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# Line 1 | Line 1
1   \documentclass[11pt]{article}
2   \usepackage{amsmath}
3   \usepackage{amssymb}
4 + \usepackage{times}
5 + \usepackage{mathptm}
6   \usepackage{setspace}
7   \usepackage{endfloat}
8   \usepackage{caption}
# Line 10 | Line 12
12   %\usepackage{booktabs}
13   %\usepackage{bibentry}
14   %\usepackage{mathrsfs}
13 %\usepackage[ref]{overcite}
15   \usepackage[square, comma, sort&compress]{natbib}
16   \usepackage{url}
17   \pagestyle{plain} \pagenumbering{arabic} \oddsidemargin 0.0cm
# Line 18 | Line 19
19   9.0in \textwidth 6.5in \brokenpenalty=10000
20  
21   % double space list of tables and figures
22 < \AtBeginDelayedFloats{\renewcommand{\baselinestretch}{1.66}}
22 > %\AtBeginDelayedFloats{\renewcomand{\baselinestretch}{1.66}}
23   \setlength{\abovecaptionskip}{20 pt}
24   \setlength{\belowcaptionskip}{30 pt}
25  
26 < %\renewcommand\citemid{\ } % no comma in optional reference note
26 < \bibpunct{[}{]}{,}{n}{}{;}
26 > \bibpunct{}{}{,}{s}{}{;}
27   \bibliographystyle{achemso}
28  
29   \begin{document}
# Line 48 | Line 48
48   %%
49  
50   %Title
51 < \title{Investigation of the Pt and Au 557 Surface Reconstructions
52 <  under a CO Atmosphere}
53 < \author{Joseph R. Michalka, Patrick W. MacIntyre and J. Daniel
51 > \title{Molecular Dynamics simulations of the surface reconstructions
52 >  of Pt(557) and Au(557) under exposure to CO}
53 >
54 > \author{Joseph R. Michalka, Patrick W. McIntyre and J. Daniel
55   Gezelter\footnote{Corresponding author. \ Electronic mail: gezelter@nd.edu} \\
56   Department of Chemistry and Biochemistry,\\
57   University of Notre Dame\\
58   Notre Dame, Indiana 46556}
59 +
60   %Date
61 < \date{Dec 15,  2012}
61 > \date{Dec 15, 2012}
62 >
63   %authors
64  
65   % make the title
# Line 65 | 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 79 | Line 82 | Industrial catalysts usually consist of small particle
82   %       Sub: Also, easier to observe what is going on and provide reasons and explanations
83   %
84  
85 < Industrial catalysts usually consist of small particles exposing
86 < different atomic terminations that exhibit a high concentration of
87 < step, kink sites, and vacancies at the edges of the facets.  These
85 < sites are thought to be the locations of catalytic
85 > Industrial catalysts usually consist of small particles that exhibit a
86 > high concentration of steps, kink sites, and vacancies at the edges of
87 > the facets.  These sites are thought to be the locations of catalytic
88   activity.\cite{ISI:000083038000001,ISI:000083924800001} There is now
89 < significant evidence to demonstrate that solid surfaces are often
90 < structurally, compositionally, and chemically {\it modified} by
91 < reactants under operating conditions.\cite{Tao2008,Tao:2010,Tao2011}
92 < The coupling between surface oxidation state and catalytic activity
93 < for CO oxidation on Pt, for instance, is widely
94 < documented.\cite{Ertl08,Hendriksen:2002} Despite the well-documented
95 < role of these effects on reactivity, the ability to capture or predict
96 < them in atomistic models is currently somewhat limited.  While these
97 < effects are perhaps unsurprising on the highly disperse, multi-faceted
98 < nanoscale particles that characterize industrial catalysts, they are
99 < manifest even on ordered, well-defined surfaces. The Pt(557) surface,
100 < for example, exhibits substantial and reversible restructuring under
101 < exposure to moderate pressures of carbon monoxide.\cite{Tao:2010}
89 > significant evidence that solid surfaces are often structurally,
90 > compositionally, and chemically modified by reactants under operating
91 > conditions.\cite{Tao2008,Tao:2010,Tao2011} The coupling between
92 > surface oxidation states and catalytic activity for CO oxidation on
93 > Pt, for instance, is widely documented.\cite{Ertl08,Hendriksen:2002}
94 > Despite the well-documented role of these effects on reactivity, the
95 > ability to capture or predict them in atomistic models is somewhat
96 > limited.  While these effects are perhaps unsurprising on the highly
97 > disperse, multi-faceted nanoscale particles that characterize
98 > industrial catalysts, they are manifest even on ordered, well-defined
99 > surfaces. The Pt(557) surface, for example, exhibits substantial and
100 > reversible restructuring under exposure to moderate pressures of
101 > carbon monoxide.\cite{Tao:2010}
102  
103 < This work is part of an ongoing effort to understand the causes,
104 < mechanisms and timescales for surface restructuring using molecular
105 < simulation methods.  Since the dynamics of the process is of
106 < particular interest, we utilize classical molecular dynamic methods
107 < with force fields that represent a compromise between chemical
106 < accuracy and the computational efficiency necessary to observe the
107 < process of interest.
