From somsak@atc.atccu.chula.ac.th Thu Dec 12 05:09:06 1996 Received: from atc.atccu.chula.ac.th for somsak@atc.atccu.chula.ac.th by www.ccl.net (8.8.3/950822.1) id EAA19226; Thu, 12 Dec 1996 04:32:47 -0500 (EST) Received: by atc.atccu.chula.ac.th (5.57/CFTHAI-2e1.ULTRIX) id AA08434; Thu, 12 Dec 96 18:55:41 GMT From: somsak@atc.atccu.chula.ac.th (Somsak Tonmunphean) Message-Id: <9612121855.AA08434@atc.atccu.chula.ac.th> Subject: How to calculate Bond Order ? To: CHEMISTRY@www.ccl.net Date: Thu, 12 Dec 1996 18:55:41 +0000 (WET) X-Mailer: ELM [version 2.4 PL20] Content-Type: text Dear Netters, I am doing my thesis with the subject of QSAR of antimalarial drugs. My available chemical calculation softwares are Gaussian 92, Hyperchem release 3, ChemPlus, Alchemy, and Molgen. From some papers, they calculated bond orders and found that these had good correlations with activity so I would like to try it but unfortunately I really don't know how to calculate the bond order of molecules. Does anybody know how to do so (if possible with the programs I have) ? Thank you very much in advance for your help. Yours sincerely, Somsak Tonmunphean. (Ph.D. Candidate) Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330 Thailand From Jeffrey.Gosper@brunel.ac.uk Thu Dec 12 10:09:08 1996 Received: from etamin.brunel.ac.uk for Jeffrey.Gosper@brunel.ac.uk by www.ccl.net (8.8.3/950822.1) id JAA20503; Thu, 12 Dec 1996 09:10:13 -0500 (EST) Received: from chem-pc-18 (actually chem-pc-18.brunel.ac.uk) by etamin.brunel.ac.uk with SMTP (PP); Thu, 12 Dec 1996 14:01:43 +0000 Date: Thu, 12 Dec 1996 14:01:39 GMT From: Jeffrey J Gosper Subject: Re: CCL:G:How to calculate Bond Order ? To: Somsak Tonmunphean cc: CHEMISTRY@www.ccl.net Message-ID: Priority: Normal MIME-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII > Dear Netters, > I am doing my thesis with the subject of QSAR of antimalarial > drugs. My available chemical calculation softwares are Gaussian 92, > Hyperchem release 3, ChemPlus, Alchemy, and Molgen. From some papers, > they calculated bond orders and found that these had good correlations > with activity so I would like to try it but unfortunately I really don't > know how to calculate the bond order of molecules. Does anybody know how > to do so (if possible with the programs I have) ? > > MOPAC can calculate bond orders (using the BONDS keyword). We are currently working on an Windows program that will take XYZ files, run MOPAC, and produce an 'extended' XYZ file that contain bond connectivities and orders which can be viewed in Re_View2. Until this is finished you can look at the degrees of bonding table in the MOPAC output. /\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\ Dr. Jeff Gosper Dept. of Chemistry BRUNEL University Uxbridge Middx UB8 3PH, UK voice: 01895 274000 x2187 facsim: 01895 256844 internet/email/work: Jeffrey.Gosper@brunel.ac.uk internet/WWW: http://www.brunel.ac.uk/~castjjg Re_View's Home page (A molecular display/animation/analysis program): http://www.brunel.ac.uk/depts/chem/ch241s/re_view/re_view.htm \/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/ From jkerins@hermes.kcc.com Thu Dec 12 11:09:11 1996 Received: from gatekeeper.kcc.com for jkerins@hermes.kcc.com by www.ccl.net (8.8.3/950822.1) id KAA21024; Thu, 12 Dec 1996 10:55:41 -0500 (EST) Received: by gatekeeper.kcc.com (5.65/fma-120691); id AA07880; Thu, 12 Dec 1996 09:57:26 -0600 Received: by hermes.kcc.com (940816.SGI.8.6.9/930416.SGI) for chemistry@www.ccl.net id JAA19871; Thu, 12 Dec 1996 09:55:06 -0600 From: "John Kerins" Message-Id: <9612120955.ZM19869@hermes.kcc.com> Date: Thu, 12 Dec 1996 09:55:06 -0600 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@www.ccl.net Subject: self-assembled monolayers Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Do any readers have data files of self-assembled monolayers they would be willing to share? I am looking for c12-c18 extended chains, packed on a flat surface at about 21 square A per chain. I am using MSI's Insight/Discover package, but am ready to do file conversions if necessary. A colleague had a minor, curiousity question on SAMs, and I wanted to show him some molecular models to keep him thinking on the atomic level, without spending too much time to build the structures. Thanks for your attention. John Kerins Kimberly-Clark Corporation Neenah, WI jkerins@kcc.com 414 721-5517 From nash@chem.wisc.edu Thu Dec 12 12:09:16 1996 Received: from humvee.doit.wisc.edu for nash@chem.wisc.edu by www.ccl.net (8.8.3/950822.1) id LAA21382; Thu, 12 Dec 1996 11:35:58 -0500 (EST) Received: from audumla.students.wisc.edu by humvee.doit.wisc.edu; id KAA25012; 8.7.5/50; Thu, 12 Dec 1996 10:35:57 -0600 Received: from [144.92.91.209] by audumla.students.wisc.edu; id KAA133474; 8.6.9W/42; Thu, 12 Dec 1996 10:35:28 -0600 X-Sender: jrnash@144.92.104.66 Message-Id: In-Reply-To: <9612121855.AA08434@atc.atccu.chula.ac.th> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 12 Dec 1996 10:35:25 -0600 To: somsak@atc.atccu.chula.ac.TH From: "John R. Nash" Subject: Re: CCL:G:How to calculate Bond Order ? Cc: CHEMISTRY@www.ccl.net somsak@atc.atccu.chula.ac.TH wrote: >Dear Netters, > I am doing my thesis with the subject of QSAR of antimalarial >drugs. My available chemical calculation softwares are Gaussian 92, >Hyperchem release 3, ChemPlus, Alchemy, and Molgen. From some papers, >they calculated bond orders and found that these had good correlations >with activity so I would like to try it but unfortunately I really don't >know how to calculate the bond order of molecules. Does anybody know how >to do so (if possible with the programs I have) ? > F. Weinhold's Natural Bond Order (NBO) calculation available with G92 (and G94) will calculate bond orders (and do decomposition of bonds into "ionic" and "covalent" parts if requested). Check the manual for details, but at its simplest, you just put "POP=NBO" in the route card and $NBO $END at the end of the input file. This gives the default NBO analysis, including bond orders. -==-John R. Nash-==-nash@chem.wisc.edu-==-UW-Madison Chem. Dept-==- --- "When in doubt, roll!" ---