SB1-Intro to Organic Chemistry

Okay then, so welcome to CH sixteen oh one. I'm Andy Smith. I'd recommend you take a handout here from the front if you want one. I'm going to be taking you through I've got nine lectures with you at the start here, followed by another series of seven lectures later on. So I'm going be taking you for 16 lectures.

0:40

You might be sick of me by the end of it, but my job is to really try and give you a core understanding of some of the major concepts. So the first nine lectures that I'm going to take you through are really going to probably the first one or two are going to be revision for many of you. I apologize if many of you know a lot of the concepts that I go through in the first two lectures, but people are starting from different points. So we want to bring everyone up to the same point for where I then go on and tell you about how we tend to think about organic chemistry in its current context. People often find these first eight or nine lectures, because I go through a lot of concepts that we apply right the way throughout this lecture course, they often question why we do it like this.

1:34

We set up a lot of concepts. They're embedded within the first two or three tutorials and then they try and set some of the core things that we use right the way throughout the course. Okay, so please don't be disheartened if you wonder why we're trying to tell you about certain concepts and we're setting it up like that, but we do that for a particular reason. Okay? And it's my job to try and guide you through those first, that first bit of the course.

2:04

So in terms of the content, I often get asked for what is the content of my lectures. I'm going to what I've sort of done here is split up the letter synopsis into the seven major sorts of areas that will list the different types of things that you might want to look at when you think about revision at the end. In terms of recommended reading, the one there are two books that are very good for this course. One is an organic chemistry book by Klein. One is the organic chemistry by Clarendon, Greaves, Warren and Wothers.

2:48

If you are a chemist and likely to be studying chemistry for four or five years, then that book number two will be a book that I would recommend that will probably take you right the way through from here, right the way through to the end of your course. The other thing that we'll recommend as we go through the course is you can buy a set of molecular models. You're allowed to take molecular models into your exam with you. A lot of people find them very useful in terms of visualizing molecules in three dimensions, which is one of the key things that we're going to be doing as we go throughout this course. They can be bought for around 15 to £20 through the online shop at the university.

3:33

They might also be available. Ian Smiley was trying to get them available through the lab as well, but I'll confirm that with you later on. A key source of information for this course will be the Moodle page. So everything will be available electronically, although I've got paper handouts here. If you would prefer to work electronically, all of the handouts are in electronic form already.

3:58

I'm going to be recording everything that I write on the board. And I'll put up that lecture podcast, try and do it within the same day that we do every lecture. Occasionally throughout my lecture handouts will be a QR code. If you scan that QR code, will give you a three-dimensional view of a structure. Because again, one of the key things that we want to try and talk you through is how we can visualize molecules in three dimensions.

4:28

Another learning aid is for every week that I'm giving you a lecture, there will be some online quizzes that you can do for self guided learning. These will help you. They're set up separately such that they were meant to cover some of the core material in the lecture such that you can test yourself. The answers are already available for you to download. There's also a video of me talking through all of the answers that's already available online.

4:57

So that's there for you as a resource. It's up to you whether you use that as you go through, but they will help when we start to talk about, when we start to look at tutorial work throughout the course. Okay. So what is organic chemistry? Okay, I love organic chemistry.

5:25

My research is in this area. And I would classify organic chemistry as a study of compounds that are composed mainly of carbon and hydrogen, but also contain other atoms. The most common atoms that will come across are oxygen, nitrogen, sulfur, silicon, and halogens. Now, I love organic chemistry. And to me, these two molecules here, you could argue, summarize to me why organic chemistry is amazing.

6:02

Okay. This has got a beautiful if I draw its proper structure correctly has got a beautiful three-dimensional structure. Both of these two molecules have significant biological responses. Does anyone know what these molecules are? I don't want to say anything about you're exactly right.

6:27

I don't want to say exactly how you know that structure. But that cocaine. But what I think is, to me, that's an amazing molecule. It looks quite small. It's composed of carbon, hydrogen, nitrogen, and oxygen.

6:43

It has a beautiful three-dimensional structure. It has an amazing, some people might say, biological response. Anyone know what this one is? Okay, that one's Viagra. So again, that again has a significant biological response.

