How Concepts Build Up In Org 1 (“The

Pyramid”)
Organic Chemistry 1 – A Roadmap For How The Course Material Builds On Itself.

I LOVE making maps. Whenever I played adventure games as a kid (or, let’s face it, as an adult)
I often made meticulous maps of how each area led to the next. Any time I really want to
understand something, I have to write everything out and make a map to connect things together
– usually after I’ve gotten myself lost a few times.

Since organic chemistry is also journey where a lot of students get lost along the way, I thought
it might be helpful to “map out” the course for my students so that they know how the different
pieces fit together.

Table of Contents

1. A Map Of A Typical Organic Chemistry 1 Course

2. The Hierarchy of Concepts – How The Material In Org 1 Builds Upon Itself
3. Week Six Is When The Sh*t Hits The Fan
4. The Alkynes Unit Is Where Synthesis Begins
5. Wild Cards: Alcohols and Spectroscopy

1. A Map Of A Typical Org 1 Course

If I was an illustrator I would draw a beautiful map like XKCD. Lacking that talent, I just use my
illustration software of choice (ChemDraw) and built a pyramid.

From my experience in seeing hundreds of different courses, I’ve made a map of what a
“typical” Org 1 course looks like and how each chapter builds on the one before. There is lots of
variation, of course, but about half the courses follow the “standard sequence” which I’ll
elaborate below (very textbook dependent – McMurry in particular likes to cover alkenes late).
Yours is probably different in some way – but the way in which concepts build up is still the
same. I welcome you to share your experiences and opinions in the comments!
2. The “Hierarchy Of Concepts” – How The Material In Org
1 Builds Upon Itself
One comes into organic chemistry from an introductory course in general chemistry. Starting
out, it’s 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. I’ve 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 wouldn’t 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
they’re 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.

3. Week Six Is When The Sh*t Really Hits The Fast-

Rotating Metal Blades Hanging From The Ceiling
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 you’ll be asked to put together all the
concepts you’ve learned previously and apply them!

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frameborder="0" allowfullscreen="allowfullscreen"></noscript>

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. It’s 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 it’s 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.

4. The Alkynes Unit Is Where Synthesis Begins

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, you’ll start to notice you’ll 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 a knowledge of the reactions and their
stereochemistry.

5. Alcohols and Spectroscopy Are A Wild Card

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 it’s 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.

For those who’ve taken the course (or teach it), how close does this follow your own experience?
Leave a comment!
Review of Atomic Orbitals for Organic
Chemistry
General Chemistry Review: Atomic Orbitals for Organic Chemistry

[Note: the following article is intended as a quick review on atomic orbitals for students enrolled
in an introductory organic chemistry class who are assumed to have taken general chemistry. It
is by no means a complete introduction to atomic orbitals. Also: this post was co-authored with
Matt Pierce of Organic Chemistry Solutions. Ask Matt about scheduling an online tutoring
session here. ]

Table Of Contents

1. The Most Important Graph Ever Made?

2. The Graph Is Explained By The Periodic Filling of Electronic Energy Levels (aka
“Orbitals”)
3. Orbitals Are Defined By The Three Quantum Numbers n, l, and m
4. A Tour Of The Electronic Configurations of The First 11 Elements
5. The 1s shell: Electronic Configuration Of Hydrogen and Helium
6. The 2s Shell: Electronic Configuration Of Lithium and Beryllium
7. The 2p Shell: Boron, Carbon, and Nitrogen
8. A Sudden Dip At Oxygen
9. The Electronic Configuration Of Fluorine
10. A Maximum At Neon
11. The 3s orbital: Sodium
12. Endnote: A Puzzle. What About A Simple Molecule Like CH4?
13. Notes

1. The Most Important Graph Ever Made?

Quote:

“If, in some cataclysm, all of scientific knowledge were to be destroyed, and only one sentence
passed on to the next generation of creatures, what statement would contain the most information
in the fewest words? I believe it is the atomic hypothesis that all things are made of atoms —
little particles that move around in perpetual motion, attracting each other when they are a little
distance apart, but repelling upon being squeezed into one another. In that one sentence, you
will see, there is an enormous amount of information about the world, if just a little imagination
and thinking are applied.”
–Richard P. Feynman

Well of course a chemist like myself is going to love a quote that extolls the central importance
of chemistry to scientific knowledge. You can always trust a barber to find an uplifting quote
about the importance of haircuts.

That caveat aside, if one had to name a single graph which could be saved from a cataclysm for
the next generation of creatures, my vote would be for this one:

What’s going on here?

 The x-axis shows every element of the periodic table, in increasing order of atomic
number.
 The y-axis shows the amount of energy required to ionize each neutral element to a
charge of +1 (the “first ionization energy”). In other words: “how easy is it to pull off an
electron off each element?”.

There is a tremendous amount of information about atomic structure embedded in this extremely
simple plot, but the concept itself isn’t so hard to understand: “how much energy does it take to
rip an electron off a neutral element?”

Two important things to note:

 First, note the broad trend: generally, as elements increase in size, the amount of energy
required to pull an electron away from the atom decreases. We can draw an analogy here
to planets orbiting the sun: all else being equal, the further away a planet (electron) is
from the sun (nucleus), the less attractive force there will be between the two (as
 measured by Newton’s law of gravitation in one case, and Coulomb’s law in the other).
Indeed that “planetary” analogy was the basis for the Bohr model of the atom.
 Second, note the periodic trend: there are certain elements (He, Ne, Ar, Kr, Xe) which
have unusually high ionization energies, followed by elements (Li, Na, K, Rb, and Cs)
with unusually low ionization energies.

2. The Graph Is Explained By The Periodic Filling of

Electronic Energy Levels (aka “Orbitals”)
Note how interpreting the diagram above flows naturally into a discussion about orbitals.

It was Bohr who first made the connection (1923) that the periodicity of atomic properties could
be explained by the periodic filling of electronic energy levels.

In an early model of the atom (1913), it was imagined that electrons occupied progressively
farther orbits around the nucleus, much like the planets in their ever-larger celestial
spheres around the sun. While the “electronic energy levels” that Bohr described are indeed now
called “orbitals”, the analogy ends there. Bohr didn’t anticipate just how weirdly-
behaved electrons can be, relative to planets. Nor did anyone else in 1913. [Note 1]

Source
for right hand image: Wikipedia

What do I mean by “weirdly-behaved”? Well, if one knows the position and momentum of
Venus, for example, then one can then calculate its positions at distant future times (such as the
transit of Venus predicted for 3:48 AM UTC on June 10, 2498).

Heisenberg showed that at the subatomic scale, there are limits to the precision with which one
can know both the position and momentum of a particle like an electron. The result is that our
knowledge of the exact positions of electrons are fuzzy; they have to be described as probability
functions. What we call “orbitals” are in fact 3-dimensional shapes where an electron with a
given set of quantum numbers has a 95% chance of being found. [Note 2]

3. Orbitals Are Defined By The Three Quantum Numbers n,

l, and m
These orbitals have properties which are defined by the three essential terms in a particular form
of the Schroedinger wave equation:

 the principal quantum number n (1, 2, 3…), which is sometimes referred to as the
“electron shell“, as it broadly relates to distance from the nucleus.
 ℓ (called the azimuthal quantum number, but knowing that name is not essential). For a
given value of n, the possible values of ℓ can range from 0 up to (n–1). So when n =
1, ℓ = 0. When n = 2, ℓ can have values of 1 or 0.
The value of ℓ determines the shape of the orbital. For ℓ = 0, the shape of the orbital is
spherical – an orbital we refer to as an s orbital.

For ℓ = 1 (which is only possible when n = 2 or above) the orbital has a dumbbell-like
shape, which we refer to as a p-orbital. The higher observed values are ℓ = 2 (d orbitals)
and ℓ = 3 (f orbitals) which are themselves fascinating, but in true organic chemistry
fashion, we will skip.
 m, which is the magnetic quantum number. The value of m depends on the value of ℓ,
and can take the values –ℓ to +ℓ, inclusive of zero. So for ℓ = 1 (the p-orbital), m can
have a value of –1, 0, or +1. The physical interpretation of this is the three orientations
possible for the p-orbital, along the x, y, and z axes. m can take on five values for the d-
orbitals (ℓ = 2) and seven values for the f orbitals (ℓ =3).

In addition to n, ℓ, and m, there is also fourth quantum number known as electronic spin, which
can take on the value +½ or –½ for electrons.

Finally, the last bullet point:

 No two electrons can have the same set of quantum numbers (which is to say, they
cannot have the same quantum state) as elucidated in Wolfgang Pauli’s exclusion
principle. (Electrons belong to a family of particles called fermions which share a
property analogous to “one seatbelt per occupant”). It’s an atom, not a clown car!

Bozos. (“bosons, shurely?” – ed. )

What this means is that electrons in atoms “build up” in energy level in a well-defined pattern,
starting with 1s (which can hold two electrons, with opposite spins), followed by 2s (which also
holds two electrons) and then 2p (which due to the three possible values of m, can hold 3 × 2 = 6
electrons, and then 3s (2 electrons) and so on.
 Image source

4. A Tour Of The Electronic Configurations of The First 11

Elements
We could go on filling up electrons, but that’s not the intended point of todays post, which is
merely to review the atomic configurations of each of the first 11 elements while referring back
to their first ionization energies as a guide.

So let’s tour the electronic configurations of the first 11 elements, shall we?

5. The 1s shell: Hydrogen and Helium

Let’s look at the (first) ionization energies for hydrogen and helium:

Hydrogen: 1312 kJ/mol

Helium: 2372 kJ/mol

Hydrogen has a single electron in the 1s orbital with spin of either +1/2 or – 1/2 (they are of the
exact same energy, except in a strong magnetic field).

We can represent the electronic configuration in two ways:

 the notation 1s1 , where 1 refers to the shell number (principal quantum number n), s is
the shape of the orbital (other values are p, d, and f) and the superscript refers to the
number of electrons in that orbital
 alternatively, with a box showing the orientation of electrons in each orbital (the
direction of the arrow noting the spin). For a half-filled orbital, the direction of the spin is
arbitrary; I’m going to draw it as “up” here and in all future examples, but it’s not
incorrect to draw it as pointing down instead.

Helium has two electrons in the 1s orbital, each with opposing spins (+1/2 and –1/2), which we
represent below.
It’s almost twice as difficult to remove an electron from helium than from hydrogen (compare:
2372 kJ/mol versus 1312 kJ/mol).

Why the higher ionization energy? Because each electron in the 1s orbital of helium now has two
protons from the nucleus pulling on it instead of just one, which results in a stronger attractive
force according to the Coulomb equation.

Note that it’s not exactly twice as much; we can rationalize the lower value as being due to
repulsion between the two electrons in the 1s orbital.

6. The 2s Shell: Lithium and Beryllium

With the 1s orbital full, the third element (lithium) must therefore have its electron placed in the
2s orbital, which is not only farther away from the nucleus, but also has the attractive force of the
nucleus partially shielded by the intervening pair of electrons in the 1s orbital. This shielding
leads the electron in the 2s orbital of lithium to only “feel” an effective nuclear charge of (3 – 2)
= +1 from the nucleus.

Hence, this electron is particularly easy to rip off, requiring a mere 520 kJ/mol (compare to 2372
kJ/mol for helium!). Lithium metal will readily participate in chemical reactions; it will react
slowly with water, for example. Helium, on the other hand, has never been observed to combine
with another element.

In contrast, the two electrons in the 1s shell of lithium never participate in reactions. We can call
these chemically inert electrons the “inner shell” electrons, as opposed to the “outer shell” , or
“valence” electron in the 2s orbital.

Since all the

interesting chemistry happens with the electrons in the 2s orbital (and not the electrons in the
“inert”, closed, 1s shell) a useful shorthand is to draw the electronic configuration of lithium
as [He] 2s1 , meaning that lithium has the electronic configuration of helium, plus a single
valence electron in the 2s orbital.

In the fourth element, beryllium, the 2s orbital becomes fully occupied with a pair of electrons
of opposite spin. Note the increased ionization energy (+379 kJ/mol from lithium) as the
electrons feel a greater attraction from the extra proton in the nucleus.
Also note that although beryllium has a filled 2s orbital, in no way does it behave like a noble
gas. Beryllium metal reacts readily with oxygen to form an oxide layer, for example. Unlike the
gap in energy between 1s and 2s, the gap in energy between the 2s orbital and the next-highest
energy level (2p) orbital is relatively small, such that these orbitals, when filled, can together
hold a combined “octet” of valence electrons.

7. The 2p Shell: Boron, Carbon, and Nitrogen

With the 2s now full, additional electrons must now be placed in an even higher energy level, the
2p orbital.

Unlike the s orbitals, which can only hold two electrons apiece, each set of p orbitals can hold
six. Our interpretation of this is that each level of p orbitals (2p, 3p, 4p, etc.) is comprised of
three individual dumbbell-shaped p orbitals that are aligned at right angles to each other along
the x, y, and z axes.

Here’s what the electronic configuration looks like for boron. (Note: we could also choose to
label the three 2p orbitals as 2px, 2py, and 2pz, but for our purposes all of these orbitals are of
equivalent energies and it serves no purpose to do so here).
Note how the ionization energy of boron is slightly lower (99 kJ/mol lower) than
that of beryllium, from which we can interpret that the 2p orbital is slightly farther away from the
nucleus than the 2s orbital. [Note 3].

The ionization energy progresses sharply upwards from boron to carbon…. (+ 286 kJ/mol)

… and then from carbon to nitrogen (+316 kJ/mol):

8. A Sudden Dip At Oxygen

Then, at oxygen, there’s a sudden dip in the ionization energy (–89 kJ/mol):
Why?

Ever got on a bus to find out there are no remaining empty seats, and you have to (horrors!) sit
next to a total stranger?

That’s essentially what’s happening here: with each of the 2p orbitals (px, py, pz) singly occupied,
any additional electrons will have to pair up. That dip in ionization energy reflects greater
electron-election repulsion in a doubly occupied orbital, making the electron (slightly) easier to
pull off.

9. The Electronic Configuration Of Fluorine

From oxygen to fluorine the ionization energy climbs again (+368 kJ/mol from oxygen):

10. A Maximum At Neon

And then, at neon we finally reach another local maximum of ionization energy (+399 kJ/mol
from fluorine):

Here we have reached the maximum capacity of the 2s and 2p orbitals (acting together as an
“octet”), where each electron in the octet will “feel” the maximum effective charge from the
nucleus. In neon, each of the eight electrons in the valence “octet” itself feels a net force of +8
from the nucleus (ten protons in the nucleus minus two electrons in the intervening 1s shell) and
a certain amount of electron-electron repulsion in the filled 2s and 2p orbitals.

