From jcf@bureau.pharmacie.unicaen.fr Tue Nov 4 04:35:06 1997 Received: from bureau.pharmacie.unicaen.fr for jcf@bureau.pharmacie.unicaen.fr by www.ccl.net (8.8.3/950822.1) id DAA00356; Tue, 4 Nov 1997 03:45:26 -0500 (EST) Received: by bureau.pharmacie.unicaen.fr (940816.SGI.8.6.9/940406.SGI.AUTO) for chemistry@www.ccl.net id JAA09033; Tue, 4 Nov 1997 09:35:23 +0100 From: "Jean-Christophe" Message-Id: <9711040935.ZM9031@bureau.pharmacie.unicaen.fr> Date: Tue, 4 Nov 1997 09:35:11 +0100 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@www.ccl.net Subject: organic molecules and chemical functions Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear CCLers, I am looking for a program to determine and to code the chemical functions (i.e., epoxide, fused rings, amines ...) of small organic molecules (I have the codes SMILES of these molecules). Would any one please give me any information about where can I find programs to do this ? Thanks a lot in advance. -- ------------------------------------------ FAUCON Jean-Christophe UFR de Pharmacie Universite de Caen FRANCE email: jcf@bureau.pharmacie.unicaen.fr ------------------------------------------ From tamasgunda@tigris.klte.hu Tue Nov 4 04:44:39 1997 Received: from tigris.klte.hu for tamasgunda@tigris.klte.hu by www.ccl.net (8.8.3/950822.1) id EAA00515; Tue, 4 Nov 1997 04:18:49 -0500 (EST) Message-Id: <199711040918.EAA00515@www.ccl.net> Received: from anti02 (anti02.chem.klte.hu) by tigris.klte.hu (MX V4.1 VAX) with SMTP; Tue, 04 Nov 1997 08:11:18 +0100 Comments: Authenticated sender is From: "Tamas Gunda" To: chemistry@www.ccl.net Date: Tue, 4 Nov 1997 08:11:17 +1 MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7BIT Subject: bromonium ion Priority: normal X-mailer: Pegasus Mail for Windows (v2.42a) Dear CCL members, My question is 50%-50% of organic and theoretical chemistry, no computers this time. I have problem with the mechanism of a strange rearrangement. Has anybody some info or knowledge about the following behavior of bromonium ion (Br+): if it is generated in a reaction when the solvent is acetonitrile, is acetonitrile capable of complexing or stabilizing this ion? I think theoretically yes, because with the triple bond of the C#N group, it could form some complex. However, I did not find any literature data so far. best regards Tamas E. Gunda ************************************************************************ Dr Tamas E. Gunda phone: (+36-52) 316666 ext 2479 Research Group of Antibiotics fax : (+36-52) 310936 L. Kossuth University e-mail: tamasgunda@tigris.klte.hu POBox 36 H-4010 Debrecen Hungary ************************************************************************ From Jeffrey.Gosper@brunel.ac.uk Tue Nov 4 06:35:08 1997 Received: from eros.brunel.ac.uk for Jeffrey.Gosper@brunel.ac.uk by www.ccl.net (8.8.3/950822.1) id FAA00785; Tue, 4 Nov 1997 05:35:17 -0500 (EST) Received: from ccns17-01.brunel.ac.uk by eros.brunel.ac.uk with SMTP-BRUNEL (PP); Tue, 4 Nov 1997 10:34:27 +0000 From: Jeffrey J Gosper Reply-To: Jeffrey.Gosper@brunel.ac.uk To: chemistry@www.ccl.net Subject: CCL:G:Vibrational Visualization of Gaussian Outputs Message-ID: Date: Tue, 4 Nov 1997 10:34:06 +0000 (GMT) Priority: NORMAL X-Mailer: Simeon for Windows Version 4.1.1 Build (16) X-Authentication: none MIME-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII > > Hello: > > I am currently looking for a program (free or inexpensive, sorry, I am > still a graduate student), that will help me to visualize the vibrational > modes of a molecule from a Gaussian 94 (or 92) output file. I am aware > of Re_view for MOPAC files, but of none for Gaussian. > > Thank you, > > Greg Dear Greg and other interested parties, Re_View2 is able to visualize G94 vibrations. You''ll need a the extra file converter GvivView that is supplied on Re_View2's