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# Line 68 | Line 68 | Notre Dame, Indiana 46556}
68   \begin{doublespace}
69  
70   \begin{abstract}
71 <
71 > We examine potential surface reconstructions of Pt and Au (557) under various CO coverages using molecular dynamics in order to find possible mechanisms and dynamics for the restructuring. The metal-CO interactions were parameterized as part of this work so that a large scale treatment of this system could be undertaken. The relative binding strengths of the metal-CO interactions were found to play a large role with regards to step edge stability and adatom diffusion. A small correlation between coverage and the size of the diffusion constant was also determined. These results appear sufficient to explain the reconstructions observed on the Pt systems and the lack of reconstructions on the Au systems.
72   \end{abstract}
73  
74   \newpage
# Line 100 | Line 100 | This work an effort to understand the mechanism and ti
100   reversible restructuring under exposure to moderate pressures of
101   carbon monoxide.\cite{Tao:2010}
102  
103 < This work an effort to understand the mechanism and timescale for
103 > This work is an attempt to understand the mechanism and timescale for
104   surface restructuring using molecular simulations.  Since the dynamics
105 < of the process is of particular interest, we utilize classical force
105 > of the process are of particular interest, we employ classical force
106   fields that represent a compromise between chemical accuracy and the
107 < computational efficiency necessary to observe the process of interest.
107 > computational efficiency necessary to simulate the process of interest.
108  
109 < Since restructuring occurs as a result of specific interactions of the
110 < catalyst with adsorbates, two metal systems exposed to carbon monoxide
111 < were examined in this work. The Pt(557) surface has already been shown
109 > Restructuring can occur as a result of specific interactions of the
110 > catalyst with adsorbates. In this work, two metal systems exposed
111 > to carbon monoxide were examined. The Pt(557) surface has already been shown
112   to reconstruct under certain conditions. The Au(557) surface, because
113   of a weaker interaction with CO, is less likely to undergo this kind
114   of reconstruction.  MORE HERE ON PT AND AU PREVIOUS WORK.
# Line 133 | Line 133 | Au-Au and Pt-Pt interactions, while modeling the CO us
133   Coulomb potential.  For this work, we have used classical molecular
134   dynamics with potential energy surfaces that are specifically tuned
135   for transition metals.  In particular, we used the EAM potential for
136 < Au-Au and Pt-Pt interactions, while modeling the CO using a rigid
136 > Au-Au and Pt-Pt interactions\cite{EAM}, while modeling the CO using a rigid
137   three-site model developed by Straub and Karplus for studying
138   photodissociation of CO from myoglobin.\cite{Straub} The Au-CO and
139   Pt-CO cross interactions were parameterized as part of this work.
# Line 164 | Line 164 | $\phi_{ij}(r_{ij})$ is an pairwise term that is meant
164   V_i =  F[ \bar{\rho}_i ]  + \sum_{j \neq i} \phi_{ij}(r_{ij})
165   \end{equation*}
166   where $F[ \bar{\rho}_i ]$ is an energy embedding functional, and
167 < $\phi_{ij}(r_{ij})$ is an pairwise term that is meant to represent the
168 < overlap of the two positively charged cores.  
167 > $\phi_{ij}(r_{ij})$ is a pairwise term that is meant to represent the
168 > repulsive overlap of the two positively charged cores.  
169  
170   % The {\it modified} embedded atom method (MEAM) adds angular terms to
171   % the electron density functions and an angular screening factor to the
# Line 176 | Line 176 | The EAM, Finnis-Sinclair, and the Quantum Sutton-Chen
176   % metals,\cite{Lee:2001qf} and also interfaces.\cite{Beurden:2002ys})
177   % MEAM presents significant additional computational costs, however.
