Archive for January, 2016

Science Makes Sense- Week 22:Transition elements, complex chemistry, d-orbitals, chelation

January 27, 2016

Have you noticed how chemists are usually depicted in magazines or advertisements? You will see serious-looking men or women in lab coats surrounded by brightly colored yellow, emerald-green or purple liquids in beakers or other containers. Nine times out of ten, most chemists pour and mix colorless, boring solutions and rarely do they create exciting-colored chemicals! The exception to this rule are those chemists who study complex chemistry and work with the transition elements.

The transition elements are the three rows or periods in the Periodic Table that are in the center between the alkaline earth metals on the left and the non- metals on the right. These are a bunch of almost 30 elements where in each row the ‘d’ shell containing ten electrons are being filled. (Ref. 1)

Most of the elements where the ‘d’ shells are being filled exhibit some interesting properties. They are metals (sometimes they are referred to as transition metals instead of transition elements), brightly colored, show different ratios in which they combine with other elements (which means they have different oxidation states) and some catalytic activity. They also combine in complex ways with metals and non-metals. (Ref. 2). In fact, the study of transition elements is a special branch of chemistry called complex chemistry. We will study why the filling up of the ‘d’ shells leads to these exceptional properties.

The definition of a transition metal is one which forms one or more stable ions which have incompletely filled ‘d’ orbitals. According to this definition, zinc, Zn, and scandium, Sc, are not really part of the transition metals, since their ions do not have any ‘d’ shell electrons.(Ref. 3)

Transition metals are good conductors of heat and electricity, less reactive than Group I alkali metals, but have high melting points, (exception is mercury,Hg, which is a liquid at room temperature), and high densities. (Ref. 4) They also form complex compounds, exhibit chelation, are good catalysts and as we already mentioned, form many colored compounds.

Let us look at four properties when we study these elements. Unlike most other metals, these transition metals do not just form simple ionic compounds like the alkali and alkaline metals. (Group I and II) Apart from the simple ionic compounds like nickel, copper, iron or cobalt chloride, they also form some complex/ coordination compounds. Many atoms or molecules called ligands, can attach themselves to these transition metals These ligands can be electron pair donor in a coordinate covalent bond. Common ligands are water, ammonia, carbon monoxide and anions (negatively charged ions) like cyanide ions, chloride ions and hydroxide ions. Sometimes these ligands are cations (positively charged ions) and electron acceptors. No wonder this branch of the study of transition metals is sometimes called complex chemistry. (Ref. 5)
Second, sometimes these ligands can be five identical carbon monoxide molecules that attach to iron, Fe, or six water ligands to nickel,Ni. These multi-dentate ligands attached to a central metal ion are called a chelating agent. ‘ Chelate’ means ‘crab-like’ and it feels like these five or six or however many ligands are like the pincers of a crab. These chelating agents have significant biological applications.(See nuggets)(Ref. 6)




Thirdly,transition metals are good catalysts. One of the reasons is that they can exist in a variety of oxidation states. This has the property of providing or withdrawing electrons from the intermediate stage of a reaction. For example, if a particular intermediate stage of a reaction is electron rich, the transition element could hold some of the electron density and facilitate the reaction. Or the transition metal might undergo oxidation- reduction reaction to achieve electron transfer to a substrate; this again allows the reaction to take place. In other words, a transition metal, existing in a variety of oxidation states and undergoing easy transitions between these oxidation states, can coordinate with a substrate, and also be a source or a sink for electrons, making it a good catalyst. (Ref. 7)

