From owner-chemistry@ccl.net Mon Jun  8 03:00:00 2009
From: "Andreas Klamt klamt||cosmologic.de" <owner-chemistry~~server.ccl.net>
To: CCL
Subject: CCL: PH-dependent ab-initio calculations
Message-Id: <-39465-090608014819-6154-OIx7Prv3tRih/ECs50966w~~server.ccl.net>
X-Original-From: Andreas Klamt <klamt/a\cosmologic.de>
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Date: Mon, 08 Jun 2009 07:47:27 +0200
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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),=20
> the pH of solvent has no influence on the properties of the molecule?=20
> Or maybe some but limited influence? If otherwise what kind of=20
> 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=20
> proteins, other than adding/subtracting H+/OH- to the chemical=20
> structure of the molecules (and the subsequent changes in structures=20
> 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=20
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=20
> <http://cosmologic.de> <owner-chemistry(!)ccl.net=20
> <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 spec=
ies
>     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 ar=
e
>     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 mode=
l,
>     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 th=
e
>     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
>
>
>
>     --=20
>     PD. Dr. Andreas Klamt
>     CEO / Geschaeftsf=FChrer
>     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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>


--=20
PD. Dr. Andreas Klamt
CEO / Geschaeftsf=FChrer
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