Organic Chemistry - Online Tutor, Practice Problems & Exam Prep

Organic chemistry emphasizes the structures, properties, and reactions of carbon-containing compounds, crucial for life. Stereochemistry involves the 3D arrangement of atoms, with stereoisomers differing in spatial configuration. Chirality centers can have R or S configurations, leading to enantiomers, which are non-superimposable mirror images. Fischer projections represent chiral compounds, where horizontal bonds pop out and vertical bonds go into the page. Resonance describes electron delocalization, stabilizing molecules. Understanding these concepts is essential for grasping molecular behavior and reactivity in organic chemistry.

Organic Chemistry & Stereochemistry

In this video, we're going to do some organic chemistry review. So recall that organic chemistry focuses on the structures, properties, and reactions of carbon-containing compounds. And what's really interesting is that carbon makes up about 62% of the dry weight of the human body, which is a very large percentage for just one element, and that goes to show how important carbon is to life. And so recall that stereochemistry refers to the spatial three-dimensional arrangements of atoms and molecules, and that stereoisomers refers to the relationships of molecules that have the same exact atomic composition but differ in their 3-D spatial arrangement. So let's take a look at our example below.

And on the left here, what we have is maleic acid, and on the right, we have fumaric acid. Now, notice that maleic acid and fumaric acid have the same exact chemical and atomic composition. So if we count up the numbers and types of atoms, they would match. Now, notice that the 3-D arrangement of these two molecules is different. Maleic acid on the left has a cis configuration of the double bond, where the two bulky groups here are found on the same side of the double bond. That's what cis configuration refers to, recall. And fumaric acid on the right has a trans configuration where the two bulky groups are actually on opposite sides of the double bond. And recall that the double bond here prevents free rotation of the molecule. So this group over here cannot rotate over to the other side because the double bond prevents it. And so, because maleic acid and fumaric acid have the same chemical composition but differ in their 3-D spatial arrangements, that makes them stereo isomers.

And so, in our next video, we're going to recap the difference between configurations and conformations. So I'll see you guys in that video.

Configurations & Conformations

Now we've already said that stereochemistry refers to the 3D spatial arrangement of an atom or molecule. But recall that stereochemistry can only be changed by breaking and reforming bonds. Whereas conformations are potentially flexible 3D arrangements that are not permanent and can be changed without breaking or reforming bonds. Now, also recall that a specific carbon atom within a molecule that has four distinct chemical groups bonded to it is called a chirality center. And you guys have learned in your previous courses that chirality centers can have up to one of 2 possible configurations, an R configuration or an S configuration. And chiral molecules that have opposite chiral configurations are called enantiomers. And enantiomers are non-superimposable mirror images that can have different chemical properties. And so the classic example is our hands. So our hands are mirror images of one another, and when we try to superimpose them or overlap them, we realize that we cannot overlap them when they're facing in the same direction, unless I were to take this thumb, rip it off, and plug it in over here, which I'm not going to do. And so our hands are non-superimposable mirror images, and they are enantiomers.

Now, down here in this example, we're going to do two things. First, we're going to label the chiral configurations of these molecules, and then we're going to analyze the ethane conformations. And so in this video, I'm not going to go over how to determine the configuration of a chiral center. But that's something that you guys need to know. So if you don't remember how to do that, watch the videos that I'm going to link you guys to in the comments below. And so notice that these two molecules only have one chiral center shown by the highlighted chiral centers configuration, whereas the one on the right has an S configuration. And, R-thalidomide here is used by doctors to treat morning sickness in pregnant women. Whereas if a doctor were to make a mistake and give a patient S-thalidomide instead of R-thalidomide, then the baby could possibly have birth defects. And so you can see how even though these two molecules look very, very similar, they are completely different and can have different chemical properties that lead to different results. So the only way that you can change R to S configurations is by breaking and reforming chemical bonds.

