Archive for November, 2015

Science Makes Sense Week 15: Organic Chemistry, organic acids, alcohol, illicit liquor and alpha-hydroxy acids.

November 30, 2015


My supervisor in Chicago used to add a slice of lemon every time he drank water.   I tried doing that for a while but that habit was short-lived.  Now I hear again about the benefits of drinking warm water in the morning with lemon-juice. (Ref.1)  Apparently it aids digestion and helps in many other ways.  Cooks also tend to use lemon zest to add zing and flavor to many salads and dishes.

Lemon juice contains citric acid, which is really an organic acid.  All citrus fruits (like oranges, grapefruit, lemons, lime) contain this  acid.

An organic acid has the general formula R-COOH, where R could be a number of carbon and hydrogen atoms arranged as straight, branched or in a cyclic arrangement.  The COOH arrangement and the formula of citric acid are shown in the second picture.

As you can see, the formula is quite complicated.  However all organic acids have one or more of the -COOH or carboxyl group and are sometimes called carboxylic acids.

Let us start with simple organic acids.  When R=H, the formula of the organic acid is HCOOH and is called formic acid.   This is the acid found in ants!  The next acid in the series has R=  CHwhich is a methyl group and the formula is CH3COOH  and is called acetic acid.   This is the acid in vinegar and vinegar products like balsamic vinegar.  The more accurate IUPAC nomenclature (naming) of organic acids would use the name methanoic acid for formic acid and ethanoic acid for acetic acid.  The next acid in the series will have three carbon atoms and the carboxyl group and will be propanoic acid and so on.

But we need to look at common organic acids besides formic and acetic acid.  Mexicans and Indians are familiar with tamarind, used in cooking especially in Indian dishes.  This adds a tart taste to dishes and contains an acid called tartaric acid.  Milk contains the acid, lactic acid.  Most organic acids are weak acids, which means the acid is not completely ionized and the percentage of the hydronium ions present is low.  Just note that all organic acids have the characteristic COOH or carboxyl group present.

Remember methane as the first in the hydrocarbon series alkanes? Replace one of the hydrogens with the hydroxyl group OH and you get your first alcohol, methyl alcohol.  Unlike inorganic compounds where the presence of the hydroxyl group, OH, implies a base, the OH  here indicates alcohols.  The next in the series is ethyl alcohol, the familiar alcohol everyone imbibes.  None of the other alcohols in the series can be ingested.   An isomer of the next alcohol (propyl alcohol) is isopropyl alcohol and is familiarly known as rubbing alcohol used for medicinal purposes.  Methyl alcohol is also called wood alcohol and is used in many applications, but lately is found to be the best fuel for automobiles.(Ref.2)

Higher organic acids/carboxylic acids, like stearic acid are used in the manufacture of soaps.(Fig.3) Acetic acid is used in food and other acids are used as preservatives.  Acetic acid is also used in the manufacture of rayon.(Ref.3)(Fig4)

Activities for Middle School Teachers:

Let students go up to 12 carbons with a COOH group to write straight chain and branched chain organic acids.  Use the IUPAC name, (explained in Nuggets of Information).

Do the same with alcohols.

Note the number of isomers in each case. What kind of isomers do you obtain? ( Position of COOH/OH as well as cis-trans isomers and mirror image isomers)

As the number of carbon atoms increase are the acids liquids or solids?

Using ball and stick models or toothpicks, raisins and cherry tomatoes and marshmallows, construct the different isomers, say for a 5-carbon acid.

Nuggets of information:

The origin of the word ‘alcohol’ comes from Arabic which literally means al kuhl and refers to kohl/ antimony powder used with ethyl alcohol on the eyes.  Years later it was used to refer just to ethyl alcohol and in chemistry generally to all alcohols. (Ref.4)

Methyl alcohol has many names besides wood alcohol: wood spirit, hydroxy methane, Colonial spirit, Columbian spirit and also methanol. It has been used for embalming bodies by the ancient Egyptians.  The word ‘methyl’ was derived from Greek where ‘methy’ means wine and ‘hyle’ means wood or path of trees.  So people have been making illicit liquor using methyl alcohol for centuries. (Ref. 5,6)  Unfortunately, in many countries like India, people have died imbibing illicit liquor, because small amounts of methyl alcohol may not harm individuals but larger amounts leads to blindness, dizziness and even death.  Small amounts are already present in the fruits we eat. (Ref.7,8)

Part of the work of the International Union of Pure and Applied Chemistry or IUPAC is to set the rules for  the nomenclature of chemical compounds. So along with common names for organic acids and alcohols we have the standard IUPAC names as well. (Ref.9)

AHAs and BHAs are now very popular facial exfoliants.  AHA s are α-hydroxy acids like malic acid (from apples), tartaric acid ( from tamarind, grapes) and citric acid from citrus fruits) (Ref.10,11) (Figs. 2,4)  These AHAs are very popular for treating dermatological problems and have even been used for Fibromyalgia.  The only BHA or β-hydroxy acid used is salicylic acid. (Ref.12) which is a cyclic compound also called 2-hydroxy benzoic acid.  Salicylic acid is the active component in aspirin as well.

