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reaction clips

High-quality visualisation of chemical reactions

A joint project of the University of Applied Arts Vienna and the University of Vienna

Background

Teaching Organic Chemistry or Medicinal Chemistry requires a lot imagination by students in order to fully understand what actually happens during a chemical reaction. The usual ways of 2-dimensional depiction is fine for quickly capturing the reaction type and the nature of reactants and products. However, a better understanding of mechanistic aspects would definitely benefit from a good animated visualisation of the entire reaction process. For this purpose, various cartoon-like animations have been utilised in chemical education in the past, but these approaches usually represent (more or less coarse) approximations and abstractions of reality. In the present project, we aim at a novel way of high-quality visualisation of a selected set of chemical reactions in combination with a highly accurate description of these reactions by state-of-the-art quantum chemistry calculations. The results are available in different formats:
  • a) high-definition video clips for lecture-hall projection
  • b) interactive 3D Flash animations for incorporation in web pages and for download
  • Calculations

    All reaction paths were obtained by ab-initio quantum chemistry calculations, using the Gaussian 09 software package at the Schrödinger III cluster (University of Vienna) and at the Vienna Scientific Cluster.

    Example clips

    These video clips can be best viewed with a dedicated video player software like VLC.
    SN1 reaction (monomolecular nucleophilic substitution)
    SN2 reaction (bimolecular nucleophilic substitution)
    bromination of benzene (electrophilic aromatic substitution)
    nitration of benzene (electrophilic aromatic substitution)
    sp3 hybridisation of carbon (explains the formation of hybrid orbitals)
    addition of MeLi to acetone (carbanion adds to a carbonyl C)

    Example clips as flash videos (flv)

    SN1 reaction (monomolecular nucleophilic substitution)
    SN2 reaction (bimolecular nucleophilic substitution)
    bromination of benzene (electrophilic aromatic substitution)
    nitration of benzene (electrophilic aromatic substitution)
    sp3 hybridisation of carbon (explains the formation of hybrid orbitals)
    addition of MeLi to acetone (carbanion adds to a carbonyl C)

    Example clips (different video file formats)

    clip name video file format
    mpg HD mpg PAL mpg PC 3g2 mobile flv HD
    SN1 reaction          
    SN2 reaction          
    bromination of benzene          
    nitration of benzene          
    sp3 hybridisation of carbon          
    addition of MeLi to acetone          

    Example 3D animations

    bromination of benzene (electrophilic aromatic substitution)
    addition of MeLi to acetone (carbanion adds to a carbonyl)

    Auxiliary material

    For special didactic purposes, Flash animations are perfectly suited to complement the video clips, e.g. for depiction of resonance structures of pi-electron systems.
    resonance structures of aniline
    resonance structures of phenolate
    resonance structures of 4-nitrophenolate

    Project partners

    Visualisation (video, 3D animations):
    Angewandte University of Applied Arts Vienna
    Institute of Technical Chemistry
    Prof. Dr.  Alfred Vendl
    Ing. Stefan Fischer

    Quantum-chemical calculations:
    Universität Wien University of Vienna
    Institute of Theoretical Chemistry
    Prof. Dr. Peter Wolschann

    Didactic concept, 2D animations:
    Universität Wien University of Vienna
    Department of Drug and Natural Product Synthesis
    Prof. Dr. Norbert Haider
    Prof. Dr. Helmut Spreitzer
    Dr. Pavel Dallakian

    Sponsored by
    BM.W_F Bundesministerium für Wissenschaft und Forschung
    Republic of Austria