R and S Configuration - Online Tutor, Practice Problems & Exam Prep

Understanding chiral centers is essential for naming stereoisomers using the Cahn-Ingold-Prelog system, commonly referred to as the R and S naming system. The process involves assigning priorities to four different groups based on atomic mass, resolving ties through a playoff system, and accounting for double or triple bonds by counting them multiple times. The final configuration is determined by tracing a path from the highest to lowest priority, with clockwise paths designated as R and counterclockwise as S. Adjustments are made if the lowest priority group is not in the back, ensuring accurate stereochemical representation.

Why stereoisomers need their own naming system.

So now that we understand what a chiral center is and we know how to recognize them on molecules, it's important that we know how to name them. So if you remember back to when I first taught you guys about simple alkane nomenclature, we talked about the IUPAC naming system. What I told you was that according to IUPAC protocol, every single molecule in the universe needs to get its own unique name. That's kind of the point of IUPAC, that now we have a systematic way to name every single molecule. Well, now that we've learned about stereoisomers, meaning molecules that possess chiral centers, that means that those stereoisomers, since they have different shapes, they're going to need to be included in the system somehow because they have a distinctive difference. Well, it turns out that all we have to do is we're going to use the same IUPAC names from before, but we're going to add just one extra step to account for those chiral centers. And that extra step is called the Cahn-Ingold-Prelog Nomenclature. I know that name is intense. So what we're going to be doing is we're not going to be using that name so much. That's kind of the technical name that's in your book. I like to just call it the R and S naming system. You'll understand why it's called R and S in a second. But for right now, just kind of take my word for it that you don't need to say Cahn-Ingold-Prelog in class. You could just say R and S, and everyone will know what you're talking about. So, in order to learn this one extra step, it's actually kind of a 5-step process. So what we'll be doing is I'll be teaching you one step at a time with a molecule so that you can apply it and see exactly how to use that rule, okay? So let's go ahead and get started with our first step.

R and S Naming- Step 1

All right. So our first step starts off pretty easy. What it states is that you're going to have to assign priorities to the 4 atoms on a chiral center based on their atomic mass in the periodic table. So let's break that down a little bit more. First of all, notice that I underlined 4 atoms. Why specifically is it the number 4? Because remember the definition of a chiral center was any atom that has 4 different groups. What I'm basically just saying here is that you find those 4 different groups and you give them priorities. How? Based on their mass in the periodic table. Okay. So let's just go ahead and look at this molecule to kind of get started with this rule. First of all, do you guys were you guys able to find an atom here that would count as a chiral center? Because that's always going to be the first step, locate your chiral center. So, do you see 1? Maybe an atom that's 4 different. Yeah. You found it. It's this one right here. Remember I can use a star to represent a chiral center. Awesome job. Notice that that carbon has 4 completely different atoms coming off of it. It has oxygen, nitrogen, hydrogen. What's that stick? Obviously, that would be a carbon. Perfect. So we've got 4 different atoms. This is definitely a chiral center. So we've got the 1st step down. The second step is that we need to assign priorities based on the periodic table. This might be the point of the video that you want to pause and grab a periodic table and then rush back over here. But we could also use this to remember our big sevens. Remember that the big seven is just a method to remember some of the most important atoms on the periodic table. Remember that the way we do this is we just draw literally a big seven And then you split the big 7 into 7 boxes. And then we would just fill these out in order of the atoms on the upper right-hand side of the periodic table. So remember that we always start off with carbon. Okay. And then we go to nitrogen, oxygen, fluorine. Now we're in the halogens and we have to go down so it'd be fluorine, chlorine, bromine, iodine. That's our big 7. Obviously this isn't comprehensive but it's a great reference point even for all the other atoms on the periodic table. Now I'm just going to trust you guys that either you're looking at the big 7 that I just drew or I have a periodic table. Let's go ahead and assign priorities. So my first question to you is which one would get the highest priority out of these 4 different atoms? Which one is the highest according to atomic mass? It has to be the oxygen, right? Because we said that we have 4 different atoms, oxygen, nitrogen, hydrogen, and carbon. So this is going to be my number one priority because it has the highest weight on the periodic table. Okay? I don't have any of the heavier atoms. So now if that's number 1, which one is number 2? Number 2 has to be nitrogen because it's a little bit lighter, so it's going to get my 2. Which one's number 3? Has to be carbon. So carbon's my number 3. And just so you guys know, if you ever see a hydrogen, that's always going to be your 4. Okay? Because nothing is lighter than hydrogen, right? So you can always just draw 4 there immediately if you just want to get good at it, okay? So that was the first step guys. It's just look at your periodic table. If you need to draw your big 7 and go ahead and compare priorities. Not so bad, right? Let's move on to the next step.

