From owner-chemistry@ccl.net Tue Mar 7 01:42:00 2006 From: "Don Steiger sd00_2002**yahoo.com" To: CCL Subject: CCL: Question for Octree and/or FMM user. Message-Id: <-31134-060307013931-11584-zLrP9BhtLs7d5nt59tzycA(-)server.ccl.net> X-Original-From: "Don Steiger" Date: Tue, 7 Mar 2006 01:39:27 -0500 Sent to CCL by: "Don Steiger" [sd00_2002###yahoo.com] For those of you that use octree data structures, I would like to know what you would consider to be an upper limit for the number of levels in the octree that you could see yourself using. Thanks in advance. From owner-chemistry@ccl.net Tue Mar 7 02:49:00 2006 From: "Raji Raji raji{:}anal.chem.tohoku.ac.jp" To: CCL Subject: CCL: Molekel Message-Id: <-31135-060307024543-10689-QMI+zUiA/P/SfMUQD4Z+tw###server.ccl.net> X-Original-From: "Raji Raji" Date: Tue, 7 Mar 2006 02:45:39 -0500 Sent to CCL by: "Raji Raji" [raji*anal.chem.tohoku.ac.jp] Dear CCL members, Since there is a problem in the Molekel software page, I can't able to download the zip files for Windows and Linux. So can anyone send me the zip files of Molekel version 4.3 (I have the latest version 4.6, which is a test release and not yet ready for the complete use) for windows platform (if not, then Linux). Thank you very much in advance. Regards, Raji. From owner-chemistry@ccl.net Tue Mar 7 05:13:00 2006 From: "Mariusz Radon mariusz.radon . gmail.com" To: CCL Subject: CCL: Multiplicity in GAMESS Message-Id: <-31136-060307051007-14680-GYEzD94zrQ6QUxQqPA3vZg[A]server.ccl.net> X-Original-From: "Mariusz Radon" Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 7 Mar 2006 11:10:02 +0100 MIME-Version: 1.0 Sent to CCL by: "Mariusz Radon" [mariusz.radon(-)gmail.com] Dear Tianxiao, AFAIK the parameter "MULT" in GAMESS determines only S_z, not S (unless you're using GUGA, when configuration-state-functions are explicitly employed and MULT stands for the real multiplicity). Because states with S>0 contain component of S_z=0 you'll always find them in "singlet" calculations. You can verify this by running this calculation again with MULT=3 -- states number 2 and 3 (clearly triplets, not singlets) should then appear as ground and the first excited state. Hope this helps. Take care, Mariusz On 3/7/06, Tianxiao Yang xiaoyang_guelph##yahoo.com wrote: > Sent to CCL by: "Tianxiao Yang" [xiaoyang_guelph~~yahoo.com] > Dear Colleagues, > > I am confusing with the S and SZ values in GAMESS. When I optimize the ground state (with MULT=1 in the input file) using MCSCF method, I got the following three roots. > > STATE 1 ENERGY= -1421.2244772662 S= 0.00 SZ= 0.00 SPACE SYM=A > STATE 2 ENERGY= -1421.1162694962 S= 1.00 SZ= 0.00 SPACE SYM=A > STATE 3 ENERGY= -1421.0552894237 S= 1.00 SZ= 0.00 SPACE SYM=A > > Is there any way to figure out STATE 2 and STATE 3 Singlet or Triplet? > > Thank you very much for your kind help. > > Xiao Yang > Department of Chemistry, > University of Guelph> > > > -- Mariusz Rado\'n e-mail: mradon/at/chemia.uj.edu.pl e-mail & im: mariusz.radon/at/gmail.com From owner-chemistry@ccl.net Tue Mar 7 07:22:00 2006 From: "John McKelvey jmmckel*_*attglobal.net" To: CCL Subject: CCL: Predicting useful properties of fluids Message-Id: <-31137-060306212156-20001-E9O266xzYOANkHnwB4ppQg{}server.ccl.net> X-Original-From: John McKelvey Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Mon, 06 Mar 2006 21:16:12 -0500 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel-,-attglobal.net] Fiona, Contact Andreas Klamt [COSMO-RS] at Klamt.{}.Cosmologic.de He specializes in this for the chemical industry. I believe, in fact, that most of his business is with ChE's in industry... John McKelvey. Fiona Case fhcase%a%hotmail.com wrote: >Sent to CCL by: "Fiona Case" [fhcase-.-hotmail.com] >Here is an important question: > >Can molecular simulations methods be used to predict industrially relevant >properties of fluids (such as viscosity, vapor pressure, heat of >vaporization, boiling temperature, heat capacity, isothermal >compressibility, thermal conductivity, vapor liquid equilibria, or infinite >dilution activity coefficients)? > >How well do the different methods and forcefields perform when compared to >experimental data, and to other, non-simulation, prediction techniques? > >The Industrial Fluid Property Simulation Collective (IFPSC) is a group of >chemists and chemical engineers from industry and NIST who want to answer >this question! We believe molecular simulation could become a breakthrough >technology that is widely accepted in the chemical industry. It has the >potential to provide a more cost-effective method for obtaining physical >property data than experiments – particularly for materials and state points >that are experimentally challenging or hazardous. > >The IFPSC have already organized two simulation challenges (in 2002 and >2004), and we are about to launch the third. The types of questions we are >considering are listed at our website: > >http://fluidproperties.org/challenge/2006proposals.html > >The CCL represents a broad cross-section of the computational chemistry >community. What do you think - do these questions represent a reasonable >test of today's leading methods and forcefields? We ask you to take the time >to answer our survey: > >http://www.surveymonkey.com/s.asp?u=35161747608 > >While you are at the website take a look at other ideas for expanding the >value and acceptance of molecular simulations and other property prediction >methods. A vision and strategic plan is available here and your comments are >welcome: > >http://fluidproperties.org/Vision-and-Strategic-Plan-5-Feb-06.pdf > > >Sincerely, >The IFPSC organizing committee > > >The IFPSC is an industry-led initiative aimed at promoting and encouraging >the development of techniques for the prediction of industrially-relevant >fluid properties. The activities of the group are supported by the >Computational Molecular Science and Engineering Forum (CoMSEF) of the >American Institute of Chemical Engineers (AIChE), the Computational >Chemistry (COMP) and Physical Chemistry (PHYS) divisions of the American >Chemical Society (ACS), The Dow Chemical Company, BP Amoco, NIST, Case >Scientific, ExxonMobil, Mitsubishi Chemical, 3M Company, and DuPont.> > > > > > > From owner-chemistry@ccl.net Tue Mar 7 07:56:00 2006 From: "Georg Lefkidis lefkidis=physik.uni-kl.de" To: CCL Subject: CCL: Multiplicity in GAMESS Message-Id: <-31138-060307020347-21743-jW4mtityKirPmvh88S6b9A(~)server.ccl.net> X-Original-From: Georg Lefkidis Content-Transfer-Encoding: 7bit Content-Type: text/plain; format=flowed; charset="utf-8" Date: Tue, 07 Mar 2006 07:26:04 +0100 Mime-Version: 1.0 Sent to CCL by: Georg Lefkidis [lefkidis=physik.uni-kl.de] Hi Xiao, state 1 is a singlet, while states 2 and 3 are triplets. You can see that by the S number. If S=0 then you have only one possibility, i.e. Sz=0, and therefore a singlet. If S=1, then you can have Sz=0, or Sz=-1 or Sz=1, so it is a triplet. There are two spin quantum numbers. The total spin S and the projection of the spin on the z axis, Sz. The total spin is depends on the number of unpaired electrons, while Sz (or sometimes called Ms) depends on how many alpha and beta electrons you have, viz. 1/2 for every alpha and -1/2 for every beta. In State 1 you have no unpaired electrons, so both numbers are zero. In states 2 and 3 you have two unpaired electrons each time, and the orientation is such that half are spin up and half are spin down. (In reality it is a bit more complicated, and the right configuration is 1/Sqrt[2]*(ab+ba) but you don't need to worry about that). For states 2 and 3 you can find degenerate states that have Sz=1 and Sz=-1 (both for each). Remember if S=x, then Sz can take the values from -x to x, and the bigger x is, the more possibilities, or in other words the higher the multiplicity. So if you are looking for singlets stick to S=0. Regards Georg Tianxiao Yang xiaoyang_guelph##yahoo.com writes: > Sent to CCL by: "Tianxiao Yang" [xiaoyang_guelph~~yahoo.com] > Dear Colleagues, > > I am confusing with the S and SZ values in GAMESS. When I optimize the ground state (with MULT=1 in the input file) using MCSCF method, I got the following three roots. > > STATE 1 ENERGY= -1421.2244772662 S= 0.00 SZ= 0.00 SPACE SYM=A > STATE 2 ENERGY= -1421.1162694962 S= 1.00 SZ= 0.00 SPACE SYM=A > STATE 3 ENERGY= -1421.0552894237 S= 1.00 SZ= 0.00 SPACE SYM=A > > Is there any way to figure out STATE 2 and STATE 3 Singlet or Triplet? > > Thank you very much for your kind help. > > Xiao Yang > Department of Chemistry, > University of Guelph > From owner-chemistry@ccl.net Tue Mar 7 15:17:00 2006 From: "PankratovAN PankratovAN#,#chem.sgu.ru" To: CCL Subject: CCL: Cyclodextrins Message-Id: <-31139-060307113237-32382-VbnlrxofR0lpINGtJSnhRg[A]server.ccl.net> X-Original-From: PankratovAN Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Tue, 7 Mar 2006 18:32:22 +0300 MIME-Version: 1.0 Sent to CCL by: PankratovAN [PankratovAN(_)chem.sgu.ru] Dear CCLers, Would somebody kindly provide me with HyperChem HIN-files for alpha, beta, and gamma cyclodextrins? Would you also advise on literature references concerning X-ray diffraction structure investigations of cyclodextrins? Thanks in advance. Sincerely yours Alexei Pankratov Professor Dr. Sc. Alexei N. Pankratov Regular Member of the American Chemical Society Department of Chemistry N. G. Chernyshevskii Saratov State University 83 Astrakhanskaya Street Saratov 410012 Russia E-mail: PankratovAN:+:chem.sgu.ru, PankratovAN:+:info.sgu.ru Web: chem.saratov.ru/pankratov From owner-chemistry@ccl.net Tue Mar 7 15:52:00 2006 From: "Scott G Flicker sflicker2=-=earthlink.net" To: CCL Subject: CCL: ISIS format MDLSK Message-Id: <-31140-060307143248-21477-Z5aO9c0AjjmDEDWTgx5RBw%server.ccl.net> X-Original-From: "Scott G Flicker" Date: Tue, 7 Mar 2006 14:32:45 -0500 Sent to CCL by: "Scott G Flicker" [sflicker2%x%earthlink.net] I am looking for any information (reading/writing etc.) on the ISIS format MDLSK that is used by ISIS/Draw. Thanks Scott Flicker sflicker2%a%earthlink.net From owner-chemistry@ccl.net Tue Mar 7 21:33:01 2006 From: "Carlos Nu ez carlos_javierna/./yahoo.com" To: CCL Subject: CCL: Cyclodextrins Message-Id: <-31141-060307183952-14178-iISZevllvk+yX9Trnayj4w],[server.ccl.net> X-Original-From: "Carlos Nu ez" Date: Tue, 7 Mar 2006 18:39:51 -0500 Sent to CCL by: "Carlos Nu ez" [carlos_javierna]-[yahoo.com] Hi, A huge number of X-ray structures of host:guest inclusion complexes of cyclodextrins can be find in the Carbohydrate Research Journal. In this field Thammarat Aree, Irene M. Mavridis & Kazuaki Harata has made abundant & recent contributions (search in http://scholar.google.com/ ). The studies of computational chemistry on cyclodextrins by Kenny Lipkowitz and Carlos Jaime are important, too. Alternatively see Chemical Reviews 1998, Vol. 98, Iss. 5, pp. 1741-2076 for reviews. regards, Carlos N. From owner-chemistry@ccl.net Tue Mar 7 22:07:00 2006 From: "Gonzalo Jimenez Oses gonzalo.jimenez*dq.unirioja.es" To: CCL Subject: CCL: PCM and dipole moment Message-Id: <-31142-060307215600-30901-nhhKhNY6qkohFTBnog9mmQ(0)server.ccl.net> X-Original-From: "Gonzalo Jimenez Oses" Date: Tue, 7 Mar 2006 21:55:59 -0500 Sent to CCL by: "Gonzalo Jimenez Oses" [gonzalo.jimenez{:}dq.unirioja.es] Dear CCL'ers: I wonder if there is any short way to stablish a coherent relationship between the free solvation energy (or, at least, the electrostatic part) obtained through a PCM method (IEF-PCM, C-PCM, D-PCM) and the dipole (or any other multipole) moment of a molecule. I have read that solvation models based on a multipole moment expansion (MPE) of the solute charge distribution, like the Onsagers original model, solvation is described explicitly in terms of a dipole moment. However, solvation models based in an apparent surface charge (ASC) like PCM seem not to take the multipole moments into consideration in a explicit way. Could anyone shed some light into this question, please? Thank you very much in advance, Gonzalo From owner-chemistry@ccl.net Tue Mar 7 23:47:00 2006 From: "Christopher Cramer cramer-.-chem.umn.edu" To: CCL Subject: CCL: PCM and dipole moment Message-Id: <-31143-060307234153-19437-6n0+YjoQTuQNmRhFA/1GxQ-.-server.ccl.net> X-Original-From: Christopher Cramer Content-Type: multipart/alternative; boundary=Apple-Mail-3-274228373 Date: Tue, 7 Mar 2006 21:56:25 -0600 Mime-Version: 1.0 (Apple Message framework v746.2) Sent to CCL by: Christopher Cramer [cramer^^^chem.umn.edu] --Apple-Mail-3-274228373 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Gonzalo, PCM uses the complete density evaluated from the wave function. As such, it is equivalent to a multipole expansion carried to infinite order (although in practice one rarely needs to go beyond about l = 12 for a moderately sized molecule before multipole expansions and PCM agree to within the noise in the respective methods -- lower still when distributed multipoles are used instead of a single-center expansion). For a complete discussion of this and some other points comparing continuum models, see Curutchet, C.; Cramer, C. J.; Truhlar, D. G.; Ruiz Lopez, M.; Orozco, M.; Luque, F. J. "Electrostatic Component of Solvation: Comparison of SCRF Continuum Models" J. Comput. Chem. 2003, 24, 284. Chris On Mar 7, 2006, at 9:13 PM, Gonzalo Jimenez Oses gonzalo.jimenez*dq.unirioja.es wrote: > Sent to CCL by: "Gonzalo Jimenez Oses" [gonzalo.jimenez{:} > dq.unirioja.es] > Dear CCL'ers: > > I wonder if there is any short way to stablish a coherent > relationship between the free solvation energy (or, at least, the > electrostatic part) obtained through a PCM method (IEF-PCM, C-PCM, > D-PCM) and the dipole (or any other multipole) moment of a molecule. > I have read that solvation models based on a multipole moment > expansion (MPE) of the solute charge distribution, like the > Onsagers original model, solvation is described explicitly in terms > of a dipole moment. > However, solvation models based in an apparent surface charge (ASC) > like PCM seem not to take the multipole moments into consideration > in a explicit way. > > Could anyone shed some light into this question, please? > > Thank you very much in advance, > > Gonzalo > > > > -= 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)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+-+ > > > -- Christopher J. Cramer University of Minnesota Department of Chemistry 207 Pleasant St. SE Minneapolis, MN 55455-0431 -------------------------- Phone: (612) 624-0859 || FAX: (612) 626-2006 Mobile: (952) 297-2575 cramer|pollux.chem.umn.edu http://pollux.chem.umn.edu/~cramer (website includes information about the textbook "Essentials of Computational Chemistry: Theories and Models, 2nd Edition") --Apple-Mail-3-274228373 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1 Gonzalo,

PCM uses the complete = density evaluated from the wave function. As such, it is equivalent to a = multipole expansion carried to infinite order (although in practice one = rarely needs to go beyond about l =3D 12 for a moderately sized molecule = before multipole expansions and PCM agree to within the noise in the = respective methods -- lower still when distributed multipoles are used = instead of a single-center expansion).

For a complete discussion = of this and some other points comparing continuum models, = see

Curutchet, C.; = Cramer, C. J.; Truhlar, D. G.; Ruiz Lopez, M.; Orozco, M.; Luque, F. J. = "Electrostatic Component of Solvation: Comparison of SCRF Continuum = Models" J. Comput. Chem. = 2003, 24, 284.

Chris

On Mar 7, = 2006, at 9:13 PM, Gonzalo Jimenez Oses gonzalo.jimenez*dq.unirioja.es = wrote:

Sent to CCL by: "Gonzalo Jimenez = Oses" [gonzalo.jimenez{:}dq.unirioja.es]
Dear = CCL'ers:

I wonder if there is any short way to stablish a = coherent relationship between the free solvation energy (or, at least, = the electrostatic part) obtained through a PCM method (IEF-PCM, C-PCM, = D-PCM) and the dipole (or any other multipole) moment of a = molecule.
I have read that solvation = models based on a multipole moment expansion (MPE) of the solute charge = distribution, like the Onsagers original model, solvation is described = explicitly in terms of a dipole moment.
However, = solvation models based in an apparent surface charge (ASC) like PCM seem = not to take the multipole moments into consideration in a explicit = way.

Could anyone shed some light into this question, = please?

Thank you very much in advance,




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--


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-3-274228373--