C9551 Structural Chemistry II

Faculty of Science
Spring 2011 - only for the accreditation
Extent and Intensity
2/0/0. 2 credit(s) (fasci plus compl plus > 4). Type of Completion: zk (examination).
Teacher(s)
prof. RNDr. Radek Marek, Ph.D. (lecturer)
doc. Mgr. Marek Nečas, Ph.D. (lecturer)
Mgr. Zdeněk Kříž, Ph.D. (lecturer)
doc. Mgr. Markéta Munzarová, Dr. rer. nat. (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.
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
there are 6 fields of study the course is directly associated with, display
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 crystal. Bragg's law. Relation between electronic structure and diffraction pattern. Scattering of X-rays on atoms. Atomic scattering factor. Automatic diffractometers - for monocrystals a powders. 5. External and internal symmetry of crystal. 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
  • Fundamentals of crystallography. Edited by Carmelo Giacovazzo. 2nd ed. Oxford: Oxford University Press, 2002, xix, 825. ISBN 0198509588. 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
The course is taught annually.
The course is taught: every week.
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 2010, Spring 2011, spring 2012 - acreditation.