2024 Faculty Courses School of Science Undergraduate major in Chemistry

Crystal Chemistry

Academic unit or major: Undergraduate major in Chemistry
Instructor(s): Hidehiro Uekusa
Class Format: Lecture (Face-to-face)
Media-enhanced courses: -
Day of week/Period (Classrooms): 5-6 Mon / 5-6 Thu
Class: -
Course Code: CHM.B333
Number of credits: 200
Course offered: 2024
Offered quarter: 2Q
Syllabus updated: Mar 14, 2025
Language: Japanese

Syllabus

Course overview and goals

The principal of crystal and molecular structure determination by X-ray diffraction method is introduced. Practice and exercise for crystal structure determination are also carried out in order to understand the practical aspect of the method.

Crystal structure analysis deals with solid-state or crystalline-state of materials by determining accurate molecular and crystal structure. The obtained structural data are not limited to determine the molecular structure, and are essential to understand the molecular and aggregation properties based on the structure. Thus, in this lecture, the principal and method for crystal structure analysis. In the first half, the principal is focused. X-ray diffraction by crystalline lattice, and concept of structure factor and electron density calculation are introduced in the first place. Also, symmetry of crystal including translation symmetry is explained. In the later half, practical analysis method is focused such as space group determination, direct method for initial structure determination, crystallographic least-squares, presenting the structure. Finally, practice of crystal structure analysis is planned which leads understanding of the latest method.

Course description and aims

The understanding of X-ray diffraction and crystal structure analysis techniques, especially how to derive the structure factor and how electron density of crystal is calculated by Fourier synthesis. Symmetry in crystal, how it is presented. Practice of crystal structure determination.

Keywords

Crystal structure, Molecular structure, X-ray, Structure analysis, X-ray diffraction

Competencies

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

Class flow

Include exercises in lecture. Practical aspect　session is scheduled in the later part.

Course schedule/Objectives

	Course schedule	Objectives
Class 1	Crystal chemistry around our life	Find crystalline state material around our life. Understand how the properties are explained by their structure.
Class 2	Symmetry elements of crystals, point group symmetry and crystal systems	Understand crystal systems from symmetry and translation conditions.
Class 3	Space groups of crystals - crystallinity including translational symmetry	Understand that space group symmetries appear, including symmetries with translational components.
Class 4	Introduction to crystal structure factor	Derive crystal structure factors from lattice planes and Bragg's equation
Class 5	From Atomic Scattering Factors to Crystal Structure Factors	Deriving Crystal Structure Factors from X-ray Scattering by Multiple Electrons
Class 6	reciprocal lattice, diffraction conditions and electron density	Derive crystal structure factors using reciprocal lattices and understand diffraction conditions and calculate electron density
Class 7	Symmetry of diffraction intensities	Understand the relationship between diffraction intensity and crystal structure symmetry and how to determine the space group from the annihilation rule.
Class 8	Phase Determination Method (1)	Understand the Patterson function method, the sequential Fourier method, and the phase determination method using the Dual Space method.
Class 9	Phase Determination Method (2)	Understand phase determination by direct and isomorphic substitution methods.
Class 10	Structural Refinement	Understand crystal structure refinement by the least squares method and related topics.
Class 11	Crystal Structure Analysis Methods - Crystal Growth	Understand the method of making single crystals, and twinning and isomorphic crystals related to single crystals.
Class 12	Crystal Structure Analysis Method - Diffraction Intensity Measurement	Practical aspect of X-ray diffraction measurement
Class 13	Crystallographic Methods - Crystal Structure Analysis	Understand the procedures for crystal structure analysis and how to use the software Crystal.
Class 14	exercises	Conducting exercises on crystal chemistry

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)

Y. Ohashi. "Crystal structure analysis by X-ray and neutron" Tokyo Kagakudojin.

Reference books, course materials, etc.

S. Ohba. "Introduction for X-ray crystal structure analysis" Kagakudojin. Other materials may be distributed in class

Evaluation methods and criteria

Understanding of crystal structure, structure analysis, related calculation method, and the application of structure. final exams (80%) and exercise problems (20%).

Related courses

CHM.B301 ： Inorganic Chemistry II
CHM.B331 ： Quantitative Chemical Analysis
CHM.B335 ： Chemistry of Solids
CHM.B305 ： Laboratory Course in Advanced Inorganic and Analytical Chemistry

Prerequisites

None