From chemistry-request@server.ccl.net Thu Oct 26 19:27:29 2000 Received: from sina.com ([202.106.187.156]) by server.ccl.net (8.8.7/8.8.7) with SMTP id TAA22390 for ; Thu, 26 Oct 2000 19:27:28 -0400 Received: (qmail 92700 invoked from network); 26 Oct 2000 23:22:44 -0000 Received: from unknown (HELO cgliu) (202.111.18.97) by 202.106.187.156 with SMTP; 26 Oct 2000 23:22:44 -0000 Message-ID: <001c01c03fa4$25e00a40$5c126fca@nju.edu.cn> From: "Chungen Liu" To: Cc: Subject: Can G2 calculate the thermodynaics properties of transition states? Date: Fri, 27 Oct 2000 07:26:18 +0800 MIME-Version: 1.0 Content-Type: text/plain; charset="gb2312" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from base64 to 8bit by server.ccl.net id TAA22391 Dear all: I am not sure if G2 or G3 or any other methods can be used to calculate the hermodynaics properties of transition states. To my knowledge, these integrated steps involving the geometry optimization which i am afraid might optimize the geometries into equilibrium states instead of transition states. Your suggestion will be very important to me. From chemistry-request@server.ccl.net Fri Oct 27 03:14:01 2000 Received: from deews1.dent.okayama-u.ac.jp (deews1.dent.okayama-u.ac.jp [150.46.202.36] (may be forged)) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA24026 for ; Fri, 27 Oct 2000 03:14:00 -0400 Received: from [150.46.162.72] (liset4.lib.okayama-u.ac.jp [150.46.162.72]) by deews1.dent.okayama-u.ac.jp (8.9.2/3.7Wpl2-oucc-1.0) with SMTP id QAA24756 for ; Fri, 27 Oct 2000 16:15:51 +0900 (JST) Message-Id: <200010270715.QAA24756@deews1.dent.okayama-u.ac.jp> Date: Fri, 27 Oct 2000 16:21:30 +0900 To: chemistry@ccl.net From: ep7@dent.okayama-u.ac.jp (Masao Masamura) Subject: CCL: Summary: MC and MD MIME-Version: 1.0 Content-Type: text/plain; charset=iso-2022-jp X-Mailer: Eudora-J(1.3.8.5-J13) Dear CCL: Sincere thanks to all who replied to my question! Below I have printed my original email and a summary of the responses: Dear Sir: I would like to ask you about (1) recent books for Monte Carlo Simulation and (2) recent books and reviews for constructing an intermolecular potential for MD and MC. Thank you M. Masamura ========================================================== One book I would recommend to you is Understanding Molecular Simulation: From Algorithm to Applications by Daan Frenkel and Berend Smit (Published 1997). Covers MC and MD and looks at algorithms (in Fortran) as well. Deepak. ********************************************************************** Deepak Singh Tel : (315)443 1739 (w) Graduate Student (315)472 9659 (h) Dept. of Chemistry Fax : (315)443 4070 Syracuse University email : desingh@syr.edu 1-014 CST, Syracuse URL : http://web.syr.edu/~desingh NY 13244 "Violence is the last refuge of the incompetent." --- Salvor Hardin ********************************************************************** From chemistry-request@server.ccl.net Fri Oct 27 08:25:53 2000 Received: from potsdam.edu (potsdam.edu [137.143.110.101]) by server.ccl.net (8.8.7/8.8.7) with SMTP id IAA26496 for ; Fri, 27 Oct 2000 08:25:52 -0400 Received: (qmail 18168 invoked by alias); 27 Oct 2000 12:25:40 -0000 Received: (qmail 18091 invoked by uid 0); 27 Oct 2000 12:25:30 -0000 Received: from comp10205.potsdam.edu (HELO comp10205) (137.143.109.46) by potsdam.edu with SMTP; 27 Oct 2000 12:25:30 -0000 Message-Id: <3.0.6.32.20001027083845.007fb380@potsdam.edu> X-Sender: marteljm@potsdam.edu X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.6 (32) Date: Fri, 27 Oct 2000 08:38:45 -0400 