The addition of HBr to alkenes is the focus of today’s video.

Fast forward to the fifteen seconds at the end for maximum awkwardness. I am an idiot when it comes to this stuff. Is making videos supposed to be brutally fricking hard? I don’t know how Gary Vaynerchuk and Salman Khan do it.

Thanks for bearing with me during this painful learning process. If you’re an expert on making videos (but not organic chemistry) and want to set up a mutually beneficial tutor-barter arrangement, drop me a line.

Loyal reader Sandy writes in with a comment about memorization:

I wish I had understood much earlier that there is a place for memorization in Orgo – like the reagents and what they contribute to a relationship, what reactions they are used with, etc. We were heavily discouraged not to memorize for the class – and I think it hurt my study plan. What we should have been told is “understand the mechanism – movement of electrons”, but you must memorize reagents, format of reactions, etc. I know he had good intentions, but he was not clear. It was at this point that I began to struggle. I did make an A, but spent the entire time between Orgo 1 and Orgo II reviewing and making sure I got the information I needed in my head.  This was the single most difficult issue I faced – trying not to memorize.

Great point.

No matter what anyone says, here’s where memorization helps: learning vocabulary, names of reactions/reagents/solvents, abbreviations, nomenclature, functional groups, and the bond-forming/bond breaking pattern of each class of reaction.

In short: vocabulary, conventions, and results obtained by experiment. Anything that answers the question “what?”is something that can be memorized. 

Where memorization doesn’t help as much is in answering the question “how?”

• how would you use [this data] to determine [this property of a molecule] ?
• how do you synthesize [this molecule] from [these molecules]?
• how will changing [this property of a molecule] change the [property of this reaction]?
• how will [this molecule] react under [these conditions] compared to [these conditions]?

See what’s going on here? We’re changing two variables at once, and the number of  possibilities (and things to memorize) increases exponentially. This is where applying concepts just becomes more efficient than memorization. I think this is what’s behind instructors’ advice to “not memorize”: it’s sound counsel.

In the best organic chemistry courses, you’re taught to apply the concepts you’ve learned to solve problems. So one piece of advice for students : ask the “how” questions a lot.* (“How does this reaction occur” is a subtly different question than “what’s the mechanism of this reaction”!).

* “Why?” is also a good question to ask, although the answer can sometimes be unsatisfying. (example “Why do we use [this reagent] for this reaction?” “Because it’s convenient, reliable, and cheap”!]

One thing has been missing from the discussion of resonance. What’s the point?

Who cares if we can write out resonance structures? What does it matter if we can figure out the two or three most stable resonance structures? So what?

Here’s the point: we can apply resonance (and electronegativity) to figure out the electron densities of molecules from first principles, and we can apply these electron densities toward understanding how a molecule will react.   

Put it another way: if you learn this skill, you will rely less on memorization for understanding reactions, because you’ll be able to figure out the chemical behavior of molecules you’ve never seen before. 

For instance: if you’re a non-chemistry major I can pretty much guarantee you’ve never seen this reaction before. But if you apply some of the principles in this post, you should be able to make some headway on it.

Let’s look at these two aspects really quickly.

1. Applying electronegativities. When you have a bond between two atoms with different electronegativities, there will be a dipole (two opposite charges separated in space). That dipole will give you a clue about the electron densities of those two atoms. For example in the molecule below, the oxygen is more electronegative than carbon which means that the C–O bond will be polarized towards oxygen (it will have a higher electron density). This is different than formal charge, which is where we have to assign a charge to an atom for “accounting” purposes.
2. Applying resonance: when you know the most stable two (or three) resonance forms, you’ll have a good idea of what the resonance hybrid looks like. The resonance hybrid also tells you electron densities, sometimes in a way that isn’t immediately apparent from electronegativity (see below).

Here’s some examples of resonance hybrids, along with the electron densities we get from applying both electronegativity and resonance. In the picture, the partial charges (δ) represent electron densities on the hybrid.

Now for the punch line.

Once you know the partial charges on a molecule, you can then use it to figure out potential chemical reactivity. How so?

Remember the “one sentence summary of chemistry”: opposite charges attract, like charges repel. 

  So any region of negative charge on a molecule will have some degree of attraction to a region of positive charge on another molecule. In reactions electrons flow from areas of high electron density to low electron density. Another way of putting it: the partial negative charge (i.e. high electron density) will go to a region of partial positive charge (i.e. low electron density).

So in the diagram below I’ve put down some of the resonance hybrids (along with other molecules), and drawn a selection of the interactions between the opposite charges. Although these arrows do not necessarily represent actual reactions (although many do!) they at least represent potentially feasible reactions. 

The key take-home skill from these examples is to be able so see how the resonance hybrid will determine electron density, and how this can end up leading to hypotheses for feasible reactions.

Let’s go back to the original question:

By applying electronegativity, we can judge that the C–Zn bond will be polarized towards carbon, which makes it electron rich; it should be attracted to the carbon of the second molecule, which both electronegativity and resonance tell us should bear a partial positive charge. In fact this is a real reaction, although we can’t fully determine how well a reaction will work from first principles. Experimental evidence is the one and only arbiter as to whether a reaction works or not.

Is this technique perfect, without exceptions? No. It’s not perfect. It’s not completely without exceptions.* But it’s a good mental model for the underlying principles of chemical reactivity.  The point here is to give you a glimpse of how to apply the concepts of electronegativity and resonance towards new and unfamiliar situations. 

*Two prominent exceptions: electronegativity isn’t the best for figuring out the reactivity of nitrile ion (CN(–) and oxymercuration of alkenes. It doesn’t predict reactivity of Cl-Cl and Br-Br, etc. which are not polarized.

**Note that this model doesn’t tell you how reactive different species will be. That will require another set of mental models.

PS – a long enough post as it is, but here are some “unproductive” interactions from the diagram above.

One of the new things I wanted to do this year was to start doing videos. Since I was starting to run out of reagents to talk about for Reagent Friday, one thought was to start talking about reactions instead – and maybe make a video for each.
So today starts a new experiment: Reaction Fridays.
There is no such thing as going from “never made a video” to “making great videos”. So the first many iterations in this series are going to be really crappy! So be it: there’s only one path to getting good – to start off crappy, risk making an ass of yourself in public, embrace your crappiness, and work upwards from there. They can always be remade, incorporating feedback as necessary.

So without further ado, here’s the first installation of Reaction Fridays: The Free-radical chlorination of alkanes!

I’d really welcome any feedback you might have. Is this useful? What could be done better? Feel free to leave a comment, send me an email, or drop an anonymous comment in the Feedback section.
Thanks!

Belated to get to this, but Jon Chui has made another beautiful graphic. You might recall his Pictorial Guide to Interpreting IR Spectra from awhile back.

Now he’s made a visual guide to Interpreting 1H NMR Spectra, and it’s lovely.

NMR is more information-rich than IR, so the task of putting *everything* on one reasonably sized graphic is an impossible task. But he’s done a great job of capturing the main concepts and key pieces of information to extract (chemical shift, integration, and multiplicity) on one graphic.

Jon has a gift for making these things, and there’s a pressing need for educational materials that not only inform, but incorporate aesthetics and design.  Maybe if enough people nag him, maybe he will keep making more of them. Here is his email. Go ahead and write him (blame me if you like).

No discussion of resonance structures would be complete without mention of how to royally screw them up. This isn’t something to feel bad about, by the way: there isn’t a chemist alive who hasn’t made one of these mistakes at some point. Think of it as a rite of passage. The trick is to make the mistakes while doing problems, not while doing an exam.

There are at least three common categories of mistakes regarding resonance structures:

• Unbalanced equations
• Moving atoms around
• Incorrect drawing of resonance arrows

Let’s first talk about unbalanced resonance equations, where something (either an atom or electrons) has been added or subtracted. Remember that in drawing resonance forms we’re only allowed to move electrons, and nothing more. That means that the two resonance forms can neither differ in the number of their electrons nor can they differ in the number of atoms.

Moving atoms around is a second category of common mistake. Although the two structures shown below have the same number of atoms and electrons, they are not resonance forms because we have broken single bonds (as opposed to π bonds) and thus moved the location of one or several atoms. The easiest way to screw this up is to move hydrogens. While these molecules are related, they are actually pairs of constitutional isomers, not resonance structures.

One way to avoid making these types of mistakes is to try to interconvert the structures using curved arrows. There are only three legal arrow-pushing moves for drawing resonance structures. Double check to make sure you aren’t breaking the rules.

The last – and by far the most common class of mistake in drawing resonance structures is to screw up the curved arrows. There is a seemingly infinite number of different ways to do this. They fall into a number of sub-categories.

First, there’s arrow-pushing moves that are wrong and cannot be redeemed. Examples A-D each depict different ways of breaking the octet rule. In A, B, and C the resonance form that would result from these arrows would have five bonds to carbon. Example D would have five bonds to nitrogen. Inconceivable! 

Examples E and F  are wrong for a different reason: remember that the curved arrow depicts the movement of a pair of electrons. In example E, the “tail” of the leftmost arrow is shown at a positive charge – a big no-no, since there isn’t a lone pair of electrons here. Likewise for F, where the positively charged nitrogen also lacks an electron pair.

Then there’s arrow pushing “moves” that are also illegal, but can be made legal through drawing an additional arrow. See if you can draw an arrow to make it work (answers at the bottom).

Then there’s the sloppy mistakes, where these arrow pushing forms are missing something important. I guess you could say this entire post is devoted to sloppy mistakes but these examples are particularly egregious because they are just one tiny little detail away from being correct. In these two cases, there is neither a lone pair of electrons (or a formal negative charge) at the tail of one of the electron-pushing arrows, which make them incorrect. Neglecting to draw the formal charge of an atom is another common sloppy mistake (albeit not unique to resonance). Note that when I say sloppy I’m not making a moral judgement here. I’m just saying it makes for imprecise and ambiguous chemical structures, which are not useful.

Finally, there are resonance structures which are not illegal, per se, but  won’t make a significant contribution to the resonance hybrid.

In both examples we have very electronegative elements (oxygen and nitrogen) with less than a full octet. Recall that electronegativity is a rough measure of the ability of an atom to stabilize negative charge? Well, the converse is true – that is, the greater the electronegativity, the more positive charge will be destabilized on that atom (clarification: by “positive charge” here I am specifically referring to having less than a full octet of electrons (like a carbocation), not the common situation where O or N with a full octet bears a formal charge of +1.)

Avoiding all of these mistakes requires careful attention to detail, bordering on paranoia. The number of atoms and electrons on the left side of the resonance arrow should balance the number of atoms and electrons on the right side of the resonance arrow. Furthermore, the changes in bonding (and charge)  of the molecule on the left side of the arrow should be accurately mapped by the appropriate curved arrow(s).

If it sounds like I’m making a case for organic chemistry being a lot like accounting, you’re right!  In the final analysis, organic chemistry equations are not unlike accounting transactions. The two sides need to balance.

P.S. Here’s the answers for the example above:

Sorry it’s taken so long to get back in the swing of things. I’ve just returned from some time Up North. What do a bunch of Canadians do when it’s –15°C outside in late December? They invite their family and friends over for a pond curling tournament!

This was the cap to a great 2011. I just wanted to take this time to thank everyone who took time out of their life to visit the site in the past year, as well as those who’ve given valuable feedback via email and comments. Having the opportunity to connect 1-on-1 with so many undergraduates (and instructors) has been invaluable in helping me learn how to teach.  A special thanks goes out to the students I’ve worked with personally and all those who helped support the site through purchasing a copy of the Reagent Guide and the Reagents app.

My mission is to make this site one of the world’s best resources for learning organic chemistry. So how can MOC be better for teaching organic chemistry in 2012?

Here’s some of the things I’m thinking about for 2012

• Video. I know there’s like maybe 2 videos on the MOC Youtube channel. I don’t want to do the whole progression of the course, Khan Academy style, but surely there are topics that  a short video would be helpful for.
• A guide to reactions. There are so many. How about a resource which organizes them all?
• Quick mini-courses on developing specific skills in organic chemistry… like determining SN1/SN2/E1/E2, or drawing resonance structures, or thinking through an NMR or synthesis problem.
• Daily tips on organic chem, delivered in your mailbox, tailored to the progression of a typical Org 1/Org 2 course.

As always, suggestions on topics to cover are always welcome. You can always write me at jamesmasterorganicchemistrycom or if you wish to remain anonymous, use the Feedback button above.

After all these posts about resonance, I thought it would be good to have a post summarizing what’s been discussed so far.