R and S Naming- Step 2

So step 2 deals with a really common issue that we face with RNS naming which is that sometimes you're going to be comparing your atoms and you have a tie because 2 of them have identical atomic weights. Well, what do you do in that situation? Well, if you do have a tie between your atomic weights, what we're then going to do is we're going to compare the next set of atoms that they're both attached to and basically have a playoff system. In the playoff system, we look at the next immediate atoms that they're both attached to and then we compare those atomic weights and we say, "Well, which of these is bigger? Which of these is heavier?" And that's going to be the winner. So let's go ahead and apply this to an example. First of all, I really hope that you guys can identify the chiral center here. Yeah, so you should be getting a little bit better at this. It's there. That's it. Okay. And now we have to figure out, first of all, are there any issues with step 1 in terms of are we able to name these priorities easily? Okay? So let's kind of just do the first step which is just figure out what all the atoms are. Well, notice that right away I have an issue because 2 of the atoms that are attached to my chiral center are the same. I have an oxygen and an oxygen. Now if I compare both of those in the periodic table, I'm obviously going to get equal atomic masses. That means I'm definitely going to have to use a playoff there no matter what. But let's continue. Maybe the other atoms, we can figure out what order they're in. Well, this is a carbon because that's a carbon group, an R group. And ET, look that up on the periodic table. You're not going to find it because that stands for ethyl. That really just stands for CH₂CH₃. I've got another two-way tie, guys. I've got another two way tie between this carbon and this carbon. So, I'm definitely having some issues with rule number 1. Okay? Now there is one thing that we can do even before this playoff system. What I can safely say is that my oxygens are going to get positions 1&2 and my carbons are going to get positions 3&4. Right? Because oxygens are bigger than carbon. That's just common sense. But I don't know which order they're going to be in. In order to figure out the order, I have to use playoffs. So let's do the oxygen playoff first. This is for spots 1&2. This will be my red oxygen. This will be my blue oxygen. What is my red oxygen attached to? It's attached immediately to an H. What is the blue oxygen attached to? That's immediately attached to ME. What does ME stand for? That's a methyl group. So a methyl group is CH₃. So it's attached to a C. Okay. So, in the playoff system, I look at what's in the bracket. Okay. It's almost like March Madness or something, but it's just a lot more boring. And, you can't win money from it unfortunately. At least I haven't developed that, that way to make money yet. So but which one is gonna win inside of that bracket? It's gonna be the carbon because carbon is heavier than hydrogen, right? So we've got a clear winner. Both my oxygens beat my carbons but the methyl beats the H. So let's move on to the carbons. So I'm going to do the same thing. I'm going to do like a color system. This will continue to be my blue carbon. I'll make this one green. So what I want to do is notice that for oxygen, oxygen is only attached to one thing more, but carbon always has 3 bonds. So I'm going to draw all 3. So for my blue one, what are the 3 additional bonds besides the chiral center because you never go backward, you only go forwards. What are the 3 atoms that that carbon is attached to? Well, it's attached to one carbon on one side. Let's just say that that is the left side. It's attached to another carbon on the right side and then it's also attached to an H that wasn't drawn. So I'm going to draw that. I'm going to put that here. So that's what's in my bracket there. Those are the 3 additional atoms attached to the carbon. Now let's look at green. So green, once again, I'm not going to look at the chiral center. I'm just going to move forward. Green is attached to 2 H's because it's CH₂ and then CH₃. It's also attached to this carbon here because obviously it's a chain, right? So it needs to be attached. What we tend to do for brackets is we put the biggest atoms first. Instead of writing this as HHC, I would actually write this as CHH. It just makes it easier to compare the brackets and see who wins. So now I know that I had a tie between the carbons. If I move into the bracket, is there a winner? Well, if you look at the first atom, there's still a tie. They're both attached to carbon. But if you look at the second set, this is where your winner is determined. It came down to the wire. It was a close game. But I'm sorry, green. You lost. Alright? So that means that my blue is going to be number 3 and my green is going to be the biggest loser at number 4 and see how we systematically did that with a playoff system. Okay? So that's all there is to it. We'll practice it more. Don't worry. But those are the basics.