7:01

But if you look at it, it's a relatively small organic molecule. But it's been designed such that it has a particular trigger. And to me that is amazing. We can make, we can put together molecules that have a certain specific structure and have a certain specific response. And to me, that's why we should be interested in organic chemistry.

7:26

I am biased, but this is why we should be interested in this area. And so to be able to come up with these molecules, what we need is we need to think about the theory and the structure of molecules such that we can understand how we can bring these components together and understand how they're held together and their structures or what is their three-dimensional structure. We want to understand reaction mechanisms such that we can predict how we can bring molecules together to make a significant structure such as this. And then these are really important, particularly in synthesis and biology, because we can then make designer molecules that have a certain response. So what I'm going to do in the rest of this lecture again, I apologize if a lot of this is really obvious.

8:21

But I'm just going to go through some of the core things that when we think about organic chemistry to bring everyone up to the same starting point. So what we're really interested in are the molecular structures of organic compounds. And you can simplify any organic structure by saying that it can consist of a hydrocarbon chain and then it has a certain functionality. A functional group that I've just shortened here as FG. These functional groups usually contain nitrogen, oxygen, sulfur, and a range of different atoms.

9:12

So what we're just going to look at are some very simple organic structures. And so if we look to start off with at a simple amino acid, that is a structure of alanine. We have a hydrocarbon chain here. It's made up of the carbon and hydrogen backbone that makes up this molecule. And then we have these core functional groups that are really key to reactivity.

10:02

When we think about functional groups, really think of these as being the reactive parts of the molecules that we're going to try and think about how we can understand the typical reactivity of many of these different structures. When we think about hydrocarbon chains, they can either be made up of simple linear chains or they can be made up of ring systems. So for example, if you look at the structure of pentane, I'm drawing this out just to try and exemplify something. If we look at a simple hydrocarbon pentane, it's got five hydrocarbons. When we start to think about the structures, it takes a long time to draw them out if you draw all of these as a big C and draw the hydrogens.

11:01

So what we typically do is we take a shortcut. We simplify them such that when we have this long chain of carbon atoms, we just draw them as a long linear chain. And we miss out the hydrogens. Okay, so any of the structures that I draw from here are just going to be representations of that. What we assume here is that we know that all of these carbon atoms are tetrahedral.

11:33

And we just assume what we're drawing in this two dimensionals, in this structure, is a representation of this. We have to remember that it's three-dimensional, but we just draw it in a linear chain. To make them look pretty, the bond angle here is approximately 120 degrees when you know the bond angle in a tetrahedral, which is at 109. But that just allows us to draw them out in a linear chain in a regular fashion. So we don't draw big Cs, we miss out the hydrogens, we roughly draw these chains at an approximate 120 bond angle 120 degree bond angle.

12:16

So if we do the same for cyclohexane, we just simplify cyclohexane to that structure. So just get used to doing that as we go through this course. The key thing to remember that I've said already is that these are two dimensional representations of three-dimensional objects. And we'll come back all the time to three dimensions. We often use abbreviations, and when I was in your position, I remember that my lecturer in organic chemistry just started throwing abbreviations at me.

13:02

So what I'm going to do is take a little bit of time to tell you some of the abbreviations that I think are important, and some of the terminology that we often use. We often use shorthand abbreviations for names of a long carbon chain. And hopefully you all know this. Are you all happy that if we have one carbon in the chain, the name of that group is usually methyl, and the simple abbreviation is ME. Is everyone familiar with that?

13:33

I'm just checking. Is anyone not familiar with that? I've stunned you into silence already. Don't you just love it? So I assume that this is okay for everyone.

13:45

And that as we increase the carbon chain, if we go to two carbons, you would go to ethyl, three up to propyl, and sorry, three up to propyl and four to butyl. The key thing is that this is a shorthand way of representing long chains, but you have to understand where they can be used. So one of the key features is that names and abbreviations can only be used for the terminal chains of a given carbon. So for example, if you look at this structure here, we have a CH3 unit at the end of this chain. So we can abbreviate that to Me.

14:33

But if you look at this structure here, we have a one, two, three, four carbon unit, but it's in the middle of that structure, not at the terminus. So we can't use that butyl abbreviation when it's in the middle of a hydrocarbon chain, only when it's at the end. And what we often like to do in organic chemistry is try to think about reactivity. And when we think about hydrocarbons, we tend to try and think that they will behave in a similar fashion. And so we generalize them and a general name for a hydrocarbon you will often see is R, where that R is just meant to mean general reactivity of an alkyl chain.

