Dynamic Science: Digital Chemistry

Outline

Digital chemistry, using computers to understand and solve chemical problems, is a rapidly developing area of modern chemistry.

Today we will introduce you to one aspect of digital chemistry, computational chemistry, where we use computers to understand chemical structure and reactivity.

We will use computer codes to solve the equations underpinning how electrons and nuclei interact within a molecule (ie run simulations). Then we use a graphical interface (gaussview) to interpret and understand the results.

By the end of this session you will have created a molecule of ammonia NH₃ in the computer, solved the Schrödinger equation to determine the most stable geometry of the molecule and generated your own animation of one of the real vibrations ammonia NH₃ undergoes, as shown to the right.

We are going to use 2 programs to do this. Gaussian is the code that runs a job (solves the equations), GaussView is the graphical interface that you interact with. When you click a button, Gaussview writes information into a file, which is then read and run by Gaussian.

The first thing to do is find the gaussview icon on the computer desktop and to click to start gaussview.

Then follow the instructions for each step below!

• creating a molecule
• running an optimisation
• looking at the output
• animating molecular vibrations
• atomic charges
• molecular orbitals

If you finish with ammonia try a small molecule of your choice!
NH₃ has been carefully chosen to make the process easy, in reality things can get complicated very quickly. Here are a few small very interesting molecules to select from:

• CH₄, methane is a problem molecule in terms of CO₂ production in the atmosphere, methane is produced by cows and so is a unique problem for NZ
• H₂O, water is ubiquitous but despite 100s of years of research, water is still not fully understood in the liquid or solid forms!
• [NO₃]¯, the nitrate anion is contained in fertiliser run-off and is negatively impacting the water quality of NZ streams and rivers
• [NH₄]⁺, the ammonium anion is the simplest cation that forms an ionic liquid, a fundamentally new type of liquid material researched in the Hunt group
• alternatively talk with Tricia to help you pick something accessible and interesting of your own choice

Please also give us some feedback! What was great? What could have been done better? Please do help us improve this dynamic science activity by filling this short online survey.