Molecular formula with centroid. Ferrocene

Hi.

I just downloaded latest version (5.9) of MarvinSketch and found we steel have this bug. I expected that bug could fixed because it is so trivial to detect.

I draw ferrocene molecule with bonds between Fe and centroid of the Cp ring. I used Add->Multicenter function to add dummy atom and than i made bond between Fe and centroid (ferrocene.mrv). Picture looks very nice but if we calculate elemental analysis i got very strange numbers: C10H8Fe.

 

I added explicit hydrogens and they also were fine. 10 hydrogen as expected. I removed bonds between iron and centroids and repeat elemental analysis calculation and at this time i got correct numbers.

Conclusions: If you have bond to centroid you have wrong numbers for molecular formula. => BUG

Seconf part is a suggestion.

Very often if you work with elemental analysis you need 0.5 molecule of solvent (H2O, CH2Cl2, etc). Is there any way we can use to do this? If no, can we add tag "weight" for each object (Atom, fragment) to control over contribution of the object into overal system. Thus, molecular formula will be calculated as Mr=weight*n*Mr(Atom)+.....over all atoms. Default value for weight is 1.

 

Thank you very much .

 

 

 

 

Hi,

Thank you for the bug report. We have not found this bug yet that is why it is not fixed so far. We will fix this.

Very often if you work with elemental analysis 

you need 0.5 molecule of solvent (H2O, CH2Cl2, etc). Is there any way we

 can use to do this? If no, can we add tag "weight" for each object 

(Atom, fragment) to control over contribution of the object into overal 

system.

It is not done by default but with a little API programming you can do this:

Attach "weight" property to the molecules in question, calculate the molecular formula for each molecule and do your suggested weight calculation.

We have fixed the bug. Marvin version 5.10 will contain the fix.

Thank you for the report.

Could you be a little bit more specific about your solution using API? Are your going to add this feature in the next realize or such functionality is available in ealrier realises?

Thank you.

PS.

 

I draw ferrocene molecule with bonds between Fe 

and centroid of the Cp ring. I used Add->Multicenter function to add 

dummy atom and than i made bond between Fe and centroid (ferrocene.mrv).

 Picture looks very nice but if we calculate elemental analysis i got 

very strange numbers: C10H8Fe.

Marvin 5.10 will contain this fix. The new result is Formula = C10H10Fe.

Very often if you work with elemental analysis
you need 0.5 molecule of solvent (H2O, CH2Cl2, etc). Is there any way we
 can use to do this? If no, can we add tag "weight" for each object
(Atom, fragment) to control over contribution of the object into overal
system.

We have no general solution for this problem, but you can do it easily using API. Do you give it a try or shall I drop a code snippet?