15:18

So you would have typically an R connected to a functional group. So when we use that, we just try to generalize that. Okay, what are some more common abbreviations that you will come across? So a common abbreviation if we have a benzene ring is to replace a benzene ring with a phenyl PH abbreviation such that we could abbreviate that phenylalanine structure. To that where we would abbreviate that.

16:08

So whenever you see the pH abbreviation, understand that that's an aromatic benzonoid ring. And so if you apply that to phenol, for example, you could abbreviate that to PHOH. So far what I've really shown you, what we've really focused on is if we have a long linear chain of hydrocarbons. But often we can have what's called a branched point. So rather than them existing in a simple chain, we could have a branch where, say, in this case, have this substituent coming off that linear chain.

16:56

So that's called a branching point. So we can either have straight or branched hydrocarbons. And for example, if we consider the structure of the formula C3H8O and we consider propanol, we can generate two different structural isomers where either we have a linear chain of that hydrocarbon connected to that alcohol functional group, Or we have a branched hydrocarbon. We can give them different names. In terms of this branch group, we would actually call this iso, we would call this isopropanol, and we would call this n buten n propanol, not butanol, sorry.

17:57

Where n refers to a linear chain. Iso refers to when you look at the longest carbon chain, you have a single methyl substituent that branches one carbon away from the terminus. So that's what that iso means. So if you have a long, you could have a long hydrocarbon which would have a branch point one carbon away from the end that would also be iso whatever the length of that carbon chain is. The key thing is that these molecules are isomers of each other.

18:34

And again, I'm going to assume that you understand that isomers are non identical molecules that have the same molecular formula. We're just going to run through a number of different isomeric compounds. So when we look, for example, at C3H6, that could either be cyclopropane or as an alternative, we could have propene. So they both have the same molecular formula, but they are very different structures. And when we think about isomers, I want to bring, what I want to start to get you to understand is that isomerism really leads to molecular complexity.

19:32

So if we move from C3H6 to C4H8O, there are a real number of different isomeric compounds and structures that you should that you could consider. One key thing that I want you to recognize here is that all of these can contain different functional groups. This contains an alcohol. This contains an These contain carbonyl groups. But when we start to think about isomerism, then the more complex the structure, the more complex the potential numbers of isomers of that compound that there can be.

20:35

And again, this is a reason why we need to be able to understand reactivity and be able to put molecules together selectively. This is only a relatively small or low molecular weight molecule. And there are already significant, significantly different numbers of ways that we can put this together. So again, understanding reactivity and putting things together selectively is one of the key things that we want to be able to do in organic chemistry. So often, when we have all our hydrocarbon connected to a functional group, I'm just going to abbreviate that.

21:32

Remember this is that wild card. That means we're just going to look at a generic hydrocarbon that connects to a functional group. Often what we need to do is to be able to describe the substitution this hydrocarbon because that can be really important for reactivity. So for example, if you make this group larger, closer to the site of the functional group, you might predict that that would react at a slower rate than something that if it wasn't as hindered. And so what we need to be able to do is to give, or what we often do is refer to the substitution of the carbon that's directly connected to the functional group.

22:28

And this is what I'm going to try and tell you about. Here, if you have your functional group that's set up by that wavy arrow, if we look at a butyl chain, so we're just looking at the four hydrocarbon chain, that R substituent that's connected to my functional group, It could either be set up in a linear fashion, and we've already described that that usually has the abbreviation of N or normal. We could have a branched point which is at this position. When you connect that to your hydrocarbon, that is one carbon away from the terminus. So that's given the abbreviation I.

23:22

So that would be an isobutyl. The alternative point that you could have a branch position would be here. And we need to differentiate between those two. And we call that S for sec. Or we could alternatively have this where we call this a T butyl or Tert butyl.

24:03

So we need to be able to use these names selectively to describe the environment that's directly attached to that functional group. S here stands for secondary. What that just means is that this carbon here, how many carbons is that bonded to? It's not a trick question. That's bonded to two.

24:29

So that's what it means. It's bonded. It's secondary because it's bonded to two carbons. If you look at this carbon here, so looking at the substitution of the carbon directly bonded to the functional group, that has three carbons attached to it. So that is then a tertiary center.

