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Organic reactions are kind of like carefully choreographed fight scenes, and nucleophilic attack is a key move. This episode of Crash Course Organic Chemistry is all about nucleophiles and electrophiles, or what happens at those molecular hot spots we’ve been talking about. We’ll also learn about what IR spectra can tell us about reactions, and how cyanide is more than just a poison from mystery stories. Let’s get to it organophiles!

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!

The word stem -phile, which is derived from the Greek “philos,” meaning “loving,” has been used with other prefixes or suffixes to suggest the love of just about everything. There's a philodendron, which is a plant that loves to climb trees, or technophile, which describes a lover of new technologies. I might consider myself a bibliophile and ailurophile, to profess my love of books and cats.

And maybe we can call ourselves organophiles, as people who love organic compounds. In this episode though, we’ll specifically be looking at two very important philes: electrophiles, lovers of electrons and nucleophiles, lovers of a molecule’s positive regions. Over the last few episodes we’ve been thinking about molecular hot spots, places on a molecule where positive charges and negative charges show up.

Now it’s time to think about what happens at these hot spots - electrophiles and nucleophiles. So, my fellow organophiles, let’s get to it! [Theme Music]. In the last episode, we discussed Brønsted-Lowry acids and bases, where the acid is a proton donor and the base is a proton acceptor.

But there are molecules out there called Lewis acids and bases, which accept or donate electron pairs instead of protons. Specifically, Lewis acids accept a lone pair of electrons and Lewis bases donate a lone pair of electrons. Lewis bases often include atoms with lone pairs like nitrogen and oxygen -- for example, ammonia and water are Lewis bases.

Other Lewis bases are negatively charged atoms like chloride, or groups of atoms like hydroxide. Generally, Lewis bases are recognizable because they have lots of electrons, so we call them electron rich. Lewis bases are also nucleophiles.

Technically if we go back to our word stem -phile, this means nucleus-loving. But when it comes to reactions in organic chemistry, being a nucleophile means they love to interact with positive charges or positive regions on another molecule. Think of, like, a superhero with a grappling hook.

A nucleophile is kinda looking for a positive charge it can throw its electrons toward and grab onto. On the flip side, Lewis acids are positively charged atoms, like a proton, or molecules that are short a pair of electrons from an octet and have an empty p orbital, like borane, BH3. Borane only has six electrons when neutral, and its empty p orbital can accept electrons.

This general definition doesn’t include compounds like phosphorous pentachloride that can be considered non-traditional Lewis acids, some of which we'll meet later in the series. Lewis acids are electron poor, which is why they're willing to accept lone pairs. And Lewis acids are also electrophiles.

Going back to our word stems, this means electron-loving. And in organic chemistry reactions, being an electrophile means they love negatively-charged electrons on other molecules and can even provoke them into interacting sometimes. To continue my grappling hook metaphor: think of an electrophile as a molecule with a big red video-game-like target on it saying "grappling hooks here!" One of the most important electrophiles we'll see throughout these videos are carbocations.

These are molecules with an sp2 hybridized carbon atom and an empty p orbital, which creates a positive charge. Keeping formal charges in mind, we can see that the carbon only has three bonds, which contribute 3 valence electrons. A neutral carbon atom has 4 valence electrons.

So 4 minus 3 is positive 1, and therefore it has a +1 formal charge. OK, now that we have nucleophiles and electrophiles as our players for today, let’s get into the fun stuff: what happens when they run into each other in a lab? When a nucleophile reacts with anything, we call that a nucleophilic attack.

If we think of organic reactions as carefully choreographed fight scenes, a nucleophilic attack is just one move in the superhero's skillset. It can be one step in a larger chemical reaction or a powerful move all on its own. In a nucleophilic attack, nucleophiles are always the aggressor and do the attacking.

So curved reaction arrows always start on the nucleophile and are drawn to the electrophile. Electrophiles aren’t just innocent bystanders though. Because they love electrons so much, they can sometimes provoke a nucleophile into attacking.

Kinda like when you want someone to do something and you keep asking and asking until they give in, or you taunt them a little to goad them on. Like I mentioned, a nucleophilic attack can be part of a larger multi-step chemical reaction. But in this episode, we're going to start simple with a one-step reaction involving a nucleophile and an electrophile.

You've gotta learn how to punch properly before you star in a martial arts film, y'know? So here we have two compounds: a hydroxide ion and 1-chlorobutane. The hydroxide has lots of electrons and that negative charge, so it’s pretty easy to figure out that it's our nucleophile.

It's a little tricker to see that 1-chlorobutane is our electrophile, though. For that, we have to remember what we learned in a previous episode about polarity: this chlorine-carbon bond is polarized. Seriously, I'm not joking when I say we're assembling an organic chemistry toolkit -- all this knowledge builds!

In this bond, the electronegative chlorine is pulling electrons toward itself, which gives the carbon a partial positive charge and the chlorine a partial negative charge. This makes that carbon an electrophile, which is pretty attractive to the hydroxide ion. So when this reaction takes place, the hydroxide attacks that carbon and donates electrons -- this is hydroxide's grappling-hook move.

I guess hydroxide is basically Batman here and the carbon chain is the side of a Gotham City building he wants to climb. Our carbon is only capable of making 4 bonds, so before we finish the reaction we have to make sure we're not breaking the rules of science. The chlorine takes a pair of electrons with it to become a chloride ion, and butan-1-ol is left behind.

Fight sequence: done! Now, there are different kinds of nucleophilic attacks that have different names. For now we can just call this particular reaction a nucleophilic substitution, because the hydroxide basically substitutes in for the chlorine.

We'll talk more about nucleophilic substitutions, and get more specific about naming them in a future episode, but it's helpful to start getting familiar with the general term for this kind of reaction now. Now you don’t have to take my word for it that this reaction happens and that our fight sequence has ended successfully with butan-1-ol. We can actually see that this reaction happened with an experimental tool we've learned in this series: infrared spectroscopy or IR.

IR provides information about the functional groups present in molecules by measuring bond vibrations. And one of the most recognizable functional groups in IR is alcohols, which we have here in butan-1-ol. So if the nucleophilic attack goes as planned, we should see a big change in the spectrum.

To see this in action, here’s the IR spectrum for 1-chlorobutane:. And here's the spectrum we get for the product of this particular reaction:. There's a strong, broad peak at 3300 wavenumbers, which is the O-H bond of an alcohol.

So we can be pretty sure that butan-1-ol was formed! So organic chemistry isn't really just magic and guessing. We can confirm what we draw on paper for our nucleophilic attack choreography with experimental tools like infrared spectroscopy.

The reaction we just looked at starred a nucleophile: hydroxide. It came in strong with a negative charge and attacked that partial-positive carbon in one fell swoop. But, like I mentioned earlier, there are strong electrophiles out there too, which pester nucleophiles into attacking.

And carbocations are some of the most pesky characters out there, taunting enough that even a weak nucleophile like water will attack them. These nucleophilic attacks are slightly more complicated fight sequences to choreograph. So they usually happen in two steps.

Let's look at this example with a carbocation as our electrophile and water as our nucleophile. The first step of the nucleophilic attack is still initiated by the nucleophile, water. A lone pair of electrons on oxygen attacks that positively-charged carbon and donates electrons.

Water shoots out a two-electron grappling hook and makes a bond! Then in the second step, a second water molecule gangs up on this grappled molecule and gets in on the action. In this case, because the second water molecule attacks a proton, we can call this a deprotonation.

It might be tempting to show the electrons going straight to the positive charge on oxygen, but be careful! Oxygen obeys the octet rule, and that move would give it ten electrons! Before we can finish the reaction we have to make sure we're not breaking the rules of science, and hydrogen can't have two bonds!

So a pair of electrons from the hydrogen-oxygen bond hops to the positively-charged oxygen atom, neutralizing the charge. And a hydronium molecule breaks away from the scuffle. Fight sequence: done.

To sum up this two-step reaction, the carbocation undergoes a nucleophilic attack by one molecule of water, then it gets deprotonated by a second molecule of water. So we're left with an alcohol and a hydronium ion. To show another two-step reaction and practice our fight choreography with slightly different characters, let's look at a different kind of nucleophile: molecules with double and triple bonds, like alkenes, alkynes and carbonyl groups.

Nucleophiles are just groups with lots of electrons, so all these fit right in! For example, let's look at the reaction of cis-but-2-ene and hydrogen bromide. Remember HBr is a strong acid and ionizes completely to form H plus and Br minus.

The alkene has a double bond, so it's our nucleophile and ready to attack our electrophile, the proton. So the double bond donates electrons by throwing out its pi electrons as a grappling hook and hooking the proton. When the alkene uses these two electrons to attack the proton, one of the two carbons previously involved in the double bond is short an electron and ends up positive.

Now we're left with a super pesky carbocation as an electrophile, and the negatively charged bromide ion as a nucleophile. The positive charge on the carbocation is irresistibly taunting to the bromide ion. So for the second step of this reaction, the bromide does a nucleophilic attack and forms 2-bromobutane.

Fight sequence: done. These two ended up as one unified dynamic duo or -- uh -- molecule. We're going to end this episode with one final nucleophile that you may have heard of before... as a potent poison in Victorian-era mystery novels and beyond: cyanide.

It's a carbon atom triple-bonded to a nitrogen atom, and the carbon carries a negative charge. But now's our chance to see cyanide as way more than just a poison. It's a pretty cool molecule because it can do a nucleophilic attack to form a carbon-carbon bond.

And being able to add carbons together is important in organic chemistry, because it helps us make super-sized molecules, such as big drug molecules in medicine. As a strong nucleophile, cyanide can attack carbon 1, in an electrophile like 1-bromo-2-methylhexane. This is another one of those nucleophilic substitutions: the cyanide latches on with a bond and pushes out the bromine as a bromide ion.

We’ll see in future episodes how carbon chains with cyanide substituents are super useful as gateways to other functional groups, or just for elongating a shorter chain. So with that, we've gotten pretty familiar with the fight choreography of a nucleophilic attack: the arrows start with the electron pairs on our nucleophile and end on the positive region on our electrophile. And with this knowledge, we're getting closer to being able to puzzle out, not memorize, lots of complicated reactions that make organic chemistry notoriously tricky!

In this episode we’ve learned that:. Nucleophiles are Lewis bases that donate electrons and attack electrophiles. Electrophiles are Lewis acids that are attacked by nucleophiles.

IR spectra can help us understand if a reaction really does happen. And cyanide is more than just a poison. Next time we’ll get further into the nitty gritty of arrow pushing and reaction mechanisms.

Let’s face it… no one wants to memorize thousands of reactions, and if we can learn how to write good mechanisms, we won’t have to! Thanks for watching this episode of Crash Course Organic Chemistry. If you want to help keep all Crash Course free for everybody, forever, you can join our community on Patreon.