Oleic acid has been found in olive oil and has been considered to be  a good dietary supplement for people with diabetes. (Ref.13)(Fig.4)

Succinic Acid is a colorless crystalline solid, used in perfume making, medicine, manufacture of lacquers and in food production.It has two carboxylic -COOH groups and has 4 carbon atoms and is also called butanedioic acid (Ref.14)(Fig.3)

Maleic and Fumaric acids are cis and trans isomers,, have 4 carbons,also two carboxyl groups,-COOH,  but with a double bond each and can be manufactured starting with a derivative of succinic acid.  They are currently being used as food additives. (Ref.15,16) (Fig.3)

Butyric acid is produced when butter turns rancid.  It also has 4 carbons and is Butanoic acid, but with only one carboxyl group, -COOH. (Ref..17)(Fig.3)

Intense exercising can lead to lactic acidosis, which really means a high build up of lactic acid in the muscles.  This could lead to nausea and stomach pain, a temporary condition. (Ref.18)(Fig4).

Many times when people eat rich food, they talk about’acid reflux’.  This is probably the stomach walls producing more acid to digest all that food. Antacids, which are bases help neutralize the acid but maybe lemon juice everyday might be a better solution.  I end with more evidence that lemons are anti-bacterial, anti-viral and aid in digestion. (Ref.19)  Worth giving that a try, why not?








6.Blum, Deborah, Poisoner’s Handbook,(Penguin Press,2010)






























































Science Makes Sense Week 14, Acids,Bases Theories, Neutralization reactions, Salts

November 23, 2015

Whenever the word ‘salt’ is used by people they usually refer to common salt or table salt with the general formula NaCl and written chemically as sodium chloride.  This is the edible salt I have spent a whole week talking about, including  chemical structure and its importance in history. (Week 9)  In Chemistry, the word salt is used more generally  and includes the product formed whenever an acid and a base ( that we studied last week) react with each other.  The reaction is called a neutralization reaction, since the original properties of the acid or the base are neutralized and a new substance, a salt, and water are formed:

HCl  +  NaOH  →  NaCl  + H2O

HCl  +  KOH     →  KCl   +  H2O

2HCl  +  Ca(OH)2   →  CaCl2  + 2H2O

HNO3   +  NaOH     →    NaNO3   +H2O

HNO3   +  KOH         →     KNO3   +  H2O

2HNO3  +  Ca(OH)2  →     Ca(NO3)2    +  2H2O

 H2SO+  2NaOH      →    Na2SO4    +  2H2O

H2SO+  2KOH         →    K2SO4    +2H2O

H2SO4   +  Ca(OH)2        →   CaSO4    +2H2O

As you can see there are several salts that can be formed when an acid and a base react. The salts are sodium chloride, potassium chloride, calcium chloride, sodium nitrate, potassium nitrate, calcium nitrate, sodium sulfate, potassium sulfate, calcium sulfate, respectively.  So with three bases and three acids we have a total of 9 salts!  The other product is always water.   So now we know that another property of an acid is that it can react with a base to form salt and water.  Of course another property of a base is that it can react with an acid to form salt and water.

Last week, we talked about H or hydrogen ion as characteristic of all acids; in actuality a hydrogen ion is just a bare proton and does not exist by itself in an aqueous (in water) solution.  It  exists as a hydronium ion shown below:


So, when hydrogen chloride HCl gas reacts with water to form hydrochloric acid, which is a liquid, it forms the aqueous hydronium ion and the chloride ion:

HCl (g)  +   H2(l)  →  H3O+(aq)   +  Cl(aq)

According to the Br∅nsted Lowry  Theory, the proton donor is the acid, HCl and the proton acceptor is the base,  H3O+, the hydronium ion.  It is important to rewrite all the above equations in the ionic form as well as remember that since the reaction can only take place in the the presence of water molecules so the hydrogen ion is  not just a proton, but a hyrodinium ion.(Ref. 1) 

Old fire extinguishers were made using baking soda and acid to generate carbon dioxide.  Baking soda is sodium bi-carbonate, NaHCO3, a salt, and the reaction takes place when the bottle containing acid is broken during use. (Ref.2)  Today we use pressurized carbon dioxide with a propellant. Sometimes water sprinklers are set up in homes without anything else for extinguishing fires.  So salts are not used these days in fire extinguishers.  (Ref. 3)

But salts play an important part in industry, medicine and everyday life. Lives are saved by UNICEF when they give people a sodium chloride and sugar solution to drink when dehydrated and suffering from heat exhaustion, thereby supplying oral re-hydration therapy. (Ref. 4)  We already know that sodium carbonate is used in the glass-making industry. Epsom salts or magnesium sulfate is used for minor home remedies and treatments.(Fig.5)  Calcium sulfate is used in food preparation, especially in making soy milk coagulate (turn solid or semi-solid) to tofu, as a calcium supplement and for minor joint aches and pains, as well as a fertilizer.(Fig.6) Needless to say, there are several more salts not mentioned, but you now have a taste of the applications of different salts in different fields.

Activities for Middle School Teachers:

We have not even considered acids like phosphoric acid, iodic acid and bromic acid.  Add to that, common bases with barium, Ba,  and lithium, Li and the list of salts increases.  To calculate the number of salts that can exist, list all the possible acids  and bases and use the multiplication principle from mathematics to calculate the total possible salts.

Starting with a single acid like hydrochloric acid,  HCl (aq), if you replace the hydogen ion, (or hydronium ion in aqueous solutions) by metal ions, check how many salts you can create! (Ref.1)

Last week we talked about moles and molarity.  Molarity is really the concentration of the acid/ base or any chemical compound, usually in water or what is known as an aqueous solution.   Knowing the moles present from an equation, you should be able to calculate the products in grams if the reactants are also given in grams.  It will be a simple proportionality problem.  Try it.

Some uses of a few salts is given above; do a study on the uses of salts in industry, medicine, manufacturing of goods.

Nuggets of Information:

Several theories have been put forward to explain acids and bases. Besides explaining their  physical properties, in 1884, Svante Arrhenius defined acids and bases as:

An Arrhenius acid solution contains an excess of H+ ions.

An Arrhenius Base solution contains an excess of  OH– ions.

Then in 1923,  Br∅nsted Lowry (a Danish and an English chemist) put forward their definitions indicated above.   Finally Lewis made it even more general by saying that  an acid accepts electrons and a base donates electrons. (Ref.1)

Hydroxides of some metals like zinc, Zn, aluminium, Al, and Chromium,Cr are  amphoteric.  This means they can act as both acids and bases.  When treated with a strong acid, they act like bases and when treated with a strong base, they will react as an acid (Ref.1):

Zn(OH)2 (s)  +  2HCl (aq)  →     ZnCl2 (aq)  +  2H2O (l)

Zn(OH)2 (s)   +  2NaOH (aq) →   Na2Zn(OH)4 (aq)

What is the ‘cool fizz’ we feel when we drink soft drinks?  Chemists say that the tingling  on our tongues is caused by chemisthesis.   This sensation does not involve taste or odor receptors, but is due to a chemically induced sensation.  Protons, Hare released when an enzyme called carbonic anydrase reacts with carbon dioxide.  The nerve-endings are acidified by the protons and hence there is tingling.(Ref.1)

As seen above, there are probably more salts than acids and bases.   Most of the rocks and minerals found in nature are some form of a salt. Metal mining involves finding metals like iron, Fe, gold, Au, and other metals as salts.  Salts are usually crystalline and have high melting and boiling points. (Ref.1)

All these compounds are ionic compounds and exist as charged particles. Just like acids and bases, salts are electrolytes. Electrolytes are substances that conduct electricity in an aqueous solution. (Ref.1)  

Some of the formations in caves called stalactites and stalagmites are nothing but salts of calcium carbonate.  Salts like carbonates and bicarbonates react with acids to release carbon dioxide, along with an ionic salt and water:

2HCl (aq)  +  Na2CO3 (aq)  →    2NaCl (aq)  + H2O (l)  + CO2 (g)

HCl (aq)  +  NaHCO3 (aq)  →     NaCl (aq)  + H2O (l)  + CO2 (g)

Last week we only considered strong acids and bases.  These are also strong electrolytes , which means that they are almost 100%  ionized in an aqueous solution.  But there are also weak inorganic acids and bases that do not dissociate completely to H+, or more exactly, H3O+,or OH. Examples of weak acids are nitrous acid, carbonic acid and weak bases include ammonia., also called weak electrolytes. These acids and base do not get ionized completely.  If you connect an electric bulb to a strong electrolyte like sodium choride, hydrochloric acid or sodium hydroxide, the bulb will glow brightly.  With weak electrolytes, the bulb will glow dimly.(Ref.1)


  1. Hein, Morris & Arena, Susan, Foundations of College Chemistry,pp.375 -79(John Wiley and sons, 2007)


Science Makes Sense, Week 13: Strong Acids, Bases, logarithms, pH, moles, Avogadro’s number.

