From acp37@rs1.rrz.Uni-Koeln.DE Mon Nov 20 07:51:04 1995 Received: from rs1.rrz.Uni-Koeln.DE for acp37@rs1.rrz.Uni-Koeln.DE by www.ccl.net (8.6.10/950822.1) id HAA19008; Mon, 20 Nov 1995 07:42:17 -0500 Received: by rs1.rrz.Uni-Koeln.DE id AA73733 (5.67b/IDA-1.5 for CCL ); Mon, 20 Nov 1995 13:41:37 +0100 Date: Mon, 20 Nov 1995 13:41:37 +0100 (MET) From: "T. Koch" To: CCL Subject: How to measure stability Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear netters, I have a question which should be of considerable interest for computational chemists. The question is: How do I measure computationally the stability of organic molecules? I study some molecules which presumably have not yet been prepared. And I would like to know if these molecules have a chance to exist. What I did so far is the most simple and obvios method: I compared the absolute electronic energy with the same quantity on a known and more or less stable isomer. But from the results I got I think that this is only a crude approximation on a "measure" of stability and reactivity. What I didn't examine yet but could be quite sensible (I think) is doing a CI or MCSCF calculation and looking at the energy gap between the frontier orbitals and comparing it to known isomers. Another way could be an examination of the computed IR-spectrum. Are there very low frequencies (shallow dips in the potential engergy surface) which could lead to "new" molecules? Is there a way to determine "centers of reactivity" ? Has someone any ideas about this topic? I will summarize it to the list, if I get any responses ;) Bye, Thorsten /-----------------------------------------------------------------\ | Thorsten Koch | | Institut fuer Physikalische Chemie II der Universitaet zu Koeln | | Luxemburger Str. 116, 50939 Koeln, Germany | | acp37@rrz.uni-koeln.de | | Tel. +49 [0]221 470 4816 | \-----------------------------------------------------------------/ From owner-chemistry@ccl.net Mon Nov 20 09:06:05 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id IAA20364; Mon, 20 Nov 1995 08:58:09 -0500 Received: from rc4.vub.ac.be for fdeprof@vub.ac.be by bedrock.ccl.net (8.7.1/950822.1) id IAA24912; Mon, 20 Nov 1995 08:57:54 -0500 (EST) Received: from orca.vub.ac.be (orcae.vub.ac.be [134.184.15.10]) by rc4.vub.ac.be (8.6.10/3.4.2.ap (rc4)) id PAA03767; Mon, 20 Nov 1995 15:00:57 +0100 Received: (fdeprof@localhost) by orca.vub.ac.be (940816.SGI.8.6.9/3.4.1.ap (orca)) id OAA10160; Mon, 20 Nov 1995 14:57:40 +0100 From: fdeprof@vub.ac.be (De Proft Frank) Message-Id: <199511201357.OAA10160@orca.vub.ac.be> Subject: DFT potentials To: chemistry@ccl.net Date: Mon, 20 Nov 1995 14:57:40 +0100 (MET) X-Mailer: ELM [version 2.4 PL23] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Dear netters, Is there anyone who has an idea about how to plot a given (DFT) exchange and correlation potential starting from an atomic alfa and beta electron density and gradient ? Are there any programs or routines for that ? Help with this problem would be highly appreciated. Please, adress all the answers to me, I will summarize afterwards. Yours sincerely, F. De Proft From huang@mazda.wavefun.com Mon Nov 20 11:06:07 1995 Received: from volvo.wavefun.com for huang@mazda.wavefun.com by www.ccl.net (8.6.10/950822.1) id KAA23749; Mon, 20 Nov 1995 10:58:44 -0500 Received: by volvo.wavefun.com (931110.SGI/930416.SGI) for chemistry@www.ccl.net id AA02964; Mon, 20 Nov 95 07:59:10 -0800 Received: from mazda.wavefun.com(198.147.95.6) by volvo.wavefun.com via smap (V1.3) id sma002962; Mon Nov 20 07:59:06 1995 Received: by mazda.wavefun.com (931110.SGI/930416.SGI) for @volvo.wavefun.com:chemistry@www.ccl.net id AA03311; Mon, 20 Nov 95 07:58:28 -0800 From: "Wayne Huang" Message-Id: <9511200758.ZM3309@mazda.wavefun.com> Date: Mon, 20 Nov 1995 07:58:28 -0800 In-Reply-To: Osawa Shuichi "CCL:Effective core potential for Gd" (Nov 17, 2:37am) References: <199511170233.LAA26054@postman.riken.go.jp> Reply-To: huang@wavefun.com X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: Osawa Shuichi , chemistry@www.ccl.net Subject: Re: CCL:Effective core potential for Gd Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 Related to the question on ECP for Gd: Gd semiempirical parameters have been developed here using PM3(tm) formalism. I could supply the initial results and run your test molecule for you. Direct your request to support@wavefun.com. --Wayne -- +---------------------------------------------------------------------+ | Wayne Huang, Ph.D. | 18401 Von Karman, Suite 370 | | Computational Chemist | Irvine, California 92715 | | Wavefunction, Inc. | (714)955-2120 Fax: (714)955-2118 | | huang@wavefun.com | World Wide Web: http://wavefun.com | +---------------------------------------------------------------------+ From yu@infiniti.wavefun.com Mon Nov 20 18:21:13 1995 Received: from volvo.wavefun.com for yu@infiniti.wavefun.com by www.ccl.net (8.6.10/950822.1) id SAA08643; Mon, 20 Nov 1995 18:18:42 -0500 Received: by volvo.wavefun.com (931110.SGI/930416.SGI) for CHEMISTRY@www.ccl.net id AA04457; Mon, 20 Nov 95 15:19:13 -0800 Received: from infinity.wavefun.com(198.147.95.8) by volvo.wavefun.com via smap (V1.3) id sma004454; Mon Nov 20 15:18:43 1995 Received: by infiniti.wavefun.com (931110.SGI/930416.SGI.AUTO) for @volvo.wavefun.com:CHEMISTRY@www.ccl.net id AA01914; Mon, 20 Nov 95 15:18:05 -0800 From: "Jianguo Yu" Message-Id: <9511201518.ZM1912@infiniti.wavefun.com> Date: Mon, 20 Nov 1995 15:18:00 -0800 Reply-To: yu@wavefun.com X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: CHEMISTRY@www.ccl.net Subject: New direction of semi-empirical? Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 Hi Netters, After working in the use and develop of semi-empirical methods a few years, while many "colleagues" of mine (all computayional chemist community) gave me many their opinions about SE, I am seriously thinking of the direction of new SE method and I believe that many people are trying or have started to develop new generation of SE. As doing any things, it certainly has enormous value to put many people's wisdom together. So I like to ask anybody's opinions about the direction of new SE and the weakness of current SE methods. I will summarize it in the net. Best regards! Jianguo Yu -- +-----------------------+------------------+-------------------------+ |Jianguo Yu, Ph.D. | ______________ | E-Mail: yu@wavefun.com | |Computational Chemist | \ _________ / | Phone: (714)955-2120 | |Wavefunction Inc. | \ \\\\\\\\/ | Fax: (714)955-2118 | |18401 Von Karman | \ \\\\\/ | "The doctrines observe | |Suite 370 | \ \\/ | nature" | |Irvine, CA 92715 | \/ | Lao-tzu (604-531 B.C.)| +-----------------------+------------------+-------------------------+ From schrecke@zinc.chem.ucalgary.ca Mon Nov 20 19:06:14 1995 Received: from zinc.chem.ucalgary.ca for schrecke@zinc.chem.ucalgary.ca by www.ccl.net (8.6.10/950822.1) id SAA09062; Mon, 20 Nov 1995 18:54:06 -0500 From: Received: by zinc.chem.ucalgary.ca (AIX 3.2/UCB 5.64/4.03) id AA21884; Mon, 20 Nov 1995 16:48:29 -0700 Message-Id: <9511202348.AA21884@zinc.chem.ucalgary.ca> Subject: NMR shift calc'n in G94. Summary To: chemistry@www.ccl.net Date: Mon, 20 Nov 1995 16:48:26 -0700 (MST) Reply-To: schrecke@zinc.chem.ucalgary.ca (Georg Schreckenbach) X-Mailer: ELM [version 2.4 PL23] Content-Type: text Content-Length: 7184 Hi everybody, recently, I posted a question regarding the calculation of NMR chemical shifts (shieldings) in G94. I got some interesting and nice replies. Here is my summary. Many thanks to all who