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# Line 20 | Line 20
20   \usepackage{graphicx}
21   \usepackage{multirow}
22   \usepackage{multicol}
23 + \usepackage{epstopdf}
24  
25   \usepackage[version=3]{mhchem}  % this is a great package for formatting chemical reactions
26   % \usepackage[square, comma, sort&compress]{natbib}
27   \usepackage{url}
28   \pagestyle{plain} \pagenumbering{arabic} \oddsidemargin 0.0cm
29   \evensidemargin 0.0cm \topmargin -21pt \headsep 10pt \textheight
30 < 9.0in \textwidth 6.5in \brokenpenalty=10000
30 > 9.0in \textwidth 6.5in \brokenpenalty=1110000
31  
32   % double space list of tables and figures
33   %\AtBeginDelayedFloats{\renewcomand{\baselinestretch}{1.66}}
# Line 86 | Line 87 | systems and the lack  of reconstruction of the Au syst
87   is sufficient to explain the reconstructions observed on the Pt
88   systems and the lack  of reconstruction of the Au systems.
89  
90 +
91 + The mechanism and dynamics of surface reconstructions of Pt(557)
92 + and Au(557) exposed to various coverages of carbon monoxide (CO)
93 + were investigated using molecular dynamics simulations. Metal-CO
94 + interactions were parameterized from experimental data and plane-wave
95 + Density Functional Theory (DFT) calculations.  The large difference in
96 + binding strengths of the Pt-CO and Au-CO interactions was found to play
97 + a significant role in step-edge stability and adatom diffusion constants.
98 + The energetics of CO adsorbed to the surface is sufficient to explain the
99 + step-doubling reconstruction observed on Pt(557) and the lack of such
100 + a reconstruction on the Au(557) surface.
101   \end{abstract}
102  
103   \newpage
# Line 117 | Line 129 | This work is an investigation into the mechanism and t
129   reversible restructuring under exposure to moderate pressures of
130   carbon monoxide.\cite{Tao:2010}
131  
132 < This work is an investigation into the mechanism and timescale for
132 > This work is an investigation into the mechanism and timescale for the Pt(557) \& Au(557)
133   surface restructuring using molecular simulations.  Since the dynamics
134   of the process are of particular interest, we employ classical force
135   fields that represent a compromise between chemical accuracy and the
# Line 126 | Line 138 | The Au(557) surface, because of a weaker interaction w
138   catalyst with adsorbates, in this work, two metal systems exposed
139   to carbon monoxide were examined. The Pt(557) surface has already been shown
140   to undergo a large scale reconstruction under certain conditions.\cite{Tao:2010}
141 < The Au(557) surface, because of a weaker interaction with CO, is seen as less
142 < likely to undergo this kind of reconstruction. However, Peters et al.\cite{Peters:2000}
143 < and Piccolo et al.\cite{Piccolo:2004} have both observed CO-induced
144 < reconstruction of a Au(111) surface. Peters et al. saw a relaxation to the
141 > The Au(557) surface, because of a weaker interaction with CO, is less
142 > likely to undergo this kind of reconstruction. However, Peters {\it et al}.\cite{Peters:2000}
143 > and Piccolo {\it et al}.\cite{Piccolo:2004} have both observed CO-induced
144 > reconstruction of a Au(111) surface. Peters {\it et al}. saw a relaxation to the
145   22 x $\sqrt{3}$ cell. They argued that only a few Au atoms
146 < become adatoms, limiting the stress of this reconstruction while
146 > become adatoms, limiting the stress of this reconstruction, while
147   allowing the rest to relax and approach the ideal (111)
148 < configuration. They did not see the usual herringbone pattern being greatly
149 < affected by this relaxation. Piccolo et al. on the other hand, did see a
148 > configuration. They did not see the usual herringbone pattern on Au(111) being greatly
149 > affected by this relaxation. Piccolo {\it et al}. on the other hand, did see a
150   disruption of the herringbone pattern as CO was adsorbed to the
151   surface. Both groups suggested that the preference CO shows for
152   low-coordinated Au atoms was the primary driving force for the reconstruction.
# Line 149 | Line 161 | adsorbates.  Since the interfaces involved are quite l
161   development of a sufficiently general yet computationally tractable
162   model of the chemical interactions between the surface atoms and
163   adsorbates.  Since the interfaces involved are quite large (10$^3$ -
164 < 10$^6$ atoms) and respond slowly to perturbations, {\it ab initio}
164 > 10$^4$ atoms) and respond slowly to perturbations, {\it ab initio}
165   molecular dynamics
166   (AIMD),\cite{KRESSE:1993ve,KRESSE:1993qf,KRESSE:1994ul} Car-Parrinello
167   methods,\cite{CAR:1985bh,Izvekov:2000fv,Guidelli:2000fy} and quantum
# Line 161 | Line 173 | Au-Au and Pt-Pt interactions.\cite{EAM} The CO was mod
173   Coulomb potential.  For this work, we have used classical molecular
174   dynamics with potential energy surfaces that are specifically tuned
175   for transition metals.  In particular, we used the EAM potential for
176 < Au-Au and Pt-Pt interactions.\cite{EAM} The CO was modeled using a rigid
176 > Au-Au and Pt-Pt interactions.\cite{Foiles86} The CO was modeled using a rigid
