A guide to organic chemistry mechanisms

academics organic chemistry premed
By Gift

The dreaded weed-out class. A pre-med’s worst nightmare. Students often approach organic chemistry with apprehension, and a particularly sore spot in the class is mechanisms. Arrows, electrons, charges, and structures all drawn out like a map. Now, make that 10 maps – or 20! What’s a pre-med to do? 

A student once said to me, “I have to memorize all of these?”

While it may seem like memorization is the only option, organic chemistry mechanisms can become quite intuitive if you follow 3 rules:

1. IDENTIFY NUCLEOPHILES AND ELECTROPHILES

Mechanisms are used to show the process of chemical synthesis! Instead of being in the lab, you’re forming new molecules on paper. A big part of this is understanding the motion of electrons: which electrons are attacking, stealing, or leaving. 

Identifying nucleophiles and electrophiles and/or atoms with nucleophilic or electrophilic properties is the key to understanding which electrons are acting and how they’re acting. 

Brush up on these definitions. Remember that nucleophiles (electron abundant and where your arrow starts) often attack other compounds and atoms with nucleophilic properties like to steal protons. Electrophiles (electron poor and where your arrow sinks) often receive electrons and atoms with electrophilic properties like to accept bonds. 

2. AVOID MIXED MEDIA ERRORS

What does that even mean? Simply put, if you’re in base, avoid forming acids. If you’re in acid, avoid forming bases.

An easy way to implement this is to identify your solution early on. Then, if you’re in an acidic solution or using an acidic workup, you should only ever have neutral or positive species in your mechanism. If you’re in a basic solution or using a basic workup, you should only ever have neutral or negative species in your mechanism. Any crossover is volatile IRL and is an immediate red flag to any TA or professor grading your work. 

Watch those charges! 

3. MOVE FORWARD 

Often, not following this seemingly simple rule is the reason many students find themselves going in circles on their mechanism sheets. 

If you’ve just added a proton to your main compound in the previous step, make sure you don’t remove that proton in the next step - you’re undoing all of your hard work. Similarly, if you’ve just made a bond, don’t break that same bond.

You should always move forward in mechanisms. 

Hint: This is aided by a strong understanding of what your end-product should look like. If you can start a mechanism by drawing out what your product should look like (something you can memorize), you’re halfway there. At each step, just check to make sure that you’re one step closer to that final product. 

Gift graduated with a 4.0/4.0 GPA from the University of Texas at Austin, where she majored in Honors Biology and obtained a certificate in creative writing. Toting a Dean’s Distinction in research and multiple recognitions in academics, Gift is now an MD candidate at Columbia University Vagelos College of Physicians and Surgeons.

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