CDROM. For further details on re_View2 see: http://www.brunel.ac.uk/depts/chem/ch241s/re_view/re_view2.htm Cheers Jeffrey J Gosper Brunel University, UK castjjg@brunel.ac.uk From d.w.price@reading.ac.uk Tue Nov 4 11:35:12 1997 Received: from sumh1.reading.ac.uk for d.w.price@reading.ac.uk by www.ccl.net (8.8.3/950822.1) id LAA02638; Tue, 4 Nov 1997 11:18:20 -0500 (EST) Received: from indyp (actually host scsgind2) by sumh1.rdg.ac.uk; Tue, 4 Nov 1997 16:17:24 +0000 Received: from Indyp by indyp via SMTP (940816.SGI.8.6.9/930416.SGI) for id QAA23560; Tue, 4 Nov 1997 16:17:12 GMT Sender: dave@reading.ac.uk Message-ID: <345F4A88.2781@reading.ac.uk> Date: Tue, 04 Nov 1997 16:17:12 +0000 From: Dave Price Organization: none-what-so-ever X-Mailer: Mozilla 3.01Gold (X11; I; IRIX 5.3 IP22) To: Comp Chem Mailing List Subject: Basis sets/pseudopotentials/plane wave sets for U or Pu MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear All, Does any one have basis sets / pseudopotentials / planewave sets for uranium or plutonium? Both molecular and periodic systems are of interest and I am also interested in programs that have already been used with these elements for molecular and periodic systems. Any information gratefully received. Cheers, Dave ------------------------------------------------------------------------ Dr. David W. Price, Tel: +44 (0)118 9875123 extn 7415 Department of Chemistry, Fax: +44 (0)118 9316331 University of Reading, mailto:d.w.price@reading.ac.uk Whiteknights, READING http://www.chem.rdg.ac.uk/g50/mmrg/dave/dave.html RG6 6AD U.K. ------------------------------------------------------------------------ From mxt43@roo.INS.CWRU.Edu Tue Nov 4 14:35:12 1997 Received: from roo.INS.CWRU.Edu for mxt43@roo.INS.CWRU.Edu by www.ccl.net (8.8.3/950822.1) id NAA03473; Tue, 4 Nov 1997 13:51:37 -0500 (EST) Received: (mxt43@localhost) by roo.INS.CWRU.Edu (8.8.6+cwru/CWRU-2.4-bsdi) id NAA16565; Tue, 4 Nov 1997 13:51:30 -0500 (EST) (from mxt43) Message-Id: <199711041851.NAA16565@roo.INS.CWRU.Edu> Date: Tue, 4 Nov 1997 13:51:30 -0500 (EST) From: mxt43@po.CWRU.Edu (Meihua Tu) To: chemistry@www.ccl.net Subject: Simulating Photosensitized Reaction Reply-To: mxt43@po.CWRU.Edu (Meihua Tu) Dear CCLers, Can anybody give me some suggestions on simulating a photosensitized reaction, like Riboflavin (Vitamin B2) sentisitized photooxidation of Tyrosine. Thank you in advance, Meihua Tu -- Tel: 216-368-3606 E-Mail: mxt43@po.cwru.edu From bersuker@eeyore.cm.utexas.edu Tue Nov 4 15:35:14 1997 Received: from eeyore.cm.utexas.edu for bersuker@eeyore.cm.utexas.edu by www.ccl.net (8.8.3/950822.1) id PAA03762; Tue, 4 Nov 1997 15:02:49 -0500 (EST) From: Received: by eeyore.cm.utexas.edu (AIX 3.2/UCB 5.64/4.03) id AA10950; Tue, 4 Nov 1997 13:55:53 -0600 Message-Id: <9711041955.AA10950@eeyore.cm.utexas.edu> Subject: Computational Chemists Wanted To: CHEMISTRY@www.ccl.net Date: Tue, 4 Nov 1997 13:55:52 -0600 (CST) X-Mailer: ELM [version 2.4 PL25] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit I am looking for young researchers - may be PhD students - with a (minimum) Masters degree in Theoretical (Computational) Chemistry, experience in quantum-chemical calculations, and good knowledge of computers and programming, to work with me on a project of modeling (calculations of) structure and properties of large and very large organometallic (metallobiochemical) systems (for an introduction see Internat. J. Quant. Chem., 63, 1051 (1997)). Interested persons please contact me via e-mail. Isaac B. Bersuker -- * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Isaac B. Bersuker | E-mail: Dept. of Chemistry | bersuker@eeyore.cm.utexas.edu Univeristy of Texas at Austin | Vox: (512) 471-4671 Austin, TX 78712 | Fax: (512) 471-8696 * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * From yliu@mail.wesleyan.edu