From owner-chemistry@ccl.net Wed Dec 10 03:31:01 2008 From: "Sebastian Kozuch kozuchs[-]yahoo.com" To: CCL Subject: CCL: translational entropy and solvation Message-Id: <-38271-081210031719-13035-+WuMetM5vo1ev41fxcB33A__server.ccl.net> X-Original-From: Sebastian Kozuch Content-Type: multipart/alternative; boundary="0-1573872474-1228896991=:80666" Date: Wed, 10 Dec 2008 00:16:31 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Sebastian Kozuch [kozuchs[#]yahoo.com] --0-1573872474-1228896991=:80666 Content-Type: text/plain; charset=us-ascii I wanted to make a small resume and add commentaries on this entropy of solvation topic. Some people (Purisima, Gilson) accurately state that the volume of the box is the same regardless of having or not a solvent in it, so ideally there should be no loss of translational entropy. I agree, although some claim that the accesible volume is reduced by the solvent. Others (Ribeiro) say that the partition function in a solvent is way to different to the Sackur-Tetrode gas phase translational entropy. I also agree. My physical chemistry university teachers told us that the solvent is reorganized around a solute molecule, and this means a loss of entropy. This effect should be considered when calculating the solvation free energy. Acording to this we should use gas phase free energy and add the solvation free energy. Sadly in most programs this doesn't work. As already posted the best values I could find are between gas phase energy and free energy. The solvent models are not good enough to account for this loss of entropy. This is clear when trying solvation at different temperatures, where the solvation free energy remains unchanged, something contrary to the free energy concept. Only molecular dynamic calculations take this into account, but this is impossible to achieve for most of quantum chemistry mortals like me. Klamt argues that COSMO-RS resolves this problem, but I have never worked with this model so I cannot comment. I'd love to see referencees or accurate data on this, but I got lost on the COSMO web page and couldn't find this information. If someone knows a paper that use this program and clearly details the solvation, please write down the cite. I want to add some referencees I could find on this, in case someone is interested. Theoretical works: (a) Tomasi, J; Persico, M. Chem. Rev. 1994, 94, 2027. (b) Tomasi, J. Theor. Chem. Acc. 2004, 112, 184. (c) Ben-Naim, A. J. Phys. Chem. 1978, 82, 792. Practical works: (a) Tamura, H.; Yamazaki, H.; Sato, H.; Sakaki, S. J. Am. Chem. Soc. 2003, 125, 16114. (b) Sakaki, S.; Takayama, T.; Sumimoto, M.; Sugimoto, M. J. Am. Chem. Soc. 2004, 126, 3332. (c) Sumimoto, M.; Iwane, N.; Takahama, T.; Sakaki, S. J. Am. Chem. Soc. 2004, 126, 10457. (d) Braga, A.; Ujaque, G.; Maseras, F. Organometallics 2006, 25, 3647. I hope I'm not making mistakes on all this issues. I'm not a specialist, I just want to be practical and as accurate as possible on my calculations. Finally I want to thank Luis Simon for starting this discussion. I feel I'm not alone in my doubts. xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx ..........Sebastian Kozuch........... xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx ...The Lise Meitner-Minerva Center... .for Computational Quantum Chemistry. ...Hebrew University of Jerusalem.... .....kozuchs/./yfaat.ch.huji.ac.il..... http://yfaat.ch.huji.ac.il/kozuch.htm xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx --0-1573872474-1228896991=:80666 Content-Type: text/html; charset=us-ascii

I wanted to make a small resume and add commentaries on this entropy of solvation topic. Some people (Purisima, Gilson) accurately state that the volume of the box is the same regardless of having or not a solvent in it, so ideally there should be no loss of translational entropy. I agree, although some claim that the accesible volume is reduced by the solvent. Others (Ribeiro) say that the partition function in a solvent is way to different to the Sackur-Tetrode gas phase translational entropy. I also agree. My physical chemistry university teachers told us that the solvent is reorganized around a solute molecule, and this means a loss of entropy. This effect should be considered when calculating the solvation free energy. Acording to this we should use gas phase free energy and add the solvation free energy.

