1
Institute of Chemistry
College of Science
University of the Philippines Diliman
CHEMISTRY 31
Elementary Organic Chemistry
A. Course Catalogue Description
1.
2.
3.
4.
5.
6.
7.
8.
Course Number:
Course Title:
Course Description:
Prerequisite:
Semester Offered:
Course Credit:
Number of Hours:
Course Goal/s:
Chemistry 31
Fundamentals of Organic Chemistry
Introduction to modern theories in organic chemistry
Chemistry 16
1st and 2nd Semester; Midyear
3.0 units
3.0 hrs/wk
To provide understanding on the basic principles of
organic chemistry
B. Rationale
Chemistry 31 is an existing course that is offered to non-Chemistry major students. This
course introduces and exposes students to modern organic chemistry theories and
provides mechanistic understanding on the basic principles of organic chemistry.
C. Course Outline
1. Course Outcomes (CO)
Upon completing the course, the students must be able to:
CO 1. Name organic compounds using IUPAC rules
CO 2. Draw structures of functional groups and their isomers
CO 3. Predict physical properties based on their functional groups
CO 4. Predict chemical properties based on their functional groups
CO 5. Predict organic reaction mechanisms based on their functional groups
CO 6. Recognize biomolecules and relate their functions with chemical structures
2.
Course Content
Course Topics
Review
1.1 Atomic Structure
1.2 Atomic orbitals of C, H, O and N
1.3 Concept of hybridization and atomic orbitals
1.4 Properties of the covalent bond
1.4.1 Bond strength (based on bond energies and bond
dissociation energies)
1.4.2 Bond length
1.4.3 Bond polarity (based on electronegativities of bonded
atoms)
No. of
Hours
I.
1.5
2
1.5 Geometry of molecule
1.6 Polarity of molecule
1.7 Intermolecular forces of attraction
II.
Nature of Organic Reactions
2.1 Types of bond cleavage
2.2 Types of organic reactions
2.3 Electrophiles and nucleophiles
2.4 Functional groups and their reactivities
2.5 Reaction mechanisms
2.6 Transition state theory
2.7 Energy changes during organic reactions
2.8 Energy of activation and reaction rate
2.9 Intermediates
Alkanes and Cycloalkanes
3.1 Structure – C sp3 orbital
3.1.1 Covalent bond properties
3.1.2 Structural formulas – line, condensed and expanded
formulas
3.1.3 Isomers
3.1.3.1 Structural isomers – chain isomers
3.1.3.2 Stereoisomers – geometric isomers and relative
stabilities of cycloalkanes, conformational (Newman
projection) isomers and optical isomers
3.2 Physical properties – boiling and melting points, solubility in
water and organic solvents
3.3 Chemical properties
3.3.1 Halogenation – free radical substitution; free radical
intermediates and relative stabilities
3.3.2 Combustion
1.5
III.
IV.
Alkenes and Cycloalkenes
4.1 Structure – C sp2 orbital
4.1.1 Isomers
4.1.2.1 Structural isomers – position isomers and
functional isomers
4.1.2.2 Stereoisomers – geometric isomers
4.2 Source - (assigned reading)
4.3 Physical properties – boiling and melting points, solubility in
water and organic
solvents
4.4 Chemical properties
4.4.1 Electrophilic addition – carbocation as intermediate;
stability and rearrangement of carbocations; relative
reactivity of alkenes
4.4.1.1 Hydrohalogenation – addition of HX (Markovnikov
addition)
4.4.1.2 Acid-catalyzed hydration – addition of H2O, H+
(Markovnikov addition)
4.4.1.3 Halogenation – addition of Br2 (anti-addition)
3.0
3.0
3
4.4.1.4 Hydroboration-oxidation – addition of (BH3)2 (syn
addition) followed by H2O2, OH- (anti-Markovnikov
addition)
4.4.1.5 Oxymercuration-demercuration – addition of
Hg(OAC)2 followed by NaBH4
4.4.1.6 Cationic polymerization - addition of alkenes, H+
4.4.2 Reduction – catalytic hydrogenation (syn addition); relation
of heats of hydrogenation and relative stabilities of alkenes
4.4.3 Oxidation of alkenes
4.4.3.1 Hydroxylation using cold, dilute, alkaline KMnO 4
4.4.3.2 Epoxidation using peroxy acids
4.4.3.3 Ozonolysis
4.5 Alkadienes
4.5.1 Isolated, conjugated, cumulated double bonds
4.5.2 Electrophilic addition: 1,2- and 1,4-addition
4.5.3 Addition of H2, metal catalyst
V.