Tue Nov 4 16:35:28 1997 Received: from mail.wesleyan.edu for yliu@mail.wesleyan.edu by www.ccl.net (8.8.3/950822.1) id QAA04306; Tue, 4 Nov 1997 16:34:42 -0500 (EST) Received: from violet.chem.wesleyan.edu (violet.chem.wesleyan.edu [129.133.20.94]) by mail.wesleyan.edu (8.8.6/8.7.3) with SMTP id QAA24764 for ; Tue, 4 Nov 1997 16:34:33 -0500 (EST) Message-Id: <2.2.32.19971104213213.00692238@mail.wesleyan.edu> X-Sender: yliu@mail.wesleyan.edu X-Mailer: Windows Eudora Pro Version 2.2 (32) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 04 Nov 1997 16:32:13 -0500 To: chemistry@www.ccl.net From: Yongxing Liu Subject: Summary: Algorithm to build 3D molecule Dear CCLers, Thanks for all who answered my questions. ********************* The Original Question **************** I am looking for algorithms to build 3D coordinates of small molecules for further refinement. The inputs are atomic element type(H,C,N,O,etc),connectivity and bond order only. The output will be the 3D coordinates for each atom. **** Answer From Professor Richard Gillilan ************ I see that the NCI database was built from connectivity files using Chem-X. There is a useful discussion about the limitations and failures of the method on http://epnws1.ncifcrf.gov:2345/dis3d/3Ddatabase/chemx/tech.html#build The page also gives a pointer to the CONCORD software (TRIPOS). The readme file that came with the version of the NCI database I downloaded a year ago talks about the Corina program: (1) Sadowski, J.; Gasteiger, J. "From Atoms and Bonds to Three- Dimensional Molecular Models: Automatic Model Builders." Chem. Rev. 1993, 93, 2567-2581. (2) Sadowski, J.; Gasteiger, J.; Klebe, G. "Comparison of Automatic Three-Dimensional Model Builders Using 639 X-Ray Structures." J. Chem. Inf. Comput. Sci. 1994, 34, 1000-1008. ****** Answer from Dr. Zhaowen Luo ********* As far as I know, CONCORD is a popurlar algorithsm for that. It is commerical available. Following is the description: CONCORD is a program developed at the University of Texas at Austin for the rapid generation of high quality approximate 3-dimensional molecular structures. I think CONCORD is a doctoral thesis. ***** Answer form Dr. Wang Arthur ***** The problem that you have encounted is called 2D to 3D conversion. No doubt many successful algorithms have been developed, such as CONCORD, CORINA, CONVERTER ... **** Many other people pointed me to their programs, Thanks too. **** Yongxing Liu Department of Chemistry Wesleyan University Middletown CT 06459 E-mail yliu@wesleyan.edu Telephone: 860-685-2777 Fax: 860-685-2211 Http://linus.chem.wesleyan.edu/yliu/ From tj@eecs.uic.edu Tue Nov 4 21:35:15 1997 Received: from mail.eecs.uic.edu for tj@eecs.uic.edu by www.ccl.net (8.8.3/950822.1) id VAA05646; Tue, 4 Nov 1997 21:26:56 -0500 (EST) Received: from ernie.eecs.uic.edu (root@ernie.eecs.uic.edu [131.193.41.33]) by mail.eecs.uic.edu (8.7.5/8.7.5) with ESMTP id UAA25470 for ; Tue, 4 Nov 1997 20:28:39 -0600 (CST) Received: from bert.eecs.uic.edu (root@bert.eecs.uic.edu [131.193.40.32]) by ernie.eecs.uic.edu (8.6.10/8.6.10) with ESMTP id UAA20838 for ; Tue, 4 Nov 1997 20:28:21 -0600 Received: from ursus.research.aa.wl.com (slip3.eecs.uic.edu [131.193.33.34]) by bert.eecs.uic.edu (8.6.10/8.6.10) with SMTP id UAA08439 for ; Tue, 4 Nov 1997 20:27:04 -0600 Message-ID: <345FD8F1.5B9E@eecs.uic.edu> Date: Tue, 04 Nov 1997 20:24:49 -0600 From: "TJ O'Donnell" Reply-To: tj@eecs.uic.edu X-Mailer: Mozilla 3.01 (Win95; I) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: Re: CCL:Guide of SMILE References: <345CA849.9CED74FF@guomai.sh.cn> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit In response to the inquiry about SMILES, links to a tutorial on SMILES are at: http://www.daylight.com/dayhtml/smiles/ TJ O'Donnell tj@eecs.uic.edu http://www.eecs.uic.edu/~tj