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 are of particular interest, we employ classical force
106 > fields that represent a compromise between chemical accuracy and the
107 > computational efficiency necessary to simulate the process of interest.
108  
109 < Since restructuring occurs as a result of specific interactions of the catalyst
110 < with adsorbates, two metals systems exposed to the same adsorbate, CO,
111 < were examined in this work. The Pt(557) surface has already been shown to
112 < reconstruct under certain conditions. The Au(557) surface, because of gold's
113 < weaker interaction with CO, is less likely to undergo such a large reconstruction.
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.
115 >
116   %Platinum molecular dynamics
117   %gold molecular dynamics
118  
117
118
119
120
121
119   \section{Simulation Methods}
120   The challenge in modeling any solid/gas interface problem is the
121   development of a sufficiently general yet computationally tractable
# Line 133 | Line 130 | Coulomb potential.  For this work, we have been using
130   typically not well represented in terms of classical pairwise
131   interactions in the same way that bonds in a molecular material are,
132   nor are they captured by simple non-directional interactions like the
133 < Coulomb potential.  For this work, we have been using classical
134 < molecular dynamics with potential energy surfaces that are
135 < specifically tuned for transition metals.  In particular, we use the
136 < EAM potential for Au-Au and Pt-Pt interactions, while modeling the CO
137 < using a model developed by Straub and Karplus for studying
138 < photodissociation of CO from myoglobin.\cite{Straub} The Au-CO and Pt-CO
139 < cross interactions were parameterized as part of this work.
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\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.
140    
141   \subsection{Metal-metal interactions}
142 < Many of the potentials used for classical simulation of transition
143 < metals are based on a non-pairwise additive functional of the local
144 < electron density. The embedded atom method (EAM) is perhaps the best
145 < known of these
142 > Many of the potentials used for modeling transition metals are based
143 > on a non-pairwise additive functional of the local electron
144 > density. The embedded atom method (EAM) is perhaps the best known of
145 > these
146   methods,\cite{Daw84,Foiles86,Johnson89,Daw89,Plimpton93,Voter95a,Lu97,Alemany98}
147   but other models like the Finnis-Sinclair\cite{Finnis84,Chen90} and
148   the quantum-corrected Sutton-Chen method\cite{QSC,Qi99} have simpler
# Line 155 | Line 152 | atomic sites is computed at atom $i$'s location,
152   core with a radially-decaying valence electron distribution. To
153   calculate the energy for embedding the core at a particular location,
154   the electron density due to the valence electrons at all of the other
155 < atomic sites is computed at atom $i$'s location,
155 > atomic sites is computed at atom $i$'s location,
156   \begin{equation*}
157   \bar{\rho}_i = \sum_{j\neq i} \rho_j(r_{ij})
158   \end{equation*}
# Line 167 | 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
172 < pairwise interaction between two
173 < atoms.\cite{BASKES:1994fk,Lee:2000vn,Thijsse:2002ly,Timonova:2011ve}
174 < MEAM has become widely used to simulate systems in which angular
175 < interactions are important (e.g. silicon,\cite{Timonova:2011ve} bcc
176 < metals,\cite{Lee:2001qf} and also interfaces.\cite{Beurden:2002ys})
177 < MEAM presents significant additional computational costs, however.
170 > % The {\it modified} embedded atom method (MEAM) adds angular terms to
171 > % the electron density functions and an angular screening factor to the
172 > % pairwise interaction between two
173 > % atoms.\cite{BASKES:1994fk,Lee:2000vn,Thijsse:2002ly,Timonova:2011ve}
174 > % MEAM has become widely used to simulate systems in which angular
175 > % interactions are important (e.g. silicon,\cite{Timonova:2011ve} bcc
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, MEAM, 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 187 | parameterized.\cite{Foiles86,PhysRevB.37.3924,Rifkin19
187   strengths and weaknesses.  One of the strengths common to all of the
188   methods is the relatively large library of metals for which these
189   potentials have been
190 < parameterized.\cite{Foiles86,PhysRevB.37.3924,Rifkin1992,mishin99:_inter,mishin01:cu,mishin02:b2nial,zope03:tial_ap,mishin05:phase_fe_ni}
190 > parameterized.\cite{Foiles86,PhysRevB.37.3924,Rifkin1992,mishin99:_inter,mishin01:cu,mishin02:b2nial,zope03:tial_ap,mishin05:phase_fe_ni}  
191  
192 < \subsection{CO}
193 < Since one explanation for the strong surface CO repulsion on metals is
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
192 > \subsection{Carbon Monoxide model}
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
204   mechanical predictions (-2.46 D~\AA)\cite{QuadrupoleCOCalc}.
