5.1: Reaction Equations vs.
Reaction Mechanisms
A simple method to show a chemical reaction is a reaction equation. A reaction
equation describes what happened, such as when two compounds react with one
another to form a third and fourth (Figure 5.1). From the following reaction equation
we know that mixing Compound A with Compound B makes Compounds C and D
(the exact reaction and compounds are not important at this stage).
A more involved method is a reaction mechanism. A reaction mechanism describes
how the reaction happened, including how many steps occurred, the order they
occurred in, and how the electrons and atoms moved during the reaction (Figure 5.2).
Reaction mechanisms are almost always theoretical; it is impossible to “prove” that a
speci c reaction follows a speci c mechanism, but we can collect evidence to support
a proposed mechanism and, more importantly, rule out other mechanisms.
Curved arrows are used to depict electron movement in reaction mechanisms. The
exact mechanism above is not important at this stage, but it is useful to see the
difference in the amount of information conveyed. For example, with this reaction
mechanism we still know that mixing Compound A with Compound B makes
Compounds C and D. We also know that a lone pair on oxygen makes a new bond to
carbon, that the carbon-bromine bond breaks with those electrons going to bromine,
and that these two things occur at the same time. The whole reaction occurs in only
one step.
5.2 Over-the-Arrow Notation in Chemical Reactions
When showing either reaction equations or mechanisms additional information is
sometimes provided. This is done is to add detail to the reaction without needing to
write a paragraph to accompany the equation. The information is added above (and
below) the reaction arrow connecting the starting material(s) and product(s) (Figure
5.3). We refer to this shorthand as “over-the-arrow” notation.
Technically there are no codi ed rules for how this is done or what information is
included/excluded. However, most sources use a similar approach.
Over-the-arrow notation can be used to convey as much or as little information as
desired (Figure 5.4). In very detailed cases all the information needed to repeat the
fi
fi
fi
reaction might be included. Commonly included information comprises reactants,
reagents, and/or catalysts, their relative amounts (as equivalents to the starting
materials), solvents, the concentration of the reaction, the temperature of the reaction,
and the length of time needed for the reaction to occur.
Usually less information is included, with only the key parts written to highlight what is
happening and any special conditions required (Figure 5.5). For example, the solvent
and temperature are important for this reaction (it will probably not work well if other
solvents or temperatures are used) but the exact equivalents of the reagent and
concentration are not (it will probably work well even if these are signi cantly
adjusted).
Remember that there is technically no requirement to be consistent with where or
what information is added. This means that some sources might not include some
information (even if it is “important”), or place it in a different order/location, or
change the style between different gures in the same document (Figure 5.6). It is
important to be able to read and interpret what information is included and
understand how it might (or might not) be important for understanding the reaction.
In some cases other information might be included. Usually this is meant to guide the
reader, such as a label for the type of reaction or mechanism that will be followed
(Figure 5.7). Often this is done when more than one reaction/mechanism is possible.
Sometimes converting a starting material into a certain product takes more than one
step, with multiple reaction conditions. Each step can be written out as a sperate
reaction equation. However, it is more convenient to avoid re-drawing things. There
are two common ways to show the overall transformation.
One approach is to discretely draw out each step’s product and use that as the
starting material for another reaction equation (Figure 5.8). Since these are sequential
reactions, the rst step must be complete before the second step can happen. This
works better for teaching materials as it allows the reader to directly see what the
exact product is for each step. However, this approach is not commonly used in
research or academic papers because it implies that the product of the rst step is
fi
fi
fi
fi
isolated (taken out of the reaction vessel, dried, and puri ed), which is often not
correct.
The other approach is to include details from the sequential steps above and/or
below a single arrow connecting the starting material(s) and the overall product(s)
(Figure 5.9). The different steps are numbered to indicate they are not all occurring at
once. Instead of discretely drawing the product of the rst reaction, it is implied that
whatever product is made is used directly as the starting material for the second
reaction. This approach works better for formal or advanced texts as it requires the
reader to already understand and visualize what the product is for each step. This also
makes it useful for examination purposes.
5.3 Drawing React Mechanisms
A common task in organic chemistry is to draw a reaction mechanism for converting a
given starting material into a desired product. This helps familiarize students with the
different types of chemical reactions and how/where they occur. It is possible to
memorize mechanisms for many different reactions. However, it is much more useful
to recognize the patterns, rules, and features of reaction mechanisms. When reaction
mechanisms are understood most chemical reactions become much easier to
interpret. Additionally, predicting products and outcomes, such as which
stereoisomer(s) can be formed, becomes signi cantly simpler.
Reaction mechanisms work by moving electrons around to form or break bonds.
When drawing a reaction mechanism it is useful to recognize areas with a high
amount of electron density. This electron density may be able to create a new bond.
Heteroatoms typically have lone pairs on them, which may be used to make a new
bond (Figure 5.10). Pi (π) bonds are higher in energy than sigma (σ) bonds. As a
result, they are easier to break. This means that electrons in π bonds might be
available to make a new bond. By de nition anions have an excess of electron
density, which again may be used to create new bonds.
When drawing a reaction mechanism it is useful to recognize areas with a low amount
of electron density. These areas may want to gain electron density in the form of a
new bond or lone pair.
fi
fi
fi
fi
Electronegative atoms tend to create polar bonds, which creates areas of lower
electron density (Figure 5.11). The atoms with less electron density may be areas
where new, less polar bonds may be formed. Pi (π) bonds are higher in energy than
sigma (σ) bonds. This means that atoms in π bonds may want to make a new σ bond
instead, gaining stability (and electron density). By de nition cations have a de ciency
of electron density, which again may result in a possible target for a new bond if the
cation has an incomplete octet.
Recall that a functional group is a collection of speci c atoms connected in a speci c
way. Since structure directly dictates reactivity, functional groups behave VERY
similarly (often identically) in each molecule they are part of. As a result, when
drawing a reaction mechanism it is useful to recognize and/or label functional groups.
This leads to pattern recognition. For example, recognizing that a primary alcohol in
one molecule undergoes a certain reaction via a certain mechanism means that a
different primary alcohol in a different molecule can probably undergo the same type
of reaction via the same type of mechanism.
Arrows are very common in organic chemistry. There are several different types of
arrows, with each used to represent a different process or concept (Table 5.1). When
drawing reaction mechanisms using the wrong kind of arrow often makes the
mechanism wrong.
Correct use of arrows is expected at an introductory level. An exception is sometimes
made when distinguishing between reversible and irreversible for a step in a reaction
mechanism; at an introductory level it may be dif cult to determine whether a step is
reversible or not. A biased reversible arrow is used when the compounds on the two
sides may interconvert, such as in equilibrium, but where one side is favoured over
the other (the longer arrow points to that side).
Curved arrows are used to show electron movement. If the end is a full arrowhead, it
represents a pair of electrons moving. If the end is a half arrowhead, it represents a
single electron moving. When a single electron moves it is called a radical. Radical
reactions are somewhat uncommon in nature. They do not follow many of the rules
for “normal” chemical reactions. As a result, they are not featured in this text.
fi
fi
fi
fi
fi
Curved arrows are used to show electron movement. In all cases the arrow starts
where the electrons are and ends where the electrons will be. Often this means the
arrow starts at an area of high electron density and points to an area of low electron
density. If a new bond is forming it will point to the atom it is being formed to (Figure
5.12). If a bond is becoming a lone pair it will point to the atom it will be associated
with.
When drawing arrows that make or break π bonds there are two conventions. Under
the old convention, the arrow points to the area where the new bond will be (Figure
5.13). This approach works well for making π bonds but may be confusing for when
they are being converted into σ bonds.
Under the new convention, the arrow points to the atom that the new bond is to
(Figure 5.14). This approach is more consistent with the formation and breaking of σ
bonds. However, it is less commonly used.
When drawing arrows that make or break π bonds using either convention is
acceptable.
When an arrow ends at an atom that atom is gaining electron density. As a result, its
formal charge may change (decrease; Figure 5.15). When an arrow points away from
an atom that atom is losing electron density. As a result, its formal charge may change
(increase). If an arrow points to an atom and another arrow points away, usually their
effects cancel, and the formal charge will not change. It may be easier to simply draw
the resulting product(s) of a series of arrows and then quickly assign formal charges
to all atoms, rather than memorize a series of new rules for the process.
This section may be considered a primer for drawing reaction mechanisms. As such, it
is likely useful to periodically revisit and review this section when encountering
reaction mechanisms in subsequent chapters.
When drawing reaction mechanisms, it is often helpful to explicitly draw in all lone
pairs. This makes it easier to see which atoms may be nucleophilic (see Section 7.2)
and helps keep track of formal charges.
When drawing reaction mechanisms, always draw all atoms involved in the
mechanism. For example, if a proton (hydrogen) will be moving in a step, draw it in
explicitly. If there are side products from a step, draw and keep track of them. This
avoids situations where a molecule “disappears” at one step but is needed for a later
step. Without having it drawn you may forget it is available.
When drawing reaction mechanisms, it is often helpful to con rm that the actual
product is obtained. Particularly with longer reaction mechanisms, it is possible to
draw many steps and end one or two steps early, resulting in an incomplete
mechanism. It is also possible to accidentally generate a different “product”, where
arrows and electrons owed but “created” a different molecule than intended.
Even chemists with years of experience and practice drawing mechanisms will
occasionally get stuck or lost when trying to determine the next step. When drawing
reaction mechanisms, it may be helpful to work backwards from the product. If some
steps forward from the starting material(s) can be proposed, and some steps
backwards from the product(s) can be proposed, it might be easier to see how the
two parts of the mechanism are related and ll in the missing steps. Additionally, this
may help nds mistakes in your proposed mechanism: you may realize that you made
an error in an early step by examining what steps must come after.
The following suggestion will not make sense without the context of later chapters
and terminology. Review it after Chapter 7, and periodically as needed.
At an introductory level the overwhelming majority of compounds can be classed as
acids, bases, nucleophiles, and/or electrophiles. Many molecules are more than one
of these things at the same time. When drawing reaction mechanisms, it is often
helpful to class each compound as an acid, base, nucleophile, and/or electrophile.
This makes it much easier to predict what steps may be possible. For example, if
compound A is an acid and a nucleophile, and Compound B is only an electrophile
(and A and B are the only compounds in the reaction), the next step is very likely to be
a nucleophilic attack of A onto B. This is especially helpful in situations where you are
stuck without any options or ideas for proposing another step.
fi
fl
fi
fi
5.4 Reaction Coordinates
When encountering reaction coordinates (energy diagrams) be aware that this is an
introductory organic chemistry text, not a physical chemistry text. However, it is
important to understand the basic terminology and applications of energy diagrams
as they can add clarity or be useful for explaining reactivity.
A generic reaction coordinate is useful for seeing important aspects of these
diagrams (Figure 5.16). The starting materials are the compounds before the reaction.
Intermediates are compounds made during the reaction that continue undergoing
transformations to eventually form the products. The products are the new
compounds made at the end of the reaction.
As the starting material becomes an intermediate, and as an intermediate becomes a
product, they pass through transition states. Transition states are NOT a different kind
of compound, they are what the compound(s) look like while undergoing a
transformation. It may help to imagine a transition state as being analogous to the
exact moment that a baseball is struck by a bat. Although we often draw the energy
surface as discrete lines, remember that the reality is (probably) a curved surface
The energy difference between a starting material/intermediate and the transition
‡
state beside it is an activation energy (usually symbolized as Ea or ΔG ; Figure 5.18).
This is the amount of energy needed for the compounds to pass through the
‡
transition state and become the next species in the pathway. If there is only one ΔG
then it is the rate-determining step (sometimes called rate-limiting step). If there are
‡
more than one ΔG then whichever is largest is the rate- determining step. Note that
this means the rate-determining step is not necessarily the transition state with the
highest energy. The difference between the transition state and what precedes it is
what is important.
In recent years the concept of a “rate-determining step” has come into question,
primarily because it only works well for a small selection of very simple reactions.
Technically the actual rate of the reaction is determined by the largest difference
between an energy minimum and a later energy maximum. This is called the energetic
‡
span. For simple reactions this is often equivalent to the largest ΔG , but not
necessarily; for many reactions the overall rate is not controlled by a single “step”. This
parameter is (much) more accurate when de ning reaction rates, but its use is not
currently as widespread.
If the nal products are lower in energy than the starting materials, then the reaction is
exergonic (“energy releasing”; Figure 5.19). If the nal products are higher in energy
than the starting materials, then the reaction is endergonic (“energy absorbing”). The
terms ‘exothermic’ and ‘endothermic’ may be more familiar, but these refer only to
enthalpy (ΔH) not free energy (ΔG). It may be useful to recall that “ΔG = ΔH – TΔS”, so
free energy is more accurate to use and also accounts for enthalpy. The energy
difference between the starting materials and the products is the change in free
° °
energy at standard conditions (ΔG RXN or ΔG ).
Although slightly beyond the scope of this text, a brief discussion of kinetics and
thermodynamics may be useful to some readers.
Kinetics relates to the overall rate of the reaction. With respect to reaction
‡
coordinates, kinetics is only concerned with ΔG values and the rate-determining step;
the energies of the starting materials, intermediates, and products are irrelevant.
Technically, the exact energies of the transition states are also irrelevant. Only the
‡
difference (ΔG ) between the energies matters. The number of steps in the reaction
also does not matter. For example, a reaction with one step (one transition state) can
be slower than a reaction with fty steps.
Thermodynamics relates to the energy absorbed or released in the reaction. With
°
respect to reaction coordinates, thermodynamics is only concerned with ΔG values;
the energies of the intermediates and transition states are irrelevant. Technically, the
exact energies of the starting materials and products are also irrelevant. Only the
°
difference (ΔG ) between the energies matters.
Most practical applications of reaction coordinates lie beyond the scope of an
introductory text. Equilibrium ratios, the Arrhenius equation, Hammond’s Postulate,
fi
fi
fi
fi
the Curtin-Hammett Principle, chemo-/regio-/stereo-selectivity arguments, and more
can use the values of (or relative positions of) species in reaction coordinates to
determine, express, or explain many things about chemical reactions.
At an introductory level, examining the reaction coordinate can reveal how many
steps are involved in a reaction. This can have important implications for describing
the mechanism (see Chapters 11 and 12).
Deciding which step is rate-determining is possible by comparing activation energies.
Then, understanding which compounds are involved in the rate- determining step
(and how the transition state looks) can help with understanding why some reactions
can be accelerated by certain effects while others cannot. The relative activation
energies of reactions can be compared to determine which of the reactions will be
faster.
When discussing “fast” reactions like acid-base chemistry (see Chapter 6) knowing if
the reaction is exergonic or endergonic can help compare relative acidities.
Comparing ΔG° values may accomplish the same task. Although a deep
understanding and application of reaction coordinates requires a great deal more
discussion and detail than appropriate at an introductory level, developing some
understanding at this stage can be very helpful both now and in further studies.