replied, I certainly enjoyed hearing from you! If anybody wants to comment further on the subject, please do so. Originally, I asked (Fri, 10 Nov 1995) > this is a question to the GAUSSIAN user's community. > > I understand that G94 can calculate NMR chemical shifts with > the GIAO scheme. Now I would like to know whether the shift > calculation is possible only on some levels of theory, > and if so, on which ones. E.g., I don't think that -- say -- > Coupled Cluster methods and shift calculations are compatible > yet in G94. In particular, I'd like to know wether G94/DFT and > shift calculations go together or not. > > Any references to papers using G94 for shift calculations would be > of interest, too. > > I am not a GAUSSIAN user, therefore I thought I ask the net; > I do so out of pure curiosity. For my part, I am working on the development > of a DFT-GIAO method for the chemical shift (shielding, to be more > precisely). It is therefore interesting to know what other people out > there are doing. > These are in fact two questions, one regarding the abilities of G94, and one about any references. As far as the first one is concerned, this is completely answered by the Gaussian people proper, and also by some other users, see below (e.g., David Case and Martin Kaupp). For the other part, my understanding is that the NMR feature (and G94 as such!) is so new that there aren't many printed papers yet. Here are the responses that I got: ------------------------------------------------------------------------------ David A. Case writes (Fri, 10 Nov 95) Hi George! The G94 manual states that shielding calculations can be done for "Hartree-Fock and pure DFT( i.e. non-hybrid ) methods." I have used it a fair amount with HF wavefunctions [one paper in press, I can send it to you if you like, concerns proton shieldings in aromatic ring systems.] I tried G94 once with DFT, but got very weird results, pretty clearly incorrect, but I have not had time to follow up on this result; it may be a result of an error on my part. If I get time to try it again, I'll let you know. Good luck on your studies. I've been using the Malkins/Salahub version of deMon for shielding calculations for bioorganic systems like peptides and sugars. Again, mainly concentration on proton shieldings. Results look pretty good (with big enough basis sets, etc.). Let me know if you want more details. Might be fun to run some test molecules in parallel, just to see how close your stuff and theirs is. ...dac ================================================================== David A. Case | internet: case@scripps.edu Dept. of Molecular Biology, MB1 | bitnet: case%scripps.edu@sdsc The Scripps Research Institute | fax: 619-554-3789 10666 N. Torrey Pines Rd. | phone: 619-554-9768 La Jolla CA 92037 USA | WWW: http://scripps.edu/case ================================================================== ------------------------------------------------------------------------------ Doug Fox (from Gaussian proper) writes (Mon Nov 13) Georg, Gaussian 94 can compute GIAO shielding tensors for both HF and DFT methods. Local gauge shielding tensors and magnetic susceptibiliities can be computed for HF and DFT using the Continuous Set of Gauge Transformations (CSGT) or the Individual Gauge for Atoms In Molecules (IGAIM) methods. We are working on extensions to post-HF methods for future releases of Gaussian. Doug Fox help@gaussian.com ------------------------------------------------------------------------------ Renee Peloquin Mattie writes (Mon, 13 Nov 1995) ACES II does NMR shifts based on coupled cluster calculations. Renee Peloquin Mattie rpmattie@omni.voicenet.com ------------------------------------------------------------------------------ Martin Kaupp writes (Mon, 13 Nov 1995) Hi