November 12, 2015


During my undergraduate days of studying chemistry, I remember a friend of mine who was in love with the subject.  She would say,” I want to keep my hands dipping in acid all my life!”  She could never have done that literally because most acids are corrosive liquids.  It was her unique and maybe bizarre way of bonding with the subject.

All acids have a sour taste and definitely are corrosive.  We shall focus on some common inorganic acids; hydrochloric acid, (HCl), nitric acid (HNO3) and sulfuric acid (H2SO4).  As you can see, the acids all have hydrogen ions H+ (cations).  The acids are ionic and exist as hydrogen ions and chloride/nitrate/sulfate ions (anions) as shown below:

HCl  →      H+ Cl

HNO3 →      H+NO3

H2SO4  →      2H+ SO42-         

(Note that the sulfate ion has two negative charges, so with the 2 hydrogen ions it will be neutral.)

The more complete this dissociation is the stronger the acid is; in other words the concentration of hydrogen ions is very high here.   These 3 acids are considered strong acids along with the following: hydrobromic acid (HBr), hydroiodic acid (HI) and perchloric acid (HClO4).(Ref. 1)

The negative logarithm of the number of hydrogen ions is called the pH of the acid.  Imagine you have a 0.01M solution of HCl.  1 mole=1M means there is 1 atomic mass in grams/g for H and Cl which is the formula for HCl, which means there is 1+ 35.5=36.5g  of HCl in 1liter of distilled water. 0.01M solution will be made taking 1 ml of this solution and adding 99ml of distilled water; one-hundredth of 1M.

The pH of this solution will be -(log0.01)= -(log 10-2 )=-(-2)=2.  Strong acids usually have a low pH near 2 or below that value.

Common acids in the house include toilet bowl cleaners (which contain some hydrochloric acid, HCl); industrial uses of acids include making fertilizers, dyes, in photography and explosives manufacturing to name a few.(Ref.2,3)


Bases are usually soapy to touch and some are very corrosive. All inorganic bases have a cation and an anion like acids, but the cation is not a hydrogen ion but usually a metal ion like lithium, sodium, potassium, etc. The anion is always a hydroxyl ion which is an OH negative ion shown like this:OH

Common bases are ionic like acids and are written as sodium hydroxide, NaOH, potassium hydroxide,KOH, calcium hydroxide,Ca(OH)2 etc but exist actually as shown for acids above, viz.,

NaOH →  Na+ OH 

KOH →       KOH–  

Ca(OH) →   Ca++   2OH–     

Again, the greater the dissociation of hydroxyl ions, the stronger is the base.  So bases are characterized by the number of hydroxyl ions, OH–  and end with hydroxide.  You can calculate the pOH of the base just like for the acids.  Again, imagine you have a .01M solution of sodium hydroxide, Na+ OH  and so the pOH of the base will be:

-(log 0.01) = -(-2)= 2.  Now pH + pOH =14, hence pH = 14-2=12.   pH of acids is below 7 and pH of bases is between 7 and 14.  Strong bases will have more hydroxyl ions and will be around 11 or 12 or even higher. Water is neither a base nor an acid and is neutral, so the pH will be around 7.

Bases like sodium hydroxide is used for making soap.  Potassium hydroxide is used in alkaline batteries and calcium hydroxide is used in bleaching powder and as an antidote for food poisoning.(Ref.4)

Next week, we will look at the reactions between acids and bases and study the resulting products.

Activities for Middle School Teachers:

Compare words like’volume’ , ‘mole’,’rational’ and ‘irrational’, generally used in the English language and in Science and Mathematics.  Let students find out other words that have different meanings inside and outside the field of Science/Mathematics, like ‘litmus test’.

pH uses logs.  Study logs or what is called logarithms.   Logs are to the base 10 ; hence log 10 is actually 1.  This can also be stated as the exponent of 10 is 1 when the base is 10 or 101   =10.  Log 100 =2, because the exponent of 10 has to be 2 to equal 100.  (Before calculators were invented, log tables were used to do complicated multiplication, division, and exponential calculations.)

Using different molarities for hydrogen ion concentrations in acids and hydroxyl ions in bases, calculate the pH of different acids and bases.

Find out more about Avogadro and Avogadro’s Number.

Why do gardeners worry about the pH of the soil? What plants need acidic soil and why?

