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# Line 58 | Line 58 | Notre Dame, Indiana 46556}
58   Notre Dame, Indiana 46556}
59  
60   %Date
61 < \date{Dec 15, 2012}
61 > \date{Mar 5, 2013}
62  
63   %authors
64  
# Line 68 | Line 68 | Notre Dame, Indiana 46556}
68   \begin{doublespace}
69  
70   \begin{abstract}
71 + We examine surface reconstructions of Pt and Au(557) under
72 + various CO coverages using molecular dynamics in order to
73 + explore possible mechanisms for any observed reconstructions
74 + and their dynamics. The metal-CO interactions were parameterized
75 + as part of this work so that an efficient large-scale treatment of
76 + this system could be undertaken. The large difference in binding
77 + strengths of the metal-CO interactions was found to play a significant
78 + role with regards to step-edge stability and adatom diffusion. A
79 + small correlation between coverage and the diffusion constant
80 + was also determined. The energetics of CO adsorbed to the surface
81 + is sufficient to explain the reconstructions observed on the Pt
82 + systems and the lack  of reconstruction of the Au systems.
83  
84   \end{abstract}
85  
# Line 100 | Line 112 | This work an effort to understand the mechanism and ti
112   reversible restructuring under exposure to moderate pressures of
113   carbon monoxide.\cite{Tao:2010}
114  
115 < This work an effort to understand the mechanism and timescale for
115 > This work is an investigation into the mechanism and timescale for
116   surface restructuring using molecular simulations.  Since the dynamics
117 < of the process is of particular interest, we utilize classical force
117 > of the process are of particular interest, we employ classical force
118   fields that represent a compromise between chemical accuracy and the
119 < computational efficiency necessary to observe the process of interest.
119 > computational efficiency necessary to simulate the process of interest.
120 > Since restructuring typically occurs as a result of specific interactions of the
121 > catalyst with adsorbates, in this work, two metal systems exposed
122 > to carbon monoxide were examined. The Pt(557) surface has already been shown
123 > to undergo a large scale reconstruction under certain conditions.\cite{Tao:2010}
124 > The Au(557) surface, because of a weaker interaction with CO, is seen as less
125 > likely to undergo this kind of reconstruction. However, Peters et al.\cite{Peters:2000}
126 > and Piccolo et al.\cite{Piccolo:2004} have both observed CO-induced
127 > reconstruction of a Au(111) surface. Peters et al. saw a relaxation to the
128 > 22 x $\sqrt{3}$ cell. They argued that only a few Au atoms
129 > become adatoms, limiting the stress of this reconstruction while
130 > allowing the rest to relax and approach the ideal (111)
131 > configuration. They did not see the usual herringbone pattern being greatly
132 > affected by this relaxation. Piccolo et al. on the other hand, did see a
133 > disruption of the herringbone pattern as CO was adsorbed to the
134 > surface. Both groups suggested that the preference CO shows for
135 > low-coordinated Au atoms was the primary driving force for the reconstruction.
136  
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.
137  
138 +
139   %Platinum molecular dynamics
140   %gold molecular dynamics
141  
142   \section{Simulation Methods}
143 < The challenge in modeling any solid/gas interface problem is the
143 > The challenge in modeling any solid/gas interface is the
144   development of a sufficiently general yet computationally tractable
145   model of the chemical interactions between the surface atoms and
146   adsorbates.  Since the interfaces involved are quite large (10$^3$ -
# Line 133 | Line 156 | Au-Au and Pt-Pt interactions, while modeling the CO us
156   Coulomb potential.  For this work, we have used classical molecular
157   dynamics with potential energy surfaces that are specifically tuned
158   for transition metals.  In particular, we used the EAM potential for
159 < Au-Au and Pt-Pt interactions, while modeling the CO using a rigid
159 > Au-Au and Pt-Pt interactions\cite{EAM}. The CO was modeled using a rigid
160   three-site model developed by Straub and Karplus for studying
161   photodissociation of CO from myoglobin.\cite{Straub} The Au-CO and
162   Pt-CO cross interactions were parameterized as part of this work.
# Line 146 | Line 169 | parameter sets. The glue model of Ercolessi {\it et al
169   methods,\cite{Daw84,Foiles86,Johnson89,Daw89,Plimpton93,Voter95a,Lu97,Alemany98}
170   but other models like the Finnis-Sinclair\cite{Finnis84,Chen90} and
171   the quantum-corrected Sutton-Chen method\cite{QSC,Qi99} have simpler
172 < parameter sets. The glue model of Ercolessi {\it et al.} is among the
172 > parameter sets. The glue model of Ercolessi et al. is among the
173   fastest of these density functional approaches.\cite{Ercolessi88} In
174   all of these models, atoms are conceptualized as a positively charged
175   core with a radially-decaying valence electron distribution. To
# Line 164 | Line 187 | $\phi_{ij}(r_{ij})$ is an pairwise term that is meant
187   V_i =  F[ \bar{\rho}_i ]  + \sum_{j \neq i} \phi_{ij}(r_{ij})
188   \end{equation*}
189   where $F[ \bar{\rho}_i ]$ is an energy embedding functional, and
190 < $\phi_{ij}(r_{ij})$ is an pairwise term that is meant to represent the
191 < overlap of the two positively charged cores.  
190 > $\phi_{ij}(r_{ij})$ is a pairwise term that is meant to represent the
191 > repulsive overlap of the two positively charged cores.  
192  
193   % The {\it modified} embedded atom method (MEAM) adds angular terms to
194   % the electron density functions and an angular screening factor to the
# Line 176 | Line 199 | The EAM, Finnis-Sinclair, and the Quantum Sutton-Chen
199   % metals,\cite{Lee:2001qf} and also interfaces.\cite{Beurden:2002ys})
200   % MEAM presents significant additional computational costs, however.
201  
202 < The EAM, Finnis-Sinclair, and the Quantum Sutton-Chen potentials
202 > The EAM, Finnis-Sinclair, and the Quantum Sutton-Chen (QSC) potentials
203   have all been widely used by the materials simulation community for
204   simulations of bulk and nanoparticle
205   properties,\cite{Chui:2003fk,Wang:2005qy,Medasani:2007uq}
206   melting,\cite{Belonoshko00,sankaranarayanan:155441,Sankaranarayanan:2005lr}
207   fracture,\cite{Shastry:1996qg,Shastry:1998dx} crack
208   propagation,\cite{BECQUART:1993rg} and alloying
209 < dynamics.\cite{Shibata:2002hh} All of these potentials have their
210 < strengths and weaknesses.  One of the strengths common to all of the
211 < methods is the relatively large library of metals for which these
212 < potentials have been
213 < parameterized.\cite{Foiles86,PhysRevB.37.3924,Rifkin1992,mishin99:_inter,mishin01:cu,mishin02:b2nial,zope03:tial_ap,mishin05:phase_fe_ni}  
209 > dynamics.\cite{Shibata:2002hh} One of EAM's strengths
210 > is its sensitivity to small changes in structure. This arises
211 > from the original parameterization, where the interactions
212 > up to the third nearest neighbor were taken into account.\cite{Voter95a}
213 > Comparing that to the glue model of Ercolessi et al.\cite{Ercolessi88}
214 > which is only parameterized up to the nearest-neighbor
215 > interactions, EAM is a suitable choice for systems where
216 > the bulk properties are of secondary importance to low-index
217 > surface structures. Additionally, the similarity of EAMs functional
218 > treatment of the embedding energy to standard density functional
219 > theory (DFT) makes fitting DFT-derived cross potentials with adsorbates somewhat easier.
220 > \cite{Foiles86,PhysRevB.37.3924,Rifkin1992,mishin99:_inter,mishin01:cu,mishin02:b2nial,zope03:tial_ap,mishin05:phase_fe_ni}  
221  
222 +
223 +
224 +
225   \subsection{Carbon Monoxide model}
226 < Since previous explanations for the surface rearrangements center on
227 < the large linear quadrupole moment of carbon monoxide, the model
228 < chosen for this molecule exhibits this property in an efficient
229 < manner. We used a model first proposed by Karplus and Straub to study
230 < the photodissociation of CO from myoglobin.\cite{Straub} The Straub
231 < and Karplus model is a rigid linear three site model which places a
232 < massless (M) site at the center of mass along the CO bond.  The
233 < geometry and interaction parameters are reproduced in Table 1. The
234 < effective dipole moment, calculated from the assigned charges, is
235 < still small (0.35 D) while the linear quadrupole (-2.40 D~\AA) is
236 < close to the experimental (-2.63 D~\AA)\cite{QuadrupoleCO} and quantum
226 > Previous explanations for the surface rearrangements center on
227 > the large linear quadrupole moment of carbon monoxide.\cite{Tao:2010}  
228 > We used a model first proposed by Karplus and Straub to study
229 > the photodissociation of CO from myoglobin because it reproduces
230 > the quadrupole moment well.\cite{Straub} The Straub and
231 > Karplus model treats CO as a rigid three site molecule with a massless M
232 > site at the molecular center of mass. The geometry and interaction
233 > parameters are reproduced in Table~\ref{tab:CO}. The effective
234 > dipole moment, calculated from the assigned charges, is still
235 > small (0.35 D) while the linear quadrupole (-2.40 D~\AA) is close
236 > to the experimental (-2.63 D~\AA)\cite{QuadrupoleCO} and quantum
237   mechanical predictions (-2.46 D~\AA)\cite{QuadrupoleCOCalc}.
238   %CO Table
239   \begin{table}[H]
240    \caption{Positions, Lennard-Jones parameters ($\sigma$ and
241      $\epsilon$), and charges for the CO-CO
242 <    interactions borrowed from Ref. \bibpunct{}{}{,}{n}{}{,} \protect\cite{Straub}. Distances are in \AA~, energies are
242 >    interactions in Ref.\bibpunct{}{}{,}{n}{}{,} \protect\cite{Straub}. Distances are in \AA, energies are
243      in kcal/mol, and charges are in atomic units.}
244   \centering
245   \begin{tabular}{| c | c | ccc |}
246   \hline
247   &  {\it z} & $\sigma$ & $\epsilon$ & q\\
248   \hline
249 < \textbf{C} & -0.6457 &  0.0262  & 3.83   &   -0.75 \\
250 < \textbf{O} &  0.4843 &   0.1591 &   3.12 &   -0.85 \\
249 > \textbf{C} & -0.6457 &  3.83 & 0.0262   &   -0.75 \\
250 > \textbf{O} &  0.4843 &  3.12 &  0.1591  &   -0.85 \\
251   \textbf{M} & 0.0 & -  &  -  &    1.6 \\
252   \hline
253   \end{tabular}
254 + \label{tab:CO}
255   \end{table}
256  
257   \subsection{Cross-Interactions between the metals and carbon monoxide}
258  
259 < Since the adsorption of CO onto a platinum surface has been the focus
259 > Since the adsorption of CO onto a Pt surface has been the focus
260   of much experimental \cite{Yeo, Hopster:1978, Ertl:1977, Kelemen:1979}
261   and theoretical work
262   \cite{Beurden:2002ys,Pons:1986,Deshlahra:2009,Feibelman:2001,Mason:2004}
263   there is a significant amount of data on adsorption energies for CO on
264 < clean metal surfaces. Parameters reported by Korzeniewski {\it et
265 <  al.}\cite{Pons:1986} were a starting point for our fits, which were
264 > clean metal surfaces. An earlier model by Korzeniewski {\it et
265 >  al.}\cite{Pons:1986} served as a starting point for our fits. The parameters were
266   modified to ensure that the Pt-CO interaction favored the atop binding
267 < position on Pt(111). This resulting binding energies are on the higher
268 < side of the experimentally-reported values. Following Korzeniewski
269 < {\it et al.},\cite{Pons:1986} the Pt-C interaction was fit to a deep
267 > position on Pt(111). These parameters are reproduced in Table~\ref{tab:co_parameters}.
268 > The modified parameters yield binding energies that are slightly higher
269 > than the experimentally-reported values as shown in Table~\ref{tab:co_energies}. Following Korzeniewski
270 > et al.,\cite{Pons:1986} the Pt-C interaction was fit to a deep
271   Lennard-Jones interaction to mimic strong, but short-ranged partial
272   binding between the Pt $d$ orbitals and the $\pi^*$ orbital on CO. The
273 < Pt-O interaction was parameterized to a Morse potential with a large
274 < range parameter ($r_o$).  In most cases, this contributes a weak
273 > Pt-O interaction was modeled with a Morse potential with a large
274 > equilibrium distance, ($r_o$).  These choices ensure that the C is preferred
275 > over O as the surface-binding atom. In most cases, the Pt-O parameterization contributes a weak
276   repulsion which favors the atop site.  The resulting potential-energy
277   surface suitably recovers the calculated Pt-C separation length
278   (1.6~\AA)\cite{Beurden:2002ys} and affinity for the atop binding
# Line 245 | Line 281 | The Au-C and Au-O cross-interactions were fit using Le
281   %where did you actually get the functionals for citation?
282   %scf calculations, so initial relaxation was of the four layers, but two layers weren't kept fixed, I don't think
283   %same cutoff for slab and slab + CO ? seems low, although feibelmen had values around there...
284 < The Au-C and Au-O cross-interactions were fit using Lennard-Jones and
284 > The Au-C and Au-O cross-interactions were also fit using Lennard-Jones and
285   Morse potentials, respectively, to reproduce Au-CO binding energies.
286 <
287 < The fits were refined against gas-surface DFT calculations with a
286 > The limited experimental data for CO adsorption on Au required refining the fits against plane-wave DFT calculations.
287 > Adsorption energies were obtained from gas-surface DFT calculations with a
288   periodic supercell plane-wave basis approach, as implemented in the
289 < {\sc Quantum ESPRESSO} package.\cite{QE-2009} Electron cores are
289 > {\sc Quantum ESPRESSO} package.\cite{QE-2009} Electron cores were
290   described with the projector augmented-wave (PAW)
291   method,\cite{PhysRevB.50.17953,PhysRevB.59.1758} with plane waves
292   included to an energy cutoff of 20 Ry. Electronic energies are
293   computed with the PBE implementation of the generalized gradient
294   approximation (GGA) for gold, carbon, and oxygen that was constructed
295   by Rappe, Rabe, Kaxiras, and Joannopoulos.\cite{Perdew_GGA,RRKJ_PP}
296 < 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
296 > In testing the Au-CO interaction, Au(111) supercells were constructed of four layers of 4
297   Au x 2 Au surface planes and separated from vertical images by six
298 < layers of vacuum space. The surface atoms were all allowed to relax.
299 < Supercell calculations were performed nonspin-polarized with a 4 x 4 x
300 < 4 Monkhorst-Pack {\bf k}-point sampling of the first Brillouin
298 > layers of vacuum space. The surface atoms were all allowed to relax
299 > before CO was added to the system. Electronic relaxations were
300 > performed until the energy difference between subsequent steps
301 > was less than $10^{-8}$ Ry.   Nonspin-polarized supercell calculations
302 > were performed with a 4~x~4~x~4 Monkhorst-Pack {\bf k}-point sampling of the first Brillouin
303   zone.\cite{Monkhorst:1976,PhysRevB.13.5188} The relaxed gold slab was
304   then used in numerous single point calculations with CO at various
305   heights (and angles relative to the surface) to allow fitting of the
306   empirical force field.
307  
308   %Hint at future work
309 < The parameters employed in this work are shown in Table 2 and the
310 < binding energies on the 111 surfaces are displayed in Table 3.  To
311 < speed up the computations, charge transfer and polarization are not
312 < being treated in this model, although these effects are likely to
313 < affect binding energies and binding site
314 < preferences.\cite{Deshlahra:2012}
309 > The parameters employed for the metal-CO cross-interactions in this work
310 > are shown in Table~\ref{tab:co_parameters} and the binding energies on the
311 > (111) surfaces are displayed in Table~\ref{tab:co_energies}.  Charge transfer
312 > and polarization are neglected in this model, although these effects are likely to
313 > affect binding energies and binding site preferences, and will be addressed in
314 > future work.
315  
316   %Table  of Parameters
317   %Pt Parameter Set 9
318   %Au Parameter Set 35
319   \begin{table}[H]
320 <  \caption{Best fit parameters for metal-CO cross-interactions.   Metal-C
321 <    interactions are modeled with Lennard-Jones potential, while the
322 <    (mostly-repulsive) metal-O interactions were fit to Morse
320 >  \caption{Best fit parameters for metal-CO cross-interactions. Metal-C
321 >    interactions are modeled with Lennard-Jones potentials. While the
322 >    metal-O interactions were fit to Morse
323      potentials.  Distances are given in \AA~and energies in kcal/mol. }
324   \centering
325   \begin{tabular}{| c | cc | c | ccc |}
# Line 295 | Line 331 | preferences.\cite{Deshlahra:2012}
331  
332   \hline
333   \end{tabular}
334 + \label{tab:co_parameters}
335   \end{table}
336  
337   %Table of energies
338   \begin{table}[H]
339 <  \caption{Adsorption energies for CO on M(111) using the potentials
340 <    described in this work.  All values are in eV}
339 >  \caption{Adsorption energies for a single CO at the atop site on M(111) at the atop site using the potentials
340 >    described in this work.  All values are in eV.}
341   \centering
342   \begin{tabular}{| c | cc |}
343    \hline
# Line 312 | Line 349 | preferences.\cite{Deshlahra:2012}
349    \textbf{Au-CO} & -0.39 & -0.40 \bibpunct{}{}{,}{n}{}{,}  (Ref. \protect\cite{TPD_Gold}) \\
350    \hline
351   \end{tabular}
352 + \label{tab:co_energies}
353   \end{table}
354  
355   \subsection{Pt(557) and Au(557) metal interfaces}
356 <
357 < Our model systems are composed of 3888 Pt atoms and XXXX Au atoms in a
358 < FCC crystal that have been cut along the 557 plane so that they are
359 < periodic in the {\it x} and {\it y} directions, and have been rotated
360 < to expose two parallel 557 cuts along the positive and negative {\it
361 <  z}-axis.  Simulations of the bare metal interfaces at temperatures
362 < ranging from 300~K to 1200~K were done to observe the relative
356 > Our Pt system is an orthorhombic periodic box of dimensions
357 > 54.482~x~50.046~x~120.88~\AA~while our Au system has
358 > dimensions of 57.4~x~51.9285~x~100~\AA.
359 > The systems are arranged in a FCC crystal that have been cut
360 > along the (557) plane so that they are periodic in the {\it x} and
361 > {\it y} directions, and have been oriented to expose two aligned
362 > (557) cuts along the extended {\it z}-axis.  Simulations of the
363 > bare metal interfaces at temperatures ranging from 300~K to
364 > 1200~K were performed to confirm the relative
365   stability of the surfaces without a CO overlayer.  
366  
367 < The different bulk (and surface) melting temperatures (1337~K for Au
368 < and 2045~K for Pt) suggest that the reconstruction may happen at
369 < different temperatures for the two metals.  To copy experimental
330 < conditions for the CO-exposed surfaces, the bare surfaces were
367 > The different bulk melting temperatures (1337~K for Au
368 > and 2045~K for Pt) suggest that any possible reconstruction should happen at
369 > different temperatures for the two metals.  The bare Au and Pt surfaces were
370   initially run in the canonical (NVT) ensemble at 800~K and 1000~K
371 < respectively for 100 ps.  Each surface was exposed to a range of CO
371 > respectively for 100 ps. The two surfaces were relatively stable at these
372 > temperatures when no CO was present, but experienced increased surface
373 > mobility on addition of CO. Each surface was then dosed with different concentrations of CO
374   that was initially placed in the vacuum region.  Upon full adsorption,
375 < these amounts correspond to 0\%, 5\%, 25\%, 33\%, and 50\% surface
376 < coverage.  Because of the difference in binding energies, the platinum
377 < systems very rarely had CO that was not bound to the surface, while
378 < the gold surfaces often had a significant CO population in the gas
375 > these concentrations correspond to 0\%, 5\%, 25\%, 33\%, and 50\% surface
376 > coverage. Higher coverages resulted in the formation of a double layer of CO,
377 > which introduces artifacts that are not relevant to (557) reconstruction.
378 > Because of the difference in binding energies, nearly all of the CO was bound to the Pt surface, while
379 > the Au surfaces often had a significant CO population in the gas
380   phase.  These systems were allowed to reach thermal equilibrium (over
381 < 5 ns) before being shifted to the microcanonical (NVE) ensemble for
381 > 5 ns) before being run in the microcanonical (NVE) ensemble for
382   data collection. All of the systems examined had at least 40 ns in the
383 < data collection stage, although simulation times for some of the
384 < systems exceeded 200ns.  All simulations were run using the open
385 < source molecular dynamics package, OpenMD.\cite{Ewald,OOPSE,OpenMD}
383 > data collection stage, although simulation times for some Pt of the
384 > systems exceeded 200~ns.  Simulations were carried out using the open
385 > source molecular dynamics package, OpenMD.\cite{Ewald,OOPSE}
386  
387 < % Just results, leave discussion for discussion section
387 >
388 >
389 >
390 > % RESULTS
391 > %
392   \section{Results}
393 < Tao {\it et al.} showed experimentally that the Pt(557) surface
394 < undergoes two separate reconstructions upon CO
395 < adsorption.\cite{Tao:2010} The first reconstruction involves a
396 < doubling of the step edge height which is accomplished by a doubling
397 < of the plateau length. The second reconstruction led to the formation
398 < of triangular clusters that arrange themselves along the lengthened
399 < plateaus.
393 > \subsection{Structural remodeling}
394 > The surfaces of both systems, upon dosage of CO, began
395 > to undergo remodeling that was not observed in the bare
396 > metal system. The surfaces to which no CO was exposed
397 > did experience minor roughening of the step-edge, but the
398 > (557) lattice was well-maintained throughout the simulation
399 > time. The Au systems were limited to greater amounts of
400 > roughening, i.e. breakup of the step-edge, and some step
401 > wandering. The lower coverage Pt systems experienced
402 > similar restructuring but to a greater extent when
403 > compared to the Au systems. The 50\% coverage
404 > Pt system formed double layers at numerous spots upon its surface.
405  
355 The primary observation and results of our simulation is that the
356 presence of CO overlayer on Pt(557) causes the same kind of
357 reconstruction observed experimentally. The 6-atom 111 facets
358 initially become disordered, and after 20-40 ns, a double-layer (with
359 a 2-atom step between terraces) forms.  However, we did not observe
360 the triangular cluster formation that was observed at longer times in
361 the experiments.  Without the CO present on the Pt(557) surface, there
362 was some disorder at the step edges, but no significant restructuring
363 was observed.
406  
407 < In these simulations, the Au(557) surface did not exhibit any
408 < significant restructuring either with or without the presence of a CO
409 < overlayer.
407 > \subsubsection{Step wandering}
408 > The 0\% coverage surfaces for both metals showed
409 > minimal movement at their respective run temperatures.
410 > As the coverage increased, the mobility of the surface
411 > also increased. Additionally, at the higher coverages
412 > on both metals, there was a large increase in the amount
413 > of observed step-wandering. Previous work by
414 > Williams\cite{Williams:1993} highlighted the entropic
415 > contribution to the repulsion felt between step-edges,
416 > and situations were that repulsion could be negated, or
417 > overcome, to allow for step coalescence or facet formation.
418  
419 < \subsection{Transport of surface metal atoms}
420 < An ideal metal surface displaying a low energy (111) face is unlikely
421 < to experience much surface diffusion because of the large vacancy
422 < formation energy for atoms at the surface.  This implies that
423 < significant energy must be expended to lift an atom out of the flat
424 < face so it can migrate on the surface.  Rougher surfaces and those
425 < that already contain numerous adatoms, step edges, and kinks, are
426 < expected to have higher surface diffusion rates.  Metal atoms that are
427 < mobile on the surface were observed to leave and then rejoin step
428 < edges or other formations. They may travel together or as isolated
429 < atoms.  The primary challenge of quantifying the overall surface
430 < mobility is in defining ``mobile'' vs. ``static'' atoms.
419 > \subsubsection{Double layers}
420 > Tao et al. have shown experimentally that the Pt(557) surface
421 > undergoes two separate reconstructions upon CO
422 > adsorption.\cite{Tao:2010} The first involves a doubling of
423 > the step height and plateau length. Similar behavior has been
424 > seen to occur on numerous surfaces at varying conditions: Ni(977), Si(111).
425 > \cite{Williams:1994,Williams:1991,Pearl} Of the two systems
426 > we examined, the Pt system showed a greater propensity for
427 > reconstruction when compared to the Au system. The amount
428 > of reconstruction is correlated to the amount of CO
429 > adsorbed upon the surface.  This appears to be related to the
430 > effect that adsorbate coverage has on edge breakup and on the surface
431 > diffusion of metal adatoms. While both systems displayed step-edge
432 > wandering, only the Pt surface underwent the doubling seen by
433 > Tao et al. within the time scales studied here.  
434 > Only the 50\% coverage Pt system exhibited
435 > a complete doubling in the time scales we
436 > were able to monitor. Over longer periods (150~ns) two more double layers formed on this interface.
437 > Although double layer formation did not occur in the other Pt systems, they show
438 > more lateral movement of the step-edges
439 > compared to their Au counterparts. The 50\% Pt system is highlighted
440 > in Figure \ref{fig:reconstruct} at various times along the simulation
441 > showing the evolution of a step-edge.
442  
443 < A particle was considered mobile once it had traveled more than 2~\AA~
444 < between saved configurations (XX ps). Restricting the transport
445 < calculations to only mobile atoms eliminates all of the bulk metal as
446 < well as any surface atoms that remain fixed for a significant length
386 < of time.  Since diffusion on a surface is strongly affected by local
387 < structures, the diffusion parallel to the step edges was determined
388 < separately from the diffusion perpendicular to these edges.  The
389 < parallel and perpendicular diffusion constants (determined using
390 < linear fits to the mean squared displacement) are shown in figure \ref{fig:diff}.
443 > The second reconstruction on the Pt(557) surface observed by
444 > Tao involved the formation of triangular clusters that stretched
445 > across the plateau between two step-edges. Neither system, within
446 > the 40~ns time scale, experienced this reconstruction.
447  
448 < %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 has been running continuously. The lowered diffusion constant at longer run times will be examined in-depth in the discussion section.
448 > \subsection{Dynamics}
449 > Previous atomistic simulations of stepped surfaces dealt largely
450 > with the energetics and structures at different conditions
451 > \cite{Williams:1991,Williams:1994}. Consequently, the most common
452 > technique utilized to date has been Monte Carlo sampling. Monte Carlo gives an efficient
453 > sampling of the equilibrium thermodynamic landscape at the expense
454 > of ignoring the dynamics of the system. Previous work by Pearl and
455 > Sibener\cite{Pearl}, using STM, has been able to show the coalescing
456 > of steps on Ni(977). The time scale of the image acquisition,
457 > $\sim$70 s/image provides an upper bound for the time required for
458 > the doubling to occur. In this section we give data on dynamic and
459 > transport properties, e.g. diffusion, layer formation time, etc.
460  
461 +
462 + \subsubsection{Transport of surface metal atoms}
463 + %forcedSystems/stepSeparation
464 + The movement or wandering of a step-edge is a cooperative effect
465 + arising from the individual movements, primarily through surface
466 + diffusion, of the atoms making up the steps. An ideal metal surface
467 + displaying a low index facet, (111) or (100), is unlikely to experience
468 + much surface diffusion because of the large energetic barrier that must
469 + be overcome to lift an atom out of the surface. The presence of step-edges
470 + on higher-index surfaces provide a source for mobile metal atoms.
471 + Breaking away from the step-edge on a clean surface still imposes an
472 + energetic penalty around $\sim$~40 kcal/mol, but this is significantly easier than lifting
473 + the same metal atom vertically out of the surface,  \textgreater~60 kcal/mol.
474 + The penalty lowers significantly when CO is present in sufficient quantities
475 + on the surface. For certain distributions of CO, the penalty can fall as low as
476 + $\sim$~20 kcal/mol. Once an adatom exists on the surface, the barrier for
477 + diffusion is negligible ( \textless~4 kcal/mol) and these adatoms are
478 + able to explore the terrace before rejoining either the original step-edge or
479 + becoming a part of a different edge. It is a more difficult process for an atom
480 + to traverse to a separate terrace although the presence of CO can lower the
481 + energy barrier required to lift or lower the adatom. By tracking the mobility of individual
482 + metal atoms on the Pt and Au surfaces we were able to determine the relative
483 + diffusion constants, as well as how varying coverages of CO affect the diffusion. Close
484 + observation of the mobile metal atoms showed that they were typically in
485 + equilibrium with the step-edges, dynamically breaking apart and rejoining the edges.
486 + At times, their motion was concerted and two or more adatoms would be
487 + observed moving together across the surfaces.
488 +
489 + A particle was considered ``mobile'' once it had traveled more than 2~\AA~
490 + between saved configurations of the system (typically 10-100 ps). An atom that was
491 + truly mobile would typically travel much greater distances than this, but the 2~\AA~cutoff
492 + was used to prevent swamping the diffusion data with the in-place vibrational
493 + movement of buried atoms. Diffusion on  a surface is strongly affected by
494 + local structures and in this work, the presence of single and double layer
495 + step-edges causes the diffusion parallel to the step-edges to be different
496 + from the diffusion perpendicular to these edges. Parallel and perpendicular
497 + diffusion constants are shown in Figure \ref{fig:diff}.
498 +
499 + \subsubsection{Dynamics of double layer formation}
500 + The increased diffusion on Pt at the higher
501 + CO coverages plays a primary role in double layer formation. However, this is not
502 + a complete explanation -- the 33\%~Pt system
503 + has higher diffusion constants but did not show
504 + any signs of edge doubling. On the
505 + 50\%~Pt system, three separate layers were formed over
506 + 150~ns of simulation time. Previous experimental
507 + work gives insight into the upper bounds of the
508 + time required for step coalescence.\cite{Williams:1991,Pearl}
509 + In this system, as seen in Figure \ref{fig:reconstruct}, the first
510 + appearance of a double layer, appears at 19~ns
511 + into the simulation. Within 12~ns of this nucleation event, nearly half of the step has
512 + formed the double layer and by 86 ns, the complete layer
513 + has been flattened out. The double layer could be considered
514 + ``complete" by 37~ns but remains a bit rough. From the
515 + appearance of the first nucleation event to the first observed double layer, the process took $\sim$20~ns. Another
516 + $\sim$40~ns was necessary for the layer to completely straighten.
517 + The other two layers in this simulation formed over periods of
518 + 22~ns and 42~ns respectively. Comparing this to the upper
519 + bounds of the image scan, it is likely that most aspects of this
520 + reconstruction occur very rapidly. A possible explanation
521 + for this rapid reconstruction is the elevated temperatures
522 + under which our systems were simulated. It is probable that the process would
523 + take longer at lower temperatures.
524 +
525 + %Evolution of surface
526   \begin{figure}[H]
527 < \includegraphics[scale=0.6]{DiffusionComparison_error.png}
527 > \includegraphics[width=\linewidth]{ProgressionOfDoubleLayerFormation_yellowCircle.png}
528 > \caption{The Pt(557) / 50\% CO system at a sequence of times after
529 >  initial exposure to the CO: (a) 258 ps, (b) 19 ns, (c) 31.2 ns, and
530 >  (d) 86.1 ns. Disruption of the (557) step-edges occurs quickly.  The
531 >  doubling of the layers appears only after two adjacent step-edges
532 >  touch.  The circled spot in (b) nucleated the growth of the double
533 >  step observed in the later configurations.}
534 >  \label{fig:reconstruct}
535 > \end{figure}
536 >
537 > \begin{figure}[H]
538 > \includegraphics[width=\linewidth]{DiffusionComparison_errorXY_remade.pdf}
539   \caption{Diffusion constants for mobile surface atoms along directions
540    parallel ($\mathbf{D}_{\parallel}$) and perpendicular
541 <  ($\mathbf{D}_{\perp}$) to the 557 step edges as a function of CO
542 <  surface coverage.  Diffusion parallel to the step edge is higher
541 >  ($\mathbf{D}_{\perp}$) to the (557) step-edges as a function of CO
542 >  surface coverage.  Diffusion parallel to the step-edge is higher
543    than that perpendicular to the edge because of the lower energy
544 <  barrier associated with going from approximately 7 nearest neighbors
545 <  to 5, as compared to the 3 of an adatom. Additionally, the observed
544 >  barrier associated with traversing along the edge as compared to
545 >  completely breaking away. Additionally, the observed
546    maximum and subsequent decrease for the Pt system suggests that the
547    CO self-interactions are playing a significant role with regards to
548 <  movement of the platinum atoms around and more importantly across
406 <  the surface. }
548 >  movement of the Pt atoms around and across the surface. }
549   \label{fig:diff}
550   \end{figure}
551  
410 %Table of Diffusion Constants
411 %Add gold?M
412 % \begin{table}[H]
413 %   \caption{}
414 %   \centering
415 % \begin{tabular}{| c | cc | cc | }
416 %   \hline
417 %   &\multicolumn{2}{c|}{\textbf{Platinum}}&\multicolumn{2}{c|}{\textbf{Gold}} \\
418 %   \hline
419 %   \textbf{Surface Coverage} & $\mathbf{D}_{\parallel}$ & $\mathbf{D}_{\perp}$ & $\mathbf{D}_{\parallel}$ & $\mathbf{D}_{\perp}$  \\
420 %   \hline
421 %   50\% & 4.32(2) & 1.185 $\pm$ 0.008 & 1.72 $\pm$ 0.02 & 0.455 $\pm$ 0.006 \\
422 %   33\% & 5.18 $\pm$ 0.03 & 1.999 $\pm$ 0.005 & 1.95 $\pm$ 0.02 & 0.337 $\pm$ 0.004  \\
423 %   25\% & 5.01 $\pm$ 0.02 & 1.574 $\pm$ 0.004 & 1.26 $\pm$ 0.03 & 0.377 $\pm$ 0.006 \\
424 %   5\%   & 3.61 $\pm$ 0.02 & 0.355 $\pm$ 0.002 & 1.84 $\pm$ 0.03 & 0.169 $\pm$ 0.004 \\
425 %   0\%   & 3.27 $\pm$ 0.02 & 0.147 $\pm$ 0.004 & 1.50 $\pm$ 0.02 & 0.194 $\pm$ 0.002  \\
426 %   \hline
427 % \end{tabular}
428 % \end{table}
552  
553 +
554 +
555   %Discussion
556   \section{Discussion}
557 + We have shown that the classical potential models are able to model the initial reconstruction of the
558 + Pt(557) surface upon CO adsorption as shown by Tao et al. \cite{Tao:2010}. More importantly, we
559 + were able to observe features of the dynamic processes necessary for this reconstruction.