205   %CO Table
206   \begin{table}[H]
207 < \caption{Positions, $\sigma$, $\epsilon$ and charges for CO geometry and self-interactions\cite{Straub}. Distances are in \AA~, energies are in kcal/mol, and charges are in $e$.}
207 >  \caption{Positions, Lennard-Jones parameters ($\sigma$ and
208 >    $\epsilon$), and charges for the CO-CO
209 >    interactions borrowed from Ref. \bibpunct{}{}{,}{n}{}{,} \protect\cite{Straub}. Distances are in \AA~, energies are
210 >    in kcal/mol, and charges are in atomic units.}
211   \centering
212   \begin{tabular}{| c | c | ccc |}
213   \hline
214 \multicolumn{5}{|c|}{\textbf{Self-Interactions}}\\
215 \hline
214   &  {\it z} & $\sigma$ & $\epsilon$ & q\\
215   \hline
216   \textbf{C} & -0.6457 &  0.0262  & 3.83   &   -0.75 \\
# Line 220 | 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}
224 > \subsection{Cross-Interactions between the metals and carbon monoxide}
225  
226 < One hurdle that must be overcome in classical molecular simulations
227 < is the proper parameterization of the potential interactions present
228 < in the system. Since the adsorption of CO onto a platinum surface has been
229 < the focus of many experimental \cite{Yeo, Hopster:1978, Ertl:1977, Kelemen:1979}
230 < and theoretical studies \cite{Beurden:2002ys,Pons:1986,Deshlahra:2009,Feibelman:2001,Mason:2004}
231 < there is a large amount of data in the literature to fit too. We started with parameters
232 < reported by Korzeniewski et al. \cite{Pons:1986} and then
233 < modified them to ensure that the Pt-CO interaction favored
234 < an atop binding position for the CO upon the Pt surface. This
235 < constraint led to the binding energies being on the higher side
236 < of reported values. Following the method laid out by Korzeniewski,
237 < the Pt-C interaction was fit to a strong Lennard-Jones 12-6
238 < interaction to mimic binding, while the Pt-O interaction
239 < was parameterized to a Morse potential with a large $r_o$
240 < to contribute a weak repulsion. The resultant potential-energy
241 < surface suitably recovers the calculated Pt-C bond length ( 1.6\AA)\cite{Beurden:2002ys} and affinity
242 < for the atop binding position.\cite{Deshlahra:2012, Hopster:1978}
226 > Since the adsorption of CO onto a platinum surface has been the focus
227 > of much experimental \cite{Yeo, Hopster:1978, Ertl:1977, Kelemen:1979}
228 > and theoretical work
229 > \cite{Beurden:2002ys,Pons:1986,Deshlahra:2009,Feibelman:2001,Mason:2004}
230 > there is a significant amount of data on adsorption energies for CO on
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). 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 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
246 > position.\cite{Deshlahra:2012, Hopster:1978}
247  
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 interaction parameters were also fit to a Lennard-Jones
252 < and Morse potential respectively, to reproduce Au-CO binding energies.
253 < These energies were obtained from quantum calculations carried out using
254 < the PBE GGA exchange-correlation functionals\cite{Perdew_GGA} for gold, carbon, and oxygen
255 < constructed by Rappe, Rabe, Kaxiras, and Joannopoulos. \cite{RRKJ_PP}.
256 < All calculations were run using the {\sc Quantum ESPRESSO} package. \cite{QE-2009}  
257 < First, a four layer slab of gold comprised of 32 atoms displaying a (111) surface was
258 < converged using a 4X4X4 grid of Monkhorst-Pack \emph{k}-points.\cite{Monkhorst:1976}
259 < The kinetic energy of the wavefunctions were truncated at 20 Ry while the
260 < cutoff for the charge density and potential was set at 80 Ry. This relaxed
261 < gold slab was then used in numerous single point calculations  with CO at various heights
262 < to create a potential energy surface for the Au-CO interaction.
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 > 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)
258 > method,\cite{PhysRevB.50.17953,PhysRevB.59.1758} with plane waves
259 > included to an energy cutoff of 20 Ry. Electronic energies are
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 > 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 > 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 fit parameter sets employed in this work are shown in Table 2 and their
277 < reproduction of the binding energies are displayed in Table 3. Currently,
278 < charge transfer is not being treated in this system, however, that is a goal
279 < for future work as the effect has been seen to affect binding energies and
280 < binding site 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  
268
269
270
271 \subsection{Construction and Equilibration of 557 Metal interfaces}
272
273 Our model systems are composed of approximately 4000 metal atoms
274 cut along the 557 plane so that they are periodic in the {\it x} and {\it y}
275 directions exposing the 557 plane in the {\it z} direction. Runs at various
276 temperatures ranging from 300~K to 1200~K were started with the intent
277 of viewing relative stability of the surface when CO was not present in the
278 system.  Owing to the different melting points (1337~K for Au and 2045~K for Pt),
279 the bare crystal systems were initially run in the Canonical ensemble at
280 800~K and 1000~K respectively for 100 ps. Various amounts of CO were
281 placed in the vacuum region, which upon full adsorption to the surface
282 corresponded to 5\%, 25\%, 33\%, and 50\% coverages. These systems
283 were again allowed to reach thermal equilibrium before being run in the
284 microcanonical ensemble. All of the systems examined in this work were
285 run for at least 40 ns. A subset that were undergoing interesting effects
286 have been allowed to continue running with one system approaching 200 ns.
