2019 Physical Chemistry III

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Academic unit or major
Undergraduate major in Life Science and Technology
Sakurai Minoru  Fujii Masaaki  Ishiuchi Shun-Ichi  Kitao Akio 
Class Format
Media-enhanced courses
Day/Period(Room No.)
Tue1-2(H121)  Fri1-2(H121)  
Course number
Academic year
Offered quarter
Syllabus updated
Lecture notes updated
Language used
Access Index

Course description and aims

The course teaches the fundamentals of quantum theory and its applications to biological systems, including the electronic structures and spectroscopic properties of biological molecules. Quantum theory is important for understanding nature, and is essential for the study not only of life science, but also of other specialized sciences and engineering. Students learn the laws governing the motions of electrons in atoms and molecules together with the mathematical description of such motions, that is, the Schrödinger equation. They will be able to solve the equation for simple process (one- or two- dimensional translational, rotational and vibrational motions), and the electronic structures of diatomic molecules and the pi-electron systems of small conjugated double bond compounds. Together with quantum theory, this course provides brief reviews of classical mechanics, wave mechanics, electromagnetism and optics, which are helpful for understanding the origin of quantum theory. This course also provides a brief introduction to computer simulations that are currently indispensable for investigating biological molecules. By the end of this course,students will understand that quantum theory is essential to interpret and predict many spectroscopic data including ultraviolet/visible, fluorescence, vibration spectra.

Student learning outcomes

By the end of this course, students will be able to:
1. Understand the basic principles of quantum theory and its application to elementary processes
2. Understand the basic concept of molecular orbital theory and its application to small molecules
3. Understand the physical origins of various inter- and intra-molecular forces
4. Understand the electronic excited states, vibrational states and dynamic properties of biological molecules by means of spectroscopic experiments and computaer simulations.
5. Understand the basic principles of classical mechanics, wave mechanics, electromagnetism, and optics as a base of quantum mechanics.


quantum theory, Schrödinger equation, wavefunction, molecular orbital theory, intermolecular and interatomic interactions, molecular spectroscopy,

Competencies that will be developed

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

Class flow

At the beginning of each class, solutions to exercise problems that were assigned during the previous class are
reviewed. Towards the end of class, students are given exercise problems related to the lecture given that day to solve.
To prepare for class, students should read the course schedule section and check what topics will be covered.

Course schedule/Required learning

  Course schedule Required learning
Class 1 Principles of quantum theory: Schrödinger equation, wavefunction, quantization, uncertainty principle Solve the Schrödinger equation for a particle that freely moves on the x-axis, and explain that the solution (wavefunction) satisfies the uncertainty principle.
Class 2 Application of quantum theory to simple processes such as translation, rotation and vibration motions Solve exercise problems 9・23, 9・23 and 9・27 on page 367 of textbook.
Class 3 The electronic structures of hydrogenic atoms: atomic orbitals and their energies Solve exercise problems 9・35, 9・36 and 9・38 on page 368 of textbook.
Class 4 The electronic stuctures of many electron atoms: the orbital approximation and the Pauli exclusion principle Find the electron configuration for each atom of H~Ca according to the Aufbau principle, and explain the relationship between the results and the periodic table.
Class 5 Valence bond theory: hybridized orbitals and diatomic molecules According to the concept of hybridization of atomic orbitals, explain the reason why the valence of carbon atom varies from 2 to 4.
Class 6 Molecular orbital theory: linear combination of atomic orbitals, homonuclear and heteronuclear diatomic molecules Solve exercise problems 10・23,10・24,10・29 and 10.30 on page 412 of textbook.
Class 7 Molecular orbital theory: polyatomic molecules and Hückel theory Solve exercise problems 10・32~10・35 on page 412 of textbook.
Class 8 Molecular orbital theory: d-Metal complexes, crystal fiels theory and computational biochemistry Explain the ligand-field theory.
Class 9 Intermolecular and interatomic interactions: electrostatic interaction, hydrogen bond and Lennard-Jones potential Solve exercise problems 11・27, 11・28 and 11・42 on pages 468~469 of textbook.
Class 10 Levels of structure: gases and liquids, the structures of biological macromolecules and membranes Solve exercise problems 11・42~11・44 and 11・50 on pages 469~470 of textbook.
Class 11 Computer simulation: molecular dynamics and Monte Carlo simulations, and quantitative structure-activity relationships Explain the difference between the molecular dynamics simulation and the Monte Carlo simulation.
Class 12 Biochemical spectroscopy: general features of spectroscopy Solve exercise problems 12・10, 11, 14, 15.
Class 13 Biochemical spectroscopy: principle of vibrational spectroscopy Solve exercise problems 12・22, 23.
Class 14 Biochemical spectroscopy: application of vibrational spectroscopy - IR and Raman spectroscopy Solve exercise problems 12・24~27.
Class 15 Biochemical spectroscopy: Electronic transition and Franck-Condon principle Explain Franck-Condon factor.


P. Atkins and J. D. Paula, Physical Chemistry for the Life Science, second edition、Oxford University Press.

Reference books, course materials, etc.

P. Atkins and J. D. Paula, Physical Chemistry, eight edition, Oxford University Press
I. Tinoco, K. Sauer, J. C. Wang, J. D. Puglisi, G. Harbison and D. Rovnyak, Physical Chemistry, Principles and Applications in Biological Sciences, fifth edition, PERSON.
D. A. McQuarrie and J. D. Simon, Physical Chemistry, A Molecular Approach, University Science Books.

Assessment criteria and methods

Learning achievement is evaluated by a final exam.

Related courses

  • LST.A201 : Physical Chemistry I
  • LST.A206 : Physical Chemistry II
  • LST.A341 : Biophysical Chemistry

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

LST.A201 : Physical Chemistry I
LST.A206 : Physical Chemistry II

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