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1 < \documentclass[11pt]{article}
1 > \documentclass[journal = jpccck, manuscript = article]{achemso}
2 > \setkeys{acs}{usetitle = true}
3 > \usepackage{achemso}
4 > \usepackage{caption}
5 > \usepackage{float}
6 > \usepackage{geometry}
7 > \usepackage{natbib}
8 > \usepackage{setspace}
9 > \usepackage{xkeyval}
10 > %%%%%%%%%%%%%%%%%%%%%%%
11   \usepackage{amsmath}
12   \usepackage{amssymb}
13   \usepackage{times}
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15   \usepackage{setspace}
16   \usepackage{endfloat}
17   \usepackage{caption}
18 < %\usepackage{tabularx}
18 > \usepackage{tabularx}
19 > \usepackage{longtable}
20   \usepackage{graphicx}
21   \usepackage{multirow}
22 < %\usepackage{booktabs}
23 < %\usepackage{bibentry}
24 < %\usepackage{mathrsfs}
25 < \usepackage[square, comma, sort&compress]{natbib}
22 > \usepackage{multicol}
23 >
24 > \usepackage[version=3]{mhchem}  % this is a great package for formatting chemical reactions
25 > % \usepackage[square, comma, sort&compress]{natbib}
26   \usepackage{url}
27   \pagestyle{plain} \pagenumbering{arabic} \oddsidemargin 0.0cm
28   \evensidemargin 0.0cm \topmargin -21pt \headsep 10pt \textheight
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32   %\AtBeginDelayedFloats{\renewcomand{\baselinestretch}{1.66}}
33   \setlength{\abovecaptionskip}{20 pt}
34   \setlength{\belowcaptionskip}{30 pt}
35 + % \bibpunct{}{}{,}{s}{}{;}
36  
37 < \bibpunct{}{}{,}{s}{}{;}
38 < \bibliographystyle{achemso}
37 > %\citestyle{nature}
38 > % \bibliographystyle{achemso}
39  
40 < \begin{document}
40 > \title{Molecular Dynamics simulations of the surface reconstructions
41 >  of Pt(557) and Au(557) under exposure to CO}
42  
43 + \author{Joseph R. Michalka}
44 + \author{Patrick W. McIntyre}
45 + \author{J. Daniel Gezelter}
46 + \email{gezelter@nd.edu}
47 + \affiliation[University of Notre Dame]{251 Nieuwland Science Hall\\
48 +  Department of Chemistry and Biochemistry\\ University of Notre
49 +  Dame\\ Notre Dame, Indiana 46556}
50  
51 + \keywords{}
52 +
53 + \begin{document}
54 +
55 +
56   %%
57   %Introduction
58   %       Experimental observations
# Line 47 | Line 71
71   %Summary
72   %%
73  
50 %Title
51 \title{Molecular Dynamics simulations of the surface reconstructions
52  of Pt(557) and Au(557) under exposure to CO}
74  
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
75   \begin{abstract}
76   We examine surface reconstructions of Pt and Au(557) under
77   various CO coverages using molecular dynamics in order to
# Line 112 | Line 117 | This work is an attempt to understand the mechanism an
117   reversible restructuring under exposure to moderate pressures of
118   carbon monoxide.\cite{Tao:2010}
119  
120 < This work is an attempt to understand the mechanism and timescale for
121 < surface restructuring by using molecular simulations.  Since the dynamics
120 > This work is an investigation into the mechanism and timescale for the Pt(557) \& Au(557)
121 > surface restructuring using molecular simulations.  Since the dynamics
122   of the process are of particular interest, we employ classical force
123   fields that represent a compromise between chemical accuracy and the
124   computational efficiency necessary to simulate the process of interest.
# Line 121 | Line 126 | The Au(557) surface, because of a weaker interaction w
126   catalyst with adsorbates, in this work, two metal systems exposed
127   to carbon monoxide were examined. The Pt(557) surface has already been shown
128   to undergo a large scale reconstruction under certain conditions.\cite{Tao:2010}
129 < The Au(557) surface, because of a weaker interaction with CO, is seen as less
130 < likely to undergo this kind of reconstruction. However, Peters et al.\cite{Peters:2000}
131 < and Piccolo et al.\cite{Piccolo:2004} have both observed CO induced
132 < reconstruction of a Au(111) surface. Peters et al. saw a relaxing of the
133 < 22 x $\sqrt{3}$ cell. They argued that a very small number of Au atoms
134 < would become adatoms, limiting the stress of this reconstruction while
135 < allowing the rest of the row to relax and approach the ideal (111)
136 < configuration. They did not see the ``herringbone'' pattern being greatly
137 < affected by this relaxation. Piccolo et al. on the other hand, did see a
138 < disruption of the ``herringbone'' pattern as CO was adsorbed to the
129 > The Au(557) surface, because of a weaker interaction with CO, is less
130 > likely to undergo this kind of reconstruction. However, Peters {\it et al}.\cite{Peters:2000}
131 > and Piccolo {\it et al}.\cite{Piccolo:2004} have both observed CO-induced
132 > reconstruction of a Au(111) surface. Peters {\it et al}. saw a relaxation to the
133 > 22 x $\sqrt{3}$ cell. They argued that only a few Au atoms
134 > become adatoms, limiting the stress of this reconstruction, while
135 > allowing the rest to relax and approach the ideal (111)
136 > configuration. They did not see the usual herringbone pattern on Au(111) being greatly
137 > affected by this relaxation. Piccolo {\it et al}. on the other hand, did see a
138 > disruption of the herringbone pattern as CO was adsorbed to the
139   surface. Both groups suggested that the preference CO shows for
140 < low-coordinated Au particles was the primary driving force for these reconstructions.
140 > low-coordinated Au atoms was the primary driving force for the reconstruction.
141  
142  
143  
# Line 144 | Line 149 | adsorbates.  Since the interfaces involved are quite l
149   development of a sufficiently general yet computationally tractable
150   model of the chemical interactions between the surface atoms and
151   adsorbates.  Since the interfaces involved are quite large (10$^3$ -
152 < 10$^6$ atoms) and respond slowly to perturbations, {\it ab initio}
152 > 10$^4$ atoms) and respond slowly to perturbations, {\it ab initio}
153   molecular dynamics
154   (AIMD),\cite{KRESSE:1993ve,KRESSE:1993qf,KRESSE:1994ul} Car-Parrinello
155   methods,\cite{CAR:1985bh,Izvekov:2000fv,Guidelli:2000fy} and quantum
# Line 156 | Line 161 | Au-Au and Pt-Pt interactions\cite{EAM}. The CO was mod
161   Coulomb potential.  For this work, we have used classical molecular
162   dynamics with potential energy surfaces that are specifically tuned
163   for transition metals.  In particular, we used the EAM potential for
164 < Au-Au and Pt-Pt interactions\cite{EAM}. The CO was modeled using a rigid
164 > Au-Au and Pt-Pt interactions.\cite{EAM} The CO was modeled using a rigid
165   three-site model developed by Straub and Karplus for studying
166   photodissociation of CO from myoglobin.\cite{Straub} The Au-CO and
167   Pt-CO cross interactions were parameterized as part of this work.
# Line 169 | Line 174 | parameter sets. The glue model of Ercolessi et al. is
174   methods,\cite{Daw84,Foiles86,Johnson89,Daw89,Plimpton93,Voter95a,Lu97,Alemany98}
175   but other models like the Finnis-Sinclair\cite{Finnis84,Chen90} and
176   the quantum-corrected Sutton-Chen method\cite{QSC,Qi99} have simpler
177 < parameter sets. The glue model of Ercolessi et al. is among the
177 > parameter sets. The glue model of Ercolessi {\it et al}. is among the
178   fastest of these density functional approaches.\cite{Ercolessi88} In
179 < all of these models, atoms are conceptualized as a positively charged
179 > all of these models, atoms are treated as a positively charged
180   core with a radially-decaying valence electron distribution. To
181   calculate the energy for embedding the core at a particular location,
182   the electron density due to the valence electrons at all of the other
# Line 208 | Line 213 | from the original parameterization, where the interact
213   propagation,\cite{BECQUART:1993rg} and alloying
214   dynamics.\cite{Shibata:2002hh} One of EAM's strengths
215   is its sensitivity to small changes in structure. This arises
216 < from the original parameterization, where the interactions
217 < up to the third nearest-neighbor were taken into account.\cite{Voter95a}
218 < Comparing that to the glue model of Ercolessi et al.\cite{Ercolessi88}
219 < which only parameterized up to the nearest-neighbor
216 > because interactions
217 > up to the third nearest neighbor were taken into account in the parameterization.\cite{Voter95a}
218 > Comparing that to the glue model of Ercolessi {\it et al}.\cite{Ercolessi88}
219 > which is only parameterized up to the nearest-neighbor
220   interactions, EAM is a suitable choice for systems where
221   the bulk properties are of secondary importance to low-index
222 < surface structures. Additionally, the similarity of EAMs functional
222 > surface structures. Additionally, the similarity of EAM's functional
223   treatment of the embedding energy to standard density functional
224 < theory (DFT) approaches gives EAM, and conclusions derived, a firm theoretical footing.
224 > theory (DFT) makes fitting DFT-derived cross potentials with adsorbates somewhat easier.
225   \cite{Foiles86,PhysRevB.37.3924,Rifkin1992,mishin99:_inter,mishin01:cu,mishin02:b2nial,zope03:tial_ap,mishin05:phase_fe_ni}  
226  
227  
# Line 228 | Line 233 | Karplus model, treats CO as a rigid three site molecul
233   We used a model first proposed by Karplus and Straub to study
234   the photodissociation of CO from myoglobin because it reproduces
235   the quadrupole moment well.\cite{Straub} The Straub and
236 < Karplus model, treats CO as a rigid three site molecule with a massless M
236 > Karplus model treats CO as a rigid three site molecule with a massless M
237   site at the molecular center of mass. The geometry and interaction
238   parameters are reproduced in Table~\ref{tab:CO}. The effective
239   dipole moment, calculated from the assigned charges, is still
# Line 267 | Line 272 | et al.,\cite{Pons:1986} the Pt-C interaction was fit t
272   position on Pt(111). These parameters are reproduced in Table~\ref{tab:co_parameters}.
273   The modified parameters yield binding energies that are slightly higher
274   than the experimentally-reported values as shown in Table~\ref{tab:co_energies}. Following Korzeniewski
275 < et al.,\cite{Pons:1986} the Pt-C interaction was fit to a deep
276 < Lennard-Jones interaction to mimic strong, but short-ranged partial
275 > {\it et al}.,\cite{Pons:1986} the Pt-C interaction was fit to a deep
276 > Lennard-Jones interaction to mimic strong, but short-ranged, partial
277   binding between the Pt $d$ orbitals and the $\pi^*$ orbital on CO. The
278   Pt-O interaction was modeled with a Morse potential with a large
279   equilibrium distance, ($r_o$).  These choices ensure that the C is preferred
280 < over O as the surface-binding atom. In most cases, the Pt-O parameterization contributes a weak
280 > over O as the surface-binding atom. In most geometries, the Pt-O parameterization contributes a weak
281   repulsion which favors the atop site.  The resulting potential-energy
282   surface suitably recovers the calculated Pt-C separation length
283   (1.6~\AA)\cite{Beurden:2002ys} and affinity for the atop binding
# Line 300 | Line 305 | zone.\cite{Monkhorst:1976,PhysRevB.13.5188} The relaxe
305   performed until the energy difference between subsequent steps
306   was less than $10^{-8}$ Ry.   Nonspin-polarized supercell calculations
307   were performed with a 4~x~4~x~4 Monkhorst-Pack {\bf k}-point sampling of the first Brillouin
308 < zone.\cite{Monkhorst:1976,PhysRevB.13.5188} The relaxed gold slab was
308 > zone.\cite{Monkhorst:1976} The relaxed gold slab was
309   then used in numerous single point calculations with CO at various
310   heights (and angles relative to the surface) to allow fitting of the
311   empirical force field.
# Line 309 | Line 314 | and polarization are neglected in this model, although
314   The parameters employed for the metal-CO cross-interactions in this work
315   are shown in Table~\ref{tab:co_parameters} and the binding energies on the
316   (111) surfaces are displayed in Table~\ref{tab:co_energies}.  Charge transfer
317 < and polarization are neglected in this model, although these effects are likely to
318 < affect binding energies and binding site preferences, and will be addressed in
314 < a future work.\cite{Deshlahra:2012,StreitzMintmire:1994}
317 > and polarization are neglected in this model, although these effects could have
318 > an effect on  binding energies and binding site preferences.
319  
320   %Table  of Parameters
321   %Pt Parameter Set 9
# Line 346 | Line 350 | a future work.\cite{Deshlahra:2012,StreitzMintmire:199
350    \multirow{2}{*}{\textbf{Pt-CO}} & \multirow{2}{*}{-1.9} & -1.4 \bibpunct{}{}{,}{n}{}{,}
351    (Ref. \protect\cite{Kelemen:1979}) \\
352   & &  -1.9 \bibpunct{}{}{,}{n}{}{,} (Ref. \protect\cite{Yeo}) \\ \hline
353 <  \textbf{Au-CO} & -0.39 & -0.40 \bibpunct{}{}{,}{n}{}{,}  (Ref. \protect\cite{TPD_Gold}) \\
353 >  \textbf{Au-CO} & -0.39 & -0.40 \bibpunct{}{}{,}{n}{}{,}  (Ref. \protect\cite{TPDGold}) \\
354    \hline
355   \end{tabular}
356   \label{tab:co_energies}
357   \end{table}
358  
359   \subsection{Pt(557) and Au(557) metal interfaces}
360 < Our Pt system has dimensions of 18~x~24~x~9 in a box of size
361 < 54.482~x~50.046~x~120.88~\AA while our Au system has
362 < dimensions of 18~x~24~x~8 in a box of size 57.4~x~51.9285~x~100~\AA.
360 > Our Pt system is an orthorhombic periodic box of dimensions
361 > 54.482~x~50.046~x~120.88~\AA~while our Au system has
362 > dimensions of 57.4~x~51.9285~x~100~\AA. The metal slabs
363 > are 9 and 8 atoms deep respectively, corresponding to a slab
364 > thickness of $\sim$21~\AA~ for Pt and $\sim$19~\AA~for Au.
365   The systems are arranged in a FCC crystal that have been cut
366   along the (557) plane so that they are periodic in the {\it x} and
367   {\it y} directions, and have been oriented to expose two aligned
368   (557) cuts along the extended {\it z}-axis.  Simulations of the
369   bare metal interfaces at temperatures ranging from 300~K to
370 < 1200~K were performed to observe the relative
370 > 1200~K were performed to confirm the relative
371   stability of the surfaces without a CO overlayer.  
372  
373 < The different bulk melting temperatures (1337~K for Au
374 < and 2045~K for Pt) suggest that any possible reconstruction should happen at
373 > The different bulk melting temperatures predicted by EAM (1345~$\pm$~10~K for Au\cite{Au:melting}
374 > and $\sim$~2045~K for Pt\cite{Pt:melting}) suggest that any possible reconstruction should happen at
375   different temperatures for the two metals.  The bare Au and Pt surfaces were
376   initially run in the canonical (NVT) ensemble at 800~K and 1000~K
377   respectively for 100 ps. The two surfaces were relatively stable at these
# Line 373 | Line 379 | coverage. Higher coverages resulted in CO double layer
379   mobility on addition of CO. Each surface was then dosed with different concentrations of CO
380   that was initially placed in the vacuum region.  Upon full adsorption,
381   these concentrations correspond to 0\%, 5\%, 25\%, 33\%, and 50\% surface
382 < coverage. Higher coverages resulted in CO double layer formation, which introduces artifacts that are not relevant to (557) reconstruction.
382 > coverage. Higher coverages resulted in the formation of a double layer of CO,
383 > which introduces artifacts that are not relevant to (557) reconstruction.
384   Because of the difference in binding energies, nearly all of the CO was bound to the Pt surface, while
385   the Au surfaces often had a significant CO population in the gas
386   phase.  These systems were allowed to reach thermal equilibrium (over
387 < 5 ns) before being run in the microcanonical (NVE) ensemble for
388 < data collection. All of the systems examined had at least 40 ns in the
389 < data collection stage, although simulation times for some of the
390 < systems exceeded 200~ns.  Simulations were run using the open
387 > 5~ns) before being run in the microcanonical (NVE) ensemble for
388 > data collection. All of the systems examined had at least 40~ns in the
389 > data collection stage, although simulation times for some Pt of the
390 > systems exceeded 200~ns.  Simulations were carried out using the open
391   source molecular dynamics package, OpenMD.\cite{Ewald,OOPSE}
392  
393 < % Just results, leave discussion for discussion section
394 < % structure
395 < %       Pt: step wandering, double layers, no triangular motifs
396 < %       Au: step wandering, no double layers
397 < % dynamics
391 < %       diffusion
392 < %       time scale, formation, breakage
393 >
394 >
395 >
396 > % RESULTS
397 > %
398   \section{Results}
399   \subsection{Structural remodeling}
400 + The bare metal surfaces experienced minor roughening of the
401 + step-edge because of the elevated temperatures, but the (557)
402 + face was stable throughout the simulations. The surface of both
403 + systems, upon dosage of CO, began to undergo extensive remodeling
404 + that was not observed in the bare systems. Reconstructions of
405 + the Au systems were limited to breakup of the step-edges and
406 + some step wandering. The lower coverage Pt systems experienced
407 + similar restructuring but to a greater extent. The 50\% coverage
408 + Pt system was unique among our simulations in that it formed
409 + well-defined and stable double layers through step coalescence,
410 + similar to results reported by Tao {\it et al}.\cite{Tao:2010}
411 +
412 +
413   \subsubsection{Step wandering}
414 + The 0\% coverage surfaces for both metals showed minimal
415 + step-wandering at their respective temperatures. As the CO
416 + coverage increased however, the mobility of the surface atoms,
417 + described through adatom diffusion and step-edge wandering,
418 + also increased.  Except for the 50\% Pt system where step
419 + coalescence occurred, the step-edges in the other simulations
420 + preferred to keep nearly the same distance between steps as in
421 + the original (557) lattice, $\sim$13\AA~for Pt and $\sim$14\AA~for Au.
422 + Previous work by Williams {\it et al}.\cite{Williams:1991, Williams:1994}
423 + highlights the repulsion that exists between step-edges even
424 + when no direct interactions are present in the system. This
425 + repulsion is caused by an entropic barrier that arises from
426 + the fact that steps cannot cross over one another. This entropic
427 + repulsion does not completely define the interactions between
428 + steps, however, so it is possible to observe step coalescence
429 + on some surfaces.\cite{Williams:1991} The presence and
430 + concentration of adsorbates, as shown in this work, can
431 + affect step-step interactions, potentially leading to a new
432 + surface structure as the thermodynamic equilibrium.
433 +
434   \subsubsection{Double layers}
435 < Tao et al. have shown experimentally that the Pt(557) surface
436 < undergoes two separate reconstructions upon CO
437 < adsorption.\cite{Tao:2010} The first involves a doubling of
438 < the step height and plateau length. Similar behavior has been
439 < seen to occur on numerous surfaces at varying conditions: Ni(977), Si(111).
440 < \cite{Williams:1994,Williams:1991,Pearl} Of the two systems
441 < we examined, the Pt system showed a larger amount of
442 < reconstruction when compared to the Au system. The amount
443 < of reconstruction is correlated to the amount of CO
435 > Tao {\it et al}.\cite{Tao:2010} have shown experimentally that the Pt(557) surface
436 > undergoes two separate reconstructions upon CO adsorption.
437 > The first involves a doubling of the step height and plateau length.
438 > Similar behavior has been seen on a number of surfaces
439 > at varying conditions, including Ni(977) and Si(111).\cite{Williams:1994,Williams:1991,Pearl}
440 > Of the two systems we examined, the Pt system showed a greater
441 > propensity for reconstruction  
442 > because of the larger surface mobility and the greater extent of step wandering.
443 > The amount of reconstruction was strongly correlated to the amount of CO
444   adsorbed upon the surface.  This appears to be related to the
445 < effect that adsorbate coverage has on edge breakup and on the surface
446 < diffusion of metal adatoms. While both systems displayed step-edge
447 < wandering, only the Pt surface underwent the doubling seen by
448 < Tao et al. within the time scales studied here.  
449 < Only the 50\% coverage Pt system exhibited
450 < a complete doubling in the time scales we
451 < were able to monitor. Over longer periods (150~ns) two more double layers formed on this interface.
452 < Although double layer formation did not occur in the other Pt systems, they show
453 < more lateral movement of the step-edges
416 < compared to their Au counterparts. The 50\% Pt system is highlighted
417 < in Figure \ref{fig:reconstruct} at various times along the simulation
418 < showing the evolution of a step-edge.
445 > effect that adsorbate coverage has on edge breakup and on the
446 > surface diffusion of metal adatoms. Only the 50\% Pt surface underwent the
447 > doubling seen by Tao {\it et al}.\cite{Tao:2010} within the time scales studied here.
448 > Over a longer time scale (150~ns) two more double layers formed
449 > on this surface. Although double layer formation did not occur
450 > in the other Pt systems, they exhibited more step-wandering and
451 > roughening compared to their Au counterparts. The
452 > 50\% Pt system is highlighted in Figure \ref{fig:reconstruct} at
453 > various times along the simulation showing the evolution of a double layer step-edge.
454  
455 < The second reconstruction on the Pt(557) surface observed by
456 < Tao involved the formation of triangular clusters that stretched
457 < across the plateau between two step-edges. Neither system, within
458 < the 40~ns time scale, experienced this reconstruction.
455 > The second reconstruction observed by
456 > Tao {\it et al}.\cite{Tao:2010} involved the formation of triangular clusters that stretched
457 > across the plateau between two step-edges. Neither metal, within
458 > the 40~ns time scale or the extended simulation time of 150~ns for
459 > the 50\% Pt system, experienced this reconstruction.
460  
461 + %Evolution of surface
462 + \begin{figure}[H]
463 + \includegraphics[width=\linewidth]{ProgressionOfDoubleLayerFormation_yellowCircle.png}
464 + \caption{The Pt(557) / 50\% CO system at a sequence of times after
465 +  initial exposure to the CO: (a) 258~ps, (b) 19~ns, (c) 31.2~ns, and
466 +  (d) 86.1~ns. Disruption of the (557) step-edges occurs quickly.  The
467 +  doubling of the layers appears only after two adjacent step-edges
468 +  touch.  The circled spot in (b) nucleated the growth of the double
469 +  step observed in the later configurations.}
470 +  \label{fig:reconstruct}
471 + \end{figure}
472 +
473   \subsection{Dynamics}
474 < Previous atomistic simulations of stepped surfaces were largely
475 < concerned with the energetics and structures at different conditions
476 < \cite{Williams:1991,Williams:1994}. Consequently, the most common
477 < technique has been Monte Carlo. Monte Carlo gives an efficient
478 < sampling of the equilibrium thermodynamic landscape at the expense
479 < of ignoring the dynamics of the system. Previous work by Pearl and
480 < Sibener\cite{Pearl}, using STM, has been able to show the coalescing
481 < of steps on Ni(977). The time scale of the image acquisition,
434 < $\sim$70 s/image provides an upper bound for the time required for
435 < the doubling to occur. In this section we give data on dynamic and
436 < transport properties, e.g. diffusion, layer formation time, etc.
474 > Previous experimental work by Pearl and Sibener\cite{Pearl},
475 > using STM, has been able to capture the coalescence of steps
476 > on Ni(977). The time scale of the image acquisition, $\sim$70~s/image,
477 > provides an upper bound for the time required for the doubling
478 > to occur. By utilizing Molecular Dynamics we are able to probe
479 > the dynamics of these reconstructions at elevated temperatures
480 > and in this section we provide data on the timescales for transport
481 > properties, e.g. diffusion and layer formation time.
482  
483  
484   \subsubsection{Transport of surface metal atoms}
485   %forcedSystems/stepSeparation
486 < The movement or wandering of a step-edge is a cooperative effect
487 < arising from the individual movements, primarily through surface
488 < diffusion, of the atoms making up the steps An ideal metal surface
444 < displaying a low index facet, (111) or (100) is unlikely to experience
486 > The wandering of a step-edge is a cooperative effect
487 > arising from the individual movements of the atoms making up the steps. An ideal metal surface
488 > displaying a low index facet, (111) or (100), is unlikely to experience
489   much surface diffusion because of the large energetic barrier that must
490 < be overcome to lift an atom out of the surface. The presence of step-edges
491 < on higher-index surfaces provide a source for mobile metal atoms.
492 < Breaking away from the step-edge on a clean surface still imposes an
493 < energetic penalty around $\sim$~40 kcal/mol, but is much less than lifting
490 > be overcome to lift an atom out of the surface. The presence of step-edges and other surface features
491 > on higher-index facets provides a lower energy source for mobile metal atoms.
492 > Single-atom break-away from a step-edge on a clean surface still imposes an
493 > energetic penalty around $\sim$~45 kcal/mol, but this is easier than lifting
494   the same metal atom vertically out of the surface,  \textgreater~60 kcal/mol.
495   The penalty lowers significantly when CO is present in sufficient quantities
496 < on the surface. For certain distributions of CO, the penalty can be as low as
496 > on the surface. For certain distributions of CO, see Discussion, the penalty can fall to as low as
497   $\sim$~20 kcal/mol. Once an adatom exists on the surface, the barrier for
498 < diffusion is negligible ( \textless~4 kcal/mol) and these adatoms are well
499 < able to explore the terrace before rejoining either the original step-edge or becoming a part
500 < of a different edge. Atoms traversing separate terraces is a more difficult
501 < process, but can be overcome through a joining and lifting stage which is
502 < examined in the discussion section. By tracking the mobility of individual
498 > diffusion is negligible (\textless~4 kcal/mol for a Pt adatom). These adatoms are then
499 > able to explore the terrace before rejoining either their original step-edge or
500 > becoming a part of a different edge. It is an energetically unfavorable process with a high barrier for an atom
501 > to traverse to a separate terrace although the presence of CO can lower the
502 > energy barrier required to lift or lower an adatom. By tracking the mobility of individual
503   metal atoms on the Pt and Au surfaces we were able to determine the relative
504   diffusion constants, as well as how varying coverages of CO affect the diffusion. Close
505   observation of the mobile metal atoms showed that they were typically in
506 < equilibrium with the step-edges, dynamically breaking apart and rejoining the edges.
506 > equilibrium with the step-edges.
507   At times, their motion was concerted and two or more adatoms would be
508 < observed moving together across the surfaces. The primary challenge in
465 < quantifying the overall surface mobility was in defining ``mobile" vs. ``static" atoms.
508 > observed moving together across the surfaces.
509  
510 < A particle was considered mobile once it had traveled more than 2~\AA~
511 < between saved configurations of the system (typically 10-100 ps). An atom that was
512 < truly mobile would typically travel much greater distances than this, but the 2~\AA~ cutoff
513 < was to prevent swamping the diffusion data with the in-place vibrational
514 < movement of buried atoms. Diffusion on  a surface is strongly affected by
510 > A particle was considered ``mobile'' once it had traveled more than 2~\AA~
511 > between saved configurations of the system (typically 10-100 ps). A mobile atom
512 > would typically travel much greater distances than this, but the 2~\AA~cutoff
513 > was used to prevent swamping the diffusion data with the in-place vibrational
514 > movement of buried atoms. Diffusion on a surface is strongly affected by
515   local structures and in this work, the presence of single and double layer
516 < step-edges causes the diffusion parallel to the step-edges to be different
517 < from the diffusion perpendicular to these edges. Parallel and perpendicular
516 > step-edges causes the diffusion parallel to the step-edges to be larger than
517 > the diffusion perpendicular to these edges. Parallel and perpendicular
518   diffusion constants are shown in Figure \ref{fig:diff}.
519  
520 < \subsubsection{Dynamics of double layer formation}
478 < The increased amounts of diffusion on Pt at the higher CO coverages plays a primary role in the formation of the double layers observed on Pt. However, this is not a complete explanation as seen by the 33\% Pt system which has higher diffusion constants but did not show any signs of undergoing the doubling. This difference will be explored more fully in the discussion. On the 50\% Pt system, three separate layers were formed over the extended run time of this system. Previous experimental work has given some insight into the upper bounds of the time required for step coalescing.\cite{Williams:1991,Pearl} In this system, as seen in Figure \ref{fig:reconstruct}, the first appearance of a double layer, a nodal site, appears at 19 ns into the simulation. Within 12 ns, nearly half of the step has formed the double layer and by 86 ns, the complete layer has been smoothed. The double layer could be considered ``complete" by 37 ns but is a bit rough or wavy. From the appearance of the first node to the first observed double layer, ignoring roughening, the process took $\sim$20 ns. Another $\sim$40 ns was necessary for the layer to completely straighten. The other two layers in this simulation form over a period of 22 ns and 42 ns respectively. Comparing this to the upper bounds of the image scan, it is likely that aspects of this reconstruction occur very quickly. A possible explanation for this rapid reconstruction is the elevated temperatures our systems were run at. It is likely that the process would take longer at lower temperatures and is an area of exploration for future work.
479 <
480 < %Evolution of surface
520 > %Diffusion graph
521   \begin{figure}[H]
522 < \includegraphics[width=\linewidth]{ProgressionOfDoubleLayerFormation_yellowCircle.png}
483 < \caption{The Pt(557) / 50\% CO system at a sequence of times after
484 <  initial exposure to the CO: (a) 258 ps, (b) 19 ns, (c) 31.2 ns, and
485 <  (d) 86.1 ns. Disruption of the (557) step-edges occurs quickly.  The
486 <  doubling of the layers appears only after two adjacent step-edges
487 <  touch.  The circled spot in (b) nucleated the growth of the double
488 <  step observed in the later configurations.}
489 <  \label{fig:reconstruct}
490 < \end{figure}
491 <
492 < \begin{figure}[H]
493 < \includegraphics[width=\linewidth]{DiffusionComparison_errorXY_remade.pdf}
522 > \includegraphics[width=\linewidth]{DiffusionComparison_errorXY_remade_20ns.pdf}
523   \caption{Diffusion constants for mobile surface atoms along directions
524    parallel ($\mathbf{D}_{\parallel}$) and perpendicular
525    ($\mathbf{D}_{\perp}$) to the (557) step-edges as a function of CO
526    surface coverage.  Diffusion parallel to the step-edge is higher
527    than that perpendicular to the edge because of the lower energy
528    barrier associated with traversing along the edge as compared to
529 <  completely breaking away. Additionally, the observed
530 <  maximum and subsequent decrease for the Pt system suggests that the
531 <  CO self-interactions are playing a significant role with regards to
532 <  movement of the Pt atoms around and across the surface. }
529 >  completely breaking away. The two reported diffusion constants for
530 >  the 50\% Pt system arise from different sample sets. The lower values
531 >  correspond to the same 40~ns amount that all of the other systems were
532 >  examined at, while the larger values correspond to a 20~ns period }
533   \label{fig:diff}
534   \end{figure}
535  
536 + The weaker Au-CO interaction is evident in the weak CO-coverage
537 + dependance of Au diffusion. This weak interaction leads to lower
538 + observed coverages when compared to dosage amounts. This further
539 + limits the effect the CO can have on surface diffusion. The correlation
540 + between coverage and Pt diffusion rates shows a near linear relationship
541 + at the earliest times in the simulations. Following double layer formation,
542 + however, there is a precipitous drop in adatom diffusion. As the double
543 + layer forms, many atoms that had been tracked for mobility data have
544 + now been buried resulting in a smaller reported diffusion constant. A
545 + secondary effect of higher coverages is CO-CO cross interactions that
546 + lower the effective mobility of the Pt adatoms that are bound to each CO.
547 + This effect would become evident only at higher coverages. A detailed
548 + account of Pt adatom energetics follows in the Discussion.
549 +
550  
551 + \subsubsection{Dynamics of double layer formation}
552 + The increased diffusion on Pt at the higher CO coverages is the primary
553 + contributor to double layer formation. However, this is not a complete
554 + explanation -- the 33\%~Pt system has higher diffusion constants, but
555 + did not show any signs of edge doubling in 40~ns. On the 50\%~Pt
556 + system, one double layer formed within the first 40~ns of simulation time,
557 + while two more were formed as the system was allowed to run for an
558 + additional 110~ns (150~ns total). This suggests that this reconstruction
559 + is a rapid process and that the previously mentioned upper bound is a
560 + very large overestimate.\cite{Williams:1991,Pearl} In this system the first
561 + appearance of a double layer appears at 19~ns into the simulation.
562 + Within 12~ns of this nucleation event, nearly half of the step has formed
563 + the double layer and by 86~ns the complete layer has flattened out.
564 + From the appearance of the first nucleation event to the first observed
565 + double layer, the process took $\sim$20~ns. Another $\sim$40~ns was
566 + necessary for the layer to completely straighten. The other two layers in
567 + this simulation formed over periods of 22~ns and 42~ns respectively.
568 + A possible explanation for this rapid reconstruction is the elevated
569 + temperatures under which our systems were simulated. The process
570 + would almost certainly take longer at lower temperatures. Additionally,
571 + our measured times for completion of the doubling after the appearance
572 + of a nucleation site are likely affected by our periodic boxes. A longer
573 + step-edge will likely take longer to ``zipper''.
574  
575  
576   %Discussion
577   \section{Discussion}
578 < In this paper we have shown that we were able to accurately model the initial reconstruction of the
579 < Pt(557) surface upon CO adsorption as shown by Tao et al. \cite{Tao:2010}. More importantly, we
580 < were able to observe the dynamic processes necessary for this reconstruction.
578 > We have shown that a classical potential model is able to model the
579 > initial reconstruction of the Pt(557) surface upon CO adsorption as
580 > shown by Tao {\it et al}.\cite{Tao:2010}. More importantly, we were
581 > able to observe features of the dynamic processes necessary for
582 > this reconstruction. Here we discuss the features of the model that
583 > give rise to the observed dynamical properties of the (557) reconstruction.
584  
585 + \subsection{Diffusion}
586 + The perpendicular diffusion constant
587 + appears to be the most important indicator of double layer
588 + formation. As highlighted in Figure \ref{fig:reconstruct}, the
589 + formation of the double layer did not begin until a nucleation
590 + site appeared. And as mentioned by Williams {\it et al}.\cite{Williams:1991, Williams:1994},
591 + the inability for edges to cross leads to an effective edge-edge repulsion that
592 + must be overcome to allow step coalescence.
593 + A greater $\textbf{D}_\perp$ implies more step-wandering
594 + and a larger chance for the stochastic meeting of two edges
595 + to create a nucleation point. Parallel diffusion along the step-edge can help ``zipper'' up a nascent double
596 + layer. This helps explain why the time scale for formation after
597 + the appearance of a nucleation site was rapid, while the initial
598 + appearance of the nucleation site was unpredictable.
599 +
600   \subsection{Mechanism for restructuring}
601 < Since the Au surface showed no large scale restructuring throughout
602 < our simulation time our discussion will focus on the 50\% Pt-CO system
603 < which did undergo the doubling featured in Figure \ref{fig:reconstruct}.
604 < Comparing the results from this simulation to those reported previously by
605 < Tao et al.\cite{Tao:2010} the similarities in the Pt-CO system are quite
606 < strong. As shown in Figure \ref{fig:reconstruct}, the simulated Pt
607 < system exposed to a large dosage of CO will restructure by doubling the terrace
608 < widths and step heights. The restructuring occurs in a piecemeal fashion, one to two Pt atoms at a time and as such is a fairly stochastic event.
609 < Looking at individual configurations of the system, the adatoms either
610 < break away from the step-edge and stay on the lower terrace or they lift
611 < up onto the higher terrace. Once ``free'', they will diffuse on the terrace
612 < until reaching another step-edge or rejoining their original edge.  
613 < This combination of growth and decay of the step-edges is in a state of
614 < dynamic equilibrium. However, once two previously separated edges
615 < meet as shown in Figure 1.B, this meeting point tends to act as a focus
616 < or growth point for the rest of the edge to meet up, akin to that of a zipper.
617 < From the handful of cases where a double layer was formed during the
618 < simulation, measuring from the initial appearance of a growth point, the
619 < double layer tends to be fully formed within $\sim$35 ns.
601 > Since the Au surface showed no large scale restructuring in any of
602 > our simulations, our discussion will focus on the 50\% Pt-CO system
603 > which did exhibit doubling featured in Figure \ref{fig:reconstruct}. A
604 > number of possible mechanisms exist to explain the role of adsorbed
605 > CO in restructuring the Pt surface. Quadrupolar repulsion between
606 > adjacent CO molecules adsorbed on the surface is one possibility.  
607 > However, the quadrupole-quadrupole interaction is short-ranged and
608 > is attractive for some orientations.  If the CO molecules are ``locked'' in
609 > a specific orientation relative to each other, through atop adsorption for
610 > example, this explanation would gain credence. The energetic repulsion
611 > between two CO molecules located a distance of 2.77~\AA~apart
612 > (nearest-neighbor distance of Pt) and both in a vertical orientation,
613 > is 8.62 kcal/mol. Moving the CO to the second nearest-neighbor distance
614 > of 4.8~\AA~drops the repulsion to nearly 0. Allowing the CO to rotate away
615 > from a purely vertical orientation also lowers the repulsion. When the
616 > carbons are locked at a distance of 2.77~\AA, a minimum of 6.2 kcal/mol is
617 > reached when the angle between the 2 CO is $\sim$24\textsuperscript{o}.
618 > The barrier for surface diffusion of a Pt adatom is only 4 kcal/mol, so
619 > repulsion between adjacent CO molecules could increase the surface
620 > diffusion. However, the residence time of CO on Pt suggests that these
621 > molecules are extremely mobile, with diffusion constants 40 to 2500 times
622 > larger than surface Pt atoms. This mobility suggests that the CO are more
623 > likely to shift their positions without dragging the Pt along with them.
624  
625 < A number of possible mechanisms exist to explain the role of adsorbed
538 < CO in restructuring the Pt surface. Quadrupolar repulsion between adjacent
539 < CO molecules adsorbed on the surface is one likely possibility.  However,
540 < the quadrupole-quadrupole interaction is short-ranged and is attractive for
541 < some orientations.  If the CO molecules are ``locked'' in a specific orientation
542 < relative to each other, through atop adsorption for example, this explanation
543 < gains some weight.  The energetic repulsion between two CO located a
544 < distance of 2.77~\AA~apart (nearest-neighbor distance of Pt) with both in
545 < a  vertical orientation is 8.62 kcal/mol. Moving the CO apart to the second
546 < nearest-neighbor distance of 4.8~\AA~or 5.54~\AA~drops the repulsion to
547 < nearly 0 kcal/mol. Allowing the CO's to leave a purely vertical orientation
548 < 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.
549 < As mentioned above, the energy barrier for surface diffusion
550 < of a Pt adatom is only 4 kcal/mol. So this repulsion between CO can help
551 < increase the surface diffusion. However, the residence time of CO on Pt was
552 < examined and while the majority of the CO is on or near the surface throughout
553 < the run, it is extremely mobile. This mobility suggests that the CO are more
554 < likely to shift their positions without necessarily dragging the Pt along with them.
625 > Another possible mechanism for the restructuring is in the destabilization of strong Pt-Pt interactions by CO adsorbed on surface Pt atoms. To test this hypothesis, a number of configurations of CO in varying quantities were arranged on the upper plateaus around a step on an otherwise clean Pt(557) surface. A few sample configurations are displayed in Figure \ref{fig:SketchGraphic}, with energy curves corresponding to each configuration in Figure \ref{fig:SketchEnergies}. Certain configurations of CO, cases (e), (g) and (h) for example, can provide significant energetic pushes for Pt atoms to break away from the step-edge.
626  
556 Another possible and more likely mechanism for the restructuring is in the
557 destabilization of strong Pt-Pt interactions by CO adsorbed on surface
558 Pt atoms.  This would then have the effect of increasing surface mobility
559 of these atoms.  To test this hypothesis, numerous configurations of
560 CO in varying quantities were arranged on the higher and lower plateaus
561 around a step on a otherwise clean Pt(557) surface. One representative
562 configuration is displayed in Figure \ref{fig:lambda}. Single or concerted movement
563 of Pt atoms was then examined to determine possible barriers. Because
564 the movement was forced along a pre-defined reaction coordinate that may differ
565 from the true minimum of this path, only the beginning and ending energies
566 are displayed in Table \ref{tab:energies}. These values suggest that the presence of CO at suitable
567 locations can lead to lowered barriers for Pt breaking apart from the step-edge.
568 Additionally, as highlighted in Figure \ref{fig:lambda}, the presence of CO makes the
569 burrowing and lifting of adatoms favorable, whereas without CO, the process is neutral
570 in terms of energetics.
627  
628 + %Sketch graphic of different configurations
629 + \begin{figure}[H]
630 + \includegraphics[width=0.8\linewidth, height=0.8\textheight]{COpathsSketch.pdf}
631 + \caption{The dark grey atoms refer to the upper ledge, while the white atoms are
632 + the lower terrace. The blue highlighted atoms had a CO in a vertical atop position
633 + upon them. These are a sampling of the configurations examined to gain a more
634 + complete understanding of the effects CO has on surface diffusion and edge breakup.