177   three-site model developed by Straub and Karplus for studying
178   photodissociation of CO from myoglobin.\cite{Straub} The Au-CO and
179   Pt-CO cross interactions were parameterized as part of this work.
# Line 174 | Line 186 | parameter sets. The glue model of Ercolessi et al. is
186   methods,\cite{Daw84,Foiles86,Johnson89,Daw89,Plimpton93,Voter95a,Lu97,Alemany98}
187   but other models like the Finnis-Sinclair\cite{Finnis84,Chen90} and
188   the quantum-corrected Sutton-Chen method\cite{QSC,Qi99} have simpler
189 < parameter sets. The glue model of Ercolessi et al. is among the
190 < fastest of these density functional approaches.\cite{Ercolessi88} In
191 < all of these models, atoms are conceptualized as a positively charged
189 > parameter sets. The glue model of Ercolessi {\it et al}.\cite{Ercolessi88} is among the
190 > fastest of these density functional approaches. In
191 > all of these models, atoms are treated as a positively charged
192   core with a radially-decaying valence electron distribution. To
193   calculate the energy for embedding the core at a particular location,
194   the electron density due to the valence electrons at all of the other
# Line 213 | Line 225 | from the original parameterization, where the interact
225   propagation,\cite{BECQUART:1993rg} and alloying
226   dynamics.\cite{Shibata:2002hh} One of EAM's strengths
227   is its sensitivity to small changes in structure. This arises
228 < from the original parameterization, where the interactions
229 < up to the third nearest neighbor were taken into account.\cite{Voter95a}
230 < Comparing that to the glue model of Ercolessi et al.\cite{Ercolessi88}
228 > because interactions
229 > up to the third nearest neighbor were taken into account in the parameterization.\cite{Voter95a}
230 > Comparing that to the glue model of Ercolessi {\it et al}.\cite{Ercolessi88}
231   which is only parameterized up to the nearest-neighbor
232   interactions, EAM is a suitable choice for systems where
233   the bulk properties are of secondary importance to low-index
234 < surface structures. Additionally, the similarity of EAMs functional
234 > surface structures. Additionally, the similarity of EAM's functional
235   treatment of the embedding energy to standard density functional
236   theory (DFT) makes fitting DFT-derived cross potentials with adsorbates somewhat easier.
237   \cite{Foiles86,PhysRevB.37.3924,Rifkin1992,mishin99:_inter,mishin01:cu,mishin02:b2nial,zope03:tial_ap,mishin05:phase_fe_ni}  
# Line 272 | Line 284 | et al.,\cite{Pons:1986} the Pt-C interaction was fit t
284   position on Pt(111). These parameters are reproduced in Table~\ref{tab:co_parameters}.
285   The modified parameters yield binding energies that are slightly higher
286   than the experimentally-reported values as shown in Table~\ref{tab:co_energies}. Following Korzeniewski
287 < et al.,\cite{Pons:1986} the Pt-C interaction was fit to a deep
288 < Lennard-Jones interaction to mimic strong, but short-ranged partial
287 > {\it et al}.,\cite{Pons:1986} the Pt-C interaction was fit to a deep
288 > Lennard-Jones interaction to mimic strong, but short-ranged, partial
289   binding between the Pt $d$ orbitals and the $\pi^*$ orbital on CO. The
290   Pt-O interaction was modeled with a Morse potential with a large
291   equilibrium distance, ($r_o$).  These choices ensure that the C is preferred
292 < over O as the surface-binding atom. In most cases, the Pt-O parameterization contributes a weak
292 > over O as the surface-binding atom. In most geometries, the Pt-O parameterization contributes a weak
293   repulsion which favors the atop site.  The resulting potential-energy
294   surface suitably recovers the calculated Pt-C separation length
295   (1.6~\AA)\cite{Beurden:2002ys} and affinity for the atop binding
# Line 314 | Line 326 | and polarization are neglected in this model, although
326   The parameters employed for the metal-CO cross-interactions in this work
327   are shown in Table~\ref{tab:co_parameters} and the binding energies on the
328   (111) surfaces are displayed in Table~\ref{tab:co_energies}.  Charge transfer
329 < and polarization are neglected in this model, although these effects are likely to
330 < affect binding energies and binding site preferences, and will be addressed in
319 < future work.
329 > and polarization are neglected in this model, although these effects could have
330 > an effect on  binding energies and binding site preferences.
331  
332   %Table  of Parameters
333   %Pt Parameter Set 9
# Line 360 | Line 371 | dimensions of 57.4~x~51.9285~x~100~\AA.
371   \subsection{Pt(557) and Au(557) metal interfaces}
372   Our Pt system is an orthorhombic periodic box of dimensions
373   54.482~x~50.046~x~120.88~\AA~while our Au system has
374 < dimensions of 57.4~x~51.9285~x~100~\AA.
374 > dimensions of 57.4~x~51.9285~x~100~\AA. The metal slabs
375 > are 9 and 8 atoms deep respectively, corresponding to a slab
376 > thickness of $\sim$21~\AA~ for Pt and $\sim$19~\AA~for Au.
377   The systems are arranged in a FCC crystal that have been cut
378   along the (557) plane so that they are periodic in the {\it x} and
379   {\it y} directions, and have been oriented to expose two aligned
# Line 369 | Line 382 | The different bulk melting temperatures (1345~$\pm$~10
382   1200~K were performed to confirm the relative
383   stability of the surfaces without a CO overlayer.  
384  
385 < The different bulk melting temperatures (1345~$\pm$~10~K for Au\cite{Au:melting}
385 > The different bulk melting temperatures predicted by EAM (1345~$\pm$~10~K for Au\cite{Au:melting}
386   and $\sim$~2045~K for Pt\cite{Pt:melting}) suggest that any possible reconstruction should happen at
387   different temperatures for the two metals.  The bare Au and Pt surfaces were
388   initially run in the canonical (NVT) ensemble at 800~K and 1000~K
# Line 396 | Line 409 | The surfaces of both systems, upon dosage of CO, began
409   %
410   \section{Results}
411   \subsection{Structural remodeling}
412 < The surfaces of both systems, upon dosage of CO, began
413 < to undergo extensive remodeling that was not observed in the bare
414 < systems. The bare metal surfaces
415 < experienced minor roughening of the step-edge because
416 < of the elevated temperatures, but the
417 < (557) lattice was well-maintained throughout the simulation
418 < time. The Au systems were limited to greater amounts of
419 < roughening, i.e. breakup of the step-edge, and some step
420 < wandering. The lower coverage Pt systems experienced
421 < similar restructuring but to a greater extent when
422 < 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}
412 > The bare metal surfaces experienced minor roughening of the
413 > step-edge because of the elevated temperatures, but the (557)
414 > face was stable throughout the simulations. The surface of both
415 > systems, upon dosage of CO, began to undergo extensive remodeling
416 > that was not observed in the bare systems. Reconstructions of
417 > the Au systems were limited to breakup of the step-edges and
418 > some step wandering. The lower coverage Pt systems experienced
419 > similar restructuring but to a greater extent. The 50\% coverage
420 > Pt system was unique among our simulations in that it formed
421 > well-defined and stable double layers through step coalescence,
422 > similar to results reported by Tao {\it et al}.\cite{Tao:2010}
423  
424  
425   \subsubsection{Step wandering}
426   The 0\% coverage surfaces for both metals showed minimal
427 < movement at their respective run temperatures. As the CO
428 < coverage increased however, the mobility of the surface,
427 > step-wandering at their respective temperatures. As the CO
428 > coverage increased however, the mobility of the surface atoms,
429   described through adatom diffusion and step-edge wandering,
430 < also increased.  Except for the 50\% Pt system, the step-edges
431 < did not coalesce in any of the other simulations, instead
432 < preferring to keep nearly the same distance between steps
433 < as in the original (557) lattice, $\sim$13\AA for Pt and $\sim$14\AA for Au.
434 < Previous work by Williams et al.\cite{Williams:1991, Williams:1994}
430 > also increased.  Except for the 50\% Pt system where step
431 > coalescence occurred, the step-edges in the other simulations
432 > preferred to keep nearly the same distance between steps as in
433 > the original (557) lattice, $\sim$13\AA~for Pt and $\sim$14\AA~for Au.
434 > Previous work by Williams {\it et al}.\cite{Williams:1991, Williams:1994}
435   highlights the repulsion that exists between step-edges even
436   when no direct interactions are present in the system. This
437 < repulsion arises because step-edge crossing is not allowed
438 < which constrains the entropy. This entropic repulsion does
439 < not completely define the interactions between steps, which
440 < is why some surfaces will undergo step coalescence, where
441 < additional attractive interactions can overcome the repulsion.\cite{Williams:1991}
442 < The presence and concentration of adsorbates, as shown in
443 < this work, can affect these step interactions, potentially leading
444 < to a new surface structure as the thermodynamic minimum.
437 > repulsion is caused by an entropic barrier that arises from
438 > the fact that steps cannot cross over one another. This entropic
439 > repulsion does not completely define the interactions between
440 > steps, however, so it is possible to observe step coalescence
441 > on some surfaces.\cite{Williams:1991} The presence and
442 > concentration of adsorbates, as shown in this work, can
443 > affect step-step interactions, potentially leading to a new
444 > surface structure as the thermodynamic equilibrium.
445  
446   \subsubsection{Double layers}
447 < Tao et al.\cite{Tao:2010} have shown experimentally that the Pt(557) surface
448 < undergoes two separate reconstructions upon CO adsorption.\cite{Tao:2010}
447 > Tao {\it et al}.\cite{Tao:2010} have shown experimentally that the Pt(557) surface
448 > undergoes two separate reconstructions upon CO adsorption.
449   The first involves a doubling of the step height and plateau length.
450 < Similar behavior has been seen on numerous surfaces
451 < at varying conditions: Ni(977), Si(111).\cite{Williams:1994,Williams:1991,Pearl}
450 > Similar behavior has been seen on a number of surfaces
451 > at varying conditions, including Ni(977) and Si(111).\cite{Williams:1994,Williams:1991,Pearl}
452   Of the two systems we examined, the Pt system showed a greater
453 < propensity for reconstruction when compared to the Au system
454 < because of the larger surface mobility and extent of step wandering.
455 < The amount of reconstruction is strongly correlated to the amount of CO
453 > propensity for reconstruction  
454 > because of the larger surface mobility and the greater extent of step wandering.
455 > The amount of reconstruction was strongly correlated to the amount of CO
456   adsorbed upon the surface.  This appears to be related to the
457   effect that adsorbate coverage has on edge breakup and on the
458 < surface diffusion of metal adatoms. While both systems displayed
459 < step-edge wandering, only the 50\% Pt surface underwent the
460 < doubling seen by Tao et al.\cite{Tao:2010} within the time scales studied here.
461 < Over longer periods, (150~ns) two more double layers formed
462 < on this interface. Although double layer formation did not occur
463 < in the other Pt systems, they show more step-wandering and
454 < general roughening compared to their Au counterparts. The
458 > surface diffusion of metal adatoms. Only the 50\% Pt surface underwent the
459 > doubling seen by Tao {\it et al}.\cite{Tao:2010} within the time scales studied here.
460 > Over a longer time scale (150~ns) two more double layers formed
461 > on this surface. Although double layer formation did not occur
462 > in the other Pt systems, they exhibited more step-wandering and
463 > roughening compared to their Au counterparts. The
464   50\% Pt system is highlighted in Figure \ref{fig:reconstruct} at
465   various times along the simulation showing the evolution of a double layer step-edge.
466  
467 < The second reconstruction on the Pt(557) surface observed by
468 < Tao involved the formation of triangular clusters that stretched
469 < across the plateau between two step-edges. Neither system, within
467 > The second reconstruction observed by
468 > Tao {\it et al}.\cite{Tao:2010} involved the formation of triangular clusters that stretched
469 > across the plateau between two step-edges. Neither metal, within
470   the 40~ns time scale or the extended simulation time of 150~ns for
471   the 50\% Pt system, experienced this reconstruction.
472  
473   %Evolution of surface
474   \begin{figure}[H]
475 < \includegraphics[width=\linewidth]{ProgressionOfDoubleLayerFormation_yellowCircle.png}
475 > \includegraphics[width=\linewidth]{EPS_ProgressionOfDoubleLayerFormation.pdf}
476   \caption{The Pt(557) / 50\% CO system at a sequence of times after
477    initial exposure to the CO: (a) 258~ps, (b) 19~ns, (c) 31.2~ns, and
478    (d) 86.1~ns. Disruption of the (557) step-edges occurs quickly.  The
# Line 474 | Line 483 | Previous atomistic simulations of stepped surfaces dea
483   \end{figure}
484  
485   \subsection{Dynamics}
486 < Previous atomistic simulations of stepped surfaces dealt largely
487 < with the energetics and structures at different conditions.
488 < \cite{Williams:1991,Williams:1994} Consequently, the most common
489 < technique utilized to date has been Monte Carlo sampling. Monte Carlo approaches give an efficient
490 < sampling of the equilibrium thermodynamic landscape at the expense
491 < of ignoring the dynamics of the system. Previous experimental work by Pearl and
492 < Sibener\cite{Pearl}, using STM, has been able to capture the coalescing
493 < 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.
486 > Previous experimental work by Pearl and Sibener\cite{Pearl},
487 > using STM, has been able to capture the coalescence of steps
488 > on Ni(977). The time scale of the image acquisition, $\sim$70~s/image,
489 > provides an upper bound for the time required for the doubling
490 > to occur. By utilizing Molecular Dynamics we are able to probe
491 > the dynamics of these reconstructions at elevated temperatures
492 > and in this section we provide data on the timescales for transport
493 > properties, e.g. diffusion and layer formation time.
494  
495  
496   \subsubsection{Transport of surface metal atoms}
497   %forcedSystems/stepSeparation
498 < The movement or wandering of a step-edge is a cooperative effect
498 > The wandering of a step-edge is a cooperative effect
499   arising from the individual movements of the atoms making up the steps. An ideal metal surface
500   displaying a low index facet, (111) or (100), is unlikely to experience
501   much surface diffusion because of the large energetic barrier that must
502   be overcome to lift an atom out of the surface. The presence of step-edges and other surface features
503   on higher-index facets provides a lower energy source for mobile metal atoms.
504 < Breaking away from the step-edge on a clean surface still imposes an
504 > Single-atom break-away from a step-edge on a clean surface still imposes an
505   energetic penalty around $\sim$~45 kcal/mol, but this is easier than lifting
506   the same metal atom vertically out of the surface,  \textgreater~60 kcal/mol.
507   The penalty lowers significantly when CO is present in sufficient quantities
508 < 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
508 > on the surface. For certain distributions of CO, see Discussion, the penalty can fall to as low as
509   $\sim$~20 kcal/mol. Once an adatom exists on the surface, the barrier for
510 < diffusion is negligible ( \textless~4 kcal/mol for a Pt adatom). These adatoms are then
510 > diffusion is negligible (\textless~4 kcal/mol for a Pt adatom). These adatoms are then
511   able to explore the terrace before rejoining either their original step-edge or
512 < becoming a part of a different edge. It is a difficult process for an atom
512 > becoming a part of a different edge. It is an energetically unfavorable process with a high barrier for an atom
513   to traverse to a separate terrace although the presence of CO can lower the
514   energy barrier required to lift or lower an adatom. By tracking the mobility of individual
515   metal atoms on the Pt and Au surfaces we were able to determine the relative
516   diffusion constants, as well as how varying coverages of CO affect the diffusion. Close
517   observation of the mobile metal atoms showed that they were typically in
518 < equilibrium with the step-edges, dynamically breaking apart and rejoining the edges.
518 > equilibrium with the step-edges.
519   At times, their motion was concerted and two or more adatoms would be
520   observed moving together across the surfaces.
521  
522   A particle was considered ``mobile'' once it had traveled more than 2~\AA~
523 < between saved configurations of the system (typically 10-100 ps). An atom that was
524 < truly mobile would typically travel much greater distances than this, but the 2~\AA~cutoff
523 > between saved configurations of the system (typically 10-100 ps). A mobile atom
524 > would typically travel much greater distances than this, but the 2~\AA~cutoff
525   was used to prevent swamping the diffusion data with the in-place vibrational
526   movement of buried atoms. Diffusion on a surface is strongly affected by
527   local structures and in this work, the presence of single and double layer
# Line 525 | Line 531 | diffusion constants are shown in Figure \ref{fig:diff}
531  
532   %Diffusion graph
533   \begin{figure}[H]
534 < \includegraphics[width=\linewidth]{DiffusionComparison_errorXY_remade_20ns.pdf}
534 > \includegraphics[width=\linewidth]{Portrait_DiffusionComparison_1.pdf}
535   \caption{Diffusion constants for mobile surface atoms along directions
536    parallel ($\mathbf{D}_{\parallel}$) and perpendicular
537    ($\mathbf{D}_{\perp}$) to the (557) step-edges as a function of CO
# Line 539 | Line 545 | The lack of a definite trend in the Au diffusion data
545   \label{fig:diff}
546   \end{figure}
547  
548 < The lack of a definite trend in the Au diffusion data in Figure \ref{fig:diff} is likely due
549 < to the weaker bonding between Au and CO. This leads to a lower observed
550 < coverage ({\it x}-axis) when compared to dosage amount, which
551 < then further limits the effect the CO can have on surface diffusion. The correlation
552 < between coverage and Pt diffusion rates conversely shows a
553 < definite trend marred by the highest coverage surface. Two
554 < explanations arise for this drop. First, upon a visual inspection of
555 < the system, after a double layer has been formed, it maintains its
556 < stability strongly and many atoms that had been tracked for mobility
557 < data have now been buried. By performing the same diffusion
558 < calculation but on a shorter run time (20~ns), only including data
559 < before the formation of the first double layer, we obtain the larger
560 < values for both $\mathbf{D}_{\parallel}$ and $\mathbf{D}_{\perp}$
561 < 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.
548 > The weaker Au-CO interaction is evident in the weak CO-coverage
549 > dependance of Au diffusion. This weak interaction leads to lower
550 > observed coverages when compared to dosage amounts. This further
551 > limits the effect the CO can have on surface diffusion. The correlation
552 > between coverage and Pt diffusion rates shows a near linear relationship
553 > at the earliest times in the simulations. Following double layer formation,
554 > however, there is a precipitous drop in adatom diffusion. As the double
555 > layer forms, many atoms that had been tracked for mobility data have
556 > now been buried resulting in a smaller reported diffusion constant. A
557 > secondary effect of higher coverages is CO-CO cross interactions that
558 > lower the effective mobility of the Pt adatoms that are bound to each CO.
559 > This effect would become evident only at higher coverages. A detailed
560 > account of Pt adatom energetics follows in the Discussion.
561 >
562  
570
571
563   \subsubsection{Dynamics of double layer formation}
564 < The increased diffusion on Pt at the higher CO coverages
565 < plays a primary role in double layer formation. However,
566 < this is not a complete explanation -- the 33\%~Pt system
567 < has higher diffusion constants but did not show any signs
568 < of edge doubling in the observed run time. On the
569 < 50\%~Pt system, one layer formed within the first 40~ns
570 < of simulation time, while two more were formed as the
571 < system was allowed to run for an additional
572 < 110~ns (150~ns total). This suggests that this reconstruction is
573 < a rapid process and that the previously mentioned upper bound
574 < will be lowered as experimental techniques continue to improve.\cite{Williams:1991,Pearl}
575 < In this system, as seen in Figure \ref{fig:reconstruct}, the first
576 < appearance of a double layer, appears at 19~ns
577 < into the simulation. Within 12~ns of this nucleation event, nearly half of the step has
578 < formed the double layer and by 86~ns, the complete layer
579 < has been flattened out. The double layer could be considered
580 < ``complete" by 37~ns but remains a bit rough. From the
581 < appearance of the first nucleation event to the first observed double layer, the process took $\sim$20~ns. Another
582 < $\sim$40~ns was necessary for the layer to completely straighten.
583 < The other two layers in this simulation formed over periods of
584 < 22~ns and 42~ns respectively. A possible explanation
585 < 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.
564 > The increased diffusion on Pt at the higher CO coverages is the primary
565 > contributor to double layer formation. However, this is not a complete
566 > explanation -- the 33\%~Pt system has higher diffusion constants, but
567 > did not show any signs of edge doubling in 40~ns. On the 50\%~Pt
568 > system, one double layer formed within the first 40~ns of simulation time,
569 > while two more were formed as the system was allowed to run for an
570 > additional 110~ns (150~ns total). This suggests that this reconstruction
571 > is a rapid process and that the previously mentioned upper bound is a
572 > very large overestimate.\cite{Williams:1991,Pearl} In this system the first
573 > appearance of a double layer appears at 19~ns into the simulation.
574 > Within 12~ns of this nucleation event, nearly half of the step has formed
575 > the double layer and by 86~ns the complete layer has flattened out.
576 > From the appearance of the first nucleation event to the first observed
577 > double layer, the process took $\sim$20~ns. Another $\sim$40~ns was
578 > necessary for the layer to completely straighten. The other two layers in
579 > this simulation formed over periods of 22~ns and 42~ns respectively.
580 > A possible explanation for this rapid reconstruction is the elevated
581 > temperatures under which our systems were simulated. The process
582 > would almost certainly take longer at lower temperatures. Additionally,
583 > our measured times for completion of the doubling after the appearance
584 > of a nucleation site are likely affected by our periodic boxes. A longer
585 > step-edge will likely take longer to ``zipper''.
586  
587  
588 + %Discussion
589 + \section{Discussion}
590 + We have shown that a classical potential model is able to model the
591 + initial reconstruction of the Pt(557) surface upon CO adsorption as
592 + shown by Tao {\it et al}.\cite{Tao:2010}. More importantly, we were
593 + able to observe features of the dynamic processes necessary for
594 + this reconstruction. Here we discuss the features of the model that
595 + give rise to the observed dynamical properties of the (557) reconstruction.
596  
597 + \subsection{Diffusion}
598 + The perpendicular diffusion constant
599 + appears to be the most important indicator of double layer
600 + formation. As highlighted in Figure \ref{fig:reconstruct}, the
601 + formation of the double layer did not begin until a nucleation
602 + site appeared. And as mentioned by Williams {\it et al}.\cite{Williams:1991, Williams:1994},
603 + the inability for edges to cross leads to an effective edge-edge repulsion that
604 + must be overcome to allow step coalescence.
605 + A greater $\textbf{D}_\perp$ implies more step-wandering
606 + and a larger chance for the stochastic meeting of two edges
607 + to create a nucleation point. Parallel diffusion along the step-edge can help ``zipper'' up a nascent double
608 + layer. This helps explain why the time scale for formation after
609 + the appearance of a nucleation site was rapid, while the initial
610 + appearance of the nucleation site was unpredictable.
611  
612 + \subsection{Mechanism for restructuring}
613 + Since the Au surface showed no large scale restructuring in any of
614 + our simulations, our discussion will focus on the 50\% Pt-CO system
615 + which did exhibit doubling. A
616 + number of possible mechanisms exist to explain the role of adsorbed
617 + CO in restructuring the Pt surface. Quadrupolar repulsion between
618 + adjacent CO molecules adsorbed on the surface is one possibility.  
619 + However, the quadrupole-quadrupole interaction is short-ranged and
620 + is attractive for some orientations.  If the CO molecules are ``locked'' in
621 + a specific orientation relative to each other, through atop adsorption for
622 + example, this explanation would gain credence. The calculated energetic repulsion
623 + between two CO molecules located a distance of 2.77~\AA~apart
624 + (nearest-neighbor distance of Pt) and both in a vertical orientation,
625 + is 8.62 kcal/mol. Moving the CO to the second nearest-neighbor distance
626 + of 4.8~\AA~drops the repulsion to nearly 0. Allowing the CO to rotate away
627 + from a purely vertical orientation also lowers the repulsion. When the
628 + carbons are locked at a distance of 2.77~\AA, a minimum of 6.2 kcal/mol is
629 + reached when the angle between the 2 CO is $\sim$24\textsuperscript{o}.
