From chemistry-request@server.ccl.net Wed Nov 8 11:00:53 2000 Received: from hotmail.com (f52.law6.hotmail.com [216.32.241.52]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA15915 for ; Wed, 8 Nov 2000 11:00:52 -0500 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Wed, 8 Nov 2000 07:58:40 -0800 Received: from 213.174.2.2 by lw6fd.law6.hotmail.msn.com with HTTP; Wed, 08 Nov 2000 15:58:39 GMT X-Originating-IP: [213.174.2.2] From: "dido dido2" To: CHEMISTRY@ccl.net Subject: hallo Date: Wed, 08 Nov 2000 15:58:39 GMT Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 08 Nov 2000 15:58:40.0057 (UTC) FILETIME=[C2EF6A90:01C0499C] Can you tell me the formulae, by which you can determine the number of isomers according to the number of carbon atoms in alkanes? if there is no formula please tell me How can i continue te row(line) of numbers,and how you do this please 1(1),1(2),1(3),2(4),3(5),5(6),9(7),18(8),35(9),75(10),..........4347(15)...... if you don`t know it please tell me someone who knows it!!! _________________________________________________________________________ Get Your Private, Free E-mail from MSN Hotmail at http://www.hotmail.com. Share information about yourself, create your own public profile at http://profiles.msn.com. From chemistry-request@server.ccl.net Wed Nov 8 12:55:47 2000 Received: from havana.ks.uiuc.edu (havana.ks.uiuc.edu [130.126.120.73]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA16422 for ; Wed, 8 Nov 2000 12:55:47 -0500 Received: from roswell.ks.uiuc.edu (roswell.ks.uiuc.edu [130.126.120.132]) by havana.ks.uiuc.edu (8.9.1/8.9.1) with ESMTP id LAA25558 for ; Wed, 8 Nov 2000 11:55:33 -0600 (CST) Received: from localhost (emad@localhost) by roswell.ks.uiuc.edu (8.9.1b+Sun/8.9.1) with ESMTP id LAA24295 for ; Wed, 8 Nov 2000 11:55:33 -0600 (CST) X-Authentication-Warning: roswell.ks.uiuc.edu: emad owned process doing -bs Date: Wed, 8 Nov 2000 11:55:33 -0600 (CST) From: Emad Tajkhorshid To: ccl CCL Subject: Different platforms for running Gaussian Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi I wonder if anybody has efficiently used SUN platforms for running quantum chemical calculations, e.g. Gaussian9x. We are considering to purchase a new machine for our group particularly for quantum chemical calculations. Among our options are SUN and Alpha machines. Any comment or suggestion with regard to this is appreciated. Thanx Emad ------------------ Emad Tajkhorshid http://www.ks.uiuc.edu/~emad Theoretical Biophysics Group Beckman Institute for Advanced Science and Technology 405 N. Mathews, Urbana, IL 61801 Tel: (217)244-5042 Fax: (217)244-6078 Email: emad@ks.uiuc.edu From chemistry-request@server.ccl.net Wed Nov 8 13:26:00 2000 Received: from gandalf.cber.nih.gov (gandalf.cber.nih.gov [128.231.52.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA16570 for ; Wed, 8 Nov 2000 13:25:59 -0500 Received: from localhost (rvenable@localhost) by gandalf.cber.nih.gov (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id NAA17116; Wed, 8 Nov 2000 13:20:12 -0500 (EST) Date: Wed, 8 Nov 2000 13:20:12 -0500 From: Rick Venable To: Marcin Krol cc: chemistry@ccl.net, charmm-bbs@csir.org Subject: Re: [charmm-bbs] Diazo dyes in CHARMM In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII See Alex MacKerell's web site at URL http://www.pharmacy.umaryland.edu/~alex/research.html for information and references on the academic parameter development process. On Wed, 8 Nov 2000, Marcin Krol wrote: > I want to simulate diazo dyes and their interactions with proteins in > CHARMM using academic, all atom forcefield. I built RTF file for my > diazo dye and chose atom types that I thought fitted 'well' with my > structure. However, I could not find proper atom types for sulphur in > SO3H- and nitrogen in -N=N- and so on. Moreover, there were 'missing > paramters'. So I used Quanta and got all atom types and > missing paramters given by Parameter Chooser. However, these atom types > and parameters belong to QUANTA_CHARMm forcefield. > > Is it safe to take them to academic par22 FF? I'm afraid it isn't. It may be or may not be safe, but it represents a significant change to existing parameters and would require significant testing on model compounds to verify or validate the changes. > Maybe someone has parameters for diazo dyes in par22, or maybe someone can tell me how to transform > parameters from CHARMm (Quanta) to CHARMM (academic)? > How can I get parameters in another way? > I know I'm asking a generic question, so I'd be also grateful if you > could refer me to a good book/article about parametrization process for > small ligand molecules. -- Rick Venable =====\ |=| "Eschew Obfuscation" FDA/CBER Biophysics Lab |____/ |=| Bethesda, MD U.S.A. | \ / |=| ( Not an official statement or Rick_Venable@nih.gov | \ / |=| position of the FDA; for that, rvenable@speakeasy.org \/ |=| see http://www.fda.gov ) From chemistry-request@server.ccl.net Wed Nov 8 15:25:21 2000 Received: from mail.rpi.edu (root@mail.rpi.edu [128.113.100.7]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA17102 for ; Wed, 8 Nov 2000 15:25:20 -0500 Received: from curtp5 (curtp5.chem.rpi.edu [128.113.21.59]) by mail.rpi.edu (8.9.3/8.9.3) with SMTP id PAA428474; Wed, 8 Nov 2000 15:25:17 -0500 Message-ID: <3A09B61D.B60@rpi.edu> Date: Wed, 08 Nov 2000 15:22:53 -0500 From: "Curt M. Breneman" Reply-To: brenec@rpi.edu Organization: RPI Department of Chemistry X-Mailer: Mozilla 3.02 (WinNT; I) MIME-Version: 1.0 To: chemistry@ccl.net CC: hayden@chemcomp.com, lockwl@rpi.edu, sundlm@rpi.edu, songm@rpi.edu, jiangb@rpi.edu, dengw2@rpi.edu, luoq@rpi.edu Subject: Another round of CCG Excellence Awards is coming! (Graduate Student Travel to ACS) Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Announcement: ===> Applications for CCG Excellence Awards are now being accepted for the Spring 2001 ACS Meeting in San Diego, CA. <=== The ACS Division of Computers in Chemistry and the Chemical Computing Group (CCG) are again pleased to announce a competition for five Graduate Student Travel Awards for ACS meeting attendance. Each of the five awards will reimburse up to $1,150 of travel and local expenses associated with attending the 221st ACS National Meeting in San Diego, CA being held during the first week of April, 2001. Preference will be given to students presenting papers or posters in one of the COMP sessions. Graduate Students may apply for the CCG Excellence award by submitting an abstract of their poster or presentation to me along with a personal statement, a letter of support from their research advisor and a one to two page CV. The