From jkl@ccl.net Tue Oct 13 09:22:06 1998 Date: Tue, 13 Oct 1998 09:22:42 -0400 To: chemistry@www.ccl.net From: Jan Labanowski Subject: John Pople -- Nobel Prize in Chemistry for 1998 Finally!!! The Nobel Institute announced that the Nobel Prize in Chemistry for 1998 is awarded to: John Pople and Walter Kohn. The Royal Swedish Academy of Sciences has awarded The 1998 Nobel Prize in Chemistry in the area of quantum chemistry to Walter Kohn, University of California at Santa Barbara, USA and John A. Pople, Northwestern University, Evanston, Illinois, USA (British citizen). The Laureates have each made pioneering contributions in developing methods that can be used for theoretical studies of the properties of molecules and the chemical processes in which they are involved. Citation: "to Walter Kohn for his development of the density-functional theory and to John Pople for his development of computational methods in quantum chemistry." See: http://www.nobel.se Jan Labanowski jkl@ccl.net From chemistry-request@www.ccl.net Sun Oct 11 10:29:22 1998 Received: from power.curtin.edu.au (root@power.curtin.edu.au [134.7.118.91]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA24395 Sun, 11 Oct 1998 10:29:19 -0400 (EDT) Received: from [192.168.0.2] (col52.columba.uwa.edu.au [130.95.222.52]) by power.curtin.edu.au (8.8.8/8.8.7) with SMTP id WAA08437 for ; Sun, 11 Oct 1998 22:29:06 +0800 Message-Id: <199810111429.WAA08437@power.curtin.edu.au> Subject: population of conformers Date: Sun, 11 Oct 1998 22:29:02 +0800 x-mailer: Claris Emailer 2.0v3, January 22, 1998 From: Andrew Rohl To: "CHEMISTRY@www.ccl.net" Mime-Version: 1.0 Content-Type: text/plain; charset="US-ASCII" Hi After performing a conformational analysis in Spartan, the energies of the lowest energy conformers are given along with their %occurrence. This is presumably calculated using some Boltzmann distribution but can anyone give the recipe for calculating these populations? Thanks Andrew -------------------------------------------------------------------------- Andrew Rohl Email: andrew@power.curtin.edu.au School of Applied Chemistry Phone: +61 8 9266 7317 (Office) Curtin University of Technology +61 8 9266 3780 (Lab) PO Box U 1987 FAX: +61 8 9266 2300 Perth, 6845 WESTERN AUSTRALIA WWW: http://www.curtin.edu.au/curtin/dept/appchem/staff/alr/alr.html -------------------------------------------------------------------------- From chemistry-request@www.ccl.net Sun Oct 11 16:54:54 1998 Received: from nano.chem.nwu.edu (nano.chem.nwu.edu [129.105.14.190]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id QAA25155 Sun, 11 Oct 1998 16:54:54 -0400 (EDT) Received: from nano.chem.nwu.edu ([129.105.14.190]) by nano.chem.nwu.edu (WESMTP 2.0 [Jun 10 1998]) with SMTP id 518007734; Sun, 11 Oct 1998 20:57:10 GMT Date: Sun, 11 Oct 1998 15:57:05 -0500 From: "G. Rechtsteiner" Subject: mass spec simulation To: CHEMISTRY@www.ccl.net X-Sender: greg@nano.chem.nwu.edu (Unverified) X-Mailer: QUALCOMM Windows Eudora Pro Version 4.0 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Message-Id: <518008734@nano.chem.nwu.edu> Hello: I was wondering if anyone has a program (windows, aix, sgi unix, or fortran to be compiled) that will "predict" a mass spectrum of a small ion. For example, if I had a series of ions C[sub n] where n = 1-6, I would want to plot a mass spectrum showing the peak center and the approximate peak widths, assuming some FWHM that would resemble the experimental spectrum, based on the isotopic pattern of the ion. I am not concerned about fragment patterns, etc. I can calculate isotopic patterns, etc. but I was wodnering if anyone has already created a program to do this. Thanks. greg rechtsteiner From chemistry-request@www.ccl.net Mon Oct 12 03:21:50 1998 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id DAA26986 Mon, 12 Oct 1998 03:21:50 -0400 (EDT) Received: from mserv.rug.ac.be (mserv.rug.ac.be [157.193.40.37]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id DAA19282 for ; Mon, 12 Oct 1998 03:21:47 -0400 (EDT) Received: from elptrs5.rug.ac.be (elptrs5.rug.ac.be [157.193.113.3]) by mserv.rug.ac.be (8.9.0/8.9.0) with SMTP id JAA09780 for ; Mon, 12 Oct 1998 09:21:35 +0200 (MET DST) Received: by elptrs5.rug.ac.be (AIX 4.1/UCB 5.64/4.03) id AA03562; Mon, 12 Oct 1998 09:16:17 +0200 Date: Mon, 12 Oct 1998 09:16:17 +0200 From: Sandra.Wauters@rug.ac.be (Sandra Wauters) Message-Id: <9810120716.AA03562@elptrs5.rug.ac.be> To: CHEMISTRY@ccl.net Subject: Morate7.8.1 calculations Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Md5: Ze2wZ1GgF4TqTDDKyaEMaQ== Hi CCLers, In order to calculate reaction rates for several reactions involving polyaromatic compounds, I am using the package MORATE7.8.1 in combination with the package MOPAC507MN. I have to use up to 50 atoms in the calculations. However, the program always aborts. This could be due to an unsufficient memory capacity. The program is able to handle up to 35 atoms. Does anyone know what memory capacity is required for the calculation of reaction rates for reactions involving up to 50 atoms ? With kind regards, Sandra From chemistry-request@www.ccl.net Mon Oct 12 03:29:31 1998 Received: from cacr.ioc.ac.ru (cacr.ioc.ac.ru [193.233.3.