How to draw mechanisms in organic chemistry

I’m going to assume here that you’re learning about organic chemistry for the first time.  I also know your friends have told you that organic chemistry is harder than riding a rabid whale across the Atlantic Ocean during a hurricane.  They’ve probably told you that organic chemistry involves a lot of memorization and whatnot, which is why they’re on that whale in the first place.

MobyDickFinal

Don’t quit, ye scurvy dogs! Our chem 110 exam is tomorrow and we’ve got to be in Liverpool before then!

However, you may have noticed by the way that “Smooth Jake” walks around your fraternity house in stained underwear that he’s not exactly the sharpest tool in the shed. To your good fortune, organic chemistry isn’t that hard at all.

Dude

Dude. Not cool.

The trick to passing organic chemistry is to not memorize anything.  Instead of committing every possible combination of reagents and products to memory, why not just figure out how they interact with each other?  After all, if you know that one sort of compound always like to do a particular sort of chemistry, you won’t have to memorize all of the specific reactions in which this takes place.

Now that I’ve convinced you that organic chemistry is simple and that all of your friends are idiots, it’s time to learn the secrets of the trade:  Reaction mechanisms.


Before we get started:  Organic Lewis structures

In general chemistry, we usually draw molecules as Lewis structures in which all of the atoms are shown and labeled.  An example of this is the compound isopropanol, which looks like this:

Oxidacao_alcool_secundario

In the world of organic chemistry, however, the molecules we deal with have lots and lots of atoms and it would be a real pain in the butt to draw them all.  As a result, we draw any alkane part of a molecule as a simple line, and only show the specific atoms present in functional groups.  As a result, isopropanol is usually drawn like this:

200px-2-propanol.svg

Where the line above the -OH is shorthand for the stuff in the expanded diagram above.


What’s a reaction mechanism?

A mechanism refers to the series of steps that the reagents undergo during a chemical reaction. Whereas a simple equation tells you what you start with and what you end with, a mechanism is a big drawing that shows you how this process takes place.  If two molecules react in a series of steps, you’ve got to show what happens in each of these steps.

The important thing to remember is that when writing reaction mechanisms, our primary interest is to show what happens to the electrons in each step.  After all, the movement of electrons results in the formation and breaking of bonds, and since chemical reactions are based on the formation and breaking of bonds, it’s important to know where these electrons go.

We show the movement of electrons with arrows.  A double-headed arrow (a normal arrow, in other words) shows that two electrons are moving, while a single headed arrow (it looks like a fishhook) shows that only one electron is moving.  It’s far more common to see two electrons moving at once, as molecules with unpaired electrons (known as “free radicals”) are extremely unstable and not as common.  Unless you know that a reaction involves free radicals, it’s best to stay away from them.


Nucleophiles and electrophiles

If you look back to the stuff I talked about regarding Lewis acids and bases, you’ll remember that a Lewis acid is something that accepts electrons and a Lewis base is something that donates electrons. For example, when ammonia reacts with hydrochloric acid, ammonia acts as a Lewis base and hydrochloric acid acts as a Lewis acid:

NH₃ + HCl → NH₄Cl

While a nice equation, it doesn’t really show what’s going on.  Let’s take a look what happens in mechanism form:

NH3+HCl

As you can see here, there’s more going on than you thought.  The lone pair of electrons on ammonia is shown pointing to the H on hydrochloric acid, which means that a bond is formed between N and H.  Likewise, the bonding electrons between H and Cl move to Cl, giving it a net negative charge.

It’s because of this that we say ammonia is a Lewis base – it donates its lone pairs to HCl to form the N-H bond.  It’s also said to be a “nucleophile”, because it likes to grab on to other atoms.

Likewise, H-Cl accepts the electrons from ammonia, which means it’s a Lewis base.  As the term “electrophile” literally means “electron-loving”, you can see why we refer to it as an electrophile.

When dealing with reaction mechanisms, the main thing to remember is that it usually involves nucleophiles grabbing onto electrophiles.  This is frequently followed by a subsequent arrangement of electrons so that everybody is happy according to the octet rule.  Some mechanisms don’t involve nucleophile-electrophile interactions (specifically, reactions in which molecules fall apart on their own), but that’s less common.


Reaction mechanism rules

A key thing to remember about reaction mechanisms is that they’re supposed to make your life easy. Sure, you can get through organic chemistry by memorizing every mechanism, but you can get through it with much less suffering by simply remembering a set of rules that generally describes how various compounds tend to combine with one another.  I’m not going to pretend that these rules describe everything, but remembering them does tend to make things simpler.

The rules:

  • “R” groups can be ignored.  Any R you see just refers to the fact that there’s something present at that location, but it isn’t involved in the reaction and can be ignored.*
  • In order for a bond to form, a two-headed arrow (representing two electrons) must move from one atom to another.  This usually takes place when a lone pair from one jumps toward the other (as seen above).
  • Lone pairs act as nucleophiles (i.e. they reach out and combine with other stuff).  Nitrogen is a very common nucleophile, as are anions of just about any variety.  ammonia as nucleophile
  • Cations and atoms with double bonds act as electrophiles.  If you’re doing some reaction mechanism and a C=O bond is present, you can usually depend on an electrophile attacking carbon at one time or another.  This can also be seen in the above diagram, where the C=O bond in the ketone is attacked by the lone pairs in ammonia.
  • Electronegativity can help you figure out where the electrons move.  It’s not very common for a lone pair on a halogen ion to act as a nucleophile because halogens are highly electronegative and want electrons.  This isn’t to say that this never happens for electronegative atoms (especially in the case where water combines with something), but it’s not very common.
  • In a good mechanism, you need to show where all of the atoms start from and where they end up. If you’ve got something ejected from a molecule, you have to show what it looks like when it’s gone. In the diagram below, all of the atoms and electrons are still present – just in a different order.F-ejected-from-fluoromethane
  • Mechanisms frequently include a number of steps.  In any mechanism it’s expected that you’ll explicitly show everything that happens in a reaction.  This means that for multistep reactions, you’ve got to show diagrams for every bond broken and formed.  In some cases you may have a lot of steps – don’t worry about this, as the world usually isn’t as simple as you were led to believe in general chemistry.
  • Intermediates (i.e. the things that are formed in one step and used up in another) don’t need to be particularly stable.  An unstable intermediate may not be very stable, but if you’ve got quadrillions of reagent molecules combining with one another, it’ll probably be formed.  Note: If you make something that’s impossible to form at all, it’s not a valid intermediate.

The biggest rule of all:  Carbon cannot have five bonds!  This may seem obvious to you, but I can guarantee that, at some point, you’ll write a mechanism in which carbon has five bonds, resulting in open mockery by your professor.  Don’t worry about it – everybody makes this mistake at least once when learning organic chemistry.

Additional resources:

  • Leah Fisch (YouTube):  The page I’ve linked to describes the reaction mechanisms for a lot of different processes, going step-by-step to understand them.  Very well done.
  • Learn 8 Organic Mechanisms at Once, Master Organic Chemistry (YouTube):  The video assumes you know the basics of organic mechanisms, but he does a great job of showing how understanding one mechanism can be generalized to eight different reactions.  This is why you don’t have to memorize every mechanism!

Footnote (*):

The “R” actually stands for “radical”, which is an older term used to describe functional groups in general.  This is much less commonly-used than it used to be, because of the prevalence of the term “free radical”, which refers to unpaired electrons.

Image credits:

 

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