To: "Chungen Liu" , From: Jaime Martell Subject: Re: CCL:Can G2 calculate the thermodynaics properties of transition states? Cc: In-Reply-To: <001c01c03fa4$25e00a40$5c126fca@nju.edu.cn> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" At 07:26 AM 10/27/00 +0800, Chungen Liu wrote: >Dear all: > >I am not sure if G2 or G3 or any other methods can be used to calculate the >hermodynaics properties of transition states. To my knowledge, these >integrated steps involving the geometry optimization which i am afraid might >optimize the geometries into equilibrium states instead of transition states. > Yes, you can, by using the opt=ts keyword. However, since these methods were optimized for equilibrium states, they have questionable accuracy for transition states. Jaime Martell, Ph.D. Assistant Professor Department of Chemistry SUNY Potsdam Potsdam, NY 13676 Phone: 315-267-2268 Fax: 315-267-3170 e-mail: marteljm@potsdam.edu WWW: http://www2.potsdam.edu/marteljm/ From chemistry-request@server.ccl.net Fri Oct 27 08:40:03 2000 Received: from ucidoor.unitedcatalysts.com ([208.23.162.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA26568 for ; Fri, 27 Oct 2000 08:40:03 -0400 Received: by ucidoor.unitedcatalysts.com; (8.8.8/1.3/10May95) id IAA28053; Fri, 27 Oct 2000 08:39:51 -0400 (EDT) Received: from 10.1.0.50 by ucismtp02.unitedcatalysts.com (InterScan E-Mail VirusWall NT); Fri, 27 Oct 2000 08:38:59 -0400 (Eastern Daylight Time) Received: from lvlxch01.unitedcatalysts.com ([10.16.100.88]) by lvlmail.unitedcatalysts.com (PMDF V6.0-24 #41777) with ESMTP id <0G3300DF99OQ50@lvlmail.unitedcatalysts.com> for chemistry@ccl.net; Fri, 27 Oct 2000 08:36:26 -0400 (EDT) Received: by lvlxch01.unitedcatalysts.com with Internet Mail Service (5.5.2650.21) id <48D99VWL>; Fri, 27 Oct 2000 08:39:40 -0400 Content-return: allowed Date: Fri, 27 Oct 2000 08:39:39 -0400 From: "Shobe, Dave" Subject: transition states with nearly free rotors To: "'CCL'" Message-id: <157A51F55AAAD3119CD70008C7B1629D63863C@lvlxch01.unitedcatalysts.com> MIME-version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id IAA26569 I'm having trouble finding a transition state (using Gaussian's opt=qst2). The problem is that the reaction involves methoxide compounds with very nearly free methyl rotors. As a result, I keep getting additional imaginary frequencies from the rotation of the methyl groups, and the program stops with an "Error termination..." Does anyone have any tricks to use in such situations? --David Shobe Süd-Chemie Inc. phone (502) 634-7409 fax (502) 634-7724 email dshobe@sud-chemieinc.com Any opinions herein are not necessarily representative of Süd-Chemie. From chemistry-request@server.ccl.net Fri Oct 27 12:00:34 2000 Received: from interlock.herc.com (interlock.herc.com [199.221.7.2]) by server.ccl.net (8.8.7/8.8.7) with SMTP id MAA27596 for ; Fri, 27 Oct 2000 12:00:33 -0400 From: Goutam.Das@betzdearborn.com Received: from csdnsg1.herc.com ([147.116.14.51]) by interlock.herc.com with SMTP id MAA26589 (InterLock SMTP Gateway for ); Fri, 27 Oct 2000 12:00:10 -0400 Subject: wax crystals To: CHEMISTRY@ccl.net X-Mailer: Lotus Notes Release 5.0.2b December 16, 1999 Message-Id: Date: Fri, 27 Oct 2000 10:58:46 -0500 X-Priority: 3 (Normal) X-Mimetrack: Serialize by Router on CSDNSG1/Servers/Herc(Release 5.0.1b|September 30, 1999) at 10/27/2000 11:50:04 AM Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear all. I am looking into designing improved wax crystal inhibitors from wax(n-paraffin) crystal structures. I would deeply appreciate if any one of you could direct me to websites containing coordinates for long n-alkane chain crystal structures and other relevant material. Any references on relevant material will also be appreciated. Thanx to all in anticipation. Have a bone chillin Haloween! Goutam Das Research Scientist BetzDearborn Division of Hercules The Woodlands, TX 77380 281.367.6201 ext 425 From chemistry-request@server.ccl.net Fri Oct 27 12:03:50 2000 Received: from toronto.acdlabs.com (toronto.acdlabs.com [207.176.233.