Neon is a local maximum where the Coulombic attractive term is maximized, and so is
ionization energy. This is what gives rise to the familar “octet rule”, where atoms are said to
“seek out full octets” and so on.
11. The 3s orbital: Sodium
Let’s just go one atom further to illustrate the dramatic difference in behaviour between sodium
and neon.

There’s a big gap between the energies of the orbitals in the n=2 shell (2s and 2p) and the
orbitals in the n=3 shell (3s and 3p).

The 3s orbital is farther away from the nucleus and the attractive force from the nucleus is
shielded by the 10 electrons in lower-energy orbitals. We say that the “effective nuclear charge”
felt by an electron in the sodium 3s orbital is just 1. (i.e. 11 – 10 = 1).

The ionization energy of sodium is a meagre 496 kJ/mol, which is 1584 kJ/mol less than neon.
Sodium gives up its valence electron readily, reacting even with water (violently!); in contrast,
no other element has ever been observed to combine with neon.

We’re going to stop at this point, but you can imagine where it goes from here. [Note 4]

12. Endnote: A Puzzle. What About A Simple Molecule Like

CH4?
So here’s a question. If the atomic configuration of carbon is [He]2s22p2, and the atomic
configuration of hydrogen is 1s1, what might we predict the structure of the simplest
hydrocarbon (CH4) to look like?

 Wouldn’t we expect to see C-H bonds along the px, py, and pz axes (bond angles of 90°)
and then a fourth C-H bond in the 2s orbital as far away from the other electrons as
possible (135° maybe) ?

 Wouldn’t we predict different bond lengths for the C-H bonds attached to p orbitals
(farther away from nucleus) than for the C-H bond attached to the s-orbital?
  Wouldn’t we expect a (small) dipole moment for CH4 ?

Instead, here’s what’s been observed about methane:

 All the C-H bonds have identical bond lengths (1.09 Angstrom).
 All C–H bond angles are identical. The hydrogens are arranged around carbon in a
perfect tetrahedron, with all H-C-H bond angles being 109.5°.
 There is no dipole moment.

What gives? How can this possibly be true, given what we now know about the s and p orbitals?
How can we explain this situation where the distinctions between the 2s and 2p orbitals have
been completely wiped out?

So what’s going on? We’ll talk about that in the next post.

Next Post: Why Is Methane Tetrahedral?

Thanks again to Matt for helping with this post. Hire Matt as your tutor!

Notes
Note 1: Nor did he (or anyone else in 1913) imagine the sublimely funky shapes of the p, d and f
orbitals. The wonders of nature can surpass the most fanciful human imagination.

Note 2: This also gives rise to strange phenomena like quantum tunnelling, where electrons have
a non-zero chance of appearing on the other side of a barrier. It’s as if Venus were to suddenly
materialize on the other side of the sun.

Note 3: although the electrons in the 2s and 2p orbitals mix and hybridize (as we’ll see) the
electrons in the 2s orbital are closer to the nucleus, which can affect certain chemical properties.
For example the unusually strong acidity of alkyne C-H bonds (pKa = 25) relative to alkanes
(pKa = 50) can be rationalized by noting that the sp-hybridized orbital are closer to the nucleus
(50% s-character) and thus more stable, relative to the pair of electrons in the sp3-hybridized
orbital of an alkyl anion (25% s-character) which are farther away.
Note 4: “He fixes the cable?”

How Do We Know Methane (CH4) Is

Tetrahedral?
What Do The Valence Electrons Of Carbon Tell Us About The Bonding In CH4?

(Hint: since the dipole moment of CH4 is zero, the answer is, “not enough”)

If the orbital configuration of carbon is 2s22p2 , then how can we use this information to figure
out what the arrangement of the orbitals are in a simple organic molecule like methane (CH4)?

It turns out that methane is tetrahedral, with 4 equal bond angles of 109.5° and 4 equal bond
lengths, and no dipole moment.

This brings up two questions. First, how do we know that CH4 is tetrahedral? And secondly, how
do we reconcile this electronic configuration (2s22p2 ) with the fact that we have four equal C–
H bonds?

That’s what this post is about.

Table of Contents

1. The Electronic Configuration Of The Valence Electrons Of Carbon Is 2s22p2

2. Can We Use This Information To Figure Out The Structure Of Methane (CH4)? (Spoiler: No)
3. Maybe Methane (CH4) Is Square Planar?
4. Disproving The Square Planar Structure Of CH4 (1874) And Proposal Of A Tetrahedral Structure
5. Tetrahedral Carbons: Not A Popular Idea In 1874
6. So What Orbitals ARE Involved?
7. Notes

1. The Electronic Configuration Of The Valence Electrons

Of Carbon Is 2s22p2
In our review of atomic orbitals, we saw that the orbital configuration of the valence electrons
of carbon is 2s22p2 as shown below:
Since the 2s orbital is lower in energy than 2p, it’s filled first. That means that there are two
electrons in the 2s orbital, and a single electron in two of the three 2p orbitals. There’s also an
empty 2p orbital.

[In addition, there are two electrons in the “inner shell” 1s orbital, which are not available for
bonding].

2. Can We Use This Information To Figure Out The

Structure Of Methane (CH4)? (Spoiler: No)
So far so good. This is fine if we’re just talking about isolated carbon atoms.

But in order to be truly useful, we need to be able to relate the orbitals of carbon to the structure
and bonding of actual organic compounds.

The simplest organic compound is methane, CH4. So let’s bring four hydrogen atoms into the
picture and try to apply what we’ve learned to come up with some hypotheses about the bonding
in this molecule.

The 3 p-orbitals in carbon are all at 90 degrees to each other, along the x, y, and z axes.
Shouldn’t we expect that the structure of methane would have three C-H bonds for each of the p
orbitals (at 90 degrees to each other) and then the fourth C-H bond attached to the 2s orbital?
Since electron pairs repel, maybe we should put that C-H bond the maximum distance away from
the other C-H bonds; this would give an H–C–H bond angle of 135°.

Following this logic would give a structure like this:

As it turns
out, it can be shown that this proposal is wrong.

Why?

Dipole moment.

Recall that each C–H bond has a small dipole due to the difference in electronegativity between
C (2.5) and H (2.2). We expect C to be partially negative and H to be partially positive.

 If the above structure accurately depicted the structure of methane, we’d expect methane to
have 3 longer C–H bonds (to the 2p orbitals) and one shorter C–H bond (to the 2s orbital, which
is closer to the nucleus)
 Furthermore, we’d expect 3 H–C–H bond angles of 90° and one H–C–H bond angle of 135°.
 When the vector sums of the C–H dipoles are added up in this structure, they would not all
cancel out.
 We would therefore expect to observe a small, but measurable dipole moment for CH4. [note 1]

However, the measured dipole moment of CH4 is zero. Therefore this cannot be the correct
structure.

This tells us that all the bond lengths and bond angles in methane are identical.
3. Maybe Methane (CH4) Is Square Planar?
Alright, you say. If all C-H bonds are of equal lengths and angles, why can’t CH4 have the
structure below, where all the bond angles are 90° and CH4 is flat, in the plane of the page. (We
call this structure “square planar”).

This was in fact the majority opinion for the arrangement of bonds around carbon until about
1880. Extremely brilliant chemists such as Berzelius went to their graves having no reason to
doubt that methane was anything but flat.

However, we now know this to be wrong. Why?

4. Disproving The Square Planar Structure Of CH4 (1874)

And Proposal Of A Tetrahedral Structure
If methane is modified so that the central carbon is attached to four different groups, the
molecule can exist as 2 different isomers that are non-superimposable mirror images (this is
called “optical isomerism” and covered later in the course).

This is possible if the arrangement of 4 groups around the central carbon is tetrahedral, but not if
the molecule is square planar. For example, the methane derivative bromochlorofluoromethane
has four different groups around carbon and can be separated into two different isomers which
rotate plane-polarized light in different directions. [As we’ll see later, these isomers are called
“enantiomers”]
This observation rules out the square planar structure. If carbon was square planar, the
molecule would be flat, and be superimposable on its own mirror image, and only one isomer
would be possible.

Jacobus Henricus van’t Hoff , a fellow at the veterinary college in Utrecht, was among the first
to address the possibility of three-dimensional carbon. In his “La Chimie dans L’Espace” (1874)
he noted that the arrangement of atoms in space has important practical consequences – a point
that had been completely neglected to that point. van’t Hoff showed that a tetrahedral
arrangement of four different groups around a carbon atom (which he called an “asymmetric
carbon“) would give rise to two different isomers, and furthermore, this would explain why
tartaric acid (with two asymmetric carbon atoms) existed in three forms (+, –, and
meso). [Source]

van’t Hoff’s work – which should be noted was purely theoretical – was not well received in
some circles.

5. Tetrahedral Carbons: Not A Popular Idea In 1874

The eminent German chemist Hermann Kolbe had this to say:
For his part, van’t Hoff flew to Stockholm on his Pegasus to receive the first Nobel Prize in
Chemistry in 1901. [

Incontrovertible proof for the tetrahedral arrangement of bonds around the carbon atom came in
1913 when Bragg determined the structure of diamond using X-ray crystallography and found it
to be a tetrahedral network of carbon atoms with C-C-C bond angles of 109.5°.

6. So What Orbitals ARE Involved?

We now rationalize the tetrahedral arrangement of atoms around methane as being due to the
repulsion of the bonding pairs of electrons with each other (a.k.a. VSEPR theory).

This doesn’t help us with understanding the orbitals involved in bonding, however.

If we accept that the arrangement of hydrogens around methane is tetrahedral, then how do we
describe the bonding orbitals of methane, given what we know about the geometry of s
and p orbitals?

After all, the 2p orbitals are all at 90 degrees to each other, but the bond angles in methane are
109.5°.

Furthermore, how do we account that each of the 4 bonds in methane are of identical lengths?
What happened to the 2s orbital, for example?

Are the electrons in the C-H bonds considered to be in p orbitals or s orbitals? Or something
else?

As it turns out, the conventional treatment is to deal with the bonds around carbon as being
in hybrid orbitals.

More on that in the next post.

Next Post: Hybrid Orbitals

Notes
Note that mono-deuterated methane (CH3D, where D is deuterium, the heavy isotope of
hydrogen) has a small dipole moment that has been measured. [ref]

Note 2: it should be noted that van’t Hoff’s Nobel Prize was for his contributions to physical
chemistry, not organic stereochemistry.

I am indebted to this page covering van’t Hoff’s “The Arrangement of Atoms In Space” for
historical perspective. Well worth reading in full.

From the same source: van’t Hoff’s tetrahedral models [from the Leiden history of science
museum; source]

From the same author, some more historical perspective on the Kolbe/van’t Hoff spat:

Obviously Kolbe was silly to be so intemperate and spiteful. He was also short-sighted, and he
guessed wrong. We can easily appreciate that in the court of history he got what was coming to
him.

The challenge is properly to respect the indispensable contributions the attitude he was
championing had made to the development of chemistry. It was by sticking close to careful
experimental observations that chemistry had gotten where it was (and is). Kolbe was trying to
keep science on a productive, intellectually justifiable path.
Hybrid Orbitals
Today’s post is all about hybrid orbitals. Here’s a quick summary:

[Note: This post was co-authored with Matthew Pierce of Organic Chemistry Solutions. Ask
Matt about scheduling an online tutoring session here. ]

Table of Contents

1. What Orbitals Are Involved In The Tetrahedral Arrangement Of C-H Bonds Around
Carbon In Methane (CH4)?
2. Hybrid Orbitals: An Explanation For Bonding At Carbon
3. A Pop Analogy: Hybrid Soda
4. sp3 Hybridization Accurately Describes The Arrangement Of Atoms In (First-Row)
Elements Bonded To Four Atoms…
5. …As Well As Situations Where The Number of [Atoms + Lone Pairs] Equals 4
6. sp2 Hybridization
7. sp Hybridization
8. Summary – Hybrid Orbitals

1. What Orbitals Are Involved In The Tetrahedral

Arrangement Of Methane (CH4)?
In the last post on the structure of methane we asked how we know that methane is tetrahedral.

Based on the orbitals of carbon (2s and 2p) we might have naively expected three of the C-H
bonds to line up along the x, y, and z axes, respectively, and have the other one at some arbitrary
angle (like 135° or so)

But then, as so often happens in science, our beautiful intuitive hypothesis was destroyed by
some annoying experimental facts:

 methane has no measurable dipole moment (our “reasonable” structure, below left, would
be expected to have a measurable dipole moment)
 the crystal structure of diamond is tetrahedral, with identical bond lengths and angles
between carbons of 109.5 degrees. This isn’t what we’d expect if we were dealing with
bonds between “pure” 2s and 2p orbitals!

In retrospect, the geometry makes sense. It happens that 109.5 degrees is the orientation that
maximizes the distance between each of the four bonding pairs, and thus minimizes their
repulsive interactions. In other words, the geometry is a direct consequence of “opposite charges
attract, like charges repel”.

But how do we describe the orbitals that are used to give that bond angle?

This is a real chin-scratcher. They can’t be pure 2s orbitals (there’s only one 2s orbital, anyway).
And they can’t be pure p orbitals, since the p orbitals are aligned at 90° to each other.

So what the heck kind of orbitals are they?

2. Hybrid Orbitals: An Explanation For Bonding At Carbon

Linus Pauling asked this same question back in his classic treatise, the Nature of the Chemical
Bond (1931) [pdf] which in large measure won him the 1954 Nobel Prize in Chemistry.

Pauling’s solution to this dilemma, which we still apply today, was the following:
  None of the bonding orbitals in methane are 100% s or 100% p. Instead, they are hybrid
orbitals that each have partial s character and partial p character.
 The three 2p orbitals and the single 2s orbital hybridize (i.e., mix) to create four hybrid
sp3 orbitals, which are arranged tetrahedrally around the central carbon atom.
 Each of the four hybrid orbitals has 25% s-character and 75% p-character.
 In the case of methane, each of these sp3 hybrid orbitals overlaps with a 1s orbital from
hydrogen to form the C-H bonds

I’ll be honest here. Many students don’t like this explanation.

Certainly, it’s confusing at first. Why?