R and S Naming- Step 3

Step 3 is pretty straightforward. It just says, if you're using the playoff system and you run into a double bond or a triple bond, the double bond is going to count twice and a triple bond is going to count 3 times. So I think the easiest way to relate to this is just to do an example. Our chiral center is where? Right here. Let's kind of figure out those 4 different atoms that we've been doing so far. So we have an H, so obviously, we can already tell what priority that's going to be, right? Out of the four numbers, which one is it going to be? 4, automatically. Good job. But these other 3, let's figure that out. I've got carbon. I've got carbon. Oh man, I have a three-way tie guys. So remember that if we have a tie where the atoms don't have different atomic weights, we have to use the playoff system. But now on top of that, I have a slightly more complicated situation because some of these carbons have double bonds on them. Let's figure out how to do the bracket playoff system like before. Let's do I'd say the easier one first, which is the blue carbon. The blue carbon, I would say what are the 3 atoms that are attached to it? Well, I definitely have 2 H's coming off of it and I have another carbon. So I'm going to put in order of atomic mass, carbon H H. So that wasn't so bad. We're used to doing that. Now let's look at the red one. The red carbon is a little bit tricky because the red carbon, notice it only has one H coming off of it and it has a carbon over here. But notice that it's double bonded to that carbon. So basically, we're going to count that as 2 separate bonds. Why? Because we need to account for all 3 bonds that the carbon makes. So to me, a double bond to carbon is just as good as 2 bonds to carbon. So I'm going to put carbon, carbon. Both of those count as the double bond and hydrogen. And then finally, I've got green, which is even a little bit crazier because notice that green is actually attached to 2 carbons, but one of them is single bonded and one of them is double bonded. So you guessed it. You're just going to add that up together. The green is attached to all carbons, C, C. 2 from the double bond, 1 from the single bond. Does that make sense? I noticed that I'm always moving forwards. I'm never moving backwards towards the chiral center. So now that we've applied that double bond rule, of course, this would also apply with triple bonds. I just don't have one drawn. Okay. What are our priorities going to be? Well, green is going to be number 1. Red would be number 2. Blue would be number 3. Okay. So I'm going to write these here. 1, 2, 3 and then obviously, our hydrogen is number 4.

Determining Priorities

So this example should have been really easy for you guys. First of all, the chiral center was right in the middle. We did have 4 different groups because even though we have 2 carbons, meaning that we're going to have to use a playoff system, they're not exactly the same. One is a methyl group and one is an ethyl group, so this does count as a chiral center. Because we have a tie, we should use the playoff system for those. But right away, I know that my number 4 priority is going to be my H. I also know that my number 1 priority is going to be the O. So really, I just need to do the playoff system for priority 2, priority 3. Now some of you guys might already be able to do this in your head, but I just want to be really careful since we've just learned this to do it really clearly. I've got a blue C. I've got a red C. The blue C is attached to 3 H's because it's a methyl group. The red C is attached to one carbon and 2 H's. And I'll just draw those H's out so you can see. So which one won? The red carbon won. This is my 2 and this is my 3. So we've got our priorities. Let's move on to the next rule.

Determining Priorities

So this one wasn't so bad either. The chiral center is right here on the side, and one thing I just want to show you guys is that this really is a chiral center. Obviously, the two substituents are different from each other. You guys might have been confused by the ring. But notice that one side of the ring is different from the other. For example, on the blue side, it takes me two carbons to get to the double bond, whereas on the green side, I immediately have a double bond right when I leave that chiral center. That means that that ring is not perfectly symmetrical, so both sides of this ring do count as different groups.