630 + The calculated barrier for surface diffusion of a Pt adatom is only 4 kcal/mol, so
631 + repulsion between adjacent CO molecules bound to Pt could increase the surface
632 + diffusion. However, the residence time of CO on Pt suggests that these
633 + molecules are extremely mobile, with diffusion constants 40 to 2500 times
634 + larger than surface Pt atoms. This mobility suggests that the CO molecules jump
635 + between different Pt atoms throughout the simulation, but will stay bound for
636 + significant periods of time.
637  
638 + A different interpretation of the above mechanism, taking into account the large
639 + mobility of the CO, looks at how instantaneous and short-lived configurations of
640 + CO on the surface can destabilize Pt-Pt interactions leading to increased step-edge
641 + breakup and diffusion. On the bare Pt(557) surface the barrier to completely detach
642 + an edge atom is $\sim$43~kcal/mol, as is shown in configuration (a) in Figures
643 + \ref{fig:SketchGraphic} \& \ref{fig:SketchEnergies}. For certain configurations, cases
644 + (e), (g), and (h), the barrier can be lowered to $\sim$23~kcal/mole. In these instances,
645 + it becomes quite energetically favorable to roughen the edge by introducing a small
646 + separation of 0.5 to 1.0~\AA. This roughening becomes immediately obvious in
647 + simulations with significant CO populations. The roughening is present to a lesser extent
648 + on lower coverage surfaces and even on the bare surfaces, although in these cases it is likely
649 + due to stochastic vibrational processes that squeeze out step-edge atoms. The mechanism
650 + of step-edge breakup suggested by these energy curves is one of the most difficult
651 + processes, a complete break-away from the step-edge in one unbroken movement.
652 + Easier multistep mechanisms likely exist where an adatom moves laterally on the surface
653 + after being ejected so it ends up alongside the ledge. This provides the atom with 5 nearest
654 + neighbors, which while lower than the 7 if it had stayed a part of the step-edge, is higher
655 + than the 3 it could maintain located on the terrace. In this proposed mechanism, the CO
656 + quadrupolar repulsion is still playing a primary role, but for its importance in roughening
657 + the step-edge, rather than maintaining long-term bonds with a single Pt atom which is not
658 + born out by their mobility data. The requirement for a large density of CO on the surface
659 + for some of the more favorable suggested configurations in Figure \ref{fig:SketchGraphic}
660 + correspond well with the increased mobility seen on higher coverage surfaces.
661  
662   %Sketch graphic of different configurations
663   \begin{figure}[H]
# Line 616 | Line 672 | Energies associated with each configuration are displa
672  
673   %energy graph corresponding to sketch graphic
674   \begin{figure}[H]
675 < \includegraphics[width=\linewidth]{stepSeparationComparison.pdf}
675 > \includegraphics[width=\linewidth]{Portrait_SeparationComparison.pdf}
676   \caption{The energy curves directly correspond to the labeled model
677   surface in Figure \ref{fig:SketchGraphic}. All energy curves are relative
678   to their initial configuration so the energy of a and h do not have the
# Line 627 | Line 683 | configurations of CO will be more likely. }
683   \label{fig:SketchEnergies}
684   \end{figure}
685  
686 < %Discussion
687 < \section{Discussion}
688 < We have shown that the classical potential models are able to model the initial reconstruction of the
689 < Pt(557) surface upon CO adsorption as shown by Tao et al. \cite{Tao:2010}. More importantly, we
690 < were able to observe features of the dynamic processes necessary for this reconstruction.
686 > While configurations of CO on the surface are able to increase diffusion,
687 > this does not immediately provide an explanation for the formation of double
688 > layers. If adatoms were constrained to their terrace then doubling would be
689 > much less likely to occur. Nucleation sites could still potentially form, but there
690 > would not be enough atoms to finish the doubling. For a non-simulated metal surface, where the
691 > step lengths can be assumed to be infinite relative to atomic sizes, local doubling would be possible, but in
692 > our simulations with our periodic treatment of the system, the system is not large enough to experience this effect.
693 > Thus, there must be a mechanism that explains how adatoms are able to move
694 > amongst terraces. Figure \ref{fig:lambda} shows points along a reaction coordinate
695 > where an adatom along the step-edge with an adsorbed CO ``burrows'' into the
696 > edge displacing an atom onto the higher terrace. This mechanism was chosen
697 > because of similar events that were observed during the simulations. The barrier
698 > heights we obtained are only approximations because we constrained the movement
699 > of the highlighted atoms along a specific concerted path. The calculated $\Delta E$'s
700 > are provide a strong energetic support for this modeled lifting mechanism. When CO is not present and
701 > this reaction coordinate is followed, the $\Delta E > 3$~kcal/mol. The example shown
702 > in the figure, where CO is present in the atop position, has a $\Delta E < -15$~kcal/mol.
703 > While the barrier height is comparable for both cases, there is nearly a 20~kcal/mol
704 > difference in energies and makes the process energetically favorable.
705  
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
706   %lambda progression of Pt -> shoving its way into the step
707   \begin{figure}[H]
708 < \includegraphics[width=\linewidth]{lambdaProgression_atopCO_withLambda.png}
709 < \caption{A model system of the Pt(557) surface was used as the framework
710 < for exploring energy barriers along a reaction coordinate. Various numbers,
711 < placements, and rotations of CO were examined as they affect Pt movement.
712 < 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 > \includegraphics[width=\linewidth]{EPS_rxnCoord.pdf}
709 > \caption{ Various points along a reaction coordinate are displayed in the figure.
710 > The mechanism of edge traversal is examined in the presence of CO. The approximate
711 > barrier for the displayed process is 20~kcal/mol. However, the $\Delta E$ of this process
712 > is -15~kcal/mol making it an energetically favorable process.}
713   \label{fig:lambda}
714   \end{figure}
715  
716 + The mechanism for doubling on this surface appears to require the cooperation of at least
717 + these two described processes. For complete doubling of a layer to occur there must
718 + be the equivalent removal of a separate terrace. For those atoms to ``disappear'' from
719 + that terrace they must either rise up on the ledge above them or drop to the ledge below
720 + them. The presence of CO helps with the energetics of both of these situations. There must be sufficient
721 + breakage of the step-edge to increase the concentration of adatoms on the surface and
722 + these adatoms must then undergo the burrowing highlighted above or some comparable
723 + mechanism to traverse the step-edge. Over time, these mechanisms working in concert
724 + lead to the formation of a double layer.
725  
726 + \subsection{CO Removal and double layer stability}
727 + Once a double layer had formed on the 50\%~Pt system it
728 + remained for the rest of the simulation time with minimal
729 + movement. There were configurations that showed small
730 + wells or peaks forming, but typically within a few nanoseconds
731 + the feature would smooth away. Within our simulation time,
732 + the formation of the double layer was irreversible and a double
733 + layer was never observed to split back into two single layer
734 + step-edges while CO was present. To further gauge the effect
735 + CO had on this system, additional simulations were run starting
736 + from a late configuration of the 50\%~Pt system that had formed
737 + double layers. These simulations then had their CO removed.
738 + The double layer breaks rapidly in these simulations, already
739 + showing a well-defined splitting after 100~ps. Configurations of
740 + this system are shown in Figure \ref{fig:breaking}. The coloring
741 + of the top and bottom layers helps to exhibit how much mixing
742 + the edges experience as they split. These systems were only
743 + examined briefly, 10~ns, and within that time despite the initial
744 + rapid splitting, the edges only moved another few \AA~apart.
745 + It is possible with longer simulation times that the
746 + (557) lattice could be recovered as seen by Tao {\it et al}.\cite{Tao:2010}
747  
748  
749  
750   %breaking of the double layer upon removal of CO
751   \begin{figure}[H]
752 < \includegraphics[width=\linewidth]{doubleLayerBreaking_greenBlue_whiteLetters.png}
752 > \includegraphics[width=\linewidth]{EPS_doubleLayerBreaking.pdf}
753   \caption{(A)  0~ps, (B) 100~ps, (C) 1~ns, after the removal of CO. The presence of the CO
754 < helped maintain the stability of the double layer and upon removal the two layers break
755 < and begin separating. The separation is not a simple pulling apart however, rather
756 < there is a mixing of the lower and upper atoms at the edge.}
754 > helped maintain the stability of the double layer and its microfaceting of the double layer
755 > into a (111) configuration. This microfacet immediately reverts to the original (100) step
756 > edge which is a hallmark of the (557) surface. The separation is not a simple sliding apart, rather
757 > there is a mixing of the lower and upper atoms at the edge.}
758   \label{fig:breaking}
759   \end{figure}
760  
# Line 771 | Line 782 | In this work we have shown the reconstruction of the P
782  
783  
784   \section{Conclusion}
785 < 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.
785 > The strength of the Pt-CO binding interaction as well as the large
786 > quadrupolar repulsion between CO molecules are sufficient to
787 > explain the observed increase in surface mobility and the resultant
788 > reconstructions at the highest simulated coverage. The weaker
789 > Au-CO interaction results in lower diffusion constants, less step-wandering,
790 > and a lack of the double layer reconstruction. An in-depth examination
791 > of the energetics shows the important role CO plays in increasing
792 > step-breakup and in facilitating edge traversal which are both
793 > necessary for double layer formation.
794  
795 +
796 +
797   %Things I am not ready to remove yet
798  
799   %Table of Diffusion Constants

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