Leah here from leah4sci.com and in this video series we're going to look at the four basic types of organic chemistry mechanisms specifically focusing on the pattern of the reaction arrows. When you first learned reactions, you simply looked at the overview. For example, molecule A reacts with molecule B to give you C plus D. A specific example would be the SN1 reaction.
where 2-butanol is reacted with hydrochloric acid to give us 2-chlorobutane plus H3O+. When you're studying mechanisms, you're looking at exactly what happens every step of the way. How does molecule A react with molecule B?
How is it that we get product C and product D? And more importantly, how would you classify every step along the way? In terms of how the electrons are moving and what they're doing in the attack.
There are four main types of mechanism patterns you'll see in organic chemistry. The nucleophilic attack, loss of leaving group, proton transfer and rearrangement. While each one is a unique pattern, they all have one thing in common, they're looking at how the electrons are moving.
If you're not comfortable with the concept of arrow pushing, review that video first, link in the description, but as a reminder. The arrow in a mechanism is showing us where the electrons are moving. Never protons, never anything else, it's specifically the electrons. And we have two types of arrows, the double headed arrow and the single headed arrow. I like to think of each arrow head telling me how many electrons are moving.
With a double headed arrow, we have a pair of electrons and this is the case for over 90% of the mechanisms you'll see in organic chemistry. The single headed arrow or the fish hook is a lone electron and you'll only see this when you're looking at radical reactions. The tail of the arrow regardless of pair or single tells us where the electrons were and the head of the arrow tells us where the electrons are going.
For example, if I want to show that molecule A with a lone pair of electrons is attacking molecule B, I would show the arrow. as starting from the electrons on A and ending towards the direction of B. This tells me the electrons of A are reaching over to attack and form a bond with B.
Then I show my yield arrow for the final product which is A bound to B where that bond is formed by the two electrons that did the initial attack. You always want to show the electrons that are about to move the arrow in the direction of where they go. where the arrowhead lands on the atom you're attacking, the yield arrow to show what happens as a result and then of course the final result in this case where we have the bond sitting between the two atoms.
Now let's take a look at the individual patterns. I don't want you memorizing these patterns when you're studying organic chemistry, don't memorize the mechanisms. Instead I want you to ask yourself what is going on here?
Why is it happening and what can I take away from this so that I can apply it to every mechanism in the future? In order to understand the nucleophilic attack, we need to explain the nucleophile and electrophile. If you see an unfamiliar word, ask yourself if you recognize something in that word.
In this case, I see the word nucleo which tells me nucleus and phile meaning loving. The nucleus is positive and something that loves the positive will seek it out so we can define a nucleophile or nucleus loving as positive seeking. What type of atom or molecule will seek positive? Opposites attract so we're looking at something negative or partially negative.
The electrophile is the opposite. Electrophile has electro which tells us electron and phile meaning loving. The charge of an electron is negative.
And something that is an electrophile will be negative seeking. What is seeking out an electrophile? Something positive or partially positive. Throughout my videos, you'll see the nucleophile represented as NU with two electrons, which is to remind you that the nucleophile has that lone pair of negative or electronegative electrons that want to do the attack.
An electrophile as E+, to show us that it's positive or partially positive. Now don't mistake seeking as going after because it's never the positive that moves, it's always the electrons so the nucleophile will seek out the electrophile. And that gives us the basics for our first pattern.
A nucleophilic attack is a nucleophile with its lone pair of electrons seeking out a positive or partially positive electrophile to form a new bond. For example, if you are working on a mechanism and you see a secondary carbocation with an iodide in solution, you'll see this intermediate in SN1 reactions or alkene addition reactions. The carbocation is positive that makes it the electrophile.
The iodide is negative which makes it the nucleophile. The pattern for this reaction is the nucleophile taking one of its lone pairs of electrons and attacking the electrophile in this case the positive carbon atom. The electrons start out on the nucleophile, the arrowhead goes towards the electrophile. And that gives us a new bond as follows. The iodine now sits next to that carbon, it still has three blue lone pairs of electrons but it now has a new bond between itself and carbon where the electrons for the new bond came from the lone pair that attacked the carbocation.
Another common type of nucleophilic attack is when you have a carbonyl being attacked at the carbonyl carbon. This molecule is harder to identify as an electrophile because we don't see an obvious positive charge the way we did with the first carbon. However, if you recognize that carbonyls have resonance, you'll find that charge.
