Water, the fundamental constituent of life, has been found
to have a critical role at both organic and inorganic
surfaces. The properties of water near surfaces, is known to be
different from water far away from the interface. This dissertation
explores the degree to which inorganic materials such as amorphous
silica (glass) and biomolecular surfaces change the properties of water. Of particular interest is the interplay between biological molecules - proteins and nucleic acids - and their aqueous environment, and how this determines biological function.
The mobility of water near protein surfaces has been of considerable
recent interest. There have been many reports in the literature
postulating that interfacial water is incapable of undergoing rapid rotational motions due to strong electrostatic forces from the protein surface. This has led to confusing and
conflicting interpretations on the molecular origin of the slow
features observed in certain experiments that probe protein
surfaces. Our theoretical studies resolve the conflicts and show that
the slow dynamics observed, originates from the protein and water
jostling in a concerted fashion. Our studies support a change in the
paradigm for the function of proteins to include both the protein and
the surrounding water as active participants in biological function.
For 80 years, scientists have employed models in which ions and water near the silica surface form a stagnant layer called the Stern layer. To account for all experimental features, these models invoke puzzling properties such as the transport of ions through immobile water. In this dissertation, we develop a realistic theoretical description of the water-amorphous
silica interface. We have successfully constructed and validated a model for the water-amorphous silica interface and have begun to examine the fate of biomolecules near this important interface. Our simulations challenge the classical textbook Stern layer model. Both ions and water exhibit a substantial degree of mobility, yet the phenomena the Stern layer was originally invoked to explain, are reproduced by our calculations.
Theoretical studies for the repair of DNA bases damaged by sunlight
demonstrate that fast water motions are critical in ensuring the
rapid repair of the bases. We have constructed a simple model
using our ground state calculations that provides
new insights into the mechanisms of efficient DNA repair
that might be deployed in the active site of the DNA repair
protein. The splitting energetics during DNA repair is
shown to modulate the charge recombination process and can
significantly affect the quantum repair yields.