From owner-chemistry@ccl.net Tue Sep 7 01:55:00 2010 From: "Michael K. Gilson mgilson-#-ucsd.edu" To: CCL Subject: CCL:G: Gsolv - pKa - Frequency Message-Id: <-42707-100907012752-24582-7ifhLpRcCvaY1Y8Njd4kVw(~)server.ccl.net> X-Original-From: "Michael K. Gilson" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Mon, 06 Sep 2010 07:53:36 -0700 MIME-Version: 1.0 Sent to CCL by: "Michael K. Gilson" [mgilson_-_ucsd.edu] I agree with Andreas that, if an implicit solvent model already implicitly accounts for changes in vibrational entropy on solvation, one needs to be careful about double-counting this contribution. just for completeness, I'd mention that, when the solute is really flexible, as for a peptide, one would still want to think about possible changes in entropy due to shifts in conformational distributions due to solvation. Regards, Mike On 9/6/2010 12:07 AM, Andreas Klamt klamt**cosmologic.de wrote: > Sent to CCL by: Andreas Klamt [klamt,+,cosmologic.de] > Hi all together, > > I think that Chris is quite right in most of his arguments, and > definitely Mike is right as well in saying that the partial molar > entropy is thermodynamically well defined and that it can be > considerably different in solution compared to the ideal gas. > > But this difference is to first order already implicitly parameterized > into every continuum solvation model that is parameterized versus exp. > dG_solv. data. Since these data do include the entropy change, the > latter is also implicitly included into the parameterized solvation > models, not based on a frequency change, but via surface proportional > corrections. > > If you try to add the same via frequency based corrections (which are > not well defined, as I mentioned earlier and as Chris mentioned in > detail), you can only make things worse! > > In a solvation model which takes into account temperature dependence, as > in COSMO-RS, you can quantify the included partial molar entropy of > solvation based on the temperature derivative of dG_solv. > > If you would like to develop a solvation model which is open for the > explicit addition of solvation entropy, you would have to do that based > on the the enthalpy (heat) of solvation, but there are much less exp. > data available for dH-solv than for dG_solv, and few people are > interested in dH_solv. The only situation for which lots of well measure > dG_solv ad dH_solv data are available, is self-solvation, which is > nothing else than free energy of vaporization (i.e. ln(vapor pressure) > and heat of vaporization). It should be noted that COSMO-RS describes > dG_vap and dH_vap consistently as self-solvation. > > Regarding your pKa problem (as for any reaction calculation) this means: > - Do the best gas phase calculation as you can afford, incl. gas-phase > entropy change, and then add the solvation free energies of educts and > products (with the right sign). > - Or use a parameterized pKa model directly based on the solution phase > energy difference of protonated and deprotonated species. > > Hope this helps. > > Andreas > > > > > > Am 05.09.2010 14:57, schrieb W Flak williamflak- -yahoo.com: >> Sent to CCL by: "W Flak" [williamflak]![yahoo.com] >> Dear CCL >> I got some questions about pKa calculation hoping to get a help here. >> * First of all, on G03 help page, it says Gsolvation=EPCMEgas, but if I >> compared delta Gsolv obtained by SCFVAC with those obtained by carrying out two >> separate jobs, I'd get difference. Why? >> Example: >> by SCFVAC >> DeltaG (solv) (kcal/mol) = -10.26 >> By two separated jobs: >> deta Gsolv = Epcm - Egas = -15.49 >> >> * Is the entropy of a molecule in gas phase different from that in a solution? >> if yes, please direct me to the undergraduate book I should read >> >> * I read many posts on pKa calculation and found some people (as Andreas >> Klamt,2006) recommended not to include frequency in pKa calculation, and the >> others include it. What do you recommend? >> >> * In G.A.A. Saracino et al. / Chemical Physics Letters 373 (2003) 411415 >> Gibbs energies have been estimated by single point HF/6-31+G(d,p) calculations >> at geometries optimised in aqueous solution at the PBE0/6-31+G(d,p) level. How >> they calculated frequency at level differs from the optimization level? >> >> Any kind of help would be appreciated >> W. Flak> >> >> > -- Michael K. Gilson, M.D., Ph.D. Professor Skaggs School of Pharm. and Pharm. Sci. University of California San Diego 9500 Gilman Drive, MC 0736 La Jolla, California, 92093-0736 Office: 858-822-0622 http://pharmacy.ucsd.edu/faculty/Gilson.shtml From owner-chemistry@ccl.net Tue Sep 7 04:23:00 2010 From: "vsuresh kumarneelamraju nvskumar123=-=yahoo.co.in" To: CCL Subject: CCL:G: optimization H-bond distance with CT deleted Message-Id: <-42708-100907041904-25967-U5wW8XM+kg1oyiI5FXOQwg : server.ccl.net> X-Original-From: vsuresh kumarneelamraju Content-Type: multipart/alternative; boundary="0-1264747415-1283845934=:11615" Date: Tue, 7 Sep 2010 00:52:14 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: vsuresh kumarneelamraju [nvskumar123===yahoo.co.in] --0-1264747415-1283845934=:11615 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear CCL Members, I read the following lines in a paper titled " Intermolecular Interactions = > from a Natural Bond orbital, Donor-Acceptor Viewpoint" Alan E. Reed, L. A. = Curtiss, F. Weinhold, Chem. Rev. 1988, 899-926. Charge transfer interactions in hydrogen bonded complex allow molecules to = approach each other closely so that they penetrate van der Waals contact di= stance. To test this effect H-bond distance can be reoptimized with CT dele= ted.=20 My question is how can we reoptimize H-bond distance with out involving cha= rge transfer interaction.=A0 I am using Gaussian03. Can any body suggest ho= w do we perform this calculation.=20 N.V. Suresh Kumar pursuing PhD CCNSB, IIIT-H HYDERABAD=0A=0A --0-1264747415-1283845934=:11615 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Dear CCL Members,

