C9551 Structural Chemistry II

Faculty of Science
Spring 2011
Extent and Intensity
2/0/0. 2 credit(s) (fasci plus compl plus > 4). Type of Completion: zk (examination).
Teacher(s)
prof. Mgr. Dominik Munzar, Dr. (lecturer)
prof. RNDr. Radek Marek, Ph.D. (lecturer)
doc. Mgr. Marek Nečas, Ph.D. (lecturer)
Mgr. Zdeněk Kříž, Ph.D. (lecturer)
Guaranteed by
prof. RNDr. Radek Marek, Ph.D.
National Centre for Biomolecular Research – Faculty of Science
Contact Person: prof. RNDr. Radek Marek, Ph.D.
Timetable
Fri 10:00–11:50 Kontaktujte učitele
Prerequisites
Structural Chemistry I (C9550)
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
Course objectives
At the end of the course students should be able to understand and explain fundamentals of X-ray diffraction and molecular modeling - two important methods of structural chemistry.
Syllabus
  • 1. Periodic systems – insight to crystal structure, forces determining the formation of crystals. 2. Solid-state NMR spectroscopy, anisotropic interactions, chemical shift tensor, dipolar interactions, magic angle spinning (MAS), cross polarisation (CP). 3. Diffraction methods. Internal structure of crystals. Crystal structure, crystal lattice and unit cell. Crystal coordinates, directions and planes. Elementary inorganic structures. Structures of metallic, ionic, and molecular crystals. 4. Diffraction. X-ray radiation properties and sources. Interaction of X-rays with crystals. Bragg's law. Relation between electronic structure and diffraction pattern. Scattering of X-rays on atoms. Atomic scattering factor. Automatic diffractometers - for single crystals and powders. 5. External and internal symmetry of crystals. Elements and operations of symmetry. Space groups. 6. Fourier series and their applications in crystallography. Structure factor. Phase problem. Structure solution and refinement. Software packages for cystallography. 7. Applications. Current crystallography - synchrotrons, determination of structures of biopolymers, structure determination from powder diffraction, charge density studies. Processing, interpretation, and presentation of crystallographic data (CIF, Mercury, DIAMOND). Crystallographic databases (CSD, ICSD, PDB). 8. Molecular modeling Introduction, principles and methods, software overview. 9. Molecular mechanics. Empirical force fields - characteristics, terms in force fields used for description of interactions, development and testing of force fields. 10. Molecular dynamics. Basic principles, parameters in MD simulation and their influence on results, constraint molecular dynamics, analysis of the MD trajectories. 11. Modeling of intermolecular interactions. Solvation of the molecules, solvation models - their applications and limitations, molecular docking - principles, software overview. 12. Modeling of crystals. Molecular clusters, periodic conditions. 13. Methods of quantum chemistry and their applications to chemical problems. Hartree-Fock method (HF) and its extensions (CI, MP). Density functional theory (DFT). Basis sets for ab initio calculations, available quantum chemical software packages. Application strategy in solving chemical problems, adequacy and requirement of individual approaches.
Literature
  • VALVODA, Václav. Základy strukturní analýzy. 1. vyd. Praha: Karolinum, 1992, 489 s. ISBN 80-200-0280-4. info
  • MASSA, Werner. Crystal structure determination. Translated by Robert O. Gould. 2nd completely updatet ed. Berlin: Springer-Verlag, 2004, xi, 210. ISBN 3540206442. info
  • LEACH, Andrew R. Molecular modelling : principles and applications. 1st pub. Essex: Longman, 1996, xvi, 595. ISBN 0582239338. info
  • Reviews in computational chemistry. Edited by Kenny B. Lipkowitz - Donald B. Boyd. New York: VCH Publishers, 1996, 414 s. ISBN 1-56081-915-4. info
Teaching methods
Lectures
Assessment methods
Oral exam
Language of instruction
Czech
Follow-Up Courses
Further Comments
Study Materials
The course is taught annually.
Teacher's information
http://www.chemi.muni.cz/nmr/radek/C9951/index.html
The course is also listed under the following terms Spring 2008 - for the purpose of the accreditation, Spring 2011 - only for the accreditation, Spring 2010, spring 2012 - acreditation.
  • Enrolment Statistics (recent)
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