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2025 (Current Year) Faculty Courses School of Life Science and Technology Undergraduate major in Life Science and Technology

Physical Chemistry III

Academic unit or major
Undergraduate major in Life Science and Technology
Instructor(s)
Yoshitaka Ishii / Akio Kitao / Takao Yasui / Ryuji Igarashi
Class Format
Lecture (Face-to-face)
Media-enhanced courses
-
Day of week/Period
(Classrooms)
1-2 Tue (M-278(H121)) / 1-2 Fri (M-278(H121))
Class
-
Course Code
LST.A211
Number of credits
200
Course offered
2025
Offered quarter
3Q
Syllabus updated
Oct 2, 2025
Language
Japanese

Syllabus

Course overview and goals

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.

Course description and aims

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.

Keywords

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

Competencies

  • 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/Objectives

Course schedule Objectives
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. Solve exercise problems 8A・4, 8A・10.

Class 2

Application of quantum theory to simple processes such as translation, rotation and vibration motions

Solve exercise problems 8B・6、8B・9 and 8B・10 on page 342 of textbook.

Class 3

The electronic structures of hydrogenic atoms: atomic orbitals and their energies

Solve exercise problems 8C・2、8C・3、8C・5 on page343 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 9B・3 , 9B・4, 9B・8 and 9B・9 on page 384 of textbook.

Class 7

Molecular orbital theory: polyatomic molecules and Hückel theory

Solve exercise problems 9C・2~9C・4、9C・7 on page 384~385 of textbook.

Class 8

Molecular orbital theory: d-Metal complexes, crystal fiels theory and computational biochemistry

Explain the ligand-field theory.

Class 9

Biochemical spectroscopy: general features of spectroscopy

Intermolecular and interatomic interactions: electrostatic interaction, hydrogen bond and Lennard-Jones potential

To be able to explain the quantum state transition related to the optical absorption and emission.simulation.

Class 10

Intermolecular and interatomic interactions: electrostatic interaction, hydrogen bond and Lennard-Jones potential

Solve exercise problems 10A・2, 10A・4 and 10A・16 on pages 431~432 of textbook.

Class 11

Computer simulation: molecular dynamics and Monte Carlo simulations, and quantitative structure-activity relationships

TExplain the difference between the molecular dynamics simulation and the Monte Carlo simulation.

Class 12

Biochemical spectroscopy: principle of vibrational spectroscopy

To be able to explain the principle of vibrational IR and Raman spectroscopy.

Class 13

Biochemical spectroscopy: Electronic transition and Franck-Condon principle

To be able to explain what factors contribute to the spectral shape of absorption and fluorescence.

Class 14

Biochemical spectroscopy: Application to biological systems

To be able to explain biological researches using spectroscopic analyses

Study advice (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.

Textbook(s)

P. Atkins and J. D. Paula, Physical Chemistry for the Life Science, third 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.

Evaluation methods and criteria

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

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