The Science of Everything Podcast - Episode 62: Organic Chemistry Demystified

Episode Date: May 31, 2014

An overview of organic chemistry, beginning with a discussion of the nature of organic compounds, the history of vitalism and its influence on the development of organic chemistry, and what makes carbon so special. I then discuss some important concepts in organic chemistry, including IUPAC nomenclature, functional groups, aromaticity, fullerenes, polymers, and organic synthesis. Recommended prelistening is Episode 15: Chemical Bonding, and Episode 23: Chemical Reactions.

You're listening to The Science of Everything podcast episode 62, Organic Chemistry. I'm your host, James Fodor. So in this episode, we're going to discuss the fundamentals of organic chemistry. Give sort of an outline to what is a very large and broad field. Organic chemistry is quite technical, and to be properly understood, requires a great deal of practice and looking at structural formulae and chemical reactions and so on, which we obviously can't do here, nor would it really be appropriate. What I will attempt to do in this episode is give an outline of some of the core issues, concepts, ideas, and findings of organic chemistry so that you can be, hopefully, after you listen to this, a bit more literate about these sorts of issues and maybe fit together some things that you've heard about and concepts that you've been exposed to before, but perhaps not properly understood.

So in this episode, we're going to look at what is organic chemistry, what is meant by organic and inorganic compounds. We'll look at the different types of organic compounds, including polymers and biochemical compounds. I'll discuss a little bit about organic chemical nomenclature, so how organic compounds are named and what some of the words there mean. Then we'll look at some interesting concepts in organic chemistry like functional groups, aromaticity and fularenes. We'll talk a bit about polymers as well. And I'll conclude by discussing a bit about the different types of organic chemical reactions and organic synthesis, so how organic molecules like drugs, for example, and new polymers are designed and constructed. So, recommended pre-listening for this episode would be

episode 23, chemical reactions, and episode 15, chemical bonding would be very important. And I think episode 9 matter and molecules would also be relevant as well. Some basic understanding of chemical bonds and chemical reactions and atoms, molecules, and that sort of thing would be pretty much essential because it would be quite difficult otherwise to follow what I'm going to say. Right, so that will be. being said, let's make a start. So first of all, we need to define what is organic chemistry, what that subject covers and what is meant. So you've probably heard the term organic before.

I think I've discussed this before, episodes two and three about organic agriculture. I think I discuss what is meant by the term organic. But when most people hear organic, they think about organic food or organic farming or something like that. Unfortunately, the term organic as used in organic food and organic as used in organic chemistry essentially have nothing to do with one another. organic food is, you know, food produced without using artificial fertilizers, and also there's a variety of other things that are used. If you're interested, look at episodes two and three techniques to use. But organic chemistry really has nothing to do with whether something is natural or man-made, because organic chemistry studies both. Organic chemistry is really the study of carbon-based compounds. That's the fundamental characterization. It's stuff with carbon in it. But it's a little bit more technical than that, because not everything that contain, not every compound that contains carbon is considered to be organic. For historical reasons, there are some carbon-containing compounds like carbides, carbonates, carbon dioxide, and carbon monoxide, are classic examples of simple oxides. So there are compounds like this that are not considered to be organic. So basically, certain very simple carbon compounds that occur in many sort of systems that are not related directly to life or living organisms are considered to be inorganic.

But that's largely for historical reasons. there's no hard and fast distinction or no firm definition as to what is organic and what is inorganic. It's a useful way of breaking up chemistry into organic and inorganic. It's a useful decomposition, useful categorization, but it's not hard and fast. There is not a clear definition. There's no universally accepted criteria as to exactly what is an organic chemical reaction and what is not, or what is it an organic compound and what is an inorganic compound. The basic criteria is whether it contains carbon, but there are some exceptions to that. So to understand organic chemistry, it's very important to understand, I think, the historical basis that it rests upon.

Originally, the distinction between organic and inorganic compounds was based on the idea of vitalism. Vitalism is an old scientific notion that organic compounds, that is compounds that are found in living organisms, are fundamentally different from inorganic compounds that you could obtain from base elements by manipulation like chemical reactions. You know, it's that stuff like salts and minerals and things like that. Those were inorganic. Those you could manipulate and form compounds through chemical reactions in the normal process, and those were sort of simple and less interesting in some sense. But the special substances were the organic compounds.

These were compounds that were found in living organisms that were produced by plants and animals and bacteria, and it was thought that they could only be produced by living organisms, and that there was something special about them. There was some vital substance, some sort of mystical almost substance, Elen Vital, it was called, and it goes by some other names, that made organic compounds special, and that it was thought that you could not convert inorganic compounds into organic compounds, because inorganic compounds lacked this vital substance, and you couldn't just create this through chemical means, and that it was this vital substance that made life special or different to non-life, that made things living.

