From peon@medchem.dfh.dk Thu Dec 18 04:41:04 1997 Received: from danpost.uni-c.dk for peon@medchem.dfh.dk by www.ccl.net (8.8.3/950822.1) id DAA08948; Thu, 18 Dec 1997 03:42:33 -0500 (EST) Received: from medchem.dfh.dk (medchem.dfh.dk [130.225.177.15]) by danpost.uni-c.dk (8.8.7/8.6) with SMTP id JAA23301 for <@danpost.uni-c.dk:chemistry@www.ccl.net>; Thu, 18 Dec 1997 09:42:33 +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 ESMTP id KAA10883 for ; Thu, 18 Dec 1997 10:21:30 +0100 Message-Id: In-Reply-To: <199712172351.SAA11152@alchemy.chem.utoronto.ca> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 18 Dec 1997 09:42:32 +0100 To: chemistry@www.ccl.net From: Per-Ola Norrby Subject: Re: CCL:MOLECULAR MECH QUESTIONS On 1997 Dec 17, E. Lewars wrote: >Molecular mechanics (MM) gives strain energies. Questions: > >Are these statements correct ? : > >(1) Strain energy differences are enthalpy differences (deltaH). > (If true, then deltaH under what conditions--zero K? room temp? I >suppose > it depends on the parameterization of the force field: k_stretch etc > might have been for, say, 0 K...?) Close enough for practical purposes. If you're a purist, read on below. >(2) MM programs that calculate frequencies can in principle calculate > entropies and thus free energies. True. You'll have to be very careful though, using the harmonic approximation for a low mode might give serious errors. This problem is not unique to MM, most QM programs also use the harmonic approximation. A few programs (both QM and MM) are smart enough to treat free rotations separately, but I don't know of any simple approximations that gives accurate entropies when you deal with intermediate modes (say, 10-50 cm-1, maybe even wider). For the purists, an elaboration on (1): Molecular mechanics energies will in principle give back the type of energies they are parameterized with. A few force fields, like CFF95 and MMFF, were parameterized from ab initio data, and will thus yield potential energies at the bottom of the energy well. The difference between this number and the enthalpy at zero K is the zero point energy, and in energy DIFFERENCES this number can frequently be neglected. Many force fields (for example, the MM2/MM3/MM4 programs) instead uses enthalpies directly, including the vibrational contribution into the potential energy surface. This gives some tricky theoretical problems when you add a vibrational analysis to something that already includes a part of the vibratinal contribution, especially when you move away from stationary points. In practice, this is ignored, and all molecular mechanics force fields are treated as if they yield a potential energy. Note that enthalpies (and free energies and entropies) in principle are properties that depend on all contributing geometries within a potential energy well. Thus, you cannot really talk about the enthalpy of a single point on the potential energy surface. From a potential energy surface, you may calculate the enthalpy for each well, but you cannot go backwards and deduce a potential energy surface from the enthalpies (other than postulating a PES and see if it gies a correct enthalpy, of course). One more note: the programs MM3 and MM4 have partially overcome the problem by an end-of-calculation analysis that converts the vibrationally averaged properties to what would be predicted from several different types of experiments (including, the "bottom-of-the-well" properties from ab initio). This seems to work well at least for bond lengths. I'd be interested to know if some better theoretician than me can find out if you can really go back to a true potential energy surface though. Holiday greetings from Per-Ola Norrby ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ * Per-Ola Norrby, Associate Professor * 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 voityuk@theochem.tu-muenchen.de Thu Dec 18 04:52:03 1997 Received: from theo1.theochem.tu-muenchen.de for voityuk@theochem.tu-muenchen.de by www.ccl.net (8.8.3/950822.1) id EAA09015; Thu, 18 Dec 1997 04:00:24 -0500 (EST) Received: (from voityuk@localhost) by theo1.theochem.tu-muenchen.de (950413.SGI.8.6.12/950213.SGI.AUTOCF) id KAA16476 for CHEMISTRY@www.ccl.net; Thu, 18 Dec 1997 10:00:19 +0100 Date: Thu, 18 Dec 1997 10:00:19 +0100 From: voityuk@theochem.tu-muenchen.de (Alexander