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A world without organic chemicals (carboxylic acids and related substances).

OK it is this time of year again, and time to teach organic chemistry to the first year chem eng students.

Now before we get going I want to tell you a story about a man and his wife who wake up one morning in a world where organic compounds have suddenly stopped existing and doing the things which they are normally doing, well to be honest I have allowed the organic chemistry in their bodies to carry on working so that they can see the chaos.

I woke up late, my alarm clock was gone. So was the bedside table and my underpants. In their place was a pile of dust, metal and bits of wire. I stumbled out of the bed which was now a mass of nasty metal springs which were poking me and my wife. Then I discovered to my horror that most of the floor was missing. The bare steel beams were all that remained, I fell past the beams into the basement. I cursed as I hit the floor in pain.

I walked through the basement which was now packed with wire and metal, I made my way to the basement door which was missing. All that remained was the nails laying on the floor where the door used to be. I walked out into the garden. The grass was gone, in its place was a loose dust covering the garden. I then saw that my fruit trees were absent, I gasped at this.

I walked up the cement steps into the house, I heard my wife calling out in terror at this horrible new world. My car was laying on the floor with no tyres, the paint was all gone from my pride and joy. My head pounded, I entered the bathroom and went to the steel cupboard where I kept a bottle of pain killers. The pain killers were gone all which remained was the sheet of foil. This is horrible, I then moved into the kitchen. I opened the bread bin to get a bite to eat and there was nothing there.

You can see how this man is having a very bad day. Wood, plastic, food, medicine, rubber, grass, cloth and paint have all vanished. I will not carry on but I am sure that you can see that life in a world with no organic chemistry is a total nightmare. Now I have your attention I was start to comment on the organic chemistry

We are starting our work with the carboxylic acids, these are chemicals which you will find in the home in several places. The soap you wash with is made up of carboxylic acid salts and the soup you drink in the kitchen has carboxylic acids (amino acids) which form polymers (proteins), your smelly socks in the wash bag smell because of carboxylic acids, the active part of dog shampoo has a carboxylic acid derivative, the rhubarb leaves in the garden have a carboxylic acid which makes them poisonous, your nylon and polyester clothing has carboxylic acid derivatives, many of the sauces in the kitchen have a carboxylic acid in it…. Do I need to continue pointing out carboxylic acids which are important in the home ?

OK let us look for a moment at one of the most simple carboxylic acids (acetic acid). Using 3Dmolecule vision we can see the carboxylic acid group bonded to the CH3 (methyl).

A moleule of acetic acid

Now as we adjust our glasses we can see the electronic properties, the red is positive while the blue is negative. We can see how the oxygen without the hydrogen is a centre which is very negative while the carbon of the carboxylic acid group is very electron poor.

Now carboxylic acids are all very well, but we need to be able to make them and do things with them. One French chemist (Grignard) did a lot of work with alkyl and aryl magnesium halides. These are organometallic compounds formed by reacting alkyl and aryl halides with magnesium in an ether. We will come back to the alkyl and aryl halides latter.

If we mix a Grignard (which is a super carbon nucleophile which seeks out electron poor centres) with carbon dioxide (CO2) we get a reaction. The carbon of the Grignard forms a bond to the carbon of the CO2 to form a carboxylate salt. Using our special 3D molecule vision (a silly name which I could not resist using) we can see how the carbon of CO2 has a partial positive charge.

After protonation (treatment with a strong acid such as HCl) we can get our carboxylic acid. Another method is to react an alkyl halide with cyanide. OK, I am sure that almost everyone has heard of the “c word” but here is an organic cyanide (Methyl cyanide) for you to look at.

The cyanide acts as a nucleophile, the carbon attacks the carbon bearing the halogen in what is known as a SN2 reaction. This is a reaction where the halogen is replaced with the cyanide, we will get back to it later so please do not lose any sleep over it.

The nitrile group can be reacted at carbon with a nucleophile (such as water) it is possible to make the nitrile carbon more reactive by protonating the nitrogen. This raises the partial charge on the carbon which makes water more able to attack the nitrile. Other nucleophiles will attack nitriles, for years I used to react nitriles with hydrazine in a related reaction to make the precursors for making metal extraction reagents.

After one water molecule has reacted with the nitrile it forms an amide. The amide is like a carboxylic acid except the OH of the carboxylic acid has been replaced with a nitrogen group such as a NH2, a NHR or a NR2. The amide can be protonated on the oxygen to make a cation which has a greater partial positive charge on the carbon. This cation is then more able to react with acidic water to form a carboxylic acid.

Below I am showing you an amide, this is the amide which would be formed from acetic acid and ammonia. But in real life it is much more easy to make it from ammonia and acetic anhydride (or acetyl chloride). To make an amide from the carboxylic acid requires a great deal of heating. If you heat the amide with P2O5 then you can make the nitrile by dehydrating the amide.

It is important to bear in mind that the hydrolysis of an amide is a hard and difficult reaction. In the past I have found that I have to boil nitriles for a long time in strong acid to make it work. This is due to the fact that the amide carbon does not have much of a positive charge on it. The lone pair on the nitrogen is delocalised through resonance onto the amide oxygen. This increases the electron density on the oxygen.

We can use the same type of mechanism as the amide hydrolysis to convert carboxylic acids into esters. An ester is like a carboxylic acid but in place of the carboxylic acid hydrogen a carbon group such as an alkyl or an aryl is present. It is important to bear in mind that esters of other types of acids can be made, I recall as a postdoc the times I worked with esters of phosphorus acids and the time I worked with (C2H5)2P(O)Cl which has the horrible ability to form tetraethyl pyrophosphate on contact with water. I will save the tale of TEPP and its irksome relatives for another day.

Back to ‘normal’ esters, the classic way to make these is to react an alcohol with the carboxylic acid using a strong acid (mineral acid) as the catalyst. Some time before christmas I mixed some soap with methanol, excess sulphuric acid and a reagent which removes any water (trimethyl orthoformate). I recall the time in Aberdeen when John Plater introduced me to the joys of trialkyl orthoforates. I think of these trialkyl orthoformates as the “thinking man’s dean stark head”. I will write about dean stark conditions another day.

After leaving it to stand over the holiday, the mixture was boiled for a day evaporated down. Then I extracted the residue with ether, the ether extract was washed with water, saturated sodium bicarbonate and brine (saturated sodium chloride solution). After I dried the ether extract with sodium sulphate, I evaporated off the ether to give me an oil.

This oil was diluted with petrol and injected into a gas chromatography machine. I looked at the GC trace and I saw a nice group of four peaks, the mass spectrum for each GC peak indicated that these compounds were methyl esters of carboxylic acids with even numbers of carbons.

The FAME (Fatty Acid Methyl Ester) profile of the soap tells me something about the soap, but I am running out of time today. Now we have seen how ester formation can be useful (GC on soap or free carboxylic acids is not normally possible) we need to think how the reaction works.

What happens is that the carboxylic acid is protonated on the carbonyl oxygen to form a cation, this cation is then attacked by the alcohol oxygen to form the new C-O bond in the ester. Below I have shown a picture of the protonated acetic acid in all its glory with the atomic charges in false colour.

 

Here is the mechanism by which the ester forms from the alcohol and the carboxylic acid under acidic conditions

PS. I will add more of  the story and more pictures in the next few days

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One Response

  1. I like this one!! The story is brilliant and makes it alot easier for my 17/18 y/os to relate to the stuff you are talking about!!

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