Finally, let us look at the reason for bright colors for transition metals. The colors of the transition metals are best described by the crystal field theory. Electrons in the d- orbital or shell are not at the same energy when there are molecules or ions attached to the metal ion. These molecules or ions are called ligands, as we already know. Ligands split the ‘d’ levels into two or more different energy levels. We see colors because the energy level differences in the ‘d’ levels is in the visible light range. When light strikes ions in solution, some of the energy with visible wavelength is absorbed by the electrons moving from a lower to a higher energy level. We see different colors because of a slight difference in energy levels that the ‘d’ levels split into. If the energy difference is greater, electrons will absorb light closer to the blue-violet end of the spectrum, and the solution will appear yellow. If the difference in the ‘d’ energy levels is less,the electrons absorb closer to the red end of the spectrum and the solution appears green; anywhere in between you will cover all the other colors. This explains why transition metals are colored. (Ref.8)

Activities for Middle School Teachers:
Before studying transition metals, students should be very familiar with the Periodic Table. They should also be able to express most elements using the electronic configuration, especially the filling up of ‘s’,’p’, and ‘d’ orbitals.
Students should understand that visible light is part of the electromagnetic spectrum and is a form of energy. They should also do research on how we perceive color in any object.
What is the role of a catalyst in any reaction? Do a comparison of enzymes and catalysts.

Nuggets of Information:
Ethylenediamine tetra acetic acid, EDTA, has 4 acetic acids,(tetra acetic acid) 2 nitrogens(diamine) on a 2 hydrocarbon chain.( Ref. 9). Chelates are biologically very signifiant. EDTA oral fluid is made up of several compounds containing transition metals and these are chelates used for curing many health issues. (Ref. 10)
Metal poisoning is treated using chelation therapy. Transition metals captures the toxic metals from the body, chelates them so that they are passed out of the excretion system of the body. (Ref. 10)
Most transition metals like iron, Fe, and chromium Cr, are key ingredients in automobiles, bridges, usually as alloys. One of the greatest applications is in cookware. They are also used in mercury thermometers, colored paints and photo reactive eye glasses. Titanium, Ti, is used to detect underwater sound, barium titanate is piezoelectric. (generates electric charge when slightly distorted)(Ref.11) Iron, Fe, along with cobalt, Co and Nickel, Ni, are magnetic and used for magnetic devices, cassette tapes, computer discs. Copper, Cu and cadmium, Cd, are used in photovoltaic cells. (Ref.11)
Human beings need two transition metals that are very essential: one is iron that is a complex compound in hemoglobin and cobalt as a complex compound in Vitamin B12.
Low iron leads to anemia and Vitamin B12 is crucial in the human diet. ( Ref.11)

REFERENCES: in transition metals in search site) (put in transition metals in search site)….ansitionmetalsrev1.html (put in ligand chemistry in search site)
7. (ask the question ” why are transition metal compounds good catalysts?”)
9. (put EDTA in search site)
10. (put biologically significant chelates)

Science Makes Sense,Week21 : The Halogens, refrigerants, toothpaste and disinfectants.

January 18, 2016

What does an older refrigerator, bleach,toothpaste and pesticides have in common?  All contain one or more halogens, the Group VII elements of the Periodic Table: fluorine, chlorine, bromine or iodine. (Astatine  is radioactive and does not behave like the other halogens.)  Today we shall study these very reactive elements, sitting so close to the most inert elements, the Noble Gases. (Ref. 1)

The word ‘ halogen’ comes from Greek, meaning ‘ salt-producing’.   The electronic configuration of all the halogens, indicate two electrons in the outermost ‘s’ shell and seven electrons in the ‘p’ shell.  This makes the halogens electrophilic and non-metals . They are ready to react with metals , which are nucleophilic. (Ref. 1)

The Halogens are diatomic molecules, i.e., they exist as two atoms sharing electrons – covalent bonding.  Astatine alone is not diatomic.  Intermolecular forces, Van der Waals forces, are very weak as one moves down the group.  This explains why the first two, F and Cl are gases.  As the forces weaken, the molecules get closer, bromine, Br is a liquid and iodine, I and astatine , At  are solids. (Ref. 2)  Since the halogens are very reactive, they are never found in the elemental form. (Ref. 1)


