The main focus of this experiment is to determine how amine compounds adsorb to clay surfaces, giving insight into possible methods of removal of these harmful compounds. The clay surfaces in question are large flat sheets that consist of silicon, aluminum and oxygen. The aluminum in the clay rings is scattered randomly in the system, as silicon is the primary element in the sheet. In the natural world, the sheets are nearly endless on the molecular level, but our system consists of one, two or three ring sheets to save on computing time. Amine pollutants adsorb to the clay sheet by means of hydrogen bonding, with an amine hydrogen bonding to the oxygen of the clay. The addition of certain organic compounds may have a desirable effect on the system by creating a stronger attraction to the amine than to the clay sheet. This is one of several possible methods of cleaning up the problems caused by fertilizer runoff and other forms of pollution.

Certain calculations done at the semi-empirical level and with density functional theory will show where these pollutants bond to the clay surface, what the lengths of these bonds are, and how tightly they are held. The semi-empirical calculations take into account thermodynamic and spectroscopic data to find an optimal geometry for the system. In other words, the calculation finds the absolute lowest energy for the system, which is what will be represented in the real world. In the semi-empirical method, only electrons in the valence shell are considered during the calculation. Density functional theory is similar to the semi-empirical method in that thermodynamic and spectroscopic data are analyzed to find an optimum geometry, but density functional theory takes the calculation a step further by incorporating more highly specialized data into the process.

Methylamine adsorbed to a clay surface. (Equilibrated geometry from a semi-empirical calculation)

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