The resonance in this case happens where the pi bond between carbon and oxygen will move up towards that oxygen atom so that the pi bond breaks and winds up as a lone pair. Oxygen still has one bond to carbon, but the pi bond It has the initial two lone pairs but that third pair comes from the pi bond that broke. This gives oxygen a formal charge of negative one and carbon a formal charge of positive one. If you're confused with this, make sure you review the video series linked below. The first one on resonance to explain the concept and the second on formal charges to help you understand where the plus and minus came from.
These are both resonance contributors but we can draw the resonance hybrid as carbon, double bound to oxygen with a dotted line representing the bond constantly moving up and down between both forms and that gives me a partial positive charge at the carbon and a partial negative charge at the oxygen. If we look at this molecule again and remember that partial positive charge, we have now identified our electrophile. If we react this with a strong group for example a methylgrineard, the carbon atom electrons that are attached to the Grignard act like a carbanion.
These electrons act like they're sitting on a C minus making them very reactive, making this molecule a nucleophile. We show the mechanism with an arrow starting at the bond between carbon and magnesium. These electrons are just sitting around carbon, don't get confused, this is actually a bond between carbon and magnesium.
We start the arrow here. and then bring them all the way to the partially positive carbonyl carbon, that's our attack. In this case, because carbon would have five bonds we have to show another set of electrons moving. We show the electrons that were already resonating upward being permanently kicked up onto the oxygen.
Draw the yield arrow to show the product and then redraw the skeleton as you see it. In this case we have the green three carbon molecule with a single bond to oxygen, two green lone pairs from the initial lone pairs and a third lone pair from the pi electrons that collapsed upward. But what happened as a result of our nucleophilic attack? It's this methyl group that is now attached to that central carbon atom and the electrons that form that new bond are the very same electrons that did the nucleophilic attack. The second common mechanism pattern is the loss of a leaving group which as the name implies is a leaving group getting lost.
For example, if we have a molecule where a chlorine is bound to a secondary carbon, in this case to chloropropane and chlorine decides it's had enough. There are two electrons forming the bond between carbon and chlorine but chlorine starts yanking on that bond. Remember this is a polar bond. There's an unequal distribution of charge and chlorine being more electronegative is hogging those electrons. It pulls and pulls and pulls until it finally pops off taking the electrons with it and breaking away.
You show the arrow starting at the bond where the electrons are about to break and ending on the atom that will wind up holding those electrons as a lone pair. As a result, the carbon is now missing a chlorine and has a formal charge of plus one. And the chlorine now has four lone pairs of electrons.
The three initial pairs that it had while bound to the molecule, and a fourth pair that came from that bond breaking and settling onto the chlorine atom, giving us chloride with a negative charge. If the leaving group breaks away and it's neutral, the resulting formal charge is minus one. If the leaving group breaks away when it's positive, the resulting charge is zero. When you gain an extra pair of electrons, the charge goes down by 1, so that plus 1 goes down to 0 and 0 goes down to negative 1. You'll see loss of a leaving group in a more advanced reaction when you study nucleophilic substitution on aromatic rings.
If you haven't learned it yet, don't be overwhelmed by what's going on, instead simply pay attention to the leaving group, in this case the chlorine. In this reaction, we're going to have a domino effect of electrons moving for resonance and ultimately kick out the leaving group. We show one of the two oxygens attacking the nitrogen to reform a pi bond.
This causes the electrons between nitrogen and carbon to resonate into the ring which causes the pi bond nearest the leaving group to come directly towards the leaving group which puts too many bonds on the carbon holding the leaving group and kicks out the leaving group. Let's redraw this exactly as we see it showing what has and hasn't changed. The black pi bond on the right hasn't moved.
Nitrogen is now only single bound. to the carbon on the ring. The oxygen on the left hasn't changed so it still has three lone pairs and a negative charge.
The oxygen on the right had three lone pairs and now has only two. It had a single bond and now it has two from these electrons forming a pi bond. On the left of the molecule, these electrons are now sitting as a pi bond in the ring and the electrons on this pi bond which will now show in blue simply moved over one position.
The carbon that initially held the Lima group now has just an OH attached and chlorine which had 3 lone pairs to begin with now has a 4th lone pair and a negative charge thanks to these electrons from the bond that broke and left with the chloride atom so that it's now sitting as 4 lone pairs on chlorine in solution. Be sure to join me in part 2 of this series where we look at proton transfer and rearrangement and then we'll look at this mechanism step by step identifying the arrow patterns for each individual step in the mechanism. You can find this entire series on my website leah4sci.com mechanism.