From owner-chemistry@ccl.net Fri Jul 7 02:07:02 1995 Received: for jkl@ccl.net by www.ccl.net (8.6.10/930601.1506) id CAA22109; Fri, 7 Jul 1995 02:04:41 -0400 Date: Fri, 7 Jul 1995 02:04:41 -0400 From: Jan Labanowski Message-Id: <199507070604.CAA22109@www.ccl.net> To: chemistry@ccl.net Subject: Please contribute new things to CCL archives In-Reply-To: Mail from 'tj ODonnell ' dated: Thu, 6 Jul 1995 15:00:10 -0500 (CDT) Cc: jkl@ccl.net TJ O'Donnell tj@eecs.uic.edu writes: > Didn't someone (Dimitris Agrafiotis) offer to collect TCL/TK programs? > I agree that TCL/TK is very powerful, in spite of its slow speed. > I am willing to collect TCL/TK programs for chemistry and maintain > an index of programs I have collected. I could make the index and > the programs available through CCL. I have NOT discussed this > with the authorities at CCL. I am just offering. > What do you all think? > Who else likes and uses TCL/TK? Just to remind you... I will most gladly put ANYTHING in the CCL archives, if it is useful for Computational Chemists. Just upload it into incoming directory to www.ccl.net by ftp and tell me what it is and what should I do with it. Give me also some README file so people know what it is. I will gladly put a directory under pub/chemistry/software/SOURCES with TCL-Tk scripts (and other scripts for that matter). Go for it... This offer will not stand forever... If you do not have ftp, send it to me via e-mail. Share your goodies... Your administrator Jan Labanowski jkl@ccl.net-- Dr. Jan K. Labanowski, Senior Research/Supercomputer Scientist/Specialist, etc. Ohio Supercomputer Center, 1224 Kinnear Rd, Columbus, OH 43212-1163 ph:(614)-292-9279, FAX:(614)-292-7168, E-mail: jkl@ccl.net JKL@OHSTPY.BITNET From owner-chemistry@ccl.net Fri Jul 7 06:36:59 1995 Received: from gw.srcc.msu.su for qsar!qsar.chem.msu.su!eugene@gamma.srcc.msu.su by www.ccl.net (8.6.10/930601.1506) id GAA24331; Fri, 7 Jul 1995 06:36:15 -0400 Received: from srcc.UUCP (uusrcc@localhost) by gw.srcc.msu.su (8.6.12/8.6.12) with UUCP id OAA01948; Fri, 7 Jul 1995 14:35:55 +0400 Received: by gamma.srcc.msu.su; Fri, 7 Jul 1995 14:35:38 +0400 Received: by qsar.chem.msu.su (dMail for DOS v1.23, 15Jun94); Fri, 7 Jul 1995 13:12:03 +0400 To: chemistry@ccl.net Cc: leclerf@medcn.umontreal.ca Message-Id: Organization: Lab. of Org.Synth., MSU Date: Fri, 7 Jul 1995 13:12:03 +0400 (MSD) From: "Eugene Radchenko" X-Mailer: dMail [Demos Mail for DOS v1.23] Subject: Summary: Methods & Principles in Medicinal Chemistry Lines: 154 Hi CCLers! Recently I posted a question concerning the book 'Methods and Principles in Medicinal Chemistry': >By any chance, can someone please mail me the series programme and ordering >information for the book series: > Methods and Principles in Medicinal Chemistry >published recently by the VCH Weinheim. Many thanks to all who replied. Following is the summary of the responses. >From: David Livingstone >Date: Sat, 24 Jun 1995 09:11:17 +0100 > >The book titles for the first three volumes are: > >QSAR: Hansch Analysis and Related Approaches. Author - H. Kubinyi, >1993, ISBN 3-527-30035-X (VCH, Weinheim) or 1-56081-768-2 (VCH, New >York). > >Chemometric Methods in Drug design. Editor - H. van de Waterbeemd, >1994 (I think) and I don't have the book so I don't know the ISBN No. > >Advanced Computer-Assisted Techniques in Drug Discovery. Editor H. >van de Waterbeemd, 1994, ISBN 3-527-29248-9 (VCH, Weinheim) > >An address for VCH in Germany is: >VCH, P.O. Box 10 11 61, D-69451, Weinheim, Germany. > >Another recent book that you may be interested in is: > >Molecular Similarity in Drug Design. Editor - P. Dean, Blackie >Academic & Professional, 1995, ISBN 0 7514 0221 4. > >Order from Chapman & Hall, 2-6 Boundary Row, London, SE1 8HN, UK. > >Finally, I have just finished a book that may be useful to you: > >Data Analysis for Chemists: Applications to QSAR and Chemical product >Design. Author - D.J. Livingstone, Oxford University Press, 1995, >ISBN 0 19 855728 0. > >This should be available in about September. > >Regards, >Dave. >------------------------------------------------------------------ >D.J. Livingstone > ChemQuest > Cheyney House, 19-21 Cheyney St., > Steeple Morden. Herts UK SG8 0LP > >Phone & Fax: +44 (0)1763 852569 >e-mail davel@chmqst.demon.co.uk ******************************************************************** >From: MARTIN@cmda.abbott.com >Date: Thu, 22 Jun 1995 15:56:20 -0500 (CDT) > >VCH is >VCH, PO Box 101161 >D-69451 Weinheim >Federal Republic of Germany > >I have just reviewed the volume on New Approaches to QSAR > >Advanced Computer-Assisted Techniques in Drug Discovery. >Edited by Han van de Waterbeemd. Weinheim; New York; Basel; >Cambridge; Tokyo: VCH 1994. (Volume 3 of Methods and >Principles in Medicinal Chemistry. Series Editors: R. >Mannhold, P. Krogsgaard-Larsen, H. Timmerman.) ISBN 3-527- >29248-9. > >This volume covers 3D quantitative structure-activity relationships, rational >use of chemical and sequence databases, advanced statistical techniques, and >neural networks and expert systems. While many chapters are not reviews of the >subject, but instead emphasize the authors' approach with no reference made to >other highly related work, all are well-written and informative. > >After an overview by the editor, Pitea, et al. discuss chemometrics and >molecular modeling to perform 3D QSAR. They illustrate their approach with >several examples. Next, Davis describes his CoMFA approach illustrated with >calcium channel agonists. Cruciani and Clementi explain GOLPE, the variable- >selection refinement of partial least-squares, and illustrate it with two >applications. > >Johnson, et. al. describe using 2D or 3D molecular similarity to select >compounds for testing, to prepare structure-activity maps, and to display 3D >properties. They also describe the mathematical procedures to apply these >concepts. Downs and Willett discuss compound selection based on clustering of >chemical structure databases. They review clustering methods and provide >examples of applications. Lewi and Moereels describe receptor mapping and >phylogenetic clustering of based on the amino acid sequences of 71 G- protein >coupled receptors. > >Continuum regression is presented by Malpass, et al., as a general technique >that encompasses multiple linear regression, partial least squares, and >principal components regression. They discuss its theoretical basis and its >performance compared to the other methods. Dor and Ojasoo present >correspondence factorial analysis, which shows the relationships between >compounds and their responses in several biological tests, using the >affinities of 187 steroids to five different receptors. Rose, et al. discuss >k- nearest neighbor and single-class discrimination to analyze biologically >active compounds surrounded by inactive compounds in descriptor space. Schaper >describes fuzzy adaptive least squares using examples of four