Message

From chemistry-request@ccl.net Fri Jun 10 00:20:16 2005 Received: from aquila.its.unimelb.EDU.AU (smtp1.unimelb.edu.au [128.250.20.111]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5A4KAFm024149 for ; Fri, 10 Jun 2005 00:20:11 -0400 Received: from CONVERSION-DAEMON.SMTP.UNIMELB.EDU.AU by SMTP.UNIMELB.EDU.AU (PMDF V6.2 #30995) id <01LPANJX0NV4ATRMEC~at~SMTP.UNIMELB.EDU.AU> for chemistry~at~ccl.net; Fri, 10 Jun 2005 12:13:38 +1000 Received: from [128.250.110.111] by SMTP.UNIMELB.EDU.AU (PMDF V6.2 #30995) with ESMTP id <01LPANJWTVLAB3OEZU~at~SMTP.UNIMELB.EDU.AU> for chemistry~at~ccl.net; Fri, 10 Jun 2005 12:13:38 +1000 Date: Fri, 10 Jun 2005 12:09:28 +1000 From: Christopher Thompson Subject: Defining orbitals To: chemistry~at~ccl.net Message-id: MIME-version: 1.0 (Apple Message framework v622) X-Mailer: Apple Mail (2.622) Content-type: multipart/alternative; boundary="Boundary_(ID_xxrOmnfSoltGu6U8J/DgyA)" X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net --Boundary_(ID_xxrOmnfSoltGu6U8J/DgyA) Content-type: text/plain; charset=US-ASCII; format=flowed Content-transfer-encoding: 7bit Gday, I would like to do an MP2 calc on a Li- species in triplet state. With one electron in the s orbital and one in a p orbital, how can you constrain the electron to say the px orbital? Cheers, cdth~at~unimelb.edu.au Christopher Thompson Laser Spectroscopy Group School of Chemistry University of Melbourne --Boundary_(ID_xxrOmnfSoltGu6U8J/DgyA) Content-type: text/enriched; charset=US-ASCII Content-transfer-encoding: 7bit Gday, I would like to do an MP2 calc on a Li- species in triplet state. With one electron in the s orbital and one in a p orbital, how can you constrain the electron to say the px orbital? Cheers, cdth~at~unimelb.edu.au Lucida GrandeChristopher Thompson Laser Spectroscopy Group School of Chemistry University of Melbourne --Boundary_(ID_xxrOmnfSoltGu6U8J/DgyA)-- From chemistry-request@ccl.net Thu Jun 9 21:34:48 2005 Received: from mail.pomona.edu (exchange1.campus.pomona.edu [134.173.71.128]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5A1Yk8O017796 for ; Thu, 9 Jun 2005 21:34:46 -0400 X-MimeOLE: Produced By Microsoft Exchange V6.5.7226.0 Content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C56D55.F3B58C1D" Subject: RE: NMR structure determination software Date: Thu, 9 Jun 2005 17:47:17 -0700 Message-ID: <658E70C89419784380590FDD04A1D91801B0DDFD~at~EVSFACULTYSTAFF.campus.pomona.edu> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: NMR structure determination software Thread-Index: AcVtHxRj2cw6wKTjRxWoENlW9ePQ5AANpX6A From: "Wayne Steinmetz" To: X-Spam-Status: No, score=0.9 required=5.0 tests=FROM_ENDS_IN_NUMS, HTML_MESSAGE,HTML_TEXT_AFTER_BODY,HTML_TEXT_AFTER_HTML autolearn=no version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net This is a multi-part message in MIME format. ------_=_NextPart_001_01C56D55.F3B58C1D Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Simple, cost effective, and useful. Meeting all criteria is a tall order. For years I have used SYBYL. However, the current version of Spartan contains many of the tools that one needs for a structure determination from NMR constraints. Warren Hehre plans to add more features to the next version. Therefore, I would recommend Spartan. =20 Wayne E. Steinmetz Carnegie Professor of Chemistry Woodbadge Course Director Chemistry Department Pomona College 645 North College Avenue Claremont, California 91711-6338 USA phone: 1-909-621-8447 FAX: 1-909-707-7726 Email: wsteinmetz~at~pomona.edu WWW: pages.pomona.edu/~wsteinmetz =20 -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request~at~ccl.net] On Behalf Of Axel Mathieu Sent: Thursday, June 09, 2005 10:15 AM To: chemistry~at~ccl.net Subject: CCL:NMR structure determination software =20 Greetings CCL'ers: =20 I was wondering if any of you were willing to share your expert opinion on the type of minimal and hopefully rather inexpensive software set-up needed to solve NMR solution structures (including visualization). I'm currently using MOE which I really like for all my modeling needs but it really has too many bells and whistles for just the NMR structure determination that we want to accomplish now. =20 I do understand that there exist many algorithms to solve NMR structures - many of which are "free" to non-profit organizations - and I do not want to embark on a discussion of how and which software is better. I simple want to see if there is a @simple@ cost-effective NMR structure determination set-up for commercial organizations. =20 If any of you offer such solutions, please do not hesitate to contact me as I am interested. Again many thanks to the community for the immense help, =20 APM =20 ------_=_NextPart_001_01C56D55.F3B58C1D Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Simple, cost effective, and = useful. Meeting all criteria is a tall order. For years I have used = SYBYL. However, the current version of Spartan contains many of the tools that one needs for = a structure determination from NMR constraints. Warren Hehre plans = to add more features to the next version. Therefore, I would recommend = Spartan.

Wayne E. = Steinmetz

Carnegie Professor of = Chemistry

Woodbadge Course = Director

Chemistry = Department

Pomona College

645 North College = Avenue

Claremont, California= 91711-6338=

USA

phone: = 1-909-621-8447

FAX: = 1-909-707-7726

Email: = wsteinmetz~at~pomona.edu

WWW: = pages.pomona.edu/~wsteinmetz

-----Original = Message-----
From: Computational = Chemistry List [mailto:chemistry-request~at~ccl.net] On Behalf Of Axel Mathieu
Sent: Thursday, June 09, 2005 10:15 = AM
To: chemistry~at~ccl.net
Subject: CCL:NMR = structure determination software

Greetings = CCL’ers:

I was wondering if any of = you were willing to share your expert opinion on the type of minimal and = hopefully rather inexpensive software set-up needed to solve NMR solution = structures (including visualization). I’m currently using MOE which I really = like for all my modeling needs but it really has too many bells and whistles = for just the NMR structure determination that we want to accomplish = now.

I do understand that there = exist many algorithms to solve NMR structures – many of which are “free” to non-profit organizations - and I do not want to = embark on a discussion of how and which software is better. I simple want to see = if there is a @simple@ cost-effective NMR structure determination set-up for = commercial organizations.

If any of you offer such = solutions, please do not hesitate to contact me as I am = interested.