Some molecules can be represented as different Lewis or line-angle structures that
have the same placement of atoms but a different placement of electrons. These are
referred to as resonance structures (Figure 5.20). For example, there are two ways to
draw the double bonds in 1,2-dimethylbenzene (o-xylene), and three different ways
of representing N,N-dimethylformamide. The structures are related to each other
using the double headed arrow for resonance
Which way is correct? There are two answers to this question: ‘all’ and ‘none’. Each
way of drawing the molecule is an equally acceptable approximation, but none of
them, by itself, is an accurate picture of the molecule. However, when considered
together they give a much more accurate picture than any on its own. This is because
they imply, together, that these bonds are not double bonds, not single bonds, but
something in between. Sometimes this is represented using dotted bonds, or a circle
in the case of aromatic compounds (Figure 5.21). These are common in biochemistry
but are heavily discouraged in this text. When represented in these ways it becomes
easy for students to lose track of how many electrons (lone pairs and π bonds) are
being shown.
Resonance is a graphical tool to approximate the ‘real’ distribution of electron density
in the molecule. Curved arrows are often used to make it easier to understand the
relationship between the two (or more) structures (Figure 5.22). They represent
imaginary electron movement between the resonance forms. Resonance is not a
physical process. The electrons are not moving along the paths of the curved arrows.
The molecule does not look like one form one second and the other the next. The
molecule looks like a weighted superposition of all resonance forms at once.
Because the electron density is shared over multiple atoms, resonance is sometimes
referred to as delocalisation (the electrons are not longer “localized” to a speci c
atom or bond). Having multiple resonance forms provides a large amount of
stabilization. The more resonance forms a group or molecule has, the more stability it
gets. Why this is true is complicated, but the most important bene t is simple: the
bonds between the atoms involved become stronger. For example, as a result of
having multiple resonance forms, the highlighted N-C bond in the left structure is
(much) stronger than the corresponding one in the right (Figure 5.23). Since the
energy in bonds is part of enthalpy (ΔH) and enthalpy is part of free energy (ΔG),
having stronger bonds provides stability to the molecule.
There are several features that make having resonance forms possible. Since having
resonance forms provides a large amount of stabilization, if a molecule can have
them, it almost certainly will. It may be initially bene cial to memorize these patterns,
but with suf cient practice it is not necessary.
Resonance is possible if there is a polar π bond (Figure 5.24). This is most commonly
found in the form of a carbon double or triple bonded to a heteroatom such as
oxygen or nitrogen.
fi
fi
fi
fi
Resonance is possible if there is a π bond directly connected to an atom with a lone
pair (Figure 5.25). The lone pair can be from a heteroatom or from an anion. At an
introductory level, assume halogens do not work for this type of resonance.
Resonance is possible if there is a π bond directly connected to an atom with an
incomplete octet (Figure 5.26). This is most commonly found in the form of a
carbocation, though other cations are possible.
Resonance is possible if there is a π bond directly connected to another π bond
(Figure 5.27). This may include adjacent alkenes. Note that this is NOT equivalent to
an atom with π bonds to two different atoms. Resonance in these cases is not possible
due to the orbitals involved being orthogonal.
Finally, resonance is possible if there is an atom with a lone pair directly connected to
an atom with an incomplete octet (Figure 5.28). This is most commonly found in the
form of a heteroatom adjacent to a carbocation.
Even in complex molecules, recognizing how smaller sub-sections of the molecule
resemble the basic examples above can be used to help construct additional
resonance forms
Always draw in all lone pair electrons before attempting to generate any resonance
structures. This is very helpful for seeing which areas satisfy the conditions needed
and ensures no areas will be overlooked.
When generating resonance structures the arrangement of atoms remains
unchanged. This is the second most common mistake and can be a quick way to
recognize that two structures are not resonance forms
When generating resonance structures σ bonds are not moved. Technically,
resonance of σ bonds is possible. This is referred to as hyperconjugation and is
usually considered too advanced for introductory material.
When generating resonance structures lone pair electrons and π bonds (double and
triple bonds) can be moved. A π bond can be moved to create another π bond. Lone
pairs can become π bonds, and π bonds can become lone pairs.
When generating resonance structures DO NOT BREAK THE OCTET RULE. This is the
most common mistake (Figure 5.31). Remember that it is possible to have less than 8
electrons (an incomplete octet), but not more.
When generating resonance structures the overall charge does not change. If the
molecule is neutral in one resonance form, then it will be overall neutral in all
resonance forms. Formal charges (cations and anions) are allowed but must cancel
out so that the overall charge is unchanged. For example, charges are visible on the
resonance forms above (Figure 5.29) but in all of them the molecule is overall neutral.
The following advice must be considered carefully. When generating resonance
structures usually do not make adjacent or unusual charges. Having a cation adjacent
to an anion is often acceptable, though in general they should match with the
electronegativity difference (i.e. the anion should be on the more electronegative
atom). However, having two anions/cations adjacent to each other is (probably) not a
reasonable resonance structure (Figure 5.32). Generating a doubly cationic or anionic
atom (+2 or -2 formal charge) is even less reasonable. In more advanced texts some
molecules may have exotic electron con gurations. For example, carbenes have a
lone pair and an incomplete octet and are usually viewed as being both cationic and
anionic on the same atom at the same time. For the purposes of this text, unusual
charges such as this are not acceptable resonance structures. Examples with them will
not feature in this text.
The overall picture of a molecule is a weighted average of all of its resonance forms.
The weighting refers to how much a given resonance form contributes to the total
image. Resonance forms do not all contribute equally (although some can). It is
possible to compare and rank contribution from multiple resonance forms. In
decreasing order of importance, higher-contribution forms have:
1. The most atoms with full octets.
2. The fewest formal charges.
fi
3. Negative formal charges on more electronegative atoms.
4. Positive formal charges on less electronegative atoms.
5. Similar charges are as far apart as possible.
6. Opposite charges are as close as possible.
It is possible to rank many resonance forms, such as those above (Figure 5.29). This is
more tedious than challenging and would not be expected. It is more reasonable to
expect comparisons of a handful of resonance forms
If many of the factors above are violated a resonance form can be “ruled out” or
classed as unreasonable
It is important to remember that resonance forms can contribute equally if all factors
are equivalent
Recall that resonance is a graphical tool to approximate the ‘real’ distribution of
electron density in the molecule. This can be approximated using dotted bonds,
though this approach is discouraged. Alternatively, delocalized systems can be
visualized by overlapping all conjugated p orbitals (Figure 5.36). This approach is
useful for seeing how the electron cloud is distributed over the entire set of atoms
involved, but can be challenging for students to draw at an introductory level.
Depending on which resonance form is depicted the hybridization of atoms may
appear to change. For example, the nitrogen in N,N-dimethylformamide appears to
3 2
be sp hybridized in the (a) and (b) forms, but sp hybridized in the (c) form (Figure
3 2
5.37). The oxygen appears to be sp hybridized in the (b) and (c) forms, but sp
2
hybridized in the (a) form. Conversely, the central carbon is sp hybridized in all three
forms.
In reality all three have trigonal planar geometries; all three atoms can be classed as
2
sp hybridized. Recall that resonance is highly stabilizing. All three atoms require p
orbitals to form a delocalized electron cloud (as in Figure 5.36). It is not possible to
3 2
have an available p orbital and be sp hybridized. They all adopt sp hybridization to
be able to participate in resonance.
This is true of any molecule that has multiple resonance forms. Technically,
each atom has the hybridization with the highest s character from all its resonance
forms. This wording is often confusing at an introductory level. An alternative phrasing
is “each atom has the hybridization made from the fewest p orbitals of all its resonance
2 3
forms”. For example, the nitrogen and oxygen above appear to be either sp or sp .
2 3
The sp orbitals are made from an s orbital and two p orbitals. The sp orbitals are
made from an s orbital and three p orbitals. Two is smaller than three, so the
2 3
hybridization on carbon, nitrogen, and oxygen above is sp instead of sp .