University of Santo Tomas

Faculty of Pharmacy

An Outcomes-Based Teaching-Learning Program for Organic Chemistry
1st Semester, A.Y. 2014-2015

Course Title: Organic Chemistry
Course Number: CHEM 200
Credit Units:: 5 units (3 units lecture and 2 units laboratory)
Contact Hours: 3 lecture hours and 6 laboratory hours per week
Course Placement: 2
nd
year, 1st sem
Prerequisite: CHEM 111 and CHEM 112 (for BS Biochemistry students)
CHEM 100 (for BS Pharmacy and BS Medical Technology students)

Course Facilitators: Prof. Angelita S. Sarile, Ph.D.,Ms. Gladys M. Ilagan and Ms. Myla R. Santiago
Course Description: The course deals with the different classes of organic compounds, their structures, properties, reactivities,
reaction mechanisms, and applications to different biochemical and health-related fields of study. It includes
training in both classical and modern semi-micro laboratory techniques in handling, preparing, separating,
purifying, identifying and characterizing organic compounds.

Prepared by: Prof. Angelita S. Sarile, Ph.D.

Reviewed by: Asst. Prof. Andrea G. Vargas, Chair, Department of Biochemistry

Approved by: Assoc. Prof. Ma. Elena J. Manansala, MSc.
Dean, Faculty of Pharmacy

Date of Approval: 14 June 2014

INSTITUTIONAL INTENDED LEARNING OUTCOME
GRADUATE ATTRIBUTE
PROGRAM INTENDED LEARNING
OUTCOME
COURSE INTENDED LEARNING OUTCOME
Academic Excellence
Show expertise in the competencies necessary to the
practice of the profession
Demonstrate creative application of concepts
and methods of pharmacy practice geared
towards the advancement of various fields and
of Pharmacy
1. Demonstrate ability to discuss the structure,
properties, nomenclature, reactivity and
reaction mechanisms of the different classes of
organic compounds
Leadership and Teamwork
Demonstrate capacity for leadership and teamwork
including the ability to motivate others, to be
responsible and reliable
Assume leadership roles as appropriate, and
work effectively and work harmoniously as
members of healthcare teams
2. Exhibit leadership roles in illustrating the
relevance and applications of the reactions and
interactions of organic molecules to the world
around us, particularly to the biochemical,
health and biological sciences
Critical Thinking and Problem-Solving Skills
Initiate innovative ideas and methods through
research responsive to the changing needs of the
society
Demonstrate critical application of principles
in pharmacy using logical and systematic
methods to provide practical solutions to real-
life professional situations
3. Develop skills in communicating chemical
information by way of designing simple
syntheses and emphasizing the relationship
between structure and reactivity
Productivity and Accountability
Develop new knowledge and understanding that will
contribute to nation-building and sustainable
development through the processes of inquiry,
research and innovation
Generate insights and new knowledge in
pharmacy that will contribute to nation-
building and sustainable development through
drug designs and development for the
prevention, diagnosis, mitigation and
treatment of diseases of man and animals
4. Explore the interrelation between mechanistic
understanding of organic reactions and
practical applications to drug design and
development, health care, energy and the
environment
Social and Ethical Responsibilities
Hold Catholic values and moral principles reflective of
the competent, committed and compassionate
Thomasian in the formation of humanely progressive
and healthy society)
Exhibit Catholic values and moral principles
reflective of the Thomasian identity;
competent, committed and compassionate, as
health care professionals in the formation of
humanely progressive and healthy society
5. Manifest Catholic values and moral principles
by developing the skills necessary to generate
less hazardous waste in the laboratory and by
learning to protect the environment by the
proper disposal or recycling of all reagents and
end products
Communication and Relational Skills
Develop effective communication competencies
through interpersonal skills and utilize information
technology responsibly as effective tool ion exploring
and expressing ideas
Apply effective communication competencies
through interpersonal skills and utilize
information technology responsibly as an
effective tool in exploring and expressing ideas
individually and collaboratively and in
maintaining therapeutic relationship s by
providing drug and health related information
6. Enhance skills in web-based learning tools and
other information technology resources.


