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2 > \usepackage{amsmath}
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4 > \usepackage{times}
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6   \usepackage{setspace}
7 < \usepackage{float}
8 < \usepackage{cite}
9 < \usepackage[pdftex]{graphicx}
10 < \usepackage[font=small,labelfont=bf]{caption}
7 > \usepackage{endfloat}
8 > \usepackage{caption}
9 > %\usepackage{tabularx}
10 > \usepackage{graphicx}
11 > \usepackage{multirow}
12 > %\usepackage{booktabs}
13 > %\usepackage{bibentry}
14 > %\usepackage{mathrsfs}
15 > \usepackage[square, comma, sort&compress]{natbib}
16 > \usepackage{url}
17 > \pagestyle{plain} \pagenumbering{arabic} \oddsidemargin 0.0cm
18 > \evensidemargin 0.0cm \topmargin -21pt \headsep 10pt \textheight
19 > 9.0in \textwidth 6.5in \brokenpenalty=10000
20  
21 + % double space list of tables and figures
22 + %\AtBeginDelayedFloats{\renewcomand{\baselinestretch}{1.66}}
23 + \setlength{\abovecaptionskip}{20 pt}
24 + \setlength{\belowcaptionskip}{30 pt}
25 +
26 + \bibpunct{}{}{,}{s}{}{;}
27 + \bibliographystyle{achemso}
28 +
29 + \begin{document}
30 +
31 +
32   %%
33   %Introduction
34   %       Experimental observations
# Line 24 | Line 47
47   %Summary
48   %%
49  
50 + %Title
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  
29 \begin{document}
30 %Title
31 \title{Investigation of the Pt and Au 557 Surface Reconstructions under a CO Atmosphere}
60   %Date
61 < \date{Dec 15,  2012}
61 > \date{Dec 15, 2012}
62 >
63   %authors
64 < \author{Joseph R.~Michalka, Patrick W. McIntyre, \& J.~Daniel Gezelter}
64 >
65   % make the title
66   \maketitle
67  
68 < \doublespacing
68 > \begin{doublespace}
69  
70 + \begin{abstract}
71  
72 + \end{abstract}
73  
74 + \newpage
75 +
76 +
77   \section{Introduction}
78   % Importance: catalytically active metals are important
79   %       Sub: Knowledge of how their surface structure affects their ability to catalytically facilitate certain reactions is growing, but is more reactionary than predictive
# Line 48 | Line 82
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 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 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 < High-index surfaces of catalytically active metals are an important area of exploration because they are typically more reactive than an ideal surface of the same metal. The greater number of low-coordinated surface atoms is likely responsible for this increased reactivity \cite{}. Additionally, the activity and specificity of many metals towards certain chemical processes has been shown to strongly depend on the structure of the surface \cite{}. Prior work has also shown that reaction conditions: high pressures, temperatures, etc. are able to cause reconstructions of the surface, either through changing the displayed surface facets or by changing the number and types of high-index sites available for reactions \cite{doi:10.1126/science.1197461,doi:10.1021/nn3015322, doi:10.1021/jp302379x}. A greater understanding of these high-index surfaces and the restructuring processes they undergo is needed as a prerequisite for more intelligent catalyst design. While current experimental work has started exploring systems at \emph{in situ} conditions, for a long time such experiments were limited to ideal surfaces in high vacuum. New techniques, such as ambient pressure XPS (AP-XPS) \cite{}, high-pressure XPS (HP-XPS) \cite{}, high-pressure STM \cite{}, environmental transmission electron microscopy (E-TEM) \cite{} and many others, are giving a clearer picture of what processes are occurring on metal surfaces when exposed to \emph{in situ} conditions. But all of these techniques still have difficulties, especially in observing what is occurring on the surfaces at an atomic level. Theoretical models and simulations in combination with experiment have proven their worth in explaining the underlying reasons for some of these reconstructions \cite{}.
104 < \\
105 < By examining two different metal-CO systems the effect the metal and the metal-CO interaction plays can be elucidated. Our first system is composed of Platinum and CO and has been the subject of many experimental and theoretical studies primarily because of Platinum's strong reactivity toward CO oxidation. The focus has primarily been on absorption energies, preferred absorption sites, and catalytic activities. The second system we examined is composed of Gold and CO. The Gold-CO interaction is much weaker than the Platinum-CO interaction and it seems likely that this difference in attraction would lead to differences in any potential surface reconstructions.
106 < %It has also been a good test for new quantum methods because of the difficulty with modeling the preference CO has for the atop binding site \cite{doi:10.1021/jp002302t}.
