From chemistry-request@www.ccl.net Tue Jan 12 04:39:11 1999 Received: from host7.lctn.u-nancy.fr (host7.lctn.u-nancy.fr [192.54.210.11]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id EAA04666 Tue, 12 Jan 1999 04:39:10 -0500 (EST) From: ferre@host7.lctn.u-nancy.fr Received: (from ferre@localhost) by host7.lctn.u-nancy.fr (AIX4.2/UCB 8.7/8.7) id KAA25238 for chemistry@www.ccl.net; Tue, 12 Jan 1999 10:11:22 +0100 (NFT) Date: Tue, 12 Jan 1999 10:11:22 +0100 (NFT) Message-Id: <199901120911.KAA25238@host7.lctn.u-nancy.fr> To: chemistry@www.ccl.net Subject: Inexpensive integrals Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-MD5: vFwjM5332y0mbzcSW3CqGw== Dear CCL During a SCF cycle (of a G94 / OPT job), I found this message : Problem detected with inexpensive integrals. Switching to full accuracy and repeating last cycle. Does anyone know what it means ? My job wasn't killed and the SCF cycle has converged normally. Thanks all. --------------------------------------------------------------------------- Nicolas FERRE Tel : 03.83.91.20.00. poste 35.32. Fax : 03.83.91.25.30. Laboratoire de Chimie Theorique Universite Henri Poincare Nancy 1 BP 239 E-mail : ferre@lctn.u-nancy.fr 54506 VANDOEUVRE-LES-NANCY Cedex --------------------------------------------------------------------------- From chemistry-request@www.ccl.net Tue Jan 12 08:20:56 1999 Received: from csb0.IPC.PKU.EDU.CN (csb0.ipc.pku.edu.cn [162.105.177.12]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id IAA05402 Tue, 12 Jan 1999 08:20:53 -0500 (EST) Received: by csb0.IPC.PKU.EDU.CN (920330.SGI/940406.SGI.AUTO) for CHEMISTRY@www.ccl.net id AA11269; Tue, 12 Jan 99 21:19:24 -0800 Date: Tue, 12 Jan 1999 21:19:22 -0800 (PST) From: Fenglou Mao To: "CHEMISTRY@www.ccl.net" Subject: ANSI C++ question? Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all, I am wondering if there is a ANSI C++ standard, and if have one, where I can find an introduction about it. And how about STL(standard template library) defined in ANSI C++, and how to find some introduction about it? Sincerely Yours, FengLou Mao ******************************* ADD:Mr. FengLou Mao Peking University BeiJing P.R.China Tel:86-10-62751490 Fax:86-10-62751725 From chemistry-request@www.ccl.net Tue Jan 12 09:50:23 1999 Received: from asia.chimfarm.unipg.it (asia.chimfarm.unipg.it [141.250.13.18]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id JAA06407 Tue, 12 Jan 1999 09:49:35 -0500 (EST) Received: from asia.chimfarm.unipg.it (localhost [127.0.0.1]) by asia.chimfarm.unipg.it (950413.SGI.8.6.12/950213.SGI.AUTOCF) via SMTP id CAA26354 for ; Sat, 2 Mar 1996 02:06:27 +0100 Sender: antonio@asia.chimfarm.unipg.it Message-ID: <31379F10.41C6@asia.chimfarm.unipg.it> Date: Sat, 02 Mar 1996 02:06:24 +0100 From: Antonio Macchiarulo Organization: Istituto di Chimica e Tecnologia del Farmaco X-Mailer: Mozilla 3.01SGoldC-SGI (X11; I; IRIX 6.3 IP32) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: Alogenation effects on benzene Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear all, How can I quantify the inductive and other possible effects of alogens on aromatic ring ?. There is any article which explains such a way ? Regards Antonio Macchiarulo ********************************************************* * Dr. Antonio Macchiarulo * * Istituto di Chimica e Tecnologia del Farmaco * * Universita' degli Studi di Perugia * * Via del Liceo 1, 06100 * * Perugia (ITALY). * * E_mail: antonio@asia.chimfarm.unipg.it * * Voice: ++ 39 75 5855114. * ********************************************************* From chemistry-request@www.ccl.net Sun Jan 10 03:52:47 1999 Received: from achilles.noc.ntua.gr (achilles.noc.ntua.gr [147.102.222.210]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id DAA22006 Sun, 10 Jan 1999 03:52:46 -0500 (EST) Received: from hermes.central.ntua.gr (hermes.central.ntua.gr [147.102.240.3]) by achilles.noc.ntua.gr (8.8.8/8.8.8) with ESMTP id KAA07777 for ; Sun, 10 Jan 1999 10:52:44 +0200 (EET) Received: by hermes.central.ntua.gr with SMTP id KAA09410 ; Sun, 10 Jan 1999 10:48:41 +0200 (EET) Message-ID: <000d01be3c76$41f16860$02df6693@titanfocalpoint> From: "Nick Fotopoulos" To: Subject: Solid state exercise setup ideas Date: Sun, 10 Jan 1999 10:50:20 +0200 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_000A_01BE3C87.0496DD40" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.72.2106.4 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 