Molecular Simulation of DNA Nucleotide-Carbon Nanotube Hybrids

  • Author / Creator
    Chehel Amirani, Morteza
  • Hybrids formed by biological entities and human-made nano-structures have been intensively studied in recent years due to their very interesting properties and applications. DNA-carbon nanotube (CNT) hybrid is one such material and the motivation of this PhD study. The interaction of DNA building blocks (nucleobases and nucleotides) with CNTs was investigated in this study using atomistic classical and quantum mechanical simulations. Depending on the size and complexity of the problem, a pure quantum mechanics (QM), a mixed quantum mechanics and molecular mechanics (QM:MM), or a classical molecular dynamics (MD) approach was employed. The interaction of DNA nucleobases with a CNT in vacuum was studied using QM with density functional theory (DFT). It was shown that the potential energy surface for DNA nucleobase-CNT system is relatively shallow and many local minima corresponding to different configurations can be found. A QM:MM model was developed in order to study the binding of DNA nucleotides with CNTs in aqueous solution. The optimized structure, binding energy, electrostatic potential, and charge transfer for the hybrids were evaluated. Our results indicated properties of DNA nucleotide-CNT hybrids strongly depend on the type of nucleotide and CNT. Finally, a classical MD simulation was performed in order to take dynamics into account. Our results showed that DNA nucleotides undergo considerable shift along the CNT axis, at a nearly constant separation distance from the CNT surface. Occasional detachment and reattachment of the nucleotides from the CNT were also observed for some systems. Comparing two ways of assigning the partial atomic charges (PAC): (1) PAC obtained from a quantum mechanical calculation for the same optimized DNA nucleotide-CNT hybrid, and (2) PAC obtained based on isolated molecules, the former gave rise to more stable hybrid with less occurrence of detachment and more tightly bound ions. This series of simulations, at different scales, not only allowed us to study the properties of the hybrids, but also provided useful information on how future simulations can be improved to enhance accuracy.

  • Subjects / Keywords
  • Graduation date
    Spring 2016
  • Type of Item
  • Degree
    Doctor of Philosophy
  • DOI
  • License
    This thesis is made available by the University of Alberta Libraries with permission of the copyright owner solely for non-commercial purposes. This thesis, or any portion thereof, may not otherwise be copied or reproduced without the written consent of the copyright owner, except to the extent permitted by Canadian copyright law.
  • Language
  • Institution
    University of Alberta
  • Degree level
  • Department
  • Supervisor / co-supervisor and their department(s)
  • Examining committee members and their departments
    • Wang, Jichang (Chemsitry, University of Windsor)
    • Ru, Chong-Qing (Mechanical Engineering)
    • Brown, Alex (Chemistry)
    • Moussa, Walied (Mechanical Engineering)
    • Tang, Tian (Mechanical Engineering)