Missing Mechanisms: H Abstraction from NH2 by Adsorbed OH

[Tingchenlee]

Topic

A possible reaction mechanism: NH2_X + OH_X <=> NH_X + H2O_X is missing in Kinetic Search (RMG website)

Context

Reactant 1: NH2 adsorbate

1 N u0 p1 c0 {2,S} {3,S} {4,S}
2 H u0 p0 c0 {1,S}
3 H u0 p0 c0 {1,S}
4 X u0 p0 c0 {1,S}

Reactant 2. OH adsorbate

1 O u0 p2 c0 {2,S} {3,S}
2 H u0 p0 c0 {1,S}
3 X u0 p0 c0 {1,S}

The result of Kinetic Search only has the product of hydroxylamine (NH2OH), however, some literature shows that H2O adsorbate would probably show up:

• Ammonia activation on platinum {1 1 1}: A density functional theory study https://doi.org/10.1016/j.susc.2006.01.031
• Pt(100)-Catalyzed Ammonia Oxidation Studied by DFT: Mechanism and Microkinetics https://pubs.acs.org/doi/10.1021/jp802489y
• Modeling ammonia oxidation over a Pt (533) surface https://doi.org/10.1016/j.susc.2011.08.014
• Structure- and Temperature-Dependence of Pt-Catalyzed Ammonia Oxidation Rates and Selectivities https://doi.org/10.1021/acscatal.8b04251

Question

Is there a missing family for the surface reaction? Or we have this family but something went wrong with the simulation?

[Tingchenlee]

The above reaction matches the template of the Surface_Abstraction_vdW while it can not be generated by this family

 *2-*3  *4             *2     *4-*3
  :     ||     ---->    |      |
~*1~ + ~*5~~          ~*1~ + ~*5~~

Not sure if we need to add L3: O-H and L4: H2O for the L1: AdsorbateVdW

L1: AdsorbateVdW
    L2: H-H
    L2: O-R
        L3: O-O
            L4: HO-OH
        L3: O-N
            L4: O-N-2R
                L5: O-NHH
            L4: O-N=R
        L3: O-C
            L4: O-C-3R
            L4: O-C=R
            L4: O-C#R
    L2: C-R
        L3: C-C
        L3: C-O
            L4: C-OH
        L3: C-N
    L2: N-R
        L3: N-N
        L3: N-O
        L3: N-C

[Tingchenlee]

Seems like it is solved by https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2062 now. The reaction mechanism can be found in Surface_Abstraction_vdW now!