JCMicrospeciesCount and majorms

Hi,

I am a new user to JChem and would like to calculate the major microspecies at a pH.

I wonder if the JCMicrospeciesCount in Excel performs the same function as majorms does in the command line. If no, is there an equivalent of majorms in JChem for Excel? If yes, how can I specify the desired pH value when I use JCMicrospeciesCount?

Thank you.

Hi Cleo, 

 

I think we already met so you cannot be new user ..

 

JCMicrospeciesCount 
Returns the number of microspecies. 

The isoelectric point (pI) is the pH at which a molecule carries no net electrical charge. The Isoelectric Point Plugin calculation considers all macro ionization states of an ionizable molecule across the pHrange. The net charge at given pH is calculated from the weighted sum of the macro distribution. 
Proteins have minimal solubility at their isoelectric point. The mobility of molecule is minimal at pI and so an important parameter for electroanalytical separation techniques. 

 

Viktor

Your  question is whether we have an overload of this function with an input parameter (pH)?

 

The other two parameters are also needed for you?

(keep explicit hyrdogens, take major tautomeric form)?

It looks like JCMicrospeciesCounts is different from what I thought.

 

What I want to do is simply obtain the chemical formula of some compounds at a certain pH, which is exactly what 'cxcalc majorms' does. I'm just looking for a way to do the same in Excel.

I understand that I can use the calculation plugin in Marvin for one compound, but unfortunately I have a lot of compounds to calculate the formula for. I am asking if there's any function in JChem which will allow me to do it all at once, rather than having to open Marvin, input pH, press OK for every single compound on the list.

Understood.

We need to add an overload for the present solution/function, which could accept the pH as a parameter.

Let me inform you tomorrow if this possible for the next week release.

 

 

Thank you, Viktor. It will be really helpful if it comes out in the release.

Hi Cleo,

We have a function called JCChemicalTerms, which is able to do calculations, which are available in ChemAxon's calculator plugins. I created a file, which contains this function with appropriate parameters for calculating the structure of major microspecies at a specific pH for a list of compounds.

Hope, this helps, but let me know if you have further questions or comments.

Anna

Anna,

The file you provided worked perfectly! Thank you.

However I can't seem to find the option 'majorMicrospecies' as an input to the function JCChemicalTerms in the online user guide (https://www.chemaxon.com/conf/JChem_for_Excel_User_Guide.pdf), and I'm wondering if there's an updated user guide, which documents the parameters that can be used in each function??

Thanks to all for replying to this thread.

Hi Cleo,

You can find the full list of functions available in chemical terms with parameters here:

https://docs.chemaxon.com/display/chemicalterms/Available+Functions

(Only a part of them is listed in JChem for Excel User's Guide, because you can find the full list here :-)

The syntax of the functions may be different when they are used in JChem for Excel, but in most of the cases, you only have to type the same string. But let me know, if you need help with this.

The documentation of how to apply Chemical Terms functions in JChem for Excel:

https://www.chemaxon.com/jchem4excel/userguide/chemical_terms.html

Anna