560  
561 < Mechanism for restructuring
561 > \subsection{Mechanism for restructuring}
562 > Since the Au surface showed no large scale restructuring throughout
563 > our simulation time our discussion will focus on the 50\% Pt-CO system
564 > which did undergo the doubling featured in Figure \ref{fig:reconstruct}.
565 > Similarities of our results to those reported previously by
566 > Tao et al.\cite{Tao:2010} are quite
567 > strong. The simulated Pt
568 > system exposed to a large dosage of CO readily restructures by doubling the terrace
569 > widths and step heights. The restructuring occurs in a piecemeal fashion, one to two Pt atoms at a time, but is rapid on experimental timescales.
570 > The adatoms either
571 > break away from the step-edge and stay on the lower terrace or they lift
572 > up onto a higher terrace. Once ``free'', they diffuse on the terrace
573 > until reaching another step-edge or rejoining their original edge.  
574 > This combination of growth and decay of the step-edges is in a state of
575 > dynamic equilibrium. However, once two previously separated edges
576 > meet as shown in Figure 1.B, this nucleates the rest of the edge to meet up, forming a double layer.
577 > From simulations which exhibit a double layer, the time delay from the initial appearance of a nucleation point to a fully formed double layer is $\sim$35 ns.
578  
579 < There are a number of possible mechanisms to explain the role of
580 < adsorbed CO in restructuring the Pt surface. Quadrupolar repulsion
581 < between adjacent CO molecules adsorbed on the surface is one
582 < possibility.  However, the quadrupole-quadrupole interaction is
583 < short-ranged and is attractive for some orientations.  If the CO
584 < molecules are locked in a specific orientation relative to each other,
585 < this explanation gains some weight.  
579 > A number of possible mechanisms exist to explain the role of adsorbed
580 > CO in restructuring the Pt surface. Quadrupolar repulsion between adjacent
581 > CO molecules adsorbed on the surface is one possibility.  However,
582 > the quadrupole-quadrupole interaction is short-ranged and is attractive for
583 > some orientations.  If the CO molecules are ``locked'' in a specific orientation
584 > relative to each other, through atop adsorption for example, this explanation
585 > gains some credence.  The energetic repulsion between two CO located a
586 > distance of 2.77~\AA~apart (nearest-neighbor distance of Pt) and both in
587 > a  vertical orientation, is 8.62 kcal/mol. Moving the CO apart to the second
588 > nearest-neighbor distance of 4.8~\AA~or 5.54~\AA~drops the repulsion to
589 > nearly 0 kcal/mol. Allowing the CO's to leave a purely vertical orientation
590 > also quickly drops the repulsion, a minimum of 6.2 kcal/mol is reached at $\sim$24 degrees between the 2 CO when the carbons are locked at a distance of 2.77 \AA apart.
591 > As mentioned above, the energy barrier for surface diffusion
592 > of a Pt adatom is only 4 kcal/mol. So this repulsion between neighboring CO molecules can
593 > increase the surface diffusion. However, the residence time of CO on Pt was
594 > examined and while the majority of the CO is on or near the surface throughout
595 > the run, most molecules are mobile. This mobility suggests that the CO are more
596 > likely to shift their positions without necessarily the Pt along with them.
597  
598 < Another possible mechanism for the restructuring is in the
598 > Another possible and more likely mechanism for the restructuring is in the
599   destabilization of strong Pt-Pt interactions by CO adsorbed on surface
600 < Pt atoms.  This could have the effect of increasing surface mobility
601 < of these atoms.  
600 > Pt atoms.  This would then have the effect of increasing surface mobility
601 > of these atoms.  To test this hypothesis, numerous configurations of
602 > CO in varying quantities were arranged on the higher and lower plateaus
603 > around a step on a otherwise clean Pt(557) surface. One representative
604 > configuration is displayed in Figure \ref{fig:lambda}. Single or concerted movement
605 > of Pt atoms was then examined to determine possible barriers. Because
606 > the movement was forced along a pre-defined reaction coordinate that may differ
607 > from the true minimum of this path, only the beginning and ending energies
608 > are displayed in Table \ref{tab:energies}. These values suggest that the presence of CO at suitable
609 > locations can lead to lowered barriers for Pt breaking apart from the step-edge.
610 > Additionally, as highlighted in Figure \ref{fig:lambda}, the presence of CO makes the
611 > burrowing and lifting of adatoms favorable, whereas without CO, the process is neutral
612 > in terms of energetics.
613  
614 < Comparing the results from simulation to those reported previously by
615 < Tao et al. the similarities in the platinum and CO system are quite
616 < strong. As shown in figure, the simulated platinum system under a CO
617 < atmosphere will restructure slightly by doubling the terrace
618 < heights. The restructuring appears to occur slowly, one to two
619 < platinum atoms at a time. Looking at individual snapshots, these
620 < adatoms tend to either rise on top of the plateau or break away from
621 < the step edge and then diffuse perpendicularly to the step direction
622 < until reaching another step edge. This combination of growth and decay
623 < of the step edges appears to be in somewhat of a state of dynamic
624 < equilibrium. However, once two previously separated edges meet as
625 < shown in figure 1.B, this point tends to act as a focus or growth
460 < point for the rest of the edge to meet up, akin to that of a
461 < zipper. From the handful of cases where a double layer was formed
462 < during the simulation, measuring from the initial appearance of a
463 < growth point, the double layer tends to be fully formed within
464 < $\sim$~35 ns.
614 > %lambda progression of Pt -> shoving its way into the step
615 > \begin{figure}[H]
616 > \includegraphics[width=\linewidth]{lambdaProgression_atopCO.png}
617 > \caption{A model system of the Pt(557) surface was used as the framework
618 > for exploring energy barriers along a reaction coordinate. Various numbers,
619 > placements, and rotations of CO were examined as they affect Pt movement.
620 > The coordinate displayed in this Figure was a representative run. As shown
621 > in Table \ref{tab:rxcoord}, relative to the energy of the system at 0\%, there
622 > is a slight decrease upon insertion of the Pt atom into the step-edge along
623 > with the resultant lifting of the other Pt atom when CO is present at certain positions.}
624 > \label{fig:lambda}
625 > \end{figure}
626  
627 +
628 +
629   \subsection{Diffusion}
630 < 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?)
630 > The diffusion parallel to the step-edge tends to be
631 > much larger than that perpendicular to the step-edge. The dynamic
632 > equilibrium that is established between the step-edge and adatom interface. The coverage
633 > of CO also appears to play a slight role in relative rates of diffusion, as shown in Figure \ref{fig:diff}.
634 > The
635 > Thus, the bottleneck of the double layer formation appears to be the initial formation
636 > of this growth point, which seems to be somewhat of a stochastic event. Once it
637 > appears, parallel diffusion, along the now slightly angled step-edge, will allow for
638 > a faster formation of the double layer than if the entire process were dependent on
639 > only perpendicular diffusion across the plateaus. Thus, the larger $D_{\perp}$, the
640 > more likely a growth point is to be formed.
641   \\
642 < \\
643 < %Evolution of surface
642 >
643 >
644 > %breaking of the double layer upon removal of CO
645   \begin{figure}[H]
646 < \includegraphics[width=\linewidth]{ProgressionOfDoubleLayerFormation_yellowCircle.png}
647 < \caption{The Pt(557) / 50\% CO system at a sequence of times after
648 <  initial exposure to the CO: (a) 258 ps, (b) 19 ns, (c) 31.2 ns, and
649 <  (d) 86.1 ns. Disruption of the 557 step edges occurs quickly.  The
650 <  doubling of the layers appears only after two adjacent step edges
651 <  touch.  The circled spot in (b) nucleated the growth of the double
652 <  step observed in the later configurations.}
646 > \includegraphics[width=\linewidth]{doubleLayerBreaking_greenBlue_whiteLetters.png}
647 > %:
648 > \caption{(A)  0 ps, (B) 100 ps, (C) 1 ns, after the removal of CO. The presence of the CO
649 > helped maintain the stability of the double layer and upon removal the two layers break
650 > and begin separating. The separation is not a simple pulling apart however, rather
651 > there is a mixing of the lower and upper atoms at the edge.}
652 > \label{fig:breaking}
653   \end{figure}
654  
655  
656 +
657 +
658   %Peaks!
659 < \begin{figure}[H]
660 < \includegraphics[width=\linewidth]{doublePeaks_noCO.png}
661 < \caption{}
662 < \end{figure}
659 > %\begin{figure}[H]
660 > %\includegraphics[width=\linewidth]{doublePeaks_noCO.png}
661 > %\caption{At the initial formation of this double layer  ( $\sim$ 37 ns) there is a degree
662 > %of roughness inherent to the edge. The next $\sim$ 40 ns show the edge with
663 > %aspects of waviness and by 80 ns the double layer is completely formed and smooth. }
664 > %\label{fig:peaks}
665 > %\end{figure}
666 >
667 >
668 > %Don't think I need this
669 > %clean surface...
670 > %\begin{figure}[H]
671 > %\includegraphics[width=\linewidth]{557_300K_cleanPDF.pdf}
672 > %\caption{}
673 >
674 > %\end{figure}
675 > %\label{fig:clean}
676 >
677 >
678   \section{Conclusion}
679 + In this work we have shown the reconstruction of the Pt(557) crystalline surface upon adsorption of CO in less than a $\mu s$. 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.
680  
681 + %Things I am not ready to remove yet
682  
683 + %Table of Diffusion Constants
684 + %Add gold?M
685 + % \begin{table}[H]
686 + %   \caption{}
687 + %   \centering
688 + % \begin{tabular}{| c | cc | cc | }
689 + %   \hline
690 + %   &\multicolumn{2}{c|}{\textbf{Platinum}}&\multicolumn{2}{c|}{\textbf{Gold}} \\
691 + %   \hline
692 + %   \textbf{Surface Coverage} & $\mathbf{D}_{\parallel}$ & $\mathbf{D}_{\perp}$ & $\mathbf{D}_{\parallel}$ & $\mathbf{D}_{\perp}$  \\
693 + %   \hline
694 + %   50\% & 4.32(2) & 1.185(8)  & 1.72(2) & 0.455(6) \\
695 + %   33\% & 5.18(3)  & 1.999(5)  & 1.95(2) & 0.337(4)   \\
696 + %   25\% & 5.01(2)  & 1.574(4)  & 1.26(3) & 0.377(6) \\
697 + %   5\%   & 3.61(2)  & 0.355(2)  & 1.84(3)  & 0.169(4)  \\
698 + %   0\%   & 3.27(2)  & 0.147(4)  & 1.50(2)  & 0.194(2)   \\
699 + %   \hline
700 + % \end{tabular}
701 + % \end{table}
702 +
703   \section{Acknowledgments}
704   Support for this project was provided by the National Science
705   Foundation under grant CHE-0848243 and by the Center for Sustainable

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