Helpful Organic Chemistry Downloads

pKa tables are everywhere, and I’m sure your class has one that will you will be expected to use. Every student will benefit immensely if they do the following: 1) learn the pKa values that we use all the time, and 2) know how to actually use the values.

Learning pKa values does include MEMORIZING them. I hate using the word memorize in organic chemistry because of the stigma the course has for being all memorization, but the reality is, this IS a time where you need to memorize. However, just memorizing the numbers without understanding their trends is going to be of limited value. You need to also put into context why some numbers are lower (or higher) than others.

Part of learning the pKa values in learning how to read a pKa table. The handout “Overview of Using pKa Values” includes information that explains how to read a pKa table (along with some drill sets and other information to help solidify the teachings). Too often a student will have a pKa table that says the pKa of methanol is about 16 and then they will show me a problem asking about the pKa of tert-butanol and tell me they don’t see it listed on their pKa table so they cannot figure out how to solve the problem. Don’t let this be you!

Page 1 lists the pKa values that every student should have memorized. These are the values I consider essential knowledge, and you will be encountering them over and over.

Page 2 lists pKa values that you will likely encounter and will benefit by knowing.

Most of the reaction mechanisms you work on will be happening in either acidic or basic conditions, and it will be important for you to know how to tell which is which.

Additionally, when you study SN2, E2, SN1, and E1, you will be using terminology of identifying weak bases and strong bases. WAAAY too many students cannot answer the question, “What is the difference between a weak base and a strong base?” without saying something like, “A slide in lecture listed strong bases as hydroxide, ethoxide, and tert-butoxide while a weak base was water.”

Sure . . . the student has not said anything inaccurate, but they haven’t really proven they know why the strong base is strong and why the weak base is weak. They proved they remembered a slide from lecture. So then when I ask a question like, "Okay, is NaNH2 a strong base?", they can't answer the question because that reagent wasn't listed on the slide.

This one-page handout seeks to make these definitions VERY SIMPLE if you understand pKa values (and pKaH values), and it also helps to see how the general chemistry pH scale of 0-14 relates to what we are doing in organic chemistry.

I literally cannot overemphasize the importance of learning pKa values and then learning how we can apply them to concepts beyond just figuring out which side of an acid-base reaction is favored.

When you study SN2, E2, SN1, and E1 (substitution and elimination), you will need to learn how to tell if a compound is likely to act as a base or as a nucleophile in various situations. Both are electron pair donors (Lewis bases), but bases grab a hydrogen while nucleophiles grab a carbon in these reactions.

Most courses teach substitution and elimination as part of the content for the second exam. This means students see this early in their process, and history has taught me that the way a student approaches learning this component of the course is critical, because it is a strong indicator of how they will approach the rest of the course. 

Most students see the distinctions of evaluating nucleophilicity versus basicity as something to be memorized from the slides they saw in class or charts off the internet, so it begins the process of thinking everything is memorization. The student misses the opportunity (and importance) early in the course to actually UNDERSTAND CONCEPTS versus memorizing some tables. This unfortunately reinforces the idea that the next barrage of information is also something to just memorize rather than to understand, and now the student is well on their way down the Organic Chemistry Highway to Hell.

This handout is on the long side (9 pages), but I promise that you will come away with a clearer picture of how to categorize - and visualize - the differences between nucleophilicity and basicity if you take the time to read and internalize it.

And hopefully, even more importantly, you will understand that we benefit by doing this type of understanding for everything in the course.

Because the more you learn the actual concepts of the stuff presented early in the course, the more likely you are to escape becoming the "memorize mountains of shit" student who doesn't understand anything and ultimately gets overwhelmed and crashes into a fiery demise.

Instead, you'll be the student who finds organic actually gets easier because you learned the tools we use in the front-end of the course, and you'll understand how to apply them to the material taught in the second part of the course.

A key difference between assigning hybridization in organic chemistry versus general chemistry is considering whether a lone pair on an atom can do resonance. If it can, we should not call the atom sp3.

An sp3 atom can never participate in resonance because it lacks the unhybridized p-orbital that is needed for making a pi bond.

This two-page handout aims to illustrate this key awareness.

This one-page handout illustrates the importance of being able to tell what type of orbitals the lone pairs are in and how this influences resonance. It also gives tips on drawing resonance structures and outlines the criteria for determining the major resonance contributor.

The saying “One Atom, One Pi” means that MOST atoms that are able to make a pi bond are able to make only one pi bond, not two. In other words, if an atom is already involved in a pi bond, you probably do not want to try drawing a second pi bond on that atom. 

Of course, an sp hybridized atom can have two pi bonds on it, but you are going to discover that we do not work with a lot of sp hybridized atoms in this course.

