From chemistry-request@server.ccl.net Fri Aug 9 08:28:47 2002 Received: from dalton.quimica.unlp.edu.ar ([163.10.18.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g79CShl20691 for ; Fri, 9 Aug 2002 08:28:46 -0400 Received: from bilbo.quimica.unlp.edu.ar (jubert4.quimica.unlp.edu.ar [163.10.18.18]) by dalton.quimica.unlp.edu.ar (8.12.5/8.12.5) with ESMTP id g79CSfkv000503 for ; Fri, 9 Aug 2002 09:28:41 -0300 Message-Id: <5.1.0.14.2.20020809090121.00a08ec0@dalton.quimica.unlp.edu.ar> X-Sender: pis_diez@dalton.quimica.unlp.edu.ar X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Fri, 09 Aug 2002 09:29:03 -0300 To: chemistry@ccl.net From: Reinaldo Pis Diez Subject: BSSE question Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Dear ccl'ers, I'm doing some bsse calculations on a system formed by two molecules interacting through a weak hydrogen bond. Don't panic, I know how to put g98 to run a bsse job and I understand (that's what I think) how the counterpoise method works. I was reading the work of Kestner and Combariza, chapter 2, Rev Comput Chem, vol 13, "Basis Set Superposition Errors: Theory and Practice" and found the usual equations defining the bsse-corrected interaction energy as E_int = E(dimer{AB}) - E(monomerA{AB}) - E(monomerB{AB}) and the definition of the BSSE energy as BSSE = E(monomerA{A}) + E(monomerB{B}) - E(monomerA{AB}) - E(monomerB{AB}) Now, the usual way to calculate E_int is by removing the nuclei and electrons of a given monomer to calculate the energy of the other monomer in the dimer basis. The only optimized geometry is that of the dimer. The energy of the monomers in the dimer basis is calculated as single point jobs (check the examples given at the end of the above paper if you're in doubt). If one is interested in a given interaction energy without bsse corrections, one should simply use E_int = E(dimer{AB}) - E(monomerA{A}) - E(monomerB{B}) with all the geometries properly optimized. Now, don't we introduce an additional error in the BSSE energy equation if we use optimized geometries for the monomers in the monomer basis and non-optimized geometries for the monomers in the dimer basis? I understand that there should be little changes in the geometries if the monomers interact weakly, but what about if one is interesting in an adduct or a chemisorption process where non-negligible changes are expected? Sorry for the long mail and thanks in advance. Regards, Reinaldo From chemistry-request@server.ccl.net Fri Aug 9 10:48:35 2002 Received: from dalton.quimica.unlp.edu.ar ([163.10.18.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g79EmVl24902 for ; Fri, 9 Aug 2002 10:48:33 -0400 Received: from bilbo.quimica.unlp.edu.ar (jubert4.quimica.unlp.edu.ar [163.10.18.18]) by dalton.quimica.unlp.edu.ar (8.12.5/8.12.5) with ESMTP id g79EmSkv003134; Fri, 9 Aug 2002 11:48:29 -0300 Message-Id: <5.1.0.14.2.20020809110905.00a10190@dalton.quimica.unlp.edu.ar> X-Sender: pis_diez@dalton.quimica.unlp.edu.ar X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Fri, 09 Aug 2002 11:48:50 -0300 To: Marcel Swart , chemistry@ccl.net From: Reinaldo Pis Diez Subject: Re: CCL:BSSE question In-Reply-To: <907F7F70-AB9F-11D6-B0E9-000393998E16@chem.vu.nl> References: <5.1.0.14.2.20020809090121.00a08ec0@dalton.quimica.unlp.edu.ar> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Marcel, >[..] Anyhow, the first thing to do for a BSSE calculation is to calculate >the energy of the monomers in the complete basis. Or: > >Eint = Eab**(ab) - Ea**(ab) - Eb**(ab) > >provided that the geometry of monomer A does not change in going from the >monomer to the dimer. Well, this has to do with the final statement of my original mail: One can accept the monomer geometries don't change for weakly-interacting systems but this will not be true at all for strongly-interacting ones. >Else you have to counteract the energy needed to bring the monomers from >their monomer-optimized geometry >to the dimer-geometry: > >Ecorr = Ea**(a) - Ea*(a) + Eb**(b) - Eb*(b) > >[Note that Ebsse is now defined as: Ebsse = Ea**(a) - Ea**(ab) + Eb**(b) - >Eb**(ab) ] But what's the meaning of Ea**(a) and Eb**(b)? If the monomers change too much when the dimer is formed, then Ea**(a) could well be a saddle point on the potential energy surface of the isolated monomer a. >So you have in total: > >Eint = Eab**(ab) - Ea**(ab) - Eb**(ab) + Ea**(a) - Ea*(a) + Eb**(b) - Eb*(b) Hmm, I cannot see how you derived that equation if your starting point is anyone of the other two eqs for Eint you gave above. >Now note that if the monomer optimized geometry is kept fixed in the dimer >geometry, the correction term is zero, Again, this is not necessarily true for strongly-interacting systems (I'm assuming that "kept fixed" is actually "changes little" above). >while if a complete basis has been used, Ebsse is zero. Yes, this is true by its definition. Well, I still think that calculating Ea**(ab) could introduce an additional error in Eint. Rei Reinaldo From chemistry-request@server.ccl.net Fri Aug 9 11:22:25 2002 Received: from dalton.quimica.unlp.edu.ar ([163.10.18.