different >biological end-points. Lastly, Clare discusses alternating conditional >expectations in QSAR, which detects the form of nonlinear relationships >between properties and bioactivity. Manallack and Livingstone discuss the >advantages and disadvantages of neural networks compared to statistical >methods. They propose experimental guidelines to prevent overtraining. Lastly, >A-Razzak and Glen discuss the artificial intelligence technique of rule >induction to discover the relationships between biological activity and >chemical properties. They propose it as a complement to conventional >statistical and pattern-recognition methods. > >Yvonne Connolly Martin >Pharmaceutical Products Division >Abbott Laboratories >100 Abbott Park Road >Abbott Park, IL 60064-3500 >June 11, 1995 *********************************************************************** >From: "Sergei Vyboishchikov" >Date: 28 Jun 95 19:50:09 MDT > > [The E-mail address of ] VCH (Verlag Chemie) is > marketing@vchgroup.de ************************************************************************ >Date: Thu, 22 Jun 1995 16:47:06 +0200 >From: Shcherbukhin Vladimir > > Hi Zhenya, > > Tha address of the distribution office is: > VCH, PO Box 101161, D-69451 Weinheim, Germany. > ----------------------------------------------------------------- >Vladimir Shcherbukhin ! phone: (+46-31)-776-2560 >ASTRA Haessle AB ! FAX: (+46-31)-776-3710 >Molndal S-43183 ! e-mail: >SWEDEN ! Vladimir.Shcherbukhin@hassle.se.astra.com *********************************************************************** Again, thanks to everyone. Eugene -- -------------------------------------------------------------------- Eugene V. Radchenko Graduate Student in Computer Chemistry E-mail: eugene@qsar.chem.msu.su Fax: +7-(095)939-0290 Ordinary mail: Chair of Organic Chemistry, Department of Chemistry, Moscow State University, 119899 Moscow, Russia ***************** Disappearances are deceptive ******************* From owner-chemistry@ccl.net Fri Jul 7 06:51:59 1995 Received: from gw.srcc.msu.su for qsar!qsar.chem.msu.su!eugene@gamma.srcc.msu.su by www.ccl.net (8.6.10/930601.1506) id GAA24337; Fri, 7 Jul 1995 06:36:46 -0400 Received: from srcc.UUCP (uusrcc@localhost) by gw.srcc.msu.su (8.6.12/8.6.12) with UUCP id OAA01950; Fri, 7 Jul 1995 14:35:58 +0400 Received: by gamma.srcc.msu.su; Fri, 7 Jul 1995 14:35:48 +0400 Received: by qsar.chem.msu.su (dMail for DOS v1.23, 15Jun94); Fri, 7 Jul 1995 14:31:47 +0400 To: chemistry@ccl.net Cc: kotelyan@che.udel.edu, yu@infinity.wavefun.com, nmills@alchemy.chem.trinity.edu, johannes.richardi@chemie.uni-regensburg.de Message-Id: Organization: Lab. of Org.Synth., MSU Date: Fri, 7 Jul 1995 14:31:47 +0400 (MSD) From: "Eugene Radchenko" X-Mailer: dMail [Demos Mail for DOS v1.23] Subject: Summary: Opinions on the quantum charges Lines: 493 Hi CCLers! Recently I asked a question on the QC-derived atomic charges: >I would like to know what is the current opinion concerning the atomic >charges calculated by the quantum-chemical methods, especially for the >charged species. I mean their strong tendency to produce over-pronounced >charge separation. I might even try to reconcile myself with slight negative >charge on nitrogen in ammonium, but rather high POSITIVE charge on carbon >in (fluorinated) carbANIONS absolutely kills me. >I wonder whether it might actually be computational artifact induced by, >for instance, improper basis set selection or atom partitioning? I have received quite a few responses. Following is the summary (in no particular order). I have also taken the liberty to comment on some points. ********************************************************************** >Date: Thu, 22 Jun 1995 08:37:08 -0500 >From: Lipkowitz > >An introductory chapter entitled "Population Analysis and Electron Densities >from Quantum Mechanics" explains all that to you. It was written by Steve >Bachrach and published in Volume 5 of Reviews in Computational Chemistry, VCH >Publishers, 1994. ************************************************************************ >Date: Thu, 22 Jun 95 15:50:55 +0200 >From: ptvd@chem.rug.nl (van duijnen) > >First, 'atomic charges' are not 'observables': they are usually obtained by >some arbitrary allocation of parts of the electronic charge distribution to >atoms. Most methods are systemitical: the Mulliken prodecure assigns >electrons to atoms via the centers of the basis functions (e.g. even if the >maximum of an a.o. lies closer to another atom onwhich it's centered!). >Two-center distributions are split equally between the two associated >atoms, regardless of where that distribution resides in space. Only the >total number of electrons is preserved. >Mulliken charges are, as a consequence strongly basis dependent, and their >use as 'chemical indicators' for extended basis sets is very doubtful. > >Second, for what are 'charges' used. If one's only interest is generating >electrostatic potentials (ESPs) outside a molecule, fitting the charges to >the expectation values of the ESP is an option. It may be combersome, >because one needs a relatively large number of 'measuring points' for which >the ESP has to be computed. The results are generally good, within the >standard multipole expansion philosophy, i.e. any set of point charges >inside the molecular volume which reproduces the ESP is acceptable. Fit >procedures are dumb but obedient: any set of charges is OK, but they don't >have to make (chemical) sense. Often the charges in two molecules (e.g. >differing only in conformation) may look very different, but both sets are >still 'good'. > >We have been satisfied with a compromise: constructing Dipole Preserving >Charges. (Theor.Chim. Acta (1983) 63 209-221). They are obtained from the >standard Mulliken analysis-by contracting the density and overlap matrices- >extented with a similar procedure for the dipole matrices. Hence, both the >total charge and the overall dipole moment is reproduced by the resulting >charges. The procedure makes sure that 'local' charge distributions are >kept as local as possible. The charges of course vary in the same way as >Mulliken charges, so their value as analytical tools are the same. > >Our experience is that the DP charges give very good ESPs. Recently we >tried to 'improve' the method (more expansion centers, higher moments,...) >but at no avail. > >There are other methods, of course. My memory tells me about Ahlrichs and >coworkers (I think it is also in Theor.Chim. Acta 1983) using a projecting >procedure which makes charges virtually basis independent. > >I hope this helps a bit. > >Best regards, Piet. > >Dr.P.Th. van Duijnen, Chemistry Department (OMAC), University of Groningen, >Nijenborgh 4, 9747 AG Groningen, The Netherlands. >tel. (int)-3150-634373 fax. (int)-3150-634296 e-mail: ptvd@chem.rug.nl ********************************************************************* >Date: Thu, 22 Jun 1995 09:50:15 -0400 >From: gilson@indigo14.carb.nist.gov (Michael K. Gilson) > >I am not expert in this field, but I do know a couple of papers that might be >relevant. They deal with the problem of fitting charges to external >electrostatic potentials computed by electronic structure calculations. > >The papers address the problem that atoms that are not near the "surface" of >the molecule need not be assigned reasonable charges. The reason is that >their charges do not influence the potential much anyway! So standard fitting >does not work too well for them. > >The references are: > >@Article{resp1, > author = "Wendy D. Cornell and Piotr Cieplak and Christopher > I. Bayly and Peter A. Kollman", > title = "Application of {RESP} charges to calculation > conformational energies, hydrogen bond energies, and > free energies of solvation.", > OPTcrossref = "", > OPTkey = "", > journal = "J. Am. Chem. Soc.", > year = "1993", > volume = "115", > OPTnumber = "", > pages = "9620-9631", > OPTmonth = "", > OPTnote = "", > OPTannote = "" >} > >@Article{resp2, > author = "Christopher I. Bayly and Piotr Cieplak and Wendy D. > Cornell and Peter A. Kollman", > title = "A well-behaved electrostatic potential based method > using charge-restraints for deriving charges: {T}he > {RESP} model.", > OPTcrossref = "", > OPTkey = "", > journal = "J. Phys. Chem.", > year = "1993", > volume = "97", > OPTnumber = "", > pages = "10269-10280", > OPTmonth = "", > OPTnote = "", > OPTannote = "" >} > >Good luck > >Mike Gilson >CARB Fellow *********************************************************************** >From: cramer@maroon.tc.umn.edu >Date: Thu, 22 Jun 1995 09:50:33 -0500 (CDT) > > Your question has been addressed ad nauseam in the literature and has been >a topic of some debate since the mid 1930's. Our own contribution has been >the development of Class IV charge models which employ semiempirical mapping >parameters to improve charges derived from other methods by fitting against >experimental dipole moments. I note that the paper is fairly recent (J. >Comput.-Aid. Mol. Des. 9 (1995) 87-110) and provides a comprehensive >listing of references to other work in the field--thus, you might find it >useful as a starting point if you decide to immerse yourself in this topic. >Moreover, it as available on the WWW at >http://wucmd.wustl.edu/jcamd/278/paper.html (kudos to ESCOM). > >Chris > >-- >Christopher J. Cramer >University of Minnesota >Department of Chemistry >207 Pleasant St. SE >Minneapolis, MN 55455-0431 >(612) 624-0859 >cramer@maroon.tc.umn.edu >http://dionysus.chem.umn.edu/ ************************************************************************ >From: tj ODonnell >Date: Thu, 22 Jun 1995 10:12:21 -0500 (CDT) > >Yes, schemes for assigning charges to atom sometimes give unexpected results. >I think it is due simply to the too-simple assumption that charge CAN be >partitioned among atoms. What I mean is: it is always an arbitrary choice one >makes when partitioning a molecular charge among its component atoms. While >nuclei may retain their identity within molecules, electrons don't - certainly >not the valence electrons. In addition, many charge schemes "look at" the >molecule from a distance (esp fitting procedures, e.g.), evaluating properties >(esp) at points which are influenced by nuclei and electrons contributed by >several atoms. Is it any wonder that this "average" effect cannot clearly be >attributed then to individual atoms? > >Just my opinion, >TJ O'Donnell >tj@eecs.uic.edu >http://www.eecs.uic.edu ************************************************************************ >From: ross@cgl.ucsf.EDU >Date: Thu, 22 Jun 1995 08:49:42 -0700 > >There is a discussion of charge fitting for molecular mechanics on >http://www.amber.ucsf.edu/amber/ under "Charge fitting philosophy." > >Bill Ross ********************************************************************** >Date: Thu, 22 Jun 95 18:52:51 +0100 >From: Johannes.Richardi@chemie.uni-regensburg.de (Johannes Richardi) > >It might be interesting for you that I am currently calculating multipole >moments of standard organic molecules by ab initio methods >(chloroform,acetone,pyridine). I compare the multipoles obtained directly and >by the partial charge models. I sometimes observe a strong derivation of some >percents. As the partial charge models are quite important for computer >simulations of liquids these results are generally interesting to my mind. > >Now concerning your remark, I believe you should compare the multipole moments >obtained directly by ab initio or experiments and by the partial charge model. >If you find a good correspondence, the results are correct, even when they >don't correspond to our chemical common sense. If not, you should try to fit >your partial charge model to the exact multipoles. I have written programms to >cope with multipoles and partial charge models and I would agree to any >cooperation. > >Please send me a copy of the answers obtained !!! > >Johannes > > >Johannes Richardi > >--------------------------------------------------------------------------- >Institut fuer Physikalische und Theoretische Chemie >- Lehrstuhl Prof. Barthel - Tel.: (+49) 941 943-4743 >Universitaet Regensburg Fax.: (+49) 941 943-4488 >Universitaetsstrasse 31 >D-93053 Regensburg >Deutschland / Germany >--------------------------------------------------------------------------- >EMail (SMTP): Johannes.Richardi@chemie.uni-regensburg.de >--------------------------------------------------------------------------- > E PUR SI MUOVE -- GALILEO GALILEI *********************************************************************** >From: breneman@XRAY.CHEM.RPI.EDU >Date: Thu, 22 Jun 1995 12:58:38 EDT > >You have entered into a very controversial subject area with your posting! >There are many different ways of approaching the "charge" problem, and >you get different results using different methods. Perhaps the use of >a common term ("charge") is not even appropriate for comparing these results. >In my opinion, a distribution of electron density can be queried for a number >of things, one of them being electrostatic potential. If one wants to >define atomic point charges which duplicate this potential (to the best fit >approximation, anyway), then this is a good model of "atomic charges". If >one wants to partition electron density and perform sub-structure quantum >mechanics, it is necessary to use a partitioning method which ultilizes >interatomic zero-flux surfaces which amount to discrete atomic boundaries. >When the electron population within these atomic volumes are subtracted from >the nuclear charge, you will get a number which is NOT to be confused with >the former electrostatic "charge" definition given above. IF, however, these >"charged" regions are considered in addition to their internal dipole moments, >the molecular dipole moments can be reproduced EXACTLY. Hence, there are >more ways to think of "charge" than most people consider. > > Curt