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2021　Physical Chemistry I

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Academic unit or major
Undergraduate major in Life Science and Technology
Instructor(s)
Ishii Yoshitaka  Kobatake Eiry  Osada Toshiya  Mie Masayasu 
Class Format
Lecture     
Media-enhanced courses
Day/Period(Room No.)
Tue1-2(W331)  Fri1-2(W833)  
Group
-
Course number
LST.A201
Credits
2
Academic year
2021
Offered quarter
1Q
Syllabus updated
2021/3/19
Lecture notes updated
-
Language used
Japanese
Access Index

Course description and aims

This course deals primarily with basic thermodynamics for bioscience and biotechnology students. It quantitatively and qualitatively describes properties of macroscopic systems, equilibrium and spontaneous changes, chemical reactions in gas and solution phase, and physical processes. The goal of the course is to understand what determines equilibrium and reactions in biological systems, and the ultimate one is to get an insight into the true nature of living organs from the view point of chemical and physical processes.

Student learning outcomes

By the end of this course, students will be able to:
1) Understand the kinetic theory of gas and explain the molecular origins and meanings of heat and temperature.
2) Understand the first law of thermodynamics and explain conservation of energies including heat and work.
3) Understand the second law of thermodynamics and the meaning of entropy, and explain equilibrium and spontaneous changes in relation to temperature and heat.
4) Understand the meaning of Gibbs energy and describe quantitatively equilibrium and changes in relation to heat, work, phase transition and concentrations of mixture components.
5) Understand the molecular interpretation of entropy and Gibbs energy, and explain the nature of thermal processes.

Keywords

thermodynamics, kinetic theory of gas, entropy, Gibbs energy, equilibrium and spontaneous changes, reactions, phase equilibrium and transition

Competencies that will be developed

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

Class flow

Over the course, students will be conducted according to the text "Physical Chemistry for the Life Sciences" with introductory and detailed explanations. In each class, students are given exercise problems related to the lecture given that day to solve.

Course schedule/Required learning

  Course schedule Required learning
Class 1 Fundamentals and kinetic theory of gas (Masayasu Mie, Takafumi Ueno) Derive the relationships of temperature with pressure and kinetic energy based on the kinetic model of gas molecules.
Class 2 Systems and surroundings, work and heat, the internal energy (Masayasu Mie, Takafumi Ueno) Understand fundamental relationships among the internal energy, heat and work in the framework of the system and surroundings.
Class 3 The first law: the conservation of energy, enthalpy, physical processes (Masayasu Mie, Takafumi Ueno) Compute enthalpy changes accompanying physical processes applying the first law, the conservation of energy.
Class 4 Chemical reactions and enthalpy: bond, formation and reaction enthalpy. Carnot cycle as a thought experiment, thermal efficiency, Clausius Inequality (Masayasu Mie, Takafumi Ueno) Compute enthalpy changes associated with chemical reactions.　Derive Clausius inequality by evaluation of energy flow as heat and work of the Carnot cycle.
Class 5 The second law: Entropy, equilibrium, the direction of spontaneous canges (Makio Tokunaga, Yoshitaka Ishii) Evaluate the direction of spontaneous changes using entropy.
Class 6 The third law, entropy changes associated with chemical reactions (Makio Tokunaga, Yoshitaka Ishii) Understand absolute entropies. Compute entropy changes associated with chemical reactions.
Class 7 Gibbs energy, equilibrium and spontaneous chages, maximum work (Makio Tokunaga, Yoshitaka Ishii) Understand the relationship between the total entropy and Gibbs energy. Evaluate Gibbs energy changes and work associated with equilibrium, spontaneous changes and chemical reactions.
Class 8 Molecular interpretaion of thermal equilibrium and irreversible changes, temperature and entropy (Makio Tokunaga, Yoshitaka Ishii) Understand the definition of entropy in statistical mechanics and the molecular interpretation of temperature.
Class 9 Boltzmann distribution, molecular interpretation of Gibbs energy, equipartition law of energy (Makio Tokunaga, Yoshitaka Ishii) Understand the molecular interpretation of Boltzmann distribution and Gibbs energy.
Class 10 Phase transition and Gibbs energy, phase diagram (Eiry Kobatake, Toshiya Osada) Evaluate Gibbs energy changes accompanying phase transitions and understand phase diagrams.
Class 11 Characteristic points, the phase diagram of water, phase transitions in biopolymers and aggregates (Eiry Kobatake, Toshiya Osada) Explain the reason of characteristic feature of water phase diagram. Evaluate phase transition of structure of nucleic acids, proteins, biological membranes.
Class 12 The thermodynamic description of mixtures, chemical potential: uniformity, solvent, solute (Eiry Kobatake, Toshiya Osada) Evaluate the variation of the chemical potentials of the solvent and the solute with concentration.
Class 13 Activities, Donnan equilibrium, entropy of mixing, the modification of boiling and freezing points, osmosis (Eiry Kobatake, Toshiya Osada) Understand the role of Donnan equilibrium in cells, and the boiling point elevation and the freezing point depression with graphs. Evaluate entropy of mixing and the van't Hoff equation.
Class 14 Osmometry, reaction Gibbs energy, reaction quotient, biological standard state (Eiry Kobatake, Toshiya Osada) Compute the molar mass by osmometry. Evaluate the variation of the reaction Gibbs energy with composition and the reaction quotient.

