3DMolSym Interactive Molecular Visualization of Symmetry Elements and Operations Chemistry Classic Award Winner Michael Sigalas, Nickolas Charistos, Department.

3DMolSymInteractive Molecular Visualization of Symmetry Elements and OperationsChemistry Classic Award Winner

Michael Sigalas, Nickolas Charistos, Department of Chemistry, Aristotle University of Thessaloniki, Greece

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Michael P. SigalasNickolas D. CharistosLaboratory of Applied Quantum ChemistryDepartment of Chemistry Aristotle University of ThessalonikiGreece



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Our Background• Laboratory of Applied Quantum Chemistry

– Computational Chemistry / Molecular Visualization

• Molwave– Development of Educational Chemistry Software

• Molecular Visualization– Own software (Adobe Director)– Jmol

• Simulations

Enantiomerix3DMolecular VisualizationDirector

Exploring ProteinsMolecular VisualizationJmol

juniorLABSimulationDirector

3DMolSymMolecular VisualizationDirector



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Our Approach• Development of Educational Chemistry Software

– A multidisciplinary field

– Multidisciplinary collaborations: Problematic

– Focus on software development

– Embody principles from multiple disciplines

– Expand our research interestsSoftware

Development

Chemical Theory

EducationalPsychology

EducationalChemistrySoftware

ChemistryLearning

ComputationalChemistry

HCI



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The Team• Michael Sigalas

– Chemistry Professor

– Project Manager \ Software Designer

• Nickolas Charistos– Chemist, PhD

– Software Developer \ Webpage Developer \ Graphic Designer

• Postgraduate Students• Chemistry Educators

Department of Chemistry, Aristotle University of Thessaloniki, Greece



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Molecular Symmetry• Symmetry Operation

– An action that, if carried out on an object (in our case a molecule) leaves it in a configuration that is indistinguishable from the original configuration.

• Symmetry Element– An abstract geometrical entity (line, plane or point) which respect to which

one or more symmetry operations can be carried out.

• The symmetry of a molecule is described by the whole set of symmetry operations that can be applied to it and hence by the whole set of symmetry elements that it possesses.

• Molecules are then classified to point groups on the basis of type and number of the symmetry elements they possess.

• The point group of a molecule determines in great extend its physicochemical behavior.



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Symmetry Elements• Axis of Rotation, Cn

– an n-fold rotation, the molecule is rotated by an angle 2π/n around a symmetry axis. If a molecule has many rotational axes, the axis with the largest n is called the principal axis.



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Symmetry Elements• Plane of Reflection, σ

– the molecule is reflected in respect to a plane. Planes including the principal axis are termed vertical planes, σv, or diagonal axes, σd, and planes perpendicular to the principal axis are called horizontal planes, σh.



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Symmetry Elements• Center of Inversion, i

– All atoms are projected through the center of symmetry.



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Symmetry Elements• Improper Rotation, Sn

– a composite operation of an n-fold rotation followed by a reflection in a plane perpendicular to this axis.



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Difficulties in Learning• Cognitive Tasks

1. Form a 3D mental image of the molecular structure

2. Imagine a possible symmetry element of the molecular structure

3. Perform the corresponding symmetry operation to the 3D image mentally

4. Check if the final 3D image is identical to the initial 3D image

• These tasks challenge students to create dynamic 3D mental models of the corresponding molecular concepts by viewing 2D symbolic representations.

• Traditional instructional media and 2D symbolic representations do not provide adequate surface features to help students visualize the dynamic nature of these concepts.



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Difficulties in Teaching• Textbooks can provide only a limited number of examples.• Only a few cases can be depicted by 2D symbolic representations• Classical media do not give the opportunity to practice and actively

explore these dynamic concepts.



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3DMolSym: Functionality• Searchable database of molecules• 3D molecular visualization• Free manipulation of models• Visualization of symmetry elements• Application of symmetry operations



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3DMolSym:Design Characteristics• Multiple representations of molecules.• Promote transformation between 2D and

3D.• Present dynamic visualizations and

animations of the corresponding chemical concepts.

• Examples that cover all characteristic cases.

• Open-ended learning environment.• Extensive practice and active exploration.



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Application in Education• Presentation tool

– to promote deeper understanding during instruction, as it provides novel visualizations that can complement the verbal representations of the tutor to exploit the dual processing capabilities of learners’ cognitive system.

• Self-pace tool– in conjunction with classical textbooks,

where the learners can actively explore the represented molecular concepts, be engaged in extensive practice with these concepts and have experiences that help them create their own knowledge



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3DMolSym: Development• Adobe Director

– Object Oriented Programming

– 3D graphics programming

– 2D graphics programming

– Database

• Text files

• Property lists



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Lets have a Look!

3DMolSym Interactive Molecular Visualization of Symmetry Elements and Operations Chemistry Classic Award Winner Michael Sigalas, Nickolas Charistos, Department.

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