awardees will be chosen by members of the COMP Executive Committee on the basis of the quality and significance of the research to be presented, the strength of the supporting materials, and standard ACS/COMP award criteria. Please submit materials to: Prof. Curt M. Breneman RPI Department of Chemistry 110 8th St Troy, NY 12180 USA Thanks for your interest. Curt Breneman RPI Chemistry COMP Treasurer Original Posting: F2000 ----------------------------------------------------------------- CHEMICAL COMPUTING GROUP ESTABLISHES STUDENT EXCELLENCE AWARDS IN CONJUNCTION WITH THE COMP DIVISION OF ACS For further information and/or to apply for the award please contact: Professor Curt M. Breneman COMP Treasurer and Fundraising Coordinator RPI Department of Chemistry brenec@rpi.edu (518) 276-2678 - phone / (518) 276-4045 - fax. ------------------------------------------------------------------- From chemistry-request@server.ccl.net Wed Nov 8 15:44:52 2000 Received: from vera.dpo.uab.edu (vera.dpo.uab.edu [138.26.1.112]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA17156 for ; Wed, 8 Nov 2000 15:44:51 -0500 Received: from asc.edu (ZeeMan.tucc.uab.edu) by vera.dpo.uab.edu (LSMTP for Windows NT v1.1b) with SMTP id <0.FDB5F6CF@vera.dpo.uab.edu>; Wed, 8 Nov 2000 14:44:50 -0600 Message-ID: <3A09BAA8.1EBA5D68@asc.edu> Date: Wed, 08 Nov 2000 14:42:16 -0600 From: "Mark A. Zottola" X-Mailer: Mozilla 4.76 [en] (Win95; U) X-Accept-Language: en MIME-Version: 1.0 To: CHEMISTRY@ccl.net Subject: Zr Parameters in Gaussian? Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Does Gaussian 's implementation of PM3 contain parameters for Zirconium? I have been trying to do some sample calculations in Gaussian98 for Zr and get the following error : NBasis= 4 NMin= 9 so simple Huckel guess is impossible. Error termination via Lnk1e in /usr/local/apps/g98.a7sv1/g98/l401.exe. Is this error message Gaussian's obtuse way of saying it does not have parameters for Zr? -- Mark A. Zottola Alabama Research and Education Network 119 Rust Research Center Computer Sciences Corporation 1801 University Boulevard VOICE: (205) 934 - 3893 Birmingham AL 35294 E-MAIL: asnmaz01@asc.edu From chemistry-request@server.ccl.net Wed Nov 8 15:50:25 2000 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA17202 for ; Wed, 8 Nov 2000 15:50:25 -0500 Received: from mailhost.msi.com (fire.msi.com [146.202.0.242]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with ESMTP id PAA27938 for ; Wed, 8 Nov 2000 15:50:23 -0500 (EST) Received: (from daemon@localhost) by mailhost.msi.com (980427.SGI.8.8.8/970903.SGI.AUTOCF) id MAA26794 for ; Wed, 8 Nov 2000 12:51:58 -0800 (PST) Received: from unknown(146.202.11.79) by mailhost.msi.com via smap (V2.0) id xma026783; Wed, 8 Nov 00 12:51:42 -0800 Message-Id: <5.0.0.25.2.20001108094942.00ad7eb0@146.202.6.130> X-Sender: dgregory@146.202.6.130 X-Mailer: QUALCOMM Windows Eudora Version 5.0 Date: Wed, 08 Nov 2000 12:44:33 -0800 To: chemistry@ccl.net (Comp. Chem. List) From: Don Gregory Subject: Re: CCL:Diazo dyes in CHARMM In-Reply-To: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Hi Marcin, Your question is one that MSI often asked. The essense of what you are asking, is "how transferrable are these prameters (between the MSI/Quanta/CHARMm force-field [Momany & Rone], and the academic CHARMM22 force-field)?" Transferrability is a common, but I think poorly understood, concept in empirical force-field usage. In the most narrow sense, it is meant to refer to the ability to optimize on small model compounds, but then use the optimized parameters is other chemical species. In this way, one can develop parameters by doing high-level QM calculations on 'peptide-like' models, and the assumption/belief is that these parameters will give reasonable results when used to calculate protein characteristics. This usage of 'transferrability' is one that I think is a reasonable one. This concept can quite easily be extended, however, to the next level, and that is your question here. "Can parameters optimized for one force-field, be used in another force-field?" The answer to that is ...... proceed with caution! My advice is to look at the other parameters you will be using, i.e. those that apply to the protein in this case, in both force-fields. If they are not too dissimilar (you have to decide) then you may feel comfortable with this level of approximation. As always, of course, an explicit description of the origin of all parameters used (even to the extent of saying 'from Quanta's Parramater Chooser') is extremely importnant. Hope this helps! DG At 06:01 PM 11/8/00 +0100, you wrote: >Dear CCLers, >I want to simulate diazo dyes and their interactions with proteins in >CHARMM using academic, all atom forcefield. I built RTF file for my >diazo dye and chose atom types that I thought fitted 'well' with my >structure. However, I could not find proper atom types for sulphur in >SO3H- and nitrogen in -N=N- and so on. Moreover, there were 'missing >paramters'. So I used Quanta and got all atom types and >missing paramters given by Parameter Chooser. However, these atom types >and parameters belong to QUANTA_CHARMm forcefield. > >Is it safe to take them to academic par22 FF? I'm afraid it isn't. >Maybe someone has parameters for diazo dyes in par22, or maybe someone can >tell me how to transform >parameters from CHARMm (Quanta) to CHARMM (academic)? >How can I get parameters in another way? >I know I'm asking a generic question, so I'd be also grateful if you >could refer me to a good book/article about parametrization process for >small ligand molecules. >Thanks in advance >Marcin Krol > > >-= 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 Dr. Don Gregory (dgregory@msi.com) CHARMm Product Marketing Manager Molecular Simulations Inc. (http://www.msi.com) 9685 Scranton Rd. San Diego, CA 92121 Office Phone: (858) 799-5331 Mobile Phone: (619) 200-3613 From chemistry-request@server.ccl.net Wed Nov 8 17:01:14 2000 Received: from thorin.eas.asu.edu (thorin.eas.asu.edu [149.169.26.91]) by server.ccl.net (8.8.7/8.8.7) with SMTP id RAA17626 for ; Wed, 8 Nov 2000 17:01:13 -0500 Received: by thorin.eas.asu.edu id AA02593; Wed, 8 Nov 2000 15:01:10 -0700 Date: Wed, 8 Nov 2000 15:01:09 -0700 (MST) From: Donghai Sun To: chemistry@ccl.net Subject: Transition State Calculation with Gaussian Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I want to use gaussian to calculate the transition state structure for Cu compound, like the zeolite ZCu adsorbed with NH3 or NOx species. What the basis set should I use in the input file? What method should I choose in