Breneman > Assoc. Prof. of Chem. > RPI, NY ************************************************************************* >Date: Thu, 22 Jun 1995 16:47:06 +0200 >From: Shcherbukhin Vladimir > >The QC charges you have written about don't look strange at all. >Especially if you consider that they are non-existing values -- there is >no *unique* way to project the electron density calculated from the >wavefunction into atomic positions. > > Yours, > Volodya > > ----------------------------------------------------------------- >Vladimir Shcherbukhin ! phone: (+46-31)-776-2560 >ASTRA Haessle AB ! FAX: (+46-31)-776-3710 >Molndal S-43183 ! e-mail: >SWEDEN ! Vladimir.Shcherbukhin@hassle.se.astra.com ************************************************************************ >From: mayer@cric.chemres.hu >Date: Mon, 26 Jun 1995 16:09:45 +0200 (DFT) > >The problem of charges is not a trivial one. The most often used >Mulliken's population analysis has a priviledged importance as far as the >MATHEMATICAL structure of the finite basis theory is concerned [cf. I. >Mayer, Chem. Phys. Letters 97, 270 (1983); THEOCHEM 255, 1 (1992)] but it >is strongly basis dependent. It usually gives chemically "reasonable" >results (especially when one interested in TRENDS in series of related >molecules) if the "well balanced" STO-3G or 6-31G** basis sets are used, >but may lead to completely mad results for other basis sets, in particular >for anions, especially if DIFFUSE functions are present in the basis - >these are formally attributed to one of the atoms but, in fact, spread >over the whole molecule. In such a case the best is to turn to >Lowdin-orthogonalized basis and calculate the charges in the latter. > >We think the over-sensibility of Muilliken's charges is partly due to some >INTRA-molecular BSSE-like effects and could be reduced by the exclusion of >the latters. However, it is to be emphasised that there exists no perfect >solution of the charge problem if an OVERLAPPING basis is used. There are >no definitions which could simultaneously fulfil the requirements: > >1. The population on each atomic orbital is always between 0 and 2; > >2. The population is related to strictly atomic quantities; > >3. The population on different AO-s (or atoms) sums up to the total > number of electrons. > >Mulliken's populations do not strictly fulfil requirement 1; the charges >calculated in Lowdin-orthogonalized basis do not fulfil requirement 2, as >are is related to some delocalized orthogonal orbitals, reflecting some >global effects, too: as a consequence, one may change them by adding some >EMPTY orbitals to the basis, i.e. without changing the wave function [c.f. >I.Mayer, Chem. Phys. Lett. 110, 440 (1984)]; the so called Robby's charge >violates requirement 3 (e.g. in the HF molecule it gives negative >resulting charge on both H and F). > >I have discussed above "partitioning the electronic charge in the Hilbert >space" of AO-s (G.G. Hall). A completely different - very useful - charge >concept emerges in Bader's "topological theory of atoms in molecules", in >which the 3-dimensional PHYSICAL space is partitioned into "atomic >domains", and the charge distribution in each of them integrates to the >atomic charges. Unfortunately, the calculation of these charges is more >complicated computationaly. > >Yours sincerely, > >Prof. Istvan Mayer > > e-mails: mayer@cric.chemres.hu > IB13LVIB@HUEARN.sztaki.hu > H1376May@ella.hu > >Central Research Institute for Chemistry >of the Hungarian Academy of Sciences >H-1525 Budapest, P.O.Box 17 >Hungary ********************************************************************* >From: Karl.F.Moschner@urlus.sprint.com >Date: Mon, 26 Jun 1995 12:04:00 -0400 > >From what I can glean from the literature, most researchers seem to agree >that HF/6-31G* MEP charges are "best" or "good" or at least adequate in >determining atom-centered charges and there is little benefit (significant >change in atom-centered charges) in going to MP2/6-31G* MEP charges. >Alternatively, to save time, scaled MNDO MEP charges may be used since they >have been shown to have a high correlation correlation to HF/6-31G* MEP >charges, at least for CHNO compounds. MEPs are generally preferred since >it is argued that they reflect what is "seen", i.e., the Coulombic >interaction experienced, by other molecules. Atom-centered charges derived >by partitioning methods, including emprical electronegativity balancing >schemes such as Del Re's (avialble QCPE) and Gasteiger methods and >semiemprical or ab initio natural atomic or Mulliken charges, are >considered to be inferior if not unreliable. However, recently, Cramer has >introduced a modified Mulliken method, for, I believe AM1, which is claimed >to reproduce MEP HF/6-31G* charges at a substantially lower computational >cost and leading to an improved semiempirical solvation model. > >As for "their strong tendency to produce over-pronounced charge separation" >and apparently odd charges, certainly MEP HF/6-31G* charges appear to >display more highly polarized molecules (larger atom-centered charges) than >the partitioning methods and one may see signifcant differences in >predicted relative charges and even charge sign changes. But which method >is correct? How can one tell? I am not aware of any correlations of >predicted/derived atom-centered charges with direct measurements, though >chemically modified STM may provide an opportunity to do so if the >resolution is fine enough. Alternatively, one might look at NMR shift >data, but this too, includes solvation effects. Might it be possible to >combine NMR with MS to measure gas phase atomic environments and therefore >the charge? I beleive some work has been done trying to correlate electron >denisty maps from X-ray studies with charge, but this too has a >partitioning problems and involves crystal lattice effects. To complicate >matters further, derived atom-centered charges may also be conformationaly >dependent! [There have been a few references on modifying empirical >partitioning methods either to include through space interactions >(Gasteiger published a variation of his method) or, I believe, to include >conformationally dependent paramters, e.g., similar to molecular mechanics >1-4 interactions. Efforts have also been made to solve such equations >directly rather than by itterative schemes so that charges may be updated >more frequently in molecular dynamics studies]. > >Many would say that atom-centered charges aren't very meaningfull anyway so >ignore them or don't worry too much. They are an artificial, albeit >methodical and reproducible construct, a convenience for counting or >partitioning electrons. But choice of charge models can have a signficant >impact on studies particularly in molecular mechanics and molecular >dynamics calculations in which accurate representation of intermolecular >potentials is crucial. > >So what is a reasearcher to do? First be