From chemistry-request@www.ccl.net Thu Feb 4 03:52:18 1999 Received: from crisv2.univ-pau.fr (crisv2.univ-pau.fr [194.167.156.212]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id DAA09352 Thu, 4 Feb 1999 03:52:17 -0500 (EST) Received: from crisv4.univ-pau.fr by crisv2.univ-pau.fr; Thu, 4 Feb 1999 09:52:15 +0100 Received: by crisv4.univ-pau.fr; Thu, 4 Feb 1999 09:52:15 +0100 (MET) Date: Thu, 4 Feb 1999 09:52:15 +0100 (MET) From: Karine Miqueu Message-Id: <199902040852.JAA18053@crisv4.univ-pau.fr> To: chemistry@www.ccl.net Subject: deshydrogenation Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Content-MD5: pMEJNrKQkM76YMXVzkWhLA== Dear CCL readers, I'm studying deshydrogenation process and I'm interesting in knowing how the H2 molecule can be eliminated (differents reactions conceivable). I would like to find all the minima and transition states for a such elimination. Does anyone know theoretical publications' references about deshydrogenation or deshydrohalogenation of compounds (example: ethylene ...,cis or trans elimination, leaving of H. or H2)? Thanks in advance Miqueu Karinne Ph. D. Student email: Karine.Miqueu@univ-pau.fr From chemistry-request@www.ccl.net Thu Feb 4 05:30:18 1999 Received: from bastion.nmrc.ucc.ie (nmrc.ucc.ie [143.239.64.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id FAA09655 Thu, 4 Feb 1999 05:30:16 -0500 (EST) Received: from odessa.nmrc.ucc.ie (odessa.nmrc.ucc.ie [143.239.64.65]) by bastion.nmrc.ucc.ie (8.9.2/8.9.2) with ESMTP id KAA12132 for ; Thu, 4 Feb 1999 10:31:59 GMT Date: Thu, 4 Feb 1999 10:32:21 +0000 From: Michael Nolan To: ccl Subject: density matrix renormalisation group methods Message-ID: <19990204103218.A1380@rennes.nmrc.ucc.ie> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Mailer: Mutt 0.95.1i Dear CCLers... We are looking at studying conjugated polymers for application in photvoltaic devices. I have seen the density matrix renormalisation group (DMRG) method used for calculation of excitations and non-linear optical properties. Does anyone have (i) any experience with using DMRG and (ii) knowledge as to where there might be an available code? (A web search is none too useful...) Thank you in advance Michael -- ************************************************************************** Mr. Michael Nolan Materials Modelling Section, Advanced Materials and Technologies Group National Microelectronics Research Centre Lee Maltings, Prospect Row Cork IRELAND mail: mnolan@nmrc.ucc.ie Tel: + 353 21 90 4113 http://nmrc.ucc.ie/projects/ape/ http://nmrc.ucc.ie/groups/AMT/modellingRes.html EMRS Call for papers: http://nmrc.ucc.ie/groups/AMT/SympMain.html **************************************************************************** From chemistry-request@www.ccl.net Thu Feb 4 06:46:23 1999 Received: from comsig.nibsc.ac.uk (comsig.nibsc.ac.uk [193.62.43.13]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id GAA09923 Thu, 4 Feb 1999 06:46:16 -0500 (EST) Received: from nibsc.ac.uk (dlinmf.nibsc.ac.uk [193.62.42.144]) by comsig.nibsc.ac.uk (980427.SGI.8.8.8/970903.SGI.AUTOCF) via ESMTP id LAA05309; Thu, 4 Feb 1999 11:44:47 GMT Message-ID: <36B98864.5DBE2B8C@nibsc.ac.uk> Date: Thu, 04 Feb 1999 11:45:40 +0000 From: Mark Forster Organization: NIBSC X-Mailer: Mozilla 4.05 [en] (Win95; I) MIME-Version: 1.0 To: Allen Adler , chemistry@www.ccl.net Subject: Re: CCL:Drawing Lewis structures References: <199902031541.JAA05098@hera.wku.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Ron and Allen For a very inexpensive windows based package look at Molecules 3D from molecular arts corporation. Some contact information on them follows. Unfortunately their WWW page (http://www.molecules.com) does not seem to be functioning. --------------------------------------------------------- Molecular Arts Corporation | Hanover Corporate Centre | CompuServe: 71644,3626 1532 E. Katella Ave., Suite 1000 | Voice: (714) 634-8100 Anaheim, California 92805, USA | FAX: (714) 634-1999 --------------------------------------------------------- > Ron A. Rumley- Van Gurp writes: > > >We are looking for software (Linux/Windows95/98 or NT) that can draw Lewis > >structures of organic molecules, depicting all electron lone pairs as well > >as bonding pairs. Is there any computer program available that generates > >such structures semi-automatically? > -- Dr Mark J Forster Ph.D. Principal Scientist Informatics Laboratory National Institute for Biological Standards and Control Blanche Lane, South Mimms, Hertfordshire EN6 3QG, United Kingdom. Tel +44 (0)1707 654753 FAX +44 (0)1707 646730 E-mail mforster@nibsc.ac.uk From chemistry-request@www.ccl.net Thu Feb 4 07:29:59 1999 Received: from mail1.one.net (0@mail.one.net [206.112.192.107]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id HAA10204 Thu, 4 Feb 1999 07:29:58 -0500 (EST) Received: from port-25-43.access.one.net ([206.112.193.44] EHLO one.net ident: IDENT-NOT-QUERIED [port 24844]) by mail.one.net with ESMTP id <12570-23933>; Thu, 4 Feb 1999 07:29:56 -0500 Message-ID: <36B99059.FC055F54@one.net> Date: Thu, 04 Feb 1999 07:19:38 -0500 From: Ray Crawford X-Mailer: Mozilla 4.5 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 To: CHEMISTRY@www.ccl.net Subject: Proline Isomerase References References: <36B8F2FB.41C6@tc.cornell.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello all! I was wondering if there are any references which affirm or disprove the following idea: Proline isomerases, because they make proline unstable by isomerizing it between the trans and cis conformation, can exhibit a protolytic effect (i.e., cause the break down of proline-rich proteins). Does anyone know if this is "true", or the correct (or more appropriate) forum to ask this question in? Thanks, Ray Crawford. From chemistry-request@www.ccl.net Thu Feb 4 07:34:43 1999 Received: from mail.rwth-aachen.de (mail.RWTH-Aachen.DE [137.226.144.9]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id HAA10293 Thu, 4 Feb 1999 07:34:37 -0500 (EST) Received: from ac.rwth-aachen.de (pae102.ac.RWTH-Aachen.DE) by mail.rwth-aachen.de (PMDF V5.1-12 #30440) with ESMTP id <01J7CISQQCAS000B3M@mail.rwth-aachen.de> for CHEMISTRY@www.ccl.net; Thu, 4 Feb 1999 13:32:13 +0100 Date: Thu, 04 Feb 1999 12:33:22 +0000 From: Krzysztof Radacki Subject: Freq in G94 Sender: root@mail.rwth-aachen.de To: CCL Message-id: <36B99392.F9FFF935@ac.rwth-aachen.de> Organization: Inst.Inorg.Chem., RWTH Aachen, Germany MIME-version: 1.0 X-Mailer: Mozilla 4.05 [en] (X11; I; Linux 2.1.132 i586) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit Dear CCLers, I have question concerning log from IR calculation in G94. Below is part of this log: > Low frequencies --- -82.8125 -5.2461 -0.0021 0.0021 0.0064 7.1252 > Low frequencies --- 10.1830 65.1288 69.2516 > ****** 1 imaginary frequencies (negative signs) ****** > Harmonic frequencies (cm**-1), IR intensities (KM/Mole), > Raman scattering activities (A**4/AMU), Raman depolarization ratios, > reduced masses (AMU), force constants (mDyne/A) and normal coordinates: > 1 2 3 > A" A" A' > Frequencies -- -82.7948 65.1108 69.2511 > Red. masses -- 1.0165 1.0212 1.1460 > Frc consts -- 0.0041 0.0026 0.0032 > IR Inten -- 0.0003 0.0653 0.8054 > Raman Activ -- 0.0000 0.0000 0.0000 > Depolar -- 0.0000 0.0000 0.0000 First frequency is 1A"= -82.7948, and I can also see it in first line that I gave: "Low frequencies --- -82.8125" The second is 65.1108 cm^-1, so my question what are this "-5.2461 -0.0021 0.0021 0.0064 7.1252 10.1830" In other calculation I can see: > Low frequencies --- -9.2092 -8.3593 0.0015 0.0037 0.0040 12.9934 > Low frequencies --- 77.1880 77.8672 96.0089 > Harmonic frequencies (cm**-1), IR intensities (KM/Mole), > Raman scattering activities (A**4/AMU), Raman depolarization ratios, > reduced masses (AMU), force constants (mDyne/A) and normal coordinates: > 1 2 3 > A' A" A' > Frequencies -- 77.1868 77.8275 96.0065 > Red. masses -- 1.4137 1.0145 1.7426 > Frc consts -- 0.0050 0.0036 0.0095 > IR Inten -- 0.8422 0.2056 0.2503 > Raman Activ -- 0.0000 0.0000 0.0000 > Depolar -- 0.0000 0.0000 0.0000 And the same question, what are in this case first 7 values? thanks in advance for any helpfull explanation Krzys Radacki _________________________---------------------------------------------------- ------------------------- e-mail: Krys.Radacki@ac.RWTH-Aachen.DE --- ------------------------- ICQ : 19021591 --- ----------------------------------------------------------------------------- From chemistry-request@www.ccl.net Thu Feb 4 09:56:06 1999 Received: from dedalus.lcc.ufmg.br (dedalus.lcc.ufmg.br [150.164.65.10]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id JAA12032 Thu, 4 Feb 1999 09:56:03 -0500 (EST) Received: from localhost by dedalus.lcc.ufmg.br (AIX 3.2/UCB 5.64/4.03) id AA09500; Thu, 4 Feb 1999 12:55:37 -0200 Organization: Universidade Federal de Minas Gerais - LCC - Brasil Date: Thu, 4 Feb 1999 12:55:37 -0200 (BDB) From: ramon kleber da rocha Reply-To: ramon kleber da rocha To: Computational Chemistry Mailing List Cc: ramon kleber da rocha Subject: Summary :CCL:DIBUG Mailing list Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi CCLers About a couple of months ago I posted a query about DIBUG mailing list. Here is my original post: -------- Does anybody have any news about DIBUG (Discover Insight Biosym Users Group) mailing list? I have been tried to find something about it on WWW without success. In fact the last new I found was about two years ago. Best regards. -------- And here is the only reply I have received: -------- Date: Thu, 10 Dec 1998 19:57:51 -0800 (PST) From: Fenglou Mao To: ramon kleber da rocha Subject: Re: CCL:DIBUG Mailing list Can you tell me the mailing list address when you get it? Thank you! Sincerely Yours, FengLou Mao ******************************* ADD:Mr. FengLou Mao Peking University BeiJing P.R.China Tel:86-10-62751490 Fax:86-10-62751725 -------- I can conclude that DIBUG mailing list is over. ________________________________________________________________________________ Ramon Kleber da Rocha, MSc. VOICE +55-31-499-5765 e-mail rkrocha@dedalus.lcc.ufmg.br FAX +55-31-499-5700 Laboratorio de QSAR e Modelagem Molecular Nucleo de Estudos em Quimica Medicinal - NEQUIM - http://www.qui.ufmg.br/~nequim Departamento de Quimica - Instituto de Ciencias Exatas Universidade Federal de Minas Gerais Av. Presidente Antonio Carlos, 6627 Campus Pampulha CEP 31-270-901 - Belo Horizonte - Minas Gerais - Brasil ________________________________________________________________________________ -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: chemistry-request@www.ccl.net -- Original Sender From: Address: rkrocha@dedalus.lcc.ufmg.br CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search Web: http://www.ccl.net/chemistry.html From chemistry-request@www.ccl.net Wed Feb 3 05:52:54 1999 Received: from dali.eis.uva.es (dali.eis.uva.es [157.88.143.190]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id FAA20261 Wed, 3 Feb 1999 05:52:43 -0500 (EST) Received: from localhost (rnunez@localhost) by dali.eis.uva.es (8.9.1/8.9.1) with SMTP id LAA25517; Wed, 3 Feb 1999 11:53:46 +0100 (MET) Date: Wed, 3 Feb 1999 11:53:46 +0100 (MET) From: Ricardo Nunez Reply-To: Ricardo Nunez To: TOPPER ROBERT cc: CHEMISTRY@www.ccl.net Subject: Re: CCL:optical activity prediction In-Reply-To: <199901291711.AA09473@zeus.cooper.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all, Our group have developed a method to calculate the optical activity from molecular geometry, I give you some references: J. Mol. Struct., vol. 354, (1995) 81-87 J. Mol. Struct., vol. 442, (1998) 135-143 J. Mol. Struct., vol. 447, (1998) 127-133 Ricardo Nunez Miguel rnunez@sorolla.eis.uva.es Departamneto de Quimica Organica ETS de Ingenieros Industriales Universidad de Valladolid Spain On Fri, 29 Jan 1999, TOPPER ROBERT wrote: > Hello all, > > An organic chemists with whom I collaborate has asked me > whether it is possible to predict the optical activity > of a mixture of enantiomers, even semiquantitatively. > (i.e., is the optical activity "big" or "small" for > a given enantiomeric excess, or e.e.). > > My own search of the Internet has failed to turn up anything. > Can anyone give us any suggestions? > > Thanks very much! > > best, > rqt > > ***************************************************************************** > Prof. Robert Q. Topper email: topper@cooper.edu > Department of Chemistry phone: (212) 353-4378 > The Cooper Union fax: (212) 353-4341 > 51 Astor Place subway: take the 6 to Astor Place > New York, NY 10003 and you're there! > http://www.cooper.edu/engineering/chemechem/ > ***************************************************************************** > The Cooper Union for the Advancement of Science and Art is a tuition-free > college in Greenwich Village, at Cooper Square and Astor Place. > ***************************************************************************** > > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: chemistry-request@www.ccl.net > -- Original Sender From: Address: topper@cooper.edu > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > > From chemistry-request@www.ccl.net Wed Feb 3 05:52:54 1999 Received: from dali.eis.uva.es (dali.eis.uva.es [157.88.143.190]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id FAA20261 Wed, 3 Feb 1999 05:52:43 -0500 (EST) Received: from localhost (rnunez@localhost) by dali.eis.uva.es (8.9.1/8.9.1) with SMTP id LAA25517; Wed, 3 Feb 1999 11:53:46 +0100 (MET) Date: Wed, 3 Feb 1999 11:53:46 +0100 (MET) From: Ricardo Nunez Reply-To: Ricardo Nunez To: TOPPER ROBERT cc: CHEMISTRY@www.ccl.net Subject: Re: CCL:optical activity prediction In-Reply-To: <199901291711.AA09473@zeus.cooper.