Date of Award




Document Type

Master's Thesis

Degree Name

Master of Science (MS)


Department of Chemistry

Content Description

1 online resource (ii, 43 pages) : color illustrations.

Dissertation/Thesis Chair

Alan Chen

Committee Members

Jia Sheng


chemistry, computational chemistry, DNA, opioid receptor, protein ligand interactions, RNA, Ligands (Biochemistry), Receptor-ligand complexes, Computational biology

Subject Categories

Chemistry | Computational Chemistry


Computational methods can be used for a wide range of applications, especially regarding DNA and RNA. Interactions such as sugar torsions, receptor-ligand interactions, ligand docking/drug docking, receptor modeling, and drug design are excellent candidates for computational analysis and in silico experiments. The use of molecular dynamics software (GROMACS) coupled with molecular design software (MOE) produce insights that may have been otherwise difficult to assess. All these problems are academic in nature but have practical uses outside of academia. Understanding alternate linkages can lead to antibiotic assays to address potential superbug epidemics. Modeling DNA superstructures can provide insight into how large proteins may co-crystallize with said DNA that would otherwise not crystallize by themselves. Lastly, designing aptamers and ligands can create new avenues of detection or treatment, such as the pesticide carbofuran, or create new ligands for receptors of interest such as the Mu-Opioid Receptor. This thesis explores the challenges in molecular design through the use of software.