Alkynes
5.1 Structure – C sp orbitals; covalent bond properties and isomers
5.2 Source – assigned reading
5.3 Physical properties – boiling and melting points; solubility in
water and organic solvents
5.4 Chemical properties
5.4.1 Electrophilic addition
5.4.1.1 Hydrohalogenation – formation of geminal
dihalides
5.4.1.2 Acid-catalyzed hydration – keto-enol
tautomerization
5.4.1.3 Halogenation
5.4.1.4 Hydroboration-oxidation – keto-enol
tautomerization
5.4.2 Acidity of terminal alkynes – formation of acetylides
5.4.3 Reduction – catalytic hydrogenation; reduction by
dissolving metals (trans-isomer) and H2, Lindlar catalyst (cisisomer)
5.4.4 Oxidation – ozonolysis
VI. Alkyl halides
6.1 Preparation
6.1.1 Recall halogenation of alkanes by free radical substitution
6.1.2 Recall hydrohalogenation of alkenes by electrophilic
addition
6.2 Physical properties – boiling and melting points; solubility in
water and organic solvents
6.3 Chemical properties
6.3.1 Nucleophilic substitution – SN1 and SN2 mechanisms
6.3.1.1 Kinetics
6.3.1.2 Solvent Effects
6.3.1.3 Stereochemistry
6.3.2 Elimination reactions – E1 and E2 mechanism (anti
addition)
1.5
4.5
4
6.3.3 Grignard reagents – formation and their reactions with H 2O,
NH3, CO2, alcohols and ethylene oxide
VII. Alcohols
7.1 Structure – hybridized orbitals of C and O
7.2 Source and preparation (assigned reading)
7.3 Physical properties – boiling and melting points; solubility in
water and organic solvents
7.4 Chemical properties
7.4.1 Acidity of alcohols – structural effects
7.4.2 Nucleophilic substitution on protonated alcohols – SN1 and
SN2 mechanisms
7.4.3 Elimination reactions on protonated alcohols – E1 and E2
mechanisms
7.4.4 Oxidation of alcohols
1.5
VIII. Ethers
8.1 Structure
8.2 Physical properties - boiling and melting points; solubility in water
and organic solvents
8.3 Preparation – Williamson synthesis
8.4 Chemical Properties – nucleophilic substitution on protonated
ethers by SN1 and SN2 mechanisms
8.5 Epoxides
8.5.1 Preparation
8.5.2 Chemical properties – reaction with Grignard reagent,
nucleophilic substitution in the presence of acids and bases
1.5
IX. Aromatic Hydrocarbons
9.1 Structure of benzene
9.1.1 Kekule structure and concept of resonance
9.1.2 Molecular orbital picture
9.1.3 Stability of benzene
9.2 Chemical properties
9.2.1 Electrophilic aromatic substitution – mechanism
9.2.1.1 Nitration – HNO3, H2SO4
9.2.1.2 Sulfonation – fuming H2SO4
9.2.1.3 Halogenation – X2, AlX3 (a Lewis acid)
9.2.1.4 Friedel Craft’s alkylation – RX, AlX3
9.2.1.5 Friedel Craft’s acylation – RCOX, AlX3
9.2.2 Electrophilic aromatic substitution on monosubstituted
benzenes
9.2.3 Arenes –reaction of the side chains
9.2.3.1 Halogenation – formation of benzylic free
radical
9.2.3.2 Oxidation – formation of benzoic acid
9.2.4 Aryl halides or halobenzenes – nucleophilic aromatic
substitution and its mechanism
9.2.5 Phenols and their chemical properties
9.2.5.1 Acidity – structural effects
9.2.5.2 Electrophilic aromatic substitution
4.5
5
X.
