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

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)
  7. ttp://

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