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.

Textbook(s)

Atkins, Paula. Physical Chemistry for the Life Sciences (2nd ed). Tokyo: Tokyo Kagakudojin, 2014; ISBN-13: 978-4807908387. (Japanese)
Atkins, Paula. Physical Chemistry for the Life Sciences (2nd revised ed). Oxford: Oxford University Press; ISBN-13: 978-0199564286. (English)

Reference books, course materials, etc.

Atkins, Paula. Atkins' Physical Chemistry I, II (8th ed). Tokyo: Tokyo Kagakudoji, 2009; ISBN-13: 978-4807906956, 978-4807906963. (Japanese)
Atkins, Paula. Atkins' Physical Chemistry (10th revised ed). Oxford: Oxford University Press, 2014; ISBN-13: 978-0199697403. (English)
Tinoco et al. Physical Chemistry: Principles and Applications in Biological Sciences (5th ed.). Tokyo: Tokyo Kagakudojin, 2015; ISBN-13: 978-4807908806. (Japanese)
Tinoco et al. Physical Chemistry: Principles and Applications in Biological Sciences (5th ed.). Upper Saddle River: Prentice Hall, 2013; ISBN-13: 978-0136056065. (English)
Reif, F. Statistical Physics ( Berkeley Physics Course, Volume 5). Tokyo: Maruzen, 2011; ISBN-13: 978-4621083437. (Japanese)
Reif, F. Complete Statistical Physics (Berkeley Physics Course, Volume 5). New York: McGraw-Hill Science, 1998; ISBN-13: 978-0070386624. (English)
Nagaoka, Yosuke. Statistical Physics. Tokyo: Iwanami shoten, 1994; ISBN-13: 978-4000079273. (Japanese)
Phillips et al. Physical Biology of the Cell (1st ed). Tokyo: Kyoritsu shuppan, 2011; ISBN-13: 978-4320057166. (Japanese)
Phillips et al. Physical Biology of the Cell (2nd ed). New York: Garland Science, 2012; ISBN-13: 978-0815344506. (English)

Assessment criteria and methods

Students' knowledge of basic matters, understanding on essential significance and abilities to apply them to problems will be assessed by assignments given by lectures. Mini-exams may be held timely.
Mini-exam and assignments 100%.

Related courses

  • LST.A206 ： Physical Chemistry II

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

There are no prior conditions for taking the course.

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