F is the most reactive of all the halogens and was a challenge to isolate it.  Even if scientists were able to get it in the elemental form, it reacted with the vessels in which it was synthesized. Finally, Henri Moisson ( 1852-1907) managed to isolate the element using electrolysis which is the process of passing an electric current to cause a chemical reaction.  Using a platinum-iridium alloy that is resistant to attack by fluorine as the electrodes, an electric current was passed through HF,which lead to the isolation of F at one of the electrodes. (Ref. 1)

Flourine is used as an oxidizing agent in rocket fuels. (Ref. 3)  As hydrogen flouride,HF, it is used to etch glass. (Ref. 1)


Sir Humphrey Davy identified this gas as a greenish- yellow gas.  Chlorine, Cl, is produced by the electrolysis of brine (sodium chloride solution).  It is reactive, but not as reactive like F. (Ref.3)

The ionic compounds of Cl are used to make disinfectants for sewage, water and for pools.  The organo compounds of Cl are used to manufacture pesticides, herbicides and fungicides. (Ref. 3)


Bromine, Br, is a foul-smelling, reddish- brown liquid isolated in 1825 by Carl Lowing and Antoine Jerome.  It is found in deposits of brine in Israel’s Dead Sea and in the U.S. in Arkansas and Michigan. The vapors are highly irritating to the throat and eyes.  Bromine is used in dyes, pesticides,disinfectants and as a flame retardant.  One of the major uses of bromine is in the manufacture of halogen lamps.  These lamps are used as automobile headlights, floodlights, spot lights.  Tungsten is used in lamps and is considered better than carbon, since it is more durable than the latter.  However,the tungsten, W, begins to thin and break causing dimming of the light source.  But the addition of bromine or other halogens inside the bulb alleviates this problem. (Ref.1)


First isolated from seaweed in 1811, the word is derived from the Greek word ‘iodos’ meaning ‘ violet colored’. (Ref. 1,3)  Ultra-pure iodine, I, may be prepared adding potassium iodide to copper sulfate.  Though I as a halogen is a non- metal, it possesses characteristics of a metal sometimes.  Radioactive isotope I-131 is used to treat thyroid disorders.  Insufficient iodine leads to goiter. (Ref. 5)

Iodine was once used in photography; today it is used in chemical analyses and the synthesis of organic compounds. (Ref. 1)


No more than 44 mg of astatine, At, are found on the earth’s crust. It is one of the rare elements, and poorly researched.  No practical applications exist right now. (Ref. 3)

Activities for Middle School Teachers:

Students can study the chemical reactions involved in adding bleach to clothes.  Is the bleaching process an oxidation reaction or not? Please explain.

When you go down the halogen group, what makes flourine the most reactive halogen and iodine the least reactive?

Look at the different chloro-flouro carbons. Find out how many different stereo isomers there are.

Nuggets of Information:

The most characteristic feature of halogens is their distinct coloration: F is pale yellow, Cl is greenish- yellow, Br is orange to red- brown, I is dark violet and At is dark black. (Ref. 2)

Flourine reacts explosively with water and is the only element to react with Noble Gases. (Ref. 3)

Henri Moisson received the Nobel Prize in 1906 for isolating the element Flourine using electrolysis. (Ref. 1)

Teflon, which is a polymer continuing Flourine is used in non-stick cookware. (Ref. 1)

Flourine was initially added to water, to prevent tooth decay.  Now it is only added to toothpaste. (Ref.1)

‘Chloros’ in Greek indicates the color , greenish-yellow, and hence the name Chlorine, for the second halogen in the series.   Chlorine is among the top ten chemicals produced in the U.S. (Ref. 3)

Cl is a highly poisonous gas that was used in World War 1 as an agent of war (Ref. 1)

In early 19th century it was use as a disinfectant during a cholera epidemic in Europe. (Ref. 1)

The single greatest use of chlorine is in the preparation of a large variety of compounds including organo-chlorides that are the starting point of plastics like PVC, polyvinyl chloride, and neoprene, a synthetic form of rubber. (Ref. 3)

