Reich

Symbolic Notation in Organic Chemistry

Chem 547

Arrow notations commonly used in organic chemistry:

Reaction arrows: Resonance arrows (indicates two resonance structures):

H2, Pt

Equilibrium arrows (reversible reactions, usually used when significant fraction of both reactant and products are
present at equilibrium):
O O
H+ Used to indicate a
+ MeOH + HOH
OMe lopsided equilibrium
OH
Retrosynthetic arrows (reverse of reaction arrow - used in planning a synthesis):

O O O O

O O O

H O O
H
β-ELEMENONE
Electron-pushing arrows (indicate movement of a pair electrons in a resonance structure or a reaction).
-

:
:
:

:
:

O O Cl
:

- -
:

: :
N≡C: + :Cl:
Cl C≡N C≡N

Single-electron pushing arrows:

Br H CH3 HBr + CH3

A few other kinds of arrows that show up occasionally: O O

Pair of electrons in an Refluxing benzene

+
energy level: solvent:

Stereochemical Notation
The bridgehead substituent in these structures is above the plane of the paper:

O O O
O
The bridgehead substituent in these structures is below the plane of the paper:

O O O O
The compound below is a mixture of stereoisomers at the bridgehead carbon:

O
For some classes of compounds the α (down) and β (up) nomenclature is used:
HO HO
O O
α-Glycoside: HO H β-Glycoside: HO
HO HO OMe
HO HO
OMe H

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 Electron Pushing in Organic Chemistry Reich
Chem 547

This handout deals with electron pushing arrows: the movement of a pair of electrons from an electron rich site (a
lone pair of electrons or a bond) to an electron poor site. Electron pushing arrows are used as a "bookkeeping"
device to easily keep track of bonding and formal charges when interconverting resonance structures or depicting
reactions. Used properly, they have tremendous value not just for understanding reactions, but also for for
predicting chemical reactivity
There are two fundamental types of electron pushing processes:

Bond breaking Bond making

- +

:
+ BF3

::
Br Br O O BF3

:
- +
N +
: :

:
O:
:

O + N
:

+ - + +

:
:

H C N: H C N: O C H :O C H

Arrow starts at a bonding pair of electrons
and ends at an atom, creating a sextet atom
(or H+) at the originating atom and new lone
pair of electrons at the terminal end.
:
Arrow starts at a lone pair of electrons and
ends at a sextet atom (or H +), creating a new
single bond, or converting a single bond to a
double bond.

In each case, the formal charge becomes one unit more positive at the starting atom and one unit more negative at
the terminal atom.

A third very commonly used type, Bond Movement, is used to depict synchronous processes. A Bond Movement
arrow starts at a σ or π bond, and ends at a sextet atom, forming a new σ or π bond:

NH2 H NH2
B H + B + + +

σ-bond movement π-bond movement

It is really shorthand for consecutive or simultaneous bond breaking and bond making processes:

NH2 NH2 H NH2

B H + B H: + B +

Bond breaking Bond making

For Bond Movement processes, neither the charge nor the total number of bonds change at the central arom, the
initial and final atoms behave as for bond breaking and bond making processes.

When a Bond Making or Bond Movement arrow ends at an octet atom, then a Bond Breaking or a second Bond
Movement processes has to "clear out" the extra pair of electron. If this cannot be done in an electronically
reasonable fashion, then the process is not feasible. In this way a series of electron movements can be strung
together. Again, all of the central carbons have no change in their charges or number of bonds, the first and last
atoms change as for Bond Making and Bond Breaking processes.
:

O -
:

: O:
-
:

:O: Cl
:

O
:

Cl
+N
:

O : O N
:

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Common problems with electron pushing

Watch for violations of the octet rule - always specifically draw in all of the atoms (including hydrogens and lone
pairs) at any atom undergoing a transformation
Draw arrows in the right direction (from donor to acceptor). We may think of a proton as attacking a double bond,
but in electron-pushing terms, it is the double bond that is attacking the proton.

Note: free protons don't actually exist in

not: solution - they are always bonded to
H+ H+ something (usually an O or N)
Clearly distinguish positive charge, and electron deficiency (a sextet atom). Cationic species like oxonium ions,
ammonium ions and the like are usually NOT electrophilic at the atom bearing the formal positive charge. Each of
the species below has electrophilic properties, but the positively charged O and N atoms are not electrophilic - it is
the atoms attached to O and N that are electrophilic and thus subject to attack by bases and nucleophiles.

Me H
+ H + +N +
Me O +O C O+ H
N +
H C N
Me
9 H

9 :Nu 9 9
However, this stricture has to be relaxed for heavier elements like P and S which are capable of forming
compounds that formally violate the octet rule

Br+ Ph Ph
+ + Ph Li Ph LiBr
P P Ph +
Ph Ph
Ph Ph
9 Ph

Similarly, make a clear distinction between formal negative charges and lone pairs of electrons - they are not
always synonymous. For boron and aluminum ate complexes, there are no lone pairs. Any donor character arises
from the sigma bonds attached to the negative charged atom.
For delocalized structures, you must pick a specific resonance structure to do any electron pushing - the "dotted
line" formulas and circle structures for aromatic systems do not work, since bonds and electron pairs are not
shown.
H H
+
9 9
:

Do not combine multiple steps into one long series of arrows. An experienced chemist may be able to get away
with this sort of behavior, but such mechanisms are confusing and can contain fatal errors. If a reaction involves a
true intermediate, your mechanism should reflect that.

Bad:
-
:

Na+ : O : O O O
The real mechanism probably involves three discrete steps:
1. Nucleophilic attack on the epoxide
OEt O 2. Nucleophilic attack of the alkoxide on the ester carbonyl
3. Loss of the ethoxy group.
O
Good: -
O:
:
- O O O
:

: OEt Na+ OEt

:

+ O O
Na :O: O
c d : e
OEt O O
OEt

O :O:
-
:

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