107 < %Now that dynamic surface events are known to play a role in many catalytic systems, additional research is being done to more closely examine many systems. Recent work by Tao et al. \cite{doi:10.1126/science.1182122} shows that a high-index platinum surface will undergo surface reconstructions when exposed to a small amount of CO, $\sim$~1 torr. Unexpectedly,  the reconstruction was metastable and reverted upon removal of the CO. Work by McCarthy et al. \cite{doi:10.1021/jp302379x} examined temperature programmed desorption's of CO from various Platinum samples and saw that species which had large amounts of low-coordinated surface atoms, highly sputtered surfaces or small nano particles, developed a higher temperature desorption peak, suggesting that binding of CO to the Platinum surface is strongly dependent on local geometry.
103 > This work an effort 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
106 > fields that represent a compromise between chemical accuracy and the
107 > computational efficiency necessary to observe 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
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  
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
122 + model of the chemical interactions between the surface atoms and
123 + adsorbates.  Since the interfaces involved are quite large (10$^3$ -
124 + 10$^6$ atoms) and respond slowly to perturbations, {\it ab initio}
125 + molecular dynamics
126 + (AIMD),\cite{KRESSE:1993ve,KRESSE:1993qf,KRESSE:1994ul} Car-Parrinello
127 + methods,\cite{CAR:1985bh,Izvekov:2000fv,Guidelli:2000fy} and quantum
128 + mechanical potential energy surfaces remain out of reach.
129 + Additionally, the ``bonds'' between metal atoms at a surface are
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 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
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 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
149 + parameter sets. The glue model of Ercolessi {\it et al.} is among the
150 + fastest of these density functional approaches.\cite{Ercolessi88} In
151 + all of these models, atoms are conceptualized as a positively charged
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,
156 + \begin{equation*}
157 + \bar{\rho}_i = \sum_{j\neq i} \rho_j(r_{ij})
158 + \end{equation*}
159 + Here, $\rho_j(r_{ij})$ is the function that describes the distance
160 + dependence of the valence electron distribution of atom $j$. The
161 + contribution to the potential that comes from placing atom $i$ at that
162 + location is then
163 + \begin{equation*}
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.  
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.
178  
179 < \section{Simulation Methods}
180 < Our model systems are composed of nearly 4000 metal atoms cut along the 557 plane. This cut creates a stepped surface of 6x(111) surface plateaus separated by a single (100) atomic step height. The large number of low-coordination atoms along the step edges provide a suitable model for industrial catalysts which tend to have a prevalence of lower CN, i.e. more reactive, sites. Drawing from experimental conclusions, the reconstructions seen for the Pt 557 surface involve doubling of the step height and the formation of triangular motifs along the steps \cite{doi:10.1126/science.1182122}. To properly observe these changes, our system size need to be greater than the periodic phenomena we are examining. The large size and the long time scales needed precluded us from using expensive quantum approaches. Thus, a forcefield describing the Metal-Metal, CO-CO, and CO-Metal interactions was parameterized.
181 < %Metal
182 < \subsection{Metal}
183 < Recent metallic forcefields, inspired by density-functional theory, including EAM\cite{doi:10.1103/PhysRevB.29.6443, doi:10.1103/PhysRevB.33.7983} and QSC\cite{} have become very popular for modeling novel metallic systems.  What makes these forcefields more suitable for metals than their pair-wise predecessors is that they work with the total electron density of the system in a manner akin to DFT. The energy contributed by a single atom is a function of the total background electron density at the point where the atom is to be embedded. The density at any given point is well-approximated by a linear superposition of the electron density as contributed by all the other atoms in the system. This description of the embedding energy allows this method to more accurately treat surfaces, alloys, and other non-bulk systems. The function describing the energy as related to the density is parameterized for each element, rather than by solving the Kohn-Sham equations which is what allows this method to be used for large systems. The embedding energy is completely enclosed within the functional $F_i[\rho_{h,i}]$ which is dependent on the host density $\rho_{h}$ at atom $i$. The density at $i$ is the sum of the density as generated by the rest of the metal. The $\phi_{ij}$ term is a purely repulsive pair-pair interaction parameterized from effective charge repulsions.
184 < %Can I increase the \sum size, not sure how...
185 < \begin{equation}
186 < E_{tot} = \sum_i F_i[\rho_{h,i}] + \frac{1}{2}\sum_i\sum_{j(\ne i)} \phi_{ij}(R_{ij})
187 < \end{equation}
188 < \begin{equation}
189 < \rho_{h,i} = \sum_{j (\ne i)} \rho_j^a(R_{ij})
190 < \end{equation}
191 < The EAM functional forms are used to model the Au and Pt self-interactions in all of our simulations.
192 < %CO
193 < \subsection{CO}
194 < Our CO model was obtained from work done by Karplus and Straub\cite{}. In their description of the biological importance of CO they developed an accurate quadrupolar model of CO which we make use of in this work. It has been suggested that the strong electrostatic repulsion that arises from this linear quadrupole may play an important role in the restructuring of metal surfaces to which CO is bound\cite{}.
