How Concepts Build Up In Org 1 (The Pyramid)

How Org 1 Builds Up (the Hierarchy of Concepts)

One comes into organic chemistry from an introductory course in general chemistry.
Starting out, its assumed you have a basic knowledge of chemical bonding, the octet rule,
VSEPR (geometry), equilibria, acids and bases, thermodynamics and so on.
Concepts build from this base. Ive made a few completely arbitrary levels to describe how
concepts progress from there. The general idea is that every level depends on concepts from
the levels below it. I wouldnt take these levels too seriously, but they might be helpful to
group together certain concepts and see how they build on each other.
Level 1 Bonding and Geometry. The first week or two of organic chemistry goes over the
key concepts of bonding from general chemistry, and
introduces hybridization, bonding (sigma and pi), dipoles,
molecular geometry, molecular orbitals, and other notions like condensed formulae. In
other words, we show how atoms bond together to form small molecules like NH3, H2O, CH4,
and so on.
Level 2 With the Level 1 concepts under our belt, we can now start to think about electron
density and electron flow. We can describe functional groups, examine their dipoles
(unequal sharing of electrons) and learn about the intermolecular forces responsible for
physical properties like boiling points. We also learn about resonance (delocalization of
electrons), and introduce the use of curved arrows to show electron flow. We can also use
the tool of curved arrows to show simple chemical reactions such as acid-base reactions,
and our lessons on electron flow help us understand the factors that influence acidity.
Level 3 Building on Level 1 concepts like bonding and geometry, we can start to examine
slightly larger molecules, and start with the simplest functional group (if you want to call it
that) alkanes. Importantly, line diagrams are introduced to show the structure of alkanes,
and we learn about structural isomers, the energies of different molecular shapes
(conformations) and the properties of cycloalkanes. Reactions are generally limited
to free-radical halogenation of alkanes (alkyl halides are important for

substitution/elimination in Level 5). The structure, bonding and geometry of alkenes (but not
their reactions) is often covered at this point as well.
These (arbitrary) levels 2 and 3 are actually pretty interchangeable in terms of the order in
which theyre covered. I chose to put electron flow on the bottom because the
conformations/cycloalkanes/alkanes chapters flow naturally into stereochemistry geometric
isomers (e.g. cis/trans isomers in cycloalkanes and alkenes) being the prime example.
Level 4- Now comes the chapter on stereochemistry, which is, in my opinion, the key
theme of Org 1, since so many of the reactions learned in subsequent chapters will use the
concepts introduced here. Here, the consequences of the three-dimensional nature of organic
molecules are first demonstrated, and we learn about stereoisomers. Seeing molecules in 3
dimensions from their depiction on a 2-dimensional page is a struggle for many introductory
students. If you start struggling here as many do get help now, because if you
wait, it might be too late.
Level 5 Three key classes of reactions are covered at this level reactions of alkenes,
nucleophilic substitution, and elimination. The order in which these topics are covered
varies considerably from course to course.
This is really the wax on, wax off moment where youll be asked to put together all the
concepts youve learned previously and apply them!
This is also where many students start to really struggle!
Why? Three reasons.
1.

ALL the concepts in the previous levels will be applied here. Its the point where you
finally start to stitch together the somewhat disconnected previous chapters into a
coherent whole. To take a specific example, truly mastering the chapter on nucleophilic
substitution reactions will require that you be able to apply an understanding of
stereochemistry, conformations, cycloalkanes, resonance, curved arrows, and acids/bases
to various types of problems, in addition to the bedrock material on chemical bonding.

2.

There are a lot of reactions presented in rapid sequence and its very easy to fall
behind.

3.

This is about 6 weeks into the course, a time where you will likely have many other
obligations (midterms in other courses, lab reports, etc). So this is the real squeeze point.

All of these combine to provide a perfect storm that leads many to drop the course at this
point.
Level 6 More reactions. Alkynes are covered after alkenes, and many important reactions of
alcohols are of the substitution/elimination variety.
There are two common sequences alkene->alkyne then substitution/elim, or
substitution/elim then alkene->alkyne.

