Dancing with molecules!

This past Tuesday, I went to the labs of Claudio Rossi, Agnese Magnani, Sylvia Martini, and Steven Loiselle with Helen and Sanet. While Helen focused on Dr. Rossi's work with carbon tagging and mathematical modeling in her blog, I wanted to share the work that Steven talked about. His research focuses on how environmental changes, such as global warming, affect the biogeochemical cycles in the African Great Lakes. Steven's lab group does most of its research not at San Miniato, but around the world. They specifically use what they call Environmental Spectroscopy, which is like the spectroscopy we, as chemistry students, have learned about over the last few years (and the same spectroscopy mentioned in this blog) but it is applied to a larger scale instead of a molecular scale; i.e. instead of a small light bulb being used as the light source, the sun is their light source.

Every body of water has its own complex dynamics that are affected by the location, climate, organisms living within the water, organisms that dine on the water, organic molecules in the water, the environment, etc. So, when one of these many contributing factors is even slightly altered, the entire dynamic of the water's ecosystem can also change. The amount of light that reaches the water surface and is absorbed or reflected is called the “underwater light field.” This light field fuels organic growth and is one of the main reasons why a body of water has certain characteristics, specifically color and opacity. As a body of water develops, the living things in and around it also develop according to the water composition.

Here's an example:

The Setting: A quiet lake community filled with environmentally-friendly families who never pollute.

The Water Source: A murky brown lake, teeming with life and brown algae, all due to the natural decomposition of carbon-containing molecules. This lake survives with little UV radiation.

The Plot: A big chemical plant is built nearby the lake during an industrial boom. Pollution fills the air. Acid rain develops.

The Result: The brown algae can't survive the increase in acidity! The brown algae perishes! The lake becomes clearer... More UV radiation reaches the depths of the lake, and the ecosystem suffers....

The End.

At the end of our lab adventure, we joined Sylvia Martini to learn how the researchers study both simple and complex molecules using MacroModel. MacroModel is a computer program with which you can create organic or inorganic molecules, manipulate them, stretch them out until their bonds should break, crunch them together like a tiny wad of paper that you could pelt at a friend's head during their Chem 260 class, and so on. If we weren't just playing around with the program and wanted to find out real information about a certain compound, the program helps figure out its most stable conformation, the lowest energy, and the temperature a lab would have to use in order to actually physically manipulate it. Sylvia told us that sometimes the researchers will just play around with the program (not often, but it made us feel like we weren't such dorks for making up a crazy molecule and turning it in constant circles while laughing for 5 minutes...) and they call it “dancing” with the molecules!