Abstract:

The use and construction of 3D visualizations, both traditional and computer-generated, plays an important role in students' development of mental models about the particulate nature of matter. Existing 3D software tools for chemistry education are generally underutilized, in part due to accessibility, functionality, or interface issues.

3DChemMol was developed as a new, freely available, web-based tool for viewing, editing, and analysing 3D models of small molecules. The interface uses JSmol as the basis for model display. It consists of new menus with several toolbars (modules) corresponding to different functionalities, and includes four help modes. Models can be loaded from the PubChem database by name or structural features. A list of 350 compounds found in essential oils is also included. Models can be displayed in a variety of standard representations and their view can be manipulated, with the ability to display multiple models simultaneously. The editing module allows the construction of new models or the editing of existing models. Structural properties of molecules can be investigated through activities such as measuring distances/angles between atoms and bonds, and constructing conformations and isomers. In addition, model symmetry can be calculated and displayed, and models can be automatically compared for isomerism. The electronegativity of models can be investigated by calculating and displaying partial atomic charges and the electrostatic potential on the molecular surface. The created visualizations can be saved as images or in interactive form. Other interface activities include interactive exercises to test student knowledge on selected topics.

The editing module of 3DChemMol was evaluated in a study of 54 university students who performed three molecular construction and editing tasks, and completed a self-report questionnaire after each task, to measure task completion, individual difficulties, and use of help. Completion rates were satisfactory and correlated with reported technical, interface, and spatial difficulties. Of the four help modes, video tutorials and hovering over toolbars with the mouse were the most frequently used. The undo function also proved essential, as it was used by the majority of students.

3DChemMol is intended for all levels of chemistry education. Its modular structure allows for both basic (e.g., model display) and more advanced applications (editing, property display, activities). It is aimed at both teachers and students and can be used in a variety of ways to support the pedagogical process, including direct instruction and self-study.

Keywords:

Learning with technology, web-based interface, 3D chemistry software, molecular modeling, representational competence.