Voityuk) Message-Id: <199712180900.KAA16476@theo1.theochem.tu-muenchen.de> To: CHEMISTRY@www.ccl.net Subject: AM1/d thermochemistry of Ti compounds Hi, Some days ago there was a question about AM1 calculation of Ti compounds. Using the AM1/d method with preliminary parameters for Ti, one can obtain quite reasonable estimation of thermochemical data and geometries of Ti containing molecules (see below). I think it would be interesting to compare AM1/d and PM3/tm results. Could anyone to provide CCLers with PM3/tm data? To finish the AM1/d parameterization for Ti more experimental or calculated data on geometries and enthalpies of formation for compounds of Ti in the gas phase are needed. Could anyone provide me with such data or/and the corresponding referencies? With best regards Alexander A. Voityuk Calculated and observed heats of formation (kcal/mol) Molecule Exp. AM1/d Ti s2d2 3F 112.3 112.3 Ti s1d3 5F 131.0 131.1 Ti+ s1d2 4F 271.2 271.2 Ti+ s0d3 4F 273.5 274.3 Ti++ s0d2 3F 585.6 585.1 Ti(CH3)4 4.3 2.0 Ti(C6H6)+ 229.2 213.4 Ti(C5H5)2H2 72.4 70.4 Ti(C5H5)2(CH3)2 1.1 12.9 TiCp2Ph2 83.7 73.8 TiCp2(CH2Ph)2 66.8 65.7 Ti(C5H5)2(N3)2 121.0 120.2 TiCp2(OPh)2 -70.9 -75.7 Ti(C5H5)2(OOCCF3)2 -512.2 -515.0 Ti(C5H5)2(OOCCCl3)2 -230.6 -232.5 TiCp2(OOC-Ph)2 -161.9 -158.7 Ti(C5H5)2(SCH3)2 -13.1 -15.2 Ti(C5H5)2(SC2H5)2 -25.2 -27.2 TiCp2(SPh)2 35.1 45.2 Ti(C5H5)2(CH3)Cl -29.8 -27.9 Ti(C5H5)2F2 -156.8 -155.1 TiCp2PhCl 9.8 1.8 Ti(C5H5)2Cl2 -63.2 -64.2 Ti(C5H5)Cl3 -121.0 -131.0 Ti(C5H5)2I2 -6.8 -17.2 Ti[N(CH3)2]4 -82.4 -78.3 TiF4 -370.8 -369.7 TiCl4 -182.4 -181.5 TiBr4 -131.5 -131.1 TiI4 -66.3 -62.1 TiOCl2 -130.4 -145.7 MEAN ERROR ( 31 comparisons ) -1.66 MEAN ABSOLUTE ERROR 4.26 Bond lengths (A) and bond angles (degrees) Molecule Variable Exp. AM1/d Ti(CH3)4 Ti-C 1.950 2.021 Ti(C5H5)2H2 Ti-C av. 2.372 2.373 TiCp2(OPh)2 Ti-Cp 2.420 2.416 Ti-O 1.907 1.838 O-Ti-O 98.1 96.8 TiCp2(OOC-Ph)2 Ti-C(Cp) 2.381 2.389 Ti-C(Cp) 2.369 2.371 Ti-C(Cp) 2.385 2.394 Ti-O 1.930 1.857 O-Ti-O 91.5 85.4 Ti(C5H5)2(SCH3)2 Mo-S 2.398 2.324 S-Mo-S 93.8 99.6 Ti(C5H5)2(SC2H5)2 Mo-S 2.395 2.324 S-Mo-S 99.3 99.7 Ti(C5H5)2Cl2 Ti-C av. 2.372 2.403 Ti-Cl 2.318 2.224 Cl-Ti-Cl 97.1 94.6 Ti(C5H5)2I2 Ti-C av. 2.372 2.406 Ti[N(CH3)2]4 Ti-N av. 2.000 1.884 N-Ti-N 109.5 110.0 TiF4 Ti-F 1.754 1.740 TiCl4 Ti-Cl 2.170 2.126 TiBr4 Ti-Br 2.340 2.341 TiI4 Ti-I 2.546 2.482 TiOCl2 Ti=O 1.601 1.594 Ti-Cl 2.239 2.168 O=Ti-Cl 115.5 111.2 From picard@ext.jussieu.fr Thu Dec 18 06:41:12 1997 Received: from shiva.jussieu.fr for picard@ext.jussieu.fr by www.ccl.net (8.8.3/950822.1) id FAA09425; Thu, 18 Dec 1997 05:55:48 -0500 (EST) Received: from idf.ext.jussieu.fr (idf.ext.jussieu.fr [134.157.81.129]) by shiva.jussieu.fr (8.8.8/jtpda-5.2.9) with ESMTP id LAA24186 for ; Thu, 18 Dec 1997 11:55:09 +0100 (CET) Received: from [134.157.11.19] by idf.ext.jussieu.fr (8.8.5/jtpda-4.0) with SMTP; Thu, 18 Dec 1997 11:55:06 +0100 (MET) Date: Thu, 18 Dec 1997 11:55:06 +0100 (MET) X-Sender: picard@idf.ext.jussieu.fr Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@www.ccl.net From: picard@ext.jussieu.fr (G.S. PICARD) Subject: Contraction sheme Dear Netters, I'm actually looking for a program which can, starting from a given basis set with a particular contraction sheme, change the contraction scheme and re-optimize the coefficients. Does anybody know such a program ? Thanks in advance Gerard S. PICARD , Directeur de Recherche au C.N.R.S., LABORATOIRE D'ELECTROCHIMIE ET DE CHIMIE ANALYTIQUE, Unite de Recherche associee au C.N.R.S. no 216, Equipe : "PROCESSUS INTERFACIAUX & REACTIVITE EN MILIEUX IONIQUES LIQUIDES" 11 rue Pierre et Marie Curie - 75231 Paris cedex 05 - FRANCE. Tel : (33) 1.55.42.63.89. Fax : (33) 1.44.27.67.50. WWW Home Page : http://alcyone.enscp.jussieu.fr/Pages/LECA/GP/ From buyong@ibmnla2.chem.uga.edu Thu Dec 18 08:41:07 1997 Received: from ibmnla2.chem.uga.edu for buyong@ibmnla2.chem.uga.edu by www.ccl.net (8.8.3/950822.1) id IAA10246; Thu, 18 Dec 1997 08:38:05 -0500 (EST) From: Received: from localhost (buyong@localhost) by ibmnla2.chem.uga.edu (AIX4.2/UCB 8.7/8.7) with SMTP id IAA18654; Thu, 18 Dec 1997 08:38:06 -0500 (EST) Date: Thu, 18 Dec 1997 08:38:05 -0500 (EST) To: Per-Ola Norrby cc: chemistry@www.ccl.net Subject: Re: CCL:MOLECULAR MECH QUESTIONS In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I agree with Professor Norrby for most of his