The work presented here can be divided into two parts: 1) an experimental and analysis section dealing with the investigation of small molecules such as methyl bromide, carbon dioxide, diatomic nitrogen, methane and methane?s photochemical derivative methyl radical adsorbed onto the Pt(111) surface, and 2) A detailed explanation of the current STM and chamber, with included designs and detailed instructions for operation and maintenance of both the STM and chamber. The investigations of the methyl bromide molecule show interesting dipole-dipole interactions on the Pt(111) surface. With a (6 x 3) lattice being described as the full monolayer that was created by overdosing and annealing to 104 K. The (6 x 3) lattice is shown to occupy top sites and three fold hollow sites on the Pt(111) surface giving rise to a very sharp and symmetrically split ν2 RAIRS mode, and the absence of the ν5 mode in RAIRS is indicative that the molecules are all aligned with their C-Br bond parallel to the surface normal. Additional sub-monolayer structures were observed that had components that were not aligned with the surface normal. The submonolayer lattices ranging from a structured 0.12 ML to a random coverages estimated at 0.20 ML, to a …

Closing report for project DOE-FG02-03ER15436. The project studied obligate autotrophy in the ammonia oxidizing bacterium Nitrosomonas europaea. Nitrosomonas europaea can obtain all of its energy and reductant for growth from the oxidation of ammonia to nitrite and is, therefore, classified as a chemolithotroph. This bacterium is also an autotroph, which can derive all cellular carbon from carbon dioxide. N. europaea seems incapable of growth with other carbon or energy sources. This restricted capability is surprising given that ammonia is a poor energy source. The main goal of the project was to examine the basis of autotrophy in N. europaea or, thought of another way, to determine the barriers to heterotrophy. The approach was enabled by the N. europaea genome sequence, stimulating new ways of thinking about this physiological paradox—an insistence on a single, albeit poor, energy source. Objective 1 was to examine the expression and regulation of the genes coding for alpha-ketoglutarate dehydrogenase, determine if the enzyme’s activity is present, and determine whether alteration of the expression levels influences autotrophic growth. Although Nitrosomonas europaea lacks measurable alpha-ketoglutarate dehydrogenase activity, the genome sequence revealed the presence of the genes encoding the enzyme. A knockout mutation was created in the sucA gene …