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Permanent link (DOI): https://doi.org/10.7939/R35M62J3B

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Molecular Simulation of DNA Nucleotide-Carbon Nanotube Hybrids Open Access

Descriptions

Other title
Subject/Keyword
Multi-scale
ONIOM
Electrostatics
DFT
Binding energy
Hybrid
Molecular Dynamics
Carbon Nanotube
Charge transfer
DNA
Molecular simulation
CNT
Density functional theory
CNT separation
QM:MM
Type of item
Thesis
Degree grantor
University of Alberta
Author or creator
Chehel Amirani, Morteza
Supervisor and department
Tang, Tian (Mechanical Engineering)
Examining committee member and department
Tang, Tian (Mechanical Engineering)
Moussa, Walied (Mechanical Engineering)
Wang, Jichang (Chemsitry, University of Windsor)
Ru, Chong-Qing (Mechanical Engineering)
Brown, Alex (Chemistry)
Department
Department of Mechanical Engineering
Specialization

Date accepted
2015-12-16T13:43:31Z
Graduation date
2016-06
Degree
Doctor of Philosophy
Degree level
Doctoral
Abstract
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.
Language
English
DOI
doi:10.7939/R35M62J3B
Rights
This thesis is made available by the University of Alberta Libraries with permission of the copyright owner solely for the purpose of private, scholarly or scientific research. 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.
Citation for previous publication
Quantum mechanical treatment of binding energy between DNA nucleobases and carbon nanotube: A DFT analysis, M Chehel Amirani, T Tang, J Cuervo, Physica E: Low-dimensional Systems and nanostructures 54, 65-71, 2013.  http://www.sciencedirect.com/science/article/pii/S138694771300204XBinding
of nucleobases with graphene and carbon nanotube: a review of computational studies, M Chehel Amirani, T Tang, Journal of Biomolecular Structure and Dynamics 33 (7), 1567-1597, 2015.  http://www.tandfonline.com/doi/abs/10.1080/07391102.2014.954315A
QM: MM model for the interaction of DNA nucleotides with carbon nanotubes, M Chehel Amirani, T Tang, Physical Chemistry Chemical Physics 17 (11), 7564-7575, 2015.  http://pubs.rsc.org/en/Content/ArticleLanding/2015/CP/C4CP05222F#!divAbstractElectrostatics
of DNA nucleotide–carbon nanotube hybrids evaluated from QM: MM simulations, M Chehel Amirani, T Tang, Nanoscale 7 (46), 19586-19595, 2015.  http://pubs.rsc.org/en/Content/ArticleLanding/2015/NR/C5NR03665H#!divAbstract

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