From chemistry-request@server.ccl.net Sun Jan 26 02:40:58 2003 Received: from [195.229.145.1] ([195.229.145.1]) by server.ccl.net (8.11.6/8.11.0) with SMTP id h0Q7eve27427 for ; Sun, 26 Jan 2003 02:40:57 -0500 Received: from no.name.available by [195.229.145.1] via smtpd (for server.ccl.net [192.153.40.39]) with SMTP; Sun, 26 Jan 2003 11:32:08 +0400 Received: from FSD1G1D (gwd1b1h.zu.ac.ae [10.10.0.23]) by macsmtp.zu.ac.ae (8.12.5/8.12.5) with ESMTP id h0Q7Xv7M011391 for ; Sun, 26 Jan 2003 11:33:57 +0400 Received: from EMBADOMAIN-MTA by FSD1G1D with Novell_GroupWise; Sun, 26 Jan 2003 11:40:00 +0400 Message-Id: X-Mailer: Novell GroupWise Internet Agent 6.0 Date: Sun, 26 Jan 2003 11:39:46 +0400 From: "Iman Boukhobza" To: Subject: Dihedral angles Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Disposition: inline Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h0Q7ewe27428 Hi I am trying to create a z matrix for a vandium complex. I have the necessary bond lengths and angles that I got from crystallography data. The problem now is dihedral angles! Any idea how these angles can be found? ps: I have worked with linear molecules, and dihedral angles were not much of a problem. Thanks Iman Boukhobza Assistant professor Zayed university From jkl@ccl.net Sun Jan 26 02:43:57 2003 -0500 Return-Path: Received: from hotmail.com (f172.law9.hotmail.com [64.4.9.172]) by ccl.net (8.11.6+Sun/8.11.6/OSC 2.1) with ESMTP id h0Q7hvj04412 for ; Sun, 26 Jan 2003 02:43:57 -0500 (EST) Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Sat, 25 Jan 2003 23:43:57 -0800 Received: from 212.138.47.29 by lw9fd.law9.hotmail.msn.com with HTTP; Sun, 26 Jan 2003 07:43:56 GMT X-Originating-IP: [212.138.47.29] From: "sabry ahmed" To: jkl@ccl.net Subject: I can't post my message Date: Sun, 26 Jan 2003 10:43:56 +0300 Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 26 Jan 2003 07:43:57.0159 (UTC) FILETIME=[AEBC5F70:01C2C50E] Dear All, I'm interested in computing the BDE(R-O2)for a series of halogenated peroxyl radicals at ab initio and DFT (B3LYP/6-31G** and B3LYP/6-311+G(2df,2p) levels. For R=CH3, values of BDE(R-O2)=30.6 and 29.1 at B3LYP/6-31G** and B3LYP/6-311+G(2df,2p), respectively, are published (J. Phys. Chem. A 1999, 103, 7094). I've tried to get these values by calculating the enthalpies of the following isogyric reaction: CH3O2 + H2 = CH3O2H + H CH3O2H + H2 = CH4 + H2O2 then, by combining these enthalpies with experimentally known heats of formation, the heat of formation of CH3O2 can be obtained. Finally, the enthalpy of the dissociation reaction: CH3O2 = CH3 + O2 , which is equal to the BDE(CH3O2)is calculated as follows: BDE(CH3O2)= heat of formation of CH3 - heat of formation of CH3O2 Unfortunately, I got BDE values of 44.4 and 37.1 kcal/mol instead of the published values 30.6 and 29.1 kcal/mol. Is there something wrong in what I've done, or something I should do more? thanks in advance, I'll summarize your responses. yours, -Sabry current address: Teachers College in Dammam P.O. Box 2375 Dammam 31451 Kingdom of Saudi Arabia From chemistry-request@server.ccl.net Sun Jan 26 08:49:50 2003 Received: from sims.csuohio.edu ([137.148.5.58]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0QDnoe17949 for ; Sun, 26 Jan 2003 08:49:50 -0500 Received: from csuohio.edu (dialup229-114.csuohio.edu [137.148.229.114]) by sims.csuohio.edu (Sun Internet Mail Server sims.4.0.1999.09.28.17.31.p2) with ESMTP id <0H9B00JNLQH2BB@sims.csuohio.edu> for chemistry@ccl.net; Sun, 26 Jan 2003 08:51:04 -0500 (EST) Date: Sun, 26 Jan 2003 08:49:42 -0500 From: Valentin Gogonea Subject: bond stretching force constant from QM data To: chemistry@ccl.net, gmx-users@gromacs.org Message-id: <05A61A48-3135-11D7-A147-003065CDB448@csuohio.edu> MIME-version: 