Intended Learning Outcomes Content Teaching-Learning Activities Assessment Tasks



1. Describe the electronic structure
of atoms
CILO1

2. Differentiate ionic from covalent
bonds
CILO1

3. Exhibit initiative to lead and
cooperate in performing assigned
tasks and/or activities
CILO 2

4. Practice social and ethical
responsibilities in the use of
facilities and resources
CILO5

5. Calculate the formal charge of the
atom
CILO1

6. Describe the hybridization of
atoms present in simple organic
compounds
CILO 6

7. Exhibit initiative to lead and
cooperate in performing assigned
tasks and/or activities
CILO 2

8. Predict the direction of polarity of
a bond
CILO1



9. Identify functional groups in
organic molecules
CILO1

Unit I: Covalent Bonding and Shapes
of Molecules

1.1 Atomic structure; atomic orbitals

1.2 Electronegativity and chemical
bonds
1.2.1 Chemical Nature of Organic
Compounds





1.3 Formal charge

1.4 Hybridization

1.4.1 Molecular Modeling of
Organic Compounds


1.5 Bond polarity
1.5.1 Extraction
1.5.2 Column and Thin layer
Chromatography
1.6 Functional groups
1.6.1 Comparative Investigation
of Organic Compounds




Assigned reading

Work along activities

Lecture forum

Note taking

Information inquiry

Small group assignment

Scientific laboratory session

Cookbook laboratory work

Brain storming



Focused listing

Objective test

Lab practical

Analytic assessment

Critique paper
Intended Learning Outcomes Content Teaching-Learning Activities Assessment Tasks


1.
Discuss the different structural effects
CILO3
2. Classify molecule as a Lewis acid or a
Lewis base
CILO1

3. Illustrate the effect of structure on pKa
and the relationship between acidity
and molecular structure
CILO6


Unit II: Acids and Bases

2.1 Structural effects

2.2 Lewis acids and Lewis bases

2.3 K
a
, pK
a
, K
b
, pK
b
, pH


Interactive Lecturing

Work Along Exercises


Problem Sets

Problem Recognition Tasks

Analytic Assessment






1. Illustrate the different kinds of
formulas
CILO1




2. Differentiate all types of isomers
CILO1

3. Classify the different types of carbon
atoms
CILO1

4. Discuss the properties and
conformations of alkanes and
cycloalkanes
CILO 6

5. Exhibit initiative to lead and cooperate
in performing assigned tasks and/or
activities
CILO 2

6. Practice social and ethical
responsibilities in the use of facilities
and resources
CILO5

Unit III: Alkanes and Cycloalkanes

3.1 Different kinds of formulas
3.1.1 Chemical Formula-writing
and Nomenclature of Organic
Compounds
3.2 Isomers
3.3 Types of carbon atoms

3.4 Boiling/melting points; solubility;
Conformations of alkanes and
cycloalkanes
3.4.5 Sublimation and Melting point
Determination



Gapped Lecture

Lecture Forum

Spontaneous Collaboration

Note taking

Information inquiry

Note taking

Information inquiry

Small group assignment
Scientific laboratory session

Cookbook laboratory work

Brain storming


Summarizing

Compare and contrast chart

Illustrating concepts and
principles

Objective Test
Intended Learning Outcomes Content Teaching-Learning Activities Assessment Tasks


1. Name and draw alkenes and
cycloalkenes
CILO1

2. Explain cis-trans isomers of alkenes
CILO1

3. Assign E,Z configurations to double
bonds
CILO1


Unit IV: Alkenes and Alkynes
4.1 Electronic structure of alkenes

4.2 Cis-trans isomers of alkenes

4.3 Sequence rules of E,Z designation


Assigned Reading

Work Along Exercises

Problem Solving Learning

Problem Sets

Problem Recognition Tasks

Documented Problem
Solution



1. Classify organic reactions
CILO1

2. Discuss the roles of radicals,
nucleophiles and electrophiles in
organic reactions
CILO4

3. Formulate the mechanism of
electrophilic addition reactions
CILO3

4. Exhibit initiative to lead and cooperate
in performing assigned tasks and/or
activities
CILO 2

5. Practice social and ethical
responsibilities in the use of facilities
and resources
CILO5

6. Explain a reaction energy diagram
CILO6

7. Predict the product of reactions of
alkenes, dienes and alkynes
CILO3

8. Demonstrate correct preparation of
alkenes and alkynes
CILO3

9. Describe the acidity of alkynes
CILO1

10. Apply the principles of different
reactions to determine the structure of an
Unit V: Reactions of Alkenes and
Alkynes