DDT which is an ogano-chloride containing two benzene rings and five chlorine atoms was used for many years as a strong pesticide. Rachel Carson, in her book written in the 60’s, called ‘ Silent Spring’ talked about the devastating environmental impact of such a pesticide and that resulted in a ban on the use of DDT in the U.S. (Ref. 4)

A series of compounds are formed by replacing the hydrogen atoms in methane by halogens. When three of the hydrogen atoms are replaced by chlorine atoms, you get the old anesthetic chloroform, or trichloromethane. When all four hydrogen atoms are replaced by chlorine atoms you get carbon tetrachloride/tetrachloro methane. This is a very common organic solvent and is also used as a refrigerant. (Ref. 3)

Chlorofluorocarbons, CFC’s, were used as refrigerants.  These are usually methane or ethane molecules where several of the hydrogen atoms are replaced by chlorine or fluorine atom/atoms.  They were given the general name Freon.  These CFC’s were found to deplete the ozone layer and were late banned. (Ref. 5)

At one time,ethylene dibromide was used by the petroleum industry as an additive to leaded gasoline. It reacted with lead to form lead bromide and cleaned out lead emissions.  In the late 70’s leaded gasoline was slowly phased out due to environmental concerns and ethylene bromide was not needed then. (Ref. 1)

Iodine, I, binds to starch and colors it deep blue; this is used as a test for iodine or starch. (Ref. 6)

Most isotopes of I are radio active, except I-127. (Ref. 6)

Solid I is blue-black and shiny, at ordinary temperatures and pressures it sublimates (converts from solid state directly to gaseous state) into a gas. (Ref. 6)

The thyroid gland uses I to make the hormones thyroxine and triodotyorine. (Ref. 6) Hormones are chemical messengers that direct cells what to do. (Ref. 7).  Insufficient iodine leads to goiter, swelling of the thyroid gland.

I deficiency is considered one of the leading causes of mental retardation. (Ref. 6)



2. familyhtml

3. science

4. Carson, Rachel, Silent Spring (Houghton Miflin, 1962)

5. biology/ss/hormones.htm



Science Makes Sense: Week 20- Chemistry and Social Justice: agents of war, mustard gas, napalm, white phosphorus.

January 10, 2016

Anyone who grew up in the ’60s will never forget that horrific, poignant picture of a young Vietnamese girl running naked with her mouth open with fear. The U.S. Forces had just dropped napalm in that village where the girl lived.  That picture galvanized the anti -war movement and could have played a significant role in ending the senseless, Vietnam War.

Napalm was originally manufactured for World War 2 and was used initially as a flame thrower against German buildings . It was a mixture of naphthenic acid and palmitic acid and the name was derived from the first syllable of each acid. (Fig. 1)(Ref. 1)

By the time of the Vietnam War, napalm was made using a mixture of plastic polystyrene, benzene and gasoline.  It creates a jelly-like substance and when ignited,sticks to everything, burning up in ten minutes. (Ref. 2) (Fig.1)

The chemical reaction is quite simple. Gasoline alone can get ignited and burn/ oxidize, but the addition of benzene (inflammable material) and a plastic allows longer burning , sticking to the clothes and skin, and in addition, the carbon dioxide formed when any hydrocarbon burns, (see Week 8) is actually converted to carbon monoxide because of incomplete combustion.  This adds to lack of oxygen and death due to difficulty breathing.