opion. However, I have a different view about MM3/MM4 PES. In the early development of MM2/MM3 force field, one was forced to only use experimental data (energy, structure...) for parameterization. Therefore, early version of MM2/MM3 was fitted to experimental enthalpy data. With accurate QM structure and energy calculated recent days, together with harmonic vibrational analysis introduced into MM3, the PES of MM3/MM4 is defined as the same from QM point of view. This means that to get enthalpy difference, vibrational correction has to be used. One more point: strain energies are comparable only for the system with identical bond structures. For different molecular systems (for example methyl ether and ethanol), heats of formation should be used. ================================================================= Dr. Buyong Ma buyong@ibmnla.chem.uga.edu Computational Center for Molecular Structure and Design Department of Chemistry University of Georgia Athens, Georgia 30602 USA Voice (706) 542-2044 ================================================================= On Thu, 18 Dec 1997, Per-Ola Norrby wrote: > On 1997 Dec 17, E. Lewars wrote: > > >Molecular mechanics (MM) gives strain energies. Questions: > > > >Are these statements correct ? : > > > >(1) Strain energy differences are enthalpy differences (deltaH). > > (If true, then deltaH under what conditions--zero K? room temp? I > >suppose > > it depends on the parameterization of the force field: k_stretch etc > > might have been for, say, 0 K...?) > > Close enough for practical purposes. If you're a purist, read on > below. > > >(2) MM programs that calculate frequencies can in principle calculate > > entropies and thus free energies. > > True. You'll have to be very careful though, using the harmonic > approximation for a low mode might give serious errors. This problem is > not unique to MM, most QM programs also use the harmonic approximation. A > few programs (both QM and MM) are smart enough to treat free rotations > separately, but I don't know of any simple approximations that gives > accurate entropies when you deal with intermediate modes (say, 10-50 cm-1, > maybe even wider). > > For the purists, an elaboration on (1): > Molecular mechanics energies will in principle give back the type > of energies they are parameterized with. A few force fields, like CFF95 > and MMFF, were parameterized from ab initio data, and will thus yield > potential energies at the bottom of the energy well. The difference > between this number and the enthalpy at zero K is the zero point energy, > and in energy DIFFERENCES this number can frequently be neglected. Many > force fields (for example, the MM2/MM3/MM4 programs) instead uses > enthalpies directly, including the vibrational contribution into the > potential energy surface. This gives some tricky theoretical problems when > you add a vibrational analysis to something that already includes a part of > the vibratinal contribution, especially when you move away from stationary > points. In practice, this is ignored, and all molecular mechanics force > fields are treated as if they yield a potential energy. > > Note that enthalpies (and free energies and entropies) in principle > are properties that depend on all contributing geometries within a > potential energy well. Thus, you cannot really talk about the enthalpy of > a single point on the potential energy surface. From a potential energy > surface, you may calculate the enthalpy for each well, but you cannot go > backwards and deduce a potential energy surface from the enthalpies (other > than postulating a PES and see if it gies a correct enthalpy, of course). > > One more note: the programs MM3 and MM4 have partially overcome the > problem by an end-of-calculation analysis that converts the vibrationally > averaged properties to what would be predicted from several different types > of experiments (including, the "bottom-of-the-well" properties from ab > initio). This seems to work well at least for bond lengths. I'd be > interested to know if some better theoretician than me can find out if you > can really go back to a true potential energy surface though. > > Holiday greetings from > > Per-Ola Norrby > > > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ > * Per-Ola Norrby, Associate Professor > * 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/ > > > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: peon@medchem.dfh.dk > -- Original Sender From: Address: peon@medchem.dfh.dk > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > > > From churca@opium.q1.fcen.uba.ar Thu Dec 18 18:41:10 1997 Received: from opium.q1.fcen.uba.ar for churca@opium.q1.fcen.uba.ar by www.ccl.net (8.8.3/950822.1) id SAA12958; Thu, 18 Dec 1997 18:12:44 -0500 (EST) Received: from localhost (churca@localhost) by opium.q1.fcen.uba.ar (8.8.0/8.8.0) with SMTP id TAA28596; Thu, 18 Dec 1997 19:41:26 -0300 Date: Thu, 18 Dec 1997 19:41:26 -0300 (ARST) From: Adrian Turjanski To: chemistry@www.ccl.net cc: mw@crystal.uwa.edu.au Subject: Molecular Modeling and Industries Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I'm sending the answers i got about my question of molecular modeling and industries. This was my question: Hi, > I had an answer to my question about molecular modeling and > indusries, and perhaps i didn't express my self correctly. > > I know that the question is too general. > > What i want is that some of you send me some brief information, > like with pharmaceuticals industries have you been working with, or > internet places where I can get some information.Or perhaps in wich subject, > like biological activity of a drug or to predict estability of a > compound etc .... > > This is only to have an idea. Perhaps it is very common for some of you > to work with industries and this questions is like " please tell me what > have you been doing in the last three years". Where I work this is not the > case, i don't know about any industrie that uses molecular modeling in > their research. > > I know that i can find some information looking at some journals or > by making a search over internet. I'm just asking for some help from those > of you that are more familiar with the subject. > > Anything that can give me some orientation or new ideas is welcome. > I'm sorry is this question my disturb some of you. > Here are the answers --------------------------------------------------------------- Hi Adrian, have a look to these pages: http://www.cray.com/solutions/examples/dupont.html http://www.cis.um.edu.mt/~phcy/symp97/jonathan.htm hope it helps a little bye Bruno ------------------------------------------------------- 1) Pfizer, Merck, Vertex, Janssen Research Foundation, Dupont-Merck, Amgen, Abbott, Parke-Davis, Schering-Plough todas estas compa~nias gigantes tienen grupos de Computational Chemistry/ Molecular Modeling. Naturalmente, cada compa~nia tiene su area de interes y especializacion que es dificil, si bien no imposible, saber. Algunas de las compa~nias mencionadas tienen grupos que desarrollan programas para estudiar en detalle las interacciones entre peque~nas moleculas y sus enzimas de interes (o receptores). ------------------------------------------------------------------------ I am afraid that I agree with Lief Norskov's answer to your original question - it is impossible to answer. Now your question is more like "where can I get some idea's or information on how Molecular Modeling is used by the industries". I think that the web pages by Molecular Simulations (MSI) would provide a suitable entrance for your question (www.msi.com). They have a comprehensive collection of modeling products covering a wide area. There are also some case studies, which could be useful to look at: http://www.msi.com/info/applications/index.html MSI is actually making a big business on this topic -- so yes, Molecular Modeling is definitely used by the industries :) Hope this helps Morten ------------------------------------------------------------------------- Dear Adrian: You might take a look at our web site (http://www.wavefun.com). There is information there on what you're looking for, and links to other places with more information... Regards, Shawn Butler --------------------------------------------------------------------------- Regarding to your recent question at CCL about Molecular Modeling in industry, I suggest you to check Web sites of software developpers like MSI (www.msi.com) or TRIPOS (www.tripos.com). In these sites you will find some industrial applications of computational chemistry software. Best regards. francois.hutschka@total.com -------------------------------------------------------------------------