24:48

Okay, so the different isomers we can name selectively. So this can be used to selectively talk about the carbon atom that directly attaches the group to the structure. The other way that we often refer to the size of groups around a given functional group is to refer to them as either primary, secondary, tertiary, or quaternary. So for example, if you look at this carbon here, if it's only connected to one carbon, we call that primary. So again, how many carbons is this connected to?

25:35

I'm looking for audience participation please, otherwise we'll be here a long time. Just one, so that's primary. If you look at this one here, how many? So that's secondary, just get used to calling things primary, secondary. Here, this carbon is bonded to three so we'd call that tertiary.

25:53

If you look at this carbon here, again, I appreciate this is one carbon away from that functional group. But I just want you to be aware that if we call something quaternary, means that this carbon here is bonded to four different carbon atoms. So we often refer to things as primary, secondary, tertiary, or quaternary. That just refers to the substitution of a given atom. And it just refers to the number of carbon atoms that are surrounding that given carbon atom.

26:22

And that's just a simple way of describing the space around it and therefore often reactivity. Okay, so what I'm going to do now for the rest of the lecture is to just run through some of the key functional groups. Again, I know that you'll be aware of many of these functional groups. What I will refer to here is something called hybridization when I talk about shape. That's something that we will cover in lecture three to start off with.

27:02

But that just refers to something about shape to start off with, okay? So if are interested, can scan these QR codes. You'll see a representation of some of these molecules in three dimensions. Okay, so when we start to think about functional groups, the first key functional group that we are going to look at is an alkene. So an alkene contains a carbon carbon double bond.

27:34

And for all of these functional groups, I'm going to try and tell you a little bit about their shape. So alkenes are planar. So when we start to think about these in three dimensions, if we just look at a very simple hydrocarbon. I'm just looking at ethene here. So when I draw these structures in three dimensions, when I draw this wedge that's meant to represent something coming out of the board.

28:13

When I draw the hash, that's representing something going into the plane of the board. So this is a flat molecule with these hydrogens and all of these atoms in the same plane as each other. We have two bonds in between that, in between these two carbons. As we go through, we will represent them as both a pi and a sigma bond. And we will refer to the hybridization of each of these carbons as SP2.

28:53

The key thing that I want you understand to start off with, how many atoms is this carbon bonded to? One, two, three. Okay, so when we think about hybridization, there are one, two, three atoms that are involved, three, sorry, three orbitals that are involved in that structure, okay? So the key thing about an alkene is that it's planar, it's sp2 hybridized, and we can come up with some relatively simple structures such as ethene. But we can also look at some natural products which again contain that alkene functionality.

29:39

Alpha pinene here and limonene on the handout. So they range from very simple to quite complex. When we go to an alkyne, that contains a carbon carbon triple bond. And the key thing about the shape here is that this has a linear shape. So if we look at the simplest alkyne, again that's ethyne, we have this triple bond that's made up of a sigma and two pi bonds between each of these carbon atoms.

30:31

If you look at that carbon, how many atoms is it bonded to? Two. So in terms of its hybridization, we would call this sp hybridization. And all that means is that we're going to mix two orbitals, an s and a p, to make that linear shape. Again, will go through that hybridization model in detail, but for now I just want you to understand how we think about shape and structure.

31:02

And actually these alkynes are very important. If you look at this complex molecule, calichomycin, we've simplified it. The R group here contains a long string of sugar molecules, but that's an anticancer molecule. And actually the trigger here is the reactive alkynes that help to try, that are really caught with biological activity. Okay, so the next functional group we're going to look at is that of an alcohol.

31:40

When we think about an alcohol, again, in terms of its structure, we have an oxygen that's bonded to a hydrogen atom and a carbon. We have two lone pairs on that oxygen. So in terms of its shape, it is actually tetrahedral at oxygen. And so we would consider that in terms of its hybridization, this is sp3. If you think about it, you have four bonding pairs around that oxygen atom.

32:21

So we need to use four s and three p's to be able to make those orbitals, to contain those electrons that point in a certain direction in space. Now again, I've just got a very complex molecule sucrose here that contains multiple hydroxyl functionalities. But the key thing that I want you to understand is the shape, the structure, and the functional group. Okay, the next functional group that I want you to be able to understand again is that of an ether. So an contains an oxygen atom that's bonded to two different hydrocarbons.

33:29

I'm just going to draw the shape of two different ones. If you look at these two ethers, remember again that we will have two lone pairs on these ethers. So again, they're going to be tetrahedral. They have four pairs of electrons around them. They are going to be sp3 hybridized or being tetrahedral in shape.

34:08

One of the most important functional groups is that of the A mean functional group. So again, generally, we're going to consider that we'd have an R with an NH2. This is functional group that we're really interested in. Does anyone know what this structure is? It's a very simple structure.

34:47

But again, I find it fascinating that something like this, again, has response. So that's a very simple structure, but that's amphetamine. Okay, again, the amine functionality is really important here to how that behaves. The key thing in terms of the structure here is that this amine again has four bonding pairs around it. So again, will be sp3 hybridized.

35:24

Any questions so far? I should always say if anyone has any questions, please put your hand up. I will be asking you lots of questions as we go through the course. But please just ask if you feel comfortable doing that. Okay, so the next class of molecule that I want to come across that I want to talk through are that of the nitro compounds.

35:50

So a nitro functional group formally contains a hydrocarbon bonded to a nitrogen that has two heteroatom oxygen atoms there. We draw this with a positive and negative charge. This would be incorrect. Remember, you can't have that would have five bonds around that nitrogen, so you can't have five bonds around there. But this nitro functionality is really key.

36:27

So for example, you have three of those nitro functionalities within that key molecule TMT here that we all know that it has these explosive properties. The next functional group that I just quickly want to run through is that of an alkyl halide. So when you have an alkyl halide, the halide functionality is often given a wildcard abbreviation X. And then we just want that to refer to fluorine, chlorine, bromine, or iodine, because again, they often have quite similar properties. So obviously an alkyl fluoride contains the fluorine containing group, a chloride, an alkyl chloride contains chlorine, so on for bromine and iodine.

37:34

But the key thing that I want you to understand is this abbreviation. We often use that RX to correspond to any alkyl halide because we often refer to their reactivity as being quite similar. Okay, the key functional group that you will come across predominantly in this lecture course as we go through is that of the carbonyl functional group. So the carbonyl functional group contains a carbon which has got a double bond to that oxygen. In terms of its shape and structure, again, we have two bonds between the carbon and that oxygen that's made up of a sigma and a pi bond.

38:34

How many atoms is that carbon bonded to? It's bonded to three again. So again, you should be able to recognize that that is sp2 hybridized. So it's a planar molecule. The key thing that we change is what the functional group here is.

38:56

So if what if this functional group with the H, then we refer to it as an aldehyde. If it's another R group, we refer to it as a ketone. And then we can also refer to it as a carboxylic acid if it's an Oh. If it's an amine, then we call this an amide. And if you have an OR, then we have an ester.

39:42

Now hopefully you'll have seen these types of functional groups already. The key thing that you need to be able to do is just recognize that they are different by variation of the substitution. You just need to be able to recognize a functional group and be able to name that. So amides are really important because proteins are made up of amides when a carboxylic acid of one amine reacts with the amino group of another. But this carbonyl functionality is gonna be really key to lots of the reactions and reactivity that we will talk through.

40:32

Okay, final couple of functional groups that I want to talk through are that of the nitriles. A nitrile contains a carbon that's bonded, triply bonded to that, to a nitrogen. I want to point out that this is very different to inorganic cyanide, but we have, because we have an organic functional group here. The key thing that again I want you to recognize is that this, because we have a triple bond between this carbon and this nitrogen, this would be linear or sp hybridized at this carbon because it would be bonded to two different atoms. Okay, so we've gone quickly through many of the functional groups that you need to be able to recognize.

41:38

One key thing that I will need to be able to point out is that we often refer to a variety of different functional groups that are at different oxidation level. So when we refer to this, what we really want to try and do is draw links between reactions and reactivity of molecules that are at the same oxidation level. And to be able to think about oxidation level in terms of carbon functional groups, all you need to do is look at where the functional group is, and look to see how many bonds to a heteroatom. So not carbon or hydrogen, the ones you'll usually see are nitrogen, oxygen, sulfur, and silicon. And count those number of bonds.

42:30

And then anything that has got a similar number of heteroatoms bonded, we argue it's at the same oxidation level. Okay. So if you look at this functional group, we've got a carboxylic acid. We're looking at the oxidation level at this carbon. How many bonds to a heteroatom does it have?

42:50

When we have a double bond here, they count as two. So we have one, two, three bonds to a heteroatom. So if you look at an ester, what we really want to try and do is see if this is at the same or a different oxidation level. So how many bonds to a heteroatom does this have? Again, this has three.

43:12

So hopefully you'll see that an ester is at the same oxidation level as an acid. So you can transform an acid to an ester without having to do an oxidation or reduction because it's at that same oxidation level. If we have an aldehyde, how many bonds to a heteroatom do we have? We only have two. If we have an alcohol, we have one.

43:37

And if we have a hydrocarbon, we don't have any bonds to a heteroatom. The key thing therefore that we need to be able to do is to say that the acid and the ester are at the same oxidation level, but to get from a compound that's got a higher oxidation level. So to go from an ester to an aldehyde, to go from a higher to a lower, we do a reduction. And if we go the opposite way around, if we need to go from an alcohol to an aldehyde, we need to do an oxidation. And you know that already, but that's the sort of language that we will use.

44:16

And basically using this methodology, we can group most of the hydrocarbons. Sorry, are the hetero atoms the carbon that is bonded to a non carbon? Yes, we're just looking at that particular carbon. Usually we're just looking at the oxidation state of the carbon that's got a functional group attached. Okay.

44:37

So using that, what you can do is you can basically look at anything that's got one bond to a heteroatom is that the alcohol oxidation level, so an alcohol, an ether, an amine, and these alkyl halides are all at the same oxidation level. And if you look at anything such as an acid, an ester, an amide, or a nitrile, that all have three bonds to a heteroatom, they all have the same oxidation level. So you can do a transformation that doesn't involve either an oxidation or a reduction. Okay. In the last couple of minutes, what I'm going to briefly do is talk about naming organic compounds.

45:32

So there are over a billion possible different ways you could put together organic molecules. There's an infinite number of possibilities effectively. So what you need to be able to do is to name them selectively such that everyone has an unambiguous name. So systematic nomenclature to name any organic compound has been introduced by IUPAC. Personally, I don't want to spend too much time on this.

46:06

It's important, I think, that you recognize how you name compounds. But for example, how I would do it is now you can just put a structure into Kendra and ask it to name it for you. But I think it's important you understand where that comes from. So just remember that all a name does is that it describes the number of hydrocarbons or the number of carbons in a given chain. It tells you where the functional groups are, and it says exactly where that functional group is attached to the skeleton.

46:36

Depending on the number of carbons in the chain, you would be able to name that parent hydrocarbon from one. Here I've gone up to 10. And so what you typically need to do is to be able to look at the length of the carbon chain within a given structure. You'd be able to look at the name of where a functional group is, and you need to state exactly where that is. So for example, if we just look at this very simple structure that is on the board, if I had a pen that worked, What we need to do here is identify the longest carbon chain.

47:26

So we can identify a one, two, three hydrocarbon chain. So you would expect to be that would be roughly named around propane. We have a sub so that's just involving these three carbons. We have a substituent coming off it here, which is a methyl. And we need to name where it is in a given position.

47:55

And we should be able to say that that methyl is at position two. So when we put that together, we would be able to name this two methylpropane. Okay? And so typically what we do is just we need to be able to look at a functional group and the length of the carbon chain and bring them two together to give itself a name. And here's hopefully a couple of obvious ones.

48:35

Here we have a single hydrocarbon based on methane. We have the alcohol functionality. We bring them together, and you can call that methanol. Here we have a ketone functionality, this carbonyl group. It's based on cyclohexane, a cyclic carbon unit.

48:54

So we would name it cyclohexanone. And all I want you to be able to do is simply to be able to name these in your own time. And what I'm going to do at the beginning of tomorrow's lecture is just very quickly tell you about the importance of the number in terms of naming specifically where a functional group is, in terms of you want to keep that number as small as possible. So again, I apologize if I've gone through quite a lot of material here, and I've gone through quite quickly and if this is revision, but I just wanted to set up the context of this for the remaining lectures. Thanks for your attention.

49:39

I'll see you tomorrow.