From magtoto@phy.ohiou.edu Wed Nov 27 00:49:33 1996 Received: from helios.phy.ohiou.edu for magtoto@phy.ohiou.edu by www.ccl.net (8.8.3/950822.1) id AAA00577; Wed, 27 Nov 1996 00:41:03 -0500 (EST) Received: by helios.phy.ohiou.edu (SMI-8.6/CLIPNET-4.1a) id AAA04179; Wed, 27 Nov 1996 00:39:34 -0500 Date: Wed, 27 Nov 1996 00:39:32 -0500 (EST) From: Noel Magtoto Sender: Noel Magtoto Reply-To: Noel Magtoto Subject: Chaos program To: chemistry@www.ccl.net In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Dear All, I noticed that this is a predominantly a forum for quantum calculations. But if there is somebody out there who can help me find a program (freeware, of course) that will allow me to analyze a time series (suspected of being chaotic) by reconstructing a chaotic attractor using Taken's time delay method and extracting the Poincare section, please show me the way. Thanks very much. Noel P. Magtoto Graduate Student Chemistry Department Ohio University Email: magtoto@helios.phy.ohiou.edu From bcnlma@hkpucc.polyu.edu.hk Wed Nov 27 04:49:39 1996 Received: from hkpa02.polyu.edu.hk for bcnlma@hkpucc.polyu.edu.hk by www.ccl.net (8.8.3/950822.1) id EAA01764; Wed, 27 Nov 1996 04:37:59 -0500 (EST) Date: Wed, 27 Nov 1996 04:37:59 -0500 (EST) Received: from [158.132.30.106] by 158.132.30.106 with SMTP; Wed, 27 Nov 1996 17:38:19 +0800 (HKT) Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: CHEMISTRY@www.ccl.net From: bcnlma@hkpucc.polyu.edu.hk (Ida N. L. Ma) Subject: electrophilic substitution Cc: bcnlma@hkpucc.polyu.edu.hk Dear CCL list member, I have been looking at elementary electrophilic substitution reactions in substituted benzene i.e. "meta", "ortho,para" directing effects with various substituents. I have tried to correlate these directioning effect using HOMO, LUMO, atomic charges (Mulliken and natural pop. analysis) and electrostatic potentials of the reactant with AM1 and HF/STO-3G* and I thought these are reasonable properties to look at. However, the correlation works sometime but not all the time and I have not been able to sort out the problem yet. Has anyone on the list have any experience with such calculations or can point me to a useful reference? yours sincerely, Ida N. L. Ma Dr. Ida N. L. Ma Dept. of App. Bio. and Chem. Tech. Hong Kong Polytechnic University Hung Hom, Hong Kong. Tel: (852)-27665620 FAX: (852)-23649932 Email: bcnlma@hkpucc.polyu.edu.hk From alain.kessi@psi.ch Wed Nov 27 07:49:39 1996 Received: from psizi1.psi.ch for alain.kessi@psi.ch by www.ccl.net (8.8.3/950822.1) id HAA02226; Wed, 27 Nov 1996 07:07:33 -0500 (EST) Received: from localhost by psizi1.psi.ch (AIX 3.2/UCB 5.64/4.03) id AA16839; Wed, 27 Nov 1996 13:11:19 +0100 Sender: kessi@psizi1.psi.ch Message-Id: <329C2FE6.794B@psi.ch> Date: Wed, 27 Nov 1996 13:11:18 +0100 From: Alain Kessi Organization: Paul Scherrer Institut, Zuerich, Switzerland X-Mailer: Mozilla 3.0 (X11; I; AIX 2) Mime-Version: 1.0 To: CCL Computational Chemistry List Subject: molecules in large electric fields Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL list members, I would appreciate any references to quantum chemical or DFT calculations of molecules in large electric fields. I will summarize to the list. Thank you for your help! Alain Kessi -- Alain Kessi (alain.kessi@psi.ch), at Paul Scherrer Institut, Zurich ++++ stop the execution of Mumia Abu-Jamal ++++ ++++ if you agree copy these 3 sentences in your own sig ++++ ++++ see: http://www.xs4all.nl/~tank/spg-l/sigaction.htm ++++ From ajit@unb.ca Wed Nov 27 08:05:11 1996 Received: from unb.ca for ajit@unb.ca by www.ccl.net (8.8.3/950822.1) id HAA02356; Wed, 