Nuggets of Information:

Hydrochloric acid,HCl, mixed with nitric acid.HNO3, is called aqua regia, literally meaning ‘royal water’.  This mixture is used in metallurgy to dissolve metals like gold Au, and platinum, Pt.(Ref. 5)

HCl is also known as muriatic acid and used to clean concrete. (Ref.2)

Did you know that  when you usually eat on time and  then sometimes you don’t, your stomach growls?  The growling is actually the secretion of hydrochloric acid, HCl, inside the walls of your abdomen getting ready to digest the food that should be there! (Ref.2)

Battery Acid in cars is sulfuric acid, H2SO.(Ref. 6)

What is a mole? Normally a mole means an animal that lives underground. But in chemistry, a mole is a number like a dozen(12) or a gross(144).  A mole is really a unit of measurement; it is a number that has the same number of particles found in 12.0 gms of Carbon-12= Avagadro’s number. This number is 6.023x 1023 .  1 mole of carbon-12 has 6.023x 1023 atoms.  1 mole of teachers = 6.023x 1023(Ref.7) , 1mole of any element will be its atomic mass and will have 6.023x 1023atoms.

Calcium Hydroxide is also known as slaked lime, sodium hydroxide is called caustic soda or lye.  The latter is used in petroleum refining, in medicines and in the manufacture of rayon. (Ref.4)

A base is also called an alkali.  The word ‘alkali’ is derived from Arabic, since the ancient Muslims in the Middle East were well-known chemists. Al Qali means the ashes.(Ref. 8)

Another well-known base/alkali is ammonium hydroxide written as NH4OH , but exists in the ionic form NH4+ OH like all the other bases and acids.  Dawn, a  dish washing liquid, contains ammonium hydroxide, or ammonia as it is commonly called.   Ammonium Hydroxide is used in the cosmetic industry,  and also as a spot and grease remover.(Ref.4) 

Ammonia and water  is in equilibrium with ammonium hydroxide :

NH+  H2O  →       NH4OH

‘Smelling salts’ have existed since the time of the Romans and was used by women whenever they had a fainting fit.   It contains water and ammonia which is essentially ammonium hydroxide (above equation). Even today, athletes in football and hockey tend to use ‘smelling salts’ to give them some boosts of energy.  The fear is the abuse of this base.(Ref. 9)

A few years ago there was a major controversy with pink slime, the addition of ammonium hydroxide in meat.  McDonald’s insisted that they had stopped its use in their products.(Ref. 10)

Don’t forget, sodium hydroxide is  used to unclog drains and is present in the famous household product, Drano.(Ref.11)

Indicator liquids change color in acidic or basic solutions; most are organic weak acids themselves.   Phenolphthalein  turns bright pink in basic solutions and is colorless (original color) in acidic solutions.   Red litmus paper turns blue in basic solutions and blue litmus paper turns red in acidic solutions.  There is also a universal indicator paper that changes color based on the pH of the solution.(Ref. 12 )

Acids also have the ability to react with metals like zinc, magnesium to produce hydrogen gas. (Ref. 13)



  13. Hein,Morris, and Arena, Susan, Foundations of College Chemistry p.374 (John Wiley and Sons 2007)

Science makes Sense Week 12: Chemistry and Social Justice-Coal and Coltan mining, coal mine disasters,black lung disease, gorillas ,guns and a ghastly life..

November 8, 2015

Just before the U.S.Presidential elections in 2008, while the Republican and Democratic candidates were sparring on various issues, there was a curious agreement on one.  Both candidates supported using coal as an energy source and called it ‘clean coal’.   A Los Angeles Times’ article during this period aptly called this phrase ‘Orwellian’. (Ref. 1)

A student with a little chemistry knows that coal is mostly carbon,C, and when you burn carbon, voila, you get carbon dioxide. Coal is also a fossil fuel.   Week 8, we have already talked in detail about the oxidation reaction of carbon compounds like hydrocarbons.  More than 50% of our energy resources comes from coal,(Ref. 2) so we are adding considerably to the carbon content in the atmosphere and contributing to climate change burning coal, besides depending more and more on automobiles and planes.(Week 8)

Years ago, it was hazardous just to go down the coal mines.  (Even today, in certain parts of the world, the conditions at work inside mines are horrific and dangerous.) (See Nuggets of Information)   Lack of oxygen and long hours inside the mines is unhealthy; add to that the inhalation of small particles of coal dust causing lung diseases and explosions.   Mine areas are constructed with minimal reinforcements and there is always the danger of collapsing of structures and trapping miners who could die a slow and terrible death underground.(Ref. 3)  Even till  the early part of the 20th century miners carried canaries with them in cages.  If the canaries died, they knew there wasn’t sufficient oxygen for the humans and the canaries had died inhaling carbon monoxide,CO.(Ref. 4)

2C  +  O2    →    2CO

C  +  O2    →         CO2

This is partial oxidation of Carbon, C.  Complete oxidation of C leads to carbon dioxide, as shown in the second equation. There is also sufficient methane in the coal mines as well.  During the coal manufacturing process mercury, Hg,  and uranium, U, are by-products.(Ref. 5)   Mercury can lead to renal, gastrointestinal and neurological,toxicity,(Ref. 6) while uranium is radioactive and can affect human cells.  As you can see,there is no part of the coal mining process that is clean.

