Naming conventions for adsorbates

cfgoldsmith / RMG-Py

Python version of the amazing Reaction Mechanism Generator (RMG).

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Naming conventions for adsorbates #65

Open rwest opened 5 years ago

rwest commented 5 years ago

In Slack, @cfgoldsmith wrote:

Hi all. Let’s start a discussion on naming conventions for the Pt species. For example, we could adopt the strategy everyone uses, such as CH3*. Or we could put the on the bonding atom (e.g. either `CH3orH3C). This becomes more important for some of the more obscure species. What should we callCNH? Right now we haveCNH, but this obscures the fact that it is bonding through carbon and looks more likeHN=C=Pt. So should we go withHNC,CNH`, or what?

rwest commented 5 years ago

For not-adsorbed things, people put the Hn as close as possible to the C, but after it.

CH3OH 
CH3CH3
CH3OCH3

Put the * at the end of the group definition, after all other ligands? worst?
```
CH3*
CNH*
CH2OH*
```
Put the * almost as close as possible to the C, but less close than the H's, and always after.
```
CH3*
C*NH
CH2*OH
CH2*CH2* (bidentate)
```
Put the * as close as possible to the C, even more close than the H's, but always after
```
C*H3
C*NH
C*H2OH
C*H2C*H2 (bidentate)
```
Can * come first? In which case could be to the left of the adatom
```
*CH3
*CNH
*CH2OH
*CH2*CH2  (bidentate)
```

I think my preference is 3 (or maybe 4 if starting with a * is never a problem?) Emily prefers 4.

I notice that only the first one (which I think is worst) makes the current CNH* that you mention.

Is this a logical way of describing the options? Did I miss any? which do you like?

cfgoldsmith commented 5 years ago

I like 3 and 4 best as well. I just checked, and we can have a species in cantera start with *, but I don't know if it would work in Chemkin.

kblondal commented 5 years ago

I like 3 and 4 too. Say we use 4 in the paper, then what about physisorbed species like (H2O), (HNO), (HCN) and (HOOH)? Also put H after the binding atom, (OH2), (NHO), (CHN), (OHOH)?

rwest commented 5 years ago

I thought physisorbed species don't have a binding atom?

rwest commented 5 years ago

Also, for what it's worth, I found some CHEMKIN II instructions saying "Species names may not begin with a number, a +, or an =, or have imbedded blanks; an ionic species may end with any number of +'s or -'s; an imbedded plus sign (+) must be enclosed in parentheses."

kblondal commented 5 years ago

Right, referring to it as binding atom because is probably not appropriate for vdW species. I mean the atom we classify the physisorbed species under in the thremo tree diagrams. Ok to have H in front for those?