Again many thanks to the = community for the immense help,

APM

=00 ------_=_NextPart_001_01C56D55.F3B58C1D-- From chemistry-request@ccl.net Thu Jun 9 21:40:47 2005 Received: from etsuex1.etsu.edu (etsuex1.etsu.edu [151.141.8.103]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5A1ehdd018015 for ; Thu, 9 Jun 2005 21:40:44 -0400 X-MimeOLE: Produced By Microsoft Exchange V6.5.7226.0 Content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Subject: RE: about excess electron transfer theoretical study Date: Thu, 9 Jun 2005 20:38:35 -0400 Message-ID: X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: about excess electron transfer theoretical study Thread-Index: AcVtPGZGNMyMLQiJQam9hBlNmZR3EQAF8gEg From: "Close, David M." To: X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id j5A1eldd018019 There are lots of paper by Yuri Berlin at Northwestern on the theory of transport in DNA. I think there are also theoretical papers by Schuster at Georgia Tech. I don't keep up with this story. I haven't liked it from the beginning. I am a radiation chemist. To say that DNA is a molecular wire is silly. You can irradiate a Cu wire all you want, and not get any free radicals. Since the wire conducts charge, the charges merely recombine. If DNA were a wire it to would have no build up of radiation induced charges. But it is well know that DNA has a very high G-value (a measure of radicals produced per unit of energy deposited). -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request|at|ccl.net] On Behalf Of jz7|at|duke.edu Sent: Thursday, June 09, 2005 1:49 PM To: CHEMISTRY|at|ccl.net Subject: CCL:about excess electron transfer theoretical study Dear all, I am reading about study on excess electron transfer (mainly thgouth DNA or pi-stack system). Although there are more and more experiments on this, I didn't find much theoretical reference talking about method study it. Is there really no such publication? Anyone who has seen it or know where I can find it please give me some help! Any information would be helpful, even reference on the conducticity of DNA would be helpful. Thanks a lot! Jeny -= This is automatically added to each message by the mailing script =- To send e-mail to subscribers of CCL put the string CCL: on your Subject: line and send your message to: CHEMISTRY|at|ccl.net Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST|at|ccl.net HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs If your is mail bouncing from ccl.net domain due to spam filters, please use the Web based form from CCL Home Page -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@ccl.net Thu Jun 9 19:31:46 2005 Received: from smtp3.Stanford.EDU (smtp3.Stanford.EDU [171.67.16.138]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j59NVfqx013865 for ; Thu, 9 Jun 2005 19:31:41 -0400 Received: from cardinal1.Stanford.EDU (cardinal1.Stanford.EDU [171.64.15.249]) by smtp3.Stanford.EDU (8.12.11/8.12.11) with ESMTP id j59NVcvS025313 for ; Thu, 9 Jun 2005 16:31:38 -0700 Date: Thu, 9 Jun 2005 16:31:38 -0700 (PDT) From: "S.I.Gorelsky" To: chemistry$at$ccl.net Subject: AOMix-CDA: analysis of charge transfer and polarization In-Reply-To: <20050510110246.GG21730$at$leitl.org> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Hello, the updated version of AOMix and AOMix-CDA is available for downloading > from http://www.sg-chem.net/ Regards, Serge Gorelsky ---------------------------------------------------------------- Dr S.I. Gorelsky, Department of Chemistry, Stanford University Box 155, 333 Campus Drive, Stanford, CA 94305-5080 USA Phone: (650) 723-0041. Fax: (650) 723-0852. ---------------------------------------------------------------- From chemistry-request@ccl.net Fri Jun 10 01:39:17 2005 Received: from smtp.dkm.cz (smtp.dkm.cz [62.24.64.34]) by server.ccl.net (8.13.1/8.13.1) with SMTP id j5A5d3hx027522 for ; Fri, 10 Jun 2005 01:39:06 -0400 Received: (qmail 8581 invoked by uid 0); 10 Jun 2005 04:39:01 -0000 Received: from j129.chello.upc.cz (HELO ?62.24.75.129?) (62.24.75.129) by smtp.dkm.cz with SMTP; 10 Jun 2005 04:39:01 -0000 Message-ID: <42A91961.5060407 +*+ uochb.cas.cz> Date: Fri, 10 Jun 2005 06:38:57 +0200 From: Daniel Svozil Reply-To: svozil +*+ uochb.cas.cz Organization: IOCB User-Agent: Mozilla Thunderbird 0.8 (Windows/20040913) X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry +*+ ccl.net Subject: Re: CCL:Reflection about the list References: <4cb6864c71e5.4c71e54cb686 +*+ imap.georgetown.edu> <42A8B644.E7E39774 +*+ panet.de> In-Reply-To: <42A8B644.E7E39774 +*+ panet.de> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net I fully agree with Guenther Meinrath, I consider sending replies back to the list as a part of Netiquete and I was also very surprised, that this is not a case in CCL (it is actually the only list I am subscribed to where it is not common practise). The value of the list is not only in the actual mail communication, but also in its web archive, and if most the answers are not present there, it becomes almost useles. Why would someone need the archive full of questions without solutions? So, please, keep replying to the list in the future. Dan -- Daniel Svozil, PhD Institute of Organic Chemistry and Biochemistry and Center for Complex Molecular Systems and Biomolecules http://www.molecular.cz/ Czech Republic phone: +420-220 410 312 rer wrote: > Dear CCL list members, > > the communication about 'reflections on the list' > meanwhile has generated some traffic. As a pretty > recent member of the list, this discussion is a > bit surprising to me. Being attached to several > mailing lists, the CCL list is the only list whee > this kind of discussion has arisen. In the other > lists (e.g. RADCH-L, ENVIRON) the questions and > responses are transfered to all subscribers. To > identify interesting topics and enjoying an > intelligent and meaningful discussion seems to be > a main motivation to join a list. Imagine: reading > an interesting question of a list member - and > never getting to know the answers! For a > scientist, this seems to me an efficient technique > of torture... > > Some days ago, I was looking for some information > about including lanthanide ions into Gaussian98 > calculations. One of the hits in the search engine > directed to 'server.ccl...'. The linked post in > CCL was very intersting to me (doing Gaussian > calculations as a kind of 'hobby'), especially > because the person posting the question was kind > enough to summarize the answers. Otherwise the > responses would not have been available. May be > the poster has aso received some answer that where > not of interest to him - but possibly to me and > other subscribers of the CCL list. > > If only the question would have been available, > what help this post would offer to others (the > community 'being the list')? In short: Replying to > the list should be a natural choice. > > Dr. habil. Guenther Meinrath > Technische Universitdt Bergakademie Freiberg > Institute of Inorganic Chemistry > Leipziger Str. 27 > D-09596 Freiberg > & > RER Consultants Passau > Schiesstattweg 3a > D-94032 Passau > > > > > Sivanesan Dakshanamurthy schrieb: > >>I too agree with the Dr.Michel Petitjean, replying to the whole list is a good idea. >>-Siva >> >>D.Sivanesan, Ph.D. >>E401, New Research Building, >>Macromolecular Core & Dept. of Oncology, >>Lombardi Cancer Center (NCI Comprehensive Cancer Center), >>Georgetown University, Washington DC 20057 >>Phone: 202-687-2347 >> > > > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: line > and send your message to: CHEMISTRY +*+ ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST +*+ ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your is mail bouncing from ccl.net domain due to spam filters, please > use the Web based form from CCL Home Page > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > From chemistry-request@ccl.net Fri Jun 10 02:51:15 2005 Received: from relay.unizar.es (ortiz.unizar.es [155.210.11.72]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5A6p79l030633 for ; Fri, 10 Jun 2005 02:51:08 -0400 Received: from [155.210.92.49] (neptuno.unizar.es [155.210.92.49]) (authenticated bits=0) by relay.unizar.es (8.13.4/8.12.3) with ESMTP id j5A6oigc003045; Fri, 10 Jun 2005 08:50:50 +0200 Message-ID: <42A93851.9070004 +*+ unizar.es> Date: Fri, 10 Jun 2005 08:50:57 +0200 From: Pablo Echenique Robba Reply-To: pnique +*+ unizar.es User-Agent: Mozilla Thunderbird 1.0 (X11/20041206) X-Accept-Language: en-us, en MIME-Version: 1.0 To: CCL list , Yo Unizar CC: Jose Luis Alonso Subject: answers to "existence of HF-SCF solutions" Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit X-Mail-Scanned: Criba 2.0 + Clamd en Unizar X-Spam-Status: No, score=0.1 required=5.0 tests=FORGED_RCVD_HELO autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net I present here the answers to my question about the existence of HF-SCF solutions and the possibility of finding them. The answers are not all from the CCL list but they are indeed interesting. --- My question ------------------------------------------------------- What I wanted to know is whether someone could indicate to me where may I find a discussion on the existence of solutions of the HF-SCF iterative procedure. I first enumerate briefly what I know: 1) The HF equations HAVE solutions (Lieb and Simon, 1977). 2) Any solution of the HF equations is an extremal, with no indication about its being a maximum, a saddle point or a minimum whatsoever. 