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all, Our group have developed a method to calculate the optical activity from molecular geometry, I give you some references: J. Mol. Struct., vol. 354, (1995) 81-87 J. Mol. Struct., vol. 442, (1998) 135-143 J. Mol. Struct., vol. 447, (1998) 127-133 Ricardo Nunez Miguel rnunez@sorolla.eis.uva.es Departamneto de Quimica Organica ETS de Ingenieros Industriales Universidad de Valladolid Spain On Fri, 29 Jan 1999, TOPPER ROBERT wrote: > Hello all, > > An organic chemists with whom I collaborate has asked me > whether it is possible to predict the optical activity > of a mixture of enantiomers, even semiquantitatively. > (i.e., is the optical activity "big" or "small" for > a given enantiomeric excess, or e.e.). > > My own search of the Internet has failed to turn up anything. > Can anyone give us any suggestions? > > Thanks very much! > > best, > rqt > > ***************************************************************************** > Prof. Robert Q. Topper email: topper@cooper.edu > Department of Chemistry phone: (212) 353-4378 > The Cooper Union fax: (212) 353-4341 > 51 Astor Place subway: take the 6 to Astor Place > New York, NY 10003 and you're there! > http://www.cooper.edu/engineering/chemechem/ > ***************************************************************************** > The Cooper Union for the Advancement of Science and Art is a tuition-free > college in Greenwich Village, at Cooper Square and Astor Place. > ***************************************************************************** > > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: chemistry-request@www.ccl.net > -- Original Sender From: Address: topper@cooper.edu > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > > From chemistry-request@www.ccl.net Wed Feb 3 08:59:35 1999 Received: from zzmkgtw.zzmk.unizh.ch (zzmkgtw.unizh.ch [130.60.67.3]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id IAA21075 Wed, 3 Feb 1999 08:59:33 -0500 (EST) Received: by zzmkgtw.zzmk.unizh.ch; (5.65v3.2/1.3/10May95) id AA22476; Wed, 3 Feb 1999 14:59:32 +0100 Message-Id: <3.0.3.32.19990203150449.006898d4@highdent> X-Sender: toukie@highdent (Unverified) X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.3 (32) Date: Wed, 03 Feb 1999 15:04:49 +0100 To: chemistry@www.ccl.net From: "Hr. Dr. S. Shapiro" Subject: Reposting Cc: toukie@zui.unizh.ch Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear Colleagues; About two weeks ago I posted a question to the CCL, and to date the response has been underwhelming, which is to say that I didn't receive any replies. It may well be that the information I seek is not yet available, though I would be a bit surprised if that were indeed the case. In any event, I am reposting this query in the hope that someone will deem to respond. The query is as follows: I am seeking published references to neutron diffraction (preferred) and/or X-ray diffraction (acceptable) data for the following two classes of compounds: (a) simple nitrophenols (with or without an additional alkyl substituent); (b) simple monoalkoxy- or monoaryloxyphenols. I am also seeking this same data for (c) 2,6-diphenylphenol If anyone has this information, or access to databases containing this information, and can dig out the relevant references, I would be very grateful. Thanks in advance to all responders, S. Shapiro toukie@zui.unizh.ch From chemistry-request@www.ccl.net Wed Feb 3 11:57:09 1999 Received: from catios.udea.edu.co ([200.24.20.180]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id LAA23413 Wed, 3 Feb 1999 11:56:50 -0500 (EST) Received: from catios.udea.edu.co (lab-carb2-059.udea.edu.co [200.24.16.227]) by catios.udea.edu.co (8.8.7/8.8.7) with ESMTP id LAA15859 for ; Wed, 3 Feb 1999 11:22:49 -0500 Message-ID: <36B8765E.A422CC02@catios.udea.edu.co> Date: Wed, 03 Feb 1999 11:16:30 -0500 From: Alejandro Montoya X-Mailer: Mozilla 4.08 [en] (Win95; I) MIME-Version: 1.0 To: "chemistry@www.ccl.net" Subject: Chemisorption Content-Type: multipart/alternative; boundary="------------404EABA60A8DA2084B3678F4" --------------404EABA60A8DA2084B3678F4 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL Readers: I sent this message last weak and unfortunately anybody reply to my question, I am very interesting in this topic and I would appreciate finding someone to know about this. the message was.. I am studying gas chemisorption on solid surface and I am interested in knowing how the CO2 can be chemisorbed (Different states of energy, any mechanical theory about that or whatever, and calculus ab initio) . If someone can help me whit any kind of information (publications/refrences) about this topic I will be very grateful. I will sumarize the massages. Thanks in advance. Alejandro Montoya E. e-mail: alemoe@catios.udea.edu.co Ph.D student University of Antioquia --------------404EABA60A8DA2084B3678F4 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit  
 Dear CCL Readers:

I sent this message last weak and unfortunately anybody reply to my question, I am very interesting in this topic and I would appreciate finding someone to know about this.  the message was..

 I am studying  gas chemisorption  on  solid surface and I am interested  in knowing how the CO2 can be chemisorbed (Different states of energy, any mechanical theory about that or whatever, and calculus ab initio)  . If someone can help me whit any kind of information  (publications/refrences) about  this topic I will be very grateful. I will sumarize the massages.

Thanks in advance.

Alejandro Montoya E.
e-mail: alemoe@catios.udea.edu.co
Ph.D student
University of Antioquia --------------404EABA60A8DA2084B3678F4-- From chemistry-request@www.ccl.net Wed Feb 3 11:57:09 1999 Received: from catios.udea.edu.co ([200.24.20.180]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id LAA23413 Wed, 3 Feb 1999 11:56:50 -0500 (EST) Received: from catios.udea.edu.co (lab-carb2-059.udea.edu.co [200.24.16.227]) by catios.udea.edu.co (8.8.7/8.8.7) with ESMTP id LAA15859 for ; Wed, 3 Feb 1999 11:22:49 -0500 Message-ID: <36B8765E.A422CC02@catios.udea.edu.co> Date: Wed, 03 Feb 1999 11:16:30 -0500 From: Alejandro Montoya X-Mailer: Mozilla 4.08 [en] (Win95; I) MIME-Version: 1.0 To: "chemistry@www.ccl.net" Subject: Chemisorption Content-Type: multipart/alternative; boundary="------------404EABA60A8DA2084B3678F4" --------------404EABA60A8DA2084B3678F4 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL Readers: I sent this message last weak and unfortunately anybody reply to my question, I am very interesting in this topic and I would appreciate finding someone to know about this. the message was.. I am studying gas chemisorption on solid surface and I am interested in knowing how the CO2 can be chemisorbed (Different states of energy, any mechanical theory about that or whatever, and calculus ab initio) . If someone can help me whit any kind of information (publications/refrences) about this topic I will be very grateful. I will sumarize the massages. Thanks in advance. Alejandro Montoya E. e-mail: alemoe@catios.udea.edu.co Ph.D student University of Antioquia --------------404EABA60A8DA2084B3678F4 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit  
 Dear CCL Readers:

I sent this message last weak and unfortunately anybody reply to my question, I am very interesting in this topic and I would appreciate finding someone to know about this.  the message was..

 I am studying  gas chemisorption  on  solid surface and I am interested  in knowing how the CO2 can be chemisorbed (Different states of energy, any mechanical theory about that or whatever, and calculus ab initio)  . If someone can help me whit any kind of information  (publications/refrences) about  this topic I will be very grateful. I will sumarize the massages.

Thanks in advance.

Alejandro Montoya E.
e-mail: alemoe@catios.udea.edu.co
Ph.D student
University of Antioquia --------------404EABA60A8DA2084B3678F4-- From chemistry-request@www.ccl.net Wed Feb 3 13:54:21 1999 Received: from chris2.u-strasbg.fr (maerker@chris2.u-strasbg.fr [130.79.34.140]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id NAA24145 Wed, 3 Feb 1999 13:54:20 -0500 (EST) Received: (from maerker@localhost) by chris2.u-strasbg.fr (8.8.8/8.8.8) id TAA00344; Wed, 3 Feb 1999 19:54:46 +0100 From: Christoph Maerker Message-Id: <199902031854.TAA00344@chris2.u-strasbg.fr> Subject: summary: problems with G94 volume runs To: chemistry@www.ccl.net (ccl) Date: Wed, 3 Feb 1999 19:54:46 +0100 (MET) Cc: maerker@chris2.u-strasbg.fr (Christoph Maerker) Organization: Laboratoire de Chimie biophysique, Institut Le Bel, Universite Louis Pasteur Postal-Address: 4, rue Blaise Pascal, F- 67000 Strasbourg FRANCE Phone: +33/3-88-41-53-19 Fax: +33/3-88-60-63-83 X-Mailer: ELM [version 2.4ME+ PL37 (25)] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: quoted-printable Content-Length: 8963 Dear CClers, here is the summary for the problems with volume runs in G9x. I have receiv= ed three very helpful answers listed below. It was true that the problems occurred on SGI's. However, the failure seems to come from Gaussian, not the OS. Larry Cuffe provided a nice patch. Doug Stack gave the hint to Gaussian test input file test232.com. I ran it both with G94 and G98 on the same SGI; G94 (RevE.2) gave the zero= =20 volume as reported before, but G98 (RevA.6) gave non-zero volumes, although different from those listed in the test232.log file. I tried other platforms as well (HP-UX and Linux), and got always different results. I do not list the numbers, because everybody can do it on his own= =20 hardware within seconds. There seems to be considerable numerical noise in= =20 the MC procedure applied, rendering the results machine-dependent. The recommended radii are less affected, whereas the volumes are. Thus, tho= se who are interested in the cavity radii and subsequent scrf=3Ddipole runs sh= ould do all computations on the VERY same machine ! Regards, Christoph Maerker PS The answers are listed according to the authors' last names. =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D From: "Dale A. Braden" Subject: Re: CCL:problem with G94 volume runs Dear Christoph, Are you running G94 on an SGI? I had this problem also, and the folks at Gaussian told me that it was due to a bug in the random number generator in the SGI operating system. It appears in some versions of IRIX but not others. Gaussian did not give me any fix for it, either, so I was forced to calculate volumes on another platform. Best wishes, Dale Dale Braden Department of Chemistry University of Oregon Eugene, OR 97403-1253 genghis@darkwing.uoregon.edu =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D From: larry@melanie.ucd.ie (Larry Cuffe) Subject: Re: SGI problems Here is the code with a reference for the random number generator at the end good luck and if there are any problems dont hesitate to contact me. Larry Cuffe The version running on the SGI failed to compute molecular volumes correc= tly. This computation is made in L604 which performs a Monte Carlo integrat= ion over a box containing the molecule in this process points within the vo= lume of the box are sampled a= t a number of points and the electron density is calculated. If the electro= n density is above a threshold value it is deemed to be part of the molecul= e At the end of this process the volume of the box is multiplied by the ra= tio of occupied to empty poin= ts and this is taken to be the molecular volume. On the SGI machine comput= ed molecular volumes returned by the program corresponded to either total o= r zero occupancy. This problem was traced back to problems with the random= number generator which is ca= lled as a machine dependant function Gran() from the module of machine depe= ndent utilities mdutil.f This source file was edited and the call to the m= achine dependent routine was replaced by a random number generator based on= the! proposals of S. D. Stearns.1. The code for the relevent changes is detailed below. Calling Routine in l604.f *Deck GnMCPt Subroutine GnMCPt(IOut,IPrint,MaxPt,NPt,NDone,XO,YO,ZO,X1,Y1,Z1, $ XYZ) Implicit Real*8 (A-H,O-Z) C C Generate the list of points for Monte-Carlo calculation C Dimension XYZ(MaxPt,3) Save One Data One/1.0d0/ 1000 Format(' Points from I=3D',I10,' through I=3D',I10) 1010 Format(' IPt=3D',I10,' XYZ=3D',3F12.6) C IFirst =3D NDone + 1 ILast =3D NDOne + NPt Lim =3D NPt / 2 Do 10 I =3D 1, Lim 10 XYZ(I,1) =3D XO + GRan(0)*X1 Do 20 I =3D 1, Lim 20 XYZ(I,2) =3D YO + GRan(0)*Y1 Do 30 I =3D 1, Lim 30 XYZ(I,3) =3D ZO + GRan(0)*Z1 Do 40 I =3D (Lim+1), NPt 40 XYZ(I,1) =3D XO + (One-GRan(0))*X1 Do 50 I =3D (Lim+1), NPt 50 XYZ(I,2) =3D YO + (One-GRan(0))*Y1 Do 60 I =3D (Lim+1), NPt 60 XYZ(I,3) =3D ZO + (One-GRan(0))*Z1 C If(IPrint.ge.3) then Write(IOut,1000) IFirst,ILast =20 Write(IOut,1010) (I,(XYZ(I,J),J=3D1,3),I=3D1,NPt) endif Return End Original Code in mdutil.f *Deck GRan Function GRan(IDummy) implicit real*8(a-h,o-z) C C Working-Precision random number. C Logical Called Integer ITime #ifdef IBM_RS6K #define USE_DRAND48 #endif #ifdef _I386_ #define USE_DRAND48 #endif #ifdef _SGI_ #define USE_RAND External Time #endif #ifdef _PMAX_ #define USE_RAND Real*4 Rand #endif #ifdef __CONVEX__ #define GRAN0_DONE Real*4 Secnds, R4Zero, Rand Save R4Zero Data R4Zero/0.0/ #endif #ifdef __HPPA #define GRAN0_DONE $NOSTANDARD SYSTEM Real*4 R4Zero Integer ISeed Data R4Zero/0.0/ #endif #ifdef IBM_PC #define GRAN0_DONE Integer*2 I2Time(2), I2, J2 Real*4 URand Equivalence (I2Time(1),ITime) #endif #ifndef GRAN0_DONE Integer Time #endif Save Called, ITime Data Called/.False. C If(Called) then #ifdef __CONVEX__ #define GRAN1_DONE ITIME=3DIrand(ITime) GRan =3D Rand(ITime) #endif #ifdef __HPPA #define GRAN1_DONE GRan =3D RAN(ISeed) #endif #ifdef IBM_PC #define GRAN1_DONE GRan =3D URand(ITime) #endif #ifdef ALPHA_VMS #define GRAN1_DONE Gran =3D getran() #endif #ifdef _SGI_ ITime =3D Time() Call SRand(ITime) #endif #ifdef USE_RAND #define GRAN1_DONE Gran =3D Rand() #endif #ifdef USE_DRAND48 #define GRAN1_DONE Gran =3D DRand48() #endif #ifndef GRAN1_DONE GRan =3D DRand(0) #endif else Called =3D .True. #ifdef __CONVEX__ #define GRAN2_DONE ITime =3D Int(20.0*Secnds(R4Zero)) ITime =3D IRand(ITime) #endif #ifdef __HPPA #define GRAN2_DONE ISeed =3D Int(20.0*Secnds(R4Zero)) #endif #ifdef IBM_PC #define GRAN2_DONE Call GetTim(I2,J2,I2Time(2),I2Time(1)) #endif #ifdef ALPHA_OSF1 #define GRAN2_DONE ITime =3D Time() Call SRand(ITime) #endif #ifdef ALPHA_VMS #define GRAN2_DONE GRan =3D getrans() #endif #ifndef GRAN2_DONE ITime =3D Time() #endif #ifdef __CONVEX__ #define GRAN3_DONE GRan =3D Rand(ITime) #endif #ifdef __HPPA #define GRAN3_DONE GRan =3D Ran(ISeed) #endif #ifdef IBM_PC #define GRAN3_DONE Gran =3D URand(ITime) #endif #ifdef ALPHA_VMS #define GRAN3_DONE #endif #ifdef USE_DRAND48 #define GRAN3_DONE Call GSR48(ITime) Gran =3D DRand48() #endif #ifdef USE_RAND #define GRAN3_DONE Call SRand(ITime) Gran =3D Rand() #endif #ifndef GRAN3_DONE GRan =3D DRand(ITime) #endif endIf Return End modified code=20 *Deck GRan Function GRan(IDummy) implicit real*8(a-h,o-z) C C Working-Precision random number. C modified LPC 8 sept 98 Logical Called Integer ITime Integer SEED Save SEED REAL*8 RANDX SEED=3D2045*SEED + 1 SEED =3D SEED - (SEED/1048576)*1048576 RANDX =3D REAL(SEED + 1)/1048577.0 GRan=3DRANDX return end 1 S. D. Stearns, "A Portable Random Number Generator for Use in Signal Proc= essing", Sandia Laboratory Technical Report (1981). =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D From: Douglas_Stack/CAS/UNO/UNEBR@unomail.unomaha.edu I've had this same problem w/ G94 running on an SGI Onynx sever (multiple processors). I ran a couple of test jobs that applied to the type of calculations I was doing. The test for molecular volume is test232.com, wh= en I performed this test, I did not get the same output as test232.log! The test232.log from Gaussian gives: Molar volume =3D 456.410 bohr**3/mol ( 40.729 cm**3/mol) Recommended a0 for SCRF calculation =3D 3.28 angstrom ( 6.20 bohr) My test232.log output was: Molar volume =3D 2389.438 bohr**3/mol (213.231 cm**3/mol) Recommended a0 for SCRF calculation =3D 5.33 angstrom ( 10.07 bohr) This the only case where I've seen the output from a local job I've run differing from the output of the Gaussian test file. I obtained my a0 for SCRF calculations by importing the molecules into Spar= tan, creating an density isosurface at the 0.01 level, and having Spartan tell m= e the volume of that surface. With the volume, I worked back to the radius, adde= d 0.5 A and used that number in SCRF. If Doug Fox see this tread, maybe he can give some insight to this problem. Regards, Douglas E. Stack Assistant Professor Department of Chemistry University of Nebraska at Omaha Omaha, NE 68182-0109 (402) 554-3647 (402) 544-3647 (fax) Douglas_Stack@unomaha.edu From chemistry-request@www.ccl.net Wed Feb 3 19:35:02 1999 Received: from bobino.sefmedia.com (www.sefmedia.com [207.164.6.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id TAA07162 Wed, 3 Feb 1999 19:35:01 -0500 (EST) Received: from sfr-qbu-pqk-vty152.as.wcom.net (sfr-qbu-pqk-vty152.as.wcom.net [206.175.229.152]) by bobino.sefmedia.com (NTMail 3.02.13) with ESMTP id qa018684 for ; Wed, 3 Feb 1999 19:34:56 -0500 Reply-To: From: "Bill Hayden" To: "John Marelius" , Subject: RE: Re: Alpha based computers in computational chemistry Date: Wed, 3 Feb 1999 19:31:54 -0500 Message-ID: <000001be4fd5$c3f69ca0$c40101c0@zman> 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 8.5, Build 4.71.2173.0 In-Reply-To: Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 Our software, MOE - the Molecular Operating Environment, is the only platform independent software on the market. It covers the full spectrum of drug discovery and runs on SGI, Sun, WinNT, Win 95 and, of particular interest to your questions, DEC Alpha NT. I invite you to visit our site at: http://www.chemcomp.com Bill Hayden@chemcomp.com -----Original Message----- From: chemistry-request@www.ccl.net [mailto:chemistry-request@www.ccl.net] On Behalf Of John Marelius Sent: February 2, 1999 5:40 AM To: chemistry@www.ccl.net Subject: CCL:Re: Alpha based computers in computational chemistry On Fri, 29 Jan 1999 shelley.jc@pg.com wrote: > > Hello, > In the context of individual research laboratories looking for > workstations or low to mid-range compute servers, are alpha based computers > used much in computational chemistry laboratories and if so how? In the group I work in we use Alpha workstations with WindowsNT for computational chemistry, mostly running our own molecular dynamics software. The Alpha + WindowsNT combination has proven to be a powerful combination of a high-performance number-cruncher and a desktop computer for word processing (MS Office etc) in one box. We find systems based on the Alpha processor not only to be the fastest but also to give the highest performance/price ratio. Systems based on the new generation of Alpha chips ("21264") are starting to become available, promising another large jump in performance. WindowsNT still has some drawbacks as a compute server operating system. * A third-party batch queue package is needed. * It's not a (simultaneous) multi-user system although remote login by telnet is possible (although sometimes problematic) by means of additional software. John Marelius +-----------------------------------------------------------------+ | John Marelius | | Dept. of Molecular Biology, Uppsala University | | E-mail: john@alpha2.bmc.uu.se | | address: Box 590, S-751 24 Uppsala, Sweden | +-----------------------------------------------------------------+ --- Administrivia: This message is automatically appended by the mail exploder: CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search Web: http://www.ccl.net/chemistry.html --- From chemistry-request@www.ccl.net Wed Feb 3 21:20:35 1999 Received: from teapot16.domain4.bigpond.com (teapot16.domain4.bigpond.com [139.134.5.164]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id VAA08090 Wed, 3 Feb 1999 21:20:31 -0500 (EST) Received: from localhost (localhost [127.0.0.1]) by teapot16.domain4.bigpond.com (NTMail 3.02.13) with ESMTP id ha332625 for ; Thu, 4 Feb 1999 12:18:40 +1000 Received: from BDIP-T-009-p-235-121.tmns.net.au ([139.134.235.121]) by mail4.bigpond.com (Claudes-Happening-MailRouter V2.2a); 04 Feb 1999 12:18:40 Message-ID: <003301be4fe4$9bdb7060$09007a81@hnlsyd8> Reply-To: "Dr Huang" From: "Dr Huang" To: Subject: RE: I uploaded my 2 software polar32.zip and polar32b.zip to ftp.ccl.net/incoming/polar/ Date: Thu, 4 Feb 1999 13:18:07 +1100 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Polar has been moved to ftp://www.ccl.net/pub/chemistry/software/MS-WIN95-NT/Polarograms ************************************************* * Dr Weiguang Huang, BS, MS, PhD, MACS * * 124 Eastern Avenue, Kingsford * * Sydney, NSW 2032, Australia * * Phone: 61 2 96620516 (h), 0413 008 019 * * email: showing@bigfoot.com, showing@fcmail.com* * http://www.bigfoot.com/~showing/ * * http://www.bigfoot.com/~VisualMath/ * ************************************************* From chemistry-request@www.ccl.net Thu Feb 4 13:08:43 1999 Received: from as1200.organik.uni-erlangen.de (as1200-1.organik.uni-erlangen.de [131.188.128.6]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id NAA14710 Thu, 4 Feb 1999 13:08:40 -0500 (EST) Received: from ccc.uni-erlangen.de (temeraire.organik.uni-erlangen.de [131.188.128.73]) by as1200.organik.uni-erlangen.de (8.8.7/8.1.11-FAU) with ESMTP id TAA20929 for ; Thu, 4 Feb 1999 19:08:41 +0100 (MET) Sender: Anselm.Horn@organik.uni-erlangen.de Message-ID: <36B9E188.AF20B9F0@ccc.uni-erlangen.de> Date: Thu, 04 Feb 1999 19:06:00 +0100 From: Anselm Horn Organization: CCC X-Mailer: Mozilla 4.5 [en] (X11; I; OSF1 V4.0 alpha) X-Accept-Language: en MIME-Version: 1.0 To: CCL Subject: Electric field in semiempirical MO theory Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL's, I'm currently working on an implementation of an uniform electric field in VAMP (a semiempirical program package similar to MOPAC or AMPAC). This feature is included as an undocumented option in MOPAC, but comments in the source are missing... Can anybody give me some references about theory or actual implementation of an electric field within semiempirical MO theory ? Any suggestions will be appreciated !! Anselm Horn -- _______________________________________________________________________ Anselm Horn, Dipl. Chem. Univ. Anselm.Horn@ccc.uni-erlangen.de ___ / __| ___ Computer Chemie Centrum | / ___ / __| | | / __|| / Naegelsbachstrasse 25 \ \__ | / | | D-91025 Erlangen \___|| | \ \__ Deutschland / Germany \ \__ \___| Tel: +49 9131/85-2-6583 * Fax: +49 9131/85-2-6565 \___| http://www.ccc.uni-erlangen.de/clark/horn/index.html _______________________________________________________________________ From chemistry-request@www.ccl.net Thu Feb 4 14:27:05 1999 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 OAA15493 Thu, 4 Feb 1999 14:27:01 -0500 (EST) Received: from cliff.nal.usda.gov (cliff.nal.usda.gov [192.54.138.2]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with SMTP id OAA07890 for ; Thu, 4 Feb 1999 14:27:01 -0500 (EST) Received: by cliff.nal.usda.gov (SMI-8.6/SMI-SVR4) id OAA09071; Thu, 4 Feb 1999 14:28:05 -0500 Date: Thu, 4 Feb 1999 14:28:05 -0500 (EST) From: "Stephen R. Heller" X-Sender: srheller@cliff To: jcicshelp , chemweb@ic.ac.uk, chminf-l@listserv.indiana.edu, orgchem@extreme.chem.rpi.edu Subject: Software for Review Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII 4 February, 1999 Subject: Computer Software for Review As the Software Review Editor for the ACS Journal of Chemical Information and Computer Science (JCICS) I often get software for review in the journal. I have three (3) new software products. I am looking for people who are willing to review these software products. In return for the review which is published in JCICS you get to keep the software or database. The review should be completed in 1-3 months. The length of the review is 4-10 double spaced typed pages. Sample reviews can be found in most of the recent issues of JCICS. Please try to give me some (short) reason to choose you over another person. I have tried this approach for about the past seven years and it is working reasonably well. (REMINDER: For those who haven't finished your reviews of software sent months and months ago, this last sentence does not apply to you!) As a result, I am continuing this new method to find reviewers using this e-mail/user group system. I reserve the right to abandon this if it is a problem, or inappropriate. I will not notify people if I have found a reviewer. If you don't hear from me within a few days I have chosen someone else to review the particular package. As I get many, many, (too many) replies to this message, please do not respond after 8 February, 1999 (Monday), as I am sure the software will be gone by then. I can be reached on Internet (SRHELLER@NIST.GOV). PLEASE BE SURE TO INCLUDE AN STREET ADDRESS, PHONE, and FAX NUMBER!!! (I often send the software by Federal Express.) Without this information I WILL NOT consider your request. Steve Heller The packages I now have are: 1. ACD/Boiling Point 3.6 software from ACD Labs (www.acdlabs.com). 2. ACD/ChemFinder 3.6 software from ACD Labs (www.acdlabs.com) 3. Elsevier Active Library on Corrosion, version 2.0 on CD-ROM. Steve Heller, Guest Researcher NIST/SRD, Mail Stop: 820/113 820 Diamond Avenue, Room 101 Gaithersburg, MD 20899-2310 USA Phone: 301-975-3338 FAX: 301-926-0416 E-mail: srheller@nist.gov WWW: www.hellers.com/~steve From chemistry-request@www.ccl.net Thu Feb 4 15:34:11 1999 Received: from email.nist.gov (email.nist.gov [129.6.2.7]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id PAA17490 Thu, 4 Feb 1999 15:34:10 -0500 (EST) Received: from feldmann.nist.gov (feldmann.nist.gov [129.6.178.78]) by email.nist.gov (8.9.1/8.9.1) with ESMTP id PAA19652; Thu, 4 Feb 1999 15:33:31 -0500 (EST) Received: from localhost (chem@localhost) by feldmann.nist.gov (8.8.8+Sun/8.8.8) with SMTP id PAA08753; Thu, 4 Feb 1999 15:24:42 -0500 (EST) Date: Thu, 4 Feb 1999 15:24:42 -0500 (EST) From: Steve Heller To: ACSMEDI@LISTS.WAYNE.EDU, amber@cgl.ucsf.edu, APPLSPEC@uga.cc.uga.edu, cache@pacificu.edu, CHEMCHAT@UAFSYSB.UARK.EDU, CHEME-L@ULKYVM.LOUISVILLE.EDU, CHEMED-L@atlantis.uwf.edu, CHEMIG@LIST.NIH.GOV, CHEMISTRY@www.ccl.net, CHMINF-L@LISTSERV.INDIANA.EDU, ICS-L@UMDD.UMD.EDU cc: srheller@nist.gov Subject: Chemisty & the Internet Meeting Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII The ChemInt'99 draft program is now available at the conference web site: www.chemint.org. The list of all invited speakers and virtually all panel members is now complete and listed in the program. ChemInt'99 will be held in at Georgetown University in Washington DC on September 25-27, 1999. Poster talks/papers submissions will be accepted only via the web site starting in the spring. The main lecturers for the meeting will be: Alan Arnold, University College (UNSW) Steven Bachrach, Northern Illinois University Robert Bovenschulte, ACS Stephen Boyer, IBM Karl Harrison, Oxford University Clemens Jochum, Deutsche Bank Gary Mallard, NIST Tom Pierce, Rohm & Haas Jerome Reichman, Vanderbilt Achim Zielesny, Bayer AG Steven S. Zumdahl, University of Illinois at Urbana-Champaign The corporate sponsors for the meeting are: ChemWeb and the Internet Journal of Chemistry Technical Sponsors are: ACS CINF Division ACS COMP Division The Chemical Structure Association (CSA) Georgetown University - Department of Chemistry International Union of Pure and Applied Chemistry (IUPAC) (pending) Japan Association for International Chemical Information (JAICI) Special Libraries Association (SLA) Chemistry Division Royal Society of Chemistry (RSC) A list of current exhibitors is on the web site. This note is also to remind people that webcasting (video/audio) and/or slides for more tha a dozen of the Chemistry and the Internet (ChemInt'98) meeting talks, held in Irvine CA in September, are also available on the ChemInt web site (www.chemint.org). A 42 page report on the meeting by Wendy Warr is also available. Steve Heller Steve Heller, Guest Researcher NIST/SRD, Mail Stop: 820/113 820 Diamond Avenue, Room 101 Gaithersburg, MD 20899-2310 USA E-mail: chem@feldmann.nist.gov From chemistry-request@www.ccl.net Thu Feb 4 15:41:47 1999 Received: from panix3.panix.com (y9N2z5gFX9ybHInuC3r6drc3SKbfJ/GK@panix3.panix.com [166.84.1.68]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id PAA17603 Thu, 4 Feb 1999 15:41:45 -0500 (EST) From: kynn@panix.com Received: (from kynn@localhost) by panix3.panix.com (8.8.5/8.8.8/PanixU1.4) id PAA20610; Thu, 4 Feb 1999 15:41:42 -0500 (EST) Date: Thu, 4 Feb 1999 15:41:42 -0500 (EST) Message-Id: <199902042041.PAA20610@panix3.panix.com> To: chemistry@www.ccl.net Subject: Histogram method, redux Thanks for the replies to my earlier query about the histogram method. I have attempted to read some of the references suggested (given below, for those interested, along with other references requested), but I must confess that I can barely understand them. Before spending any more time trying to make sense of them, it would be wise to determine whether these methods would actually serve my purposes. So here I give a schematic description of the problem I'm dealing with, in the hope that someone may be able to tell me whether the "multiple histogram method" would be of any use. Consider a model of protein folding dynamics, with the following features: 1. The folding is perfectly two-state, the two states being designated U (unfolded) and F (folded). Moreover, the two states are well separated in terms of energy; i.e., if we were able to produce an energy histogram at the folding transition temperature (Tf), the distribution would be distinctly bimodal, with a largely unpopulated region separating the peaks corresponding to F and U. 2. Let t_F(T) and t_U(T) be the mean passage times for the folding (U->F) and the unfolding (F->U) transitions, respectively, as functions of the temperature T. 3. We distinguish three temperature regimes I < II < III. In regime I, for all practical purposes, t_U(T) is infinite, while t_F(T) is "reasonably small". Conversely, in regime III, t_F(T) is practically infinite, while t_U(T) is small. 4. In regime II, a narrow neighborhood of the folding transition temperature Tf, both t_F(T) and t_U(T) are roughly equal, and both are extremely large (of the order of 2-3 CPU-weeks on our workstations). (Of course, no sharp boundaries separate these three temperature regimes; t_F(T) and t_U(T) grow rapidly, as one approaches regime II from regime I and III, respectively.) 5. Because of the slowing down described in 4, it is extremely difficult to determine Tf. The single histogram method (which I described in my original post) would require a single run near Tf, long enough to sample both the F and U states in a way that actually reflects their relative probabilities. For the reason mentioned in (4) and (5) this is impractical, which seems to rule out this method. But it was suggested by a few responders to my earlier post that the *multiple* histogram method may be useful in this case. The only way I can see to apply this method is by producing two histograms, one at temperature T1 in regime I to sample F, and one at temperature T3 in regime III to sample U. Then, if we "absorb" the temperature into the definition of the Hamiltonian (as Ferrenberg and Swendsen do, see reference below), then this could be construed a case of having two "Hamiltonians", H/(k*T1) and H/(k*T2), (where H is the actual Hamiltonian, in the standard nomeclature). Then I would use the method of Bennett (see reference below) to obtain a free energy difference between these two states (as a function of T). Is this correct? (The method of Ferrenberg and Swendsen is a generalization of Bennett's method to more than two histograms, if I've understood them correctly). These multiple histogram methods require a certain amount of overlap between the histograms, which leads, for the system described above, to a somewhat paradoxical situation: the greater the overlap between the two states (meaning that neither P(U;T)/P(F;T) nor P(F;T)/P(U;T) is too small), the closer the simulation temperatures have to be to Tf, and therefore the longer it would take to adequately sample the phase space (as remarked in (4) above). This suggests that the multiple histogram method would not be very useful either. Am I right? Thanks for your patience. Below are the references mentioned above. Regards, KJ Papers that report using the histogram method: @ARTICLE{klimov-thirumalai98, AUTHOR = {D. K. Klimov and M. R. Betancourt and D. Thirumalai}, TITLE = {Virtual atom representation of hydrogen bonds in minimal off-lattice models of alpha helices: effect on stability, cooperativity and kinetics}, JOURNAL = {Folding and Design}, VOLUME = 