Archive for September, 2015

Science Makes Senses Week 6: Sulfur, brimstone, rubber,sulfa drugs and alliums

September 27, 2015

Pope Francis is visiting the United States, and I could not help but think of the Catholic nuns in school who would scare us with words like ‘fire’ and ‘brimstone’.They would warn us about sinning and hell. ‘Brimstone’ was just another word for sulfur which is supposed to be burning forever in that nether place.

The word ‘sufra’ in Arabic means yellow and sulfur’s name could have been derived from it. Also in Sanskrit, sulfur was called ‘Shulbari’ which means ‘enemy of copper’ From ancient times it was known that metals like copper reacted with sulfur.

For years, people have believed that sulfur springs were good for their health and took daily dips in them. In fact, there are places in Texas and Florida named Sulphur Springs! Sulfur was also used as a fumigant (to control pests) thousands of years ago.Today I will talk about this useful element that we have known for so long and hope to separate myth from reality.

The chemical symbol is S. When sulfur burns in the presence of oxygen, it burns with a blue flame. and has a distinctive odor:

S +O2    →   SO2

                          ( Sulfur plus oxygen gives sulfur dioxide)

Match heads made of sulfur when burnt would lead to the same odor: same oxidation reaction, leading to sulfur dioxide.

Sulfur is lemon-yellow in color and is a non-metal. In the Periodic Table it is just under Oxygen, or in the same Group as Oxygen. (The rows in a Periodic Table are called the ‘periods’ and the columns are called ‘groups’.)

week 6 sweek 6 ssweek6

Many vegetables we cook with have sulfur compounds in them including onions, garlic, cabbage. Eggs contain sulfur and rotten eggs have a distinctive smell because of hydrogen sulfide  H2S (a compound of 2 atoms of hydrogen and one atom of sulfur). Sulfur is found offshore in Texas and Louisiana and is not usually mined directly, since hydrogen sulfide, a toxic gas, is often present, along with sulfuric acid fumes. The sulfur is mined by the Frasch process, where hot water is pumped to the levels where sulfur is deposited and fairly pure sulfur is obtained. Actually, more and more extraction of sulfur takes place during petroleum production. However, in countries like Indonesia and parts of South America, even to this day sulfur is mined directly from volcano craters,  a job filled with hazards for the miners.

Sulfur is used in the vulcanization of rubber. Natural rubber tends to stretch or get hardened easily.Vulcanization is the addition of sulfur to natural rubber which then increases its tensile strength; an important property in the manufacture of tires. Today tires in the United States are mostly made using synthetic rubber versus rubber from a tree(natural rubber).

Most of the sulfur that is extracted is used in the manufacture of sulfuric acid and most of the sulfuric acid is used to make fertilizers and batteries. Sulfur is also used as a fungicide.

Before the manufacture of antibiotics we had sulfa drugs, chemically synthesized organo-sulfur compounds used to treat bacterial infections. (An organo-sulfur compound is a multi carbon,multi hydrogen and sulfur containing compound  with covalent bonding) (I will talk soon in my blogs about covalent bonding) In 1930, the first case is recorded where a sulfa- drug, a sulfanilamide molecule, cured bacterial infection successfully. Chemists were eager to synthesize more sulfa drugs and between 1935-46, over five thousand different variations of the sulfanilamide molecule was made.(Don’t be scared by the big name, this is an organic compound containing sulfur-‘sulfa’; the nitrogen with hydrogen indicates the ‘ amide’. As we continue to study Organic Chemistry, all these so-called complicated names will make sense.) Out of all the molecules synthesized, three more stand out: Sulfapyridine, used for the treatment of pneumonia, Sulfathiazole for the treatment of gastro-intestinal infections and Sulfacetamide for the treatment of urinary tract infections.

In fact, during World War I, (1914-18) there was no effective treatment available for bacterial infections. Because of infections like gangrene many soldiers had to have their limbs amputated or unfortunately, sometimes they died. During World War II, (1939-45) with the discovery of sulfa drugs Sulfapyridine and Sulfathiasole, veterans’ limbs and lives were saved. Sulfa drugs cured thousands of lives at home suffering from pneumonia and in the battlefield and were considered ‘wonder drugs’.Some of us born in the ’50s and ’60s are well aware of using these sulfa drugs.