Today it is not just coal that is being mined.  There are  areas in the Congo where ‘Coltan’ mining takes place.  This is short for Columbite and Tantalite, compounds of Niobium and Tantalum.(Ref. 7) These two elements, Niobium,Nb, and Tantalum,Ta, are in the same Group and below Vanadium, V, in the Periodic Table.  They are part of the Transition Elements, also called rare metals.  The transition metals are where the 10 electrons in the ‘d’ shell are being filled. (Ref. 8)  

What is so special about these two elements?  Tantalum, or Ta, when powdered with its oxide is used in mobile cellular phones and other electronic devices as a capacitor. (Ref.9) A capacitor stores electrical charge and controls the flow of electrical current, also called a condenser.(Ref.10)  Ta is extremely good at conducting heat as well as electricity, making it a favorite metal to use in small electronic devices (Ref.9)  Nb, on the other hand is not used in electronic devices, but is very widely used in making stainless steel, in the construction of space ships and for making jewellery.(Ref.11)  It just happens to be found alongside Tantalum as Coltan.

The mining process in the Congo is not as tedious and hazardous; however the conditions for the workers is deplorable. Teenage and child workers are usually working long hours in the mines. Rwanda which is next door is involved in a Civil War with the Congo, fighting for rights on the Coltan mines, exploiting and killing people in the process.  In addition, the digging of mountains and areas in that region is affecting the gorilla and other wildlife population considerably.  But there is a lot of money that can be obtained from mining Coltan, so people, the army, the rebel forces are rushing in to grab what they can, extracting money from the workers. (Ref.12) This reminds one of the Gold Rush days of North America in the 19th century.  There have been attempts made by electronic companies that sell smart phones to look for other sources in the world for Coltan. However war-torn Central Africa still supplies one-fourth of the world’s supply and the rest comes from the Amazon area in South America, and maybe parts of Australia. (Ref.13) Unfortunately, conditions are similar to what is happening in the Congo; only the venue has changed.

Meanwhile, the craze for the latest smart tablet or phone is never-ending as well as our thirst for fossil fuel energy from coal.  We as a society have to decide if human rights violations, health of humans and the degradation of the environment and fauna and flora is worth this madness for the latest technological marvel or our continuing dependence on fossil fuel.  Can we as a species arrive at a meaningful and sustainable solution?


Activities for Middle School Teachers:

Watch the movie by John Sayles about West Virginia coal miners called “Matewan’.(Ref.14)

Let the students look at coal mine disasters in the 21st century, throughout  the world.

Study the gold rush, oil rush and today’s Coltan rush and document the similarities and differences.

Do an experiment studying capacitors.  Capacitors store electrical energy and springs store mechanical energy, graph charge versus voltage for capacitors and force versus displacement for springs. (Ref. 15 )

Tantalum and Niobium along with Cobalt and few metalloids are called rare metals, and the  rare earth elements are the Lanthanides and Actinides in the Periodic Table. (Ref.16,17)

Compare and contrast properties and uses of these two: rare metals and rare earth elements.

The origins of the names for Tantalum and Niobium comes from Greek mythology.  Find out the significance of this.

Nuggets of information:

This year,2015, marks the bicentenary of the Safety Lamp created by Humphrey Davy and Stephenson who both independently worked on a lamp for miners.  Both fought for rights for the discovery, but the lamp was named after Sir Humphrey Davy, called the Davy Safety Lamp. The flame in the lamp changed color if methane gas was found in the mines and was carried by miners inside the coal mines. (Ref.18)

The 5 largest coal mining/producing areas in the U.S. are Wyoming with almost 40% of the total U.S. production; next is West Virginia (12%), followed by Kentucky (8%) and Illinois and Pennsylvania (5% each). (Ref.19)

If you look at the number of coal mine disasters in West Virginia over a 110 year period, from the late 19th century till recently, one sees that there is an average of more than one mine disaster per year!  Most of them are because of some sort of explosion in the mine.(Ref.20)  The latest well-known mine disaster there occurred in 2010 in the Upper Big Branch Mine  owned by Massey Energy where 29 miners lost their lives and was due to methane gas leaking with resulting explosions. Compensation and law suits are still being settled.(Ref.21)