When it comes to learning about carbocation stability, most students will be able to quote the party line that the tertiary carbocation is the most stable while the primary is the least stable. However, things begin to fall apart when: (a) they are asked to explain WHY this is true, (b) they are asked to identify what type of carbocation is forming (tertiary, secondary, primary, etc.), and (c) they overlook resonance as being an even more important aspect of carbocation stabilization than the number of substituents spewing out of the carbocation.

This one-page handout outlines the important aspects of carbocation stabilization while also illustrating what hyperconjugation is and why it makes alkyl groups electron donating and therefore stabilizing to the carbocation. Remember, we make a yucky positive charge get smaller (less reactive) by donating electrons towards it.

It is a predictable phenomenon that students will initially struggle with learning how to convert wedge-dash structures into the Newman projection, and vice-versa. This two-page handout aims to break it down into an easy conversion.

The importance of understanding what a meso structure is cannot be overstated. Meso structures are achiral molecules that have chiral centers, and these show up everywhere when students are being tested on stereochemistry.

Many classes spend a few minutes discussing this concept and students often end up not realizing how ubiquitous these things are in the types of exam questions they are going to see. Meso structures are ideal molecules for fooling the noob into mistakenly calling them chiral, or to label them as an enantiomer of a similar looking structure.

The typical thing students learn about meso structures is “they have a plane of symmetry” . . . not going to say this is incorrect, but the reality is most meso structures will not be presented in a conformation where we can immediately see the plane of symmetry. Additionally, many students don't actually know what a plane of symmetry is, so they are trying to identify something they don't know how to recognize.

I recommend students follow the guidance on the handout where you learn to spot what I call “meso potential”, and then know how to do R and S and evaluate the results.

Too often, students make things harder on themselves by trying to memorize the stereochemistry outcomes of every individual reaction they learn as if it is yet another disjointed factoid they need to add to their list of crap to memorize. Those who are doing this are typically not realizing there is a much easier and sensible approach.

Trying to memorize stereochemistry outcomes of individual reactions can be a sign that the student isn’t recognizing a repeating pattern that governs almost every reaction we cover. The goal of this one-page handout is to shed light on the reality that pretty much all the stereochemistry outcomes are following a predictable pattern if you understand the difference between bonding to an sp2 atom verses bonding to an sp3 atom.

I am a firm believer that students will learn organic chemistry reactions with better retention if they understand the repeating mechanistic steps of the reactions. Understanding the mechanisms will automatically fill in the knowledge that too many students think they need to memorize in a disjointed manner.

Alkene additions are usually some of the first reactions students are exposed to where they start making flashcards and sheets similar to the handout I have for you. These tools are meant to organize and centralize information and then make it easier to learn. However, if you just try memorizing the information without recognizing the sensibility of repeating behaviors, you are putting yourself at high risk of becoming the student who falls apart on exams.

My document is color coded to group together reactions that are following the same mechanistic pathway. So for example, the first 3 listed in that pink/salmon color will be seen by most students as 3 separate reactions that need to be memorized individually, but I would say that is really only one mechanism pathway that finishes with different nucleophiles bonding to the carbocation, and it is these different nucleophiles that end up creating different functional groups in the end.

In other words, the first 3 are the result of an alkene meeting a strong acid (strong acid is defined as pKa less than zero), a carbocation is formed, then ultimately the carbocation is closed by having a nucleophile attaching to it. That nucleophile can vary depending on what we add, and this is how we can have multiple options for what functional group is created.

Reactions in blue are all making a triangle intermediate – we get that when the alkene (acting as the donor) reaches for an atom that contains a non-bonded lone pair. That lone pair can beam back to form the triangle intermediate which allows us to sidestep the carbocation that would form if the alkene were instead grabbing an acidic hydrogen (hydrogen has no lone pair available to beam down). Sidestepping the carbocation means avoiding the unfilled octet.

I'm pointing these out as quick examples to illustrate why looking for repeating concepts in our mechanisms helps us make sense of these reactions and learn them faster.

When it comes to learning about substitutions and eliminations, the E2 reaction has the most nuance that needs to be learned. One of the quintessential characteristics of this reaction is the requirement that the leaving group and the next-door neighbor hydrogen (also called the beta hydrogen) be anti-periplanar to each other for the orbitals to align correctly to make the reaction possible. This anti-periplanar alignment is the exact same orientation we discuss when we say two groups are anti on a staggered Newman projection.

ALL schools love to heavily test E2 on cyclohexane because it combines crucial understandings of E2 along with the fun of the axial and equatorials in the cyclohexane chair flip. This one-page handout outlines two rules that we all need to learn regarding the requirements of making an alkene form via the E2 reaction between two carbons of a cyclohexane.

The goal here is to make it obvious when we can and cannot do E2 WITHOUT having to go through the work of drawing out actual chair structures and doing their flips.