So this notion is a very old notion, it goes back to ancient Greece, and was believed, you know, through, up until to the early 19th century, when it began to be questioned, when there were a series of chemists who began to develop, who began to sort of draw, close the gap in a sense between inorganic and organic compounds. So the real clincher came with a decisive experiment by Volha in 1828 when he was able to synthesize urea, which was long recognized to be a clear example of an organic compound, from the inorganic salts, potassium cyanate and ammonium sulfate. So two clearly inorganic substances, he were able to react them together to form what was clearly an organic substance. And this was not the only such experiment that was conducted around the time, but it was sort of one of the key decisive ones that really disprove this notion that there was anything special or that there was any special vital substance inherent to organic compounds, that in fact it was just a different type of matter,

and that you could create organic substances from inorganic substances through the correct reactions. So basically around the early to mid-19th century, with the progress of chemistry, this notion of vitalism was discredited. However, the old distinction between organic and inorganic compounds remained, and is still why they're used to date to separate out chemistry. So if you study chemistry, there's sort of quite distinct approaches, I suppose, or differences in subject matter between whether you're studying organic or inorganic. Fundamentally, it's all the same stuff. It's all atoms and bonds. The sort of physics behind it's basically the same stuff. but there are important differences in methodologies and I guess just the way it tends to be approached,

partly historical, partly because of the nature of carbon compounds are quite special, which means that they are, it's useful to keep them as sort of separate disciplines, or at least to have like specialisations there, but there is no hard and fast, clearly distinct difference. The old vitalist notion is long discredited, but I think it's useful to understand that that's where the origin of this notion of an organic substance came from.

Okay, so having laid that historical background, let me talk a bit about some of the different types of organic compounds. One of the key things to understand is that organic compounds are very, very diverse. In fact, there are far more organic compounds than inorganic compounds. Organic compounds are those that contain carbon. Usually they also contain hydrogen and oxygen and nitrogen and some other things like that. But there's a small, I mean, they can contain any element, but there's a small number of elements that are particularly common in organic compounds,

hydrogen, nitrogen, oxygen, phosphorus, etc. Organic chemistry essentially studies carbon and some of those other elements that commonly occur with it. Inorganic chemistry studies basically all the rest of the periodic table, over 100 other elements. But organic compounds, I think there are several million known and named classified organic compounds and a few hundred thousand inorganic compounds. So almost all known compounds are organic compounds, and that's because of the ridiculous diversity and flexibility of carbon,

which we'll talk about in a moment. But just to give an idea of some of the different types of organic compounds, so you know what we're talking about, one big class are essentially natural compounds. These are biomolecules produced by plants and animals and bacteria. And most of these are still extracted from natural sources because it's either impossible or just too expensive to produce them artificially. So it's still the case that most drugs are developed from plants

or other natural sources and often still extracted from. them or groaning bacteria or something like that. Substances themselves, they're not produced artificially in a lab because it's too expensive. Another good example of this is natural gas and oil and coal still extracted from the ground. These are also organic substances. So examples of biochemical compounds that are important, carbohydrates, enzymes, hormones, lipids, neurotransmitters, nucleic acids, proteins, proteins, vitamins, fats and oils, all of these things are organic compounds. Essentially anything that's in the body is an organic compound, with a few exceptions,

but overwhelmingly everything in most of the things that form life are organic compounds, or predominantly organic compounds. So that's the sort of natural class of naturally occurring organic compounds, but there are also a very large class of inorganic or synthetic compounds. These do not occur naturally and a man-made. The biggest classes of these are plastics and rubbers. So you probably know that plastic is an organic compound. It's made from hydrocarbon, so essentially it's made from oil.

That's a simplification, but that's essentially correct. Rubber also is a synthetic polymer. So, some of the polymer, as I've mentioned before, is a long molecule, a big long molecule that is comprised of a long interlinked chain of smaller components, which are called monomers. So you have a monomer, a particular type of monomer, you string a bunch of them together, you chain them up by chemical bonds, and you form what's called a polymers. So DNA is an example of a polymer because it's comprised of individual nucleic acids, which you string them in a big long chain together in that double helic structure and you form a polymer. Synthetic polymers, like the plastics on the rubbers, are formed using a similar idea, but the monomers are different.

Plastic is a broad term that's used to describe a wide class of synthetic organic compounds, which are polymers that they're made by chain together lots of organic monomers. I think it's interesting just to think about the different types of plastic to perhaps give you a bit of an understanding of how this fits together. So all plastics are polymers, well, all plastics I know of are polymers, and there's certainly all organic substances, which means they're mostly made from carbon. Well, carbon and hydrogen. So some of the different types of plastics include polypropylene. Polyethylene is the type of plastic that's used in plastic bags. So polyethylene is the most common type of plastic. It's used in very thin form in things like plastic bags, but it's also used just.

just as a generic plastic to make... So, you know, just small plastic toys or a plastic keyboard or a plastic door handle. There's a problem that made of polyethylene. And polyethylene is very simple. It's basically just literally a chain of carbons with hydrogens bonded around them. So hydrogens and hydrogen, that's really all it is. And, you know, it has to be cool and set in particular way, so there's more complexity there. But essentially, that's what polyethylene is.

