S12-THE MOLECULES IN ORGANIC CHEMISTRY

By PragyanSharma Polavarapu

In the old days 55 years ago I vaguely remember there was a list of 92 elements (the very interesting Mendeleev Periodic Table) .

The Trans-uranium elements subsequently included in the Periodic Table have increased the number of elements to 118 . But the transuranium elements are mostly unstable radioactive elements and are created in laboratories or in nuclear reactors and particle accelerators . But being a simple worshipper of old Daltonian chemistry I am not interested.

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Out of the old periodic table list of 92 elements 17 are non metals .Here I am concerned only with the old familiar non-metals like C, H2, N2 and O2 ,S –all of which are important in organic chemistry. A few words about non-metals in general.

While metals have a special metallic shine and and conduct heat and electricity easily,the solid non-metallic elements — carbon, sulphur, phosphorous, silicon, boron etc.— are brittle, do not bend and do not possess the mirror like shine of metal.( Bromine is a liquid non-metal).

The gases oxygen, nitrogen, hydrogen, chlorine, etc are treated as non-metals because their chemical reactions are identical with the reactions of the solid non metals.(Hydrogen is sometimes treated as metal and sometimes as non-metal based on its chemical properties).

Even scientists thought till 300 or 400 years ago that pure unpolluted air was an element. But it was found that air is a mechanical mixture of oxygen ( 21% ) and nitrogen ( 78%).Water too was treated as an element but when electrolyzed broke into the two elemental gases oxygen and hydrogen. It is a chemical compound.

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Everybody knows that elements, whether metals or nonmetals, are composed of extremely minute unbreakable particles called atoms. The sharp point of a pin can accommodate thousands of millions of atoms! (The correct number is many times more) .There are now 118 elements and so 118 types of atoms .But we are now interested only in the first 92 elements of the old Mandeliev periodic table.

The smallest particles of a chemical compound is the molecule. Molecules are groups of atoms strongly tied by bonds made of electron pairs . In another way we may say that molecules are just like boxes in which atoms are fixed rigidly in a 3D structure.

Understanding Organic Reactions

After two or three centuries of modern research scientists could realize that the slow organic chemical reactions in bodies of humans,plants, fishes,animals are entirely similar in nature to the inorganic chemical reactions in mineral substances. Only the rates(speeds) of the reactions are different. Inorganic chemical reactions are generally instantaneous while the organic chemical reactions take hours or even a day to complete.

Even in modern age scientists thought for a long time that a “vital force”( un-understandable strange force) manages the organic reactions and that the organic reactions cannot be explained by rules of inorganic chemistry. Scientists are now agreed that inorganic and organic reactions are completely similar and that there is no need for any vital force. Of course there are vast differences in the way inorganic and organic chemical reactions proceed.

(1) In molecules of mineral substances (inorganic substances) only very few atoms , at the most ten atoms, exist in participating or resultant molecules . But in the world of organic chemistry a molecule( participating molecule or resultant molecule) may contain hundreds of atoms !

(2)Almost every molecule in chemical reactions in living beings should contain atoms of element carbon. Reason is that all organic chemical compounds are created based on “hydrocarbons” which contain a long chain of carbon atoms to which a large number of hydrogen atoms are attached

(3) The inorganic chemical reaction is instantaneous but the chemical reactions on organic substances proceed very slowly taking hours or even a day or more.

(4) There are said to be around 20 million “organic chemical compounds” classified and studied in science laboratories. In comparison the inorganic compounds classified in science laboratories are only about half a million i.e. around 500,000.

Organic chemical reactions

Here we study organic chemical reactions in a few special situations

(a) Abundance of water

On planet earth the most important and extensive thing is water –mainly the ocean water. For nearly two to three billion years only single celled organisms lived in water . Only after the atmosphere was filled with oxygen and only after plants prepared carbohydrate food living creatures migrated to land surface away from water.

( b) Abundance of air

Scientists say that in the oldest atmosphere of earth 4500 billion years ago(when earth was a burning ball of melted rocks and melted metal) there were only helium and hydrogen in air . There was no oxygen. This was the “first atmosphere” of earth .

The earth started to cool quickly after it moved very far away from sun and entered its orbit in extremely cold cosmic space. Thick semi-solid stony plates of continent-size and above them a solid crust formed on earth. The temperature was around 70 to 80 degrees in the oceans . It might have rained for hundreds of years. There were thousands of volcanoes.There was pungent and suffocating atmosphere. It was called “second atmosphere”.

Scientists say that after several hundred millions later the temperatures further came down to 30 to 40 degrees . Green cyanobacteria containing chlorophyll started manufacturing carbohydrate during sunlight hours and also released oxygen in to atmosphere for a billion years or more . The great “oxygen atmosphere” the life giver was created and modern species very slowly developed in the long millions of years. This is called “third atmosphere” of planet earth.

(c) The oxygen reaction region called fire

All substances like petroleum and diesel, vegetable oils,and things like paper,wood,dry leaves,cotton,seeds,sugar are all hydrocarbon based substances. Even a burning candle,burning paper,burning match stick etc have a temperature of 1500degrees and can burn any hydrocarbon substance. Most fires on earth relate to hydrocarbon burning only. In every fire involving hydrocarbons ,water vapour and carbon dioxide gas are formed with release of great amounts of heat energy.

(d) In presence of sunlight and lightnings — The sunlight and lightning are always present at some area of the sphere of earth —whether on land or on ocean surface or in a deep forest. Photosynthesis by plants(whether on land or in sea) is entirely dependent on sunlight as sun is the supplier of energy. The lightnings help produce lot of nitrogenous fertilized in soil.

( d ) The slow organic reaction

While the reactions in inorganic chemistry are completed in seconds , the organic metabolic reactions occurring inside living creatures are so slow that they may take hours or even a day or more for completion of reaction. Respiration, digestion, fermentation for alcohol, formation of curd from milk, ripening of fruit and even putrefaction —all are combinations of hundreds of organic chemical reactions.