I think that when we initially learn about orbitals, we intuitively think of them as containers –
sort of like atomic Tupperware for holding electrons that happen to come in a variety of cutesy
shapes.

Electrons, then, can be imagined to behave like the “fruits” that rattle around in these containers
(strict limit: 2 per container!). It’s not so surprising to our intuition when we learn that they can
move from container to container within an atom or even leave the atom altogether.
What is surprising is when we open up the fridge and find that our cute little sphere- and
dumbbell-shaped Tupperware containers have changed their shape and merged their properties
with each other! This violates our intuition about how containers behave!

What the…?! Hybridized tupperware containers?

This is the quantum world, folks! If this doesn’t mystify you… it f*&king should!

Going forward, I don’t ask that you understand or even “believe in” hybridization on a deep
mathematical or theoretical level. That’s not necessary for our purposes [Pauling was a great
teacher. You can always read the original Pauling paper, here, if you choose]

I merely advise that you try to suspend your disbelief going forward, because using this
hybridization model will help us rationalize a lot of molecular structure, geometry, and
behaviour.

3. A Pop Analogy: Hybrid Soda

Before we dive in any further, here’s what I consider to be a helpful little analogy (thx, Steven)
that might help to get the point across.

 Imagine you have four bottles of pop: one bottle of Sprite (S) and three bottles of Pepsi
(P).
 Now imagine pouring them out, mixing them all together, and then re-filling each bottle
with the mixture.
 The Law of Conservation of Pop says that you still have four bottles worth of liquid. But
now the pop is neither pure Sprite or pure Pepsi; it is a hybrid between the two.
 Specifically, each bottle now has 25% Sprite character and 75% Pepsi character.
 We can call this “hybrid” pop, if you like, sp3
That’s a little bit like what has happened to our 2s and 2p orbitals. By mixing the 2s and three 2p
orbitals, we now have four orbitals which have 25% s character and 75% p character. (Although,
importantly, it’s the shapes of the bottles that are changing, not just the contents).

The final step is to arrange these four orbitals at the corners of a tetrahedron, which allows for
the maximum distance between the four electron pairs (like charges repel!)

How does this rationalization help us?

 It explains the tetrahedral molecular geometry of methane, with 4 identical H–C–H bond
angles (109.5°)
 It explains the 4 identical C–H bond lengths (and bond strengths) in methane
 It explains the lack of a dipole moment in methane, since the tetrahedral arrangement of
the electron pairs allows for all partial charges to cancel (i.e. the vectors sum to zero)
 The model even helps to rationalize how certain reactions occur, which we won’t go into
right now [e.g. backside attack in the SN2 reaction occurs into the empty “antibonding”
orbital 180° to the bonding C–H orbital, if you’ve been reading ahead]

4. sp3 Hybridization Accurately Describes The Arrangement

Of Atoms In (First-Row) Elements Bonded To Four
Atoms…
This doesn’t just apply to methane. It applies to any situation where a (first-row) element is
bonded to four atoms. Obviously tetrahedral carbon is the most prominent example we will
explore, but it also applies to tetrahedral nitrogen [e.g. NH4(+)] and even tetrahedral boron [e.g.
BF4(-)].
5….As Well As Situations Where The Number of [Atoms +
Lone Pairs] Equals 4
The tetrahedral arrangement of the orbitals holds even when one or more pairs of electrons is a
non-bonded lone pair (If you’ve run across VSEPR theory, which most people have by the time
that they arrive in organic chem, this shouldn’t come as a shock.)

For instance, ammonia (NH3), the “methyl anion” (CH3 – ) and the hydronium ion (H3O+) all
have a central atom with 4 pairs of electrons: 3 pairs of bonding electrons and one pair of non-
bonded electrons. As we’ve seen, the ideal geometry for arranging four pairs of electrons is
tetrahedral, which makes the hybridization of the central atom sp3. This leaves the molecule
with a “piano stool” arrangement of atoms about the central atom, which we call “trigonal
pyramidal” geometry.

Another way of putting it is that the central atom has tetrahedral orbital geometry (sp3) and
trigonal planar molecular
geometry.
An interesting fact is that the bond angles in these are compressed from the ideal angle of 109.5°.
The H-N-H bond angles in ammonia, for instance, are 107 degrees. We rationalize this as being
due to the fact that a non-bonded lone pair is more repulsive than a “normal” bonding pair –
likely because it’s closer to the atom and exerts a stronger influence.

This deviation from “ideal” bond angles is even greater in H2O (water) which has two lone pairs.
The hybridization is still sp3, the orbital geometry is still tetrahedral, but the shape (“molecular
geometry”) of the resulting molecule is “bent”.

Indeed, one of the notable achievements of Pauling’s hybridization model is that it correctly
accounts for the dipole moment of water. If water were perfectly “linear”, as many of us might
have naively assumed before we learned any chemistry, the dipoles would cancel each other out.

Another example of “bent” geometry is found in the amide anion NH2– which has two lone pairs
on nitrogen.

A quick table might help to summarize everything we’ve established about sp3 hybridization:

6. sp2 Hybridization
Let’s go back to our pop-bottle analogy. Say we only mix our Sprite with two bottles of Pepsi,
not three.

What does that leave us with?

This gives us three hybrid bottles of pop, and one leftover unhybridized bottle.

By analogy, if we mix the 2s orbital with two 2p orbitals, we obtain three sp2 hybrid orbitals,
and one left over, unhybridized p orbital.

When these three sp2 orbitals are filled with electron pairs, the bond angle that maximizes their
distance apart is 120°.

This gives us a “trigonal planar” arrangement of sp2 orbitals, with the unhybridized p orbital at
right angles to the plane. It kind of resembles a Mercedes Benz symbol.

A classic example of this trigonal planar geometry is seen in borane, BH3 , which has three pairs
of bonding electrons arranged at 120° to each other. The trigonal planar geometry is also found
in carbocations, such as the methyl cation, CH3+ .

You might wonder: where is the unhybridized p orbital?

At right angles to the plane. Recall that each of the three p orbitals are at right angles to each
other. So whichever two p-orbitals hybridize, the third (leftover) p orbital will be at right angles
to the plane that they form (just like the z axis is perpendicular to the xy plane)

In the case of BH3 and carbocations, the unhybridized p-orbital is empty.

There is another very common situation where sp2 geometry is observed, however. If adjacent
atoms have single electrons in unhybridized p-orbitals, and if those p-orbitals can overlap, a bond
can result. This is a phenomenon known as “pi-bonding“. (We’ll have a lot more to say about it
later.)

Pi bonds – which are often just called, “double bonds” – require an unhybridized p orbital in
order to form.

The carbon, oxygen, and nitrogen atoms in the examples below, which all have pi bonds (double
bonds) are sp2 hybridized. The orbitals are separated by angles of approximately 120°.

Note that lone pairs can be in sp2-hybridized orbitals, just as we saw in NH3 and H2O in the case
of sp3 hybridization. Also note that in the midde molecule (formaldehyde), the oxygen has two
lone pairs (each in sp2 hybridized orbitals) and in the top right molecule the nitrogen has a single
lone pair in a sp2 hybridized orbital.

When a lone pair is present, the bond angles will be slightly less than 120° since the lone pair
can be thought of taking up more “room”.

7. sp Hybridization
Let’s examine the last possible case. What if only one p orbital hybridizes with the s orbital?

This gives us two hybrid ” sp ” orbitals separated by the maximum angle apart: 180 degrees. We
call this arrangement, “linear”. Each hybrid sp orbital has 50% s character and 50% p character.
The two unhybridized p-orbitals are each at right angles to the sp hybrid orbitals.

For instance, here’s what the orbitals look like in beryllium chloride (BeCl2) where the Cl-Be-Cl
bond angle is 180°. If we consider the Cl-Be-Cl bond to be along the x-axis, the two
(unhybridized) p-orbitals will be along the y and z axes, respectively.

sp-hybridization is more commonly observed in situations where there are two pi bonds on a
single atom. The most prominent examples are “triple bonds”, as seen in alkynes, nitriles, and
carbon monoxide (CO). In these cases, not only are the carbon atoms sp-hybridized, but so are
the nitrogen (in nitriles) and oxygen (in carbon monoxide) atoms.
Note also that lone pairs can be in sp-hybridized orbitals, as seen in nitriles and carbon
monoxide.

sp-hybridization is not exclusive to triple bonded atoms – for example, the central carbons in
allene and ketene participate in two pi bonds and are therefore sp-hybridized – but triple bonds
are the most immediately recognizable examples.

8. Summary – Hybrid Orbitals

OK. Here are the main points of this unintentionally very long post:

 Electron pairs repel. In the absence of orbital hybridization, the bond angles around CH4
would be confined to the geometry of the p-orbitals (90°). It’s energetically favorable for
the s and p orbitals to hybridize to form sp3 orbitals which results in a greater separation
of the electron pairs and bond angles of 109° (i.e. at the apices of a tetrahedron). This
also holds for central atoms with non-bonding electron pairs such as NH3 and H2O.
 When only two p orbitals participate in hybridization, three sp2 hybrid orbitals result that
adopt a trigonal planar orbital geometry. The remaining (unhybridized) p orbital, which is
at right angles to the trigonal plane, can either be empty (as in BH3) or singly-occupied
(as seen in molecules containing pi bonds).
 When only one p orbital participates in hybridization, the result is two sp hybrid orbitals
and a linear orbital geometry. The two remaining p orbitals are available for pi-bonding
(as in triply-bonded organic compounds such as alkynes and nitriles) or can be empty (as
in BeCl2).
 Note that the number of orbitals around the central atom is always 4. Orbitals are neither
created nor destroyed by hybridization; they are merely transformed.

In the next post we will just provide a super simple trick for quickly determining the
hybridization of a central atom.

Thanks again to Matt for co-authoring. Ask Matt about scheduling an online tutoring
session here.

How To Determine Hybridization: A Shortcut

A Shortcut For Determining The Hybridization Of An Atom In A Molecule
Here’s a shortcut for how to determine the hybridization of an atom in a molecule. This will save
you a lot of time.

–BEGIN SHORTCUT–

Here’s what you do:

1. Look at the atom.

2. Count the number of atoms connected to it (atoms – not bonds!)
3. Count the number of lone pairs attached to it.
4. Add these two numbers together.

 If it’s 4, your atom is sp3.

 If it’s 3, your atom is sp2.
 If it’s 2, your atom is sp.

(If it’s 1, it’s probably hydrogen!)

This works in at least 95% of the cases you will see in Org 1.

–END SHORTCUT–

Some Simple Worked Examples Of The Hybridization

Shortcut
sp3 hybridization: sum of attached atoms + lone pairs = 4

sp2 hybridization: sum of attached atoms + lone pairs = 3

sp hybridization: sum of attached atoms + lone pairs = 2

Where it can start to get slightly tricky is in dealing with line diagrams containing implicit
(“hidden”) hydrogens and lone pairs. Chemists like time-saving shortcuts just as much as
anybody else, and learning to quickly interpret line diagrams is as fundamental to organic
chemistry as learning the alphabet is to written English.

Remember:

 Just because lone pairs aren’t drawn in on oxygen, nitrogen, and fluorine doesn’t mean
they’re not there.
 Assume a full octet for C, N, O, and F with the following one exception: a positive
charge on carbon indicates that there are only six electrons around it. [Nitrogen and
oxygen bearing a formal charge of +1 still have full octets].

[Advanced: a quick note on determining the hybridization of atoms in some weird cases like free
radicals, carbenes and nitrenes ]

How To Determine Hybridization: Two Exercises

Here’s an exercise. Try picking out the hybridization of the atoms in this highly poisonous
molecule made by the frog in funky looking pyjamas, below right.
[Don’t worry if the molecule looks a little crazy: just focus on the individual atoms that the
arrows point to (A, B, C, D, E). A and B especially. If you haven’t mastered line diagrams yet
(and “hidden” hydrogens) maybe get some more practice and come back to this later.]

[Answers here]

Here are some more examples.

[Answers here.]

Are there any exceptions?

Sure. Although as with many things, explaining the shortcut takes about 2 minutes, while
explaining the exceptions takes about 10 times longer.

Helpfully, these exceptions fall into two main categories. It should be noted that by the time your
course explains why these examples are exceptions, it will likely have moved far beyond
hybridization.

Bottom line: these probably won’t be found on your first midterm.

Exception #1: Lone pairs adjacent to pi-bonds

The main exception is for atoms bearing lone pairs that are adjacent to pi bonds.

Quick shortcut: Lone pairs adjacent to pi-bonds (and pi-systems) tend to be in unhybridized p
orbitals, rather than in hybridized spn orbitals. So when a nitrogen that you might expect to be
trigonal pyramidal sp3 is adjacent to a pi bond, its hybridization is actually sp2 (trigonal planar).
Why? The quick answer is that lowering of energy from conjugation more than makes up for any
gain in energy through increased steric hindrance. [see this post: “Conjugation and Resonance“]

What’s the long answer?

Let’s think back to why atoms hybridize in the first place: minimization of electron-pair
repulsion.

For a primary amine like methylamine, adoption of a tetrahedral (sp3) geometry by nitrogen
versus a trigonal planar (sp2) geometry is worth about 5 kcal/mol [roughly 20 kJ/mol]. That
might not sound like a lot, but for two species in equilibrium, a difference of 5 kcal/mol in
energy represents a ratio of about 4400:1] . [How do we know this? See this (advanced) Note on
nitrogen inversion]

What if there was some compensating effect whereby a lone pair unhybridized p-orbital was
actually more stable than if it was in a hybridized orbital?

This turns out to be the case in many situations where the lone pair is adjacent to a pi bond! The
most common and important example is that of amides, which constitute the linkages between
amino acids. The nitrogen in amides is planar (sp2), not trigonal pyramidal (sp3), as proven by x-
ray crystallography.

The difference in energy varies widely, but a typical value is about 10 kcal/mol favouring the
trigonal planar geometry. [We know this because many amides have a measurable barrier to
rotation a topic we also talked about in the Conjugation and Resonance post]

Why is trigonal planar geometry favoured here? Better orbital overlap of the p orbital with
the pi bond vs. the (hybridized) sp3 orbital.
The drawing below tries to show how a change in hybridization from sp3 to sp2 brings the p-
orbital closer to the adjoining p-orbitals of the pi bond, allowing for better orbital overlap. Better
orbital overlap allows for stronger pi-bonding between the nitrogen lone pair and the carbonyl p-
orbital, which results in an overall lowering of
energy.