179 > The EAM, Finnis-Sinclair, and the Quantum Sutton-Chen 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}
183 > melting,\cite{Belonoshko00,sankaranarayanan:155441,Sankaranarayanan:2005lr}
184 > fracture,\cite{Shastry:1996qg,Shastry:1998dx} crack
185 > propagation,\cite{BECQUART:1993rg} and alloying
186 > dynamics.\cite{Shibata:2002hh} All of these potentials have their
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}  
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
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{$\sigma$, $\epsilon$ and charges for CO self-interactions\cite{}. 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 | ccc |}
212 > \begin{tabular}{| c | c | ccc |}
213   \hline
214 < \multicolumn{4}{|c|}{\textbf{Self-Interactions}}\\
214 > &  {\it z} & $\sigma$ & $\epsilon$ & q\\
215   \hline
216 < &  $\sigma$ & $\epsilon$ & q\\
216 > \textbf{C} & -0.6457 &  0.0262  & 3.83   &   -0.75 \\
217 > \textbf{O} &  0.4843 &   0.1591 &   3.12 &   -0.85 \\
218 > \textbf{M} & 0.0 & -  &  -  &    1.6 \\
219   \hline
88 \textbf{C} &  0.0262  & 3.83   &   -0.75 \\
89 \textbf{O} &   0.1591 &   3.12 &   -0.85 \\
90 \textbf{M} & -  &  -  &    1.6 \\
91 \hline
220   \end{tabular}
221   \end{table}
94 %Cross
95 \subsection{Cross-Interactions}
96 To finish the forcefield, the cross-interactions between the metals and the CO needed to be parameterized. Previous attempts at parameterization have used two different functional forms to model these interactions\cite{}. A LJ model was fit for the Metal-Carbon interaction and a Morse potential was parameterized for the Metal-Oxygen interaction. The parameter sets chosen, as shown in Table 2, did a suitable job at reproducing experimental adsorption energies as shown in Table 3, but more importantly, they were able to capture the binding site preference. The Pt-CO parameters show a slight preference for the atop binding site which matches the experimental observations.
222  
223 + \subsection{Cross-Interactions between the metals and carbon monoxide}
224  
225 + Since the adsorption of CO onto a platinum surface has been the focus
226 + of much experimental \cite{Yeo, Hopster:1978, Ertl:1977, Kelemen:1979}
227 + and theoretical work
228 + \cite{Beurden:2002ys,Pons:1986,Deshlahra:2009,Feibelman:2001,Mason:2004}
229 + there is a significant amount of data on adsorption energies for CO on
230 + clean metal surfaces. Parameters reported by Korzeniewski {\it et
231 +  al.}\cite{Pons:1986} were a starting point for our fits, which were
232 + modified to ensure that the Pt-CO interaction favored the atop binding
233 + position on Pt(111). This resulting binding energies are on the higher
234 + side of the experimentally-reported values. Following Korzeniewski
235 + {\it et al.},\cite{Pons:1986} the Pt-C interaction was fit to a deep
236 + Lennard-Jones interaction to mimic strong, but short-ranged partial
237 + binding between the Pt $d$ orbitals and the $\pi^*$ orbital on CO. The
238 + Pt-O interaction was parameterized to a Morse potential with a large
239 + range parameter ($r_o$).  In most cases, this contributes a weak
240 + repulsion which favors the atop site.  The resulting potential-energy
241 + surface suitably recovers the calculated Pt-C separation length
242 + (1.6~\AA)\cite{Beurden:2002ys} and affinity for the atop binding
243 + position.\cite{Deshlahra:2012, Hopster:1978}
244  
245 + %where did you actually get the functionals for citation?
246 + %scf calculations, so initial relaxation was of the four layers, but two layers weren't kept fixed, I don't think
247 + %same cutoff for slab and slab + CO ? seems low, although feibelmen had values around there...
248 + The Au-C and Au-O cross-interactions were fit using Lennard-Jones and
249 + Morse potentials, respectively, to reproduce Au-CO binding energies.
250  
251 < %\subsection{System}
252 < %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.
251 > The fits were refined against gas-surface DFT calculations with a
252 > periodic supercell plane-wave basis approach, as implemented in the
253 > {\sc Quantum ESPRESSO} package.\cite{QE-2009} Electron cores are
254 > described with the projector augmented-wave (PAW)
255 > method,\cite{PhysRevB.50.17953,PhysRevB.59.1758} with plane waves
256 > included to an energy cutoff of 20 Ry. Electronic energies are
257 > computed with the PBE implementation of the generalized gradient
258 > approximation (GGA) for gold, carbon, and oxygen that was constructed
259 > by Rappe, Rabe, Kaxiras, and Joannopoulos.\cite{Perdew_GGA,RRKJ_PP}
260 > 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 > Au x 2 Au surface planes and separated from vertical images by six
264 > layers of vacuum space. The surface atoms were all allowed to relax.
