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new bidentate families to consider #8
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From discussion on another PR.; 1. Surface_DoubleBond_to_Bidentate
where Worth doing. 2. Surface_PiBond_to_DiSigmaThen, additionally, the pi- to -di-sigma would be:
where Worth doing. |
Reaction 1 and DoubleBond_to_Bidentate are the same, so I modified the original post. I would call reaction 2 "PiBond_to_DiSigma" |
Here is another reaction involving bidentate species: Surface_Bidentate_Dissociation (or Association_to_Bidentate in reverse):For disigma species that contain a single bond, break that bond and increase the bond order with the surface:
Note that the bonds between This could be useful for something like |
Regarding yesterday’s weekly telecon, one of Katrin’s action items it to check out how we’re estimating the thermo for bidentate species. As a pre-requisite, we need to turn on reactions that form bidentate species. Currently, we have two in the development branch: Surface_Adsorption_Bidentate and Surface_Bidentate_Dissociation. I have a few thoughts. First, I think that these two reactions are not going to be the most important in terms of generating bidentate species. The second reaction family (which I probably added?), Surface_Bidentate_Dissociation, is third order overall and second order in vacant sites. Furthermore, I think that particular name is better suited for a different reaction. I propose that we add the following reaction families in this order: Surface_Bidentate_DissociationA bidentate species with a single bond dissociates. The reverse reaction is when two adsorbates, each with double-bonds or higher to the surface, come together and form a single bond between them, thereby reducing the bond orders to the surface. Surface_DoubleBond_to_BidentateIf an adsorbate has an internal double bond, then it can fall over onto a vacant site, creating a bidentate. Surface_PiBond_to_DiSigmaIf a vdW species has a double bond, then convert it to a bidentate with singe bonds. |
Those three sound good. I edited the comments above this to get the names consistent. |
Regarding how the thermo is estimated for bidentate species, the current approach is to use double the binding site area in the partition function calculation. So now the translational partition function is calculated by: I added the three bidentate reaction families to a new branch bidentate_families with made up activation energies and approximated pre-exponentials. I now have the last one defined in the reverse reaction, Surface_DiSigma_to_PiBond. Does it matter which direction it is defined in if the reactions are reversible? Perhaps depending on the kinetic parameters? |
Update regarding the DoubleBond_to_Bidentate family: I ran a test where a part of the surface is initially covered by *CHO for that and it seems to work correctly, as it can do the following: *CHO + * => *=CH*O *=CH*O + *=> *O + **=CH |
Update regarding the DiSigma_to_PiBond family: it seems to work as it should. At least so far I have seen that it was able to make pi-bonded O2 from bidentate O2. |
For the comment (two above) about DoubleBond_to_Bidentate it is trying to do this
but doesn't realize the C is already bonded and is doing this
|
I have not expanded the bidentate family set much, because we still haven't worked out how to handle them in the thermo tree. Once we do, here are two families to add:
DoubleBond_to_Bidentate:
If the binding atom has a double bond, form a new surface bond with a vacant site:
This could be useful for something like
*CH=O + * --> *CH*O
. Note: adsorbed vinyl would be another example, except that we don't have thermo for that species.And another form of bond dissociation,
name? (previously Bidentate_Dissociation, but I think that name is better used elsewhere):
If the binding atom has a double bond, and that double-bond has a single bond, break that single bond:
EDIT: because this is third order, I would de-emphasize it in the short term.
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