3) The SCF method DOES NOT always converge. Of course, when it does converge, the wave function that results is indeed a solution of the HF equations. Again, with no indication about its being a maximum, a saddle point or a minimum. My two questions are related to point 3: a) When does the SCF converge? b) How do we know, if it converged, that it did it to a minimum (and not to a maximum or to a saddle point)? I would thank very much any hint to articles or books discussing this. I mean, further than the typical "we hope it converge because our basis sets and our starting point are so good". --- Answers ----------------------------------------------------------- By now, there are indeed some results going further, from numerical mathematics experts; see for example Volume X of the series "Handbook of Numerical Analysis", which is a special volume on Computational Chemistry (Elsevier, 2003). In the first chapter, a 268 pages long textbook on computational quantum chemistry in itself, discusses results to at least some aspects of your question. Hope this helps, Bernd --- Prof. Dr. Bernd Hartke e-mail: hartke +*+ phc.uni-kiel.de Theoretical Chemistry phone : +49-431-880-2753 Institute for Physical Chemistry fax : +49-431-880-1758 University of Kiel http://ravel.phc.uni-kiel.de/ Olshausenstrasse 40 24098 Kiel GERMANY ----------------------------------------------------------------------- Dear Pablo, We have been working on globally convergent iterative methods for HF-SCF equations (J. Chem. Phys. 121, pp. 10863-10878 (2004)) and we have discussed in that paper some properties of the HF equations in that sense. Also Cancis and Le Bris published a paper on the properties of SCF methods, in which they discuss the convergence of the classical fixed-point iteration (Math. Modell. Numer. Anal. 34, 749 (2000)) and introduce some interesting scf methods. For an analysis of the HF problem in a very theoretical perspective (also much more difficult to follow) you can check the work of P. L. Lions (COMM. MATH. PHYS. 109 (1): 33-97 1987). We are now working on new methods and we now know several properties of the scf energy, if you are interested we send you the paper when it is ready. As far as we know, we can't know whether the solution found is a minimum, saddle point or maximum, but we know that the lower the energy the better it is. The book suggested by Bernd probably contains the results of Cances and Le Bris on that subject. Best regards, Leandro. ----------------------------------------------------------------------- Hello Pablo, I can suggest you two references (although they are perhaps made superfluous by the more recent reference cited by Bernd Hartke): M. Defranceschi, C. Le Bris, "Computing a Molecule: A Mathematical viewpoint", J. of Math. Chem. 21, 1 (1997) M. Defranceschi, C. Le Bris, "Computing a Molecule in its Environment: A Mathematical viewpoint", Int. J. of Quant. Chem. 71, 227 (1999) ----------------------------------------------------------------------- Hi Pablo, I see two issues here. One is the analicity of the HF equations. And they do have solutions. The other issue is the computational or numerical procedure used to find those solutions. Regarding b), we know that the converged solution is a minimum by calculating the second derivative of the solution wrt the (MO) coeficients, this is the "stability" check found in some computer programs. Regarding a), there are many different SCF algorithms. Some first order (use only 1st derivatives wrt to coeficients), other second order (use 1st and 2nd derivatives) and quasi-second order (use some approximation to the 2nd derivatives). Each type has diffrent convergence properties, and pratical/observed convergence depends on the region of the coeficient space which you start your optimization. There are many reviews on these subjects, try: author = "T. Helgaker", title = "Optimization of Minima and saddle points", booktitle = "Lectures Notes in Quantum Chemistry - European Summer School in Quantum Chemistry", editor = "B. O. Roos", year = 1992, volume = 1, publisher = "Springer-Verlag", pages = {295-324}, address = "Berlin", or author = "H. B. Schlegel", title = "Optimization of equilibrium geometries and transition structures", journal = "Adv. Chem. Phys." , year = 1987, volume = 67, pages = {249-286}, Hope it helps, ------------------------------------------------------------------------ >Dear Guilherme, >> >> Thank you very much for your precise and useful answer. I have one more >> question however: when you answer to my point b), you don't mention >> anything about checking that the minimum is not only local but also >> global. Are there checks for this? > > Ha, thats a completely different business! Yes, I am only saying about a local minimum. Wether this is the global one, there is no mathematical or heuristic approach to be sure. The only way to be sure we have found a global minimum, is to find all the other (local) minimum! heheheh G ----------------------------------------------------------------------------------------------------- Hi, Maybe the following paper could be a good starting point: Eric Cances and Claude Le Bris, Int. J. Quantum Chem. 79 (2000) 82-90 -- *********** Dr. Nicolas Ferre' *********** Laboratoire de Chimie Theorique et de Modelisation Moleculaire UMR 6517 - CNRS Universites Aix-Marseille Case 521 Centre de Saint-Jerome 13397 - Marseille Cedex 20, France Tel : (+33)4.91.28.27.33 Fax : (+33)4.91.28.87.58 http://www.up.univ-mrs.fr/wsrep/ctheo/lctmm.html *************************************************************** --------------------------------------------------------------------------------------------------- Thats all, hope it helps. Pablo Echenique Guilherme Regards, Lorenzo Lodi -- ------------------------------------ Pablo Echenique Robba Departamento de Fisica Teorica & Instituto de Biocomputacion y Fisica de los Sistemas Complejos BIFI Universidad de Zaragoza 50009 Zaragoza Spain Tel.: 34 976761260 E-mail: pnique +*+ unizar.es ------------------------------------ From chemistry-request@ccl.net Fri Jun 10 05:38:12 2005 Received: from mail.chem.tamu.edu (mail.chem.tamu.edu [165.91.176.8]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5A9c6ca006781 for ; Fri, 10 Jun 2005 05:38:07 -0400 Received: by mail.chem.tamu.edu (CommuniGate Pro PIPE 4.2.8) with PIPE id 2985157; Fri, 10 Jun 2005 04:38:06 -0500 Received: from [83.78.155.205] (account singleton *o* mail.chem.tamu.edu) by mail.chem.tamu.edu (CommuniGate Pro WebUser 4.2.8) with HTTP id 2985155 for chemistry *o* ccl.net; Fri, 10 Jun 2005 04:37:52 -0500 From: "Daniel A. Singleton" Subject: CCL:Reflection about the list To: chemistry *o* ccl.net X-Mailer: CommuniGate Pro WebUser Interface v.4.2.8 Date: Fri, 10 Jun 2005 04:37:52 -0500 Message-ID: In-Reply-To: <42A8B644.E7E39774 *o* panet.de> References: <4cb6864c71e5.4c71e54cb686 *o* imap.georgetown.edu> <42A8B644.E7E39774 *o* panet.de> MIME-Version: 1.0 Content-Type: text/plain; charset="ISO-8859-1"; format="flowed" Content-Transfer-Encoding: 8bit X-Chemistry_Department-MailScanner-Information: Chemistry_Helpdesk X-Chemistry_Department-MailScanner: Found to be clean X-MailScanner-From: singleton *o* mail.chem.tamu.edu X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net I would like to point out that the old problem of getting too many emails from a list is no longer an issue for me, and I suspect this is true for many of the suscribers on the list. I filter everything with 'CCl' in the Subject line, putting it in a separate mailbox that I examine at my leisure. I use the CCl mailbox as a type of database, and it is more important to me that answers to questions be findable in the database than that I get fewer emails. Also, I will admit that the possibility that an easy question has already been answered by someone else has kept me from answering a great many questions - if someone else has already answered a question, why should I bother? So overall, I think the list would end up more useful to people if the responses went to the whole list. Dan Singleton From chemistry-request@ccl.net Fri Jun 10 06:13:26 2005 Received: from exchange21.fed.cclrc.ac.uk (exchangegw03.rl.ac.uk [130.246.135.202]) by server.ccl.net (8.13.1/8.13.1) with SMTP id j5AADMds008389 for ; Fri, 10 Jun 2005 06:13:22 -0400 Received: from exchange33.fed.cclrc.ac.uk ([172.16.133.33]) by exchange21.fed.cclrc.ac.uk with Microsoft SMTPSVC(6.0.3790.211); Fri, 10 Jun 2005 10:26:14 +0100 X-MimeOLE: Produced By Microsoft Exchange V6.5.7226.0 Content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C56D9E.72959B0F" Subject: RE: NMR structure determination software Date: Fri, 10 Jun 2005 10:26:14 +0100 Message-ID: X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: NMR structure determination software Thread-Index: AcVtHxRj2cw6wKTjRxWoENlW9ePQ5AANpX6AABIonMA= From: "Flaig, R $Ralf$" To: X-OriginalArrivalTime: 10 Jun 2005 09:26:14.0835 (UTC) FILETIME=[72CEE830:01C56D9E] X-Spam-Status: No, score=0.1 required=5.0 tests=FORGED_RCVD_HELO,HTML_MESSAGE autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net This is a multi-part message in MIME format. ------_=_NextPart_001_01C56D9E.72959B0F Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Have a look at the crystallography & NMR system. =20 http://cns.csb.yale.edu/v1.1/ =20 =20 Hope this helps, Ralf -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request :: ccl.net] On Behalf Of Wayne Steinmetz Sent: 10 June 2005 01:47 To: chemistry :: ccl.net Subject: CCL:NMR structure determination software =09 =09 Simple, cost effective, and useful. Meeting all criteria is a tall order. For years I have used SYBYL. However, the current version of Spartan contains many of the tools that one needs for a structure determination from NMR constraints. Warren Hehre plans to add more features to the next version. Therefore, I would recommend Spartan. =20 Wayne E. Steinmetz Carnegie Professor of Chemistry Woodbadge Course Director Chemistry Department Pomona College 645 North College Avenue Claremont, California 91711-6338 USA phone: 1-909-621-8447 FAX: 1-909-707-7726 Email: wsteinmetz :: pomona.edu WWW: pages.pomona.edu/~wsteinmetz =20 -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request :: ccl.net] On Behalf Of Axel Mathieu Sent: Thursday, June 09, 2005 10:15 AM To: chemistry :: ccl.net Subject: CCL:NMR structure determination software =20 Greetings CCL'ers: =20 I was wondering if any of you were willing to share your expert opinion on the type of minimal and hopefully rather inexpensive software set-up needed to solve NMR solution structures (including visualization). I'm currently using MOE which I really like for all my modeling needs but it really has too many bells and whistles for just the NMR structure determination that we want to accomplish now. =20 I do understand that there exist many algorithms to solve NMR structures - many of which are "free" to non-profit organizations - and I do not want to embark on a discussion of how and which software is better. I simple want to see if there is a @simple@ cost-effective NMR structure determination set-up for commercial organizations. =20 If any of you offer such solutions, please do not hesitate to contact me as I am interested. Again many thanks to the community for the immense help, =20 APM =20 ------_=_NextPart_001_01C56D9E.72959B0F Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Message

