. PHZ derivatives at the beginning were used as antipyretics, but as they have toxic effects on red blood cells which made their use dangerous.5 PHZ was used for many years in experimental induction of anaemia in animal until it was suggested that, it can be used as a drug for polycythemia vera.6

1.3.2 Benzimidazole:

This is an example of a fused ring system containing an aromatic (benzenoid) carbocyclic ring (on the right-hand side) and an aromatic heterocyclic ring.

Benzimidazole and its derivatives have been extensively studied compared to the most other heterocyclic compounds, and have got a good attention from synthetic organic and medicinal chemists. Benzimidazole has many applications in several areas such as biological activities. Compounds containing benzimidazole nuclei show antineoplastic, anticancer, antibacterial, antiinfective, antifungal and many other activities. 7

1.3.3 Phenols:

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Mercantile applications of phenols are prevalent. The tree isomers (o-cersol, catecho and resorcinol) are used in the manufacture of dyes and indicators. O-cersol is used to prepare 4,6-dinitro-o-cresol (DNOC) and 2-methyl-p-chlorophenoxyacetic acid (MCPA). DNOC is used as a spray insecticide against. For example, locusts and is a contact herbicide for the control of board-leaved weeds and treatment of potatoes and leguminous crop. MCPA is also used to control broad-leaved weeds. There are two compounds which have been synthesised from phenols, and those compounds are used as antioxidants in food industry. One of them is BHA (butylated hydroxyanisole) and the other one is BHT (butylated hydroxytoluene), and those compounds are labelled as E320 and E321 respectively on food packaging.5

o-Cresol Catechol Resorcinol

1.4 Methods:

This part will briefly consider the infrared spectra and nuclear magnetic resonance spectroscopy. Both methods are widely used in organic chemistry, infrared (IR) provides the function groups in the compound and nuclear magnetic resonance allows the chemist to put the skeleton.

1.4.1 Infrared spectra (IR):

As it has been mentioned, IR is a method which can be used to identify some function groups in the compound. Because many function groups give special frequency in IR spectra. However, there are some peaks cannot be identify in IR spectra and those peaks or area of peaks are called fingerprinter region. The functions which will be discussed are very common in organic compounds and they have characteristic frequencies in IR spectra, those groups are stated in the next table with some examples:8

Function group



2850-2960 (s)

C- CH3


C-H (aromatic)

3000-3100 (w)


2100-2200 (w)

-OH (carboxylic acid)

3300-3600 (w)


1180-1300 (s, m)

N-H (amine)

3100-3500 (m)

-C=N- (imine)

1590-1690 (w)

-C-N (aromatic amine)

1250-1360 (w)

C=O (Ketone)

1710 (s)

S=strong, m= medium, w= weak

There is an important effect which should be mentioned here, this effect is called conjugation. '' When the carbonyl group in aldehyde or ketone is separated from a carbon-carbon double bond (or an aromatic ring) by only a single bond, the carbonyl group is said to be conjugated with the double bond (or the ring)''.9

A ketone or aldehyde in which the carbonyl group is conjugated has a lower carbonyl stretching frequency than does a ketone or aldehyde in which there is no such conjugation.

Single bonds are easier to stretch than double bonds and, therefore, adsorb at lower frequencies.

For example in e-p-anisalacetophenone where the carbonyl group is conjugated with double bond gives frequency at 1655.5 cm-1, while in carbonyl group is not conjugated with double bond gives frequency at 1710 cm-1.

1.4.1 Nuclear magnetic resonance:

The phenomenon of nuclear magnetic resonance was first observed in 1946, and it has been applied in organic chemistry in 1960. Nowadays, nuclear magnetic resonance (NMR) spectroscopy is a routine laboratory technique. Besides its application for the identification of compounds, NMR can be used to follow reactions, measure rate and equilibrium constants and study the dynamic behaviour of molecules. It also has medical application in MRI (magnetic resonance imaging) and can be used to determine the structure of large biomolecules.8

1.6 The Diels-Alder reaction:

One of the most important reactions of conjugated dienes is the 1,4-addition of another multiple bond to the conjugated system to give a six-membered ring. A classic example of this reaction is the formation of a substituted cyclohexene from 1,3-butadiene and maleic anhydride.

The reaction of 1,3-butadiene with maleic anhydride is an example of the Diels-Alder reaction, named after the two German chemists, Otto Diels and Kurt Alder. This type of addition reaction always has two reactions. One is a conjugated diene, which may have many different types of substituents on it. The other reactant always has a double or a triple bond in it and is known as the dienophile, a compound that is attracted to and reacts with the diene. The dienophile may be a simple alkene or part of a diene system. The most reactive dienophile usually have a carbonyl group or another electron-withdrawing group such as a cyano or nitro group conjugated with a carbon-carbon double bond.9

1.7 Aim:

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The aim of this project is to synthesis some ring compounds and identify those compounds by using infrared spectroscopy (IR) and nuclear magnetic resonance (NMR), and discuss the data of those two methods.