From peon@medchem.dfh.dk Tue Nov 26 01:49:24 1996 Received: from danpost.uni-c.dk for peon@medchem.dfh.dk by www.ccl.net (8.8.3/950822.1) id BAA21937; Tue, 26 Nov 1996 01:43:19 -0500 (EST) Received: from medchem.dfh.dk (medchem.dfh.dk [130.225.177.15]) by danpost.uni-c.dk (8.7.5/8.6) with SMTP id HAA19833; Tue, 26 Nov 1996 07:43:17 +0100 (MET) Received: from [130.225.177.59] (compmac2 [130.225.177.59]) by medchem.dfh.dk (950413.SGI.8.6.12/950213.SGI.AUTOCF) via SMTP id HAA23877; Tue, 26 Nov 1996 07:45:14 +0100 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 26 Nov 1996 07:43:19 +0100 To: E.Tajkhorshid@DKFZ-Heidelberg.de From: peon@medchem.dfh.dk (Per-Ola Norrby) Subject: Re: CCL:pKa calculation Cc: chemistry@www.ccl.net >I have calculated the energy (HF) of a set of protonated molecules and compared >them with the ones of non protonated species. After inclusion of vibrational >and thermal corrections you can get a figure which can be refered as 'proton >affinity' of the studied molecule. I want to know if there is any relationship >between this proton affinity and pKa of the molecule. Any comment in this >regard will be appreciated. > >Thanx in advance > >-- >Emad Dear Emad, What you have here is a "gas phase pKa". If you want the aqueous pKa, you have to perform the calculations in solvent. Some solvation models are available, I'm not sure I really trust them, but you could try. Also, trying to calculate any kind of absolute pKa requires very high levels, in my experience HF is not nearly good enough. Something that COULD be fairly reliable is calculating RELATIVE pKa from an isodesmic comparison, eg: R3N + NH4+ <-> R3NH+ + NH3 Thus you could calculate values relative to one standard, this should be good enough for most applications. I recommend the book "Ab initio molecular orbital theory" by Hehre, Radom, Schleyer, and Pople. With an isodesmic comparison, you MIGHT get away with adding solvent contributions as single point calculations for all species in the above equation. In my experience, the most reliable published methods for this are the SMx models, available in many programs with semi-empirical calculations, ie AM1-SM2 or PM3-SM3. If you want to do it at the ab initio level (not necessarily better), you could look into Tomasi's PCM-method. Regards, Per-Ola Norrby ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ * Per-Ola Norrby * The Royal Danish School of Pharmacy, Dept. of Med. Chem. * Universitetsparken 2, DK 2100 Copenhagen, Denmark * tel. +45-35376777-506, +45-35370850 fax +45-35372209 * Internet: peon@medchem.dfh.dk, http://compchem.dfh.dk/ From chpajt@bath.ac.uk Tue Nov 26 03:49:22 1996 Received: from goggins.bath.ac.uk for chpajt@bath.ac.uk by www.ccl.net (8.8.3/950822.1) id CAA22256; Tue, 26 Nov 1996 02:51:20 -0500 (EST) Received: from bath.ac.uk (actually host midge.bath.ac.uk) by goggins.bath.ac.uk with SMTP (PP); Tue, 26 Nov 1996 07:51:16 +0000 Date: Tue, 26 Nov 1996 07:51:11 +0000 (GMT) From: A J Turner To: Per-Ola Norrby cc: E.Tajkhorshid@dkfz-heidelberg.de, chemistry@www.ccl.net Subject: Re: CCL:pKa calculation In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi! Whilst what you are saying is very interesting as far as it goes, it takes no account of the entropic change on solvation. The only method of which I am aware that will do this would be QM/MM FEPT. This can be done at all levels of ab-initio theory - if you have a big enough computer! Hoever - I am begining to believe that it will give reasonable results at AM1 level - and thus be do-able for small systems - on a work-station. Best wishes Alex ------------------------------------------------------------------- |Alexander J Turner |A.J.Turner@bath.ac.uk | |Post Graduate |http://www.bath.ac.uk/~chpajt/home.html| |School of Chemistry |+144 1225 8262826 ext 5137 | |University of Bath | | |Bath, Avon, U.K. |Field: QM/MM modeling | ------------------------------------------------------------------- From peon@medchem.dfh.dk Tue Nov 26 04:06:24 1996 Received: from danpost.uni-c.dk for peon@medchem.dfh.dk by www.ccl.net (8.8.3/950822.1) id DAA22598; Tue, 26 Nov 1996 03:16:42 -0500 (EST) Received: from medchem.dfh.dk (medchem.dfh.dk [130.225.177.15]) by danpost.uni-c.dk (8.7.5/8.6) with SMTP id JAA25686; Tue, 26 Nov 1996 09:16:41 +0100 (MET) Received: from [130.225.177.59] (compmac2 [130.225.177.59]) by medchem.dfh.dk (950413.SGI.8.6.12/950213.SGI.AUTOCF) via SMTP id JAA26406; Tue, 26 Nov 1996 09:18:41 +0100 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 26 Nov 1996 09:16:43 +0100 To: A J Turner From: peon@medchem.dfh.dk (Per-Ola Norrby) Subject: Re: CCL:pKa calculation Cc: chemistry@www.ccl.net Hi Alex, >Whilst what you are saying is very interesting as far as it goes, it takes >no account of the entropic change on solvation. Well, it does! Some continuum solvation models (like the Cramer-Truhlar models) calculate solvation free energies. It's true that many ab initio-based models only calculate the electrostatic contribution, and for an isodesmic comparison that may actually be enough, but the SMx models do give free energies of solvation. Combining those with a normal mode analysis for the remaining thermodynamic contributions should be a very cost-effective way of getting the overall equilibrium free energies. >The only method of which I am aware that will do this would be QM/MM >FEPT. This can be done at all levels of ab-initio theory - if you have a >big enough computer! Hoever - I am begining to believe that it will give >reasonable results at AM1 level - and thus be do-able for small systems >- on a work-station. I'm very interested in QM/MM methods, but if you use them for FEP, can you calculate any practical systems (say, 10-15 heavy atoms + a couple of hundred water) this millenium, on ANY computer? Also, FEP is only theoretically defensible if you have a good description of the potential energy surface at low energy non-stationary points, and we all know that AM1 will give substantial errors even for relative energies of stationary points. Of course, as long as it works and gives good results, I wont insist on a perfect theoretical background, but I'd like to see comparison to experiment for a couple of hundred cases first. Regards, Per-Ola Norrby ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ * Per-Ola Norrby * The Royal Danish School of Pharmacy, Dept. of Med. Chem. * Universitetsparken 2, DK 2100 Copenhagen, Denmark * tel. +45-35376777-506, +45-35370850 fax +45-35372209 * Internet: peon@medchem.dfh.dk, http://compchem.dfh.dk/ From dok889@mbp-sun8.inet.dkfz-heidelberg.de Tue Nov 26 09:49:25 1996 Received: from ns1.DKFZ-Heidelberg.de for dok889@mbp-sun8.inet.dkfz-heidelberg.de by www.ccl.net (8.8.3/950822.1) id JAA24499; Tue, 26 Nov 1996 09:05:20 -0500 (EST) Received: from mbp-sun8.inet.dkfz-heidelberg.de (mbp-sun8.inet.dkfz-heidelberg.de [193.174.48.244]) by ns1.DKFZ-Heidelberg.de (8.7.3/DKFZ-8.6.4) with SMTP id PAA05296 for ; Tue, 26 Nov 1996 15:03:42 +0100 (MET) Received: from localhost by mbp-sun8.inet.dkfz-heidelberg.de (5.x/SMI-SVR4) id AA28328; Tue, 26 Nov 1996 15:08:58 +0100 Date: Tue, 26 Nov 1996 15:08:57 +0100 (MET) From: "w.han@dkfz-heidelberg.de" To: CHEMISTRY@www.ccl.net Subject: N2 and CO dielectric constants Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers: Can anybody tell me the dielectric constants of N2 and CO? I would like to use them as solutions in SCRF (G94) calculations. Thank you very much! Wen-Ge E-mail: w.han@dkfz-heidelberg.de From joubert@ext.jussieu.fr Tue Nov 26 10:06:32 1996 Received: from shiva.jussieu.fr for joubert@ext.jussieu.fr by www.ccl.net (8.8.3/950822.1) id IAA24473; Tue, 26 Nov 1996 08:59:44 -0500 (EST) Received: from idf.ext.jussieu.fr (idf.ext.jussieu.fr [134.157.81.129]) by shiva.jussieu.fr (8.8.3/jtpda-5.2) with ESMTP id OAA28734 for ; Tue, 26 Nov 1996 14:59:34 +0100 (MET) Received: from [134.157.11.17] by idf.ext.jussieu.fr (8.6.10/jtpda-4.0) with SMTP; Tue, 26 Nov 1996 14:59:13 +0100 X-Sender: joubert@idf.ext.jussieu.fr Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 26 Nov 1996 16:05:31 +0200 To: chemistry@www.ccl.net From: joubert@ext.jussieu.fr (Laurent Joubert) Subject: Tools for SciAn/G94 [2] Dear Netters, The versions 1.1 of the little programs "Transcube", "Transfreq" and "Molnff" are now available on the net : http://134.157.11.11/Pages/LECA/GP/Laurent/Laurent.html These versions correct some little bugs. You can now compile these programs with both SGI and IBM Risc 6000 compilers. If somebody finds any errors during the compilation (or running one of these programs), please contact me. Laurent Joubert ******************************************************** * Laurent JOUBERT (PhD student) * * * * Ecole Nationale Superieure de Chimie de Paris * * Laboratoire d'Electrochimie et de Chimie Analytique * * 11, rue Pierre et Marie Curie * * 75231 PARIS CEDEX 05- FRANCE * * * * Tel : 44-27-66-94 * * Fax : 44-27-67-50 * * * * E-Mail : joubert@ext.jussieu.fr * * http://www.enscp.jussieu.fr * ******************************************************** From cmerlot@cit.enscm.fr Tue Nov 26 10:14:25 1996 Received: from cit.enscm.fr for cmerlot@cit.enscm.fr by www.ccl.net (8.8.3/950822.1) id JAA24701; Tue, 26 Nov 1996 09:26:21 -0500 (EST) Received: from argent.enscm.fr by cit.enscm.fr (AIX 4.1/UCB 5.64/4.03) id AA16668; Tue, 26 Nov 1996 15:25:26 +0100 Sender: merlot@cit.enscm.fr Message-Id: <329AFFBE.3452@cit.enscm.fr> Date: Tue, 26 Nov 1996 15:33:34 +0100 From: Cedric Merlot X-Mailer: Mozilla 2.0 (X11; I; SunOS 5.5 sun4m) Mime-Version: 1.0 To: "William R. Smith" Cc: chemistry@www.ccl.net Subject: Re: Molecule Builder References: <210A71D1AB6@msnet.nw.uoguelph.ca> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit William R. Smith wrote: > > Hi again, > > I received several helpful replies to my previous posting: > -------------------------------------------------------------------------- > Does anyone know of a simple Windows 3.1/NT/95 product that can be used > to build molecules? > -------------------------------------------------------------------------- > > I'm sorry I didn't make my question more explict. What I want is a .DLL > (or .VBX(preferably) or .OCX) that I can incorporate within other software. > i.e. I don't want a stand-alone product. I don't think any of the > replies refer to products that can be used this way (but the individual > posters should please contact me if I'm wrong) Preferably, the price would > also be right :- ) > > Best Regards, > > W. R. Smith Professor > Dept. of Mathematics and Statistics Hi all I'm interested in Molecule Builders (2D and 3D) for PC too. More exactly, I'm searching C or C++ source code in public domain. Builders don't have to be very accurate, but I'm looking for an idea. http://schiele.organik.uni-erlangen.de/cactvs/toolidx.html gives source code in CSH (I believe) and the main idea is quite hard to understand. Could anyone help me ? Thanks -- Cedric Merlot cmerlot@cit.enscm.fr From qftramos@usc.es Tue Nov 26 10:49:25 1996 Received: from uscmail.usc.es for qftramos@usc.es by www.ccl.net (8.8.3/950822.1) id KAA25491; Tue, 26 Nov 1996 10:46:04 -0500 (EST) Received: by uscmail.usc.es (5.67b/1.34) id AA00469; Tue, 26 Nov 1996 16:44:47 +0100 Date: Tue, 26 Nov 1996 16:44:46 +0100 (MET) From: Antonio Fernandez Ramos To: Lista computacional Subject: Rate constants Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear netters: I am very interested in experimental rate constants in gas phase for the intramolecular proton transfer in malonaldehyde and derivatives, tropolone and derivatives etc. I would like to know if exists information about this and where is available. Thanks in advance. Antonio Fernandez Ramos E-mail:qftramos@usc.es Dpto de Quimica-Fisica Facultad de Quimica Avda das Ciencias s/n 15706 Santiago de Compostela SPAIN From Jeffrey.Gosper@brunel.ac.uk Tue Nov 26 10:57:03 1996 Received: from ceres.brunel.ac.uk for Jeffrey.Gosper@brunel.ac.uk by www.ccl.net (8.8.3/950822.1) id KAA25117; Tue, 26 Nov 1996 10:07:59 -0500 (EST) From: Received: from loki.brunel.ac.uk by ceres.brunel.ac.uk with SMTP (PP); Tue, 26 Nov 1996 15:06:32 +0000 Message-Id: <1274.199611261506@loki.brunel.ac.uk> Subject: Re: CCL:G:PED programs To: mtulio@dragoeiro.uma.pt (Mario Tulio Rosado) Date: Tue, 26 Nov 1996 15:06:23 +0000 (GMT) Cc: Chemistry@www.ccl.net In-Reply-To: <9611251506.AA19943@dragoeiro.uma.pt> from "Mario Tulio Rosado" at Nov 25, 96 03:06:57 pm X-Mailer: ELM [version 2.4 PL24] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit > > Dear CCL, > > I am looking for FREE (preferably) program runing on a PC that can do PED > analysis and possibly animation of vibrational modes obtained from MO > programs (Gaussian, Mopac). > Can anybody help me? > > > Thanks in advance > > Mario Tulio Rosado > Dept. of Chemistry > University of Madeira > PORTUGAL > > > Re_View is a Windows program that can animate the vibrations from MOPAC6/7. Re_View2 also works with MOPAC93, GAMESS, and can interface to other program such as TURBOMOL, GAUSSIAN via a 'standard' vibartion file (called a Re_View2 vibration file .rv2). I am currently writing a converter for FREQCHK and output files from Gaussian94. For further information on Re_View see http://www.brunel.ac.uk/depts/chem/ch241s/re_view/re_view.htm Yours sincerely Jeff Gosper From neuber@exp.bessy.de Tue Nov 26 11:03:32 1996 Received: from metaxa.exp.bessy.de for neuber@exp.bessy.de by www.ccl.net (8.8.3/950822.1) id KAA25114; Tue, 26 Nov 1996 10:07:44 -0500 (EST) Received: by exp.bessy.de (MX V4.1 VAX) id 3; Tue, 26 Nov 1996 16:07:26 MET Sender: neuber@exp.bessy.de Date: Tue, 26 Nov 1996 16:07:25 MET From: Michael Neuber To: chemistry@www.ccl.net Message-ID: <009ABF3C.60F3ED0F.3@exp.bessy.de> Subject: summary: pi-pi and tm-params with semiemp methods Dear all! It is coming late and I have to excuse for that, but I don't want to miss to give a summary on the correspondence I had after my question here from Nov 5th: Dear all, in "Semiempirical Molecular Orbital Methods" (Rev.Comp.Chem. 2(1990)pp 45-81) J.J.P. Stewart describes 'strong and weak points of NDDO semiempirical methods'. What I am interested in is whether there is any further reference regarding the value of semiempiric methods (AM1, PM3, also ZINDO-1) especially for the description of intermolecular pi-pi interaction of aromatic molecules. I would appreciate any hint on reported results or experience with that, will summarize if it seems appropriate. Greetings Michael Neuber @ Berlin As a quick summary: all of the standart semiempiric methods (up to AM1 and PM3) fail to correctly describe pi-pi interactions, and only the ZINDO methods are parameterized to treat transition metals. However it is believed that new methods named below will give better results especially with transition metals, so it is worth following the development in this area: Warren Hehre's PM3(tm) (Spartan) Andrew Holder's SAM1 (AMPAC) Walter Thiel's MNDO/d (also Spartan (?), info not yet complete....) Thanks to everyone who took time to supply some info on the capability of the semiempiric methods, and further, the development and state of implementation of new code in the different software packages. I still expect several results on further (literature) research regarding these issues. But as I will be busy with other duties in the next time, here is some type of interim report. Regards Michael Neuber --------------------------------------------------------------------------- Dr. Michael Neuber Universitaet Heidelberg c/o BESSY (ESCASCOPE) Lentzeallee 100 D-14195 Berlin Phone (++49/0) 30 82004-237/-176 FAX ..-149 e-mail neuber@exp.bessy.de --------------------------------------------------------------------------- ############################################################################# ############################################################################# __________________________________________________________________________ Michael, I have tried unsuccessfully to model Aromatic pi-pi interactions using AM1 and PM3. I was able to observe the interaction at the ab initio level, either with HF or MP2 (probably better). I have not published on this yet. Ned ****************************************************************************** Ned H. Martin, DeLoach Professor and Chair 910-962-3453 Department of Chemistry Fax: 910-962-3013 University of North Carolina at Wilmington 601 S. College Rd Wilmington, NC 28403-3297 Email: martinn@vxc.uncwil.edu ******************************************************************************* ______________________________________________________________________________ Hi Michael, You asked: > What I am interested in is whether there is any further reference > regarding the value of semiempiric methods (AM1, PM3, also ZINDO-1) > especially for the description of intermolecular pi-pi interaction > of aromatic molecules. I don't have a reference to hand, but I have some experience which is probably relevant. The weakness of the semiempirical methods will be more with the "intermolecular" part of your question rather than the "pi-pi" part. I have tried to model charge transfer complexes and some stacked aromatic systems with AM1 and PM3, but these methods wouldn't find a stable geometry: the aromatic molecules just drifted farther and farther apart, or collapsed down to a prismane type compound. Ultimately, molecular mechanics gave the most reasonable geometries. The problem is primarily that the semiempirical parameterizations were developed with minimal basis sets. There aren't diffuse functions as such, so long range, ie. intERmolecular interactions, are poorly modeled. You might have some success if you have X-ray structure data, or can get reasonable geometries with mechanics, and then apply semiempirical calculations to examine the orbitals. Better, would be to do the geometry optimization at an ab initio HF or DFT method with a better basis set, if your system isn't too large. It may be that one of the newer parameterizations which include d-orbitals (Andy Holder's SAM1, Warren Hehre's PM3(tm), or Walter Thiele's MNDO/d) will also work better for longer range interactions. I wouldn't count on getting a useful geometry with the standard semiempirical methods, though. If you do have some success, please let me know what worked! EC --- Chamot Laboratories, Inc. 530 E. Hillside Rd. Naperville, Illinois 60540 Phone/Fax: (630) 637-1559 echamot@xnet.com http://www.xnet.com/~chamotlb ________________________________________________________________________________ Dear Michael From my experience, pi-pi interactions are not described in semi- empirical methods. As a matter of fact, James Stewart has told me literally that interactions like that are not included in any of the MOPAC-type methods. We will elaborate some more on that in a paper on my PhD work I've submitted to JCS Dalton (Kranenburg, Kamer, van Leeuwen, Veldman, Spek). Best regards, Mirko Kranenburg Dr. Mirko Kranenburg DSM Research, PO-PC P.O. Box 18 6160 MD Geleen The Netherlands Telephone +31-46-4767019 Telefax +31-46-4760503 E-mail m.kranenburg@research.dsm.nl _________________________________________________________________________________ Dear Michael, Since acceptance and publication will probably take a while, I'll include a small excerpt with relevant references (most of which I got from the CCL by the way! There is a summary in the CCL-archives.) Good luck! Mirko _ The importance of attractive interactions between p-systems is well recognised, 34 but semi-empirical SCF techniques have not been very successful in describing these interactions. 35,36 None of the MOPAC calculations reproduces the p-stacking interaction (34) C. A. Hunter and J. K. M. Sanders, J. Am. Chem. Soc. 1990, 112, 5525. (35) M. D. Gordon, T. Fukunaga and H. E. Simmons, J. Am. Chem. Soc. 1976, 98, 8401. (36) T. Bally, Faraday Discussion, J. Chem. Soc. Faraday Trans 1994, 90, 1799. (37) J. J. P. Stewart, Personal communication. (38) Y. Kurita, C. Takayama and S. Tanaka, J. Comput. Chem. 1994, 15, 1013. (39) J. Perlstein, J. Am. Chem. Soc. 1994, 116, 11420. _ Dr. Mirko Kranenburg DSM Research, PO-PC P.O. Box 18 6160 MD Geleen The Netherlands Telephone +31-46-4767019 Telefax +31-46-4760503 E-mail m.kranenburg@research.dsm.nl ________________________________________________________________________________ DEar Michael, I would be interested in getting any response you receive for your question. Thanks in advance. Satyam ----------------------------------------------------- Dr. Satyam Priyadarshy 914, Chevron, Department of Chemistry University of Pittsburgh, Pittsburgh, PA 15260, U.S.A Fon/Fax: +1-412-624-8200(Extn 1217or 8589) / 624-8552 email: satyam+@pitt.edu OR satyam@hathi.chem.pitt.edu ----------------------------------------------------- _________________________________________________________________________________ Hi, Michael. > Could you please comment on the plans of HyperCube, especially whether > or not you will implement the SAM1, PM3(tm) or MNDO/D methods within HyperChem ? Some development is being done to include d orbitals in our semi-empirical methods, but it will be a significant amount of work; I cannot predict when it might be completed. "PM3(tm)" is proprietary to Wavefunction, I think; we will probably offer similar functionality in some future release but it will probably have a different name. > Is there any experience or knowledge how these methods (esp. MNDO/D) > compare to the HyperChem implementations of ZINDO ? I asked my colleague who is doing that development work. He tells me that some parameters and results have been published for the main-group elements and structures containing them, but there have not yet been any publications of parameters or results for transition metal compounds for MNDO/D. The parameters are available for PM3(tm) but I think that no description of the method is available, let alone a description of its results. We do not even have parameters for SAM1. > Have there been any improvements or changes for the AM1, PM3 and > ZINDO parametrizations within HyperChem in the last Versions since HC 3.0 ? As far as I can tell, the only changes have been the addition of some parameters for "capping atoms" for PM3 and ZINDO/1 so that these methods could be used more easily for calculating fragments of structures. The only method that has had a lot of new parameters added is Extended Huckel. Regards, Joel polowin@hyper.com ________________________________________________________________________________ Hi, In July 95 there was a very similar question posted to CCL You might want to rummage through the CCL archive (the subject line for that thread was; CCL:pi-stacking in MOPAC? ) I made a note of two references that were mentioned in the replies. although I never needed to get them, so exactly how helpful they will be I cannot say. T. Ishida & K. Ohno, "The Influence of Basis Sets on Wave Function Tails", Int. J. Quantum Chem, 35 (1989) 257-66. Kurita, Y.; Takayama, C.; Tanaka, S. J. Comput. Chem. 1994, 15, 1013-1018. Regards Michael -- ______________________________________________________________________ | Michael Shephard. | M.Shephard@unsw.EDU.AU | | University of New South Wales. | michaels@jake.chem.unsw.EDU.AU | | Australia | | _______________________________________________________________________________ Hello Paul ! Recently I saw your question in the CCL list from 10/1995... >Dear CCl's, >I am interested in using the SAM1 method and ZINDO to correlate >the redox properties of various Iron II and III complexes with computed >parameters such as HOMO energy, IP potential. >Has anyone come across similar work or would like to suggest the best >approach. >Any useful replies will be summarised. > > Paul Heelis > North East Wales Institute, UK > Heelisp@newi.ac.uk It is not quite the same problem I am working on, but more some organometallic adsorption reactions. Now, what I am looking for is software like SAM1, MNDO/D or PM3(tm) which are said to contain parameters for transition metals and better suited parameters to take pi-pi interactions into account. Perhaps you are still working with such stuff and can give any advice where to get such programs and also how they compare to ZINDO? Any comment is appreciated! (I already contacted Prof Holder (SAM1) but didn't get a response so far.) Greetings from Berlin Michael Neuber _________________________________________________________________________________ Dear Dr Neuber, I am sorry, but if I recall, I did not get much from that notice on CCL. Our own experience is that SAM1 gives good geometry, but we have not done much work with it to be honest. We have just started using MOMEC, a molecular mechanics programme specificaly parametised for transition metals. Maybe you know it? Sorry this is not much help. Paul Dr. P.Heelis Faculty of Science and Innovation North East Wales Institute Mold Rd Wrexham Ll11 2AW UK ________________________________________________________________________________ Dear Dr Heelis ! Could you give some info where you got the SAM1 program as well as the MOMEC software ? Is it only commercially available software ? Regards Michael Neuber _________________________________________________________________________________ Hi, the SAM1 was part of AMPAC from semichem, usa, ~ 500$, amd momec is from Germany , WWW: http://www.docadchem.com/ , this was around 1000DM. Bye, Paul Dr. P.Heelis Faculty of Science and Innovation North East Wales Institute Mold Rd Wrexham Ll11 2AW UK ________________________________________________________________________________ Hi Michael, I'll give you some statements I got concerning the TM/semi-empirical question. But partly in my own words (one answer was in swedish). Actually, I got no reply of the type I had hoped for, i.e. some sort of (independent) comparison/review. Probably some new information is now available, since both Spartan and Semichem should announce news in August on a ACS meeting. _Uebrigens, ich hatte ein Paper am ECOSS, glaube ich. Ich arbeitete frueher in der Liquid-ESCA-Gruppe hier in Uppsala. Aber 92 war ich schon Post-doc in Wuerzburg.... _So long, Fredrik ----------------------- 1) From Mark Stave "Prof. Walter Thiel's latest version of his semiempirical program, MNDO96, is scheduled to be released soon.Prof. Thiel recently sent me a message indicating MNDO96 will have parameters for the following transition metals: Ti,Zr,Hf,Fe,Ni,Pd,Cu,Ag,Zn,Cd,Hg You may consider contacting Prof. Thiel directly at thiel@oci.unizh.ch I would also like to mention that the Thiel's MNDO program is a part of the UniChem molecular modeling package. If you'd like more information about UniChem, please let me know." 2) "I have heard both Andy Holder and Warren Hehre present results of validation testing at ACS meetings to establish the accuracy of their parameterizations for transition metals. The current status seems to be that: MNDO/d parameterization is focused on main group elements rather than transition metals; PM3(tm) is adding transition metals rapidly, but is focused on good geometries rather than energies; and SAM1 is progressing slower, but is focused on being theoretically consistent and may give better energies." 3) ...Extended Hueckel gives front orbitals, ZINDO electronic spectra, neither of them should be used for geometry optimizations.... ...PM3(tm) (Spartan) seems to give good geometries, but have failed several times for me... ...Others have said that PM3(tm) is a "quick-and-dirty"-parametrization, has to be used with caution... ...The rumours say that SAM1 should be much better than PM3(tm)... ...SAM1 will probably be in the next version of AMPAC, but with very few metals (Fe, Cu, Zn?)... ------------------------- Fredrik Boekman Dept of Organic Chemistry email: Fredrik.Bokman@kemi.uu.se Uppsala University phone: +46/18/183794 P.O. Box 531 fax: +46/18/508542 S-75121 Uppsala Sweden ________________________________________________________________________________ ... Rob O'Brien wrote: > Thiel & Voityuk (ref 2 and 3), have published parameters that extend > the sp basis set used in the AM1, PM3 etc. programs in Hyperchem to include > the d orbitals. I suspect that my calculation problems is related to the > sp rather than spd nature of the chlorine basis set. Ok, there probably is a misunderstanding here. MNDO, AM1 and PM3 are semiempirical *methods* defined by: MNDO: {M.J.S. Dewar and W. Thiel, {\sl J. Am. Chem. Soc.}, {\bf 99}, 4899, 4907 (1977) AM1: {M.J.S. Dewar, E.G. Zoebisch, E.F. Healy, and J.J.P. Stewart, {\sl J. Am. Chem. Soc.}, {\bf 107}, 3902 (1985)} and PM3: {J.J.P. Stewart, {\sl J. Comp. Chem.}, {\bf 10}, 209, 221 (1989)}, respectively. Some of the relevant issues (such as parameters for the elements not parametrized in the original work and a few technical details) are discussed elsewhere, but these three pretty much describe the *methods* themselves. Hyperchem (or Mopac, or Ampac, or VAMP, or MNDO94, or Gaussian, or Spartan, or whatever) are all *programs* implementing the *methods*. All and every of them should be equivalent (modulo the implementation bugs) *if* *they* *implement* *the* *method* you are interested in. Now, MNDO/d, despite a seemingly insignificant difference in the name from MNDO, is a different method, and in some aspects quite a different method from (although sharing a lot of ideas and even some parameters with) the original MNDO. To get an impression of the difference, take a look at the publication describing the two-electron repulsion integrals in MNDO/d: {W. Thiel and A.A. Voityuk, {\sl Theor. Chim. Acta}, {\bf 81}, 391 (1992); {\bf 93}, 315 (1996)} and compare it with the MNDO reference above. Implementing all the necessary integrals is fairly non-trivial, and several pitfalls are there for the unwary (I was there, so I know ;-). The situation is complicated by the fact what most of the semiempirical codes out there attempt to use simplifications arising from the sp nature of the basis set in the MNDO,AM1 and PM3 aggressively, and chasing all the cases where the original author of the code (which may be not available for the comment by now, or may not remember himself, even if he is) cut the corner, knowing that he'll newer ever use anything but s and p functions, might easily become a nightmare. To my knowledge (which is admittedly incomplete), only two codes out there (Thiel's MNDO94 and on, and Wavefunction's Spartan) actually implement the MNDO/d. (Slight differences between these two implementations were rumored, which are probably due to Spartan implementing the original TCA 92 publication to the letter, despite a few typografic errors, which were corrected in TCA 96, but I do not *know* for sure.) The bottom line is clear: until the esteemed Hyperchem team *implements* the MNDO/d method in their program, you won't be able to use MNDO/d parameters with Hyperchem. If you don't want to wait for this to happen (Joel should know better whether and when it will or not, but he probably can't tell anyway), you'd have to try your look with other programs. Regards, /Serge.P ps@ocisgi7.unizh.ch (Serge Pachkovsky) ________________________________________________________________________________ > The bottom line is clear: until the esteemed Hyperchem team *implements* the > MNDO/d method in their program, you won't be able to use MNDO/d parameters > with Hyperchem. If you don't want to wait for this to happen (Joel should > know better whether and when it will or not, but he probably can't tell anyway), > you'd have to try your look with other programs. Thanks for the summary. You are correct: we are working on this, but I can't -- in any sense of "cannot" -- predict when d orbitals might be included in the HyperChem semi-empirical methods other than E.H. and the two ZINDO calculations. Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com WWW: http://www.hyper.com/ Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 _______________________________________________________________________________ On Tue, 12 Nov 1996, rprf526-int wrote: > Collegues: > > I am looking for parameters of metals, mainly > transition ones, for MOPAC (MNDO or PM3) > I really appreciate any information! > > Regards, > > Manuel J. Goncalves > Proccess Department > Intevep > New version of Spartan has PM3(tm) with some transition metals. Atomic parameters for MOPAC can be obtained from corresponding Spartan's parameter files. _ Serge Gorelsky Inorganic Chemistry Laboratory Department of Chemistry, York University 4700 Keele St., North York, Toronto, Ontario M3J 1P3, Canada tel.(416) 736-2100 ext#77720 ________________________________________________________________ From cramer@maroon.tc.umn.edu Tue Nov 26 11:49:44 1996 Received: from mhub2.tc.umn.edu for cramer@maroon.tc.umn.edu by www.ccl.net (8.8.3/950822.1) id KAA25595; Tue, 26 Nov 1996 10:59:01 -0500 (EST) Received: from maroon.tc.umn.edu by mhub2.tc.umn.edu; Tue, 26 Nov 96 09:59:02 -0600 Received: by maroon.tc.umn.edu; Tue, 26 Nov 96 09:59:02 -0600 Message-Id: <329b13c63f3b002@maroon.tc.umn.edu> From: Christopher J Cramer Subject: Re: CCL:pKa calculation To: peon@medchem.dfh.dk (Per-Ola Norrby) Date: Tue, 26 Nov 1996 09:59:01 -0600 (CST) Cc: chpajt@bath.ac.uk, chemistry@www.ccl.net In-Reply-To: from "Per-Ola Norrby" at Nov 26, 96 09:16:43 am X-Mailer: ELM [version 2.4 PL25] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit A small point of clarification on this thread: > > >Whilst what you are saying is very interesting as far as it goes, it takes > >no account of the entropic change on solvation. > > Well, it does! Some continuum solvation models (like the > Cramer-Truhlar models) calculate solvation free energies. It's true that > many ab initio-based models only calculate the electrostatic contribution, > and for an isodesmic comparison that may actually be enough, but the SMx > models do give free energies of solvation. > Even the electrostatic component of solvation as calculated by most continuum models formally has the status of a free energy (it's just not ALL of the free energy of solvation). That is because one usually invokes linear response theory to account for the "cost" of solvent distortion in order to solvate the solute, and that includes both enthalpic and entropic terms. So, the Born formula, the Onsager formula, etc., all calculate free energies. Several studies on the validity of linear response theory have appeared, and the consensus seems to be that it works fine for solutes that do not concentrate large amounts of charge over very small volumes (e.g., singly charged atoms are OK, but doubly and higher charged atoms are not). Naturally, however, there are some dissenters. In any case, SCRF models almost always use a Hamiltonian that includes the cost of solvent distortion and build a Fock operator to minimize the expectation value for that Hamiltonian, the result then being a mixture of potential energy (from the usual components of the Fock operator) and free energy (from the solute/solvent mutual polarization). As for the rest of the free energy of solvation, the SMx models, and modifications of other continuum models like Rivail/Rinaldi, Tomasi's PCM, COSMO, etc., typically assume a proportionality between this quantity and molecular surface area and by parameterization against experiment they predict the full free energy of solvation -- THE ONLY PHYSICAL OBSERVABLE since the components are not measureable with the possible exception of very special systems where certain components must be zero. More complicated approaches to estimating dispersion, cavitation, etc. have been proposed, but in the absence of these properties being experimentally accessible, it is difficult to decide whether they are worth the extra effort (opinions on this subject vary). Chris -- Christopher J. Cramer University of Minnesota Department of Chemistry 207 Pleasant St. SE Minneapolis, MN 55455-0431 -------------------------- Phone: (612) 624-0859 || FAX: (612) 626-7541 cramer@maroon.tc.umn.edu http://pollux.chem.umn.edu/~cramer From ahocquet@tamarugo.cec.uchile.cl Tue Nov 26 12:49:28 1996 Received: from tamarugo.cec.uchile.cl for ahocquet@tamarugo.cec.uchile.cl by www.ccl.net (8.8.3/950822.1) id MAA26215; Tue, 26 Nov 1996 12:13:00 -0500 (EST) Received: from ([146.83.10.50]) by tamarugo.cec.uchile.cl (5.0/SMI-SVR4(Thom)) id AA08421; Tue, 26 Nov 1996 14:12:22 +0400 Message-Id: <329B6AD3.39CF@tamarugo.cec.uchile.cl> Date: Tue, 26 Nov 1996 14:10:27 -0800 From: Alexandre Hocquet X-Mailer: Mozilla 2.02 (Win16; I) Mime-Version: 1.0 To: E.Tajkhorshid@DKFZ-Heidelberg.de Cc: chemistry@www.ccl.net Subject: pKa calculations Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Per Ola Norrby wrote : >What you have here is a "gas phase pKa". If you want the aqueous >pKa, you have to perform the calculations in solvent. = Or another thing to do is to compare your calculations to experimental = gas phase pKa. In an article that will be published soon in the Journal = of Chemical Research, i compare calculated pKas with both solution and = gas phase pKas for carboxylic acids. The original reference for the gas = phase pKa determination was in the Canadian Journal of Chemistry, in 1970 but i dont remember the exact references. Maybe someone in the CCL has it at hand or knows more recent references. I would be interested too Regards, -- = Alexandre HOCQUET Laboratorio de Cristalograf=EDa Facultad de Ciencias F=EDsicas Universidad de Chile Blanco Encalada, 2008 Santiago Chile fax : 56 2 696 73 59 email : ahocquet@tamarugo.cec.uchile.cl From ponder@dasher.wustl.edu Tue Nov 26 15:49:30 1996 Received: from dasher.wustl.edu for ponder@dasher.wustl.edu by www.ccl.net (8.8.3/950822.1) id PAA27507; Tue, 26 Nov 1996 15:09:07 -0500 (EST) From: Received: from comet.wustl.edu by dasher.wustl.edu (5.65v3.2/1.1.10.5/06Aug96-0509PM) id AA11104; Tue, 26 Nov 1996 14:09:07 -0600 Received: from localhost by comet.wustl.edu (5.65v3.2/1.1.10.5/28Jun96-0443PM) id AA00514; Tue, 26 Nov 1996 14:09:07 -0600 Message-Id: <9611262009.AA00514@comet.wustl.edu> Reply-To: ponder@dasher.wustl.edu To: chemistry@www.ccl.net Cc: ponder@dasher.wustl.edu Subject: TINKER Version 3.2 is Available Date: Tue, 26 Nov 96 14:09:07 -0600 X-Mts: smtp Dear CCL Members, We want to announce, for the first time to the "general public", the availability of our TINKER program package for molecular mechanics and dynamics. A brief description is given below, and further information is available from the TINKER web site at http://dasher.wustl.edu/tinker/. The TINKER molecular modeling software is a complete package for molecular mechanics and dynamics of molecules, especially polypeptides. TINKER has the ability to use any of several common parameter sets, such as AMBER/OPLS, CHARMM22, MM2, MM3, AMBER-95, ENCAD, MMFF-94, MM4 (last 3 in progress) and our own TINKER set. It also implements a variety of novel algorithms such as: a new distance geometry metrization method that is much faster than standard algorithms, Elber's reaction path methods, modified versions of Scheraga's Straub's global optimization via potential smoothing, multipole expansion Macromodel GB/SA solvation, our own truncated Newton (TNCG) local optimizer, surface areas and volumes with derivatives, a simple free energy perturbation facility, normal mode analysis, minimization in torsional space, a new spherical energy cutoff method, reaction field treatment of long range electrostatics, and much more.... The distribution version of TINKER, with full source code, is made available free of charge to anyone who wants it. The distributed code is written in a clean, simple subset of Fortran77. A working f2c translated version in C is also provided. We do not and will not provide binaries, as it is expected that users will build the package on their local machines. The basic package has been used by the Ponder lab and others at Washington University since about 1991 and should be fairly robust. All we ask is that you notify us of any bugs, features you would like added, or major code extensions that you add youself. If you make significant use of the package, please return the enclosed license form. Comments are welcome and should be sent via email to ponder@comet.wustl.edu. -------- Jay W. Ponder Phone: (314) 362-4195 Biochemistry, Box 8231 Fax: (314) 362-7183 Washington University Medical School 660 South Euclid Avenue Email: ponder@comet.wustl.edu St. Louis, Missouri 63110 USA WWW: http://dasher.wustl.edu/ From shawn@wavefun.com Tue Nov 26 19:49:30 1996 Received: from volvo.wavefun.com for shawn@wavefun.com by www.ccl.net (8.8.3/950822.1) id SAA29447; Tue, 26 Nov 1996 18:50:24 -0500 (EST) Received: by volvo.wavefun.com (931110.SGI/930416.SGI) for chemistry@www.ccl.net id AA29375; Tue, 26 Nov 96 15:52:04 -0800 Date: Tue, 26 Nov 96 15:52:04 -0800 Received: from fiat.wavefun.com(198.147.95.116) by volvo.wavefun.com via smap (V1.3) id sma029373; Tue Nov 26 15:51:51 1996 X-Sender: shawn@nissan Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@www.ccl.net From: shawn@wavefun.com (Shawn Butler) Subject: New Software Dear CCLers: Wavefunction, Inc. announces release of PC Spartan (same as MacSpartan) and MacSpartan Plus (MacSpartan + Inorganics/Organometallics). Both new products are complete molecular visualization and computational tools. More information is available at http://www.wavefun.com, sales@wavefun.com, or (714) 660-6101. Best wishes for the holidays. Regards, Shawn Butler shawn@wavefun.com From guojx@xx1.icas.ac.cn Tue Nov 26 21:49:29 1996 Received: from xx1.icas.ac.cn for guojx@xx1.icas.ac.cn by www.ccl.net (8.8.3/950822.1) id VAA00115; Tue, 26 Nov 1996 21:32:39 -0500 (EST) Received: (from guojx@localhost) by xx1.icas.ac.cn (8.6.12/8.6.9) id KAA09968; Wed, 27 Nov 1996 10:37:14 +0800 Date: Wed, 27 Nov 1996 10:37:14 +0800 (CST) From: Guo Jian-Xin To: chemistry@www.ccl.net Subject: Interaction between the anion and cation? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters: I would like to calculation the interaction between the radical anion and cation. for the first step, the geometry of the radical-ion pairs should be obtained. My question is: 1. how can we deal with the charge? In my knowledge, I have not found a program that can finish this work. 2. The coulumb attractive force between the two charge can not be calculated. a better method is to add a potential to the Hamitonian. are there any other method in the quantum chemical calculation? I will summarize the replies if interested. Thank in advances. Jianxin Guo ********************************************************************* * Guo, Jian-xin * Telephone: (++86+010) 2563101 * * Ph. D. student * Fax: (++86+010) 2569564 * * State Key Lab for Structral * Email: guojx@xx1.icas.ac.cn * * Chemistry of Unstable * guojx@infoc3.icas.ac.cn * * and Stable Species, * * * Institute of Chemsitry * * * Chinese Academy of Sciences * * * BeiJing 100080 * * * P. R. CHINA * * *********************************************************************