Now over here, we have our ethane conformations. And we're showing a specific type of molecular depiction known as a Newman projection. So recall that a Newman projection is like looking down the barrel of a molecule. And so if we have our ethane here with its hydrogens, it's almost as if we are looking right down the barrel of this molecule this way. And so notice that there are two possible conformations. There's a staggered conformation and an eclipsed conformation. The staggered conformation, notice that the hydrogens are very spread apart from one another. Whereas in the eclipsed conformation, the hydrogens on opposite carbons are essentially overlapping in space. And so, this is why it's called an eclipsed conformation. And so, you don't need to break or reform bonds to change from a staggered conformation to an eclipsed conformation. And it is possible to convert between the two, even though the staggered conformation is more stable and more prevalent. And so this is a good summary of configurations and conformations, and I'll see you guys in our next video when we talk about resonance.

Organic Chemistry

Here's your RNS naming cheat sheet. Remember there are 4 main rules to be able to figure out the configuration or RNS of any molecule. Let's go ahead and use these examples to apply these four rules.

The first rule is that you assign priorities 1 through 4 on the chiral center by atomic mass. So what we would do is we would look at the atomic mass of each atom that's around the chiral center and try to figure out which one's heaviest, that would get 1. What we see is that for both of these, hydrogen is going to lose and it's going to get 4, but for the other ones all I have is carbons. Carbon, carbon, and carbon. So I have a three-way tie, so I can't use the atomic mass rule for this atom. Let's go next. So it says double bonds count twice, triple bonds count 3 times. So what I would do is, in this case this is what's going to break my tie, this is a single carbon, this gets counted as 2 carbons, and this gets counted as 3 carbons. So in my prioritization, this would now get 3, 2, and 1, and the same thing would apply to this one over here. Okay?

If there is a tie still, then compare the next set of adjacent atoms. I don't need to do that because I don't have a tie anymore. But if I still had any ties, then I'd have to go to the next set of atoms and then compare those in a playoff system. Rule 2, if 4 is on the dash, number 4 is on the dash, then just simply trace paths from 1 to 2 to 3, and you're done. You can name your RNS. So are any of these already in the configuration of having a 4 in the back or on the dash? Yes. This one right here. So that means I can already go ahead and go from 1 to 2, from 2 to 3, and from 3 to 1, you always ignore 4. And since it's counterclockwise, that means this is going to be an S. Great.

So what about if your 4 is not on the dash, which is actually most of the time. Notice that for this molecule, 4 is on the wedge, not on the dash. We're going to have to swap whatever's on the dash with 4. So, and by the way, not all professors do it this way, but this is the way that I do it and it's helped thousands of students all over the country. So I would recommend, just sticking to one method and then just going with it. I like my method, but if you have a different way of doing it, that's fine. So what I would do is I would switch the 4 with with the dash. So my dash is 3, and my 4 is always going to be 4. I'm going to replace that with now a 4 here and a 3 here. You don't always, you would not always replace 43. I just happen to be replacing 3 in this case because that's the one on the dash. Great. Now I can trace my path from 1 to 2, from 2 to, from 2 to 3, from 3 to 1, I ignore 4 and it looks like an S, but because I start off with an S, I need to change it to an R. So this is an R. Okay.

So now we just found our configurations for these 2 molecules using rules 1 through 3. And I just want to remind you of the last rule, which is that if you have multiple configurations on the same molecule as multiple chiral centers, then you should use locations and parenthesis to describe them. In this case, you can only use S, you only need to use R because there's only one chiral center. But if there's more, then you should include the location of where that chiral center is, and you should put it all together in parenthesis. Alright? So that was your R and S naming summary. If you want more information on this topic, just click on the link below.

