Pharmaceutical Organic Chemistry

1

Introduction to Organic Chemistry

Organic chemistry is the major branch of chemistry which deals with the scientific study of preparation, structure, properties, composition and reactions of carbon containing compounds. In organic chemistry, not only hydrocarbons are studied but also compounds in which carbon is bonded with any other atoms like oxygen, halogens, nitrogen, phosphorus and sulfur etc. Almost all organic compounds contain at least one carbon hydrogen bond (C-H) in it.

Origin of Organic Chemistry

The history of organic chemistry can be traced back to ancient times when the tribes extracted chemicals from plants and animals to treat their ailments. But they did not name it as organic chemistry. The records what they kept are useful in the development of modern organic chemistry.

In 1700s, the French noble man and chemist, Antonie-Laurent De Lavoisier showed that nearly all substances of plant origin are composed of carbon, hydrogen and oxygen. Organic compounds of animal’s origin also consist of similar three elements but frequently contain nitrogen, phosphorous or sulphur either alone or in combination.

The German scientist John Jakob Berzelius, was the first scientist who defined organic chemistry as a branch of modern science in early 1800’s. He had classified the chemical compounds into organic and inorganic compounds with the following definition.

Organic compounds: Compounds derived from living organisms were believed to contain an immeasurable vital force and the essence of life called organic compounds.

Inorganic compounds: Compounds derived from minerals and those lacking of that vital force were called inorganic compounds.

The Vital Force Theory Essence of Life

According to the Berzelius discovery, the chemists could create a life in the laboratory; they assumed that they could not create any compound with a vital force. This vital force theory put forwarded by Berzelius had no scientific background but held the field till 1828. A German chemist Friedrich Wohler synthesized an organic compound named urea by heating ammonium cyanate, a compound that did not come from a living organism. 

For the first time an organic compound is obtained from something other than living system without the aid of any kind of vital force.

The synthesis of urea was indicated by the leading chemists of the day. The vital force concept (essence of life) did not die quickly. It was only after the synthesis of acetic acid by Kolbe in 1845 and the synthesis of methane in 1856 the belief in the essence of life theory was abandoned. Thus, we see that the vital force theory died only a lingering death.

Definition of Organic Chemistry

From the beginning of synthesis of urea, methane and acetic acid in the laboratory, chemists needed a new definition for organic compounds.

Organic compounds are now defined as compounds that contain carbon. Then the next question arises Why is an entire branch of organic chemistry devoted to the study of carbon containing compounds? The so called organic compounds have been found to be mainly compounds of carbon and hydrogen (called hydrocarbons) and their derivatives. Finally, organic chemistry is defined today as The chemistry of hydrocarbons and their derivatives". There is no sharp line of demarcation between organic and inorganic chemistry, the difference between organic and inorganic compounds is still being retained as a matter of convenience than of principle.

Reasons for Treating Organic Chemistry as a Separate Branch of Chemistry

The following number of characteristics of organic compounds justifies the treatment of organic chemistry as a separate branch of chemistry.

(i) Large number or Catenation (making bond with all other atoms easily) property of carbon: Compared with the compounds of other elements, the number of organic compounds is very large. About more than one million organic compounds are already known and more being added to the list everyday by chemists all over the world. Why are so many organic compounds present? What makes carbon so special? The answer is the position of carbon in the periodic table. In periodic table, carbon is present in the centre of the second row of elements. The atoms to the left of carbon have a tendency to give up electrons, whereas the atoms to the right of carbon have a tendency to accept electrons (Fig. 1.1).

Figure 1.1 Shows the position of carbon atom in periodic table (second row elements).

Since carbon is in the middle, it neither readily gives up nor readily accepts electrons, instead it shares the electrons. Carbon not only can share the electrons with different kind of atoms, it can also share electrons with other carbon atoms which allow it to form the vast variety of chain like molecules. Because carbon can share electrons with atoms other than carbon also adds to the range of stable carbon containing compounds. Consequently it also forms millions of more stable compounds with various ranges of chemical properties by sharing its electrons.

This peculiar property of carbon is known as Catenation (ability of carbon atom to make a bond with all atoms). It is not possible to add all these huge carbon compounds in the chapter on carbon in any textbook and hence organic compounds need to be studied separately.

(ii) Complexity of molecules: Some types of organic molecules have more complex structures and possess high molecular weight than inorganic molecules. For example, molecular weight of proteins ranges from several thousands to million.

(iii) Isomerism: Representation of more than one organic compound for the same molecular formula is called as isomers and this phenomenon is known as isomerism. For example, the molecular formula C4H10O stands for three types of ether and four types of alcohol.

