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When we venture to new places, we need navigational tools to guide us. In organic chemistry, those are reaction mechanisms! In this episode of Crash Course Organic Chemistry, we’ll learn all about how to write reaction mechanisms. Having this super useful skill means we don’t have to worry about memorizing every reaction that has ever existed.

Series Sources:
Brown, W. H., Iverson, B. L., Ansyln, E. V., Foote, C., Organic Chemistry; 8th ed.; Cengage Learning, Boston, 2018.
Bruice, P. Y., Organic Chemistry, 7th ed.; Pearson Education, Inc., United States, 2014.
Clayden, J., Greeves, N., Warren., S., Organic Chemistry, 2nd ed.; Oxford University Press, New York, 2012.
Jones Jr., M.; Fleming, S. A., Organic Chemistry, 5th ed.; W. W. Norton & Company, New York, 2014.
Klein., D., Organic Chemistry; 1st ed.; John Wiley & Sons, United States, 2012.
Louden M., Organic Chemistry; 5th ed.; Roberts and Company Publishers, Colorado, 2009.
McMurry, J., Organic Chemistry, 9th ed.; Cengage Learning, Boston, 2016.
Smith, J. G., Organic chemistry; 6th ed.; McGraw-Hill Education, New York, 2020.
Wade., L. G., Organic Chemistry; 8th ed.; Pearson Education, Inc., United States, 2013.

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Hi! I’m Deboki Chakravarti and welcome to Crash Course Organic Chemistry!

Whether it's GPS, a fold-out map, or directions like "head to the big maple tree and turn left," we need navigational tools to help us know where to go. Especially as we venture to new places. But there are highways, freeways, roundabouts, stop lights, construction signs, bicycle lanes, and so many other kinds of navigational signs and symbols.

All the details might be overwhelming at first! But with time, we can build up familiarity so we can travel quickly and maybe even effortlessly. Chemical reactions have their own navigational language, too, in reaction mechanisms.

As we get more practice interpreting these roadmaps, we'll be able to use reaction mechanisms to see patterns, predict products, and successfully track electrons as they make and break bonds. For instance, in the last episode we learned that we only show nucleophilic attack happening with an arrow drawn from the nucleophile to the electrophile. That’s an important freeway, but there are a lot of organic chemistry navigation skills left to learn, so let’s get to it! [Theme Music].

Every chemical reaction has a beginning and an end: we start with one or more reactants and our destination is one or more products. Reaction mechanisms are detailed maps that show us the routes we can take, and many notable pit stops along the way. In non-metaphorical words, a reaction mechanism is a step-by-step sequence that helps us keep track of electron movements, bonds that break and form, and any molecules that show up over the course of a chemical reaction.

Before we get into specific examples, we need to get comfy with some basic navigational symbols: lots of arrows. Some you might recognize from earlier in this series, but I want to make sure we're all on the same page. We can use 6 types of straight arrows to describe the relationship between different molecules, like chemical reactions or resonance structures.

A straight arrow pointing in one direction means a forward reaction, showing reactants becoming products. Two straight arrows, one on top of the other, mean that the reaction can go in both directions, forward and reverse. If they melt into each other, this means a step is at equilibrium.

Sometimes the reactions in an equilibrium will be unbalanced, and we'll see more of some chemicals and less of others in our mixture. The longer arrow tells us the direction the equilibrium lies. If the long arrow points right, the forward reaction happens more, and the products are favored.

If the long arrow points left, the backward reaction happens more, and the reactants are favored. Next we have an arrow to represent resonance structures, where we move a charge around one molecule. This arrow has a single line with two heads going in opposite directions -- so it's distinct from an equilibrium arrow.

We use curved arrows to show electrons moving around within or between molecules, whether we're dealing with resonance structures within molecules or chemical reactions. A curved arrow with a regular arrowhead means we're pushing two electrons. And a curved arrow with a harpoon head or fishhook arrowhead means we're only pushing a single electron, also known as a radical.

In general, electron-rich atoms or molecules-- called nucleophiles -- are attracted to electron-poor atoms or molecules -- called electrophiles. And these arrows will connect them as electrons get shuffled around and bonds get made and broken. We're gonna put all the arrows we're gonna see throughout organic chemistry in a handy chart.

So, take notes if you want! It might be useful as we're still getting familiar with all these symbols. Now that we know a few basic symbols, we can start looking at whole maps of chemical reactions.

Some reaction mechanisms can be multistep and really complex, while others are rather simple. In the last episode we talked about nucleophilic attack, which involves two types of molecules: electrophiles and nucleophiles. An electrophile is electron-loving, so it's something like a carbocation that might have an empty orbital and a positive formal charge.

A super detailed way to represent a carbocation in a reaction mechanism is by drawing out everything, including the empty p orbital and its molecular geometry. A nucleophile is a molecule with electrons that are ready to react, so it usually has a negative charge or lone pairs. Nucleophiles are ready to attack any molecule with a complete or partial positive charge.

So our nucleophile is the starting point for our electrons and the electrophile is their destination. We can fill in the rest of our reaction mechanism map with directional, curved arrows. When our bromide ion sees the carbocation's empty orbital, the nucleophile attacks the electrophile and donates a pair of electrons.

Using the symbols we've learned, we show that electron movement with a regular curved arrowhead. That makes a bond, which creates a neutral molecule as the product. To show that it's our next (and final) stop in this reaction mechanism, we draw a straight arrow pointing in one direction and the product that’s made.

Done! This kind of reaction mechanism map has a lot of detailed information, but drawing out orbitals and the geometry of molecules takes a while and makes it hard to focus on just the reaction. So in reaction mechanisms moving forward, we’ll mostly focus on how the electrons are moving.

We just draw arrows, without the extra flair like orbitals. Sometimes we need maps to check that we know where we're going, like when you look up your favorite restaurant just to be positive you take the right freeway exit. And navigational tools like maps and road signs are so helpful because they can help us go somewhere we've never been before.

In organic chemistry, what that means is we can use reaction mechanisms and electron pushing to help us predict products in chemical reactions. We don't have to memorize every single reaction that has ever existed! We just have to navigate carefully through each step of our journey.

For example, let's look at this reaction. We're given the start of a roadmap with three compounds and an arrow that tells us the reaction can go in both directions. We're not given the product, but we can figure out what it is.

To start, we have to look for the functional groups on the starting molecule and then what's written above the reaction arrow and think about what they might do. Here, we've got an alkene and some water and sulfuric acid. Sulfuric acid is a super strong acid -- almost as strong as hydrochloric acid or hydrobromic acid -- which means its most acidic proton completely dissociates in water.

We talk about acidity in more detail in episode 11, so rewatch that video if you need a refresher. But simply, sulfuric acid doesn’t argue when the water molecule grabs a proton to form a hydronium ion -- H3O+. After puzzling through that road sign, we can properly start our reaction mechanism journey with 2 reactants.

We have cis-but-2-ene, which has an electron-rich double bond -- a nucleophile. And we have a hydronium ion, which has a positive formal charge -- an electrophile. We can mark these regions in red and blue, respectively, to see our reaction hot spots.

Because double bonds have a lot of electrons between just two atoms, they're attracted to positive regions. So we know where the first reaction will happen! Let's draw a regular curved arrow that starts on the electrons in the double bond and does a nucleophilic attack on the electrophilic hydronium ion.

Remember, even though it might be tempting to show the electrons going straight to the positive charge on oxygen, that move would give oxygen ten electrons, which is not allowed! It's also not okay for hydrogen to have two bonds in organic chemistry mechanisms. So we have to draw one arrow to attack a hydrogen, and a second arrow to move a pair of electrons to the positively-charged oxygen atom, which neutralizes the charge.

Since the double bond attacks a proton--an electrophile--this step is called electrophilic addition of a proton to an alkene. Now we have a plain old water molecule and a carbocation, which is quite reactive, so we're not done yet! This is just a pit stop, and we still have farther to go on our road map.

Specifically, this is a prime setup for another nucleophilic attack, this time with water as the nucleophile and the carbocation as the electrophile. So next, we can draw a curved arrow from a lone pair of electrons on the oxygen in water to the positively-charged carbon in the carbocation. This electron-push forms a bond and gives us a protonated alcohol called an oxonium ion.

That's the oxygen atom with a carbon-oxygen bond, two hydrogen-oxygen bonds, a positive charge, and a lone pair. The pKa of this protonated alcohol is very low. As another refresher from the acidity episode: a low pKa means a stronger acid that's more willing to give up its hydrogen.

So we're still not done yet! After a second pit stop, we have one final acid-base reaction. There are still water molecules floating around, so our reactants are a water molecule (as our base) and the oxonium ion (as our acid).

We can draw one last curved arrow from a lone pair of electrons on the oxygen in water to deprotonate the oxonium ion and reform the hydronium ion catalyst we started with. As final products, we have regenerated our hydronium ion catalyst and made butan-2-ol. There’s nothing left in solution that's interesting to the butan-2-ol….

So that means we’ve reached our destination! We could draw out a comprehensive reaction mechanism with all of these steps, including our starting point, our destination, and all the pit stops. But it's often simpler to sum up our work with the overall reaction:.

It was a long and winding road trip to get here, but we predicted a product! Not even the most celebrated Nobel-prize-winning organic chemist knows every single reaction from start to finish. Knowing the navigational language of reaction mechanisms and how to push electrons can help us solve any problem step-by-step.

Now, I don't want to amp up the difficulty too much, but let's practice our basic reaction mechanism skills once more with a slightly different example. In this reaction, we're given the start of a roadmap with an arrow meaning a forward reaction… but we're given lots of different chemicals here. And it might look a little overwhelming!

But don't worry. Let's start, again, by looking at the functional groups and what's written near the reaction arrow and figure out what it means. In this puzzle, the 1 and the 2 represent two steps that have to take place in that order.

So we need a little more road signage to help us with our journey. We'll start with the reactants labeled 1 and our cyclohexanone. Sodium acetylide is dissociated in solution as an ionic salt, the negative carbon of the triple bond is very reactive so it does the driving while the sodium is just along for the ride.

That means the acetylide is our nucleophile and the partially positive carbon of the carbon-oxygen double bond in cyclohexanone is its electrophile target. With our players identified, we can draw the nucleophilic attack with a regular curved arrow from the lone pair on the acetylide to the partially positive carbon. We can't take a pit stop there, though, because that would be 5 bonds to carbon and break science!

Well, for this typical organic compound, at least. So we have to push electrons to the electronegative oxygen and then we're done. So this molecule is the first pit stop on our roadmap, and the positively-charged sodium ion is just hanging around stabilizing the negatively charged oxygen.

Now, we could stop here for dinner, this sodium salt is stable in our reaction flask, but we know that there's a better BBQ joint just down the street, so we’ll keep on driving. Now that we've followed number 1 on the reaction arrow, we can move onto the directions listed in number 2. We've got some water and hydrochloric acid, which is super strong and completely dissociates.

So just like the last puzzle, this road sign basically means add in a hydronium ion! This negatively charged ion doesn't have resonance stabilization, so just like the conjugate base of ethanol we met in episode 11, this is a strong base. Our hydronium ion is a strong acid, so the proton is transferred from the acid to the base, and presto, we’ve made a neutral product.

And with that final bond, we’re done. We've got some side products like water and sodium chloride, but most importantly we have 1-ethynylcyclohexan-1-ol. In summary, the reaction mechanism looks like this:.

Don’t panic, all the atoms are there, I promise! But by convention, side products like water and sodium chloride aren’t shown in a summary reaction, we just show the major organic product. We made it through this journey by using a few key navigational tools, and without a whole bunch of memorization.

We'll keep building up our toolkit even more in episodes to come. In this episode, we learned:. How to write reaction mechanisms or maps of reactions.

That strong acids in water should be considered hydronium ions or sources of protons. And electron rich atoms or regions of molecules are attracted to electron-poor atoms or regions of molecules. Next time we’ll look more closely at that positively charged carbon with the empty p-orbital as we begin reactions of alkenes.

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