27 Nov 1996 07:35:34 -0500 (EST) Received: (from ajit@jupiter.sun.csd.unb.ca [131.202.3.10]) by unb.ca (8.7.6/961016-08:40) id IAA23450 for ; Wed, 27 Nov 1996 08:35:33 -0400 (AST) Received: from localhost by jupiter.sun.csd.unb.ca (8.8.3/960921-23:08) id IAA02619; Wed, 27 Nov 1996 08:35:32 -0400 (AST) Date: Wed, 27 Nov 1996 08:35:32 -0400 (AST) From: "Ajit J. Thakkar" X-Sender: ajit@jupiter To: chemistry@www.ccl.net Subject: CCL: Student Huckel program available Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII A free instructional Huckel MO program is available http://www.simtel.net/pub/simtelnet/msdos/chemstry/hmo10.zip ftp://ftp.simtel.net/pub/simtelnet/msdos/chemstry/hmo10.zip 103636 bytes hmo10.zip Student Huckel molecular orbital calculator HMO performs Huckel theory calculations on planar conjugated hydrocarbons. Undergraduate students find HMO easy to learn and use. HMO accepts input interactively with helpful suggestions. It traps and diagnoses common student input errors. HMO calculates molecular orbital coefficients and energies, pi-electron populations (densities), bond orders, bond lengths, free valences and self polarizabilities. Basic information on use of reactivity indices is presented. HMO requires less than 120KB of free memory. Special requirements: None. Freeware. Uploaded by the author. Ajit J. Thakkar, Chemistry Department, University of New Brunswick ajit@unb.ca http://www.unb.ca From MB@neurosearch.dk Wed Nov 27 08:49:39 1996 Received: from post.neurosearch.dk for MB@neurosearch.dk by www.ccl.net (8.8.3/950822.1) id IAA02697; Wed, 27 Nov 1996 08:31:27 -0500 (EST) Received: by post.neurosearch.dk with SMTP (Microsoft Exchange Server Internet Mail Connector Version 4.0.994.63) id <01BBDC6F.C8C14310@post.neurosearch.dk>; Wed, 27 Nov 1996 14:32:15 +0100 Message-ID: From: Maj - Britt Buch To: "'chemistry@www.ccl.net'" Subject: phosphorus-related parameters Date: Wed, 27 Nov 1996 14:32:13 +0100 X-Mailer: Microsoft Exchange Server Internet Mail Connector Version 4.0.994.63 MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Hi !Where can I obtain phosphorus-related parameters ?I want to phosphorylate a tyrosine residue and then run some dynamics.But in the proces of creating the phosphotyrosine, some problems turn up.After exchanging the hydroxyl hydrogen with a -PO3(2-) group, the amberforcefield can't assign potential type to the tyr:cz, and the totalformal charge doesn't equal the total partial charge. The formal chargeare set correct, with a charge of -1 on each of the two singel-bondedoxygen atoms, but the partiel charge is 0.00 for all atoms in thetyrosine residue. How do I get the correct partiel charges assigned ? Is it nessesary todefine a new atom type, and if so how do I do that ?Thank you for your helpMaj-Britt From tajkhors@mbp-sgi7.inet.dkfz-heidelberg.de Wed Nov 27 08:59:57 1996 Received: from ns1.DKFZ-Heidelberg.de for tajkhors@mbp-sgi7.inet.dkfz-heidelberg.de by www.ccl.net (8.8.3/950822.1) id IAA02686; Wed, 27 Nov 1996 08:29:42 -0500 (EST) Received: from mbp-sgi7.inet.dkfz-heidelberg.de (mbp-sgi7.inet.dkfz-heidelberg.de [193.174.48.96]) by ns1.DKFZ-Heidelberg.de (8.7.3/DKFZ-8.6.4) with ESMTP id OAA20913 for ; Wed, 27 Nov 1996 14:28:17 +0100 (MET) Received: (tajkhors@localhost) by mbp-sgi7.inet.dkfz-heidelberg.de (940816.SGI.8.6.9/DKFZ-8.6.4) id OAA11864 for chemistry@www.ccl.net; Wed, 27 Nov 1996 14:27:23 +0100 From: "Emadeddin Tajkhorshid" Message-Id: <9611271427.ZM11862@mbp-sgi7.inet.dkfz-heidelberg.de> Date: Wed, 27 Nov 1996 14:27:22 +0100 Reply-To: E.Tajkhorshid@DKFZ-Heidelberg.de X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@www.ccl.net (Computational Chemistry List) Subject: pKa calc. Summary Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 8bit Dear CCLers It is the summary of the responses I got for my pKa calculation problem: ******************************************************************************* Original Q: 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. ******************************************************************************** And the answers I got: ******************************************************************************* Date: Mon, 25 Nov 1996 9:49:11 -0600 (CST) From: YONG HUANG To: E.Tajkhorshid@DKFZ-Heidelberg.de Subject: RE: CCL:pKa calculation pKa and proton affinity (/\H) or basicity (/\G) have no relationship with each other. This is not explicitly told in undergraduate courses in America. However, we can safely say that the higher (lower) the pKa of MH, the higher (lower) the proton affinity or basicity of M-, which is _the conjugate base of MH_. Similarly, the higher proton affinity (basicity) of M, the less acidic MH+ is. The above is from simple manipulation of chemical equations. On the other hand, if you look at tables of acidity (or the negative trend of pKa) and basicity of _the same_ species in a reference book, you'll find that _usually_ the more acidic the less basic. But there's no guarantee. H2O is both less basic and less acidic than CH3OH in gas phase. Yong ******************************************************************************* 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 | ------------------------------------------------------------------- ******************************************************************************* 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/ ******************************************************************************* Hi! Unless you have included an explicit solvation term for the products and the reactants - and got at the delta - S then you don't really have an estimation of pKa. That is not to say that the above terms are not computable. If someone comes up with a 'rule of thumb' way of getting pKa from the proton affinity - I would love to here of it though. 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 | ------------------------------------------------------------------- ******************************************************************************* Emad, I am very interested in this topic, in connection with a calculation for the pKa of coordinated water that I and a collaborator want to do. To get a pKa COMPLETELY ab initio requires that you also include the energetics of the solvated proton after dissociation, which is not a straightforward problem. It seems to me that it is more realistic to connect the computed proton affinities to shifts in pK from an experimental value. In our case, the exp. pKa of water is available, so by computing the shift in energy difference between the protonated and unprotonated forms of water for the isolated and complexed cases, you can compute a pK shift (the proton solvation contribution is the same in either case). The question is what level of theory needs to be applied to get decent estimates.. Regards, Randy All opinions expressed here are mine, not my employer's ///////////////////////////////////////////////////////////////////////// \\ Randy J. Zauhar, PhD | E-mail: zauhar@tripos.com // \\ Tripos, Inc. | : zauhar@cyberjunction.com // \\ 1699 S. Hanley Rd., Suite 303 | Phone: (314) 647-1099 Ext. 3382 // \\ St. Louis, MO 63144 | // ///////////////////////////////////////////////////////////////////////// ** ** ** "If you have conceptions of things that you can have no conception ** ** of, then the conception and the thing appear to co-incide." ** ** --- C.G. Jung ** ************************************************************************* 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/ ******************************************************************************* 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 Cristalografía Facultad de Ciencias Físicas Universidad de Chile Blanco Encalada, 2008 Santiago Chile fax : 56 2 696 73 59 email : ahocquet@tamarugo.cec.uchile.cl ******************************************************************************* 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 ******************************************************************************* Many thanx to all people who replied me. -- Emad ********************************************************************* E. Tajkhorshid German Cancer Research Center; DKFZ Tel: +49 6221 42 2339 Dept. Molecular Biophysics (0810) FAX: +49 6221 42 2333 P.O.Box 101949 Email: E.Tajkhorshid@DKFZ-Heidelberg.DE 69009 Heidelberg, FRG *********************************************************************** * A friend may well be reckoned a masterpiece of the nature (Emerson) * *********************************************************************** From LIN@ubaclu.unibas.ch Wed Nov 27 09:49:44 1996 Received: from swiba9.unibas.ch for LIN@ubaclu.unibas.ch by www.ccl.net (8.8.3/950822.1) id JAA02959; Wed, 27 Nov 1996 09:24:35 -0500 (EST) Received: from balu.urz.unibas.ch by swiba9.unibas.ch with SMTP (PP); Wed, 27 Nov 1996 15:23:15 +0100 Received: from ubaclu.unibas.ch by ubaclu.unibas.ch (PMDF V4.3-7 #7496) id <01ICCFPBI8O0937DJ3@ubaclu.unibas.ch>; Wed, 27 Nov 1996 15:22:58 +0100 Date: Wed, 27 Nov 1996 15:21:17 +0100 From: Shu-Kun Lin Subject: IUPAC name To: chemistry@www.ccl.net Message-id: <01ICCFT49RZ8937DJ3@ubaclu.unibas.ch> Organization: University of Basel, Switzerland MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Dear Colleagues: Where can I get a software for me to generate IUPAC names if I have 2D structures or Daylight SMILES or MDL MolFiles? Shu-Kun ------------------------------------------------------------ Dr. Shu-Kun Lin emails: LIN@mdpi.org Molecules/MDPI LIN@ubaclu.unibas.ch Saengergasse 25 100700.1527@compuserve.com CH-4054 Basel Tel. +41 79 322 3379 Switzerland Fax +41 61 302 8918 MDPI: http://mdpi.org/ Molecules: http://science.springer.de/molec/molecule.htm ------------------------------------------------------------ From tajkhors@mbp-sgi7.inet.dkfz-heidelberg.de Wed Nov 27 09:58:42 1996 Received: from ns1.DKFZ-Heidelberg.de for tajkhors@mbp-sgi7.inet.dkfz-heidelberg.de by www.ccl.net (8.8.3/950822.1) id JAA03124; Wed, 27 Nov 1996 09:48:05 -0500 (EST) Received: from mbp-sgi7.inet.dkfz-heidelberg.de (mbp-sgi7.inet.dkfz-heidelberg.de [193.174.48.96]) by ns1.DKFZ-Heidelberg.de (8.7.3/DKFZ-8.6.4) with ESMTP id OAA21316 for ; Wed, 27 Nov 1996 14:57:42 +0100 (MET) Received: (tajkhors@localhost) by mbp-sgi7.inet.dkfz-heidelberg.de (940816.SGI.8.6.9/DKFZ-8.6.4) id OAA11900 for chemistry@www.ccl.net; Wed, 27 Nov 1996 14:56:48 +0100 From: "Emadeddin Tajkhorshid" Message-Id: <9611271456.ZM11898@mbp-sgi7.inet.dkfz-heidelberg.de> Date: Wed, 27 Nov 1996 14:56:48 +0100 In-Reply-To: peon@medchem.dfh.dk (Per-Ola Norrby) "Re: CCL:pKa calculation" (Nov 26, 7:43am) References: Reply-To: E.Tajkhorshid@DKFZ-Heidelberg.de X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@www.ccl.net (Computational Chemistry List) Subject: pKa calculation (2) Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear Per-Ola