You can think of this as leading to a stronger “partial” C–N bond. Two important consequences
of this interaction are restricted rotation in amides, as well as the fact that acid reacts with amides
on the oxygen, not the nitrogen lone pair (!)

The oxygen in esters and enols is also also sp2 hybridized, as is the nitrogen in enamines and
countless other examples.

As you will likely see in Org 2, some of the most dramatic cases are those where the “de-
hybridized” lone pair participates in an aromatic system. Here, the energetic compensation for a
change in hybridization from sp3 to sp2 can be very great indeed – more than 20 kcal/mol in
some cases.

For this reason, the most basic site of pyrrole is not the nitrogen lone pair, but on the carbon (C-
2) (!).

[Are there exceptions to this exception? Rare ones – see below]

Exception #2. Geometric Constraints

Another example where the actual hybridization differs from what we might expect from the
shortcut is in cases with geometric constraints. For instance in the phenyl cation below, the
indicated carbon is attached two two atoms and zero lone pairs. What’s the hybridization?
From our shortcut, we might expect the hybridization to be sp.

In fact, the geometry around the atom is much closer to sp2. That’s because the angle strain
adopting the linear (sp) geometry would lead to far too much angle strain to be a stable molecule.

A quote passed on to me from Matt seems appropriate:

“Geometry determines hybridization, not the other way around”

Well, that’s probably more than you wanted to know about how to determine the hybridization of
atoms. Suffice to say, any post from this site that contains shortcut in the title is a sure fire bet to
have over 1000 words and >10 figures.

Thanks to Matt Pierce of Organic Chemistry Solutions for important contributions to this
post. Ask Matt about scheduling an online tutoring session here.

Answers to Q1: A) sp3 B) sp3 C) sp D) sp2 E) sp3

Answers to Q2: A) sp3 B) sp2 C) sp2 D) sp2 E) sp F) sp G) sp H) sp

Notes

Note 1. Some weird cases.

Unlikely to encounter these, but here goes:

What about higher block elements like sulfur and phosphorus?

Third row elements like phosphorus and sulfur can exceed an octet of electrons by incorporating
d-orbitals in the hybrid. This is more in the realm of inorganic chemistry so I don’t really want
to discuss it. Here’s an example for the hybridization of SF4 from elsewhere. (sp3d orbitals).

Note 2: For the 5 kcal/mol figure, see here. [Tetrahedron Lett, 1971, 37, 3437].

An amine connected to three different substituents (R1 R2 and R3) should be chiral, since it has in
total 4 different substituents (including the lone pair). However, all early attempts to prepare
enantiomerically pure amines met with failure. It was later found that amines undergo inversion
at room temperature, like an umbrella being forced inside-out by a strong wind.

In the transition state for inversion the nitrogen is trigonal planar. One can thus calculate the
difference in energy between the sp3 and sp2 geometries by measuring the activation barrier for
this process (notably by the work of Kurt Mislow (RIP)].

Note 3:A fun counter-example would be Coelenterazine .

One would not expect both nitrogen atoms to be sp2 hybridized, because that would lead to a
cyclic, flat, conjugated system with 8 pi electrons : in other words, antiaromatic. I can’t find a
crystal structure of the core molecule to confirm (but would welcome any additional
information!)

Orbital Hybridization And Bond Strengths

How Orbital Hybridization Affects Bond Strengths

Understanding the concept of hybrid orbitals (see previous post) lets you make accurate
predictions about trends in bond strengths. In this post we’ll give several examples of how to
do this.

Table of Contents

1. A Quick Quiz (On Bond Dissociation Energy)

2. Key Principle On Orbital Hybridization And Bond Strengths: The Greater The s-
character, The Stronger The Bond
 3. Electrons In s-Orbitals Are Closer To the Nucleus Than Electrons In The Corresponding
p-Orbitals
4. Summary: All Else Being Equal, The Greater The s-Character, The Stronger The Bond
5. Bonus Section: An Answer To A Question A Few People Might Be Asking
6. Homolytic versus Heterolytic Bond Cleavage
7. A Test For You
8. One Last Thing: This Concept Also Explains Why CH3+ Is More Stable Than NH3+
9. Notes

1. A Quick Quiz
Let’s start with a quick quiz.

What’s the strongest C–H bond, below?

(In other words, which C–H bond has the highest bond-dissociation energy?)

The answer is C.

 In a), the carbon is sp3 hybridized and the bond dissociation energy is 105 kcal/mol
 In b), the carbon is sp2 hybridized and the bond dissociation energy is 110 kcal/mol
 In c), the carbon is sp hybridized and the bond dissociation energy is 126 kcal/mol

2. Key Principle On Orbital Hybridization And Bond

Strengths: The Greater The s-character, The Stronger The
Bond

Note that the trend for bond strengths, above, is sp > sp2 > sp3
In other words, the more s-character on carbon, the stronger the bond.

Let’s try this again. What about these three C–C bonds?

Hopefully you ranked them A > B > C .

All else being equal: an sp-sp3 bond is stronger than an sp2-sp3 bond, which in turn is
stronger than an sp3-sp3 bond.

Why?

3. Electrons In s-Orbitals Are Closer To the Nucleus Than

Electrons In The Corresponding p-Orbitals
On average: electrons in s orbitals are closer to the nucleus (and therefore feel a greater effective
positive charge) than electrons in the corresponding p orbitals.

Electrons in an sp orbital (50% s-character) will therefore experience a greater attractive force to
the nucleus than electrons in an sp2 (33% s-character) or sp3 (25% s-character) orbital.

“Bond dissociation energy” (BDE) mentioned above, is a measure of the energy required
for homolytic cleavage of a bond (homo = same; lysis = breaking). [See post: Bond Dissociation
Energies = Homolytic Cleavage]

That is, it measures the energy required for breakage of the bond such that each atom ends up
with the same number of electrons, such as the reactions below:
In the homolytic cleavage reactions above, a single electron is removed from the C–H molecular
orbital and placed on hydrogen, which dissociates. The other electron remains on carbon.

The bond dissociation energy for the sp–H bond is higher than that for sp3–H because more
force (energy) is required to remove an electron from the more tightly-held sp–H molecular
orbital and place it exclusively on the hydrogen atom.

So electrons in an orbital with more s character will be closer to the nucleus and feel a stronger
electrostatic force.

This helps to explain the higher bond energy.

Recognizing the type of bonds in molecules is a key skill. (see also: C-C sigma bonds come
in six varieties, C-C pi bonds come in one).

For most purposes, this ends the key lesson of the post.

4. Summary: All Else Being Equal, The Greater The s-

Character, The Stronger The Bond
But… if you find yourself trying to reconcile an apparent contradiction that comes from another
part of the course, read on.

5. Bonus Section: An Answer To A Question A Few People

Might Be Asking
Alkynes (pKa 25) are stronger acids than typical alkanes (pKa > 50).

For example, alkynes are readily deprotonated by strong bases such as NaNH2, whereas alkanes
are not:
Why? Because the C–H bond in an alkyne has more s-character, and the resulting lone pair on
carbon is held more tightly to the nucleus, rendering the conjugate base more stable.

Oh dear. There seems to be an angry mob approaching.

WAIT! You just said that alkyne C–H bonds are stronger than alkane C–H bonds because they
have more s-character and now you are saying that they are easier to break because they have
more s-character.

Shouldn’t that make alkynes less acidic because the C–H bonds have more s-character?

HEY! If sp-H Bonds Are So

Strong, Then why are alkyne C-H bonds so acidic!!!???

Put away the pitchforks! There is a perfectly logical explanation for this!

6. Homolytic versus Heterolytic Bond Cleavage

What’s the source of the confusion here?

Let’s follow the electrons.

Ultimately the resolution to this dilemma is recognizing the difference

between homolytic cleavage (which is what bond dissociation energy measures)
and heterolytic cleavage (which is what occurs in an acid-base reaction, the loss of H+ ).

Let’s look at these two processes.

In homolytic cleavage of a C–H bond, an electron is completely removed from the vicinity of the
carbon and placed on hydrogen. Because of the greater s-character of the bond, it is more
difficult to remove an electron from an sp-hybridized carbon than from an sp3 hybridized carbon.
As we said above, that’s why the bond-dissociation energies for alkyne C–H bonds are higher
than for alkane C–H bonds.
In an acid-base reaction, the C–H bond also breaks, but it breaks in such a way that the pair of
electrons stays on the carbon atom. Since the bond breaks in a way that leads to an uneven
distribution of electrons, it is called heterolytic bond cleavage (hetero = different, lysis =
breaking).

Let’s say that again: in an acid base reaction, the pair of electrons stays on carbon, resulting in
a negatively-charged carbon atom (a “carbanion”).

Acidity, as measured by pKa, is a measure of the equilibrium between an acid and its conjugate
base. The more that the equilibrium favours the conjugate base, the lower the pKa and the
stronger the acid. In other words:

Any factor which makes the conjugate base more stable, increases acidity.

 In the conjugate base of an alkyne, the lone pair is held in an sp- orbital with 50% s-
character.
 In the conjugate base of an alkane, the lone pair is held in an sp3 orbital with 25% s-
character.

What lone pair will be more stable?

The lone pair held more tightly to the nucleus – that is, the sp-orbital.

That’s why alkynes are more acidic than alkanes: the conjugate base is more stable.

Hopefully this makes it clearer that stronger C–H bonds and greater C–H acidity are two sides of
the same phenomenon.

[You might find it helpful to think of sp orbitals as having a greater effective electronegativity
than sp2 orbitals, which in turn have a greater electronegativity than sp3 orbitals. So the reason
for the greater acidity of alkynes relative to alkenes is not really so different than the greater
acidity of H–F relative to H2O. ]

7. A Test For You

At the risk of droning on, there is a third side of this phenomenon to consider.

Homolytic cleavage can only happen one way. But there are two ways to draw heterolytic
cleavage of a C–H bond, and you might have noticed that I only showed one.

There’s a second (albeit unlikely) way heterolytic cleavage can happen. The pair of electrons in
the C–H bond could migrate instead to hydrogen, not carbon, resulting in a hydride anion and a
carbocation. [Again, very unlikely, but bear with me here].

Here’s a test I have for you. Based on everything we’ve gone through so far, which of the two
products below (A or B) would be more stable?

Think it through.

 To form A, we have to remove a pair of electrons from an sp-hybridized carbon.

 To form B, we have to remove a pair of electrons from an sp3-hybridized carbon.

What’s more favourable?

 Reaction to give A would require removing two electrons from an sp-hybridized carbon.
 Reaction to give B would require removing two electrons from an sp3 hybridized carbon.
The reaction to give B should be much easier, because the electrons are less tightly held. And
indeed, sp3-hybridized carbocations have been observed and even isolated.

In contrast, sp-hybridized carbocations such as A are extremely unstable and have never been
observed directly. [note 2]

This observation is also consistent with all the observations above!

8. One Last Thing: This Concept Also Explains Why CH3+

Is More Stable Than NH3+
As I said above, it can be helpful to think of sp-hybridized carbons as having a greater effective
electronegativity than sp2-hybridized carbons, which in turn have greater electronegativity than
sp3 hybridized carbons. We used this to rationalize why alkynes are stronger acids than alkanes,
similarly to why H-F is a stronger acid than H2O.

This can also be flipped around, just as in our carbocation example above.

The greater the electronegativity of the atom, the more unstable electron-deficient species
become.

This helps to explain why, for example, H3C+ (with six valence electrons) is much more stable
than H3N+ (also with six valence electrons) which in turn is far more stable than oxygen or
fluorine with six valence electrons; increasing electronegativity has the same effect on the
stability of electron-deficient species as increasing s-character.

OK. Enough!

Notes
Note 1: Here’s a notable attempt to make sp-hybridized carbocations. The only application of
helium in organic chemistry that I have ever seen.

Sigma bonds come in six varieties: Pi bonds

come in one
You may recall from Gen chem (and no doubt your first week of o-chem as well), that orbitals
on carbon come in two flavors: s and p.
s orbitals should be familiar as the spherical-shaped orbitals. The electrons of hydrogen, for
instance, are in a 1s orbital.

p orbitals are shaped like figure-eights, or loops. The electrons in p orbitals are slightly farther
away from the nucleus than those in s orbitals, so they are a little bit higher in energy. The p
orbitals therefore fill with electrons only after the s orbitals are filled.

Hybridization is a concept that hasn’t been addressed here yet, but there’s an excellent video
discussion of it here.

What’s observed from analyzing the structure of molecules such as CH4 is that the shapes cannot
result from the electrons being in s or p orbitals alone, but instead are a consequence of the
electrons in s and p orbitals mixing to form hybrid orbitals. If you draw an analogy to how we
could make a “hybrid” soft drink by mixing different proportions of Sprite and Pepsi, these new
orbitals aren’t fully s or fully p, but are a combination of both. The “flavor” of each bond
depends on the relative proportions of s orbital and p orbital content:

sp3 = 25% s character, 75% p character

sp2 = 33% s character, 66% p character

sp = 50% s character, 50% p character.

It is these hybrid orbitals that form sigma bonds (σ bonds). Sigma bonds are created from the
head-on overlap of orbitals. Those orbitals will be some combination of s orbitals and p orbitals.

[What’s happened to the missing p orbitals for sp2 and sp hybridized carbon? Well, these p
orbitals aren’t involved in hybridization or in sigma bonding – instead, they maintain 100% p
character, are available to form π bonds, which are created by the side-by-side overlap of
orbitals. π bonding involves p orbitals exclusively.*]

Since carbon can exist in one of these three hybridization states, we can therefore have six
varieties of carbon-carbon sigma bonds:

Now, recall that for any given quantum number, s orbitals are lower in energy than p orbitals.
The electrons in s orbitals are held more closely to the nucleus than electrons in p orbitals. Take
a look at the relative bond lengths and strengths for each of these six situations.
General principle – the more s character the bond has, the more tightly held the bond will
be.

[Note that this is also why the protons in acetylene are more acidic than those in ethene and
ethane – the electrons in the conjugate base are more tightly held, making them more stable. If it
seems contradictory that the bond is both stronger and yet more easily broken, remember that
bond energies measure homolytic cleavage]

Now, the number of π bonds that can form will be dependent on the number of unhybridized p
orbitals available – 1 for sp2 hybridized carbons, 2 for sp hybridized carbons (the two π
bonds will be at right angles to each other in the latter case).

In contrast to sigma orbitals, there is only one way to form a C-C π bond – from the
overlap of two p orbitals.