265 > Supercell calculations were performed nonspin-polarized with a 4 x 4 x
266 > 4 Monkhorst-Pack {\bf k}-point sampling of the first Brillouin
267 > zone.\cite{Monkhorst:1976,PhysRevB.13.5188} The relaxed gold slab was
268 > then used in numerous single point calculations with CO at various
269 > heights (and angles relative to the surface) to allow fitting of the
270 > empirical force field.
271  
272 + %Hint at future work
273 + The parameters employed in this work are shown in Table 2 and the
274 + binding energies on the 111 surfaces are displayed in Table 3.  To
275 + speed up the computations, charge transfer and polarization are not
276 + being treated in this model, although these effects are likely to
277 + affect binding energies and binding site
278 + preferences.\cite{Deshlahra:2012}
279  
280   %Table  of Parameters
281   %Pt Parameter Set 9
282   %Au Parameter Set 35
283   \begin{table}[H]
284 < \caption{Best fit parameters for metal-adsorbate interactions. Distances are in \AA~and energies are in kcal/mol}
284 >  \caption{Best fit parameters for metal-CO cross-interactions.   Metal-C
285 >    interactions are modeled with Lennard-Jones potential, while the
286 >    (mostly-repulsive) metal-O interactions were fit to Morse
287 >    potentials.  Distances are given in \AA~and energies in kcal/mol. }
288   \centering
289   \begin{tabular}{| c | cc | c | ccc |}
290   \hline
291 < \multicolumn{7}{| c |}{\textbf{Cross-Interactions} }\\
291 > &  $\sigma$ & $\epsilon$ & & $r$ & $D$ & $\gamma$ (\AA$^{-1}$) \\
292   \hline
115 &  $\sigma$ & $\epsilon$ & & $r$ & $D$ & $\gamma$ \\
116 \hline
293   \textbf{Pt-C} & 1.3 & 15  & \textbf{Pt-O} & 3.8 & 3.0 & 1 \\
294   \textbf{Au-C} & 1.9 & 6.5  & \textbf{Au-O} & 3.8 & 0.37 & 0.9\\
295  
# Line 123 | Line 299 | To finish the forcefield, the cross-interactions betwe
299  
300   %Table of energies
301   \begin{table}[H]
302 < \caption{Absorption energies in eV}
302 >  \caption{Adsorption energies for CO on M(111) using the potentials
303 >    described in this work.  All values are in eV}
304   \centering
305   \begin{tabular}{| c | cc |}
306 < \hline
307 < & Calc. & Exp. \\
308 < \hline
309 < \textbf{Pt-CO} & -1.9 & -1.4~\cite{Kelemen}-- -1.9~\cite{Yeo} \\
310 < \textbf{Au-CO} & -0.39 & -0.44~\cite{TPD_Gold_CO} \\
311 < \hline
306 >  \hline
307 >  & Calculated & Experimental \\
308 >  \hline
309 >  \multirow{2}{*}{\textbf{Pt-CO}} & \multirow{2}{*}{-1.9} & -1.4 \bibpunct{}{}{,}{n}{}{,}
310 >  (Ref. \protect\cite{Kelemen:1979}) \\
311 > & &  -1.9 \bibpunct{}{}{,}{n}{}{,} (Ref. \protect\cite{Yeo}) \\ \hline
312 >  \textbf{Au-CO} & -0.39 & -0.40 \bibpunct{}{}{,}{n}{}{,}  (Ref. \protect\cite{TPD_Gold}) \\
313 >  \hline
314   \end{tabular}
315   \end{table}
316  
317 <
139 <
317 > \subsection{Pt(557) and Au(557) metal interfaces}
318  
319 + Our model systems are composed of 3888 Pt atoms and 3384 Au atoms in a
320 + FCC crystal that have been cut along the 557 plane so that they are
321 + periodic in the {\it x} and {\it y} directions, and have been rotated
322 + to expose two parallel 557 cuts along the positive and negative {\it
323 +  z}-axis.  Simulations of the bare metal interfaces at temperatures
324 + ranging from 300~K to 1200~K were done to observe the relative
325 + stability of the surfaces without a CO overlayer.  
326  
327 + The different bulk (and surface) melting temperatures (1337~K for Au
328 + and 2045~K for Pt) suggest that the reconstruction may happen at
329 + different temperatures for the two metals.  To copy experimental
330 + conditions for the CO-exposed surfaces, the bare surfaces were
331 + initially run in the canonical (NVT) ensemble at 800~K and 1000~K
332 + respectively for 100 ps.  Each surface was exposed to a range of CO
333 + that was initially placed in the vacuum region.  Upon full adsorption,
334 + these amounts correspond to 0\%, 5\%, 25\%, 33\%, and 50\% surface
335 + coverage.  Because of the difference in binding energies, the platinum
336 + systems very rarely had CO that was not bound to the surface, while
337 + the gold surfaces often had a significant CO population in the gas
338 + phase.  These systems were allowed to reach thermal equilibrium (over
339 + 5 ns) before being shifted to the microcanonical (NVE) ensemble for
340 + data collection. All of the systems examined had at least 40 ns in the
341 + data collection stage, although simulation times for some of the
342 + systems exceeded 200ns.  All simulations were run using the open
343 + source molecular dynamics package, OpenMD.\cite{Ewald,OOPSE,OpenMD}
344  
345   % Just results, leave discussion for discussion section
346 + % structure
347 + %       Pt: step wandering, double layers, no triangular motifs
348 + %       Au: step wandering, no double layers
349 + % dynamics
350 + %       diffusion
351 + %       time scale, formation, breakage
352   \section{Results}
353 < \subsection{Diffusion}
354 < 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.
353 > \subsection{Structural remodeling}
354 > Tao {\it et al.} showed experimentally that the Pt(557) surface undergoes
355 > two separate reconstructions upon CO adsorption.\cite{Tao:2010} The first
356 > reconstruction involves a doubling of the step height and plateau length. Similar
357 > behavior has been seen to occur on numerous surfaces at varying conditions.\cite{Williams:1994,Williams:1991,Pearl}
358 > Of the two systems we examined, the Platinum system showed the most surface
359 > reconstruction. Additionally, the amount of reconstruction appears to be
360 > dependent on the amount of CO adsorbed upon the surface. This result is likely
361 > related to the effect that coverage has on surface diffusion. While both systems
362 > displayed step edge wandering, only the Pt surface underwent doubling within
363 > the time scales we were modeling. Specifically only the 50 \% coverage Pt system
364 > was observed to undergo a complete doubling in the time scales we were able to monitor.
365 > This event encouraged us to allow that specific system to run continuously during which two
366 > more double layers were created. The other systems, not displaying any large scale changes
367 > of interest, were all stopped after 40 ns of simulation. Neverthless, the other Platinum systems tended to show
368 > more cumulative lateral movement of the step edges when compared to the Gold systems.
369 > The 50 \% Pt system is highlighted in figure \ref{fig:reconstruct} at various times along the
370 > simulation showing the evolution of the system.
371  
372 < %Table of Diffusion Constants
373 < %Add gold?M
374 < \begin{table}[H]
375 < \caption{Platinum 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. There were two approaches of analysis. One looking at the surface atoms that had moved more than a prescribed amount over the run time and the other looking at all surface atoms. Units are \AA\textsuperscript{2}/ns}
376 < \centering
153 < \begin{tabular}{| c | ccc | ccc | c |}
154 < \hline
155 < \textbf{System Coverage} & $\mathbf{D}_{\parallel}$ & $\mathbf{D}_{\perp}$ & \textbf{Atoms} & $\mathbf{D}_{\parallel}$ & $\mathbf{D}_{\perp}$ & \textbf{Atoms} & \textbf{Time (ns)}\\
156 < \hline
157 < &\multicolumn{3}{c|}{\textbf{Mobile}}&\multicolumn{3}{c|}{\textbf{Surface Atoms}} & \\
158 < \hline
159 < 50\% & 3.74 & 0.89 & 497 & 2.05 & 0.49 & 912 & 116 \\
160 < 50\% & 5.81 & 1.59 & 365 & 2.41 & 0.68 & 912 & 46   \\
161 < 33\% & 6.73 & 2.47 & 332 & 2.51 & 0.93 & 912 & 46   \\
162 < 25\% & 5.38 & 2.04 & 361 & 2.18 & 0.84 & 912 & 46  \\
163 < 5\% & 5.54 & 0.63 & 230 & 1.44 & 0.19 & 912 & 46  \\
164 < 0\% & 3.53 & 0.61 & 282 & 1.11 & 0.22 & 912 & 56  \\
165 < \hline
166 < 50\%-r & 6.91 & 2.00 & 198 & 2.23 & 0.68  & 925 & 25\\
167 < 0\%-r  & 4.73 & 0.27 & 128 & 0.72 & 0.05 & 925 & 43\\
168 < \hline
169 < \end{tabular}
170 < \end{table}
372 > The second reconstruction on the Pt(557) surface observed by Tao involved the
373 > formation of triangular clusters that stretched across the plateau between two step edges.