the calculation? Would you please give me more positive suggestion on such calculation? Thanks for your kind favor! donghai Donghai Sun Department of Bio, Chemical and Materials Engineering Arizona State University Tel: 480-965-8509 (O) (FAX) 480-446-8666 (H) Email: sun@thorin.eas.asu.edu From chemistry-request@server.ccl.net Wed Nov 8 20:51:52 2000 Received: from panic.csc.cuhk.edu.hk (root@panic.csc.cuhk.edu.hk [137.189.6.35]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id UAA18517 for ; Wed, 8 Nov 2000 20:51:50 -0500 Received: from l (dialup2-019.csc.cuhk.edu.hk [137.189.209.19]) by panic.csc.cuhk.edu.hk (8.9.3/8.9.3) with SMTP id JAA05568 for ; Thu, 9 Nov 2000 09:51:42 +0800 (HKT) Message-ID: <001901c049ef$b0fa9f00$13d1bd89@l> Reply-To: "Kiniu WONG Kin-Yiu" From: "Kiniu WONG Kin-Yiu" To: Subject: calculation of excitation energies for some elements in Group II Date: Thu, 9 Nov 2000 09:49:29 +0800 Organization: Physics CUHK MIME-Version: 1.0 Content-Type: text/plain; charset="big5" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 Dear all, Recently, I've used Gaussian to calculate excitation energies for some elements in Group II. However, I didn't get a satisfactory result with the standard CIS method. On the other hand, using the same basis function, good results could be obtained by finding the difference of energies between two different multiplicity of the same atom (multiplicity= 1 and = 3). I have calculated the excitation energies for Be, Mg and Ca. The highlight of input and output is attached below. My question is why the results obtained by the difference of energies between two different multiplicity atoms are much better than that computed by CIS method? Is the CIS the standard method to calculate excitation energies? Are there any other references about computation of excitation energies? Any kind of help is welcome! I know CASSCF can calculate excitation energies in high accuracy, so how can I use CASSCF to give excellent results for theses three atoms (Be, Mg and Ca)? I'm a beginner to computational chemistry, any helps are useful. Thank you very much in advance. ---- Beryllium: experimental excitation energy = 2.725eV, input1 : #P UCIS(50-50,Nstates=10)/6-31G(d) SCF=(Tight, direct,MaxCycle=128) Beryllium excitation energy 0 1 Be output1: 1st excitation energy = 1.6551eV, error = 39% input2: #P UCID/6-31G(d) SCF=(Tight, direct, MaxCycle=128) Beryllium excitation energy 0 1 Be output2: CID = -14.6131258 H input3: #P UCID/6-31G(d) SCF=(Tight, direct, MaxCycle=128) Beryllium excitation energy 0 3 Be output3: CID = -14.5108488 H ==> excitation energy = output3 - output2 = 2.78eV, error = 2% Magnesium: experimental excitation energy = 2.71eV, input1 : #P UCIS(50-50,Nstates=10)/6-31G(d) SCF=(Tight, direct,MaxCycle=128) Magnesium excitation energy 0 1 Mg output1: 1st excitation energy = 1.8747eV, error = 45% input2: #P UCID/6-31G(d) SCF=(Tight, direct, MaxCycle=128) Magnesium excitation energy 0 1 Mg output2: CID = -199.6289369H input3: #P UCID/6-31G(d) SCF=(Tight, direct, MaxCycle=128) Magnesium excitation energy 0 3 Mg output3: CID = -199.5323995H ==> excitation energy = output3 - output2 = 2.63eV, error = 3% Calcium: experimental excitation energy = 1.88eV, input1 : #P UCIS(50-50,Nstates=10)/6-31G(d) SCF=(Tight, direct,MaxCycle=128) Calcium excitation energy 0 1 Ca output1: 1st excitation energy = 1.0897eV, error = 42% input2: #P UCID/6-31G(d) SCF=(Tight, direct, MaxCycle=128) Calcium excitation energy 0 1 Ca output2: CID = -36.2418938H input3: #P UCID/6-31G(d) SCF=(Tight, direct, MaxCycle=128) Calcium excitation energy 0 3 Ca output3: CID = -36.1760326H ==> excitation energy = output3 - output2 = 1.79eV, error = 5% Regards, Kiniu ---- Kiniu WONG Kin-Yiu Undergraduate student Department of Physics The Chinese University of Hong Kong Email: kiniu@cuhk.edu.hk or kyiwong@phy.cuhk.edu.hk From chemistry-request@server.ccl.net Wed Nov 8 22:01:40 2000 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id WAA18800 for ; Wed, 8 Nov 2000 22:01:40 -0500 Received: from mercury.chem.csiro.au (mercury.chem.CSIRO.AU [138.194.50.8]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with ESMTP id WAA04105 for ; Wed, 8 Nov 2000 22:01:33 -0500 (EST) Received: from [138.194.46.107] (cpr-46107.chem.csiro.au [138.194.46.107]) by mercury.chem.csiro.au (8.9.3/8.9.3) with ESMTP id OAA14920; Thu, 9 Nov 2000 14:01:11 +1100 (EST) X-Sender: win097@clex1.vic.csiro.au Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 9 Nov 2000 14:01:10 +1100 To: CHMINF-L@LISTSERV.INDIANA.EDU, chemistry@ccl.net From: "Dr. Dave Winkler" Subject: Major chemistry conference in Brisbane July 2001 The Royal Australian Chemical Institute is hosting the IUPAC World Chemistry Congress in Brisbane, Australia, in July 2001. This meeting comprises the IUPAC congress, the AIMECS01 medicinal chemistry meeting of the Asian Federation of Medicinal Chemistry, and the 9th Asian Chemical Congress. The Congress web site, http://www.ccm.com.au/wcc, contains detailed information on the program, speakers etc and the First Circular can be downloaded as a PDF. Please register by 3 December for 'early bird' discount. Convention speakers include: Yuan T. Lee, President, Academia Sinica, Taiwan Jean-Marie Lehn, University of Strasbourg, France Richard Lerner, CEO, Skaggs Institute, Scripps Research Institute, USA F. Sherwood Rowland, University of California, Irvine USA Sir John Meurig Thomas, Royal Institution, UK Cheers, Dave Dr. David A. Winkler Email: dave.winkler@molsci.csiro.au Senior Principal Research Scientist Voice: 61-3-9545-2477 CSIRO Molecular Science Fax: 61-3-9545-2446 Private Bag 10,Clayton South MDC 3169 http://www.csiro.au Australia http://www.molsci.csiro.au From chemistry-request@server.ccl.net Thu Nov 9 05:03:33 2000 Received: from gamma.dou.dk (gamma.dou.dk [130.225.130.7]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA02482 for ; Thu, 9 Nov 2000 05:03:33 -0500 Received: from localhost (frj@localhost) by gamma.dou.dk (8.9.3/8.9.3) with ESMTP id JAA07571 for ; Thu, 9 Nov 2000 09:58:31 +0100 (MET) Date: Thu, 9 Nov 2000 09:58:30 +0100 (MET) From: Frank Jensen To: chemistry@ccl.net Subject: G94 - SUN Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I would be interested in knowing if anybody has a working SUN version of Gaussian-94 still around. I do have both Gaussian-98 and -94, but they are giving me some discrepancies in the SGI version. I have G98 running on a SUN machine, but the makefile for G94 is set up for SUN-OS 5 and compiler version 2, and I don't have access to that kind of vintage machines. Thus I would be interested in either a working set of executables for G94, or a G94 makefile for the more recent SUN-OS (7/8) and compilers (5/6). Frank -------------------------------------------------- | Frank Jensen, Department of Chemistry | | SDU Odense University, DK-5230 Odense, Denmark | | FAX +45 66 15 87 80 , Voice +45 65 50 25 07 | | http://bogense.chem.ou.dk/~frj | -------------------------------------------------- From chemistry-request@server.ccl.net Thu Nov 9 04:13:06 2000 Received: from gpo.munich.msi-eu.com (cam.msi-eu.com [192.190.183.254]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA02306 for ; Thu, 9 Nov 2000 04:13:05 -0500 Received: from woernitz.munich.msi-eu.com (woernitz.munich.msi-eu.com [172.29.64.178]) by gpo.munich.msi-eu.com (8.9.3/8.9.3/Debian 8.9.3-21) with ESMTP id JAA20165; Thu, 9 Nov 2000 09:06:00 +0100 Received: (from jxh@localhost) by woernitz.munich.msi-eu.com (8.8.8/8.8.8) id JAA29309; Thu, 9 Nov 2000 09:05:58 +0100 (MET) From: "Joerg-Ruediger Hill" Message-Id: <10011090905.ZM29305@woernitz.munich.msi-eu.com> Date: Thu, 9 Nov 2000 09:05:53 +0100 X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: lutz.ehrlich@lionbioscience.com Subject: Re: CCL:RevCompChem bibtex style? Cc: CHEMISTRY@server.ccl.net Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="PART-BOUNDARY=.110011090905.ZM29305.munich.msi-eu.com" --PART-BOUNDARY=.110011090905.ZM29305.munich.msi-eu.com Content-Description: Text Content-Type: text/plain ; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable X-Zm-Decoding-Hint: mimencode -q -u Hi, > could somebody point me to a BIBTEX style file that complies to > the reference style for 'Reviews in Computational Chemistry' ? > If you know of a solution (even a half-baked one) I would appreciate if= > you emailed me personally. Attached you'll find the BIBTEX style file I have created for Reviews in Computational Chemistry. Best Regards J=F6rg-R=FCdiger Hill -- = -------------------------------------------------------------------------= ----- Dr. Joerg-Ruediger Hill | Phone +49 89 61459-413 | The opinions express= ed in Molecular Simulations | Fax +49 89 61459-400 | this message are my p= erso- Inselkammerstrasse 1 | E-mail jxh@msi-eu.com | nal opinions and no = offi- D-82008 Unterhaching | | cal statements of Mo= lecu- Germany | http://www.msi.com/ | lar Simulations Inc. -------------------------------------------------------------------------= ----- --PART-BOUNDARY=.110011090905.ZM29305.munich.msi-eu.com X-Zm-Content-Name: revcompchem.bst Content-Description: Text Content-Type: text/plain ; name="revcompchem.bst" ; charset=us-ascii % BibTeX bibliography style `revcompchem' for Reviews in Computational Chemistry % 4/28/98 Joerg-R. Hill % % version 0.99a for BibTeX versions 0.99a or later, LaTeX version 2.09. % Copyright (C) 1985, all rights reserved. % Copying of this file is authorized only if either % (1) you make absolutely no changes to your copy, including name, or % (2) if you do make changes, you name it something other than % btxbst.doc, plain.bst, unsrt.bst, alpha.bst, and abbrv.bst. % This restriction helps ensure that all standard styles are identical. % The file btxbst.doc has the documentation for this style. % % Fixed article, book references 11/10/92---CLF ENTRY { address author booktitle chapter edition editor howpublished institution journal key month note number organization pages publisher school series title type volume year } {} { label } INTEGERS { output.state before.all mid.sentence after.sentence after.block after.item author.or.editor } FUNCTION {init.state.consts} { #0 'before.all := #1 'mid.sentence := #2 'after.sentence := #3 'after.block := #4 'after.item := } FUNCTION {add.semicolon} { duplicate$ #-1 #1 substring$ "}" = { #-2 #1024 substring$ ";} " * } { "; " * } if$ } STRINGS { s t } FUNCTION {output.nonnull} { 's := output.state mid.sentence = { ", " * write$ } { output.state after.block = { add.semicolon write$ newline$ "\newblock " write$ } { output.state before.all = 'write$ { output.state after.item = { " " * write$ } { add.period$ " " * write$ } if$ } if$ } if$ mid.sentence 'output.state := } if$ s } FUNCTION {output} { duplicate$ empty$ 'pop$ 'output.nonnull if$ } FUNCTION {output.check} { 't := duplicate$ empty$ { pop$ "empty " t * " in " * cite$ * warning$ } 'output.nonnull if$ } FUNCTION {output.bibitem} { newline$ "\bibitem{" write$ cite$ write$ "}" write$ newline$ "" before.all 'output.state := } FUNCTION {fin.entry} { add.period$ write$ newline$ } FUNCTION {new.block} { output.state before.all = 'skip$ { after.block 'output.state := } if$ } FUNCTION {new.sentence} { output.state after.block = 'skip$ { output.state before.all = 'skip$ { after.sentence 'output.state := } if$ } if$ } FUNCTION {new.item} { duplicate$ empty$ { skip$ } { output.state mid.sentence = { after.item 'output.state := } { skip$ } if$ } if$ } FUNCTION {not} { { #0 } { #1 } if$ } FUNCTION {and} { 'skip$ { pop$ #0 } if$ } FUNCTION {or} { { pop$ #1 } 'skip$ if$ } FUNCTION {new.block.checka} { empty$ 'skip$ 'new.block if$ } FUNCTION {new.block.checkb} { empty$ swap$ empty$ and 'skip$ 'new.block if$ } FUNCTION {new.sentence.checka} { empty$ 'skip$ 'new.sentence if$ } FUNCTION {new.sentence.checkb} { empty$ swap$ empty$ and 'skip$ 'new.sentence if$ } FUNCTION {new.item.checka} { empty$ 'skip$ 'new.item if$ } FUNCTION {field.or.null} { duplicate$ empty$ { pop$ "" } 'skip$ if$ } FUNCTION {emphasize} { duplicate$ empty$ { pop$ "" } { "{\em " swap$ * "}" * } if$ } FUNCTION {boldface} { duplicate$ empty$ { pop$ "" } { "{\bf " swap$ * "}" * } if$ } FUNCTION {paren} { duplicate$ empty$ { pop$ "" } { "(" swap$ * ")" * } if$ } INTEGERS { nameptr namesleft numnames } FUNCTION {format.names} { 's := #1 'nameptr := s num.names$ 'numnames := numnames 'namesleft := { namesleft #0 > } { s nameptr "{f.