Avogadro Program for Chemistry Education: To What Extent can Molecular Visualization and Three-dimensional Simulations Enhance Meaningful Chemistry Learning?

Baraa Rayan¹ and Anwar Rayan^{1, 2,}

¹Science Education Department, Al-Qasemi Academic College, Baka EL-Garbiah, Israel

²Institute of Applied Research- the Galilee Society, 20200 Shefa-'Amr, Israel;Head of Drug Discovery Informatics Lab, QRC - Qasemi Research Center, Al-Qasemi Academic College, Baka EL-Garbiah, Israel

Cite this paper:
Baraa Rayan and Anwar Rayan. Avogadro Program for Chemistry Education: To What Extent can Molecular Visualization and Three-dimensional Simulations Enhance Meaningful Chemistry Learning?. World Journal of Chemical Education. 2017; 5(4):136-141. doi: 10.12691/wjce-5-4-4

Abstract

In developing this study, we hypothesized that the integration of computerized techniques and modeling tools into traditional face-to-face instruction can produce a better hybrid model of teaching, capable of motivating students and improving their attitude toward science in general, and toward chemistry in particular. We tested how molecular visualizations and three-dimensional simulations affect students’ conceptual understanding of chemistry and their attitudes toward learning chemistry. During the academic year 2016-2017, we incorporated Avogadro software into teaching and tested how it affected students’ performance on chemistry exams in their courses. The difference in average scores between the two groups (8.2 points for the experimental group and 6.4 points for the control group) was significant. Student feedback following the initiative was positive and encouraging. Most students indicated that learning chemistry with Avogadro was extremely helpful, bringing the microscopic world of molecules closer to them, and they felt that they would like to see such software integrated into their chemistry studies from day one. Other parameters will be tested in continuation of this study, such as students' attitudes toward learning chemistry and their inquiry skills.

Keywords:
chemistry education molecular structure computer-based learning three-dimensional simulations meaningful chemistry learning Avogadro software

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References:

[1]	Chandrasegaran AL, Treagust DF, & Mocerino M. (2008). An evaluation of a teacher intervention to promote students’ ability to use multiple levels of representation when describing and explaining chemical reactions. Research in Science Education, 38(2), 237-248.
[2]	Dori YJ, & Hameiri M. (2003). Multidimensional analysis system for quantitative chemistry problems— symbol, macro, micro and process aspects. Journal of Research in Science Teaching, 40, 278-302.
[3]	Dori Y.J. and Kaberman Z. (2012). Assessing high school chemistry students' modeling sub-skills in a computerized molecular modeling learning environment. Instructional Science, 40, 69-91.
[4]	Pappalardo M, Rayan M, Abu-Lafi S, Leonardi M.E, Milardi D, et al. (2017). Homology-based modeling of rhodopsin-like family members in the inactive state: structural analysis and deduction of tips for modeling and optimization. Molecular Informatics. 2017 Apr 4.[Epub ahead of print].
[5]	Michaeli A, & Rayan A. (2016). Modeling ensample of loop conformations by Iterative Stochastic Elimination, Letters in Drug Design and Discovery. 13(7): 646-651.
[6]	Goldblum A, Glick M, & Rayan A. (1993). Extending Crystallographic Information with Semiempirical Quantum Mechanics and Molecular Mechanics: A Case of Aspartic Proteinases. J. Chem. Inform. Comp. Sci. 33(2): 270-274.
[7]	Barak M, & Hussein-Farraj R. (2012). Integrating model-based learning and animations for enhancing students' understanding of proteins structure and function. Research in Science Education, 43(2), 619-636.
[8]	Gilbert JK. (2005). Visualization: A metacognitive skill in science and science education. Visualization in Science Education, Models and Modeling in Science Education. 1: 9-27. Publisher: Springer Netherlands.
[9]	Barak M, & Dori YJ. (2011). Science education in primary schools: Is an animation worth a thousand pictures? Journal of Science Education and Technology, 20(5), 608-620.
[10]	AAAS. (2011). Vision and Change in undergraduate biology education. Retrieved from http://visionandchange.org/files/2011/03/Revised-Vision-and-Change-Final-Report.pdf.
[11]	Spitznagel, B., Pritchett, P.R., Messina, T.C., Goadrich, M., Rodriguez, J. (2016). An undergraduate laboratory activity on molecular dynamics simulations. Biochem Mol Biol Educ. doi: 10.1002/bmb.20939. [Epub ahead of print].
[12]	Hofstein A, & Mamlok-Naaman R. (2011). High-School Students’ Attitudes toward and Interest in Learning Chemistry. 2011 international year of chemistry. Educ. quím., publicado en línea el 19 de enero de 2011, Universidad Nacional Autónoma de México.
[13]	Mamlok-Naaman R. (2011). How can we motivate high school students to study science? Science Education International. 22:1, 5-17.
[14]	Raiyn J, & Rayan A. (2015). How Chemicals’ Drawing and Modeling Improve Chemistry Teaching in Colleges of Education. World Journal of Chemical Education 3, 1: 1-4.
[15]	Movahedzadeh F. (2011). Improving Students’ Attitude Toward Science Through Blended Learning. Science education and civic engagement 3:2, 13-19.
[16]	Hanwell MD, Curtis DE, Lonie DC, Vandermeersch T, Zurek E, et al. (2012). Avogadro: an advanced semantic chemical editor, visualization, and analysis platform. Journal of Chemoinformatics 4, 1-17.
[17]	Baugh EH, Lyskov S, Weitzner BD, & Gray JJ. 2011. Real-time pymol visualization for rosetta and pyrosetta. PLoS One, 6(8), e21931.
[18]	Moll A, Hildebrandt A, Lenhof HP & Kohlbacher O. (2005) Ballview: An object-oriented molecular visualization and modeling framework. J Comput Aided Mol Des, 19(11), 791-800.
[19]	Milner N, Ben-Zvi R, & Hofstein A. (1987). Variables that affect students enrollment in science courses. Research in Science and Technological Education, 5, 201-208.