Resonance

So recall that resonance is the delocalization of electrons within a molecule. And all that means is that these electrons can shift within a molecule. And the delocalization of electrons creates an energy stabilizing effect that stabilizes a molecule. And so if we take a look at our example below, what you'll notice is that we have a lone pair of electrons on this nitrogen that can be delocalized, and then we have a pi bond or a double bond here on the carbonyl group, which also has the ability for some electron delocalization. And so what you'll see is that these arrows here, recall, represent the movement of 2 electrons, and so we have the lone pair going to this bond here, and we have the pi bond here or the double bond electron density shifting up onto the oxygen. And so that creates an oxygen, atom here with a full negative charge, a nitrogen atom with a full positive charge, and this carbon and nitrogen bond here with a double bond character. And so recall that these transient states are not actually existing in a molecule. So there's never a moment where there's a full negative charge or a full positive charge. And in fact, what a hybrid between these two resonance structures is more appropriate in the best representation, and that's shown below. So you can see here in this representation, the oxygen has a partial negative charge, which is different from a full negative charge. The nitrogen has a partial positive charge, and then we have a dotted line here, from the oxygen to the nitrogen, showing that these bonds have double bond character to them. And so this is the best representation of the resonance happening in this molecule. And this concludes our lesson on resonance, and I'll link you guys to videos, in the comments section if you guys need some more practice, and I'll see you guys in our practice videos.

A) Identify the chirality centers in the molecule.

B) Determine the configuration of each chirality center.

Alright. So here's a 2-part practice problem that's broken up into part a up above and part b down below. And part a is asking us to identify the chirality centers in the molecule that's over here on the far right. And so, again, if you guys don't remember how to determine the configuration of a chirality center from your old organic chemistry courses, then make sure you guys rewatch these videos that I'm linking you to in the comment section down below. Recall from our previous lesson videos that a chirality center is literally just a carbon atom. It's a special carbon atom. It's a carbon atom that is chemically bonded to 4 distinct chemical groups or 4 distinct chemical pathways. Essentially, what we can see is this first carbon atom in our molecule, notice that it is double-bonded to a single chemical group of an oxygen atom. And so we have 2 pathways, 2 bonds, so this bond here and this bond over here, that are leading to the same chemical group. So we don't have 4 distinct chemical groups attached to this carbon atom. And for that reason, this carbon atom right here is not a chirality center, and we don't need to worry about its configuration. Now, the same applies for this carbon atom over here on the far right because we know that even though they're not shown, these carbon atoms are bonded to 4 groups. And so essentially, we know that there's going to be a hydrogen atom on a dash, as well as another hydrogen atom on a wedge. And so essentially because this, path right here and this path right here are leading to this same exact chemical group of a hydrogen atom, that means that there are not 4 distinct chemical groups attached to this carbon atom right here. And so this carbon atom is not a chirality center, and we don't need to worry about its configuration. Now, when we look at this carbon atom, on the other hand, notice that again, it has 4 distinct chemical groups. And so we know that there's going to be a hydrogen on a dash going down here, and we know that because, the hydroxyl group is on a wedge, so the hydrogen must be going on a dash. And no matter which chemical, path you look at, whether you look at this path here, this path this way, this path going this way, or this path going down, all 4 pathways have a distinct chemical group or a different chemical group. And so, for that reason, we can actually say that this carbon atom right here is a chirality center. And, the same applies for this carbon atom over here as well. So, no matter which chemical path you take, we know that there's going to be a hydrogen atom coming up on a wedge here, because we have the hydroxyl group on a dash. And so essentially, no matter which chemical path you take, whether you take this path this way, this one going down this way, this one going this way, or this one going up, all 4 chemical groups are chemically distinct. And so that means that this carbon atom here, shown here, is also a chirality center. And so what that means is we have 2 chirality centers in this molecule, these 2 carbon atoms that are shown, and we've identified the chirality centers in this molecule. So part a is complete. Now, moving on to part b, it says to determine the configuration of each chirality center. And so, again, if you don't remember how to determine the configuration of a chirality center, make sure that you watch the videos that I'm linking you to in the comments section below. But, over here in this box, we have a little refresher to help you guys refresh the basics. And so we know that there are 2 configurations orientation of priorities number 123 are, orientation of priorities number 123 are, going to be in a clockwise orientation. And then s configuration is when the orientation of priorities 1,2,3 is in a counterclockwise orientation. And so, something that we need to keep in mind, is that, if the 4th priority is not on a dash, then we actually need to flip the configuration that it looks like. And so the 4th priority is going to be really important, as well to keep in mind. And remember that the way we determine priorities is by comparing the atomic numbers of the atoms that are connected to each of these carbon atoms. And so, if we take a look at these 2 chirality centers, we're first going to look at this chirality center here and determine its configuration. And so, looking at this pathway going here, notice that the first atom that's attached is an oxygen atom. Going in this pathway this way, the first atom is a carbon atom that's attached. And also going this way, the first atom is a hydrogen atom. And so, by comparing these atoms here that are in red, the 2 carbons, the hydrogen and the oxygen, we're going to be comparing the atomic numbers. And so, notice that of these 4 atoms, oxygen has the highest atomic number. And so that means that the path that's leading to the oxygen is going to have the highest priority, priority number 1. So we can put a 1 here to remind us that this pathway here is priority number 1 for this chirality center. Now, going to the right and to the left, we know that we have 2 carbon atoms over here, and those 2 have a higher priority than the hydrogen, since the hydrogen has an atomic number of 1, so it has the lowest priority. And so essentially, what we can say is that this hydrogen is going to be priority number 4. So now what we need to do is determine which of these two pathways is actually going to have a higher priority. Which one's going to get priority 2, and which one's going to get priority 3? And so, in order to determine that, what we need to do is compare the atoms in each of the paths. So what we're going to say is the path going to the left will be path number 1 over here, and then the path going to the right is going to be path number 2. And so, essentially, what we'll see is that both of these paths initially lead to a carbon atom that's directly connected. And so, from that point, what we need to do is look at the constituents of these carbon atoms. And so the constituents are just the chemical groups that are bonded to those carbon atoms. And so notice for this carbon atom over here, which is this carbon atom right here, it leads to 2, it has two paths leading to an oxygen atom. And so, what that means is we can put an oxygen atom twice, and then also going this way, we have a hydrogen atom that's attached. So those are the constituents of this carbon atom here. Now we need to do the same for this carbon atom over here, which is this carbon carbon atom right here. So going up, notice that the first(atom is an oxygen atom, so we can put an oxygen right here. And then going down this way, the first atom is a carbon atom, so we can put this carbon atom over here. And then going up this way, the first atom is a hydrogen atom. And so now that we have the constituents, we can do a play playoff type system where we compare each of the atoms and compare the atomic numbers to determine which path is going to get a higher priority. So comparing these two atoms right here, they have the same atom of a carbon, so they have the same atomic number, and there's a tie here, between both paths. And the same applies to these 2 atoms, these 2 oxygen atoms. But looking at the oxygen and the carbon atom, notice that the oxygen atom has a higher atomic number than the carbon atom. And so what that means is that path number 1 here is the winner, and it's going to have a higher priority than path number 2. And so, remember, path number 1 is this red path that's going this way right here. And so what that means is we can label it as being priority number 3, I'm sorry, priority number 2, because it has a higher priority than this blue path, which is going to be priority number 3. And so now that we've determined the priorities for all 4 chemical groups on this chirality center, we now can draw arrows from priority 1 to priority 2, priority 2 to priority 3, and priority 3 back to priority number 1, skipping priority number 4. And so, notice that the orientation of priorities 1, 2, and 3 is a clockwise orientation where it goes from 1 to 2, 2 to 3, and 3 back to 1 in a clockwise fashion. And a clockwise orientation is suggesting an R configuration for this chirality center here. Now, remember that we always need to take into account the 4th priority. And so if the 4th priority is not on a dash, then we need to flip the configuration that it looks like. But looking at our 4th priority here of this hydrogen, notice that it is on a dash. So we don't have to worry about flipping the configuration, and the configuration is going to be exactly what it looks like, which is an R configuration with a clockwise orientation of priorities 1, 2, 3. So we can label this chirality center right here as being an R configuration. And for our answer over here, we can put an R. And so really, that is it for the configuration of this chirality center. Now remember that our molecule has 2 chirality centers, and we only determine the configuration of this one. So we need to repeat this process on this chirality center, which is this carbon atom over here. So what we can do is get rid of these arrows over here, so that we can repeat this same process on this carbon atom right here. And so, essentially, what we'll see is that this oxygen atom going up is going to have a higher priority than either of the other atoms that are connected to the other pathways. And so what that means is that this pathway going up is going to have priority number 1. And so we can put priority number 1 next to this hydroxyl group. And then, again, our hydrogen atom going this way is going to have the lowest priority of priority number 4. So then all we need to do is determine which of these pathways, this pathway or this pathway here, is going to get a higher priority of priority 2, and which one's going to get priority 3. And so, comparing, we'll say that this pathway going to the left will be path number 1 here, and then, this pathway going to the right here will be path number 2. And so, notice that both atoms of these paths are going to be a carbon atom. So we can put a carbon atom there. And then, what we need to do is look at the constituents of these carbon atoms or the chemical groups bonded to those carbon atoms. And so essentially, notice that this carbon atom over here, which is this carbon atom right here, is bonded to an oxygen atom directly. So over here we can put an oxygen atom. And it's also bonded to a carbon atom going this way, so we can put a carbon atom over there. And it's also bonded to a hydrogen atom, so we can put a hydrogen atom down here as well. Now looking at path number 2, notice that it is bonded to essentially this carbon atom right here. Notice that it is bonded to an oxygen atom going this way, so we can put an oxygen atom here. And then it's bonded to 2 hydrogen atoms, so we can put hydrogen down here. So we have oxygen here and 2 hydrogens right here. And so now that we have our atoms, what we can do is do our direct comparison. And so the carbon with the carbon here is the same atomic number, so there's a tie between these two paths. The oxygen and the oxygen, again, there's a tie between these two paths. And then the carbon with the hydrogen right here, notice that the carbon atom has a higher atomic number, and is going to be the winner, and it's going to have a higher priority than path number 2. And path number 1, again, is this red path that's shown right here. So what that means is we can show this red path, going this way as being priority number 2. And then, of course, that means that this other path over here will be priority number 3. And so now that we've assigned priorities to all chemical groups of this chirality center, we can draw arrows from 1 to 2, 2 to 3, and 3 back to 1 skipping priority number 4. And so looking at this, notice that our, the orientation of our priorities looks like a counterclockwise orientation. And a counterclockwise orientation of priorities 1, 2, 3 suggests an S configuration. So this might be tempting to put as an S configuration. However, we cannot forget that we always have to consider the 4th priority. And if the 4th priority is not on a dash, then we have to flip the configuration that it looks like. And so even though this looks like an S configuration because it's going counterclockwise, notice that our 4th priority of this hydrogen here is not on a dash. And so that means that we need to flip the configuration that it looks like. And so even though this looks like an S configuration counterclockwise, it's actually going to be an R configuration. And so, what that means is over here we can put R. And so essentially what we've determined is that our priorities are chirality centers, so both of these chirality centers, this one right here and this one right here, both have an R configuration. And that concludes this practice problem, so I'll see you guys in our next video.