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA27659 for ; Fri, 27 Oct 2000 12:03:50 -0400 Received: from gavin (gavin.acdlabs.com [207.176.233.80]) by toronto.acdlabs.com (8.9.0/8.9.0) with SMTP id MAA18447; Fri, 27 Oct 2000 12:02:28 -0400 (EDT) From: "Gavin Shear" To: "Gerd Bruno Rocha" Cc: Subject: RE: Databases Date: Fri, 27 Oct 2000 12:06:39 -0400 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) In-Reply-To: <39F5DADF.48979D4E@npd.ufpe.br> X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Importance: Normal ACD offers a free (though limited) example crystallographic database available at: http://www.acdlabs.com/download/db/chemfold.html Be sure to first install ChemSketch 4.5 freeware, and the ChemFolder trial in order to view the database. This database mainly serves as an example of the type and structure of information that you are able to store and search within ChemFolder. Many thanks, Gavin Shear From chemistry-request@server.ccl.net Fri Oct 27 12:41:00 2000 Received: from dasher.wustl.edu (dasher.wustl.edu [128.252.68.48]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA27882 for ; Fri, 27 Oct 2000 12:41:00 -0400 Received: from dasher.wustl.edu by dasher.wustl.edu (8.8.8/1.1.20.8/08Dec99-1053AM) id LAA0000163298; Fri, 27 Oct 2000 11:45:20 -0500 (CDT) Sender: ponder@dasher.wustl.edu Message-ID: <39F9B120.1198E229@dasher.wustl.edu> Date: Fri, 27 Oct 2000 11:45:20 -0500 From: Jay Ponder Organization: Biochemistry, Washington University Medical School X-Mailer: Mozilla 4.72 [en] (X11; U; OSF1 V5.0 alpha) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: TINKER 3.8 is Now Available Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL, A new release of the TINKER Molecular Modeling Package, version 3.8 dated October 2000, is available from the TINKER web site at http://dasher.wustl.edu/tinker/ or via anonymous ftp download from dasher.wustl.edu in the /pub/tinker area. TINKER is a modular, general package for molecular mechanics and dynamics with some special facilities and parameter sets for biopolymers. It supports several common force fields, including AMBER, CHARMM, MM2, MM3, OPLS-AA, OPLS-UA, and our own TINKER polarizable atomic multipole force field. The package contains advanced algorithms for energy minimization, distance geometry and global search that are not readily available elsewhere. TINKER version 3.8 contains the following new features and updates from version 3.7: (1) replacement of previous conjugate gradient minimizer with a more efficient L-BFGS algorithm, (2) updated parameter sets for several distributed 3rd-party force fields, (3) a new nucleic acid building module for generating DNA or RNA structures from sequence, (4) "final" parameters for the TINKER polarizable atomic multipole water model, (5) faster and more flexible GB/SA continuum solvation models including several literature variants, (6) Ewald summation for polarizable multipole electrostatics, (7) new programs to compute radial distribution functions, diffusion constants and power spectra from MD