Tag Archives: Molecule

Optical Isomerism

Everything is identical about these twins. Number of atoms, type of atoms are same. Only difference is the spatial arrangement of atoms or groups of atoms attached to the carbon atoms. There is one more trait of these twins-they are mirror images of one another. They are called stereoisomers. Stereo means spatial.

There is a slight differences in the reactivity of these members. One very interesting property of these molecules is that they rotate the light passing through their solution in equal and opposite directions called Levo and Dextro.

When such compounds are synthesized in the laboratory, we obtain both isomers in equal amounts and there is no optical activity because effect of one type isomers is nullified by the effect in opposite direction.

But in nature, synthesis of macro-molecules like carbohydrates, lipids and oils by the biological enzyme driven reactions we exclusively obtain only one kind of isomers-mostly levo-rotatary. This is due to enzymes which are proteins and very specific catalysts whereas industrial catalysts are surface active and both isomers are manufactured in equal amounts. Special techniques are required to separate them into pure Levo or Dextro isomers. Due to this reason the cost of these isomers increases manifolds. It has been found that some diseases respond to specific isomers. Such medicine are called stereo-specific medicine.

Advertisements

Bacteria in Oilfields

Bacteria can thrive on almost anything and adapt themselves to very diverse environments. They can eat subsist on substances like cellulose which we humans cannot assimilate. They can breakdown poisonous gases like hydrogen sulfide and absorb nitrogen from atmosphere and fix them into the roots of many plants which plants use as fertilizer.

Bacteria can even breakdown crude oil. Crude oil consists of millions of hydrocarbons which are composed from carbon and hydrogen. These compounds range from the simplest molecule called methane made from 1 carbon atom to giant molecules containing even more than 50 carbon atoms.

Many of these bacteria live in the upper crust of the soil. They have attained the capability to use lighter hydrocarbon gases namely methane, ethane, propane and also the higher molecular hydrocarbons as the source of the carbon nutrient for energy. These are called aerobic bacteria and commonly termed as methanotrophs, propanotrophs and so on. They use like us the atmospheric oxygen to oxidize the hydrocarbons and end result is energy, carbon dioxide and water, the same products as are generated during the digestion of food by us. Of course, they also need so many other nutrients like electrolytes, trace elements which they use to synthesize enzymes which help in carrying out degradation reactions at much lower temperatures.

But this is not the end of story. There are bacteria which can survive in the anoxic (without oxygen) environment such as deeply buried bacteria which breakdown the organic matter. They extract the oxygen required to breakdown the organic matter from the sulfate ions present in the water associated with the organic matter. They breakdown the organic matter to methane and one strain of them is aptly called methanogens.

One may wonder if such bacteria exist deep down and breakdown the oil why have they eaten up all the oil present inside the reservoirs. The answer is that they are sloths in nature. They multiply with speeds nowhere near to the aerobic bacteria. Experimenters working in proliferating and separating the pure strains are often frustrated with there laziness.

The hypothesis that all the biogenic gas has been produced by aerobic bacteria is being challenged because biogenic gas has been found in the deeper sediments generated under anaerobic conditions. Researchers say that the methane trapped inside the ice crystals called gas hydrates has been the handiwork of methanogens.

Graphene: Size Zero Allotrope

Carbon is the atom on which the life on the earth is based. Though it is not a complicated element having only 6 atomic number, it ability to form compounds with hydrogen, oxygen, sulfur and host of other atoms and its ability for catenation makes it the most distinguished element for us. We owe our existence to it. Most of the macromolecules which are bodies are composed of contain carbon, hydrogen and oxygen.

This simple element show another very surprising properties. One of them is the allotropy. Two allotrope are two different arrangements in which an element can exist. Till 2004, two allotropes of carbon, diamond and graphite were recognized. A simple change in the way atoms are arranged geometrically can drastically alter their properties.

Diamond is network of tetrahedrons in which each carbon is joined with 4 other carbon atoms and so on. This forms a network which is the hardest material in the world. It sparkles in the light as the light is refracted at so many faces and unable to escape.

Graphite on the other hand is the form in which carbon atoms form honeycomb structures of hexagons joined to each other in the layers. The attraction between layers is not much and layers can slip over one another giving it a lubrication ability. Since there are are free electrons between the layers on each carbon, they form a tunnel in which electrons can move. Thus graphite also conducts electricity.

Now comes the Graphene. If you peel each layer, you have a two dimensional material which is thinnest material in the world. It is only 1 carbon atom thick and but at the same time it is the strongest material in the world, 100 times stronger than the steel.

Only limitation presently is its manufacture on commercial level in the purest form because contamination of even in single alien atom can spoil all the properties.

So many uses are already envisaged for this material. Since it conducts electricity better than any other material and unbreakable and very thin, future cellphones and other electronic touch screen gadgets shall be made from this. These shall be very thin, would not break on falling and could be folded to suit the pockets.

Another use shall be in the bionic devices because it is flexible and highly resistant to the corrosion caused by electrolytes present in the cells of human beings. These devices can be inserted at any place for many years without worrying for replacement.

At present scientists are trying to explore methods of making it on commercial scale. May be some genius like Kary Mullis device something like Polymerase chain reaction (PCR)  to multiply it million folds from a single copy. Nothing is impossible.

Chemistry by Nature

Nature is a great chemist. It synthesizes millions of compounds every moment ranging from simple molecules like methane to very complex molecules like carbohydrates, cellulose and proteins. Most of these compounds are synthesized by plants. From the plants they are passed on to animals because the animals cannot synthesize their food by themselves. But there are many chemical reactions occurring inside the cells like breaking down the complex molecules and unlocking the energy which is stored in them.

Where does all the energy locked inside the different molecules come from? Most of it is derived from the Sun light. In many cultures like Hindus and Egyptians, Sun is worshiped as the harbinger of life. They may not be knowing the scientific facts behind it. Energy tries to dissipate and some storage is required to held it at one place and use it whenever required. Cells are the prime example.

How do the plants get hold of the energy. They carry out a reaction called photosynthesis in which they combine carbon dioxide and water in the presence of sunlight. All this work is done with the help of a big organic molecule called Chlorophyll. The products of this reaction are sugar and oxygen. When human beings consume the sugar, they break it down again to carbon dioxide and water and energy absorbed from the sun is unlocked and nourishes our bodies.

This reaction is a fuel burning reaction. But unlike the burning of fuels it happens at a very low temperature (body temperature) in our bodies although both reactions are exothermic in nature. How is this achieved? First of all, only those reactions are possible which results in products having lower energy than the reactants. But to initiate the reaction, the system has to cross a energy hill called energy of activation.

Catalysts are capable of making the reactions occur at low temperatures because they lower the energy of activation. In our bodies there are specialized proteins which are called enzymes which act as catalysts. These are very specific and one enzyme is specialized for only one task.

Catalysts also determine the kind of product that is synthesized. For example, the hydrogenation of unsaturated oils can be carried out by reaction with hydrogen. In the case of using a catalyst, only cis addition to the double bond is allowed whereas without catalyst in addition to elevated temperature and pressure conditions, the product formed is a mixture of both cis and trans products.

Since in the nature most of the reactions are carried out at ambient conditions, enzymes are generally utilized by the nature. In the case of molecules having asymmetric carbon centres a mixture of 50:50 ratio is produced without enzymes. These are called stereo-isomers and rotate the light in left and right direction. But in nature only one of these forms is synthesized. After all animals consume only one form of stereoisomers.

So nature is a great chemist.

Achievements of a wandering mind

Many a times you must have experienced in your life that you cannot recall a certain incident, name of a person or a book or author although at other times you remembered it so well. In those circumstances, the harder you try to recall more it eludes you. It is not the case of poor memory or age as it happens with everyone at one time or another. You leave it frustrated and become busy in some other work and in a flash the things will come to your mind. The same has happened to many great scientists and authors.

August Kekulé von Stradonitz, the great chemist who elucidated the structure of benzene did it in reverie while riding a horse drawn bus. As he will doze off, he saw the atoms dancing before his eyes. These atoms caught hold of each other. The bigger ones held more than one smaller atoms and so on. Thus he was able to arrive at the ring structure of the benzene molecule. Not only that, he was able to draw the structure of molecules with same molecular formula but different physical properties. He was talking about geometrical isomers. It was left to his brilliant young student Vant Hoff to discover the sterochemistry of carbon molecules in which for different groups are attached to a carbon atom. Such carbon atoms are said to be asymmetric and stereo isomerism imparts a property of deflecting light to right or left from its path when light travels through the solution of such substances. Such molecules are called optically active compounds with dextro (right) rotatory and levo (left) rotatory categories. Whenever such compounds are synthesized in the laboratory we end up with 50:50 mixtures of both forms which are optically inactive because the deflection caused by one set to left is countered by another set to the right. To separate these mixture into pure forms, these mixtures are reacted with a pure levo or dextro rotatory compound resulting in two salts of different melting of boiling points which are easily separable. After separation the add on moelcule has to be detached to obtain the pure compound of levo or dextro nature. n nature, we encountered only single type of compounds either levo-rotatory or dextro rotatory because most of the natural compounds are synthesized by different routes using the enzymes. It was the great Luis Pasteur who separated the two optically active  forms of tartaric acid crystals using tweezers and demonstrated the optical activity. The weather of France also assisted him because the tartaric acid obtained from the raw grapes formed large beautiful crystals.

Another example of great achievements of wandering mind is that of Greek mathematician Archimedes. He was given the commission by the King to know whether the crown he ordered to be made was really of Gold or of gold alloy. Archimedes thought and thought about solving the problem from many angles but was frustrated and he decided to leave aside the problem for sometimes. He ordered his servant to make a bath for  him. As he lowered himself into the bath, he saw the level of water rising. The idea that same weights of different elements displace the different volume of water suddenly flashed to his mind. This way he can find the volume that a certain weight of gold will occupy perhaps by comparing the crown weight by same weight pure gold. He was so elated that he jumped out of the bath and ran naked towards the palace shouting the now famous word  “Eureka”

The story of H2O Molecule

I am a molecule of water. Hydrogen and Oxygen are two elements which combine in the ratio of 2 to 1 to create me. I have abundant siblings on the earth. In fact we make up for about 70% of the earth. I am so small that I can enter into smallest of spaces. My birth place is in the space. We all are so identical that it is impossible to label us with names. We all have only one name and that is water. there are species called homo sapiens  After birth I along with my other brothers began living in a place which people started calling the seas. In the beginning we all lived in one place but many upheavals separated us and we were divided into many parts.

We are always in the ceaseless state of movement. Never had time to rest. We chase each other, collide with each other and collide with surroundings. Some of us move and dance faster than others. When the agile ones get tired, they slow down and hand over the baton to sluggards who in turn become agile. But we are bound to each other. But when the Sun is angry and it is hot, some of us are thrown out from the sea and fly up and up. Then we float aimlessly in the atmosphere. We wander from here and there. But we again come together at places which are cool such as above the mountains and rich vegetation. We join one another so tightly that we cannot remain afloat. We begin to fall towards earth.

So of us fall on the mountains where temperatures are so low that we become hibernated and enter a deeper and longer sleep. Others fall directly on the earth where they flow collectively as one body and travels from high altitudes to low altitudes. Some of us are very curious and collect inside the depression and become confined there for very long periods.  Other more adventurous even penetrate the earth and go deep inside it and remain there for thousands of years. During our journey on the land we take with us members of other communities which disintegrate inside us into their individual entities. Some of us joined on the way with others become a mammoth creature called the river and flow towards our home at sea. It can take us 2 to 6 months time for reaching back.

Our brothers in the confined places called lakes and ponds have to wait  much much longer to reach home. When Sun smiles benignly on them, some of us again escape into the atmosphere and if lucky go back either falling directly into the sea or falling again on the earth and joining the other which have already begun their journey towards home in the form of river.

All for You

What you will say,

We will say also.

Brine is mud,

mud brine.

Deep is shallow and

Shallow deep.

Pigeons crows and

Crows pigeons.

What you will say,

We will say also.

Sun comes in night,

Moon in the day.

Night is bright,

Dark is the day.

DNA is RNA,

RNA DNA.

Oil is heavy,

Water lighter,

Gas is heaviest.

What you will say,

We will say also.

Our faith unshakable,

in you is blind.

No questions, No queries,

No F&A Q s.

Your word is final,

O’ Nimrod!, bless us bless us!