25 June 2013

7 Factors that stabilize negative charge in organic chemistry

It’s good – but not enough – to recognize partial charges and to figure out where they interact.

Since reactions involve processes that lead to the gain or loss of charges, understanding the factors that stabilize (or destabilize) charge have a tremendous impact on how likely a reaction is given to occur! Let’s talk about negative charge today.

Let’s talk about a concrete example. For instance if a reaction leads to the formation of a very unstable negative charge, it’s unlikely to occur. But if it leads to the loss of a very unstable negative charge, it’s considerably more likely.

For instance, that’s why one of these reactions of methane is likely and the other is unlikely. That’s going to be explored in more detail in future posts.

So what factors lead to the stabilization of negative charge? Two main things.

negative charge is stabilized by adjacent positive charge (opposite charges attract!)
negative charge tends to be less stable when it’s concentrated and more stable when it’s dispersed.

Think about that as you look at this list of seven factors that stabilize negative charge.

1. High charge densities are unstable

This one’s fairly straightforward to understand. High charge densities are unstable. So as we move from water to OH(-) to O(2-), we are getting progressively more unstable here.

2. Electronegativity

Electronegativity is a rough measure how effectively the positively charged nucleus of an atom can “pull” electrons toward it. (Opposite charges attract.) Electronegativity increases as we go across the periodic table. So if you compare the anions going from C , N, O to F across the periodic table, the stability of the negative charge will increase.

3. Polarizability

Down the periodic table, it’s a little more helpful to think “dispersal of charge is good!” rather than “opposite charges attract”. Compare fluorine and iodine. The size of the fluorine ion (radius: 119 pm) is much smaller than iodine (radius: 206 pm). However, they both have a charge of negative 1.

Imagine two balls, each weighing one pound. But one is made of iron, and the other is made of rubber. Which ball is going to be smaller? The iron ball (smaller and harder) is like fluorine, and the rubber ball (larger and squishier) is like iodine. And a certain “squishiness” helps to stabilize charge, since it isn’t as concentrated over a small volume. That’s a way of expressing the greater polarisability of iodine.

4. Resonance

Along the same lines, a negative charge that is adjacent to one or more Pi bonds can disperse its negative charge over multiple atoms. We describe this phenomenon as “resonance”. So in the example below, the negatively charged alkane on the left is much less stable than the adjacent negatively charged species, where the negative charge can be dispersed over multiple carbons through resonance.

5. Electron withdrawing groups.

This one falls more into the auspices of “opposite charges attract”. A negative charge that is adjacent to an atom with electron withdrawing groups on it will be stabilized greater than one that is not. In the extreme case of CCl3(-), the resulting ion is many orders of magnitude more stable than H3C(-) itself. (This is the basis of the haloform reaction).

6. Orbitals.

s orbitals are closer to the nucleus than p orbitals are. So electrons that are in s orbitals will be closer to the nucleus than electrons in p orbitals – and therefore, lower energy (“opposite charges attract”). For this reason, electrons that are in sp orbitals are lower energy than sp2, which is lower energy than sp3, since they have greater s character (33% for sp2) than sp3 (25%). This makes the anions more stable.

7. Aromaticity.

This is a special case, covered in detail in organic chemistry 2. Certain molecules possess a special stability – called aromaticity – that is enormously stabilizing, kind of like qualifying for an huge tax break from the government. Certain negatively charged molecules – such as the cyclopentadienyl anion, pictured below – are aromatic, and therefore possess much greater stability than they would have otherwise.

So how the heck do we keep track of all of this?

Seven factors?!!! So how do we know which is most important? That’s a great question! These trends can interact with each other in unpredictable ways, and it’s hard to judge which is most important.

Thankfully, there’s a concept you’ve probably already met for figuring out the stability of these species, which can be readily measured. It’s called basicity. These factors determine how stable a base will be!

The basicity of a species tells you about how stable its lone pair of electrons are.

How do we find a good measure of basicity? Simple. It’s in the Pka table , a collection of measurements that’s been compared to the table of hand strengths in poker.

Bottom line:

Two factors to watch out for: opposite charges attract, and dispersal of charge.
unstable anions will tend to be at the intial tails of arrows (form bonds).
stable anions will tend to be at the final heads of arrows (likely to be leaving groups)

Common Mistakes: How not to draw resonance curved arrows

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 arrowsThere are only three legal arroe 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 beaccurately 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:

The 8 Types of Arrows In Organic Chemistry, Explained

To my knowledge there are 8 different types of arrows you meet in organic chemistry. Here’s a little guide to them.

1. The forward arrow, otherwise known as the “reaction arrow”. The purpose of this arrow is to show action. Now, “BH3, then NaOH/H2O2″ might not exactly seem like your idea of “action”, but put yourself in the alkene’s position – it’s double bond is being ripped asunder in order to form new bonds to boron and hydrogen, and then with the addition of H2O2, the bond to boron is replaced with one to oxygen. That’s a pretty eventful day in the life of an alkene.