Different type of ethers

Different type of alcohols

All the above isomers possess different properties due to different arrangement of an atom. In contrast, in inorganic chemistry, one molecular formula stands for only one compound. For example H2SO4 indicates only sulphuric acid and nothing else (only a few inorganic complex compounds also show isomerism).

(iv) Polymerism: When the molecular formula of one organic compound is a simple multiple of the other (i.e., both of them have the same empirical formula), they exhibit polymerism.

For example: benzene exhibits polymerism with acetylene (Benzene is a polymer of acetylene)

A large number of organic compounds exhibit polymerism but a very few inorganic compounds show polymerism.

(v) Non-ionic character of organic compounds: Organic compounds have covalent bonds and therefore do not get ionize when dissolved in water.

For example: Chloroform (CHCl3) is insoluble in water and does not give white precipitation with sliver nitrate solution (a characteristic property of inorganic chloride salts).

On the other hand, the inorganic compounds usually ionize in water and therefore mainly all inorganic reactions undergo ionic reactions. For example; all chloride salts react with silver nitrate solution and produces white precipitate which is a characteristic reaction of chloride ions.

(vi) Comparative instability of organic compounds: The covalent bond nature of organic compounds makes them more liable to heat and light. On heating the covalent bond, it easily undergoes decomposition. Hence all of the organic molecules possess low melting point and boiling point.

But all the inorganic compounds have ionic bonds which cannot be decomposed at low temperature. More amount of energy is needed for breaking the bond. Hence all inorganic compounds have high melting and boiling point.

(vii) Solubility: Organic compounds, unlike inorganic compounds are mostly soluble in organic solvents such as alcohol, ether, acetone, benzene etc. and they are sparingly soluble (formation of weak hydrogen bond) or insoluble in water (lack of formation of hydrogen bond with water).

(viii) Homologues series: Organic compounds are classified into families or groups called as homologues series. Different members belonging to a homologues series are known as homologues and they are characterized by the presence of a particular characteristic group so can be indicated by a general formula. The common difference between the consecutive members in the homologues series is CH2. These members possess similar chemical properties and regular gradation in their physical properties. They are prepared by general methods of preparation as described in the individual chapters.

This property of organic compounds reduced the studies of over a million of organic compounds to few homologues series. Similar properties of different homologues are the properties of the functional group in each one of them.

(ix) Action of heat: Most of the organic compounds burns in air to give carbon dioxide and water and some of them decompose on heating to leave a black residue (ash or charcoal). But generally inorganic compounds are stable towards heat.

(x) Structure: The arrangement of atoms or structure in most of the organic molecules is well established. But it is more difficult to determine the structure of inorganic compounds. A comparatively very few of them have been completely worked out.

(xi) Origin: Most of the organic compounds are obtained from animal or vegetable kingdom in comparison to the inorganic compounds which are obtained from mineral origin.

(xii) Rates of organic reactions: Due to the reversibility and invariability accompanied by side reactions, most of the reactions between organic compounds are slow. It indicates the activity of molecules rather than ions. They rarely proceed to completion and their yield is generally low.

Rise of Organic Chemistry

After the various discoveries of Wohler (1882), Kolbe (1840) and Berthelot (1850’s), chemists found that it was not the vital force which imparted uniqueness to organic chemistry rather a simple fact that organic compounds were all compounds of carbon. The perfection in technique of combustion analysis of carbon and oxygen gave new dimension to organic chemistry. Hence, the first time accurate formulae were available for a good number of fairly complicated organic compounds. Various theories were advanced in order to describe the complexities of substitution, isomerism etc.

Frankland, in 1852 discovered the concept of valence. In 1858 Kekule & Cooper proposed the tetravalency concept of carbon and its ability to link with each other. In 1858, Cannizaro and Avogadro discovered a hypothesis for the determination of accurate molecular weight. Chemists started thinking about molecular structure and chemical bond related terms. Kekule introduced the idea about a bond between atoms.

Nowadays, organic chemistry has matured as a major scientific discipline. Over 95 % the known chemical compounds are organic in nature and roughly half of the present-day chemists are organic chemists. Rapid and fast growth in the field of organic chemistry is due to the fact that organic chemical industry contributes a major role in the world economy and organic compounds are literally the "stuff of life".

Need for Studying Organic Chemistry

Organic chemistry is an essential aspect in biological and medical field. All the living organisms are composed of organic substances. Evolution of life postulated that life started from a single organic compound, nucleotide which polymerises or joined together to form a building blocks of life known as DNA.