287 All simulations were run using the open source molecular dynamics package, OpenMD. \cite{Ewald, OOPSE}
288
289
290
291
292
293
294 %\subsection{System}
295 %Once equilibration was reached, the systems were exposed to various sub-monolayer coverage of CO: $0, \frac{1}{10}, \frac{1}{4}, \frac{1}{3},\frac{1}{2}$. The CO was started many \AA~above the surface with random velocity and rotational velocity vectors sampling from a Gaussian distribution centered on the temperature of the equilibrated metal block.  Full adsorption occurred over the period of approximately 10 ps for Pt, while the binding energy between Au and CO is smaller and led to an incomplete adsorption. The metal-metal interactions were treated using the Embedded Atom Method while the Pt-CO and Au-CO interactions were fit to experimental data and quantum calculations. The raised temperature helped shorten the length of the simulations by allowing the activation barrier of reconstruction to be more easily overcome. A few runs at lower temperatures showed the very beginnings of reconstructions, but their simulation lengths limited their usefulness.
296
297
283   %Table  of Parameters
284   %Pt Parameter Set 9
285   %Au Parameter Set 35
286   \begin{table}[H]
287 < \caption{Best fit parameters for metal-adsorbate interactions. Distances are in \AA~and energies are in kcal/mol}
287 >  \caption{Best fit parameters for metal-CO cross-interactions.   Metal-C
288 >    interactions are modeled with Lennard-Jones potential, while the
289 >    (mostly-repulsive) metal-O interactions were fit to Morse
290 >    potentials.  Distances are given in \AA~and energies in kcal/mol. }
291   \centering
292   \begin{tabular}{| c | cc | c | ccc |}
293   \hline
294 < \multicolumn{7}{| c |}{\textbf{Cross-Interactions} }\\
294 > &  $\sigma$ & $\epsilon$ & & $r$ & $D$ & $\gamma$ (\AA$^{-1}$) \\
295   \hline
308 &  $\sigma$ & $\epsilon$ & & $r$ & $D$ & $\gamma$ \\
309 \hline
296   \textbf{Pt-C} & 1.3 & 15  & \textbf{Pt-O} & 3.8 & 3.0 & 1 \\
297   \textbf{Au-C} & 1.9 & 6.5  & \textbf{Au-O} & 3.8 & 0.37 & 0.9\\
298  
299   \hline
300   \end{tabular}
301 + \label{tab:co_parameters}
302   \end{table}
303  
304   %Table of energies
305   \begin{table}[H]
306 < \caption{Adsorption energies in eV}
306 >  \caption{Adsorption energies for CO on M(111) using the potentials
307 >    described in this work.  All values are in eV}
308   \centering
309   \begin{tabular}{| c | cc |}
310 < \hline
311 < & Calc. & Exp. \\
312 < \hline
313 < \textbf{Pt-CO} & -1.9 & -1.4~\cite{Kelemen:1979}-- -1.9~\cite{Yeo} \\
314 < \textbf{Au-CO} & -0.39 & -0.44~\cite{TPD_Gold_CO} \\
315 < \hline
310 >  \hline
311 >  & Calculated & Experimental \\
312 >  \hline
313 >  \multirow{2}{*}{\textbf{Pt-CO}} & \multirow{2}{*}{-1.9} & -1.4 \bibpunct{}{}{,}{n}{}{,}
314 >  (Ref. \protect\cite{Kelemen:1979}) \\
315 > & &  -1.9 \bibpunct{}{}{,}{n}{}{,} (Ref. \protect\cite{Yeo}) \\ \hline
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}
323  
324 + Our model systems are composed of 3888 Pt atoms and 3384 Au atoms in a
325 + FCC crystal that have been cut along the 557 plane so that they are
326 + periodic in the {\it x} and {\it y} directions, and have been rotated
327 + to expose two parallel 557 cuts along the positive and negative {\it
328 +  z}-axis.  Simulations of the bare metal interfaces at temperatures
329 + ranging from 300~K to 1200~K were done to observe the relative
330 + stability of the surfaces without a CO overlayer.  
