![]() The total time to complete all tasks is approximately three to four hours. Students were asked to complete a two-page worksheet that comprises of four sets of tasks. Student worksheet in Additional file 1 was developed and continually revised. The computer-delivered molecular model activity has been adopted in a first-year chemistry lab at Mahidol University since 2019. displaying animations, dipole-moment, spectra and surfaces (orbitals and densities). Visualize molecules in various representations (ball-and-stick or space-filling) as well as displaying bond length, bond angle and torsional angle. Read different types of files (xyz or z-matrix geometry, check point file, frequency calculation output).īuild and edit molecules by graphic user interface and optimize structures by built-in molecular mechanics force fields. We use only the following abilities of the programs. The programs are also available for Linux but the installation may not be trivial.Īs mentioned earlier, in this paper, we do not intend to introduce beginners to run any calculations or work with any macromolecules. Each program requires minimal disk space (< 50 MB) and, for most users, downloading and installing can take less than 5 min. They offer a range of features to run and analyze calculations. Both programs are light-weight and easy to install. Description of software and featuresĪvogadro and IQmol are open-source and cross-platform for both Mac and Windows, launched in 20 respectively. Due to the clear separation of laboratory and lecture in the curriculum, we do not intend to teach the underlying concepts but only provide tools and practices to support their learning. Instructions are designed so that students can easily follow even without prior knowledge in chemistry and students can also appreciate producing textbook-quality pictures. To use some additional visualization features of the software related to those discussed in general chemistry course without running a quantum chemical calculation (Tasks 2 and 3 below). To use the virtual tool in the same way that physical molecular models are used (Tasks 1 and 4 below) The aims of this four-hour session with the software are The class can be taken independently of the lecture class. The laboratory course is the first laboratory in chemistry for science students. To the best of our knowledge, our work is the first paper that explicitly describes educational uses of molecular graphics software for this audience level. Advanced features traditionally associated with using these programs are intentionally left out. The lesson was designed to maximize alignment to the content taught in general chemistry. ![]() This paper describes our experience in using two programs, Avogadro and IQmol, for a lesson in an introductory-level chemistry laboratory class. However, educational exercises of introductory-level chemistry are limited as these programs are regarded as specialized and used mainly for research. A number of papers have described the use of these software for upper-level undergraduate teaching. ![]() The issue here is therefore how to bring these dynamic and interactive visualization programs as scaffolding tools for student learning. Most molecular graphics programs allow users to construct, edit and visualize molecules in 3D, and hence, are viable alternatives to conventional teaching materials. With open-source licensing, the cost and availability of the software is no longer an issue. Until recently, these programs were intended for sophisticated users of quantum and molecular mechanics modelling and were licensed at high price. Molecular graphics software has been available in the market for many decades.
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