Subject: Effects of pH - summary

From: "Mire Zloh" <[email-masked]>
Date: Sun, 16 Dec 2001 17:42:53 -0000

Dear all,

thanks to all who answered my question regarding the studies of pH effects on quantum-chemistry
 calculations.
I am a bit wiser, although there is no strightforward solutions and more investigations into this problem are necessary. 

Best regards,

Mire

From: "Shobe, Dave" <[email-masked]>

Solution studies are still pretty crude at this point (usually just the
dielectric constant of the solvent is modeled), and I don't think you could
study the effects of pH using these.  One might be able to estimate the pKa
of the molecule, but that's about it.  
 
Molecular dynamics is a completely different story, because there you
explicitly add solvent molecules (and can have a certain "concentration" of
them protonated or deprotonated).  But the sacrifice is that the
representation of the molecules are fairly crude, and you will get very
little in the way of "electronic properties".  
 
If someone actually suggests a way of doing what you want I would be
interested in hearing about it.

----- Original Message ----- 
From: "Amiram Goldblum" <[email-masked]>

 Maybe I can help a little, but I never used Gamess or MOPAC,
 while I have much experience with MNDO (which has been part of MOPAC).
 
 One way is to study the direct protonation of the molecule, but this can
 not be done partially. I am not aware of any such applications,
 to study continous effects of pH variations on properties,
 but maybe you could just keep  a proton (or oxonium)
 at varying distances from your molecule in different
 directions (or maybe a few protons) and recalculate. That would have
 a differential polarizing effect . In ab initio you will have to
 take care of the Basis Set Superposition Error (BSSE) - there's
 quite a lot written about that. The strategy
 may strongly depend on the structure of your molecules.
 
 Many years ago, in the end of the 70's and the during the 80's,
 Steve Scheiner had a series of papers on the effects of protonation
 and external charges on molecules. It was really impressive work,
 done by ab initio mostly. Maybe you should look for them.

 The average distance of protons is the main effect of pH. You could
 calculate it from the concentration (probably will be very remote...).

From: "Robinson, James" <[email-masked]>

 Umm good, errr.. crumbs, I usually add protons or remove them  for the
 appropriate species. AS for a general pH affect, crumbs.. How about adding
 H3O+ or OH- in the environment? Or adjust the dielectric constant for acid
 or basic media. Cant really think of anything else.