331  
332 + The different bulk (and surface) melting temperatures (1337~K for Au
333 + and 2045~K for Pt) suggest that the reconstruction may happen at
334 + different temperatures for the two metals.  To copy experimental
335 + conditions for the CO-exposed surfaces, the bare surfaces were
336 + initially run in the canonical (NVT) ensemble at 800~K and 1000~K
337 + respectively for 100 ps.  Each surface was exposed to a range of CO
338 + that was initially placed in the vacuum region.  Upon full adsorption,
339 + these amounts correspond to 0\%, 5\%, 25\%, 33\%, and 50\% surface
340 + coverage.  Because of the difference in binding energies, the platinum
341 + systems very rarely had CO that was not bound to the surface, while
342 + the gold surfaces often had a significant CO population in the gas
343 + phase.  These systems were allowed to reach thermal equilibrium (over
344 + 5 ns) before being shifted to the microcanonical (NVE) ensemble for
345 + data collection. All of the systems examined had at least 40 ns in the
346 + data collection stage, although simulation times for some of the
347 + systems exceeded 200ns.  All simulations were run using the open
348 + source molecular dynamics package, OpenMD.\cite{Ewald,OOPSE,OpenMD}
349  
334
335
350   % Just results, leave discussion for discussion section
351 + % structure
352 + %       Pt: step wandering, double layers, no triangular motifs
353 + %       Au: step wandering, no double layers
354 + % dynamics
355 + %       diffusion
356 + %       time scale, formation, breakage
357   \section{Results}
358 < \subsection{Diffusion}
359 < While an ideal metallic surface is unlikely to experience much surface diffusion, high-index surfaces have large numbers of low-coordinated atoms which have a much easier time overcoming the energetic barriers limiting diffusion, leading to easier surface reconstructions. Surface movement was divided between the parallel ($\parallel$) and perpendicular ($\perp$) directions relative to the step edge. We were then able to calculate diffusion constants as a function of CO coverage. As can be seen in Table 4, the presence and amount of CO directly affects the diffusion constants of surface platinum atoms. The presence of two 50\% coverage systems is to show how the diffusion process is affected by time. The majority of the systems were run for approximately 50 ns while the half monolayer system been running continuously. The lowered diffusion constant at longer run times will be examined in-depth in the discussion section.
358 > \subsection{Structural remodeling}
359 > Tao {\it et al.} showed experimentally that the Pt(557) surface undergoes
360 > two separate reconstructions upon CO adsorption.\cite{Tao:2010} The first
361 > reconstruction involves a doubling of the step height and plateau length. Similar
362 > behavior has been seen to occur on numerous surfaces at varying conditions.\cite{Williams:1994,Williams:1991,Pearl}
363 > Of the two systems we examined, the Platinum system showed the most surface
364 > reconstruction. Additionally, the amount of reconstruction appears to be
365 > dependent on the amount of CO adsorbed upon the surface. This result is likely
366 > related to the effect that coverage has on surface diffusion. While both systems
367 > displayed step edge wandering, only the Pt surface underwent doubling within
368 > the time scales we were modeling. Specifically only the 50 \% coverage Pt system
369 > was observed to undergo a complete doubling in the time scales we were able to monitor.
370 > This event encouraged us to allow that specific system to run continuously during which two
371 > more double layers were created. The other systems, not displaying any large scale changes
372 > of interest, were all stopped after 40 ns of simulation. Neverthless, the other Platinum systems tended to show
373 > more cumulative lateral movement of the step edges when compared to the Gold systems.
374 > The 50 \% Pt system is highlighted in figure \ref{fig:reconstruct} at various times along the
375 > simulation showing the evolution of the system.
376  
377 < %Table of Diffusion Constants
378 < %Add gold?M
379 < \begin{table}[H]
380 < \caption{Platinum and gold diffusion constants parallel and perpendicular to the 557 step edge. As the coverage increases, the diffusion constants parallel and  perpendicular to the step edge both initially increase and then decrease slightly. Units are \AA\textsuperscript{2}/ns}
381 < \centering
346 < \begin{tabular}{| c | cc | cc | c |}
347 < \hline
348 < \textbf{System Coverage} & $\mathbf{D}_{\parallel}$ & $\mathbf{D}_{\perp}$ & $\mathbf{D}_{\parallel}$ & $\mathbf{D}_{\perp}$  & \textbf{Time (ns)}\\
349 < \hline
350 < &\multicolumn{2}{c|}{\textbf{Platinum}}&\multicolumn{2}{c|}{\textbf{Gold}} & \\
351 < \hline
352 < 50\% & 4.32 $\pm$ 0.02 & 1.185 $\pm$ 0.008 & 1.72 $\pm$ 0.02 & 0.455 $\pm$ 0.006 & 40 \\
353 < 33\% & 5.18 $\pm$ 0.03 & 1.999 $\pm$ 0.005 & 1.95 $\pm$ 0.02 & 0.337 $\pm$ 0.004 & 40   \\
354 < 25\% & 5.01 $\pm$ 0.02 & 1.574 $\pm$ 0.004 & 1.26 $\pm$ 0.03 & 0.377 $\pm$ 0.006 & 40  \\
355 < 5\%   & 3.61 $\pm$ 0.02 & 0.355 $\pm$ 0.002 & 1.84 $\pm$ 0.03 & 0.169 $\pm$ 0.004 & 40  \\
356 < 0\%   & 3.27 $\pm$ 0.02 & 0.147 $\pm$ 0.004 & 1.50 $\pm$ 0.02 & 0.194 $\pm$ 0.002  & 40  \\
357 < \hline
358 < \end{tabular}
359 < \end{table}
377 > The second reconstruction on the Pt(557) surface observed by Tao involved the
378 > formation of triangular clusters that stretched across the plateau between two step edges.
379 > Neither system, within our simulated time scales, experiences this reconstruction. A constructed
380 > system in which the triangular motifs were constructed on the surface will be explored in future
381 > work and is shown in the supporting information.