So now we just have to do priorities. My number one priority is going to be the nitrogen. It has to be because nitrogen is heavier than carbon. But notice that once again, I'm going to have a three-way tie between atoms. I have a blue carbon, a red carbon, and a green carbon. How did you guys figure this out? Hopefully, you guys used playoffs. For the green carbon, we're going to use the "double bond counts twice" rule. So I'm going to say it's attached to a carbon, a carbon, and an H. The red carbon is attached to one carbon and two Hs. Those Hs are right here. And the blue one is a methyl. So we know that methyls are only attached to hydrogen, and those are your priorities right there. Our priorities were that green was my 2, red is my 3, and now in this case, my methyl group is actually my 4. Hydrogen doesn't always have to be your 4th, meaning let me say that back. Let me say that the other way. Your 4th doesn't necessarily need to be hydrogen. If you don't have any hydrogens by themselves on your chiral center, you're just going to go with whichever group is the biggest loser. That's your number 4. If you happen to have a hydrogen, then of course, that's going to be your biggest loser because there's nothing smaller than it. Let's move on to the next step.

R and S Naming- Step 4

So finally in step 4, we're going to learn how to name these guys. Step 4 starts off by saying that if your last priority group is in the back I'm not even going to read the rest yet. Let's just define that first part. The last priority group is always going to be which group? Group number 4. Let's actually just redefine that as 4 because that's the easiest way to say it. If 4 is in the back, now what does the back mean? In 3D structures, that always means a dash. So this is actually starting off by saying that if 4 is on the dash, then we're going to trace a path from the highest priority to the lowest priority. Now what that literally means is that we’re gonna draw arrows from my number 1 priority to my number 2 and from my number 2 priority to my number 3. But remember, there are 4 groups. What happens to number 4? Do I also draw an arrow to that one? No, because you're always going to ignore group number 4 because it's on the dash. Since it's in the back of the molecule, I don’t look at it. I only look at groups 1, 2, and 3. So now I trace that path and if that path happens to look like a clockwise path, meaning does it look in the direction that a clock would move in? Okay. Now, for this, you're gonna need to know what an analog clock looks like. I know that for maybe some of you younger folks, maybe you’re not used to seeing those too often but we're just going to have to stretch ourselves a little bit. Clockwise rotation is going to get an R letter. And a counterclockwise rotation is going to get an S letter, hence the name R and S. Let's just use, bring that down, that example that we did before. Those priorities are going to be the exact same priorities and let's see if we can assign an R or an S to this chiral center. Those priorities should be correct. This is my chiral center. So now the first thing I have to ask myself is, is my number 4 on the dash? Perfect. It is. So that means I can use this rule. This next rule says, I draw arrows from 1 to 2, from 2 to 3, and then finally back from 3 to 1. What about number 4? I ignore it because it’s in the back. I don't want to use number 4. So is this a clockwise rotation or a counterclockwise rotation? This is clockwise folks. And since it's clockwise, this is going to be considered an R isomer. We haven't learned how to incorporate this into the full name yet, but this is considered an R. Awesome, right? Awesome. So let's go ahead and move on to step number 5.

R and S Naming- Step 5

Step number 4 is really easy to use but it has a major limitation: it only works if your number 4 is on the dash. And guess what? Your professor is often going to give you molecules where your number 4 is not on the dash. It might be in the front or it might be on the side. Why would he do such a thing? Obviously, to make your life harder, okay? In that case, we're going to have to move down to step 5, which is kind of like your contingency plan. If your number 4, the last priority group, is not in the back, which I'm sorry to tell you is most of the time, then we're going to have to make an adjustment because it turns out that the method we use for step 4 is actually the easiest way to figure this out. But my number 4 needs to be on the dash in order to use it. What we're going to do is we're going to cheat a little bit and we're going to swap number 4 with whatever is on the dash already. Meaning that whatever number is on the dash, let's say it's 2 or 3, we're going to redraw those numbers and swap them so that we can pretend like number 4 is on the dash, even though it really isn't on the dash. We're just going to pretend. Now, there's no free lunch. We're cheating here. I just told you this is like a game of make-believe. We're going to pretend like the 4 is on the back even though it isn't. So, in order to make up for that, we're going to have to swap whatever sign we get to make up for the fact that we swapped the groups. This is really easy. It just means that if you trace your path and it looks like an R, you're actually going to give it an S. If it looks like an S, you're actually going to give it an R. Let's go ahead and do an example where we bring down the priorities from before and see how it works out. Remember that this was number 1, number 2, number 3, and number 4. Okay? So is my number 4 on dash? No, it's not. It's actually in the front. So what are we going to do? Well, in order to use the system from before, I have to swap out. The rule says the number 4 has to swap with whatever is on the dash. What's on the dash? 1. Now I want to warn you guys against other methods of doing this. Some online tutorials like YouTube, or even your professor, will sometimes tell you to redraw the molecule with this pretend switch. I think that's really unnecessary and that's really confusing. It's a lot easier just to swap out the numbers. I'm going to scratch out 4. We know that that's moving to the back. We're going to scratch out 1. We know that's swapping. And I'm going to redraw just the numbers. Now that my 4 is in the back, I can ignore it and I can draw my path. So my path goes from 1 to 2, from 2 to 3, from 3 to 1. Remember that I ignore 4. What does that look like to you? It looks like an R. Is this actually going to be an R? No, because I had to swap that group in the beginning, so I'm actually going to consider this to be an S isomer. Okay? And that's the final answer. So this really isn't that hard. You just have to remember to swap at the end to make up for the fact that you swapped at the beginning. Great. Let's move on to an example.

Provide the full name for the following molecule, taking stereochemistry into account.

• A. (S)-3-hydroxy-2,2,4,5-tetramethylhexanol
• B. (S)-2,2,4,5-tetramethyl-3-hexanol
• C. (R)-2,2,4,5-tetramethyl-3-hexanol
• D. (R)-4-hydroxy-2,3,5,5-tetramethylhexanol

Provide the full name for the following molecule, taking stereochemistry into account.

• A. (S)-2-Cyclobutenol
• B. (R)-2-hydroxy-Cyclobutene
• C. (S)-Cyclobut-2-en-1-ol
• D. (R)-3-hydroxy-2-cylcobutene

Provide the full name for the following molecule, taking stereochemistry into account.

• A. (2E,4S)-4-methylhexene
• B. (4E,3R)-3-methyl-4-hexene
• C. (2E,4R)-4-methyl-2-hexene
• D. (2E,3R)-3-methyl-2-hexene

Here’s what students ask on this topic:

What is the Cahn-Ingold-Prelog priority rule in R and S configuration?

The Cahn-Ingold-Prelog priority rule is used to assign priorities to the four groups attached to a chiral center based on their atomic masses. The atom with the highest atomic mass gets the highest priority (1), and the one with the lowest atomic mass gets the lowest priority (4). If two atoms have the same atomic mass, you compare the next set of atoms they are attached to, continuing this process until a difference is found. This system helps in determining the R (rectus) or S (sinister) configuration of the chiral center.

How do you determine R and S configuration when the lowest priority group is not in the back?

If the lowest priority group (4) is not in the back (on a dash), you need to swap it with the group that is on the dash. After swapping, trace the path from the highest priority (1) to the lowest (3), ignoring the fourth group. If the path is clockwise, it is R; if counterclockwise, it is S. Since you swapped groups, you must reverse the final configuration: if it looks like R, it is actually S, and vice versa.

What is a chiral center and how do you identify it?

A chiral center, also known as a stereocenter, is an atom (usually carbon) that has four different groups attached to it. This creates a non-superimposable mirror image, giving rise to chirality. To identify a chiral center, look for a carbon atom bonded to four distinct groups. If all four groups are different, the carbon is a chiral center.

How do double and triple bonds affect the priority assignment in R and S configuration?

In the Cahn-Ingold-Prelog system, double and triple bonds are treated as if the bonded atoms are duplicated or triplicated. For example, a double bond to carbon (C=C) is considered as two single bonds to carbon (C-C and C-C). Similarly, a triple bond (C≡C) is treated as three single bonds to carbon (C-C, C-C, and C-C). This method ensures that the priority assignment accurately reflects the bonding environment.

What is the significance of R and S configuration in organic chemistry?

The R and S configuration is crucial in organic chemistry because it helps distinguish between different stereoisomers, which can have vastly different chemical and biological properties. For example, the R and S forms of a drug may have different therapeutic effects or side effects. Accurate R and S naming ensures clear communication and understanding of a molecule's 3D structure and its potential interactions.