Fundamentally, it's made of the same material as oil is. It's just in a slightly different structure. It's just carbon and hydrogen. Another third common type of plastic is called polyvinyl chloride or PVC. That's used as a particularly hard type of plastic, which is often used to construction like plastic pipes. That's polyvinyl chlorine. And essentially, it's similar to polyethylene,

but it's got chlorine atoms substitute for some hydrogens, which adds some strength to it. And there's also some other things like nylon and Teflon. There's many, many organic polymers. But these are all synthetic polymers. they're made in labs, often using inputs of hydrocarbons to provide the raw materials, essentially, to produce the polymers. So, as you might have hopefully been able to gather from the types of organic compounds that I've mentioned, that organic compounds are ubiquitous. They're everywhere.

Synthetic and natural organic compounds are just ubiquitous in contemporary society. So that's why organic chemistry is so important. But why carbon? Why is carbon? Why is carbon? carbon so special or important? Organic chemistry is very important, and organic chemistry is essentially the study of carbon compounds, but why carbon, like why single that out? The reason is because carbon has an essentially unique ability to form very long chains of interconnecting bonds, carbon-carbon bonds. This is probably called concatenation.

This is important because the ability of carbon to be so useful is precisely because it forms these polymers. Many of the things that I mentioned before, the three different types of plastic, as the synthetic polymers and the other things in life, like the lipids, your proteins, and your enzymes and your hormones and your nucleic acids. These are all polymers, and the reason that they can do such interesting things is because they can be such long molecules, which allows them to fall up into interesting shapes and carry interesting functions in the case of proteins, or to store lots of energy in the case of lipids, or to be very light and strong in the case

of plastics. But it's the longness and the complexity or the potential complexity associated with that, that allows carbon compounds to be so useful. So that concatenation, that ability to form very long chains is crucial. And carbon is not completely unique, but largely unique among the elements in being able to do that, because it has a valence of four. It normally has four bonding sites, because it has four, essentially four empty spots for electrons to fill that need to be filled by electrons, and those electrons come from other atoms. So it has four valent sites.

That means four bonds that it conform with other atoms. That four is a special number because it's essentially allows for a very symmetrical arrangement that allows you to form very long chains. Whereas other elements that don't have that symmetry, if you try and form a long chain of them, it'll either like it'll bend around and come back on itself or the chain just won't be stable because of the kinks and other things like that. So essentially being able to form long, straight, concatenated bonds is crucial to be able to form long, complex polymers. And that's what carbon does, because it has a valence of four.

Silicon also has a valence of four, and that's partly why it's also quite useful in many applications, but it's not as light and versatile. It doesn't form and break bonds as as carbon does. That's another thing that makes carbon so useful. It's very light and simple element, so it just forms bonds with lots and lots of different things and can be relatively easily made to form double bonds or to break double bonds, and you can add elements and take them off. It's just very flexible, very versatile. And so therefore it's able to form this very large class of complex and intricate molecules. One of the simplest forms of organic molecules is called hydrocarbons, which I mentioned before.

These are a family of organic molecules that are purely composed of hydrogen and carbon, so just hydrogen, carbon-hens, and hydrocarbon. And fossil fuels, so coal and oil and natural gas are sort of the canonical examples of hydrocarbons, because that's what they are. They're just carbon and hydrogen. and when we burn them, essentially what we're doing is we're breaking up those bonds between the carbon atoms, and we're reacting the carbon with oxygen in the atmosphere to form carbon dioxide, and we also form water as well. We react some of the oxygen in the atmosphere with hydrogens found in the hydrogon to form water, H2O. So the energy stored in the carbon-to-carbon and carbon-hydrogen bonds is extracted by reaction with oxygen in the atmosphere,

and energy released, and then we use that to fuel our energy. economy. So that's why hydrocarbons are so useful. They're also used, as I mentioned before, to produce plastics, and so synthetic polymers. They provide the raw material in a sense for that. Okay, so that's the conclusion of sort of the introductory part of this, the what is organic chemistry, the types of organic compounds and why carbon special. I now want to look at a few more specific elements. First, I want to start by talking about the nomenclature. So nomenclature is a very important component of organic chemistry, and there's a systematized way of referring to, what, naming and referring to organic compounds.

As is unsurprising, because as I mentioned, there are so many of them, we have to have rigorous and clear rules for naming them. So these are, these rules for the nomenclature are agreed upon by the International Union of Pure and Applied Chemistry, so IUPAC. They have, you know, very strict and very technical rules about exactly how names are put together. Essentially, the idea is that you look at the longest chain of carbons that is present in a molecule. There might be lots of different chains and subchains and so on. You look at the longest possible one and you base the name on that and then you describe the molecule based on

the position of different side chains along the main chain. So if your main chain, your longest chain of carbons has 10 carbons on it, then you name the molecule after saying, well, what is branched off from the second carbon and what is branched off from the third carbon and what is branched off from the fourth carbon? And then maybe there are sub-brances of that and so you name those appropriately. And, you know, Each different type of bond or molecule that could be attached to it has its own name. And so you basically just build up bigger and longer names according to where the different chains or subgroups appear on the main chain of carbons. Now, the rules are far too technical to go into here. I'm just trying to give an illustration of how nomenclature works and what it's used for.