China, India, Japan, South Africa, Wales,to name a few countries, have had several coal mine disasters over the years.(Ref.22) There is also child labor involved in some countries, especially in Northeast India even today. Several non-profit agencies are trying to find opportunities for children to avoid the dangerous and often fatal work in India.(Ref.23)  BP , the oil company states that India, US, Russia, China and Australia have the highest coal reserves.(Ref.24)

Mountain top removal is the latest way of looking for coal, especially in the Appalachian Mountains in the Eastern United States. This strips the land causing water shortages, the land is laid out to waste and frequent floods and health problems affect the people who live there. (Ref 25)

Black lung disease was very common  before the 70s in the US. This is a disease that is usually found in miners with prolonged exposure to coal dust.  One would have thought with the regulations imposed after the 1970s, cases of this disease would disappear.  Unfortunately, many of the 29 men who died in the mine disaster from West Virginia suffered from this disease.(Ref.26)

There is mining of not just coal and Coltan in the world that causes environmental and human rights violations. There are mines for manganese, gold, silver, copper tin and diamonds. and in all these cases there is small-scale and large-scale mining.  There are jobs created but there are many diseases, lack of clean water and all the other problems mentioned above(Ref.27)

One meaningful way to lower the demand for more Coltan is to recycle old, unused electronic devices; many neighborhood programs conduct such recycling programs.

Since coal is not really clean energy, we need to be. investing more in solar and wind energy here in the U.S.









8.Hein, Morris & Arena, Susan, Foundations of College Chemistry,pp.215,6 (John Wiley and sons, 2007)
























Science Makes Sense, Week 11: Organic Chemistry, isomers,stereo and structural isomers, cis-platin, cancer treatment and my eye!

November 1, 2015

Siddhartha Mukherjee in his Pulitzer Prize-winning biography of cancer called The Emperor of All Maladies, talks about the efficacy of using cis-platin or cis-Platinum to cure certain specific types of cancer.  Cis-platin chemically reacts with DNA making these DNA -damaged cells unable to duplicate their genes, halting the spread of the cancer.(Ref. 1)  Today I will talk about the structure of these compounds using simpler models to illustrate stereo and structural isomers.

What are isomers?  An isomer of a compound has the same chemical formula but different arrangement of atoms.  Week 7, I talked about these isomers briefly but today we will look at more examples.  First we will look at the structure of cis and trans-platin.  Unlike organic chemistry molecules, these molecules do not have carbon as the central atom.  Platinum,Pt from the transition metal series, is the central atom with 4 bonds: two are with ammonia molecules (NH3) and two are with chlorine (Cl) atoms as shown.  Notice the cis structure has both Cl atoms on the same side of the Pt, whereas the trans structure has the Cl atoms on opposite sides of the Pt. (First picture) 

Week 7 we saw isomers of cis-2-butene and trans-2-butene. The nomenclature of these organic compounds is not too difficult to understand. The carbon compound is an alkene with general formula CnH2n where n=4, so it is a butene. Since the double bond is between the second and third carbon atom it is called 2-butene.  The relative positions of H (hydrogen), CH3(methyl) decides if it is a cis or trans 2-butene.  When the methyl groups are on the same side, it is called a cis isomer and when they are on opposite sides , it is called a trans isomer.(Look at the picture from Week 7)  Wherever there is a difference in geometry of atoms or group of atoms  in space, the isomer is called a sterioisomer.   Note that the chemical formula is still the same for cis and trans-butene viz., C4H8.  Cis and trans isomers are usually found around double bonds where there is limited rotation, but also found around heavy metals like Platinum Pt, as well.

In Week 7, we noticed the straight and branched chain with butene which caused two more isomers. These are called structural isomers, since the arrangement of the atoms has changed. Here it is not the spatial arrangement, but the structural  arrangement of carbon atoms that is different.  Saturated carbon atoms, like alkanes also  exhibit structural isomerism.  Stereo-isomerism may be absent since there is free rotation around the C-C bond unlike in the case of a C=C bond in 2-butene which restricts rotation.

Butane has two structural isomers: A straight chain of the 4 carbon atoms gives you butane, but when they branch, you get isobutane  or 2-methyl propane.(Second Picture)  As the number of carbon atoms increases, the possibility of more isomers exist.  (The best way to understand isomers, is to actually make the models with ball and stick kits or other kits that are available.   You could also construct them using toothpicks and marshmallows, cherry tomatoes or other objects that stick on to the toothpicks).   Remember all the possible structures are called isomers akin to saying, “We are 4 siblings or I have 2 sisters and a brother”.  In other words, butane has 2 isomers or normal or straight-chain butane has 1 other isomer that is a branched chain.

