From chemistry-request@server.ccl.net Tue Aug 13 05:19:58 2002 Received: from mailgate.rz.uni-karlsruhe.de (exim@[129.13.64.97]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7D9Jvl17750 for ; Tue, 13 Aug 2002 05:19:57 -0400 Received: from rz70.rz.uni-karlsruhe.de (cd95@rz70.rz.uni-karlsruhe.de [129.13.97.243]) by mailgate.rz.uni-karlsruhe.de with esmtp (Exim 3.36 #1) id 17eXqF-0007C3-00; Tue, 13 Aug 2002 11:19:55 +0200 Date: Tue, 13 Aug 2002 11:19:55 +0200 (CES) From: Harald Svedung To: Arturas cc: CCL Subject: Re: CCL:ET at short distances In-Reply-To: <2330392762.20020812173436@vaidila.vdu.lt> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id g7D9Jwl17754 Hello Arturas and all. How is life on Gediminas Avenue? At 3 AA, a first order SCF calculation should do the job. That is to say an intermolecular interaction is then dominated by exchange repulsion. This corresponds to a Born-Meyer repulsion in the Electron Gas Density Functional method: C. Nyeland, J. P. Toennies, Chem. Phys., 188, (1994), 205. We tested this in: H. Svedung, S. Nordholm, C. Nyeland, PCCP, 3, (2001), 2209. V(Born-Meyer) = A exp(-b*r), and we found, e.g., that b for an He-He interaction is 2.35 and for an Ar-Ar interaction 1.93. The density and shape of the HOMO clearly comes into play, but unless the LUMO is very close, or if you consider extremly strong collisions, the LUMO will probably not mix into the solution. That is if we are talking about the interaction between two molecules. The environment of the interacting centra will change the results as the electron density is changed, but the effects are not huge.... depending on how sencitive you are. :-) /Harald On Mon, 12 Aug 2002, Arturas wrote: > Hello CCL'ers, > > Got qustion, if anybody back at work again :) > > It is postulated that in long range ET there is exponential dependence > and the main factor controling ET is distance. Here is distances above > 5 Angstroms. If we have two molecules at distance shorter than 5; say > about 3-4 Å. > > How large can be ET deviation depending on structural arrengments for > each other (Acceptor-Donor) ??? Can some orientation retard ET so that > ET rate would drop significantly ??? Do any structural things play any > influence in short distance or, in opposite, in short distances all > depends on HOMO/LUMO properties saying roughly ??? > > Would like to get just any short profesinal comments. > > -- > Best regards, > Arturas Z. > > mailto:a3arzi@vaidila.vdu.lt > http://biologija.vdu.lt/person/ziemar/index.html > > > > > -= 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 > > > > > > Dr. Harald Svedung cellphone: +49-175 736 2576 Institut für Physikalische Chemie or: +46-709-223 206 Universität Karlsruhe Fritz-Haber-Weg 4 D-761 28 Karlsruhe Tyskland Tel: +49-721 608 2108 Fax:+49-721 608 6524 From chemistry-request@server.ccl.net Tue Aug 13 07:15:40 2002 Received: from hamlin.cc.boun.edu.tr ([193.140.192.230]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7DBFcl21064 for ; Tue, 13 Aug 2002 07:15:39 -0400 Received: by hamlin.cc.boun.edu.tr (Postfix, from userid 757) id E213320AE; Tue, 13 Aug 2002 14:08:16 +0300 (EET DST) Received: from localhost (localhost [127.0.0.1]) by hamlin.cc.boun.edu.tr (Postfix) with ESMTP id D60021C0D for ; Tue, 13 Aug 2002 14:08:16 +0300 (EET DST) Date: Tue, 13 Aug 2002 14:08:16 +0300 (EET DST) From: Nurcan Senyurt X-Sender: senyurtn@hamlin.cc.boun.edu.tr To: chemistry@ccl.net Subject: NBO Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL users I have two different conformers of a molecule. I guess that in one of them, there are hyperconjugative interactions that stabilize it with respect to the other. I have performed NBO analysis and checked the donor-acceptor interactions. My question is: Is it logical to sum all the donor-acceptor interactions and deduce that the one with the higher sum is stabilized more than the other by the hyperconjugative interactions. Or should I choose specific donor-acceptor interactions among the tabulated in NBO analysis? My worry is; in the first