178  
179 < The EAM, Finnis-Sinclair, and the Quantum Sutton-Chen potentials
179 > The EAM, Finnis-Sinclair, and the Quantum Sutton-Chen (QSC) potentials
180   have all been widely used by the materials simulation community for
181   simulations of bulk and nanoparticle
182   properties,\cite{Chui:2003fk,Wang:2005qy,Medasani:2007uq}
# Line 190 | Line 190 | Since previous explanations for the surface rearrangem
190   parameterized.\cite{Foiles86,PhysRevB.37.3924,Rifkin1992,mishin99:_inter,mishin01:cu,mishin02:b2nial,zope03:tial_ap,mishin05:phase_fe_ni}  
191  
192   \subsection{Carbon Monoxide model}
193 < Since previous explanations for the surface rearrangements center on
194 < the large linear quadrupole moment of carbon monoxide, the model
195 < chosen for this molecule exhibits this property in an efficient
196 < manner.  We used a model first proposed by Karplus and Straub to study
197 < the photodissociation of CO from myoglobin.\cite{Straub} The Straub and
198 < Karplus model is a rigid three site model which places a massless M
199 < site at the center of mass along the CO bond.  The geometry used along
200 < with the interaction parameters are reproduced in Table~1. The effective
193 > Previous explanations for the surface rearrangements center on
194 > the large linear quadrupole moment of carbon monoxide.  
195 > We used a model first proposed by Karplus and Straub to study
196 > the photodissociation of CO from myoglobin because it reproduces
197 > the quadrupole moment well.\cite{Straub} The Straub and
198 > Karplus model, treats CO as a rigid three site molecule which places a massless M
199 > site at the center of mass position along the CO bond.  The geometry used along
200 > with the interaction parameters are reproduced in Table~\ref{tab:CO}. The effective
201   dipole moment, calculated from the assigned charges, is still
202   small (0.35 D) while the linear quadrupole (-2.40 D~\AA) is close
203   to the experimental (-2.63 D~\AA)\cite{QuadrupoleCO} and quantum
# Line 218 | Line 218 | mechanical predictions (-2.46 D~\AA)\cite{QuadrupoleCO
218   \textbf{M} & 0.0 & -  &  -  &    1.6 \\
219   \hline
220   \end{tabular}
221 + \label{tab:CO}
222   \end{table}
223  
224   \subsection{Cross-Interactions between the metals and carbon monoxide}
# Line 230 | Line 231 | position on Pt(111). This resulting binding energies a
231   clean metal surfaces. Parameters reported by Korzeniewski {\it et
232    al.}\cite{Pons:1986} were a starting point for our fits, which were
233   modified to ensure that the Pt-CO interaction favored the atop binding
234 < position on Pt(111). This resulting binding energies are on the higher
235 < side of the experimentally-reported values. Following Korzeniewski
234 > position on Pt(111). These parameters are reproduced in Table~\ref{tab:co_parameters}
235 > This resulted in binding energies that are slightly higher
236 > than the experimentally-reported values as shown in Table~\ref{tab:co_energies}. Following Korzeniewski
237   {\it et al.},\cite{Pons:1986} the Pt-C interaction was fit to a deep
238   Lennard-Jones interaction to mimic strong, but short-ranged partial
239   binding between the Pt $d$ orbitals and the $\pi^*$ orbital on CO. The
240 < Pt-O interaction was parameterized to a Morse potential with a large
241 < range parameter ($r_o$).  In most cases, this contributes a weak
240 > Pt-O interaction was parameterized to a Morse potential at a larger
241 > minimum distance, ($r_o$).  This was chosen so that the C would be preferred
242 > over O as the binder to the surface. In most cases, this parameterization contributes a weak
243   repulsion which favors the atop site.  The resulting potential-energy
244   surface suitably recovers the calculated Pt-C separation length
245   (1.6~\AA)\cite{Beurden:2002ys} and affinity for the atop binding
# Line 245 | Line 248 | The Au-C and Au-O cross-interactions were fit using Le
248   %where did you actually get the functionals for citation?