1.0 X-Mailer: Apple Mail (2.551) Content-type: text/plain; format=flowed; charset=US-ASCII Content-transfer-encoding: 7BIT Dear CCLers and GMX users, I am trying to estimate the force constant for Fe-S bond stretching > from QM calculations and use it with Gromos87 force field (gromacs). I carried out UB3LYP/6-31+G** calculations for Fe-SCH3 (charge=+1,multip=5) and Fe-Imidazole (+2,5) with G98 and I got the following force constants (I used a conversion factor from mDyne/A to KJ/(mol nm2) of 60230): mDyne/A kJ/(mol nm2) Gromos87 Fe-S 1.839 110763 Fe-N 0.757 45594 418400 1) Is it acceptable to scale properly (using the QM and Gromos Fe-N force constants) the Fe-S force constant to be in the same range as the Fe-N force constant in the Gromos87 force field. Did anybody use this kind of approach or there is a better way to estimate and adjust the QM determined force constant to a force field force constant? 2) For an angle bending the force constant required in the forcefield has units of kJ/(mol rad2), while the one obtained from QM calculations has units of kJ/(mol nm2). I believe that the former can be obtained > from the latter if one assumes that the oscillator length for this particular normal mode is the distance between the endpoints of the angle. This should be valid for a torsion angle too. Is this correct? I would appreciate any insight that I can get from the list and I thank you for your help. Valentin Gogonea Department of Chemistry Cleveland State University Received: from out004.verizon.net (out004pub.verizon.net [206.46.170.142]) by ccl.net (8.11.6+Sun/8.11.6/OSC 2.1) with ESMTP id h0QMuCj22722 for ; Sun, 26 Jan 2003 17:56:12 -0500 (EST) Received: from anick000 ([63.16.3.212]) by out004.verizon.net (InterMail vM.5.01.05.20 201-253-122-126-120-20021101) with ESMTP id <20030126225610.ORDI2505.out004.verizon.net@anick000> for ; Sun, 26 Jan 2003 16:56:10 -0600 From: "David J Anick" To: chemistry@ccl.net Subject: How to resolve overlapping Gaussians in the UV Spectrum? Message-ID: <002701c2c5a6$e23bad40$d403103f@anick000> Date: Sun, 26 Jan 2003 17:53:24 -0800 Dear CCL-ers, I have a complex line shape from a spectrum that I would like to represent as a sum of overlapping Gaussians. More precisely, I have a function y=f(x), a < x < b, given as about 500 (x,y) points, where f(a)=f(b)=0, and I would like to find a small number (typically 3 to 8, perhaps) of Gaussians whose sum approximates f. I.e. I want to generate parameters {c_i,s_i,b_i} for which the function F(x) = SIGMA_i c_i exp(-s_i*(x-b_i)^2) is a very good approximation to f. Can anyone please point me to software, free or not, Linux or Windows, that can do this? Thank you. I will summarize responses. David Anick PhD MD David.Anick@gte.net (Harvard Medical School) From chemistry-request@server.ccl.net Sun Jan 26 17:41:39 2003 Received: from mail012.syd.optusnet.com.au ([210.49.20.170]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0QMfZe28616 for ; Sun, 26 Jan 2003 17:41:38 -0500 Received: from mail.eburwd1.vic.optushome.com.au (c18842.eburwd1.vic.optusnet.com.au [210.49.181.184]) by mail012.syd.optusnet.com.au (8.11.1/8.11.1) with ESMTP id h0QMfYq24296 for ; Mon, 27 Jan 2003 09:41:35 +1100 Message-ID: <200301270941350375.003705C1@mail.eburwd1.vic.optushome.com.au> X-Mailer: Calypso Version 3.30.00.00 (4) Date: Mon, 27 Jan 2003 09:41:35 +1100 Reply-To: fburden@optushome.com.au From: "Frank Burden" To: chemistry@ccl.net Subject: SciPredict: Update Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====_10436208951102=_" --=====_10436208951102=_ Content-Type: text/plain; charset="us-ascii" There have been a few reports of difficulties with SciPredict > from users with locked Windows directories (File