From Angstroms to Microns: Studies of Interfaces and Macromolecules with Geochemical Implications Using Computational and Nonlinear Optical Tools

Open Access
Author:
Campen, Richard Kramer
Graduate Program:
Geosciences
Degree:
Doctor of Philosophy
Document Type:
Dissertation
Date of Defense:
May 29, 2007
Committee Members:
  • James David Kubicki, Committee Chair
  • Eric Borguet, Committee Member
  • William Blaine White, Committee Member
  • Janna Kay Maranas, Committee Member
  • Christopher Howard House, Committee Member
Keywords:
  • carbohydrate
  • colloid chemistry
  • second harmonic generation
  • density functional theory
Abstract:
Quantitatively describing biogeochemical cycles or groundwater contaminant mobility and fate is challenging. Much of the challenge lies in the fact that such descriptions must be multiscale. For example, the fate of nitrogen added to agricultural soils depends on the atomic level interaction of the particular nitrogen species with soil components,the micron to kilometer scale dynamics of mineral and organic colloids in the subsurface,the local abundance and activity of particular microbial populations, the geological characteristics of the subsurface and weather. My interest in this dissertation is the lower half of this continuum: describing how to move from the atomic to the micron scale in environmentally relevant chemistry. In some instances this is straightforward, the specific heat of water can be rationalized from the properties of small clusters of water molecules, in other cases it is less so, the details of how atomic scale interactions combine to produce micron scale structures are nonlinear. This nonlinearity in moving across spatial scales is often found in environmental chemistry in two areas: the solid/water interface and the chemistry of macromolecules. Sugars of varying lengths are macromolecules of particular interest as they are ubiquitous and both have relatively long lifetimes and a defined chemical structure(to ease subsequent analysis). In this dissertation I develop tools to aid in the characterization of both the solid particle/water interface and the calculation of sugar properties: I apply second harmonic generation spectroscopy to characterize adsorption on chemically heterogeneous colloid particles and the surface potential of the mineral colloid/water interface and investigate the appropriate level of electronic structure theory for the calculation of sugar properties, test the application of several atomistic materials force fields to sugars and apply replica exchange molecular dynamics to investigate hydrogen bonding in disaccharides in vacuum. Taken together this work lays the foundation for full experimental and computational characterization of the mineral/water,cell/water and cell/mineral interfaces: the groundwork for quantitative description of atomic through micron scale phenomena in the environment.