Alkynes are a blank canvas they can be transformed into essentially any functional group
we choose. Once reactions of alkynes are covered, youll start to notice youll get an
increasing number of synthesis questions. Synthesis is the art of planning how to build a
target molecule from starting materials using a sequence of reactions, and success will
require you to master ALL of the skills you gain in levels 1-5, most importantly knowledge of
the reactions and their stereochemistry.
Alcohols are a wild card. The chapter on alcohols contains many substitution and elimination
reactions, and furthermore includes reactions of epoxides (generally built from alkenes).
Because Org 1 covers so much ground, alcohols are often pushed back to Org 2, but they
really belong in Org 1.
Another wild card is Spectroscopy the main tool we use to determine the structures of
molecules. This needs to get covered somewhere, so its usually shoved near the end of Org 1
or the beginning of Org 2. Alternatively some instructors stagger it out through the courses of
Org 1 and Org 2. Lots of variation on this point.
How Concepts Build Up In Org 2
OK. Having looked at the Org 1 Concept Map, lets ask the next logical question: what does a
typical Org 2 course look like?
One general observation: the way functional groups are covered in your typical two-semester
organic chemistry course generally follows the oxidation ladder. Look at the progression:
alkanes (low oxidation state) first, then alkyl halides, alkenes, alcohols (medium oxidation
state), then ketones, aldehydes, and carboxylic acid derivatives (higher oxidation state).
[Amines break this pattern theyre usually covered near the end, but for reasons Ill describe
at the bottom its probably best that amines arent covered in Org 1. ]
Org 1 is largely about sp3 hybridized (i.e. tetrahedral) carbon. We learn about bonding,
geometry, conformations, -> stereochemistry < (notice the subtle highlighting) and
reactions of sp3hybridized carbon. Even when we cover the reactions of sp and sp 2 hybridized
carbon (i.e. alkenes and alkynes) we are largely focusing on the sp 3-hydbridized products
obtained, and describing their regiochemistry and stereochemistry.
Org 2 once you get the unit on alcohols out of the way is largely about sp 2 hybridized
carbon. Stereochemistry, which was such an integral part of org 1, does not play as important
a role. Nor does conformational analysis you likely wont be seeing many Newman
projections or even cyclohexane chairs! Instead, the common thread that runs through the
key chapters can be described as -systems, molecular orbital theory, or, perhaps more
crudely resonance. Another key difference is that Org 2 isnt as blatantly conceptual. Unlike
Org 1, which is maybe 50% conceptual chapters and 50% chapters on reactions, Org 2 is
pretty much all reactions.There are really only two fundamental new concepts introduced
aromaticity and orbital symmetry. [Note that Im not counting spectroscopy here, which is
usually wedged in somewhere either at the end of Org 1 or the beginning of Org 2]. If Org 1
is Star Wars: A New Hope, which begins slowly and has to introduce all the main
characters, Org 2 is The Empire Strikes Back: action, action, action from
beginning to end.

Org 2 truly begins with a chapter on -systems (i.e. conjugation). This chapter covers bonding in molecules where there are more than two adjacent p orbitals dienes, allylic
systems and explores how the molecular orbitals build up. An understanding of molecular
orbital theory is essential to be able to grasp the key reactions of aromatic systems, pericyclic
reactions, and carboxylic acid derivatives, so this chapter is truly the bedrock of Org 2.
Instead of building up like a pyramid, like Org 1 does, I tend to see Org 2 as proceeding along
three main forks, with a somewhat disconnected section on biomolecules at the end.
The three forks are:

Aromaticity and reactions of aromatics

Pericyclic reactions and orbital symmetry

Carbonyl derivatives

Heres my map of what I think it looks like:

Fork 1: Aromaticity
From molecular orbital theory the course can then progress to an introduction of aromaticity
( a new fundamental concept describing why certain unsaturated cyclic compounds are
unusually stable) and then the reactions of aromatic derivatives. This is a good arena to reintroduce multi-step synthesis, as the substituents on aromatic rings have a great deal of

influence on their reactivity. These lessons will be useful when the course turns to carbonyl
chemistry, where synthesis will require a lot of detailed planning.
Fork 2: Pericyclic Reactions
The Diels Alder reaction of dienes is a fundamentally different type of reaction from those that
have been encountered before in the course, and a grasp of molecular orbital theory is
necessary to understand 1) why it works the way it does, and 2) how it gives rise to different
patterns of regioselectivity and stereoselectivity. Time permitting, the course can also go into
further reactions in the same family, including electrocyclic ring opening/closing, the Cope
rearrangement, and others.
Fork 3: Carbonyls, Carboxylic Acid derivatives, Enolates (main sequence).
The third and largest thrust proceeds from the chapter on alcohols through aldehydes,
ketones, esters, carboxylic acids, and the reactions of their enolates. Molecular orbital
theory isnt as key here as for aromaticity or orbital symmetry, but can certainly help when
understanding the reactivity of different carboxylic acid derivatives. [E.g. why are esters
cleaved more easily by nucleophiles than amides?]
Amines and Biomolecules
From the chapter on enolates the course then usually proceeds through amines a mish mash
of many different reaction types encountered throughout Org 1 and Org 2 and then ends
with a few units on biomolecules, including carbohydrates, amino acids, and (sometimes)
nucleic acids/terpenes/fatty acids. The good news is that these latter chapters are relatively
self-contained. Be forewarned that the chapter on carbohydrates includes a lot of reactions
and nomenclature that only get used within a very narrow context.
So what makes Org 2 so difficult?
Its really no secret. The pace at which new reactions are introduced makes Org 2 a
very challenging course. And its not merely a matter of volume, either there are network
effects too. As the course progresses, so does the complexity of synthesis problems which
will ask you to bring your knowledge of these reactions to bear on describing reaction
sequences that will build up complex molecules from simpler precursors. Reactions from Org 1
(such as nucleophilic substitution) are not excluded, by the way.
A sub-problem in the lots of new reactions category is that unless you put in a lot of time
working problems, many of the reactions will look very similar (especially with carbonyls). Its
common to get the feeling that theres some deeper patterns and organization but you cant
quite put your finger on it. Finding time to put it all together in your head is hard, especially
with things moving so fast its can be like trying to play Jenga in the back of a racecar.
Lets conclude. So whats the point of all of this, anyway?
In my view, the real jewel of organic chemistry 2 is the skill of synthesis. By the end of Org 2,
youve toured all the major functional groups, and should be able to take a simple small-

molecule target with a functional group or two and be able to figure out a sequence of
reactions that will build it from smaller building blocks. This requires learning a tremendous
amount of new material and concepts, putting them all together in your head, and then being
able to apply this knowledge to solve problems. It takes a lot of work and a lot of time to get
right but its an extremely powerful feeling. For me, it was a feeling of being on a
mountaintop after a tremendous amount of slogging in the weeds. Putting everything
together to make a coherent whole, and then realizing, oh geez, weve really only scratched
the surface here. Theres a reason why people make the study of organic chemistry their
lifes work its extremely deep.
P.S. Where does Org 2 end and Org 3 begin? Id say its when we start having to deal
withmultiple functional groups in the same molecule that can potentially react. From Org 3
onwards, we really start to focus on the issue of selectivity: selectivity between functional
groups (chemoselectivity), selectivity for synthesis of various stereoisomers
(stereoselective synthesis), and designing the synthesis of ever more complex molecules
from an ever-growing arsenal of reactions.

What To Expect In Organic Chemistry 2

A large part of organic chemistry 1 is devoted to laying the foundations: introducing structural
concepts such as bonding, geometry, stereochemistry, conformations, resonance, and steric
effects, while introducing concepts in chemical reactivity such as nucleophilicity,
electrophilicity, acidity, basicity and so on.
While there are several important new concepts introduced in Org 2 (especially in the context
of pi-bonding) you will find that it largely builds on the foundations of Org 1 and assumes that
you fully understand these concepts. The focus in Org 2 will be much more on reactions.
If I had to name an overall theme for Org 2, it would be : the chemistry of pi
bonds.Understanding resonance will be very important!
Here is a brief introduction to some of the highlights of Org 2. By the end of the course, the
answers to the following questions hopefully wont seem as mysterious.
1. Conjugation

Why is it that diene A is more stable than diene B? How is it that replacing a single
substituent on an alkene can drastically affect the reactivity? For example, why is it that
alkene C does not react with electrophiles such as alkyl halides, but alkene
D does. And alkene E does not react with nucleophiles, but alkene F does. How do we explain
this?
2. Thermodynamic and kinetic control.

In the addition of HBr to an isolated alkene such as, say, 1-butene, there is only one product
possible (not counting stereoisomers). However, if we add HBr to butadiene, we can get two
products, A and B. At low temperature, we obtain A as the dominant product, but at high
temperature, B is dominant. Why is this?
3. Cycloaddition reactions.

When the diene (cyclopentadiene) is added to ethene, no reaction occurs. But when we use
the middle alkene instead, there is a rapid reaction to provide a new cyclic compound. What is
different about this alkene that allows this reaction to occur? And why will this alkene react
readily with cyclopentadiene, but when it is added to ethene, nothing happens?
4. Aromaticity

Normal alkenes (like cyclohexene) give trans dibromides when treated with Br2. But the cyclic
triene in the middle (benzene) doesnt react with bromine at all (unless you add a catalyst,
and even then you get a different product!) Why the difference in reactivity? And why is this

behavior similar for molecules like furan, pyrrole, and pyridine, but a molecule
like cyclooctatetraene(bottom) will also add Br2?
5. Carbonyl chemistry

Grignard reagents react readily with aldehydes and ketones, but not amides. What causes the
difference in reactivity?
When an alcohol is added to a carboxylic acid, the flask has less mojo than
a Shakermeetinghouse. But when just a drop of acid is added, they readily combine to form an
ester. Why is this?
6. Biomolecules
Your body is made up of proteins, sugars, and fats. What do these molecules look like? What
are their properties? How can we make them in the laboratory, and potentially modify their
structures?
In Short
Its vitally important to: make sure you have a firm handle on the key concepts and reactions
from organic 1, because it will be assumed that you know it all.
The biggest challenge will be: getting a handle on the large number of reactions to learn,
especially in carbonyl chemistry.

