Date of Award


Document Type


Degree Name

Doctor of Philosophy (PhD)

Legacy Department


Committee Chair/Advisor

Dr. Steven J. Stuart

Committee Member

Dr. Robert A. Latour

Committee Member

Dr. Brian Dominy

Committee Member

Dr. Jason McNeill


ABSTRACT Molecular Dynamics (MD) is an effective method to study diverse systems to gain atomistic level details from the trajectories of particles in the system. MD require a potential which describes the interaction of the particles within the system, which is then used to solve Newton's equation of motion to obtain the trajectories of the particles. For an accurate simulation of a system, an appropriate potential should be used for the MD simulations. The Adaptive Interactive Reactive Empirical Bond Order (AIREBO) potential is a promising potential for MD simulations of systems involving bond breakage or formation [1, 2]. The AIREBO potential is a Tersoff-style bond order potential which adds LJ and torsional interactions to REBO potential developed by Brenner et al [3, 4]. Currently, the AIREBO potential is well parameterized to study carbonaceous and hydrocarbon systems. In the first part of this study, the AIREBO potential is used in MD simulations to study the welding of single wall carbon nanotubes (SWCNTs) through Ar bombardment. SWCNTs have unique electronic properties which make them an appropriate candidate to use in nanoscale transistor and nanocomputer studies. An optimum conductivity through SWCNTs is required for these applications in electronic devices and it is achieved by the bonding arrangements of the carbon atoms in the junction area. This spatial bonding between SWCNTs can be obtained by various experimental methods such as electron beam radiation, fast atom bombardment and chemical vapor deposition. This study focuses on simulating Ar bombardment over cross junction of two SWCNTs placed on an imaginary Lennard-Jones surface perpendicular to each other. The cross junction area of SWCNTs was bombarded with Ar atoms of various kinetic energies in microcanical ensemble which is followed by annealing at various temperatures. The main goal of this study is to find optimum conditions to obtain the highest number of connections between the SWCNTs and the smallest number of sp2 C atoms whose coordination numbers are changed from sp2 to sp or sp3 during the bombardment and annealing cycle. Junction quality measured is defined as the ratio between the number or connections between SWCNTs and the number of sp2 C atoms whose coordination numbers are changed from sp2 to sp or sp3and it was used to assess the results of MD simulations. Since each connection requires 2 sp2 C atoms changing to sp3, the expected junction quality measure is 0.5. It has been found that SWCNTs give the highest junction quality measure for Ar bombardment with 100 eV impact energy and annealing temperature and time of 3000 K and 8 ps, respectively. In the second part of the present study, the AIREBO potential is parameterized to find the optimal empirical parameters to study hdyrofluorocarbon systems. The new reparameterized AIREBO potential is a promising candidate to study reactive hydroflorocarbon sytems such as fluorination of CNTs. These empirical parameters are electrostatic parameters to define the electrostatic properties of atoms, covalent parameters to define covalent interactions between each pair of atoms, many-body parameters to define the noncovalent interactions between atoms more than 3, LJ parameters to define van der Waals interactions between atoms, and torsional parameters to define the torsional interactions. The electrostatic parameters are fitted to bond polarizabilities of FF, HH and CC bonds and dipole moments of fluorinated methanes. For the covalent parameters, there are many properties used in the parameterization process. The properties for HH, FF and HF pairs are bond lengths, bond dissociation enthalpy, bond force constant, bond length at predetermined potential and the slope at that bond length. The bond length and bond dissociation enthalpies are obtained from MD simulation of H2, F2 and HF molecules at 298 K in canonical ensemble and the other 3 properties are calculated using the AIREBO potential. For CH and CF parameters, instead of bond dissociation enthalpies and force constants, bond atomization enthalpy and vibrational modes of CH4 and CF4 are used to assess the progress of parameterization and are obtained through MD simulation of CH4 and CF4. Covalent CC parameters are fitted to 19 properties. These are bond lengths and bond force constants of single, double and triple CC bond lengths in ethane, diamond, ethane, graphite and acetylene; atomization enthalpies of C2Hx (x=6,4,2) molecules, graphite and diamond; c11 and c¬12 elastic constants of diamond and graphite; CC bond length at predetermined potential and slope of CC potential at that bond length. The reparameterized AIREBO potential results in a reasonable fit to experimental properties. Finally, g(cosθkij), the contribution of k atom to the bond-order between atoms i and j through the angle between k, i and j atoms has been found using a new method which will replace complex sixth order polynomial and contains one parameter, λkij, and energies of various hydrofluorocarbons using the AIREBO potential are compared to their DFT energies in the fitting process. Pij(NT,NC) are the corrections to the effect of the atoms on atom i to the bond-order between atom i and j atoms and is a bicubic spline that depends on the number of C atoms and the number of constituent not including the atom in the bond. The values at the spline knots are fitted to the experimental formation enthalpies of a set of 56 hydrofluorocarbon molecules. Formation enthalpies are calculated using the energies obtained from MD simulations at 298 K in canonical ensemble and these formation enthalpies are compares to experimental values to assess the goodness of the values at the spline knots where these values are used to calculate parameters of bicubic spline. The fitting process of the values at spline knots produced an average absolute error of 99.53 kJ/mol which can will be improved in the next rounds at this step of parameterization.

Included in

Chemistry Commons



To view the content in your browser, please download Adobe Reader or, alternately,
you may Download the file to your hard drive.

NOTE: The latest versions of Adobe Reader do not support viewing PDF files within Firefox on Mac OS and if you are using a modern (Intel) Mac, there is no official plugin for viewing PDF files within the browser window.