Date of Award:

5-2014

Document Type:

Dissertation

Degree Name:

Doctor of Philosophy (PhD)

Department:

Chemistry and Biochemistry

Committee Chair(s)

Steve Scheiner (Committee Chair), Tapas Kar (Committee Co-Chair)

Committee

Steve Scheiner

Committee

Tapas Kar

Committee

David Farrelly

Committee

Alexander I. Boldyrev

Committee

Bradley S. Davidson

Committee

T. C. Shen

Abstract

Molecular interactions play key role in the existence of biomolecules like proteins and nucleic acids, and various materials. Molecular interactions are weak forces that hold different molecules or different fragments of the same molecule together, and are often referred to as noncovalent interactions. Due to the complexity in biomolecules, these interactions are still poorly understood. This dissertation presents results from quantum mechanical simulations of various types of noncovalent interactions, which are extremely important for the structure and functions of biomolecules and materials.

A new sort of noncovalent interaction is identified. This new sort of interaction originates from a direct interaction between two electronegative atoms. This interaction is represented as BA···D, where A and D are electronegative atoms, and B is some substituent. In most cases, this new sort of interaction is found to be more stable than regular hydrogen bonds. These new interactions are found to have some potential to allow the development of materials with unusual physical properties.

This dissertation also explores the role of supposedly weaker CH hydrogen bonds on the configuration of peptide-peptide interactions, secondary structure of proteins, and mechanism of methyl transfer reaction in enzymes. Similarly, putative hydrogen bonding at the tips of functionalized carbon nanotubes is studied, which reveals the absence of OH and COOH groups together at the tips of carbon nanotubes.

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