The intriguing  fact is that these sulfa drugs do not kill the bacteria, which is what an anti-bacterial agent is supposed to do. Bacteria need folic acid to thrive and multiply inside our bodies. (Most of our folic acid comes from leafy vegetables that we eat.) The remarkable fact is that the middle portion of the folic acid  structure looks a lot like the structure of the sulfa drug. So the bacteria takes in the sulfa drug, thinking it is folic acid and dies.

Without sulfur chemists could not have synthesized these wonder drugs. Of course, today we have penicillin (naturally occurring substance that contains sulfur) and other antibiotics that are more effective , but we still use a few sulfa drugs for certain kinds of infections. This lemon-colored solid called sulfur plays a significant role in our lives. It is the 17th most abundant element on earth and the 10th most abundant element in the universe.

Activities for Middle School Teachers: If you have access to a laboratory, create some of the allotropes of sulfur, so students can observe the various crystalline shapes.

Collaborate with the geography/social studies instructor to find where sulfur is mined from volcanoes, where sulfur is extracted using the Frasch process and where sulfur is obtained during petroleum production.

Connect with history to look at young adult fiction based on World War I and II.Read books where veterans returned from World War I with limbs amputated.*

Let students interview family members (great uncles, great grandparents, great aunts etc) and learn about the use of sulfa drugs in their younger days during bacterial infections.

Nuggets of information: Sulfur dioxide was used as a refrigerant to create the first artificial ice-skating rink.

Elemental sulfur has several allotropes. When an element has one or more allotropes of itself it means it can be found having different structures. Sulfur exists as monoclinic, rhombic and plastic sulfur.

Hair,skin and  feathers contain a lot of sulfur,

Why do we cry when we cut onions? The cells of the onions release a sulfur containing compound that breaks down basically into sulfuric acid and other sulfur compounds, enters our eyes and reacts with the water there to sting our eyes and makes it water to flush the acid out.

Onions, leeks, chives, garlic all belong to the Allium family and they are all monocotyledons not dicotyledons. (i.e., when they sprout they have single leaves instead of two leaves.) Alliums absorb sulfur from the soil.


Le Couteur, Penny and Burreson,Jay,   Napolean’s Buttons: How 17 molecules changed History,(Jeremy P. Tarcher Putnam,2003)


Science Makes Sense Week 5: Wonderful water, The Ghost Map and Weeping Willow

September 20, 2015

Every time I open the faucet to wash dishes or drink some water, I have to remind myself of the fact that thousands of people, mostly women, all over the world, are right now searching for/storing water and fuel for their daily survival.  I also think of California now using gray water (water used for washing/bathing) whenever possible to water gardens after going through a severe drought and forest fires. Water is such a precious commodity but we take it for granted when there seems to be plenty available. All trees, plants, animals need this liquid to survive but a tree like the weeping willow, would hardly grow without a constant flow of water.Today we will look at water, first as a chemist and then its significance in 19th century England.


A water molecule (a molecule is a combination of atoms) is made up of two atoms of hydrogen and one atom of oxygen and the chemical formula is written as H2O. The structure is planar (unlike methane, CH4 , which is 3-dimensional, a tetrahedron) and can be depicted with the H-O-H angle as 1050  

and is shown as:IMG_2265

Also, the molecule is polar since the electronic cloud in each bond, moves a little closer to the oxygen atom and therefore the hydrogen atom is slightly positive(δ+) and the oxygen atom is slightly negative (δ-). This allows the different molecules of water to form a connection with each other like this:IMG_2264This is called hydrogen bonding.

Water has some unique properties because of its polarity; it dissolves  many solids and is used as the first test to detect chemicals in the laboratory: is the substance soluble or insoluble in water? Water is called the universal solvent and allows us to absorb many nutrients when we eat, because they dissolve in water readily. Substances that dissolve in water are called hydrophilic and those that repel water( like oil) are called hydrophobic. 

