ORGANIC CHEMISTRY INTRODUCTION

1. University of Santo Tomas
Faculty of Pharmacy
SCHOLIA TUTORIAL CLUB
ORGANIC
CHEMISTRY
First Grading Period
Prepared by: Hajime Q. Nakaegawa
BS Biochemistry 2018
AY 2016-2017

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• All are being used for the sake of discussing
necessary information for the course.
• To whoever holds a copy of this, it must be used
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owner.

3. Outline of Topics to be
discussed:
• Introduction to Organic Chemistry – Definition, Hydrocarbon
and its Derivatives, Structural Formula Formats
• Nomenclature – How to name organic compounds.
• Carbon, Carbon, Carbon – Review on importance of carbon,
principles involved, hybridization, bonds
• Isomers and Stereochemistry – definition, types and
classifications
• Chirality of Molecules - Introduction, Stereoisomers,
Conformational Isomers (Straight Chain and Cyclic,
Orientations (Axial and Equatorial), Configurational Isomers,
Meso Compounds
• Relative and Absolute Configuration – Meaning
• Structural Effects – Electron delocalization, resonance, CH
hyperconjugation, LPD, inductive effect, steric effect, and
angle strain

4. Lesson 1
Introduction to
Organic Chemistry
Definition, Hydrocarbon and its
Derivatives, Structural Formula Formats

5. Organic Chemistry
• Study of carbon and its compounds?
• Study of organic compounds? …duh.
• Study of hydrocarbon compounds and its derivatives
TWO THINGS INVOLVED IN ORGCHEM
1. HYDROCARBON 2. HYDROCARBON
DERIVATIVES

6. Few more notes to
consider:
• The building block of structural organic chemistry is
the tetravalent carbon atom
• With few exceptions, carbon compounds can be
formulated with four covalent bonds to each
carbon, regardless of whether the combination is
with carbon or some other element.

7. 1. HYDROCARBONS
• A hydrocarbon is an organic compound consisting
entirely of hydrogen and carbon ONLY.
1. HYDROCARBON
Aliphatic (R) Aromatic (Ar)
Uncyclic / Open Structure Factors to consider:
1. Should be cyclic (closed
structure / no terminal
point)
2. Planar (2D structure)
3. Has conjugated double
bond (alternating)
4. Follows Huckel’s Rule
#pi e- = 4n + 2
Saturated Unsaturated
No pi bond
formation or all
are single
bonded
Ex. Alkanes
Contain pi bonds
/ has double or
triple bonds
Ex.
Alkenes/Alkynes

8. General Rule for knowing
if its Aromatic or
Aliphatic.
If the organic compound does NOT
follow the four general factors of an
aromatic compound, then it’s
aliphatic.

9. 2. Hydrocarbon
Derivatives
• Hydrocarbon
derivatives are
formed when
there is a
substitution of a
functional
group at one or
more of these
positions.
• Order of priority
MUST be
observed

13. Kekule Formulas
• A Lewis structure in which bonded electron pairs in
covalent bonds are shown as lines.
• FYI: Kekulé was the first to suggest a sensible structure for
benzene. He said The carbons are arranged in a
hexagon, and he suggested alternating double and
single bonds between them.

14. Condensed Formula
• To save space and time in the representation of
organic structures, it is common practice to use
"condensed formulas" in which the bonds are not
shown explicitly.
• In using condensed formulas, normal atomic
valences are understood throughout.

15. 3D Structural Formula
• Sample:
• Acetone
• IUPAC Name:
2-propanone

16. Skeletal Formula
• Also called the Line-Angle Formula
• It is represented in two dimensions, as on a page of
paper.
• A skeletal formula shows the skeletal
structure or skeleton of a molecule, which is
composed of the skeletal atoms that make up the
molecule.

17. Lesson 2
Nomenclature
HOW TO NAME ORGANIC
COMPOUNDS

18. Introduction
• The primary goal of the International Union of Pure
and Applied Chemistry (IUPAC) naming system is to
create an unambiguous relationship between the
name and structure of a compound.
• With the conventions established by IUPAC, no two
distinct compounds have the same name. The
IUPAC naming system greatly simplifies chemical
naming.

