Molecular Field Trips

Jan 02, 2010

When I look back at my school days in the seventies and early eighties I remember some great teachers, a lot of last minute swotting and some really inspiring events. There was a physics trip to Jodrell Bank to listen to far off pulsars. A geography field trip took us over the unique limestone pavement at Ingleton in the Yorkshire Dales and an English Lit trip took us to Stratford-upon-Avon to see Othello performed in Shakespeare's home town.


It isn't that easy to go on a Molecular field trip - the size factor of ten to the power of minus nine doesn't help. However it struck me that in addition to all the guided e-learning, simulating, and molecular modelling, Odyssey also provided a kind of Molecular field trip. It takes students on a fascinating and inspiring field trip into the molecular world that was simply not available a few years ago. Imagine demonstrating a real-time 3D chemical reaction in the classroom!

 

Well, here it is - without Odyssey's motion of course:

 

Chemistry Field trip

Molecules in Motion: The Basic Idea Behind Dynamic Simulations

Jun 01, 2009

Odyssey’s simulations are very different from the simulations you may have encountered in other science media products. The motion of molecules does not arise because a human designer used a software tool to create an animation. Instead, Odyssey uses the basic laws of nature in order to represent molecular matter. The motion of molecules is an outcome of applying these laws, very much like the forces of gravity determine how the planets in the solar system move. In short, there is no "movie" file anywhere in Odyssey.

When you watch a simulation of liquid water in Odyssey, the computer is calculating "time steps". (The program actually makes several steps between screen updates.) The steps are separated by approximately one picosecond of physical time — a very short time indeed! Typically, the computer calculates several thousand time steps during a simulation (up to hundreds of thousands of steps for some systems). Each frame also calculates:

 

  • Intermolecular attractive energy: an energy term that represents van der Waals forces (dispersion forces) between non-bonded atoms.
  • Intermolecular repulsive energy: a steeply repulsive energy term for steric interactions at short distance that makes a close "overlap" of non-bonded atoms very unlikely.
  • Coulomb energy (both inter- and intramolecular): energy term due to the assignment of "effective charges” to all the atoms of a molecule; at the intermolecular level, this energy represents charge-charge, charge-dipole, and dipole-dipole interactions

As you can see, there's a lot going on in each rendered frame. This explains why Odyssey provides such engaging scientifically sound molecular simulations.

Two Clicks Away

Jun 01, 2009

I’ve just completed mapping Odyssey Version 3 to the A-level Chemistry Course Specifications - Edexcel, AQA, OCR, Salters etc. This means you are only 2 clicks away from interactive tutorials and 3D molecular models relevant to your current topic. In Version 3 there are about 100 new interactive tutorials, so the syllabus coverage is now approaching 90%. It’s a great time to buy!

 

You can see the course mapping for your A-level Chemistry course here.