Question: Relative to sigma bonds, do you think p-p bonds (π bonds) would be stronger or
weaker?

1) What’s their % s-character?

2) Energy required to break C-C bond in ethane:

Energy required to break apart the C=C bond in ethene:

*green text = not the whole truth! ( but close enough for your course)

(Advanced) References And Further Reading

1. Tables of bond lengths determined by X-ray and neutron diffraction. Part 1. Bond
lengths in organic compounds. Allen, F. H.; Kennard, O.; Watson, D. G. ; Brammer, L.;
Orpen, A. G.; Taylor, R. J. Chem. Soc., Perkin Trans. 2, 1987, S1-S19
DOI: 10.1039/P298700000S1
A useful reference, this paper collects bond lengths of various organic compounds
determined from X-ray crystal diffraction data.

A Key Skill: How to Calculate Formal

Charge
Hey! Welcome to Master Organic Chemistry, just in case you’re a first time visitor.
In this blog post I explain how to calculate formal charge for molecules. However, you
might find my videos containing 10 solved examples of formal charge problems to be even
more useful. Just thought you should know!

Need to figure out if an atom is negative, positive, or neutral? Here’s the formula for figuring
out the “formal charge” of an atom:

Formal charge = [# of valence electrons] – [electrons in lone pairs + 1/2 the number of bonding
electrons]

This formula explicitly spells out the relationship between the number of bonding electrons and
their relationship to how many are formally “owned” by the atom. However, since the “number
of bonding electrons divided by 2” term is also equal to the number of bonds surrounding the
atom, here’s the shortcut formula:

Formal Charge = [# of valence electrons on atom] – [non-bonded electrons + number of bonds].

Let’s apply it to some examples. for example BH4 (top left corner).

 The number of valence electrons for boron is 3.

 The number of non-bonded electrons is zero.
 The number of bonds around boron is 4.

So formal charge = 3 – (0 + 4) = 3 – 4 = –1

The formal charge of B in BH4 is negative 1.

Let’s apply it to :CH3 (one to the right from BH4)

 The number of valence electrons for carbon is 4

 The number of non-bonded electrons is two (it has a lone pair)
 The number of bonds around carbon is 3.

So formal charge = 4 – (2 +3) = 4 – 5 = –1

The formal charge of C in :CH3 is negative 1.

Same formal charge as BH4!

Let’s do one last example. Let’s do CH3+ (with no lone pairs on carbon). It’s the orange one on
the bottom row.

 The number of valence electrons for carbon is 4

 The number of non-bonded electrons is zero
 The number of bonds around carbon is 3.

So formal charge = 4 – (0 +3) = 4 – 3 = +1

You can apply this formula to any atom you care to name.
Here is a chart for some simple molecules along the series B C N O . I hope beryllium and
fluorine aren’t too offended that I skipped them, but they’re really not that interesting for the
purposes of this table.

Note the interesting pattern in the geometries (highlighted in colour): BH4(–), CH4, and NH4(+)
all have the same geometries, as do CH3(–), NH3, and OH3(+). Carbocation CH3(+) has the same
electronic configuration (and geometry) as neutral borane, BH3. The familiar bent structure of
water, H2O, is shared by the amide anion, NH2(–). These shared geometries are one of the
interesting consequences of valence shell electron pair repulsion theory (VSEPR – pronounced
“vesper“, just like “Favre” is pronounced “Farve”.)

The formal charge formula also works for double and triple bonds:

Here’s a question. Alkanes, alkenes, and alkynes are neutral, since there are four bonds and no
unbonded electrons: 4 – [4+0] = 0. For what other values of [bonds + nonbonded electrons]
will you also get a value of zero, and what might these structures look like? (You’ll meet some
of these structures later in the course).

One final question – why do you think this is called “formal charge”?
Think about what the formal charge of BF4 would be. Negative charge on the boron. What’s the
most electronegative element here? Fluoride, of course, with an electronegativity of 4.0, with
boron clocking in at 2.0. Where do you think that negative charge really resides?

Well, it ain’t on boron. It’s actually spread out through the more electronegative fluoride ions,
which become more electron-rich. So although the “formal” address of the negative charge is on
boron, the electron density is actually spread out over the fluorides. In other words, in this case
the formal charge bears no resemblance to reality.

Partial Charges Give Clues About Electron

Flow
There’s a hidden layer of detail beneath chemical structures that students new to organic
chemistry often miss.

I’m talking about partial charges.

Although each of these bonds appears to be covalent, the electronegativity of each atom
determines how “greedy” it is for electrons – and this means that many bonds that look “neutral”
are actually polarized.

Why is this important? Because attraction between opposite charges is the ultimate driving force
in so many chemical reactions. You can see how these “hidden” partial charges provide an
important clue for how these reactions proceed.

Note – the arrows show the movement of a pair of electrons (electrons truly are to organic
chemistry what currency is to economics – it’s all about the study of their flow).

Note how the arrows always flow from negative to positive – never the opposite way.
It’s why a knowledge of electronegativity trends is absolutely crucial to doing well in organic
chemistry

The Four Intermolecular Forces and How

They Affect Boiling Points
Properties like melting and boiling points are a measure of how strong the attractive forces are
between individual atoms or molecules. (We call these intermolecular forces –
forces between molecules, as opposed to intramolecular forces – forces within a molecule. )

It all flows from this general principle: as bonds become more polarized, the charges on the
atoms become greater, which leads to greater intermolecular attractions, which leads to higher
boiling points.

There are four major classes of interactions between molecules and they are all different
manifestations of “opposite charges attract”.

Now available – Download this awesome (free) 3-page handout on how to solve common
boiling point problems. With 10 examples of solved problems! (Also contains all the key
points discussed in this post)

MOC_Boiling_Point_Handout (PDF)

The four key intermolecular forces are as follows:

Ionic bonds > Hydrogen bonding > Van der Waals dipole-dipole interactions > Van der
Waals dispersion forces.

Let’s look at them individually, from strongest to weakest.

Ionic forces
Ionic are interactions between charged atoms or molecules (“ions”). Positively charged ions,
such as Na(+) , Li(+), and Ca(2+), are termed cations. Negatively charged ions, such as Cl(–),
Br(–), HO(–) are called anions (I always got this straight through remembering that the “N” in
“Anion” stood for “Negative”) The attractive forces between oppositely charged ions is
described by Coulomb’s Law, in which the force increases with charge and as decreases as the
distance between these ions is increased. The highly polarized (charged) nature of ionic
molecules is reflected in their high melting points (NaCl has a melting point of 801 °C) as well
as in their high water solubility (for the alkali metal salts, anyway; metals that form multiple
charges like to leave residues on your bathtub)
Hydrogen bonding
Hydrogen bonding occurs in molecules containing the highly electronegative elements F, O,
or N directly bound to hydrogen. Since H has an electronegativity of 2.2 (compare to 0.9 for
Na and 0.8 for K) these bonds are not as polarized as purely ionic bonds and possess some
covalent character. However, the bond to hydrogen will still be polarized and possess a dipole.

The dipole of one molecule can align with the dipole from another molecule, leading to an
attractive interaction that we call hydrogen bonding. Owing to rapid molecular motion in
solution, these bonds are transient (short-lived) but have significant bond strengths ranging from
(9 kJ/mol (2 kcal/mol) (for NH) to about 30 kJ/mol (7 kcal) and higher for HF. As you might
expect, the strength of the bond increases as the electronegativity of the group bound to hydrogen
is increased.

So in a sense, HO, and NH are “sticky” – molecules containing these functional groups will tend
to have higher boiling points than you would expect based on their molecular weight.

Van Der Waals Dipole-Dipole Interactions

Other groups beside hydrogen can be involved in polar covalent bonding with strongly
electronegative atoms. For instance, each of these molecules contains a dipole:

These dipoles can interact with each other in an attractive fashion, which will also increase the
boiling point. However since the electronegativity difference between carbon (electronegativity
= 2.5) and the electronegative atom (such as oxygen or nitrogen) is not as large as it is for
hydrogen (electronegativity = 2.2), the polar interaction is not as strong. So on average these
forces tend to be weaker than in hydrogen bonding.

Van der Waals Dispersion Forces (“London forces”)

The weakest intermolecular forces of all are called dispersion forces or London forces. These
represent the attraction between instantaneous dipoles in a molecule. Think about an atom like
argon. It’s an inert gas, right? But if you cool it to –186 °C, you can actually condense it into
liquid argon. The fact that it forms a liquid it means that something is holding it together. That
“something” is dispersion forces. Think about the electrons in the valence shell. On average,
they’re evenly dispersed. But at any given instant, there might be a mismatch between how many
electrons are on one side and how many are on the other, which can lead to an instantaneous
difference in charge.
It’s a little like basketball. On average, every player is covered one-on-one, for an even
distribution of players. But at any given moment, you might have a double-team situation where
the distribution of players is “lumpy” (it also means that somebody is open). In the valence shell,
this “lumpiness” creates dipoles, and it’s these dipoles which are responsible for intermolecular
attraction.

The polarizability is the term we use to describe how readily atoms can form these instantaneous
dipoles. Polarizability increases with atomic size. That’s why the boiling point of argon (–186
°C) is so much higher than the boiling point of helium (–272 °C). By the same analogy, the
boiling point of iodine, (I-I, 184 °C) is much higher than the boiling point of fluorine (F-F, –
188°C).

For hydrocarbons and other non-polar molecules which lack strong dipoles, these dispersion
forces are really the only attractive forces between molecules. Since the dipoles are weak and
transient, they depend on contact between molecules – which means that the forces increase with
surface area. A small molecule like methane has very weak intermolecular forces, and has a low
boiling point. However, as molecular weight increases, boiling point also goes up. That’s
because the surface over which these forces can operate has increased. Therefore, dispersion
forces increase with increasing molecular weight. Individually, each interaction isn’t worth
much, but if collectively, these forces can be extremely significant. How can a gecko lizard walk
on walls? Look at its feet.

[Determining trends for hydrocarbons can get a little bit tricky depending on the exact structure –
symmetry also plays a role in boiling points and melting points. I talked about this in detail
previously.]

Bottom line:
1. Boiling points are a measure of intermolecular forces.
2. The intermolecular forces increase with increasing polarization of bonds.
3. The strength of intermolecular forces (and therefore impact on boiling points) is ionic >
hydrogen bonding > dipole dipole > dispersion
4. Boiling point increases with molecular weight, and with surface area.

For another discussion of these principles see Chemguide

3 Trends That Affect Boiling Points

Now available – Download this awesome (free) 3-page handout on how to solve common
boiling point problems. With 10 examples of solved problems! (Also contains all the key
points discussed in this post)

MOC_Boiling_Point_Handout (PDF)

Figuring out the order of boiling points is all about understanding trends. The key thing to
consider here is that boiling points reflect the strength of forces between molecules. The more
they stick together, the more energy it will take to blast them into the atmosphere as gases.

There are 3 important trends to consider.

1. The relative strength of the four intermolecular forces is: Ionic > Hydrogen bonding >
dipole dipole > Van der Waals dispersion forces. The influence of each of these attractive
forces will depend on the functional groups present.
2. Boiling points increase as the number of carbons is increased.
3. Branching decreases boiling point.

Let’s have a closer look:.

Trend #1: The relative strength of the four intermolecular

forces .
Compare the different butane alcohol derivatives shown below. Molecules of diethyl ether,
C4H10 O, are held together by dipole-dipole interactions which arise due to the polarized C-O
bonds. Compare its boiling point of (35 °C)with that of Its isomer butanol (117 °C). The greatly
increased boiling point is due to the fact that butanol contains a hydroxyl group, which is capable
of hydrogen bonding. Still, the attractive forces in butanol pale in comparison to those of the salt
sodium butoxide, which melts at an extremely high temperature (well above 260 °C) and actually
decomposes before it can turn into a liquid.

Then think about butane, C4H10, which contains no polar functional groups. The only attractive
forces between individual butane molecules are the relatively weak Van der Waals dispersion
forces. The result is that butane boils at the temperature at which water freezes (0° C), far below
even that of diethyl ether.
Moral of the story: among molecules with roughly similar molecular weights, the boiling points
will be determined by the functional groups present.

You could tell a similar tale for the similar amine and carboxylic acid isomers shown below.

For a previous discussion of the 4 intermolecular forces, see here. For the reference in Reusch’s
textbook, see here.

Trend #2 – For molecules with a given functional group,

boiling point increases with molecular weight.
Look at the dramatic increases in boiling points as you increase molecular weight in all of these
series:
Here’s the question: How, exactly do intermolecular forces increase as molecular weight
increases?

Well, the key force that is acting here are Van der Waals dispersion forces, which are
proportional to surface area. So as you increase the length of the chain, you also increase the
surface area, which means that you increase the ability of individual molecules to attract each
other.

On an intuitive level, you could compare these long molecules to strands of spaghetti – the
longer the noodles, the more work it takes to pull them apart. As the chain length increases, there
will be regions where they can line up next to each other extremely well.

Individually, each interaction might not be worth very much, but when you add them all up over
the length of a chain, Van der Waals dispersion forces can exert tremendous effects.

3. Symmetry (or lack thereof).

This is another byproduct of the surface-area dependence of Van der Waals dispersion forces –
the more rod-like the molecules are, the better able they will be to line up and bond. To take
another intuitive pasta example, what sticks together more: spaghetti or macaroni? The more
spherelike the molecule, the lower its surface area will be and the fewer intermolecular Van der
Waals interactions will operate. Compare the boiling points of pentane (36°C) and 2,2-dimethyl
propane (9 °C).
It can also apply to hydrogen bonding molecules like alcohols – compare the boiling points of 1-
pentanol to 2-pentanol and 3-pentanol, for instance. The hydroxyl group of 1-pentanol is more
“exposed” than it is in 3-pentanol (which is flanked by two bulky alkyl groups), so it will be
better able to hydrogen bond with its fellows.

In summary, there are three main factors you need to think about when confronted with a
question about boiling points. 1) what intermolecular forces will be present in the molecules? 2)
how do the molecular weights compare? 3) how do the symmetries compare?

One last quick question for the road (see comments for answer).

P.S. New! Check out this free 3-page handout on solving common boiling point exam
problems!

How To Use Electronegativity To Determine

Electron Density (and why NOT to trust
formal charge)
Last time we talked about how electrons are the “currency” of chemistry and every reaction is a
transaction of electrons between atoms. That means that if we really want to understand a
reaction, we have to understand where the electrons are (and aren’t).

There’s two factors to employ when doing this. The first is electronegativity. That’s what today’s
post is about: using electronegativity to determine electron densities. (The second is
resonance BTW – more on that in future posts)

I’m assuming you know how to draw Lewis structures and understand the concepts of
electronegativity and formal charge, as well as being able to interpret line drawings, but that’s
it. If you’re not at that level, back up and read up on those concepts.

OK. Let’s start with the first question: how do we tell where the electrons are in a molecule?

The first skill is being able to draw proper Lewis structures for a molecule. To succeed in
organic chemistry you absolutely need to be able to do this in your sleep. The Lewis
structure should account for all the electrons around an atom, including the often-hidden lone
pairs of electrons if applicable. Let’s have a look.
The second skill lies in being able to apply electronegativity to determine partial charges in
bonds.

See, our drawings of chemical structures can sometimes get in the way of what is really going
on with the electrons.

If we just paid attention to the drawings themselves, the lines we draw between atoms –
“covalent bonds” – are electron pairs that are shared equally between the two.

However, the difference between the idealized sharing of electrons in a covalent bond versus the
reality of different electron densities is, to use an analogy, not unlike the difference between a
utopian socialist worker-state, and Soviet Russia.

Remember electronegativity – a ranking of an atom’s “greed” for electrons, in other words? In a

bond, the more electronegative element will have a greater share of the electrons, and a
partial negative charge to reflect this greater electron density. The less electronegative
element will have a partial positive charge to reflect the lack of electron density.

Let’s look at a few simple molecules and analyze the dipoles in their bonds by comparing
relative electronegativities. Remember the mnemonic for electronegativity? “Phone call bro….
CSI is on, please hold…. bye” .
Why is it important to go through all of this? Because in chemical reactions, electrons will
flow from areas of high electron density to areas of low electron density. Knowing where
the partial charges are is an important first step in determining where the molecule will
react. Covalent bonds with large dipoles (i.e. large differences in electronegativity) are worth
looking paying attention to: frequently, this will be where the “action” is.
“Hold on”, you might say. “I thought electron densities were reflected by their charges, like in
H3O+, BF4-, and NH2- !” No no no no no. This is one of the first real curveballs that gets
thrown at you in organic chemistry, and one that continually gives students fits.

Formal charge is NOT the same as electron density.

“Formal charge” gives us a bit of a dilemma. When a molecule bears a charge (either positive or
negative), for bookkeeping purposes, we have to denote one atom as “bearing” that charge.
However it’s important to realize that this “bookkeeping” is NOT the same as electron density,
which is the real sources of reactivity. Sure, there are lots of examples of molecules where the
charge actually *does* represent the electron density. But then again, there are a lot of counter
examples too – like BH4(-), NH4(+), H3O(+) and others.
Make sure you understand this because it might be hard to get your head around the first time.

The O in H3O+ might have a “formal” charge of +1, but it is actually the most electron-rich (i.e.
negatively charged) atom on the molecule!

So although the molecule H3O(+) has a charge of +1, that positive charge is actually not on the
oxygen itself, but is “spread out” – dispersed – around the molecule, but particularly around the
hydrogens.( Click here to see a potential energy map of H3O(+) ). However, for “book-keeping”
we assign a charge of +1 on the oxygen, because of the underlying assumption in bond diagrams
that electrons are shared equally between atoms.

Bottom line: if H3O(+) is reacting with an electron rich species, those electrons will go to the
hydrogens (since they are electron poor), NOT the oxygen!!

If you use formal charge to determine electron densities you will get screwed over on a
regular basis.

I apologize for writing such a long post but let’s finish by applying this concept toward some
potential attractive and repulsive interactions between molecules. These are not meant to depict
actual reactions, although as we will later see, reactions will begin with an attractive interaction
between two molecules. Conversely, where we line up two like charges (positive-positive and
negative-negative) these are sites where repulsion will occur (and reactions between these atoms
will not occur).

Bottom line #2: If you learn electronegativities and how to assign partial charges, you will
be always be able to figure out where the electron rich and electron poor areas of a
molecule are, and we can apply this toward reactions.
Things will get a bit more complicated when resonance is possible. More on that in the next
post.

Note how on the last part of the 3rd slide I threw in some new words – “electrophilic” and
“nucleophilic” to denote “electron-poor” and “electron-rich” respectively. Much more on these
later.
Here’s an excellent online resource on the topic of electrostatic potential in organic chemistry
from Reed College.

Introduction to Resonance
Last time we talked about how to use electronegativity to find the electron densities in a
molecule – and when to ignore formal charge.

However I didn’t mention a second key factor that can complicate the analysis of electron
densities: the presence of double bonds (π bonds). In this post we will see how combining an
understanding of dipoles with an understanding of the “best” distribution of pi-electrons in a
molecule will give us an overall picture of where electrons are in a molecule.

[Further down the line, an understanding of where the electrons are will help us understand
where the molecule will participate in reactions. ]

Applying Electronegativity Differences To Understand

Electron Densities In Molecules With Pi Bonds – Simple
Examples
But let’s start with the simple stuff. In many cases, an analysis of electronegativities can give you
a very accurate idea of where electron densities are in molecules with π bonds. This can tell you
where the “dipoles” are.

Which atom is more electronegative? That’s the one that will be “delta-negative”. Simple
enough.

By the way, this model is very effective for finding the reactive sites in these molecules. Here are
two examples.

See how the H+ is attracted to the partially negative oxygen, and the HO- is attracted to the
partially positive carbon.
Experiments support our prediction that the positively charged acid (i.e. “H+”) will react at the
“negative” atom bearing the electrons (oxygen in this case) while negatively charged hydroxide
(HO-) will react at the atom bearing the partially positive charge (C in this case).

So far so good.

The problem with our model so far is that it doesn’t allow us to make accurate predictions in
some cases.

Two Cases Where “Applying Electronegativity Differences”

Fails To Accurately Predict Electron Density
Part of the experience of being a scientist is watching your very simple, appealing
hypotheses/models get ripped to shreds by experimental evidence (or lack thereof).

Look at these two molecules below. The Lewis structure of the first molecule (“acetate ion”)
appears to tell us that one oxygen is more negative than the other.

The Lewis structure of the second molecule (the “allyl carbocation”) suggests that one carbon
bears the positive charge and the others are neutral.

We’d predict from this model that the more “negative” oxygen would be more reactive than the
neutral oxygen, and likewise for the “positive” and neutral carbons. However, if we test this
model by using labelled compounds, we find that our simple model is inconsistent with
experiment.

What happens with the first molecule (acetate ion) is that each of the two oxygens is equally
reactive with H+.

And in the second example, each of the terminal carbons is equally reactive with
nucleophiles.
Something is clearly lacking in our model. Let’s look at these molecules again.

If you look closely it’s possible to draw two different Lewis structures for these molecules.

From the experiments above, the molecules behave like they are a 1:1 mixture of these two
compounds. [They are not, but they behave that way!]

Let’s introduce a new concept: Resonance.

In These Two Cases The “True” Electron Densities Are

Reflected By A “Hybrid” of Two Resonance Structures
When we can draw two (or more) forms of the same molecule that differ only in the placement of
their electrons, these are called “resonance forms” (or “resonance structures”). We can also
say these forms are “in resonance”. Sometimes they are also called resonance “isomers” although
this will get a hand-slap in many circles, as they are not technically isomers.
It is tempting (and very wrong!) to think that these two forms are in “equilibrium” between each
other. Avoid this common mistake!

Why is this wrong? Because were this true, the bond lengths of the C=O double bond and the
C–O single bond in the acetate ion would be different. (1.21 vs. 1.36 Angstrom). However
experimental evidence (from X-ray crystal structures) shows us that each bond length is exactly
the same (1.26 Angstrom). This observation has been made for countless other resonance
isomers as well, such as benzene, carbonate, nitro groups, and many more.

What this means is that the true structure of the acetate ion (and the allyl carbocation) is a
“hybrid” of two resonance forms. We use a special arrow to depict the two resonance forms (the
double-headed arrow).

What this means is that the formal charge of –1 in the acetate ion is distributed evenly between
the two oxygens. And the formal charge of +1 in the allyl carbocation is distributed equally
between the two terminal carbons. [Note 1]. As we learned last time, formal charge can be a
poor guide to electron densities, so here we see another example where it’s inaccurate.

Again: electron densities are what really matters for understanding the reactivity of a
molecule. Lewis structures and formal charges are imperfect guides to fully describing electron
densities in molecules, but they’re so useful in many other contexts that we have to learn to live
with their flaws.

However, a combination of understanding dipoles (electronegativity differences) and resonance

will complete the picture for us.

Next post we’ll talk about another accounting system we will use to describe the movement of
electrons: the curved arrow formalism.

Next Post: Introduction to Curved Arrows (2): Curved Arrows!

[Note 1: These are simple examples. Charge distribution will not always be evenly divided, and
resonance forms will not always be of equal energy – more on that in future posts]
How To Use Curved Arrows To Interchange
Resonance Forms
Last time in this series on resonance, we saw that resonance forms represent two (or more)
different ways to draw the same molecule, which differ only in their distribution of electrons.

What’s different in the molecules below? Specifically, what bonds formed and broke? Where did
the electrons actually go?

In both cases the resonance form on the right contains all the same atoms of the molecule on the
right, but the electrons have been moved around (or to be more specific, electron pairs).

There are two places we will find electron pairs: they will either be found in bonds or as lone
pairs on atoms. That’s it. For the purposes of discussing resonance, we’ll confine our discussion
of “bonds” to π bonds exclusively.

Here’s the punch line: we can convert one resonance form into another by showing the
movement of electrons between bonds and lone pairs (or vice versa).

We just need a graphical tool to do it. Thankfully, Robert Robinson devised such a tool for us to
use. It’s called the “curved arrow”.
The curved arrow shows “movement” of a pair of electrons. It’s an extremely useful accounting
system that lets us keep track of changes in bonding and also in charge. Since electron pairs are
present either in bonds or in lone pairs, there are really only four combinations of “moves”. Only
three of them are actually legal.

Every resonance form for a molecule can be found through the application of these three
moves.

Let’s look at them in detail.

If you look closely, with each arrow we are changing the formal charge by 1. The charges
change at the tail, which becomes more positive (since it’s giving away electrons), and the head,
which becomes more negative (since it’s gaining electrons).

Note that last example, lone pair to lone pair, is not legal. It’s illegal because we are changing
the formal charge at each carbon by 2 units (from –1 to +1 and from +1 to –1). This is not
allowed for a single arrow.

Here’s some common “dumb” questions about curved arrows.

 Does it matter which side of the bond the arrows are on? No
 If an atom has multiple lone pairs, does it matter which one you use? No
 Are we ever allowed to give an atom more than 8 electrons? NOOOOOO (at least not
with C, N, O, F).
 I’m lazy. Can’t I just draw the “tail” as coming from the negative charge and skip putting
in the lone pairs? YES

This brings up an excellent point. When it comes to drawing, chemists are ingenious at finding
ways to be lazy. We can also draw the tail of curved arrows as coming from negative
charges (as long as there are electrons on that atom, remember how formal charge can be
misleading).

This makes our lives a little easier because who really wants to draw lone pairs if they don’t have
to? From now on in this series I’m only going to draw in the lone pairs if absolutely
necessary. Otherwise I’ll just draw the curved arrow as coming from the negative charge.

Just be careful, however – if the atom is neutral, you MUST draw in a lone pair of electrons.
Never draw the tail of a curved arrow from an atom with no lone pairs.

This covers the basics of the curved arrow formalism. Now that we can start to use curved
arrows to draw resonance structures, we can also think about how to evaluate the relative
importance of some simple resonance structures. That’s the subject of the next post.

Next Post: Evaluating Resonance Forms (1): The Rule of Least Charges

Just to show another application I’ve drawn in a second, detailed breakdown of arrow pushing in
the carboxylate ion we discussed last time. Yes, it’s ridiculous in detail but sometimes that helps.
Evaluating Resonance Forms (1) – The Rule
of Least Charges
So far I’ve talked about resonance, and introduced the curved arrow formalism to show the
movement of electrons. Importantly, we’ve talked about how the “true” picture of a molecule is a
hybrid of its resonance forms (and not an equilibrium between forms).

Here’s a recap of the different “moves” we can perform on a molecule to get different resonance
forms. Every resonance form we can draw for a molecule can be made through a combination of
these three moves.
We can apply these “moves” so long as we don’t break the octet rule. The thing is that if we
start looking at even simple molecules, we can soon get lost in a maze of potential resonance
forms if we apply the arrow-pushing rules willy-nilly. So let’s cut to the main problem: how do
we evaluate the stability of different resonance forms? In other words, which are lower
energy (more significant) and which are higher energy (less significant).

Here’s the punch line for today:

Let’s look at three examples. Really simple ones, but they’ll do.

The simplest molecule with a π bond is ethene. If we draw a resonance form for it, we can move
the π bond to the lone pair of one of the end carbons (doesn’t matter which one) to give a
carbocation and a lone pair. This is a “legal” resonance form, since we’re not breaking the octet
rule.

The question is, how significant is the resonance form with the two charges? The answer from
experiment is: not very much. If you measure the electronic and structural properties of ethene,
it’s clear that the carbon-carbon bond length is shorter than that of a normal carbon-carbon single
bond, implying a strong interaction between the two atoms. Furthermore, if the resonance form
on the right were significant, we’d expect ethene to have a relatively high boiling point (since it’s
charged) and be quite soluble in polar solvents like water. In fact, ethene boils at a very low
temperature (–88 C) and is practically insoluble in polar solvents. So it’s safe to conclude that
the resonance form on the right is quite insignificant.

(One thing to note – the NET charge of each resonance form is the same here (i.e. they both have
a net charge of zero) since on the resonance form on the right, the opposite charges cancel).
Let’s now look at the resonance forms of the allyl carbocation. The net charge on the allyl
carbocation is +1. When we apply the relevant arrow-pushing “moves” to it, we get something
like this, with 4 resonance forms – A, A’ , B, and C. Resonance forms A and A’ both have one
charge. Resonance forms B and C have three charges. [Although again, note that B and C each
have a net charge of +1 when you cancel the opposite charges].
So what does experiment tell us? Our best experimental evidence for the structure of the allyl
carbocation tells us that the positive charge is distributed equally between the two end carbons,
with a bond length intermediate between that of a C–C single bond (1.50 Å) and a C–C π bond
(1.40 Å). That is to say, the resonance hybrid of fhe allyl carbocation is a 1:1 mixture of
resonance forms A and A’. Resonance forms B and C don’t contribute to the resonance hybrid to
any significant extent.

Finally, let’s look at the allyl anion. We can use a similar application of the arrow pushing rules
to get the different resonance forms, although here’s a twist. Note that we can’t move the end
lone pair to form a new π bond without breaking the octet rule! So in this case we actually have
to draw two arrows to make it legal. This gets us to the equivalent resonance form, A’.

On the other hand the other resonance forms (B and C) can be obtained through a fairly
straightforward process (move a π bond to form a lone pair on either carbon.) Again, however,
these resonance forms don’t contribute much to the overall resonance hybrid. Experiment tells us
that the electron density on the allyl anion is on the ends, and the bond lengths are again
intermediate between a C–C single bond and a C–C π bond. The best interpretation of this data
is that the allyl carbanion is a 1:1 mixture of the resonance forms A and A’.

So again, the bottom line is that the most stable (and significant) resonance forms will be
those with the fewest charges.

You’ve probably noticed however that these examples are pretty simple – we’re just dealing with
carbon atoms. What happens when we deal with unsymmetrical resonance forms? We’ll need to
introduce a new principle for that.
Next Post: Evaluating Resonance Forms (2): Applying Electronegativity

Edit: removed “we’d expect to see a dipole for ethene” from the paragraph beginning with “The
question is?..”. Thanks Jess for the tip.

Evaluating Resonance Forms (2): Applying

Electronegativity
The last time I talked about evaluating resonance structures the molecules were, to be honest –
pretty simple. Evaluating the resonance structures of ethene, the allyl carbocation, and the allyl
carbanion are a pretty far cry from some of the more complicated structures you’ll see in a
typical course. So today I thought I’d start to talk about the (much more common) situation when
you have a π bond between two dissimilar atoms. How do you evaluate the resonance forms in
these cases?

We’re going to have to go back to using our old friendly measuring stick, electronegativity for
this task. Here’s the bottom line lesson for the resonance structures we’ll evaluate today.

Hopefully this makes some sense! Charged resonance forms are less stable than neutral
resonance forms. So if we absolutely must form a charged resonance form, it makes sense to put
the negative charge on the atom best able to stabilize it. How do we know which atoms stabilize
negative charge the best? Well, a pKa table will give you a really good idea. But beyond that, if
you look at the five key factors that influence acidity, one of the most important factors is the
electronegativity of an atom. After all, electronegativity is ultimately a measure of to what
extent an atom is able to stabilize negative charge.

So hopefully it should come as no surprise as we walk through these three examples that the
second-best resonance forms are the ones where negative charge ends up on the more
electronegative atom.

Let’s start by looking at a simple carbonyl compound, acetone (2-propanone).

If we look at the possible curved-arrow “moves” for drawing the resonance forms of this
molecule, there’s two possibilities. In the first possibility, we draw an arrow from the π bond to
the oxygen atom, putting a negative charge on the oxygen and leaving behind a positive charge
on the carbon. In the second, we’re making the carbon negative and leaving behind a positive
charge on the oxygen. Not only is there a positive charge on the oxygen, it has less than a full
octet. This is an extremely unstable situation. So hopefully it’s clear that the resonance form
where there is a negative charge on oxygen is the second-best resonance form next to the neutral
one, and the resonance form where there is a negative charge on carbon is insignificant.
Experiment bears this out. Calculations of the charge density on acetone reveal that the carbon is
electropositive and the oxygen is electronegative, as per what we’d expect from electronegativity
differences. So the molecule can be thought of as a hybrid of the best and second-best resonance
forms.
Likewise, the resonance forms for the imine below similar behavior. As expected, calculations of
electron density for this imine show that there is considerable positive charge density on the
carbon and a high density of negative charge on the nitrogen. As you’d expect, the resonance
form where there’s negative charge on carbon gets very little weight.
Finally we come to the acetate ion, which we discussed previously. Again, the second-best
resonance form is that where there’s a positive charge on the carbon (and the worst is the one
where it bears a negative charge).

With these examples in mind, can you apply the rule to determine the “second-best” resonance
forms for each of these molecules?
Click here for answers

Next time I’ll go into a few more details on evaluating resonance forms based on lessons we
learn from acidity and basicity.

Next Post: Evaluating Resonance Forms (3) – Where to Put Negative Charges

Evaluating Resonance Forms: Factors That

Stabilize Negative Charges
So far in discussing resonance forms we’ve mentioned two important principles that govern
which resonance form will be most important.

1. Minimize total point charges: the resonance form with the fewest charges will be the
most important. (which is OK think of as “most stable”, even if resonance forms don’t actually
exist).

2. How to break π bonds. If you absolutely must break a π bond to make a resonance form, dit
is best to do it in a way so that the pair of electrons end up on the more electronegative
atom of the π bond.

That second rule is a handy one to live by, but it’s just a representation of a more general
principle when it comes to resonance (and organic chemistry in general):

All else being equal, a resonance form with a negative charge

on a less basic atom will be more important than a negative
charge on a more basic atom.
You could argue that this definition is circular, because basicity is essentially a measure of the
stability of an anion. OK, fine. The more stable an anion is, the less basic it is. So how do we
go about finding out information on basicity? My suggestion is to visit your best friend, the pKa
table. Or you could familiarize yourself with the key trends that affect acidity, and apply these
concepts to resonance forms.

Let’s go these trends them one by one.

Factor 1: Electronegativity
Recall that basicity decreases as the electronegativity of an atom increases.

That means that in comparing two resonance forms of equal charge, we can determine which is
more stable by examining the electronegativity. In the examples above, we can tell that the
resonance forms on the left are more stable than the resonance forms on the right, since the
electronegativity of O > N and also O > C. There are a lot of chemical structures that have
resonance forms with alternating charges on C and N (or O), so this is a particularly useful rule.

Factor 2: Polarizability.
The basicity of an atom decreases as the polarizability increases. This trend especially applies for
atoms in the same column of the periodic table, such as O and S.
Factor 3: Inductive effects.
Basicity decreases as the negative charge is stabilized by adjacent electron withdrawing groups.
So in the cases below, the more stable resonance form is the one where the negative charge is on
the atom with the extra electron withdrawing groups. [Note 1]

But it ain’t always straightforward. Organic chemistry being what it is, it’s common to have
situations where we have to weigh the effects of multiple variables. Like in these examples.

What do we do here? We rely on experimental results. One body of work in this area is the
pKa table, an experimentally derived guide to the multi-variable dependent phenomenon of
acidity. Another is to compute the relative energies computationally. Or, a third is simply to
apply the 4 principles we’ve discussed earlier to the situation at hand and see which act in the
same direction and which oppose. At least 3 of the examples here should be fairly
straightforward to figure out .

Make Friends With The pKa Table

So to make a long story short, as I’ve said many times before, the pKa table is your friend. For
three good reasons.

1. It tells you about the relative strengths of acids and bases (itself very important)

2. It gives you an idea of which atoms will bear negative charge the best (useful for
determining the stability of resonance structures). (Weakly basic atoms bear negative charge the
best.)

3. When you learn about substitution and elimination reactions, it also is the Rosetta Stone for
determining leaving group ability. (Good leaving groups = weak bases)

Next Post: Evaluating Resonance Forms (4): Where to put the positive charges?

[Note 1] . it should also be pointed out that theres going to be some repulsion in charge between
the oxygen & negative charge or the fluorines & negative charge. Furthermore once the electron
withdrawing group can participate in resonance we have to think about π donation and π
accepting.

Note 2: What about hybridization? Doesn’t that affect stability of negative charges too? After all,
the reason why alkynes are more acidic than alkenes which are more acidic than alkanes is
because the ability of orbitals to stabilize negative charge increases as increase the amount of s
character [sp3 to sp2 to sp ]. So shouldn’t that apply, for example, in the instance below?
From examining these two resonance forms we might be tempted to believe that the nitrogen on
the left (the one bearing a hydrogen) is sp2 in one version and sp3 in another. If you think about
what resonance forms represent, however – different ways of depicting electron density – you
will realize that this can not actually the case since that would involve moving atoms around
[re-hybridizing from sp2 (trigonal planar) to sp3 (tetrahedral). ]. Both nitrogen atoms are, in
fact, sp2 hybridized, and their stabilities cannot be distinguished based on this characteristic.
[Thank you to reader Brian E. for correcting an earlier version of this post. In fact, Brian informs
me that calculations indicate the right-hand resonance form makes a significantly higher
contribution to the resonance hybrid than does the left-hand resonance form].

Evaluating Resonance Forms (4): Positive

Charges
As I mentioned before, the resonance form(s) of lowest energy are those where the charges are
minimized. However, sometimes you can’t get around it: you have to put a charge somewhere.
Last time I talked about the principles involved in deciding where best to put a negative charge:
on the least basic atom. Today I’ll talk about the opposite situation: where to put a positive
charge.

There are really one main principle to think about when deciding which site will stabilize
positive charge the best. Recall the one sentence summary of chemistry: opposite charges attract,
like charges repel. Electron-poor atoms are stabilized by adjacent electron-rich atoms. Electron
poor atoms are destabilized by electron-poor atoms.

To be more specific, there are three main ways this plays out when evaluating resonance
structures.

It’s probably this first principle which causes the most confusion of all. Let’s look at the “best”
and “second-best” resonance forms for these positively charged species. Notice how in each one,
the second-best resonance form has a carbocation – that is, a carbon with six valence electrons.
The best resonance form has a new π bond that has been formed through the donation of a pair of
electrons on the adjacent atom (O, N, Cl, F). In the process we put a positive charge on that
atom.
Why is this weird? Because up to this point, you’re probably used to thinking of atoms like F, O,
Cl, and N as the “electron Scrooges” of the periodic table. Due to their high electronegativity
they take electrons away from whatever they’re attached to. Here’s an important new concept:
When atoms with a lone pair are adjacent to an atom with an empty orbital, formation of a
π bond will be favored. Remember that formation of a chemical bond is an energy-lowering
event. The “loss” of a full lone pair on the donating atom is more than compensated for by the
energy released through formation of a new π bond to the empty orbital.

We call this π donation. It’s such an important concept there will be much more to say about it in
a subsequent post, but if you want to anthropomorphize matters here, you can compare F, O, N
and Cl to famous Scrooges such as John D. Rockefeller, Andrew Carnegie, and even Bill
Gates: while they may have been thought of as greedy, they also have a philanthropic side.

Just one thing to note: although it might look “bad” to put a positive charge on electronegative
atoms such as O, N, Cl, and F, this is OK in these cases because if you look closely there is a
full octet of electrons on each of these atoms. Recall that the “positive charge” we draw is
actually formal charge, and remember that formal charge does not always reflect electron
density. So in these cases these atoms are not actually electron-deficient.

However it’s important to distinguish between these types of positively charged atoms, and those
in the diagram below which lack a full octet. It is extremely energetically unfavorable for atoms
like F, O, and N to have less than a full octet of electrons. Avoid!
 Here comes the
second most important principle when it comes to stabilizing positive charge: if possible, it is
best to place the positive charge on the most substituted carbon atom. As I often say to my
students, “if you’re poor, it helps to have rich neighbors”. The stability of carbocations increases
with the number of attached alkyl groups. It might be useful to review the 3 factors that stabilize
carbocations.

The last factor to keep in mind is essentially the inverse of what we just discussed. Carbocations
are destabilized when adjacent to electron-withdrawing groups. Now it’s important to add the
caveat – electron withdrawing groups that cannot donate a lone pair. So we can put groups such
as CF3, NR3,(+) COOR, COOH, SO3H, NO2, and others in this category. Let’s have a look.
Note that in each case the carbocation is attached to a group which is removing elecron density
from it *without* being able to donate a lone pair of electrons. Again, it might be useful to
review the 3 factors which destabilize carbocations.
So hopefully that (mostly) covers an introduction to evaluating the stability of different
resonance forms. In the next few posts, we’ll start to look at how to apply resonance to find the
reactive sites on a molecule.

Next Post: Applying Resonance (1): Pi-donation

Exploring Resonance: Pi-Donation

You’d think after five or six posts on resonance, that would be enough. But NO, friends, it just
keeps going. I promise that today’s post is actually useful, although to be honest it’s probably
most applicable if you’re in (or going into) org 2, since the chemistry of the functional groups
discussed here don’t really come up until then.

Anyway. The topic of today’s post is “π donation”, which is just a way of describing what can
occur in certain resonance forms where an atom with a lone pair can form a π bond with an
adjacent atom of appropriate hybridization. Now this has been talked about before, sure – but
here, the difference is that we’ll primarily be discussing situations where the “best” resonance
form is neutral, and the “second-best” resonance form is charged.

Let’s look at the resonance forms of an enol (shown) and use what has already been discussed to
evaluate their relative importance. Note that in order to draw resonance form D we have to do
two arrow moves to avoid breaking the octet rule.
  Resonance form A has the fewest charges.
 Resonance form D has two charges, but all atoms have full octets.
 Resonance forms B and C each have two charges, but have empty octets on the carbons.

In evaluating these resonance forms, A will be most important due to the rule of fewest
charges. D will be the second-most important since we always give atoms full octets if
possible. And B and C will be the least important because each of them have atoms with less
than full octets.

While that’s nice, you should go on more than just some Internet dude’s appraisal of what
resonance forms are most important. What about experimental evidence?

Here’s three pieces of experimental evidence to support the proposal that resonance form D is
more important than B and C.

 reactivity profile (shown below) – enols tend to react with electropositive groups such as
protons (H+ ) at the site where they bear a partial negative charge (opposite charges
attract, remember). This supports a resonance form such as D being more important than,
say B.
 proton NMR spectroscopy is a good guide to electron density, and protons on the enolate
carbon are shifted downfield relative to alkenes (this indicates the carbon is more electron
rich, which supports the importance of resonance form D).
 electrostatic potential maps (although I can’t find a good one for the enol shown, here’s
one for a related species. Note how there is less positive charge on one of the carbons).
Furthermore, molecules like the ones below would be expected to show similar behavior – and
they do.

Enamines (the one on the left) are well known to react with positive species at the end carbon
(C1). Vinyl chlorides, although less reactive, will also react with positive species at the end
carbon (C-1)

Take home message: alkenes attached to an atom with a lone pair such as O, N, Cl, S, etc.
(often called “heteroatoms“) have an important resonance form with a negative charge
adjacent to the carbon-atom bond.

