Naming conventions for adsorbates

[rwest]

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 C*H3 or H3C*). This becomes more important for some of the more obscure species. What should we call CNH? Right now we have CNH*, but this obscures the fact that it is bonding through carbon and looks more like HN=C=Pt. So should we go with HNC*, C*NH, or what?

[rwest]

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

CH3OH 
CH3CH3
CH3OCH3

1. Put the * at the end of the group definition, after all other ligands? worst?

CH3*
CNH*
CH2OH*

2. 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)

3. 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)

4. 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]

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]

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]

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

[rwest]

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]

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?