Intermolecular Forces in the Dynamic Molecule
We used Interactive Physics to explore the consequences of inter-molecular forces in aggregates.
While Charged Strings does all of the calculations and presents a new protein shape, students can use Interactive Physics to see how the components of a molecular string interact with each other and with water, and see the process of formation. This commercially available simulation package runs dynamic simulations based on first principles. The software allows the user to define shapes and to interconnect these shapes with rods, springs, and other constraints. Then the shapes can be given initial positions and velocities and the resulting motion simulated. The software supports electrostatic forces between charged particles.
We built model water molecules from two small positively charged "hydrogen" atoms colored red and a negatively charged "oxygen" atom colored blue. The hydrogen atoms were connected by a massless rod that could pivot around the center of the oxygen. A spring between the hydrogen atoms allowed the hydrogen atoms to vibrate around their rest position.
The figure illustrates a polarized five-protein molecule surrounded by water. When this simulation is run without water, the protein folds into a tight U-shape and oppositely charged tails touch. With water present, the more favorable final state has water between the protein tails, as shown.
This software was also used to permit student to explore the hydration of ions and the resulting solubility of ions as well as exploring the interactions of two or more proteins. Using Interactive Physics, students could actually try to build protein-like machines to take certain shapes or accomplish certain functions.
Build charged letters using Interactive Physics.
