COMPREHENSIVE HANDOUT FOR ORGANIC CHEMISTRY

COMPREHENSIVE
HANDOUT
FOR
ORGANIC
CHEMISTRY
Prepared by:
Ser Loisse R. Mortel
with major contributions from Justin Redd B. Mapalo

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PART 1. INTRODUCTION
Chemistry – the scientific study of properties of and
changes in matter.
Organic Chemistry – branch of Chemistry that deals with
properties and changes in organic compounds.
Organic Compound – historically defined as a compound
that originates from living creatures.
- now more correctly and conveniently defined as any
compound that contains carbon (proven by synthesis of
organic compound Urea from inorganic sources by
Friedrich Wohler).
Given that organic compounds are not just existent in
living systems, it would be present in practically every
place here in the biosphere. Living creatures like you and
plants and bacteria, plastic, wood, fabric, paper, most
drugs, and many more are organic compounds.
Learning Organic Chemistry
Organic Chemistry discussion will be divided through
using groups of similar compounds. General chemistry
essentials of interest in organic chemistry are discussed
first, followed by reactions specific for those similar
compounds.
Functional group – a small identifiable chemical entity
that should always be seen in a family of organic
compounds.
Functional Groups
Most atoms that comprise the functional groups are non-
metals and most of the time are connected by covalent
bonds. Because of this, we give a name for that small
functional group as well as a distinct collective name for
the family of organic compounds bearing the functional
group (For example, organic compounds with an amino (-
NH3) group are called “amines”).
Functional Group Family of Organic
Compounds
Carboxyl Carboxylic acids
Acyloxycarbonyl Acid anhydrides
Alkoxycarbonyl Esters
Alkylthiocarbonyl Thioesters
Halocarbonyl Acid halides
Aminocarbonyl/
Carbamoyl
Amides
Cyano Nitriles
Formyl Aldehydes
Carbonyl Ketones
Hydroxyl Alcohols
Mercaptan/Thiol Thiols
Amino Amines
Alkoxy Ethers
Alkylthio Sulfides
Carbon-carbon triple bond Alkynes
Carbon-carbon double
bond
Alkenes
Carbon-carbon single bond Alkanes
Halogen Organic halides
Table P1. Table depicting some names of functional
groups, and corresponding name (or family)
of organic compounds with the functional group.
PART 2. STRUCTURAL FORMULAS
Before the structure, function and reactivity of organic
compounds can even be discussed, it is imperative for
one to be trained as much as possible in identifying the
structure and giving the name of a presented organic
compound.
In this, the formula and nomenclature (system of
naming) of organic compounds is a good starting topic to
kick off Organic Chemistry.
Chemical Formula - is a written depiction of a chemical
compound by using the letter symbols of the elements as
written in the periodic table of elements.
Organic compounds’ function and reactivity are so much
better explained through depicting them as atoms
connected together by specific bonds with specific
shapes rather than using letters alone, so we use
structural chemical formulas instead.
Structural (chemical) formula, where the atoms are
written as they are bonded to each other in space.
Structural Formula Formats
There are several ways of writing chemical formula. They will be listed down from basic to advanced (not necessarily
becoming more complicated along the way). As a note, in case the reader is still confused on how many hydrogens to
attach to another atom (like carbon or oxygen), it would depend on the atom itself (and we will know why later on).
Ccarbon should always have 4 bonds, oxygen 2 bonds, nitrogen 3 bonds and halogens (F, Cl, Br, I) 1 bond.
Name of Structural
Formula
Definition Example (Compound used: 1-butanol)
A. Straight-line/ Kekule
Structure
Encountered in general chemistry. Here, a
chemical bond is depicted by a straight line,
and lone electrons are depicted as dots.
(Recall: Lewis structures still depict a
chemical bond by two dots)
B. Condensed Structure The only difference with the kekule
structure is that a single bond between two
atoms is not anymore drawn. Only double or
triple bonds are drawn (sometimes not at
all; people have different preferences)

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C. 3D (Dash-Wedge-
Line) Structure
Takes into consideration the three-
dimensional perspective of the atoms.
Wedged – the substituent faces the reader.
Dashes – the substituent is far from the
reader.
Lines – the substituent is at the plane of the
paper.
D. Skeletal Formula This formula treats any end pointin a
written structural formula as a carbon atom
with all other C-H bonds implied.
Table P2. The different structural formulas used in organic chemistry.
PART 3. NOMENCLATURE
Like people with real names and nicknames
Whether people call you by complete name, nickname or a combination of both, those names pertain only to you. This is
true to organic compounds. They too have real names and nicknames.
Systematic name – real name of compounds based on specialized naming rules. Itaims to describe the number, location
and precise structure of the compound in question.
Trivial name – nick name of compounds based solely on tradition and familiarization by people. It does not depict the
precise structure of the compound in question.
Semi-systematic – names of compounds describe only partially the structure of the compound in question because a set of
rules were not employed.
Figure P1. Ethanoic acid is a systematic name, depicting the number of carbon atoms (“eth” means two according to rules),
acetic acid is semi-systematic (“acet” means two, but does not follow current naming rules) and its diluted form has the
trivial name vinegar.
Systematic Names: Prefixes, Parents, and Suffixes
The International Union of Pure and Applied Chemistry (IUPAC) governs most of the rules in naming organic compounds. By
their rules, the systematic name must contain three essential parts: the parent, prefix, and suffix.
PREFIX-PARENT-SUFFIX
The parent is the part of the compound that represents it. In the name, it is between the prefix and suffix.
The prefix is written before the parent name, and means all other parts of the compound branching out from the parent
(called substituents). Substituents may be further named clearer in the prefix by using locants, descriptors, and multipliers.
a. Locant – may be any number or italicized letter (ex. N) that designates on which part of the parent chain a
particular substituent is placed. Locants are also used in suffixes.
b. Descriptor – a necessary prefix that describes a certain structural aspect of a compound, usually
stereochemistry (ex. cis-trans, E-Z, S-R)
c. Multiplier – a prefix that indicates a number of identical substituents.
The suffix is written after the parent name, and means either carbon-carbon multiple bonds or the highest priority
functional group.
GENERAL RULES IN NOMENCLATURE
Portion of
Systematic
Name
Rule/s
(If there is a rule “a”, “b” onwards, the first rule
overrules all others next to it)
Demonstration

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Parent 1a. On assigning the parent chain:
The parent is the carbon chain that bears the most
functional groups.
Note: If there are two candidates for this rule, choose
the one with a higher total priority of substituents (in
accordance to hierarchy of functional groups).
Demonstration: Some people may think that rule 1b
(longest chain rule) will apply here, but 1a overrules it.
1b. The parent is the longest carbon chain.
Demonstration: Since the 5-carbon and 7-carbon chain
both have the same number of substituents (1), pick
the longer chain.
1c. Cyclic chains take precedence over linear chains.
Demonstration: Since both chains can either have 1
substituent and are of equal length, the cyclic chain
becomes the parent.
2. On writing the parent in the name:
The parent shall be named according to the carbon
chain length. The first few prefixes are listed below.
#Carbons Carbon length prefix
1 Meth-
2 Eth-
3 Prop-
4 But-
5 Pent-
6 Hex-
7 Hept-
8 Oct-
9 Non-
10 and so on Dec- and so on
Table P3. Carbon length prefixes.
Propane.
Prefix 1a. On assigning locants:
Locants will be assigned starting from the carbon of a
terminal functional group (carboxyl, carboxyl derived
group, formyl, nitrile).
Demonstration: The functional group at the right is a
carboxyl group. It is terminal, and so the carbon there
will be the number 1 carbon.
NOTE: Systematic naming only allows numbers as
locants (1, 2, 3, etc). Trivial names allow locant
assignment as greek letters (alpha, beta, gamma) and
will also follow this rule about terminal functional
groups.
Demonstration: On the compound at the right, the NH2
group is placed on the 4
th
carbon, “gamma” in greek.
NOTE: If you don’t need locants, DO NOT use them.
3-bromobutanoic acid
Left: Butyric acid (trivial)
Right: gamma-aminobutyric acid (trivial)

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1b. Lowest sum rule: Locants will be assigned in a way
that they add up to the lowest possible sum in the
final name.
1-bromo-2-methylpentane
1c. First point of difference rule: If you can start on
two different functional groups interchangeably
without violating the lowest sum rule, locants shall
start from the higher priority group.
Demonstration: The cyclopropyl has 3 carbons while
the methyl has 1, and like how we decide parents, we
prioritize the longer chain.
4-methyl-2-cyclopropylpentane
EXCEPTION: If you can start on a double bond and
triple bond can be named interchangeably without
violating rule of first difference, locants shall start
from the double bond. Hex-1-en-5-yne
2. On writing the prefixes (punctuations):
Upon writing the compound name, the punctuations
are:
Hyphen (-) – between a letter and a number and
between a letter/number and parenthesis.
Comma (,) – between two numbers
Nothing is placed between two letters. Spaces are
used when a specific nomenclature calls for them.
2,4-dimethylhexanoic acid
3. On writing the prefixes (precedence):
The prefixes shall be listed alphabetically, with the
locant always immediately before the substituent it
locates.
Multiplier prefixes, listed below, as well as the prefix
cyclo and all descriptors (that we will not yet discuss)
are not part of the alphabetization.
# Similar
substituents
Multiplier prefix
2 Di-
3 Tri-
4 Tetra-
5 Penta-
6 and so on Hexa- and so on
Table P4. Multiplier prefixes.
2-Methyl-2-cycloPropylpentane
2-Hydroxy-2,4-diMethylbutane
4. On writing the prefixes (complex substituents):
If there are substituents on a substituent, enclose that
“secondary” substituent in a parenthesis.
Demonstration: The 4C chain holds the higher priority
keto group, overruling the 5C chain with hydroxyl. The
chain with the hydroxyl is treated as substituent. The
hydroxyl is the substituent in the substituent. 2-(2-hydroxypropyl)-3-oxobutanoic acid
Suffix 1. Highest priority rule:
The highest priority functional group will occupy the
suffix portion, still with the appropriate locant. (The
hierarchy that determines which group is of the
highest priority is in part 4.) NOTE: If the functional
group is terminal, no locant should be placed because
rule 1a in prefixes implies that the functional group is
on carbon 1.
Demonstration: Hydroxy and keto groups are of lower
priority than the carboxyl group. Thus, the carboxyl
group will occupy the suffix of this compound’s name.
2-(2-hydroxypropyl)-3-oxobutanoic acid

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2. Multiple suffixes due to double/triple bonds:
Double and triple bonds, whether highest priority or
not, are named with suffixes. Between the two, the
triple bond is the priority group. Hex-1-en-5-yne
3. On elision (removal of letters)
No two vowels or two consonants may be beside each
other. For vowels, one of the two is removed. For
consonants, a vowel may be placed in between.
Propan-2-ol, not propane-2-ol
PART 4. NOMENCLATURE HIERARCHY: SUBSTITUENTS AND SUFFIXES
As said in suffix rule 1, there is a hierarchy being followed for functional groups. This arose from the case wherein a parent
compound contains more than one functional group (A polyfunctional compound). In the current rules, the highest priority
functional group determines the suffix of the compound, and the lower functional groups will be treated as substituents of
the compound. Thus, given the fact that only one functional group is present, their suffix will be used.
The table below lists the accordingsuffix and substituent names of compounds with that functional group.
Functional Group Prefix Suffix
Carboxyl Carboxy- -oic acid/ -carboxylic acid
Acyloxycarbonyl - -oic anhydride/ -carboxylic
anhydride
Alkoxycarbonyl Alkoxycarbonyl- -oate/ -carboxylate
Alkylthiocarbonyl Alkylthiocarbonyl- -thioate/ -carbothioate
Halocarbonyl Halocarbonyl- -oyl halide/ -carbonyl halide
Aminocarbonyl/ Carbamoyl Carbamoyl- -amide/ -carboxamide
Cyano Cyano- -nitrile/ -carbonitrile
Formyl Oxo- -al/ -carbaldehyde
Carbonyl Oxo- -one
Hydroxyl Hydroxy- -ol
Thiol Mercapto- -thiol
Amino Amino- -amine
Alkoxy * Alkoxy- Ether
Alkylthio * Alkylthio- Sulfide
Carbon-carbon triple bond - -yne
Carbon-carbon double bond - -ene
Carbon-carbon single bond - -ane
As longas hydrocarbon Alkyl- -e
Halogen * Halo- Halide
Table P5. List of functional groups along with their prefixes and suffixes in naming.
* - the suffix is used only in the trivial name of a organic compound, and thus, the systematic name uses purely the prefix of
the compound even if the functional group is the highest priority.
Do not worry about the tables and asterisks, as the next part will be a walkthrough of how to actually use the table above.
PART 5. IUPAC NOMENCLATURE DIVIDED BY ORGANIC CLASS
A. NOMENCLATURE OF ALKANES AND ALKYL
HALIDES
Alkanes, agreeably the simplest of all organic compounds
are those which contain purely only carbon and
hydrogen atoms, all connected through single bonds.
Naming
1. The substituent alkanes use the prefix corresponding
to the carbon chain length plus the suffix –yl, written
with their correspondinglocant.
2. The parent is written after substituents are
chronologically arranged, by use of the prefix
corresponding to the carbon chain length plus the
suffix –ane.
3. For cyclic alkanes as well as alkenes and alkynes, the
prefix cyclo- will simply be added.
Figure P2. Methane
Figure P3. 3-methylpentane
Figure P4. Methylcyclohexane

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Alkyl Halides are alkanes with halides as substituents.
The only additional naming rule is that the halides use
the following substituent names:
Halide Substituent Name
F Fluoro-
Cl Chloro-
Br Bromo-
I Iodo-
Table P6. Prefixes for halides substituents.
Ex.
Figure P5. 1-bromopropane
Figure P6. 1,1-difluoroethane
B. NOMENCLATURE OF ALKENES AND ALKYNES
Alkenes differ only from alkanes in that there is at least
one carbon-carbon double bond, the functional group
corresponding to this class of organic compounds.
Naming
1. Follow as in alkanes.
2. The suffix of the parent chain must use the suffix –
ene, preceded by the locant for the double bond.
3. If there is a triple bond, the suffix for the triple bond
is the ultimate suffix of the parent chain, with the –
ene suffix being trimmed to –en-.
Ex.
Figure P7. Propene
Figure P8. Penta-1,2-diene
Alkynes only differ from alkanes in that there is atleast
one carbon-carbon triple bond, the functional group
corresponding to this class of organic compounds.
Naming
2. The suffix of the parent chain must use the suffix –
yne, preceded by the locant for the triple bond.
3. If there is a double bond, the –yne will prevail as the
ultimate suffix of the parent chain.
Figure P9. But-2-yne
Figure P10. Hep-2-en-4-yne
C. NOMENCLATURE OF AMINES
Amines are organic compounds which contain an amino
group (-NH2) attached to the parent.
Naming Amines
1. If there are any carbon chains attached to the
nitrogen other than the parent, label them as
substituent with the locant designated the letter N-.
In this, N is treated as a number.
2. Write the parent chain, changing the suffix from –
ane to –amine.
Figure P11. N-ethyl-N-methylbutanamine
D. NOMENCLATURE OF ALCOHOLS, THIOLS AND
PHENOLS
Alcohols are organic compounds which contain atleast
one hydroxyl group (-OH) attached to an aliphatic chain
(aliphatic and aromatic compounds discussed more on
Proper 5). Phenols are organic compounds with atleast
one hydroxyl group attached to an aliphatic chain and
may also refer to the compound hydroxybenzene. Thiols
are actually the sulfur analogs (or version) of alcohols,
and instead of a hydroxyl group, the thiol or mercapto (-
SH) group is attached.
Naming Alcohols and Thiols
1) Follow as in alkanes.
2a) The suffix must be changed from –ane to –ol, with
the correspondinglocant.
Figure P12. Butan-1-ol
2b) The suffix must be changed from –ane to –thiol, with
the correspondinglocant.
Figure P13. Butane-2-thiol
Naming substituent hydroxyls and thiols
1) Follow as in alkanes
2a) Use the substituent name –hydroxyl,
attached to the parent name.
Figure P14. 2-hydroxyethanoic acid
2b) Use the substituent name –mercapto,
attached to the parent name.