So what does it matter? Although it deserves a post of its own, the concept of π donation is
probably the most important application of resonance you learn in Org 2. It influences
everything covered in that course: reactions of aromatic rings, reactions of dienes, and especially
reactions of carbonyl compounds.

Here’s the key point of this post.

This will have tremendous consequences for chemical reactivity, which will be the subject of a
later post. For the moment I’ll just leave with a final application of π donation. And a question.

For which of these molecules do you think π donation is going to be the most important? That is,
what types of atoms would be more likely to to give away their lone pairs to form π bonds?

Hint: it has something to do with electronegativity. [Note 1]

In the next (and for now hopefully last ) post on resonance concepts, I’ll talk about the opposite
of π donation: π accepting.

Next Post: Applying Resonance (2): Pi Acceptors

[Note 1] Across a row, π donation is inversely related to electronegativity. However caution is

advised when using electronegativity to compare π donation when going down the periodic table
– other effects, such as orbital overlap, also come into play.

Exploring Resonance: Pi-acceptors

Last time I talked about π donation and π donors, which are atoms capable of forming a new π
bond with an adjoining C-C π bond. The upshot of π donation is that these molecules will have
an important resonance form where the carbon at the far end of the π bond (away from the π
donor) has a negative charge.
Todays topic is π acceptors, which is, as you might imagine, exactly the opposite phenomenon as
π donation.

Recall that in π bonds that are polarized toward a more electronegative atom, we have an
important resonance form where the less electronegative atom (usually carbon) bears a positive
charge. That would be the one on the left, below.

However, when we have an

additional double bond attached to an electron withdrawing group, we can also draw an
additional resonance form where there is a positive charge on the far carbon. That would be the
one on the right.

These are both important resonance forms. Note that they both have an equal number of charges
(two) and they are polarized so as to put the negative charge on the most electronegative atom
(oxygen). They will each make an important contribution to the resonance hybrid of this
molecule.

(The question of which resonance form is more important for the purposes of reactivity is an
important question I’m deferring to a later date. The short answer is that it depends greatly on the
reaction conditions chosen).

Now: see how the double bond has “moved” toward the electron-withdrawing group? For this
reason, we call these types of substituents “π acceptors”, because they can “accept” a π bond.
This is a general phenomenon not just for functional groups containing C=O and C=N groups,
but also for functional groups such as nitriles, nitro groups, sulfonyls… essentially any polarized
group containing a π bond.

You can also think of it as an extension of a phenomenon we observe for resonance forms that
have an empty p orbital, such as carbocations and other groups that contain an empty p orbital
(such as this boronic acid, pictured).
Here’s the quick summary of this phenomenon:

This is the last big post planned on introducing resonance concepts for the time being. After a
summary, and then some examples of what NOT to do, I want to show how you can apply this
skill (that of evaluating resonance forms in determining electron density on a molecule) toward
figuring out the reactivity of a given molecule.

Next Post: In Summary – Resonance

In Summary: Resonance
Four key factors that determine the importance of resonance forms in organic chemistry are:

 Rule #1: Minimize charges

 Rule #2: Full octets are favored
 Rule #3: How stable are the negative charges?
 Rule #4: How stable are the positive charges?

After all these posts about resonance, I thought it would be good to have a post summarizing
what’s been discussed so far.

One of the key skills in analyzing the reactivity of a molecule is to be able to figure out where
the electrons are.

As I wrote here, if we’re dealing with single bonds, it’s a relatively straightforward matter of
figuring out the differences in electronegativities.

However if multiple bonds (π bonds) are present, then we start to run into a little problem: there
can be multiple ways to distribute electrons on the same molecule (i.e. different resonance
forms). Therefore, in order to understand electron density on a molecule where pi bonds
are present, we must first understand the importance of its various resonance forms.
How can we “find” resonance forms for a given molecule? It’s possible to do it through trial-
and-error, but one surefire way is to do so is to apply the curved arrow formalism, which is a
way of depicting the “movement” of electrons.

There are three “legal” ways to move electrons using curved arrows: from pi bond to lone pair,
from lone pair to pi bond, and from pi bond to pi bond:

Here’s an important point about resonance forms. It is tempting (and very wrong!) to think that
these resonance forms are in “equilibrium” between each other. Avoid this common mistake!

Instead, the “true” state of the molecule will be a “hybrid” of these resonance forms.

For example in the acetate and allyl cation examples below, the “true” structure of the molecule
is represented through a 50:50 combination of the two resonance forms.

In this case both resonance forms are equal in energy, so the “hybrid” is a 1:1 mixture of the two.
However this is only rarely the case, for instance in this ketone below, which has 3 different
resonance forms.

Not all resonance forms will be of equal significance. How do we evaluate how important
they are?
 Principle #1: The rule of least charges
Resonance forms become less significant as the number of charges are increased. For example,
in the ketone above, the resonance form with zero charges will be the most significant. (Note
however, that each resonance form has a net charge of zero.

Principle #2: The octet principle

Resonance forms where all atoms have full octets will be more significant than resonance forms
where atom(s) lack a full octet. Importantly, it’s a good general rule never to place less than a
full octet on nitrogen or oxygen, as in the example above, right. Since these atoms are highly
electronegative, these resonance forms are extremely unstable and will be insignificant.

Principle #3: Stabilization of negative charges

Negative charges are most stable when placed on the least basic atom. There are four main trends
to consider here:

 Electronegativity: across a row of the periodic table, negative charge becomes more
stable as electronegativity is increased.
 Polarizability: down a column of the periodic table, negative charge becomes more
stable as polarizability increases
 Electron withdrawing groups stabilize negative charge through inductive effects.
 Hybridization: negative charge becomes more stable as the s-character of the atom is
increased. sp (most stable) > sp2 > sp3 (least stable

Note that stability is the opposite of basicity.

Principle #4: Stabilization of positive charges
When dealing with positive charges, the resonance form where all octets are filled will be the
best (see principle #2). Between resonance forms where there is a positive charge that has less
than a full octet (that is, a carbocation), then follow these principles:

1. Place positive charge on the most substituted carbon

2. Avoid placing positive charge adjacent to electron withdrawing groups if possible
3. Place positive charge preferentally on sp3 > sp2 > sp
Application #1: Pi donation

When double bonds are connected to an atom with a lone pair of electrons, the molecule will
have a significant resonance form where there is negative charge on the adjacent carbon.

Application #2: Pi accepting

When double bonds are connected to a polarized π bond, the molecule will have a significant
resonance form where there is positive charge on the adjacent carbon.

For now, that does it for a summary of the important themes in resonance. Next stop (after a post
about some common mistakes) will be to apply these principles to chemical reactivity.

Drawing Resonance Structures: 3 Common

Mistakes To Avoid
No discussion of resonance structures would be complete without mention of how to royally
screw them up. This isn’t something to feel bad about, by the way: there isn’t a chemist alive
who hasn’t made one of these mistakes at some point. Think of it as a rite of passage. The trick
is to make the mistakes while doing problems, not while doing an exam.

There are at least three common categories of mistakes regarding resonance structures:

 Unbalanced equations
 Moving atoms around
 Incorrect drawing of resonance arrows

Mistake #1 : Unbalanced Resonance Equations

Let’s first talk about unbalanced resonance equations, where something (either an atom or
electrons) has been added or subtracted. Remember that in drawing resonance forms we’re only
allowed to move electrons, and nothing more. That means that the two resonance forms can
neither differ in the number of their electrons nor can they differ in the number of atoms.

Mistake #2 :Moving atoms around

A second category of common mistake is to move atoms around. Although the two structures
shown below have the same number of atoms and electrons, they are not resonance forms
because we have broken single bonds (as opposed to π bonds) and thus moved the location of
one or several atoms. The easiest way to screw this up is to move hydrogens. While these
molecules are related, they are actually pairs of constitutional isomers, not resonance structures.

One way to avoid making these types of mistakes is to try to interconvert the structures using
curved arrows. There are only three legal arrow-pushing moves for drawing resonance structures.
Double check to make sure you aren’t breaking the rules.

Mistake #3 : Incorrectly Drawing Curved Arrows

The last – and by far the most common class of mistake in drawing resonance structures is to
screw up the curved arrows. There is a seemingly infinite number of different ways to do this.
They fall into a number of sub-categories.

Breaking The Octet Rule

First, there’s arrow-pushing moves that are wrong and cannot be redeemed. Examples A-D
each depict different ways of breaking the octet rule. In A, B, and C the resonance form that
would result from these arrows would have five bonds to carbon. Example D would have five
bonds to nitrogen. Inconceivable!
Examples E and F are wrong for a different reason: remember that the curved arrow depicts the
movement of a pair of electrons. In example E, the “tail” of the leftmost arrow is shown at a
positive charge – a big no-no, since there isn’t a lone pair of electrons here. Likewise for F,
where the positively charged nitrogen also lacks an electron pair.

Missing A Curved Arrow

Then there’s arrow pushing “moves” that are also illegal, but can be made legal through
drawing an additional arrow. See if you can draw an arrow to make it work (answers at the
bottom).

Forgetting To Draw In Lone Pairs

Then there’s the sloppy mistakes, where these arrow pushing forms are missing something
important. I guess you could say this entire post is devoted to sloppy mistakes but these
examples are particularly egregious because they are just one tiny little detail away from being
correct. In these two cases, there is neither a lone pair of electrons (or a formal negative charge)
at the tail of one of the electron-pushing arrows, which make them incorrect. Neglecting to draw
the formal charge of an atom is another common sloppy mistake (albeit not unique to resonance).
Note that when I say sloppy I’m not making a moral judgement here. I’m just saying it makes for
imprecise and ambiguous chemical structures, which are not useful.

Finally, there are resonance structures which are not illegal, per se, but won’t make a significant
contribution to the resonance hybrid.

Insignificant Resonance Structures

In both examples we have very electronegative elements (oxygen and nitrogen) with less than a
full octet. Recall that electronegativity is a rough measure of the ability of an atom to stabilize
negative charge? Well, the converse is true – that is, the greater the electronegativity, the more
positive charge will be destabilized on that atom (clarification: by “positive charge” here I am
specifically referring to having less than a full octet of electrons (like a carbocation), not the
common situation where O or N with a full octet bears a formal charge of +1.)

How To Avoid Making Mistakes Drawing Resonance

Structures
Avoiding all of these mistakes requires careful attention to detail, bordering on paranoia. The
number of atoms and electrons on the left side of the resonance arrow should balance the number
of atoms and electrons on the right side of the resonance arrow. Furthermore, the changes in
bonding (and charge) of the molecule on the left side of the arrow should be accurately
mapped by the appropriate curved arrow(s).

If it sounds like I’m making a case for organic chemistry being a lot like accounting, you’re
right! In the final analysis, organic chemistry equations are not unlike accounting
transactions. The two sides need to balance.

Next Post: How To Apply Resonance and Electronegativity To Understand Reactivity

P.S. Here’s the answers for the example above:

How to apply electronegativity and resonance
to understand reactivity
One thing has been missing from the discussion of resonance. What’s the point?

Who cares if we can write out resonance structures? What does it matter if we can figure out the
two or three most stable resonance structures? So what?

Here’s the point: we can apply resonance (and electronegativity) to figure out the electron
densities of molecules from first principles, and we can apply these electron densities toward
understanding how a molecule will react.

Put it another way: if you learn this skill, you will rely less on memorization for understanding
reactions, because you’ll be able to figure out the chemical behavior of molecules you’ve
never seen before.

For instance: if you’re a non-chemistry major I can pretty much guarantee you’ve never seen this
reaction before. But if you apply some of the principles in this post, you should be able to make
some headway on it.

Let’s look at these two aspects really quickly.

1. Applying electronegativities. When you have a bond between two atoms with different
electronegativities, there will be a dipole (two opposite charges separated in space). That
dipole will give you a clue about the electron densities of those two atoms. For example
in the molecule below, the oxygen is more electronegative than carbon which means that
the C–O bond will be polarized towards oxygen (it will have a higher electron density).
This is different than formal charge, which is where we have to assign a charge to an
atom for “accounting” purposes.
2. Applying resonance: when you know the most stable two (or three) resonance forms,
you’ll have a good idea of what the resonance hybrid looks like. The resonance hybrid
also tells you electron densities, sometimes in a way that isn’t immediately apparent from
electronegativity (see below).
Here’s some examples of resonance hybrids, along with the electron densities we get from
applying both electronegativity and resonance. In the picture, the partial charges (δ) represent
electron densities on the hybrid.
Now for the punch line.

Once you know the partial charges on a molecule, you can then use it to figure out potential
chemical reactivity. How so?

Remember the “one sentence summary of chemistry”: opposite charges attract, like charges
repel.

So any region of negative charge on a molecule will have some degree of attraction to a region
of positive charge on another molecule. In reactions electrons flow from areas of high electron
density to low electron density. Another way of putting it: the partial negative charge (i.e. high
electron density) will go to a region of partial positive charge (i.e. low electron density).

So in the diagram below I’ve put down some of the resonance hybrids (along with other
molecules), and drawn a selection of the interactions between the opposite charges. Although
these arrows do not necessarily represent actual reactions (although many do!) they at least
represent potentially feasible reactions.
The key take-home skill from these examples is to be able so see how the resonance hybrid will
determine electron density, and how this can end up leading to hypotheses for feasible reactions.

Let’s go back to the original question:

By applying electronegativity, we can judge that the C–Zn bond will be polarized towards
carbon, which makes it electron rich; it should be attracted to the carbon of the second molecule,
which both electronegativity and resonance tell us should bear a partial positive charge. In fact
this is a real reaction, although we can’t fully determine how well a reaction will work from
first principles. Experimental evidence is the one and only arbiter as to whether a reaction
works or not.

Is this technique perfect, without exceptions? No. It’s not perfect. It’s not completely without
exceptions.* But it’s a good mental model for the underlying principles of chemical
reactivity. The point here is to give you a glimpse of how to apply the concepts of
electronegativity and resonance towards new and unfamiliar situations.

*Two prominent exceptions: electronegativity isn’t the best for figuring out the reactivity of
nitrile ion (CN(–) and oxymercuration of alkenes. It doesn’t predict reactivity of Cl-Cl and Br-
Br, etc. which are not polarized.
**Note that this model doesn’t tell you how reactive different species will be. That will require
another set of mental models.

PS – a long enough post as it is, but here are some “unproductive” interactions from the diagram
above.