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id DAA27015 Mon, 12 Oct 1998 03:29:14 -0400 (EDT) Received: from cacr.ioc.ac.ru (nmr-v [193.233.3.213]) by cacr.ioc.ac.ru (8.8.8/EM.SRV.10.8) with ESMTP id LAA08684 for ; Mon, 12 Oct 1998 11:28:20 +0400 (MSD) Message-ID: <36224CDE.BD45C77E@cacr.ioc.ac.ru> Date: Mon, 12 Oct 1998 11:39:26 -0700 From: val Reply-To: val@cacr.ioc.ac.ru Organization: IOC X-Mailer: Mozilla 4.04 [en] (Win16; I) MIME-Version: 1.0 To: CCL_post Subject: PCM for TM Content-Type: text/plain; charset=koi8-r Content-Transfer-Encoding: 7bit Dear CCL'ers, I am looking for the examples of PCM solvation model usage for energy and geometry corrections in the case of transition metal (TM) complexes. Particularly, platinum complexes are of most interest, however, any other TM references are also very welcome. Thanks! sincerely, Valentin. PS Of course, a summary of the replies (if any) will be made. ==================================================================== , , , , Valentin P. Ananikov |\\\\ ////| /////| NMR Group | \\\|/// | ///// | ND Zelinsky Institute of Organic Chemistry | |~~~| | |~~~| | Leninsky Prospect 47 | |===| | |===| | Moscow 117913 | | | | | | | Russia | | A | | | Z | | \ | | / | | / e-mail: val@cacr.ioc.ac.ru \|===|/ |===|/ http://nmr.ioc.ac.ru/Staff/AnanikovVP/ '---' '---' Fax +7 (095)1355328 Phone +7 (095)9383536 ==================================================================== From chemistry-request@www.ccl.net Mon Oct 12 04:35:36 1998 Received: from edda.vcp.monash.edu.au (edda.vcp.monash.edu.au [130.194.216.165]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id EAA27284 Mon, 12 Oct 1998 04:35:33 -0400 (EDT) Received: from localhost (david@localhost) by edda.vcp.monash.edu.au (980427.SGI.8.8.8/970903.SGI.AUTOCF) via ESMTP id SAA18554 for ; Mon, 12 Oct 1998 18:35:31 +1000 (EST) Date: Mon, 12 Oct 1998 18:35:30 +1000 From: David Chalmers X-Sender: david@edda.vcp.monash.edu.au To: CHEMISTRY@www.ccl.net Subject: Utility to superimpose pdb files Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi all, I am after a utility to perform a best fit superimposition of two pdb files that I can incorporate in to a shell or perl script. Does anybody have such a useful thing? Thanks David _____________________________________________________________________________ David Chalmers Lab: 9903 9623 Victorian College of Pharmacy Fax: 9903 9582 381 Royal Pde, Parkville, Vic 3053 http://synapse.vcp.monash.edu.au Australia David.Chalmers@vcp.monash.edu.au _____________________________________________________________________________ From chemistry-request@www.ccl.net Mon Oct 12 04:58:54 1998 Received: from chu.Chem.nthu.edu.tw (Chu.Chem.nthu.edu.tw [140.114.45.233]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id EAA27334 Mon, 12 Oct 1998 04:58:38 -0400 (EDT) Received: by chu.Chem.nthu.edu.tw (AIX 3.2/UCB 5.64/4.03) id AA12163; Mon, 12 Oct 1998 16:42:12 +0800 From: lin@chu.Chem.nthu.edu.tw (Chiu-Ling Lin) Message-Id: <9810120842.AA12163@chu.Chem.nthu.edu.tw> Subject: 6-31G* basis set of I, Te and Sb? To: CHEMISTRY@www.ccl.net Date: Mon, 12 Oct 1998 16:42:11 +0800 (TAIST) X-Mailer: ELM [version 2.4 PL25] Content-Type: text Dear Netters, Can any one provide us the 6-31G* basis set of I, Te, Sb, Sn and In in Gaussisn Program form? Any hits will be helpful! Regards, Wang Kang Bing ------------------------------------ lin@chu.chem.nthu.edu.tw ------------------------------------ From chemistry-request@www.ccl.net Mon Oct 12 05:40:31 1998 Received: from rc1.vub.ac.be (rc1.vub.ac.be [134.184.129.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id FAA27418 Mon, 12 Oct 1998 05:40:29 -0400 (EDT) Received: from mach.vub.ac.be (mach.vub.ac.be [134.184.129.3]) by rc1.vub.ac.be (8.8.8/%I%.0.ap (rc1)) id LAA05298; Mon, 12 Oct 1998 11:38:04 +0200 (MET DST) for Received: from [134.184.36.157] (algcmc12.vub.ac.be [134.184.36.157]) by mach.vub.ac.be (8.8.5/%I%.1.ap (mach.test)) id LAA19623; Mon, 12 Oct 1998 11:40:22 +0200 (MET DST) for X-Sender: wlangen@pop.vub.ac.be Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Mon, 12 Oct 1998 11:40:06 +0200 To: chemistry@www.ccl.net From: Wilfried Langenaeker Subject: delta E (singlet-triplet) Dear CCL, I wonder if someone could help me find the energy differences between the singlet and doublet states of some atoms and ions. The atoms we are interested in are : Li+,Be,F-,Ne,Na+,Cl- and Ar. Thanking you in advance, Wilfried ============================================================================= Wilfried Langenaeker Postdoctoral Fellow - FWO Flanders Fax : +32 - 2 - 629 33 17 Vrije Universiteit Brussel Phone : +32 - 2 - 629 36 73 Eenheid Algemene Chemie E-mail : wlangen@vub.ac.be Faculteit Wetenschappen http://homepages.vub.ac.be/~wlangen/ Pleinlaan 2, 1050 Brussel, Belgium ============================================================================= From chemistry-request@www.ccl.net Mon Oct 12 07:01:07 1998 Received: from infomail.es (ncc1.infomail.es [194.224.53.134]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id HAA27553 Mon, 12 Oct 1998 07:01:06 -0400 (EDT) Received: from teleline.es ([195.53.209.253]) by infomail.es (Tid InfoMail Exchanger v2.20) with SMTP id #908190269.159710001; Mon, 12 Oct 1998 13:04:29 +0200 Message-ID: <3621E106.BFD6C5CA@teleline.es> Date: Mon, 12 Oct 1998 12:59:18 +0200 From: Manu Reply-To: mm29@ukc.ac.uk X-Mailer: Mozilla 4.03 [es] (Win95; I) MIME-Version: 1.0 To: CHEMISTRY@www.ccl.net Subject: Re: CCL:Re: CCL:xafs / exafs References: <3.0.32.19980929001113.00717738@146.202.6.217> <361412E2.E84B750F@ukc.ac.uk> Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Infomail-Id: 908190269.3E63010A811066.30269 Status: RO Content-Length: 1445 Manu escribió: > > This page is a bit old, but hopefully useful. > http://www.esrf.fr/computing/expg/subgroups/theory/xafs/xafs_software.html > > Regarding this, I would like to point out that, the MSI software, at > least the module of cerius2 3.5 regarding to EXAFS (hopefully I will be > right the version number) was based upon excurve92. > > My best wishes > > Manu > > _____________________________________________________ > "Freedon is just another word for nothing to loose" > Me and Bobby Mc. Gee - Kris Kristofferson > ______________________:::::::::::::::::::::::::: > Manuel Melle Franco :Another PROUD Linux user: > Ph.D. Student : RH 4.2, 5.0, SW 3.4 : > :::::::::::::::::::::::::: > School of Physical Sciences > University of Kent at Canterbury -England- > http://cmr.ukc.ac.uk/postgrads/manu.html > ________________________________________________ -- _____________________________________________________ "Freedon is just another word for nothing to loose" Me and Bobby Mc. Gee - Kris Kristofferson ______________________:::::::::::::::::::::::::: Manuel Melle Franco :Another PROUD Linux user: Ph.D. Student : RH 4.2, 5.0, SW 3.4 : :::::::::::::::::::::::::: School of Physical Sciences University of Kent at Canterbury -England- http://cmr.ukc.ac.uk/postgrads/manu2.html ________________________________________________ From chemistry-request@www.ccl.net Mon Oct 12 07:24:05 1998 Received: from chem-sci.cairo.eun.eg ([193.227.11.50]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id HAA27581 Mon, 12 Oct 1998 07:23:57 -0400 (EDT) Received: by chem-sci.cairo.eun.eg; (5.65v3.2/1.1.8.2/13Aug96-0241PM) id AA21635; Mon, 12 Oct 1998 12:26:00 +0200 Date: Mon, 12 Oct 1998 12:26:00 +0200 (EET) From: Adel Abbas El-Azhary Subject: Gaussian problem To: chemistry@www.ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters: I am using Gaussian94 installed on a sgi machine and doing geometry optimization on a molecule with 600 primitive gaussians and 318 basis functions at the rb3lyp/6-31g* level. I am getting a write error in the first geometry optimization step. The error is ============================================ Cycle 5 Pass 1: Errorneous write -1 instead 405768. fd = 5 writwa. ============================================== It is clear to me that this is a read/write problem. Did anyone experience this problem before or have an idea how to fix it. Best regard, Adel El-Azhary Chemistry Department Faculty of Science Cairo University Giza, Egypt From chemistry-request@www.ccl.net Mon Oct 12 11:15:51 1998 Received: from van-der-Waals.pc.uni-koeln.de (tom@van-der-waals.pc.Uni-Koeln.DE [134.95.49.173]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id LAA22316 Mon, 12 Oct 1998 11:15:47 -0400 (EDT) Received: from localhost (tom@localhost) by van-der-Waals.pc.uni-koeln.de (8.8.8/8.8.8) with SMTP id RAA01831 for ; Mon, 12 Oct 1998 17:16:53 +0200 Date: Mon, 12 Oct 1998 17:16:53 +0200 (MEST) From: Thomas Kraska To: chemistry@www.ccl.net Subject: Workshop on Global Phase Diagrams Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear colleagues, we would like to announce a workshop on Global Phase Diagrams. Enclosed you will find a brief information about the workshop and and a WWW-address for more information and registration. For questions you can send email to the addresses below. Please forward this announcement to colleagues who might be interested in this workshop. Yours, U. K. Deiters, L. Z. Boshbov, T. Kraska Announcement for the 1st Workshop on Global Phase Diagrams Walberberg near Cologne, Germany March 21-24, 1999 -------------------------------------------------------------------------- Global Phase Diagrams as introduced by van Konynenburg and Scott are maps providing an overview over the phase behavior of binary fluid mixtures. The investigation of Global Phase Diagrams is a powerful method for understanding phase equilibria phenomena of mixtures in general. The objective of the workshop is to report about achievements and recent developments in this area and its extension to new fields of application. Invited are theoretical or experimental papers which deal with the systematic investigation of * the influence of interaction parameters on mixing phenomena * equations of states or lattice models for pure, binary or multi-component mixtures * the influence of interaction or geometry parameters on adsorption phenomena or separation factors * interference of solid and fluid phases in mixtures * phase phenomena in reacting systems * classification of phase diagrams -------------------------------------------------------------------------- For details and registration see the workshop WWW-page at: http://van-der-Waals.pc.uni-koeln.de/1stGPD/register.html -------------------------------------------------------------------------- Prof. Dr. Ulrich K. Deiters Dr. Leonid Z. Boshkov Priv.-Doz. Dr. Thomas Kraska Institute of Physical Chemistry Thermodynamics Center University at Cologne State Academy of Luxemburger Str. 116 Refrigeration D-50939 Koeln, Odessa Germany Ukraine phone: +49 221 470-4543 fax: +49 221 470-4900 e-mail: deiters@stthd0.pc.uni-koeln.de e-mail: Kraska@stthd0.pc.uni-koeln.de -------------------------------------------------------------------------- From chemistry-request@www.ccl.net Mon Oct 12 11:30:15 1998 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id LAA24468 Mon, 12 Oct 1998 11:30:14 -0400 (EDT) Received: from mhub1.lvs.dupont.com (mhub1.lvs.dupont.com [206.241.18.2]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id LAA28535 for ; Mon, 12 Oct 1998 11:30:12 -0400 (EDT) Received: from mhub2.lvs.dupont.com by mhub1.lvs.dupont.com with ESMTP; Mon, 12 Oct 1998 11:28:04 -0400 Received: from cdcln24.lvs.dupont.com by mhub2.lvs.dupont.com; Mon, 12 Oct 1998 11:28:02 -0400 Received: by CDCLN24.LVS.DUPONT.COM(Lotus SMTP MTA SMTP v4.6 (462.2 9-3-1997)) id 8525669B.0054EDC2 ; Mon, 12 Oct 1998 11:27:38 -0400 X-Lotus-FromDomain: DUPONT@DUPONT_MHUB From: "Ya-Jun Zheng" To: CHEMISTRY@ccl.net Message-Id: <8525669B.00547ECB.00@CDCLN24.LVS.DUPONT.COM> Date: Mon, 12 Oct 1998 11:27:18 -0400 Subject: Rotational barrier in C6H5-NH2 Mime-Version: 1.0 Content-type: text/plain; charset=us-ascii Hi, Does anyone know the rotational barrier of the amino group in C6H5-NH2? Any info will be appreciated. Please reply to my e-mail address directly. Thanks. Yajun Zheng From chemistry-request@www.ccl.net Mon Oct 12 12:26:52 1998 Received: from eagle.molsoft.com (eagle.molsoft.com [209.122.85.34]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id MAA01870 Mon, 12 Oct 1998 12:26:51 -0400 (EDT) Received: by eagle.molsoft.com (5.65v4.0/1.1.19.2/13Jun98-0140AM) id AA16656; Mon, 12 Oct 1998 12:25:33 -0400 Date: Mon, 12 Oct 1998 12:25:33 -0400 From: Molsoft Info Message-Id: <199810121625.AA16656@eagle.molsoft.com> Subject: A One Day Course on Computational Structural Biology Apparently-To: chemistry@www.ccl.net Dear Colleague, Molsoft announces a one day course in computational structural biology. Lecturer and instructor: Dr. Ruben Abagyan Date: Thursday, October 29, 1998 Location: Molsoft LLC office, 200 Middlesex-Essex Tpke, Iselin, New Jersey NJ Turnpike, exit 11 Garden State Parkway, exit 131-A/B Time: 10 a.m. - 4 p.m. The