From owner-chemistry@ccl.net Mon Dec 8 05:47:01 2008
From: "Wolfram Altenhofen wolfram(0)chemcomp.com" <owner-chemistry^server.ccl.net>
To: CCL
Subject: CCL: Upcoming MOE Training Courses in Europe in Spring 2009
Message-Id: <-38260-081208053641-31491-FTXi51Bp2IOE0vnDhT/gXA^server.ccl.net>
X-Original-From: "Wolfram Altenhofen" <wolfram**chemcomp.com>
Date: Mon, 8 Dec 2008 05:36:37 -0500
Sent to CCL by: "Wolfram Altenhofen" [wolfram%x%chemcomp.com]
Chemical Computing Group is pleased to annouce the following MOE training
courses offered in Europe during Spring 2009:
* Feb 4th - 6th hosted by the University of Leuven, Belgium
* Feb 16th - 18th hosted by the CESCA, Barcelona, Spain
* March 2nd - 4th hosted by the University of Bonn, Germany
* April 27th - 29th hosted by the University of Strasbourg, France
The first two days will cover MOE applications focusing on
Small Molecule Modeling, HTS Analysis, SAR and QSAR, Library Design (day one)
and Protein Modeling and Structure Basd Design (day two)
Day three offers an introduction to CCG's Scientific Vector Language (SVL).
In all cases the content will be tuned to match the requirements and level of experience of the attendees as much as possible.
The courses are free of charge, refreshments are included; food and
accommodation have to be organized and covered individually.
Should you feel that someone else in your group would be more interested but
may not have received this mail, please feel free to forward.
For further questions and to register please contact Tracey Nixon
(tnixon[a]chemcomp.com or +44 1223 422319) at the Cambridge CCG office.
We look forward to welcome you,
Dr. Wolfram Altenhofen
Director of Scientific Services
Chemical Computing Group
AG Kaiser-Wilhelm-Ring 11
50672 Koeln
Germany
From owner-chemistry@ccl.net Mon Dec 8 06:22:00 2008
From: "Pierre Archirel pierre.archirel{=}lcp.u-psud.fr" <owner-chemistry[*]server.ccl.net>
To: CCL
Subject: CCL: translational entrpy in solvent
Message-Id: <-38261-081205121324-11149-I2y4EO06zp0fYAceLc81kg[*]server.ccl.net>
X-Original-From: Pierre Archirel <pierre.archirel-,-lcp.u-psud.fr>
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Date: Fri, 05 Dec 2008 17:31:46 +0100
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Sent to CCL by: Pierre Archirel [pierre.archirel+/-lcp.u-psud.fr]
Dear colleagues,
1- I wonder that your disputation makes no reference to densities of
states...
Translation entropy in solution should be smaller than in the vacuum
because due to caging
effects the density of states decreases. The same should be true for
rotation.
Actually both vacuum translation and rotation become vibrations of the
global system,
it can be in principle evaluated with harmonic analysis of the solute +
1 solvent shell system.
2- I summit the following test to your commentaries:
take the two reactions A+A->A2 and A2->A+A in the gas phase:
each of the three species has -TStrans=-0.5 eV at 300K (it only weakly
depends on masses)
Hence in the first case Delta(-TStrans) amounts to +0.5 eV, in the
second case to -0.5 eV
This means that in the gas phase translation entropy always tends to
inhibate association
and to favor dissociation.
THIS HAS BEEN EXPERIMENTALLY VERIFIED
(see for example S. Le Caer et al, PCCP 4 1855-1865 (2002))
3- Is there any clue that this general law is true in solution? 0.5eV
is huge!
My current PCM calculations suggest that it is false, I best compare to
experiment
when simply adding vacuum vibrational free energies to PCM electrostatic and
non electrostatic solvation free energies.
This means that the translation entropy probably behaves like in the
vacuum, but with
much smaller values, not 0.5 eV!!
Any comment will be appreciated.
Pierre Archirel
LCP, bat 349
Universite Paris-Sud
Orsay, France
__________________________________________________________
Pierre Archirel
Groupe de Chimie Th�orique
Laboratoire de Chimie Physique Tel: 01 69 15 63 86
Bat 349 Fax: 01 69 15 61 88
91405 Orsay Cedex
France pierre.archirel:-:lcp.u-psud.fr
__________________________________________________________
From owner-chemistry@ccl.net Mon Dec 8 13:59:01 2008
From: "Raphael Ribeiro raphaelri(-)hotmail.com" <owner-chemistry:server.ccl.net>
To: CCL
Subject: CCL: translational entropy in solvent
Message-Id: <-38262-081208135819-1181-8kYPQipGRdZwBT9ElcxU0A:server.ccl.net>
X-Original-From: "Raphael Ribeiro" <raphaelri(a)hotmail.com>
Date: Mon, 8 Dec 2008 13:58:16 -0500
Sent to CCL by: "Raphael Ribeiro" [raphaelri%%hotmail.com]
Dear Pierre,
It is quite obvious that the translational entropy changes while going from the ideal gas phase to a solvated phase. What is also obvious in my opinion is that the translational/rotational/vibrational components of free energy (and also entropy) calculated using implicit solvents are not going to reproduce the quantities from the real system in a good way. I've said earlier that one of the biggest failures of the implicit solvent models is that they do not represent in a true way the phase space of the system. The density of states calculated using the implicit model for solvation does not represent the reality at all, and that is why it is not a good idea to calculate components of the free energy with PCM, COSMO, etc.