19. STEPS IN
NAMING

20. 1. Identify the Longest Carbon Chain Containing the
Highest-Order Functional Group
• This will be called the parent chain and will be used to
determine the root of the name.
• Keep in mind that if there are double or triple bonds
between carbons, they must be included
• If one of the functional groups would provide a suffix for
the compound (for example, an alcohol, which will be
discussed later), then the parent chain must contain this
functional group.
• Keep in mind that the highest-priority functional group
(with the most oxidized carbon) will provide the suffix.

21. 2. Number the Chain
• As a convention, the carbon numbered 1 will be the
one closest to the highest-priority functional group.
• If the functional groups all have the same priority,
numbering the chain should make the numbers of the
substituted carbons as low as possible.

22. 3. Name the Substituents
• Substituents are functional groups that are not part of
the parent chain.
• A substituent’s name will be placed at the beginning of
the compound name as a prefix, followed by the name
of the longest chain.

23. 4. Assign a Number to Each
Substituent
• Pair the substituents that you have named to the
corresponding numbers in the parent chain.
• Multiple substituents of the same type will get both the
di–, tri–, and tetra– prefixes that we have previously
noted and also a carbon number designation—even if
they are on the same carbon.

24. 5. Complete the Name
• Names always begin with the names of the substituents
in alphabetical order, with each substituent preceded
by its number.
• Note: Prefixes like di–, tri–, and tetra– as well as the
hyphenated prefixes like n– and tert– are ignored while
alphabetizing.
• Nonhyphenated roots that are part of the name,
however, are included; these are modifiers like iso–,
neo–, or cyclo–.
• The numbers are separated from each other with
commas, and from words with hyphens.
• Finally, we finish the name with the name of the
backbone chain, including the suffix for the functional
group of highest priority.

25. Example

27. PRACTICE EXERCISE

28. Answer Key

29. • View Practice Questions pg.55

30. Lesson 3
Carbon, carbon,
carbon…
Review on importance of carbon,
principles involved, hybridization,
bonds

31. Why Carbon?
• Molecules with carbon are ORGANIC.
• Carbon dioxide and molecules without carbon are
INORGANIC.
• FACTORS WHY CARBON IS IMPORTANT
• 1. They are versatile. Can form up to four bonds (single,
double, or triple) in rings or in chains
• 2. Bonds formed are high in energy. Ex. Diamond
• Functional groups in organic molecules
o Are LESS stable than the carbon backbone but
are more likely to participate in chemical reactions
o Determine the characteristics and chemical
reactivity of organic molecules.

32. Principles involved
• 1. Aufbau Principle - electron will successfully occupy the
available electrons in increasing energy. German term
meaning building up
• In short, lowest energy first.
• 2. Hund’s Rule of Multiplicity – When there are more than
one orbital at a particular energy level, only one electron
will fill each orbital until each has one electron. After this,
pairing will occur with the addition of one electron to
each orbital.
• In short, degenerate orbitals must have 1 electron first
• 3. Pauli’s Exclusion Principle (by Wolfgang Pauli) – In a
given atom, no two electrons can have the same set of
four quantum numbers, therefore each orbital can only
hold two electrons.
• In short, two electrons only and must be of opposite spin.

33. Hybridization
• All atoms undergo hybridization red + white = pink…
• PURPOSE OF HYBRIDIZATION? Form equivalent orbitals
(orbitals with the same shape)

35. Lesson 4
Isomers and
Stereochemistry
Definition, types and classifications

36. Stereochemistry
• the branch of chemistry concerned with the three-
dimensional arrangement of atoms and molecules and
the effect of this on chemical reactions.
• Branch of chemistry that studies isomers (duh), and a
property of a compound to have isomers.
• IMPORTANT NOTES TO TAKE:
- We need at least one sp3-hybridized carbon
- To represent molecules as 3D objects.

37. ISOMERS
• Isomers - each of two or more compounds with the
same molecular formula but a different arrangement of
atoms in the molecule and different properties.
• They can differ in:
a. ARRANGEMENT OF BONDS – refers to actual bonds
between atoms, isomers with a different connectivity of
their atoms
b. CONFIGURATION – refers to the permanent spatial
positions of two isomers with the same attachments.
Two configurational isomers are never identical to each
other.
c. CONFORMATION – refers to temporary spatial positions,
and two conformational isomers can be identical at
one point.