course is directed at scientists with an interest in protein structure and structure prediction who wish to learn what can be accomplished with the cutting edge methods of computational structural biology. The following topics will be covered: Sensitive sequence searches Multiple sequence alignments and trees Secondary structure prediction, pattern recognition, functional annotation Modeling by homology Structure-based analysis of sequence conservation Protein surfaces and structure analysis Introducing mutation Ab initio peptide folding Advanced molecular vizualization For additional information and registration please visit our web-site at www.molsoft.com. From chemistry-request@www.ccl.net Mon Oct 12 14:33:42 1998 Received: from ghiberti.pch.nat.tu-bs.de (ghiberti.pch.nat.tu-bs.de [134.169.41.187]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id OAA17287 Mon, 12 Oct 1998 14:33:40 -0400 (EDT) Received: from brunelleschi.pch.nat.tu-bs.de by ghiberti.pch.nat.tu-bs.de (5.65v4.0/1.1.19.2/05Mar98-0504) id AA24318; Mon, 12 Oct 1998 20:33:40 +0200 From: Robert Gdanitz Received: by brunelleschi.pch.nat.tu-bs.de (5.65v4.0/1.1.10.5/02Mar98-0611PM) id AA24927; Mon, 12 Oct 1998 20:33:40 +0200 Message-Id: <9810121833.AA24927@brunelleschi.pch.nat.tu-bs.de> Subject: Atomic masses for He2! To: chemistry@www.ccl.net (Computational Chemistry List) Date: Mon, 12 Oct 1998 20:33:40 +0200 (MET DST) X-Mailer: ELM [version 2.4 PL23] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Dear Colleagues: On September 30, I posted the question whether atomic or nuclear masses should be used for the computation of molecular constants like or D_0 from the interaction potential of He_2. In their recent work on He_2, Bukowski, Jeziorski, Korona, Szalewicz, and Williams [Chem. Phys. Lett. 262 (1996) 431; J. Chem. Phys. 106 (1997) 5109], and Janzen and Aziz [J. Chem. Phys. 107 (1997) 914] use *nuclear* masses. The latter paper also contains an acknowledgment to LeRoy "for pointing out the necessity of using nuclear mass in the calculation." After I received only one answer (from Frank Jensen) to my CCL request, I di- rectly contacted several scientists I consider as experts on the topic and came to the following conclusions: o The treatment of the coupling between nuclear and electronic motion in molecu- lar systems is still a topic of present research. An excellent review by Kutzelnigg "Die adiabatische Naeherung" (unfortunately in German) exists as a contribution to the "Arbeitstagung Mariapfarr 1997" and may be downloaded by anonymous ftp from "ftp.kfunigraz.ac.at/dep/tch/kutz.zip" (this is a compres- sed Postscript file which - after a rename to e.g. "kutz.gz" - may be de-com- pressed with "gunzip"). Kutzelnigg is presently preparing another review on this subject. Yet another review called "The idea of a potential energy sur- face" written by Sutcliffe will appear in "Lecture Notes in Chemistry" (I re- ceived a preprint from the author). o With the present state of affairs, I believe it is best to first analyze the physical properties of the system of investigation and then choose an appro- priate theoretical formalism, instead of starting with the latter. Following this paradigm, one observes that in He_2, which most of the time slowly vibra- tes around ~ 100 au, the He atoms are only slightly perturbed. Thus each of the two electron pairs is mostly located on its ``private'' nucleus, the charges of the other nucleus and the other electrons are almost perfectly shielded, and electron exchange is rather unimportant. One may therefore con- clude, that the use of an *atomic* reduced mass, i.e. including the electrons, is to be preferred. o With a very recently computed interaction potential [Submitted to Mol. Phys], the usage of *nuclear* masses instead, increases by 0.5 A and decreases D_0 by 0.03 mK. These changes are found to be insignificant within the accura- cy obtained in this work. I would like to thank the following individuals for writing me their opinion on the present problem: N. Handy, W. Jakubetz, F. Jensen, W. Kutzelnigg, and B. Sutcliffe. Robert Gdanitz -- Robert J. Gdanitz Institut f. Physikalische u.Theoretische Chemie Phone: +49 531 391-5370 Technische Universitaet Braunschweig Fax: +49 531 391-5396 Hans-Sommer-Str. 10 email: r.gdanitz@tu-bs.de D-38106 Braunschweig, Germany From chemistry-request@www.ccl.net Mon Oct 12 16:10:33 1998 Received: from postal.ucc.uno.edu (postal.ucc.uno.edu [137.30.1.80]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id QAA10682 Mon, 12 Oct 1998 16:10:24 -0400 (EDT) Received: from slater (slater.chem.uno.edu [137.30.57.87]) by postal.ucc.uno.edu (PMDF V5.2-29 #33240) with SMTP id <0F0Q00ON6D7LMW@postal.ucc.uno.edu> for chemistry@www.ccl.net; Mon, 12 Oct 1998 15:06:57 -0500 (CDT) Date: Mon, 12 Oct 1998 15:06:13 -0500 From: Howard Alper Subject: Parameterization - summary Sender: heacm@slater.chem.uno.edu To: chemistry@www.ccl.net Cc: halper@uno.edu Message-id: <36226135.41C6@uno.edu> Organization: University of New Orleans MIME-version: 1.0 X-Mailer: Mozilla 3.0 (X11; U; AIX 1) Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: 8BIT Hello, Several weeks back I asked this list for help with the process of parameterizing a model of Nitromethane for molecular dynamics simulation. Many people on the list responded, with much helpful information as to how I should proceed (being a total novice in parameter development). Thanks to their help, and some off-line conversations, I am now happy immersed in the parameterization process, and will hopefully converge to reasonable parameters for Nitromethane in the near future. Many thanks to all who responded. The summary is below. Howard ____________________________________________________________________ My original post was the following: Hello, I'm sorry if this is a repeat, but as far as I could tell this message did not post when I originally sent it - twice. Several weeks back I wrote about parameterization and units in simulation (still waiting for some replies...) Now I have some questions about parameterization to create forcefields for MD simulations. Specifically, I am interested in parameterizing Nitromethane. While any information regarding a set of parameters (bond, angle, torsion, out-of-plane,charges,van der Waals, etc) would be welcome, we are interested in generating the neccesary parameters, and in a form suitable for use in CHARMM. To this end I have several questions: 1) I need to derive, somehow, structural parameters and force constants for bond-stretching and angle-binding. The force constants should be in units of energy/(angstroms**2) and energy/(radian**2) (I have seen some force constants in old papers that give force constants in units of millidynes/angstroms, but I do not understand how that relates to the case of angle-bending constants...) I can perform an optimization and frequency calculation in Gaussian, for example, but >from what I can tell the resulting frequencies and force constants are for the normal modes of the molecule, not bonds and angles/etc. Does anyone know if Gaussian has any options to derive the type of force constants I require? Or, does anyone know of a post-Gaussian analysis program that would do the above? 2) I also need to derive van der Waals parameters. One person I asked said something on the order of "you can derive that from the interaction of two nitromethane molecules". To a parameterization novice, that is not very specific advice. Could anyone clarify what in detail needs to be done, provide references, describe how programs like Guassian might be used to get VDW parameters, etc? (If one calculates the interaction energy of two nitromethane molecules at verious distances and orientations, is not the total energy for a configuration the sum of coulombic and VDW terms? Does that mean the charges must first be derived?) Thanks in advance, Howard Alper ____________________________________________________________________ And now your responses: ____________________________________________________________________ From: Craig Burkhart Hello Howard, Some ideas, etc on your request: Howard Alper wrote: > 1) I need to derive, somehow, structural parameters and force constants > for bond-stretching and angle-binding. The force constants should > be in units of energy/(angstroms**2) and energy/(radian**2) (I have > seen some force constants in old papers that give force constants > in units of millidynes/angstroms, but I do not understand how that > relates to the case of angle-bending constants...) I can perform > an optimization and frequency calculation in Gaussian, for example, but > from what I can tell the resulting frequencies and force constants > are for the normal modes of the molecule, not bonds and angles/etc. > Does anyone know if Gaussian has any options to derive the type of > force constants I require? Or, does anyone know of a post-Gaussian > analysis program that would do the above? The conversion from mdyn/Ang to kcal/mole/Ang^2 is a throwback to the old days when forcefields were used for spectroscopic purposes (see the Allinger MMx implementations for the conversions). Ab initio-based parameterization is growing in importance, largely due to Allinger's and Hagler's groups work. Hagler, Hwang and Stockfish wrote a nice article, circa 1994, on using ab initio methods to parameterize their newest 2nd generation forcefield. If my memory is correct, they used small random displacements in bonds, angles and torsions to parameterize their forcefield for the valence terms. > 2) I also need to derive van der Waals parameters. One person I asked > said something on the order of "you can derive that from the interaction > of two nitromethane molecules". To a parameterization novice, that is > not very specific advice. Could anyone clarify what in detail needs to > be done, provide references, describe how programs like Guassian might > be used to get VDW parameters, etc? (If one calculates the interaction > energy of two nitromethane molecules at verious distances and > orientations, is not the total energy for a configuration the sum > of coulombic and VDW terms? Does that mean the charges must first > be derived?) This part is a bit more tricky. How you do the nonbonded interactions is going to depend upon your usage. If you are interested in ideal gas-phase simulations, then maybe you only have to do a set of random configurations with a pair of molecules (perfect pairwise interactions). If you want to do more concentrated systems, then you have to worry about how to incorporate the many-body interactions (higher order virial terms) into your forcefields. In liquids, for example, the parameterization is performed against thermodynamic data such as heats of vaporization, and so on. Jorgensen's group has used this approach with a great deal of success in their OPLS implementations. The long and the short of this is: if you want to do ideal gas phase simulations of nitromethane, then a correlated ab initio method (Muller-Plesset, for example) is probably going to be necessary if you want really high quality pairwise parameters. You can use Hartree-Fock if you want lesser quality, as the dispersion interaction will not be handled adequately. And yes, you will need to obtain the partial charges separately, usually by electrostatic potential-derived charges. Even here, you must be careful. If you want to do liquids, then using ELP in a continuum solvent field would be indicated on initial inspection, as the liquid state will polarize your molecule--causing the partial charges to increase on each atom (CHARMM is a nonpolarizable forcefield). Most people ignore this complication, as you would have to have a table or "nomograph" of partial atomic charges for each atom type as a function of dielectric constant and molecular environment (Karasawa and Goddard did some nice work in this area about 10 years ago using a variation of charge equilibration via a classical grand canonical ensemble. They could update the charges on-the-fly). You will also need to use bulk thermodynamic data to create "effective" nonbonded van der Waals parameters. I don't know if Bill Jorgensen would release his parameterization codes, but I believe that Jay Ponder's Tinker suite has that capability--and the last time I checked, his software is freely obtainable from his website ( http://dasher.wustl.edu). Hope this helps... Craig ____________________________________________________________________ From: ulf@hugin.teokem.lu.se (Ulf Ryde) To: Dear Dr. Alper, I have implemented a simple version of the procedure suggested by Seminario (Int. J. Quantum Chem.: Quantum. Chem. Symp. 30(96)59-65). It converts the Hessian matrix produced by the Gaussian program to internal force constants and it is said to be invariant to the choice of internal coordinates. I find this procedure useful for a rapid determination of force constants. Please note, however, that this is only an approximate procedure since it ignors the interactions between parameters of different types and it is not the method used in standard parameterisations. For more accurate methods, you should look in the original papers of the MMFF, Amber, CHARMM, etc. force fields and references therein, e.g . Cornell, et al, J. Am. Chem. Soc. 117(95)5179 Halgren, J. Comput. Chem. 17(96)490-641 Paverlites et al, J. Comput. Chem. 18(97)221-239. Good Luck, Ulf ____________________________________________________________________ From: Jaromir MAREK > Hello, > > Specifically, I am interested in parameterizing Nitromethane. > While any information regarding a set of parameters (bond, angle, > torsion, out-of-plane,charges,van der Waals, etc) would be welcome, > we are interested in generating the neccesary parameters, and in a form > suitable for use in CHARMM. To this end I have several questions: Hi Howard ! Some general informations are at AMBER WWW pages http://www.amber.ucsf.edu/amber/amber.html and http://www.amber.ucsf.edu/amber/newparams.html Regards, Jaromir ____________________________________________________________________ From: "Donald E. Williams" Check my home page www.louisville.edu/~dewill01. Program nbp will accept dimer data for optimization of the force field. -- Dr. Donald E. Williams email:dew01@xray5.chem.louisville.edu Department of Chemistry University of Louisville phone:502-852-5975 Louisville, KY 40292 fax: 502-852-8149 ____________________________________________________________________ From: ss@CLEMSON.EDU (Steven J. Stuart) Howard, Some direct & indirect answers to your CCL post questions: 1) I don't have any specific numbers for you. However, if you get normal mode frequencies from Gaussian, it will be possible to turn those into bond stretches and angle bends. I can't answer whether Gaussian has options to do this or whether there are postprocessing tools to do it for you. But as a worst-case scenario, you could do the calculation by hand. Tedious, but possible. See Wilson, Decius, and Cross "Molecular Vibrations" for details. Nitromethane is small enough that it might even be worked out for you. 2) LJ parametrization is more my forte. One approach, that you partially described, would be to: (a) evaluate interaction energy vs. distance for 2 nitromethane molecules at fairly distant separations, for a given orientation, using Gaussian or ; (b) select LJ parameters which reproduce the PE vs r curve. In general, this will not completely specify the LJ parameters for your 4 different atoms, and you will have to do this for several different configurations. Choose these either based on symmetry or based on selecting configurations such as H-bonding arrangements that are expected to contribute heavily in your applications. Another very common approach is to steal some of your LJ constants from similar compounds. The LJ constants for C and H are not likely to be very different in nitromethane and other substituted methane species. You are right that you will need to know the partial charges before doing the LJ fit. There are lots of ways to select these. You will need to reproduce the molecule's dipole moment (either in gas phase or in solution, depending on your particular application and the potential you are combining it with). This will not uniquely specify the charges, though. Beyond that, you can optimize the charges to reproduce the electrostatic potential around the molecule, or to give the correct dimer energies when optimized in conjunction with the LJ parameters, or any of several other methods. I suspect I haven't been as explicit as you'd like. If so, ask more questions and I'll try to provide more details where I can. -Steve Stuart ss@clemson.edu ____________________________________________________________________ Guido Germano Organization: Physics Department University of Bristol You asked a 1 million $ question. I have, perhaps, an answer to this curiosity of yours: > I have seen some force constants in old papers that give force > constants in units of millidynes/angstroms, but I do not understand > how that relates to the case of angle-bending constants You can treat bending as a (1,3) stretching. More in general, the equilibrium bonds and angles can be easily found with Gaussian; the force constants not, they must be guessed, but for quick and dirty calculations it's not difficult, as the order of magnitude of strecthing constants is always the same and ten times higher than the bending ones, which are again more or less the same and higher than the torsional ones, etc. The hardest parameters to guess are the VdW ones. In principle you need to do test MD runs with lots of molecules and calibrate physical observables like the density by trial and error. I don't think ab initio calculations on couples are enough, if the objects are not spherical. Bottomline: if you find any new papers or algorithms to extract e.g. stretching and bending constants in an automatic fashion from a normal mode analysis, let me know (I suspect it's an ill-determined problem: once you have a set of constants, you can check with the normal modes; but I have never gone this much into detail). Regards Guido Germano ____________________________________________________________________ From: Ya-Jun Zheng Hi Howard, Since you are trying to get parameters to use in Charmm, you may not need very accurate force field parameters. One simple approach is as follow: For internal parameters, you could take the ab initio bond lengthes and angles. For the torsion parameters, you could use either experimental or ab initio (e.g., HF/6-31G*) values. For charges, use ESP fitted charges. van der Waals parameters could be obtained by analogy (for example using the normal carbonyl O parameters for the nitro O). The bond and angle force constants can be obtained by trying to reproduce the IR spectra of CH3NO2 (normal model analysis in Charmm). Unless you are trying to simulate nitromethane liquid, otherwise the above approach should give you reasonable parameters. You could also use the ab initio CH3NO2---H2O interaction energy to refine your van der Waals parameters. Allinger and coworkers published MM3 (or MM2) parameters few years ago in J. Mol. Structure. You could use some of these parameters as initial guess. As for the two questions you asked, the simple answer is as follow: 1. Basicaly, you need a transformation program to do that. There is an old program called G-matrix that some people use to do the transformation. I had a hardcopy of that program, but never had the chance to make it work, 2. You could check some of the papers by former Biosym people (A. Hagler and others), which gave detailed description of how to do parameterization >from ab initio data. Yajun Zheng ******************************************************** Dr. Ya-Jun Zheng DuPont Stine-Haskell Research Center P. O. Box 30 Newark, DE 19714 E-mail: Ya-Jun.Zheng@usa.dupont.com ******************************************************** ____________________________________________________________________ From: "Alexander D. MacKerell, Jr." Howard, If you want to determine parameters that are compatible with CHARMM you should follow the same procedures used for that force field. The appropriate references are on my web page, along with the recent release of charmm parameters. Those papers include the use of normal modes in the optimzation procedure (note that any normal mode is a combination of individual internal coordinates, you just change the parameters associated with those coordinates to reproduce the desired frequency). Concerning the vdw parameters, i would use default values from CHARMM as a first (and quite reasonable) guess. Using these optimize the rest of your force field. When that is complete, then reconsider the quality of the vdw params. Note that optimization of the vdw params is, in my opinion, the most difficult aspect of parameter optimazation. good luck, alex -- Alex MacKerell, Ph.D. Associate Professor School of Pharmacy University of Maryland 20 North Pine Street Baltimore, MD 21201 410-706-7442 410-706-0346 (fax) alex@mmiris.ab.umd.edu or alex@rx.umaryland.edu http://www.pharmacy.ab.umd.edu/~alex/ ____________________________________________________________________ From: Wayne Steinmetz The frequencies of the vibrational normal modes can be expressed in terms of the local force constants which you require. The details are given in the classic E. B. Wilson, J. C. Decius, and P. C. Cross, Molecular Vibrations, McGraw-Hill (1955). With some luck, a moelcular spectroscopist has performed an exhaustive study of the Raman and infra-red spectra of normal nitromethane and isotopic modifications and has completed a normal coordinate analysis. A complete study should include the parameters that you require. An example of what you might find can be found in T. Shimanouchi, H. Matsuura, Y. Ogawa, and I. Harada, J. Physical Chemical Reference Data, Vol. 7 , pp. 1323-1443 (1978). Unfortunately nitromethane is not in this paper but the paper that I cited is Part 9 of the series entitled Tables of Molecular Vibrational Frequencies. Some of Takehiko Shimanouchi's other papers in this series might contain what you require. Since nitromethane is a small molecule with no internal rotation, I would be surprised that no one has beaten it to death. A source of chem abstract with keywords such as nitromethane and normal coordinate analysis might lead the path to your data. Another possible source of references is JANAF Thermochemical Tables. The spectroscopic data that form the basis for the thermodynamic data are provided that stat mech is the basis for the thermo. I checked my copy but nitromethane is not present but I have an older edition. ____________________________________________________________________ From: ross@cgl.ucsf.EDU See http://www.amber.ucsf.edu/amber/newparams.html probably all but the "improper torsions" part would be a decent intro for your purposes. Bill Ross ____________________________________________________________________ From: Rick Venable On Wed, 16 Sep 1998, Howard Alper wrote: > Now I have some questions about parameterization to create forcefields > for MD simulations. Specifically, I am interested in parameterizing > Nitromethane. While any information regarding a set of parameters > (bond, angle, torsion, out-of-plane,charges,van der Waals, etc) would > be welcome, we are interested in generating the neccesary parameters, > and in a form suitable for use in CHARMM. To this end I have several > questions: I've omitted the questions, because I'm not answering them directly, but supplying some references from Alex MacKerell's web site at http://www.pharmacy.umab.edu/~alex/research.html The papers below describe the development of various topology and parameter sets which are distributed with the academic version of CHARMM; additional citations and the parameter sets themselves (in CHARMM format) are also available on the web page. Typically, force constants for bond stretching and angle bending are derived from published IR/Raman spectroscopic data, after conversion to the CHARMM system of units. Atomic point charges and VDW radii parameters require extensive ab initio calculations, while torsions are usually