382  
383 + \subsection{Dynamics}
384 + While atomistic-like simulations of stepped surfaces have been performed before \cite{}, they tend to be
385 + performed using Monte Carlo techniques\cite{Williams:1991,Williams:1994}. This allows them to efficiently sample the thermodynamic
386 + landscape but at the expense of ignoring the dynamics of the system. Previous work, using STM \cite{Pearl},
387 + has been able to visualize the coalescing of steps of (system). The time scale of the image acquisition, ~ 70 s/image
388 + provides an upper bounds for the time required for the doubling to actually occur. While statistical treatments
389 + of step edges are adept at analyzing such systems, it is important to remember that the edges are made
390 + up of individual atoms and thus can be examined in numerous ways.
391  
392 + \subsubsection{Transport of surface metal atoms}
393 + %forcedSystems/stepSeparation
394 + The movement of a step edge is a cooperative effect arising from the individual movements of the atoms
395 + making up the step. An ideal metal surface displaying a low index facet (111, 100, 110) is unlikely to
396 + experience much surface diffusion because of the large energetic barrier to lift an atom out of the surface.
397 + For our surfaces however, the presence of step edges provide a source for mobile metal atoms. Breaking away
398 + from the step edge still imposes an energetic penalty around 40 kcal/mole, but is much less than lifting the same metal
399 + atom out from the surface,  > 60 kcal/mole, and the penalty lowers even further when CO is present in sufficient quantities
400 + on the surface, ~20 kcal/mole. Once an adatom exists on the surface, its barrier for diffusion is negligible ( < 4 kcal/mole)
401 + and is well able to explore its terrace. Atoms traversing terraces is more difficult, but can be overcome through a joining and lifting stage.
402 + By tracking the mobility of individual metal atoms on the Platinum and Gold surfaces we were able to determine
403 + the relative diffusion rates and how varying coverages of CO affected the rates. Close
404 + observation of the mobile metal atoms showed that they were typically in equilibrium with the
405 + step edges, constantly breaking apart and rejoining. Additionally, at times their motion was concerted and
406 + two or more atoms would be observed moving together across the surfaces. The primary challenge in quantifying
407 + the overall surface mobility was in defining ``mobile" vs. ``static" atoms.
408  
409 + A particle was considered mobile once it had traveled more than 2~\AA~ between saved configurations
410 + of the system (10-100 ps). An atom that was truly mobile would typically travel much greater than this, but
411 + the 2~\AA~ cutoff was to prevent the in-place vibrational movement of atoms from being included in the analysis.
412 + Since diffusion on  a surface is strongly affected by local structures, in this case the presence of single and double
413 + layer step edges, the diffusion parallel to the step edges was determined separately from the diffusion perpendicular
414 + to these edges. The parallel and perpendicular diffusion constants are shown in figure \ref{fig:diff}.
415 +
416 + \subsubsection{Double layer formation}
417 + The increased amounts of diffusion on Pt at the higher CO coverages appears to play a role in the
418 + formation of double layers, seeing as how that was the only system within our observed simulation time
419 + that showed the formation. Despite this being the only system where this reconstruction occurs, three separate layers
420 + were formed over the extended run time of this system. As mentioned earlier, previous experimental work has given some insight into
421 + the upper bounds of the time required for enough atoms to move around to allow two steps to coalesce\cite{Williams:1991,Pearl}.
422 + As seen in figure \ref{fig:reconstruct}, the first appearance of a double layer, a nodal site, appears at 19 ns into
423 + the simulation. Within 12 ns, nearly half of the step has formed the double layer and by 86 ns, a smooth complete
424 + layer has formed. The double layer is complete by 37 ns but is a bit rough.
425 + From the appearance of the first node to the initial doubling of the layers ignoring their roughness took ~20 ns.
426 + Another ~40 ns was necessary for the layer to completely straighten. The other two layers in this simulation form
427 + over a period of 22 ns and 42 ns respectively.
428 +
429 + %Evolution of surface
430 + \begin{figure}[H]
431 + \includegraphics[width=\linewidth]{ProgressionOfDoubleLayerFormation_yellowCircle.png}
432 + \caption{The Pt(557) / 50\% CO system at a sequence of times after
433 +  initial exposure to the CO: (a) 258 ps, (b) 19 ns, (c) 31.2 ns, and
434 +  (d) 86.1 ns. Disruption of the 557 step edges occurs quickly.  The
435 +  doubling of the layers appears only after two adjacent step edges
436 +  touch.  The circled spot in (b) nucleated the growth of the double
437 +  step observed in the later configurations.}
438 +  \label{fig:reconstruct}
439 + \end{figure}
440 +
441 + \begin{figure}[H]
442 + \includegraphics[width=\linewidth]{DiffusionComparison_errorXY_remade.pdf}
443 + \caption{Diffusion constants for mobile surface atoms along directions
444 +  parallel ($\mathbf{D}_{\parallel}$) and perpendicular
445 +  ($\mathbf{D}_{\perp}$) to the 557 step edges as a function of CO
446 +  surface coverage.  Diffusion parallel to the step edge is higher
447 +  than that perpendicular to the edge because of the lower energy
448 +  barrier associated with going from approximately 7 nearest neighbors
449 +  to 5, as compared to the 3 of an adatom. Additionally, the observed
450 +  maximum and subsequent decrease for the Pt system suggests that the
451 +  CO self-interactions are playing a significant role with regards to
452 +  movement of the platinum atoms around and more importantly across
453 +  the surface. }
454 + \label{fig:diff}
455 + \end{figure}
456 +
457 +
458 +
459 +
460   %Discussion
461   \section{Discussion}
462 < Comparing the results from simulation to those reported previously by Tao et al. the similarities in the platinum and CO system are quite strong. As shown in figure 1, the simulated platinum system under a CO atmosphere will restructure slightly by doubling the terrace heights. The restructuring appears to occur slowly, one to two platinum atoms at a time. Looking at individual snapshots, these adatoms tend to either rise on top of the plateau or break away from the step edge and then diffuse perpendicularly to the step direction until reaching another step edge. This combination of growth and decay of the step edges appears to be in somewhat of a state of dynamic equilibrium. However, once two previously separated edges meet as shown in figure 1.B, this point tends to act as a focus or growth point for the rest of the edge to meet up, akin to that of a zipper. From the handful of cases where a double layer was formed during the simulation. Measuring from the initial appearance of a growth point, the double layer tends to be fully formed within $\sim$~35 ns.
