CCL: PH-dependent ab-initio calculations



 Sent to CCL by: Andreas Klamt [klamt. a .cosmologic.de]
 Dear Yutao Yue,
 
just upfront: COSMOtherm is the name of our COSMO-RS program. The theory itslef has the name COSMO-RS. Just to avoid confusion.
 Let me try to answer your further questions:
 
Is it true that for those molecules without any chance of grabbing and releasing H+ (protonation state) or OH- (not sure how to name that), the pH of solvent has no influence on the properties of the molecule? Or maybe some but limited influence? If otherwise what kind of influence would it be? (I assume that solvent are always neutral while separate charges H3O+ and OH- have very low concentration comparing to the solvent itself)
 Yes, that is true.
 
On the other hand, for molecules like individual amino acids or proteins, other than adding/subtracting H+/OH- to the chemical structure of the molecules (and the subsequent changes in structures and other properties), are there any other significant influence of pH on the molecules?
Even for amino acids and proteins: The pH influences the balance of the different protonation forms. This then has an influence on the structure and properties.
 Andreas
 
 
Sorry for bringing up more questions and I really appreciate your time and help.
 Regards,
 Yutao Yue
 
On Fri, Jun 5, 2009 at 2:19 AM, Andreas Klamt klamt++cosmologic.de <http://cosmologic.de>; <owner-chemistry(!)ccl.net <mailto:owner-chemistry%28%21%29ccl.net>> wrote:
     Sent to CCL by: Andreas Klamt [klamt(a)cosmologic.de
     <http://cosmologic.de>;]
     Dear Yutao,
     pH-dependent ab-initio calculations in general are impossible. The
     pH of
     the solvent does change the equilibrium between protonated and
     deprotonated species, but you will always have to decide which species
     you want to consider in your ab-initio calculation. (in the
     following I
     assume that you mean generally QM methods, including DFT, when you say
     ab-initio). Beyond the H3O+ and OH- concentrations, which anyway are
     very small, the pH does not change the solvent properties
     significantly.
     I.e. what you need to do is to calculate the protonated and
     deprotonated
     species in your solvent (usually water) using a good solvation model,
     calculate the pKa from the free energy difference of both solvated
     species, and then calculate the population of the species at a
     given pH.
     Our COSMOtherm program in combination with a QM propgram being able to
     write the required DFT/COSMO files, e.g. TURBOMOLE, does provide the
     infrastructure to do so, not only in water but in any solvent.
     Andreas
     Yutao Yue Yutao.Yue*_*gmail.com <http://gmail.com>; schrieb:
         Sent to CCL by: "Yutao  Yue" [Yutao.Yue^_^gmail.com
         <http://gmail.com>;]
         Hello dear friends, does anybody know how to do an ab-initio
         calculation of a molecular system under a certain PH value?
         Has there been much development on PH-dependent ab-initio
         methods? Maybe some PH-dependent empirical methods? Thanks for
         any information.
         Regards,
         Yutao Yue
 
-- PD. Dr. Andreas Klamt
     CEO / Geschaeftsführer
     COSMOlogic GmbH & Co. KG
     Burscheider Strasse 515
     D-51381 Leverkusen, Germany
     phone   +49-2171-731681
     fax     +49-2171-731689
     e-mail  klamt|*|cosmologic.de <http://cosmologic.de>;
     web     www.cosmologic.de <http://www.cosmologic.de>;
     HRA 20653 Landgericht Koeln, GF: Dr. Andreas Klamt
     Komplementaer: COSMOlogic Verwaltungs GmbH
     HRB 49501 Landgericht Koeln, GF: Dr. Andreas Klamt
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 --
 PD. Dr. Andreas Klamt
 CEO / Geschaeftsführer
 COSMOlogic GmbH & Co. KG
 Burscheider Strasse 515
 D-51381 Leverkusen, Germany
 phone  	+49-2171-731681
 fax    	+49-2171-731689
 e-mail 	klamt a cosmologic.de
 web    	www.cosmologic.de
 HRA 20653 Landgericht Koeln, GF: Dr. Andreas Klamt
 Komplementaer: COSMOlogic Verwaltungs GmbH
 HRB 49501 Landgericht Koeln, GF: Dr. Andreas Klamt