3, NUMBER = 6, PAGES = {481--496}, YEAR = 1998 } @ARTICLE{guo-brooks97, AUTHOR = {Zhuyan Guo and Charles L. {Brooks~III}}, TITLE = {Thermodynamics of Protein Folding: A Statistical Mechanical Study of a Small All-$\beta$ Protein}, JOURNAL = {Biopolymers}, VOLUME = 42, PAGES = {745--757}, YEAR = 1997 } @ARTICLE{berriz-shakhnovich97, AUTHOR = {Gabriel F. Berriz and Alexander M. Gutin and Eugene I. Shakhnovich}, TITLE = {Cooperativity and Stability in a {L}angevin Model of Proteinlike Folding}, JOURNAL = {Journal of Chemical Physics}, VOLUME = 106, NUMBER = 22, PAGES = {9276--9285}, YEAR = 1997 } @ARTICLE{socci-onuchic95, AUTHOR = {Nicholas D. Socci and Jos\'{e} N. Onuchic}, TITLE = {Kinetics and thermodynamic analysis of proteinlike heteropolymers: Monte Carlo histogram technique}, JOURNAL = {Journal of Chemical Physics}, VOLUME = 103, NUMBER = 11, PAGES = {4732--4744}, YEAR = 1995 } @ARTICLE{sali-karplus94, AUTHOR = {Andrej \u{S}ali and Eugene Shakhnovich and Martin Karplus}, TITLE = {How Does a Protein Fold?}, JOURNAL = {Nature}, VOLUME = 369, PAGES = {248--251}, YEAR = 1994 } Methodological papers: @ARTICLE{bennett76, AUTHOR = {Charles H. Bennett}, TITLE = {Efficient Estimation of Free Energy Differences from {M}onte {C}arlo Data}, JOURNAL = {Journal of Computational Physics}, VOLUME = 22, PAGES = {245--268}, YEAR = 1976 } @ARTICLE{ferrenberg-swendsen88, AUTHOR = {Alan M. Ferrenberg and Robert H. Swendsen}, TITLE = {New {M}onte {C}arlo Technique for Studying Phase Transitions}, JOURNAL = {Physical Review Letters}, VOLUME = 61, NUMBER = 23, PAGES = {2635--2638}, YEAR = 1988 } @ARTICLE{ferrenberg-swendsen89, AUTHOR = {Alan M. Ferrenberg and Robert H. Swendsen}, TITLE = {Optimized {M}onte {C}arlo Data Analysis}, JOURNAL = {Physical Review Letters}, VOLUME = 63, NUMBER = 12, PAGES = {1195--1198}, YEAR = 1989 } @ARTICLE{kumar-rosenberg92 AUTHOR = {Shankar Kumar and Djamal Bouzida and Robert H. Swendsen and Peter A. Kollman and John M. Rosenberg}, TITLE = {The Weighted Histogram Analysis Method for Free-Energy Calculations on Biomolecules. {I}. {T}he Method}, JOURNAL = {Journal of Computational Chemistry}, VOLUME = 13, NUMBER = 8, PAGES = {1011--1021}, YEAR = 1992 } From chemistry-request@www.ccl.net Thu Feb 4 16:08:10 1999 Received: from mail.rwth-aachen.de (mail.RWTH-Aachen.DE [137.226.144.9]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id QAA17900 Thu, 4 Feb 1999 16:08:09 -0500 (EST) Received: from zosia (zosia.dorf.RWTH-Aachen.DE) by mail.rwth-aachen.de (PMDF V5.1-12 #30440) with SMTP id <01J7D0ROKIK20008B5@mail.rwth-aachen.de> for chemistry@www.ccl.net; Thu, 4 Feb 1999 22:06:46 +0100 Date: Thu, 04 Feb 1999 22:07:58 +0100 From: Krzysztof Radacki Subject: Re: CCL:G:Freq in G94 In-reply-to: X-Sender: kradacki@mail.rwth-aachen.de To: chemistry@www.ccl.net Message-id: <3.0.6.32.19990204220758.007d04f0@mail.rwth-aachen.de> MIME-version: 1.0 X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.6 (32) Content-type: text/plain; charset="us-ascii" References: <36B99392.F9FFF935@ac.rwth-aachen.de> Dear CCLers, I would like to thank all people who answerd my question. Below is one of first answers I get ( from Frank Jensen): >These are the 6 modes corresponding to overall translation >and rotation of the molecule. The three 0.00xx modes are the T-modes, >which should be identically zero, but are not due to numerical >inaccuracies. The other 3 are the R-modes, which also should be >zero, but are not since the gradient is not exactly zero. The >second set of frequencies are obtained by diagonalizing the >force constant matrix after explicit removal of these 6 >T+R modes. Once more thank you all. Regards Krzys Radacki _________________________---------------------------------------------------- ------------------------- e-mail: Krys.Radacki@ac.RWTH-Aachen.DE --- ---------------------------------------------------------------------------- - From chemistry-request@www.ccl.net Thu Feb 4 17:51:05 1999 Received: from mailserv.molienergy.bc.ca (fireserv.molienergy.bc.ca [207.216.249.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id RAA19435 Thu, 4 Feb 1999 17:51:04 -0500 (EST) Received: by MAILSERV.molienergy.bc.ca with Internet Mail Service (5.0.1458.49) id ; Thu, 4 Feb 1999 14:49:36 -0800 Message-ID: <71B30885B657D111809D080009EEBBF34FE70D@MAILSERV.molienergy.bc.ca> From: Jan Reimers To: "'kynn@panix.com'" Cc: "'CHEMISTRY@www.ccl.net'" Subject: RE: G:Histogram method, redux Date: Thu, 4 Feb 1999 14:49:36 -0800 X-Priority: 3 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.0.1458.49) Content-Type: text/plain I will try once more to explain with the magnetism analogy (as used by Ferrenberg and Swendsen). Magnetism Protein folding You tune Temp & Field (T,Hm) Temp & "FoldingField" (T,Hfold) MC measures Energy & Magnetization (E,m) Energy & Degree of folding (E,f) In the magnetic system below Tc the free energy F(m) becomes bimodal with minima at +m and -m. The MC time required to jump from the +m to -m grows exponentially with (Tc-T), so it is hopeless to measure the relative probability of the two states at low T. You need a way to get around this. For the multi histogram method we have to options for data collection, 1) sweep various T values and store energy histograms H(E), m(e), m^2(e) etc. (as do Ferrenberg and Swendsen) or 2) sweep H values and store H(m), E(m), E^2(m) etc. Joining histograms H(E) provides information on the relative probabilities of the various energy states P(E), not the probabilities of magnetization states. For the latter you need to build up H(m), which is most efficiently done sweeping the external field that couples to m in the Hamiltonian, Hm. Enough magnetism. For protein folding the story is similar, joining H(E) histograms does not help you determine H(f). f=degree of folding). You need to define a folding parameter (doesn't sound too hard) and add a term Hfold*f to your Hamiltonian. Hfold now "pushes" your system towards folded (Hfold>0) and unfolded (Hfold<0) states. In the end you calculate P(f) (or the log) using the multi histogram method for a value of Hfold=0, so the fact that Hfold is unphysical is irrelvant to the final number, it just forces the metropolis algorithm to sample states that are extremly low probability when Hfold=0. ________________________ Jan N. Reimers (Ph.D.) Manager, Materials Research NEC Moli Energy (Canada) Ltd. ________________________