The purpose is so that ideally every single organic compound should have a unique and unambiguous name from which you can determine its structural formula. That is the exact relationship of all the atoms in the molecule. So that's why the names have to be very precise and technical, because they literally describe exactly the structure of the molecule. It's not a name in the usual sense, because we could just call the molecule, you know, molecule 4-7-8, and that might be enough. Or we could call it Bob.

You could just have a name to refer it to. But the technical nomenclature in organic chemistry actually specifies precisely the structure of the molecule so that a chemist could just look at the name, and in theory at least, draw up the molecule, and they'd know exactly what it looked like. But in practice, because these technical structural names are very long and complicated, chemists don't really use them very much in actually referring to compounds.

What they tend to do is use either structural formula, which is essentially like a diagram of the molecule, if it's complicated, or if it's simple enough, just use its common name, or a trivial name they're also called. Now, sometimes things are simple enough that the trivial name is the same as its proper name. So carbon dioxide, well, that's not an organic molecule, but it'll do for our purposes here. Carbon dioxide is its proper name. That's probably what it's called. Water would be an example of a trivial name. That's not its proper name. Its proper chemical name would be a dihydrogen oxide or dihydrogen monoxide.

But water is just commonly used because it's easier. Or you just write H2O. But to give some examples, so tataric acid is a type of organic acid that's found in wine. Generally, you just refer to as tartaric acid because it's easier and simpler. but its proper systematic name is 2-3-dhydroxy-butane-di-oic acid. Let's break that down a bit. So 2-3, what does that mean? Well, those numbers refer to the carbon atoms along the main chain,

and it says that something happens on, there's something attached to carbons 2 and 3. Well, what is attached to those carbons? Well, the next bit of the name tells us that, dihydroxy. The dye tells us that there are 2. Okay, well, 2 what? Hydroxy. Well, that's essentially just OH molecule.

That's a functional group, which we'll talk about in a moment. So dihydroxy, there's two of those OH things bonded to the second and third carbon atoms. Okay. What are these second and third carbon atoms part of? What's the main chain? Well, the next bit of the name tells us that, butane. Butte means four. So there are four carbons in the big chain.

And A-N means there are no double bonds. It's all single bonds. EIN means there are double bonds, and iron means there are triple bonds. But don't worry too much about that. But you can indicate the type of bonds in the name. And the last bit, dioeic acid, tells us essentially that it's an old. organic acid. So that tells us also that there's another functional group that's going to be attached there. But it actually tells us that there are two of them. There'll be acids,

acid groups at either end. But the key point is that you can refer to the acidic properties of the molecule by the final component, which is the oic acid. Dioic acid means there's actually two of those acidic groups on the end. So overall, we have the name two, three, dihydroxybutane, dioic acid. So that specifies completely the structure of the molecule and where everything is, the different functional groups and the different types of bonds. But you can see that that's kind of long and annoying, so tartaric acid's easier. Now, I can't resist giving an example of a much longer name, because tartaric acid is actually a relatively simple organic compound.

Beta-carotene is a pigment found in certain fruits and vegetables, so it's responsible for the color of some of these, and it's classified as a hydrocarbon. It's a fair bit more complicated than tartaric acid, so it's sort of trivial name is beta-carotene. What is its IUPIC name? Well, its Iupic name is as follows. 133, trimethyl 2, 1E3E, 5E, 7e, 9e, 11, 11, e 13, e 15E, 17E, 3,712, tetramethyl-Methyl-Exene, 1-E0, 2-6-3Methyl-Exene, 1-Ele,

octadeca 1-3-5-7-9-11, 13, 15, 17, non-anil cyclohexene. So that's the full name. Now, as you can imagine, no one actually uses that name. It's much easier either to call it beta-carotene or to just draw the structure, the structural formula. And all of those numbers, by the way, are just referring to the different carbons along the position of the main backbone chain, the longest chain of carbon molecules, the positions that the different groups occur. So if you look at beta-carotene, it's got a couple of rings at each end, and there's a long chain of carbons in between, and there's some double bonds periodically. there's a few other sort of small side branches. But that's what the name is referring to.

It's just specifying exactly where all those side branches occur and where the double bonds occur. So that's that big list of numbers that I gave, for example. It was specifying where the double bonds were. But anyway, the purpose is to give it as an illustration of how one puts these big names together and also why they're not really used that much. Also, one point that I want to make about this

is you might sometimes hear that, like, the longest word ever is some, the name of some chemical compound that has like a thousand letters or whatever. These are not usually considered to be real words because no one really uses them. Technically, you can name a compound. There's no limit to how long the name could be, just however long the chain was. You could give its full IPEC chemical name. But scientists really don't use that. There's no real point to that name.