5.1 Kinds of organic reactions
5.2 Organic reaction intermediates


5.3 Electrophilic addition reactions

5.3.1 Classification Tests for
Hydrocarbons




5.4 Reaction energy diagrams and
transition states
5.5 Reactions of alkenes, dienes, and
alkynes
5.6 Preparation of alkenes and alkynes

5.7 Alkyne acidity
5.8 Structure elucidation


Gapped Lecture

Lecture Forum

Three-Minute Essay

Note taking

Information inquiry

Small group assignment

Scientific laboratory session

Cookbook laboratory work

Brain storming



Focused Listing

Whats the Principle

Analytic Assessment

Lab practical

Analytic assessment

Critique paper
Intended Learning Outcomes Content Teaching-Learning Activities Assessment Tasks
unknown compound
CILO3





1.
Discuss chirality and optical activity
CILO6
2. Locate stereocenters in molecules
CILO1

3. Differentiate enantiomers from
diastereomers; meso compounds from
racemic mixture
CILO3

4. Designate the configuration of a
stereocenter
CILO1

Unit VI: Chirality: The Handedness of
Molecules

6.1 Chirality and optical activity

6.2 Stereocenter
6.3 Enantiomers and diastereomers,
meso compounds and racemic
mixture
6.4 R , S convention



Gapped Lecture

Lecture Forum

Three-Minute Essay

Problem Solving Learning



Focused Listing

Whats the Principle

Analytic Assessment

Documented Problem
Solution


1. Illustrate the mechanisms of S
N
1 and
S
N
2 reactions
CILO3

2. Differentiate S
N
1 from S
N
2 reactions
CILO3

3. Exhibit initiative to lead and cooperate
in performing assigned tasks and/or
activities
CILO 2

4. Practice social and ethical
responsibilities in the use of facilities
and resources
CILO5

5. Describe elimination reactions: E1 and
E2
CILO1

6. Identify reactions as S
N
1, S
N
2, E1, and
E2
CILO1

7. Predict the products of reactions of
alkyl halides and the effects of changes
in reaction conditions on substitution
and elimination reactions
CILO3

Unit VII: Haloalkanes

7.1 Mechanisms of S
N
2 and S
N
1
Reactions
7.2 Comparison of S
N
2 and S
N
1
Reactions
7.2.1 Classification Tests for
Organic Halides




7.3 Elimination reactions: E1 and E2

7.4 Competition between substitution
and elimination
7.5 Factors affecting substitution and
elimination



Interactive Lecturing

Work Along Activities

Note taking

Information inquiry

Small group assignment

Scientific laboratory session

Cookbook laboratory work

Brain storming


Problem Sets

Documented Problem
Solution

Analytic Assessment

Objective test

Lab practical

Critique paper
Intended Learning Outcomes Content Teaching-Learning Activities Assessment Tasks


1. Differentiate alcohols from phenols;
ethers from epoxides; and thiols from
sulfides
CILO1

2. Exhibit initiative to lead and cooperate
in performing assigned tasks and/or
activities
CILO 2

3. Practice social and ethical
responsibilities in the use of facilities
and resources
CILO5

4. Compare the physical and chemical
properties of alcohols, phenols, and
ethers
CILO3


5. Discuss synthesis alcohols, ethers, and
phenols
CILO3

6. Predict the products of reactions
involving alcohols, phenols, and ethers
CILO3

Unit VIII: Alcohols, Ethers, and Thiols

8.1 Alcohols, phenols, ethers,
epoxides, thiols, and sulfides

8.1.1 Classification Tests for
Hydroxyl Compounds




8.2 Properties of alcohols, ethers and
phenols: H-bonding, acidity
8.2.1 Simple and Fractional
Distillation
8.3 Synthesis of alcohols, phenols,
and ethers
8.4 Reactions of alcohols, phenols,
and ethers




Lecture Forum

Assigned Reading

Workshop

Note taking

Information inquiry

Small group assignment

Scientific laboratory session

Cookbook laboratory work

Brain storming




Summarizing

Analytic Assessment

Objective test

Lab practical

Analytic assessment

Critique paper
.

1. Determine whether a substance is
aromatic or antiaromatic
CILO1

2. Formulate the mechanisms of
electrophilic aromatic substitution
reactions
CILO3

3. Predict the reactivity and orientation
of the aromatic ring and substituents
in electrophilic aromatic substitution
reactions
CILO3

4. Discuss aromaticity in nonbenzene
rings and polycyclic compounds
CILO3

Unit IX: Benzene and Its Derivatives

9.1 Benzene structure and stability
9.2 Aromaticity and Antiaromaticity
9.3 Electrophilic aromatic substitution
reactions of benzene

9.4 Substituent effects in electrophilic
aromatic substitutions


9.5 Polycyclic aromatic compounds



Gapped Lecture

Lecture Forum

Work Along Exercises

Web-Enhanced Activity


Summarizing

Analytic Assessment

Online Assessment
Intended Learning Outcomes Content Teaching-Learning Activities Assessment Tasks
5. Outline the synthesis of substituted
benzene through various reaction
pathways
CILO4

9.6 Organic synthesis


1. Differentiate 1
o
, 2
o
, 3
o
, and 4
o
amines
CILO1

2. Exhibit initiative to lead and cooperate
in performing assigned tasks and/or
activities
CILO 2

3. Practice social and ethical
responsibilities in the use of facilities
and resources
CILO5

4. Evaluate the base strength of amines
CILO3

5. Discuss the reactions and synthesis of
amines
CILO3


Unit X: Amines

10.1 Different types of amines
10.1.1 Classification Test for Amines






10.2 Basicity of amines

10.3 Reactions and synthesis of
amines



Gapped Lecture

Lecture Forum

Three-Minute Essay

Note taking

Information inquiry

Small group assignment

Scientific laboratory session

Cookbook laboratory work

Brain storming


Focused Listing

Whats the Principle

Analytic Assessment

Objective test

Lab practical

Critique paper


1. Compare the reactivities of aldehydes
with that of ketones
CILO3

2. Discuss the different reactions of
aldehydes and ketones
CILO4
3. Exhibit initiative to lead and cooperate
in performing assigned tasks and/or
activities
CILO 2

4. Practice social and ethical
Unit XII: Aldehydes and Ketones

12.1 Electronic structure of carbonyl
group
12.2 Reactions of aldehydes and
ketones
12.2.1 Classification Tests for
Carbonyl Containing
Compounds



Lecture Forum

Reflective Lecturing

information inquiry

Small group assignment



Summarizing

Problem Sets

Objective test

Lab practical

Intended Learning Outcomes Content Teaching-Learning Activities Assessment Tasks
responsibilities in the use of facilities
and resources
CILO5


Scientific laboratory session

Cookbook laboratory work

Brain storming
Analytic assessment

Critique paper


1. Name and draw structural formulas for
carboxylic acids
CILO1

2. Compare acidity of carboxylic acids
CILO3

3. Outline the necessary steps for the
syntheses of various drugs
CILO4
4. Exhibit initiative to lead and cooperate
in performing assigned tasks and/or
activities
CILO 2
5. Practice social and ethical
responsibilities in the use of facilities
and resources
CILO5


Unit XIII Carboxylic Acids

13.1 Nomenclature and structure of
carboxylic acids
13.2 Acidity of carboxylic acids
13.3 Chemical transformations and
syntheses
13.1.1 Synthesis of Aspirin




Problem Solving Learning

Assigned Reading

Lecture forum

Note taking

Information inquiry

Small group assignment

Scientific laboratory session

Cookbook laboratory work

Brain storming



Summarizing

Analytic Assessment

Objective test

Lab practical

Critique paper



1. Identify the functional derivatives of
carboxylic acids
CILO1


2. Discuss the physical and chemical
properties of acid derivatives
CILO1

Unit XIV: Functional Derivatives of
Carboxylic Acids

14.1 Nomenclature and structures of
carboxylic acid derivatives

14.2 Properties of acid derivatives




Problem Solving Learning

Assigned Reading

Lecture forum



Summarizing

Analytic Assessment

Objective test
Intended Learning Outcomes Content Teaching-Learning Activities Assessment Tasks
3. Compare reactivities of carboxylic acid
derivatives
CILO3

4. Exhibit initiative to lead and cooperate
in performing assigned tasks and/or
activities
CILO 2

5. Practice social and ethical
responsibilities in the use of facilities
and resources
CILO5

6. Formulate mechanisms of simple
nucleophilic acyl substitution reactions
CILO6

14.3 Reactivities of carboxylic acid
derivatives
14.3.1 Synthesis of Soap and
Detergent




14.4 Characteristic reactions of
carboxylic acid derivatives
14.4.1 Classification Tests for
Carboxylic Acids and
Derivatives