consistent; don't mix charge >models. Next, from a completely pragmatic standpoint, use the charge model >which best fits your set of data. Don't be overly concerned with absolute >values unless there is corroborative direct or indirect evidence that they >are "wrong" or inconsitent with other observations. > >What's wrong with a negative charge on N in amonnium compounds? That is, >why is it important and what significance does it have? Does it lead to >incorrect conformations? Presumably one might be more interested in the >charge on the -N+H protons which might be expected to reflect H-bonding >potential and acidity, i.e., compared with water, methanol, etc., and that, >no doubt, has to be more positive to compensate for the negative N. > >Positive C-charge on flourinated carbanions? Why is this a problem? Does >it disagree with chemical reactivity, i.e., nuclephilicity of the >carbanion? Is it more positive than the neutral compound? > >In my own work, I have also observed "bothersome" charges but more often >than not such observations are distractions and not relevant to the study. > >In the end, there is no easy answer. This controversy is likely to go on >for some time until methods permit us to reliably measure charges of >individual atoms. > >My appologies for not referencing the many researchers who have made >valuable contributions to this area of research. > >Karl > _______________________________________________________________________ >/ \ >| Comments are those of the author and not Unilever Research U. S. | >| | >| Karl F. Moschner, Ph. D. | >| | >| Unilever Research U. S. e-mail: Karl.F.Moschner@urlus.sprint.com | >| 45 River Road Phone: (201) 943-7100 x2629 | >| Edgewater, NJ 07020 FAX: (201) 943-5653 | >\_______________________________________________________________________/ ************************************************************************** >Date: Thu, 22 Jun 1995 15:41:12 -0400 >From: "E. Lewars" > >There was a question about QM charges and fluorocarbanions reccently. >Some of these species were said to show a positive C, and the question of the >reliability of quantum mechnically calc charges arose. > There seems to be no one, right way to calc charges on atoms in molecules, >and these charges evidently can't be measured ("are not QM observables") -- >but see Pearlman and Kim, J Mol Biol 211 p 171 (1990). >General refs to calculating charges: >Wiberg et al, J Comp Chem 14 p1504 (1993) >Basis set dependence: >Rodrigues et al, J Comp Chem 14 p922 (1993) >Other refs: > >JACS 107 p1829 (1985) >JACS 113 p 5203 (1991) >JACS 115 p614 (1993) >JACS 115 p1084 (1993) >JACS 116 p6812 (1994) >J Comp Chem 14 p530 (1993) >J Comp Chem 14 799 (1993) >J Comp Chem 15 200 (1994) >Rev in Comp Chem II, 219 (1991) > >I did a few calcs on some fluorocarbanions: the electrostatic potential charges >look very reasonable, and hardly change with the basis: > >H-F level CH3- F-CH2- F-CH-F- >charge on >C 3-21G/6-31G* -1.53/-1.43 -1.07/-1.03 -0.70/-0.71 >F " / " ----- -0.26/-0.27 -0.24/-0.22 >H " / " 0.18/0.14 0.17/0.15 0.17/0.15 ******************************* (But I really seen the positive values for CHF2 and CF3 anions. they must have been Mulliken ones ;-) Evidently, any QM charges can be used to characterize the qualitative tendencies within a series of compounds and do nicely correlate with ESCA and NMR shifts. (Although qualitative tendencies usually can be formulated without any (let alone non-empirical) calculations at all. It is the comparison within diverse sets that usually requires computations :-). The MEP charges seem more chemically reasonable and more suited in the context of the molecular recognition. Concerning the question of what exactly bothers me in the charges (see the posting by K.F.Moschner above). As to ammonium cation, I evidently overlooked the fact that the actual charge in NH3 is anything but the formal zero. Sorry. As to carbanions, I think that although nucleophilicity is not solely controlled by charge (it is orbital interaction, not electrostatic), positive charge on C might be expected to shift major nucleophilic center >from C to F atoms. Moreover, as the electronegativity of carbon is greater than that of hydrogen, carbon in (neutral) hydrocarbons should have slight negative charge. Also, it raises interesting ambiguity. One might expect positively charged Lewis base to have very compact lone pair and consequently to be very hard base. On the other hand, inductive delocalization caused by F atoms might be expected to increase the base softness. I would like to know whether someone have studied this problem. Thank you for your time Eugene -- -------------------------------------------------------------------- Eugene V. Radchenko Graduate Student in Computer Chemistry E-mail: eugene@qsar.chem.msu.su Fax: +7-(095)939-0290 Ordinary mail: Chair of Organic Chemistry, Department of Chemistry, Moscow State University, 119899 Moscow, Russia ***************** Disappearances are deceptive ******************* From owner-chemistry@ccl.net Fri Jul 7 09:52:16 1995 Received: from garam.kreonet.re.kr for moon@kistmail.kist.re.kr by www.ccl.net (8.6.10/930601.1506) id JAA25981; Fri, 7 Jul 1995 09:37:55 -0400 Received: from kistmail.kist.re.kr (kistmail.kist.re.kr [161.122.12.3]) by garam.kreonet.re.kr (8.6.9H1/8.6.9) with SMTP id WAA22055 for ; Fri, 7 Jul 1995 22:40:34 +0900 Received: by kistmail.kist.re.kr (5.65/KISTMAIL-0.1) id AA05491; Fri, 7 Jul 95 22:35:05 +0900 Date: Fri, 7 Jul 95 22:35:05 +0900 From: moon@kistmail.kist.re.kr (Moon Tae Sung) Message-Id: <9507071335.AA05491@kistmail.kist.re.kr> To: chemistry@ccl.net Subject: Ab initio ? Dear Netter I want to know reference papers about ab initio (theory and method). I am doing MD simulation, and I want to develope potential parameter in some cases. Wait for reply. Tae-Sung Moon moon@kistmail.kist.re.kr .. From owner-chemistry@ccl.net Fri Jul 7 10:07:02 1995 Received: from ohstpw.mps.ohio-state.edu for L330%SUEARN2.BITNET@mps.ohio-state.edu by www.ccl.net (8.6.10/930601.1506) id KAA26665; Fri, 7 Jul 1995 10:03:30 -0400 From: Received: from SUEARN2.BITNET (MAILER@SUEARN2) by MPS.OHIO-STATE.EDU (PMDF V5.0-3 #9122) id <01HSL2C54OBK9KM1SU@MPS.OHIO-STATE.EDU> for CHEMISTRY@ccl.net; Fri, 07 Jul 1995 10:03:27 -0400 (EDT) Date: Fri, 07 Jul 95 17:59 MSK Subject: G92/G94 and KAP To: CHEMISTRY@ccl.net Message-id: <01HSL2C58YN69KM1SU@MPS.OHIO-STATE.EDU> Content-transfer-encoding: 7BIT Dear CCLers ! We have in our institute few RISC workstations from different companies : SGI, DEC, Sun etc. How important in the sense of performance may be using of KAP preprocessor for translation of typical quantum chemical programs: G92/G94, GAMESS, MOPACK etc ? Dr. Nickolay Anikin, N.D. Zelinsky Institute of Organic Chemistry Moscow From owner-chemistry@ccl.net Fri Jul 7 10:22:03 1995 Received: from quimica.urv.es for ricart@quimica.urv.es by www.ccl.net (8.6.10/930601.1506) id KAA26918; Fri, 7 Jul 1995 10:14:36 -0400 Received: by quimica.urv.es (AIX 3.2/UCB 5.64/4.03) id AA25899; Fri, 7 Jul 1995 16:12:54 +0200 From: ricart@quimica.urv.es (Josep M. Ricart) Message-Id: <9507071412.AA25899@quimica.urv.es> Subject: CAT -96 now in the WEB To: chemistry@ccl.net Date: Fri, 7 Jul 1995 16:12:54 +0200 (DFT) X-Mailer: ELM [version 2.4 PL24] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 385 Dear colleage: It is a pleasure to announce that all the information concerning the 6th INTERNATIONAL CONFERENCE ON THEORETICAL ASPECTS OF HETEROGENEOUS CATALYSIS (CAT96) Tarragona, Spain, June 2-7, 1996 can be accessed in the net through WWW: http://www.quimica.urv.es/~cat96/cat96.html For any questions contact the conference e-mail: cat96@quimica.urv.es F. Illas & J. M. Ricart From owner-chemistry@ccl.net Fri Jul 7 10:34:12 1995 Received: from quimica.urv.es for ricart@quimica.urv.es by www.ccl.net (8.6.10/930601.1506) id KAA26864; Fri, 7 Jul 1995 10:10:17 -0400 Received: by quimica.urv.es (AIX 3.2/UCB 5.64/4.03) id AA38217; Fri, 7 Jul 1995 16:08:54 +0200 From: ricart@quimica.urv.es (Josep M. Ricart) Message-Id: <9507071408.AA38217@quimica.urv.es> Subject: no subject (file transmission) To: CAT@quimica.urv.es, now@quimica.urv.es, in@quimica.urv.es, the@quimica.urv.es, WEB@quimica.urv.es, chemistry@ccl.net Date: Fri, 7 Jul 1995 16:08:54 +0200 (DFT) X-Mailer: ELM [version 2.4 PL24] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 385 Dear colleage: It is a pleasure to announce that all the information concerning the 6th INTERNATIONAL CONFERENCE ON THEORETICAL ASPECTS OF HETEROGENEOUS CATALYSIS (CAT96) Tarragona, Spain, June 2-7, 1996 can be accessed in the net through WWW: http://www.quimica.urv.es/~cat96/cat96.html For any questions contact the conference e-mail: cat96@quimica.urv.es F. Illas & J. M. Ricart From owner-chemistry@ccl.net Fri Jul 7 10:37:05 1995 Received: from mtolympus.ari.net for ars@ari.net by www.ccl.net (8.6.10/930601.1506) id KAA26875; Fri, 7 Jul 1995 10:11:40 -0400 Received: from arsoftware.ari.net (arsoftware.ari.net [198.69.192.82]) by mtolympus.ari.net (8.6.5/8.6.5) with SMTP id KAA29864 for ; Fri, 7 Jul 1995 10:11:22 -0400 Date: Fri, 7 Jul 1995 10:11:22 -0400 Message-Id: <199507071411.KAA29864@mtolympus.ari.net> X-Sender: ars@mtolympus.ari.net (Unverified) X-Mailer: Windows Eudora Version 1.4.4 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@ccl.net From: ars@ari.net (ARSoftware Corporation) Subject: Re: Docking Program Dear Netter: > >I am looking for a docking program that does more global >conformational search. I would be happy to summarize all responses. > >If you can point out possible ftp site for the programs, that would be >really helpful > >Thanks in advance > >Song Liu >Postdoctoral Researcher >Institute of Biomedical Science >Academia Sinica, Taiwan > > >-------This is added Automatically by the Software-------- >-- Original Sender Envelope Address: owner-chemistry@ccl.net >-- Original Sender From: Address: sliu@mastermodel.ps.uci.edu >CHEMISTRY@ccl.net -- everyone | CHEMISTRY-REQUEST@ccl.net -- coordinator >MAILSERV@ccl.net: HELP CHEMISTRY | Gopher: www.ccl.net 73 >Anon. ftp www.ccl.net | CHEMISTRY-SEARCH@ccl.net -- archive search >http://www.ccl.net/chemistry.html | for info send: HELP SEARCH to MAILSERV > >One suggestion might be PCModel, a windows(also available for the macintosh) based software program. PCModel has the true docking as well as other capabilities. For more information e-mail us your fax number or your postal address. John Parikh > ===================================================== ARSoftware Corporation 8201 Corporate Drive Landover, MD 20785 Phone: (301) 459-3773 FAX: (301) 459-3776 e-mail: ars@ari.net From owner-chemistry@ccl.net Fri Jul 7 11:07:03 1995 Received: from saturn.kent.edu for raeker@saturn.kent.edu by www.ccl.net (8.6.10/930601.1506) id LAA28495; Fri, 7 Jul 1995 11:03:43 -0400 Received: by saturn.kent.edu (AIX 3.2/UCB 5.64/4.03) id AA13110; Fri, 7 Jul 1995 10:52:52 -0400 Date: Fri, 7 Jul 1995 10:52:51 -0400 (EDT) From: "Todd J. Raeker" To: CCL Subject: Summary of molecular integrals Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello all, A couple of weeks ago I asked about good source of information on molecular integrals. Here is a summary of all replies I have recieved. I have edited the replies to just site the refernces. Some comments are removed. ******* 1 ******** A couple of good papers, from the Gamess manual, are: "Numerical Integration Using Rys Polynomials" H.F.King and M.Dupuis J.Comput.Phys. 21,144(1976) "Evaluation of Molecular Integrals over Gaussian Basis Functions" M.Dupuis,J.Rys,H.F.King J.Chem.Phys. 65,111-116(1976) "Molecular Symmetry and Closed Shell HF Calculations" M.Dupuis and H.F.King Int.J.Quantum Chem. 11,613(1977) "Computation of Electron Repulsion Integrals using the Rys Quadrature Method" J.Rys,M.Dupuis,H.F.King J.Comput.Chem. 4,154-157(1983) An excellent paper to start with is "The Gaussian Function in Calculations of Statistical Mechanics and Quantum Mechanics" I.Shavitt in _Methods in Computational Physics_ 2,1(1963) ******* 2 ******** Computational Techniques in Quantum Chemistry and Molecular Physics Diercksen, Sutcliffe, and Veillard. -Contains a chapter called 'Introduction to Molecular Integral Evaluation' which discusses integrals of slater and of gaussian type orbitals. ETO Multicenter Molecular Integrals Edited by Charles A. Weatherford and Herbert W. Jones. J. Fernandez Rico, J.Chem.Phys. 91 (7), 1989 to latr dates ******* 3 ******** For a good review of the efficient calculation of quantum chemical integrals, see P. M. W. Gill, Advan. Quantum Chem. 25, 141 (1994). ******* 4 ******** S. Obara and A. Saika, J. Chem. Phys. 84 (1986) 3963. S. Obara and A. Saika, J. Chem. Phys. 89 (1988) 1540 It is a self-contained reference, it goes straight to the point, it contains formulas for all integrals you normally need: overlap (easy!), nuclear attraction, electron-electron repulsion, kinetic energy, multipole moments, electric field and e.f. gradient, angular momentum, and spin-orbit. Dr. Todd J. Raeker | Department of Chemistry raeker@saturn.kent.edu | Kent State University Phone (216)-672-2986 | Kent, OH 44242-0001 From owner-chemistry@ccl.net Fri Jul 7 11:37:13 1995 Received: from mail.eecs.uic.edu for tj@eecs.uic.edu by www.ccl.net (8.6.10/930601.1506) id LAA28868; Fri, 7 Jul 1995 11:22:13 -0400 Received: from bert.eecs.uic.edu (bert.eecs.uic.edu [128.248.166.23]) by mail.eecs.uic.edu (8.6.11/8.6.10) with ESMTP id KAA26760 for ; Fri, 7 Jul 1995 10:23:17 -0500 From: tj ODonnell Received: (tj@localhost) by bert.eecs.uic.edu (8.6.10/8.6.10) id KAA20310 for chemistry@ccl.net; Fri, 7 Jul 1995 10:23:16 -0500 Message-Id: <199507071523.KAA20310@bert.eecs.uic.edu> Subject: Tcl/Tk information To: chemistry@ccl.net (CCL) Date: Fri, 7 Jul 1995 10:23:15 -0500 (CDT) X-Mailer: ELM [version 2.4 PL23] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 367 Hi All, For those of you who are interested in further investigation of Tcl/Tk, please check out: http://www.sco.com/Technology/tcl/Tcl.html TJ -- *---------------------------------------------------------------------* | Dr. TJ O'Donnell > tj@eecs.uic.edu < http://www.eecs.uic.edu/~tj/ | *---------------------------------------------------------------------* From owner-chemistry@ccl.net Fri Jul 7 12:22:08 1995 Received: from azure.CCIT.Arizona.EDU for POLLARD@CCIT.ARIZONA.EDU by www.ccl.net (8.6.10/930601.1506) id MAA01022; Fri, 7 Jul 1995 12:08:57 -0400 From: Received: from CCIT.ARIZONA.EDU by CCIT.ARIZONA.EDU (PMDF V4.3-13 #2381) id <01HSL0B32I7K8ZFKLW@CCIT.ARIZONA.EDU>; Fri, 07 Jul 1995 09:08:43 -0700 (MST) Date: Fri, 07 Jul 1995 09:08:43 -0700 (MST) Subject: ab-initio and TM's To: chemistry@ccl.net Message-id: <01HSL0B34NDE8ZFKLW@CCIT.ARIZONA.EDU> X-Envelope-to: chemistry@ccl.net X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-transfer-encoding: 7BIT I was wondering if get peoples opinion on the best (or most accepted) method to perform ab-initio calculations with second and third row TM complexes. I am familiar with all the semi-empirical approaches but am not with any ab-initio. What basis sets work best? Relativistic effects? Thank you and I look forward to responses. J. Pollard From owner-chemistry@ccl.net Fri Jul 7 13:07:06 1995 Received: from cric.chemres.hu for ccl@cric.chemres.hu by www.ccl.net (8.6.10/930601.1506) id MAA02162; Fri, 7 Jul 1995 12:58:15 -0400 From: Received: by cric.chemres.hu (AIX 3.2/UCB 5.64/4.03) id AA12005; Fri, 7 Jul 1995 18:51:41 +0200 Date: Fri, 7 Jul 1995 18:51:41 +0200 (DFT) To: Kui Zhang Cc: Computational Chemistry List Subject: Re: CCL:BSSE Correction for Protonation Energy In-Reply-To: <01HSIOI1VN989CCTYV@phem3.acs.ohio-state.edu> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Wed, 5 Jul 1995, Kui Zhang wrote: > > Dear Netters, > > One of our projects is the calculation of protonation energy > for some interesting compounds using high level ab initio calculations. > Recently I have been trying to correct calculated protonation energies > with BSSE. I first used CH3NH2 as model compound to do testing > calculations at HF, MP2 and MP4 levels with several basis sets. The > calculations were carried out using Gaussian 92 with MASSAGE method. > The following is a set of calculated values of the BSSE correction for > CH3NH2: > BSSE Correction (kcal/mol) > > HF/6-31G*//HF/6-31G* 0.60 > HF/6-31+G**//HF/6-31+G** 0.84 > HF/6-31+G(2d,2p)//HF/6-31+G(2d,2p) 0.31 > MP2/6-31+G**//HF/6-31+G** 6.87 > MP4/6-31+G**//HF/6-31+G** 7.20 > MP2/6-31+G**//MP2/6-31+G** 14.15 > > It can be obviously seen that the MP and HF give a such huge > difference that there is absolutely not comprimise between HF and MP > values. The same situation was also observed in another compound > similar to CH3NH2. Can any of you help me handle this problem? My > question is that which method I should trust in term of the BSSE > computation, MP or HF? I would greatly appreciate any direction, > suggestion and comment. Thank you very much in advance. > > > Kui Zhang > Department of Chemistry > Miami University > Oxford, OH 45056 > USA > > That is O.K. - i.e. what should have been obtained. The BSSE is normally much larger at electron correlation level than at the SCF one. This is because our SCF wave functions are much closer to the HF limit than we can account electron correlation. In other words, when the basis is paractically saturated for SCF, it is still very far from that when correlation is concerned. (SCF requires much simpler functions.) Obviously, SCF energies should be corrected for BSSE at the SCF level, MP2 ones at the MP2 level etc. (Although it is not clear to what extent counterpoise corrections can "overcorrect" at the MPn level - we are working on this problem, too.) The most serious problem I see that optimizing the geometry without BSSE correction and correcting BSSE only afterwards may be dangerous - while optimizing the geometry with BSSE correction is not a trivial problem (c.f. I. Mayer, P.R. Surjan, Chem. Phys. Lett. 191, 497, 1992). Yours sincerely, Istvan Mayer e-mails: mayer@cric.chemres.hu IB13LVIB@HUEARN.sztaki.hu H1376May@ella.hu Central Research Institute for Chemistry of the Hungarian Academy of Sciences H-1525 Budapest, P.O.Box 17 Hungary From owner-chemistry@ccl.net Fri Jul 7 13:52:06 1995 Received: from gkcl.ists.ca for lin@gkcl.ists.ca by www.ccl.net (8.6.10/930601.1506) id NAA03879; Fri, 7 Jul 1995 13:51:43 -0400 Received: by gkcl.ists.ca (5.61/1.34) id AA02348; Fri, 7 Jul 95 13:55:03 -0400 From: lin@gkcl.ists.ca (Delin Shen) Message-Id: <9507071755.AA02348@gkcl.ists.ca> Subject: Problems with DeFT program To: chemistry@ccl.net Date: Fri, 7 Jul 95 13:55:02 ADT X-Mailer: ELM [version 2.2 PL0] Dear Netters, We are currently installing DeFT program of Dr. St-Amant in several computer systems. we came cross one section of the program that we think might has a minor mistake: subroutine delphidr.f >>130 call delphi(ndelphi,ncenters,nptcharges,ngrid,ngridby2,natomtype, >>131 & iwkvec,epsilon,coord,wkvec(jf),coordptcharge,ptcharge, >>132 & wkvec(ja),wkvec(jb),wkvec(jc),wkvec(jd),wkvec(je), >>133 & wkvec(ig),wkvec(jh)) ^^ Should it be "jg" instead of "ig"? There also some other sections of the program that don't conform standard Fortran. We sent Dr. St-Amant a message more than month ago about this and haven't got any answers yet. We have reproduced all sample output. The problem we have right now is a test run we did with benzene optimization using a fine and random grid: D6h symmetry input gives nonsymmetrical result. Since it is optimization without conserving the symmetry, we are not expecting output with D6h symmetry. What bothers us is that C-H bond distances differ about 0.03 A. Any comments on these problems are appreciated. Thank you. DeLin Shen Chemistry Department York University Ontario, Canada From owner-chemistry@ccl.net Fri Jul 7 14:22:06 1995 Received: from tigger.jvnc.net for palres.dnet.sandoz.com!bowlus@sandoz.com by www.ccl.net (8.6.10/930601.1506) id OAA04174; Fri, 7 Jul 1995 14:08:51 -0400 Received: from sndzeh.UUCP by tigger.jvnc.net with UUCP id AA24373 (5.65c/IDA-1.4.4 for chemistry@ccl.net); Fri, 7 Jul 1995 14:08:50 -0400 Message-Id: <199507071808.AA24373@tigger.jvnc.net> Date: Fri, 7 Jul 95 13:54:47 -0400 From: bowlus@palres.dnet.sandoz.com (Steve Bowlus) To: "chemistry@ccl.net"@SNDZEH.dnet.sandoz.com Cc: BOWLUS@sandoz.com Subject: MOPAC "TRANS" keyword I would appreciate any pointers on the use of the MOPAC 6 or -93 keyword TRANS=n We wish to do some thermochemical calculations on systems with several rotable bonds. In such systems, how is "n" determined? Some options which might seem reasonable: n = # of "rotable" bonds, where some judgement is used to exclude bonds with large barriers (e.g. amides) from the count n = # of negative/imaginary roots to the Hessian. I've found for floppy systems, even with small gnorms, there might be several, small (< 100 cm-1) negative roots. Heretofore, I have used only the delta H from MOPAC for these systems, since the entropy estimates were so dubious. I expect TRANS may improve the situation, but not solve it. Opinions or experience on this point would be appreciated. I will summarize to the list if there is interest. sb =========================================================================== Stephen B. Bowlus, Ph.D. Computer-Aided Molecular Design Research Division e-mail: bowlus@sandoz.com Sandoz Agro, Inc. Phone: + 1 415 354 3904 975 California Ave. Fax: + 1 415 857 1125 Palo Alto, CA 94304 =========================================================================== From owner-chemistry@ccl.net Fri Jul 7 20:07:09 1995 Received: from theory.chem.uottawa.ca for st-amant@theory.chem.uottawa.ca by www.ccl.net (8.6.10/930601.1506) id UAA10029; Fri, 7 Jul 1995 20:03:26 -0400 Received: by theory.chem.uottawa.ca (AIX 3.2/UCB 5.64/4.03) id AA25887; Fri, 7 Jul 1995 19:36:08 -0400 Date: Fri, 7 Jul 1995 19:36:08 -0400 From: st-amant@theory.chem.uottawa.ca (Alain St-Amant) Message-Id: <9507072336.AA25887@theory.chem.uottawa.ca> To: CHEMISTRY@ccl.net Subject: Potential Problems with DeFT lin@gkcl.ists.ca (Delin Shen) writes: > >Dear Netters, > > We are currently installing DeFT program of Dr. St-Amant in several >computer systems. we came cross one section of the program that we think >might has a minor mistake: > > subroutine delphidr.f > > >>130 call delphi(ndelphi,ncenters,nptcharges,ngrid,ngridby2,natomtype, > >>131 & iwkvec,epsilon,coord,wkvec(jf),coordptcharge,ptcharge, > >>132 & wkvec(ja),wkvec(jb),wkvec(jc),wkvec(jd),wkvec(je), > >>133 & wkvec(ig),wkvec(jh)) > ^^ > Should it be "jg" instead of "ig"? Sorry about that. Yes it should be "jg" instead of "ig". For those using the code, don't worry about it. `delphi' is the module having to do with the program's solvation model, which I never got around to finishing up. It's very similar to the Honig/Friesner work. As it is, there's nothing in the input deck that you can add to make this routine jump into action. > There also some other sections of the program that don't conform standard > Fortran. We sent Dr. St-Amant a message more than month ago about this and > haven't got any answers yet. Sorry about the delay in getting back. To anybody who doesn't get a reply within a day or two, just e-mail me again. Again, don't worry about it. Answers are in no way affected. The problem that arose is that one of the subroutines (gradxxds1.f) had an extra (or *bonus* :-)) argument at the end of its argument list (grad). This argument is never used throughout the course of the subroutine. The calls to this subroutine therefore seem to have one too few arguments. Since the missing argument is the never used last argument, no problem. No wonder it slipped my attention. But to make everything nice, people should remove 'grad' from the 'gradxxd1.f' argument list. > We have reproduced all sample output. The problem we have right now >is a test run we did with benzene optimization using a fine and random grid: >D6h symmetry input gives nonsymmetrical result. Since it is optimization >without conserving the symmetry, we are not expecting output with D6h >symmetry. What bothers us is that C-H bond distances differ about 0.03 A. This is way too big a variation. True, the grids can't maintain the symmetry of benzene, and there will be variations in bond lengths, but nowhere near this large. I've run it, and I get nowhere near the errors^H^H^H^H^H^H noise (:-) you're getting. All C--C bonds are within 0.0001 Angstroms of each other and all C--H bonds are within 0.0001 Angstroms of each other, which of course is but a fraction of the inherent errors of DFT relative to experiment. This is actually better than usual. Don't be shocked with something of the order of 0.001-0.002 Angstroms. A fine grid slaps on about 3000 points per atoms. Send me a copy of your input deck, and I'll check it for potential problems. For those wondering why we can't maintain D6H symmetry: Unfortunately, the grids used don't have the symmetry of the molecule in question and symmetry is broken. We could enforce symmetry, but that would be sweeping the problem under a rug. Randomizing the orientation of the angular points on the radial shells is an attempt to smooth out the noise in the total energy (at the cost of losing symmetry in systems that actually could maintain their symmetry with the grids in question). Hope this helps. Nicely recovering from the coronary I had when I saw 0.03 Angstroms, Alain P.S. DeFT is available for free from the OSC archives. If you want, just come over to the U. of Ottawa Chemistry WWW site and there will be a hyperlink to the specific place in the archives where DeFT is stored. From owner-chemistry@ccl.net Fri Jul 7 20:22:13 1995 Received: from condor.CC.UMontreal.CA for hinsenk@ERE.UMontreal.CA by www.ccl.net (8.6.10/930601.1506) id UAA10165; Fri, 7 Jul 1995 20:15:32 -0400 Received: from eole.ERE.UMontreal.CA (eole.ERE.UMontreal.CA [132.204.10.20]) by condor.CC.UMontreal.CA with ESMTP id SAA13471 (8.6.11/IDA-1.6); Fri, 7 Jul 1995 18:13:22 -0400 Received: from cyclone.ERE.UMontreal.CA by eole.ERE.UMontreal.CA (950221.405.SGI.8.6.10/5.17) id SAA03441; Fri, 7 Jul 1995 18:13:21 -0400 Received: by cyclone.ERE.UMontreal.CA (950221.405.SGI.8.6.10/5.17) id SAA11863; Fri, 7 Jul 1995 18:13:18 -0400 Date: Fri, 7 Jul 1995 18:13:18 -0400 From: hinsenk@ERE.UMontreal.CA (Hinsen Konrad) Message-Id: <199507072213.SAA11863@cyclone.ERE.UMontreal.CA> To: states@rucola.WUStL.EDU CC: chemistry@ccl.net In-reply-to: <9507062015.ZM2504@rucola.wustl.edu> (states@rucola.WUStL.EDU) Subject: Re: CCL:TCL/TK Tcl without Tk does not really offer much over perl, or for that matter basic, True, and Tk has been integrated into some other languages in the meantime, which are more powerful (at least in my opinion). Examples are Scheme, Perl and Python. really have the power to support scientific computing. Smalltalk with graphical extensions is also a precursor, but most non-smalltalk programmers find the philosophy of smalltalk programming hard to deal with and the commercial On the contrary, Smalltalk is one of my preferred languages. I'd really like to have a similar environment, but suitable for scientific work (i.e. for numerical work). A combination that I consider very promising for scientific programming is C++ with Python tied together with ILU. All three can be had for free, and together they allow everything from high-performance code to scripts to be written in a coherent object-oriented style. ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsenk@ere.umontreal.ca Departement de chimie | Tel.: +1-514-343-6111 ext. 3953 Universite de Montreal | Fax: +1-514-343-7586 C.P. 6128, succ. 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