2020 Organic Chemistry I (alkanes and haloalkanes)

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Academic unit or major
Undergraduate major in Life Science and Technology
Nakamura Hiroyuki  Seio Kohji  Mori Toshiaki  Ohkubo Akihiro  Matsuda Tomoko  Tsutsumi Hiroshi 
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Mode of instruction
Day/Period(Room No.)
Tue7-8(H101)  Fri7-8(H101)  
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Syllabus updated
Lecture notes updated
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Course description and aims

The objects of bioscience and biotechnology are apparently organic compounds. Thus, this lecture systematically and comprehensively describes fundamental topics necessary for the use of or the research on organic compounds, including the knowledge and theory on their nomenclature, nature, analysis, reactions, synthesis, and utility. The contents consist of the IUPAC nomenclature, the electronic states and bonding of molecules, three-dimensional structures of molecules, the instrumental analysis of molecular structures (NMR, IR, Ms), reactions of each functional group, the carbon-carbon bond formation and organic synthesis, and utility of natural and artificial organic compounds, which will be lectured according to the textbook, with the theoretical background and relationship between the topics being mentioned.
At the outset, this course allows the student to firmly learn the general knowledge and theory common to individual topics, such as the nomenclature of compounds, electronic states and bonding of molecules and their nature and structures owing to the former, and the electronic theory of organic chemistry essential to the description of reaction mechanisms. At the next stage, the students will proceed to study reactions unique to each functional group and the instrumental analysis of molecular structures, which are not only memorized but also well interpreted by them on the basis of the above general notion. While reviewing the previous two steps, the students are requested to increase their ability to understand the application of the fundamental topics, for example, the synthesis of organic compounds and utility of natural and artificial compounds. As a whole, this lecture will provide students basic knowledge and theory of organic chemistry and, at the same time, its covering area of utility of organic compounds.

Student learning outcomes

By the end of this course, students will be able to:
1. Give names to organic compounds, with seeing their structures, and vice versa.
2. Understand the electronic states and bonding of organic molecules and explain their nature and structures based on the former.
3. Discuss reaction mechanisms with appropriate flow of electrons based on the electronic theory of organic chemistry.
4. Show characteristic reactions of individual functional groups.
5. Make synthetic plans of organic compounds by the functional-group manipulation and carbon-carbon bond formation.
6. Imagine synthetic utility of natural and artificial organic compounds.


Structure and Bonding in Organic Molecules, Structure and Reactivity (Acids and Bases, Polar and Nonpolar Molecules), Reactions of Alkane, Cycloalkanes, Stereoisomers, Properties and Reactions of Haloalkanes (Bimolecular Nucleophilic Substitution), Further Reactions of Haloalkanes (Unimolecular Substitution and Pathways of Elimination)

Competencies that will be developed

Specialist skills Intercultural skills Communication skills Critical thinking skills Practical and/or problem-solving skills

Class flow

The lecture is to be done in order according to the textbook. (Thus, students are encouraged to familiarize the expected pages of the textbook in advance to the class and to review them after the class.) Three professors are responsible for this course.

Course schedule/Required learning

  Course schedule Required learning
Class 1 cancelled
Class 2 Ionic and Covalent Bonds The Octet Rule, Lewis Structures, Resonance Forms
Class 3 Hybrid Orbitals Atomic Orbitals, Molecular Orbitals, Hybrid Orbitals
Class 4 Acids and Bases Acids and Bases, Kinetics and Thermodynamics of Chemical Reactions, Electrophiles and Nucleophiles, Functional Groups
Class 5 Structural and Physical Properties of Alkanes Straight-Chain and Branched Alkanes, Naming the Alkanes, Rotation about Single Bonds
Class 6 Structure of Alkyl Radicals Strength of Alkane Bonds, Hyperconjugation, The Radical Chain Mechanism
Class 7 Names and Physical Properties of Cycloalkanes Ring Strain and the Structure of Cycloalkanes, Polycyclic Alkanes
Class 8 Chiral Molecules Optical Activity, Absolute Configuration (R-S Sequence Rules),Fischer Projections
Class 9 Stereochemistry in Chemical Reactions Racemic Mixtures, Enantiomers, Separation of Enantiomers
Class 10 Stereochemistry of the SN2 Reaction Frontside or Backside Attack, Structure and SN2 Reactivity (The Leaving Group and the Nucleophile)
Class 11 Unimolecular Nucleophilic Substitution Stereochemical Consequences of SN1 Reactions, Effects of Solvent, Leaving Group, and Nucleophile on Unimolecular SN1 Nucleophilic Substitution
Class 12 Unimolecular Elimination E1, Competition Between Substitution and Elimination
Class 13 Bimolecular Elimination E2, Competition Between Substitution and Elimination
Class 14 cancelled

Out-of-Class Study Time (Preparation and Review)

To enhance effective learning, students are encouraged to spend approximately 100 minutes preparing for class and another 100 minutes reviewing class content afterwards (including assignments) for each class.
They should do so by referring to textbooks and other course material.


Organic Chemistry - Structure and Function, 8th ed., K. P. C. Vollhardt and N, E. Schore, W. H. Freeman and Co., New York,; The Japanese translation, 8th ed., Kagakudojin, Kyoto (Japanese)

Reference books, course materials, etc.

Study Guide and Solutions - Manual for Organic Chemistry, N, E. Schore, W. H. Freeman and Co., New York

Assessment criteria and methods

The home works assigned by each professor (100%).

Related courses

  • LST.A207 : Organic Chemistry II (alcohols and alkenes)
  • LST.A212 : Organic Chemistry III (benzene and ketones)
  • LST.A217 : Organic Chemistry IV (carbonyl compounds and amines)
  • LST.A333 : Bioorganic Chemistry
  • LST.A343 : Pharmaceutical Chemistry

Prerequisites (i.e., required knowledge, skills, courses, etc.)

No prerequisites.

Contact information (e-mail and phone)    Notice : Please replace from "[at]" to "@"(half-width character).

Akihiro Ohkubo (aohkubo[at]bio.titech.ac.jp) Hiroyuki Nakamura (hiro[at]res.titech.ac.jp)

Office hours

All the questions must be through e-mail.


As there is no duplication of the contents from Organic Chemistry I (alkanes and haloalkanes) to IV (carbonyl compounds and amines), the systematic study in this order will maximize its efficiency. Therefore, students are advised to enroll all of them in serial order. After completion of these courses, more advanced lectures, Bioorganic Chemistry and Pharmaceutical Chemistry, are available. Thus, students can proceed to the higher level of organic chemistry by taking one or both of them, dependent on their interest.

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