38. ISOMERS
Red means ‘difference in’
Structural / Constitutional Isomers
Arrangement
Skeletal
Stereoisomers
Spatial position
Positional Functional
Attachment Placement
of functional
group
Actual functional
group
Configurational Conformational
tetrahedral Unsaturated/cyclic
Geometric
Enantiomers Diastereomers
Mirror images Non Mirror images
Optical Isomers
Permanent
spatial
difference
Temporary
spatial
difference

39. Flowchart of Isomer Relationship

41. Exercise1 2
3
6
4
5
7
8

42. Answer Key
1. Positional Isomers – because they differ in the
placement of their functional groups
2. Functional Isomers – one is aldehyde, another is
ketone
3. Enantiomers – they are optical and mirror images
4. Geometric Isomers - there is a restricted rotation of
the double bond due to the pi bond which means
they don't readily interconvert
5. Skeletal Isomers
6. Positional Isomers – because they differ in the
placement of their functional groups
7. Diastereomers
8. Diastereomers

43. Lesson 5
Chirality of Molecules
Introduction, Stereoisomers, Conformational
Isomers (Straight Chain and Cyclic,
Orientations (Axial and Equatorial),
Configurational Isomers, Meso Compounds

44. Introduction
• Stereoisomers – have the same molecular formula and
connectivity of atoms in their molecules, but different 3D
orientation of their atoms in space.
• Enantiomers – (1)non superimposable mirror images, (2)
the term itself always refers to pairs, and (3) majority of
biomolecules and one-half of the used medications
used in human medicine exhibit enantiomerism
• The most common cause of enantiomerism is a carbon
bonded to four different groups.

45. Conformational vs
Configuration
• Conformational isomers or conformers differ in
rotation around single (σ) bonds
• Configurational isomers can be interconverted only
by breaking bonds.

46. Conformational Isomers
• Conformational isomers are, in fact, the same molecule,
only at different points in their natural rotation around
single (σ) bonds.
• While double bonds hold molecules in a specific position
(as explained with cis–trans isomers later), single bonds
are free to rotate.
• Conformational isomers arise from the fact that varying
degrees of rotation around single bonds can create
different levels of strain.
• Conformations are easy to see when the molecule is
depicted in a Newman projection, in which the
molecule is visualized along a line extending through a
carbon–carbon bond axis.

47. Straight-Chain
Conformations
• For butane, the most stable conformation occurs when the
two methyl groups (containing C-1 and C-4) are oriented
180° (duh) away from each other.
• WHY 180?? In this position, there is minimal steric repulsion
between the atoms’ electron clouds because they are as
far apart as they can possibly be.
• Thus, the atoms are “happiest” BECAUSE they are in their
lowest-energy state. Because there is no overlap of atoms
along the line of sight (besides C-2 and C-3), the molecule is
said to be in a staggered conformation.
• Specifically, it is called the anti conformation because the
two largest groups are antiperiplanar (in the same plane, but
on opposite sides) to each other.
• This is the most energetically favorable type of staggered
conformation. (parang sa pagmamahal lang yan)

48. • The other type of staggered conformation,
called gauche (means unsophisticated or
awkward), occurs when the two largest
groups are 60° apart.
• When the two methyl groups directly
overlap each other with 0° separation, the
molecule is said to be totally eclipsed and
is in its highest-energy state. Totally eclipsed
conformations are the least favorable,
energetically, because the two largest
groups are synperiplanar (in the same
plane, on the same side)
Nothing I can say
A total eclipse of the
heart

50. Cyclic Conformations
• Cycloalkanes can be either fairly stable compounds, or fairly
unstable—depending on ring strain. Ring strain arises from
three factors: angle strain, torsional strain, and nonbonded
strain (sometimes referred to as steric strain).
• Angle strain results when bond angles deviate from their
ideal values by being stretched or compressed.
• Torsional strain results when cyclic molecules must assume
conformations that have eclipsed or gauche interactions.
• Nonbonded strain (van der Waals repulsion) results when
nonadjacent atoms or groups compete for the same space.
• Nonbonded strain is the dominant source of steric strain in
the flagpole interactions of the cyclohexane boat
conformation.

51. Conformations of Cycloalkanes
• To alleviate the strain, cycloalkanes attempt to adopt various
nonplanar conformations.
• Cyclobutane puckers into a slight “V” shape.
• Cyclopentane adopts what is called an envelope
conformation.
• Cyclohexane exists mainly in three conformations called the
chair, boat, and twist- or skew-boat forms.
• The most stable conformation of cyclohexane is the chair
conformation, which eliminates all three types of strain.

52. Axial-Equatorial
Orientation
• The hydrogen atoms that are perpendicular to the
plane of the ring (sticking up or down) are called
axial, and those parallel (sticking out) are called
equatorial.
• The axial–equatorial orientations alternate around the
ring; that is, if the wedge on C-1 is an axial group, the
dash on C-2 will also be axial, the wedge on C-3 will
be axial, and so on.

53. • Cyclohexane can undergo a chair flip in which one
chair form is converted to the other.
• In this process, all axial groups become equatorial,
and all equatorial groups become axial.
• All dashes remain dashes, and all wedges remain
wedges. This interconversion can be slowed if a bulky
group is attached to the ring;
• tert-butyl groups are classic examples of bulky groups
on the MCAT. For substituted rings, the bulkiest
• group will favor the equatorial position to avoid
nonbonded strain (flagpole interactions) with axial
• groups in the molecule

55. Cis and trans
• If both groups are located on the same side of the
ring, the molecule is called cis; if they are on
opposite sides of the ring, it is called trans

56. Cis/trans vs E/Z
• In simple compounds with only one substituent on
either side of the immovable bond, we use the
terms cis and trans. For more complicated
compounds with polysubstituted double bonds,
(E)/(Z) nomenclature is used instead.

57. Configurational Isomers
• Unlike conformational isomers that interconvert by
simple bond rotation, configurational isomers can only
change from one form to another by breaking and
reforming covalent bonds.
• The two categories of configurational isomers are
enantiomers and diastereomers.
• Both enantiomers and diastereomers can also be
considered optical isomers because the different
spatial arrangement of groups in these molecules
affects the rotation of plane-polarized light.

58. • An object is considered chiral if its mirror image
cannot be superimposed on the original object.
• This implies that the molecule lacks an internal plane
of symmetry.

59. • Two molecules that
are
nonsuperimposable
mirror images of each
other are called
enantiomers.
• Molecules may also
be related as
diastereomers. These
molecules are chiral
and share the same
• connectivity, but are
not mirror images of
each other. This is
because they differ
at some (but not all)
of
• their multiple chiral
centers.

60. Polarized and Optical
Activity
• Optical activity refers to the rotation of this plane-
polarized light by a chiral molecule.
• At the molecular level, one enantiomer will rotate
plane-polarized light to the same magnitude but in
the opposite direction of its mirror image (assuming
concentration and path lengths are equal).
• A compound that rotates the plane of polarized light
to the right, or clockwise, is dextrorotatory (d-) and is
labeled (+).
• A compound that rotates light toward the left, or
counterclockwise, is levorotatory (l-) and is labeled (–
). The direction of rotation cannot be determined
from the structure of a molecule and must be
determined experimentally.

61. Polarizer

62. Diastereomers
• Diastereomers are non-mirror-image configurational
isomers.
• Diastereomers occur when a molecule has two or
more stereogenic centers and differs at some, but
not all, of these centers.
• This means that diastereomers are required to have
multiple chiral centers. For any molecule with n
chiral centers, there are 2n possible stereoisomers.

64. Meso compound
• For a molecule to have optical activity, it must not
only have chiral centers within it, but must also lack
a plane of symmetry.
• Thus, if a plane of symmetry exists, the molecule is
not optically active, even if it possesses chiral
centers. This plane of symmetry can occur either
through the chiral center or between chiral centers.
• A molecule with chiral centers that has an internal
plane of symmetry is called a meso compound.

65. • As shown in this image, D- and L-tartaric acid are both
optically active, but meso-tartaric acid has a plane of
symmetry and is not optically active.
• This means that even though meso-tartaric acid has two
chiral carbon atoms, the molecule as a whole does not
display optical activity.
• Meso compounds are essentially the molecular
equivalent of a racemic mixture.

66. Lesson 6
Relative and Absolute
Configuration
Meaning

67. • The configuration of a stereoisomer refers to the spatial
arrangement of the atoms or groups in the molecule.
• The relative configuration of a chiral molecule is its
configuration in relation to another chiral molecule
(often through chemical interconversion).
• We can use the relative configuration to determine
whether molecules are enantiomers, diastereomers, or
the same molecule.
• Absolute conformation of a chiral molecule describes
the exact spatial arrangement of these atoms or
groups, independent of other molecules.