I read the following= lines in a paper titled " Intermolecular Interactions from a Natural Bond = orbital, Donor-Acceptor Viewpoint" Alan E. Reed, L. A. Curtiss, F. Weinhold= , Chem. Rev. 1988, 899-926.

Charge transfer interactions in hydrogen= bonded complex allow molecules to approach each other closely so that they= penetrate van der Waals contact distance. To test this effect H-bond dista= nce can be reoptimized with CT deleted.

My question is how can we r= eoptimize H-bond distance with out involving charge transfer interaction.&n= bsp; I am using Gaussian03. Can any body suggest how do we perform this cal= culation.

N.V. Suresh Kumar
pursuing PhD
CCNSB, IIIT-H
HYD= ERABAD

--0-1264747415-1283845934=:11615-- From owner-chemistry@ccl.net Tue Sep 7 07:33:01 2010 From: "Rene Thomsen rt%molegro.com" To: CCL Subject: CCL: Structure presentation software Message-Id: <-42709-100907014232-19643-wKUB9Wm7NfEg8MHTN7gtYw(0)server.ccl.net> X-Original-From: Rene Thomsen Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 6 Sep 2010 16:59:13 +0200 MIME-Version: 1.0 Sent to CCL by: Rene Thomsen [rt*o*molegro.com] Dear W. Flak, You can also try out Molegro Molecular Viewer. It is a free cross-platform application for visualization of molecules with a built-in raytracer for making high-quality images. To download Molegro Molecular Viewer, please visit our company website at: http://www.molegro.com/mmv-product.php Kind regards, Rene Thomsen --- Molegro C. F. Moellers Alle 8, Bldg. 1110 DK-8000 Aarhus C Denmark www.molegro.com On Fri, Sep 3, 2010 at 7:18 AM, W. Flak williamflak_-_yahoo.com wrote: > > Sent to CCL by: "W.  Flak" [williamflak++yahoo.com] > Dear CCL > I was wondering which program do you use to present a protein structure in a > paper? > I use GaussView, but the picture looks sillly > Thanks in advance > W. Flak From owner-chemistry@ccl.net Tue Sep 7 08:08:00 2010 From: "Jack Young jayoung50^^aim.com" To: CCL Subject: CCL: NUMOL code Message-Id: <-42710-100907031134-24797-MmonEiKqA90YuluI7WZEag~!~server.ccl.net> X-Original-From: "Jack Young" Date: Tue, 7 Sep 2010 03:11:33 -0400 Sent to CCL by: "Jack Young" [jayoung50(a)aim.com] Dear all, Can anyone point me to the direction of the latest version of the basis set free program NUMOL by Becke and Dickinson? I tried searching google but no luck. Mant thanks. Best, Jack From owner-chemistry@ccl.net Tue Sep 7 12:17:01 2010 From: "Decai Yu decaiyu23(a)yahoo.com" To: CCL Subject: CCL:G: multiplicity for two fragments Message-Id: <-42711-100907111507-28417-ofpkhNDYzxiXdESuqv+NBA/a\server.ccl.net> X-Original-From: "Decai Yu" Date: Tue, 7 Sep 2010 11:15:06 -0400 Sent to CCL by: "Decai Yu" [decaiyu23 ~~ yahoo.com] Dear All, I am calculating the adsorption of Nitrogen Oxide to a transition metal ion (for example Mn). The NO has one unpaired electron, while Mn has five unpaired electrons. In such a case, how do I determine the multiplicity of the adsorbed structure. Shoud I use '0 7' or should I use '0 5' (considering they are antiferromagetic)? If the actual ground state is antiferromagnetic, should I follow the broken symmetry procedure as outlined in Gaussian? For the counterpoise calculations, should I use '0 5 0 6 0 2'? Any advice on these questions would be highly appreciated. Regards, Decai