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Figure P15. 2-mercaptoethanoic acid
Naming Phenols
1) Name the substituents outside the hydroxyl group of
the aromatic ring.
2) Use phenol exclusively as the suffix.
Figure P16. 3-methylphenol
Figure P17. 2,4-diiodophenol
E. NOMENCLATURE OF ETHERS AND SULFIDES
Ethers are organic compounds with an alkoxy functional
group (-OR), one where an oxygen is attached to a
carbon chain other than the parent. Sulfides are organic
compounds with the alkylthio functional group, the
sulfur analogs of ethers.
Naming Ethers and Sulfides
1) Follow as in alkanes.
2a) Indicate the presence of the alkoxy group by using
the carbon length prefix followed by –oxy.
2b) Indicate the presence of the alkylthio group by using
the carbon length prefix followed by –thio.
2) Indicate the parent chain.
Figure P18. 2-methoxybutane
Figure P19. 2-methylthiobutane
Figure P20. 2-methoxy-2-ethylthioheptane
F. NOMENCLATURE OF KETONES AND ALDEHYDES
Ketones are organic compounds with the carbonyl (C=O)
functional group,a carbon double bonded to an oxygen.
Aldehydes are organic compounds with the formyl (CHO)
functional group,a carbonyl group attached to a
hydrogen. Note that the formyl group requires three
bonds other than the parent, and will always be terminal.
Naming Ketones
1. Follow as in alkanes
2. Change the suffix from –ane to –one, with the
correspondinglocant.
Figure P21. Pentan-2-one
Naming carbonyl as substituent
2. Indicate presence of carbonyl group by
using the prefix oxo-.
3. Indicate parent chain
Figure P22. 3-oxobutanoic acid
Naming Aldehydes
1) Because the formyl group is terminal,assign the
formyl carbon the locant number 1.
2) Indicate all substituents.
3) Change the suffix from –ane to –al, without anymore
the locant.
Figure P23. 2-hydroxyheptanal
4) Cyclic aldehydes use the suffix –carbaldehyde
instead.
Figure P24. 2-hydroxycyclohexanecarbaldehyde
Naming formyl as substituent
2. Indicate presence of formyl group by using
the prefix oxo-.
3. Indicate parent chain.
Figure P25. 3-oxopropanoic acid

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G. NOMENCLATURE OF CARBOXYLIC ACIDS AND
ITS DERIVATIVES
Carboxylic acids are organic compounds with the
carboxyl functional group (-COOH), a carbonyl-hydroxyl
functional group. The carboxylic acid derivatives are
those which can be produced with the carboxylic acid as
starting material, and may not necessarily always show a
functional group similar to a carboxyl.
Amides are carboxylic acid derivatives with the
carbamoyl (CONH2) functional group.
Acid halides are carboxylic acid derivatives with the
halocarbonyl (COX) functional group.
Esters and thioesters are carboxylic acid derivatives with
the alkoxycarbonyl (COOR) and alkylthiocarbonyl (COSR)
group, respectively.
Acid anhydrides are carboxylic acid derivatives wherein
two carboxylic acids are bonded to each other through
an oxygen atom.
Nitriles are carboxylic acid derivatives with a cyano or
carbonitrile group (CN).
Because carboxylic acids or their derivatives are usually
the highest priority group in a compound, their
nomenclature as substituents will not anymore be
discussed.
Naming Carboxylic Acids
2. Change the suffix from –ane to –oic acid, without
anymore using the locant.
Figure P26. 4-hydroxybut-2-enoic acid
Naming Amides
1. If there are any carbon chains attached to N, name
as if naming amines.
2. Follow as in alkanes for the parent chain.
3. Change the suffix from –ane to –amide.
Figure P27. N-methylethanamide
4. Cyclic amides use the suffix –carboxamide instead.
Figure P28. N-methylcyclobutylcarboxamide
Naming Acid halides
2. Change the suffix from –ane to –oyl halide.
Figure P29. Butanoyl chloride
3. Cyclic acid halides use the suffix –carbonyl halide
instead.
Figure P30. 4-hydroxycyclohexanecarbonyl bromide
Naming Esters and Thioesters
1. Treat the carbon chain connected to the single
bonded oxygen as the substituent.
2. Treat the carbon chain connected to the carbonyl
carbon as the parent.
3. Change the suffix of the parent from –ane to –oate
or –thioate, respectively.
Figure P31. Ethyl propanoate
Figure P32. Ethyl propanethioate
4. Cyclic esters and thioesters use suffixes –carboxylate
and –carboxythiolate instead.
Figure P33. Ethyl cyclopropanecarboxylate
Figure P34. Ethyl cyclopropanecarbothiolate
Naming Acid Anhydrides
1. If the two chains are of same identity, just identify
one and change the suffix from –ane to –oic
anhydride.
Figure P35. Propanoic anhydride
2. If the two chains are of different identity, identify
both, change their suffixes from –ane to –oic and
end with the word anhydride.

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Figure P36. Ethanoic methanoic anhydride
3. Cyclic anhydrides use the suffix –carboxylic
anhydride instead.
Figure P37. Cyclohexanyl butyl carboxylic anhydride
Naming Nitriles
2. Change the suffix from –ane to –nitrile.
Figure P38. 2-hydroxybutanenitrile
3. Cyclic nitriles use the suffix –carbonitrileinstead.
Figure P39. 2-hydroxycyclobutanecarbonitrile

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PART 6. PROPERTIES OF ORGANIC COMPOUNDS ARISING FROM STRUCTURE
Organic Chemistry is not without properties specific for its discussion. The following are terms that describe an organic
compound based on their structure alone (and not their function or innate chemical properties).
Property Classification of the property Example
Ring closure/ being cyclic Linear compounds – no ring.
Carbocyclic compounds are those whose ring
consists entirely of carbon.
Heterocyclic compounds are those whose ring
consists of at least one atom other than carbon
(aka heteroatom).
Saturation - refers to the
saturation of content of
hydrogen atoms in the
compound.
Saturated – no wasted double or triple bond
(wasted instead of being used to bond to
hydrogen)
Unsaturated – double or triple bond exists and
wastes maximum bonding with more
hydrogens.
Multiple double bond
pattern – how many single
bonds separate two double
bonds?
Conjugated – there is exactly one single bond
in between two or more double bonds.
Isolated – there is no single bond in between
the two double bonds.
Cumulated – there is more than one single
bond in between the two double bonds.
REVIEW PROPER 1: MOLECULAR ANATOMY
While there is a blurry division between topics focused in this review topic and the second, the goal of this particular
portion is to introduce the very structure and behavior of a single atom or compound while the second focuses on how an
atom or compound behaves towards others.
PART 1. SUB-ATOMIC PARTICLES AND THE ATOMIC
MODEL
The structure of the atom is first tackled in order to get a
clearer idea going into the reactivity of actoms towards
each other.
Atoms are generally understood to contain three sub-
atomic particles classified according to their charge (or
absence of):
Protons - positively charged subatomic particles.
Electrons - negatively charged subatomic particles.
Neutrons - chargeless subatomic particles.
The atomic model is the generally understood
composition and structural property of the atom, with
regard to its subatomic particles, their location, number
and reactivity.
Two statements from it important in organic chemistry:
1) The atom is electrically neutral having equal number of
protons and electrons to minimize its potential electric
energy (and attain stability);
2) Electrons are distributed in energy levels, and
moreover have so much to deal with the atom’s behavior
towards other atoms. Do not forget that opposite
charges attract.
PART 2. CHEMICAL BONDING AND QUANTUM
NUMBERS
Electrons are the ones responsible for the creation of the
chemical bonds we know (aka covalent and ionic bonds).
However, be clarified that bonds in chemistry are not all
chemical bonds.
Chemical bond – a combination of electrons from two
different atoms that is permanent and forms a new
identity (ex. Oxygen and two hydrogens form water by
chemical bonding). The most known chemical bonds are
the covalent and ionic bonds.
Physical bond – a.k.a. forces of attraction - “weaker”
bonds that are temporary and determine only the
compactness of a compound and not identity (ex. Water
vapor has weak physical bonds, liquid water has stronger
physical bonds,and ice has the strongest physical bonds).

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The most known forces of attraction are van der Waals
forces, dipole-dipole interactions and hydrogen bonds.
We will characterize these bonds later.
Quantum Mechanics
Quantum Mechanics is a quite a fancy term but it only
pertains to the study of understanding how the electrons
move about in the atom: where they are located and
what energy they are possessing at the moment.
General Chemistry helped us understand the gist of
quantum mechanics by representing them in symbols
known as quantum numbers.
1. Principal Quantum Number, (n) refers to the energy
level, or a wide estimated orbit where electrons can
move about.
2. Azimuthal Quantum Number (l) refers to the even
smaller areas of the energy level where electrons more
likely rotate about called subshells.
3. Magnetic Quantum Number refers to the orbitals, or
slots within the electron shell where two electrons of
different spins (determined by 4. Spin Quantum
Number) can occupy.
Quantum number Symbols What it
represents
Principal (n) 1, 2, 3, 4, 5… Energy shell
Azimuthal (l) s, p, d, f… Subshell
Magnetic (ml) …-2, -1, 0, 1,
2…
Orbital
Spin (ms) -1/2, +1/2 Electron spin
Table 1.1. The quantum numbers.
Figure 1.1. The shapes of orbitals in s and p subshells. The
sphere shape of s and dumbbell shape of p play a role in
multiple bonding.
An energy shell contains even more specific spaces
wherein electrons move about called orbitals, and these
orbitals have shapes as depicted above. This should erase
our mindset that because we draw a chemical bond as
two dots or as a line, electrons just stay in a line. They
stay movingin these orbitals.
Figure 1.2. Kekule structure and orbital shape diagram of
ethene. The symbols enclosed in parenthesis (pi and
sigma) are discussed later.
Electronegativity: Basis of Chemical Bonds
Even the formation of a single Carbon-Hydrogen bond
requires the understanding of electronegativity, the
property of an atom to attract electrons (by its protons)
toward itself.
A more electronegative atom has the tendency to pull a
less electronegative atom towards it because they will
share orbital spaces and reduce instability.
Octet rule is followed in atom stability, where eight
valence electrons are considered the most stable.
Differing valence electrons mean different number of
electrons required by different atoms.
Figure 1.3. Note here that sodium achieves the octet rules
because by giving its one valence electron on its 3
rd
energy level, all eight electrons on its 2
nd
energy level
automatically become valence electrons following the
octet rule.
Element(s) Valence
Electrons
Electrons more to
reach octet rule/
stability
Carbon 4 4
Nitrogen 5 3
Oxygen 6 2
Fluorine, Chlorine,
Bromine, Iodine
7 1
Hydrogen 1 1
Table 1.2. Common elements in organic chemistry along
with their valence electrons and electrons needed to
follow the octet rule.
Formal and Partial Charges: A little more that just “positive and negative”
A positively charged atom has its own degrees of positivity, and vice-versa for negatively charged ones. Formally
charged ones are those with an actual charge such as +1, +2 and so on. An already bonded atomis partially

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charged if it already follows the octet rule, but is bonded to an atom much more electronegative than it. The
small letter delta (δ) represents a partial charge.
Forces of Attraction
Name of Bond Involved molecules Example
Hydrogen bond Already bonded very electronegative atom (F, N,
O) and already bonded hydrogen (H) atom
Dipole-dipole forces Already bonded very electronegative atom and
already bonded partially positive atom (usually
carbon)
Van der waals Any two or more atoms bonded together,
without even a partial charge
Chemical bonds
Ionic bond One metal and one non-metal
Covalent bond Two non-metals
Table 1.3. Summary of chemical bonds or interactions.
Intermolecular Forces (Forces of Attraction)
1. Hydrogen bond –as said, being a weak chemical bond,
the hydrogen bond does not create new compounds. If
water can hydrogen bond another water molecule, they
just attract each other, without forming a new
compound in the process.
a. Intramolecular Hydrogen Bonding –
hydrogen bonding occurs within the same
molecule.
b. Intermolecular Hydrogen Bonding –
hydrogen bonding occurs among different
molecules.
2. Other forces of attraction – includingion-dipole
interactions, dipole-dipole interactions, van der waals
interactions and others contribute to the amount of
compaction the molecules have with each other (thus,
forces of attraction). Thus, it can be said that from gas to
liquid to solid, the intermolecular forces get stronger.
Electronegativity difference: Polarity of Intramolecular
Forces
Once a bond is made, regardless of combination of
electrons there is a disparity in the movement of
electrons between the two atoms.
Polarity – denotes opposite charges (thus, “polar”) on
two bonded atoms, the positive and negative.
The simplistic reality is that ionic bonds and covalent
bonds are the same, just different in their level of
polarity.
One way to measure polarity is by calculating their
numerical electronegativity difference. The greater this
difference, the greater polarity between the two, greater
instability alone and greater tendency to be bonded
together.
1. Ionic Bond – highly polar bond as to represent a gain
on the metal and loss of electron on the non-metal.
Basis of electronegativity difference – 2.0 and higher
Examples: Most inorganic compounds

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KCl – formed by the reaction between K
+
and Cl
-
;
EN = 2.2
NaCH3COO – formed by the reaction between
Na
+
and CH3COO
-
; EN = 2.6; (focus on the bond
between the sodium cation and oxygen anion)
2. Covalent Bond – sharing of electrons on both atoms
being bonded.
Basis of electronegativity difference will lead to two
further types of covalent bonds.
a. Polar-covalent bond –one atom has a greater
share of electrons than other because itis
relatively more electronegative.
Basis of electronegativity difference, 0.6 to 1.9
(greater ED than the other type of covalent
bond)
Example: C-O and CN
C-O – EN = 1.0
CN – EN = 0.5
b. Non-polar covalent bond – electrons are
equally shared between two atoms being
bonded, because neither are significantly more
electronegative than the other.
Basis of electronegativity difference, 0 to 0.4
(lesser ED than the first type of covalent bond)
Example: C-C bonds
C-C – EN = 0
PART 3. MOLECULAR GEOMETRY AND HYBRIDIZATION
We now know how electrons move about through
quantum theory, but don’t know why we have to draw
them with consistent appearancein our notes and in the
books.
Valence Shell Electron-Pair Repulsion (VSEPR) Theory -
faithful to the concept that stability of molecules is based
on lowest energy because shapes of the molecules are
caused by repelling of electrons to be the farthest away
possible from each other.
Electron domains - “groups” that repel each other.
Tthey are either other atoms (thus a bonding pair) or
lone pairs (a non-bonding pair)). This is why you cannot
see a methane molecule written like this.
Figure 1.4. “Move away!” said the electrons in this wrong
drawing of methane, a supposedly tetrahedral molecule.
This is also why instability is caused when there are too
much chemical bonds crumpled together in a molecule.
Figure 1.5. The fact that all hydrogen atoms have the
same tendencies to repel electrons make it possible for
methane to have equal angles between H atoms.
The most well-known shapes are listed below, based on
the number of bonding pairs or chemical bonds (more
accurately electron domains) and the number of their
electron domains.
Molecular
Geometry
#BP #LP
Linear 2 0
Trigonal planar 3 0
Trigonal planar 2 1
Tetrahedral 4 0
Tetrahedral 3 1
Tetrahedral 2 2
Trigonal bipyramid 5 0
Octahedral 6 0
Octahedral 5 1
Octahedral 4 2
Table 1.4. The well-known molecular geometries.
“Molecular geometry” here is specifically the electron
domain geometry (refer to other sources).
When there are different substituents such as a lone pair
or more electronegative atom (instead of H), the angles
become a little greater or lesser between domains to
maximize distance between each other.
Figure 1.7. Because a lone pair is closer to oxygen
compared to a bonding pair, the repulsion is greater
causing the angle to increase JUST A LITTLE BIT (>109.5)
as to maintain tetrahedral shape.
Hybridization and Multiple Bonds
The second quantum number tells us that we have
different subshells. In organic chemistry, we only need
the s and p subshells. The s orbital is closer to the
positive nucleus, and their charges neutralize more than
p orbitals. P orbitals are less stable and can be utilized for
reactions, this property being called polarizability.

SLRM/JRBM| 15
Sigma bond – s orbitals on head-head overlap.
The first bond is always and only the sigma bond
between two atoms.
Pi-bond – p orbitals on side-side overlap.
Because s orbitals are spherical, they cannot pi bond.
Moreover, since there cannot be more than one sigma
bond, p orbitals cannot sigma bond.
THUS, sigma = s orbital; pi = p orbital
Figure 1.6. The s orbital occupies the lower energy state
and is closer to the nucleus, which the electrons would
prefer compared to the more unstable p orbital.
The great problem in Organic Chemistry is that Carbon
only has two outer electrons that can bond, but even in
the simplest molecule (CH4) carbon has FOUR bonds.
Why?
Hybridization – theory where in at the excited state, the
valence s and p orbitals can fuse to share their
characteristics. The more important fact is that p orbitals
gain s orbital characteristics: p orbitals can now sigma
bond.
Figure 1.8 In the ground state, two electrons reside in the
lower s orbital. At the excited state, s electrons disperse.
Still, the excited state of this carbon is not consistent with
the 4 sigma bond observation in methane.
Figure 1.9. Hybridization theory states that upon
excitation, electrons disperse and orbitals share their
characteristics. This means the s orbital shares it sigma
bonding characteristic with the p orbitals. Problem
solved.
One atom may have different hybridizations as time passes by. When the atoms bonded to it demand additional sigma or pi
bonds as needed, the hybridization of an atom will adjust accordingly to fit the situation.
Carbon in particular has three hybridization states: sp3,sp2 and sp.
The three hybridized orbitals are named after how much subshells have hybridized together, where only those in parenthesis
possess the character of the s orbital:
Hybridized
orbital
names
Description Orbital diagram Resulting
molecular
geometry
sp
3
One s orbital and all three
p orbitals combine, giving
way for four sigma bonds.
Because all bonds form sigma bonds, no pi bonds can be
formed, but there is still some polarizability inherited from
Tetrahedral

SLRM/JRBM| 16
the p orbitals (25%).
sp
2
One s orbital and two of
the three p orbitals
combine, giving way for
three sigma bonds and
one pi bond courtesy of
the one unhybridized p
orbital. One pi bond can be formed due to one solo unhybridized
p. (33.3% estimated polarizability)
Planar
sp One s orbital and one of
the three p orbitals
combine, giving way for
three sigma bonds and
two pi bonds.
The bottom orbital shape diagram shows the side view of
the compound, showing the right angle between two p
orbitals.
Two pi bonds can be formed due to two solo unhybridized
p’s. (50% estimated polarizability)
Linear
Table 1.5. The hybridizations of carbon.
Figure 1.10. Propane-1,2-diene is an example of compound with carbons having different hybridizations. The middle carbon
has sp hybridization (with 2 pi bonds), while the side carbons have sp2 hybridization (with only 1 pi bond each).
Counting  and  Bonds
a. For carbon-carbon single bonds (sp
3
) – there is always one  and no bonds
Ex. C-C = 1  and 0 , C-C-C-C-C = 4  and 0 
b. For carbon-carbon double bonds (sp
2
) – there is always one  and one  bond
Ex. C=C = 1  and 1 , C=C-C=C-C = 4  and 2 
c. For carbon-carbon triple bonds (sp) – there is always one  and two  bonds
Ex. CC = 1  and 2 , CC-C=C-C = 4  and 3 
How about the hybridization for nitrogen and oxygen? The theory definitely holds true for them and their molecular
geometries still remain the same (ex. If sp3 carbon is tetrahedral, sp3 O and N are also tetrahedral), only in that a nother
thing has to be mentioned for N and O: if a valence orbital already has two paired electrons, there cannot anymore be any
bond made for that orbital.

SLRM/JRBM| 17
Figure 1.11. Even if all orbitals of N and O share s character, filled orbitals cannot anymore participate in bonding. Take note
that oxygen cannot have sp hybridization because both sp orbitals (in bracket) are already filled. Examples for sp3 and sp2
hybridized nitrogen and oxygen atoms are drawn below the orbital configurations.
PART 4. ISOMERS AND STEREOCHEMISTRY
An isomer is a compound that is defined only in relation to another compound like someone being another’s relative.
Stereochemistry - both the branc h of chemistry thatstudies isomers, and a property of a compound to have isomers.
Identical – the two compounds being compared are exactly the same.
Isomers – the two (or more) compounds have the same molecular formula but are not identical. They can differ in a)
arrangement of bonds, b) configuration (permanent spatial positions) or c) conformation. The definitions of these terms
are defined in the caption of the figure below.
Figure 1.12. Difference between the terms “arrangement”, “configuration”, and “conformation”.
Arrangement refers to actual bonds between atoms. It may give the most “non-related” isomers.
Configuration refers to permanent spatial positions of two isomers with the same attachments. Two configurational isomers
are never identical to each other.
Conformation refers to temporary spatial positions, and two conformational isomers can be identical at one point.
ISOMERS
arrangement spatial position
Constitutional Isomer Stereoisomer
attachment placement offx group actual fx group
configuration conformation
SKELETAL POSITIONAL FUNCTIONAL
CONFORMATIONAL
tetrahedral
unsaturated/cyclic
Optical Isomers
GEOMETRIC
mirror images not mirror images
ENANTIOMERS DIASTEREOMERS
Figure 1.13. Classification scheme for isomers.

SLRM/JRBM| 18
1. Constitutional Isomers
Constitutional isomers differ in arrangement of bonds, and most likely have different systematic and trivial names (ex.
In a, pentane and isopentane are isomers even though they have different names).
a. Structural or Skeletal Isomers – the skeletal components are rearranged to give different molecules.
Ex. Pentane and Isopentane both have the same empirical formula, C5H12, but are drawn differently.
Figure 1.14. Pentane Figure 1.15. Isopentane or 2-methylpentane
b. Positional Isomers – the placement of the functional group differs.
Ex. Butan-1-ol and Butan-2-ol are both written as C4H9OH but are drawn differently.
Figure 1.16. Butan-1-ol
Figure 1.17. Butan-2-ol
c. Functional Isomers – possess different functional groups.
Ex. Ethanol and Dimethyl Ether (Methoxymethane) are both written as C2H6O but one is drawn as an alcohol and
the other as an ether.
Figure 1.18. Ethanol Figure 1.19. DImethyl Ether or Methoxymethane
2. Stereoisomers
Also called spatial isomers, stereoisomers are those which either differ in configuration or conformation, with identical
or exactly the same arrangement of bonds among atoms. Because the identity of these isomers are most of the time
nearly identical due to identical bond arrangements, the names of these isomers are usually the same, only given an
additional term to distinguish each other (ex. Cis-trans isomers are almost identical)
2a. Configurational Isomers – stereoisomers with permanent spatial differences.
a. Optical isomers – stereoisomers different in configuration resulting from having at least one central atom
that is attached to four distinct groups (this property is called chirality)+.
i. Enantiomers – op (discussion of chirality in RX compounds).
ii. Diastereomers – are stereoisomers different in configuration but not having the property of chirality.
b. Geometric Isomers – are stereoisomers of a carbon-containing compound resulting from inability to
rotate. There are two situations: when there is a double bond and when the compound is cyclic.
Figure 1.20. Inability to rotate in compounds with double bonds or cyclic structures.
Unlike conformational isomers which can beidentical, two geometric isomers can never be identical and thus
needs a way of naming. When out of the four substituents, two are hydrogen and the other two are same
(ex. Chlorine), the cis-trans nomenclature is used. When there is atleast another different substituent (ex. 2
hydrogens, chlorine and bromine), the E-Z nomenclature is used.
c1. Cis-trans nomenclature
We use the cis-trans nomenclature when each of the two carbons have one substituent, and one of their
attachments is actually part of the parent chain.
i. Cis – the substituents for the two carbons are at the same side
ii. Trans – the substituents for the two carbons are at the opposite side
Ex. Cis-1,2-dichlorocyclohexane and Trans-1,2-dichlorocyclohexane

SLRM/JRBM| 19
Figure 1.21. Cis-1,2-dichlorocyclohexane Figure 1.22. Trans-1,2-dichlorocyclohexane
c2. E,Z notation
Look at 1-bromo-2-fluoropropene. In carbon 2, the methyl substituents is part of the parent chain, but
carbon 1 is not attached to any other substituent which is part of the parent chain. This means atleast
one of the two carbons has more than one substituent (like carbon 1 here, having Br and H has
substituents). To name these tri- or tetra-substituted alkenes properly, we use priorities for each of the
two carbons.
Figure 1.23. You cannot designate cis or trans notations for this compound because the alkene is tri-
substituted. We use the E-Z notation instead.
Example (with steps)
1) Prioritize the two constituents per carbon based on their molecular weight (I > Br > Cl > > O etc.)
2) Label the heavier 1 and the lighter 2.
3) If the substituents labeled 1 are on the same side, use Z (as if you’re labeling them cis). If
otherwise, use E (as if you’re labeling them trans).
Figure 1.24. The E and Z isomers of 1-bromo-2-fluoropropene.
2b. Conformational isomers – are stereoisomers with temporary spatial differences. To demonstrate it, we introduce
two additional structural formula formats: the sawhorse and the newman projection formulas.
Sawhorse Representation
Views carbon-carbon bonds at an oblique angle.
Figure 1.25. Sawhorse Representation of Ethane
Newman Projection
Views the whole structure directly from one end of the alkane.
Carbon atoms are represented by circles.
Figure 1.26. Left: stagerred conformation of ethane. Right: eclipsed conformation of ethane.

SLRM/JRBM| 20
Staggered conformation - substituents do not overimpose each other in the newman projection are more stable
Eclipsed conformation - substituents overimpose each other in the newman projection and are less stable.
Again, at one point, one molecule may twist by itself due to random motion and be the same exact conformational
isomer as the other.
Figure 1.27. The staggered ethane can move about to become eclipsed.
The conformation of cyclohexane is quite different. Because it’s quite complex compared to something like ethane
above, it has a special shape that conforms to its actual shape (in order to make the atoms as far away from each
other as possible also). The two most famous conformations are the chair and boat conformation.
Figure 1.28. The boat and chair conformations of cyclohexane.
Both consist of axial (vertical) bonds and equatorial (diagonal) bonds. However, since the chair sets the two pointed
carbons apart more, it is the most preferred formula for cyclohexane.
You may be asked to be able to recognize the axial from the equatorial bond. Justimagine a tripod. Every point in the
chair conformation gives you two out of three feet. Supply the remaining foot (equatorial) and the other is the stand
(axial).
Figure 1.29. Identifying equatorial and axial bonds.

SLRM/JRBM| 21
REVIEW PROPER 2: MOLECULAR FUNCTION AND REACTIVITY
Although most of the concepts in this proper are intertwined with the chapter on alkanes, for a smoother logical flow these
concepts that can be used as foundational knowledge were lifted out and inserted into this “introductory” proper.
PART 1. PERIODIC TRENDS AND REVIEW OF ELECTRONEGATIVITY
Periodic trends, properties of atoms that increase or decrease as a reader proceeds horizontally or vertically through a
periodic table are not entirely needed for organic chemistry. Some of these are only important when we differentiate non-
metals from the many metals in the table, but organic chemistry only deals with the very few non-metals. The most
significant periodic property of atoms in this course is electronegativity, which we have already discussed.
Electronegativity increases as one progresses from the left to the right and from the bottom to the top of the periodic table.
Figure 2.1. Electronegativity trend in the periodic table.
When two atoms are bonded together, electronegativity induces polarity or disturbance of positive and negative charges.
Although covalently bonded atoms aresupposed to have no charges, the atoms’ electronegative property gives them
partial charges (Recall formal and partial charges). In chloromethane, the chlorine atom, being the more electronegative
atom, attracts electrons fromits covalent bond with carbon. This gives it a partially negative charge. Carbon, having “lost”
its electrons to the chlorine atom, gains a partially positive charge.
Figure 2.2. Electron flow and partial charges in chloromethane.
The direction of the electron cloud shift is indicated by a crossed arrow. The electronegativity of bonds may also be
computed by subtracting the electronegativity value (or EN) of the less electronegative atom from the EN of the more
electronegative atom. We should also know now how to use electronegativity differences in order to know if a chemical
bond is covalent non-polar (EN = 0.0 – 0.4), covalent polar (EN = 0.5-1.9) or ionic (2.0 and above).
PART 2. SOME VISIBLE PROPERTIES OF MATTER
In the field of physical chemistry, many observable
properties of chemicals such as elasticity, viscosity, flow
and thermodynamics are discussed, but it is enough in
this course to know about the following visible/physical
properties of matter:
A. Melting and Boiling Points
The melting and boiling points of a substance are the
temperatures at which the solid form of the substance
turns into liquid (melting point) and at which the liquid
form of the substance turns into gas (boiling point).
Melting and boiling points simply reflect the degree of
the forces of attraction in them. In short, as the forces of
attraction in a substance become stronger, the greater
energy (in this context, heat) required to break them and
consequently turn solid into liquid (melting) or turn liquid
into gas (boiling).
Two factors influence the melting/boiling points:
1. Strength of force of attraction (stronger means
higher melting/boiling points)
2. Length of the compound chain (longer or larger
compounds share greater forces, thus higher
melting/boiling points)
Order of the attractive forces (Strongest to weakest):
Hydrogen bonds > Dipole-Dipole > Van der waals
Figure 2.3. There might be arguments on order between 2
and 3, but the strength of attractive forces is usually
more significant than the chain length of the compound/
B. Solubility
In other chemistry subjects, molecules will be too large
to be dissolved in a like solvent. This means that size can
interfere with the solubility of a molecule. Molecules in

SLRM/JRBM| 22
organic chemistry however are small enough to bypass
this concept.
Thus, the principle of polarity governs solubility in
organic chemistry. With that said, like dissolves like and
no additional solubility guidelineis used.
Amphipathic compound – one which dissolves in both
polar and non-polar solvents (the process is called
partition, in unequal amounts).
Figure 2.4. A short carboxylic acid is amphipathic
because it has polar and non-polar portions.
Since forces of attraction induce those small charges
responsible for polarity, the strength of forces of
attraction also play the major rolein solubility.
Order of the forces of attraction (in dissolving on polar
solvent like water)
Hydrogen bonds (contribute most charge and thus
greatest polarity) > Dipole-dipole > Van der waals
Example:
Figure 2.5. The solubility rules for polar and non-polar
compounds are opposite of each other as demonstrated
here.
C. Acidity/Alkalinity
The terms acid and base are used to describe
compounds, whether organic or inorganic, which have
electron or hydrogen atom accepting or donating
capabilities.
Brønsted-Lowry Definition
1. Acids – capable of donating hydrogen ions
Examples: HCl, HBr, HF, H2SO4
2. Bases – capable of accepting hydrogen
atoms
Examples: NH3, H2O
HCl is a Brønsted-Lowry acid sinceit provides the
hydrogen ion in its aqueous solution. NH3 is the
Brønsted-Lowry base since it accepts a hydrogen.
Lewis Definition
1. Acids – capable of accepting electron pairs
Examples:
Compounds containinga polar bond with
hydrogen (HCl, HBr, HNO3)
Li
+
and Mg
2+
AlCl3, FeCl3, TiCl4,and ZnCl2
2. Bases – capable of donating electron pairs
with which to react with Lewis acids
Examples: NaOH, Ca(OH)2, NH3, H2O
Amphoteric compound – one which can act both as an
acid and as a base.
Water is in itself amphoteric. Recall that water auto-
ionizes into its constituent hydrogen and hydroxide ions
(can become a Brønsted-Lowry acid and Lewis base) or
accept a hydrogen to become hydronium (can become
Brønsted-Lowry base and Lewis acid)
Figure 2.6. Water is amphoteric because it can act as an
acid and a base. You may use the different definitions of
acid and base to prove this.
PART 3. STRUCTURAL EFFECTS
Stability and Reactivity: The reasons for understanding
structural effects
The reader recall greater stability and lesser reactivity
are two ideas for the same result, the lowering of an
atom’s or compound’s potential energy.
The electrical instability in a compound can sometimes
permit it to induce polarities within itself by passing
around electrons in several ways to stabilize the
compound.
Structural Effects - are momentary interactions
happening within atoms of the same molecule or within
molecules that aim to stabilize the compound as much as
possible.
The following are the structural effects most
encountered in the course:
1. Electron Delocalization
Utilizes the polarizability of electrons in pi bonds
to stabilize them around sp2 hybridized carbons.
This means thatinstead of staying in place, the pi
electrons shuffle around all adjacent p orbitals.
We demonstrate delocalization by drawing
“instantaneous”structural formulas called
canonical structures. These several canonical
structures (at least 2) represent the total
movement of electrons around the sp2 system.

SLRM/JRBM| 23
A structural formula of a compound without
delocalization yet is counted as one canonical
structure.
Figure 2.7. At home, your electric fan may have
different instantaneous pictures but it really
rotates. The same concept applies for electrons
delocalized around adjacent p orbitals as shown
by dashed lines.
a. π –electron Delocalization (Resonance)
The delocalized electrons mainly come from a pi
bond. Recognize that a conjugated diene is
actually a sp2 system, and will demonstrate
resonance.
Figure 2.8. Resonance in a conjugated system.
b. σ –electron Delocalization (CH Hyper-
conjugation)
The delocalized electrons come from a sp3
hybridized carbon.
Figure 2.9. Hyperconjugation in propene .
Each hydrogen in a carbon that can
hyperconjugate gives one canonical structure. (If
that C has 3 hydrogens, we have 3 canonical
structures already). Thus, in the structure above,
we have (3 hydrogens + undelocalized formula) 4
possible canonical structures.
c. Lone pair delocalization
The delocalized electrons mainly come from a
lone pair, most often from a nitrogen or oxygen
atom.
Figure 2.10. Lone pair delocalization in an amine adjacent
to a sp2 carbon. (In advanced text, an carbon with both
double bond and amino group may initiate transfer of
double bond from the carbon to the nitrogen.)
2. Inductive Effect – movement caused by polarity. This is demonstrated exactly the same as how we indicate
movement of atoms in a polar bond in the introduction (an arrow pointing to the more electronegative atom).
a. Electron Attracting or Withdrawing Inductive Effect
Electrons are drawn towards atoms with:
1. Excess positive charges as those in the quaternary ammonium and ammonium cations
2. Electronegative atoms in the amino group (-NH2), hydroxyl group (-OH), methoxy
(-OCH3) group, and halo group (-F, -Cl, -Br)
3. Atoms with increased electronegativity due to more electrons such as in nitriles (triple bond) and
benzene (extensive resonance)
Figure 2.11. Electron attraction of the oxygen in a compound with positive charge, compound with electronegative
atom (oxygen) and electron dense compounds. Also notice how benzene and chlorine are fighting for the electrons.

SLRM/JRBM| 24
b. Electron Repelling or Donating Inductive Effect
Electrons are repelled by:
1. Less electronegative atoms (such as carbon)
2. Negatively charged functional groups (-COO
-
, -S
-
, -O
-
)
Figure 2.12. Electron donation of carbon atoms in 2-methylpentan-1-ol and electron donation of the nitrogen atom
in 1-aminopentane.
Inductive Effects and Acidity/Alkalinity
In organic chemistry, the two previous definitions of acids and bases translates to the ability to release hydrogen
(Bronsted-Lowry acidity) and ability to donate electrons (Lewis basicity).
If the inductive effect contributes to making the compound more stable after kickinga hydrogen, then the
compound doesn’t have to kick it out (lesser acidity = more alkalinity). If however the compound is less stable,
kicking out a hydrogen would make it more stable and the tendency for kicking itis higher (greater acidity).
Figure 2.13. The more stable compound doesn’t have to kick a hydrogen because carbons feed the oxygen, and
thus the occurrence of such is low. The less stable compound would be stabilized from release of the electron in
hydrogen and therefore is more acidic.
Figure 2.14. Note that acidity does not only apply to oxygen compounds such as above. Anything electron dense
would have the ability to kick out protons (and be acidic). This is why even unsaturated compounds have very
slight acidic property.
3. Steric Effect
Electrical instability caused by closingin of
electron dense atoms (recall VSEPR).
Atoms in molecules occupy certain amounts of
space. If they are brought too close to each other,
their electron clouds may repel each other causing
a steric strain that may affect the reactivity of the
molecule.
Figure 2.15. Steric effect in a multi-substituted
benzene.
4. Angle Strain
Electrical instability in atoms closingin with
small angles in cyclic compounds.
Atoms in cyclic molecules share a certain angle
between each other. The ideal is 109.5 degrees
(property of cyclohexane). As the angle goes
farther or lower than that, the repelling effect of
electrons on each other increases.
Figure 2.16. Angle strain in cyclopropane. 60 degrees is
a very far cry from 109.5, making cyclopropane a very
unstable compound.

SLRM/JRBM| 25
Structural Effects stabilize and destabilize
Instead of actually being a stabilizing structural effect, steric effect and angle strain are an unstable effects and are
avoided by compounds to maintain stability.
Figure 2.17. A good example of avoiding destabilizing effects. If a reaction produces more than one product, most
of the product is the more (or most) stable of all. The first shows avoidance to steric effect, and the second shows
avoidance to angle strain.
The corollary to knowing that structural effects may stabilize or destabilize a compound is that the more stable
product may either contain less destabilizing effects and have more stabilizing effects.
Figure 2.18. In this reaction, the lower one is preferred for being the carbocation because it is more supported by CH
hyperconjugation.
PART 4. REACTION FUNDAMENTALS
Knowing the reactants and products in a reaction doesn’t
cut it for those who have chemistry-intensive
professions. Chemical kinetics (how fast), reaction
mechanisms (how), and chemical equilibrium (how
complete) of a reaction have to be known also.
A. CHEMICAL KINETICS AND REACTION MECHANISM
Chemical Kinetics deals with both the rate of reactions
and the energetics of the reaction. Moreover, the
mechanism of the reaction where the actual breakage
and formation of new bonds are seen, was discussed.
Energetics
The energy diagram below will review the
reader to the way energy moves in a reaction
and prove the consistency of the principles
written before.
Figure 2.19. An example of an energy diagram.
Going up means increase in energy and vice-
versa.
Transition state – point A to point B, where
change in energy is employed (“transition” from
the reactant towards the product.)
Activation energy – amount of energy needed
to go through the transition state. Ea is the
highest amount of energy in the reaction
because the breakage and formation of bond at
the same time is very energy requiring.
Any energy that is less than Ea will mean no
reaction.
Figure 2.20. Interpretation of the reaction AB + C
-> AC + B in the energy diagram. If the EA cannot
be met, C cannot substitute B and no product is
formed.
Reaction Intermediates
The reactant at reaching the transition state
turns into a reaction intermediate where the
bond cleavage has already occured. In organic
chemistry, most intermediates are those of
carbon because most bonds are concentrated
on it. The following are the most common
carbon intermediates:

SLRM/JRBM| 26
a. Carbanion (C
-
) – a negatively charged
carbon intermediate, attracted to
positive charges
b. Carbocation (C
+
) – a positively charged
carbon intermediate, attracted to
negative charges
c. Carbon free radical (C
●
) – a carbon
intermediate with a single electron,
and is highly reactive to other free
radicals
B. CHEMICAL EQUILIBRIUM
If you were asked to read a book and you like the book,
you would perhaps finish it. If however you don’t like the
book, even if you were forced to read you would stop
somewhere where you can’t stand it anymore. This
analogy goes for the energetics of the reaction.
Chemical equilibrium – state of a reaction where some
reactants remain as reactants and some turn into
products. This is the point where the energy in the
mixture of reactants and products is at the lowest,
resisting further change.
The other concepts regarding chemical equilibrium will
not anymore be reviewed, but it is important to note
that a significant number of organic reactions are in
chemical equilibrium.
Figure 2.21. Format of a chemical equilibrium. Note the
double pointed arrow.
C. GENERAL TYPES OF CHEMICAL REACTIONS
In organic chemistry, other than this itis imperative to know whether the reaction involves charged intermediates
(carbanions or carbocations) or radical intermediates (carbon free radical) in addition to knowing how much reactants or
products there are. Thus, the followingscheme is used to classify a chemical reaction:
(Organic) Chemical Reaction
is characterized by its
1. Attacking group 2. Scheme
resulting from
A) Addition
homolytic heterolytic B) Elimination
cleavage cleavage C) Substitution
(includes redox and combustion)
1) Free Radicals (R
●
) 2) Electrophilic (E
+
) D) Rearrangement
3) Nucleophilic (Nu
-
)
Figure 2.22. A system for characterizing reactions.
1. BY ATTACKING GROUPS
Attacking groups - the reactant other than the one other being discussed (if we discuss an alkane, the other reactant is the
attacking group).
Attacking groups are classified according to their presence or absence of electrons. We list first the two bond
breakages/cleavage that give rise to these attacking groups.
a. Homolytic Bond Cleavage – “symmetrical” breaking of a covalent bond leaving each of the atoms with a single
unpaired electron. The attacking intermediates are free radicals which contain one unpaired electron, making
it highly unstable and very reactive. One homolytic cleavage yields two free radical intermediates. The
reactions initiated by free radicals are called free radical reactions.
Figure 2.23. Homolytic cleavage.
b. Heterolytic Bond Cleavage – “asymmetrical” breaking of a covalent bond leaving one atom with a positive
charge (electrophile) and another atom with a negative charge (nucleophile). One heterolytic cleavage only
produces one electrophile intermediate and one nucleophile intermediate. The reactions initiated by
electrophiles and nucleophiles are called polar reactions.
Figure 2.24. Heterolytic cleavage.
Polar Reactants: Electrophiles and Nucleophiles.

SLRM/JRBM| 27
Because in polar reactions, we are talking about reactants with charges as intermediates, we can classify a
reactant based on the charge it possesses as an intermediate.
a. Electrophiles (E
+
) – electron-loving; electron-poor atoms with a partial positive charge, turns
into a carbocation intermediate.
b. Nucleophile (N
-
) – nucleus-loving or proton-loving; electron-rich atoms with a partial negative
charge, turns into a carbanion intermediate
2. BY SCHEME (NUMBER OF REACTANTS AND PRODUCTS)
Reaction Type with definition and example Simple Representation with Example
Addition (A) – two or more reactants, one product
Ex. Ethene reacts with hydrochloric acid to
form chloroethane.
A + B -> AB
Elimination (E) – one reactant, two or more products
Ex. Ethanol gives off ethene and water
when subjected to an acid catalyst
AB -> A + B
Substitution (S) – one of the substituents in a
molecule is substituted with a different atom or
functional group to give off a new product
AB + CD -> AD + CB
Redox – increase or decreasein oxidation state of two
participating compounds.
By observing the scheme, it is a substitution reaction
between the reactant and the catalyst.
* [O] designates oxidation in a chemical equation,
and [H] designates reduction.
A -> B (A with higher or lower oxidation state)
Combustion – “oxidation of carbon”
Complete combustion – all of the reactant is oxidized
to carbon dioxide with water
Incomplete combustion – unsufficient oxygen; excess
carbon is seen as black soot.
By observing the scheme, it is a substitution reaction
between the organic compound and the oxygen.
Ex. The complete combustion of methane
into carbon dioxide and water
CH + O2 -> CO2 + H2O + Heat (complete)
CH + O2 -> C + CO2 + Heat (incomplete)
Rearrangement/Isomerism – the substituents or
components of a compound become rearranged to
form a new product.
Ex. But-1-ene, under an acid catalyst, will
rearrange to form but-2-ene.
A -> B (rearranged A)
Table 2.1. Classification of reactions by scheme.
REVIEW PROPER 3: ALKANES
Alkanes consist of nothing more than hydrocarbons. Each
carbon atom is joined together by a single bond. All
carbon atoms are sp
3
hybridized. Alkanes may be
straight chains, branched chains, or cyclic.
1. Also known as paraffins from the Latin parum
affinis meaning little affinity. They are known such
because they are stable and unreactive
compounds.
2. Non-polar, hydrophobic,and soluble in other
hydrocarbon compounds. Alkanes areimmiscible
with water. (Review solubility due to forces of
attraction)
3. The longer and flatter the carbon chain, the
higher the boiling point, and the less the polarity.
(Review melting/boiling points due to forces of
attraction)
4. The greater the number of branches, the lower
the boiling point. (due to smaller area for van der
waals forces).
5. Recall that cyclic compounds have cis-trans
isomerism, and so are cycloalkanes.

SLRM/JRBM| 28
Inherent Stability of Alkanes
Recall thatin multiple bonding, pi bonds are more
polarizable. Because alkanes have no pi bonds,it is
expected that all their bonds are strongsigma bonds. For
this explanation, alkanes are unreactive to nucleophiles
or electrophiles.
Figure 3.1. Alkanes do not react with Nu
-
or E
+
.
PART 2. PREPARATION OF ALKANES
Alkanes cannot become reactants to form other products, but other compounds which are more reactive than them can
react to form alkanes. When we talk about a class of organic compounds becoming products, we can call the reaction a
preparation of that particular class of organic compounds.
Preparation of alkanes can be done in several reactions. Because this is the first time any specific reaction will be
considered, we cannot talk in detail about the reactants involved, but we can already know the names of the reactants and
the reactions involved.
1. Hydrogenation of Unsaturated Hydrocarbons – the pi bonds in the unsaturated hydrocarbons are polarizable to
hydrogen ions, and under the reaction favoring such event, saturated hydrocarbons (a.k.a. alkanes) are formed.
Specific Reaction Name Reactant Example
1. Dehydrogenation * Alkenes
Alkynes
(Will be discussed in unsaturated hydrocarbons)
* - mechanism has not yet been discussed.
PART 3. REACTION MECHANISM: FREE-RADICAL SUBSTITUTION
The formation of radicals occurs from the homolytic cleavage of a bond resultingin two intermediates each possessing an
unpaired electron. Again, this product is known as a radical which is highly reactive. The stability of radicals depends on the
number of substituents attached to the atom possessing the unpaired electron that could exhibit more structural effects.
Thus, tertiary radicals are more stable than secondary radicals, which,i n turn, are more stable than primary radicals. The
most unstableis the methyl radical.
Figure 3.2. Stability of radicals.
Halogenation of Alkanes
If the alkane can be turned into a radical,it could react with another radical. The most known way by which an alkane
radical can be produced is by use of sunlight (UV). The radical reaction is usually represented by the addition of a halogen
such as chlorine to an alkane, and has the followingsteps:
1. Initiation – UV cleaves both a chlorine molecule to give chlorine free radicals.
Cl-Cl + uv  2 Cl 
2. Propagation
a. One chlorine radical breaks a C-H bond on an alkane while passing the electron to the carbon. This yields a
carbon free radical bearinga chlorine atom. On the other hand, the removed hydrogen and the other chlorine
radical form hydrogen chloride.
CH3-H + 2Cl   ClCH3 + HCl
b. This continues until no hydrogen can be substituted.
CH3 + ClCH3 Cl2CH2 + HCl
CH3 + Cl2CH2  Cl3CH + HCl
CH3 + Cl3CH  CCl4 + HCl
3. Termination – chlorine radicals that cannot anymore substitute alkanes bond to each other (as if the reverse of
initiation). The reaction stops.
2 Cl   Cl-Cl
Because the attacking group (Cl) is a free radical and the general relation of reactant to products constitute a substitution,
we call the total mechanism a free-radical Substitution (SR). Note that halogenation SR uses chlorine or bromine gas under
high temperatures or ultraviolet radiation; bromine, though less reactive, is more selective.

SLRM/JRBM| 29
PART 4. OTHER REACTIONS
1. Cracking – the unsaturation of saturated hydrocarbons
Ex. Unsaturation of ethane into ethene or ethyne
H3C-CH3  H2C=CH2 + H2 or HCCH + 2 H2
2. Catalytic Reforming – dehydrogenation, isomerization, and aromatization of high molecular weight alkanes
Ex. Dehydrogenation and subsequent aromatization of methylcyclohexane into methylbenzene or toluene
Figure 3.3. Aromatization and Dehydrogenation of methylcyclohexane
3. Grignard Reaction - uses the organic compound as a carbanion to bond with partially or formally positive nucleophiles.
The preparation of the negative carbon compound occurs only when an alkyl halideis present. This is when a metal like
magnesium can bond in the middle.
Figure 3.4. Addition of magnesium yields the Grignard reagent, RMgX.
The greatest use of Grignard reactions lies in the fact that it can overpower a pi bond of a partially or formally positive
element (such as a partially positive carbon or a carbocation) and take its place.
Figure 3.5. Grignard reaction followed by hydration on an aldehyde. More on this on review propers 7 and 8.
REVIEW PROPER 4. UNSATURATED HYDROCARBONS (ALKANES AND
ALKYNES)
Unsaturated hydrocarbons are not completely saturated
with hydrogens due to presence of pi bonds (double or
triple). Those with double bonds are called alkenes, and
those with triple bonds are called alkynes.
Alkenes –one or more carbon-carbon double bonds.
A linear alkene has the general formula of CnH2n.
Vinylic carbons - carbon atoms directly double bonded to
each other.
Allylic carbons - carbons directly bonded to vinylic
carbons.
The alkene carbons bearing the double bond (except
cumulated dienes) have planar geometry, and cumulated
dienes have linear geometry.
Figure 4.1. The vinylic and allylic carbons of an alkene.
Alkynes –one or more carbon-carbon triple bonds.
A linear alkyne has the general formula of CnH2n -2.
All alkyne carbons bearing the triple bond have linear
geometry.A linear shape has no edge, so a linear formula
has no bends.
Figures 4.2 and 4.3. The skeletal formulas at the bottom
are initially awkward to see, but those are the correct
ways of drawing a sp hybridized carbon.

SLRM/JRBM| 30
Enyne – a hydrocarbon with atleast one double bond
and one triple bond.
PART 2: PROPERTIES OF ALKENES
 are non-polar, and liquid at room temperature.
 have densities of less than 1.0 g/mL.
 are more reactive than alkanes and alkynes
because of their diffuse electron clouds.
Alkynes’ reactivity are weakened due to
overcrowding of electrons in the triple bond.
 Trans isomers are more stable than cis isomers
in acyclic alkenes.
o 2n
= for mula to get #cis-trans isomers
where “n” is the number of double bonds
 The more substituents present around the
vinylic carbon, the more stable the molecule.
(Why)
 Internal alkenes are more stable than terminal
alkenes. (use canonical structures to justify)
INDEX OF HYDROGEN DEFICIENCY (IHD)
- gives the number of H2 molecules needed to fully
saturate a hydrocarbon. In the laboratory, IHD of
alkenes/alkynes is called the degree of unsaturation.
- IHD can help in predicting the structure of a
hydrocarbon that may possess a ring or pi bonds (or
both).
- Notice that for every pi bond or ring closure, TWO
hydrogens are removed from the compound. This is why
each IHD value corresponds to TWO hydrogen atoms.
Steps for calculating #IHD:
1.Count the number of carbon and hydrogen atoms
of the given, then write its molecular formula
(CxHy).
2. Using the given’s #carbons (n), compute for its
linear alkane formula using CnH2n +2
3.Subtract the #hydrogens from given to #hydrogens
of the linear alkane.
4.Divide the difference by 2 since one IHD value
corresponds to two hydrogens. The quotient will
give you the #IHD.
Example: Given C6H6, compute for the #IHD and propose
possiblestructures for the unsaturated hydrocarbon.
1. The molecular formula is already given.
2. The linear alkane counterpart of the given
(where n = 6) is C6H14.
3. #Halkane - #Hgiven = 14 – 6 = 8
4. #IHD = 8/2 = 4
To find out the possible structures of the given
unsaturated hydrocarbon, one can use these “options”
to “buy” one IHD value:
1. A pi bond takes one IHD. Thus, a double bond
takes 1 IHD, and a triple bond takes 2 IHD
values.
2. A ring takes one IHD value. Thus, monocyclic
compound takes 1 IHD, a bicyclic one takes 2
IHD, and so forth.
Below are justsome possible structures of C6H6 (kekule structures are used to show hydrogen count):
Possible options (4 IHD) Structure Possible options (4 IHD) Structure
4 double bonds
(4 x 1 = 4)
3 double bonds 1 ring
(3 + 1 = 4)
2 triple bonds
(2 x 2 = 4)
1 ring, 1 triple bond, 1
double bond
(1 + 2 + 1 = 4)
2 double bonds, 1 triple
bond
(2 + 2 = 4)
Table 4.1. Possible structures of C6H6. Other possible structures of C6H6 were not anymore drawn.
PART 3. PREPARATION OF ALKENES
The reaction involving alkanes had already been discussed, and the reaction involving alcohols and alkyl halides will be
discussed again in the future.
Specific Reaction Name Reactant Example
1. Catalytic Reforming/
Dehydrogenation
Alkanes
(Has been illustrated in alkanes.)

SLRM/JRBM| 31
2. Dehydration *
1. Catalyst: Sulfuric Acid and
Heat
Alcohols
3. Dehydrohalogenation of
Alkyl Halides *
Catalyst: KOH in ethanol
2.
Alkyl Halides
* - reaction has not yet been previously discussed and will beillustrated instead in the future.
PART 4. REACTION MECHANISM: ELECTROPHILIC ADDITION
The pi bond is easier to disrupt than the sigma bond. Because alkanes do not have pi bonds, the reactions of alkenes and
alkynes that are not seen in alkanes are due to the presence of their pi bonds. Given that the double or triple bond is
electron rich,itis attracted to electrophiles. Thus, the reaction is, first, electrophilic.
In exchange of the pi electrons, atoms (from the electrophile) were added. Because the entire electrophile was inserted to
the alkene and no atom from the alkene was substituted, the reaction scheme is addition.
In this, the total reaction mechanismis called Electrophilic Addition (AE).
Markovnikov’s rule - states that for asymmetric reagents, the hydrogen atom is added to the vinylic carbon with more
hydrogens, and the non-hydrogen atom is added to the vinylic carbon with less hydrogens.
Specific Reaction Name Example
1. (Catalytic) Hydrogenation
Reagent: H2
Catalysts: Pd/C (palladium on carbon) or PtO2
Product: Alkane
2. Halogenation
Reagent: Cl2 or Br2 on a solvent (DCM or CCl4)
Product: trans-Vicinal dihalide
NOTE: Vicinal means two same functional groups are
placed 1,2.
3. Hydrohalogenation
Reagent: HCl or HBr on ether
Product: Alkyl halide
4. (Acid-catalyzed) Hydration
Reagent: H2O
Catalyst: Acid Catalyst
Product: Alcohol
5. Hydroboration
Reagent: BH3, THF, NaOH, H2O2
Product: Alcohol (anti-Markovnikov)
6. Addition of Alcohols
Reagent: Alcohol
Catalyst: Acid Catalyst
Product: Ether
7. Mild Oxidation (Basic Hydroxylation)
Reagent: KMnO4 in NaOH
Product: cis-Vicinal diol
8. Strong Oxidation (Oxidative Cleavage)
Reagent: KMnO4 in an acidic medium
Product: Refer to oxidative cleavage
Refer to oxidative cleavage.

SLRM/JRBM| 32
9. Epoxidation
Catalyst: Peroxyacid
Product: Epoxide
9. Hydroxylation of Epoxides (Epoxide Ring Opening)
Catalyst: Acid
Product: cis-Vicinal diol
10. Addition Reactions of Conjugated Dienes
Reagent: Hydrogen halide
Product: 1,2 and 1,4 addition products
(review canonical structures in conjugated sp
2
systems, one canonical structure yields + and –
charges on opposite ends)
11. Polymerization
Reagent: Free radical
Product: Polymer of length n + 1 monomers
Unlike in alkanes where the number of hydrogens
limits the free radical reaction, each added alkene
adds another pi bond, which allows alkene polymers
to become very long chains.
(Initiation -> propagation -> termination)
PART 5. ELECTROPHILIC ADDITION OF ALKYNES
- Take note that because two pi bonds are removed for every triple bond, two moles of reagent must be used to
remove both pi bonds (ex. one mole reagent only removes one pi bond)
1. Hydrogenation
Reagent: H2
Catalyst: Pd/C or Lindlar catalyst
Product: Alkane (if Pd/C), Alkene (if Lindlar)
2. Halogenation
Reagent: Cl2 or Br2
Product: trans-Vicinal dihalide per mole reagent
3. Hydrohalogenation
Reagent: HCl or HBr
Product: Alkyl halide
NOTE: Markovnikov’s rule is essential in this case
4. Hydration (followed by Tautomerization)
Reagent: H2O
Catalyst: H2SO4, HgSO4
Product: Enol Intermediate  Ketone
NOTES:
i) An enol is unstable, so it tautomerizes to a ketone/aldehyde
ii) The enol turns into an aldehyde if the alkyne is ethyne (Why?)
ii) Tautomerization is a rearrangement reaction where the
difference between the two isomers is the placement of one
hydrogen atom.
5. Strong Oxidation
Reagent: KMnO4 in an acidic medium
Product: Refer to “Oxidative Cleavage” below
Refer below.
Oxidative Cleavage Strong oxidation is enough to break an
unsaturated compound into two halves.

SLRM/JRBM| 33
The two halves that would be cut would dictate
the products.
The cleavage products of alkenes (and alkynes)
can be determined by looking at the vinylic
carbons and counting the number of “oxidizable
sites” which are either
a) Bonds of the carbon that were cleaved; or
b) Hydrogen atoms directly bonded to the carbon
Figure 4.4. Illustration of the guidelines for
cleavage products.
The guideline is as follows:
4 oxidizable sites – carbon dioxide (CO2)
3 oxidizable sites – carboxylic acid product
2 oxidizable sites – ketone product
Figure 4.5. Examples of oxidative cleavage reactions.
Keep track of the halves being cleaved and count the
oxidizable sites per half.
Nucleophilic Substitution (SN) of the Acetylide Ion
As discussed in the polar reaction mechanisms for unsaturated hydrocarbons, the nature of the electron dense double and
triple bonds are great sites for electrophiles, but the following reaction creates a positively charged ion, this time attack
sites by nucleophiles.
1. Acetylide Anion Formation
This reaction is possible only for alkynes. The reaction name refers to the product, the acetylide anion.
Reagent: NaNH2 (sodium amide) in ammonia
Product: Acetylide Anion and Ammonia
Figure 4.6. Acetylide Anion Formation by Ethyne
2. Nucleophilic Substitution of the Acetylide Anion
Reagent: Alkyl halide
Product: Terminal Alkyne (if ethyne), Internal Alkyne (if alkyne chain possesses more than two carbon atoms)
Figure 4.7. SN of the Acetylide ion.
REVIEW PROPER 5: AROMATIC HYDROCARBONS
A compound has to follow several qualifications before it
can be called aromatic. This is governed by three
properties: Being cyclic, being completely planar, and
following of Debye-Hückel’s Rule (popularly Hückel’s
Rule).
If any one of the properties are not met, the compound
is automatically non-aromatic (aka aliphatic)
Rule Qualifying Property
1. Being cyclic The compound MUST be cyclic.
2. Being The ring in the compound must be

SLRM/JRBM| 34
planar PLANAR (must have conjugated
arrangement with all ring members in
sp
2
hybridization.
3. Hückel’s
Rule
4n + 2 number of pi electrons in the
ring.
Table 5.1. Three requirements that must be followed to
conclude the aromaticity of a compound.
- Hückel’s Rule - given by the equation e
-
= 4n + 2
where n must be a whole number. The e to be
counted are those of the pi bonds present within the
ring. Lone pairs of heteroatoms may also be counted
when two additional pi electrons are needed.
- Aromatic compounds are also termed as arenes.
Take benzene as an example. We validate its aromaticity.
Figure 5.1. Benzene.
1) The nin 4n + 2 must be a whole number;benzene has 6 pi
electrons, and so we calculate:
4n + 2 = 6
4n = 6 - 2
n = (6 - 2)/4 = 4/4 = 1
Since nis a whole number, benzene follows Huckel's rule.
2) Benzene is cyclic.
3) All atoms in the ring are of sp
2
hybridization.
Thus, benzene is aromatic.
PART 2. REACTION MECHANISM: ELECTROPHILIC SUBSTITUTION
You may see benzene as an alkene, so you might initially assume it reacts like one (through electrophilic addition). But this
is not the case.
Benzene is indeed, an alkene, but more importantly, itis conjugated, which also makes it resonant (recall structural effects).
If it would react like an alkene, one pi bond would be broken, and thus its aromaticity and resonance will be destroyed; it
will become unstable. Because we all know that compounds prefer to be stable, benzene cannot react in this manner.
Figure 5.2. Theoretical comparison of the energy possessed by benzene and a similar ring without resonance.
Thus, if we look below, we would be able to conclude the reaction mechanism of benzene which retains its aromaticity and
resonance: substitution.
Figure 5.3. The substitution scheme retains the aromaticity of benzene, and is preferred between the two.
The benzene ring is obviously electron rich, thus,it attracts electrophiles. Therefore, its reaction mechanism is electrophilic.
Thus, the complete reaction mechanism for benzene and aromatic compounds is electrophilic substitution (SE).

SLRM/JRBM| 35
PART 3. REACTIONS ON BENZENE
1. Halogenation
Reagent: X2
Catalyst: FeX3
Product: Halobenzene
2. Nitration
Reagent: HNO3
Catalyst: H2SO4
Product: Nitrobenzene
3. Sulfonation
Reagent: SO3 + H2SO4 (Fuming Sulfuric Acid)
Catalyst: H2SO4
Product: Benzenesulfonic acid
4. Friedel-Crafts Alkylation
Reagent: Alkyl Chloride
Catalyst: AlCl3
Product: Alkylbenzene
5. Friedel-Crafts Acylation
Reagent: Acyl Halide
Catalyst: AlCl3
Product: Acylbenzene
NOTE: The productis usuallya ketone, but in the case of a
methanoyl halide, do you still get a ketone? (Answer by drawing)
6. Hydrogenation
Reagent: H2
Catalyst: PtO2
Product: Cyclohexane
7. Oxidation
Reagent: KMnO4, H2O
Product: Benzoic Acid
PART 4. SUBSTITUENTS AND SUBSTITUENT EFFECTS
For a benzene ring that already has a substituent to it, two consequences immediately occur:
CHANGE 1: The reactivity of the substituted benzene is altered (increased or decreased); and
CHANGE 2: The existing substituent will direct the new electrophile to a specific carbon in the benzene ring.
For this explanation, the substituents in the ring are described as a combination of two classifications: if it activates or
deactivates (activator/deactivator), and on which relative carbon of the ring (ortho, meta, para) it will direct new
substituents.
The substituents can also undergo reactions, but the focus will first be on the benzene ring itself.
CHANGE 1: Activators and Deactivators
A substituent may increase or decrease reactivity of the ring due to whatever structural effects the substituent will bring to
the benzene ring. Because benzene attracts electrophiles,increasing electron density makes it more reactive.
A substituent that increases the ring’s electron density activates it,
and any that decreases its electron density deactivates it.
The strongest activators give free electrons as lone pairs, followed by those which may occasionally delocalize electrons to
the ring (additional resonance or hyperconjugation).
Lone pair delocalization (ex. Amines) > Resonance (ex. Conjugated alkyl groups) = CH hyperconjugation (ex. Alkyls)
The strongest deactivators have formal positive charges, followed by electron attraction by electronegative atoms (such as
halogens), followed by those which possess only a partial positive charge (as in partially positive carbons).
Formal positive charge (ex. Nitro group) > Electronegativity (ex. Halogens) > Partial positive charge (ex. Carbonyl)

SLRM/JRBM| 36
Figure 5.4. Substituent effects on reactivity of the aromatic ring.
CHANGE 2: Ortho, Para and Meta Orientations
The directing effect of a substituent in the ring is actually influenced by the same reason why it activates or deactivates (by
altering electron density in the ring). There are three orientations in which the new substituent may be placed (in relation
to the existingsubstituent):
a. Ortho (o) – new substituent is placed at carbon #2 from the existing substituent (1,2 orientation)
b. Meta (m) – new substituent is placed at carbon #3 from the existing substituent (1,3 orientation)
c. Para (p) – new substituent is placed at carbon #4 from the existingsubstituent (1,4 orientation)
Figure 5.5. ortho, meta, and para orientations of dimethylbenzene (traditional name “xylene”)
Some substituents at the benzene ring are ortho-/ para- directing, while others are meta- directing.
A substituent makes certain carbons (but not all) more active than others: whatever carbons become more activated will be
the attack site of new substituents, and the less activated carbons will not be attacked (ex. meta directing substituents
make the carbons meta to it more activated than those ortho/para to it)
The following table shows diagrammatical explanations on how certain activators or deactivators direct in ortho/para or
meta orientations.
Orientation Diagram and Explanation
Meta
Figure 5.6. Meta directing mechanism.
Deactivating substituents decrease electron density in the ring. They lessen the tendency of the
pi electrons to settle in the ortho/para positions, while the meta positions are not deactivated.
(This is why most meta directors are deactivators)
NOTE: HALOGENS are the only deactivators that direct in the ortho/para directions
Ortho/Para
Figure 5.7. Ortho/para directing mechanism.
Activatingsubstituents increase electron density in the ring. They increase the tendency of the pi
electrons to settle in the ortho/para positions, while the meta positions are not activated.
(This is why most ortho/para directors are activators)

SLRM/JRBM| 37
PART 5. ALIPHATIC REACTIONS ON ARENES
While the focus in the previous part was on the benzene ring, its substituents are also free to undergo reactions. There are
no stated limitations on what reactions can possibly happen to these substituents. Examples are shown below.
Figure 5.6. Bromination SR, oxidation, and epoxidation of
alkane, aldehyde, and alkene substituents respectively on a ring.
Exercises:
In synthesis of most organic compounds, multiple reactions have to be done to yield the desired product. Some examples
are given below. It is important to write the correct sequence of reactions when dealing with rings because each new
substituent gives a certain directing effect.
Ex. 1: Synthesis of para-Xylene from benzene
a. Friedel-Crafts Alkylation – places a methyl group on the benzene ring
b. Friedel-Crafts Alkylation – places another methyl to generate ortho and para isomers. Isolate para-Xylene.
Figure 5.7. Steps in exercise 1 for organic synthesis.
Ex. 2: Synthesis of 2-bromo-1,4-dimethylbenzene from benzene
b. Friedel-Crafts Alkylation – places methyl groups producing ortho and para isomers of dimethylbenzene.
c. Bromination – isolating the para-isomer, bromine has is directed to go ortho by any of the two methyl groups.
Will we get 2-bromo-1,4-dimethylbenzene if we::
1) We rearrange the steps to alkylation -> bromination -> alkylation? (Answer: YES)
If we do this, we just get the ortho isomer after bromination (instead of the p -isomer in the example), then do the second
alkylation (draw to verify).
2) We rearrange the steps to bromination -> 2x alkylation? (Answer: YES)
Similar explanation as 1 (draw to verify).
Ex. 3: Synthesis of 4-chlorobenzoic acid from benzene
b. Chlorination – places a chloro group on the methylbenzene ring on an ortho- and para- position from the
existing methyl group
c. Oxidation – oxidizes the methyl group into a carboxyl group regardless of chlorine’s deactivating effect.

SLRM/JRBM| 38
Will we get 4-chlorobenzoicacid if we:
1) We rearrange the steps to alkylation -> oxidation -> chlorination? (Answer: NO)
Oxidizing the alkyl group will yield a carboxyl group, a deactivator and a meta director; because we know that we want a para
oriented product, we cannot get it from this sequence of reactions (draw to verify).
2) We rearrange the steps to oxidation ->alkylation -> chlorination? (Answer: NO)
This sequence does not make sense because if oxidation is done first, nothing will happen because there is nosubstituent to be
oxidized in the first place.
REVIEW PROPER 6: RX COMPOUNDS
R-X: R is any carbon chain,and X is a functional group
distinct for each class. X for alkyl halides is halogen, OH
for alcohols, and NH2 for amines.
RX compounds (alkyl halides, alcohols (with other oxygen
compounds) and amines) exhibitsome similar reactivities
and properties.
An RX is usually classified according to how many
substituents other than the “X” are attached to the “R”:
1. Methyl – C is bonded to X and 3 H
Ex. Chloromethane, methanol, methylamine
2. Primary (1◦) – C is bonded to X, 1 R, 2 H
Ex. Chloroethane, ethanol, ethylamine
3. Secondary (2◦) – C is bonded to X, 2 R, 1 H
Ex. 2-chloropropane, isopropyl alcohol, 2-
aminopropane
4. Tertiary (3◦) – C is bonded to X and 3 R
Ex. 2-chloro-2-methylpropane, isobutyl alcohol,
2-methyl-2-aminopropane
Figure 6.1. Classification of an alcohol based on R
substituents.
PART 2. REACTIONS MECHANISMS OF THE RX’S
There are two general mechanisms shared by the RX’s.
1) Nucleophilic substitution. R -> carbocation and
X -> nucleophile.
R will attract nucleophiles. X will leave R and a
nucleophile will take place of X (substitution).
Thus, many reactions of RX compounds have the
mechanism of nucleophilic substitution.
Figure 6.2. General mechanism of nucleophilic
substitution.
2) Beta-elimination. X is not substituted; bases swipe a
proton in the form of hydrogen to the carbon beside the
one bearing the X (called the beta-hydrogen).
Because X had been released and no additional atom or
functional group has been added, elimination has
occurred. Thus, RX compounds also have the mechanism
of beta elimination.
Figure 6.3. General mechanism of beta elimination. The
encircled hydrogen is the beta-hydrogen.
PART 3. OPTICAL ISOMERISM
Recall that optical isomers in organic compounds are
made possible due to attachment to four different
substituents of a central carbon. This gives rise to
enantiomers, diastereomers and meso compounds.
Chirality and Enantiomerism
Remember that optical isomers are configuration
isomers, where spatial differences are permanent around
four substituents. (So non-tetrahedral carbons cannot
have optical isomerism).
Chirality (also known as handedness) - property of a
tetrahedral carbon to have four different groups
attached to it, such that they cannot superimpose exactly
when one is placed over another.

SLRM/JRBM| 39
Chiral center/ stereogenic center/ chiral carbon –
carbon that possesses chirality
Enantiomers - isomers which are “mirror images” of each
other and rotate a plane of polarized light (clockwise or
counterclockwise).
Our concern now is simply how to know enantiomers
when drawn. One compound is an enantiomer of
another if it looks like the other compound when put in
front of a mirror.
Figure 6.4. A simple diagram of two enantiomers in
relation to each other.
Are there isomers with chiral centers that are not
enantiomeric? This is a case when we have more than
one chiral isomer.
Figure 6.5. Carbon 1s in the two isomers are mirrors of
each other, but carbon 2s don’t mirror each other.
Diastereomer – optical isomers with two or more chiral
centers that are not really mirrors of each other because
at least one chiral center is identical in both compounds
(not mirrors).
Special Nomenclature for Enantiomers: The Cahn-
Ingold-Prelog Sequence
We have assigned descriptors for geometric isomers (the
only other configurational isomers other than optical
isomers). The way we assign descriptors for optical
isomers is the same: by priorities.
The Cahn-Ingold-Prelogsequence for chiral compounds
makes use of the 3D structural formula. Below is an
example of how a single compound can be drawn in
multiple ways.
Figure 6.6. The three compounds look different, but in the
3D configuration they are all the same compound, just
being rotated in view. Below is the top view of the
compounds, with the south being the front of the 3D
formula.
Steps:
1. Label all the substituents from 1 to 4, 1 belonging to
the substituent with the heaviest first atom downwards.
If two substituents have the same atom, go a bond
farther and find the first difference.
2. Put the number 4 substituent at the back (dash if we
use the 3D formula).
3. Determine if the direction from substituent 1 towards
3 is clockwise or counterclockwise.
4. If counterclockwise, give the descriptor (R) to the
compound. If clockwise, the give the descriptor (S).
Figure 6.7. Example of the R/S naming sequence for 1-
chloroethan-1-ol.
(R)-Chloroethanol is at the left, (S)-Chloroethanol is at the
right.
Meso compounds - contain chirality centers, but are
achiral as a whole. This happens when two or more chiral
centers exist (have 4 different substituents) but the
compound as a whole has a plane of symmetry.
Figure 6.8. A visualization of a (1R,2S) compound. Using
the plane of symmetry as a scissor, the two halves are
actually identical and thus cancels out the possibilities for
polarized light to rotate on it.
PART 4. MOLECULARITY OF REACTIONS
Let us give a new name for the R in RX which becomes
into a carbocation: substrate, and that the carbon
directly attached to X is the alpha carbon (recall rule on
greek designations). Molecularity is a topic under
kinetics, and the kinetics of the reaction of RX
compounds is significant as we will see later.
We know that the carbon of R bearing X can be methyl,
primary, secondary or tertiary and that this tetrahedral
carbon can give optical isomers. Now, chemists know
that the first factor influences the second.
Molecularity - tells how much of the reactants can
participate in one distinct step of a reaction.
Polar reactions can have two molecularities because for
sure, we have E
+
and Nu
-
.
Unimolecular – only either the E+ or Nu- participate in
every step of the reaction. This means we have 2 steps.

SLRM/JRBM| 40
Bimolecular – both E+ or Nu- participate in obviously
only one step of the reaction.
Bimolecularity translates to One-Step reactions
A generally accepted idea for bimolecularity is the
attacking group is strong enough to be the cause of bond
breakage and bond formation on the substrate in only
one step.
SN2 –the attacking nucleophile is strong enough
to cause a one-step reaction,simultaneously
attacking a substrate and kicking off what we
call the leaving group. Because SN reactions in
RX compounds have some stereochemistry in it,
it will be discussed more in the next part.
E2 – the base is strong enough to aggressively
swipe the beta-hydrogen from the substrate,
even if the leaving group may not be a very
good one.
Unimolecularity translates to Two-Step reactions and
Racemization
A generally accepted idea for unimolecularity is the
attacking group is not strong enough to be the cause of
bond breakage and bond formation on the substrate,
forcing two steps: one to kick the leaving group and
another one to finish the reaction.
SN1 –the attacking nucleophile cannot attack
the substrate unless the substrate gains a
charge, made possible when the leaving group
separates from the substrate.
E1 - the base doesn’t have to be strong enough
to impart electrons to the beta hydrogen
because the leaving group will go away first.
Figure 6.9. E1 and E2 reactions. Note the
absence of an intermediate in E2 and the
carbocation intermediate in E1.
E1cB – the beta carbon is so acidic thatit can
kick out a beta hydrogen even before the
leaving group leaves (making R
-
carbanion,
which we used to know as a conjugate base).
Figure 6.10. E1cB. The beta carbon is willing to
kick a beta hydrogen.
PART 5. REACTION STEREOCHEMISTRY FOR
SUBSTITUTION
This is the time appropriate for us to discuss how a
reaction of an RX compound can influence its
stereochemistry.
The bond breakage caused by the cleavage in
preparation of SN results in a carbocation intermediate.
Experiments show that the hybridization of the
carbocation intermediate is planar with a sp2
hybridization, and thus we go from tetrahedral to planar
from RX to R
+
.
Figure 6.11. The tetrahedral shape of a carbon with four
bonds (and thus with sp3 hybridization) had a three-
dimensional appearance like everything in your study
table except paper. The carbocation shifts the shape into
only two-dimensional.
This gives one important detail: when a nucleophile
attacks,it would now matter where exactly it would
bond. Look at the figure below.
Figure 6.12. Possible sites of attack for nucleophiles make
significant result in the configuration of the final product.
When a nucleophile hits area 1, R2 is pushed to the back
and the nucleophile takes the previous place of R2
(because the order is inverted, we call its resulting
stereochemistry inversion). If it hits area 2, it would
simply insert itself in the back (retention).
Bimolecularity hits the back
The detail known in bimolecular substituent is the “back-
attack” mechanism where the Nu
-
is at the farthest from
the L relative to R (in short, behind R)to get the most
attraction from R, kicking the leaving group in the
process.
Because of this, the R/S stereochemistry is inverted.
Thus, we assume that all SN2 reactions cause an
inversion in the stereochemistry of the product.

SLRM/JRBM| 41
Figure 6.13. The sneaky strong nucleophile strikes at the
back to kick the leaving group away.
Unimolecularity hits anywhere
The carbocation itself is the target of weak nucleophiles,
and since no leaving groups are present, the nucleophiles
are free to either attack the back or the front.
Experimentally discovered, 50% of products have
inverted stereochemistry and 50% have retained
stereochemistry. This process where there is a 1:1
inversion:retention ratio is called racemization.
Thus, we assume that all SN1 reactions cause a
racemization in the stereochemistry of the productS.
Figure 6.14. The nucleophile is free to attack the front or
the back areas between R2 and R3. This results in
racemization.
If you want to visualize and verify whether inversion or
retention is happening, below is an example:
Figure 6.15. Racemization process (inversion and
retention) for SN1 reaction. OH is the leaving group.
Practice the rotation of the S isomer to put priority 4 at
the back)
PART 6. REACTION STEREOCHEMISTRY FOR
ELIMINATION
While we cannot have stereochemistry for tetrahedral
centers when we talk about elimination, we do have
stereochemistry for positional isomerism. Look at the
equation below:
Figure 6.16. Where should the double bond go?
Zaitsev’s rule - states that the double bond will be
created between the alpha carbon and the most stable
beta carbon. The most stable beta carbon is the one
which has most canonical structures based on CH
hyperconjugation.
Figure 6.17. Look at the disparity between the canonical
structures of the carbanionabove and below. Obviously,
the one above is the preferred intermediate.
However, not 100% of the reactant turns into the
product with the more stable intermediate. This means
that we can still have a small percent of the other
compound as product.
Figure 6.18. Just for discussion’s sake, the percentages
are invented to comparethe ratio of products formed
based on Zaitsev’s rule. Assume reaction to be 100%
complete.

SLRM/JRBM| 42
PART 7. FACTORS AFFECTING NUCLEOPHILIC
SUBSTITUTION AND ELIMINATION
1. Leaving group
Generally, the most unstable X is the best leaving group.
Two factors contribute to the instability of the leaving
group.
a. Electronegativity – those atoms (like O, F, Cl, Br, I) can
be good leaving groups because the electronegativity
causes electrical instability between them and the alpha
carbon.
b. Size – causes instability because of electron density.
Actually, size is more important than electronegativity.
This is why iodine, even if less electronegative than
fluorine, is a better leaving group.
I > Br > Cl > F > O > N > less electronegative atoms
2. Substrate
The factor we need to see in a good substrate is different
per molecularity of reaction.
a. Unimolecular reactions – because good leaving groups
are there, the best substrate should have the most
stable alpha carbon possible.
Unimolecular: 3 > 2 > 1 > methyl
b. Bimolecular reactions - because the nucleophile or
base needs to attack the substrate quickly, any additional
substituents can block the way by steric effect. The least
shielded alpha carbon would create the best substrate.
Bimolecular: methyl > 1 > 2 > 3
3. Solvent
If we were to really perform the experiment for SN and E
reactions on RX compounds, we have to use a suitable
solvent.
We can first classify the solvent in several categories, and
their effects on the molecularity are as follows:
Non-polar solvents – repel the charges of the polar RX
molecule. Remember that polar and non-polar molecules
do not mix? Thus, non-polar solvents are NOT used in RX
reactions.
Polar solvents – can cause hydrogen bonds or dipole-
dipole attractions toward the RX molecule, which is
useful when RX becomes a carbocation. Thus, this is the
preferred solvent for RX reactions.
Protic – refers to the ability of a solvent to release
protons (H+). Thus, the ability to be protic is analogous to
the ability of being acidic. Obviously, one which cannot
release protons is aprotic.
Figure 6.19. Example of a protic and an aprotic
compounds that can be used as solvents.
Hydrogen ions will bond to the more negative atoms.
Figure 6.20. Notice where hydrogen ions go in
unimolecular and bimolecular reactions.
Thus, hydrogen ions (and thus, protic solvents) are
preferred in unimolecular reactions because they clear
up the leaving group while they are not welcome in
bimolecular reactions (and thus, aprotic solvents are
preferred) because the nucleophile bonds with them
instead of the substrate.
4. Nucleophile/base
The nucleophile or baseis the fourth factor, and had
already been discussed in molecularity.
The table below correlates the four factors and their
influence on SN1, SN2, E1 and E2 reactions.
Below is a table summarizing the preferred
characteristics of the factors in substitution/elimination
reactions:
Factor SN1/E1 SN2/E2
Leaving group Strong Weak
Substrate Most stable Least sterically
hindered
Solvent Polar protic Polar aprotic
Nucleophile/Base Weak Strong
PART 8 THE REALITY: SUBSTITUTION AND ELIMINATION
COMPETE
By now, it is not weird to notice how some things in
substitution and elimination are similar. Realize now that
some reagents can act BOTH as nucleophile and a base.
We know from this point that NaOH is a strong
nucleophile, but even from Chem 100 you should know
that it is also a strong base! This means that NaOH can
induce both SN2 and E2 reactions.
Substitution and elimination compete against each other
because a reagent has competing nucleophilic and basic
properties.
Increased temperature favors elimination because
elimination reactions require more energy (more bond
breaking and forming) compared to substitution (which
usually consists of only one bond breakage and one bond
formation).

SLRM/JRBM| 43
REVIEW SUBPROPER 1: ALKYL HALIDES
PART 1: INTRODUCTION
The only reason why we are dividing the RX compounds is they are prepared in their own special ways. Thus, these
are shortsubpropers with any notable discussions specific only to a particular class of RX compounds.
PART 2: PREPARATION
Luckily, all the reaction mechanisms for the following preparation methods have been discussed. They are tabulated
below.
Reaction Reactant Equation
Hydrohalogenation SR
Reagent: X2
Catalyst: UV
Alkanes
(Has been illustrated in alkanes.)
Hydrohalogenation AE
Reagent: HX in ether solvent
Alkenes/ Alkynes (Has been illustrated in unsaturated
hydrocarbons.)
Halogenation SN
Reagent (Nu-): SOCl2
(Chlorination), PBr3
(Bromination)
Reagent: Alkyl Chloride/
Bromide
Alcohol
PART 3: SPECIFIC SN AND E REACTIONS
The following reaction names which are specific to alkyl halides are listed below. Luckily, these have already been
previously discussed:
Reaction name What it really means
Friedel-Crafts Alkylation
Reagent: Benzene
Catalyst: AlX3
Electrophilic substitution of benzene with the alkyl halide as the
electrophile
Dehalogenation
Reagent: KOH in EtOH solvent
Product: Alkene
Elimination of alkyl halides
Hydration SN
Reagent: Strong nucleophile (like
NaOH) or water (a weak nucleophile)
Product: Alcohol
Nucleophilic substitution with OH as final attachment.
REVIEW SUBPROPER 2: OXYGEN COMPOUNDS AND THEIR ANALOGS
PART 1: INTRODUCTION AND THE OXIDATION
STATE
The hydroxyl group imparts all alcohols the
inductive effect of oxygen, making it partially
negative and the hydrogen partially positive. Thus,
two alcohol molecules can exhibit hydrogen
bonding.
Figure 6b.1. There is extensive hydrogen bonding
between the alcohol (R-O-H) molecules.
The hydrogen bonds also give the tendency of the
OH group to release its Hatoms. In other terms,

SLRM/JRBM| 44
an alcohol can have a slight acidity. The inductive
effect of oxygen on the carbon bearing the
hydroxyl makes the carbon unstable, and kicking
off the hydroxyl’s hydrogen would stabilize the
compound.
Figure 6b.2. The effect of electron repelling
inductive effect of carbons on the acidity.
Analog – modified version.
Oxygen groups have their sulfur analogs.
Oxygen group (Class)
(General formula)
Sulfur analog (Class)
(General formula)
Hydroxyl on aliphatic
chain (alcohols)
ROH
Thiol/mercapto- (thiols)
RSH
Alkoxy (ethers)
ROR
Alkylthio (sulfides or
thioethers)
RSR
Hydroxyl on aromatic
chain (phenols)
Ar-OH
No direct equivalent
While oxygen and sulfur both have six valence
electrons, sulfur is a larger atom and increases
instability by its own. This means the sulfur would
prefer to kick a hydrogen more than oxygen (thus,
thiols are more acidic than alcohols).
The immense electron density of aromatic
compounds further increases acidity. In the case
of phenol, release of hydrogen yields a phenoxide
ion.
Figure 6b.3. Release of hydrogen from phenol
produces phenoxide and hydrogen (hydronium)
ion.
Note that phenol can mean two things: the group
of aromatic alcohols , and phenol itself
(hydroxybenzene).
Oxidation States and Redox Reactions
Whether alcohols are methyl, primary, secondary or tertiary, other than being substrates for either bimolecular or
unimolecular reactions are important in their redox reactions. The ability of the oxygen to raise or lower the
oxidation state of the entire compound is evident in part 3.
Figure 6b.4. As more oxygens become more bonded with the compound, their oxidation state continues to increase.
PART 2: PREPARATION
As much as alcohols can undergo redox reactions to form other products, the reverse can happen: other organic
compounds can turn into alcohols (and not just by redox reactions only; hydration and Grignard reactions can also
take part). The followingare the reactions used to prepare alcohols.
Reactions producing alcohols
Hydration AE
Reagent: H2O
Catalyst: Acid catalyst
Product: Alcohol
Alkenes
(Has been illustrated in unsaturated hydrocarbons.)
Hydration SN
Reagent: Strong
nucleophile (like NaOH) or
water (a weak nucleophile)
Product: Alcohol
Any other RX compound
(alkyl halides, amines)
(Has been illustrated in alkyl halides)
Reactions producing diols
The diols (double hydroxylated alcohols) are not the ones we will discuss in reactions of alcohols (which only have 1
hydroxyl group).

SLRM/JRBM| 45
Mild Oxidation
Reagent: KMnO4 in basic
solvent
Product: Vicinal (1,2-) diol
Alkene
Epoxide Ring Opening
Reagent: H2O, acid catalyst
Product: Vicinal (or 1,2-)
diol
Epoxides
PART 3: REDOX REACTIONS OF OXYGEN-CONTAINING COMPOUNDS
PARTIAL AND FULL REDOX
The property of oxygen to raise or lower the oxidation state of all oxygen-containing compounds gives rise to
“partial” and “full” oxidation reactions. The reason why an alcohol can be oxidized is that it has H atoms that can be
polarized and altered. If none of these h atoms exist (aka tertiary alcohols), the alcohol is unreactive to redox
reactions.
Figure 6b.5. Encircled are those H atoms that can be used for redox.
It matters now whether the alcohol is primary or secondary if we talk about redox. If two H atoms are available, one
can be used to form the carbonyl double bond, and the second can be used to oxygen. However, if only one H atom
is available, only the carbonyl double bond can be created.
Figure 6b.6. The first H atom gives rise to the double bond in the carbonyl.
The second H atom gives rise to attachment to an OH group or other nucleophiles.
Hydrogen atoms have been numbered for easier tracking.
The reader should know the class of organic compounds produced just by the diagramjust above. Primary alcohols
yield aldehydes or carboxylic acids, and secondary alcohols yield ketones.
This seems all clear until one may wonder how to determine if a primary alcohol would become an aldehyde or a
carboxylic acid. Because of this, we use the terms partial and full redox.
Figure 6b.7. Author’s representation of partial and full redox.
Only the jump from alcohol to carboxyl compounds (forward and back) is “full”.

