C5060 Methods of Chemical Research I.

Faculty of Science
Autumn 2010
Extent and Intensity
2/0/0. 2 credit(s) (fasci plus compl plus > 4). Recommended Type of Completion: zk (examination). Other types of completion: k (colloquium).
prof. RNDr. Miroslav Holík, CSc. (lecturer)
RNDr. Aleš Kroupa, CSc. (lecturer)
doc. RNDr. Pavel Kubáček, CSc. (lecturer)
doc. RNDr. Jaromír Marek, Ph.D. (lecturer)
prof. Mgr. Jan Preisler, Ph.D. (lecturer)
doc. RNDr. Jiří Toužín, CSc. (lecturer)
prof. RNDr. Libuše Trnková, CSc. (lecturer)
prof. RNDr. Michaela Vorlíčková, DrSc. (lecturer)
prof. RNDr. Zdirad Žák, CSc. (lecturer)
Guaranteed by
doc. RNDr. Pavel Kubáček, CSc.
Department of Chemistry - Chemistry Section - Faculty of Science
Contact Person: doc. RNDr. Pavel Kubáček, CSc.
Tue 10:00–11:50 A12-311
Passing out lectures C4660 and C4020.
Parallel hearing of the lectures from Chemical Structure recommended.
Course Enrolment Limitations
The course is offered to students of any study field.
Course objectives
By the end of the course, students should be able to understand principle and basic applications of the following methods.
Electron microscopy. Symmetry of molecules. X-ray structural analysis. Protein crystallography. Raman and IR spectroscopy. NIR spectroscopy. Cyclic voltammetry. Optical rotation (ORD, CD) in structural analysis. Electron paramagnetic resonance. Luminescence.
  • 1. Electron microscopy. Interaction of electrons with solid phase. Electro microscope (electromagnetic lenses, electron jet, vacuum system), building of the picture, creation of contrast. Diffraction on singlecrystal and polycrystal. Sample preparation etching.
  • 2. Roentgen diffraction. Elementary crystallography symmetry of the structure, space group symmetry, diffraction of Roentgen radiation, structural factor. Basis of structural analysis data collection, data reduction, phase problem and its solution, improvement of the structural model, structure evaluation.
  • 3. Crystallography of proteins. Macromolecular techniques of crystallization, methods of sitting and hanging drop, seedings. Diffraction experiment:sources of X-ray, detectors, cryo-crystallography. Methods of solving phase problem in proteins. Method of molecular replacement. Methods of heavy atom derivatives (SIR, MIR, MIRAS), MAD and Se-proteins. Maps of electron density. Building of structural model and model refinement.
  • 4. Fluorescence spectroscopy. Fluorescence and other luminescence methods, life time, quantum yield. Fluorescence intensity. Switch-out and selfquenching. Excitation and emission spectra. Quasiline fluorescence and fluorescence in solid phase. Spectrometer and measurement procedure.
  • 5. Techniques of Raman spectroscopy. Elastic and non-elastic dispersion of irradiation (Rayleigh, Stokes and anti-Stokes lines); selection rules - polarisability and transition integral, polarization of Raman lines; electronic, resonance and surface enhanced Raman effects; nonlinear effects – stimulated-, inverse-, hyper-Raman effects, coherent anti-Stokes Raman spectroscopy.
  • 6. Methods of IR spectroscopy. Origin of IR bands, selection rules – dipole moment and transition integral; basic and overtones, combination lines; experimental technique of IR spectroscopy, materials and solvents used, sample preparation. Application in qualitative, structural, and quantitative analysis, study of binding characteristics (bond order and strength).
  • 7. Near-infrared spectroscopy. NIR as a method without sample preparation: low sensitivity and low resolution. Mathematic methods for qualitative and quantitative analysis. Industrial analytic transfer of signal by glass fiber. Quality control at automatic production.
  • 8. Circular bichroism. Absorption of irradiation in monomers and polymers; absorption in nucleic acids. Advantages end disadvantages of the method. Vibration circular bichroism and linear bichroism.
  • 9. Modern electrochemical methods: fundamentals and applications Electrode system and electrode reaction. Voltammetry and coulometry. Potentiostatic and galvanostatic regime. Trends and hyphenated methods.
  • 10. Electron Paramagnetic Resonance as the method for study of systems with non-zero electron spin. Nature of the effect and the experiment, characteristics of EPR signals, hyperfine structure. Use of EPR in structural and analytical chemistry.
  • 11. Symmetry of molecules. Elements and operations of point symmetry. Applications of symmetry in chemistry.
  • Toužín, Jiří-Příhoda, Jiří. Spektrální a magnetické metody studia anorganických sloučenin. 1.vyd.Praha:Státní pedagogické nakladatelství, 1986
Teaching methods
The two-hour lectures will be given by internal or external specialist in the respective areas.
Assessment methods
The final examination has a oral form (examiner: prof. Holík).
Language of instruction
Further Comments
Study Materials
The course is taught annually.
The course is also listed under the following terms Autumn 2007 - for the purpose of the accreditation, Autumn 1999, Autumn 2010 - only for the accreditation, Autumn 2000, Autumn 2001, Autumn 2002, Autumn 2003, Autumn 2004, Autumn 2005, Autumn 2006, Autumn 2007, Autumn 2008, Autumn 2009, Autumn 2011, Autumn 2011 - acreditation, Autumn 2012, Autumn 2013, Autumn 2014, Autumn 2015, Autumn 2016, autumn 2017, Autumn 2018, Autumn 2019.
  • Enrolment Statistics (Autumn 2010, recent)
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