12 minutes reading time (2314 words)

    Western Australia Branch Bayliss Youth Lecture Organic Chemistry - It's Everywhere!


    Ira Remsen (1846-1927) has often been described as the father of chemical research in America, and it is both amusing and constructive to read about one of his early experiments(2):
    "While reading a textbook on chemistry, I came upon the statement 'nitric acid acts upon copper'. I was getting tired of reading such absurd stuff and I determined to see what this meant. The spirit of adventure was upon me. Having nitric acid and copper, I had only to learn what the words 'acts upon' meant. Then, the statement, 'nitric acid acts upon copper' would be something more than mere words.

    "All was still. In the interest of knowledge I was even willing to sacrifice one of the few copper cents then in my possession. I put one of them on a table, opened the bottle marked 'nitric acid', poured some of the liquid on the copper and prepared to make an observation.

    "But what was this wonderful thing which I beheld? The cent was already changed, and it was no small change either. A greenish blue liquid foamed and fumed over the cent and over the table. The air in the neighbourhood of the performance became dark red. A great coloured cloud arose. This was disagreeable and suffocating - how should I stop this? I tried to get rid of the objectionable mess by picking it up and throwing it out of the window, which I had meanwhile opened. I learned another fact - nitric acid not only acts upon copper but it acts upon fingers. The pain led to another unpremeditated experiment, I drew my fingers across my trousers and another fact was discovered. Nitric acid also acts upon trousers."


    Like Ira Remsen, instead of being content with just reading about things, look around, what do you SEE? Outside - green trees, black soil, some water; inside - a piece of string, a packet of salt, a bag of sugar, a bowl of red jelly, a loaf a mouldy bread. All of these things are MATTER - stuff that we can see, feel or smell, something tangible.

    Matter, molecules and atoms

    What is this MATTER? Generally, it consists of MOLECULES, those CHEMICALS made up from ATOMS of the various ELEMENTS found on our Earth, A CHEMIST needs to know much about the various elements (there are about one hundred of them), and so they are collected together in the PERIODIC TABLE.

    The periodic table

    What is the Periodic Table? Well, it is a bit like a cemetery for the various elements, with each element having a different headstone. Let us consider the headstone for the element SODIUM:

     This tells us that sodium has an atomic number of eleven, and an atomic mass of about twenty three. Sodium is one of the alkali metals, and occurs in the same place in the Periodic Table as lithium and potassium, two other such metals.

    The alkali metals are very reactive, acting as reducing agents and forming stable cations, eg.

    Na → Na+ + e-

    Let us consider a common reaction of the alkali metals.

    The reduction of water

    Into a dish of water containing a little phenolphthalein, add a small piece of lithium metal - what do you SEE? Bubbles of gas, a pink colour appearing! All is explained:
    2Li + 2H2O → 2LiOH + H2
    Repeat the experiment with sodium and with potassium (a very small speck is advisable!) - such is the reactivity of the potassium metal that a mauve light is emitted.

    Making salt

    Not a constructive thing to do, you say, but certainly something that shows further the reactivity of sodium metal. Fill up a jar with come CHLORINE gas and, into it, plunge some molten sodium contained in a deflagrating spoon - a vigorous reaction ensues, and a fine white solid (sodium chloride, salt) is deposited on the inside of the jar. The reaction lasts for several minutes, and a beautiful yellow light (one of the emission lines of the sodium atom, the same light that gives us yellow street lights) is emitted. Again, we have a redox reaction:
    2Na + Cl2 → 2NaCl

    An organic chemist and the periodic table

    An ORGANIC CHEMIST puts few demands on the Periodic Table, seeing that most organic molecules contain only CARBON, HYDROGEN, OXYGEN, NITROGEN, SULFUR and PHOSPHORUS. Let us consider the element CARBON, present in all organic molecules:

     The simplest organic molecule is METHANE, CH4, one€ carbon atom somehow joined (bonded) to four hydrogen atoms:

     Other simple organic molecules are METHANOL, CH3OH, ETHYLENE, C2H4 and CARBON DIOXIDE, CO2:

     (note that ethylene and carbon dioxide both contain DOUBLE bonds, and that carbon is TETRAVALENT in all three molecules).