path unknown). Also the closing-down routine left SciPredict running in the background. This is almost indiscernible except when trying to uninstall SciPredict. For those interested a modified SciPredict is now available on www.scimetrics.com/software Download the program and you will get to access the Vapor Pressure model for a (new) 10 days free trial. Models available for purchase are Vapor Pressure, LogP, Henry's law and Water Solubility. Please send queries and comments to: Dr Frank Burden SciMetrics 23 Harrow Street Blackburn South VIC 3130 Australia frank.burden@scimetrics.com --=====_10436208951102=_ Content-Type: text/html; charset="us-ascii"
There have been a few reports of difficulties with SciPredict from users with locked Windows directories (File path unknown).
Also the closing-down routine left SciPredict running in the background. This is almost indiscernible except when trying to uninstall SciPredict.
 
For those interested a modified SciPredict is now available on www.scimetrics.com/software
 
Download the program and you will get to access the Vapor Pressure model for a (new) 10 days free trial.
Models available for purchase are Vapor Pressure, LogP, Henry's law and Water Solubility.
 
Please send queries and comments to:
 
Dr Frank Burden
SciMetrics
23 Harrow Street
Blackburn South
VIC 3130   Australia
frank.burden@scimetrics.com
--=====_10436208951102=_-- From chemistry-request@server.ccl.net Sun Jan 26 17:06:41 2003 Received: from smtp01.mrf.mail.rcn.net ([207.172.4.60]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0QM6fe27571 for ; Sun, 26 Jan 2003 17:06:41 -0500 Received: from ms05.mrf.mail.rcn.net ([207.172.4.19]) by smtp01.mrf.mail.rcn.net with esmtp (Exim 3.35 #4) id 18cuvJ-0000yj-00 for chemistry@ccl.net; Sun, 26 Jan 2003 17:06:41 -0500 Received: from 207.172.190.132 by ms05.mrf.mail.rcn.net (Mirapoint Messaging Server MOS 3.2.2-GA) with HTTP/1.1; Sun, 26 Jan 2003 17:06:41 -0500 Date: Sun, 26 Jan 2003 17:06:41 -0500 From: simulationchallenge@rcn.com Subject: Industrial Fluid Properties Simulation Challenge To: chemistry@ccl.net X-Mailer: Webmail Mirapoint Direct 3.2.2-GA MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Message-Id: Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from base64 to 8bit by server.ccl.net id h0QM6fe27572 In June 2001 a workshop was held at NIST on the use of "Simulation Methods to Predict the Thermophysical Properties of Fluids". The participants (chosen to represent industry, academia and government labs) concluded that a major limitation to the practical application of simulation methods was a lack of validation and comparison studies on industrially relevant properties and materials. This limitation was also recognized in a detailed study of the future of the U.S. chemical industry: “Technology Vision 2020”, and in the “Technology Roadmap for Computational Chemistry”. To address this problem the Industrial Fluid Properties Simulation Challenge was established. In the first Challenge the modeling community was asked to predict densities, viscosity and VLE for a specified set of materials. Predictions were compared with accurate experimental data (obtained specifically for this contest at NIST and the Dow Chemical Company). The results, and publications by most of the entrants describing the methods they used, will be published in an upcoming edition of Fluid Phase Equilibria. We are now planning a second Challenge. We are seeking input (brainstorming) on the types of physical properties we should include. If you are an industrial modeler or work with industry, please send us your suggestions. We will be selecting the physical properties to be included in the next Challenge based on three criteria: 1) Industrial