--- trunk/COonPt/firstTry.tex	2012/12/11 18:22:20	3810
+++ trunk/COonPt/firstTry.tex	2012/12/13 22:42:37	3811
@@ -106,16 +106,20 @@ High-index surfaces of catalytically active metals are
 accuracy and the computational efficiency necessary to observe the
 process of interest.
 
-High-index surfaces of catalytically active metals are an important area of exploration because they are typically more reactive than an ideal surface of the same metal. The greater number of low-coordinated surface atoms is believed responsible for this increased reactivity \cite{}. Additionally, the activity and specificity of many metals towards certain chemical processes has been shown to strongly depend on the structure of the surface \cite{}. Prior work has also shown that reaction conditions, such as high pressures and high temperatures are able to cause reconstructions of the metallic surface, either through changing the displayed surface facets or by changing the number and types of high-index sites available for reactions \cite{doi:10.1126/science.1197461,doi:10.1021/nn3015322, doi:10.1021/jp302379x}. A greater understanding of these high-index surfaces and the restructuring processes they undergo is needed as a prerequisite for more intelligent catalyst design. While current experimental work has started exploring systems at \emph{in situ} conditions, for a long time such experiments were limited to ideal surfaces in high vacuum. New techniques, such as ambient pressure XPS (AP-XPS) \cite{}, high-pressure XPS (HP-XPS) \cite{}, high-pressure STM \cite{}, environmental transmission electron microscopy (E-TEM) \cite{} and many others, are providing clearer pictures of the processes that are occurring on metal surfaces under these conditions. Nevertheless, all of these techniques still have limitations, especially in observing what is occurring at an atomic level. Theoretical models and simulations in combination with experiment have proven their worth in explaining the underlying reasons for some of these reconstructions \cite{}. 
-\\
-By examining two different metal-CO systems the effect that the metal and the metal-CO interaction plays can be elucidated. Our first system is composed of platinum and CO and has been the subject of many experimental and theoretical studies primarily because of platinum's strong reactivity toward CO oxidation. The focus has primarily been on adsorption energies, preferred adsorption sites, and catalytic activities. The second system we examined is composed of gold and CO. The gold-CO interaction is much weaker than the platinum-CO interaction and it seems likely that this difference in attraction would lead to differences in any potential surface reconstructions.
-%It has also been a good test for new quantum methods because of the difficulty with modeling the preference CO has for the atop binding site \cite{doi:10.1021/jp002302t}. 
-%Now that dynamic surface events are known to play a role in many catalytic systems, additional research is being done to more closely examine many systems. Recent work by Tao et al. \cite{doi:10.1126/science.1182122} shows that a high-index platinum surface undergoes surface reconstructions when exposed to a small amount of CO, $\sim$~1 torr. Unexpectedly,  the reconstruction was metastable and reverted upon removal of the CO. Work by McCarthy et al. \cite{doi:10.1021/jp302379x} examined temperature programmed desorption's of CO from various platinum samples and saw that species which had large amounts of low-coordinated surface atoms, highly sputtered surfaces or small nano particles, developed a higher temperature desorption peak, suggesting that binding of CO to the platinum surface is strongly dependent on local geometry. 
+Since restructuring occurs as a result of specific interactions of the catalyst
+with adsorbates, two metals systems exposed to the same adsorbate, CO,
+were examined in this work. The Pt(557) surface has already been shown to 
+reconstruct under certain conditions. The Au(557) surface will provide a
+useful counterpoint
 
+%Platinum molecular dynamics
+%gold molecular dynamics
 
 
 
