how to get formula at certain pH?

Hello!

i am dealing with some compounds at pH8 while i already have the SMILES for each compound. Is there any way i could get the according formula at that pH with marvin commandline programs?? Or maybe i should just add or take away hydrogen atoms from the formula.

THX!

You can use Chemical Terms Evaluator to do this.

Examples:

$ evaluate -e 'formula(majorms("2.0"))' "CCCCN"
C4H12N

$ evaluate -e 'formula(majorms("12.0"))' "CCCCN"
C4H11N

Examples show how to return formula at pH 2 and pH 12.

$ evaluate -e 'formula(majorms("2.0"))' "CCCCN"
C4H12N

$ evaluate -e 'formula(majorms("12.0"))' "CCCCN"
C4H11N

it doesn't work. i type in the example and it only returns

formula(majorms(2.0))

is it a new function developed in the latest version of marvin? i downloaded the software some time ago.

No it's not new. Did you use the quotation marks in the command? Please copy here the text from your console,  include the command and the result as well.

Yes i just copied the example and paste it in my commandline. here is the result:

C:\Documents and Settings\Administrator>evaluate -e 'formula(majorms("2.0"))' "CCCN"

formula(majorms(2.0))

Thanks!

Please use this command, it will work on Windows OS:

evaluate -e "formula(majorms('2.0'))" "CCCN"
C3H10N

yeah it works correctly this time. Thanks a lot !!