Sadly in most programs this doesn't work. As already posted the best values I could find are between gas phase energy and free energy. The solvent models are not good enough to account for this loss of entropy. This is clear when trying solvation at different temperatures, where the solvation free energy remains unchanged, something contrary to the free energy concept. Only molecular dynamic calculations take this into account, but this is impossible to achieve for most of quantum chemistry mortals like me.

Klamt argues that COSMO-RS resolves this problem, but I have never worked with this model so I cannot comment. I'd love to see referencees or accurate data on this, but I got lost on the COSMO web page and couldn't find this information. If someone knows a paper that use this program and clearly details the solvation, please write down the cite.

I want to add some referencees I could find on this, in case someone is interested.
Theoretical works: (a) Tomasi, J; Persico, M. Chem. Rev. 1994, 94, 2027. (b) Tomasi, J. Theor. Chem. Acc. 2004, 112, 184. (c) Ben-Naim, A. J. Phys. Chem. 1978, 82, 792.
Practical works: (a) Tamura, H.; Yamazaki, H.; Sato, H.; Sakaki, S. J. Am. Chem. Soc. 2003, 125, 16114. (b) Sakaki, S.; Takayama, T.; Sumimoto, M.; Sugimoto, M. J. Am. Chem. Soc. 2004, 126, 3332. (c) Sumimoto, M.; Iwane, N.; Takahama, T.; Sakaki, S. J. Am. Chem. Soc. 2004, 126, 10457. (d) Braga, A.; Ujaque, G.; Maseras, F. Organometallics 2006, 25, 3647.

I hope I'm not making mistakes on all this issues. I'm not a specialist, I just want to be practical and as accurate as possible on my calculations.
Finally I want to thank Luis Simon for starting this discussion. I feel I'm not alone in my doubts.
 
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
..........Sebastian Kozuch...........
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
...The Lise Meitner-Minerva Center...
.for Computational Quantum Chemistry.
...Hebrew University of Jerusalem....
.....kozuchs/./yfaat.ch.huji.ac.il.....
http://yfaat.ch.huji.ac.il/kozuch.htm
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx


--0-1573872474-1228896991=:80666-- From owner-chemistry@ccl.net Wed Dec 10 05:46:00 2008 From: "Tristan Youngs t.youngs-*-qub.ac.uk" To: CCL Subject: CCL: Aten v1.0 released. Message-Id: <-38272-081210054513-18236-94+BrEb0MOhaIIfrZnCuNg(~)server.ccl.net> X-Original-From: "Tristan Youngs" Date: Wed, 10 Dec 2008 05:45:10 -0500 Sent to CCL by: "Tristan Youngs" [t.youngs===qub.ac.uk] Dear all, For your information, Aten v1.0 is now available from the new website at www.projectaten.net (.org and .com will point there in the next few weeks). Consider this an early Christmas gift designed to help with your input preparation, coordinate generation, and visualisation (but without a receipt). The code is generally more rounded and stable, but of course suggestions and bug reports are always most welcome. www.projectaten.net is the place to air your views, ask for help, or even offer a helping hand should the need overtake you. Best regards, Tris. From owner-chemistry@ccl.net Wed Dec 10 09:56:01 2008 From: "Vjeran Gomzi vgomzi#,#irb.hr" To: CCL Subject: CCL:G: G03: Is it possible to actually RESTART job at a definite step? Message-Id: <-38273-081210060403-26320-N+L5B/xwtZYyb9E0zwVpxg-#-server.ccl.net> X-Original-From: "Vjeran Gomzi" Date: Wed, 10 Dec 2008 06:03:59 -0500 Sent to CCL by: "Vjeran Gomzi" [vgomzi~!~irb.hr] Dear CClers, I have found myself confused, since it seems that the restart option to Opt keyword only knows how to take the last step and then try to continue the optimization. This is not very useful in the cases in which one would like to restart the job from some previous geometry, but not erase all the previous steps from optimization. Which is probably done by using Opt (without restart) and Geom=(check, step=N). Specifically, the problem is, if I use the latter option, would the optimization still take into account the previous (good or bad) steps in the optimization? If that is not the case, it it possible at all within G03 Optimizations? How? Thank You for any information whatsoever, Vjeran Gomzi, PhD OCB Dept, QOC Group Rudjer Boskovic Institute, Zagreb, CROATIA From owner-chemistry@ccl.net Wed Dec 10 13:10:01 2008 From: "Ben Vail p26j3[-]unb.ca" To: CCL Subject: CCL:G: PM3 on pure boron clusters Message-Id: <-38274-081210103209-18149-WHMdOwdiAMMuaDJQp+4Mzg!=!server.ccl.net> X-Original-From: "Ben Vail" Date: Wed, 10 Dec 2008 10:32:06 -0500 Sent to CCL by: "Ben Vail" [p26j3_-_unb.ca] Hi, I'm trying to run some PM3 calculations using Gaussian 03 on various sized pure boron clusters, but it seems like it doesn't have the parameters to do these calculations. Any help on how to make it work would be greatly appreciated. Thanks, Ben From owner-chemistry@ccl.net Wed Dec 10 14:21:01 2008 From: "Sahar Shamseldden ABDALLA sahar_shams20#,#hotmail.com" To: CCL Subject: CCL: error termination in scrf calculation usin G03 Message-Id: <-38275-081210141508-18202-g+bOJAsHUFZje39bJoPcpg#,#server.ccl.net> X-Original-From: "Sahar Shamseldden ABDALLA" Date: Wed, 10 Dec 2008 14:15:05 -0500 Sent to CCL by: "Sahar Shamseldden ABDALLA" [sahar_shams20]~[hotmail.com] Dear all, I am trying to calculate the energy and vibrational frequency for some subistituted five member rings using b3lyp/6-31G+(d,p)scrf=(pcm,solvent water,read) as keywords. I only change the radii form UAO as default to UFF.The calcutions wer verg good , but when i add few water molecules in the molecular cavity i faced problem and the calculation ended with errors such as following the errors as described below. Although I can restart the crashed calculations and some times after restart calculations can finish, many times it gives one of these errors again. I already have optimized these structures in gas phase without any problem. I will be very grateful if someone can help me to understand at least one or more of these errors. The errors are as follows. error 1 Inv2 failed in DMIVCL. Error termination via Lnk1e error2 AdVTs1: ISph= 1182 is engulfed by JSph= 1182 but Ae( 1181) is not yet zero! Error termination via Lnk1e error-3 Excessive number of vertices on a tessera. Error termination via Lnk1e error-4 BldSpC: Error generating genealogic tree for sphere 281 at level 15 Error termination via Lnk1e From owner-chemistry@ccl.net Wed Dec 10 19:40:00 2008 From: "John McKelvey jmmckel\a/gmail.com" To: CCL Subject: CCL:G: PM3 on pure boron clusters Message-Id: <-38276-081210183515-31487-j8ppfD0XmOM3I47Sop+tSQ(0)server.ccl.net> X-Original-From: "John McKelvey" Content-Type: multipart/alternative; boundary="----=_Part_77763_20145411.1228952101360" Date: Wed, 10 Dec 2008 18:35:01 -0500 MIME-Version: 1.0 Sent to CCL by: "John McKelvey" [jmmckel[#]gmail.com] ------=_Part_77763_20145411.1228952101360 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Try PM6 in the newest MOPAC.. free to academics.. Google "mrmopac" to get info.. John McKelvey On Wed, Dec 10, 2008 at 10:32 AM, Ben Vail p26j3[-]unb.ca < owner-chemistry###ccl.net> wrote: > > Sent to CCL by: "Ben Vail" [p26j3_-_unb.ca] > Hi, I'm trying to run some PM3 calculations using Gaussian 03 on various > sized pure boron clusters, but it seems like it doesn't have the parameters > to do these calculations. Any help on how to make it work would be greatly > appreciated. > Thanks, > Ben> > > ------=_Part_77763_20145411.1228952101360 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Try PM6 in the newest MOPAC.. free to academics..  Google "mrmopac" to get info..

John McKelvey

On Wed, Dec 10, 2008 at 10:32 AM, Ben Vail p26j3[-]unb.ca <owner-chemistry###ccl.net> wrote:

Sent to CCL by: "Ben  Vail" [p26j3_-_unb.ca]
Hi, I'm trying to run some PM3 calculations using Gaussian 03 on various sized pure boron clusters, but it seems like it doesn't have the parameters to do these calculations. Any help on how to make it work would be greatly appreciated.
Thanks,
Ben



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