Water exhibits cohesion, adhesion and surface tension as well because of its polarity. Cohesion means water sticks well to other water molecules and adhesion means that water sticks to other substances as well. Because of adhesion, water spreads out well on a glass plate. The high surface tension of water leads to more of cohesion versus  adhesion causing water to act like the surface is a stretched transparent plastic sheet. Surface tension is why water beads up on a waxed car or on the surface of leaves/fruits (that have a waxy, oily surface) after a rainfall, or when you wash them.The meniscus of water is curved such that it has a concave shape, more on the sides of the container and less in the middle, away from the container. Adhesion and water’s high surface tension are responsible for the shape of the meniscus.

The hydrogen bonding leads to some unique properties as well. Water has a very high specific heat, which means it takes a long time to heat up. (I will talk again about specific heat later) But to me, the most interesting and useful application of water is in the way it freezes. All liquids, when they cool down sufficiently become solids and almost always the solids are denser than their liquid form, which means they will sink to the bottom of a container containing the liquid.  Water, however, behaves differently. As you start cooling water, the density (ratio of mass over volume) increases, but at  40C it starts getting less dense. (Remember that water freezes to ice at 00C)This has a lot to do with the lattice-like structure due to hydrogen bonding that leads to a lot of open spaces between the water molecules.(When volume increases, density decreases.) So, when the weather gets cold and the local pond or river starts freezing, the ice forms a layer on the top, does not sink down and all aquatic life continues to live in cold weather,since the water body does not freeze solid; amazing!

In the middle of the 19th century, London was already a very congested city. The book, The Ghost Map, written by Steven Johnson, is a true account of the mysterious high number of deaths that was happening suddenly in a part of London. At that time, the prevalent notion was that because there were many people living together, there was ‘bad air’ that caused this epidemic. However, a physician Dr Snow, figured out where the deaths were taking place and did a detailed mapping of that area to find out that the abnormal high mortality rate was because of contaminated drinking water from the same source; a water pump. For the first time, a water-borne disease like cholera were correctly diagnosed. As you can see here, water the universal solvent, can also lead to terrible consequences.

Activities for Middle School Teachers: Work collaboratively with the math instructor on gathering statistical data (like the data collected by Dr. Snow in the book) .

You could also collaborate with the Social Studies instructor to read the book The Ghost Map to understand the importance of water in figuring out how the epidemic spread.

During  the early winter season, take students on a field trip to view lakes, ponds that have a thin upper layer of ice. Ask students, “Why do ice cubes float and not sink in water?”  Take students to the nearest water filtration area for them to understand how local water is purified.Students can learn how to measure the volume of water in a measuring cylinder by looking at the lower meniscus at eye level. In addition, students could improve their geography skills and locate big cities around the world close to a water source.

Nuggets of information: Stop drinking bottled water, you are wasting money and adding more plastic to the environment.The water is not any different from tap water, and is slightly treated. Contrary to popular belief, this bottled water does not come from some mysterious sparkling spring somewhere.

John Snow mentioned in The Ghost Map,is considered the Father of Epidemiology. This means the science  of the patterns , causes  and effects of diseases  and health in a defined population.


The Ghost Map The Story of London’s Most Terrifying Epidemic — and How It Changed Science, Cities, and the Modern World

by Steven Johnson Riverhead Books, New York, 2006.

Science makes Sense Week 4: Chemistry and Social Justice, fracking, natural gases, pollutants, water

September 14, 2015

“Drill baby drill!’ was the rallying cry in 2008 before the Presidential Elections by a certain party in the United States. It did not matter that the opposing party won the elections since drilling for oil in Alaska and fracking in several states is being continued with no stoppage.

Last week, I talked about the petroleum industry and the heavy dependence on all the by-products for our energy needs here in the United States. The spread of Chemistry and its applications has been exciting and fruitful in industry, pharmaceuticals, cosmetics (to name a few) especially for the past century. Along with the benefits, there has been side effects that have adversely affected the human race as well as the environment around us. Every fourth week we shall look at this under the sub heading” Chemistry and Social Justice” Today I will focus on the popularity of fracking to extract natural gases from shale oil.

Most petroleum products are extracted using oil rigs that look for fossil fuels in land and water (called off-shore drilling) However, in the early 14th century, shale oil deposits ( layer of rock sometimes thousands of feet below) were discovered and used in Switzerland and Austria, for fuel and lighting. This deeper layer was not used much after the discovery of oil in the mid 19th century from under the ground in the United States.But, now once again, shale oil extraction, called fracking, is prevalent in the 20th and 21st century.

What is fracking? Fracking, also known as ‘hydraulic fracturing’ is the process used to force water under pressure through a vertical and horizontal tubing  under ground to the shale oil depth. The diagram illustrates the setup while Reference #2 explains fracking clearly. The forced water along with a tubing that enters the pipe causes fissures (breakages) in the soil forcing natural gas and petroleum to seep into the pipes and get pumped out. Natural gas is made up of methane (CH4) and ethane (C2H6). while the other petroleum by products could range from propane (C3H8) and higher alkanes of the general formula  CnH2n+2 . (Last week’s blog explains the chemistry a little more.)


As one can see, the fracking process is fraught with problems. First, a lot of water is used that will definitely deplete the water table levels. People and livestock in the area will be affected by less water availability. Second, the water table could be contaminated by all the chemicals used in the fracking process. (These chemicals could seep into the water table.) What are these chemicals?

There are more than 50 chemicals used and the fracking industry is secretive/ignorant about some of the chemicals . Many of the chemicals listed are known carcinogens and methane, one of the products collected, is extremely flammable. Also, methane has been documented to play a critical role in climate change. Xylene and toluene, hydrocarbons that have a ring like structure are also present, very toxic and easily inhaled since they are volatile liquids. (Any liquid that can convert to gas molecules at room temperature is called volatile, just like gasoline.)

“Gasland”, the documentary made a few years ago, clearly illustrates how people living in the area where fracking took place were afraid to open their faucets. This was because the water was mixed with methane and cloudy. When the faucet was opened, sometimes, flames would appear at the mouth of the faucet if a lighted match was placed there.

Fourth, earthquakes are prone to happen in the areas where fracking takes place, since the soil layers, thousands of feet below the ground, have been disturbed considerably. There are  more reasons outlined in one of the references,but these four are sufficient to reconsider fracking and look for alternative sources of energy like electric, wind , hydro and solar for our energy needs.

Additions/ Corrections: Natural gas is used not just for cooking but for heating purposes as well.

Activities for Middle School teachers:compare the gold rush of 1849 with the oil rush that began in 1859 and continues till today. This could be a combined project with the social studies teacher.Students could also research news articles about fracking in their states/ neighboring states and the public opposition to it.

Nuggets of information: Southern Illinois is where most of the fracking takes place in Illinois; however there are fracking sites in McHenry County as well.

The United States contains three-quarters of the world’s shale oil reserves.

Even though the United States is moving towards renewable energy sources, It is still among the top consumers/ producers of petroleum along with natural gas and coal, all non-renewable energy sources.


“Oil Shale” (PDF). Colorado School of Mines. 2008. p. 2. Retrieved 2008-12-24

Science Makes Sense Week 3: Organic Chemistry-Nomenclature,hydrocarbons, alkanes, whales and petroleum

September 7, 2015

Man has always been in need of energy sources; starting with the discovery of fire. From the middle of the 17th century till the late 19th century , whale hunting was prevalent to such an extent, that certain kinds of whales, like the blue whale, the sperm whale ,were hunted for their oil till they almost became extinct. Whale oil was a necessary source of fuel and heat including whale oil for lighting, as well as for candle waxes and even in the processing of textiles and soap. An unexpected gush of oil discovery in Pennsylvania, USA,  is considered the beginnings of the use of fossil fuels for Western energy sources in the 19th century. In China and Iran, seep oil as it was called,  was used for fuel from early times. (4th century through 16th century)

What are fossil fuels and why do we call them that? Basically it is animal remains under great pressure and temperature over years and years that converts to crude petroleum. The distillation of petroleum leads to myriad products that literally fuels our every day life.(Distillation is a chemical process that starts with heating crude petroleum obtained from oil rigs and separated into several solids, liquids and gases used for fuel and other purposes.)

Every third week we will study organic chemistry. If you look at  the Periodic Table, you find that the 6th element is carbon. Carbon is such a busy element because it can combine with other elements to form hundreds of carbon compounds. The study of these compounds has been named Organic Chemistry to distinguish it from Inorganic Chemistry, which is the study of the rest of the elements in the Periodic Table!

