"One thing to consider is that PCM type models are = parameterized models, and the values of the parameters have been derived = to fit experiments, _without_ an explicit first solvation shell. A large = fraction of solvation is the first shell, and that has been absorbed by = the parameters. Introducing an explicit solvation shell and then put a = PCM on top of that may therefore give you a kind of double counting. Of = course the cavity changes, and there are the usual problems of electron = density outside the cavity, etc.... In short, there is a risk that the = results will _deteriorate_ when putting in an explicit first solvation = shell.
I am not aware of any study = where the performance of PCM type models where the first solvation shell = is considered explicitly, but if you find any, I would appreciate the = reference(s). In principle such an approach should be able to provide = more accurate results than a pure continuum model, but the PCM = parameters may have to be returned. This, of course, is not trivial, and = the optimal set of parameters may depend on which method you use for the = solvent molecules (HF, DFT, MP2, etc). Sorting this out should keep you = busy for a while ;-)"

Rare for me to disagree with Frank, but I = would say that, if you "materialize" a solvent molecule out of the = continuum, your results should not change if you are using a decent = continuum model. The exception to this rule is simple -- when the = solvent molecule being materialized is in fact not behaving at all like = a solvent molecule, but instead is part of a supersolute because it = enjoys some uniquely strong interaction with the solute. There are many = examples of this, e.g., the first coordination shell of highly charged = monatomic ions (where, indeed, we do not refer to the ion as an isolated = species, but as an aquo complex, if the solvent is water, for example). = Or, again using water because it is simple, an organic molecule with a = hydrogen bond donor and an acceptor separated by exactly one water = molecule's width (i.e., that water snuggles right in there and becomes = an intimate part of the molecule, not a typical solvent).

It is true that good continuum models are parameterized to = account for the deviation of the first shell from bulk electrostatic = behavior. But, of course, if they ARE good then the materialization of = the solvent molecule (or the "explicitization", if you will) covers the = surface area being excluded with exactly the effects that the model is = losing, and exposes new first-shell area (the area about the new piece = of the supersolute) that itself will now have first solvation shell = effects. Way, way back in 1992 we considered this to be an important = test for a solvation model, and we showed, for instance, that the = aqueous solvation free energy for piperidine using the SM2 and SM3 = solvation models remained unaffected by materializing first one and then = a second water molecule, hydrogen bonding to the two secondary amine = groups. (Of course, one must use the proper thermodynamic cycle to = evaluate this, where the sum of the gas-phase free energy of = complexation plus the free energy of continuum solvation for the cluster = must equal the sum of the solvation free energies of the isolated solute = and isolated water molecules.) See=A0Cramer, C. J.; Truhlar, D. G. "Comparative = Analysis of the AM1-SM2 and PM3-SM3 Parametrized SCF Solvation Models = for Free Energies in Aqueous Solution" J. Comput.-Aid. = Mol. Des. = 1992, 6, 629.

More recently, we have = evaluated this in the context of our latest solvation model, SM6, where = we showed that it is indeed important to materialize at leat one water = in order to compute accurate solvation free energies for ions having = concentrated charge, and that adding more waters did not have much = effect when the charge was only +/- 1. See=A0Kelly, C. P.; = Cramer, C. J.; Truhlar, D. G. "Aqueous Solvation Free Energies of Ions = and Ion-Water Clusters Based on An Accurate Value for the Absolute = Aqueous Solvation Free Energy of the Proton" J. Phys. Chem. = B = 2006, 110, 16066. and its precursor=A0Kelly, C. P.; = Cramer, C. J.; Truhlar, D. G. "SM6: A Density Functional Theory = Continuum Solvation Model for Calculating Aqueous Solvation Free = Energies of Neutrals, Ions, and Solute-Water Clusters" J. Chem. = Theory Comput. 2005, 1, 1133.