It will make your life easier if you look for underlying trends and themes and see that
underneath what appears to be tremendous variety, there are really only a handful of
mechanisms.
The most important skill the course will provide: being able to design and plan multiple-step
syntheses of relatively complicated molecules. Furthermore, the course will give you a much
greater understanding of the chemistry of biologically important molecules such as amino
acids, lipids, and sugars. It will be a lot of work, but youll see the world around you in a
different way.

The Six Pillars of Organic Chemistry

A few weeks ago Jeremy at The Chemistry Blog wrote a post called Common Student
Difficulties in Organic Chemistry. Since I was flying home for vacation at the time, I missed
out the discussion, but buried in the comment section was a reference to a recent article by
Joseph J. Mullins of Le Moyne College in Syracuse NY called The Six Pillars of Organic
Chemistry [J Chem Ed, 2008, p. 83 behind a paywall, but most academic institutions will
have it].
Paraphrasing the authors words, the six pillars arent meant to represent all the concepts
required for organic chemistry or to define precisely what concepts were meant to be
included, but instead provide a framework. Prof. Mullins six pillars are the following:
1.

Electronegativity - in an example provided, going across a period leads to increasing

nucleophilicity with decreasing electronegativity. For example, nucleophilicity follows the

following order:
2.

Polar covalent bonding when bonds form between atoms of unequal

electronegativity, the resulting dipole has a positively charged terminus and a negatively
charged terminus, which will provide insight into its preferred mode of chemical reactivity.
So in the above example, the C-Cl bond is polarized whereas the C-H bonds (C and H
having relatively similar electronegativities) are not, resulting in selective breakage of the
carbon-halogen bond during the SN2 instead of the carbon-hydrogen bonds.

3.

Steric effects the rate of the SN2 is greatly affected by the presence of neighboring
bulky groups. So the trend for the above reaction would be:

4.

Inductive effects. The author gives the example of Markovnikoffs rule as an example
of inductive effects, where increasing substitution on carbon leads to increasing inductive

stabilization of the carbocation [he also notes that hyperconjugation, a more

fundamentally sound explanation, can be covered in the resonance section, below].
5.

Resonance resonance effects are widespread in organic chemistry. One example is

that they explain the selective bromination of cyclohexene at the allylic position under
free-radical conditions, versus competing bromination at the secondary (or vinylic
positions). Another example is the planarity of peptide bonds due to the donation of
electrons into the carbonyl * orbital.

6.

Aromaticity Aromaticity is an important driving force in chemical reactions and a

powerful stabilizing influence on molecules. The decreased reactivity of benzene in
bromination reactions versus, say, cyclohexene is an extension of resonance stabilization,
which helps to explain why tryptophan is not considered a basic amino acid even though
(like lysine) it contains a nitrogen in tryptophan, the nitrogen lone pair is tied up in the
system.

I really enjoy thinking about things like this. Overall I think its extremely helpful to
develop a framework that boils down organic chemistry into a short set of useful
principles. Thats essentially the goal of this site, after all. I think the ideal set will, to some
extent, depend on the professors audience of students. In some undergraduate organic
chemistry courses (particularly community colleges) the first half consists of lessons on
chemical structure and reactivity followed by a strong dose of biochemistry. Im not certain,
but I think this the type of course that Prof. Mullins is teaching. In more research-oriented
schools, where the second half of the course is essentially a rapid series of new reagents and
transformations, students are stuggling to drink from a firehose. It would probably be more
helpful in these circumstances to include principles that more explicitly assist with
understanding the driving forces of most reactions in organic chemistry. Nucleophile attacks
electrophile, for example, is an extremely simplifying way of looking at chemical reactions,
and recognizing the patterns of electron flow helps to avoid an excessive reliance on
memorization.
I think the best quote of the article is the following:
It is therefore sensible when teaching the subject to remember to explicitly refer to the
underlying principles, and not to assume that learners are recognizing the physical forces.
Bingo. I make this mistake all the time. Sage advice.
For educators reading this: what would be your six pillars?