Aldehydes and Ketones
10.1 Structure
10.2 Preparation
10.2.1 Recall hydration of alkynes by electrophilic addition
10.2.2 Recall Friedel Craft’s acylation by electrophilic
aromatic substitution
10.2.3 Recall oxidation of alcohols
10.2.4 Recall ozonolysis of alkenes
10.3 Physical Properties – boiling and melting points, solubility in
water and organic solvents
10.4 Chemical properties
10.4.1 Nucleophilic addition – mechanism
10.4.1.1 Addition of HCN to form cyanohydrins
10.4.1.2 Addition of hydrides (NaBH4 and LiAlH4) to
form alcohols (reduction)
10.4.1.3 Addition of water to form geminal diols
10.4.1.4 Addition of Grignard reagents to form
alcohols
10.4.1.5 Addition of alcohols to form acetals/ketals
10.4.1.6 Addition of derivatives of ammonia to form
imines and other derivatives
10.4.2 Reactions due to acidity of -hydrogen
10.4.2.1 Enols and enolates
10.4.2.2 Alpha-halogenation
10.4.2.3 Aldol condensation
10.4.3 Reduction of aldehydes and ketones to alcohols
10.4.4 Oxidation of aldehydes to carboxylic acids
10.5 Carbohydrates (4.5 hours)
10.5.1 Classification
10.5.2 Monosaccharides
10.5.2.1 Open-chain structure (Fischer projection) of
simple aldoses and their relation to glycerides
10.5.2.2 Structure of ketoses
10.5.2.3 Stereoisomerism and optical activity –
enantiomers, epimers
10.5.2.4 Cyclic hemiacetal structure – formation of
anomers
10.5.3 Chemical properties of monosaccharides
10.5.3.1 Isomerization of ketoses to aldoses
10.5.3.2 Oxidation using Tollen’s reagent, Br 2 in H2O,
HNO3
10.5.3.3 Reduction
10.5.3.4 Kiliani-Fischer synthesis
10.5.3.5 Osazone formation
10.5.3.6 Ruff degradation
10.5.4 Disaccharides – glycosidic linkage, reducing and nonreducing disaccharides
10.5.5 Polysaccharides
XI. Carboxylic Acids and Derivatives
4.5
4.5
6
11.1 Structure
11.2 Physical properties
11.3 Preparation
11.3.1 Recall oxidation of alcohols, aldehydes and arenes
11.3.2 Hydrolysis of nitriles
11.3.3 Carbonation of Grignard reagent
11.4 Chemical properties
11.4.1 Acidity of carboxylic acids – structural effects
11.4.2 Nucleophilic acyl substitution – mechanism
11.4.2.1 Formation of carboxylic acid derivatives and
their interconversion
11.4.2.2 Relative reactivities of carboxylic acid and
derivatives
11.4.2.3 Hydrolysis of carboxylic acid derivatives
11.4.3 Reaction of esters with Grignard reagents
11.5 Fats
11.5.1 Structure of mono-, di- and triglycerides (simple and
mixed)
11.5.2 Acid and base-catalyzed hydrolysis
XII. Amines
12.1 Structure
12.2 Physical properties
12.3 Chemical properties
12.3.1 Basicity – structural effects
12.3.2 Reactions with carboxylic acid derivatives to form
amides
12.3.3 Reactions with HONO to form diazonium ions and Nnitroso compounds
12.3.4 Diazonium ions and their substitution and coupling
reactions
12.3.5 Hinsberg reaction
12.4 Amino Acids and Peptides
12.4.1 Amino acids
12.4.1.1 Structure – zwitterions and isoelectric point
12.4.1.2 Classification according to the nature of the
side chain – polar and non-polar
12.4.2 Peptides
12.4.2.1 Structure
12.4.2.2 Determination of chain sequence by terminal
residue analysis
12.4.2.2.1 N-terminal analysis
12.4.2.2.1.1Reaction with
phenylisothiocyanate – Edman
degradation
12.4.2.2.1.2 Reaction with 2,4dinitrofluorobenzene – Sanger method
13.1.1 12.4.2.2.2 C-terminal analysis – use of
carboxypeptidase
4.5
7
3.
Course Coverage
Week
Learning outcome/s
Course Topic*
Essential or Key
Questions
1
I. Review
At the end of this topic, the
students are expected to:
1. Recall the concepts learned
in General Chemistry on the
formation of covalent bonds
using the valence bond theory
2. Recall the properties of
covalent molecules based on
the hybrid orbital used by the
central atom
3. Recognize functional groups
4. Predict covalent properties
of functional groups
5. Predict intermolecular forces
of attractions (IMF) of
functional groups
6. Relate IMFs with the
physical properties of organic
molecules
• What are the
intermolecular
forces of
attractions
between an
organic
compounds?
• What are the
different functional
groups?
• How does IMFs
affect the physical
properties of
organic molecules?
1
II. Nature of Organic
At the end of this topic, the
students are expected to:
Reactions
1. Identify the types of organic
reactions
2. Differentiate chemical
reactivities of functional groups
3. Differentiate organic reaction
mechanisms of functional
groups
• What are the types
of organic
reactions?
• What are the
reactivities of
different functional
groups?
Suggested
Teaching and
Learning
Activities
Suggested
Assessment
Tools/
Activities
• Lectures
• Discussion
• Exercises
• Problem
Set
• Quiz
• Exam
• Lectures
• Discussion
• Exercises
• Problem
Set
• Quiz
• Exam
8
4. Recall the collision theory
5. Recall the construction of
potential energy diagrams
2
At the end of topics 3-12, the
students are expected to:
1. Recognize the different
organic functional groups
based on molecular structure
and nomenclature
a. draw a molecular
structure from
compound name
b. name a compound
based on molecular
structure
c. differentiate
compounds based on
functional groups
d. recognize functional
groups in a
macromolecule
e. know functional group
test
2. Correlate physical properties
with functional groups
a. identify relative
polarities
b. identify relative boiling
and melting points
c. identify relative
solubility in water
d. identify other distinct
physical properties e.g.
odor and taste
III. Alkanes and
Cycloalkanes
•
•
•
•
•
•
What are the
physical properties
of alkanes and
cycloalkanes?
What are the
chemical
reactivities of
alkanes and
cycloalkanes?
How are physical
properties of
alkanes and
cycloalkanes
related to their
structures?
What are the
different
stereoisomers of
alkanes and
cycloalkanes?
What are the
different methods
of preparation of
alkanes?
What are the
mechanisms
involved in the
chemical reactions
of alkanes and
cycloalkanes?
• Lectures
• Discussion
• Exercises
• Problem
Set
• Quiz
• Exam
9
3. Recognize stereoisomers
a. recognize and relate
chirality with optical
activity
b. differentiate and
recognize types of
configurational isomers
c. draw different
stereochemical
representation for a
molecular structure
d. recognize and
designate between R
and S configuration
e. draw representations of
conformations of a
molecule and analyze
its conformational
energies
f. elate by example
stereochemistry of
molecules with
biological activity
g. operate Spartan
software for molecular
modeling and
stereochemical
comparisons
4. Assess the reactivity of each
functional group
a. predict the reactivity of
a molecule based on
functional group
10
b. identify the different
reactions of each
functional group
c. propose a reaction
mechanism based on
the functional group
d. predict product/s, sideproducts and conditions
for each reaction
e. enumerate the
appropriate reagents for
each reaction
f. explain the chemical
basis of the reaction
depending on the
functional group
g. assess the feasibility of
each reaction
h. enumerate industrially
important reactions
5. Enumerate the usefulness of
each functional group
a. enumerate the practical
use of a compound
based on the functional
group
b. enumerate the hazards
related to each group
3
The same as in topic 3
IV. Alkenes and
Cycloalkenes
•
The same key
questions as in
topic 3.