Also, in most of the implicit models there are empirical parameters (in the non-electrostatic contributions) which are not physical. Implicit solvation models were created to give nice solvation free energies (as a whole) and that is why they are in most of the times not suitable to reproduce other physical properties in a good way.
For your association/dissociation problem I recommend you the following article: http://biophysics.med.jhmi.edu/amzel/people/siebert/strsl_2col_bw_letter.pdf
In this article the authors create a model for calculating the loss of translational entropy in associations accurately. They use molecular dynamics.
The last thing to say is that the free energy of solvation generated by implicit solvent models already include all of the components of the free energy (free energy of solvation = free energy of the solvated phase system - free energy of the gas phase system) and as Andreas Klamt already remarked, the addition of translational, rotational and vibrational free energy contributions in solutions will lead to double counting of effects already implicitly taken into account in solvation models and are not recommended at all.
Raphael Ribeiro
From owner-chemistry@ccl.net Mon Dec 8 16:25:01 2008
From: "Sebastian Kozuch kozuchs!^!yahoo.com" <owner-chemistry---server.ccl.net>
To: CCL
Subject: CCL:G: Translational entropy in solvent
Message-Id: <-38263-081208143036-17639-IswKAodyLVcrj0lj7gdZkg---server.ccl.net>
X-Original-From: Sebastian Kozuch <kozuchs-,-yahoo.com>
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Date: Mon, 8 Dec 2008 10:30:19 -0800 (PST)
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Sent to CCL by: Sebastian Kozuch [kozuchs{}yahoo.com]
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Dear CCLers:
The problem of the entropy component in solvent was tackled for instance in J. Am. Chem. Soc. 2004, 126, 10457 and Organometallics 2006, 25, 3647 by simply deleting the rotational and translational entropy. This extreme approach can be sometimes more accurate than putting all the free energy components in the same basket with the solvation. Comparing my simple gaussian values with the more accurate ones of J. Chem Phys 107, 1997, 1981, convinced me that for charged molecules in high dielectric solvents it's better to delete the entropy in gas phase.
For a Ni neutral complex in THF solvent I found that the accurate values where roughly in the middle between full free energy and E+ZPE. This compared to experimental values and considering my DFT calculations accurate enough. Clearly gaussian overestimates the translational and rotational entropies. It would have been nice a manual that explains this behaviour. I've heard of programs that correct this, but still I couldn't find a good manual for them also.
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
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<div style="font-family: arial,helvetica,sans-serif; font-size: 10pt;">Dear CCLers:<br>The problem of the entropy component in solvent was tackled for instance in J. Am. Chem. Soc. 2004, 126, 10457 and Organometallics 2006, 25, 3647 by simply deleting the rotational and translational entropy. This extreme approach can be sometimes more accurate than putting all the free energy components in the same basket with the solvation. Comparing my simple gaussian values with the more accurate ones of J. Chem Phys 107, 1997, 1981, convinced me that for charged molecules in high dielectric solvents it's better to delete the entropy in gas phase.<br>For a Ni neutral complex in THF solvent I found that the accurate values where roughly in the middle between full free energy and E+ZPE. This compared to experimental values and considering my DFT calculations accurate enough. Clearly gaussian overestimates the translational and rotational entropies. It would have been
nice a manual that explains this behaviour. I've heard of programs that correct this, but still I couldn't find a good manual for them also.<br><br><div> </div><span style="font-family: courier,monaco,monospace,sans-serif;">xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx</span><br style="font-family: courier,monaco,monospace,sans-serif;"><span style="font-family: courier,monaco,monospace,sans-serif;">..........Sebastian Kozuch...........</span><br style="font-family: courier,monaco,monospace,sans-serif;"><span style="font-family: courier,monaco,monospace,sans-serif;">xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx</span><br style="font-family: courier,monaco,monospace,sans-serif;"><span style="font-family: courier,monaco,monospace,sans-serif;">...The Lise Meitner-Minerva Center...</span><br style="font-family: courier,monaco,monospace,sans-serif;"><span style="font-family: courier,monaco,monospace,sans-serif;">.for Computational Quantum Chemistry.</span><br
style="font-family: courier,monaco,monospace,sans-serif;"><span style="font-family: courier,monaco,monospace,sans-serif;">...Hebrew University of Jerusalem....</span><br style="font-family: courier,monaco,monospace,sans-serif;"><span style="font-family: courier,monaco,monospace,sans-serif;">.....kozuchs_-_yfaat.ch.huji.ac.il.....</span><br style="font-family: courier,monaco,monospace,sans-serif;"><a rel="nofollow" target="_blank" href="http://yfaat.ch.huji.ac.il/kozuch.htm"><span style="font-family: courier,monaco,monospace,sans-serif;">http://yfaat.ch.huji.ac.il/kozuch.htm</span></a><br style="font-family: courier,monaco,monospace,sans-serif;"><span style="font-family: courier,monaco,monospace,sans-serif;">xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx</span><div><br></div></div></div><br>
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