And, finally, if I may = plagiarize myself (assuming Wiley will be reluctant to sue me), Section = 12.5.4 of Essentials of Computational Chemistry, entitled Mixed = Explicit/Implicit Models opines:

Having identified the strongest points of the = explicit and implicit solvent models, it seems an obvious step to try to = combine them in a way that takes advantage of the strengths of each. For = instance, to the extent first-solvation-shell effects are qualitatively = different from those deriving from the bulk, one might choose to include = the first solvation shell explicitly and model the remainder of the = system with a continuum (see, for instance, Chalmet, Rinaldi, and = Ruiz-Lopez, 2001).
There are certain = instances where this approach may be regarded as an attractive option. = For example, Cossi and Crescenzi (2003) found that accurate computation = of 17O NMR chemical shifts for alcohols, ethers, and carbonyls in = aqueous solution required at least one explicit solvent shell, but that = beyond that shell a continuum could be used to replace what would = otherwise be a need for a much larger cluster. However, just as the = strengths of the two models are combined, so are the weaknesses. A = typical first shell of solvent for a small molecule may be expected to = be composed of a dozen or so solvent molecules. The resulting = supermolecular cluster will inevitably be characterized by a large = number of accessible structures that are local minima on the cluster = PES, so that statistical sampling will have to be undertaken to obtain a = proper equilibrium distribution. Thus, QM methods require a substantial = investment of computational resources. In addition, certain technical = points require attention, e.g., how does one keep the first solvent = shell from =91exchanging=92 with the continuum since both, in principle, = foster identical solvation interactions?
So,= while there is growing interest in hybrid models of all sorts (as = discussed in more detail in the next chapter), the choice of a mixed = solvent model is not necessarily intrinsically better than a pure = explicit or pure implicit model. In general, unless there is a strong = suspicion that first-solvation-shell effects are drastically different = > from those more typically encountered, there is no particularly = compelling reason to pursue a mixed modeling strategy. An example of = such a situation might be the aqueous coordination sphere surrounding a = highly charged metal cation. In that case, the electrostriction of the = first shell makes the water molecules more ligand-like than = solvent-like, and their explicit inclusion in the solute complex is = entirely warranted.

where = the references are:=A0=A0Chalmet, S., Rinaldi, D., and Ruiz-L=ABopez, M. = F. 2001. Int. J. Quantum Chem., 84, 559 and=A0Cossi, M. and Crescenzi, = O. 2003. J. Chem. Phys., 118, 8863.

Returning= to the original post, I would say that the energy changes that were = reported upon inclusion of a specific solvent molecule are not unusual = for a case where one (or more) solvent molecules are indeed playing a = role as part of a supersolute. Sadly, the only way to determine this is = to do the experiment, but one's intuition can often be good after a bit = of experience.

Chris

--

Christopher J. Cramer

University of Minnesota

Department of Chemistry

207 Pleasant St. = SE

Minneapolis, MN 55455-0431

--------------------------
=
Phone:=A0 (612) 624-0859 || FAX:=A0 (612) 626-2006

Mobile: (952) = 297-2575

cramer*pollux.chem.umn.edu<= /FONT>

http://pollux.chem.umn.edu/~cr= amer

(website = includes information about the textbook "Essentials

=A0 =A0 of Computational = Chemistry:=A0 Theories and = Models, 2nd Edition")