• Lectures
• Discussion
• Exercises
• Problem
Set
• Quiz
• Exam
11
4
4-5
5
6
The same as in topic 3
The same as in topic 3
The same as in topic 3
The same as in topic 3
V. Alkynes
VI. Alkyl Halides
VII. Alcohols
VIII. Ethers
•
•
•
•
The same key
questions as in
topic 3.
The same key
questions as in
topic 3.
The same key
questions as in
topic 3.
The same key
questions as in
topic 3.
• Lectures
• Discussion
• Exercises
• Problem
Set
• Quiz
• Exam
• Lectures
• Discussion
• Exercises
• Problem
Set
• Quiz
• Exam
• Lectures
• Discussion
• Exercises
• Problem
Set
• Quiz
• Exam
• Lectures
• Discussion
• Exercises
• Problem
Set
• Quiz
• Exam
12
7-8
8-9
The same as in topic 3
The same as in topic 3
10-11 The same as in topic 3
11-12 The same as in topic 3
IX. Aromatic Hydrocarbons •
X. Aldehydes and Ketones
•
XI. Carboxylic Acids and
Derivatives
•
XII. Nitrogen-containing
Compounds
•
*Refer to Course Content for complete list of course topic
The same key
questions as in
topic 3.
The same key
questions as in
topic 3.
The same key
questions as in
topic 3.
The same key
questions as in
topic 3.
• Lectures
• Discussion
• Exercises
• Problem
Set
• Quiz
• Exam
• Lectures
• Discussion
• Exercises
• Problem
Set
• Quiz
• Exam
• Lectures
• Discussion
• Exercises
• Problem
Set
• Quiz
• Exam
• Lectures
• Discussion
• Exercises
• Problem
Set
• Quiz
• Exam
13
4.
Course Requirements
1.
2.
3.
2 lecture examinations
short quizzes
final examination
TOTAL
300 pts
100 pts
200 pts
600 pts
(150 pts per exam)
A student may be exempted from taking the final examination provided his pre-final class
standing is 2.5 or better (at least 256 points)
Coverage of lecture examinations:
First examination – Review to Ethers (Apr 24-25, 2021)
Second examination – Aromatic hydrocarbons to Amino Acids (June 12-13, 2021)
Grading:
Grad
e
1.0
1.25
1.5
1.75
2.0
2.25
2.5
2.75
3.0
4.0
5.0
%
95-100
90-94
85-89
80-84
75-79
70-74
65-69
60-64
55-59
49-54
Below
49
Raw Score BEFORE
Finals
380-400
360-379
340-359
320-339
300-319
280-299
260-279
Raw Score AFTER Finals
570-600
540-569
510-539
480-509
450-479
420-449
390-419
360-389
330-359
294-329
Below 294
Policies:
1. The final examination is departmental.
2. There are NO make-up exams for missed examinations. If the student misses an
examination, then his grade is INC provided his class standing is passing.
3. There is NO make-up for missed quizzes.
4. A grade of 5.0 may be given in the following cases:
o Cheating in an exam or quiz.
o No final exam and the class standing is failing. (If the student is unable to take
the finals but his standing is passing, then his grade is INC.
o Unofficial dropping, i.e., the student stopped attending classes and did not
provide the instructor with the instructor’s copy of the dropping slip. It is the
responsibility of the student who officially dropped the course to provide the
instructor with a copy of the dropping slip.
D.
Textbook Reference
1.
John McMurry. Organic Chemistry (latest edition)