249   %scf calculations, so initial relaxation was of the four layers, but two layers weren't kept fixed, I don't think
250   %same cutoff for slab and slab + CO ? seems low, although feibelmen had values around there...
251 < The Au-C and Au-O cross-interactions were fit using Lennard-Jones and
251 > The Au-C and Au-O cross-interactions were also fit using Lennard-Jones and
252   Morse potentials, respectively, to reproduce Au-CO binding energies.
253 <
254 < The fits were refined against gas-surface DFT calculations with a
253 > The limited experimental data for CO adsorption on Au lead us to refine our fits against DFT.
254 > Adsorption energies were obtained from gas-surface DFT calculations with a
255   periodic supercell plane-wave basis approach, as implemented in the
256   {\sc Quantum ESPRESSO} package.\cite{QE-2009} Electron cores are
257   described with the projector augmented-wave (PAW)
# Line 257 | Line 260 | Ionic relaxations were performed until the energy diff
260   computed with the PBE implementation of the generalized gradient
261   approximation (GGA) for gold, carbon, and oxygen that was constructed
262   by Rappe, Rabe, Kaxiras, and Joannopoulos.\cite{Perdew_GGA,RRKJ_PP}
263 < Ionic relaxations were performed until the energy difference between
261 < subsequent steps was less than $10^{-8}$ Ry.  In testing the CO-Au
262 < interaction, Au(111) supercells were constructed of four layers of 4
263 > In testing the Au-CO interaction, Au(111) supercells were constructed of four layers of 4
264   Au x 2 Au surface planes and separated from vertical images by six
265 < layers of vacuum space. The surface atoms were all allowed to relax.
266 < Supercell calculations were performed nonspin-polarized with a 4 x 4 x
267 < 4 Monkhorst-Pack {\bf k}-point sampling of the first Brillouin
265 > layers of vacuum space. The surface atoms were all allowed to relax
266 > before CO was added to the system. Electronic relaxations were
267 > performed until the energy difference between subsequent steps
268 > was less than $10^{-8}$ Ry.   Nonspin-polarized supercell calculations
269 > were performed with a 4~x~4~x~4 Monkhorst-Pack {\bf k}-point sampling of the first Brillouin
270   zone.\cite{Monkhorst:1976,PhysRevB.13.5188} The relaxed gold slab was
271   then used in numerous single point calculations with CO at various
272   heights (and angles relative to the surface) to allow fitting of the
273   empirical force field.
274  
275   %Hint at future work
276 < The parameters employed in this work are shown in Table 2 and the
277 < binding energies on the 111 surfaces are displayed in Table 3.  To
278 < speed up the computations, charge transfer and polarization are not
279 < being treated in this model, although these effects are likely to
280 < affect binding energies and binding site
281 < preferences.\cite{Deshlahra:2012}
276 > The parameters employed for the metal-CO cross-interactions in this work
277 > are shown in Table~\ref{co_parameters} and the binding energies on the
278 > (111) surfaces are displayed in Table~\ref{co_energies}.  Charge transfer
279 > and polarization are neglected in this model, although these effects are likely to
280 > affect binding energies and binding site preferences, and will be added in
281 > a future work.\cite{Deshlahra:2012,StreitzMintmire}
282  
283   %Table  of Parameters
284   %Pt Parameter Set 9
# Line 295 | Line 298 | preferences.\cite{Deshlahra:2012}
298  
299   \hline
300   \end{tabular}
301 + \label{tab:co_parameters}
302   \end{table}
303  
304   %Table of energies
# Line 312 | Line 316 | preferences.\cite{Deshlahra:2012}
316    \textbf{Au-CO} & -0.39 & -0.40 \bibpunct{}{}{,}{n}{}{,}  (Ref. \protect\cite{TPD_Gold}) \\
317    \hline
318   \end{tabular}
319 + \label{tab:co_energies}
320   \end{table}
321  
322   \subsection{Pt(557) and Au(557) metal interfaces}

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