Skip to main content
Open Access Publications from the University of California

UC Berkeley

UC Berkeley Electronic Theses and Dissertations bannerUC Berkeley

X-ray Absorption Spectroscopy of Biologically Relevant Systems


The relationship of biologically relevant molecules to their aqueous environment remains an active area of current research. In this dissertation, I present research biologically relevant molecules in an aqueous environment using X-ray spectroscopy and accompanying calculations.

Chapter 1 is a more thorough introduction to the topic of near edge X-ray absorption fine structure (NEXAFS) spectroscopy with stress on the experimental set up used, and computational methods. Additionally, in Chapter 1 there is a more detailed outline on the topics in subsequent chapters.

Chapters 2 and 3 detail an examination of the model system of carboxylate (CH3COO-) with a variety of metals. These studies were to examine the preferential ion pairing of different cations by NEXAFS. In chapter 2, I investigate the interactions of carboxylate with the monovalent cations lithium, sodium, and potassium; chapter 3, is an examination of the strength of interactions of carboxylate with the following divalent cations: magnesium, calcium, strontium, copper, manganese, and zinc.

During the course of my graduate work, the need for improved computational results became apparent. The development of the current technique employed within my research group is detailed within Chapter 4 using prototypical gas phase molecules as example systems.

In chapter 5, I compare both experimental and computational results of a monopeptide, alanine, compared to one of its synthetic analogues, a monopeptoid, sarcosine. These results compare the spectral importance of hydration versus conformation, in addition to conclusions concerning the spectral impact of microhydration versus bulk hydration.

I present preliminary results for other biological molecules in Chapter 6. The molecules studied are the amino acids arginine and valine, and the RNA nucleobases uracil and cytosine, and their respective nucleosides, uridine and cytidine. The chapter includes both preliminary experimental and theoretical spectra.

In Chapter 7, I look to the future with a brief discussion of improvements and advice to future coworkers.

Main Content
For improved accessibility of PDF content, download the file to your device.
Current View