In most of the chemical industries and pharmaceutical companies in and around us, we encounter organic reactions. Maximum number of life saving drugs are organic compounds only, hence any field e.g. chemical engineering, food and flavoring industry, electrical engineering (liquid crystals displays for digital watches) is surrounded by basics of organic chemistry only. Doctor or Pharmacist are surrounded by organic compounds throughout their life because maximum numbers of life saving drugs are organic compounds only.

For the discipline of biochemistry, molecular biology or another branch of life sciences, a good background of organic chemistry is essential. Specialization in any other branch of chemistry needs good knowledge of organic chemistry.

Apart from these, study of organic chemistry extremely stimulate intellectual pursuit and promotes logical thinking. Organic compounds are vital for the sustenance of all life. Many medical disorders or diseases are due to disruption of organic molecules in the body. Enzymes, proteins, carbohydrates, lipids and catalysts present in our body are organic substances which play a major role in our day to day life.

Classification of Organic Compounds

Organic compounds are categorized into two major groups such as

1. Open chain or acyclic compounds or aliphatic compounds.

2. Cyclic compounds or closed chain compounds.

1. Open chain or acyclic compounds: Carbon compounds having open chain of carbon atoms whether branched or unbranched are called as open chain compounds. The name aliphatic was derived from the Greek word aleipher (meaning fat) as the earliest known compounds of this type were obtained from fats.

Saturated compounds: A hydrocarbon (compounds that contains only carbon and hydrogen) contains only one carbon-carbon (C-C) single bond are called as saturated compounds (Four valency of carbon atom is saturated with different atoms or groups).

Unsaturated compounds: A hydrocarbon having carbon-carbon double bond (C=C) or carbon-carbon triple bond ( C C) are called as unsaturated compounds.

2. Cyclic compounds or closed chain compounds: Organic compounds with a closed chain of atoms are called as closed chain or cyclic compounds.

Polycyclic compounds: Molecules containing two or more ring system is known as polycyclic compounds.

Homocyclic or carbocyclic compounds: The cyclic compounds entirely composed of carbon atom are called as homocyclic or carbocyclic compounds.

These are further sub divided in to two important groups.

Aromatic compounds: Compounds containing a ring structure of six carbon atom of benzene are known as benzenoid or aromatic compounds as shown in following examples.

Most of the organic compounds occur in plants and many of them have fragrant odour, so they are named as aromatic compounds (Greek aroma = sweet smell).

Alicyclic compounds or aliphatic cyclic compounds: Some of the homocyclic compounds contain a ring structure but behave like aliphatic compounds, hence, they are named alicyclic or cyclic aliphatic compounds. It includes the important compounds of polymethylenes or their derivatives as shown below.

Heterocyclic compounds: Cyclic compounds in which one or more carbon atoms are replaced by other atoms are called as heterocyclic compounds. The non carbon atoms present in the ring are called as hetero atoms. Examples are nitrogen, oxygen and sulphur. Some of the examples for heterocyclic compounds are shown below. 

Organic Chemistry in the Service of Mankind

All molecules such as proteins, amino acids, enzymes, lipids, DNA & RNA which make life possible contain carbon atoms and the great majority of the chemical reactions that occur within body or living system are organic reactions. We depend on organic compounds that occur in nature for our day to day life needs as given below:

Foods: Starch, sucrose, glucose, fats, vitamins, proteins etc.

Household and commercial articles: Soap, ointments, oils, cosmetics, flavoring agents, paints, varnishes etc.

Drugs and disinfectants: Aspirin, sulphonamides, penicillin, chloroform, dettol, lysol etc.

Poisons: Strychnine, opium and different kind of insecticides.

Perfumes: Camphor, ionone and vanillin.

Dyes: Indigo, malachite green, congored etc.

Explosives: Trinitrotoluene, nitroglycerin, dynamite and picric acid etc.

War gases: Lewisite, mustard gas and chloropicrin.

Hence, organic compounds penetrate into each and every phase of our life. We look and count on an organic chemist for the manufacture of the above compounds and for the development of various chemical industries.

Various sources of organic compounds: As mentioned earlier, organic compounds are mainly obtained from the natural sources and synthesized in laboratory.

Plants and animal sources: By using suitable method of isolation, various types of organic compounds are obtained directly from plant and animal sources. For example: carbohydrates (sugars, starch, cellulose), proteins (silk, wool, food proteins, casein), alkaloids (morphine, quinine, strychnine), fats and oils (soyabean oil, cotton seed oil, sunflower oil, butter), hormones, vitamins, resins, perfumes and flavouring agents.

1. Natural gas and petroleum: These are used as fuels as well as the major source for organic compounds. Through various types of synthetic organic reaction, natural gas and fuels are used as a source for the preparation of hundreds of useful organic substances such as explosives, solvents, synthetic rubber and plastics.

2. Coal: It is another major source of lot of organic compounds. Pyrolysis or the destructive distillation of coal produces coke and coal tar. Nearly more than 200 varieties of organic compounds are isolated from coal tar. The coal tar produces the starting materials for the manufacture of thousands of useful aromatic compounds such as drugs, dyes, perfumes and others.

3. Synthesis: By using synthetic strategies and reactions, the simple organic compounds obtained from petroleum and coal tar have been converted in to thousands of useful materials.

Many examples can be cited of synthetic organic compounds replacing those obtained from natural sources but it need volumes. In several cases, the synthetic compounds obtained are more superior to natural compounds. We will study the basic principles of organic chemistry which will help us to learn complex organic compounds and their chemistry in further stages.

Probable Questions

1. Define vital force theory. Why was it abandoned?

2. What is meant by isomerism and polymerism? Write the various isomers of C4H10O.

3. Write the importance of organic chemistry in medicines or medical field.

4. Write a brief note on the rise and development of organic chemistry.

5. Define organic chemistry, and how will you justify organic compounds belongs to separate branch of chemistry?

6. Write a short note on organic chemistry in the service of mankind.

2

Nomenclature of Organic Compounds

Introduction

In early days, scientists named the compounds based on historic background. For example, wood spirit was named so because it was obtained from distillation of wood. Later it was named as methanol based on Greek words (methu = wine and hale = wood). Similarly, the name acetic acid was derived from vinegar (Latin; acetum = vinegar), because the acetic acid is the major constituent of vinegar. These are called as common names or trivial names.

As the number of compounds were discovered more, naming by history becomes difficult. Hence systematic naming becomes important. The systematization of names was carried out by the International congress of leading chemistry held in Geneva, 1892.

Rational system of nomenclature was formed and it is called as Geneva system of nomenclature. Slight revision and improvements were carried out time to time. One such being held at Liege (Belgium) 1930 by International Union of Chemistry and it is called as IUC system of nomenclature. The IUC was later modified by the International Union of Pure and Applied Chemistry in 1958 and it is called as IUPAC system of nomenclature.

To name the organic compound according to IUPAC nomenclature a set of rules were framed and all the compounds are named accordingly. However, even today some of the common names are used for organic compounds. Hence the chemists should also be aware of the common names apart from IUPAC nomenclature.

Non-systemic nomenclature of organic compounds like common name, trivial name etc are described in individual chapters.

IUPAC System of Nomenclature

IUPAC nomenclature is been used now a days to name organic compounds. However, some of the simple compounds are named by trivial names. Earlier names have been continued even today but complex organic compound can be given using IUPAC nomenclature only. Various rules are followed for naming compounds by IUPAC system:

Rule 1: Longest chain rule: In the given organic compound longest possible chain of carbon atoms is selected and the compound is named as a derivative of this alkane.

For example, the compound given below have five carbons in horizontal line and six carbons in the longest chain hence we should select it as a hexane derivative only.

Rule 2: Lowest number for substituents rule: After selecting the longest chain, the numbering should be given from one end to the other end. While giving the number, the substituents should be given lowest possible number.

For example, the compound given below is named in two ways.

In first case, naming 4,7-dimethyl octane is not correct because 2,5-di methyl octane have lowest numbers for the substituents.

If different alkyl groups are in equivalent positions in relation to the end of the chain, preference is given to the end where the radical has fewer carbon atoms (methyl, ethyl, etc).

In the following example, the first case of naming is correct because methyl group is given preference over ethyl group. 

If identical radicals are at equal distance in the chain then the numbering starts from the end where it is more branched.

In the following example, the first way of naming is correct where the branching end is given preference.

If two sets of numbers are possible for the given chain, then order of prefix in the name will decide the numbering (alphabetical order of the substituents).

For example, the given compound can be named as 1-bromo-4-chloro butane or 1-chloro-4-bromo butane. As the prefix bromo is first, the first name is correct.

If chains of equal length are competing for selection as the parent chain in a branched alkane, the preference goes to the chain carrying more branches.

For example, in the given organic compound first way of naming i.e., 3-ethyl-2,6-dimethyl heptane is correct where as 5-isopropyl-2-methyl heptane is wrong.

Rule 3: Arrangement of prefixes: When there is more than one group attached in the chain, they should be arranged alphabetically. If same group is presented in two or three places of chain then the prefix di or tri etc are used.

For example, the given organic compound is named as 5-ethyl-2,3-dimethyl heptane.

Rule 4: Lowest number for functional group: When the functional group is present in the chain, it should be given first preference even if it violates lowest number rule 2. Double bond or triple bond also considered as functional groups.

The order of preference of numbering is as follows.

(i) To the principal functional group of a compound.

(ii) To the double or triple bond.

(iii) To the substituent atoms or groups.

When more than one functional group present in the compound, then the order of preference is as follows.

1. Carboxylic acids

2 . Carboxylic acid derivatives

3 . Aldehydes

4. Nitriles

5 . Ketones

6. Alcohols

7. Amines

8. Ethers

9. Olefins

10. Acetylenes

Systematic name for allyl alcohol is

For nomenclature purpose the following functional groups are considered as substituents not as functional groups (halo, nitroso and azo as they do not have ending).

When there is more than one functional group in the compound, one is principal functional group and the other is secondary functional group. The prefixes and suffixes used for various functional groups are depicted in the following Table 2.1.

Table 2.1 Groups cited only as prefixes. 

Table 2.2 Groups cited as prefixes or suffixes.

Rule 5: Writing names for compounds containing more than one functional group: Whenever more than one functional group are present in the given compound then the ending is suitably modified. Carbon - carbon multiple bonds and second functional groups are combined in endings or the important functional group is considered as substituent.

Some of the examples are shown below.

Name of some compounds containing two or more functional groups are shown in Table 2.3.

Table 2.3 Nomenclature of some simple polyfunctional compounds.

Table 2.4 Nomenclature of some unsaturated compounds of Simple Functions.

Table 2.5 Nomenclature of some compounds of complex Functions.

Rule 6: Treatment of like things alike: All groups of one kind which occurs in a single molecule should be given the same treatment as far as possible.

For example, in the given example carboxylic acid is the main functional group, the parent compound should include two or three functional groups as possible.

Rule 7: Functional groups and the selected chain: Maximum number of functional groups must be included in the carbon chain even if it violates longest chain rule (Rule 1), as shown in the following example.

When there is a side chain with side chain, the latter is numbered and the name of the complex is considered to start with the first letter of its complete name, as shown in the following example.

In addition to these rules, following points mentioned are also useful in writing IUPAC name of compound.

Steps involved in writing IUPAC name of the compound

Step 1: Locate the longest chain containing principal functional group and as many as secondary functional group and carbon-carbon multiple bonds.

Step 2: Select the root word corresponding to the chain length. For example Hex for six carbon atom chain.

Step 3: Number the longest chain selected from the end near to the principal functional group.

Step 4: Based on the carbon-carbon bonds C — C, C = C, C≡C attach the suffix -ane, -ene or yne respectively to the root word of carbon chain.

Step 5: Add suitable prefixes and suffixes with numerals to indicate the number and position of each side chain, substituent, or functional group.

Example:

Notes:

1. Position of numerals used in the enumeration of substituents: Numerals representing location of unsaturation or functional groups are placed before the name stem as

2. Writing names: The names of radical replacing hydrogen atom in compound are carried out. For example, Chlorotoluene (chlorine replaced H atom of toluene).

Elision of vowels: To avoid ambiguity vowels, whether pronounced or silent are generally retained in systematic naming. This results in using of double vowels, e,g, cyclooctane.

However it has been accepted to elide following vowel a,e and o in the following circumstances.

(i) When preceding the suffix name of a functional group, example

Propanol not propaneol

Hexamine not hexane amine.

(ii) Naming Alkenes and Alkynes on the same compound-example Pentenyne not penteneyne.

3. Punctuation marks: Most commonly used punctuation in naming organic compounds are hyphens, commas and enclosing brackets.

(i) Hyphens:

(a) Used to connect numbers and letters serving as a locants.

For example: 2-Chloropropanone 1-Bromo-3-chlorobutane.

(b) Used to connect the prefixes like cis, trans (configurational prefixes) or structural prefixes (sec, tert, neo) with the compound name.

For example: Cis-2-butene, tert-butyl alcohol

The prefixes cis, trans, iso, neo, tert etc should be in italics.

(ii) Commas: Used to separate individual members of a series of locants.

Example: 1,1,2-Trichloro propane.

(iii) Enclosing brackets: Parenthesis ( ) and square [ ] are used as demarcation symbols when the locants are related to complete names. Example: 4-amino-N-(hydroxyl ethyl) butyramide.

Writing the structural formula from the given IUPAC name: To write the chemical strcture of a given compound from the IUPAC name, the following steps are to be adopted.