simulations. TINKER is distributed with full source code, a User's Guide, and several examples and test molecule files. Directions are supplied for building the package on most commonly used CPU/OS combinations. Prebuilt executables limited to a maximum of 10000 atoms are also provided for Linux, Windows, and Macintosh. Please see the web site above for further information. Comments, questions and suggestions for future improvements can be sent to ponder@dasher.wustl.edu. Jay Ponder -- Jay W. Ponder Phone: (314) 362-4195 Biochemistry, Box 8231 Fax: (314) 362-7183 Washington University Medical School 660 South Euclid Avenue Email: ponder@dasher.wustl.edu St. Louis, Missouri 63110 USA WWW: http://dasher.wustl.edu/ From chemistry-request@server.ccl.net Fri Oct 27 11:34:50 2000 Received: from snoopy.qc.ag-berlin.mpg.de (snoopy.qc.ag-berlin.mpg.de [141.20.73.58]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA27495 for ; Fri, 27 Oct 2000 11:34:33 -0400 Received: from qc.ag-berlin.mpg.de ([127.0.0.1]) by snoopy.qc.ag-berlin.mpg.de (8.10.2/8.10.2/SuSE Linux 8.10.0-0.3) with ESMTP id e9RFc7h04415 for ; Fri, 27 Oct 2000 17:38:07 +0200 X-Authentication-Warning: snoopy.qc.ag-berlin.mpg.de: Host [127.0.0.1] claimed to be qc.ag-berlin.mpg.de Sender: mh@snoopy.qc.ag-berlin.mpg.de Message-ID: <39F9A15F.22001283@qc.ag-berlin.mpg.de> Date: Fri, 27 Oct 2000 17:38:07 +0200 From: "Max C. Holthausen" Organization: HUB X-Mailer: Mozilla 4.74 [en] (X11; U; Linux 2.2.16 i686) X-Accept-Language: en MIME-Version: 1.0 To: computational chemistry list Subject: Re: Can G2 calculate ...transition states? Content-Type: text/plain; charset=iso-8859-15 Content-Transfer-Encoding: 8bit I have seen excellent results for Peterssons CBS-QB3 in applications to transition structure energies (to be published). For the method, see J. Chem. Phys. 110, 2822 (1999). This now is a(nother) black box procedure in Gaussian98. DFT of course does a good job for TS geometries and the S^^2 dependent correction term in the energy extrapolation apparently ameliorates the situation for a (more or less single reference) description of breaking bonds. Technically, use opt=TS for transition structure optimizations. Regards, Max At 07:26 AM 10/27/00 +0800, Chungen Liu wrote: >Dear all: > >I am not sure if G2 or G3 or any other methods can be used to calculate the >hermodynaics properties of transition states. To my knowledge, these >integrated steps involving the geometry optimization which i am afraid might >optimize the geometries into equilibrium states instead of transition states. > -- --------------------------------------------------------------------- Dr. Max C. Holthausen Institut für Chemie Email: mh@qc.ag-berlin.mpg.de Humboldt Universität Phone: Int + (30) 20192 314 Jägerstr. 10/11 Fax: Int + (30) 20192 302 D-10117 Berlin, Germany --------------------------------------------------------------------- From chemistry-request@server.ccl.net Fri Oct 27 16:58:32 2000 Received: from usc.edu (root@usc.edu [128.125.253.136]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA29211 for ; Fri, 27 Oct 2000 16:58:31 -0400 Received: from chem2.usc.edu (chem2.usc.edu [128.125.8.63]) by usc.edu (8.9.3.1/8.9.3/usc) with ESMTP id NAA07840 for ; Fri, 27 Oct 2000 13:58:31 -0700 (PDT) Received: from localhost (devlin@localhost) by chem2.usc.edu (8.9.3.1/8.9.3/usc) with SMTP id NAA15148 for ; Fri, 27 Oct 2000 13:58:27 -0700 X-Authentication-Warning: chem2.usc.edu: devlin owned process doing -bs Date: Fri, 27 Oct 2000 13:58:27 -0700 (PDT) From: "Frank J. Devlin" To: chemistry@server.ccl.net Subject: Dimer structures Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCl, Is it possible to optimize dimeric structures using Gaussian? Any pointers, references, etc. would be very helpful. I will summarize to the list. Thank you, Dr. Frank Devlin. From chemistry-request@server.ccl.net Fri Oct 27 17:30:45 2000 Received: from Mercury.acs.unt.edu (mercury.acs.unt.edu [129.120.220.