68. (E) and (Z) nomenclature
• (E) and (Z) nomenclature is used for compounds with
polysubstituted double bonds.
• Using the Cahn–Ingold–Prelog priority rules, priority is
assigned based on the atom bound to the double-
bonded carbons.
• The alkene is named (Z) (German: zusammen,
“together”) if the two highest-priority substituents on
each carbon are on the same side of the double
bond and (E) (entgegen, “opposite”) if they are on
opposite sides.

69. The simple priority rules
• The higher the atomic number, the higher the
priority. If the atomic numbers are equal, priority is
determined by the next atoms outward; again,
whichever group contains the atom with the
highest atomic number is given top priority.
• If a tie remains, the atoms in this group are
compared one-by-one in descending atomic
number order until the tie is broken.
• Z = “z”ame sid; E = “e”pposite side
• View Practice Questions pg.103

70. Lesson 7
Structural Effects

71. Structural Effects
• Effect of the structure on STABILITY and REACTIVITY of the
organic compound.
• 1. Electron Delocalization
• A. pi electron delocalization
• B. sigma (σ) electron delocalization / CH
hyperconjugation
• C. Lone pair delocalization
• 2. Inductive Effect
• A. Electron Attracting or Withdrawing Inductive Effect
• B. Electron Repelling or Donating Inductive Effect
• 3. Steric Effect
• 4. Angle Strain

72. 1. Electron Delocalization
• Electrons belonging to certain molecules are not attached
to a particular atom or bond in that molecule.
• These electrons are said to be "delocalized" because they
do not have a specific location (are not localized); they
cannot be drawn in a simple Lewis structure. Rather, they
exist in orbitals that include several atoms and/or bonds.
• You can imagine these orbitals as clouds surrounding parts
of the molecule.
• Delocalization gives molecules resonance stability, stronger
acidiy and based on the resonance stability, we can
determine the range of absorbtion of ultraviolet and visible
light of a molecule in the light spectrum.
• The actual structure with delocalized electrons is called a
resonance hybrid.

73. Molecular Orbital Theory
• Delocalization is characteristic of the molecular
orbital theory concerning the structure of atoms.
• Rather than the lone pair of electrons contained in
specific bonds (as in the valence-bond theory), the
MO (molecular-orbital theory) theorizes that
electrons exist in orbitals that are spread over the
entire molecule.
• The MO theory explains molecules such as ozone
and benzene, which cannot be drawn satisfactorily
with one Lewis structure, and are therefore
described as resonance hybrids. Molecular orbitals
solve this issue through the concept of delocalized
electrons.

74. A. Pi 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.

75. B. Sigma pi delocalization
(CH hyperconjugation)
• Delocalized electrons come from a sp3 hybridized
carbon.

76. C. Lone pair
delocalization
• The delocalized electrons mainly come from a lone
pair, most often from a nitrogen or oxygen atom.

77. 2. Inductive Effect
• An inductive effect is an electronic effect due to the
polarization of σ bonds within a molecule or ion. This
is typically due to an electronegatvity difference
between the atoms at either end of the bond.
• The more electronegative atom, the more it pulls
the electrons in the bond towards itself creating
some bond polarity
• Basis here is the polarity.
• Three considerations:
• 1). electronegativity, 2). bonding order and charge
and 3). position within a structure.

78. Electron attracting or
Withdrawing Inductive Effect
• Has a Negative inductive effect (-I)
• Electrons are draw on towards atoms with:
• 1. Excess positive charges
• 2. Electronegative atoms
• 3. Atoms with increased electronegativity due to
more electrons

79. Electron donating
inductive effect
• Has a positive inductive effect (+I)
• Electrons are repelled by:
• 1. Less electronegative atoms (ex. C)
• 2. Negatively charged functional groups

80. 3. Steric Effect
• Electrical instability caused by closing in of electron
dense atoms.
• 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.

81. 4. Angle Strain
• Electrical instability in atoms closing in with small
angles in cyclic compounds.
• Atoms in cyclic molecules share a certain angle
between each other. The ideal is 109.5 degrees. As
the goes farther or lower than that, the repelling
effect of electrons on each other increases.

82. END
Failure is the opportunity to begin again, more
intelligently.