462 > In this paper we have shown that we were able to accurately model the initial reconstruction of the
463 > Pt (557) surface upon CO adsorption as shown by Tao et al. \cite{Tao:2010}. More importantly, we
464 > were able to capture the dynamic processes inherent within this reconstruction.
465  
466 + \subsection{Mechanism for restructuring}
467 + The increased computational cost to examine this system using molecular dynamics rather than
468 + a Monte Carlo based approach was necessary so that our predictions on possible mechanisms
469 + and driving forces would have support not only from thermodynamic arguments but also from the
470 + actual dynamics of the system.
471 +
472 + Comparing the results from simulation to those reported previously by
473 + Tao et al. the similarities in the platinum and CO system are quite
474 + strong. As shown in figure \ref{fig:reconstruct}, the simulated platinum system under a CO
475 + atmosphere will restructure slightly by doubling the terrace
476 + heights. The restructuring appears to occur slowly, one to two
477 + platinum atoms at a time. Looking at individual snapshots, these
478 + adatoms tend to either rise on top of the plateau or break away from
479 + the step edge and then diffuse perpendicularly to the step direction
480 + until reaching another step edge. This combination of growth and decay
481 + of the step edges appears to be in somewhat of a state of dynamic
482 + equilibrium. However, once two previously separated edges meet as
483 + shown in figure 1.B, this point tends to act as a focus or growth
484 + point for the rest of the edge to meet up, akin to that of a
485 + zipper. From the handful of cases where a double layer was formed
486 + during the simulation, measuring from the initial appearance of a
487 + growth point, the double layer tends to be fully formed within
488 + $\sim$~35 ns.
489 +
490 + There are a number of possible mechanisms to explain the role of
491 + adsorbed CO in restructuring the Pt surface. Quadrupolar repulsion
492 + between adjacent CO molecules adsorbed on the surface is one
493 + possibility.  However, the quadrupole-quadrupole interaction is
494 + short-ranged and is attractive for some orientations.  If the CO
495 + molecules are ``locked'' in a specific orientation relative to each other however,
496 + this explanation gains some weight.  The energetic repulsion between two CO
497 + located a distance of 2.77~\AA~apart (nearest-neighbor distance of Pt) with both in a
498 + vertical orientation is 8.62 kcal/mole. Moving the CO apart to the second nearest-neighbor
499 + distance of 4.8~\AA~or 5.54~\AA~drops the repulsion to nearly 0 kcal/mole. SHOW A NUMBER FOR ROTATION.
500 + As mentioned above, the energy barrier for surface diffusion of a platinum adatom is only 4 kcal/mole. So this
501 + repulsion between CO can help increase the surface diffusion. However, the residence time of CO was examined
502 + and while the majority of the CO is on or near the surface throughout the run, it is extremely mobile. This mobility
503 + suggests that the CO are more likely to shift their positions without necessarily dragging the platinum along
504 + with them.
505 +
506 + Another possible and more likely mechanism for the restructuring is in the
507 + destabilization of strong Pt-Pt interactions by CO adsorbed on surface
508 + Pt atoms.  This could have the effect of increasing surface mobility
509 + of these atoms.  To test this hypothesis, numerous configurations of
510 + CO in varying quantities were arranged on the higher and lower plateaus
511 + around a step on a otherwise clean Pt (557) surface. One representative
512 + configuration is displayed in figure \ref{fig:lambda}. Single or concerted movement
513 + of platinum atoms was then examined to determine possible barriers. Because
514 + of the forced movement along a pre-defined reaction coordinate that may differ
515 + from the true minimum of this path, only the beginning and ending energies
516 + are displayed in table \ref{tab:energies}. The presence of CO at suitable
517 + sites can lead to lowered barriers for platinum breaking apart from the step edge.
518 + Additionally, as highlighted in figure \ref{fig:lambda}, the presence of CO makes the
519 + burrowing and lifting nature favorable, whereas without CO, the process is neutral
520 + in terms of energetics.
