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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}
9 < %\usepackage{tabularx}
10 < \usepackage{graphicx}
1 > \documentclass[journal = jpccck, manuscript = article]{achemso}
2 > \setkeys{acs}{usetitle = true}
3 > \usepackage{achemso}
4 > \usepackage{natbib}
5   \usepackage{multirow}
6 < %\usepackage{booktabs}
7 < %\usepackage{bibentry}
8 < %\usepackage{mathrsfs}
9 < \usepackage[square, comma, sort&compress]{natbib}
6 > \usepackage{wrapfig}
7 > \usepackage{fixltx2e}
8 > %\mciteErrorOnUnknownfalse
9 >
10 > \usepackage[version=3]{mhchem}  % this is a great package for formatting chemical reactions
11   \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
12  
13 < % double space list of tables and figures
14 < %\AtBeginDelayedFloats{\renewcomand{\baselinestretch}{1.66}}
23 < \setlength{\abovecaptionskip}{20 pt}
24 < \setlength{\belowcaptionskip}{30 pt}
13 > \title{Molecular Dynamics simulations of the surface reconstructions
14 >  of Pt(557) and Au(557) under exposure to CO}
15  
16 < \bibpunct{}{}{,}{s}{}{;}
17 < \bibliographystyle{achemso}
16 > \author{Joseph R. Michalka}
17 > \author{Patrick W. McIntyre}
18 > \author{J. Daniel Gezelter}
19 > \email{gezelter@nd.edu}
20 > \affiliation[University of Notre Dame]{251 Nieuwland Science Hall\\
21 >  Department of Chemistry and Biochemistry\\ University of Notre
22 >  Dame\\ Notre Dame, Indiana 46556}
23  
24 + \keywords{}
25 +
26   \begin{document}
27  
28 <
28 >
29   %%
30   %Introduction
31   %       Experimental observations
# Line 47 | Line 44
44   %Summary
45   %%
46  
50 %Title
51 \title{Molecular Dynamics simulations of the surface reconstructions
52  of Pt(557) and Au(557) under exposure to CO}
47  
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{Mar 5, 2013}
62
63 %authors
64
65 % make the title
66 \maketitle
67
68 \begin{doublespace}
69
48   \begin{abstract}
49 < We examine potential surface reconstructions of Pt and Au(557)
50 < under various CO coverages using molecular dynamics in order
51 < to explore possible mechanisms for any observed reconstructions and their dynamics.
52 < The metal-CO interactions were parameterized as part of this
53 < work so that an efficient large-scale treatment of this system could be
54 < undertaken. The large difference in binding strengths of the metal-CO
55 < interactions was found to play a significant role with regards to
56 < step-edge stability and adatom diffusion. A small correlation
57 < between coverage and the magnitude of the diffusion constant was
58 < also determined. An in-depth examination of the energetics of CO
59 < adsorbed to the surface provides results that appear sufficient to explain the
60 < reconstructions observed on the Pt systems and the corresponding lack  
61 < on the Au systems.
49 >  The mechanism and dynamics of surface reconstructions of Pt(557) and
50 >  Au(557) exposed to various coverages of carbon monoxide (CO) were
51 >  investigated using molecular dynamics simulations.  Metal-CO
52 >  interactions were parameterized from experimental data and
53 >  plane-wave Density Functional Theory (DFT) calculations.  The large
54 >  difference in binding strengths of the Pt-CO and Au-CO interactions
55 >  was found to play a significant role in step-edge stability and
56 >  adatom diffusion constants.  Various mechanisms for CO-mediated step
57 >  wandering and step doubling were investigated on the Pt(557)
58 >  surface.  We find that the energetics of CO adsorbed to the surface
59 >  can explain the step-doubling reconstruction observed on Pt(557) and
60 >  the lack of such a reconstruction on the Au(557) surface.  However,
61 >  more complicated reconstructions into triangular clusters that have
62 >  been seen in recent experiments were not observed in these
63 >  simulations.
64   \end{abstract}
65  
66   \newpage
# Line 112 | Line 92 | This work is an attempt to understand the mechanism an
92   reversible restructuring under exposure to moderate pressures of
93   carbon monoxide.\cite{Tao:2010}
94  
95 < This work is an attempt to understand the mechanism and timescale for
96 < surface restructuring by using molecular simulations.  Since the dynamics
97 < of the process are of particular interest, we employ classical force
98 < fields that represent a compromise between chemical accuracy and the
99 < computational efficiency necessary to simulate the process of interest.
100 < Since restructuring typically occurs as a result of specific interactions of the
101 < catalyst with adsorbates, in this work, two metal systems exposed
102 < to carbon monoxide were examined. The Pt(557) surface has already been shown
103 < to reconstruct under certain conditions. The Au(557) surface, because
104 < of a weaker interaction with CO, is less likely to undergo this kind
105 < of reconstruction.  
106 <
107 <
95 > This work is an investigation into the mechanism and timescale for the
96 > Pt(557) \& Au(557) surface restructuring using molecular simulation.
97 > Since the dynamics of the process are of particular interest, we
98 > employ classical force fields that represent a compromise between
99 > chemical accuracy and the computational efficiency necessary to
100 > simulate the process of interest.  Since restructuring typically
101 > occurs as a result of specific interactions of the catalyst with
102 > adsorbates, in this work, two metal systems exposed to carbon monoxide
103 > were examined. The Pt(557) surface has already been shown to undergo a
104 > large scale reconstruction under certain conditions.\cite{Tao:2010}
105 > The Au(557) surface, because of weaker interactions with CO, is less
106 > likely to undergo this kind of reconstruction. However, Peters {\it et
107 >  al}.\cite{Peters:2000} and Piccolo {\it et al}.\cite{Piccolo:2004}
108 > have both observed CO-induced modification of reconstructions to the
109 > Au(111) surface. Peters {\it et al}. observed the Au(111)-($22 \times
110 > \sqrt{3}$) ``herringbone'' reconstruction relaxing slightly under CO
111 > adsorption. They argued that only a few Au atoms become adatoms,
112 > limiting the stress of this reconstruction, while allowing the rest to
113 > relax and approach the ideal (111) configuration.  Piccolo {\it et
114 >  al}. on the other hand, saw a more significant disruption of the
115 > Au(111)-($22 \times \sqrt{3}$) herringbone pattern as CO adsorbed on
116 > the surface. Both groups suggested that the preference CO shows for
117 > low-coordinated Au atoms was the primary driving force for the
118 > relaxation.  Although the Au(111) reconstruction was not the primary
119 > goal of our work, the classical models we have fit may be of future
120 > use in simulating this reconstruction.
121  
122   %Platinum molecular dynamics
123   %gold molecular dynamics
124  
125   \section{Simulation Methods}
126 < The challenge in modeling any solid/gas interface problem is the
127 < development of a sufficiently general yet computationally tractable
128 < model of the chemical interactions between the surface atoms and
129 < adsorbates.  Since the interfaces involved are quite large (10$^3$ -
130 < 10$^6$ atoms) and respond slowly to perturbations, {\it ab initio}
126 > The challenge in modeling any solid/gas interface is the development
127 > of a sufficiently general yet computationally tractable model of the
128 > chemical interactions between the surface atoms and adsorbates.  Since
129 > the interfaces involved are quite large (10$^3$ - 10$^4$ atoms), have
130 > many electrons, and respond slowly to perturbations, {\it ab initio}
131   molecular dynamics
132   (AIMD),\cite{KRESSE:1993ve,KRESSE:1993qf,KRESSE:1994ul} Car-Parrinello
133   methods,\cite{CAR:1985bh,Izvekov:2000fv,Guidelli:2000fy} and quantum
# Line 146 | Line 139 | Au-Au and Pt-Pt interactions\cite{EAM}, while modeling
139   Coulomb potential.  For this work, we have used classical molecular
140   dynamics with potential energy surfaces that are specifically tuned
141   for transition metals.  In particular, we used the EAM potential for
142 < Au-Au and Pt-Pt interactions\cite{EAM}, while modeling the CO using a rigid
143 < three-site model developed by Straub and Karplus for studying
142 > Au-Au and Pt-Pt interactions.\cite{Foiles86} The CO was modeled using
143 > a rigid three-site model developed by Straub and Karplus for studying
144   photodissociation of CO from myoglobin.\cite{Straub} The Au-CO and
145   Pt-CO cross interactions were parameterized as part of this work.
146    
# Line 159 | Line 152 | parameter sets. The glue model of Ercolessi et al. is
152   methods,\cite{Daw84,Foiles86,Johnson89,Daw89,Plimpton93,Voter95a,Lu97,Alemany98}
153   but other models like the Finnis-Sinclair\cite{Finnis84,Chen90} and
154   the quantum-corrected Sutton-Chen method\cite{QSC,Qi99} have simpler
155 < parameter sets. The glue model of Ercolessi et al. is among the
156 < fastest of these density functional approaches.\cite{Ercolessi88} In
157 < all of these models, atoms are conceptualized as a positively charged
158 < core with a radially-decaying valence electron distribution. To
159 < calculate the energy for embedding the core at a particular location,
160 < the electron density due to the valence electrons at all of the other
161 < atomic sites is computed at atom $i$'s location,
155 > parameter sets. The glue model of Ercolessi {\it et
156 >  al}.\cite{Ercolessi88} is among the fastest of these density
157 > functional approaches. In all of these models, atoms are treated as a
158 > positively charged core with a radially-decaying valence electron
159 > distribution. To calculate the energy for embedding the core at a
160 > particular location, the electron density due to the valence electrons
161 > at all of the other atomic sites is computed at atom $i$'s location,
162   \begin{equation*}
163   \bar{\rho}_i = \sum_{j\neq i} \rho_j(r_{ij})
164   \end{equation*}
# Line 192 | Line 185 | properties,\cite{Chui:2003fk,Wang:2005qy,Medasani:2007
185   The EAM, Finnis-Sinclair, and the Quantum Sutton-Chen (QSC) potentials
186   have all been widely used by the materials simulation community for
187   simulations of bulk and nanoparticle
188 < properties,\cite{Chui:2003fk,Wang:2005qy,Medasani:2007uq}
188 > properties,\cite{Chui:2003fk,Wang:2005qy,Medasani:2007uq,mishin99:_inter}
189   melting,\cite{Belonoshko00,sankaranarayanan:155441,Sankaranarayanan:2005lr}
190 < fracture,\cite{Shastry:1996qg,Shastry:1998dx} crack
191 < propagation,\cite{BECQUART:1993rg} and alloying
192 < dynamics.\cite{Shibata:2002hh} All of these potentials have their
193 < strengths and weaknesses.  One of the strengths common to all of the
194 < methods is the relatively large library of metals for which these
195 < potentials have been
196 < parameterized.\cite{Foiles86,PhysRevB.37.3924,Rifkin1992,mishin99:_inter,mishin01:cu,mishin02:b2nial,zope03:tial_ap,mishin05:phase_fe_ni}  
190 > fracture,\cite{Shastry:1996qg,Shastry:1998dx,mishin01:cu} crack
191 > propagation,\cite{BECQUART:1993rg,Rifkin1992} and alloying
192 > dynamics.\cite{Shibata:2002hh,mishin02:b2nial,zope03:tial_ap,mishin05:phase_fe_ni}
193 > One of EAM's strengths is its sensitivity to small changes in
194 > structure. This is due to the inclusion of up to the third nearest
195 > neighbor interactions during fitting of the parameters.\cite{Voter95a}
196 > In comparison, the glue model of Ercolessi {\it et
197 >  al}.\cite{Ercolessi88} was only parameterized to include
198 > nearest-neighbor interactions, EAM is a suitable choice for systems
199 > where the bulk properties are of secondary importance to low-index
200 > surface structures. Additionally, the similarity of EAM's functional
201 > treatment of the embedding energy to standard density functional
202 > theory (DFT) makes fitting DFT-derived cross potentials with
203 > adsorbates somewhat easier.
204  
205   \subsection{Carbon Monoxide model}
206 < Previous explanations for the surface rearrangements center on
207 < the large linear quadrupole moment of carbon monoxide.  
208 < We used a model first proposed by Karplus and Straub to study
209 < the photodissociation of CO from myoglobin because it reproduces
210 < the quadrupole moment well.\cite{Straub} The Straub and
211 < Karplus model, treats CO as a rigid three site molecule which places a massless M
212 < site at the center of mass position along the CO bond.  The geometry used along
213 < with the interaction parameters are reproduced in Table~\ref{tab:CO}. The effective
214 < dipole moment, calculated from the assigned charges, is still
215 < small (0.35 D) while the linear quadrupole (-2.40 D~\AA) is close
216 < to the experimental (-2.63 D~\AA)\cite{QuadrupoleCO} and quantum
206 > Previous explanations for the surface rearrangements center on the
207 > large linear quadrupole moment of carbon monoxide.\cite{Tao:2010} We
208 > used a model first proposed by Karplus and Straub to study the
209 > photodissociation of CO from myoglobin because it reproduces the
210 > quadrupole moment well.\cite{Straub} The Straub and Karplus model
211 > treats CO as a rigid three site molecule with a massless
212 > charge-carrying ``M'' site at the center of mass. The geometry and
213 > interaction parameters are reproduced in Table~\ref{tab:CO}. The
214 > effective dipole moment, calculated from the assigned charges, is
215 > still small (0.35 D) while the linear quadrupole (-2.40 D~\AA) is
216 > close to the experimental (-2.63 D~\AA)\cite{QuadrupoleCO} and quantum
217   mechanical predictions (-2.46 D~\AA)\cite{QuadrupoleCOCalc}.
218   %CO Table
219   \begin{table}[H]
220    \caption{Positions, Lennard-Jones parameters ($\sigma$ and
221 <    $\epsilon$), and charges for the CO-CO
222 <    interactions borrowed from Ref.\bibpunct{}{}{,}{n}{}{,} \protect\cite{Straub}. Distances are in \AA, energies are
223 <    in kcal/mol, and charges are in atomic units.}
221 >    $\epsilon$), and charges for CO-CO
222 >    interactions. Distances are in \AA, energies are
223 >    in kcal/mol, and charges are in atomic units.  The CO model
224 >    from Ref.\bibpunct{}{}{,}{n}{}{,}
225 >    \protect\cite{Straub} was used without modification.}
226   \centering
227   \begin{tabular}{| c | c | ccc |}
228   \hline
229   &  {\it z} & $\sigma$ & $\epsilon$ & q\\
230   \hline
231 < \textbf{C} & -0.6457 &  0.0262  & 3.83   &   -0.75 \\
232 < \textbf{O} &  0.4843 &   0.1591 &   3.12 &   -0.85 \\
231 > \textbf{C} & -0.6457 &  3.83 & 0.0262   &   -0.75 \\
232 > \textbf{O} &  0.4843 &  3.12 &  0.1591  &   -0.85 \\
233   \textbf{M} & 0.0 & -  &  -  &    1.6 \\
234   \hline
235   \end{tabular}
# Line 241 | Line 243 | clean metal surfaces. Parameters reported by Korzeniew
243   and theoretical work
244   \cite{Beurden:2002ys,Pons:1986,Deshlahra:2009,Feibelman:2001,Mason:2004}
245   there is a significant amount of data on adsorption energies for CO on
246 < clean metal surfaces. Parameters reported by Korzeniewski {\it et
247 <  al.}\cite{Pons:1986} were a starting point for our fits, which were
246 > clean metal surfaces. An earlier model by Korzeniewski {\it et
247 >  al.}\cite{Pons:1986} served as a starting point for our fits. The parameters were
248   modified to ensure that the Pt-CO interaction favored the atop binding
249 < position on Pt(111). These parameters are reproduced in Table~\ref{tab:co_parameters}
250 < This resulted in binding energies that are slightly higher
249 > position on Pt(111). These parameters are reproduced in Table~\ref{tab:co_parameters}.
250 > The modified parameters yield binding energies that are slightly higher
251   than the experimentally-reported values as shown in Table~\ref{tab:co_energies}. Following Korzeniewski
252 < et al.,\cite{Pons:1986} the Pt-C interaction was fit to a deep
253 < Lennard-Jones interaction to mimic strong, but short-ranged partial
252 > {\it et al}.,\cite{Pons:1986} the Pt-C interaction was fit to a deep
253 > Lennard-Jones interaction to mimic strong, but short-ranged, partial
254   binding between the Pt $d$ orbitals and the $\pi^*$ orbital on CO. The
255 < Pt-O interaction was parameterized to a Morse potential at a larger
256 < minimum distance, ($r_o$).  This was chosen so that the C would be preferred
257 < over O as the binder to the surface. In most cases, this parameterization contributes a weak
255 > Pt-O interaction was modeled with a Morse potential with a large
256 > equilibrium distance, ($r_o$).  These choices ensure that the C is preferred
257 > over O as the surface-binding atom. In most geometries, the Pt-O parameterization contributes a weak
258   repulsion which favors the atop site.  The resulting potential-energy
259   surface suitably recovers the calculated Pt-C separation length
260   (1.6~\AA)\cite{Beurden:2002ys} and affinity for the atop binding
# Line 263 | Line 265 | The limited experimental data for CO adsorption on Au
265   %same cutoff for slab and slab + CO ? seems low, although feibelmen had values around there...
266   The Au-C and Au-O cross-interactions were also fit using Lennard-Jones and
267   Morse potentials, respectively, to reproduce Au-CO binding energies.
268 < The limited experimental data for CO adsorption on Au lead us to refine our fits against DFT.
268 > The limited experimental data for CO adsorption on Au required refining the fits against plane-wave DFT calculations.
269   Adsorption energies were obtained from gas-surface DFT calculations with a
270   periodic supercell plane-wave basis approach, as implemented in the
271 < {\sc Quantum ESPRESSO} package.\cite{QE-2009} Electron cores are
271 > Quantum ESPRESSO package.\cite{QE-2009} Electron cores were
272   described with the projector augmented-wave (PAW)
273   method,\cite{PhysRevB.50.17953,PhysRevB.59.1758} with plane waves
274   included to an energy cutoff of 20 Ry. Electronic energies are
# Line 280 | Line 282 | zone.\cite{Monkhorst:1976,PhysRevB.13.5188} The relaxe
282   performed until the energy difference between subsequent steps
283   was less than $10^{-8}$ Ry.   Nonspin-polarized supercell calculations
284   were performed with a 4~x~4~x~4 Monkhorst-Pack {\bf k}-point sampling of the first Brillouin
285 < zone.\cite{Monkhorst:1976,PhysRevB.13.5188} The relaxed gold slab was
285 > zone.\cite{Monkhorst:1976} The relaxed gold slab was
286   then used in numerous single point calculations with CO at various
287   heights (and angles relative to the surface) to allow fitting of the
288   empirical force field.
289  
290   %Hint at future work
291   The parameters employed for the metal-CO cross-interactions in this work
292 < are shown in Table~\ref{co_parameters} and the binding energies on the
293 < (111) surfaces are displayed in Table~\ref{co_energies}.  Charge transfer
294 < and polarization are neglected in this model, although these effects are likely to
295 < affect binding energies and binding site preferences, and will be added in
294 < a future work.\cite{Deshlahra:2012,StreitzMintmire:1994}
292 > are shown in Table~\ref{tab:co_parameters} and the binding energies on the
293 > (111) surfaces are displayed in Table~\ref{tab:co_energies}.  Charge transfer
294 > and polarization are neglected in this model, although these effects could have
295 > an effect on binding energies and binding site preferences.
296  
297   %Table  of Parameters
298   %Pt Parameter Set 9
299   %Au Parameter Set 35
300   \begin{table}[H]
301 <  \caption{Best fit parameters for metal-CO cross-interactions. Metal-C
302 <    interactions are modeled with Lennard-Jones potential, while the
303 <    metal-O interactions were fit to Morse
301 >  \caption{Parameters for the metal-CO cross-interactions. Metal-C
302 >    interactions are modeled with Lennard-Jones potentials, while the
303 >    metal-O interactions were fit to broad Morse
304      potentials.  Distances are given in \AA~and energies in kcal/mol. }
305   \centering
306   \begin{tabular}{| c | cc | c | ccc |}
# Line 316 | Line 317 | a future work.\cite{Deshlahra:2012,StreitzMintmire:199
317  
318   %Table of energies
319   \begin{table}[H]
320 <  \caption{Adsorption energies for CO on M(111) at the atop site using the potentials
320 >  \caption{Adsorption energies for a single CO at the atop site on M(111) at the atop site using the potentials
321      described in this work.  All values are in eV.}
322   \centering
323   \begin{tabular}{| c | cc |}
# Line 326 | Line 327 | a future work.\cite{Deshlahra:2012,StreitzMintmire:199
327    \multirow{2}{*}{\textbf{Pt-CO}} & \multirow{2}{*}{-1.9} & -1.4 \bibpunct{}{}{,}{n}{}{,}
328    (Ref. \protect\cite{Kelemen:1979}) \\
329   & &  -1.9 \bibpunct{}{}{,}{n}{}{,} (Ref. \protect\cite{Yeo}) \\ \hline
330 <  \textbf{Au-CO} & -0.39 & -0.40 \bibpunct{}{}{,}{n}{}{,}  (Ref. \protect\cite{TPD_Gold}) \\
330 >  \textbf{Au-CO} & -0.39 & -0.40 \bibpunct{}{}{,}{n}{}{,}  (Ref. \protect\cite{TPDGold}) \\
331    \hline
332   \end{tabular}
333   \label{tab:co_energies}
334   \end{table}
335  
335 \subsection{Pt(557) and Au(557) metal interfaces}
336  
337 < Our model systems are composed of 3888 Pt atoms and 3384 Au atoms in a
338 < FCC crystal that have been cut along the (557) plane so that they are
339 < periodic in the {\it x} and {\it y} directions, and have been oriented
340 < to expose two aligned (557) cuts along the extended {\it
341 <  z}-axis.  Simulations of the bare metal interfaces at temperatures
342 < ranging from 300~K to 1200~K were performed to observe the relative
343 < stability of the surfaces without a CO overlayer.  
337 > \subsection{Validation of forcefield selections}
338 > By calculating minimum energies for commensurate systems of
339 > single and double layer Pt and Au systems with 0 and 50\% coverages
340 > (arranged in a c(2x4) pattern), our forcefield selections were able to be
341 > indirectly compared to results shown in the supporting information of Tao
342 > {\it et al.} \cite{Tao:2010}. Five layer thick systems, displaying a 557 facet
343 > were constructed, each composed of 480 metal atoms. Double layers systems
344 > were constructed from six layer thick systems where an entire layer was
345 > removed from both displayed facets to create a double step. By design, the
346 > double step system also contains 480 atoms, five layers thick, so energy
347 > comparisons between the arrangements can be made directly. The positions
348 > of the atoms were allowed to relax, along with the box sizes, before a
349 > minimum energy was calculated. Carbon monoxide, equivalent to 50\%
350 > coverage on one side of the metal system was added in a c(2x4) arrangement
351 > and again allowed to relax before a minimum energy was calculated.
352  
353 < The different bulk (and surface) melting temperatures (1337~K for Au
354 < and 2045~K for Pt) suggest that any possible reconstruction may happen at
355 < different temperatures for the two metals.  The bare Au and Pt surfaces were
356 < initially run in the canonical (NVT) ensemble at 800~K and 1000~K
357 < respectively for 100 ps. These temperatures were chosen because the
358 < surfaces were relatively stable at these temperatures when no CO was
359 < present, but experienced additional instability upon addition of CO in the time
360 < frames we were examining. Each surface was exposed to a range of CO
361 < that was initially placed in the vacuum region.  Upon full adsorption,
362 < these amounts correspond to 0\%, 5\%, 25\%, 33\%, and 50\% surface
355 < coverage. Higher coverages were tried, but the CO-CO repulsion was preventing
356 < a higher amount of adsorption.  Because of the difference in binding energies, the Pt
357 < systems very rarely had CO that was not bound to the surface, while
358 < the Au surfaces often had a significant CO population in the gas
359 < phase.  These systems were allowed to reach thermal equilibrium (over
360 < 5 ns) before being run in the microcanonical (NVE) ensemble for
361 < data collection. All of the systems examined had at least 40 ns in the
362 < data collection stage, although simulation times for some of the
363 < systems exceeded 200ns.  All simulations were run using the open
364 < source molecular dynamics package, OpenMD.\cite{Ewald,OOPSE}
353 > Energies for the various systems are displayed in Table ~\ref{tab:steps}. Examining
354 > the Pt systems first, it is apparent that the double layer system is slightly less stable
355 > then the original single step. However, upon addition of carbon monoxide, the
356 > stability is reversed and the double layer system becomes more stable. This result
357 > is in agreement with DFT calculations in Tao {\it et al.}\cite{Tao:2010}, who also show
358 > that the addition of CO leads to a reversal in the most stable system. While our
359 > results agree qualitatively, quantitatively, they are approximately an order of magnitude
360 > different. Looking at additional stability per atom in kcal/mol, the DFT calculations suggest
361 > an increased stability of 0.1 kcal/mol per Pt atom, whereas we are seeing closer to a 0.4 kcal/mol
362 > increase in stability per Pt atom.
363  
364 < % Just results, leave discussion for discussion section
365 < % structure
366 < %       Pt: step wandering, double layers, no triangular motifs
367 < %       Au: step wandering, no double layers
368 < % dynamics
371 < %       diffusion
372 < %       time scale, formation, breakage
373 < \section{Results}
374 < \subsection{Structural remodeling}
375 < Tao et al. showed experimentally that the Pt(557) surface
376 < undergoes two separate reconstructions upon CO
377 < adsorption.\cite{Tao:2010} The first involves a doubling of
378 < the step height and plateau length. Similar behavior has been
379 < seen to occur on numerous surfaces at varying conditions (Ni 977, Si 111, etc).
380 < \cite{Williams:1994,Williams:1991,Pearl} Of the two systems
381 < we examined, the Pt system showed a larger amount of
382 < reconstruction when compared to the Au system. The amount
383 < of reconstruction appears to be correlated to the amount of CO
384 < adsorbed upon the surface.  We believe this is related to the
385 < effect that adsorbate coverage has on edge breakup and surface
386 < diffusion of adatoms. While both systems displayed step-edge
387 < wandering, only the Pt surface underwent the doubling seen by
388 < Tao et al., within the time scales we were modeling. Specifically,
389 < only the 50~\% coverage Pt system was observed to have a
390 < step-edge undergo a complete doubling in the time scales we
391 < were able to monitor. This event encouraged us to allow that
392 < specific system to run for much longer periods during which two
393 < more double layers were created. The other systems, not displaying
394 < any large scale changes of interest, were all stopped after running
395 < for 40 ns in the microcanonical ensemble. Despite no observation
396 < of double layer formation, the other Pt systems tended to show
397 < more cumulative lateral movement of the step-edges when
398 < compared to the Au systems. The 50\% Pt system is highlighted
399 < in Figure \ref{fig:reconstruct} at various times along the simulation
400 < showing the evolution of the system.
364 > The gold systems show a much smaller energy difference between the single and double
365 > systems, likely arising from their lower energy per atom values. Additionally, the weaker
366 > binding of CO to Au is evidenced by the much smaller energy change between the two systems,
367 > when compared to the Pt results. This limited change helps explain our lack of any reconstruction
368 > on the Au systems.
369  
402 The second reconstruction on the Pt(557) surface observed by
403 Tao involved the formation of triangular clusters that stretched
404 across the plateau between two step-edges. Neither system, within
405 our simulated time scales, experiences this reconstruction. A constructed
406 system in which the triangular motifs were constructed on the surface
407 will be explored in future work and is shown in the supporting information.
370  
371 < \subsection{Dynamics}
372 < While atomistic-like simulations of stepped surfaces have been
373 < performed before, they tend to be performed using Monte Carlo
374 < techniques\cite{Williams:1991,Williams:1994}. This allows them
375 < to efficiently sample the equilibrium thermodynamic landscape
376 < but at the expense of ignoring the dynamics of the system. Previous
377 < work by Pearl and Sibener\cite{Pearl}, using STM, has been able to
378 < visualize the coalescing of steps of Ni(977). The time scale of the image
379 < acquisition, $\sim$70 s/image provides an upper bounds for the time
380 < required for the doubling to actually occur. Statistical treatments of step-edges
381 < are adept at analyzing such systems. However, in a system where
382 < the number of steps is limited, examining the individual atoms that make
383 < up the steps can provide useful information as well.
371 > %Table of single step double step calculations
372 > \begin{table}[H]
373 > \caption{Minimized single point energies of unit cell crystals displaying (S)ingle or (D)double steps. Systems are periodic along and perpendicular to the step-edge axes with a large vacuum above the displayed 557 facet. The addition of CO in a 50\% c(2x4) coverage acts as a stabilizing presence and suggests a driving force for the observed reconstruction on the highest coverage Pt system. All energies are in kcal/mol.}
374 > \centering
375 > \begin{tabular}{| c | c | c | c | c | c | c |}
376 > \hline
377 > \textbf{Step} & \textbf{N}\textsubscript{M} & \textbf{N\textsubscript{CO}} & \textbf{Unit-Cell Energy} & \textbf{Energy per M} & \textbf{Energy per CO} & \textbf{Difference per M} \\
378 > \hline
379 > Pt(557)-S & 480 & 0 & -61142.624 & -127.381 & - & 0 \\
380 > Pt(557)-D & 480 & 0 & -61027.841 & -127.141 & - & 0.240 \\
381 > \hline
382 > Pt(557)-S & 480 & 40 & -62960.289 & -131.167 & -45.442 & 0 \\
383 > Pt(557)-D & 480 & 44 & -63040.007 & -131.333 & -45.731 & -0.166\\
384 > \hline
385 > \hline
386 > Au(557)-S & 480 & 0 & -41879.286 & -87.249 & - &0 \\
387 > Au(557)-D & 480 & 0 & -41799.714 & -87.084 & - & 0.165 \\
388 > \hline
389 > Au(557)-S & 480 & 40 & -42423.899 & -88.381 & -13.615 & 0 \\
390 > Au(557)-D & 480 & 44 & -42428.738 & -88.393 & -14.296 & -0.012 \\
391 > \hline
392 > \end{tabular}
393 > \label{tab:steps}
394 > \end{table}
395  
396  
397 < \subsubsection{Transport of surface metal atoms}
398 < %forcedSystems/stepSeparation
399 < The movement or wandering of a step-edge is a cooperative effect
400 < arising from the individual movements, primarily through surface
401 < diffusion, of the atoms making up the step. An ideal metal surface
402 < displaying a low index facet, (111) or (100) is unlikely to experience
403 < much surface diffusion because of the large energetic barrier that must
404 < be overcome to lift an atom out of the surface. The presence of step-edges
405 < on higher-index surfaces provide a source for mobile metal atoms.
406 < Breaking away from the step-edge on a clean surface still imposes an
407 < energetic penalty around $\sim$~40 kcal/mole, but is much less than lifting
408 < the same metal atom out from the surface,  \textgreater~60 kcal/mole, and
409 < the penalty lowers even further when CO is present in sufficient quantities
437 < on the surface. For certain tested distributions of CO, the penalty was lowered
438 < to $\sim$~20 kcal/mole. Once an adatom exists on the surface, its barrier for
439 < diffusion is negligible ( \textless~4 kcal/mole) and is well able to explore the
440 < terrace before potentially rejoining its original step-edge or becoming a part
441 < of a different edge. Atoms traversing separate terraces is a more difficult
442 < process, but can be overcome through a joining and lifting stage which is
443 < examined in the discussion section. By tracking the mobility of individual
444 < metal atoms on the Pt and Au surfaces we were able to determine the relative
445 < diffusion rates and how varying coverages of CO affected the rates. Close
446 < observation of the mobile metal atoms showed that they were typically in
447 < equilibrium with the step-edges, constantly breaking apart and rejoining.
448 < At times their motion was concerted and two or more adatoms would be
449 < observed moving together across the surfaces. The primary challenge in
450 < quantifying the overall surface mobility was in defining ``mobile" vs. ``static" atoms.
397 > \subsection{Pt(557) and Au(557) metal interfaces}
398 > Our Pt system is an orthorhombic periodic box of dimensions
399 > 54.482~x~50.046~x~120.88~\AA~while our Au system has
400 > dimensions of 57.4~x~51.9285~x~100~\AA. The metal slabs
401 > are 9 and 8 atoms deep respectively, corresponding to a slab
402 > thickness of $\sim$21~\AA~ for Pt and $\sim$19~\AA~for Au.
403 > The systems are arranged in a FCC crystal that have been cut
404 > along the (557) plane so that they are periodic in the {\it x} and
405 > {\it y} directions, and have been oriented to expose two aligned
406 > (557) cuts along the extended {\it z}-axis.  Simulations of the
407 > bare metal interfaces at temperatures ranging from 300~K to
408 > 1200~K were performed to confirm the relative
409 > stability of the surfaces without a CO overlayer.  
410  
411 < A particle was considered mobile once it had traveled more than 2~\AA~
412 < between saved configurations of the system (10-100 ps). An atom that was
413 < truly mobile would typically travel much greater than this, but the 2~\AA~ cutoff
414 < was to prevent the in-place vibrational movement of non-surface atoms from
415 < being included in the analysis. Diffusion on  a surface is strongly affected by
416 < local structures and in this work the presence of single and double layer
417 < step-edges causes the diffusion parallel to the step-edges to be different
418 < from the diffusion perpendicular to these edges. This led us to compute
419 < those diffusions separately as seen in Figure \ref{fig:diff}.
411 > The different bulk melting temperatures predicted by EAM
412 > (1345~$\pm$~10~K for Au\cite{Au:melting} and $\sim$~2045~K for
413 > Pt\cite{Pt:melting}) suggest that any reconstructions should happen at
414 > different temperatures for the two metals.  The bare Au and Pt
415 > surfaces were initially run in the canonical (NVT) ensemble at 800~K
416 > and 1000~K respectively for 100 ps. The two surfaces were relatively
417 > stable at these temperatures when no CO was present, but experienced
418 > increased surface mobility on addition of CO. Each surface was then
419 > dosed with different concentrations of CO that was initially placed in
420 > the vacuum region.  Upon full adsorption, these concentrations
421 > correspond to 0\%, 5\%, 25\%, 33\%, and 50\% surface coverage. Higher
422 > coverages resulted in the formation of a double layer of CO, which
423 > introduces artifacts that are not relevant to (557) reconstruction.
424 > Because of the difference in binding energies, nearly all of the CO
425 > was bound to the Pt surface, while the Au surfaces often had a
426 > significant CO population in the gas phase.  These systems were
427 > allowed to reach thermal equilibrium (over 5~ns) before being run in
428 > the microcanonical (NVE) ensemble for data collection. All of the
429 > systems examined had at least 40~ns in the data collection stage,
430 > although simulation times for some Pt of the systems exceeded 200~ns.
431 > Simulations were carried out using the open source molecular dynamics
432 > package, OpenMD.\cite{Ewald,OOPSE,openmd}
433  
434 < \subsubsection{Double layer formation}
435 < The increased amounts of diffusion on Pt at the higher CO coverages appears
436 < to play a primary role in the formation of double layers, although this conclusion
437 < does not explain the 33\% coverage Pt system. On the 50\% system, three
438 < separate layers were formed over the extended run time of this system. As
439 < mentioned earlier, previous experimental work has given some insight into the
440 < upper bounds of the time required for enough atoms to move around to allow two
441 < steps to coalesce\cite{Williams:1991,Pearl}. As seen in Figure \ref{fig:reconstruct},
442 < the first appearance of a double layer, a nodal site, appears at 19 ns into the
443 < simulation. Within 12 ns, nearly half of the step has formed the double layer and
444 < by 86 ns, a smooth complete layer has formed. The double layer is ``complete" by
445 < 37 ns but is a bit rough. From the appearance of the first node to the initial doubling
446 < of the layers ignoring their roughness took $\sim$~20 ns. Another ~40 ns was
447 < necessary for the layer to completely straighten. The other two layers in this
448 < simulation form over a period of 22 ns and 42 ns respectively. Comparing this to
449 < the upper bounds of the image scan, it is likely that aspects of this reconstruction
478 < occur very quickly.
434 >
435 > % RESULTS
436 > %
437 > \section{Results}
438 > \subsection{Structural remodeling}
439 > The bare metal surfaces experienced minor roughening of the step-edge
440 > because of the elevated temperatures, but the (557) face was stable
441 > throughout the simulations. The surfaces of both systems, upon dosage
442 > of CO, began to undergo extensive remodeling that was not observed in
443 > the bare systems. Reconstructions of the Au systems were limited to
444 > breakup of the step-edges and some step wandering. The lower coverage
445 > Pt systems experienced similar step edge wandering but to a greater
446 > extent. The 50\% coverage Pt system was unique among our simulations
447 > in that it formed well-defined and stable double layers through step
448 > coalescence, similar to results reported by Tao {\it et
449 >  al}.\cite{Tao:2010}
450  
451 + \subsubsection{Step wandering}
452 + The bare surfaces for both metals showed minimal step-wandering at
453 + their respective temperatures. As the CO coverage increased however,
454 + the mobility of the surface atoms, described through adatom diffusion
455 + and step-edge wandering, also increased.  Except for the 50\% Pt
456 + system where step coalescence occurred, the step-edges in the other
457 + simulations preferred to keep nearly the same distance between steps
458 + as in the original (557) lattice, $\sim$13\AA~for Pt and
459 + $\sim$14\AA~for Au.  Previous work by Williams {\it et
460 +  al}.\cite{Williams:1991, Williams:1994} highlights the repulsion
461 + that exists between step-edges even when no direct interactions are
462 + present in the system. This repulsion is caused by an entropic barrier
463 + that arises from the fact that steps cannot cross over one
464 + another. This entropic repulsion does not completely define the
465 + interactions between steps, however, so it is possible to observe step
466 + coalescence on some surfaces.\cite{Williams:1991} The presence and
467 + concentration of adsorbates, as shown in this work, can affect
468 + step-step interactions, potentially leading to a new surface structure
469 + as the thermodynamic equilibrium.
470 +
471 + \subsubsection{Double layers}
472 + Tao {\it et al}.\cite{Tao:2010} have shown experimentally that the
473 + Pt(557) surface undergoes two separate reconstructions upon CO
474 + adsorption.  The first involves a doubling of the step height and
475 + plateau length.  Similar behavior has been seen on a number of
476 + surfaces at varying conditions, including Ni(977) and
477 + Si(111).\cite{Williams:1994,Williams:1991,Pearl} Of the two systems we
478 + examined, the Pt system showed a greater propensity for reconstruction
479 + because of the larger surface mobility and the greater extent of step
480 + wandering.  The amount of reconstruction was strongly correlated to
481 + the amount of CO adsorbed upon the surface.  This appears to be
482 + related to the effect that adsorbate coverage has on edge breakup and
483 + on the surface diffusion of metal adatoms. Only the 50\% Pt surface
484 + underwent the doubling seen by Tao {\it et al}.\cite{Tao:2010} within
485 + the time scales studied here.  Over a longer time scale (150~ns) two
486 + more double layers formed on this surface. Although double layer
487 + formation did not occur in the other Pt systems, they exhibited more
488 + step-wandering and roughening compared to their Au counterparts. The
489 + 50\% Pt system is highlighted in Figure \ref{fig:reconstruct} at
490 + various times along the simulation showing the evolution of a double
491 + layer step-edge.
492 +
493 + The second reconstruction observed by Tao {\it et al}.\cite{Tao:2010}
494 + involved the formation of triangular clusters that stretched across
495 + the plateau between two step-edges. Neither of the simulated metal
496 + interfaces, within the 40~ns time scale or the extended time of 150~ns
497 + for the 50\% Pt system, experienced this reconstruction.
498 +
499   %Evolution of surface
500   \begin{figure}[H]
501 < \includegraphics[width=\linewidth]{ProgressionOfDoubleLayerFormation_yellowCircle.png}
502 < \caption{The Pt(557) / 50\% CO system at a sequence of times after
503 <  initial exposure to the CO: (a) 258 ps, (b) 19 ns, (c) 31.2 ns, and
504 <  (d) 86.1 ns. Disruption of the (557) step-edges occurs quickly.  The
501 > \includegraphics[width=\linewidth]{EPS_ProgressionOfDoubleLayerFormation}
502 > \caption{The Pt(557) / 50\% CO interface upon exposure to the CO: (a)
503 >  258~ps, (b) 19~ns, (c) 31.2~ns, and (d) 86.1~ns after
504 >  exposure. Disruption of the (557) step-edges occurs quickly.  The
505    doubling of the layers appears only after two adjacent step-edges
506    touch.  The circled spot in (b) nucleated the growth of the double
507    step observed in the later configurations.}
508    \label{fig:reconstruct}
509   \end{figure}
510  
511 + \subsection{Dynamics}
512 + Previous experimental work by Pearl and Sibener\cite{Pearl}, using
513 + STM, has been able to capture the coalescence of steps on Ni(977). The
514 + time scale of the image acquisition, $\sim$70~s/image, provides an
515 + upper bound for the time required for the doubling to occur. By
516 + utilizing Molecular Dynamics we are able to probe the dynamics of
517 + these reconstructions at elevated temperatures and in this section we
518 + provide data on the timescales for transport properties,
519 + e.g. diffusion and layer formation time.
520 +
521 +
522 + \subsubsection{Transport of surface metal atoms}
523 + %forcedSystems/stepSeparation
524 +
525 + The wandering of a step-edge is a cooperative effect arising from the
526 + individual movements of the atoms making up the steps. An ideal metal
527 + surface displaying a low index facet, (111) or (100), is unlikely to
528 + experience much surface diffusion because of the large energetic
529 + barrier that must be overcome to lift an atom out of the surface. The
530 + presence of step-edges and other surface features on higher-index
531 + facets provides a lower energy source for mobile metal atoms.  Using
532 + our potential model, single-atom break-away from a step-edge on a
533 + clean surface still imposes an energetic penalty around
534 + $\sim$~45~kcal/mol, but this is certainly easier than lifting the same
535 + metal atom vertically out of the surface, \textgreater~60~kcal/mol.
536 + The penalty lowers significantly when CO is present in sufficient
537 + quantities on the surface. For certain distributions of CO, the
538 + energetic penalty can fall to as low as $\sim$~20~kcal/mol. The
539 + configurations that create these lower barriers are detailed in the
540 + discussion section below.
541 +
542 + Once an adatom exists on the surface, the barrier for diffusion is
543 + negligible (\textless~4~kcal/mol for a Pt adatom). These adatoms are
544 + then able to explore the terrace before rejoining either their
545 + original step-edge or becoming a part of a different edge. It is an
546 + energetically unfavorable process with a high barrier for an atom to
547 + traverse to a separate terrace although the presence of CO can lower
548 + the energy barrier required to lift or lower an adatom. By tracking
549 + the mobility of individual metal atoms on the Pt and Au surfaces we
550 + were able to determine the relative diffusion constants, as well as
551 + how varying coverages of CO affect the diffusion. Close observation of
552 + the mobile metal atoms showed that they were typically in equilibrium
553 + with the step-edges.  At times, their motion was concerted, and two or
554 + more adatoms would be observed moving together across the surfaces.
555 +
556 + A particle was considered ``mobile'' once it had traveled more than
557 + 2~\AA~ between saved configurations of the system (typically 10-100
558 + ps). A mobile atom would typically travel much greater distances than
559 + this, but the 2~\AA~cutoff was used to prevent swamping the diffusion
560 + data with the in-place vibrational movement of buried atoms. Diffusion
561 + on a surface is strongly affected by local structures and the presence
562 + of single and double layer step-edges causes the diffusion parallel to
563 + the step-edges to be larger than the diffusion perpendicular to these
564 + edges. Parallel and perpendicular diffusion constants are shown in
565 + Figure \ref{fig:diff}.  Diffusion parallel to the step-edge is higher
566 + than diffusion perpendicular to the edge because of the lower energy
567 + barrier associated with sliding along an edge compared to breaking
568 + away to form an isolated adatom.
569 +
570 + %Diffusion graph
571   \begin{figure}[H]
572 < \includegraphics[width=\linewidth]{DiffusionComparison_errorXY_remade.pdf}
572 > \includegraphics[width=\linewidth]{Portrait_DiffusionComparison_1}
573   \caption{Diffusion constants for mobile surface atoms along directions
574    parallel ($\mathbf{D}_{\parallel}$) and perpendicular
575    ($\mathbf{D}_{\perp}$) to the (557) step-edges as a function of CO
576 <  surface coverage.  Diffusion parallel to the step-edge is higher
577 <  than that perpendicular to the edge because of the lower energy
578 <  barrier associated with traversing along the edge as compared to
579 <  completely breaking away. Additionally, the observed
501 <  maximum and subsequent decrease for the Pt system suggests that the
502 <  CO self-interactions are playing a significant role with regards to
503 <  movement of the Pt atoms around and across the surface. }
576 >  surface coverage.  The two reported diffusion constants for the 50\%
577 >  Pt system correspond to a 20~ns period before the formation of the
578 >  double layer (upper points), and to the full 40~ns sampling period
579 >  (lower points).}
580   \label{fig:diff}
581   \end{figure}
582  
583 + The weaker Au-CO interaction is evident in the weak CO-coverage
584 + dependance of Au diffusion. This weak interaction leads to lower
585 + observed coverages when compared to dosage amounts. This further
586 + limits the effect the CO can have on surface diffusion. The correlation
587 + between coverage and Pt diffusion rates shows a near linear relationship
588 + at the earliest times in the simulations. Following double layer formation,
589 + however, there is a precipitous drop in adatom diffusion. As the double
590 + layer forms, many atoms that had been tracked for mobility data have
591 + now been buried, resulting in a smaller reported diffusion constant. A
592 + secondary effect of higher coverages is CO-CO cross interactions that
593 + lower the effective mobility of the Pt adatoms that are bound to each CO.
594 + This effect would become evident only at higher coverages. A detailed
595 + account of Pt adatom energetics follows in the Discussion.
596 +
597 + \subsubsection{Dynamics of double layer formation}
598 + The increased diffusion on Pt at the higher CO coverages is the primary
599 + contributor to double layer formation. However, this is not a complete
600 + explanation -- the 33\%~Pt system has higher diffusion constants, but
601 + did not show any signs of edge doubling in 40~ns. On the 50\%~Pt
602 + system, one double layer formed within the first 40~ns of simulation time,
603 + while two more were formed as the system was allowed to run for an
604 + additional 110~ns (150~ns total). This suggests that this reconstruction
605 + is a rapid process and that the previously mentioned upper bound is a
606 + very large overestimate.\cite{Williams:1991,Pearl} In this system the first
607 + appearance of a double layer appears at 19~ns into the simulation.
608 + Within 12~ns of this nucleation event, nearly half of the step has formed
609 + the double layer and by 86~ns the complete layer has flattened out.
610 + From the appearance of the first nucleation event to the first observed
611 + double layer, the process took $\sim$20~ns. Another $\sim$40~ns was
612 + necessary for the layer to completely straighten. The other two layers in
613 + this simulation formed over periods of 22~ns and 42~ns respectively.
614 + A possible explanation for this rapid reconstruction is the elevated
615 + temperatures under which our systems were simulated. The process
616 + would almost certainly take longer at lower temperatures. Additionally,
617 + our measured times for completion of the doubling after the appearance
618 + of a nucleation site are likely affected by our periodic boxes. A longer
619 + step-edge will likely take longer to ``zipper''.
620  
621  
509
622   %Discussion
623   \section{Discussion}
624 < In this paper we have shown that we were able to accurately model the initial reconstruction of the
625 < Pt(557) surface upon CO adsorption as shown by Tao et al. \cite{Tao:2010}. More importantly, we
626 < were able to observe the dynamic processes necessary for this reconstruction.
624 > We have shown that a classical potential is able to model the initial
625 > reconstruction of the Pt(557) surface upon CO adsorption, and have
626 > reproduced the double layer structure observed by Tao {\it et
627 >  al}.\cite{Tao:2010}. Additionally, this reconstruction appears to be
628 > rapid -- occurring within 100 ns of the initial exposure to CO.  Here
629 > we discuss the features of the classical potential that are
630 > contributing to the stability and speed of the Pt(557) reconstruction.
631  
632 < \subsection{Mechanism for restructuring}
633 < Comparing the results from simulation to those reported previously by
634 < Tao et al.\cite{Tao:2010} the similarities in the Pt-CO system are quite
635 < strong. As shown in Figure \ref{fig:reconstruct}, the simulated Pt
636 < system under a CO atmosphere will restructure by doubling the terrace
637 < heights. The restructuring occurs slowly, one to two Pt atoms at a time.
638 < Looking at individual configurations of the system, the adatoms either
639 < break away from the step-edge and stay on the lower terrace or they lift
640 < up onto the higher terrace. Once ``free'' they will diffuse on the terrace
641 < until reaching another step-edge or coming back to their original edge.  
642 < This combination of growth and decay of the step-edges is in a state of
643 < dynamic equilibrium. However, once two previously separated edges
644 < meet as shown in Figure 1.B, this meeting point tends to act as a focus
645 < or growth point for the rest of the edge to meet up, akin to that of a zipper.
530 < From the handful of cases where a double layer was formed during the
531 < simulation, measuring from the initial appearance of a growth point, the
532 < double layer tends to be fully formed within $\sim$~35 ns.
632 > \subsection{Diffusion}
633 > The perpendicular diffusion constant appears to be the most important
634 > indicator of double layer formation. As highlighted in Figure
635 > \ref{fig:reconstruct}, the formation of the double layer did not begin
636 > until a nucleation site appeared.  Williams {\it et
637 >  al}.\cite{Williams:1991,Williams:1994} cite an effective edge-edge
638 > repulsion arising from the inability of edge crossing.  This repulsion
639 > must be overcome to allow step coalescence.  A larger
640 > $\textbf{D}_\perp$ value implies more step-wandering and a larger
641 > chance for the stochastic meeting of two edges to create a nucleation
642 > point.  Diffusion parallel to the step-edge can help ``zipper'' up a
643 > nascent double layer. This helps explain the rapid time scale for
644 > double layer completion after the appearance of a nucleation site, while
645 > the initial appearance of the nucleation site was unpredictable.
646  
647 < A number of possible mechanisms exist to explain the role of adsorbed
648 < CO in restructuring the Pt surface. Quadrupolar repulsion between adjacent
649 < CO molecules adsorbed on the surface is one likely possibility.  However,
650 < the quadrupole-quadrupole interaction is short-ranged and is attractive for
651 < some orientations.  If the CO molecules are ``locked'' in a specific orientation
652 < relative to each other, through atop adsorption perhaps, this explanation
653 < gains some weight.  The energetic repulsion between two CO located a
654 < distance of 2.77~\AA~apart (nearest-neighbor distance of Pt) with both in
655 < a  vertical orientation is 8.62 kcal/mole. Moving the CO apart to the second
656 < nearest-neighbor distance of 4.8~\AA~or 5.54~\AA~drops the repulsion to
657 < nearly 0 kcal/mole. Allowing the CO's to leave a purely vertical orientation
658 < also quickly drops the repulsion, a minimum is reached at $\sim$24 degrees
659 < of 6.2 kcal/mole. As mentioned above, the energy barrier for surface diffusion
660 < of a Pt adatom is only 4 kcal/mole. So this repulsion between CO can help
661 < increase the surface diffusion. However, the residence time of CO was
662 < examined and while the majority of the CO is on or near the surface throughout
663 < the run, it is extremely mobile. This mobility suggests that the CO are more
664 < likely to shift their positions without necessarily dragging the Pt along with them.
647 > \subsection{Mechanism for restructuring}
648 > Since the Au surface showed no large scale restructuring in any of our
649 > simulations, our discussion will focus on the 50\% Pt-CO system which
650 > did exhibit doubling. A number of possible mechanisms exist to explain
651 > the role of adsorbed CO in restructuring the Pt surface. Quadrupolar
652 > repulsion between adjacent CO molecules adsorbed on the surface is one
653 > possibility.  However, the quadrupole-quadrupole interaction is
654 > short-ranged and is attractive for some orientations.  If the CO
655 > molecules are ``locked'' in a vertical orientation, through atop
656 > adsorption for example, this explanation would gain credence. Within
657 > the framework of our classical potential, the calculated energetic
658 > repulsion between two CO molecules located a distance of
659 > 2.77~\AA~apart (nearest-neighbor distance of Pt) and both in a
660 > vertical orientation, is 8.62 kcal/mol. Moving the CO to the second
661 > nearest-neighbor distance of 4.8~\AA~drops the repulsion to nearly
662 > 0. Allowing the CO to rotate away from a purely vertical orientation
663 > also lowers the repulsion. When the carbons are locked at a distance
664 > of 2.77~\AA, a minimum of 6.2 kcal/mol is reached when the angle
665 > between the 2 CO is $\sim$24\textsuperscript{o}.  The calculated
666 > barrier for surface diffusion of a Pt adatom is only 4 kcal/mol, so
667 > repulsion between adjacent CO molecules bound to Pt could indeed
668 > increase the surface diffusion. However, the residence time of CO on
669 > Pt suggests that the CO molecules are extremely mobile, with diffusion
670 > constants 40 to 2500 times larger than surface Pt atoms. This mobility
671 > suggests that the CO molecules jump between different Pt atoms
672 > throughout the simulation.  However, they do stay bound to individual
673 > Pt atoms for long enough to modify the local energy landscape for the
674 > mobile adatoms.
675  
676 < Another possible and more likely mechanism for the restructuring is in the
677 < destabilization of strong Pt-Pt interactions by CO adsorbed on surface
678 < Pt atoms.  This would then have the effect of increasing surface mobility
679 < of these atoms.  To test this hypothesis, numerous configurations of
680 < CO in varying quantities were arranged on the higher and lower plateaus
681 < around a step on a otherwise clean Pt(557) surface. One representative
682 < configuration is displayed in Figure \ref{fig:lambda}. Single or concerted movement
683 < of Pt atoms was then examined to determine possible barriers. Because
684 < the movement was forced along a pre-defined reaction coordinate that may differ
685 < from the true minimum of this path, only the beginning and ending energies
686 < are displayed in Table \ref{tab:energies}. These values suggest that the presence of CO at suitable
687 < locations can lead to lowered barriers for Pt breaking apart from the step-edge.
688 < Additionally, as highlighted in Figure \ref{fig:lambda}, the presence of CO makes the
689 < burrowing and lifting of adatoms favorable, whereas without CO, the process is neutral
690 < in terms of energetics.
676 > A different interpretation of the above mechanism which takes the
677 > large mobility of the CO into account, would be in the destabilization
678 > of Pt-Pt interactions due to bound CO.  Destabilizing Pt-Pt bonds at
679 > the edges could lead to increased step-edge breakup and diffusion. On
680 > the bare Pt(557) surface the barrier to completely detach an edge atom
681 > is $\sim$43~kcal/mol, as is shown in configuration (a) in Figures
682 > \ref{fig:SketchGraphic} \& \ref{fig:SketchEnergies}. For certain
683 > configurations, cases (e), (g), and (h), the barrier can be lowered to
684 > $\sim$23~kcal/mol by the presence of bound CO molecules. In these
685 > instances, it becomes energetically favorable to roughen the edge by
686 > introducing a small separation of 0.5 to 1.0~\AA. This roughening
687 > becomes immediately obvious in simulations with significant CO
688 > populations. The roughening is present to a lesser extent on surfaces
689 > with lower CO coverage (and even on the bare surfaces), although in
690 > these cases it is likely due to random fluctuations that squeeze out
691 > step-edge atoms. Step-edge breakup by direct single-atom translations
692 > (as suggested by these energy curves) is probably a worst-case
693 > scenario.  Multistep mechanisms in which an adatom moves laterally on
694 > the surface after being ejected would be more energetically favorable.
695 > This would leave the adatom alongside the ledge, providing it with
696 > five nearest neighbors.  While fewer than the seven neighbors it had
697 > as part of the step-edge, it keeps more Pt neighbors than the three
698 > neighbors an isolated adatom has on the terrace. In this proposed
699 > mechanism, the CO quadrupolar repulsion still plays a role in the
700 > initial roughening of the step-edge, but not in any long-term bonds
701 > with individual Pt atoms.  Higher CO coverages create more
702 > opportunities for the crowded CO configurations shown in Figure
703 > \ref{fig:SketchGraphic}, and this is likely to cause an increased
704 > propensity for step-edge breakup.
705  
706 + %Sketch graphic of different configurations
707 + \begin{figure}[H]
708 + \includegraphics[width=\linewidth]{COpaths}
709 + \caption{Configurations used to investigate the mechanism of step-edge
710 +  breakup on Pt(557). In each case, the central (starred) atom was
711 +  pulled directly across the surface away from the step edge.  The Pt
712 +  atoms on the upper terrace are colored dark grey, while those on the
713 +  lower terrace are in white.  In each of these configurations, some
714 +  of the atoms (highlighted in blue) had CO molecules bound in the
715 +  vertical atop position.  The energies of these configurations as a
716 +  function of central atom displacement are displayed in Figure
717 +  \ref{fig:SketchEnergies}.}
718 + \label{fig:SketchGraphic}
719 + \end{figure}
720 +
721 + %energy graph corresponding to sketch graphic
722 + \begin{figure}[H]
723 + \includegraphics[width=\linewidth]{Portrait_SeparationComparison}
724 + \caption{Energies for displacing a single edge atom perpendicular to
725 +  the step edge as a function of atomic displacement. Each of the
726 +  energy curves corresponds to one of the labeled configurations in
727 +  Figure \ref{fig:SketchGraphic}, and the energies are referenced to
728 +  the unperturbed step-edge.  Certain arrangements of bound CO
729 +  (notably configurations g and h) can lower the energetic barrier for
730 +  creating an adatom relative to the bare surface (configuration a).}
731 + \label{fig:SketchEnergies}
732 + \end{figure}
733 +
734 + While configurations of CO on the surface are able to increase
735 + diffusion and the likelihood of edge wandering, this does not provide
736 + a complete explanation for the formation of double layers. If adatoms
737 + were constrained to their original terraces then doubling could not
738 + occur.  A mechanism for vertical displacement of adatoms at the
739 + step-edge is required to explain the doubling.
740 +
741 + We have discovered one possible mechanism for a CO-mediated vertical
742 + displacement of Pt atoms at the step edge. Figure \ref{fig:lambda}
743 + shows four points along a reaction coordinate in which a CO-bound
744 + adatom along the step-edge ``burrows'' into the edge and displaces the
745 + original edge atom onto the higher terrace.  A number of events
746 + similar to this mechanism were observed during the simulations.  We
747 + predict an energetic barrier of 20~kcal/mol for this process (in which
748 + the displaced edge atom follows a curvilinear path into an adjacent
749 + 3-fold hollow site).  The barrier heights we obtain for this reaction
750 + coordinate are approximate because the exact path is unknown, but the
751 + calculated energy barriers would be easily accessible at operating
752 + conditions.  Additionally, this mechanism is exothermic, with a final
753 + energy 15~kcal/mol below the original $\lambda = 0$ configuration.
754 + When CO is not present and this reaction coordinate is followed, the
755 + process is endothermic by 3~kcal/mol.  The difference in the relative
756 + energies for the $\lambda=0$ and $\lambda=1$ case when CO is present
757 + provides strong support for CO-mediated Pt-Pt interactions giving rise
758 + to the doubling reconstruction.
759 +
760   %lambda progression of Pt -> shoving its way into the step
761   \begin{figure}[H]
762 < \includegraphics[width=\linewidth]{lambdaProgression_atopCO.png}
763 < \caption{A model system of the Pt(557) surface was used as the framework
764 < for exploring energy barriers along a reaction coordinate. Various numbers,
765 < placements, and rotations of CO were examined as they affect Pt movement.
766 < The coordinate displayed in this Figure was a representative run. As shown
767 < in Table \ref{tab:rxcoord}, relative to the energy of the system at 0\%, there
768 < is a slight decrease upon insertion of the Pt atom into the step-edge along
578 < with the resultant lifting of the other Pt atom when CO is present at certain positions.}
762 > \includegraphics[width=\linewidth]{EPS_rxnCoord}
763 > \caption{Points along a possible reaction coordinate for CO-mediated
764 >  edge doubling. Here, a CO-bound adatom burrows into an established
765 >  step edge and displaces an edge atom onto the upper terrace along a
766 >  curvilinear path.  The approximate barrier for the process is
767 >  20~kcal/mol, and the complete process is exothermic by 15~kcal/mol
768 >  in the presence of CO, but is endothermic by 3~kcal/mol without CO.}
769   \label{fig:lambda}
770   \end{figure}
771  
772 + The mechanism for doubling on the Pt(557) surface appears to require
773 + the cooperation of at least two distinct processes. For complete
774 + doubling of a layer to occur there must be a breakup of one
775 + terrace. These atoms must then ``disappear'' from that terrace, either
776 + by travelling to the terraces above or below their original levels.
777 + The presence of CO helps explain mechanisms for both of these
778 + situations. There must be sufficient breakage of the step-edge to
779 + increase the concentration of adatoms on the surface and these adatoms
780 + must then undergo the burrowing highlighted above (or a comparable
781 + mechanism) to create the double layer.  With sufficient time, these
782 + mechanisms working in concert lead to the formation of a double layer.
783  
784 + \subsection{CO Removal and double layer stability}
785 + Once the double layers had formed on the 50\%~Pt system, they remained
786 + stable for the rest of the simulation time with minimal movement.
787 + Random fluctuations that involved small clusters or divots were
788 + observed, but these features typically healed within a few
789 + nanoseconds.  Within our simulations, the formation of the double
790 + layer appeared to be irreversible and a double layer was never
791 + observed to split back into two single layer step-edges while CO was
792 + present.
793  
794 < \subsection{Diffusion}
795 < As shown in the results section, the diffusion parallel to the step-edge tends to be
796 < much larger than that perpendicular to the step-edge, likely because of the dynamic
797 < equilibrium that is established between the step-edge and adatom interface. The coverage
798 < of CO also appears to play a slight role in relative rates of diffusion, as shown in Figure \ref{fig:diff}.
799 < The
800 < Thus, the bottleneck of the double layer formation appears to be the initial formation
801 < of this growth point, which seems to be somewhat of a stochastic event. Once it
802 < appears, parallel diffusion, along the now slightly angled step-edge, will allow for
803 < a faster formation of the double layer than if the entire process were dependent on
804 < only perpendicular diffusion across the plateaus. Thus, the larger $D_{\perp}$, the
805 < more likely a growth point is to be formed.
596 < \\
794 > To further gauge the effect CO has on this surface, additional
795 > simulations were run starting from a late configuration of the 50\%~Pt
796 > system that had already formed double layers. These simulations then
797 > had their CO molecules suddenly removed.  The double layer broke apart
798 > rapidly in these simulations, showing a well-defined edge-splitting
799 > after 100~ps. Configurations of this system are shown in Figure
800 > \ref{fig:breaking}. The coloring of the top and bottom layers helps to
801 > show how much mixing the edges experience as they split. These systems
802 > were only examined for 10~ns, and within that time despite the initial
803 > rapid splitting, the edges only moved another few \AA~apart. It is
804 > possible that with longer simulation times, the (557) surface recovery
805 > observed by Tao {\it et al}.\cite{Tao:2010} could also be recovered.
806  
598
807   %breaking of the double layer upon removal of CO
808   \begin{figure}[H]
809 < \includegraphics[width=\linewidth]{doubleLayerBreaking_greenBlue_whiteLetters.png}
810 < %:
811 < \caption{(A)  0 ps, (B) 100 ps, (C) 1 ns, after the removal of CO. The presence of the CO
812 < helped maintain the stability of the double layer and upon removal the two layers break
813 < and begin separating. The separation is not a simple pulling apart however, rather
814 < there is a mixing of the lower and upper atoms at the edge.}
809 > \includegraphics[width=\linewidth]{EPS_doubleLayerBreaking}
810 > \caption{Behavior of an established (111) double step after removal of
811 >  the adsorbed CO: (A) 0~ps, (B) 100~ps, and (C) 1~ns after the
812 >  removal of CO.  Nearly immediately after the CO is removed, the
813 >  step edge reforms in a (100) configuration, which is also the step
814 >  type seen on clean (557) surfaces. The step separation involves
815 >  significant mixing of the lower and upper atoms at the edge.}
816   \label{fig:breaking}
817   \end{figure}
818  
819  
611
612
820   %Peaks!
821 < \begin{figure}[H]
822 < \includegraphics[width=\linewidth]{doublePeaks_noCO.png}
823 < \caption{At the initial formation of this double layer  ( $\sim$ 37 ns) there is a degree
824 < of roughness inherent to the edge. The next $\sim$ 40 ns show the edge with
825 < aspects of waviness and by 80 ns the double layer is completely formed and smooth. }
826 < \label{fig:peaks}
827 < \end{figure}
821 > %\begin{figure}[H]
822 > %\includegraphics[width=\linewidth]{doublePeaks_noCO.png}
823 > %\caption{At the initial formation of this double layer  ( $\sim$ 37 ns) there is a degree
824 > %of roughness inherent to the edge. The next $\sim$ 40 ns show the edge with
825 > %aspects of waviness and by 80 ns the double layer is completely formed and smooth. }
826 > %\label{fig:peaks}
827 > %\end{figure}
828  
829  
830   %Don't think I need this
831   %clean surface...
832   %\begin{figure}[H]
833 < %\includegraphics[width=\linewidth]{557_300K_cleanPDF.pdf}
833 > %\includegraphics[width=\linewidth]{557_300K_cleanPDF}
834   %\caption{}
835  
836   %\end{figure}
# Line 631 | Line 838 | In this work we have shown the reconstruction of the P
838  
839  
840   \section{Conclusion}
841 < In this work we have shown the reconstruction of the Pt(557) crystalline surface upon adsorption of CO in < $\mu s$. Only the highest coverage Pt system showed this initial reconstruction similar to that seen previously. The strong interaction between Pt and CO and the limited interaction between Au and CO helps explain the differences between the two systems.
841 > The strength and directionality of the Pt-CO binding interaction, as
842 > well as the large quadrupolar repulsion between atop-bound CO
843 > molecules, help to explain the observed increase in surface mobility
844 > of Pt(557) and the resultant reconstruction into a double-layer
845 > configuration at the highest simulated CO-coverages.  The weaker Au-CO
846 > interaction results in significantly lower adataom diffusion
847 > constants, less step-wandering, and a lack of the double layer
848 > reconstruction on the Au(557) surface.
849  
850 + An in-depth examination of the energetics shows the important role CO
851 + plays in increasing step-breakup and in facilitating edge traversal
852 + which are both necessary for double layer formation.
853 +
854   %Things I am not ready to remove yet
855  
856   %Table of Diffusion Constants
# Line 655 | Line 873 | In this work we have shown the reconstruction of the P
873   % \end{tabular}
874   % \end{table}
875  
876 < \section{Acknowledgments}
877 < Support for this project was provided by the National Science
878 < Foundation under grant CHE-0848243 and by the Center for Sustainable
879 < Energy at Notre Dame (cSEND). Computational time was provided by the
880 < Center for Research Computing (CRC) at the University of Notre Dame.
881 <
876 > \begin{acknowledgement}
877 >  We gratefully acknowledge conversations with Dr. William
878 >  F. Schneider and Dr. Feng Tao.  Support for this project was
879 >  provided by the National Science Foundation under grant CHE-0848243
880 >  and by the Center for Sustainable Energy at Notre Dame
881 >  (cSEND). Computational time was provided by the Center for Research
882 >  Computing (CRC) at the University of Notre Dame.
883 > \end{acknowledgement}
884   \newpage
885 < \bibliography{firstTryBibliography}
886 < \end{doublespace}
885 > \bibstyle{achemso}
886 > \bibliography{COonPtAu}
887 > %\end{doublespace}
888 >
889 > \begin{tocentry}
890 > \begin{wrapfigure}{l}{0.5\textwidth}
891 > \begin{center}
892 > \includegraphics[width=\linewidth]{TOC_doubleLayer}
893 > \end{center}
894 > \end{wrapfigure}
895 > A reconstructed Pt(557) surface after 86~ns exposure to a half a
896 > monolayer of CO.  The double layer that forms is a result of
897 > CO-mediated step-edge wandering as well as a burrowing mechanism that
898 > helps lift edge atoms onto an upper terrace.
899 > \end{tocentry}
900 >
901   \end{document}

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