374 > Neither system, within our simulated time scales, experiences this reconstruction. A constructed
375 > system in which the triangular motifs were constructed on the surface will be explored in future
376 > work and is shown in the supporting information.
377  
378 + \subsection{Dynamics}
379 + While atomistic-like simulations of stepped surfaces have been performed before \cite{}, they tend to be
380 + performed using Monte Carlo techniques\cite{Williams:1991,Williams:1994}. This allows them to efficiently sample the thermodynamic
381 + landscape but at the expense of ignoring the dynamics of the system. Previous work, using STM \cite{Pearl},
382 + has been able to visualize the coalescing of steps of (system). The time scale of the image acquisition, ~ 70 s/image
383 + provides an upper bounds for the time required for the doubling to actually occur. While statistical treatments
384 + of step edges are adept at analyzing such systems, it is important to remember that the edges are made
385 + up of individual atoms and thus can be examined in numerous ways.
386  
387 + \subsubsection{Transport of surface metal atoms}
388 + %forcedSystems/stepSeparation
389 + The movement of a step edge is a cooperative effect arising from the individual movements of the atoms
390 + making up the step. An ideal metal surface displaying a low index facet (111, 100, 110) is unlikely to
391 + experience much surface diffusion because of the large energetic barrier to lift an atom out of the surface.
392 + For our surfaces however, the presence of step edges provide a source for mobile metal atoms. Breaking away
393 + from the step edge still imposes an energetic penalty around 40 kcal/mole, but is much less than lifting the same metal
394 + atom out from the surface,  > 60 kcal/mole, and the penalty lowers even further when CO is present in sufficient quantities
395 + on the surface, ~20 kcal/mole. Once an adatom exists on the surface, its barrier for diffusion is negligible ( < 4 kcal/mole)
396 + and is well able to explore its terrace. Atoms traversing terraces is more difficult, but can be overcome through a joining and lifting stage.
397 + By tracking the mobility of individual metal atoms on the Platinum and Gold surfaces we were able to determine
398 + the relative diffusion rates and how varying coverages of CO affected the rates. Close
399 + observation of the mobile metal atoms showed that they were typically in equilibrium with the
400 + step edges, constantly breaking apart and rejoining. Additionally, at times their motion was concerted and
401 + two or more atoms would be observed moving together across the surfaces. The primary challenge in quantifying
402 + the overall surface mobility was in defining ``mobile" vs. ``static" atoms.
403  
404 + A particle was considered mobile once it had traveled more than 2~\AA~ between saved configurations
405 + of the system (10-100 ps). An atom that was truly mobile would typically travel much greater than this, but
406 + the 2~\AA~ cutoff was to prevent the in-place vibrational movement of atoms from being included in the analysis.
407 + Since diffusion on  a surface is strongly affected by local structures, in this case the presence of single and double
408 + layer step edges, the diffusion parallel to the step edges was determined separately from the diffusion perpendicular
409 + to these edges. The parallel and perpendicular diffusion constants are shown in figure \ref{fig:diff}.
410 +
411 + \subsubsection{Double layer formation}
412 + The increased amounts of diffusion on Pt at the higher CO coverages appears to play a role in the
413 + formation of double layers, seeing as how that was the only system within our observed simulation time
414 + that showed the formation. Despite this being the only system where this reconstruction occurs, three separate layers
415 + were formed over the extended run time of this system. As mentioned earlier, previous experimental work has given some insight into
416 + the upper bounds of the time required for enough atoms to move around to allow two steps to coalesce\cite{Williams:1991,Pearl}.
417 + As seen in figure \ref{fig:reconstruct}, the first appearance of a double layer, a nodal site, appears at 19 ns into
418 + the simulation. Within 12 ns, nearly half of the step has formed the double layer and by 86 ns, a smooth complete
419 + layer has formed. The double layer is complete by 37 ns but is a bit rough.
420 + From the appearance of the first node to the initial doubling of the layers ignoring their roughness took ~20 ns.
421 + Another ~40 ns was necessary for the layer to completely straighten. The other two layers in this simulation form
422 + over a period of 22 ns and 42 ns respectively.