Georg, As you know, we are using the DFT(IGLO) approach of Malkin et al., mainly connected with deMon, but recently also with interfaces to other programs. As I have G94, I have also played around with its NMR features. The NMR shift calculations are at present possible with HF and 'pure' DFT (uncoupled KS, same as you are doing). I have actually already seen some posters and even one paper of people who claim to have used a hybrid DFT/HF functional, although this is not supported in the manual. Indeed, if you use the corresponding key-words, you get some resonably-looking results. However, it is not clear at all how it's done, uncoupled for the KS part, coupled for the HF part ? Also, I have seen no publication whatsoever describing G94's NMR features. Apart from GIAOs, the program also supports some other choices of gauge origin: CSGT (continuous set of gauge transformations), IGAIM (individual gauge for atoms in molecules), and of course common gauge origin. Best regards, Martin ------------------------------------------------------------------ | Dr. Martin Kaupp | | Max-Planck-Institut fuer Festkoerperforschung, | | Heisenbergstrasse 1, D-70569 Stuttgart, Germany, | | Tel.: country-code+711/689-1532 | | Fax.: country-code+711/689-1562 | | email: kaupp@vsibm1.mpi-stuttgart.mpg.de | | | | and Institut fuer Theoretische Chemie, Universitaet Stuttgart, | | Pfaffenwaldring 55, D-70569 Stuttgart, Germany | | Tel.: country-code+711/685-4399 | | Fax.: country-code+711/685-4442 | ------------------------------------------------------------------ ------------------------------------------------------------------------------ Frederic Bouyer writes (Mon, 13 Nov 1995) Hi Georg, Could I share with you replies you could receive? I am highly interested in NMR spectra on molecules from ab-initio calculations. Thank you very much in advance. Frederic Bouyer ------------------------------------------------------------------------------ Frederic BOUYER Laboratoire d'Electrochimie et de Chimie Analytique E.N.S.C.P. 11, rue Pierre et Marie Curie 75231 PARIS Cedex 05-France Tel: (33)-1-44-27-67-51/66-94 ou (33)-1-43-54-53-84 Fax: (33)-1-44-27-67-50 http://alcyone.enscp.jussieu.fr/Pages/LECA/GP/FB/ ------------------------------------------------------------------------------ ============================================================================== Georg Schreckenbach Tel: (Canada)-403-220 8204 Department of Chemistry FAX: (Canada)-403-289 9488 University of Calgary Email: schrecke@zinc.chem.ucalgary.ca 2500 University Drive N.W., Calgary, Alberta, Canada, T2N 1N4 ============================================================================== From quchunxu@bio.titech.ac.jp Mon Nov 20 20:51:15 1995 Received: from titbio-gw.bio.titech.ac.jp for quchunxu@bio.titech.ac.jp by www.ccl.net (8.6.10/950822.1) id UAA10445; Mon, 20 Nov 1995 20:39:56 -0500 Received: by titbio-gw.bio.titech.ac.jp (5.67+1.6W/tit-mx1.1); Tue, 21 Nov 95 10:36:23 JST Date: Tue, 21 Nov 95 10:36:23 JST From: Qu Chunxu Message-Id: <9511210136.AA25319@titbio-gw.bio.titech.ac.jp> To: chemistry@www.ccl.net Subject: cavity volume calculation Dear netters, I met a problem on cavity volume calculation. I am studying on the thermostability of 3-isopropylmalate dehydrogenase. Protein engineering showed that at a certain site, Ala-->Leu mutation increased the stability of protein. Crystallography analysis showed that the sidechain of Leucine reduced the cavity around mutation site. Although the dot surface illustration can show this point very well, we are asked to give the cavity volume in each case. However, we have no such a program. Could you help me? Thanks in advance. your sincerely Chunxu Qu Chunxu Qu Faculaty of Bioscience & Biotechnology Tokyo Institute of Technology Japan