= --Apple-Mail-34--324735766-- From owner-chemistry@ccl.net Wed Oct 11 09:49:01 2006 From: "mire.zloh mire.zloh++pharmacy.ac.uk" To: CCL Subject: CCL: Second Workshop on Computational Chemistry and Its Applications (Part of ICCS 2007)/ Call for Paper Message-Id: <-32764-061011052441-4820-YmmI2mdmh04vSPfK74ridw(-)server.ccl.net> X-Original-From: "mire.zloh" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 11 Oct 2006 09:47:04 +0100 MIME-Version: 1.0 Sent to CCL by: "mire.zloh" [mire.zloh|a|pharmacy.ac.uk] Hi, Delete =20 from the end of the link, Correct link is: http://pages.intnet.mu/ramasami/iccs_2007.htm Best regards, Mire -----Original Message----- > From: owner-chemistry__ccl.net [mailto:owner-chemistry__ccl.net] Sent: 11 October 2006 08:56 To: Zloh, Mire Subject: CCL: Second Workshop on Computational Chemistry and Its Applications (Part of ICCS 2007)/ Call for Paper Sent to CCL by: Karol Langner [karol.langner .. kn.pl] On Wednesday 11 of October 2006 07:29, Dr. Ponnadurai Ramasami ramchemi__intnet.mu wrote: > Please visit http://pages.intnet.mu/ramasami/iccs_2007.htm=20 This link does not work from where I am. -- written by Karol Langner Wed Oct 11 08:49:30 CEST 2006http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Wed Oct 11 10:58:00 2006 From: "Rajarshi Guha rajarshi.guha---gmail.com" To: CCL Subject: CCL: SMILE to 2D structure Message-Id: <-32765-061011100526-19009-lSE/tHwMl4VLZ292wxVQgw#,#server.ccl.net> X-Original-From: "Rajarshi Guha" Content-Type: multipart/alternative; boundary="----=_Part_25042_1725099.1160572160744" Date: Wed, 11 Oct 2006 09:09:20 -0400 MIME-Version: 1.0 Sent to CCL by: "Rajarshi Guha" [rajarshi.guha]*[gmail.com] ------=_Part_25042_1725099.1160572160744 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Content-Disposition: inline On 10/11/06, Nehru Viji Shankaran chat2viji#,#gmail.com < owner-chemistry],[ccl.net> wrote: > > Sent to CCL by: "Nehru Viji Shankaran" [chat2viji^-^gmail.com] > Dear all, > > I want a program which would convert the SMILE strings (simple)into > 2D structure probably a connection table,z-matrix. > If possible kindly provide me with the source code for it. > The CDK will do this. Example code is at http://cheminfo.informatics.indiana.edu/~rguha/code/java/#smi2sdf -- Rajarshi Guha ------=_Part_25042_1725099.1160572160744 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline

On 10/11/06, Nehru Viji Shankaran chat2viji#,#gmail.com <owner-chemistry],[ccl.net> wrote:
Sent to CCL by: "Nehru Viji Shankaran" [chat2viji^-^gmail.com]
Dear all,

       I want a program which would convert the SMILE strings (simple)into
       2D structure probably a connection table,z-matrix.
       If possible kindly provide me with the source code for it.

The CDK will do this. Example code is at
http://cheminfo.informatics.indiana.edu/~rguha/code/java/#smi2sdf

--
Rajarshi Guha ------=_Part_25042_1725099.1160572160744-- From owner-chemistry@ccl.net Wed Oct 11 11:32:00 2006 From: "gonzalo jimenez oses gonzalo.jimenez++dq.unirioja.es" To: CCL Subject: CCL: PCM vs. explicit water with PCM - effect on reaction profile Message-Id: <-32766-061011110634-5358-s3FozE7ZELazZrJurhZ2dw_-_server.ccl.net> X-Original-From: "gonzalo jimenez oses" Date: Wed, 11 Oct 2006 11:06:33 -0400 Sent to CCL by: "gonzalo jimenez oses" [gonzalo.jimenez[A]dq.unirioja.es] Dear CCL'ers This short message is only to thank all the valuable opinions reported with respect to explicit/implicit solvation, specially those coming from Chris Cramer. His comments are always very accurate and, in fact, I strongly recommend the reading of his "Essentials..." to have a deep view of these kind of concepts. I also would like to thank the reported references, which is always the most straightforward way to obtain the different viewpoints. Best regards, Gonzalo From owner-chemistry@ccl.net Wed Oct 11 13:59:00 2006 From: "Barry Hardy barry.hardy[*]tiscalinet.ch" To: CCL Subject: CCL: Invitation to Open Event on Screening, ELNs, KM in R&D & Comp Chem Message-Id: <-32767-061011135438-22753-p6aXGvYBHq/1KgFeroNVtA,,server.ccl.net> X-Original-From: Barry Hardy Content-Type: multipart/alternative; boundary="=====================_22020412==_.ALT" Date: Wed, 11 Oct 2006 19:57:26 +0200 Mime-Version: 1.0 Sent to CCL by: Barry Hardy [barry.hardy{}tiscalinet.ch] --=====================_22020412==_.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed For those in the neighborhood of Philadelphia next week and interested in the topics of Virtual Screening, Electronic Lab Notebooks (ELNs), Knowledge Management in R&D & Chemistry Research - please consider coming along for the Open Event & Knowledge Cafe at Thomas Great Hall, Bryn Mawr College, the evening of Tuesday Oct 17th starting from 16.00 and running to 21.00. The event is free to attend and includes food, refreshments, good networking and an interactive format. To take a place on the guest list simply RSVP with your name and organization by forwarding a copy of this email to innovationwell [at] douglasconnect.com and indicate with xs which of the activities below you would like to join. Activities: * Screening Forum on "Could we take a Community Approach to Comparing Virtual Screening Methods?" [ ] or * Presentation and Discussion of ELNs [ ] and * Panel Discussion on Knowledge Management in R&D [ ] and * Knowledge Cafe (i.e., more informal group discussions at tables with food and refreshments) [ ] One table's theme at the Knowledge Cafe will be Computational Chemistry Research and ELNs whose discussion I would like to join [ ] More Information at: Knowledge Management in R&D and ELNs: http://barryhardy.blogs.com/theferryman/2006/09/electronic_lab_.html or http://www.echeminfo.com/COMTY_conferenceopenevent/ and Post on Comparing Virtual Screening Methods recently posted by John Irwin (UCSF) and I at http://barryhardy.blogs.com/cheminfostream/2006/10/could_we_take_a.html best regards Barry Hardy eCheminfo Community of Practice Douglas Connect, Switzerland +41 61 851 0170 (office) www.douglasconnect.com --=====================_22020412==_.ALT Content-Type: text/html; charset="us-ascii" For those in the neighborhood of Philadelphia next week and interested in the topics of Virtual Screening, Electronic Lab Notebooks (ELNs), Knowledge Management in R&D & Chemistry Research - please consider coming along for the Open Event & Knowledge Cafe at Thomas Great Hall, Bryn Mawr College, the evening of Tuesday Oct 17th starting from 16.00 and running to 21.00.

The event is free to attend and includes food, refreshments, good networking and an interactive format.

To take a place on the guest list simply RSVP with your name and organization by forwarding a copy of this email to innovationwell [at] douglasconnect.com and indicate with xs which of the activities below you would like to join.

Activities:
* Screening Forum on "Could we take a Community Approach to Comparing Virtual Screening Methods?" [ ]
or
* Presentation and Discussion of ELNs [   ]
and
* Panel Discussion on Knowledge Management in R&D [   ]
and
* Knowledge Cafe (i.e., more informal group discussions at tables with food and refreshments) [   ]

One table's theme at the Knowledge Cafe will be Computational Chemistry Research and ELNs whose discussion I would like to join [ ]

More Information at:
Knowledge Management in R&D and ELNs:
http://barryhardy.blogs.com/theferryman/2006/09/electronic_lab_.html
or
http://www.echeminfo.com/COMTY_conferenceopenevent/
and
Post on Comparing Virtual Screening Methods recently posted by John Irwin (UCSF) and I at http://barryhardy.blogs.com/cheminfostream/2006/10/could_we_take_a.html

best regards
Barry Hardy
eCheminfo Community of Practice
Douglas Connect, Switzerland
+41 61 851 0170 (office)
www.douglasconnect.com --=====================_22020412==_.ALT-- From owner-chemistry@ccl.net Wed Oct 11 16:23:00 2006 From: "Gilles Marcou gilles.marcou/./pharma.u-strasbg.fr" To: CCL Subject: CCL: SMILE to 2D structure Message-Id: <-32768-061011141606-4905-l7EkcGOGDesiXY3R07zEjw]~[server.ccl.net> X-Original-From: Gilles Marcou Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-15" Date: Wed, 11 Oct 2006 20:27:55 +0200 MIME-Version: 1.0 Sent to CCL by: Gilles Marcou [gilles.marcou/./pharma.u-strasbg.fr] Hi all, In fact I like very much Cactvs. http://www2.chemie.uni-erlangen.de/software/cactvs/ It is able to do that. It is not as pretty as other tools but it is 100% Tcl/Tk and it is very robust. Ciao, > > I want a program which would convert the SMILE strings > > (simple)into 2D structure probably a connection table,z-matrix. > > If possible kindly provide me with the source code for it. > > The CDK will do this. Example code is at > http://cheminfo.informatics.indiana.edu/~rguha/code/java/#smi2sdf -- Gilles Marcou Université Louis Pasteur de Strasbourg Institut de Chimie de Strasbourg Laboratoire d' infochimie, UMR7077 4, rue Blaise Pascal, 67000 Strasbourg eMail: g.marcou^chimie.u-strasbg.fr From owner-chemistry@ccl.net Wed Oct 11 21:46:00 2006 From: "Wolf-D. Ihlenfeldt wdi|a|xemistry.com" To: CCL Subject: CCL: SMILE to 2D structure Message-Id: <-32769-061011213202-29176-SNVYbEydnRdCr0LeodD5Wg*o*server.ccl.net> X-Original-From: "Wolf-D. Ihlenfeldt" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 11 Oct 2006 20:31:40 -0400 MIME-Version: 1.0 Sent to CCL by: "Wolf-D. Ihlenfeldt" [wdi_-_xemistry.com] Gilles, thanks for the praise! However, that dowmload location has only ancient versions of the toolkit. The official download site for the toolkit for academic users is www.xemistry.com/academic. For commercial customers, dedicted batch conversion and depiction programs are available. Btw, it is *not* 100% Tcl/Tk. There is a very powerful Tcl scripting layer for rapid application prototyping, and lots of sample programs which were scripted in Tcl or Tk, but the core library is written in ANSI C, including the 2D layout algorithms. The Tcl/Tk components are available as source, but not the core. W. D. Ihlenfeldt Xemistry GmbH wdi]^[xemistry.com > -----Original Message----- > From: owner-chemistry]^[ccl.net [mailto:owner-chemistry]^[ccl.net] > Sent: Wednesday, October 11, 2006 4:29 PM > To: Ihlenfeldt, W.d. > Subject: CCL: SMILE to 2D structure > > Sent to CCL by: Gilles Marcou [gilles.marcou/./pharma.u-strasbg.fr] > Hi all, > > In fact I like very much Cactvs. > http://www2.chemie.uni-erlangen.de/software/cactvs/ > > It is able to do that. It is not as pretty as other tools but > it is 100% Tcl/Tk and it is very robust. > > Ciao, > > > > I want a program which would convert the SMILE strings > > > (simple)into 2D structure probably a connection table,z-matrix. > > > If possible kindly provide me with the source code for it. > > > > The CDK will do this. Example code is at > > http://cheminfo.informatics.indiana.edu/~rguha/code/java/#smi2sdf > > > -- > Gilles Marcou > Université Louis Pasteur de Strasbourg > Institut de Chimie de Strasbourg > Laboratoire d' infochimie, UMR7077 > 4, rue Blaise Pascal, > 67000 Strasbourg > eMail: g.marcou_-_chimie.u-strasbg.fr > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, > please change> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, > Password: search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > -+-+-+-+-+ > > > > From owner-chemistry@ccl.net Wed Oct 11 22:50:00 2006 From: "Zhijian Wu zhijw..hotmail.com" To: CCL Subject: CCL: solid molecular N2 Message-Id: <-32770-061011042439-14179-Pb0G1G1it9Xbsq47c8Upew|server.ccl.net> X-Original-From: "Zhijian Wu" Content-Type: text/html; format=flowed Date: Wed, 11 Oct 2006 03:10:41 -0400 Mime-Version: 1.0 Sent to CCL by: "Zhijian Wu" [zhijw],[hotmail.com]
Hi,

Does anybody know the cell constants and fractional coordinates of solid molecular N2 (nitrogen gas) in ALPHA-phase?

Thank you very much for any of your input.

Regards,

Zhijian WU