(i) Locate the parent alkane: From the name write the number of carbon atoms of the alkane in a straight chain and number them from any one of the end.

(ii) Locate the suffix: Locating suffix gives information about chain length, nature of functional group along with the positions.

(iii) Locate the groups/substituents: As mentioned in prefix locates the groups position in the chain.

(iv) Add hydrogen atoms if required to satisfy: Four valencies of each carbon atoms to get the formula.

Thus, for writing the structural formulae of 3-ethyl-2,5-dimethyl-1,4-octadiene.

(i) Parent alkane is octane. Write eight carbon atoms in a straight chain and number it.

(ii) The suffix diene indicates two double bonds in 1 and 4 points.

(iii) To locate the groups mentioned in prefix we attach ethyl group on 3rd C and methyl groups to 2nd C and 5th C to get the desired compounds.

(iv) Finally to satisfy valencies hydrogen atoms are added.

Probable Questions

3. What do you understand about IUPAC nomenclature system? and write the various rules and steps involved in it.

6. Mention the IUPAC names of the various compounds represented by the molecular formula C4H10O.

7. Write the IUPAC name for the following compounds.

9. Write the IUPAC nomenclature following compounds.

3

Structure of Organic Molecules and their Relative Properties

Introduction to Atom/Molecule

The wide diversity of chemical behavior of different compounds is due to the difference in the internal structure of constituting atoms of these compounds.

We know that the atom is made up of certain fundamental particles like electrons, protons, neutrons and subatomic particles like mesons and positrons. The protons and neutrons are present in the nucleus while electrons are present in the extra nuclear part which is divided into different orbitals. Electrons are the basic constituent of all atoms.

Wave nature of electrons and wave equations: Louis de Broglie, a French scientist in 1924 suggested that the electrons in an atom possess both particle and wave like properties. The properties of electrons in atoms can be better described as waves rather than particles.

There are two types of waves. One is travelling waves and another is standing waves. Example for travelling waves is sound waves and standing waves are waves found inside an organ pipe.

An electron in an atomic orbital is like a stationary, bound such as vibration: a standing wave. The three-dimensional standing wave features of an orbital are easily explained by using a guitar string as onedimensional analogy.

If we pluck a guitar string at its middle it produce standing waves. This vibration has spread into the upward and downward direction equally in a second (with equal time). If we draw an instantaneous diagram of the wave form, it shows the string displaced in a smooth curve either upward or downward, depending on the exact instant of the picture.

Now, 1s orbital of an atom is considered a string on a guitar (except 3D direction). The orbital is described by its wave equation ψ. Wave equation is a mathematical description of the shape of the wave as it vibrates. All of the waves are positive sign for a brief instant and then it is negative sign. The density of an electron at any point is given by ψ². The 1s orbital is spherical in shape and symmetrical, so it is indicated by a circle with the nucleus in centre and with a plus and minus sign to represent the instantaneous sign of the wave function (Fig. 3.1).

Figure 3.1 Similarity of the 1s orbital with fundamental vibration of guitar string.

The wave function square provides electron density. The spherically symmetrical orbital is represented by a circle with a nucleus.

When we gently place our finger at the centre of a guitar string while plucking the string from moving, the position at the midpoint is always zero so this point is node. The string vibrates in two halves at the mid point of string and the two halves are vibrating in opposite side. i.e., upward and downward displacement (the two halves of the string is out of phase). Fig. 3.2 shows the first harmonic of the guitar string.

Figure 3.2 The first harmonic of the guitar resembles 2p-orbital.

The two lobes of 2p orbital are separated by a nodal plane. The two lobes are out of phase with each other. When one lobe has plus sign, the other lobe has minus sign as shown in Fig. 3.2 (a)

Figure 3.2(a) The two lobes of 2p orbital are separated by a nodal plane.

The wave nature of the electron is indicated by following equation.

Wave equation or Schrodinger wave equation

Where, x, y, z = Three space coordinates.

ψ (psi) = Wave equation of the electron.

m = Mass of electron.

E = Total energy.

P.E. = Potential energy.

h = Planck’s constant.

The above equation indicates the state of an electron in terms of its mass, total energy, its potential energy relative to the nucleus, Planck’s constant and a quantity, ψ (psi) known as the wave function of the electron. Hence if we know the all other terms in Schrodinger equation, we can calculate ψ.