423 +
424 + %Evolution of surface
425 + \begin{figure}[H]
426 + \includegraphics[width=\linewidth]{ProgressionOfDoubleLayerFormation_yellowCircle.png}
427 + \caption{The Pt(557) / 50\% CO system at a sequence of times after
428 +  initial exposure to the CO: (a) 258 ps, (b) 19 ns, (c) 31.2 ns, and
429 +  (d) 86.1 ns. Disruption of the 557 step edges occurs quickly.  The
430 +  doubling of the layers appears only after two adjacent step edges
431 +  touch.  The circled spot in (b) nucleated the growth of the double
432 +  step observed in the later configurations.}
433 +  \label{fig:reconstruct}
434 + \end{figure}
435 +
436 + \begin{figure}[H]
437 + \includegraphics[width=\linewidth]{DiffusionComparison_errorXY_remade.pdf}
438 + \caption{Diffusion constants for mobile surface atoms along directions
439 +  parallel ($\mathbf{D}_{\parallel}$) and perpendicular
440 +  ($\mathbf{D}_{\perp}$) to the 557 step edges as a function of CO
441 +  surface coverage.  Diffusion parallel to the step edge is higher
442 +  than that perpendicular to the edge because of the lower energy
443 +  barrier associated with going from approximately 7 nearest neighbors
444 +  to 5, as compared to the 3 of an adatom. Additionally, the observed
445 +  maximum and subsequent decrease for the Pt system suggests that the
446 +  CO self-interactions are playing a significant role with regards to
447 +  movement of the platinum atoms around and more importantly across
448 +  the surface. }
449 + \label{fig:diff}
450 + \end{figure}
451 +
452 +
453 +
454 +
455   %Discussion
456   \section{Discussion}
457 < 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.
457 > In this paper we have shown that we were able to accurately model the initial reconstruction of the
458 > Pt (557) surface upon CO adsorption as shown by Tao et al. \cite{Tao:2010}. More importantly, we
459 > were able to capture the dynamic processes inherent within this reconstruction.
460  
461 < \subsection{Diffusion}
462 < 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?)
463 < \\
464 < \\
465 < %Evolution of surface
461 > \subsection{Mechanism for restructuring}
462 > The increased computational cost to examine this system using molecular dynamics rather than
463 > a Monte Carlo based approach was necessary so that our predictions on possible mechanisms
464 > and driving forces would have support not only from thermodynamic arguments but also from the
465 > actual dynamics of the system.
466 >
467 > Comparing the results from simulation to those reported previously by
468 > Tao et al. the similarities in the platinum and CO system are quite
469 > strong. As shown in figure \ref{fig:reconstruct}, the simulated platinum system under a CO
470 > atmosphere will restructure slightly by doubling the terrace
471 > heights. The restructuring appears to occur slowly, one to two
472 > platinum atoms at a time. Looking at individual snapshots, these
473 > adatoms tend to either rise on top of the plateau or break away from
474 > the step edge and then diffuse perpendicularly to the step direction
475 > until reaching another step edge. This combination of growth and decay
476 > of the step edges appears to be in somewhat of a state of dynamic
477 > equilibrium. However, once two previously separated edges meet as
478 > shown in figure 1.B, this point tends to act as a focus or growth
479 > point for the rest of the edge to meet up, akin to that of a
480 > zipper. From the handful of cases where a double layer was formed
481 > during the simulation, measuring from the initial appearance of a
482 > growth point, the double layer tends to be fully formed within
483 > $\sim$~35 ns.
484 >
485 > There are a number of possible mechanisms to explain the role of
486 > adsorbed CO in restructuring the Pt surface. Quadrupolar repulsion
487 > between adjacent CO molecules adsorbed on the surface is one
488 > possibility.  However, the quadrupole-quadrupole interaction is
489 > short-ranged and is attractive for some orientations.  If the CO
490 > molecules are ``locked'' in a specific orientation relative to each other however,
491 > this explanation gains some weight.  The energetic repulsion between two CO
492 > located a distance of 2.77~\AA~apart (nearest-neighbor distance of Pt) with both in a
493 > vertical orientation is 8.62 kcal/mole. Moving the CO apart to the second nearest-neighbor
494 > distance of 4.8~\AA~or 5.54~\AA~drops the repulsion to nearly 0 kcal/mole. SHOW A NUMBER FOR ROTATION.
495 > As mentioned above, the energy barrier for surface diffusion of a platinum adatom is only 4 kcal/mole. So this
496 > repulsion between CO can help increase the surface diffusion. However, the residence time of CO was examined
497 > and while the majority of the CO is on or near the surface throughout the run, it is extremely mobile. This mobility
498 > suggests that the CO are more likely to shift their positions without necessarily dragging the platinum along
499 > with them.
500 >
501 > Another possible and more likely mechanism for the restructuring is in the
502 > destabilization of strong Pt-Pt interactions by CO adsorbed on surface
503 > Pt atoms.  This could have the effect of increasing surface mobility
504 > of these atoms.  To test this hypothesis, numerous configurations of
505 > CO in varying quantities were arranged on the higher and lower plateaus
506 > around a step on a otherwise clean Pt (557) surface. One representative
507 > configuration is displayed in figure \ref{fig:lambda}. Single or concerted movement
508 > of platinum atoms was then examined to determine possible barriers. Because
509 > of the forced movement along a pre-defined reaction coordinate that may differ
510 > from the true minimum of this path, only the beginning and ending energies
511 > are displayed in table \ref{tab:energies}. The presence of CO at suitable
512 > sites can lead to lowered barriers for platinum breaking apart from the step edge.
513 > Additionally, as highlighted in figure \ref{fig:lambda}, the presence of CO makes the
514 > burrowing and lifting nature favorable, whereas without CO, the process is neutral
515 > in terms of energetics.
516 >
517 > %lambda progression of Pt -> shoving its way into the step
518   \begin{figure}[H]
519 < \includegraphics[scale=0.5]{ProgressionOfDoubleLayerFormation_yellowCircle.png}
520 < \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.}
519 > \includegraphics[width=\linewidth]{lambdaProgression_atopCO.png}
520 > \caption{A model system of the Pt 557 surface was used as the framework for a reaction coordinate.
521 > Various numbers, placements, and rotations of CO were examined. The one displayed was a
522 > representative sample. As shown in Table , relative to the energy at 0\% there is a slight decrease
523 > upon insertion of the platinum atom into the step edge along with the resultant lifting of the other
524 > platinum atom.}
525 > \label{fig:lambda}
526   \end{figure}
527  
528  
529  
530 + \subsection{Diffusion}
531 + As shown in the results section, the diffusion parallel to the step edge tends to be
532 + much faster than that perpendicular to the step edge. Additionally, the coverage
533 + of CO appears to play a slight role in relative rates of diffusion, as shown in figure \ref{fig:diff}
534 + Thus, the bottleneck of the double layer formation appears to be the initial formation
535 + of this growth point, which seems to be somewhat of a stochastic event. Once it
536 + appears, parallel diffusion, along the now slightly angled step edge, will allow for
537 + a faster formation of the double layer than if the entire process were dependent on
538 + only perpendicular diffusion across the plateaus. Thus, the larger $D_{\perp}$, the
539 + more likely a growth point is to be formed.
540 + \\
541  
191 %Peaks!
192 \includegraphics[scale=0.25]{doublePeaks_noCO.png}
193 \section{Conclusion}
542  
543 + %breaking of the double layer upon removal of CO
544 + \begin{figure}[H]
545 + \includegraphics[width=\linewidth]{doubleLayerBreaking_greenBlue_whiteLetters.png}
546 + \caption{Hi}
547 + \label{fig:breaking}
548 + \end{figure}
549  
550  
551  
552  
553 + %Peaks!
554 + \begin{figure}[H]
555 + \includegraphics[width=\linewidth]{doublePeaks_noCO.png}
556 + \caption{}
557 + \label{fig:peaks}
558 + \end{figure}
559  
560 + %clean surface...
561 + \begin{figure}[H]
562 + \includegraphics[width=\linewidth]{557_300K_cleanPDF.pdf}
563 + \caption{}
564  
565 + \end{figure}
566 + \label{fig:clean}
567 + \section{Conclusion}
568  
569  
570 + %Things I am not ready to remove yet
571  
572 + %Table of Diffusion Constants
573 + %Add gold?M
574 + % \begin{table}[H]
575 + %   \caption{}
576 + %   \centering
577 + % \begin{tabular}{| c | cc | cc | }
578 + %   \hline
579 + %   &\multicolumn{2}{c|}{\textbf{Platinum}}&\multicolumn{2}{c|}{\textbf{Gold}} \\
580 + %   \hline
581 + %   \textbf{Surface Coverage} & $\mathbf{D}_{\parallel}$ & $\mathbf{D}_{\perp}$ & $\mathbf{D}_{\parallel}$ & $\mathbf{D}_{\perp}$  \\
582 + %   \hline
583 + %   50\% & 4.32(2) & 1.185(8)  & 1.72(2) & 0.455(6) \\
584 + %   33\% & 5.18(3)  & 1.999(5)  & 1.95(2) & 0.337(4)   \\
585 + %   25\% & 5.01(2)  & 1.574(4)  & 1.26(3) & 0.377(6) \\
586 + %   5\%   & 3.61(2)  & 0.355(2)  & 1.84(3)  & 0.169(4)  \\
587 + %   0\%   & 3.27(2)  & 0.147(4)  & 1.50(2)  & 0.194(2)   \\
588 + %   \hline
589 + % \end{tabular}
590 + % \end{table}
591  
592 < \end{document}
592 > \section{Acknowledgments}
593 > Support for this project was provided by the National Science
594 > Foundation under grant CHE-0848243 and by the Center for Sustainable
595 > Energy at Notre Dame (cSEND). Computational time was provided by the
596 > Center for Research Computing (CRC) at the University of Notre Dame.
597 >
598 > \newpage
599 > \bibliography{firstTryBibliography}
600 > \end{doublespace}
601 > \end{document}

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