case antibond-antibond interactions are also considered and in the latter case it is hard to make a wise selection among the donor-acceptor interactions. I appreciate any comments to my question. Thank you in advance. Nurcan Tuzun Bogazici University Chem Department 80815 Bebek, Istanbul Turkey From chemistry-request@server.ccl.net Tue Aug 13 10:35:46 2002 Received: from keep-n-touch.net ([161.58.167.54]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7DEZkl28528 for ; Tue, 13 Aug 2002 10:35:46 -0400 Received: from urgs (p3E99271D.dip.t-dialin.net [62.153.39.29]) by keep-n-touch.net (8.11.6) id g7DEZVe70213; Tue, 13 Aug 2002 08:35:32 -0600 (MDT) From: herta@mantik.de To: chemistry@ccl.net Date: Tue, 13 Aug 2002 16:50:12 +0200 MIME-Version: 1.0 Subject: computation of the protonation Message-ID: <3D5938C4.23880.162D5B3@localhost> Priority: normal X-mailer: Pegasus Mail for Windows (v4.01) Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Content-description: Mail message body Dear CCLs, I want to compute the protonation of nitrogen in organic molecules solved in water. In other words: how many h-atoms are connected to a specific nitrogen atom. The total charge of the molecule is unknown. Is there an easy method to perform this? Is the computation of gasteiger charges an easy way (computation of the partial charge of possible h-atoms)? Or is a better method the use of neural networks? Much thanks in advance for any feedback. Sincerely, christian herta From chemistry-request@server.ccl.net Tue Aug 13 16:14:55 2002 Received: from totalchem.com.br ([200.210.178.14]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g7DKErl07117 for ; Tue, 13 Aug 2002 16:14:54 -0400 Message-Id: <200208132014.g7DKErl07117@server.ccl.net> From: "TotalChem Internet Services S/A" To: Subject: Mensagem importante Sender: "TotalChem Internet Services S/A" Mime-Version: 1.0 Content-Type: text/plain; charset="ISO-8859-1" Content-Transfer-Encoding: 8bit Date: Tue, 13 Aug 2002 17:15:13 -0300 Reply-To: "TotalChem Internet Services S/A" Existem, no TOTALCHEM, empresas procurando seus produtos e serviços. Cadastre seus estoques ativos e inativos. GRATUITAMENTE. Acesse www.totalchem.net. Veja as categorias mais produradas: PRODUTOS Químicos Equipamentos Embalagem e Unitização SERVIÇOS Logística Segurança e Meio Ambiente Sua privacidade é importante para nós. Se você não deseja receber mais email desta divulgação, por favor envie um email para newsletter@mcq.com.br. Nosso intuito é divulgar serviços úteis ao público em geral e, ofertas não desejadas serão canceladas conforme sua solicitação. From chemistry-request@server.ccl.net Tue Aug 13 19:01:18 2002 Received: from sd.accelrys.com ([64.165.22.62]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7DN1Gl14112 for ; Tue, 13 Aug 2002 19:01:17 -0400 Received: (from jnauss@localhost) by sd.accelrys.com (8.11.0/8.11.0) id g7DNAG201214 for chemistry@ccl.net; Tue, 13 Aug 2002 16:10:16 -0700 From: Jeffrey Nauss Received: from sandmail01.sd.accelrys.com (sandmail01.sd.accelrys.com [172.30.160.90]) by sd.accelrys.com (8.11.0/8.11.0) with ESMTP id g7DNAGf01205 for ; Tue, 13 Aug 2002 16:10:16 -0700 To: chemistry@ccl.net Subject: Accelrys bioinformatics workshops in Europe MIME-Version: 1.0 X-Mailer: Lotus Notes Release 5.0.9a January 7, 2002 Message-ID: Date: Tue, 13 Aug 2002 16:01:08 -0700 X-MIMETrack: Serialize by Router on sandmail01/Server/Accelrys(Release 5.0.9 |November 16, 2001) at 08/13/2002 04:01:10 PM, Serialize complete at 08/13/2002 04:01:10 PM Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g7DN1Il14113 Accelrys Ltd. will be holding three Bioinformatics workshops at our office in Cambridge, UK in September On September 17th-18th, the workshop "Wisconsin Package and SeqLab" will be offered. The Wisconsin Package® is the most widely used Bioinformatics suite in the world. Containing over 130 programs, it covers almost every aspect of sequence analysis. This workshop describes the use of the Wisconsin Package through the X-Windows interface SeqLab®. Many of the basic functions are described in detail with enough theoretical description to obtain an understanding of many of the programs. No prior experience with the Wisconsin Package is required but some knowledge of bioinformatics techniques will be helpful. On September 19th, the one-day "SeqWeb Workshop" will be offered. This workshop is relevant to customers who already know about the Wisconsin Package but who would like to use a web-based interface. SeqWeb provides intranet access to some of the more popular applications in the Wisconsin Package from a web browser. A prerequisite for this course is experience with the Wisconsin Package or completion of the "Wisconsin Package and SeqLab Workshop". Finally, on September 20th, the one-day "Desktop Visualization and Communication with ViewerPro Workshop" will be conducted. This workshop is designed for chemists, biochemists, biologists, or anyone else who wants high-quality molecular modeling, visualization, and analysis on their desktop. This one-day workshop focuses on the use of Viewer Pro with Microsoft desktop products for communication and integration. It is an excellent complement to the Wisconsin Package training for the visualization of protein structures. Fees per individual for the 2-day "Wisconsin Package and SeqLab Workshop " are $1200 commercial, $900 government/non-profit, and $660 academic. Fees for either the "SeqWeb" or the "Desktop Visualization and Communication with ViewerPro" workshops are $600 commercial, $450 government/non-profit, or $330 academic each. Registration is on-line at URL http://www.accelrys.com/training/bioinf/schedule.html. Further detailed information about this and other Accelrys training workshops can be found at the Accelrys website (http://www.accelrys.com/training/index.html). Please do not hesitate to contact me should you have any questions. Thank you very much. Elizabeth Crookenden Training Coordinator + 44 1223 228691 -- Jeffrey L. Nauss, Ph.D. Manager, Discovery Studio Training Accelrys Inc. 9685 Scranton Road San Diego, CA 92121-3752 Phone: 858-799-5555 Fax: 858-799-5100 E-mail: jnauss@accelrys.com http://www.accelrys.com/training From chemistry-request@server.ccl.net Tue Aug 13 14:51:33 2002 Received: from web20208.mail.yahoo.com ([216.136.226.63]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g7DIpXl04623 for ; Tue, 13 Aug 2002 14:51:33 -0400 Message-ID: <20020813185133.72907.qmail@web20208.mail.yahoo.com> Received: from [130.83.244.130] by web20208.mail.yahoo.com via HTTP; Tue, 13 Aug 2002 11:51:33 PDT Date: Tue, 13 Aug 2002 11:51:33 -0700 (PDT) From: Hatice Can Subject: CASSCF-Active Space To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear All, My compound has 7 pi bonds and 8 lonepairs.It is singlet and cation.So I noticed that with CIS calculations the excitation is occured from pi to pi*.It has only S1 state that was published as experimentall work. I am really confused with the calculations of determining the active space orbitals. First of all, I have done the following calculations to choice the orbitals for active space.My first question is: which method should I use RFH or UHF with pop= full or naturalorbitals or reg keywords? I am using Gaussian98. My input: %chk=tiy.chk #T RHF/STO-3G Test Pop=Full 1 1 molecule --Link1-- %Chk=tiy.chk #T CAS(14,10) Guess=(Read,Only,Local) Test Geom=Check 1 1 I selected my orbitals from the results of CAS calculations. I decided to alter only two orbitals.One pair is in the occupied orbitals, and the other is in virtuals. At the end of my alteration job, I obtained empty one-electron symbolic density matrix. So why did I obtain that empty matrix? And also I noticed that the message in the output as" WARNING! : large rotation I J = 67 31. What is the meaning of that large rotation? I would like to thank you so much for all the attentions and suggestions. Thank you in advance. Hatice Can Chemistry Dep. TU-Darmstadt Germany __________________________________________________ Do You Yahoo!? HotJobs - Search Thousands of New Jobs http://www.hotjobs.com