As a widely applied theory that has found success across many fields, density functional theory (DFT) is largely taught. Typically, the most effective way to convey DFT concepts is through illustrative examples that are currently lacking in available resources. In this work, we demonstrate total energy calculations for H[subscript 2] using…

The process of diffusion is intimately related to random molecular displacement and is central to many problems in chemistry. Here, we provide an intuitive derivation of the diffusion equation based on the analysis of the random trajectories of particles generated and plotted by simple MATLAB and Python scripts. The codes are very simple and…

The introduction of Computational Chemistry via "Molecular Modelling and Drug Design" course at undergraduate level has opened wide possibilities for students to expand their knowledge of quantum chemistry, organic reaction mechanisms, protein-ligand interactions, drug design, and probable "in vivo" behavior of drug candidates.…

The crystalline sponge method allows for direct and precise molecular structure determination of liquid and gaseous targets and thus has been recognized as a revolutionary breakthrough in crystallography. To expose undergraduates to this cutting-edge technique, we have developed a comprehensive laboratory experiment with reaction conditions and…

The rise of virtual and online education in recent years has led to the development and popularization of many online tools, notably three-dimensional (3D) models and augmented reality (AR), for visualizing various structures in chemical sciences. The majority of the developed tools focus on either small molecules or biological systems, as…

The application of chemistry concepts in biological settings plays an important role in the interdisciplinary field of drug discovery and development. This is true for molecular docking, where an understanding of intermolecular forces and noncovalent interactions is useful for rational drug design and development. Here we report the design and use…

Teaching chemistry and biology students about biologics design remains challenging despite its increasing importance in pharmaceutical development. Monoclonal antibodies, commonly called mAbs, are the most popular biologics. They have been developed into drugs to treat various diseases in the past decades. Multiple challenges exist for designing…

3D printers have facilitated a wealth of 3D printed molecular models illustrating key structural concepts for student learning. However, general adoption of 3D printed models in the organic chemistry classroom proceeds slowly as the majority of consumer-grade 3D (fused deposition modeling (FDM) and resin) printers are inherently monochromatic,…

We report a molecular modeling study for undergraduate students aimed at carrying out an analysis of small molecules using a systematic conformational search with VEGA ZZ, a freely available software program. Conformational analyses were performed using a systematic search based on variations of torsion angles. First, the conformations of n-butane…

Having a deeper understanding of molecules in their structural forms allows students to grasp biochemical and general chemical concepts in a more profound manner. Through the use of visualization software, we have shown that students gain confidence and insight into the chemical workings of molecular structure and can then utilize this knowledge…

This article reports a workshop from the 2021 IUBMB/ASBMB Teaching Science with Big Data conference held virtually in June 2021 where participants learned to explore and visualize large quantities of protein PBD data using Jupyter notebooks and the Python programming language. This activity instructs participants using Jupyter notebooks, Python…

The biology education literature includes compelling assertions that unfamiliar problems are especially useful for revealing students' true understanding of biology. However, there is only limited evidence that such novel problems have different cognitive requirements than more familiar problems. Here, we sought additional evidence by using…

While chemistry exists in three dimensions, it is presented in two. This down-conversion results in a significant loss in information and often necessitates multiple images/figures to convey the complexity, intricacy, and beauty of a given structure. Currently, three-dimensional models are built to allow students to interact with molecules.…

Understanding the relationship between protein structure and function can be challenging for students. Molecular visualization software aids students in this problem by allowing manipulation of structures from new and deeper perspectives. In this communication, an activity using iMolview Lite, structure visualization software for portable devices,…

Recently there is an increasing need for experiments that can be conducted remotely. In this sense, this paper presents three experiments about materials science and an X-ray diffraction (XRD) technique that can be taught and performed entirely remotely. The first experiment is about the calculation of lattice parameters, atomic radii, and…