Thanx for your helpful response to my first question. Actually I am mainly interested in the change of pKa value with regard to conformational changes. Therefore we may bypass the calculation of ABSOLUTE pKa and go to RELATIVE one. I may compare the gas phase proton affinity of teh same species in different conformations. Now is it possible to convert the obtained difference, even very rough, to pH units? For example is there anything like "1Kcal can be related to .6 pH unit"? Any reference and comment is highly appreciated. Thanx -- Emad ********************************************************************* E. Tajkhorshid German Cancer Research Center; DKFZ Tel: +49 6221 42 2339 Dept. Molecular Biophysics (0810) FAX: +49 6221 42 2333 P.O.Box 101949 Email: E.Tajkhorshid@DKFZ-Heidelberg.DE 69009 Heidelberg, FRG *********************************************************************** * A friend may well be reckoned a masterpiece of the nature (Emerson) * *********************************************************************** From zac@servidor.unam.mx Wed Nov 27 10:49:41 1996 Received: from servidor.dgsca.unam.mx for zac@servidor.unam.mx by www.ccl.net (8.8.3/950822.1) id KAA03449; Wed, 27 Nov 1996 10:48:30 -0500 (EST) Received: by servidor.dgsca.unam.mx (5.0/SMI-SVR4) id AA16930; Wed, 27 Nov 1996 09:49:10 +0600 Date: Wed, 27 Nov 1996 09:49:09 -0600 (CST) From: Garcia Zacarias Angelica-FQ To: Chemistry-List 2 Subject: ADF RESTART Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello fellow ccl's I was wondering if you could help me with a problem with ADF. I'm trying to run a particularly large molecule with the restart option but every time ADF gets to the RESTART command it crashes, I've tryed using the results from calculations without the RESTART but it still sends the same error message, something about a superindex having a wrong format but I'm not sore what that means. Can anyone help me please!!! :). Thanks in Advance Angelica Zacarias Claudia Angelica Garcia Zacarias Fisica y Quimica Teorica, DEPg. or Q.Inorganica, DEPg. Fac.Quimica, UNAM email: zacarias@papalotl.pquim.unam.mx Ciudad Universitaria, Mexico D.F.04510 zac@servidor.unam.mx Tel: (52 5) 622 3776 From Giulia.Caron@ict.unil.ch Wed Nov 27 11:49:42 1996 Received: from unilmta3.unil.ch for Giulia.Caron@ict.unil.ch by www.ccl.net (8.8.3/950822.1) id LAA03858; Wed, 27 Nov 1996 11:40:15 -0500 (EST) Received: from pcbep5008b.unil.ch by unilmta3.unil.ch with SMTP inbound; Wed, 27 Nov 1996 17:39:15 +0100 Message-Id: <2.2.16.19961127174702.64cf38c8@ulys.unil.ch> X-Sender: gcaron@ulys.unil.ch X-Mailer: Windows Eudora Pro Version 2.2 (16) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@www.ccl.net From: "Giulia Caron (la Perla di Losanna)" Subject: About VAMP Date: Wed, 27 Nov 1996 16:39:16 +0000 Dear CCLers, I like before giving correct assignment to NMR spectra, to have predictions of chemical shift by semi empirical methods. VAMP 5.1 (Oxford Molecular) uses neural nets to extimate from the wave function the spectroscopic properties of molecules but I don't know how it works. Can you help me? Thank you very much! Giulia \\|// ( @ @ ) .---------------------oOOo----(_)----oOOo-----------------------------------. | La Perla di Losanna | ICT | | Giulia Caron | Section de Pharmacie | | mail : giulia.caron@ict.unil.ch | UNIVERSITE DE LAUSANNE | | tel: ++41 21/692-4528 | BEP CH-1015 Lausanne | | fax : +41 21/692-4505 Oooo. | Switzerland | | ( ) Oooo. | | .----------------------------\ (----( )-----------------------------------. \_) ) / (_/ From Eugenia.Migliavacca@ict.unil.ch Wed Nov 27 13:49:42 1996 Received: from unilmta3.unil.ch for Eugenia.Migliavacca@ict.unil.ch by www.ccl.net (8.8.3/950822.1) id NAA04347; Wed, 27 Nov 1996 13:03:35 -0500 (EST) Message-Id: <199611271803.NAA04347@www.ccl.net> Received: from pcbep5005c.unil.ch by unilmta3.unil.ch with SMTP inbound; Wed, 27 Nov 1996 19:02:53 +0100 X-Sender: emigliav@ulys.unil.ch X-Mailer: Windows Eudora Version 2.1.1 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Wed, 27 Nov 1996 19:05:25 +0100 To: Computational Chemistry Mailing List From: Jenny Subject: radical cations in solution Dear CCLers, I am interested in the calculation of minimum energy conformations of a radical cation (17 heavy atom: C, O, N) in solution (water). Can continuum solvation models be used to investigate geometries and relative energies of different conformers? Is AMSOL a good choice? Please, reply directly to me (Eugenia.Migliavacca@ict.unil.ch). I will summarize the answers for the CCL. Thank you in advance and best regards, Jenny Jenny Migliavacca Institut de Chimie Therapeutique Ecole de Pharmacie Universite de Lausanne CH-1015 Dorigny-Lausanne Tel: 021 / 692.45.29 Fax: 021 / 692.45.05 Email: Eugenia.Migliavacca@ict.unil.ch From C.Wigglesworth@open.ac.uk Wed Nov 27 17:49:43 1996 Received: from venus.open.ac.uk for C.Wigglesworth@open.ac.uk by www.ccl.net (8.8.3/950822.1) id RAA07187; Wed, 27 Nov 1996 17:03:56 -0500 (EST) Received: from tyne.open.ac.uk by venus.open.ac.uk with SMTP Local (PP) id <26783-0@venus.open.ac.uk>; Wed, 27 Nov 1996 22:03:45 +0000 Received: (from cw9@localhost) by tyne.open.ac.uk (8.7.6/8.6.12) id WAA27023 for chemistry@www.ccl.net; Wed, 27 Nov 1996 22:03:44 GMT From: Chris Wigglesworth Message-Id: <199611272203.WAA27023@tyne.open.ac.uk> Subject: Sternheimer antishielding factors To: chemistry@www.ccl.net Date: Wed, 27 Nov 1996 22:03:43 +0000 (GMT) X-Mailer: ELM [version 2.4ME+ PL17 (25)] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Dear CCLers, I am currently trying to calculate electric field gradients for ionic solid state systems using point charge models and ab initio methods. To do this I require values for the Sternheimer antishielding factor for a number of heavy/transition metals, in particular Vanadium and Lanthanum. I would therefore appreciate any references to where I might find values for the Sternheimer antishielding factor for heavy/transition metals. I will summarise the results. Yours sincerely, Chris Wigglesworth Chemistry Deparment The Open University Walton Hall Milton Keynes MK7 6AA e-mail: c.wigglesworth@open.ac.uk From peon@medchem.dfh.dk Wed Nov 27 17:58:48 1996 Received: from danpost.uni-c.dk for peon@medchem.dfh.dk by www.ccl.net (8.8.3/950822.1) id QAA07120; Wed, 27 Nov 1996 16:58:39 -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 WAA00462; Wed, 27 Nov 1996 22:58:38 +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 XAA01846; Wed, 27 Nov 1996 23:02:54 +0100 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Wed, 27 Nov 1996 22:58:39 +0100 To: E.Tajkhorshid@DKFZ-Heidelberg.de From: peon@medchem.dfh.dk (Per-Ola Norrby) Subject: Re: CCL:pKa calculation (2) Cc: chemistry@www.ccl.net Dear Emad, >Now is it possible to convert the obtained difference, even very rough, to pH >units? For example is there anything like "1Kcal can be related to .6 pH >unit"? Sure, since .Delta.G = -RT ln(Ka) and pKa = -log(Ka), it follows that .Delta.G = RT ln(10) pKa Therefore, for the reaction AH+ + B <-> A + BH+ : .Delta.G = RT ln(10) .Delta.pKa I would still add a semi-empirical solvation term to .Delta.G, as the conformers may be solvated differently. 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/