 
+
+
 \section{Simulation Methods}
 The challenge in modeling any solid/gas interface problem is the
 development of a sufficiently general yet computationally tractable
@@ -199,10 +203,10 @@ to the experimental (-2.63 D~\AA\cite{}) and quantum m
 site at the center of mass along the CO bond.  The geometry along with the interaction
 parameters are reproduced in Table 1. The effective dipole moment is still
 small (0.35 D) while the linear quadrupole (-2.40 D~\AA) is close
-to the experimental (-2.63 D~\AA\cite{}) and quantum mechanical predictions (WHAT VALUE, Coriana et al?).
+to the experimental (-2.63 D~\AA)\cite{QuadrupoleCO} and quantum mechanical predictions (-2.46 D~\AA)\cite{QuadrupoleCOCalc}.
 %CO Table
 \begin{table}[H]
-\caption{Positions, $\sigma$, $\epsilon$ and charges for CO geometry and self-interactions\cite{}. Distances are in \AA~, energies are in kcal/mol, and charges are in $e$.}
+\caption{Positions, $\sigma$, $\epsilon$ and charges for CO geometry and self-interactions\cite{Straub}. Distances are in \AA~, energies are in kcal/mol, and charges are in $e$.}
 \centering
 \begin{tabular}{| c | c | ccc |}
 \hline
@@ -218,8 +222,27 @@ The cross-interactions between the metals and the CO n
 \end{table}
 
 \subsection{Cross-Interactions}
-The cross-interactions between the metals and the CO needed to be parameterized. Previous attempts at parameterization have used two different functional forms to model these interactions\cite{}. A LJ model was fit for the Metal-Carbon interaction and a Morse potential was parameterized for the Metal-Oxygen interaction. The parameter sets chosen, as shown in Table 2, did a suitable job at reproducing experimental adsorption energies as shown in Table 3, but more importantly, they were able to capture the binding site preference. The Pt-CO parameters show a slight preference for the atop binding site which matches the experimental observations.
 
+One hurdle that must be overcome in classical molecular simulations 
+is the proper parameterization of all of the potential interactions present
+in the system. CO adsorbed on a platinum surface has been the focus of
+many experimental \cite{Yeo, Hopster:1978, Ertl:1977, Kelemen:1979} and theoretical studies. 
+\cite{Beurden:2002ys,Pons:1986,Deshlahra:2009,Feibelman:2001,Mason:2004} 
+We started with parameters reported by Korzeniewski et al. \cite{Pons:1986} and then
+modified them to ensure that the Pt-CO interaction favored 
+an atop binding position for the CO upon the Pt surface. Following the method 
+laid out by Korzeniewski, the Pt-C interaction was fit to a strong 
+Lennard-Jones 12-6 interaction to mimic binding, while the Pt-O interaction
+was parameterized to a Morse potential. The resultant potential-energy
+surface suitably recovers the calculated Pt-CO bond length (1.1 \AA)\cite{Deshlahra:2012} and affinity
+for the atop binding position.\cite{Deshlahra:2012, Hopster:1978}
+
+The Au-C and Au-O interaction parameters were fit to a Lennard-Jones and Morse potential respectively. The binding energies were obtained from quantum calculations carried out using <functional> for gold. 
+
+Numerous single point calculations were performed at various distances of the CO
+
+
+
 \subsection{Construction and Equilibration of 557 Metal interfaces}
 
 Our model systems are composed of approximately 4000 metal atoms cut along the 557 plane. The bare crystals were initially run in the Canonical ensemble at 1000K and 800K respectively for Pt and Au. The difference in temperature is necessary because of the two metals different melting points. Various amounts of CO were added to the simulation box and allowed to absorb to the metal surfaces over a short period of 100 ps. After further thermal relaxation the simulations were all run for at least 40 ns. A subset of the runs that showed interesting effects were allowed to run longer. The system
@@ -261,7 +284,7 @@ Our model systems are composed of approximately 4000 m
 \hline
  & Calc. & Exp. \\
 \hline
-\textbf{Pt-CO} & -1.9 & -1.4~\cite{Kelemen}-- -1.9~\cite{Yeo} \\
+\textbf{Pt-CO} & -1.9 & -1.4~\cite{Kelemen:1979}-- -1.9~\cite{Yeo} \\
 \textbf{Au-CO} & -0.39 & -0.44~\cite{TPD_Gold_CO} \\
 \hline
 \end{tabular}
