THEORETICAL INVESTIGATIONS OF PI-PI AND SULFUR-PI INTERACTIONS AND THEIR ROLES IN BIOMOLECLUAR SYSTEMS
The study of noncovalent interactions between aromatic rings and various functional groups is a very popular topic in current computational chemistry. The research presented in this thesis takes steps to bridge the gap between theoretical prototypes and real-world systems.
The non-additive contributions to the interaction energy in stacked aromatic systems are measured by expanding the prototype benzene dimer into trimeric and tetrameric systems. We show that the three- and four-body interaction terms generally do not contribute significantly to the overall interaction energy, and that the two-body terms are essentially the same as in the isolated dimer.
The sulfur-pi interaction is then studied by using the hydrogen sufide-benzene dimer as a prototype system for theoretical predictions. We obtain higly-accurate potential energy curves, as well as an interaction energy extrapolated to the complete basis set limit. Energy decomposition analysis using symmetry-adapted perturbation theory shows that the sulfur-pi interaction is primarily electrostatic in nature.
These theoretical results are then compared to an analysis of real sulfur-pi contacts found by searching protein structures in the Brookhaven Protein DataBank. We find that the most frequently seen configuration does not correspond to the theoretically predicted equilibrium for sydrogen sulfide-benzene, but instead to a configuration that suggests an alkyl-pi interaction involving the carbon adjacent to the sulfur atom. We believe our findings indicate that environmental effects within proteins are altering the energetics of the sulfur-pi interaction so that other functional groups are preferred for interacting with the aromatic ring.
Advisor:Bredas, Jean-Luc; Sherrill, C. David; Hernandez, Rigoberto
School:Georgia Institute of Technology
School Location:USA - Georgia
Source Type:Master's Thesis
Keywords:chemistry and biochemistry
Date of Publication:11/28/2005