Note taking

Information inquiry

Small group assignment

Scientific laboratory session

Cookbook laboratory work

Brain storming

Web-Enhanced Activity

Lab practical

Critique paper

Online Assessment
REFERENCES:
Bathan, G.I., Bayquen, A.V., Crisostomo, A.B.C., Cruz, C.T., de Guia, R.M., Farrow, F.L., Pea, G.T., Sarile,A.S. and Torres, P.C. (eds.) (2014).
Laboratory Manual in Organic Chemistry. Quezon City,Philippines: C & E Publishing, Inc.
Brown, W. H. and Poon, T. (2014). Introduction to Organic Chemistry. 5
th
ed. New Jersey: John Wiley & Sons, Inc.
Hart H., Craine LE, Hart DJ, and Hadad CM. (2012). Organic Chemistry A Brief Course. 13
th
ed. Brooks/Cole, CENGAGE Learning
Klein, David R. (2012) Organic Chemistry New Jersey: John Wiley & Sons, Inc.
Lim-Sylianco, Clara Y. Principles of Organic Chemistry. 6
th
ed. Aurum Technical Books.
McMurry J. (2011). Fundamentals of Organic Chemistry. 7
th
ed. Thomson Brooks/Cole, Belmont, CA, USA.
Solomons, T.W. G., Fryhle, C.B., Snyder, S.A. (2014). Organic Chemistry. 11
th
ed. John Wiley and Sons, Inc., New York.









GRADING SYSTEM:
The overall grade is composed of 20% monthly grade, 40% preliminary grade and 40% final grade. The preliminary and final grades consist of
60% lecture and 40% laboratory. The lecture and laboratory grades are computed as follows.

LECTURE
LABORATORY
Prelims Finals
Departmental Examination 50% 30% 30%
Quizzes 40% 30% 20%
Class Standing (Attendance/Performance/ Conduct) 10% 10% 10%
Formal Reports --------- 15% 15%
Pre-lab Assignment --------- 5% 5%
Data Sheet --------- 5% 5%
Post-lab Assignment --------- 5% 5%
Practical Exam --------- --------- 10
TOTAL 100% 100% 100%

COURSE POLICY: At least with an 80% attendance
Passing rate: 75%

Prepared by: Prof. Angelita S. Sarile, Ph.D.

Reviewed by: Asst. Prof. Andrea G. Vargas, Chair, Department of Biochemistry

Approved by: Assoc. Prof. Ma. Elena J. Manansala, MSc.
Dean, Faculty of Pharmacy

Date of Approval: 14 June 2014



TENTATIVE COURSE CALENDAR:

WEEK CONTENT
1 Covalent Bonding; Acids and Bases
2 Alkanes and Cycloalkanes
3 Reactions of Alkenes and Alkynes
4
5 Benzene and its Derivatives
6 MONTHLY
7 Haloalkanes
8
9 Chirality
10 Alcohols, Thiols, and Ethers
11
12 PRELIMS
13 Aldehydes and Ketones
14
15 Carboxylic Acids
16 Carboxylic Acid Derivatives
17
18 FINALS


Introduction to Organic Chemistry
5
th
ed. Brown, W. and Poon, T.
EXERCISES

Unit I

1.17
1.22
1.25
1.27 d, f, i, l,o
1.33
1.37
1.51
1.55
1.64
Unit III

3.14
3.20
3.26
3.33
3.36
3.49
PIT # 10 and 11

Unit V

5.13
5.16
5.19
5.28
5.32
5.46
5.51
Unit VII

7.11 b,d,f
7.22 b,d,f
7.26 a,c,e
7.35 b,c,d
7.36
7.43
7.44 a,d,g
7.46

Unit IX

9.11 b,d,f,h
9.23
9.26 f,g,h,i,j
9.28
9.31
9.36
9.41
9.47


Unit XII

12.13
12.14 d,f,g,h
12.21
12.40 a,b,c
12.44

Unit XIV

14.15
14.21
14.29
14.45
14.46 f,g,h
Unit II

2.10
2.17
2.19
2.28
2.29
2.36
2.39
Unit IV

4.12
4.18 a,c,e
4.19 b,c,d
4.21 b,d,f
4.22 a,c,e
4.27
4.36
Unit VI

6.13
6.22
6.24
PIT # 6,7 and 14
Unit VIII

8.13 b,d,e,h
8.15 a,c,e
8.24
8.25
8.29
8.38
8.42
8.47

Unit X

10.12
10.14
10.15
10.22
10.36
10.43
Unit XIII

13.17
13.30
13.32
13.39
13.46