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g79FMKl26144 for ; Fri, 9 Aug 2002 11:22:23 -0400 Received: from bilbo.quimica.unlp.edu.ar (jubert4.quimica.unlp.edu.ar [163.10.18.18]) by dalton.quimica.unlp.edu.ar (8.12.5/8.12.5) with ESMTP id g79FMIkv003670; Fri, 9 Aug 2002 12:22:18 -0300 Message-Id: <5.1.0.14.2.20020809120034.00a1e350@dalton.quimica.unlp.edu.ar> X-Sender: pis_diez@dalton.quimica.unlp.edu.ar X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Fri, 09 Aug 2002 12:22:40 -0300 To: Patrick Bultinck , chemistry@ccl.net From: Reinaldo Pis Diez Subject: Re: CCL:BSSE question In-Reply-To: References: <5.1.0.14.2.20020809090121.00a08ec0@dalton.quimica.unlp.edu.ar> Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1"; format=flowed Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g79FMPl26147 Patrick, >[...] The trick I use is then to define a >"deformation" energy, that accounts for the energy needed to deform >monomer geometries, in the monomer basis set. >So : Energy for the the reaction A+B -> E is calculated in these steps : >- optimize the geometry of AB. >- split it in A and B, with geometries as they were in the complex >- calculate the energies of A and B in the dimer basis set, this gives E(int) >- calculate the energies of A and B in the monomer basis set in the >"complex" geoņetries. Call these Am,c and Bm,c. >- calculate the energies of A and B in the monomer basis set for their >global minimum geometries. Call these energies Am,g and Bm,g >Now calculate the distortion or deformation energies as >Am,c-Am,g and similar for B. > >The total interaction energy for the formation of AB from A and B in >their global minima is then just E(int)+Edis,a+Edis,b. > >Make sense ? It is clear the origin of E(int)+Edis,a+Edis,b. This is the same eq Marcel Swart wrote in his mail and I didn't understand. Well, it seems that there's a well-established recipe to deal with the bsse problem. Thanks, Reinaldo From chemistry-request@server.ccl.net Fri Aug 9 09:02:25 2002 Received: from fsuj20.rz.uni-jena.de ([141.35.1.18]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g79D2Ol21705 for ; Fri, 9 Aug 2002 09:02:25 -0400 Received: from virusscan.rz.uni-jena.de (virusscan.rz.uni-jena.de [141.35.1.23]) by fsuj20.rz.uni-jena.de (8.12.0.Beta7/8.11.1) with ESMTP id g79D2LZJ002801 for ; Fri, 9 Aug 2002 15:02:22 +0200 (MET DST) Received: from virusscan.rz.uni-jena.de (localhost [127.0.0.1]) by virusscan.rz.uni-jena.de (8.11.6/8.11.6) with ESMTP id g79D2KG13121 for ; Fri, 9 Aug 2002 15:02:20 +0200 Received: from lill (lill.iomc.uni-jena.de [141.35.147.47]) by fsuj27.rz.uni-jena.de (8.11.1/8.11.1) with ESMTP id g79D2JU02491 for ; Fri, 9 Aug 2002 15:02:19 +0200 Content-Type: text/plain; charset="us-ascii" From: Sten Nilsson lill Reply-To: sten.nilsson-lill@uni-jena.de To: chemistry@ccl.net Subject: Negative hyperconjugation and DFT Date: Fri, 9 Aug 2002 15:02:21 +0200 User-Agent: KMail/1.4.2 MIME-Version: 1.0 Message-Id: <200208091502.21053.c2nist@rz.uni-jena.de> Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g79D2Pl21710 Dear colleagues, I would appreciate your thoughts and comments on the use of hybrid density functionals for studying negative hyperconjugation (anomeric effect). Is B3LYP appropriate to use or should I use an exchange functional with improved long-range behaviour as in mpw1pw91 or mpw1k. The delocalisation I'm looking at is a nitrogen lone-pair interacting either with a C-S or C-N bond (i.e. the antibonding orbital) and I want to compare these interactions. I will summarise the answers from you for you. Thanks in advance! Sten Nilsson Lill From chemistry-request@server.ccl.net Thu Aug 8 16:27:13 2002 Received: from ucismtp02.unitedcatalysts.com ([208.23.162.6]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g78KR6l12362 for ; Thu, 8 Aug 2002 16:27:06 -0400 Received: from 10.1.0.50 by ucismtp02.unitedcatalysts.com (InterScan E-Mail VirusWall NT); Thu, 08 Aug 2002 16:23:13 -0400 Received: from lvlxch01.unitedcatalysts.com ([10.16.100.88]) by lvlmail.unitedcatalysts.com (PMDF V6.0-24 #41777) with ESMTP id <0H0J00E6GKH7T3@lvlmail.unitedcatalysts.com>; Thu, 08 Aug 2002 16:19:55 -0400 (EDT) Received: by lvlxch01.unitedcatalysts.com with Internet Mail Service (5.5.2653.19) id ; Thu, 08 Aug 2002 16:23:04 -0400 Content-return: allowed Date: Thu, 08 Aug 2002 16:23:00 -0400 From: "Shobe, Dave" Subject: RE: SUMMARY:Equilibrium Constants To: "'knauerc'" , chemistry@ccl.net Message-id: <157A51F55AAAD3119CD70008C7B1629D01C15F2F@lvlxch01.unitedcatalysts.com> MIME-version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-type: text/plain; charset=iso-8859-1 Actually I only wrote the first part of this response; someone else must have contributed the part about gas vs. aqueous phases. --Dave S. 5) David Shobe (dshobe@sud-chemieinc.com) The NIST WebBook (http://webbook.nist.gov/chemistry/) has thermochemical data as a function of temperature, and you can calculate equilibrium constants in the usual way. (Also note that the answers and necessary data sets will differ considerably for gas-phase and aqueous-phase equilibrium constants). From chemistry-request@server.ccl.net Fri Aug 9 10:07:52 2002 Received: from ultra3000.ifqsc.sc.usp.br ([143.107.228.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g79E7pl23645 for ; Fri, 9 Aug 2002 10:07:52 -0400 Received: from floyd (floyd.ifqsc.sc.usp.br [143.107.228.51]) by ultra3000.ifqsc.sc.usp.br (8.11.0/8.11.0) with SMTP id g79EDpA06730 for ; Fri, 9 Aug 2002 11:13:51 -0300 Message-ID: <000801c23fad$9022ff60$33e46b8f@if.sc.usp.br> From: "Alexandre Suman de Araujo" To: References: <20020717093630.A5976@ks.uiuc.edu> Subject: Calixarenes simulations Date: Fri, 9 Aug 2002 11:03:39 -0300 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 Hi guys I'm trying to perform some simulations of calixarenes. I saw in some paper that the most common force field used to do this simulations is AMBER. Some people use the AMBER program package too. Well, what I'd like to know is if somebody had done simulations of calixarenes with another package(GROMACS, TINKER, etc.)? Waiting answers. Thanks Alexandre Suman de Araujo IFSC - USP - São Carlos UIN: 6194055 ----- Original Message ----- From: "Robert Brunner" To: Sent: Wednesday, July 17, 2002 11:36 AM Subject: CCL:JMV Molecular Viewer Support within BioCoRE > JMV Molecular Viewer Support within BioCoRE > > July 3, 2002: > > Urbana, Illinois - The Theoretical Biophysics Group at the University of > Illinois is proud to announce an exciting new feature of BioCoRE, a > Biological Collaborative Research Environment. BioCoRE is freely > accessible at the Theoretical Biophysics Group website and development > is supported by the NIH National Center for Research Resources. > > JMV version 1.0 can now be > accessed from within BioCoRE. JMV, a molecular viewer written using Java > and Java 3D, can be used to view molecular files stored within the > BioFS, BioCoRE's shared filesystem. JMV provides several molecular > representations, multiple coloring styles, lighting controls, and > stereoscopic rendering capabilities. Version 1.0 of JMV is currently > only available within BioCoRE, and a standalone release is upcoming. > > In addition, several other BioCoRE components have seen key improvements > recently: > > * The BioCoRE Control Panel can now be run as a standalone Java > application using Java Web Start. This frees users from the constraints > of running the Control Panel as a Java applet, which allows increased > flexibility and improved robustness since browser crashes no longer kill > the Control Panel. > > * Improved overall "look and feel". The BioCoRE web pages no longer rely > on Javascript menus. This makes pages load faster and provides > compatibility with more browsers. > > * Users can save JPEG files of states from VMD into BioCoRE > automatically. This allows researchers to browse states visually and > load desired configurations directly into VMD. > > * You can now create Interactive accounts within Job Management. > Interactive accounts allow BioCoRE to submit jobs to any computer that > you can log into via SSH. This can be used to run jobs on machines that > BioCoRE doesn't officially support yet. (BioCoRE has built in support > for machines at PSC, NCSA and Globus sites using the Alliance > certificates) > > * BioCoRE job management can now upload files to the remote > supercomputer center of your choice before submitting a job. This allows > researchers to keep their input files in the BioCoRE shared filesystem > and let BioCoRE automatically stage the files. > > > For details, please visit the BioCoRE website at > . > > The Theoretical Biophysics group encourages BioCoRE users to be closely > involved in the development process through reporting bugs, contributing > fixes, periodical surveys and via other means. Questions or comments may > be directed to biocore@ks.uiuc.edu. > > We are eager to hear from you, and thank you for using our software! > > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > >