** Reference to paper:

https://pubs.acs.org/doi/10.1021/acs.jpcc.9b05757

** DOI:

10.1021/acs.jpcc.9b05757

** Title:

Dynamical Study of the Dissociative Chemisorption of CHD3 on Pd(111)

** Authors:

Gerrits, Nick; Chadwick, Helen; Kroes, Geert-Jan

** Contact e-mail:

n.gerrits@lic.leidenuniv.nl
g.j.kroes@chem.leidenuniv.nl

** Abstract:

The specific reaction parameter (SRP) approach to density functional theory has been shown to model reactions of polyatomic molecules with metal surfaces important for heterogeneous catalysis in the industry with chemical accuracy.
However, transferability of the SRP functional among systems in which methane interacts with group 10 metals remains unclear for methane + Pd(111).
Therefore, in this work, predictions have been made for the reaction of CHD3 on Pd(111) using Born–Oppenheimer molecular dynamics while also performing a rough comparison with experimental data for CH4 + Pd(111) obtained for lower incidence energies.
Hopefully, future experiments can test the transferability of the SRP functional among group 10 metals also for Pd(111).
We found that the reactivity of CHD3 on Pd(111) is intermediate between and similar to either Pt(111) or Ni(111), depending on the incidence energy and the initial vibrational state distribution.
This is surprising because the barrier height and experiments performed at lower incidence energies than investigated here suggest that the reactivity of Pd(111) should be similar to that of Pt(111) only.
The relative decrease in the reactivity of Pd(111) at high incidence energies is attributed to site specificity of the reaction and to dynamical effects such as the bobsled effect and energy transfer from methane to the surface.

** Description per file:
Note that many files/scripts are missing for how to perform the calculations as they are the same as the ones provided in 2018_jcp_CHD3_cu_alloys.
Therefore, in this folder mainly the results and new scripts are provided.
Furthermore, not all analysis scripts are included, as they essentially just gather data generated by check-CHD3.py contained in the PostAnalysis.dat

The program used for DFT is VASP v5.3.5 with a special modification in order to use a SRP functional and with VTST (http://theory.cm.utexas.edu/vtsttools/index.html).

** Folder Barrier:
The barrier geometries obtained for Pt(111), Pd(111), and Ni(111) are provided.

** Folder Equilibrated_slabs:
Contains all the equilibrated slabs and their snapshots used in the AIMD for the initial conditions.

All figures are made with matplotlib 1.5.1, except figure 1 which was made with Blender 1.79 and annoted with GIMP

** Folder Figure01:
angles.pdf

** Folder Figure02:
reactionprobability_comparison.pdf
plotstickingcomparison.py - generates the plot

** Folder Figure03:
cleavage_comparison.pdf
plotcleavage_comparison.py - generates the plot

** Folder Figure04:
aimd_angles_comparison.pdf
plotangles.py - generates the plot
ni_angles_reac.dat pd_angles_reac.dat pt_angles_reac.dat - data files containing the theta, beta, and phi angles at the initial time step and moment of reaction (r=r_ts)
These data files are required for making the plot

** Folder Figure05:
Zc_ts_comparison.pdf
plotr_ts_comparison.py - generates the plot

** Folder Figure06:
energytransfer_comparison.pdf
plotenergytransfer_comparison.py - generates the plot

** Folder Figure07:
probabilityreactionsite_comparison.pdf
plotreactionsite_comparison.py - generates the plot

** Folder Figure08:
probabilityreactionsite_p.pdf
plotreactionsite_probability.py - generates the plot

** Folder Figure09:
reactionprobability_exp.pgf - this is the plot, but should be included in a latex document in order to render it
plotstickingcomparison_exp2.py - generates the plot

** Folder FigureS01:
convergence.pdf
plotconvergence.py - generates the plot

** Folder FigureS02:
probabilityreactionsite_p_add.pdf
plotreactionsite_probability_additive.py - generates the plot

** Folder FigureS03:
site_analytical.pdf
Analysis_dist_plot_analytical.py - generates the plot, but requires the AIMD data and the PostAnalysis.dat generated with the check-CHD3.py file

Other files:
check-CHD3.py - analysis the trajectories
Analysis_angle.py - generates the angle data files, and the average
Analysis_rts.py - Obtains the average and standard error of Z_COM at the moment of reaction from the PostAnalysis.dat