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA29414 for ; Fri, 27 Oct 2000 17:30:44 -0400 Received: from jove.acs.unt.edu (10759@jove.acs.unt.edu [129.120.220.41]) by Mercury.acs.unt.edu (8.8.8/8.8.8) with ESMTP id QAA27154; Fri, 27 Oct 2000 16:29:50 -0500 (CDT) Received: from localhost (tdp0006@localhost) by jove.acs.unt.edu (8.8.8/8.8.8) with ESMTP id QAA04352; Fri, 27 Oct 2000 16:29:49 -0500 (CDT) Date: Fri, 27 Oct 2000 16:29:49 -0500 (CDT) From: TREVOR D POWER To: "Frank J. Devlin" cc: chemistry@server.ccl.net Subject: Re: CCL:Dimer structures In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Frank, What kind of dimeric structures are you interested in calculating? With symmetry constraints? Regards, David Power Department of Chemistry University of North Texas Nt Station, Box 305070 Denton, Texas 76203-5070 tdp0006@unt.edu On Fri, 27 Oct 2000, Frank J. Devlin wrote: > > Dear CCl, > > Is it possible to optimize dimeric structures using Gaussian? > Any pointers, references, etc. would be very helpful. > > I will summarize to the list. > > Thank you, > > Dr. Frank Devlin. > > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > From chemistry-request@server.ccl.net Fri Oct 27 19:02:53 2000 Received: from usc.edu (root@usc.edu [128.125.253.136]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id TAA29909 for ; Fri, 27 Oct 2000 19:02:52 -0400 Received: from chem2.usc.edu (chem2.usc.edu [128.125.8.63]) by usc.edu (8.9.3.1/8.9.3/usc) with ESMTP id QAA26939; Fri, 27 Oct 2000 16:02:51 -0700 (PDT) Received: from localhost (devlin@localhost) by chem2.usc.edu (8.9.3.1/8.9.3/usc) with SMTP id QAA15236; Fri, 27 Oct 2000 16:02:50 -0700 X-Authentication-Warning: chem2.usc.edu: devlin owned process doing -bs Date: Fri, 27 Oct 2000 16:02:49 -0700 (PDT) From: "Frank J. Devlin" To: TREVOR D POWER cc: chemistry@server.ccl.net Subject: Re: CCL:Dimer structures In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi Trevor, Consider dimethylsulfoxide (DMSO). It is known experimentally that DMSO forms dimers in solution i.e. IR bands for dimer can be observed. Now I would like to model the dimer system to determine the structure that exists in solution. Is it like this for example CH3 O CH3 \ / \ / S S / \ / \ CH3 O CH3 or are the DMSO molecules oriented in some other way? So, I want to optimize the geometries of likley dimer structures and calculate their IR spectra. Regards, Frank. On Fri, 27 Oct 2000, TREVOR D POWER wrote: > Frank, > What kind of dimeric structures are you interested in calculating? > With symmetry constraints? > > Regards, > David Power > Department of Chemistry > University of North Texas > Nt Station, Box 305070 > Denton, Texas 76203-5070 > tdp0006@unt.edu > > > > On Fri, 27 Oct 2000, Frank J. Devlin wrote: > > > > > Dear CCl, > > > > Is it possible to optimize dimeric structures using Gaussian? > > Any pointers, references, etc. would be very helpful. > > > > I will summarize to the list. > > > > Thank you, > > > > Dr. Frank Devlin. > > > > > > > > > > -= This is automatically added to each message by mailing script =- > > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > > > > > > > >