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# Line 86 | Line 86 | systems and the lack  of reconstruction of the Au syst
86   is sufficient to explain the reconstructions observed on the Pt
87   systems and the lack  of reconstruction of the Au systems.
88  
89 +
90 + The mechanism and dynamics of surface reconstructions of Pt(557)
91 + and Au(557) exposed to various coverages of carbon monoxide (CO)
92 + were investigated using molecular dynamics simulations. Metal-CO
93 + interactions were parameterized from experimental data and plane-wave
94 + Density Functional Theory (DFT) calculations.  The large difference in
95 + binding strengths of the Pt-CO and Au-CO interactions was found to play
96 + a significant role in step-edge stability and adatom diffusion constants.
97 + The energetics of CO adsorbed to the surface is sufficient to explain the
98 + step-doubling reconstruction observed on Pt(557) and the lack of such
99 + a reconstruction on the Au(557) surface.
100   \end{abstract}
101  
102   \newpage
# Line 117 | Line 128 | This work is an investigation into the mechanism and t
128   reversible restructuring under exposure to moderate pressures of
129   carbon monoxide.\cite{Tao:2010}
130  
131 < This work is an investigation into the mechanism and timescale for
131 > This work is an investigation into the mechanism and timescale for the Pt(557) \& Au(557)
132   surface restructuring using molecular simulations.  Since the dynamics
133   of the process are of particular interest, we employ classical force
134   fields that represent a compromise between chemical accuracy and the
# Line 126 | Line 137 | The Au(557) surface, because of a weaker interaction w
137   catalyst with adsorbates, in this work, two metal systems exposed
138   to carbon monoxide were examined. The Pt(557) surface has already been shown
139   to undergo a large scale reconstruction under certain conditions.\cite{Tao:2010}
140 < The Au(557) surface, because of a weaker interaction with CO, is seen as less
141 < likely to undergo this kind of reconstruction. However, Peters et al.\cite{Peters:2000}
142 < and Piccolo et al.\cite{Piccolo:2004} have both observed CO-induced
143 < reconstruction of a Au(111) surface. Peters et al. saw a relaxation to the
140 > The Au(557) surface, because of a weaker interaction with CO, is less
141 > likely to undergo this kind of reconstruction. However, Peters {\it et al}.\cite{Peters:2000}
142 > and Piccolo {\it et al}.\cite{Piccolo:2004} have both observed CO-induced
143 > reconstruction of a Au(111) surface. Peters {\it et al}. saw a relaxation to the
144   22 x $\sqrt{3}$ cell. They argued that only a few Au atoms
145 < become adatoms, limiting the stress of this reconstruction while
145 > become adatoms, limiting the stress of this reconstruction, while
146   allowing the rest to relax and approach the ideal (111)
147 < configuration. They did not see the usual herringbone pattern being greatly
148 < affected by this relaxation. Piccolo et al. on the other hand, did see a
147 > configuration. They did not see the usual herringbone pattern on Au(111) being greatly
148 > affected by this relaxation. Piccolo {\it et al}. on the other hand, did see a
149   disruption of the herringbone pattern as CO was adsorbed to the
150   surface. Both groups suggested that the preference CO shows for
151   low-coordinated Au atoms was the primary driving force for the reconstruction.
# Line 149 | Line 160 | adsorbates.  Since the interfaces involved are quite l
160   development of a sufficiently general yet computationally tractable
161   model of the chemical interactions between the surface atoms and
162   adsorbates.  Since the interfaces involved are quite large (10$^3$ -
163 < 10$^6$ atoms) and respond slowly to perturbations, {\it ab initio}
163 > 10$^4$ atoms) and respond slowly to perturbations, {\it ab initio}
164   molecular dynamics
165   (AIMD),\cite{KRESSE:1993ve,KRESSE:1993qf,KRESSE:1994ul} Car-Parrinello
166   methods,\cite{CAR:1985bh,Izvekov:2000fv,Guidelli:2000fy} and quantum
# Line 161 | Line 172 | Au-Au and Pt-Pt interactions.\cite{EAM} The CO was mod
172   Coulomb potential.  For this work, we have used classical molecular
173   dynamics with potential energy surfaces that are specifically tuned
174   for transition metals.  In particular, we used the EAM potential for
175 < Au-Au and Pt-Pt interactions.\cite{EAM} The CO was modeled using a rigid
175 > Au-Au and Pt-Pt interactions.\cite{Foiles86} The CO was modeled using a rigid
176   three-site model developed by Straub and Karplus for studying
177   photodissociation of CO from myoglobin.\cite{Straub} The Au-CO and
178   Pt-CO cross interactions were parameterized as part of this work.
# Line 174 | Line 185 | parameter sets. The glue model of Ercolessi et al. is
185   methods,\cite{Daw84,Foiles86,Johnson89,Daw89,Plimpton93,Voter95a,Lu97,Alemany98}
186   but other models like the Finnis-Sinclair\cite{Finnis84,Chen90} and
187   the quantum-corrected Sutton-Chen method\cite{QSC,Qi99} have simpler
188 < parameter sets. The glue model of Ercolessi et al. is among the
189 < fastest of these density functional approaches.\cite{Ercolessi88} In
190 < all of these models, atoms are conceptualized as a positively charged
188 > parameter sets. The glue model of Ercolessi {\it et al}.\cite{Ercolessi88} is among the
189 > fastest of these density functional approaches. In
190 > all of these models, atoms are treated as a positively charged
191   core with a radially-decaying valence electron distribution. To
192   calculate the energy for embedding the core at a particular location,
193   the electron density due to the valence electrons at all of the other
# Line 213 | Line 224 | from the original parameterization, where the interact
224   propagation,\cite{BECQUART:1993rg} and alloying
225   dynamics.\cite{Shibata:2002hh} One of EAM's strengths
226   is its sensitivity to small changes in structure. This arises
227 < from the original parameterization, where the interactions
228 < up to the third nearest neighbor were taken into account.\cite{Voter95a}
229 < Comparing that to the glue model of Ercolessi et al.\cite{Ercolessi88}
227 > because interactions
228 > up to the third nearest neighbor were taken into account in the parameterization.\cite{Voter95a}
229 > Comparing that to the glue model of Ercolessi {\it et al}.\cite{Ercolessi88}
230   which is only parameterized up to the nearest-neighbor
231   interactions, EAM is a suitable choice for systems where
232   the bulk properties are of secondary importance to low-index
233 < surface structures. Additionally, the similarity of EAMs functional
233 > surface structures. Additionally, the similarity of EAM's functional
234   treatment of the embedding energy to standard density functional
235   theory (DFT) makes fitting DFT-derived cross potentials with adsorbates somewhat easier.
236   \cite{Foiles86,PhysRevB.37.3924,Rifkin1992,mishin99:_inter,mishin01:cu,mishin02:b2nial,zope03:tial_ap,mishin05:phase_fe_ni}  
# Line 272 | Line 283 | et al.,\cite{Pons:1986} the Pt-C interaction was fit t
283   position on Pt(111). These parameters are reproduced in Table~\ref{tab:co_parameters}.
284   The modified parameters yield binding energies that are slightly higher
285   than the experimentally-reported values as shown in Table~\ref{tab:co_energies}. Following Korzeniewski
286 < et al.,\cite{Pons:1986} the Pt-C interaction was fit to a deep
287 < Lennard-Jones interaction to mimic strong, but short-ranged partial
286 > {\it et al}.,\cite{Pons:1986} the Pt-C interaction was fit to a deep
287 > Lennard-Jones interaction to mimic strong, but short-ranged, partial
288   binding between the Pt $d$ orbitals and the $\pi^*$ orbital on CO. The
289   Pt-O interaction was modeled with a Morse potential with a large
290   equilibrium distance, ($r_o$).  These choices ensure that the C is preferred
291 < over O as the surface-binding atom. In most cases, the Pt-O parameterization contributes a weak
291 > over O as the surface-binding atom. In most geometries, the Pt-O parameterization contributes a weak
292   repulsion which favors the atop site.  The resulting potential-energy
293   surface suitably recovers the calculated Pt-C separation length
294   (1.6~\AA)\cite{Beurden:2002ys} and affinity for the atop binding
# Line 314 | Line 325 | and polarization are neglected in this model, although
325   The parameters employed for the metal-CO cross-interactions in this work
326   are shown in Table~\ref{tab:co_parameters} and the binding energies on the
327   (111) surfaces are displayed in Table~\ref{tab:co_energies}.  Charge transfer
328 < and polarization are neglected in this model, although these effects are likely to
329 < affect binding energies and binding site preferences, and will be addressed in
319 < future work.
328 > and polarization are neglected in this model, although these effects could have
329 > an effect on  binding energies and binding site preferences.
330  
331   %Table  of Parameters
332   %Pt Parameter Set 9
# Line 360 | Line 370 | dimensions of 57.4~x~51.9285~x~100~\AA.
370   \subsection{Pt(557) and Au(557) metal interfaces}
371   Our Pt system is an orthorhombic periodic box of dimensions
372   54.482~x~50.046~x~120.88~\AA~while our Au system has
373 < dimensions of 57.4~x~51.9285~x~100~\AA.
373 > dimensions of 57.4~x~51.9285~x~100~\AA. The metal slabs
374 > are 9 and 8 atoms deep respectively, corresponding to a slab
375 > thickness of $\sim$21~\AA~ for Pt and $\sim$19~\AA~for Au.
376   The systems are arranged in a FCC crystal that have been cut
377   along the (557) plane so that they are periodic in the {\it x} and
378   {\it y} directions, and have been oriented to expose two aligned
# Line 369 | Line 381 | The different bulk melting temperatures (1345~$\pm$~10
381   1200~K were performed to confirm the relative
382   stability of the surfaces without a CO overlayer.  
383  
384 < The different bulk melting temperatures (1345~$\pm$~10~K for Au\cite{Au:melting}
384 > The different bulk melting temperatures predicted by EAM (1345~$\pm$~10~K for Au\cite{Au:melting}
385   and $\sim$~2045~K for Pt\cite{Pt:melting}) suggest that any possible reconstruction should happen at
386   different temperatures for the two metals.  The bare Au and Pt surfaces were
387   initially run in the canonical (NVT) ensemble at 800~K and 1000~K
# Line 396 | Line 408 | The surfaces of both systems, upon dosage of CO, began
408   %
409   \section{Results}
410   \subsection{Structural remodeling}
411 < The surfaces of both systems, upon dosage of CO, began
412 < to undergo extensive remodeling that was not observed in the bare
413 < systems. The bare metal surfaces
414 < experienced minor roughening of the step-edge because
415 < of the elevated temperatures, but the
416 < (557) lattice was well-maintained throughout the simulation
417 < time. The Au systems were limited to greater amounts of
418 < roughening, i.e. breakup of the step-edge, and some step
419 < wandering. The lower coverage Pt systems experienced
420 < similar restructuring but to a greater extent when
421 < 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}
411 > The bare metal surfaces experienced minor roughening of the
412 > step-edge because of the elevated temperatures, but the (557)
413 > face was stable throughout the simulations. The surface of both
414 > systems, upon dosage of CO, began to undergo extensive remodeling
415 > that was not observed in the bare systems. Reconstructions of
416 > the Au systems were limited to breakup of the step-edges and
417 > some step wandering. The lower coverage Pt systems experienced
418 > similar restructuring but to a greater extent. The 50\% coverage
419 > Pt system was unique among our simulations in that it formed
420 > well-defined and stable double layers through step coalescence,
421 > similar to results reported by Tao {\it et al}.\cite{Tao:2010}
422  
423  
424   \subsubsection{Step wandering}
425   The 0\% coverage surfaces for both metals showed minimal
426 < movement at their respective run temperatures. As the CO
427 < coverage increased however, the mobility of the surface,
426 > step-wandering at their respective temperatures. As the CO
427 > coverage increased however, the mobility of the surface atoms,
428   described through adatom diffusion and step-edge wandering,
429 < also increased.  Except for the 50\% Pt system, the step-edges
430 < did not coalesce in any of the other simulations, instead
431 < preferring to keep nearly the same distance between steps
432 < as in the original (557) lattice, $\sim$13\AA for Pt and $\sim$14\AA for Au.
433 < Previous work by Williams et al.\cite{Williams:1991, Williams:1994}
429 > also increased.  Except for the 50\% Pt system where step
430 > coalescence occurred, the step-edges in the other simulations
431 > preferred to keep nearly the same distance between steps as in
432 > the original (557) lattice, $\sim$13\AA~for Pt and $\sim$14\AA~for Au.
433 > Previous work by Williams {\it et al}.\cite{Williams:1991, Williams:1994}
434   highlights the repulsion that exists between step-edges even
435   when no direct interactions are present in the system. This
436 < repulsion arises because step-edge crossing is not allowed
437 < which constrains the entropy. This entropic repulsion does
438 < not completely define the interactions between steps, which
439 < is why some surfaces will undergo step coalescence, where
440 < additional attractive interactions can overcome the repulsion.\cite{Williams:1991}
441 < The presence and concentration of adsorbates, as shown in
442 < this work, can affect these step interactions, potentially leading
443 < to a new surface structure as the thermodynamic minimum.
436 > repulsion is caused by an entropic barrier that arises from
437 > the fact that steps cannot cross over one another. This entropic
438 > repulsion does not completely define the interactions between
439 > steps, however, so it is possible to observe step coalescence
440 > on some surfaces.\cite{Williams:1991} The presence and
441 > concentration of adsorbates, as shown in this work, can
442 > affect step-step interactions, potentially leading to a new
443 > surface structure as the thermodynamic equilibrium.
444  
445   \subsubsection{Double layers}
446 < Tao et al.\cite{Tao:2010} have shown experimentally that the Pt(557) surface
447 < undergoes two separate reconstructions upon CO adsorption.\cite{Tao:2010}
446 > Tao {\it et al}.\cite{Tao:2010} have shown experimentally that the Pt(557) surface
447 > undergoes two separate reconstructions upon CO adsorption.
448   The first involves a doubling of the step height and plateau length.
449 < Similar behavior has been seen on numerous surfaces
450 < at varying conditions: Ni(977), Si(111).\cite{Williams:1994,Williams:1991,Pearl}
449 > Similar behavior has been seen on a number of surfaces
450 > at varying conditions, including Ni(977) and Si(111).\cite{Williams:1994,Williams:1991,Pearl}
451   Of the two systems we examined, the Pt system showed a greater
452 < propensity for reconstruction when compared to the Au system
453 < because of the larger surface mobility and extent of step wandering.
454 < The amount of reconstruction is strongly correlated to the amount of CO
452 > propensity for reconstruction  
453 > because of the larger surface mobility and the greater extent of step wandering.
454 > The amount of reconstruction was strongly correlated to the amount of CO
455   adsorbed upon the surface.  This appears to be related to the
456   effect that adsorbate coverage has on edge breakup and on the
457 < surface diffusion of metal adatoms. While both systems displayed
458 < step-edge wandering, only the 50\% Pt surface underwent the
459 < doubling seen by Tao et al.\cite{Tao:2010} within the time scales studied here.
460 < Over longer periods, (150~ns) two more double layers formed
461 < on this interface. Although double layer formation did not occur
462 < in the other Pt systems, they show more step-wandering and
454 < general roughening compared to their Au counterparts. The
457 > surface diffusion of metal adatoms. Only the 50\% Pt surface underwent the
458 > doubling seen by Tao {\it et al}.\cite{Tao:2010} within the time scales studied here.
459 > Over a longer time scale (150~ns) two more double layers formed
460 > on this surface. Although double layer formation did not occur
461 > in the other Pt systems, they exhibited more step-wandering and
462 > roughening compared to their Au counterparts. The
463   50\% Pt system is highlighted in Figure \ref{fig:reconstruct} at
464   various times along the simulation showing the evolution of a double layer step-edge.
465  
466 < The second reconstruction on the Pt(557) surface observed by
467 < Tao involved the formation of triangular clusters that stretched
468 < across the plateau between two step-edges. Neither system, within
466 > The second reconstruction observed by
467 > Tao {\it et al}.\cite{Tao:2010} involved the formation of triangular clusters that stretched
468 > across the plateau between two step-edges. Neither metal, within
469   the 40~ns time scale or the extended simulation time of 150~ns for
470   the 50\% Pt system, experienced this reconstruction.
471  
# Line 474 | Line 482 | Previous atomistic simulations of stepped surfaces dea
482   \end{figure}
483  
484   \subsection{Dynamics}
485 < Previous atomistic simulations of stepped surfaces dealt largely
486 < with the energetics and structures at different conditions.
487 < \cite{Williams:1991,Williams:1994} Consequently, the most common
488 < technique utilized to date has been Monte Carlo sampling. Monte Carlo approaches give an efficient
489 < sampling of the equilibrium thermodynamic landscape at the expense
490 < of ignoring the dynamics of the system. Previous experimental work by Pearl and
491 < Sibener\cite{Pearl}, using STM, has been able to capture the coalescing
492 < 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.
485 > Previous experimental work by Pearl and Sibener\cite{Pearl},
486 > using STM, has been able to capture the coalescence of steps
487 > on Ni(977). The time scale of the image acquisition, $\sim$70~s/image,
488 > provides an upper bound for the time required for the doubling
489 > to occur. By utilizing Molecular Dynamics we are able to probe
490 > the dynamics of these reconstructions at elevated temperatures
491 > and in this section we provide data on the timescales for transport
492 > properties, e.g. diffusion and layer formation time.
493  
494  
495   \subsubsection{Transport of surface metal atoms}
496   %forcedSystems/stepSeparation
497 < The movement or wandering of a step-edge is a cooperative effect
497 > The wandering of a step-edge is a cooperative effect
498   arising from the individual movements of the atoms making up the steps. An ideal metal surface
499   displaying a low index facet, (111) or (100), is unlikely to experience
500   much surface diffusion because of the large energetic barrier that must
501   be overcome to lift an atom out of the surface. The presence of step-edges and other surface features
502   on higher-index facets provides a lower energy source for mobile metal atoms.
503 < Breaking away from the step-edge on a clean surface still imposes an
503 > Single-atom break-away from a step-edge on a clean surface still imposes an
504   energetic penalty around $\sim$~45 kcal/mol, but this is easier than lifting
505   the same metal atom vertically out of the surface,  \textgreater~60 kcal/mol.
506   The penalty lowers significantly when CO is present in sufficient quantities
507 < 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
507 > on the surface. For certain distributions of CO, see Discussion, the penalty can fall to as low as
508   $\sim$~20 kcal/mol. Once an adatom exists on the surface, the barrier for
509 < diffusion is negligible ( \textless~4 kcal/mol for a Pt adatom). These adatoms are then
509 > diffusion is negligible (\textless~4 kcal/mol for a Pt adatom). These adatoms are then
510   able to explore the terrace before rejoining either their original step-edge or
511 < becoming a part of a different edge. It is a difficult process for an atom
511 > becoming a part of a different edge. It is an energetically unfavorable process with a high barrier for an atom
512   to traverse to a separate terrace although the presence of CO can lower the
513   energy barrier required to lift or lower an adatom. By tracking the mobility of individual
514   metal atoms on the Pt and Au surfaces we were able to determine the relative
515   diffusion constants, as well as how varying coverages of CO affect the diffusion. Close
516   observation of the mobile metal atoms showed that they were typically in
517 < equilibrium with the step-edges, dynamically breaking apart and rejoining the edges.
517 > equilibrium with the step-edges.
518   At times, their motion was concerted and two or more adatoms would be
519   observed moving together across the surfaces.
520  
521   A particle was considered ``mobile'' once it had traveled more than 2~\AA~
522 < between saved configurations of the system (typically 10-100 ps). An atom that was
523 < truly mobile would typically travel much greater distances than this, but the 2~\AA~cutoff
522 > between saved configurations of the system (typically 10-100 ps). A mobile atom
523 > would typically travel much greater distances than this, but the 2~\AA~cutoff
524   was used to prevent swamping the diffusion data with the in-place vibrational
525   movement of buried atoms. Diffusion on a surface is strongly affected by
526   local structures and in this work, the presence of single and double layer
# Line 539 | Line 544 | The lack of a definite trend in the Au diffusion data
544   \label{fig:diff}
545   \end{figure}
546  
547 < The lack of a definite trend in the Au diffusion data in Figure \ref{fig:diff} is likely due
548 < to the weaker bonding between Au and CO. This leads to a lower observed
549 < coverage ({\it x}-axis) when compared to dosage amount, which
550 < then further limits the effect the CO can have on surface diffusion. The correlation
551 < between coverage and Pt diffusion rates conversely shows a
552 < definite trend marred by the highest coverage surface. Two
553 < explanations arise for this drop. First, upon a visual inspection of
554 < the system, after a double layer has been formed, it maintains its
555 < stability strongly and many atoms that had been tracked for mobility
556 < data have now been buried. By performing the same diffusion
557 < calculation but on a shorter run time (20~ns), only including data
558 < before the formation of the first double layer, we obtain the larger
559 < values for both $\mathbf{D}_{\parallel}$ and $\mathbf{D}_{\perp}$
560 < at the 50\% coverage as seen in Figure \ref{fig:diff}.
556 < This places the parallel diffusion constant more closely in line with the
557 < expected trend, while the perpendicular diffusion constant does not
558 < drop as far. A secondary explanation arising from our analysis of the
559 < mechanism of double layer formation focuses on the effect that CO on the
560 < surface has with respect to overcoming surface diffusion of Pt. If the
561 < coverage is too sparse, the Pt engages in minimal interactions and
562 < thus minimal diffusion. As coverage increases, there are more favorable
563 < arrangements of CO on the surface allowing for the formation of a path,
564 < a minimum energy trajectory, for the adatom to explore the surface.
565 < As the CO is constantly moving on the surface, this path is constantly
566 < changing. If the coverage becomes too great, the paths could
567 < potentially be clogged leading to a decrease in diffusion despite
568 < their being more adatoms and step-wandering.
547 > The weaker Au-CO interaction is evident in the weak CO-coverage
548 > dependance of Au diffusion. This weak interaction leads to lower
549 > observed coverages when compared to dosage amounts. This further
550 > limits the effect the CO can have on surface diffusion. The correlation
551 > between coverage and Pt diffusion rates shows a near linear relationship
552 > at the earliest times in the simulations. Following double layer formation,
553 > however, there is a precipitous drop in adatom diffusion. As the double
554 > layer forms, many atoms that had been tracked for mobility data have
555 > now been buried resulting in a smaller reported diffusion constant. A
556 > secondary effect of higher coverages is CO-CO cross interactions that
557 > lower the effective mobility of the Pt adatoms that are bound to each CO.
558 > This effect would become evident only at higher coverages. A detailed
559 > account of Pt adatom energetics follows in the Discussion.
560 >
561  
570
571
562   \subsubsection{Dynamics of double layer formation}
563 < The increased diffusion on Pt at the higher CO coverages
564 < plays a primary role in double layer formation. However,
565 < this is not a complete explanation -- the 33\%~Pt system
566 < has higher diffusion constants but did not show any signs
567 < of edge doubling in the observed run time. On the
568 < 50\%~Pt system, one layer formed within the first 40~ns
569 < of simulation time, while two more were formed as the
570 < system was allowed to run for an additional
571 < 110~ns (150~ns total). This suggests that this reconstruction is
572 < a rapid process and that the previously mentioned upper bound
573 < will be lowered as experimental techniques continue to improve.\cite{Williams:1991,Pearl}
574 < In this system, as seen in Figure \ref{fig:reconstruct}, the first
575 < appearance of a double layer, appears at 19~ns
576 < into the simulation. Within 12~ns of this nucleation event, nearly half of the step has
577 < formed the double layer and by 86~ns, the complete layer
578 < has been flattened out. The double layer could be considered
579 < ``complete" by 37~ns but remains a bit rough. From the
580 < appearance of the first nucleation event to the first observed double layer, the process took $\sim$20~ns. Another
581 < $\sim$40~ns was necessary for the layer to completely straighten.
582 < The other two layers in this simulation formed over periods of
583 < 22~ns and 42~ns respectively. A possible explanation
584 < for this rapid reconstruction is the elevated temperatures
595 < under which our systems were simulated. It is probable that the process would
596 < take longer at lower temperatures. Additionally, our measured times for completion
597 < of the doubling after the appearance of a nucleation site are likely affected by our
598 < constrained axes. A longer step-edge will likely take longer to ``zipper''. However,
599 < the first appearance of a nucleation site will likely occur more quickly due to its stochastic nature.
563 > The increased diffusion on Pt at the higher CO coverages is the primary
564 > contributor to double layer formation. However, this is not a complete
565 > explanation -- the 33\%~Pt system has higher diffusion constants, but
566 > did not show any signs of edge doubling in 40~ns. On the 50\%~Pt
567 > system, one double layer formed within the first 40~ns of simulation time,
568 > while two more were formed as the system was allowed to run for an
569 > additional 110~ns (150~ns total). This suggests that this reconstruction
570 > is a rapid process and that the previously mentioned upper bound is a
571 > very large overestimate.\cite{Williams:1991,Pearl} In this system the first
572 > appearance of a double layer appears at 19~ns into the simulation.
573 > Within 12~ns of this nucleation event, nearly half of the step has formed
574 > the double layer and by 86~ns the complete layer has flattened out.
575 > From the appearance of the first nucleation event to the first observed
576 > double layer, the process took $\sim$20~ns. Another $\sim$40~ns was
577 > necessary for the layer to completely straighten. The other two layers in
578 > this simulation formed over periods of 22~ns and 42~ns respectively.
579 > A possible explanation for this rapid reconstruction is the elevated
580 > temperatures under which our systems were simulated. The process
581 > would almost certainly take longer at lower temperatures. Additionally,
582 > our measured times for completion of the doubling after the appearance
583 > of a nucleation site are likely affected by our periodic boxes. A longer
584 > step-edge will likely take longer to ``zipper''.
585  
586  
587 + %Discussion
588 + \section{Discussion}
589 + We have shown that a classical potential model is able to model the
590 + initial reconstruction of the Pt(557) surface upon CO adsorption as
591 + shown by Tao {\it et al}.\cite{Tao:2010}. More importantly, we were
592 + able to observe features of the dynamic processes necessary for
593 + this reconstruction. Here we discuss the features of the model that
594 + give rise to the observed dynamical properties of the (557) reconstruction.
595  
596 + \subsection{Diffusion}
597 + The perpendicular diffusion constant
598 + appears to be the most important indicator of double layer
599 + formation. As highlighted in Figure \ref{fig:reconstruct}, the
600 + formation of the double layer did not begin until a nucleation
601 + site appeared. And as mentioned by Williams {\it et al}.\cite{Williams:1991, Williams:1994},
602 + the inability for edges to cross leads to an effective edge-edge repulsion that
603 + must be overcome to allow step coalescence.
604 + A greater $\textbf{D}_\perp$ implies more step-wandering
605 + and a larger chance for the stochastic meeting of two edges
606 + to create a nucleation point. Parallel diffusion along the step-edge can help ``zipper'' up a nascent double
607 + layer. This helps explain why the time scale for formation after
608 + the appearance of a nucleation site was rapid, while the initial
609 + appearance of the nucleation site was unpredictable.
610  
611 + \subsection{Mechanism for restructuring}
612 + Since the Au surface showed no large scale restructuring in any of
613 + our simulations, our discussion will focus on the 50\% Pt-CO system
614 + which did exhibit doubling. A
615 + number of possible mechanisms exist to explain the role of adsorbed
616 + CO in restructuring the Pt surface. Quadrupolar repulsion between
617 + adjacent CO molecules adsorbed on the surface is one possibility.  
618 + However, the quadrupole-quadrupole interaction is short-ranged and
619 + is attractive for some orientations.  If the CO molecules are ``locked'' in
620 + a specific orientation relative to each other, through atop adsorption for
621 + example, this explanation would gain credence. The calculated energetic repulsion
622 + between two CO molecules located a distance of 2.77~\AA~apart
623 + (nearest-neighbor distance of Pt) and both in a vertical orientation,
624 + is 8.62 kcal/mol. Moving the CO to the second nearest-neighbor distance
625 + of 4.8~\AA~drops the repulsion to nearly 0. Allowing the CO to rotate away
626 + from a purely vertical orientation also lowers the repulsion. When the
627 + carbons are locked at a distance of 2.77~\AA, a minimum of 6.2 kcal/mol is
628 + reached when the angle between the 2 CO is $\sim$24\textsuperscript{o}.
629 + The calculated barrier for surface diffusion of a Pt adatom is only 4 kcal/mol, so
630 + repulsion between adjacent CO molecules bound to Pt could increase the surface
631 + diffusion. However, the residence time of CO on Pt suggests that these
632 + molecules are extremely mobile, with diffusion constants 40 to 2500 times
633 + larger than surface Pt atoms. This mobility suggests that the CO molecules jump
634 + between different Pt atoms throughout the simulation, but will stay bound for
635 + significant periods of time.
636  
637 + A different interpretation of the above mechanism, taking into account the large
638 + mobility of the CO, looks at how instantaneous and short-lived configurations of
639 + CO on the surface can destabilize Pt-Pt interactions leading to increased step-edge
640 + breakup and diffusion. On the bare Pt(557) surface the barrier to completely detach
641 + an edge atom is $\sim$43~kcal/mol, as is shown in configuration (a) in Figures
642 + \ref{fig:SketchGraphic} \& \ref{fig:SketchEnergies}. For certain configurations, cases
643 + (e), (g), and (h), the barrier can be lowered to $\sim$23~kcal/mole. In these instances,
644 + it becomes quite energetically favorable to roughen the edge by introducing a small
645 + separation of 0.5 to 1.0~\AA. This roughening becomes immediately obvious in
646 + simulations with significant CO populations. The roughening is present to a lesser extent
647 + on lower coverage surfaces and even on the bare surfaces, although in these cases it is likely
648 + due to stochastic vibrational processes that squeeze out step-edge atoms. The mechanism
649 + of step-edge breakup suggested by these energy curves is one of the most difficult
650 + processes, a complete break-away from the step-edge in one unbroken movement.
651 + Easier multistep mechanisms likely exist where an adatom moves laterally on the surface
652 + after being ejected so it ends up alongside the ledge. This provides the atom with 5 nearest
653 + neighbors, which while lower than the 7 if it had stayed a part of the step-edge, is higher
654 + than the 3 it could maintain located on the terrace. In this proposed mechanism, the CO
655 + quadrupolar repulsion is still playing a primary role, but for its importance in roughening
656 + the step-edge, rather than maintaining long-term bonds with a single Pt atom which is not
657 + born out by their mobility data. The requirement for a large density of CO on the surface
658 + for some of the more favorable suggested configurations in Figure \ref{fig:SketchGraphic}
659 + correspond well with the increased mobility seen on higher coverage surfaces.
660  
661   %Sketch graphic of different configurations
662   \begin{figure}[H]
# Line 627 | Line 682 | configurations of CO will be more likely. }
682   \label{fig:SketchEnergies}
683   \end{figure}
684  
685 < %Discussion
686 < \section{Discussion}
687 < We have shown that the classical potential models are able to model the initial reconstruction of the
688 < Pt(557) surface upon CO adsorption as shown by Tao et al. \cite{Tao:2010}. More importantly, we
689 < were able to observe features of the dynamic processes necessary for this reconstruction.
685 > While configurations of CO on the surface are able to increase diffusion,
686 > this does not immediately provide an explanation for the formation of double
687 > layers. If adatoms were constrained to their terrace then doubling would be
688 > much less likely to occur. Nucleation sites could still potentially form, but there
689 > would not be enough atoms to finish the doubling. For a non-simulated metal surface, where the
690 > step lengths can be assumed to be infinite relative to atomic sizes, local doubling would be possible, but in
691 > our simulations with our periodic treatment of the system, the system is not large enough to experience this effect.
692 > Thus, there must be a mechanism that explains how adatoms are able to move
693 > amongst terraces. Figure \ref{fig:lambda} shows points along a reaction coordinate
694 > where an adatom along the step-edge with an adsorbed CO ``burrows'' into the
695 > edge displacing an atom onto the higher terrace. This mechanism was chosen
696 > because of similar events that were observed during the simulations. The barrier
697 > heights we obtained are only approximations because we constrained the movement
698 > of the highlighted atoms along a specific concerted path. The calculated $\Delta E$'s
699 > are provide a strong energetic support for this modeled lifting mechanism. When CO is not present and
700 > this reaction coordinate is followed, the $\Delta E > 3$~kcal/mol. The example shown
701 > in the figure, where CO is present in the atop position, has a $\Delta E < -15$~kcal/mol.
702 > While the barrier height is comparable for both cases, there is nearly a 20~kcal/mol
703 > difference in energies and makes the process energetically favorable.
704  
636 \subsection{Diffusion}
637 As shown in Figure \ref{fig:diff}, for the Pt systems, there
638 is a strong trend toward higher diffusion constants as
639 surface coverage of CO increases. The drop for the 50\%
640 case being explained as double layer formation already
641 beginning to occur in the analyzed 40~ns, which lowered
642 the calculated diffusion rates. Between the parallel and
643 perpendicular rates, the perpendicular diffusion constant
644 appears to be the most important indicator of double layer
645 formation. As highlighted in Figure \ref{fig:reconstruct}, the
646 formation of the double layer did not begin until a nucleation
647 site appeared. And as mentioned by Williams et al.\cite{Williams:1991, Williams:1994},
648 the inability for edges to cross leads to an effective repulsion.
649 This repulsion must be overcome to allow step coalescence.
650 A greater $\textbf{D}_\perp$ implies more step-wandering
651 and a larger chance for the stochastic meeting of two edges
652 to form the nucleation point. Upon that appearance, parallel
653 diffusion along the step-edge can help ``zipper'' up the double
654 layer. This helps explain why the time scale for formation after
655 the appearance of a nucleation site was rapid, while the initial
656 appearance of said site was unpredictable.
657
658 \subsection{Mechanism for restructuring}
659 Since the Au surface showed no large scale restructuring throughout
660 our simulation time our discussion will focus on the 50\% Pt-CO system
661 which did undergo the doubling featured in Figure \ref{fig:reconstruct}.
662 Similarities of our results to those reported previously by Tao et al.\cite{Tao:2010}
663 are quite strong. The simulated Pt system exposed to a large dosage
664 of CO readily restructures by doubling the terrace widths and step heights.
665 The restructuring occurs in a piecemeal fashion, one to two Pt atoms at a
666 time, but is rapid on experimental timescales. The adatoms either break
667 away from the step-edge and stay on the lower terrace or they lift up onto
668 a higher terrace. Once ``free'', they diffuse on the terrace until reaching
669 another step-edge or rejoining their original edge. This combination of
670 growth and decay of the step-edges is in a state of dynamic equilibrium.
671 However, once two previously separated edges meet as shown in Figure 1.B,
672 this nucleates the rest of the edge to meet up, forming a double layer.
673 From simulations which exhibit a double layer, the time delay from the
674 initial appearance of a nucleation point to a fully formed double layer is $\sim$35~ns.
675
676 A number of possible mechanisms exist to explain the role of adsorbed
677 CO in restructuring the Pt surface. Quadrupolar repulsion between adjacent
678 CO molecules adsorbed on the surface is one possibility.  However,
679 the quadrupole-quadrupole interaction is short-ranged and is attractive for
680 some orientations.  If the CO molecules are ``locked'' in a specific orientation
681 relative to each other, through atop adsorption for example, this explanation
682 gains some credence. The energetic repulsion between two CO located a
683 distance of 2.77~\AA~apart (nearest-neighbor distance of Pt) and both in
684 a vertical orientation, is 8.62 kcal/mol. Moving the CO apart to the second
685 nearest-neighbor distance of 4.8~\AA~or 5.54~\AA~drops the repulsion to
686 nearly 0 kcal/mol. Allowing the CO to rotate away from a purely vertical orientation
687 also lowers the repulsion. A minimum of 6.2 kcal/mol is reached at when the
688 angle between the 2 CO is $\sim$24\textsuperscript{o}, when the carbons are
689 locked at a distance of 2.77 \AA apart. As mentioned above, the energy barrier
690 for surface diffusion of a Pt adatom is only 4 kcal/mol. So this repulsion between
691 neighboring CO molecules can increase the surface diffusion. However, the
692 residence time of CO on Pt was examined and while the majority of the CO is
693 on or near the surface throughout the run, the molecules are extremely mobile,
694 with diffusion constants 40 to 2500 times larger, depending on coverage. This
695 mobility suggests that the CO are more likely to shift their positions without
696 necessarily the Pt along with them.
697
698 Another possible and more likely mechanism for the restructuring is in the
699 destabilization of strong Pt-Pt interactions by CO adsorbed on surface
700 Pt atoms. To test this hypothesis, numerous configurations of
701 CO in varying quantities were arranged on the higher and lower plateaus
702 around a step on a otherwise clean Pt(557) surface. A few sample
703 configurations are displayed in Figure \ref{fig:SketchGraphic}, with
704 energies at various positions along the path displayed in Table
705 NO TABLE. Certain configurations of CO, cases B and D for
706 example, can have quite strong energetic reasons for breaking
707 away from the step-edge. Although the packing of these configurations
708 is unlikely until CO coverage has reached a high enough value.
709 These examples are showing the most difficult cases, immediate
710 adatom formation through breakage away from the step-edge, which
711 is why their energies at large distances are relatively high. There are
712 mechanistic paths where an edge atom could get shifted to onto the
713 step-edge to form a small peak before fully breaking away. And again,
714 once the adatom is formed, the barrier for diffusion on the surface is
715 negligible. These sample configurations help explain CO's effect on
716 general surface mobility and step wandering, but they are lacking in
717 providing a mechanism for the formation of double layers. One possible
718 mechanism is elucidated in Figure \ref{fig:lambda}, where a burrowing
719 and lifting process of an adatom and step-edge atom respectively is
720 examined. The system, without CO present, is nearly energetically
721 neutral, whereas with CO present there is a $\sim$ 15 kcal/mol drop
722 in the energy of the system.
723
705   %lambda progression of Pt -> shoving its way into the step
706   \begin{figure}[H]
707   \includegraphics[width=\linewidth]{lambdaProgression_atopCO_withLambda.png}
708 < \caption{A model system of the Pt(557) surface was used as the framework
709 < for exploring energy barriers along a reaction coordinate. Various numbers,
710 < placements, and rotations of CO were examined as they affect Pt movement.
711 < The coordinate displayed in this Figure was a representative run.  relative to the energy of the system at 0\%, there
731 < is a slight decrease upon insertion of the Pt atom into the step-edge along
732 < with the resultant lifting of the other Pt atom when CO is present at certain positions.}
708 > \caption{ Various points along a reaction coordinate are displayed in the figure.
709 > The mechanism of edge traversal is examined in the presence of CO. The approximate
710 > barrier for the displayed process is 20~kcal/mol. However, the $\Delta E$ of this process
711 > is -15~kcal/mol making it an energetically favorable process.}
712   \label{fig:lambda}
713   \end{figure}
714  
715 + The mechanism for doubling on this surface appears to require the cooperation of at least
716 + these two described processes. For complete doubling of a layer to occur there must
717 + be the equivalent removal of a separate terrace. For those atoms to ``disappear'' from
718 + that terrace they must either rise up on the ledge above them or drop to the ledge below
719 + them. The presence of CO helps with the energetics of both of these situations. There must be sufficient
720 + breakage of the step-edge to increase the concentration of adatoms on the surface and
721 + these adatoms must then undergo the burrowing highlighted above or some comparable
722 + mechanism to traverse the step-edge. Over time, these mechanisms working in concert
723 + lead to the formation of a double layer.
724  
725 + \subsection{CO Removal and double layer stability}
726 + Once a double layer had formed on the 50\%~Pt system it
727 + remained for the rest of the simulation time with minimal
728 + movement. There were configurations that showed small
729 + wells or peaks forming, but typically within a few nanoseconds
730 + the feature would smooth away. Within our simulation time,
731 + the formation of the double layer was irreversible and a double
732 + layer was never observed to split back into two single layer
733 + step-edges while CO was present. To further gauge the effect
734 + CO had on this system, additional simulations were run starting
735 + from a late configuration of the 50\%~Pt system that had formed
736 + double layers. These simulations then had their CO removed.
737 + The double layer breaks rapidly in these simulations, already
738 + showing a well-defined splitting after 100~ps. Configurations of
739 + this system are shown in Figure \ref{fig:breaking}. The coloring
740 + of the top and bottom layers helps to exhibit how much mixing
741 + the edges experience as they split. These systems were only
742 + examined briefly, 10~ns, and within that time despite the initial
743 + rapid splitting, the edges only moved another few \AA~apart.
744 + It is possible with longer simulation times that the
745 + (557) lattice could be recovered as seen by Tao {\it et al}.\cite{Tao:2010}
746  
747  
748  
# Line 741 | Line 750 | in the energy of the system.
750   \begin{figure}[H]
751   \includegraphics[width=\linewidth]{doubleLayerBreaking_greenBlue_whiteLetters.png}
752   \caption{(A)  0~ps, (B) 100~ps, (C) 1~ns, after the removal of CO. The presence of the CO
753 < helped maintain the stability of the double layer and upon removal the two layers break
754 < and begin separating. The separation is not a simple pulling apart however, rather
755 < there is a mixing of the lower and upper atoms at the edge.}
753 > helped maintain the stability of the double layer and its microfaceting of the double layer
754 > into a (111) configuration. This microfacet immediately reverts to the original (100) step
755 > edge which is a hallmark of the (557) surface. The separation is not a simple sliding apart, rather
756 > there is a mixing of the lower and upper atoms at the edge.}
757   \label{fig:breaking}
758   \end{figure}
759  
# Line 771 | Line 781 | In this work we have shown the reconstruction of the P
781  
782  
783   \section{Conclusion}
784 < In this work we have shown the reconstruction of the Pt(557) crystalline surface upon adsorption of CO in less than a $\mu s$. Only the highest coverage Pt system showed this initial reconstruction similar to that seen previously. The strong interaction between Pt and CO and the limited interaction between Au and CO helps explain the differences between the two systems.
784 > The strength of the Pt-CO binding interaction as well as the large
785 > quadrupolar repulsion between CO molecules are sufficient to
786 > explain the observed increase in surface mobility and the resultant
787 > reconstructions at the highest simulated coverage. The weaker
788 > Au-CO interaction results in lower diffusion constants, less step-wandering,
789 > and a lack of the double layer reconstruction. An in-depth examination
790 > of the energetics shows the important role CO plays in increasing
791 > step-breakup and in facilitating edge traversal which are both
792 > necessary for double layer formation.
793  
794 +
795 +
796   %Things I am not ready to remove yet
797  
798   %Table of Diffusion Constants

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