Have a=20 look at the crystallography & NMR system.

http://cns.csb.yale.edu/v1.1/<= /FONT>

Hope=20 this helps,

Ralf

-----Original Message-----
From: = Computational=20 Chemistry List [mailto:chemistry-request :: ccl.net] On Behalf Of = Wayne=20 Steinmetz
Sent: 10 June 2005 01:47
To:=20 chemistry :: ccl.net
Subject: CCL:NMR structure determination=20 software

Simple, = cost=20 effective, and useful. Meeting all criteria is a tall = order. =20 For years I have used SYBYL. However, the current version of = Spartan=20 contains many of the tools that one needs for a structure = determination from=20 NMR constraints. Warren Hehre plans to add more features to the = next=20 version. Therefore, I would recommend Spartan.

Wayne E.=20 Steinmetz

Carnegie = Professor of=20 Chemistry

Woodbadge = Course=20 Director

Chemistry=20 Department

Pomona = College

645 North = College=20 Avenue

Claremont, = California = 91711-6338

USA

phone:=20 1-909-621-8447

FAX:=20 1-909-707-7726

Email:=20 wsteinmetz :: pomona.edu

WWW:=20 pages.pomona.edu/~wsteinmetz

-----Original=20 Message-----
From:=20 Computational Chemistry List [mailto:chemistry-request :: ccl.net] = On Behalf Of Axel = Mathieu
Sent: Thursday, June 09,=20 2005 10:15=20 AM
To: = chemistry :: ccl.net
Subject: CCL:NMR structure = determination=20 software

Greetings=20 CCL’ers:

I was wondering if any = of you were=20 willing to share your expert opinion on the type of minimal and = hopefully=20 rather inexpensive software set-up needed to solve NMR solution = structures=20 (including visualization). I’m currently using MOE which I = really like for all=20 my modeling needs but it really has too many bells and whistles for = just the=20 NMR structure determination that we want to accomplish = now.

I do understand that = there exist=20 many algorithms to solve NMR structures – many of which are = “free” to=20 non-profit organizations - and I do not want to embark on a discussion = of how=20 and which software is better. I simple want to see if there is a = @simple@=20 cost-effective NMR structure determination set-up for commercial=20 organizations.

If any of you offer such = solutions, please do not hesitate to contact me as I am=20 interested.

Again many thanks to the = community=20 for the immense help,

APM

------_=_NextPart_001_01C56D9E.72959B0F-- From chemistry-request@ccl.net Fri Jun 10 10:16:09 2005 Received: from server.ccl.net (ccl [127.0.0.1]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5AEG8PB018798 for ; Fri, 10 Jun 2005 10:16:08 -0400 Received: (from apache@localhost) by server.ccl.net (8.13.1/8.13.1/Submit) id j5AEG8r2018797 for chemistry !! ccl.net; Fri, 10 Jun 2005 10:16:08 -0400 Date: Fri, 10 Jun 2005 10:16:08 -0400 Message-Id: <200506101416.j5AEG8r2018797 !! server.ccl.net> X-Authentication-Warning: server.ccl.net: apache set sender to chemistry-request !! ccl.net using -f From: "JIM, , LI" To: chemistry !! ccl.net X-Web-Message-Number: 050610101426-18701 Subject: W:fluorescence spectra calculation X-Spam-Status: No, score=0.2 required=5.0 tests=ALL_TRUSTED,DEAR_SOMETHING, FORGED_YAHOO_RCVD autolearn=no version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Dear Sirs: I am interested in calculating fluorescence spectra and looking for help. Please let me know which computer program(s) I can use to calculate fluorescence spectra. Thanks. Jim From chemistry-request@ccl.net Fri Jun 10 11:40:28 2005 Received: from sys12.mail.msu.edu (sys12.mail.msu.edu [35.9.75.112]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5AFeOVt023515 for ; Fri, 10 Jun 2005 11:40:24 -0400 Received: from chieny by sys12.mail.msu.edu with local (Exim 4.44 #1) id 1Dgk0W-0002Oy-Pg for chemistry !! ccl.net; Fri, 10 Jun 2005 09:57:12 -0400 References: <4cb6864c71e5.4c71e54cb686 !! imap.georgetown.edu> <42A8B644.E7E39774 !! panet.de> In-Reply-To: From: "Yao-Ying Chien" To: chemistry !! ccl.net Subject: Re: CCL:Reflection about the list Date: Fri, 10 Jun 2005 09:57:12 -0400 Mime-Version: 1.0 Content-Type: text/plain; format=flowed; charset="utf-8" Content-Transfer-Encoding: 7bit Message-Id: X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Hi, I did the similar too. One ccl folder where contains ccl_in, ccl_save, and ccl_delete. ccl_in is where the files are filtered in. ccl_delete is where the files will be deleted next week. Yao Daniel A. Singleton writes: > > I would like to point out that the old problem of getting too many > emails from a list is no longer an issue for me, and I suspect this is > true for many of the suscribers on the list. I filter everything with > 'CCl' in the Subject line, putting it in a separate mailbox that I examine > at my leisure. > I use the CCl mailbox as a type of database, and it is more important > to me that answers to questions be findable in the database than that I > get fewer emails. Also, I will admit that the possibility that an easy > question has already been answered by someone else has kept me from > answering a great many questions - if someone else has already answered a > question, why should I bother? So overall, I think the list would end up > more useful to people if the responses went to the whole list. > > Dan Singleton > > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: > line > and send your message to: CHEMISTRY !! ccl.net > > Send your subscription/unsubscription requests to: > CHEMISTRY-REQUEST !! ccl.net HOME Page: http://www.ccl.net | Jobs Page: > http://www.ccl.net/jobs > > If your is mail bouncing from ccl.net domain due to spam filters, please > use the Web based form from CCL Home Page > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > From chemistry-request@ccl.net Fri Jun 10 12:02:55 2005 Received: from web50308.mail.yahoo.com (web50308.mail.yahoo.com [206.190.38.62]) by server.ccl.net (8.13.1/8.13.1) with SMTP id j5AG2prU024608 for ; Fri, 10 Jun 2005 12:02:51 -0400 Received: (qmail 28927 invoked by uid 60001); 10 Jun 2005 16:02:50 -0000 DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=yahoo.com; h=Message-ID:Received:Date:From:Subject:To:MIME-Version:Content-Type:Content-Transfer-Encoding; b=xMkS0uk0774zD5AcoWMWiyRhIQDRf7+Sj1max+zgv2qk2KfUNODsd22OQbLChwA9iy43k+r7fvSP9E2LGZfKLCtpkzHFtbWfzPb39vclH0g9iEbeQyDY52rR2DYKBezlNrrtYjdc3hBBfexqeCjXChk0PDHRKTF+BSV4bO6LeYE= ; Message-ID: <20050610160250.28925.qmail{at}web50308.mail.yahoo.com> Received: from [164.68.15.202] by web50308.mail.yahoo.com via HTTP; Fri, 10 Jun 2005 09:02:50 PDT Date: Fri, 10 Jun 2005 09:02:50 -0700 (PDT) From: Nhat Le Minh Subject: UFF modification in Gaussian To: CHEMISTRY{at}ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Spam-Status: No, score=1.8 required=5.0 tests=DNS_FROM_RFC_ABUSE, DNS_FROM_RFC_POST autolearn=no version=3.0.3 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Dear CCL subscribers: My name is Alex Le. I'm trying to find a way to modify the UFF parameters to incorporate a new atom type. I wonder if there is anyone who has been successfully at customizing the parameters in any software. And if it is possible, would you please tell me the procedure? I have tried to add the customized parameter at the end of a G03 input com file but still, there is something missing and the manual of G03 about the MM Force Field is not adequate in terms of explanation. I hope to receive some hints or suggestion soon. With best regards, Alex Le. Nhat Minh Le (Alex Le) Delta Chi - Brotherhood of a Lifetime nworld3d{at}yahoo.com www.247lfc.com | www.sr3d.net __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From chemistry-request@ccl.net Fri Jun 10 13:45:35 2005 Received: from chemail.tamu.edu (CHENOV3.TAMU.EDU [165.91.142.133]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5AHjVd3029649 for ; Fri, 10 Jun 2005 13:45:31 -0400 Received: from che y0w9065 [165.91.227.17] by chemail.tamu.edu with NetMail SMTP Agent $Revision: 1.1.1.1 $ on Novell NetWare; Fri, 10 Jun 2005 12:02:27 -0500 Message-ID: <015c01c56dde$2f7262c0$11e35ba5@che> From: "yixuan wang" To: Subject: energy of Cr Date: Fri, 10 Jun 2005 12:02:29 -0500 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0159_01C56DB4.46826A20" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2900.2180 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2900.2180 X-Spam-Status: No, score=0.8 required=5.0 tests=FROM_ENDS_IN_NUMS, FROM_HAS_MIXED_NUMS,HTML_MESSAGE autolearn=no version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net This is a multi-part message in MIME format. ------=_NextPart_000_0159_01C56DB4.46826A20 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear All, I tried a few combinations by varing SCF and Integral with G03 = B04 (C02) for a lot of transition metals. Most of them reasonably = differ. However, I was surprised by the results of Cr. The details are = as follows. =20 a) # b3lyp/gen pseudo=3Dread b) #b3lyp/gen pseudo=3Dread = c) b3lyp/gen pseudo=3Dread integral(grid=3Dultrafine) scf=3Dqc = scf=3Dqc = integral(grid=3Dultrafine) 0 5 Cr Cr 0 LanL2dz **** Cr 0 LanL2dz Energy: -86.2396491893au -86.2396526553 = -86.148570844 =20 In addition, G98 A11 gives -86.2396549360 and -86.2396550127 for the = cases b and c, respectively. Yixuan Wang Texas A&M Univ =20 ------=_NextPart_000_0159_01C56DB4.46826A20 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Dear All,

I = tried a few=20 combinations by varing SCF and Integral with G03 B04 (C02) for a lot=20 of transition metals. Most of them reasonably differ. However, I = was=20 surprised by the results of Cr. The details are as = follows. =20

   =20 a)  # b3lyp/gen=20 pseudo=3Dread       =20 b)   #b3lyp/gen=20 pseudo=3Dread    c) = b3lyp/gen=20 pseudo=3Dread
         &n= bsp;integral(grid=3Dultrafine)       &= nbsp;           sc= f=3Dqc           &= nbsp;           &n= bsp;           &nb= sp;scf=3Dqc
         &nbs= p;            = ;            =             &= nbsp;           &n= bsp;           &nb= sp;           &nbs= p;            = ;          =20 integral(grid=3Dultrafine)

0 =20 5
= Cr

         Cr=20 0
        =20 LanL2dz
         = ****

Cr =20 0
LanL2dz

=20 Energy:=20 -86.2396491893au &nb= sp; -86.2396526553 &n= bsp; &nb= sp; =20 -86.148570844

In = addition, G98=20 A11 gives -86.2396549360 and -86.2396550127 for the cases b and c, = respectively.

Yixuan Wang

Texas A&M Univ

------=_NextPart_000_0159_01C56DB4.46826A20-- From chemistry-request@ccl.net Fri Jun 10 15:59:13 2005 Received: from lgsx14.lg.ehu.es (lgsx14.lg.ehu.es [158.227.2.29]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5AJx72V001642 for ; Fri, 10 Jun 2005 15:59:08 -0400 Received: from lgsx14.lg.ehu.es (localhost [127.0.0.1]) by lgsx14.lg.ehu.es (8.12.10/8.12.10) with ESMTP id j5AJJKp8027070 for ; Fri, 10 Jun 2005 21:19:20 +0200 (MEST) Received: from Amphiaraus.sq.ehu.es (sqpc99.sq.ehu.es [158.227.161.199]) by lgsx14.lg.ehu.es (8.12.10/8.12.10) with ESMTP id j5AJJFL9027046 for ; Fri, 10 Jun 2005 21:19:20 +0200 (MEST) From: Txema Mercero Organization: EHU To: chemistry.-at-.ccl.net Subject: Re: CCL:energy of Cr Date: Fri, 10 Jun 2005 21:18:07 +0200 User-Agent: KMail/1.7.1 References: <015c01c56dde$2f7262c0$11e35ba5@che> In-Reply-To: <015c01c56dde$2f7262c0$11e35ba5@che> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit Content-Disposition: inline Message-Id: <200506102118.07658.jm.mercero.-at-.ehu.es> X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Have you checked that these results correspond to the same electronic state?, i.e., are the electrons in the same orbitals? Friday 10 June 2005 19:02-ean, yixuan wang-k idatzi zuen: > Dear All, > > I tried a few combinations by varing SCF and Integral with G03 B04 > (C02) for a lot of transition metals. Most of them reasonably differ. > However, I was surprised by the results of Cr. The details are as follows. > > a) # b3lyp/gen pseudo=read b) #b3lyp/gen pseudo=read c) > b3lyp/gen pseudo=read integral(grid=ultrafine) scf=qc > scf=qc integral(grid=ultrafine) > > 0 5 > Cr > > Cr 0 > LanL2dz > **** > > Cr 0 > LanL2dz > > Energy: -86.2396491893au -86.2396526553 > -86.148570844 > > In addition, G98 A11 gives -86.2396549360 and -86.2396550127 for the > cases b and c, respectively. > > > Yixuan Wang > Texas A&M Univ -- Ikus e-mail helbide berria! Be aware of the new e-mail address! e-mail: jm.mercero.-at-.ehu.es From chemistry-request@ccl.net Fri Jun 10 16:07:27 2005 Received: from zproxy.gmail.com (zproxy.gmail.com [64.233.162.195]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5AK7Nww002017 for ; Fri, 10 Jun 2005 16:07:23 -0400 Received: by zproxy.gmail.com with SMTP id 13so1138232nzp for ; Fri, 10 Jun 2005 13:07:22 -0700 (PDT) DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=beta; d=gmail.com; h=received:message-id:date:from:reply-to:to:subject:in-reply-to:mime-version:content-type:content-transfer-encoding:content-disposition:references; b=rNWulKSvMypguMgcFP8ikVC/KTl1p+fmL2TXPcw9DuhNBLba6GRc7Mpp/rRHwCV0poVfxY1EAeKVkBtd+6ECf0l/8eCy6LnNNKiwQL40ZZ4CSkoGlcgj8jKtVhHeTQrq4LqARFLi7294ZHtiQmcEdIl8V/N4egrUUsYWWx6BF1E= Received: by 10.36.68.5 with SMTP id q5mr93395nza; Fri, 10 Jun 2005 13:07:22 -0700 (PDT) Received: by 10.36.7.4 with HTTP; Fri, 10 Jun 2005 13:07:22 -0700 (PDT) Message-ID: Date: Fri, 10 Jun 2005 16:07:22 -0400 From: Gustavo Seabra Reply-To: To: chemistry..at..ccl.net Subject: Re: CCL:NMR structure determination software In-Reply-To: Mime-Version: 1.0 Content-Type: text/plain; charset=WINDOWS-1252 Content-Disposition: inline References: X-Spam-Status: No, score=1.4 required=5.0 tests=RCVD_BY_IP,REPLY_TO_EMPTY autolearn=no version=3.0.3 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from base64 to 8bit by server.ccl.net id j5AK7Rww002021 On 6/9/05, Axel Mathieu wrote: > > > > Greetings CCL'ers: > > > > I was wondering if any of you were willing to share your expert opinion on > the type of minimal and hopefully rather inexpensive software set-up needed > to solve NMR solution structures (including visualization). I'm currently > using MOE which I really like for all my modeling needs but it really has > too many bells and whistles for just the NMR structure determination that we > want to accomplish now. > > > > I do understand that there exist many algorithms to solve NMR structures > many of which are "free" to non-profit organizations - and I do not want to > embark on a discussion of how and which software is better. I simple want to > see if there is a @simple@ cost-effective NMR structure determination set-up > for commercial organizations. > > > > If any of you offer such solutions, please do not hesitate to contact me as > I am interested. > > Again many thanks to the community for the immense help, > > > > APM Hi, There was a project called "Seneca" > From their web page: " SENECA is a program package for Computer Assisted Structure Elucidation (CASE). It attempts to find the constitution of an unknown molecule upon evidence from spectroscopic data, in particular from NMR" (see http://seneca.sourceforge.net/SENECA_Intro.html) SENECA is now part of the CDK (Chemistry Development Kit) which, AFAIK, is free: http://almost.cubic.uni-koeln.de/cdk/ -- --------------------------------------------------------------------------------------------- Gustavo Seabra Postdoctoral Associate Quantum Theory Project University of Florida Registered Linux user number 381680 Say NO! to software patents: http://www.nosoftwarepatents.com --------------------------------------------------------------------------------------------- If at first you don't succeed... ...skydiving is not for you. From chemistry-request@ccl.net Fri Jun 10 16:46:00 2005 Received: from mail.pomona.edu (exchange1.campus.pomona.edu [134.173.71.128]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5AKjvCO003161 for ; Fri, 10 Jun 2005 16:45:58 -0400 X-MimeOLE: Produced By Microsoft Exchange V6.5.7226.0 Content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C56DFD.6471E525" Subject: RE: Defining orbitals Date: Fri, 10 Jun 2005 13:45:52 -0700 Message-ID: <658E70C89419784380590FDD04A1D91801B0DDFF..at..EVSFACULTYSTAFF.campus.pomona.edu> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: Defining orbitals Thread-Index: AcVtf9T6jOK0I4jOThiRt9csA1EDMgAfTfIg From: "Wayne Steinmetz" To: X-Spam-Status: No, score=0.9 required=5.0 tests=FROM_ENDS_IN_NUMS, HTML_MESSAGE,HTML_TEXT_AFTER_BODY,HTML_TEXT_AFTER_HTML autolearn=no version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net This is a multi-part message in MIME format. ------_=_NextPart_001_01C56DFD.6471E525 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable The electrons belong to the entire atom and are not constrained to any orbital. One uses orbitals to construct the wave function. One must be sure that the set of orbitals, i.e. the basis set, is sufficiently flexible to describe completely the molecular species. You are dealing with an atomic species so a polarization basis set is probably not needed. =20 Wayne E. Steinmetz Carnegie Professor of Chemistry Woodbadge Course Director Chemistry Department Pomona College 645 North College Avenue Claremont, California 91711-6338 USA phone: 1-909-621-8447 FAX: 1-909-707-7726 Email: wsteinmetz..at..pomona.edu WWW: pages.pomona.edu/~wsteinmetz =20 -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request..at..ccl.net] On Behalf Of Christopher Thompson Sent: Thursday, June 09, 2005 6:09 PM To: chemistry..at..ccl.net Subject: CCL:Defining orbitals =20 Gday,=20 =20 I would like to do an MP2 calc on a Li- species in triplet state.=20 =20 With one electron in the s orbital and one in a p orbital,=20 how can you constrain the electron to say the px orbital?=20 =20 Cheers,=20 cdth..at..unimelb.edu.au=20 =20 Christopher Thompson=20 Laser Spectroscopy Group=20 School of Chemistry=20 University of Melbourne=20 ------_=_NextPart_001_01C56DFD.6471E525 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

The electrons belong to the entire atom and are not constrained to any = orbital. One uses orbitals to construct the wave function. One must be sure = that the set of orbitals, i.e. the basis set, is sufficiently flexible to = describe completely the molecular species. You are dealing with an atomic = species so a polarization basis set is probably not needed.

Wayne E. = Steinmetz

Carnegie Professor of = Chemistry

Woodbadge Course = Director

Chemistry = Department

Pomona College

645 North College = Avenue

Claremont, California = 91711-6338

USA

phone: = 1-909-621-8447

FAX: = 1-909-707-7726

Email: = wsteinmetz..at..pomona.edu

WWW: = pages.pomona.edu/~wsteinmetz

-----Original = Message-----
From: Computational = Chemistry List [mailto:chemistry-request..at..ccl.net] On Behalf Of Christopher Thompson
Sent: Thursday, June 09, = 2005 6:09 PM
To: chemistry..at..ccl.net
Subject: CCL:Defining = orbitals

Gday,

I would like to do an MP2 calc on a Li- = species in triplet state.

With one electron in the s orbital and one in = a p orbital,

how can you constrain the electron to say the = px orbital?

Cheers,

cdth..at..unimelb.edu.au

Christopher = Thompson

Laser = Spectroscopy Group

School of = Chemistry

University of = Melbourne

=00 ------_=_NextPart_001_01C56DFD.6471E525-- From chemistry-request@ccl.net Fri Jun 10 20:47:50 2005 Received: from LaTech.edu (selene.LaTech.edu [138.47.18.25]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5B0liIQ011089 for ; Fri, 10 Jun 2005 20:47:44 -0400 Received: from localhost (localhost [127.0.0.1]) by LaTech.edu (Postfix) with ESMTP id E81CD309333 for ; Fri, 10 Jun 2005 18:44:56 -0500 (CDT) Received: from LaTech.edu ([127.0.0.1]) by localhost (selene.latech.edu [127.0.0.1]) (amavisd-new, port 10024) with LMTP id 64251-01-64 for ; Fri, 10 Jun 2005 18:44:54 -0500 (CDT) Received: from helius.latech.edu (helius.LaTech.edu [138.47.18.18]) by LaTech.edu (Postfix) with ESMTP id 6F2BC308981 for ; Fri, 10 Jun 2005 18:44:54 -0500 (CDT) Received: from MobilPacha (unknown [138.47.56.69]) by helius.latech.edu (Postfix) with SMTP id 4B0F799203 for ; Fri, 10 Jun 2005 18:44:54 -0500 (CDT) Message-ID: <023b01c56e16$60d7d2e0$10982f8a@MobilPacha> From: "Derosa-Latech" To: References: <658E70C89419784380590FDD04A1D91801B0DDFF :: EVSFACULTYSTAFF.campus.pomona.edu> Subject: Re: CCL:Defining orbitals Date: Fri, 10 Jun 2005 18:44:44 -0500 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0238_01C56DEC.77EAE780" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2900.2180 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2900.2180 X-Virus-Scanned: amavisd-new at latech.edu X-Spam-Status: No, score=1.5 required=5.0 tests=DNS_FROM_RFC_BOGUSMX, HTML_MESSAGE autolearn=no version=3.0.3 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net This is a multi-part message in MIME format. ------=_NextPart_000_0238_01C56DEC.77EAE780 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable I am puzzled by the question. If I understand correctly, by constraining = electrons to particular atomic orbitals, you already define a wave = function which is now not a result of your calculation and thus may or = may not be a solution of the Schr=F6dinger equation (what is an = eigenvalue problem). What is it that you want to do, get the energy of = the system in that particular state?=20 ----- Original Message -----=20 From: Wayne Steinmetz=20 To: chemistry :: ccl.net=20 Sent: Friday, June 10, 2005 3:45 PM Subject: CCL:Defining orbitals The electrons belong to the entire atom and are not constrained to any = orbital. One uses orbitals to construct the wave function. One must be = sure that the set of orbitals, i.e. the basis set, is sufficiently = flexible to describe completely the molecular species. You are dealing = with an atomic species so a polarization basis set is probably not = needed. Wayne E. Steinmetz Carnegie Professor of Chemistry Woodbadge Course Director Chemistry Department Pomona College 645 North College Avenue Claremont, California 91711-6338 USA phone: 1-909-621-8447 FAX: 1-909-707-7726 Email: wsteinmetz :: pomona.edu WWW: pages.pomona.edu/~wsteinmetz -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request :: ccl.net] = On Behalf Of Christopher Thompson Sent: Thursday, June 09, 2005 6:09 PM To: chemistry :: ccl.net Subject: CCL:Defining orbitals Gday,=20 I would like to do an MP2 calc on a Li- species in triplet state.=20 With one electron in the s orbital and one in a p orbital,=20 how can you constrain the electron to say the px orbital?=20 Cheers,=20 cdth :: unimelb.edu.au=20 Christopher Thompson=20 Laser Spectroscopy Group=20 School of Chemistry=20 University of Melbourne=20 ------=_NextPart_000_0238_01C56DEC.77EAE780 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

I am puzzled by the question. If I = understand=20 correctly, by constraining electrons to particular atomic orbitals, you = already=20 define a wave function which is now not a result of your = calculation and=20 thus may or may not be a solution of the Schr=F6dinger equation (what is = an=20 eigenvalue problem). What is it that you want to do, get the = energy of the=20 system in that particular state?

----- Original Message -----
From:=20 Wayne=20 Steinmetz
To: chemistry :: ccl.net

Sent: Friday, June 10, 2005 = 3:45 PM

Subject: CCL:Defining = orbitals

The=20 electrons belong to the entire atom and are not constrained to any=20 orbital. One uses orbitals to construct the wave function. = One=20 must be sure that the set of orbitals, i.e. the basis set, is = sufficiently=20 flexible to describe completely the molecular species. You are = dealing=20 with an atomic species so a polarization basis set is probably not=20 needed.

Wayne E.=20 Steinmetz

Carnegie = Professor of=20 Chemistry

Woodbadge = Course=20 Director

Chemistry=20 Department

Pomona=20 College

645 North = College=20 Avenue

Claremont, = California=20 91711-6338

USA

phone:=20 1-909-621-8447

FAX:=20 1-909-707-7726

Email:=20 wsteinmetz :: pomona.edu

WWW:=20 pages.pomona.edu/~wsteinmetz

-----Original=20 Message-----
From:=20 Computational Chemistry List [mailto:chemistry-request :: ccl.net] = On Behalf Of Christopher=20 Thompson
Sent: = Thursday, June=20 09, 2005 6:09 PM
To:=20 chemistry :: ccl.net
Subject:=20 CCL:Defining orbitals

Gday, =

I would like to do an MP2 = calc on a Li-=20 species in triplet state.

With one electron in the s = orbital and=20 one in a p orbital,

how can you constrain the = electron to say=20 the px orbital?

Cheers, =

cdth :: unimelb.edu.au=20

Christopher=20 Thompson

Laser=20 Spectroscopy Group

School of=20 Chemistry

University=20 of Melbourne

------=_NextPart_000_0238_01C56DEC.77EAE780-- From chemistry-request@ccl.net Fri Jun 10 20:05:10 2005 Received: from zproxy.gmail.com (zproxy.gmail.com [64.233.162.203]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5B056I6008930 for ; Fri, 10 Jun 2005 20:05:06 -0400 Received: by zproxy.gmail.com with SMTP id 13so1232952nzp for ; Fri, 10 Jun 2005 17:05:06 -0700 (PDT) DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=beta; d=gmail.com; h=received:message-id:date:from:reply-to:to:subject:in-reply-to:mime-version:content-type:content-transfer-encoding:content-disposition:references; b=RtnI233hvR/Q4iF8IH/qoT2lP4p5OptCuWMMl28QOzwiJLAFGGg1qe9iXXMGIeBANDuOm5fv8uiN+/f753NSuGbenYoUPDDF74b+6us1e6cxGbXSTBq7CBOA6F8yL1bRAtWs9hk5OhFloRaJakwGmyjQ0groimAk7kW0vrR2xKA= Received: by 10.36.222.70 with SMTP id u70mr1652303nzg; Fri, 10 Jun 2005 17:05:06 -0700 (PDT) Received: by 10.36.7.4 with HTTP; Fri, 10 Jun 2005 17:05:06 -0700 (PDT) Message-ID: Date: Fri, 10 Jun 2005 20:05:06 -0400 From: Gustavo Seabra Reply-To: To: chemistry [a] ccl.net Subject: Re: CCL:about excess electron transfer theoretical study In-Reply-To: Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Disposition: inline References: X-Spam-Status: No, score=1.4 required=5.0 tests=RCVD_BY_IP,REPLY_TO_EMPTY autolearn=no version=3.0.3 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id j5B05AI6008934 Did you try Google Scholar? http://www.scholar.google.com/scholar?as_q=%22electron+transfer%22+theoretical&num=10&btnG=Search+Scholar&as_epq=&as_oq=DNA+%22pi-stacked%22&as_eq=&as_occt=any&as_sauthors=&as_publication=&as_ylo=&as_yhi=&hl=en&lr= hth. On 6/9/05, jz7 [a] duke.edu wrote: > Dear all, > > I am reading about study on excess electron transfer (mainly thgouth DNA > or pi-stack system). Although there are more and more experiments on this, > I didn't find much theoretical reference talking about method study it. Is > there really no such publication? Anyone who has seen it or know where I > can find it please give me some help! Any information would be helpful, > even reference on the conducticity of DNA would be helpful. > > Thanks a lot! > > Jeny > > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: line > and send your message to: CHEMISTRY [a] ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST [a] ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your is mail bouncing from ccl.net domain due to spam filters, please > use the Web based form from CCL Home Page > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > -- --------------------------------------------------------------------------------------------- Gustavo Seabra Postdoctoral Associate Quantum Theory Project University of Florida Registered Linux user number 381680 Say NO! to software patents: http://www.nosoftwarepatents.com --------------------------------------------------------------------------------------------- If at first you don't succeed... ...skydiving is not for you. From chemistry-request@ccl.net Fri Jun 10 22:32:35 2005 Received: from mxout1.cac.washington.edu (mxout1.cac.washington.edu [140.142.32.134]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5B2WSNZ023908 for ; Fri, 10 Jun 2005 22:32:29 -0400 Received: from smtp.washington.edu (smtp.washington.edu [140.142.33.9]) by mxout1.cac.washington.edu (8.13.4+UW05.04/8.13.4+UW05.05) with ESMTP id j5B1J95X007459 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=OK) for ; Fri, 10 Jun 2005 18:19:09 -0700 Received: from u.washington.edu (wgibbs.bchem.washington.edu [128.95.235.4]) (authenticated authid=ohucke) by smtp.washington.edu (8.13.4+UW05.04/8.13.4+UW05.05) with ESMTP id j5B1J9pa024919 (version=TLSv1/SSLv3 cipher=RC4-MD5 bits=128 verify=NOT) for ; Fri, 10 Jun 2005 18:19:09 -0700 Message-ID: <42AA3C0C.3090805 = u.washington.edu> Date: Fri, 10 Jun 2005 18:19:08 -0700 From: Oliver Hucke Reply-To: ohucke = u.washington.edu User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.0.2) Gecko/20030208 Netscape/7.02 X-Accept-Language: en-us, en MIME-Version: 1.0 To: CCL Subject: FLO & Allegrow Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Dear CCLer's can somebody point me to information on the commercial availability of the programs FLO+ and Allegrow, written by Colin McMartin and Regine Bohacek? Any hints are highly appreciated. Oliver -- _______________________________________________________________ Oliver Hucke, Dr. Health Sciences Building - K418C University of Washington 1959 NE Pacific St. Dept. of Biochemistry phone: (206) 685 7046 Box 357742 fax : (206) 685 7002 Seattle, WA 98195-7742 email: ohucke = u.washington.edu _______________________________________________________________