Man has always looked for  chemical weapons during war.  Before World War 2, mustard gas was used in World War 1.  The structure is shown in Fig. 1; a four carbon hydrocarbon with sulfur, S, in the middle and two chlorine , Cl atoms, one at each end. (Ref. 3)

Mustard gas, is chemically known as 1,1, thio bis (2-chloro ethane).  ‘ Thio’ is for the sulfur and ‘bis’ implies 2 pieces of 2 carbon atoms, viz.,ethane each having a chlorine atom. (Fig. 1)

The chemical reaction steps of how mustard gas reacts on the human body is shown here:

Mustard gas converts due to nucleophilic attack of carbon by the sulfide to a sulfonium salt; this is attacked by water present as moisture in the human body to a hemi mustard and HCl, hydrochloride acid.  This is attacked by water to form a Thio- glycol plus HCl, and the final step has HCl once more as a by-product. Mustard gas and hemi- mustard are vesicants and the three molecules of HCl is also a strong skin irritant. (Ref. 4)

The next war weapon we will look at is White Phosphorus.  It is actually a polyatomic molecule, having four P atoms in a tetrahedral arrangement.  It is one of the three allotropes of Phosporus. (Week 17)(Fig. 1)

White Phosphorus has been used several times in war as a chemical weapon.  It is considered illegal to use this as a weapon of war. Originally, though, in World War 1, it was used as a smoke screen and for flares.  However, in the late 20th century and early 21st century, USA, Russia and Israel have been accused of illegal use. (Ref. 5)

White Phosphorus oxidizes in the presence of oxygen to form phosphorus pentoxide. (Week 17)  This oxide is extremely hygroscopic, which means it absorbs moisture very readily.  If it comes into contact with skin, it will definitely cause severe blisters. It is difficult to extinguish and keeps on burning as long as oxygen is present. (Ref. 5)  One can only imagine the horrible burns and death it can cause.

The ancient Mayas had a noble tradition, whereby they gave their enemies a decent burial. But the human race now with the use of chemical weapons like napalm,mustard gas and white phosphorus, to name only a few, are intent on bringing cruel and inhumane ways of attacking the enemy which many times includes innocent civilians.

Activities for Middle School Teachers:

Let students do a time line of chemical agents used in war.  What kinds of  such weapons were used besides vesicants and napalm?

Study how many of these chemical weapons contain chlorine.  How many contain sulfur?  What, if any is the most common element or group of elements found  in these chemical weapons?

Besides chemical weapons, there has been biological weapons used, let students make a list of these war agents as well.  How do they cause harm to humans?

Nuggets of Information: 

Dr. Louis F. Fieser created an aluminium soap mixed with naphthenic and palmitic acid.  The name napalm came from the first syllables of the two acids. This combined with gasoline, was a brutally effective weapon. (Fig. 1)(Ref. 1)

In World War 2, the German word “bombenbrandscrumpfeichen” was created in response to napalm bombing of German bunkers. Soldiers in the bunkers would be baked by the heat and the word means ” firebomb shrunken flesh”. (Ref. 1)

Kurt Vonegut’s book, Slaughterhouse Five, is about a controversial campaign where 35,000 to 135,000 German soldiers died due to napalm in World War 2. (Ref. 1)

During the Vietnam War, napalm (b) was formulated that caused even more terrible destruction of soldiers and civilians. (Ref.1)(Fig. 1)

That terrified little girl from the first paragraph, Kim Phuc, survived miraculously and is today a U.N.Goodwill Ambassador. (Ref.1)

But napalm may still have been used, despite protests and bans by the U.N., during the Persian Gulf War by U.S. forces. (Ref. 1)

Mustard gas is a vessicant, which means an agent that induces blistering. (Ref. 6)

Though this gas is always seen as a nasty poison, resulting in a slow, painful death and causes cancer, yet, ironically, it has also been used to treat cancer!  In 1919, after the first usage of mustard gas,it was noted that victims had a low blood cell count.  In 1946, nitrogen mustards (replace sulfur,S, by a nitrogen,N) reduced tumor growth in mice as well as humans.  Now nitrogen mustards have become a modern chemotherapy therapy treatment for lymph glands Hodgkin’s Disease. (Ref. 4)

White Phosphorus was also called Willie Peat during  World War 1. (Ref. 5)



1. (put in ‘napalm’ in search line)


3. (put in ‘ white phosphorus’ in search line) (put in ‘vesicant’ in search line)




Week 19: Science Makes Sense-Organic Chemistry-aldehydes, ketones

January 4, 2016

When my mother was young, the perfume that young women of her time would crave for was Chanel No. 5!  I remember my sister getting her first whiff of this exquisite perfume at a wealthy girlfriend’s house and raving about it.

Aldehydes played a quiet role in creating that popular perfume. (Ref. 1).     Today we shall study aldehydes and ketones and note their structure and everyday uses.

Let us start with the simplest aldehyde: commonly known as formaldehyde,but the IUPAC name is methanal.  Note the ‘al’ ending, whereas for alcohols, the ending is ‘ol’.  All aldehydes have H-C=O structure, so the first aldehyde is shown with an additional H or hydrogen atom.  The next aldehyde, ethanal or acetaldehyde has a methyl group instead of the H, or hydrogen atom. Fig. 1 has the first four in the series. (Ref. 2)

Ketones are very similar to aldehydes, but they do not have the H-C=O structure; only the C=O structure, or the carbonyl structure. The carbon atom could have two methyl groups and then could be more carbon atoms. Again, Fig.1 has the first four in the ketone series. (Ref. 2)

Since aldehydes have the hydrogen present, they are not as stable as ketones and can be oxidized.  Since ketones do not have that hydrogen atom, they are resistant to oxidation. (Ref. 3)

The carbonyl group,C=O,is characteristic of both aldehydes and ketones.      The oxygen atom is far more electronegative than the carbon atom and the presence of the extra bond (double bond) increases the pull of the electrons towards the O. The high polarity of this bond in aldehydes and ketones results in higher boiling points relative to comparative hydrocarbons. (Ref. 3)

Smaller molecules of aldehydes and ketones are soluble in water; they hydrogen bond with water molecules.  As chain length increases, the hydrocarbon ‘tails'(all hydrocarbon bits apart from the carbonyl group) of the molecule come in the way of hydrogen bonding. (Ref. 3)

Uses of aldehydes and ketones: Formaldehyde and acetaldehyde (methanal and ethanal) are used extensively in industry,resins.   Butyraldehyde or butanal,is used as a plasticizer.  Higher aldehydes are used as deodorants, favors and detergents. (Ref. 3)

Ketones are used mainly in pharmaceuticals,polymers, solvents. Ketones play a significant role in biochemistry. (Ref. 3)

So once again, organic compounds play a vital role in our daily lives.

Activities for Middle School Teachers:

Let students write straight and branched carbon groups for aldehydes and ketones for the first ten in the series.  How many isomers can you get? Are there any enantiomers, stereo- isomers? Name them all using the IUPAC nomenclature.

Nuggets of Information:

Many aldehydes are derived from the de- hydrogenation of corresponding alcohols, hence the name ‘ al-dehyde’.  (Ref. 4).  

Certain foods and flavors in our diet contain aldehydes.  Cinnamon, almonds and vanilla are examples of aldehydes cinnamaldehyde, benzaldehyde and vanillin respectively. (Ref. 5).   All these compounds have a benzene ring.

Aldehydes and ketones play an important role in the chemistry of carbohydrates.  A carbohydrate is literally a hydrate of carbon.  The sugars, glucose and fructose are carbohydrates.  Glucose is an aldehyde and fructose is a ketone. (Ref. 5)

When the body uses fat for energy,ketones are generated during fat metabolism.  The fat gets converted to A T P.  Ketones are produced as part of the process.  When people eat less carbohydrate,the bodies turn to fat for energy, naturally more ketones are generated then.  This is called ketosis. ( Ref.6)

Most cells use ketones for at least part of their energy. (Ref.6)

Ketones and aldehydes exhibit tautomerism: this is a special kind of isomerism, where the carbonyl group, C=O, converts to the hydroxyl group,OH group and a double bond.  This is called keto-enol tautomerism.  The u-tube illustrates it. (Ref. 7)image


1. perfume






7.u-tube, keto-enol tautomerism, Khan Academy