Fischer Projections

So recall from your previous organic chemistry courses that Fischer projections are actually a type of molecular drawing style that are commonly used, especially to portray chiral compounds. Now, Fischer projections actually have 2 very important key features that we always have to consider. The first key feature is that all of the horizontal bonds, or the bonds that go from side to side, are always popping out of the page at you, so they're always coming out of the page at you. And even though they're normally not presented as wedges, they really should be presented as wedges. And so we can see that in our example below. And so what you can see is that the horizontal bonds, the ones that go from side to side here, they're being presented as wedges that are popping out of the page at you. But in a typical Fischer projection, all of the bonds are flat and so you don't see any wedges being presented. But you still have to remember that the horizontal bonds are still popping out of the page at you. So that's a very important key feature to remember. Now, the second important key feature to remember is that all of the vertical bonds, or the bonds that go up and down in a Fischer projection, they are always going into the page away from you. So they should really be presented as dashes. They should be presented as dashes even though they're normally not, and we can also see that in our example below. So you can see here that we have the vertical bonds, the ones that go up and down, and they are being presented as dashes that are going into the page away from you. And so in a typical Fischer projection, notice that again the vertical bonds are presented as just normal lines. But you have to remember that these vertical bonds here are actually going into the page away from you.

Alright. So if we take a look at our example for determining the R and S configuration of a Fischer projection, you have to keep in mind these 2 key features. And so we're going to, first look at the chiral carbon. So if we look at this carbon in the center here shown as this dot, it is a chiral carbon because it has 4 distinct chemical groups bonded to it. And we're going to go through our normal RNS system for determining the R and S configuration. And so we'll go through our priorities. The nitrogen here gets priority number 1. This group up top gets priority 2, and the methyl gets priority 3. The hydrogen, of course, is going to get the lowest priority, which is priority number 4. And so then we go and we draw our arrows. So our arrows go from 1 to 2, from 2 to 3, and then from 3 back to 1. And this looks like a clockwise configuration, and the clockwise configuration would be an R configuration. But because this is a Fischer projection, we have to remember that the horizontal bonds, the ones that go side to side, really are popping out of the page at us even though they're not presented as wedges. So this horizontal bond here, the one that's connecting our 4th priority, is actually really popping out of the pages at us. So we can imagine it being a wedge. And so if the 4th priority is on a wedge, all you need to do is flip the configuration that it looks like. So this looks like, clockwise R configuration, but because the 4th priority is popping out of the page at us, we have to flip the configuration. And it's actually an S configuration. So the configuration of this chirality center and the center is S. And so, we're going to get a little bit more practice determining the R and S configuration of Fischer projections in our next practice videos. So I'll see you guys there.

Here’s what students ask on this topic:

What is the difference between stereoisomers and enantiomers in organic chemistry?

Stereoisomers are molecules with the same molecular formula and sequence of bonded atoms (constitution), but they differ in the 3D orientations of their atoms in space. Enantiomers are a specific type of stereoisomer that are non-superimposable mirror images of each other. They have identical physical properties except for their interaction with plane-polarized light and reactions in chiral environments. For example, the R and S configurations of a chiral center in a molecule can lead to enantiomers, which can have drastically different biological activities, as seen with the drug thalidomide.

How do you determine the R and S configuration of a chiral center?

To determine the R and S configuration of a chiral center, follow these steps: 1) Assign priorities to the four substituents based on atomic number, with the highest atomic number getting the highest priority. 2) Orient the molecule so that the lowest priority group (usually hydrogen) is pointing away from you. 3) Trace a path from the highest priority (1) to the second (2) and then to the third (3). If the path is clockwise, the configuration is R (rectus); if counterclockwise, it is S (sinister). If the lowest priority group is not pointing away, you may need to swap groups and reverse the configuration at the end.

What is a Fischer projection and how is it used in organic chemistry?

A Fischer projection is a 2D representation of a 3D organic molecule, commonly used to depict chiral centers. In a Fischer projection, horizontal lines represent bonds coming out of the plane (towards the viewer), while vertical lines represent bonds going into the plane (away from the viewer). This projection is particularly useful for comparing the stereochemistry of molecules. When determining R and S configurations using Fischer projections, remember that the horizontal bonds are wedges (out of the plane) and the vertical bonds are dashes (into the plane).

What is resonance in organic chemistry and why is it important?

Resonance in organic chemistry refers to the delocalization of electrons within a molecule, which can be represented by multiple resonance structures. These structures depict different possible arrangements of electrons, particularly π electrons and lone pairs, that contribute to the overall hybrid structure. Resonance is important because it stabilizes molecules by allowing electron density to be distributed over multiple atoms, reducing the overall energy of the molecule. This concept is crucial for understanding the reactivity and stability of many organic compounds, such as benzene and carboxylate ions.

How do staggered and eclipsed conformations differ in terms of stability?

Staggered and eclipsed conformations refer to different spatial arrangements of atoms around a single bond in a molecule, often visualized using Newman projections. In a staggered conformation, the atoms or groups on adjacent carbons are positioned as far apart as possible, minimizing repulsive interactions and thus being more stable. In an eclipsed conformation, the atoms or groups are aligned with each other, leading to increased repulsive interactions and higher energy, making it less stable. The staggered conformation is generally more prevalent due to its lower energy state.