    Carbon dioxide

    This organic molecule plays a pivotal role in our lives in that plants, during PHOTOSYNTHESIS, harness the energy of the sun and produce sugars and oxygen. We eat the sugars, and breathe the oxygen, so surviving and again producing carbon dioxide:

    Let us show how the body produces carbon dioxide. Into a dish, place some water, a little phenolphthalein and just enough dilute sodium hydroxide solution so that the solution goes pink. Now blow into this solution (using a piece of plastic tubing) - the colour slowly fades as the pH drops (the solution becomes less basic):

    CO2 + OH- → HCO3-

    Sugar (sucrose)

    An organic chemist represents SUCROSE, C12H22O11 as

     If you want to make a spectacular mess, put 70g of sugar and 70 mL of concentrated sulfuric acid in a tall jar (with a plastic tray underneath for safe keeping!) and stand back. A smelly, hissing black column slowly forms(3):

    c. H2SO4
    C12H22O11 → 12C + 11H2O

    A bowl of red jelly

    Apart from being mostly water, jelly contains sugar, gelatin (the setting agent, a protein) and COLOURING. All food additives are carefully screened by regulatory bodies to protect our health, so the AZO DYES are now rarely used as colouring agents in foodstuffs. However, they are such excellent dyes that they are used extensively elsewhere, and they are easy to prepare:
    Take any aromatic primary amine (careful - check for the individual toxicity of these compounds), dissolve it in some concentrated hydrochloric acid, cool the solution to 0-5°C in an ice bath and add some sodium nitrite solution in portions; keep the final mixture (A) cold. Into a dish place any phenol, a little ethanol and some 2M sodium hydroxide solution (B). Now add a few drops of A to all of B, and swirl. Depending on your choice of amine(s) and phenol(s), a whole range of beautiful colours (azo dyes) may be obtained:

    A loaf of mouldy bread

    This usually lurks in the recesses of your refrigerator and, depending on the conditions and the mould which has invaded your bread, can look spectacularly yukky! How can anything so smelly and horrible have been so good to mankind? Before the second World War, Alexander Fleming had cause to examine some culture plates that he had inoculated with a Staphylococcus bacterium. Serendipitously, the plates had been contaminated by a stray mould and, after incubation, appeared thus:

     The mould had produced a chemical which inhibited the growth of the Staphylococcus bacterium, It was up to a pathologist, Howard Florey, and a biochemist, Ernest Chain, to isolate and purify the chemical (termed PENICILLIN) and to develop it as a life-saving drug:

     Well, penicillin is a successful, broad-spectrum ANTIBIOTIC against various bacteria, but has little or no effect on a VIRUS, such as the one that is supposed to cause acquired immune deficiency syndrome (AIDS).

    AIDS - drug therapy or immunisation?

    Much chemical research has gone into the development of an effective drug for the AIDS virus. One such chemical, AZT, is only partly effective in the treatment of AIDS, and serious side-effects are common:

     What of the chances of developing a VACCINE against infection by the AIDS virus? About 1800 (well before the time of Nobel prizes), a medical practitioner by the name of Edward Jenner noticed that milkmaids, although visibly affected by cowpox, never died from the dreaded disease, smallpox. In a moment of inspiration, Jenner took fluid from one of the lesions on the skin of a milkmaid and injected it into a male volunteer. After an incubation period, Jenner then injected the same male with real smallpox material (!) and the boy survived. IMMUNISATION and vaccines were born!

    What was behind this remarkable discovery? The cowpox material (ANTIGEN) had caused the immune system of the boy to produce an ANTIBODY. This antibody was sufficiently broad-spectrum in its action that it was able to negate the infective smallpox antigen.

    Antibodies, proteins and enzymes

    What is an antibody? It is basically a PROTEIN, a high molecular weight polymer of AMINO ACIDS.
    Another type of protein is an ENZYME, large molecules capable of speeding up (catalysing) the chemical reactions that go on in nature, and in us. One such enzyme, CATALASE, is found in potatoes.

    Catalase and hydrogen peroxide

    Take a potato, cut it into pieces and blend with a little water. Strain the sludge through cheese cloth into a bowl and discard the cloth and contents.
    Now take about 25 ml of hydrogen peroxide solution (about 3%, from the local pharmacy) and place it into a large test tube:

    What is happening - absolutely nothing! Now add about 1O mL of your potato extract to the test tube and rapidly connect to the rest of your apparatus for collecting any liberated gas. If you are efficient and quick, you will be rewarded by the appearance of bubbles, the enzyme catalysing the decomposition of the hydrogen peroxide:

    H2O2 → 2H2O + O2
    Repeat the experiment, but this time add a squirt of copper sulfate solution (3g in 100 ml of H2O) to the hydrogen peroxide solution before the addition of the potato extract. What happens - absolutely nothing again! What is going on?

    Enzymes and enzyme inhibitors

    In the above experiment, the copper ions (Cu++) have acted as an ENZYME INHIBITOR - no oxygen is produced from the hydrogen peroxide. A related and really interesting example of enzyme inhibition is found with another enzyme, ACETYLCHOLINESTERASE, a chemical present in your body.
    Say you pick up a hot object which threatens to burn your fingers - a simple molecule in your body, acetylcholine, is involved in the transmission of a message to the brain which causes a muscle response, and you drop the hot object. All is well, you say. But what if I tell you that the acetylcholine left behind is a poison to your body, and must be removed. This is where the enzyme, acetylcholinesterase, comes into play, catalysing the following reaction:

     Again all is well, but what if something happens to inhibit the action of the enzyme, acetylcholinesterase, and the level of acetylcholine builds up? What type of molecule could be an inhibitor of the enzyme - an ANTI-CHOLINESTERASE?

    Well, you probably have these anti-cholinesterases in your house, for use as insecticides, and they work very well to kill lawn beetles and the like. But what if some perverted mind decided to try these same chemicals on humans? Would they kill humans? Yes, and so the NERVE GASES were born, compounds so toxic that less than one milligram can kill an adult.

    The structure of nerve gases

    These are relatively simple chemicals:

     Just a collection of carbon, hydrogen, oxygen, nitrogen and phosphorus atoms which can be cleverly put together by a trained chemist:

    All that is needed is phosphoric acid, hydrogen cyanide, ethanol and dimethylamine.

    How do enzyme inhibitors work?

    Essentially, the inhibitor has the correct SHAPE to fit into the ACTIVE SITE of the enzyme, thus blocking the approach of the natural substrate(s):

    The shapes of molecules

    Let us return to the simple molecule, METHANE, CH4. Although we depicted it as a planar arrangement of four hydrogen atoms around a central atom, this was just a convenience. Methane actually has a shape, a tetrahedron:

     Consider now a different molecule, CHFClBr, a central carbon atom joined to four different atoms: hydrogen, fluorine, chlorine and bromine. Again the shape is a tetrahedron, but look, two different arrangements are possible:

    We can say that the two arrangements have a different SENSE OF SHAPE (you may recognise that they are, in fact, mirror images). What are the ramifications of this 'sense of shape'?

    Oil of spearmint and oil of caraway

    If you somehow extract the fragrant oils from spearmint leaves and caraway (or dill), you have essentially the same chemical in the extract, CARVONE. But then why do these oils smell so differently - one like chewing gum, the other like rye bread or dill pickles? The answer lies in the 'sense of shape' of the carvone:

    The receptor sites in your nose recognize the 'sense of shape' and different smells result.

    The tragedy of thalidomide

    About 1960, thalidomide was developed in Europe for the treatment of morning sickness in pregnant women. The drug appeared to be a very good one, until reports started to appear of serious malformation in babies born by mothers who had been prescribed thalidomide. After an intensive investigation, the cause of the horrible tragedy became apparent. The thalidomide prescribed to the women contained both 'senses of shape':

    One shape was an excellent sedative that controlled morning sickness very well, the other was a teratogenic molecule that caused gross malformation in a developing foetus.

    On this sombre note I close my lecture. I hope that I have been able to entertain you, to interest you, and to show you that we live in a world of vibrant (organic) chemistry.

    1. The preparation and delivery of the 1991 Bayliss Youth Lecture would not have been possible without the advice, skill, help and enthusiasm of Dr. Mauro Mocerino.
    2. Getman, F.H., J.Chem.Ed., 1940,17, 9-10.
    3. Shakhashiri, B.Z., "Chemical Demonstrations" (Univ. Wisconsin Press), 1983,1,77-8,
    4. Summerlin, L.R., Borgford, C.L., and Ealy, J.B., "Chemical Demonstrations" (American Chemical Society), 1987, 2, 150-1.
    5. Reproduced, with kind permission, from Brown, W.H., and Rogers, E,P., "General, Organic, and Biochemistry" (Brooks/Cole, 3rd ed.), 1987, 646.

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