Dear CCLer's, I am seting up an exercise for engineering students that will present = them with the current achievements & capabilities of computational = chemistry (especially in the solid state field as many of them follows = electrical engineering). The final target is to stimulate and prepare = them to use the readily available s/w tools or at least be able to = operate in interdisciplinary projects. The exercise approach is molecule --> supramolecular aggr. --> = macromolecules ---> solid state I have already finalized the first 3 phases using freely available s/w = PCGAMESS-US, Hyperchem 5.0 (almost), and Molden.on WIN95 platform, = explaining the various uses of CompChem at differenr levels of theory. I am also aware of BiconEdit program capabilities for DOS and Brillouin = zones prediction at EHMO level. Could you suggest me solid state systems and/or other material that = would be relevant to form a good teaching basis ? Also, are you aware of software capable for solid state calculations at = a level of theory greater than EHMO? I will summarise to the list. Best regards and wishes for a happy & fruitful new year, Dr. Nick Fotopoulos National Technical Univ. of Athens From chemistry-request@www.ccl.net Sun Jan 10 03:52:49 1999 Received: from mail.matav.hu (mail.matav.hu [145.236.224.244]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id DAA22009 Sun, 10 Jan 1999 03:52:48 -0500 (EST) Received: (qmail 12883 invoked from network); 10 Jan 1999 09:52:43 +0100 Received: from unknown (HELO inhale) (195.70.54.253) by mail.matav.hu with SMTP; 10 Jan 1999 09:52:43 +0100 Message-ID: <3697B311.E8D65392@chemaxon.com> Date: Sat, 09 Jan 1999 20:50:41 +0100 From: Ferenc Csizmadia Organization: ChemAxon X-Mailer: Mozilla 4.01 [en] (WinNT; I) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: New ideas for chemistry software X-Priority: 3 (Normal) Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit A few weeks ago I posted the following letter to CCL: ===== I would like to know your opinion about future trends in chemical software development. What will be the hottest topics in the near future? What are the areas that need new approaches from program developers? ===== Thank you for the contributions. Here are the answers I received so far. 1. ===== I would like to submit an idea which is based on the article of Mok, Neumann and Handy, J. Phys. Chem. 1996, 100, 6225-6230. Precise calculations (approaching FCI-quality) should be quite possible, at a cost scaling as CASSCF, if one were to include only excitations corresponding to nondynamical correlation in a CASSCF calculation, and afterwards using a correlation functional fittet to only dynamical correlation (He or Ne) in a DFT calculation based on densities from the CASSCF calculation. Thomas Bligaard Pedersen University of Strasbourg and Technical University of Denmark 2. ===== It seems nearest future trends in chemistry are more or less visible. To make it short: Biology, Biochemistry and related topics. >From the clear domination of physics up to the middle of our century scientific world is moving into "the living cell". You can proof it by analyzing the number of publications, impact-factors of various journals, the number of grants in difference fields of chemistry, and activity of funding organizations in general. Even in this List, proteins and DNA modeling and visualization, docking, MD, structure determination, ..., are the topics discussed quite often. Significant contribution and support are coming from the medicine related applications, i.e., QSAR, screening, drug design, etc. I am not to say that I like the situation, but one has to accept obvious things. Concerning the possible arias of software development, very likely it could be a structure calculation, refinement, prediction and analyzing programs for the most important biological molecules like proteins, DNA, etc. Of course all of the above with up to date Graphics User Interface. So, if you are going to start new software project, try to collect more info about structural biochemistry stuff. Valentin P. Ananikov NMR Group ND Zelinsky Institute of Organic Chemistry 3. ===== It would be nice to have a Windows program that would calculate the enthalpy of formation at 0K and at 298.15 K, and a program that would calculate rate constants. You would take the output file from a Gaussian 94 or Gaussian 98 calc and drag it into the Chemaxon window, click Start, and the program would calculate heats of formation or rate. For heat of formation the Gaussian output might be a G2, G2(MP2) or CBS job. The algorithm could be bases onA. Nicolaides, A. Rauk, M. N. Glukhovtsev, L. Radom, JPC, 1996, 100, 17460. for rate constants, methods might come from standard books on statistical thermodynamics (e.g. Steinfeld, Francisco and Hase). E. Lewars 4. ===== How to determine crystal structures from powder diffraction data is still hot topic. The 5 last years have seen the emergence of many ways of locating optimally a molecular model inside a cell (Monte Carlo, simulated annealing, genetic algorithm, packing considerations, optimized grid search,...). It seems that developers believe that pharmaceutical companies are, or will be interested. You cannot find any of these new softwares in the public domain, nor in the commercial one! See http://www.cristal.org/iniref.html for more details Structure/properties prediction is the way to continue to explore, not really new, but not really successful till now. Armel Le Bail - Université du Maine, Laboratoire des Fluorures 5. ===== In my humble opinion, linear scaling SCF theory will continue to get hotter, as applications become more wide spread and algorithms get more robust. Matt Challacombe Los Alamos National Laboratory Theoretical Division email: mchalla@t12.lanl.gov 6. ===== I think that some of the types of calculations that exist, but are seldom done, will become more widely used. Here are some of my picks. relativistic calculations solvent effects band structure calculations mesoscale calculations synthesis route prediction ab initio molecular dynamics Dave Young 7. ===== I am just reading -- again -- a very nice and very general article by Martin Head-Gordon that appeared in the centennial issue of J. Phys. Chem. He lists a lot of trends and challenges for electronic structure theory, and almost all of them are longer term, and still valid today. The reference is J. Phys. Chem. 1996, 100, 13213. In fact, the entire issue is worth a look as it contains various general reviews. Georg Schreckenbach 8. ===== I think the new ideas for chemistry software is: 1. Better organized interface. It is easy to learn. 2. Moved to cheaper but hign performance PC. FengLou Mao Peking University 9. ===== I think that simulation using virtual reality in all branches of chemistry. Jorge Arce Molina Instituto Superior Minero Metalurgico Las Coloradas s/n. 10. ===== I think we don t really need a lot of _new_ programmes; rather, we need a lot of extant programmes/source codes to be ported into Win95/WinNT executables. Now that the price of RAM is so low and we will soon have PCs with clock speeds exceeding 500 MHz, we should be able to run a lot of programmes on the PC that heretofore have been restricted to Unix workstations. For example, so far as I know, there is no simple, stand-alone programme for the PC that will calculate the molecular volume or solvent-accessible surface of a macromolecule (or even of a small molecule) from its .ent or .mol2 file. This would be a very useful tool for the community of PC computational chemists. Whilst MOPAC and AMPAC have been ported to DOS/Win, I know of no DOS/Win programme that can perform a conformational search in order to identify the (most likely) global energy minimum of a molecule _in an aqueous environment_. I believe that MacroModel contains a module which does this, so in principle it is possible to obtain a DOS/Win executable that can also do this. So far as I am aware, there are no publically-available DOS/Win programmes that use genetic algorithms for optimal selection of variables for linear regression analysis. Neither, so far as I know, does there exist a recent version of GOLPE that runs under DOS/Win. These would be very valuable chemometric tools for the PC compurtational chemist. Around April 1999 the C source code for the programme LigBuilder should be released. When it is, it will be a very useful addition to the PC computational chemistry armamentarium, if only someone would port it to a DOS/Win executable. The JPC solvent version was recently described [J. Chem. Phys. 109(1): 260 ( 98)]. However, there is no DOS/Win-compatible release of this method; such a release would be a valuable addition to the PC computational chemist s methodological arsenal. And there are other programmes so far available only for Unix which ought to be made available to PC users: PARM and GRID are two which spring to mind at the moment. And, of course, there remains a need for new and better ways of quickly calculating log P, log D, pKa, aqueous solubility, &., &c. S. Shapiro ===== The discussion is still open. If anyone would like to contribute please send a letter to CCL or me. Ferenc ~~~~~~ Ferenc Csizmadia, Ph.D. ChemAxon Ltd. Valyog u. 7, H-1032 Budapest, Hungary http://www.chemaxon.com T:+3620 9570988 mailto:fcsiz@chemaxon.com From chemistry-request@www.ccl.net Sun Jan 10 20:28:57 1999 Received: from Mercury.unix.acs.cc.unt.edu (mercury.acs.unt.edu [129.120.220.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id UAA24398 Sun, 10 Jan 1999 20:28:56 -0500 (EST) Received: from jove.acs.unt.edu (6930@jove.acs.unt.edu [129.120.220.41]) by Mercury.unix.acs.cc.unt.edu (8.8.8/8.8.8) with ESMTP id TAA23370; Sun, 10 Jan 1999 19:28:56 -0600 (CST) Received: from localhost (aiz0001@localhost) by jove.acs.unt.edu (8.8.8/8.8.8) with SMTP id TAA25088; Sun, 10 Jan 1999 19:28:55 -0600 (CST) Date: Sun, 10 Jan 1999 19:28:55 -0600 (CST) From: Anita Ilze Zvaigzne To: Ferenc Csizmadia cc: chemistry@www.ccl.net Subject: Re: CCL:New year -> new ideas for chemistry software In-Reply-To: <369384E9.24EE747D@chemaxon.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Wed, 6 Jan 1999, Ferenc Csizmadia wrote: > I would like to know your opinion about future trends in chemical > software development. What will be the hottest topics in the near > future? What are the areas that need new approaches from program > developers? > ===== > > It seems nearest future trends in chemistry are more or less visible. > To make it short: Biology, Biochemistry and related topics. > With regard to this discussion, I would like to add that the REASON why computational approaches and software are so enticing in biology, biochemistry, etc. is because of the difficulty in obtaining high-quality experimental data -- quickly and at low cost. The suggestion was made later in this discussion that if one wanted to start a new software project that one should look at structural biochemistry. I don't think that someone starting a new software project should necessarily limit themselves to this one area. There are many pressing needs in biology, biochemistry and molecular medicine OTHER than in structural modeling. There are many pressing needs in other areas of chemistry and engineering. Certainly, a software developer should also NOT neglect to examine the development of low-cost "user-friendly" software for data acquistion and control of analytical and chemical instrumentation. If profit and funding are the sole criteria for determining what software/computational project to start, then our accomplishments as scientists are doomed. I don't think that someone starting a new project should fall victim to the "bandwagon effect". From a business standpoint, it is difficult for a new software developer to break into a saturated market. It seems that profit and funding are the result of how we PROMOTE the results or application of the work to a potential grant agency, industrial user, etc. Our prime consideration in the work done should be how IMPORTANT is the problem solved or the application. Respectfully, Anita I. Zvaigzne From chemistry-request@www.ccl.net Sun Jan 10 23:44:23 1999 Received: from gate-sl1.mdli.com (ns2.mdli.com [208.200.221.3]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id XAA24700 Sun, 10 Jan 1999 23:44:22 -0500 (EST) Received: (from smap@localhost) by gate-sl1.mdli.com (8.8.8/8.8.8) id UAA07094; Sun, 10 Jan 1999 20:36:35 -0800 (PST) Received: from puffin.mdli.com(191.254.19.10) by gate-sl1.mdli.com via smap (V2.1) id xma007092; Sun, 10 Jan 99 20:36:32 -0800 Received: from shepherd.mdli.com by puffin.mdli.com (8.8.5/BCH1.0) id UAA02096; Sun, 10 Jan 1999 20:43:43 -0800 (PST) Received: by shepherd.mdli.com with Internet Mail Service (5.5.2232.9) id ; Sun, 10 Jan 1999 20:44:51 -0800 Message-ID: <8E13FBBA26A9DA119ED400A0C9AB2CE55A7873@shepherd.mdli.com> From: Guenter Grethe To: CHMINF-L , Computational Chemistry List , Derwent List , Diversity LIst , isisforum , Medicinal Chemistry List Cc: Gerald Maggiora , Guenter Grethe , Jacques Weber , Janet Ash , John Blackmore , Johnny Gasteiger , Peter Willett , Rainer Moll , Vincent van Geerestein Subject: Fifth International Conference on Chemical Structures - Call for Papers ---A Reminder Date: Sun, 10 Jan 1999 20:44:46 -0800 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2232.9) Content-Type: text/plain Dear colleagues, just a reminder that the deadline for submitting abstracts for oral or poster presentations at the Fifth International Conference on Chemical Structures is January 15, 1999. This is your chance to present your research at this important conference and to interact with your peers. For details about the conference and submitting abstracts please check our website at http://ChemWeb.com/conference/5iccs/5iccs.html Hope to hear from you soon. Sincerely yours, Guenter Grethe Conference Chair From chemistry-request@www.ccl.net Mon Jan 11 00:04:12 1999 Received: from exstudent3.levels.unisa.edu.au (EXSTUDENT3.Levels.UniSA.Edu.Au [130.220.22.184]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id AAA24761 Mon, 11 Jan 1999 00:03:21 -0500 (EST) Received: by EXSTUDENT3.Levels.UniSA.Edu.Au with Internet Mail Service (5.5.2232.9) id ; Mon, 11 Jan 1999 15:32:58 +1030 Message-ID: From: "Soar, Terri Jacqueline - SOATJ001" To: chemistry@www.ccl.net Subject: SUMMARY: error/accuracy determinations for S.E. application Date: Mon, 11 Jan 1999 15:32:56 +1030 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2232.9) Content-Type: text/plain; charset="iso-8859-1" Hi all. Thanks to those 3 people who replied to my plea for any ideas/help (these are listed below). (Thanks Andrew, I have read your paper) I have a few other resources to check out before I decide what will be the best way to go on this topic. If there are any other delayed thoughts about this problem that may be of use to me, it's not too late to post them! Regards, Terri ------------------------------------------------------------------------- Ms. Terri Soar, PhD student, Ian Wark Research Institute, tel: +61 8 8302 3706 University of South Australia, fax: +61 8 8302 3683 The Levels Campus, Mawson Lakes, S.A. 5095, AUSTRALIA email: soatj001@students.unisa.edu.au -------------------------------------------------------------------------- REPLIES TO MY QUERY (as shown last on this list): ------------------------- take a look at: Gale, J. D., Rohl, A. L., Watling, H. R., Parkinson, G. M., Theoretical Investigation of the Nature of Aluminum-Containing Species Present in Alkaline Solution, The Journal of Physical Chemistry B; 1998; 102(50); 10372-10382. Andrew :-) Andrew Rohl [andrew@power.curtin.edu.au] ------------------------ Well, I think the state of the art (I'm a full time follower but only a part time practicioner (sp?)) for systems with no direct experimental counterpart is to choose your simples system (say a dimer) and model it with increasingly sofisticated ab inito methods until the answer doesn't change any more. If this is similar to your calculated results then the semi empirical results are valid. By the way, heats of formation themselves are somewhat meaningless. Relative heats of formation mean more (such as delta Hf between 2 monomers and a dimer, or a solvated dimer vs an unsolvated dimer. Good luck. I wish there was a simple solution. I would be interested in reading your other responses. Kimberley Cousins Associate Professor of Chemistry California State University, San Bernardino 5500 University Parkway San Bernardino, CA 92407 (909)880-5391 kcousins@csusb.edu http://chem.csusb.edu/~kcousins ----------------- Just a quick note to say that I was involved in something like this previously, although the system/species were different. Si/AL(O)x(OH)y clusters relating to zeolites but we have published the results. Here I think we discussed some thoughts relating to the accuracy and how we might be able to extrapolate the results to chemically related systems regarding the formation of Lowensteins Rule in zeolites. Hopefully it might be of some help C.R.A. Catlow, A.R. George & C.M. Freeman, "Ab-initio and Molecular Mechanics Studies of Aluminosilicate Fragments and the Origin of Lowenstein's Rule.", Chem. Comm., 1311-1312, (1996). I've also cc this to Prof. Richard Catlow who is still very active in the area but I feel does not have time to follow the group. Hope this helps Cheers Ashley ---------------------------------------------------------------------- Ashley George, Phone : 0118-977-3133 Cerebrus Direct : 0118-989-9317 613 Reading Rd. Fax : 0118-989-9300 Winnersh, Berks Email : A.George@cerebrus.ltd.uk RG41 5UA. UK URL : http://www.cerebrus.ltd.uk ---------------------------------------------------------------------- ---------------------------------- My original query was: Hi CCLers. I'm after some ideas, pointers or even just people's thoughts as to the topic of calculating the accuracy of calculations. This is the situation...For my PhD in physical and inorganic chemistry about one quarter of my work has involved applying computational chemistry. The computational chemistry work has focused on a range of aluminium-oxyhydroxide species (monomer, dimer, trimer, tetramer and some polymers) that may exist in aging caustic aluminate solutions where crystalline Al(OH)3, i.e. gibbsite, finally precipitates out. We are using MOPAC93 with AM1 (i.e. semi-empirical quantum mechanical methodology) and also with and without COSMO (to include solvent effects) to perform geometry optimisations and SADDLE calculations on these species where our main interest is the stability and also the relative energetics of the species (wrt to heats of formation and reaction and also Gibbs free energy of formation and reaction) to indicate what species are more likely to exist in these solutions and participate in reactions possibly leading to gibbsite formation. So, how would I go about estimating errors and determining accuracy for this work (keeping in mind that many of the solution species we've modelled cannot be measured experimentally (i.e. heats of formation))? As I've said above, I'm after any answers to this question in addition to people's thoughts as to what may be expected in the way of accuracy determinations for this type of work. Thanks in advance and, of course, a summary will be produced. Terri From chemistry-request@www.ccl.net Mon Jan 11 06:04:07 1999 Received: from swan2.uspnet.usp.br (swan2.uspnet.usp.br [143.107.253.69]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id GAA26253 Mon, 11 Jan 1999 06:04:05 -0500 (EST) Received: from ligquim ([143.107.194.89]) by swan2.uspnet.usp.br (8.9.1a/8.9.1) with SMTP id JAA19345 for ; Mon, 11 Jan 1999 09:02:24 -0200 (EDT) Message-ID: <001e01be3d50$fac14240$0100005a@ligquim.ffclrp.usp.br> From: "=?iso-8859-1?B?U+lyZ2lv?=" To: Subject: convergence in NBO Date: Mon, 11 Jan 1999 08:54:59 -0200 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Content-Transfer-Encoding: 7bit Dear Netters, In order to determine the energy of stabilization due to resonance, I am trying to delete Fock matrix elements of some (or all) unbonded (stared) orbitals. But the SCF calculation without these elements does not converge. How can I obtain the convergence. Thanks, Sergio From chemistry-request@www.ccl.net Mon Jan 11 12:38:00 1999 Received: from magnum.cooper.edu (magnum.cooper.edu [199.98.16.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id MAA00052 Mon, 11 Jan 1999 12:38:00 -0500 (EST) Received: from zeus.cooper.edu by magnum.cooper.edu with SMTP id AA12852 (5.65c/IDA-1.4.4 for ); Mon, 11 Jan 1999 12:34:48 -0500 Received: by zeus.cooper.edu id AA25564 (5.67b/IDA-1.5 for CHEMISTRY@www.ccl.net); Mon, 11 Jan 1999 12:36:42 -0500 From: TOPPER ROBERT Message-Id: <199901111736.AA25564@zeus.cooper.edu> Subject: Re: CCL:G:SUMMARY OF RATE/ACTIVATION ENERGY To: CHEMISTRY@www.ccl.net Date: Mon, 11 Jan 1999 12:36:41 -0500 (EST) Cc: topper@cooper.edu (TOPPER ROBERT) X-Mailer: ELM [version 2.4 PL24alpha3] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Hi. Just a note, after reading the TST summary just distributed to the CCL. I have to disagree somewhat with some of the comments made by Dr. Chan: > Someone recommend you using Don Truhlar's program POLYRATE. > I've never used Truhlar's program but I know it specialize > in microcanonical variational transition state theory > and tunneling rate coefficent. Such method is required for > reaction without a sharp barrier (like some dissociation reactions) > or low-temperature reactions that involve proton transfer. > Such method is terribly time consuming (it requires > caculation of a reaction pathyway and a number of > hessian along the pathway) and require quite a bit of expertise. > Truhlar's program is an inappropriate................. > recommendation for evaluation of rate for isomerisation > and most reactions with a barrier height. I was once a postdoc with Prof. Truhlar, so a little bias follows. One of my UNDERGRADUATE chemical engineering students installed POLYRATE and MORATE on an SGI computer in an afternoon without any help or advice from me. He was able to use POLYRATE to do calculations within 2 weeks. The code is incredibly powerful but I would say that it is comparable to MORATE in terms of ease of use. The documentation is INCREDIBLY good. But are some calculations time-consuming? Yes. However, there are many methods in POLYRATE, and some of them are computationally expensive and some are cheap. One does not, for example, need to calculate the entire reaction pathway in order to get a good result from POLYRATE, as Truhlar et.al. have discussed in a number of recent articles. Also, POLYRATE is not merely a microcanonical TST code, but rather is capable of a full suite of canonical and microcanonical TST calculations. It's comparable to GAUSSIAN in its sheer range of capabilities, and represents the current state-of-the-art. Also, POLYRATE has been used on isomerization reactions with excellent success. See Y.P. Liu et.al., JACS 115, p. 2408 (1993); ibid., p.7806 (1993) for papers on the treatment of kinetic isotope effects in sigmatropic rearrangement. As long as classical/nonclassical recrossing of the TST is not an important quantitative effect, there's no reason not to use TST on an isomerization reaction. For some clues as to when recrossing might be important, you may like to consult a review article I wrote on classical recrossing dynamics (shameless plug): R.Q. Topper, Reviews in Computational Chemistry 10, p.101 (1997). Fundamentally, if the density of states of the product is high, recrossing may not be much of an issue well above threshold. IMHO, tunneling is typically the biggest issue for reactions involving proton transfer. And POLYRATE is equipped to carry out a variety of tunneling corrections. ***************************************************************************** Robert Q. Topper email: topper@cooper.edu Department of Chemistry phone: (212) 353-4378 The Cooper Union fax: (212) 353-4341 51 Astor Place subway: take the 6 to Astor Place New York, NY 10003 and you're there! http://www.cooper.edu/engineering/chemechem/ ***************************************************************************** The Cooper Union for the Advancement of Science and Art is a tuition-free college in Greenwich Village, at Cooper Square and Astor Place. ***************************************************************************** From chemistry-request@www.ccl.net Tue Jan 12 12:17:02 1999 Received: from hermes.hrz.uni-bielefeld.de (hermes.hrz.uni-bielefeld.de [129.70.4.55]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id MAA08831 Tue, 12 Jan 1999 12:16:58 -0500 (EST) Received: from tc1.chemie.uni-bielefeld.de (fddi-gateway.chemie.uni-bielefeld.de [129.70.40.2]) by hermes.hrz.uni-bielefeld.de (8.8.6/8.8.6) with SMTP id SAA13404 for ; Tue, 12 Jan 1999 18:16:28 +0100 (MET) Received: by tc1.chemie.uni-bielefeld.de (1.37.109.4/16.2) id AA03127; Tue, 12 Jan 99 18:18:07 +0100 From: Carola Begemann Message-Id: <9901121718.AA03127@tc1.chemie.uni-bielefeld.de> Subject: Diradicals or Diradicaloid? To: chemistry@www.ccl.net Date: Tue, 12 Jan 99 18:18:07 MEZ Mailer: Elm [revision: 70.85] Dear fellow computational chemists, I calculated the electronic structure of some molecules with two electrons in two nearly degenarate frontier orbitals. I used a two configuration SCF for the singlet state and a rohf for the triplet state. My problem is how to refer to the species. Are the singlet molecules real diradicals or just diradicaliod Molecules. All the texts I read so far (the book by Borden titled Diradicals and the Article by Salem and Rowland, Angew. chem. int. ed. 11 p92 (1972)) only state that a Diradical has two electrons in two closely spaced orbitals. Some say molecules with a triplet ground state are diradicals while the ones with a singlet ground state are diradicaloids. My professor thinks it is not that easy and wants me to read '' the article by Dewar that appeared in the J. Am. Chem. soc. sometime between 1970 and about 1980''. I could'nt locate that specific article. My question: Does one of you have the full citation or even better can provide a clear definition of the terms diradical and diradicaloid? Thanks in advance and I will summarize. Carola Begemann ---------------------------------------------- Carola Begemann email: carola@tc1.chemie.uni-bielefeld.de adress: Schackenburger Strasse 204a, 33818 Leopoldshoehe, Germany ----------------------------------------------