You would just use the structural formula or have other ways of describing it, and you would have a common name or a trivial name to refer to it simply and concisely. But anyway, that's some stuff on nomenclature. Now, let me talk about functional groups. I mentioned functional groups before because they're very important in naming molecules. You need to specify what functional groups are part of them, but what are functional groups? Well, functional groups are specific groups of atoms or sometimes bonds within molecules that are responsible for characteristic types of behavior or characteristic types of reactions

that these molecules participate in. So the same functional group will undergo similar reactions regardless of what particular molecule it's part of or how big the molecule is. So that's why functional groups are important because they're groups of atoms that participate in the same types of reactions or the same type of chemical functions regardless of where you find them.

So it's very useful to be able to identify functional groups because you can then predict, at least probabilistically, the types of behaviors are chemical species, is likely to exhibit. So you see, well, it's got this functional group, so it's probably going to behave this way, or it's got this couple of functional groups, and so it's probably going to behave in some other way, or it's got this functional group, so that means it's more likely to engage in this type of reaction, or less likely to participate in this type of reaction. So functional groups are really, really useful in organic chemistry for dealing with the ridiculous

complexity of the hundreds of thousands and millions of different compounds. You see, you break it up by what functional groups are present. Indeed, that's a way of studying organic chemistry, you just study the different types of functional groups, and what types of reactions there what types of reactions they participate in and what properties they exhibit and so on. So I'm now going to go through a list, a brief list of some of the many functional groups that are found in organic chemistry. And I don't expect people to remember all of these or really follow it in all detail. I'm trying to give the flavor of organic chemistry and what it's about. And so I hope to do that by going through some of these functional groups here.

Also, you may have heard of some of them before, or at least some of the names. So don't worry if you can't remember them all or fit names with properties. That's not so important. Just try and get the gist of how this works. So, let me go through a few. Al-canes I mentioned before. Al-canes have single carbon-carbon bonds. Al-keens, that's got an E instead of an A, an A, that's where you have a double-carbon carbon bond, and an al-Kine, where you have a Y, that's a triple bond. And so these tend to engage in particular types of reactions. So we talk about al-keens, al-Kains, and al-Kines. An example of the difference would be saturated versus unsaturated fats. saturated fats are, that means they have all of the hydrogens they could possibly have,

that means they have no double bonds. So they're alkanes. They have no double bonds because they've got the maximum possible number of hydrogens. They're saturated with hydrogens. If we take out some hydrogens, that means that instead of bonding to a hydrogen, two with the carbons bond to each other, and so you form a double bond. That's an alken. So that's an unsaturated fan, or an unsaturated compound.

So that's an application of the difference between alkanes and alkanes. and they tend to exhibit particular types of functionality, and they have different properties, like saturated fats are more likely to be solid, unsaturated fats more likely to be liquid. Another type of function groups are haloalkanes. So halogens are chlorine, bromine, fluorine, and iodine. They're the atoms right to the right-hand side of the periodic table, or the second-to-right-most group. So not the noble gases, one before that, which have one free spot for. or an electron, basically. So they're very reactive because they're only one extra electron to form a stable outer shell.

And halogens are particularly useful as solvents and flame retardants and an amnative synthesis reactions because you can often sort of swap out a halogen for some other molecule for some other atom. So it's a very, so hallowalkane is very useful. And an example of a heliocaine that I mentioned before was PVC, polyvinyl chloride, that the chloride is a halogen, so that's a that's a hello alcane there. alcohol's very important functional group and alcohol is the functional group there is a carbon bonded to an

OH group. So the OH group is sort of what we refer to as the functional group itself. It's an oxygen and an oxygen. If you have an oxygen and a hydrogen whacked on somewhere in your organic compound, it's an alcohol or at least it may be. It has an alcohol functional group because you can have more than one functional group. So some common alcohols, ethanol, that's when you have two carbons, that's the alcohol you drink, or some people drink. Rubbing alcohol is called isopropyl alcohol, that's when you have three carbons in your chain. Methanol is when you have one carbon, and that's very volatile and can be used as fuel. So basically, ethanol, methanol, and

isopropyl alcohol are very similar in structure. There's just, you've got an OH group attached to some number of carbons, one in the case of methanol, two in the case of ethanol, three in the case of isopropyl alcohol. But their properties are, well, some of them are similar, like they're all flammable, but they certainly are quite different. Like ethanol, people drink, very strongly recommend against drinking isopropyl alcohol or methanol because they're quite toxic. I mean, I suppose ethanol is toxic to an extent as well, but the other types are particularly problematic. So alcohol is a very important functional group, and that's what makes something in alcohol, it's just that OH group. Ketones, that's a ketone is when you have a carbon double bonded

to an oxygen, and that's it. That's the functional group. It's the C and the double O bond. That's all. Many important reactions in industry use ketones. aldehydes, that's when you have a carbon double bonded to an oxygen and separately single bonded to a hydrogen. It's found in many fats and oils and fragrances. Another type of compound that is commonly found in fragrances are called esters, and that's where you have a carbon double bonded to an oxygen and single bonded to a second oxygen, which in turn bonds to another carbon. Again, don't worry if you can't follow that.

The point is that you can see that many of these important functional groups are fairly small. It's just, you know, you have oxygens or hydrogens combined in a particular way and a slight change in the way that they're bonded means that it's a different functional group. So many of the functional groups are actually quite similar in terms of you just look at them. The structure is quite similar, but their properties can be quite different. So, as I mentioned, esters and aldehydes are very commonly found in fragrances and oils and fats, and particularly esters have very distinctive fruit-like odors. So many artificial colorings and flavorings that are used in foods are actually esters.

So that banana smell, for instance. I don't know exactly what compound is, but I'm pretty sure that's an ester. most of those types of things are esters, a particular types of compounds with a particular functional group. Carbohylic acids, that's when you have a carbon double bonded to an oxygen and also double bonded to an OH group, the hydroxyl group.

Very common in organic acids, acetic acid vinegar, that has the carbocytic acid functional group. Nitriles, that's when you have a carbon triple bonded to a nitrogen. That's used in many drugs. Thyl, that's when you have a sulfur bonded to a carbon and a hydrogen. Many of those uses odorants. So, for example, the smell of natural gas,

When you say, you know, you can smell gas. Well, natural gas is methane, which is just C-CH4. It doesn't smell. You can't see it, taste, it, smell it, or anything. So when you say you smell gas, you don't smell methane. You can't smell methane. What you're smelling is thyls that are added as odorants to the natural gas precisely so that we can smell it. Phosphates are another important functional group.

That's four oxygens bonded to a central phosphorus atom and then also connected often to a carbon. It's important for any getransmissions. So it has applications in biochemistry, so you might have heard of, ADP or ATP energy molecules used in cells. That's Identicing Triphosphate. They've got these phosphate groups. So very common applications in biology there. So that gives you an outline of some of the functional groups.

You may have heard of some of them before, the aldehydes or the carbonylacillic acids, esters, helloalkanes, alcohols, ketones. Very important for understanding and categorizing organic molecules and predicting their properties and reactivities. So now I want to move on to talk about another property of organic compounds. which is called aromaticity. Now, aromaticity describes essentially when you have a ring of unsaturated carbon atoms connected together. It's six carbon atoms connected in a ring. It's a particular structure.

That phenomena is called aromaticity. The reason it's important is because essentially the six carbon atoms share electrons between all of them. It's sort of like one big covalent bond in some sense between all six of the atoms. That's not quite right, but it's a way of thinking about it. It's a special structure that has particularly low energy. You can spread out the electrons across a sort of a wider space, which means that the repulsive force between the electrons is lower, which essentially means you have a lower potential energy.

It's more stable. That's the key. It's more stable because you can spread out the electrons more. And so these aromatic rings, as they're called, are common in many types of organic compounds, and they're a particularly stable way for carbon to form, so that they're very common. These aromatic rings are also called benzene rings.

and you may have seen them before because they're occasionally used in a sort of stylistic way, like in logos or on products or things like that. It's essentially just a hexagon of lines, and sometimes you'll have a circle in the middle or something like that. This is basically a benzene ring or stylized versions of benzene rings. I'll post the pictures of some of these things on the Facebook so you can get an idea of what I'm talking about. But I think it's useful to have an idea of what this thing is. It's very important in organic chemistry because it appears all the time and has many important properties. The reason it's called aromatic, by the way, is because originally it was associated with odourants.

Many odorses do have aromatic rings, but certainly not all of them do. So the name is sort of a historical accident, like many things in science and organic chemistry as a whole. But the phenomena is not fragrance. Like, that's not what makes something aromatic in organic chemistry. It's to do with this conjugation stabilization property of the spreading out of the electrons across the six hydrogen atoms. That's what aromaticity is. It's not actually about whether it smells or not. That's just the word.

So, for example, four amino acids are aromatic. Histidine, phenolalinine, tryptophan, and tyrosine. Each of them have at least one aromatic ring in them. All of the five nucleotides, adenine, thymine, cytosine, and guine and urosyl have a number of rings. And so they form a key component of their structure. Steroid hormones are made out of a number of aromatic rings. Moving on to another very interesting property of organic compounds. Things called fullerines, and I can't help but mention these things.

A fullerine is any molecule that is composed entirely of carbon in the form of some sort of hollow structure. So it could be a sphere or a tube or an ellipsoid or some substance like that. So diamond is composed completely of carbon. There's nothing else in it, if it's pure diamond. But it's not hollow, it's a dense structure. Whereas there are things called bucket. balls or spherical fullerines, which are basically spheres of 60 carbon atoms in a very particular

arrangement. They're actually exactly the same structure as many footballs or soccer balls are. So if you think about that shape with how it has like those flat surfaces all linked together, that's really exactly the shape, or very close to exactly the shape of a bucky ball. Obviously they're just a lot smaller, and they're made of carbon atoms, and they're only made of carbon, and they're hollow on the inside. Solyurgical versions of this where you basically have a sheet of carbon and roll it up into a tube, These are called carbon nanotubes, and some people may have heard of these before because they're sort of recent developments in nanotechnology and chemistry. And there's a lot of excitement about some of their properties because fullerines tend to be very strong, very high tensile strength.

They're also very good conductors of electricity and heat, but they're also fairly inactive, that is chemically inactive, because they don't have any exposed atoms that can easily be displaced. They're sort of wound up as a sphere or a hollow tube. And there aren't any reactive functional groups like the alcohols or the esters or whatever to cause problems. The carbon by itself just sort of sits there. It's very stable. It's not reactive. But it's very strong and conductive. And so this combination of lightweight, strong, unreactive and highly conductive means it has these have potential applications in computing,

developing new computing technologies or new microchips. New potential applications in producing very high, strong but lightweight materials for use in construction or in manufacture of machinery. and other things like that. So it's very much early days for exactly what this will be used for. But I couldn't help mentioning them because they're an interesting application of organic chemistry and people talk about them periodically. So carbon nanotubes are just tubes of carbons rolled up together, and they're an example of fullerines, hollow substances composed entirely of carbons. Very interesting, very interesting things. Okay, so I'll come to the end now by saying a little bit about organic reactions and organic synthesis. This is making organic molecules, basically.

So organic chemistry has a tradition of naming specific reactions after their inventor or co-inventors. And there are literally hundreds of these. There's a big list on Wikipedia you can check out, and I certainly won't really go through any of them. But each of these reactions, in order to specify a particular organic reaction, ideally what one does is establish what's called a mechanism, a reaction mechanism. And this refers to a sequence of steps, very small steps, that specifies exactly what reaction. with what in each stage of the reaction. So exactly how you get from the reactants to the products.

So that includes specifying any intermediate states, which might be like high energy states that don't last for very long, or activated complexes, transition states, exactly which bonds are broken, what order the bonds are broken in, exactly which new bonds are formed and what order they form in. Electron transfers, whether there are double bonds or whether there's conjugation. Also, you'd want to include the stereochemistry, which is the exact shape of the molecule,

which products are formed in what order they're formed, exactly what reacts with what. You also would want to include the rates of reaction, any catalysts that are used. So it's literally in exact detail everything that reacts and how it reacts in the order that reacts. And that's what a reaction mechanism is. So when you establish a reaction mechanism, describe exactly what the products are and the reactants are, and all of that in detail, then you've established what the reaction is and you've given a name. And there are many, many, many of those. But it's very useful to understand these reaction mechanisms because then we can understand how they work and make predictions about, well, what if I changed something, how would

the reaction change, or how would the rates change, how would the rate depend on the different concentrations of the reactants, for example, all sorts of things like that. There are a few basic types of reactions, classes of reactions that occur commonly in organic chemistry. The three that I'll mention here are addition reactions, elimination reactions, and substitution reactions. And I think I have discussed these before when I talked about chemical reactions more broadly, because these can, there are inorganic versions of these as well. But in an organic sense, an addition reaction is when two or more molecules combine to form a bigger molecule. Often this involves adding new species across a double bond. So a class example of this is the polymerization reactions

to form organic, to form those long polymers, because usually what happens is we start with the double bond between two carbons, we break open the double bond, and then we break open the double bond, and then we add things across that double bond, maybe it's hydrogens or maybe it's new functional groups or something like that, using the extra space that's been made there. And one, you can potentially use that to form longer chains of molecules. The reverse of an addition reaction is an elimination reaction where we have two substituents that are removed from a larger bigger molecule,

so you break up a big molecule into smaller molecules. And this is just the exact opposite of addition reaction. You remove things, often hydrogens or other functional groups, and form double bonds between the adjacent carbons instead. Substitution reactions is just when you have one atom or a functional group and swapped out for a different one. Halogens are very common. The haloalcines that I mentioned before, the chlorine and the iodine and bromine,

are often used in substitution reactions because they're really good to essentially swap out for other atoms, so they're very handy there. Organic synthesis, which is a direct application of organic reactions, is the process of preparing a particular organic compound or species, as it's called, from given reactants. A total synthesis is a sort of more specific phrase. In principle, a total synthesis is the complete chemical synthesis of some complex organic molecule from simpler pieces without the aid of biological processes. So not using cells to do it for us. This is doing it in the lab through chemical processes so that we control at each stage.

So if we just inject a gene into bacteria and get that to produce something for us, that's not really a total synthesis because we're just getting the biology to do it for us. Total synthesis is when we do it in the lab, controlling all the steps. Usually the idea of a total synthesis is that you start with simple pieces that are commercially available that you can get reasonably easy access to. Carbon dioxide would be a simple example. And then you combine these in a way that ultimately leads to the product that you want, which could be very much more complicated. And often that requires many, many steps. You don't go straight from the reactors to the products. You go through a long chain of intermediates. you gradually build up more and more and more complex molecules until you get to the final end product that you're interested in.

And so at each stage of the process, each stage of the synthesis, you have to decide what chemical reaction to use, what reagents and products will be produced, what conditions are necessary, how fast the reaction will occur. So that's the rate of the reaction, because if the reaction is too slow, then that's not really viable. You also need to consider the yield, which means that what proportion of the product is what you want and what is other stuff that you don't want. So you always want to get a good yield because otherwise, again, it's too slow and too expensive. You want to consider the purity of the product, whether they're going to be contaminants, whether you can figure out a different way of getting to the same product that has a higher yield or a greater purity or that has a faster rate. There's also another complication because most complex natural products are chiral.

I talked about carav carality in the previous organic episode. It essentially means like right-handed and left-handed versions. as a mirror image of the same molecule. But the activity of the molecule, of most biomolecules, depends on which version it is, whether it's the right-handed or the left-handed version. Traditionally, many total synthesis yielded mixtures of both the left-handed and the right-handed,

and that's a problem because you only want half of them, and how do you separate out the two halves when they're almost exactly the same thing, like they're the same weight, for example, so you can't really use centrifusion to do that. More recently, there have been new and very clever methods of trying to separate out these mixtures, or even better, just to produce, to devise a total synthesis that only produces

one, whichever stereo isomis or whichever handedness you're interested in. And there's clever ways you can do that, but that's another complexity that you have to consider, like whether it's going to be right-handed or left-handed and which one you want, and how you're going to separate out the mixture if there is one. So a technique that's used for this these days is called retro synthesis. And this is basically, you start with what you want to end up with, you start with your design product, and then you break it down into something a little bit simpler. So you break one bond, say, you break this carbon-carbon bond,

or imagine detaching this part. And then you say, okay, well, now I've got two things that are slightly simpler. How can I get those? Suppose I had those. If I had these two things, then I could make my end product because I just react them together in the way that I know. Okay, but how do I get these two things? Well, then I break each of those down into smaller bits.

But how do I get the smaller bits? So you keep breaking, breaking down, until you reach a stage where you say, oh, I can buy that. this is something that's commercially available, and so I don't need to produce it. And so the idea is you just keep breaking down, you keep going down the chain,

breaking up each piece into more small and smaller components until at every stage in the process you've reached something that's commercially available. At that stage, you've constructed a total synthesis because you've figured out how to produce the end product using substances that they're available, assuming all of the reaction stages, of course, are possible and plausible, and then you have to consider rates and the yield and other things like that.

But that's the basic idea of retrocensus. You start at the end and break up, and break the product up into smaller pieces and then figure out how you could get that. And so you'd supply the process recursively. So organic synthesis is a really complicated area and it's the product of a lot of research. Obviously there's a lot of money here in terms of drug design in terms of treating diseases, in terms of developing new polymers and new material. So there's lots of interest in the industry for this sort of thing.

But it's very hard as well because there are millions of organic compounds and literally an infinitude of possibilities of the structures that you could have and ways that you could react things together. And there's no, like, algorithm you can just apply to follow a set set of steps, like, just to solve the equation and figure out how to do it. There's a lot of sort of ingenuity and, you know, knowledge of the different chemical reactions and how there's similar problems have been solved in the past,

and so there's much complexity there, which is why there's a, you know, still a lot of demand for chemists who understand this sort of stuff. But we now have reached the conclusion of this podcast. I hope you found it interesting. I think organic chemistry is something that can be, dry. I mean, it definitely can be quite dry, you know, if you're just learning reaction after reaction. Hopefully, the way I presents it at least made it a little bit more

interesting and accessible. I try to present some of the things that are more relevant, some of the knowledge that you might have heard, or concepts that you can perhaps relate to. So try and think about some of the things I talked about. I talked about what is organic chemistry? I talked about the types of organic molecules, both biomolecules and also synthetic polymers. I talked about why carbon is special, the special properties it has. I talked about the different types of functional groups and what those are. I talked about organic nomenclature, so how we name organic molecules. I talked about some other special properties of organic compounds, aromaticity, fullerines,

and I talked about organic synthesis and reactions and the different types of reactions, and I'll talk about retrosynthesis and how that's done. If you enjoyed this podcast, please jump on to iTunes and give the podcast a favorable review. It really helps to increase the image and the exposure of the podcast. So if you can do that, that's much appreciated. Also, give our Facebook page a like. Just go to Facebook, type in The Science of Everything podcast. You should be able to find the Facebook page.

There I post periodic updates and also images and visualizations to accompany the audio material of the podcast. So check that out. And even aside from that, just give us a like so that you can boost the visibility of the podcast. The website is Fods12.podbean.com. If you're interested in checking that out, you can also send me an email, at FODS12, that's FODDS12 at gmail.com, and there you can send me any recommendations you might have, things you'd like to learn more about at future topics or suggestions of how the podcast could be improved, or just let me know that you listen and like the episode.

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