Today we will look at one of the combinations of carbon and hydrogen or compounds comprising hydrogen and carbon; these are called hydrocarbons. ( A compound is a chemical combination of two or more elements.) The first series of hydrocarbons have the general formula shown below and are called alkanes or paraffins.


The first alkane in the series has n=1 which makes 1 carbon atom combine with 2×1+2=4 hydrogen atoms to give :

C1Hor CH4

as we commonly write it (when there is only one atom of any element you do not need the subscript 1 for it)

This hydrocarbon compound is named methane. Methane is also called ‘marsh gas’.  As the second name suggests,  it  is a gas and is also highly flammable. Methane is the main component of natural gas used at homes and other places for cooking purposes:IMG_2239IMG_2237

Now let us make n= 2 and  we get the second compound in the series called ethane;  (n=2, so there are 2 carbon atoms and 2×2+2=6 hydrogen atoms) and the formula is   C2H6 for ethane.

The next compound in the series (n=3) will be three carbon atoms combined with 2×3+2 =8 hydrogen atoms called propane

written like this/ chemical formula : C3H8

When n=4, we have 4 carbon atoms combined with 2×4+2=10 hydrogen atoms called butane and written like this/ chemical formula: C4H10         

So far we have seen methane, ethane, propane and butane; all four are gases at room temperature. Notice all end in ‘ane’ and are all called alkanes.

When n=5 we have 5 carbon atoms combined with 2×5+2=12 hydrogen atoms and the name is pentane. From now on the names will be the latin word for the number so 6 carbon atoms will be called hexane and 7, heptane. 8, octane, and so on. As you notice the formula for pentane will be  C5H12 , for hexane : C6H14, for heptane; C7H16 , and for octane: C8H18.

The first four alkanes were named before the nomenclature (a fancy word that means ‘naming process’)was decided.

Ethane is also used along with methane as natural gas for cooking purposes. Propane is used in propane tanks for outdoor grills. Butane is the fuel used in cigarette lighters and butane torches. Pentane is a low-boiling liquid used as a solvent and in the creation of plastic foams, hexane( liquid) is used in gasoline, and in industry as a solvent. Heptane has 0 octane rating and is not used as a fuel for gasoline since it causes high engine knock., it is used as a solvent in industry. Octane has good octane rating ( obviously) and is a major component of gasoline.

We have looked at the formula and uses of at least 8 alkanes, but it is important to picture how the arrangements of atoms or structure of these compounds looks like. Using simple materials like toothpicks and marshmallows or raisins one can construct these compounds. Here is a picture of the first three alkane compounds: methane, ethane and propane. As you can see, they are three-dimensional structures; for methane, one can see the tetrahedral structure of the compound.(The carbon atom is depicted by a tomato, and the hydrogen atom is depicted as a marshmallow here. The toothpicks are supposed to indicate the bond between the atoms; distances between the atoms, sizes of the atoms here are not accurate, but these models help understand structure.)


Next time (Week 6) we might be able to look at structure a little more closely and learn more about structural differences.Most of the alkanes studied today are the by-products in the distillation of crude petroleum. As you can see they are invaluable in our everyday life. However, next week as we look at Chemistry and Social Justice, we will talk about the problems in our society as a result of our over-dependence on petroleum/ fossil fuels.Careening from the near extinction of whales we are now at the point of near exhaustion of our fossil fuel energy resources.

Activities for middle school teachers: Let students figure out the structures of nonane, (9 carbon), decane etc till , say n=20. Students can also draw a graph using graph paper, making the number of carbon atoms on the x-axis, and the number of hydrogen atoms on the y-axis and plot a graph.(For example the x point for methane will be 1 unit and the y point will be 4 units.) What will be the shape of the plotted points? Why? Can the student now predict the structure of any alkane from that plotted graph? How will they do it?

If the language arts teacher is reading “Moby Dick” by Herman Melville, students will have an idea about the hunting of whales for whale oil two centuries back.

Nuggets of Information:The word ‘petroleum’ comes from 2 Greek words,’petra’ for rock and ‘oleum’ for oil.

Only the Inuit people have the legal rights to hunt whales today.

In 1859,workers in USA discovered petroleum jelly as a by-product in the oil rigs . They were not too happy with the sticky product, but found it was effective in the treatment of minor scratches and bruises. Today it is sold as Vaseline.