The "Yet Another extended Hu¨ckel Molecular Orbital Package" (YAeHMOP) has been merged with the Avogadro open-source molecular editor and visualizer. It is now possible to perform YAeHMOP calculations directly from the Avogadro graphical user interface for materials that are periodic in one, two, or three dimensions, and to visualize…

A bioinformatics laboratory experiment was designed to help undergraduate students learn RNA structure and function in biochemistry courses. In this laboratory experiment, students used 5S rRNAs as material to predict secondary structure and visualize three-dimensional (3D) structure. Students first downloaded molecular information from the 5S…

Students undertaking courses in the field of chemistry need to integrate their spatial skills and conceptual knowledge. However, model perception along with the understanding of spatial processes and spatial structures of molecules has been a cause of difficulty for students as conventional teaching methods cannot fully aid student comprehension.…

Hands-on exercises are designed for undergraduate physical chemistry students to derive two-dimensional quantum chemistry from scratch for the H atom and H[subscript 2] molecule, both in the ground state and excited states. By reducing the mathematical complexity of the traditional quantum chemistry teaching, these exercises can be completed…

Molecular visualizations have been widely endorsed by many chemical educators as an efficient way to convey the dynamic and atomic-level details of chemistry events. Research indicates that students who use molecular visualizations are able to incorporate most of the intended features of the animations into their explanations. However, studies…

A series of interactive, instructional units have been developed that integrate computational molecular modelling and visualization to teach fundamental chemistry concepts and the relationship between the molecular and macro-scales. The units span the scale from atoms, small molecules to macromolecular systems, and introduce many of the concepts…

Within high school chemistry the topic of acids, bases, and pH is particularly challenging because robust understanding of the topic depends heavily on the student possessing deep concepts of atoms, molecules, ions, and chemical reactions. Since knowledge is acquired and stored in a dynamic structure, it was investigated in this study how…

The Water and Molecular Networks (WAMNet) Project uses graduate student written Reduced Instruction Set Computing (RISC) computer simulations of the molecular structure of water to assist high school students learn about the nature of water. This study examined: (1) preconceptions concerning the molecular structure of water common among high…

This study reports the efforts of the Water and Molecular Networks Project (WAMNet), a program in which high school chemistry students use computer simulations developed at Boston University (Massachusetts) to model the three-dimensional structure of molecules and the hydrogen bond network that holds water molecules together. This case study…