Quantum Mechanics

Quantum mechanics uses mathematical equation that explains the wave motion of electrons. According to this theory, the wave motion of guitar string is used to describe the motion of electron around the nucleus. In 1926, Erwin-Schrodinger proposed a wave equation of an electron. Wave equations possess a series of solution that are called as wave functions. Solving this wave equation for a given electron tells us the volume of space around the nucleus where the electron is likely to be present and is known as orbital.

Atomic Orbitals involved in Organic Molecules

Electrons move forth and back about the nucleus hence it would not be visible as a particle but it gives the appearance of diffused spherical cloud due to its motion. This is called as electron cloud. This concept can be explained by referring ceiling fan. At rest or slow movement, blades of fan occupy only a part of space but at high speed it occupies entire circular space. Similarly electrons occupy entire space around the nucleus but at some time it is found somewhere in space (Fig. 3.3 & 3.3(a)).

An orbital is a region in space where there is a maximum probability of finding the moving electron. Hence atomic orbital can also be defined as one electron wave function denoted by ψ, is the probability of finding an electron at that point. Therefore it is a mathematical symbol or representation of electron density distribution which has all the properties associated with waves. It has a numerical value which may be positive or negative (corresponding to the crest or trough of the wave respectively) or zero (which corresponds to a node which is a region where a crest and trough meet).

Figure 3.3 Only a portion of the circle occupied by a fan, but whole circular space is occupied when it rotates rapidly. Formation of a cloud when electron moves briskly in a shell is also similar to this.

Figure 3.3(a) Spinning of an electron around its own axis in clockwise and anticlockwise direction.

Shells, Sub-shells and Orbitals

The nucleus of an atom remains intact in most of the organic reactions and the outermost electrons only take part in chemical reactions. From the electronic structure of atoms, it is understood that atoms of elements heavier than hydrogen contain more than one electron which occupy definite orbitals. These orbitals further divided into several shells depending upon the principal quantum number n. The shell corresponding to a principal quantum number 1 is also called the K shell and the shell corresponding to principal quantum number 2 is also called the L shell. Likewise, the shells corresponding to higher principal quantum number 3, 4, 5, 6 and 7 are termed M, N, O, P and Q respectively.

Quantum Numbers

Principal quantum number (n, refers to the size of orbital): It denotes energy and distance of the electron from the nucleus. It cannot have value equal to zero which shows that electrons are not in nucleus as proved by Rutherford.

Azimuthal or subsidary quantum number (l, refers to the shape of the orbital): It is the geometric shape and the direction in which the electron is most likely to be found in an atom. It may have whole number values from 0 to (n-1). The area corresponding to the azimuthal quantum number is called subshells. The sub shells with respect to l = 0, 1, 2, and 3 are also designated by letters s, p, d and f respectively. The solid number of subshells in a shell is equal to its principal quantum number. For example, 1 or K shell has only one sub shell l (1s), 2 or L shell has two subshells (2s and 2p) and 3 or M shell has three subshells (3s, 3p and 3d). Similarly, four subshells in the 4 or N shells are the 4s, 4p, 4d and 4f. The term 2p⁴ means that there are four electrons in the p shell of the second or L shell.

The arrangement of shells, subshells and orbitals in an atom and the distribution of electrons are shown in Fig 3.4 and 3.4 a.

Magnetic quantum number (m, refers to the orientation of the orbital): It is the behavior of the electron in the magnetic field. It can have all integral values from - l to 0 to +l. Thus for 1s electrons, since l = 0; it can have only one value 0 which means that s orbital will not change in the magnetic field. When l = 1 i.e., for p orbital, m can have values -1, 0 and 1 which means that the p-orbital will orient itself in three different direction in the magnetic field represented by three axes. Such, orbitals are termed as pχ py and pz orbitals and are represented as shown in Fig. 3.5a. Similarly, the d- orbitals (l = 2) will give rise to five values of the magnetic quantum number (-2, -1, 0, 1, 2) and therefore d orbitals will split into five different orbitals while f orbital will split into seven different f orbitals corresponding to seven values of magnetic quantum number (m = -3, -2 -1, 0, 1, 2 and 3) when placed in the magnetic field.

Figure 3.4 Arrangement of shells and subshells in an atom.

Figure 3.4(a) Distribution of electrons in shells and subshells.

Figure 3.5 s orbital-Geometrical representation.

Spin quantum number (s, refers the direction of the spin of the electron about its own axis): It is a behavior of the electrons in the electrical field. It can be either + ½ or - ½ corresponding to each magnetic quantum number, as difference between the spin quantum numbers is always unity. Thus each of the p-orbitals (pχ py and pz) will have two electrons corresponding to spin quantum number of either + ½ or - ½. The p-sub shell therefore has six electrons (2 × 3 p-orbitals), d-orbitals ten electrons (2 × 5 d-orbitals) and /-orbitals fourteen electrons (2 × 7 f-orbitals).

