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# Line 117 | Line 117 | This work is an investigation into the mechanism and t
117   reversible restructuring under exposure to moderate pressures of
118   carbon monoxide.\cite{Tao:2010}
119  
120 < This work is an investigation into the mechanism and timescale for
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
# Line 126 | 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 relaxation 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
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 being greatly
137 < affected by this relaxation. Piccolo et al. on the other hand, did see a
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 atoms was the primary driving force for the reconstruction.
# Line 149 | 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 161 | 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 174 | 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 213 | 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}
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) 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}  
# Line 272 | 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 314 | 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
319 < future work.
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 360 | Line 359 | dimensions of 57.4~x~51.9285~x~100~\AA.
359   \subsection{Pt(557) and Au(557) metal interfaces}
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.
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$19~\AA~for Au.
365   The systems are arranged in a FCC crystal that have been cut
366   along the (557) plane so that they are periodic in the {\it x} and
367   {\it y} directions, and have been oriented to expose two aligned
# Line 369 | Line 370 | The different bulk melting temperatures (1345~$\pm$~10
370   1200~K were performed to confirm the relative
371   stability of the surfaces without a CO overlayer.  
372  
373 < The different bulk melting temperatures (1345~$\pm$~10~K for Au\cite{Au:melting}
373 > The different bulk melting temperatures predicted by EAM (1345~$\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
# Line 396 | Line 397 | The surfaces of both systems, upon dosage of CO, began
397   %
398   \section{Results}
399   \subsection{Structural remodeling}
400 < The surfaces of both systems, upon dosage of CO, began
401 < to undergo extensive remodeling that was not observed in the bare
402 < systems. The bare metal surfaces
403 < experienced minor roughening of the step-edge because
404 < of the elevated temperatures, but the
405 < (557) lattice was well-maintained throughout the simulation
406 < time. The Au systems were limited to greater amounts of
407 < roughening, i.e. breakup of the step-edge, and some step
408 < wandering. The lower coverage Pt systems experienced
409 < similar restructuring but to a greater extent when
410 < compared to the Au systems. The 50\% coverage
410 < Pt system was unique among our simulations in that it
411 < formed numerous double layers through step coalescence,
412 < similar to results reported by Tao et al.\cite{Tao:2010}
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 < movement at their respective run temperatures. As the CO
416 < coverage increased however, the mobility of the surface,
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, the step-edges
419 < did not coalesce in any of the other simulations, instead
420 < preferring to keep nearly the same distance between steps
421 < as in the original (557) lattice, $\sim$13\AA for Pt and $\sim$14\AA for Au.
422 < Previous work by Williams et al.\cite{Williams:1991, Williams:1994}
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 arises because step-edge crossing is not allowed
426 < which constrains the entropy. This entropic repulsion does
427 < not completely define the interactions between steps, which
428 < is why some surfaces will undergo step coalescence, where
429 < additional attractive interactions can overcome the repulsion.\cite{Williams:1991}
430 < The presence and concentration of adsorbates, as shown in
431 < this work, can affect these step interactions, potentially leading
432 < to a new surface structure as the thermodynamic minimum.
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.\cite{Tao:2010} have shown experimentally that the Pt(557) surface
436 < undergoes two separate reconstructions upon CO adsorption.\cite{Tao:2010}
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 numerous surfaces
439 < at varying conditions: Ni(977), Si(111).\cite{Williams:1994,Williams:1991,Pearl}
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 when compared to the Au system
442 < because of the larger surface mobility and extent of step wandering.
443 < The amount of reconstruction is strongly correlated to the amount of CO
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
446 < surface diffusion of metal adatoms. While both systems displayed
447 < step-edge wandering, only the 50\% Pt surface underwent the
448 < doubling seen by Tao et al.\cite{Tao:2010} within the time scales studied here.
449 < Over longer periods, (150~ns) two more double layers formed
450 < on this interface. Although double layer formation did not occur
451 < in the other Pt systems, they show more step-wandering and
454 < general roughening compared to their Au counterparts. 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
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  
# Line 474 | Line 471 | Previous atomistic simulations of stepped surfaces dea
471   \end{figure}
472  
473   \subsection{Dynamics}
474 < Previous atomistic simulations of stepped surfaces dealt largely
475 < with the energetics and structures at different conditions
476 < \cite{Williams:1991,Williams:1994}. Consequently, the most common
477 < technique utilized to date has been Monte Carlo sampling. Monte Carlo approaches give an efficient
478 < sampling of the equilibrium thermodynamic landscape at the expense
479 < of ignoring the dynamics of the system. Previous experimental work by Pearl and
480 < Sibener\cite{Pearl}, using STM, has been able to capture the coalescing
481 < of steps on Ni(977). The time scale of the image acquisition,
485 < $\sim$70~s/image provides an upper bound for the time required for
486 < the doubling to occur. By utilizing Molecular Dynamics we were able to probe the dynamics of these reconstructions and in this section we give data on dynamic and
487 < 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
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 and other surface features
491   on higher-index facets provides a lower energy source for mobile metal atoms.
492 < Breaking away from the step-edge on a clean surface still imposes an
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, see Figures \ref{fig:sketchGraphic} and \ref{fig:sketchEnergies}, the penalty can fall to 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 for a Pt adatom). These adatoms are then
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 a difficult process for an atom
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.
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
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
# Line 539 | Line 533 | The lack of a definite trend in the Au diffusion data
533   \label{fig:diff}
534   \end{figure}
535  
536 < The lack of a definite trend in the Au diffusion data in Figure \ref{fig:diff} is likely due
537 < to the weaker bonding between Au and CO. This leads to a lower observed
538 < coverage ({\it x}-axis) when compared to dosage amount, which
539 < then further limits the effect the CO can have on surface diffusion. The correlation
540 < between coverage and Pt diffusion rates conversely shows a
541 < definite trend marred by the highest coverage surface. Two
542 < explanations arise for this drop. First, upon a visual inspection of
543 < the system, after a double layer has been formed, it maintains its
544 < stability strongly and is no longer a good source for adatoms and so
545 < atoms that had been tracked for mobility data have now been buried. By
546 < performing the same diffusion calculation but on a shorter run time
547 < (20~ns), only including data before the formation of the double layer, we obtain
548 < the larger values for both $\mathbf{D}_{\parallel}$ and $\mathbf{D}_{\perp}$ at the 50\% coverage.
549 < This places the parallel diffusion constant more closely in line with the
556 < expected trend, while the perpendicular diffusion constant does not
557 < drop as far. A secondary explanation arising from our analysis of the
558 < mechanism of double layer formation focuses on the effect that CO on the
559 < surface has with respect to overcoming surface diffusion of Pt. If the
560 < coverage is too sparse, the Pt engages in minimal interactions and
561 < thus minimal diffusion. As coverage increases, there are more favorable
562 < arrangements of CO on the surface allowing the formation of a path,
563 < a minimum energy trajectory, for the adatom to explore the surface.
564 < As the CO is constantly moving on the surface, this path is constantly
565 < changing. If the coverage becomes too great, the paths could
566 < potentially be clogged leading to a decrease in diffusion despite
567 < their being more adatoms and step-wandering.
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  
569
570
551   \subsubsection{Dynamics of double layer formation}
552 < The increased diffusion on Pt at the higher
553 < CO coverages plays a primary role in double layer formation. However, this is not
554 < a complete explanation -- the 33\%~Pt system
555 < has higher diffusion constants but did not show
556 < any signs of edge doubling in the observed run time. On the
557 < 50\%~Pt system, one layer formed within the first 40~ns of simulation time, while two more were formed as the system was run for an additional
558 < 110~ns (150~ns total). Previous experimental
559 < work gives insight into the upper bounds of the
560 < time required for step coalescence.\cite{Williams:1991,Pearl}
561 < In this system, as seen in Figure \ref{fig:reconstruct}, the first
562 < appearance of a double layer, appears at 19~ns
563 < into the simulation. Within 12~ns of this nucleation event, nearly half of the step has
564 < formed the double layer and by 86~ns, the complete layer
565 < has been flattened out. The double layer could be considered
566 < ``complete" by 37~ns but remains a bit rough. From the
567 < appearance of the first nucleation event to the first observed double layer, the process took $\sim$20~ns. Another
568 < $\sim$40~ns was necessary for the layer to completely straighten.
569 < The other two layers in this simulation formed over periods of
570 < 22~ns and 42~ns respectively. Comparing this to the upper
571 < bounds of the image scan, it is likely that most aspects of this
572 < reconstruction occur very rapidly. A possible explanation
573 < for this rapid reconstruction is the elevated temperatures
594 < under which our systems were simulated. It is probable that the process would
595 < take longer at lower temperatures.
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 + 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 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 bound to Pt 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 different interpretation of the above mechanism, taking into account the large
626 + mobility of the CO, looks at how instantaneous and short-lived configurations of
627 + CO on the surface can destabilize Pt-Pt interactions leading to increased step-edge
628 + breakup and diffusion. On the bare Pt(557) surface the barrier to completely detach
629 + an edge atom is $\sim$~43~kcal/mol, as is shown in configuration (a) in Figures
630 + \ref{fig:SketchGraphic} \& \ref{fig:SketchEnergies}. For certain configurations, cases
631 + (e), (g), and (h), the barrier can be lowered to $\sim$~23~kcal/mole. In these instances,
632 + it becomes quite energetically favorable to roughen the edge by introducing a small
633 + separation of 0.5 to 1.0~\AA. This roughening becomes immediately obvious in
634 + simulations with significant CO populations, although it is present to a lesser extent
635 + on lower coverage surfaces and even on the bare surfaces. In these cases it is likely
636 + due to stochastic vibrational processes that squeeze out step-edge atoms. The mechanism
637 + of step-edge breakup suggested by these energy curves is one the most difficult
638 + processes, a complete break-away from the step-edge in one unbroken movement.
639 + Easier multistep mechanisms likely exist where an adatom moves laterally on the surface
640 + after being ejected so it is sitting on the edge. This provides the atom with 5 nearest
641 + neighbors, which while lower than the 7 if it had stayed a part of the step-edge, is higher
642 + than the 3 it could maintain located on the terrace. In this proposed mechanism, the CO
643 + quadrupolar repulsion is still playing a primary role, but for its importance in roughening
644 + the step-edge, rather than maintaining long-term bonds with a single Pt atom which is not
645 + born out by their mobility data. The requirement for a large density of CO on the surface
646 + for some of the more favorable suggested mechanisms in Figure \ref{fig:SketchGraphic}
647 + correspond well with the increased mobility seen on higher coverage surfaces.
648  
649   %Sketch graphic of different configurations
650   \begin{figure}[H]
# Line 623 | Line 670 | configurations of CO will be more likely. }
670   \label{fig:SketchEnergies}
671   \end{figure}
672  
673 < %Discussion
674 < \section{Discussion}
675 < We have shown that the classical potential models are able to model the initial reconstruction of the
676 < Pt(557) surface upon CO adsorption as shown by Tao et al. \cite{Tao:2010}. More importantly, we
677 < were able to observe features of the dynamic processes necessary for this reconstruction.
673 > While configurations of CO on the surface are able to increase diffusion,
674 > this does not immediately provide an explanation for the formation of double
675 > layers. If adatoms were constrained to their terrace then doubling would be
676 > much less likely to occur. Nucleation sites could still potentially form, but there
677 > would not be enough atoms to finish the doubling. Real materials, where the
678 > step lengths can be taken as infinite, local doubling would be possible, but in
679 > our simulations with our periodic treatment of the system, this is not possible.
680 > Thus, there must be a mechanism that explains how adatoms are able to move
681 > amongst terraces. Figure \ref{fig:lambda} shows points along a reaction coordinate
682 > where an adatom along the step-edge with an adsorbed CO ``burrows'' into the
683 > edge displacing an atom onto the higher terrace. This mechanism was chosen
684 > because of similar events that were observed during the simulations. The barrier
685 > heights we obtained are only approximations because we constrained the movement
686 > of the highlighted atoms along a specific concerted path. The calculated $\Delta E$'s
687 > are the more interesting results from this investigation. When CO is not present and
688 > this reaction coordinate is followed, the $\Delta E > 3$~kcal/mol. The example shown
689 > in the figure, where CO is present in the atop position, has a $\Delta E < -15$~kcal/mol.
690 > While the barrier height is comparable to the non-CO case, that is a nearly a 20~kcal/mol
691 > difference in energies and moves the process from slightly unfavorable to energetically favorable.
692  
632 \subsection{Diffusion}
633 As shown in Figure \ref{fig:diff}, for the Pt systems, there
634 is a strong trend toward higher diffusion constants as
635 surface coverage of CO increases. The drop for the 50\%
636 case being explained as double layer formation already
637 beginning to occur in the analyzed 40~ns, which lowered
638 the calculated diffusion rates. Between the parallel and
639 perpendicular rates, the perpendicular diffusion constant
640 appears to be the most important indicator of double layer
641 formation. As highlighted in Figure \ref{fig:reconstruct}, the
642 formation of the double layer did not begin until a nucleation
643 site appeared. And as mentioned by Williams et al.\cite{Williams:1991, Williams:1994},
644 the inability for edges to cross leads to an effective repulsion.
645 This repulsion must be overcome to allow step coalescence.
646 A greater $\textbf{D}_\perp$ implies more step-wandering
647 and a larger chance for the stochastic meeting of two edges
648 to form the nucleation point. Upon that appearance, parallel
649 diffusion along the step-edge can help ``zipper'' up the double
650 layer. This helps explain why the time scale for formation after
651 the appearance of a nucleation site was rapid, while the initial
652 appearance of said site was unpredictable.
653
654 \subsection{Mechanism for restructuring}
655 Since the Au surface showed no large scale restructuring throughout
656 our simulation time our discussion will focus on the 50\% Pt-CO system
657 which did undergo the doubling featured in Figure \ref{fig:reconstruct}.
658 Similarities of our results to those reported previously by Tao et al.\cite{Tao:2010}
659 are quite strong. The simulated Pt system exposed to a large dosage
660 of CO readily restructures by doubling the terrace widths and step heights.
661 The restructuring occurs in a piecemeal fashion, one to two Pt atoms at a
662 time, but is rapid on experimental timescales. The adatoms either break
663 away from the step-edge and stay on the lower terrace or they lift up onto
664 a higher terrace. Once ``free'', they diffuse on the terrace until reaching
665 another step-edge or rejoining their original edge. This combination of
666 growth and decay of the step-edges is in a state of dynamic equilibrium.
667 However, once two previously separated edges meet as shown in Figure 1.B,
668 this nucleates the rest of the edge to meet up, forming a double layer.
669 From simulations which exhibit a double layer, the time delay from the
670 initial appearance of a nucleation point to a fully formed double layer is $\sim$35~ns.
671
672 A number of possible mechanisms exist to explain the role of adsorbed
673 CO in restructuring the Pt surface. Quadrupolar repulsion between adjacent
674 CO molecules adsorbed on the surface is one possibility.  However,
675 the quadrupole-quadrupole interaction is short-ranged and is attractive for
676 some orientations.  If the CO molecules are ``locked'' in a specific orientation
677 relative to each other, through atop adsorption for example, this explanation
678 gains some credence. The energetic repulsion between two CO located a
679 distance of 2.77~\AA~apart (nearest-neighbor distance of Pt) and both in
680 a vertical orientation, is 8.62 kcal/mol. Moving the CO apart to the second
681 nearest-neighbor distance of 4.8~\AA~or 5.54~\AA~drops the repulsion to
682 nearly 0 kcal/mol. Allowing the CO to rotate away from a purely vertical orientation
683 also lowers the repulsion. A minimum of 6.2 kcal/mol is reached at when the
684 angle between the 2 CO is $\sim$24\textsuperscript{o}, when the carbons are
685 locked at a distance of 2.77 \AA apart. As mentioned above, the energy barrier
686 for surface diffusion of a Pt adatom is only 4 kcal/mol. So this repulsion between
687 neighboring CO molecules can increase the surface diffusion. However, the
688 residence time of CO on Pt was examined and while the majority of the CO is
689 on or near the surface throughout the run, the molecules are extremely mobile,
690 with diffusion constants 40 to 2500 times larger, depending on coverage. This
691 mobility suggests that the CO are more likely to shift their positions without
692 necessarily the Pt along with them.
693
694 Another possible and more likely mechanism for the restructuring is in the
695 destabilization of strong Pt-Pt interactions by CO adsorbed on surface
696 Pt atoms. To test this hypothesis, numerous configurations of
697 CO in varying quantities were arranged on the higher and lower plateaus
698 around a step on a otherwise clean Pt(557) surface. A few sample
699 configurations are displayed in Figure \ref{fig:lambdaTable}, with
700 energies at various positions along the path displayed in Table
701 \ref{tab:rxcoord}. Certain configurations of CO, cases B and D for
702 example, can have quite strong energetic reasons for breaking
703 away from the step-edge. Although the packing of these configurations
704 is unlikely until CO coverage has reached a high enough value.
705 These examples are showing the most difficult cases, immediate
706 adatom formation through breakage away from the step-edge, which
707 is why their energies at large distances are relatively high. There are
708 mechanistic paths where an edge atom could get shifted to onto the
709 step-edge to form a small peak before fully breaking away. And again,
710 once the adatom is formed, the barrier for diffusion on the surface is
711 negligible. These sample configurations help explain CO's effect on
712 general surface mobility and step wandering, but they are lacking in
713 providing a mechanism for the formation of double layers. One possible
714 mechanism is elucidated in Figure \ref{fig:lambda}, where a burrowing
715 and lifting process of an adatom and step-edge atom respectively is
716 examined. The system, without CO present, is nearly energetically
717 neutral, whereas with CO present there is a $\sim$ 15 kcal/mol drop
718 in the energy of the system.
719
693   %lambda progression of Pt -> shoving its way into the step
694   \begin{figure}[H]
695   \includegraphics[width=\linewidth]{lambdaProgression_atopCO_withLambda.png}
# Line 729 | Line 702 | in the energy of the system.
702   \label{fig:lambda}
703   \end{figure}
704  
705 + The mechanism for doubling on this surface appears to be a convolution of at least
706 + these two described processes. For complete doubling of a layer to occur there must
707 + be the equivalent removal of a separate terrace. For those atoms to ``disappear'' from
708 + that terrace they must either rise up on the ledge above them or drop to the ledge below
709 + them. The presence of CO helps with both of these situations. There must be sufficient
710 + breakage of the step-edge to increase the concentration of adatoms on the surface.
711 + These adatoms must then undergo the burrowing highlighted above or some comparable
712 + mechanism to traverse the step-edge. Over time, these mechanisms working in concert
713 + led to the formation of a double layer.
714  
715 + \subsection{CO Removal and double layer stability}
716 + Once a double layer had formed on the 50\%~Pt system it
717 + remained for the rest of the simulation time with minimal
718 + movement. There were configurations that showed small
719 + wells or peaks forming, but typically within a few nanoseconds
720 + the feature would smooth away. Within our simulation time,
721 + the formation of the double layer was irreversible and a double
722 + layer was never observed to split back into two single layer
723 + step-edges while CO was present. To further gauge the effect
724 + CO had on this system, additional simulations were run starting
725 + from a late configuration of the 50\%~Pt system that had formed
726 + double layers. These simulations then had their CO removed.
727 + The double layer breaks rapidly in these simulations, already
728 + showing a well-defined splitting after 100~ps. Configurations of
729 + this system are shown in Figure \ref{fig:breaking}. The coloring
730 + of the top and bottom layers helps to exhibit how much mixing
731 + the edges experience as they split. These systems were only
732 + examined briefly, 10~ns, and within that time despite the initial
733 + rapid splitting, the edges only moved another few \AA~apart.
734 + It is possible with longer simulation times that the
735 + (557) lattice could be recovered as seen by Tao {\it et al}.\cite{Tao:2010}
736  
737  
738  

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