There isn’t any hard and fast rule about what is supposed to go above or below the arrow, although reagents tend to go above and solvents tend to go below. You’ll often see a sequence of reactions placed over the arrow and numbered “1) , 2), 3), etc. These represent individual steps that could often be shown with individual arrows of their own, but they are placed in series here over the arrow to save space.

2. The Equilibrium arrow. This shows a reaction that is reversible, usually in the context where the reversibility is being highlighted (such as in a reaction mechanism). To further highlight the position of an equilibrium, you may also occasionally see one of the arrows being longer than the other, showing that the equilibrium favors the starting materials or products.

3. The Resonance arrow. Not to be confused with the equilibrium arrow, this double-headed arrow shows two (or more) species that are resonance structures of each other. That is to saythey differ in the arrangements of their electrons and nothing else. Although it’s a separate discussion, it’s important to note that the molecule *does not* shuffle back and forth between these forms, but instead the “true picture” of the molecule is a combination or hybrid of these structures.

4. The Dashed Arrow. This is often used to show a speculative or theoretical transformation, where conditions might have yet to be discovered. Alternatively in a test situation it’s a way of visually depicting the question, “How would you do this?”

5. The Curved Arrow (double headed). The curved arrow formalism is such an important tool that entire books have been devoted to it (for instance, I highly recommend checking out “Arrow Pushing in Organic Chemistry” by Daniel Levy). The point of the curved, double-headed arrow is to show the movement of an electron pair. They start at the tail and end up at the head. Hugely important for following how mechanisms work. Deserving of a series of posts in itself.

6. The Curved Arrow (single headed). The single-headed (or “single-barbed”) arrow depicts the movement of a single electron. Useful in discussions of radical chemistry mechanisms in particular. Identical in all other respects to the double-headed arrow.

7. The Broken Arrow. This is used to show reactions that don’t work: fluorine is a bad leaving group in nucleophilic substitutions, for example. And quinine can definitely not be synthesized from the oxidation of aniline.

8. The Retrosynthesis Arrow. The open arrow here doesn’t actually show a “reaction”, per se, but instead more of a mental exercise. The retrosynthetic arrow is meant to depict the process of breaking down a complex molecule to simpler starting materials. This is useful as a planning device to highlight a key strategy used for building a molecule.

Curved Arrows and Addition Reactions

Not only can lone pairs act as nucleophiles…. but π bonds can too! Alkenes are a lot more exciting than they’re often given credit for. That means that given a sufficiently frisky electrophile, they can donate their pair of π electrons to form a new sigma bond.

Like this!

However, there’s one little problem here. See that curved arrow? What does it really mean? If you weren’t given the product, would you be able to draw it, given that curved arrow?

See the problem here: Which atom of the alkene is actually forming the bond to hydrogen? When we were dealing with lone pairs, it was easy: atoms clearly “own” their lone pairs, and we can tell exactly which atom is forming a bond to which. With alkenes, it’s different: since they “share” that pair of electrons, we’re going to have to somehow show which atom gets the new atom and which is left behind as a carbocation.

Here’s the conventional way it’s done. If we want to show the bottom carbon forming the bond, the usual way to do this is to draw this loop like this, to show the “path” of the electrons coming in an arc from this direction. The carbon on the alkene “closest” to the hydrogen is the one that ends up bonded to it.

Similarly, if we wanted to show the left carbon forming the bond, we’d “arc” the bond like this:

One problem with this: it’s kind of a kludge. The curved arrow notation is limited in that all we can really do is decide where the tail should go (at the π bond, obviously) and where the head should go (to form the new bond). But the question of which carbon forms the bond is still ambiguous.

And if there’s one thing organic chemists hate, it’s ambiguity.

Give me clear definitions or give me death!

To try and deal with this issue, organic chemists have come up with two potential solutions. They’re worth looking at if you’re finding this issue confusing.

Modified Curved Arrow Convention #1: “Bouncy” Arrows.

Instead of showing the curved arrow as a big sweeping arc, one solution is to put an extra bounce into the arrow. The idea here is that we’re showing the pair of electrons travelling to the carbon in question, and from there moving on to form the new sigma bond. No more ambiguity here. [Literature reference]

This solves the ambiguity problem at the expense of putting in an extra hump in the arrow. Although it doesn’t seem like a big deal, the extra bounce has likely been the reason why this convention hasn’t taken off. However well intentioned, the trouble with a convention like this is humanity’s natural tendency towards laziness: taking the time to consistently draw an extra hump into the arrow – even if it takes only 5 seconds – represents extra work that is skipped unless absolutely necessary. Behavioral change is very difficult.

