Graduate School

Selected Topics from Molecular Spectroscopy

This course is part of the programme:
Materials (Third Level)

Objectives and competences

The primary goal of this course is to give students the theoretical and practical knowledge of modern molecular spectroscopies and their application in research field. The main stress is on acquirement of practical knowledge from the applied spectroscopies

Prerequisites

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Content (Syllabus outline)

1. Advanced techniques in infrared and Raman spectroscopy

  • reflection measurements
  • attenuated total reflection
  • thin films
  • polarization measurements
  • rapid scan
  • step scan
  • 2-D vibrational spectroscopy
  • modern methods of solving the vibrational problem

2. Selected topics from the applications of the vibrational spectroscopy

  • polymer chemistry
  • chemistry of dyes and coatings

  • characterization of materials
  • application of vibrational spectroscopy in biochemistry, medicine, biophysics and pharmacy
  • characterization of hydrogen bonding
  • structure and dynamics of proteins
  • structure and dynamics of DNK molecules
  • structure and dynamics of amphiphilic molecules
  • application of vibrational analysis in analytical and food chemistry

3. Advanced methods of high resolution NMR spectroscopy

  • multidimensional pulse sequences
  • study of macromolecules
  • study of conformational flexible molecules
  • study of intermolecular interactions
  • application of NMR spectroscopy in structural organic and medical chemistry
  • application of the NMR spectroscopy in pharmaceutical industry

4. Selected topics of UV-VIS and fluorescent spectroscopy

Intended learning outcomes

Knowledge and understanding:

Students learn the principles of different molecular spectroscopic methods They acquire basic knowledge about the application of the modern spectroscopies and techniques in practice. Students gain know-how on the whole process from preparation the sample, measurement on particular spectrometer and the analysis followed by the interpretation of different kind of molecular spectra. With practical work on examples from research practice, they learn advanced techniques of the evaluation and interpretation of obtained spectra. Students learn which combination of spectroscopic methods and techniques are optimal for solving the specific scientific problem.

Readings

    • CHALMERS J. M. and GRIFFITHS P.R., Handbook of Vibrational Spectroscopy Vol.I-V, Wiley & Sons, LTD, Chichester, 2002.
    • NAKAMOTO K., Infrared and Raman Spectra of Inorganic and Coordination Compounds, Wiley, New York, 1997.
    • PERKAMPUS H.H., UV-VIS Spectroscopy and Its Applications Springer-Verlag, 2002.
    • LAKOWITZ J. R., Principles of Fluorescent Spectroscopy Kulwer Academic/Plenum Publisher, 1999.
    • DEWEY T.G., Biophysical and Biochemical Aspects of Fluorescencence Spectroscopy Plenum Press, 1991.
    • MIRTIČ, Andreja, GRDADOLNIK, Jože. The structure of poly-L-lysine in different solvents. Biophysical chemistry, 2013, vol. 175-176, str. 47-53.
    • GRDADOLNIK, Jože, MOHAČEK-GROŠEV, Vlasta, BALDWIN, Robert Lesh, AVBELJ, Franc. Populations of the three major backbone conformations in 19 amino acid dipeptides. Proc. Natl. Acad. Sci. U. S. A., 2011, vol. 108, no. 5, str. 1794-1798.
    • GROBELNIK, Barbara, GRDADOLNIK, Jože. Calculation of the absorption spectrum from an ATR infrared experiment. Acta chim. slov., 2008, vol. 55, no. 4, str. 978-984.
    • GRDADOLNIK, Jože, GOLIČ GRDADOLNIK, Simona, AVBELJ, Franc. Determination of conformational preferences of dipeptides using vibrational spectroscopy. J. phys. chem., B Condens. mater. surf. interfaces biophys., 2008, vol. 112, no. 9, str. 2712-2718.
    • GRDADOLNIK, Jože. Infrared difference spectroscopy. Part I, Interpretation of the difference spectrum. Vibr. spectrosc., 2003, vol. 31, no. 2, str. 279-288.
    • GRDADOLNIK, Jože. ATR-FTIR spectroscopy: its advantages and limitations. Acta chim. slov., 2002, vol. 49, no. 3, str. 631-642.
    • GRDADOLNIK, Jože, MARÉCHAL, Yves. Bovine serum albumin observed by infrared spectrometry. I, Methodology, structural investigation, and water uptake. Biopolymers, 2001, vol. 62, no. 1, str. 40-53.

Assessment

The overall assessment is combined from seminar and oral exam (50/50). The first part is the assessment from the oral defense of a written seminary work. The second part of the assessment is oral exam from the themes lectured at lectures. (50/50)

Lecturer's references

Full professor of Physics at the University of Nova Gorica.

1. MIRTIČ, Andreja, MERZEL, Franci, GRDADOLNIK, Jože. The amide III vibrational circular dichroism band as a probe to detect conformational preferences of alanine dipeptide in water. Biopolymers, ISSN 0006-3525, Jul. 2014, vol. 101, iss. 7, str. 814-818, [COBISS.SI-ID 5482522 ].

2. GRDADOLNIK, Jože, MOHAČEK-GROŠEV, Vlasta, BALDWIN, Robert Lesh, AVBELJ, Franc. Populations of the three major backbone conformations in 19 amino acid dipeptides. Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 2011, vol. 108, no. 5, str. 1794-1798, [COBISS.SI-ID 4611098].

3. STARE, Jernej, PANEK, Jaroslaw J., ECKERT, Jürgen, GRDADOLNIK, Jože, MAVRI, Janez, HADŽI, Dušan. Proton dynamics in the strong chelate hydrogen bond of crystalline picolinic acid n-oxide. A new computational approach and infrared, Raman and INS study. The journal of physical chemistry. A, Molecules, spectroscopy, kinetics, environment, & general theory, ISSN 1089-5639, 2008, vol. 112, no. 7, str. 1576-1586. [COBISS.SI-ID 3876890].

4. GRDADOLNIK, Jože, GOLIČ GRDADOLNIK, Simona, AVBELJ, Franc. Determination of conformational preferences of dipeptides using vibrational spectroscopy. The journal of physical chemistry. B, Condensed matter, materials, surfaces, interfaces & biophysical, ISSN 1520-6106, 2008, vol. 112, no. 9, str. 2712-2718. [COBISS.SI-ID 3877146].

5. AVBELJ, Franc, GOLIČ GRDADOLNIK, Simona, GRDADOLNIK, Jože, BALDWIN, Robert Lesh. Intrinsic backbone preferences are fully present in blocked amino acids. Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 2006, vol. 103, no. 5, str. 1272-1277. [COBISS.SI-ID 3425306].

University course code: 3FIi03*

Year of study: 1

Lecturer:

ECTS: 6

Workload:

  • Lectures: 15 hours
  • Exercises: 15 hours
  • Seminar: 15 hours
  • Individual work: 135 hours

Course type: elective

Languages: english

Learning and teaching methods:
lectures, exercises on state of the software for the analysis of vibrational spectra , presentation and interpretation of project results to other students in open discussion under supervision of the lecturer