635 + Energies associated with each configuration are displayed in Figure \ref{fig:SketchEnergies}.}
636 + \label{fig:SketchGraphic}
637 + \end{figure}
638 +
639 + %energy graph corresponding to sketch graphic
640 + \begin{figure}[H]
641 + \includegraphics[width=\linewidth]{stepSeparationComparison.pdf}
642 + \caption{The energy curves directly correspond to the labeled model
643 + surface in Figure \ref{fig:SketchGraphic}. All energy curves are relative
644 + to their initial configuration so the energy of a and h do not have the
645 + same zero value. As is seen, certain arrangements of CO can lower
646 + the energetic barrier that must be overcome to create an adatom.
647 + However, it is the highest coverages where these higher-energy
648 + configurations of CO will be more likely. }
649 + \label{fig:SketchEnergies}
650 + \end{figure}
651 +
652 +
653 +
654   %lambda progression of Pt -> shoving its way into the step
655   \begin{figure}[H]
656 < \includegraphics[width=\linewidth]{lambdaProgression_atopCO.png}
656 > \includegraphics[width=\linewidth]{lambdaProgression_atopCO_withLambda.png}
657   \caption{A model system of the Pt(557) surface was used as the framework
658   for exploring energy barriers along a reaction coordinate. Various numbers,
659   placements, and rotations of CO were examined as they affect Pt movement.
660 < The coordinate displayed in this Figure was a representative run. As shown
579 < in Table \ref{tab:rxcoord}, relative to the energy of the system at 0\%, there
660 > The coordinate displayed in this Figure was a representative run.  relative to the energy of the system at 0\%, there
661   is a slight decrease upon insertion of the Pt atom into the step-edge along
662   with the resultant lifting of the other Pt atom when CO is present at certain positions.}
663   \label{fig:lambda}
664   \end{figure}
665  
666 + \subsection{CO Removal and double layer stability}
667 + Once a double layer had formed on the 50\%~Pt system it
668 + remained for the rest of the simulation time with minimal
669 + movement. There were configurations that showed small
670 + wells or peaks forming, but typically within a few nanoseconds
671 + the feature would smooth away. Within our simulation time,
672 + the formation of the double layer was irreversible and a double
673 + layer was never observed to split back into two single layer
674 + step-edges while CO was present. To further gauge the effect
675 + CO had on this system, additional simulations were run starting
676 + from a late configuration of the 50\%~Pt system that had formed
677 + double layers. These simulations then had their CO removed.
678 + The double layer breaks rapidly in these simulations, already
679 + showing a well-defined splitting after 100~ps. Configurations of
680 + this system are shown in Figure \ref{fig:breaking}. The coloring
681 + of the top and bottom layers helps to exhibit how much mixing
682 + the edges experience as they split. These systems were only
683 + examined briefly, 10~ns, and within that time despite the initial
684 + rapid splitting, the edges only moved another few \AA~apart.
685 + It is possible with longer simulation times that the
686 + (557) lattice could be recovered as seen by Tao {\it et al}.\cite{Tao:2010}
687  
688  
587 \subsection{Diffusion}
588 As shown in the results section, the diffusion parallel to the step-edge tends to be
589 much larger than that perpendicular to the step-edge, likely because of the dynamic
590 equilibrium that is established between the step-edge and adatom interface. The coverage
591 of CO also appears to play a slight role in relative rates of diffusion, as shown in Figure \ref{fig:diff}.
592 The
593 Thus, the bottleneck of the double layer formation appears to be the initial formation
594 of this growth point, which seems to be somewhat of a stochastic event. Once it
595 appears, parallel diffusion, along the now slightly angled step-edge, will allow for
596 a faster formation of the double layer than if the entire process were dependent on
597 only perpendicular diffusion across the plateaus. Thus, the larger $D_{\perp}$, the
598 more likely a growth point is to be formed.
599 \\
689  
690  
691 +
692 +
693   %breaking of the double layer upon removal of CO
694   \begin{figure}[H]
695   \includegraphics[width=\linewidth]{doubleLayerBreaking_greenBlue_whiteLetters.png}
696 < %:
606 < \caption{(A)  0 ps, (B) 100 ps, (C) 1 ns, after the removal of CO. The presence of the CO
696 > \caption{(A)  0~ps, (B) 100~ps, (C) 1~ns, after the removal of CO. The presence of the CO
697   helped maintain the stability of the double layer and upon removal the two layers break
698   and begin separating. The separation is not a simple pulling apart however, rather
699   there is a mixing of the lower and upper atoms at the edge.}
# Line 614 | Line 704 | more likely a growth point is to be formed.
704  
705  
706   %Peaks!
707 < \begin{figure}[H]
708 < \includegraphics[width=\linewidth]{doublePeaks_noCO.png}
709 < \caption{At the initial formation of this double layer  ( $\sim$ 37 ns) there is a degree
710 < of roughness inherent to the edge. The next $\sim$ 40 ns show the edge with
711 < aspects of waviness and by 80 ns the double layer is completely formed and smooth. }
712 < \label{fig:peaks}
713 < \end{figure}
707 > %\begin{figure}[H]
708 > %\includegraphics[width=\linewidth]{doublePeaks_noCO.png}
709 > %\caption{At the initial formation of this double layer  ( $\sim$ 37 ns) there is a degree
710 > %of roughness inherent to the edge. The next $\sim$ 40 ns show the edge with
711 > %aspects of waviness and by 80 ns the double layer is completely formed and smooth. }
712 > %\label{fig:peaks}
713 > %\end{figure}
714  
715  
716   %Don't think I need this
# Line 658 | Line 748 | In this work we have shown the reconstruction of the P
748   % \end{tabular}
749   % \end{table}
750  
751 < \section{Acknowledgments}
751 > \begin{acknowledgement}
752   Support for this project was provided by the National Science
753   Foundation under grant CHE-0848243 and by the Center for Sustainable
754   Energy at Notre Dame (cSEND). Computational time was provided by the
755   Center for Research Computing (CRC) at the University of Notre Dame.
756 <
756 > \end{acknowledgement}
757   \newpage
758   \bibliography{firstTryBibliography}
759 < \end{doublespace}
759 > %\end{doublespace}
760 >
761 > \begin{tocentry}
762 > %\includegraphics[height=3.5cm]{timelapse}
763 > \end{tocentry}
764 >
765   \end{document}

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