How many isomers does pentane have?  Again, start with  a straight chain and see how many branched chains you can form.  You see only 3 isomers of pentane: n-pentane, 2-methyl butane and 2,2-dimethyl propane.(Third picture)  Hexane has 6 isomers well illustrated in the U-tube example.(Ref. 2).  When we get to heptane there are 9 isomers.(Ref. 3).  Note the stick model without showing the C or the CH3, H atoms attached to the C shown in the second, third pictures. This will be helpful later when we talk about cyclic hydrocarbons without indicating all the C, H atoms but just showing the geometric stick figure or closed polygons.

Why is it important to talk about isomers? Many isomers of alkanes and other organic compounds play a very important part in our daily life. Iso-octane is a very vital component of fuel for automobiles.  We just saw how cis-platin is invaluable in the successful treatment of certain kinds of cancer.  But one of the most exciting applications of cis and trans isomers is what happens in less than a picosecond (1×10-12of a second) when we see something!  Light reflected from objects undergo a chemical change, and the brain makes sense of the visual information to create an object.   The eye is somewhat like a camera.  The pupil allows light to enter the eye, focused by the lens and strikes  light-sensitive detectors in the retina which is at the back of the eyeball.  The light-sensitive detectors are called rods and cones (shaped that way). The cones provide color information while the rods are extremely sensitive detectors of white light and help with night vision.  The rods when hit with light, 11 cis -retinal (a chemical in the retina) isomerizes to all trans-retinal.  So every time we see, a small step in the process utilizes isomers.(Ref.4) The whole process of isomerization might take 200 femtoseconds to 1 picosecond! (Ref.5)


Activities for Middle School Teachers:

What is a femtosecond? It is 1×10-15 of a second.  Let students learn all the various names for these minute time elapses, like pico, nano etc. These prefixes can also be applied to other measurements like length, volume, mass.

To find isomers for higher alkanes, students need to carry out the following operations:

  1. First write the structure of the longest chain .
  2. Next write the possible structures of the branched chain with one C removed  and placed at various positions attached to a C
  3. Next write the possible structures of the branched chain with two C removed
  4. Repeat this process till you have no duplicates.

Look for cis and trans isomers among alkenes and alkynes. 2-butene was the first to exhibit these isomers.Go up to n=10 to explore these isomers. Also calculate the straight chain and branched chain isomers with alkenes and alkynes from n=2 till n=10.

The word, ‘iso’ implies same. Look for other words that start with iso, eg., isotherm, isobar, isometric, isotopes. What do they mean?

Today we use words like cis- gender and trans-gender. Knowing what you do about the meaning of cis and trans isomers can you see the appropriateness of these definitions for people and their preferences?


Nuggets of Information:

Enantiomers are another kind of stereo-isomers. These are non-superimposable structures that  have the same chemical formula, but are mirror-images of each other. (Fourth Picture)  A methane molecule where three of the H (hydrogen atoms) are replaced by Cl(chlorine), F(fluorine), and Br(bromine)atoms respectively, has 2 enantiomers.(Ref.6)

The carbon C atom in the center of these enantiomers which have four different atoms attached are called the chiral center or the stereogenic center. (Ref.6)

Acute promyelocytic leukemia (simply stated, cancer of the white blood cells, also known as ACL), has been effectively treated using a trans-isomer this time along with chemotherapy.  The isomer is called trans-retinoic acid.(Ref.1)  Retinoic acid is a 19 carbon organic acid (while vinegar is a one carbon organic acid) also known as Vitamin A acid. (Ref.7)

There are 3 kinds of structural isomers. The first involves straight chain and branched chain carbon compounds. The second is seen where there are double or triple bonds in the carbon compound and will depend on the position of the unsaturated bond.  The third will involve entirely different compounds with the same chemical formula, like an ether and an alcohol which can both contain carbon, hydrogen and oxygen atoms.(Ref. 8)   As we study more organic chemistry, the third isomer will make more sense!

Isomers are part of the world of big protein molecules in biochemistry; no wonder so many isomers play a role in medicine and naturally occurring substances like α- and β- glucose. Some of these proteins are so large and bulky that they change their shapes causing isomers that are called topoisomers. (Ref. 9)

The role of isomers is critical in what we can or cannot eat. Starch, found in corn, rice, wheat, potatoes is the main source of food for many cultures. But cellulose which has a similar structure, is inedible for humans and most animals but is a strong fibre . Both starch and cellulose are polymers of the monomer glucose, with just a difference in the arrangements of each monomer. (A polymer is many units of the same unit; here it is a glucose unit; a cyclic arrangement of carbon and hydrogen atoms, which is the monomer.)  The monomers of one is arranged like a mirror image, viz., an enantiomer of the other. (Ref. 9,10)


  1. Mukherjee, Siddhartha, The Emperor of All Maladies(Scribner, 2010)
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