So, the four quantum numbers give the following information:

1. n (Principal quantum number) defines the shell and determines the size of the orbital along with the energy of orbital. There are n subshells in the nth shell.

2. l (Azimuthal quantum number) identifies the subshell and determines the shape of the orbital. There are (2l + 1) orbitals present in each type of a subshell that is, one s orbital (l = 0), three p orbitals (l = 1) and five d-orbitals (l = 2) per sub shell. The l also determines the energy of the orbital in a multielectron atom to some extent.

3. m (Magnetic quantum number) indicates the orientation of the orbital. For a given value of l, m1 has (2l + 1) values, the same as the number of orbitals per subshell i.e., the number of orbitals is equal to the number of ways in which they are oriented.

4. s (Spin quantum number) indicates the orientation of the spin of the electron about its own axis.

Shapes of Atomic Orbitals

The directional properties of atomic orbitals play a major role in the determination of molecular shape. Hence in the formation of covalent bond only s and p orbitals are involved.

Shape of s orbital: According to wave mechanical calculations, the s orbital is spherical in shape (Fig. 3.5(a)) and symmetrical about the nucleus which is indicated by (+) sign. All atomic s orbitals possess spherical shape but only differ in their size i.e., size of the orbital increases with higher shell number. Thus 1s < 2s < 3s. Hence 1s orbital is surrounded by the larger 2s orbitals which in turn surrounded by still larger 3s orbital and so on. There is a space between every two s adjacent orbitals (between 1s and 2s) where the probability of finding an electron is zero (a spherical nodal space).

Figure 3.5(a)

Shape of p orbital: The p orbital is not spherical and symmetrical (Fig 3.5(b)) but it consists of two lobes to form a dumb-bell shaped structure. The three orbitals are identical in shape and energy but differ in their orientation about the x, y and z axes. The three orbitals are represented as px py and pz depending upon its orientation along the coordinate axes. The two lobes of the p orbitals do not touch with each other at the nucleus and are concentric with the nucleus which is called as node. In this node where the probability of finding an electron is zero and the plane passing through this point is termed as nodal plane that separates the two lobes of each dumb-bell.

Figure 3.5(b) p orbitals-Geometrical representation.

Rules for Distribution of Electrons into various Shells, Subshells and Orbitals

Based on the spectroscopic, magnetic, experimental and theoretical considerations, various rules for distribution of electrons into different shells, subshells and orbitals can be summarized as follows:

1. The maximum number of electrons in any shell is 2n² where n is the principal quantum number of the shell. Hence the maximum number of electrons in the first shell is 2, in the second shell is 8; in the third shell is 18; and the fourth shell is 32.

2 . The electrons always enter into the available orbital of the lowest energy. The new electron enters the orbital where (n+1) is minimum. Whenever (n+1) has the same value for two or more orbitals, the new electron enters the orbital where n is minimum. This is known as the Aufbau principle (Electrons are filled in the orbitals with increasing order of energy). Few orbitals arranged in the order of increasing energy are as follows:

The order may be remembered by the direction of the arrows which gives the order of filling of orbitals that is starting from right top to bottom left (Fig. 3.6)

Figure 3.6 Order of filling of orbitals.

3. Pauli exclusion principle: Only two electrons may exist in the same orbital and these electrons must have opposite spin.

4. As long as empty orbitals are available electrons will never pair, this is called as Hund’s rule of maximum multiplicity. That is pairing of electrons begins only with the introduction of second electron in the s-orbital, the fourth electron in p-orbital, the sixth electron in the d-orbital, and the eigth electron in the f-orbital. For example, two p-electrons in carbon are unpaired and three p electrons in nitrogen are also unpaired. Pairing begins with the introduction of fourth electron in p orbitals as in oxygen.

5. Stability of subshells: Completely full or exactly half-full, subshells are more stable. For example, nitrogen, with its p-orbitals half-full, is more stable than both of its neighbours, carbon and oxygen.

6. To explain the above points, electronic configuration of orbital elements from hydrogen (atomic number = 1) to neon (atomic number = 10) is given below in Table 3.1 & 3.1(a).

Table 3.1 & 3.1(a) Electron configuration of first ten elements.

Probable Questions

1. Define atom and write a brief note on atomic number and mass number of an atom.

2. Mention the wave equation and write its significance.

3. Explain in detail about the wave nature of electron and its properties.

4. What is meant by Schrodinger’s equation? and write its uses.

5. Define electron cloud