SLRM/JRBM| 46
Thus, the oxidation of an alcohol to a carboxyl compound (such as carboxylic acid) is a full oxidation and reduction of a
carboxyl compound to an alcohol is a full reduction and require a strong oxidizing and strong reducing agent,
respectively. All other redox reactions are partial, and it doesn’t matter if a strong or weak oxidizing/reducing agent is
used.
OXIDATION OF PHENOLS
Phenols can be oxidized to form quinones (aromatic ketones). An example below is oxidation of benzene to
benzoquinone. A quinone can then be reduced to hydroquinone, a benzene ring with two hydroxyl groups in the
para-orientations.
The redox reactions of alcohols are tabulated below:
Reaction Equation
Partial Oxidation of Primary Alcohols
Reagent: PCC/ Periodinane
Product: Aldehydes
Oxidation of Secondary Alcohols
Reagent: PCC/ Periodinane
Product: Ketones
Full Oxidation
Reagent: CrO3
Product: Carboxylic acids
Oxidation of phenols
Reagent (OA): Na2Cr2O7
Product: Quinones
Reduction of quinone
Reagent (RA): SnCl2 in H2O
Product: Hydroquinones
PART 4: POLAR REACTIONS: SPECIFIC SN AND E REACTIONS
The following reaction names which are specific to alcohols are listed below:
Reaction name What it really means
Williamson Ether Synthesis
Reagent (Nu
-
): Alkyl halide
Product: Ether
Nucleophilic substitution where the alcohol is actually the
nucleophile (Better nucleophilicity, recall why)
Dehydration
Reagent: H2SO4
Product: Alkene
Elimination of alcohols
PART 5: ETHERS AND EPOXIDES
We know that ethers are a class of organic compounds with an alkoxy group (-OR) as a functional group. While cyclic
ethers have some crazy trivial names we wouldn’t bother memorizing in this course yet, we have dealt with the three
membered ether: the epoxide. We have discussed this in the AE reactions of alkenes. It’s good that we review the
cleavage of epoxides:

SLRM/JRBM| 47
Reaction name Equation
Hydration of Epoxides
Product: Vicinal (or 1,2-) diol
REVIEW SUBPROPER 3:AMINES
The amines have the opposite nature of alcohols:
being basic. The low electronegativity of the
nitrogen atom gives amines the basic property.
Being less electronegative than the oxygen atom,
the nitrogen can donate its one lone pair more
readily.
Figure 6c.1. Unlike oxygen which pulls its lone pairs
close to it, nitrogen atoms can readily offer their
lone pair to other compounds or atoms.
Like alcohols, the stability of the carbon directly
attached to the amino group will dictate the
basicity of the compound. As the electron
repelling effect increases, the nitrogen becomes
more negative, further making the lone pairs
available to others.
Figure 6c.2. As more electron repelling effect
reaches the nitrogen atom, the lone pairs
become more dispersed and available for other
compounds.
PART 2: PREPARATION
The followingis a table that shows possible reactions from other classes that yield amines.
Nucleophilic Substitution
Reagent: R-NH2
Other RX compounds
(Has been illustrated in amines.)
REVIEW PROPER 7: CARBONYL COMPOUNDS
In this proper, the two classes of compounds are indeed
carbonyl compounds. These two groups are the ketones
and aldehydes, which are the most commonly referred
organic compounds when we say the words carbonyl
compounds.
Oxygen in the carbonyl group acts similarly to that in the
hydroxyl group:initiates partial positive charge on the
carbon, which in turn becomes a relatively electron
lacking site.
Another consideration in aldehydes and ketones is that
they possess only a C-C or C-H bond, and these don’t
make any good leaving group. This means no existing
sigma bond can be destroyed unlike that in RX’s and any
nucleophilic attack will break only the weaker pi bond
between C and O.
Figure 7.1. The keto group in the left and formyl group in
the right have nosigma bond that is easy to break due to
low dipoles (aka electronegativity difference).
It is now known that it is easier to break a pi bond than
these strong C-H or C-O bonds, the aldehyde/ketone and
the attacking nucleophile will merge into one, and thus
the addition scheme of reaction is observed.
In totality, the general reaction mechanism of ketones or
aldehydes is nucleophilic addition (AN).

SLRM/JRBM| 48
Figure 7.2. Illustration of AN based on the explanation in this introductory part.
R may be H (for aldehydes) and a carbon chain (for ketones).
If ketones and aldehydes have the same reaction scheme, what is their difference? That difference i s the ability of an
aldehyde to be further oxidized into a carboxylic acid (recall that polarizable hydrogens can be replaced by another oxygen),
something the ketone cannot undergo due to absence of any polarizable hydrogen.
PART 2: PREPARATION
The ability of an aldehyde and ketone to be reduced into a primary alcohol and secondary alcohol respectively has been
tackled in the subproper on alcohols. Tabulated below is a review on these reactions.
Oxidation
Reagent: PCC/Periodinane/CrO3
Product: Ketone
Secondary Alcohols
(Has been illustrated in alcohols.)
Partial Oxidation
Reagent: PCC/Periodinane
Product: Aldehyde
Primary Alcohols
Hydration followed by
Tautomerization
Product: Ketone
Alkyne
(Has been illustrated in unsaturated
hydrocarbons.)
PART 3: REDOX REACTIONS
Because redox reactions are reversible, itis possible that we get a product out of something we used to get alcohols and
ketones from. Because of these, from aldehydes we can get the other oxygen-containing compounds. Reactions are
tabulated below.
Reaction Equation
Reduction of an Aldehyde
Reagent: NaBH4/LiAlH4
Product: Primary Alcohol
Reduction of a Ketone
Reagent: NaBH4/LiAlH4
Product: Secondary Alcohol
Oxidation of an Aldehyde
Reagent: CrO3
Product: Carboxylic acid

JRBM/SLRM2013 | 49
PART 4: POLAR REACTIONS: NUCLEOPHILIC ADDITION
As said, the polar reactions involve a nucleophilic attack towards breakage of the pi bond in the carbonyl functional group.
The products from nucleophilic attack by a certain nucleophile have specific names and are tabulated below.
Nucleophile (actual
attacking group)
Product name
(from aldehyde/ from ketone)
Structure
(R may be H or another carbon chain)
Water (lone pair of H2O) Hydrate (also known as geminal
diol)
Dehydration (reversal of above
reaction)
Ketone/Aldehyde from hydrates
Reagent: H2SO4
Mechanism:
Alcohol (1 mole) (lone pair
of ROH)
Hemiacetal/ hemiketal
Alcohol (2 moles) (lone pair
of ROH)
Acetal/ ketal
Amine (lone pair of RHN)
* R may be H or another
carbon chain
Aldimine/ ketimine
Special Topic 1: Acetals/Ketals and ANE
If a second ROH bonds with the hemiketal/hemiacetal, the hydroxyl (being the better leaving group) is kicked out,
and the H from the second ROH bonds with the hydroxyl to form water. The reaction for acetal/ketal formation is
still AN but because a functional group is kicked out (hydroxyl), elimination has occurred. The total mechanism of
an acetal/ketal formation is ANE.
Figure 7.3. The bond is first formed, the those kicked out seem to
form a by product from the substrate and nucleophile.An ANE mechanism.
Special Topic 2: The Imines
Instead of expecting an amino alcohol when we add an amine to a carbonyl compound, the hydroxyl group is
kicked off and the carbanion shares its electrons to the nitrogen to form a double bond with nitrogen. A C=N bond
is commonly called an imino bond, and thus the organic compounds from this reaction are called imines: the
aldimines and ketimines.

JRBM/SLRM2013 | 50
Because water is removed from the two reactants, the nucleophilic ddition is followed by elimination. Thus, the
total reaction is also ANE.
Figure 7.4. The unstable amino alcohol from AN undergoes removal of the hydroxyl
group to ultimately form an imino bond.
Grignard Reactions
Grignard reactions for the two carbonyl compounds utilize the double bond in the carbonyl group, breaking the pi bond and
replacing it to create a new bond with whatever carbon chain is bonded to the magnesium ion (Recall: Grignard reactions
and the carbanion). The reaction mechanism stays AN.
Reaction Equation
Grignard Reaction (Aldehyde)
Reagent: Mg
Product: Secondary Alcohol
Grignard Reaction (ketone)
Reagent: Mg
Product: Tertiary Alcohol
REVIEW PROPER 8: CARBOXYLIC ACIDS AND THEIR DERIVATES
The carboxyl group (COOH), aside from being the
functional group thatseparates carboxylic acids from
other organic compounds,also gives the reactivity
specific only to those which hold the COOH group.
Both the carbonyl and hydroxyl functional groups have
an oxygen that pulls electrons away from the carbon, and
two things happen:
1) The compound becomes polar (even more polar
compared to alcohols and carbonyl compounds) and
2) The hydroxyl group is more stabilized even without
the hydrogen atom (thus, this stability causes an easier
release of H+, or higher acidity). This is why the carboxyl
containing compound is called an acid in the first place.
The stabilizingstructural effects on the carboxyl group:
1) Lone pair delocalization, paving the way for
2) Resonance (recall sp2 hybridization and structural
effects).
- A lone pair from the hydroxyl can jump to the carbonyl
carbon and onto the carbonyl oxygen, ultimately allowing
the two oxygen atoms to resonate. Thus, the hydroxyl
initiates resonance.
Figure 8.1. Lone-pair delocalization followed by
resonance stabilizes the carboxyl group immensely.
Carboxylic acid derivatives (acid halides,anhydrides,
esters and amides) have different stabilities because th
new substituent replaces the hydroxyl group.
- This means that any reaction that turns a carboxylic acid
to become a derivative substitutes the hydroxyl group
(substitution) and that hydroxyl acts as a leaving group
(as water). The carbon becomes a carbocation and
attracts nucleophiles. Thus, the total reaction scheme for
carboxylic acids is (acyl) nucleophilic substitution
(SNAcyl).

JRBM/SLRM2013 | 51
Figure 8.2. The hydroxyl group leaves as water, leaving a
carbocation intermediate, in other words becoming an
electrophile ready to accept different nucleophiles.
Figure 8.3. General scheme for SNAcyl. Water is always a
by-product because it is actually the leaving group.
Reactivity Issues
Because the attacking group are nucleophiles, the substituent that donates electrons better deactivates the carboxylic acid
derivative, and the substituent that donates electrons better (or even pulls them) activates the carboxylic acid derivative.
Figure 8.4. The attached substituents arranged according to reactivity/instability.
Structural effects per attachment is also depicted.
Let’s explain why this is the order through structural effects.
1) Acid halides – halogen withdraws electrons and therefore activates
2) Anhydrides –acyl group pulls electrons + oxygen withdraws electrons and consequently activates.
3) Esters – alkoxy group carbons hyperconjugate + repel electrons stabilizes more than how the oxygen electron
withdrawal effect activates. Carboxylic acids are usually at par with esters because its hydroxyl groups also has an
oxygen.
4) Amide – nitrogen has lone pair delocalization that stabilizes more than how its electron attractinginductive effect
activates
This shows that even though the carboxylic acids and derivatves have similar structures, their small differences in structure
reflect differences in reactivity.

JRBM/SLRM| 52
PART 2: PREPARATION
Preparation of carboxylic acids had already been discussed both in the full oxidation of primary alc ohols and
oxidation of aldehydes. They are tabulated below for review purposes:
Oxidation
Reagent: CrO3
Aldehyde
(Has been illustrated in carbonyl compounds.)
Full Oxidation
Reagent: CrO3
Primary alcohol
PART 3: REDOX REACTIONS
Redox reactions of other organic compounds have been discussed to yield carboxylic acids. The table below
reverses all those reactions.
Reaction Equation
Full Reduction
Reagent: LiAlH4
Product: Primary Alcohol
(Previously illustrated already in preparation of alcohols.)
Partial Reduction
Reagent: NaBH4 only
Product: Aldehyde
(Previously illustrated already in preparation of carbonyl
compounds.)
Reduction (amides and
nitriles)
Reagent: LiAlH4
Product: Amines
(Previously illustrated already in reactions of amines.)
PART 4: POLAR REACTIONS: ACYL NUCLEOPHILIC SUBSTITUTION
The following are the reactions that form one carboxyl compound from each other. RCOX as shown in the
equations could be any of the ones listed in the second column.
Reaction RCOX could
be:
Equation
Amide Formation
Nucleophile: Amine/
ammonia
Product: Amide
Acids, halides,
anhydrides

JRBM/SLRM| 53
Fischer Esterification
Nucleophile: Alcohol
Product: Ester
Acids, halides,
anhydrides,
esters (trans)
Anhydride
Formation
Nucleophile:
Carboxylic acid
Product: Anhydride
Acid halides
Acid Halide
(Chloride only)
Formation
Reagent: SOCl2
Product: Acid Halide
Acids
Trans-esterification is another term for an esterification of an ester.
Grignard reaction for carboxylic acids are similar to the carbonyl compounds in a way that the pi bond in the
carbonyl group is utilized to form a sigma bond between a new carbon group.
Reaction Possible
reactant
Equation
Grignard Reaction
Reagent: Mg forming
RMgX
Product: Secondary
alcohol
Carboxylic acid
Grignard Reaction
Reagent: Mg forming
RMgX (2 moles)
Product: Tertiary
alcohol
Ester
References
1) Campbell, M., Farell, S. (2012). Biochemistry 7th
Edition. Belmont, CA: Thomson Brooks/Cole.
2) McMurry J. (2011). Fundamentals of Organic Chemistry 7th
Edition. Belmont, CA: Brooks/Cole.
3) Brown, W., Poon, T. (2011). Introduction to Organic Chemistry 4th
Edition. New York: John Wiley &
Sons.
4) Whitten et al. (2010). Chemistry 9th
Edition. Belmont, CA: Brooks/Cole.
5) Boyer, R. (2006). Concepts in Biochemistry 3rd
Edition. New York: John Wiley & Sons.
6) Brown, T.L., LeMay, H.E., Bursten, B.E.(2004). Chemistry: The Central Science Ninth Edition. San
Francisco: Pearson Education, Inc.
7) Ouelette, R.J. (1994). Organic Chemistry: A Brief Introduction. New York: Macmillan, Inc.

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