parameterized to match experimentally determined rotational barriers and/or conformational distributions. MacKerell, Jr., A. D.; Bashford, D.; Bellott, M.; Dunbrack Jr., R.L.; Evanseck, J.D.; Field, M.J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F.T.K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D.T.; Prodhom, B.; Reiher, III, W.E.; Roux, B.; Schlenkrich, M.; Smith, J.C.; Stote, R.; Straub, J.; Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. All-atom empirical potential for molecular modeling and dynamics Studies of proteins. Journal of Physical Chemistry B, 1998, 102, 3586-3616. Yin, D. and MacKerell, Jr. A.D. Combined Ab initio/Empirical Approach for the Optimization of Lennard-Jones Parameters. Journal of Computational Chemistry, 1998, 19: 334-338. Pavelites, J.J., Bash, P.A., Gao, J. and MacKerell, Jr., A.D. A Molecular Mechanics Force Field for NAD+, NADH, and the Pyrophosphate Groups of Nucleotides. Journal of Computational Chemistry, (1997) 18:221-239. A.D. MacKerell Jr., J. Wi-rkiewicz-Kuczera and M. Karplus, An All-Atom Empirical Energy Function for the Simulation of Nucleic Acids, Journal of the American Chemical Society (1995) 117:11946-11975. -- Rick Venable =====\ |=| "Eschew Obfuscation" FDA/CBER Biophysics Lab |____/ |=| Bethesda, MD U.S.A. | \ / |=| ( Not an official statement or rvenable@deimos.cber.nih.gov | \ / |=| position of the FDA; for that, http://www.erols.com/rvenable \/ |=| see http://www.fda.gov ) ____________________________________________________________________ From: Per-Ola Norrby Howard Alper wrote: ..... > Specifically, I am interested in parameterizing Nitromethane. >While any information regarding a set of parameters (bond, angle, >torsion, out-of-plane,charges,van der Waals, etc) would be welcome, >we are interested in generating the neccesary parameters, and in a form >suitable for use in CHARMM.... ..... Dear Howard, We just published a method for parameterization, specifically implemented for MacroModel, but we put a lot of effort into making the routines general enough so that you should be able to use it in a similar manner with any MM program running under Unix. Anything force field specific is handled by Unix scripts, you only need to be able to handle Unix to modify the method for the force field you are interested in. The method is described in J. Comput. Chem., 1998, 19, 1146-1166. I'll share the routines (note! they are NOT user-friendly, and you definitely need the article to make sense of them). Send me an email if you're interested. The stuff I'm distributing right now is a year old, I'm right in the middle of putting together an updated version, should be ready in a couple of weeks.' Best regards, 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: Konrad Hinsen > Specifically, I am interested in parameterizing Nitromethane. > While any information regarding a set of parameters (bond, angle, > torsion, out-of-plane,charges,van der Waals, etc) would be welcome, > we are interested in generating the neccesary parameters, and in a form > suitable for use in CHARMM. To this end I have several questions: Have a look at 21) K. Hinsen, B. Roux An accurate potential for simulating proton transfer in acetylacetone J. Comp. Chem. 18, 368 (1997) It describes a complete parametrization procedure, although of course for a different molecule and probably with different priorities. ____________________________________________________________________ From:"Klaus-D. Warzecha" At 17:04 14.09.98 -0500, you wrote: >[...] Now I have some questions about parameterization to create >forcefields for MD simulations. >Specifically, I am interested in parameterizing Nitromethane. >While any information regarding a set of parameters (bond, angle, >torsion, out-of-plane,charges,van der Waals, etc) would be welcome, >we are interested in generating the neccesary parameters, and in a form >suitable for use in CHARMM. >[...] Howard, unfortunately I'm no expert in computational chemisty and therefore not sure whether the following will be helpful at all, but you might consider to have a look at an earlier article on Molecular Mechanics Force-Field Parametrization Procedures. A. J. Hopfinger, R. A. Pearlstein, J. Computational Chemistry, 1984, 5, 486-499. I have to admit that I never used it myself and thus won't be able to give you any help on that, sorry. Greetings, Klaus-D. Warzecha Klaus-D. Warzecha Max-Planck-Institut für Strahlenchemie Mülheim an der Ruhr Germany ____________________________________________________________________ -- Howard E. Alper, Ph.D. Dept. of Chemistry and The Advanced Materials Research Institute University of New Orleans New Orleans, LA 70148 504-280-7216 - Helping molecules find happiness for almost a 5th of a century. From chemistry-request@www.ccl.net Mon Oct 12 21:20:46 1998 Received: from guomai.sh.cn ([202.96.206.71]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id VAA03085 Mon, 12 Oct 1998 21:20:44 -0400 (EDT) Received: from guomai.sh.cn (email-53 [210.0.0.53]) by guomai.sh.cn (8.9.1/8.9.1) with ESMTP id JAA27613 for ; Tue, 13 Oct 1998 09:17:58 +0800 (CST) Message-ID: <3622AB0A.8D88A635@guomai.sh.cn> Date: Tue, 13 Oct 1998 09:21:14 +0800 From: Yubo Fan Reply-To: yubofan@guomai.sh.cn Organization: Department of Chemistry, Fudan University X-Mailer: Mozilla 4.03 [en] (Win95; I) MIME-Version: 1.0 To: CHEMISTRY@www.ccl.net Subject: Pyrolysis Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers, I am dealing with some pyrolysis reactions. The problem is how I can get the temperature the reactions begin. For example, at which temperature the reaction 2 H2O = 2 H2 + O2 begins. Is it possible to use quantum calculation to get this temperature? Thank you very much Y. Fan -- ============================================================= Yubo Fan Email: yubofan@guomai.sh.cn Organic Synthesis Lab The Department of Chemistry Fudan University Phone: 8621-65648139 No. 220 Handan Road Fax: 8621-65641740 Shanghai, 200433 P. R. China =============================================================