~}{vv~}{ll}{, jj}" format.name$ 't := nameptr #1 > { namesleft #1 > { ", " * t * } { numnames #2 > { "," * } 'skip$ if$ t "others" = { " et~al." * } { " and " * t * } if$ } if$ } 't if$ nameptr #1 + 'nameptr := namesleft #1 - 'namesleft := } while$ } FUNCTION {format.authors} { author empty$ { "" } { #1 'author.or.editor := author format.names } if$ } FUNCTION {format.editors} { editor empty$ { "" } { #2 'author.or.editor := editor format.names editor num.names$ #1 > { ", Eds." * } { ", Ed." * } if$ } if$ } FUNCTION {format.title} { title empty$ { "" } { title "t" change.case$ } if$ } FUNCTION {n.dashify} { 't := "" { t empty$ not } { t #1 #1 substring$ "-" = { t #1 #2 substring$ "--" = not { "--" * t #2 global.max$ substring$ 't := } { { t #1 #1 substring$ "-" = } { "-" * t #2 global.max$ substring$ 't := } while$ } if$ } { t #1 #1 substring$ * t #2 global.max$ substring$ 't := } if$ } while$ } FUNCTION {format.date} { year empty$ { month empty$ { "" } { "there's a month but no year in " cite$ * warning$ month } if$ } { month empty$ { year paren } { month " " * year paren } if$ } if$ } FUNCTION {format.bdate} { year empty$ { "there's no year in " cite$ * warning$ } 'year if$ } FUNCTION {format.btitle} { title emphasize } FUNCTION {tie.or.space.connect} { duplicate$ text.length$ #3 < { "~" } { " " } if$ swap$ * * } FUNCTION {either.or.check} { empty$ 'pop$ { "can't use both " swap$ * " fields in " * cite$ * warning$ } if$ } FUNCTION {format.bvolume} { volume empty$ { "" } { "Vol. " volume tie.or.space.connect series empty$ 'skip$ { " of " * series emphasize * } if$ "volume and number" number either.or.check } if$ } FUNCTION {format.number.series} { volume empty$ { number empty$ { series field.or.null } { output.state mid.sentence = { "number" } { "Number" } if$ number tie.or.space.connect series empty$ { "there's a number but no series in " cite$ * warning$ } { " in " * series * } if$ } if$ } { "" } if$ } FUNCTION {format.edition} { edition empty$ { "" } { output.state mid.sentence = { edition "l" change.case$ " ed." * } { edition "t" change.case$ " ed." * } if$ } if$ } INTEGERS { multiresult } FUNCTION {multi.page.check} { 't := #0 'multiresult := { multiresult not t empty$ not and } { t #1 #1 substring$ duplicate$ "-" = swap$ duplicate$ "," = swap$ "+" = or or { #1 'multiresult := } { t #2 global.max$ substring$ 't := } if$ } while$ multiresult } FUNCTION {format.pages} { pages empty$ { "" } { pages multi.page.check { "pages" pages n.dashify tie.or.space.connect } { "page" pages tie.or.space.connect } if$ } if$ } FUNCTION {format.vol.num.pages} { volume boldface field.or.null number empty$ 'skip$ { "(" number * ")" * * volume empty$ { "there's a number but no volume in " cite$ * warning$ } 'skip$ if$ } if$ pages empty$ 'skip$ { duplicate$ empty$ { pop$ format.pages } { ", " * pages n.dashify * } if$ } if$ } FUNCTION {format.chapter.pages} { chapter empty$ 'format.pages { type empty$ { "chapter" } { type "l" change.case$ } if$ chapter tie.or.space.connect pages empty$ 'skip$ { ", " * format.pages * } if$ } if$ } FUNCTION {format.in.ed.booktitle} { booktitle empty$ { "" } { editor empty$ { "in " booktitle emphasize * } { "in " format.editors * ", " * booktitle emphasize * } if$ } if$ } FUNCTION {format.in.booktitle.ed} { booktitle empty$ { "" } { editor empty$ { "in " booktitle emphasize * } { "in " booktitle emphasize * ", " * format.editors * } if$ } if$ } FUNCTION {format.pub.address} { publisher empty$ { "" } { address empty$ { publisher } { publisher ", " * address *} if$ } if$ } FUNCTION {empty.misc.check} { author empty$ title empty$ howpublished empty$ month empty$ year empty$ note empty$ and and and and and { "all relevant fields are empty in " cite$ * warning$ } 'skip$ if$ } FUNCTION {format.thesis.type} { type empty$ 'skip$ { pop$ type "t" change.case$ } if$ } FUNCTION {format.tr.number} { type empty$ { "Technical Report" } 'type if$ number empty$ { "t" change.case$ } { number tie.or.space.connect } if$ } FUNCTION {format.article.crossref} { key empty$ { journal empty$ { "need key or journal for " cite$ * " to crossref " * crossref * warning$ "" } { "In {\em " journal * "\/}" * } if$ } { "In " key * } if$ " \cite{" * crossref * "}" * } FUNCTION {format.crossref.editor} { editor #1 "{vv~}{ll}" format.name$ editor num.names$ duplicate$ #2 > { pop$ " et~al." * } { #2 < 'skip$ { editor #2 "{ff }{vv }{ll}{ jj}" format.name$ "others" = { " et~al." * } { " and " * editor #2 "{vv~}{ll}" format.name$ * } if$ } if$ } if$ } FUNCTION {format.book.crossref} { volume empty$ { "empty volume in " cite$ * "'s crossref of " * crossref * warning$ "In " } { "Volume" volume tie.or.space.connect " of " * } if$ editor empty$ editor field.or.null author field.or.null = or { key empty$ { series empty$ { "need editor, key, or series for " cite$ * " to crossref " * crossref * warning$ "" * } { "{\em " * series * "\/}" * } if$ } { key * } if$ } { format.crossref.editor * } if$ " \cite{" * crossref * "}" * } FUNCTION {format.incoll.inproc.crossref} { editor empty$ editor field.or.null author field.or.null = or { key empty$ { booktitle empty$ { "need editor, key, or booktitle for " cite$ * " to crossref " * crossref * warning$ "" } { "in {\em " booktitle * "\/}" * } if$ } { "in " key * } if$ } { "in " format.crossref.editor * } if$ " \cite{" * crossref * "}" * } FUNCTION {article} { output.bibitem format.authors "author" output.check crossref missing$ { journal emphasize "journal" output.check format.vol.num.pages output new.item format.date "year" output.check new.sentence format.title "title" output.check } { format.article.crossref output.nonnull format.pages output } if$ fin.entry } FUNCTION {book} { output.bibitem author empty$ { format.editors "author and editor" output.check } { format.authors output.nonnull crossref missing$ { "author and editor" editor either.or.check } 'skip$ if$ } if$ format.btitle "title" output.check crossref missing$ { format.bvolume output format.number.series output format.pub.address "publisher" output.check } { format.book.crossref output.nonnull } if$ format.edition output format.bdate "year" output.check new.block fin.entry } FUNCTION {booklet} { output.bibitem format.authors output new.item format.title "title" output.check howpublished address new.block.checkb howpublished output address output format.date output new.block fin.entry } FUNCTION {inbook} { output.bibitem author empty$ { format.editors "author and editor" output.check } { format.authors output.nonnull } if$ format.in.booktitle.ed "booktitle" output.check crossref missing$ { format.pub.address "publisher" output.check format.bdate "year" output.check new.block format.bvolume output new.block format.chapter.pages "chapter and pages" output.check new.block format.number.series output } { format.chapter.pages "chapter and pages" output.check new.block format.book.crossref output.nonnull } if$ format.edition output title empty$ { "need title for " cite$ * warning$ } { format.title output } if$ new.block fin.entry } FUNCTION {incollection} { output.bibitem format.authors "author" output.check new.item crossref missing$ { format.in.booktitle.ed "booktitle" output.check format.bvolume output format.number.series output new.block format.pub.address "publisher" output.check format.edition output format.bdate "year" output.check new.block format.chapter.pages output } { format.incoll.inproc.crossref output.nonnull format.chapter.pages output } if$ new.block fin.entry } FUNCTION {inproceedings} { output.bibitem format.authors "author" output.check new.item crossref missing$ { format.in.ed.booktitle "booktitle" output.check format.bvolume output format.number.series output format.pages output address empty$ { organization publisher new.sentence.checkb organization output publisher output format.bdate "year" output.check } { address output.nonnull format.bdate "year" output.check new.sentence organization output publisher output } if$ } { format.incoll.inproc.crossref output.nonnull format.pages output } if$ new.block fin.entry } FUNCTION {conference} { inproceedings } FUNCTION {manual} { output.bibitem format.title "title" output.check new.sentence author empty$ { organization empty$ 'skip$ { organization output.nonnull address output } if$ } { format.authors output.nonnull new.item } if$ author empty$ { organization empty$ { address new.block.checka address output } 'skip$ if$ } { organization address new.block.checkb organization output address output } if$ format.edition output format.date output new.block fin.entry } FUNCTION {mastersthesis} { output.bibitem format.authors "author" output.check new.item format.title "title" output.check new.item "Master's thesis" format.thesis.type output.nonnull school "school" output.check address output format.date "year" output.check new.block fin.entry } FUNCTION {misc} { output.bibitem format.authors output format.title output howpublished new.item.checka howpublished output format.bdate output new.block fin.entry empty.misc.check } FUNCTION {phdthesis} { output.bibitem format.authors "author" output.check new.item format.btitle "title" output.check new.item "PhD thesis" format.thesis.type output.nonnull school "school" output.check address output format.date "year" output.check new.block fin.entry } FUNCTION {proceedings} { output.bibitem editor empty$ { organization output } { format.editors output.nonnull new.item } if$ new.block format.btitle "title" output.check format.bvolume output format.number.series output address empty$ { editor empty$ { publisher new.sentence.checka } { organization publisher new.sentence.checkb organization output } if$ publisher output format.date "year" output.check } { address output.nonnull format.date "year" output.check new.sentence editor empty$ 'skip$ { organization output } if$ publisher output } if$ new.block fin.entry } FUNCTION {techreport} { output.bibitem format.authors "author" output.check new.item format.title "title" output.check new.item format.tr.number output.nonnull institution "institution" output.check address output format.date "year" output.check new.block fin.entry } FUNCTION {unpublished} { output.bibitem format.authors "author" output.check new.item % format.title "title" output.check new.item note "note" output.check format.date output fin.entry } FUNCTION {default.type} { misc } MACRO {jan} {"January"} MACRO {feb} {"February"} MACRO {mar} {"March"} MACRO {apr} {"April"} MACRO {may} {"May"} MACRO {jun} {"June"} MACRO {jul} {"July"} MACRO {aug} {"August"} MACRO {sep} {"September"} MACRO {oct} {"October"} MACRO {nov} {"November"} MACRO {dec} {"December"} MACRO {bbrc} {"Biochem. Biophys. Res. Commun."} MACRO {jacs} {"J. Amer. Chem. Soc."} MACRO {jbc} {"J. Biol. Chem."} MACRO {pnas} {"Proc. Natl. Acad. Sci."} MACRO {jmb} {"J. Mol. Biol."} MACRO {embo} {"EMBO J."} MACRO {tibs} {"Trends Biochem. Sci."} MACRO {protsfg} {"Proteins: Struct. Func. Gen."} MACRO {ieeetcad} {"IEEE Transactions on Computer-Aided Design of Integrated Circuits"} MACRO {ipl} {"Information Processing Letters"} MACRO {jacm} {"Journal of the ACM"} MACRO {jcss} {"Journal of Computer and System Sciences"} MACRO {scp} {"Science of Computer Programming"} MACRO {sicomp} {"SIAM Journal on Computing"} MACRO {tocs} {"ACM Transactions on Computer Systems"} MACRO {tods} {"ACM Transactions on Database Systems"} MACRO {tog} {"ACM Transactions on Graphics"} MACRO {toms} {"ACM Transactions on Mathematical Software"} MACRO {toois} {"ACM Transactions on Office Information Systems"} MACRO {toplas} {"ACM Transactions on Programming Languages and Systems"} MACRO {tcs} {"Theoretical Computer Science"} READ STRINGS { longest.label } INTEGERS { number.label longest.label.width } FUNCTION {initialize.longest.label} { "" 'longest.label := #1 'number.label := #0 'longest.label.width := } FUNCTION {longest.label.pass} { number.label int.to.str$ 'label := number.label #1 + 'number.label := label width$ longest.label.width > { label 'longest.label := label width$ 'longest.label.width := } 'skip$ if$ } EXECUTE {initialize.longest.label} ITERATE {longest.label.pass} FUNCTION {begin.bib} { preamble$ empty$ 'skip$ { preamble$ write$ newline$ } if$ "\begin{thebibliography}{" longest.label * "}" * write$ newline$ } EXECUTE {begin.bib} EXECUTE {init.state.consts} ITERATE {call.type$} FUNCTION {end.bib} { newline$ "\end{thebibliography}" write$ newline$ } EXECUTE {end.bib} --PART-BOUNDARY=.110011090905.ZM29305.munich.msi-eu.com-- From chemistry-request@server.ccl.net Thu Nov 9 06:36:18 2000 Received: from lgsx01.lg.ehu.es (lgsx01.lg.ehu.es [158.227.2.34]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA02957 for ; Thu, 9 Nov 2000 06:36:17 -0500 Received: from [158.227.47.250] (lcmxfy.lc.ehu.es [158.227.47.250]) by lgsx01.lg.ehu.es (8.11.0/8.11.0) with ESMTP id eA9AV7b06713; Thu, 9 Nov 2000 11:31:07 +0100 (MET) Message-Id: <200011091031.eA9AV7b06713@lgsx01.lg.ehu.es> X-Mailer: Microsoft Outlook Express Macintosh Edition - 4.5 (0410) Date: Thu, 09 Nov 2000 11:33:28 +0100 Subject: Change basis set in G98 From: "Pablo Vitoria" To: fan@mail.chem.tamu.edu, CCL Mime-version: 1.0 X-Priority: 3 Content-type: text/plain; charset="US-ASCII" Content-transfer-encoding: 7bit Hi Huajun, You can use guess=read with DFT and HF methods when changing basis set, geometry of the molecule and even if you add some atoms to your molecule, for example calculating a dimer after the monomer as long as you keep the order of the atoms. (It works!) In fact, I use this method very often in calculations involving transition metal elements, which have convergence problems. I run a calculation with a "small" basis set, faster and easier to converge, check if it converged to the correct electronic state, and then I run a final calculation with a bigger basis set using guess=read. I am not an expert in G98 internals, but as far as I know, the program reads the orbitals from the checkpoint file, and then proyects them to the new basis set. Best regards Pablo ----------------------------------------- Pablo Vitoria Garcia Dpto. Quimica Inorganica, Facultad de Ciencias Universidad del Pais Vasco (UPV/EHU) Aptdo. 644 E-48080 Spain Phone: +34 94 6015529/5522 Fax: +34 94 4648500 ----------------------------------------- From chemistry-request@server.ccl.net Thu Nov 9 10:13:08 2000 Received: from fep6.online.sh.cn ([202.96.209.79]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA04711 for ; Thu, 9 Nov 2000 10:13:07 -0500 Received: from cadd ([61.151.177.42]) by fep6.online.sh.cn (InterMail vM.4.01.02.39 201-229-119-122) with SMTP id <20001109140817.HXGC450.fep6.online.sh.cn@cadd> for ; Thu, 9 Nov 2000 22:08:17 +0800 Date: Thu, 9 Nov 2000 22:10:21 +0800 From: Ji Hai-tao To: "chemistry@ccl.net" Subject: conformer population Organization: School of pharmacy, second military medical university X-mailer: FoxMail 2.1 [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: 7bit Message-Id: <20001109140817.HXGC450.fep6.online.sh.cn@cadd> Hi,CCLers! I want to calculate the population of some conformer.I know that Boltzmann law is needed.As the conformers have been calculated by ab initio Single Point Energy calculation.but I don't know if T=298K, R=8.31.Whether I should make frequency calculation so that I can get some thermodynamic value?Can the single point energy be used directly? then what are the values for R and T? Song Yunlong songyunlong@263.net From chemistry-request@server.ccl.net Thu Nov 9 10:23:31 2000 Received: from fep1.mail.online.sh.cn ([202.96.209.74]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA04771 for ; Thu, 9 Nov 2000 10:23:30 -0500 Received: from cadd ([61.151.177.42]) by fep1.mail.online.sh.cn (InterMail vM.4.01.02.39 201-229-119-122) with SMTP id <20001109141843.EOBR541.fep1.mail.online.sh.cn@cadd> for ; Thu, 9 Nov 2000 22:18:43 +0800 Date: Thu, 9 Nov 2000 22:20:48 +0800 From: Ji Hai-tao To: "chemistry@ccl.net" Subject: help Organization: School of pharmacy, second military medical university X-mailer: FoxMail 2.1 [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: 7bit Message-Id: <20001109141843.EOBR541.fep1.mail.online.sh.cn@cadd> Hi,CCLers, I am performing conformational analysis on a drug molecule.I want to know the exact population of each conformer. I want to know how to calculation the conformation population analysis based on Boltzmann law? Can you supply me with the equation and make an explicit explanation of how to use it.Especially I use single point energy,am I need some correction so that T=298K ? From chemistry-request@server.ccl.net Thu Nov 9 11:09:21 2000 Received: from icaro.cti.unav.es (icaro.cti.unav.es [159.237.12.44]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA05099 for ; Thu, 9 Nov 2000 11:09:18 -0500 Received: from aldebaran.cti.unav.es (aldebaran.cti.unav.es [159.237.6.33]) by icaro.cti.unav.es (8.10.0/8.10.0) with ESMTP id eA9F3qV02410 for ; Thu, 9 Nov 2000 16:03:52 +0100 Received: from alumni.unav.es (baldomero.cti.unav.es [159.237.6.143]) by aldebaran.cti.unav.es (8.10.0/8.10.0) with ESMTP id eA9F3pT04270 for ; Thu, 9 Nov 2000 16:03:52 +0100 (MET) Sender: luis@unav.es Message-ID: <3A0ACA9C.DA361D84@alumni.unav.es> Date: Thu, 09 Nov 2000 16:02:36 +0000 From: Luis Gracia Organization: Unidad de Modelizacion Molecular (http://www.unav.es/organica/umm/)Dpto. Quimica Organica y Farmaceutica. Universidad de Navarra. X-Mailer: Mozilla 4.7 [en] (X11; I; IRIX 6.2 IP20) X-Accept-Language: en, es, de MIME-Version: 1.0 To: CCL list Subject: latex style for protein alignments Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, does anybody know about a latex style that manage protein alignments properly? Thanks in advance. Luis Gracia Valen Unidad de Modelizacion Molecular Dpto. Q. Organica y Farmaceutica Universidad de Navarra C/ Irunlarrea 1, Pamplona 31080, Espana Tel: +34 948 425600 ext 6292 o 6359 lgracia2@alumni.unav.es http://www.unav.es/organica/luis/ From chemistry-request@server.ccl.net Thu Nov 9 13:18:45 2000 Received: from cougar.it.wsu.edu (root@cougar.it.wsu.edu [134.121.1.10]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA05784 for ; Thu, 9 Nov 2000 13:18:43 -0500 Received: from ucis (ucis.chem.wsu.edu [134.121.41.180]) by cougar.it.wsu.edu (8.9.3/8.9.3) with SMTP id JAA11215; Thu, 9 Nov 2000 09:13:32 -0800 (PST) Message-ID: <007101c04a70$60566080$b4297986@chem.wsu.edu> From: "Phillip D. Matz" To: "Ji Hai-tao" , References: <20001109140817.HXGC450.fep6.online.sh.cn@cadd> Subject: Re: CCL:conformer population Date: Thu, 9 Nov 2000 09:13:27 -0800 MIME-Version: 1.0 Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.3018.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.3018.1300 Hello! The single-point energy should not be used to calculate Boltzmann distributions. The zero-point energy (ZPE) for each conformer must be included along with the single-point energies to be used in a Boltzmann population distribution model. This would not be the case if the ZPE were identical between conformers, unfortunately the ZPE is different between conformers so it must be included. Respectfully, Phillip Matz matz@wsunix.wsu.edu ----- Original Message ----- From: "Ji Hai-tao" To: Sent: Thursday, November 09, 2000 6:10 AM Subject: CCL:conformer population > Hi,CCLers! > I want to calculate the population of some conformer.I know that > Boltzmann law is needed.As the conformers have been calculated by > ab initio Single Point Energy calculation.but I don't know if T=298K, > R=8.31.Whether I should make frequency calculation so that I can get > some thermodynamic value?Can the single point energy be used directly? > then what are the values for R and T? > > > Song Yunlong > songyunlong@263.net > > > > -= 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 Thu Nov 9 13:13:43 2000 Received: from cougar.it.wsu.edu (root@cougar.it.wsu.edu [134.121.1.10]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA05746 for ; Thu, 9 Nov 2000 13:13:42 -0500 Received: from ucis (ucis.chem.wsu.edu [134.121.41.180]) by cougar.it.wsu.edu (8.9.3/8.9.3) with SMTP id JAA06870; Thu, 9 Nov 2000 09:08:33 -0800 (PST) Message-ID: <005601c04a6f$ae898fd0$b4297986@chem.wsu.edu> From: "Phillip D. Matz" To: "Kiniu WONG Kin-Yiu" , References: <001901c049ef$b0fa9f00$13d1bd89@l> Subject: Re: CCL:calculation of excitation energies for some elements in Group II Date: Thu, 9 Nov 2000 09:08:29 -0800 MIME-Version: 1.0 Content-Type: text/plain; charset="big5" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.3018.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.3018.1300 Hello! What you have stated is true. CIS uses the ground state optimized orbitals to determine the excited state wave function. Thus the orbitals are not optimized for the excited state like they are for the ground state. So if you perform a Hartree-Fock calculation on a triplet ground state, the energy will be less than the energy from a CIS(triplets) calculation because the Hartree-Fock calculation will optimize the orbitals for the triplet while the CIS will not. Respectfully, Phillip Matz ----- Original Message ----- From: "Kiniu WONG Kin-Yiu" To: Sent: Wednesday, November 08, 2000 5:49 PM Subject: CCL:calculation of excitation energies for some elements in Group II > Dear all, > > Recently, I've used Gaussian to calculate excitation energies for some > elements in Group II. However, I didn't get a satisfactory result with the > standard CIS method. On the other hand, using the same basis function, good > results could be obtained by finding the difference of energies between two > different multiplicity of the same atom (multiplicity= 1 and = 3). I have > calculated the excitation energies for Be, Mg and Ca. The highlight of > input and output is attached below. My question is why the results obtained > by the difference of energies between two different multiplicity atoms are > much better than that computed by CIS method? Is the CIS the standard > method to calculate excitation energies? Are there any other references > about computation of excitation energies? Any kind of help is welcome! > > I know CASSCF can calculate excitation energies in high accuracy, so how > can I use CASSCF to give excellent results for theses three atoms (Be, Mg > and Ca)? I'm a beginner to computational chemistry, any helps are useful. > Thank you very much in advance. > > ---- > Beryllium: > experimental excitation energy = 2.725eV, > > input1 : #P UCIS(50-50,Nstates=10)/6-31G(d) SCF=(Tight, > direct,MaxCycle=128) > Beryllium excitation energy > 0 1 > Be > output1: 1st excitation energy = 1.6551eV, error = 39% > > input2: #P UCID/6-31G(d) SCF=(Tight, direct, MaxCycle=128) > Beryllium excitation energy > 0 1 > Be > output2: CID = -14.6131258 H > > input3: #P UCID/6-31G(d) SCF=(Tight, direct, MaxCycle=128) > Beryllium excitation energy > 0 3 > Be > output3: CID = -14.5108488 H > > ==> excitation energy = output3 - output2 = 2.78eV, error = 2% > > > Magnesium: > experimental excitation energy = 2.71eV, > > input1 : #P UCIS(50-50,Nstates=10)/6-31G(d) SCF=(Tight, > direct,MaxCycle=128) > Magnesium excitation energy > 0 1 > Mg > output1: 1st excitation energy = 1.8747eV, error = 45% > > input2: #P UCID/6-31G(d) SCF=(Tight, direct, MaxCycle=128) > Magnesium excitation energy > 0 1 > Mg > output2: CID = -199.6289369H > > input3: #P UCID/6-31G(d) SCF=(Tight, direct, MaxCycle=128) > Magnesium excitation energy > 0 3 > Mg > output3: CID = -199.5323995H > > ==> excitation energy = output3 - output2 = 2.63eV, error = 3% > > > Calcium: > experimental excitation energy = 1.88eV, > > input1 : #P UCIS(50-50,Nstates=10)/6-31G(d) SCF=(Tight, > direct,MaxCycle=128) > Calcium excitation energy > 0 1 > Ca > output1: 1st excitation energy = 1.0897eV, error = 42% > > input2: #P UCID/6-31G(d) SCF=(Tight, direct, MaxCycle=128) > Calcium excitation energy > 0 1 > Ca > output2: CID = -36.2418938H > > input3: #P UCID/6-31G(d) SCF=(Tight, direct, MaxCycle=128) > Calcium excitation energy > 0 3 > Ca > output3: CID = -36.1760326H > > ==> excitation energy = output3 - output2 = 1.79eV, error = 5% > > Regards, > Kiniu > > ---- > Kiniu WONG Kin-Yiu > Undergraduate student > Department of Physics > The Chinese University of Hong Kong > Email: kiniu@cuhk.edu.hk or kyiwong@phy.cuhk.edu.hk > > > > -= 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 Thu Nov 9 13:20:48 2000 Received: from cheviot1.ncl.ac.uk (root@cheviot1.ncl.ac.uk [128.240.233.15]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA06094 for ; Thu, 9 Nov 2000 13:20:46 -0500 Received: from aidan.ncl.ac.uk (nbwt@aidan.ncl.ac.uk [128.240.233.1]) by cheviot1.ncl.ac.uk (8.10.1/8.10.1) with ESMTP id eA9IKeG16776; Thu, 9 Nov 2000 18:20:40 GMT Received: from localhost (nbwt@localhost) by aidan.ncl.ac.uk (8.9.3+Sun/8.9.0) with ESMTP id SAA13644; Thu, 9 Nov 2000 18:20:39 GMT X-Authentication-Warning: aidan.ncl.ac.uk: nbwt owned process doing -bs Date: Thu, 9 Nov 2000 18:20:39 +0000 (GMT) From: "Bruce. Tattershall" X-Sender: nbwt@aidan.ncl.ac.uk To: "Phillip D. Matz" cc: Ji Hai-tao , chemistry@ccl.net Subject: Re: CCL:conformer population In-Reply-To: <007101c04a70$60566080$b4297986@chem.wsu.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Filter-Version: 1.8 (cheviot1.ncl.ac.uk) If one has done a calculation for a gas-phase molecule, but one is interested in conformer ratio in solution (and is prepared to ignore any differential solvent effects), then should one take 'Sum of electronic and zero-point Energies' from the Gaussian freq output or 'Sum of electronic and thermal Energies' ? The first is, I think, independent of temperature. I had supposed that populations of vibrational levels might be similar between gas phase and solution phase molecules, though I am not a Physical Chemist and have no grounds for this assumption. Therefore using differences in thermal energies between conformers should give a better value of delta E. Total entropy printed by Gaussian is dominated by translational and rotational terms, so I suppose the entropy calculation has no transferability to the solution phase, and one should be content to use delta U rather than delta G in calculating K. I should be pleased to receive authoritative advice from experts in this field. Bruce Tattershall Personal Email: Bruce.Tattershall@newcastle.ac.uk Postal address: Dr. B.W. Tattershall Department of Chemistry, University of Newcastle Newcastle upon Tyne, NE1 7RU, England From chemistry-request@server.ccl.net Thu Nov 9 18:09:35 2000 Received: from hutsult3.hutch.com.au (hutsult3.hutch.com.au [203.12.80.7]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA07314 for ; Thu, 9 Nov 2000 18:09:32 -0500 From: Weiguang.Huang@eurorscg.com.au Received: from Sydney2.eurorscg.com.au ([203.30.131.4]) by hutsult3.hutch.com.au (8.9.3/8.9.3) with SMTP id KAA25520 for ; Fri, 10 Nov 2000 10:00:26 +1100 (EST) Received: by Sydney2.eurorscg.com.au(Lotus SMTP MTA v4.6.3 (778.2 1-4-1999)) id 4A256993.00004785 ; Fri, 10 Nov 2000 10:03:03 +1000 X-Lotus-FromDomain: EURORSCG_SYD To: chemistry@ccl.net Message-ID: <4A256993.000045B5.00@Sydney2.eurorscg.com.au> Date: Fri, 10 Nov 2000 09:57:44 +1000 Subject: ZDNet Review and rate software Polar as 4 stars Mime-Version: 1.0 Content-type: text/plain; charset=us-ascii Content-Disposition: inline ZDNet Review and rate software Polar as 4 stars. 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