One of the key skills in analyzing the reactivity of a molecule is to be able to figure out where the electrons are.

 As I wrote here, if we’re dealing with single bonds, it’s a relatively straightforward matter of figuring out the differences in electronegativities.

However if multiple bonds (π bonds) are present,  then we start to run into a little problem:  there can be multiple ways to draw the same molecule – and thus, figuring out electron densities on a given molecule is not always as straightforward.

This situation – when we can draw two (or more) forms of the same molecule that differ only in the placement of their electrons – is called resonance, and the different structures we draw are called resonance forms.

How can we “find” resonance forms for a given molecule? It’s possible to do it through trial-and-error, but one surefire way is to do so is to apply the curved arrow formalism, which is a way of depicting the “movement” of electrons.

Here’s an important point about resonance forms. It is tempting (and very wrong!) to think that these  resonance forms are in “equilibrium” between each other. Avoid this common mistake!

Instead, the “true” state of the molecule will be a “hybrid” of these resonance forms.

For example in the acetate and allyl cation examples below, the “true” structure of the molecule is represented through a 50:50 combination of the two resonance forms.

In this case both resonance forms are equal in energy, so the “hybrid” is a 1:1 mixture of the two. However this is only rarely the case, for instance in this ketone below, which has 3 different resonance forms.

Not all resonance forms will be of equal significance. How do we evaluate how important they are? 

 Principle #1: The rule of least charges

Resonance forms become less significant as the number of charges are increased. For example, in the ketone above, the resonance form with zero charges will be the most significant. (Note however, that each resonance form has a net charge of zero.

 Principle #2: The octet principle

Resonance forms where all atoms have full octets will be more significant than resonance forms where atom(s) lack a full octet. Importantly, it’s a good general rule never to place less than a full octet on nitrogen or oxygen, as in the example above, right. Since these atoms are highly electronegative, these resonance forms are extremely unstable and will be insignificant.

Principle #3: Stabilization of negative charges

Negative charges are most stable when placed on the least basic atom. There are four main trends to consider here:

• Electronegativity: across a row of the periodic table, negative charge becomes more stable as electronegativity is increased.
• Polarizability: down a column of the periodic table, negative charge becomes more stable as polarizability increases
• Electron withdrawing groups stabilize negative charge through inductive effects.
• Hybridization: negative charge becomes more stable as the s-character of the atom is increased.  sp (most stable) > sp2 > sp3 (least stable

Note that stability is the opposite of basicity.

Principle #4: Stabilization of positive charges

When dealing with positive charges, the resonance form where all octets are filled will be the best (see principle #2). Between resonance forms where there is a positive charge that has less than a full octet (that is, a carbocation), then follow these principles:

1. Place positive charge on the most substituted carbon
2. Avoid placing positive charge adjacent to electron withdrawing groups if possible
3. Place positive charge preferentally on sp3 > sp2 > sp

Application #1: Pi donation

When double bonds are connected to an atom with a lone pair of electrons, the molecule will have a significant resonance form where there is negative charge on the adjacent carbon.

Application #2: Pi accepting

When dobule bonds are connected to a polarized πbond, the molecule will have a significant resonance form where there is positive charge on the adjacent carbon.

For now, that does it for a summary of the important themes in resonance. Next stop (after a post about some common mistakes) will be to apply these principles to chemical reactivity.

Last time I talked about π donation and π donors, which are atoms capable of forming a new π bond with an adjoining C-C π bond.  The upshot of π donation is that these molecules will have an important resonance form where the carbon at the far end of the π bond (away from the π donor) has a negative charge.

Todays topic is π acceptors, which is, as you might imagine, exactly the opposite phenomenon as π donation.

Recall that in π bonds that are polarized toward a more electronegative atom, we have an important resonance form where the less electronegative atom (usually carbon) bears a positive charge. That would be the one on the left, below.

 However, when we have an additional double bond attached to an electron withdrawing group, we can also draw an additional resonance form where there is a positive charge on the far carbon. That would be the one on the right.

These are both important resonance forms. Note that they both have an equal number of charges (two) and they are polarized so as to put the negative charge on the most electronegative atom (oxygen). They will each make an important contribution to the resonance hybrid of this molecule.

(The question of which resonance form is more important for the purposes of reactivity is an important question I’m deferring to a later date. The short answer is that it depends greatly on the reaction conditions chosen).

Now: see how the double bond has “moved” toward the electron-withdrawing group? For this reason, we call these types of substituents “π acceptors”, because they can “accept” a π bond.

This is a general phenomenon not just for functional groups containing C=O and C=N groups, but also for functional groups such as nitriles, nitro groups, sulfonyls… essentially any polarized group containing a π bond.

You can also think of it as an extension of a phenomenon we observe for resonance forms that have an empty p orbital, such as carbocations and other groups that contain an empty p orbital (such as this boronic acid, pictured).

Here’s the quick summary of this phenomenon:

This is the last big post planned on introducing resonance concepts for the time being. After a summary, and then some examples of what NOT to do,  I want to show how you can apply this skill (that of evaluating resonance forms in determining electron density on a molecule) toward figuring out the reactivity of a given molecule.  

Next Post: In Summary – Resonance 

You’d think after five or six posts on resonance, that would be enough. But NO, friends, it just keeps going. I promise that today’s post is actually useful, although to be honest it’s probably most applicable if you’re in (or going into) org 2, since the chemistry of the functional groups discussed here  don’t really come up until then.

Anyway. The topic of today’s post is “π donation”, which is just a way of describing what can occur in certain resonance forms where an atom with a lone pair can form a π bond with an adjacent atom of appropriate hybridization. Now this has been talked about before, sure – but here, the difference is that we’ll primarily be discussing situations where the “best” resonance form is neutral, and the “second-best” resonance form is charged.

Let’s look at the resonance forms of an enol (shown) and use what has already been discussed to evaluate their relative importance. Note that in order to draw resonance form D we have to do two arrow moves to avoid breaking the octet rule.

• Resonance form A has the fewest charges.
• Resonance form D has two charges, but all atoms have full octets.
• Resonance forms B and C each have two charges, but have empty octets on the carbons.

In evaluating these resonance forms, A will be most important due to the rule of fewest charges. D will be the second-most important since we always give atoms full octets if possible. And C and D will be the least important because each of them have atoms with less than full octets.

While that’s nice, you should go on more than just some Internet dude’s appraisal of what resonance forms are most important. What about experimental evidence?

Here’s three pieces of experimental evidence to support the proposal that resonance form D is most important.

• reactivity profile (shown below) – enols tend to react with electropositive groups such as protons (H+ ) at the site where they bear a partial negative charge (opposite charges attract, remember). This supports a resonance form such as D being more important than, say B.
• proton NMR spectroscopy is a good guide to electron density, and protons on the enolate carbon are shifted downfield relative to alkenes (this indicates the carbon is more electron rich, which supports resonance form D).
• electrostatic potential maps (although I can’t find a good one for the enol shown, here’s one for a related species. Note how there is less positive charge on one of the carbons).

Furthermore, molecules like the ones below would be expected to show similar behavior – and they do.

Enamines (the one on the left) are well known to react with positive species at the end carbon (C1).  Vinyl chlorides, although less reactive, will also react with positive species at the end carbon (C-1)

Take home message: alkenes attached to an atom with a lone pair such as O, N, Cl, S, etc. (often called  ”heteroatoms“) have an important resonance form with a negative charge adjacent to the carbon-atom bond. 

So what does it matter? Although it deserves a post of its own, the concept of π donation is probably the most important application of resonance you learn in Org 2. It influences everything covered in that course: reactions of aromatic rings, reactions of dienes, and especially reactions of carbonyl compounds.

Here’s the key point of this post.

This will have tremendous consequences for chemical reactivity, which will be the subject of a later post. For the moment I’ll just leave with a final application of π donation. And a  question.

For which of these molecules do you think π donation is going to be the most important? That is, what types of atoms would be more likely to  to give away their lone pairs to form π bonds?

Hint: it has something to do with electronegativity. [Note 1]

In the next (and for now hopefully last ) post on resonance concepts, I’ll talk about the opposite of π donation: π accepting.

Next Post: Applying Resonance (2): Pi Acceptors

[Note 1] Across a row, π donation is inversely related to electronegativity. However caution is advised when using electronegativity to compare π donation when going down the periodic table – other effects, such as orbital overlap, also come into play.