Tag Archives: Carbon

Elements necessary for humans

At present there are 118 elements listed in the periodic table. Some of these elements are commonly found on the earth in the form of ores. Some are radioactive and have very short half lives. Many such elements have been synthesized in the laboratory and live for a very short time.

Human body like other things existing is made of compounds which are made from the elements. Out of these 118 only some elements are connected with the human body.

Although elements as such don’t make up the body it is the combined form that is molecules constitute the human body. But elemental composition is as follows by mass.

Oxygen: 65%

Carbon: 18%

Hydrogen: 10%

Nitrogen: 3%

Other elements: 4%

Other elements include Calcium, Potassium, Phosphorus, Sulphur, Sodium, Chlorine, Magnesium, Boron, Chromium, Cobalt, Copper,  Fluorine, Iodine, Iron, Manganese, Molybdenum, Selenium, Silicon, Tin, Vanadium and Zinc.

Although these elements are used in very minor amount, they are crucial to some body processes.

Elements can be divided into different groups according to the functions they perform.

Building Blocks

The main building blocks of the body are proteins which are synthesized from amino acids. For these elements used are Hydrogen, Carbon, Nitrogen, Oxygen, Phosphorus and Sulphur. DNA also contains these elements except Sulphur. DNA is the genetic code.


Enzymes are chemicals which are catalysts for carrying out chemical reactions like breakdown of sugars and other macro molecules. Such enzymes use some elements like Magnesium, Manganese, Copper, Zinc, Selenium and Molybdenum. Enzymes play role in respiration, digestion, metabolism and immune system.

Nerves and Control

Brain sends messages to different parts of the body and this is a two way communication. Electrical signals are carried through electrolytic solutions like brines. Sodium, Potassium and Calcium ions this play the role of transmitting the signals. Similarly Chloride ions regulate the water in and out of cells. Iodine is used to make hormones which regulate metabolism.

Bones and Teeth

Bones make the template on which our body is hoisted. Strong bones and teeth are essential for the healthy body.  Bones and Teeth are made of Calcium and phosphate. Phosphate contains Phosphorus and Oxygen. Manganese element makes more stronger and resistance to breaking.


Blood is the lifeline of the body. Blood carries oxygen to the cells and removes the carbon-dioxide gas which is the byproduct of combustion reaction. Oxygen is carried by blood due to the presence of iron which binds the Oxygen. Other elements which are constituents of blood are Carbon, Oxygen, Iron and Cobalt. Cobalt is essential to make red blood cells.

Respiration and Energy

Respiration is inhalation of Oxygen. Adinosine Triphosphate (ATP) is formed during respiration which is the compound used by body as energy. Main elements involved here are Carbon, Nitrogen, Phosphorus and Oxygen.

Source: c&en magazine of American Chemical Society (ACS)

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.

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.

A Soccer Ball and C60 Molecule

Carbon, a small atom with atomic weight of 12 amu and atomic number of 6, is the element on which the life on this planet is based. Carbon atom forms 4 single electron bonds of sp3 configuration and hence can combine with 4 different atoms including carbon atoms. Thus it can form giant or macromolecules often found in nature. Some examples are carbohydrates, hydrocarbons, proteins, lipids and so on.

Buckminster Fuller

Carbon as such exists in two allotropic forms namely diamond and graphite with very different physical properties. While diamond is the hardest material and inert towards chemicals, graphite is active, chemically not inert and conducts electricity with ease and has a structure made of hexagonal sheets separated by electron clouds. There sheets can slip over each other making graphite a lubricant. Scientists has been able to separate these 1 atom thick sheets which have extraordinary properties like many times stronger than steel, easily foldable and superconductor of electricity. These sheets has been named Graphene.

Possibilities do not end here. In the interstellar dust, giant molecules of carbon which are very stable and inert have been detected. One of them is C60 molecule. If it was to be superstable and chemically inert, it should have a closed structure. Smalley and Kroto who were awarded Nobel Prize for the discovery looked towards the domes constructed by Buckminster Fuller outlined above. They called this molecule Buckminsterfullerene in his honor. A soccer ball is known as truncated icosahedron which has 60 vertices, 32 faces: 12 of which are pentagonal and 20 hexagonal. Famous architect Buckminster Fuller constructed biosphere structures which are very stable and energy efficient because a sphere has maximum volume but minimum surface area.

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.

Cyclohexane: A Chemical Chair

Cyclohexane belongs to the category of hydrocarbons called naphthenes. It has a chemical formula of C6H12. Naphthenes are found in crude oil. Most abundant are mono ring compounds of which cyclohexane is the perfect example. In fact, the poly ring naphthenes are found in the high boiling fractions of naphtha and the name seems to have been derived from naphtha. The term Naphthene has become almost redundant except in petroleum industry.The other fractions present in the crude oil are paraffins which are long chain alkanes  with formula CnH2n+1. For example, when n=6, then we have hexane with formula C6H14. High molecular weight paraffins are the main constituents of waxes. Another important category of compounds present in the crude oil is called aromatics. The most celebrated and simplest molecule of the category is Benzene with chemical formula C6H6. The overall properties of crude oil depend on the relative amounts of these fractions.

So, we observe that normal hexane, cyclohexane and benzene have six carbons but number of hydrogen atoms go on decreasing while going from paraffins to aromatics. This indicates that we are progressing towards graphite with the loss of hydrogen atoms. Crude oils derived from the marine sources are lighter in nature meaning they have lesser amounts of waxy paraffins. This helps them to be lighter and survive in under sea hydrostatic pressure. On the other hand, plants in the arid climates have wax on their leaves which helps in the prevention of moisture evaporation and is absolutely necessary for the survival of plants under harsh conditions. Thus the crude derived from terrestrial plants have higher wax content.

Anyway, we come to cyclohexane. The carbon atoms try to have tetrahedral geometry around them when combining to 4 atoms. But this is not possible here. So they settle for a compromise for stability. Cyclohexane twists to have a shape like a chair with alternate carbons in two parallel planes and hydrogen atoms arranged in two directions. They are in positions called axial and equatorial positions with axial hydrogen atoms almost perpendicular to the carbon atoms plane with alternating up and down positions.

How was this structure confirmed? It was confirmed by using the tool called Nuclear Magnetic Resonance (NMR) which is used these days in the medical science under the name of MRI. The protons  (hydrogen atoms) behave like tiny magnets and spin around their axis. As we know from the magnets, when we place a small magnet near a strong magnet, smaller one aligns itself along the axis of stronger magnet. Energy is required to flip it back to its original position. Thus the principle of NMR is that molecules are placed in a powerful magnetic field and swept with electromagnetic energy. This will be of no useful tool if all the hydrogen atoms absorb the energy at same wavelength. Fortunately, the magnetic moments of hydrogen atoms are modified by the electronic environment around it a molecule which may be due to the presence of hetero atoms and groups or different number of groups. Thus due to the different environment, the hydrogen atoms absorb energy at different wavelengths. From this we come to know the chemical environment of different hydrogen atoms and thus elucidate its structure. In our brain, we have so many molecules which contain hydrogen atoms and these are affected by the state of our mind.

When cyclohexane is placed in a NMR cell, we get only a single signal indicating that all the hydrogen atoms are equivalent. But this is true only at normal temperature. The reason is that axial and equatorial hydrogen atoms flip up and down because energy required for this is very small and room temperature provides it. But as we cool the sample, less energy is available and a temperature reaches 40K, the atoms sort of freeze in their locations and two peaks begin to appear. These peaks are indicative of up and down orientation hydrogen atoms. This confirms a chair configuration of cyclohexane.

Buckyballs, Fullerenes & Diamondoids

Carbon has a special place amongst all the elements. It is king of covalent compounds and a separate branch of chemistry called organic chemistry is devoted to the carbon compounds. These organic compounds are formed by the bonds formed between carbon and carbon or carbon and hydrogen or oxygen atoms. Carbon can form 4 covalent bonds and hence there are endless possibilities of compounds. Organic compounds are major constituents of our bodies and food.

Carbon has atomic number of six. This means that it has 4 electrons in the outer L shell and thus is tetravalent and combines with 4 atoms. The arrangement of atoms about carbon is tetrahedral in nature. Ranging from the hydrocarbons which are the constituents of the petroleum to carbohydrates there is a plethora of carbon based compounds.

Elemental carbon in itself is very interesting element. Till recently, it was supposed to be existing in two allotropic forms which were called graphite and diamonds. Allotrope differ in their physical properties like melting point, hardness and electrical conductivity but chemical properties are almost same though the rates of reaction shall differ due to the different energy requirements to break the structures. Graphite has two dimensional layers consisting of repeating hexagons like a honeycomb. These layers exist parallel to one another. Due to this, they can slip over under stress. This property makes it an lubricant. In between the layers are clouds of electrons which make the graphite a good conductor of electricity.

Diamond,on the other hand, is known to be the hardest elements due to its compact structure formed by joining the tetrahedrons. They are as everyone knows are the most sought after items of jewelry. Many of them had been the cause of wars between kingdoms and bad luck for their possessors. They are the bad conductors of electricity.

So this was the status till recently. But there was one addition to the two allotropes. This new allotrope is called as Fullrenes and was found by Robert Curl, Harold Kroto and Richard Smalley on analyzing the products formed when carbon is evaporated in the vacuum in the inert atmosphere. The structures contain up to 60 to 70 carbons. The special one which has 60 carbon atoms resembles a football and has been named “Buckyball” after the architect Buckminster Fuller who had designed the Geodesic Globe. The balls surface contains pentagons and hexagons juxtaposed.

Why were these not recognised for so many years? Why did they eluded the scientists for so long? . One reason is the miniscule amount of these which exists only in the stars. With the advent of latest instruments like Mass spectrometers and ingenuity of the some brilliant human beings, these have been synthesised in micro scale in the laboratory. Experiments are on to develop the affordable commerical methods for their productions.

Fullrenes and buckyballs belong to class of nanomolecules. They have certain properties which will revolutionize the future science. Some of the applications include the synthesis of special molecules inside them becuase they act like a cage and trap molecules of many types. Fullrenes are cylindrical tubes which are the lightest but very strong. There are vast possibilities for their use. Beginning from construction of efficient air planes and energy efficient machines and in the construction of super conducting materials.

Incidentally, there is another class of carbon compounds called diamondoids. These are compounds like the Bucky balls but having few hydrogen atoms in the place of carbon atoms. These compounds have been found in the petroleum. These are also detected by mass spectrometry and NMR. They also belong to the category of nano-molecules and hold promise for many new applications in the metallurgy, super conducting materials and shed the light on the formation, generation and migration of petroleum.

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”