Modified Curved Arrow Convention #2: “Pre-bonds”.

Another way of dealing with this is to insert the equivalent of “training wheels” into our curved arrows. Since the curved arrow is itself ambiguous, to clarify things we put in a dashed line that precisely delineates where the new bond is forming. Then, we draw the arrow with the tail comingfrom the electron source (the π bond) and the head going to the new bond. We can put the arrow right on the dashed line itself. This has the advantage of not modifying the curved arrow convention itself, just adding in an optional “guide” that makes its application more clear. [For an application of this technique I recommend checking out Dr. Peter Wepplo's blog, where I first found this convention used]

If you find yourself confused following the movement of electrons in the reactions of alkenes with electrophiles, these supplementary conventions might be of use to you.

Markovnikov’s Rule (2) – Why It Works

Understanding Why Markovnikov’s Rule Works

Let’s assemble all the facts we know about the reactions of alkenes with an acid like HCl so far.

Regio chemistry: as we saw in the last post, reactions of alkenes with acids like HCl followMarkownikoff's rule: the major product formed is that where the hydrogen adds to the carbon containing the most hydrogens.

Stereochemistry: as we saw in the stereochemistry, this reaction provides a mixture of “syn” and “anti” products (when the reactant makes this possible).

Rearrangements. The last post briefly touched on another issue. In some cases, the reaction of alkenes with acids like HCl can lead to rearrangements such as hydride shifts or alkyl shifts.

So how does this reaction work? Any mechanism we propose would have to be consistent with all of these facts.

Furthermore, we need to think about this reaction in terms of what we already know about electron flow. Electrons flow from areas of high electron density (“electron rich”, or “nucleophilic” areas) to areas of low electron density (“electron poor” or “electrophilic” areas). Remember how electrons are polarized in a molecule like H-Br ? Hydrogen is less electronegative, and therefore more electron poor. Bromine is more electronegative and therefore more electron rich. In an alkene, the relevant electrons we will consider are in the π bond, which form a kind of “π electron cloud” above and below the plane of the alkene.

Here’s the best hypothesis we have on how this reaction works so far.

In this reaction, electrons flow from the electron-rich carbon-carbon π bond to the electron poor hydrogen. [Step 1, arrow A] leading to breakage of the H-Cl bond (arrow B). [Recall that this isn't such a bad state of affairs for Cl- as it is a weak base and therefore a good leaving group]. This forms an intermediate carbocation, which is then attacked by the chloride ion (Step 3, arrow C) leading to formation of the alkyl halide.

Why does this hypothesis fit with the data?

Regioselectivity. As we saw in the last post, reactions of alkenes with acids like HCl follow Markovnikov’s rule: the major product formed is that where the hydrogen adds to the carbon containing the most hydrogens. This is consistent with the carbocation model, since carbocation stability increases as hydrogens are replaced with carbons.

Stereochemistry. The observation of syn and anti products is also consistent with a carbocation intermediate. The second step of the reaction involves attack of the nucleophile (Cl- in this case) upon the empty p orbital of a free carbocation. Since this can occur from either direction (“top” or “bottom” faces of the carbocation) we should expect a mixture of syn and anti products here. And that’s what we see:

Note that in the above reaction, the two faces of this carbocation are not precisely equal. The bottom face is shielded by the methyl group adjacent to the carbocation, which occupies more space than the corresponding hydrogen on the top face. Therefore we should expect (and in fact do observe) more of the syn product relative to the anti product. However, both products are still observed.

Rearrangements. Rearrangements can occur in situations where a hydride or alkyl shift can lead to a more stable carbocation. More on this in a subsequent post (this is getting long) but for similar examples, see the posts on rearrangements in substitution and elimination reactions.

A Reformulation of Markovnikov’s Rule

With these facts in mind, and having proposed this new hypothesis, we can now propose arephrasing of Markovnikov’s rule. In its previous incarnation, Markovnikov’s rule sounds pretty arbitrary (H adds to the carbon with the most hydrogens? Why?). In this rephrasing, we can say exactly why these reactions proceed this way.

In the reaction of alkenes with hydrogen halides, the reaction will proceed through the most stable carbocation.

As we’ll see this will not only apply to the reaction of alkenes with hydrogen halides but also with acid in the presence of other nucleophiles (like water and alcohols).

One last note. If you look above, for the first time we’re using the arrow pushing formalism to show electrons flowing from a π bond to form a new sigma bond. In other words, it’s acting as a nucleophile! This arrow might look a little weird.

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25 June 2013

7 Factors that stabilize negative charge in organic chemistry

Common Mistakes: How not to draw resonance curved arrows

The 8 Types of Arrows In Organic Chemistry, Explained

Curved Arrows and Addition Reactions

Markovnikov’s Rule (2) – Why It Works

20 June 2013

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Organic chemistry multiple choice questions with answers

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