Formal Charge at pH using chemical terms

In cxcalc, it is possible to calculate the formal charge of a structure at a given pH. Unfortunately, this seems to be missing from the JChem chemical terms. 

Here you can provide a pH argument, but here you cannot pass in the pH option.

Is it possible to perform this calculation through the chemical term? I am trying to calculate this value through the web service we have setup (using the chemical terms API).

Thanks,

Craig

It can be done in Chemical Terms, here are some examples:

$ evaluate -e "formalCharge(majorMicrospecies('1.0'))" "NCC(O)=O"
1

$ evaluate -e "formalCharge(majorMicrospecies('7.4'))" "NCC(O)=O"
0

$ evaluate -e "formalCharge(majorMicrospecies('11.0'))" "NCC(O)=O"
-1

The parameter of the formalCharge() function can be the major microspecies of a molecule generated by the majorMicrospecies() function.

 

Dear ChemAxon Team/ users

Is it possible to calculate the formal charge of a compound using JChemWebservices? What are the parameters?

 

1) I have tried the following options. However, all I get is the structure as a result. I would like to stick with JchemWebservices, instead of importing Chemical Terms or calling cxcalc or any other library. Could you please help here?

"include": ["cd_id","charge"],

"parameters":{

    "formalCharge": {

"type": "TOTAL",

"implicitHydrogens": true,

"takeResonantStructures": true,

"takeMicrospecies": false

}

 

2) Regarding zwitterions: Is it OK to say that a zwitterion must have: (i) an isoelectic point AND (ii) a formal charge = 0?

 

Thanks,

MrYan 

Hi MrYan,

The current version of the "charge" calculator in the Web Services does not contain formalCharge, but you can access it through chemical terms with a request like this:

{
    "include": ["cd_id"],
    "additionalFields": {
            "formalCharge": "chemicalTerms(formalCharge)"
		}
}

or you can add this to your original request:

 {
    "include": ["cd_id","charge"],
    "additionalFields": {
            "logp": "chemicalTerms(formalCharge)"
		},
	"parameters":{
		"charge": {
			"type": "TOTAL",
			"implicitHydrogens": true,	
			"takeResonantStructures": true,
			"takeMicrospecies": false
		}
	}
}

Regards,
Peter