521 +
522 + %lambda progression of Pt -> shoving its way into the step
523 + \begin{figure}[H]
524 + \includegraphics[width=\linewidth]{lambdaProgression_atopCO.png}
525 + \caption{A model system of the Pt 557 surface was used as the framework for a reaction coordinate.
526 + Various numbers, placements, and rotations of CO were examined. The one displayed was a
527 + representative sample. As shown in Table , relative to the energy at 0\% there is a slight decrease
528 + upon insertion of the platinum atom into the step edge along with the resultant lifting of the other
529 + platinum atom.}
530 + \label{fig:lambda}
531 + \end{figure}
532 +
533 +
534 +
535   \subsection{Diffusion}
536 < As shown in the results section, the diffusion parallel to the step edge tends to be much faster than that perpendicular to the step edge. Additionally, the coverage of CO appears to play a slight role in relative rates of diffusion, as shown in Table 4. Thus, the bottleneck of the double layer formation appears to be the initial formation of this growth point, which seems to be somewhat of a stochastic event. Once it appears, parallel diffusion, along the now slightly angled step edge, will allow for a faster formation of the double layer than if the entire process were dependent on only perpendicular diffusion across the plateaus. Thus, the larger $D_{\perp}$, the more likely a growth point is to be formed. One driving force behind this reconstruction appears to be the lowering of surface energy that occurs by doubling the terrace widths. (I'm not really proving this... I have the surface flatness to show it, but surface energy?)
536 > As shown in the results section, the diffusion parallel to the step edge tends to be
537 > much faster than that perpendicular to the step edge. Additionally, the coverage
538 > of CO appears to play a slight role in relative rates of diffusion, as shown in figure \ref{fig:diff}
539 > Thus, the bottleneck of the double layer formation appears to be the initial formation
540 > of this growth point, which seems to be somewhat of a stochastic event. Once it
541 > appears, parallel diffusion, along the now slightly angled step edge, will allow for
542 > a faster formation of the double layer than if the entire process were dependent on
543 > only perpendicular diffusion across the plateaus. Thus, the larger $D_{\perp}$, the
544 > more likely a growth point is to be formed.
545   \\
546 < \\
547 < %Evolution of surface
546 >
547 >
548 > %breaking of the double layer upon removal of CO
549   \begin{figure}[H]
550 < \includegraphics[scale=0.5]{ProgressionOfDoubleLayerFormation_yellowCircle.png}
551 < \caption{Four snapshots at various times a) 258 ps b) 19 ns c) 31.2 ns d) 86.1 ns. Slight disruption of the surface occurs fairly quickly. However, the doubling of the layers seems to be very dependent on the initial linking of two separate step edges. The focal point in b, appears to be a growth spot for the rest of the double layer.}
550 > \includegraphics[width=\linewidth]{doubleLayerBreaking_greenBlue_whiteLetters.png}
551 > \caption{Hi}
552 > \label{fig:breaking}
553   \end{figure}
554  
555  
556  
557  
558   %Peaks!
559 < \includegraphics[scale=0.25]{doublePeaks_noCO.png}
559 > \begin{figure}[H]
560 > \includegraphics[width=\linewidth]{doublePeaks_noCO.png}
561 > \caption{}
562 > \label{fig:peaks}
563 > \end{figure}
564 >
565 > %clean surface...
566 > \begin{figure}[H]
567 > \includegraphics[width=\linewidth]{557_300K_cleanPDF.pdf}
568 > \caption{}
569 >
570 > \end{figure}
571 > \label{fig:clean}
572   \section{Conclusion}
573  
574  
575 + %Things I am not ready to remove yet
576 +
577 + %Table of Diffusion Constants
578 + %Add gold?M
579 + % \begin{table}[H]
580 + %   \caption{}
581 + %   \centering
582 + % \begin{tabular}{| c | cc | cc | }
583 + %   \hline
584 + %   &\multicolumn{2}{c|}{\textbf{Platinum}}&\multicolumn{2}{c|}{\textbf{Gold}} \\
585 + %   \hline
586 + %   \textbf{Surface Coverage} & $\mathbf{D}_{\parallel}$ & $\mathbf{D}_{\perp}$ & $\mathbf{D}_{\parallel}$ & $\mathbf{D}_{\perp}$  \\
587 + %   \hline
588 + %   50\% & 4.32(2) & 1.185(8)  & 1.72(2) & 0.455(6) \\
589 + %   33\% & 5.18(3)  & 1.999(5)  & 1.95(2) & 0.337(4)   \\
590 + %   25\% & 5.01(2)  & 1.574(4)  & 1.26(3) & 0.377(6) \\
591 + %   5\%   & 3.61(2)  & 0.355(2)  & 1.84(3)  & 0.169(4)  \\
592 + %   0\%   & 3.27(2)  & 0.147(4)  & 1.50(2)  & 0.194(2)   \\
593 + %   \hline
594 + % \end{tabular}
595 + % \end{table}
596 +
597   \section{Acknowledgments}
598   Support for this project was provided by the National Science
599   Foundation under grant CHE-0848243 and by the Center for Sustainable

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