relevance 2) Possibility of prediction using a simulation approach 3) The degree of challenge in experimental evaluation (if the property is harder to measure, simulation is more likely to be used) Any comments about the desired (industrially useful) accuracy for a prediction would also be helpful (+/- 0.1%, 1%, 10%?) We will post a summary of suggestions received by the 14th February, and later we will post a full description of the problem sets and details on how you can participate in this contest. Thank you The Industrial Fluids Properties Simulation Challenge Committee: Chair: Raymond Mountain - NIST Anne Chaka - NIST Daniel Friend - NIST Russell Johnson - NIST Dave Frurip - Dow Chemical Company Jonathan Moore - Dow Chemical Company James Olson - Dow Chemical Company Fiona Case - Colgate Palmolive Joseph Golab - BP Petr Kolar - Mitsubishi Martin Schiller - E.I. du Pont de Nemours and Company Email: simulationchallenge@rcn.com Simulation Challenge website: http://www.cstl.nist.gov/FluidSimulationChallenge/ Reports of the 2001 NIST workshop: http://www.ctcms.nist.gov/~fstarr/ptpfms/home.html Chemical Industry Vision 2020 Technology Partnership, sponsored by AIChE, ACS, and CCR, http://www.chemicalvision2020.org/ "Chemical Industry of the Future, Technology Roadmap for Computational Chemistry", 1999, http://www.ccrhq.org/vision/index/roadmaps/complete.html From chemistry-request@server.ccl.net Sun Jan 26 23:38:51 2003 Received: from smtp1.Stanford.EDU ([171.64.14.23]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0R4coP03423 for ; Sun, 26 Jan 2003 23:38:50 -0500 Received: from smtp1.Stanford.EDU ([127.0.0.1]) by smtp1.Stanford.EDU (8.12.6/8.12.6) with ESMTP id h0R4cnHL012439 for ; Sun, 26 Jan 2003 20:38:50 -0800 (PST) Received: from SERGE (DNab407cfb.Stanford.EDU [171.64.124.251]) by smtp1.Stanford.EDU (8.12.6/8.12.6) with SMTP id h0R4clpi012434; Sun, 26 Jan 2003 20:38:48 -0800 (PST) Message-ID: <000801c2c5bd$fc549e50$fb7c40ab@SERGE> From: "S. I. Gorelsky" To: "David J Anick" Cc: References: <002701c2c5a6$e23bad40$d403103f@anick000> Subject: Re: CCL:How to resolve overlapping Gaussians in the UV Spectrum? Date: Sun, 26 Jan 2003 20:38:48 -0800 Organization: Stanford University MIME-Version: 1.0 Content-Type: text/plain; charset="koi8-r" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1106 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 Hello, Here is one program to do exactly what you want: http://www.obbligato.com/software/swizard/ You can model your spectrum as a sum of Gaussians, a sum of Lorentzian functions, or their mixture. With regards, S. Gorelsky Department of Chemistry, Stanford University, 333 Campus Drive, Stanford, CA 94305-5080 Fax: (650) 723-0553 Phone: (650) 723-0041 http://www.stanford.edu/~gorelsky/ ----- Original Message ----- From: "David J Anick" To: Sent: Sunday, January 26, 2003 4:25 PM Subject: CCL:How to resolve overlapping Gaussians in the UV Spectrum? > Date: Sun, 26 Jan 2003 17:53:24 -0800 > > Dear CCL-ers, > > I have a complex line shape from a spectrum that I would like to > represent as a sum of overlapping Gaussians. More precisely, > I have a function y=f(x), a < x < b, given as about 500 (x,y) > points, where f(a)=f(b)=0, and I would like to find a small > number (typically 3 to 8, perhaps) of Gaussians whose sum > approximates f. I.e. I want to generate parameters {c_i,s_i,b_i} > for which the function > F(x) = SIGMA_i c_i exp(-s_i*(x-b_i)^2) > is a very good approximation to f. > > Can anyone please point me to software, free or not, Linux or > Windows, that can do this? > > Thank you. I will summarize responses. > > David Anick PhD MD > David.Anick@gte.net > (Harvard Medical School) > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > >