From owner-chemistry@ccl.net Tue Aug 8 03:47:30 1995 Received: from chu.chem.nthu.edu.tw for ccluser@chu.chem.nthu.edu.tw by www.ccl.net (8.6.10/930601.1506) id DAA11315; Tue, 8 Aug 1995 03:40:11 -0400 From: Received: by chu.chem.nthu.edu.tw (AIX 3.2/UCB 5.64/4.03) id AA18358; Tue, 8 Aug 1995 15:40:18 +0900 Message-Id: <9508080640.AA18358@chu.chem.nthu.edu.tw> Subject: SCRF in Gaussian 94 ? To: Chemistry@ccl.net Date: Tue, 8 Aug 95 15:40:17 TAIDT X-Mailer: ELM [version 2.4dev PL17] Dear list members, I am attempting to calculation with the keyword, " SCRF=PCM " -- in Gaussian 94,but i have been encountered problems about it's input . From user's reference, i know it needs dielectric constant of solvent and the number of points per sphere ,so i write input like following, ________________________________________________________________ 1 $ RunGaus 2 #n hf/3-21g scrf=pcm scfcyc=100 test 3 4 Gaussian 94 Test Job 1 5 flouride anion 6 7 -1 1 8 f 9 10 80.0 1.0 ____________________________________________________________________ I don't know what's wrong with my input? Any reply on this problem is appreciated! Sincerely, ===================================================================== San-Yan Chu | E-mail: ccluser@chu.chem.nthu.edu.tw Department of chemistry | National Tsing Hua University | Phone: 886-35-721634 Hsinchu, Taiwan 30043 | Fax: 886-35-711082 ===================================================================== From owner-chemistry@ccl.net Tue Aug 8 08:17:32 1995 Received: from rs2.hrz.th-darmstadt.de for schulte@ws09.pc.chemie.th-darmstadt.de by www.ccl.net (8.6.10/930601.1506) id IAA13745; Tue, 8 Aug 1995 08:11:51 -0400 Received: from ws09.pc.chemie.th-darmstadt.de by rs2.hrz.th-darmstadt.de with SMTP id AA24453 (5.65c/IDA-1.4.4 for ); Tue, 8 Aug 1995 14:11:22 +0200 Received: by ws09.pc.chemie.th-darmstadt.de (AIX 3.2/UCB 5.64/4.03) id AA12271; Tue, 8 Aug 1995 14:11:34 +0200 From: schulte@ws09.pc.chemie.th-darmstadt.de (Joachim Schulte) Message-Id: <9508081211.AA12271@ws09.pc.chemie.th-darmstadt.de> Subject: Problems with point group recognition in MOPAC 7.0 To: chemistry@ccl.net Date: Tue, 8 Aug 1995 14:11:33 +0200 (CST) X-Mailer: ELM [version 2.4 PL23] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 1054 Dear Ladies and Gentlemen, With Mopac 7.0 I have some problems concerning the recognition of some point groups. Provided with an icosahedral C60 geometry MOPAC does not recognize any point group, not even a subgroup of Ih. The output simply is '????'. The degeneracy scheme of the molecular orbital energies is looking correct (3-, 4- and fivefold degeneracies). This happens both for cartesian coordinates and Z-matrix coordinates (Mopac and Gaussian style). But also with simpler molecules there seem to be problems, e.g. cyclopentadienyl-anion. Mopac returns C5H in that case. Other molecules, as benzene or methane are correctly(D6H and TD). These problems seem to be hardware-independent (Tried on a Pentium running Linux and a DECstation running Ultrix). I want to do some calculations on fullerenes and I am therefore very interested in getting Mopac to recognize molecular symmetry correctly. Are problems like the ones mentioned above already known? Sincerely Yours Joachim Schulte (schulte@ws09.pc.chemie.th-darmstadt.de) From owner-chemistry@ccl.net Tue Aug 8 09:02:30 1995 Received: from condor.CC.UMontreal.CA for larouche@CHIMCN.UMontreal.CA by www.ccl.net (8.6.10/930601.1506) id IAA14280; Tue, 8 Aug 1995 08:54:46 -0400 Received: from chims1.CHIMCN.UMontreal.CA (chims1.CHIMCN.UMontreal.CA [132.204.11.106]) by condor.CC.UMontreal.CA with ESMTP id IAA10629 (8.6.11/IDA-1.6 for ); Tue, 8 Aug 1995 08:53:46 -0400 Received: from osiris.CORG.UMontreal.CA by chims1.CHIMCN.UMontreal.CA (940816.SGI.8.6.9/5.17) id IAA18242; Tue, 8 Aug 1995 08:56:56 -0400 Received: by osiris.CORG.UMontreal.CA (940816.SGI.8.6.9/5.17) id IAA12736; Tue, 8 Aug 1995 08:56:46 -0400 From: larouche@CHIMCN.UMontreal.CA (Benoit Larouche) Message-Id: <199508081256.IAA12736@osiris.CORG.UMontreal.CA> Subject: Parameters for Phosphonamides To: chemistry@ccl.net Date: Tue, 8 Aug 1995 08:56:45 -0400 (EDT) Cc: cantindl@CHIMCN.UMontreal.CA MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 450 Dear Netters, I am looking for molecular mechanics parameters for phosphonamides. Does anybody have parameters that they would be prepared to give me or can anybody direct me towards an appropriate reference? I will post a summary to the group. -- Benoit Larouche | INTERNET : larouche@chimcn.umontreal.ca Department of Chemistry | larouche@ere.umontreal.ca Universite de Montreal | PHONE : (514) 343-6111 x3969 From owner-chemistry@ccl.net Tue Aug 8 10:17:41 1995 Received: from faui45.informatik.uni-erlangen.de for goeller@organik.uni-erlangen.de by www.ccl.net (8.6.10/930601.1506) id KAA16114; Tue, 8 Aug 1995 10:08:54 -0400 Received: from derioc1.organik.uni-erlangen.de by uni-erlangen.de with SMTP; id AA17772 (5.65c-7/7.3w-FAU); Tue, 8 Aug 1995 16:08:07 +0200 Received: by organik.uni-erlangen.de; id AA18575 (5.64/7.4b-FAU); Tue, 8 Aug 95 16:08:00 +0200 From: Andreas Goeller Message-Id: <9508081408.AA18575@derioc1.organik.uni-erlangen.de> Subject: Summary electronegativity To: chemistry@ccl.net Date: Tue, 8 Aug 95 16:07:59 METDST X-Mailer: ELM [version 2.3 PL11] Hello netters, thanks very much for the informative news about group electronegativities. I summarize it in this mail: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >I'm searching for values of electronegativities for some functional groups. >I'm doing investigations concerning EN vs. bond lenth etc. The ligands in the >systems are > > F OH Cl NH2 Br I CH3 H >This would be the "right" order, if you take into account only the EN of >the atoms. Some other suggestions or literature? > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ I also found some references: **L. Pauling, The nature of the chemical bond, 3rd ed., Cornell Univ. Press Ithaka, NY 1960. **R.S. Mulliken, J. Chem Phys 2 (1934) 782 **R.S. Mulliken, J. Chem Phys 3 (1935) 573 **A.L.Allred, E.R. Rochow, J. Inorg. Nucl. Chem. 5 (1958) 264 **W. Gordy, Phys Rev 69 (1946) 604. ******************************************************************** >From JMULLAY@aol.com Sun Aug 6 20:04:52 1995 The question of group electronegativity can be a tricky one. Suggest sticking to one consistent method for your work. My favorite is: JACS, 1985, 107,7271. John Mullay ******************************************************************** From: "E. Lewars" In response to a query, here are some refs to electroneg's of atoms and gps: J Cioslowski and T. Mixon [Nixon?], J Am Chem Soc, 115 (1993) 1084 R. J. Boyd and S. L. Bord, J Am Chem Soc, 114 (1992) 1652 C. L. Perrin, J Am Chem Soc, 113 (1991) 2865 ========== Errol Lewars ===== ******************************************************************** >From RSTOLOW@PEARL.TUFTS.EDU Fri Aug 4 19:15:10 1995 Dear Andreas, I have been using the atomic electronegativities published by M. L. Huggins, J. Am. Chem. Soc. 1953, 75, 4123 (Table II). The Huggins values for H, F, Cl, Br and I are given there. I would be interested in all references you may gather to electronegativities for the CH3 and CF3 groups. Bob Stolow Department of Chemistry Tufts University Medford, MA 02155 USA email: rstolow@pearl.tufts.edu ******************************************************************** >From hase@IQM.Unicamp.BR Fri Aug 4 18:34:05 1995 Dear Andreas, I suggest you to check literature "Structure and Bonding. Vol.66 Electronegativity", ed. by K.D.Sen and C.K.Jorgensen, Springer-Verlag (1987). There are TABLEs of Group ENs. (p.165), Bondlength's versus EN diference (p.169), Proton affinities versus EN of lone pairs (p.179), etc. Good luck! Yoshiyuki Hase Instituto de Quimica, Universidade Estadual de Campinas, Campinas, SP (Brasil) e-mail: hase@iqm.unicamp.br ******************************************************************** >From stephan.irle@itc.univie.ac.at Fri Aug 4 17:17:21 1995 Hallo Andreas, The conzepts of group elektronegativities are relative old. There are some scales. - S.G. Bratsch, J. Chem. Educ. {\bf 62} (1985), 101 - N. Inamoto, S. Masuda, Chem. Lett. (1982), 1003 - R.T. Sanderson, ``Polar Covalence'', Academic Press, New York, (1983), 41 - J.E. Huheey, J. Phys. Chem. {\bf 70} (1966), 2086 You have to be careful if the groups are at aromatic or aliphatic compounds. Viele Gruesse, Stephan ******************************************************************** >From GDURST@DOWELANCO.COM Fri Aug 4 16:48:23 1995 Dear Andreas, I recently saw an article for calculating group electronegativities: Qian Xie, Hongmei Sun, Guirong Xie & Jiaju Zhou, "JCICS", v35(1), 1995, 106-109. The PC program developed by the authors is available on request to do the calculations. Regards, Greg ******************************************************************** >From hlee@slaughterhouse.niehs.nih.gov Fri Aug 4 16:49:13 1995 Hi, Check out Parr and Yang's book "Density-Functional Theory of Atoms and Molecules", Appendix F. -- Dr. Dummy, ******************************************************************** There is a volume entitled "Electronegativity" in the Springer-Verlag series on Bonding in Chemistry....Is a GREAT reference for what you mention. Regards, John -- John M. McKelvey email: mckelvey@Kodak.COM Computational Science Laboratory phone: (716) 477-3335 2nd Floor, Bldg 83, RL Eastman Kodak Company Rochester, NY 14650-2216 ******************************************************************* --------------------------------------------------------------- Andreas Goeller Computer Chemie Centrum der Dipl.-Chem. Universitaet Erlangen/Nuernberg Naegelsbachstr. 25 phone: +49(0)9131-856583 D-91052 Erlangen fax: +49(0)9131-856565 Germany email: goeller@organik.uni-erlangen.de http://www.organik.uni-erlangen.de --------------------------------------------------------------- From owner-chemistry@ccl.net Tue Aug 8 11:02:32 1995 Received: from ENH.NIST.GOV for jbrown@indigo17.carb.nist.gov by www.ccl.net (8.6.10/930601.1506) id KAA17749; Tue, 8 Aug 1995 10:52:43 -0400 Received: from indigo17.carb.nist.gov by ENH.NIST.GOV (PMDF V5.0-3 #10952) id <01HTTTAWCCE800MQTH@ENH.NIST.GOV> for chemistry@ccl.net; Tue, 08 Aug 1995 10:50:50 -0400 (EDT) Received: by indigo17.carb.nist.gov (940816.SGI.8.6.9/930416.SGI) for chemistry@ccl.net id KAA06922; Tue, 08 Aug 1995 10:39:09 -0400 Date: Tue, 08 Aug 1995 10:39:09 -0400 From: "Dr. James Brown" Subject: Structure for cyclodextrins To: chemistry@ccl.net Message-id: <9508081039.ZM6920@indigo17.carb.nist.gov> MIME-version: 1.0 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7BIT I am looking for the structure of cyclodextrins (neutron or x-ray) to give me a starting point for some mechanics calculations. Does anyone know where I could get them without having to go to the CSD? Thanks, James From owner-chemistry@ccl.net Tue Aug 8 11:10:57 1995 Received: from SLVAXA.umsl.edu for C1790@SLVAXA.UMSL.EDU by www.ccl.net (8.6.10/930601.1506) id KAA17731; Tue, 8 Aug 1995 10:51:18 -0400 Received: from SLVAXA.UMSL.EDU by SLVAXA.UMSL.EDU (PMDF V4.3-7 #2503) id <01HTTRAQXXS69OCV2T@SLVAXA.UMSL.EDU>; Tue, 8 Aug 1995 09:53:24 CDT Date: Tue, 08 Aug 1995 09:53:24 -0500 (CDT) From: BILL WELSH Subject: Steric Effects in Polymers To: chemistry@ccl.net Message-id: <01HTTRAQXXS89OCV2T@SLVAXA.UMSL.EDU> X-VMS-To: in%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT I need literature references to cases where strong interactions between sidechains and the main chain have greatly influenced the spatial configuration of the polymer. I understand that examples can be found among the polyolefins, vinyl polymers, and even polysaccharides, but I need specific references to the literature. Any help is greatly appreciated. Bill Welsh Dept. of Chem. Univ. of Missouri-St. Louis From owner-chemistry@ccl.net Tue Aug 8 11:17:33 1995 Received: from mail.barrnet.net for jstewart@fujitsuI.fujitsu.com by www.ccl.net (8.6.10/930601.1506) id LAA17959; Tue, 8 Aug 1995 11:04:19 -0400 Received: from fujitsu1.fujitsu.com (fujitsu1.fujitsu.com [133.164.254.1]) by mail.barrnet.net (8.6.10/MAIL-RELAY-LEN) with SMTP id IAA14395 for ; Tue, 8 Aug 1995 08:04:19 -0700 Received: by fujitsu1.fujitsu.com (4.1/SMI-4.1) id AA13669; Tue, 8 Aug 95 08:05:33 PDT Date: Tue, 8 Aug 95 08:05:33 PDT From: jstewart@fujitsu.com (Dr. James Stewart) Message-Id: <9508081505.AA13669@fujitsu1.fujitsu.com> To: CHEMISTRY@ccl.net Subject: Symmetry in MOPAC Joachim Schulte writes: > With Mopac 7.0 I have some problems > concerning the recognition of some point groups. Provided with an > icosahedral C60 geometry MOPAC does not recognize any point group, > not even a subgroup of Ih. The output simply is '????'. The degeneracy > scheme of the molecular orbital energies is looking correct (3-, 4- and > fivefold degeneracies). This happens both for cartesian coordinates > and Z-matrix coordinates (Mopac and Gaussian style). > But also with simpler molecules there seem to be problems, e.g. > cyclopentadienyl-anion. > Mopac returns C5H in that case. Other molecules, as benzene or > methane are correctly(D6H and TD). > These problems seem to be hardware-independent (Tried on a Pentium > running Linux and a DECstation running Ultrix). MOPAC 7 was not designed to recognize C60. MOPAC 7 was limited to systems for which the principal axis is either perpendiculer to a set of atoms (Benzene) or goes through some of the atoms. In C60, the principal axis is through the middle of a pentagon. For routine use, MOPAC 93 is recommended over MOPAC 7. MOPAC 93 will recognize C60 as being Ih, and a whole slew of weird and wonderful systems - truncated icosahedra (like C60), truncated cubes and tetrahedra, and `twisted' icosahedra (point-group `I') At the risk of sounding repetitive: Users of MOPAC are encouraged to use MOPAC 93, and are advised not to use MOPAC 7. MOPAC 7 is intended to be used only when a public domain code MUST be used. MOPAC 7 has a large number of known minor faults - such as the inability to recognize the symmetry of many systems. This makes it particularly irritating, compared to MOPAC 93, when it is used for routine work. MOPAC 7 and MOPAC 93 are both available through the QCPE. Jimmy Stewart From owner-chemistry@ccl.net Tue Aug 8 11:32:37 1995 Received: from rookery.acns.nwu.edu for lnorris@rookery.acns.nwu.edu by www.ccl.net (8.6.10/930601.1506) id LAA18291; Tue, 8 Aug 1995 11:21:44 -0400 Received: from kiwi.acns.nwu.edu by rookery.acns.nwu.edu with ESMTP (1.37.109.16/20.1) id AA001345304; Tue, 8 Aug 1995 10:21:45 -0500 Message-Id: <199508081521.AA001345304@rookery.acns.nwu.edu> Received: by kiwi.acns.nwu.edu (1.37.109.16/16.2) id AA136045304; Tue, 8 Aug 1995 10:21:44 -0500 From: "Lawrence S. Norris" Subject: Formaldehyde Force Field To: chemistry@ccl.net Date: Tue, 08 Aug 1995 10:21:43 CDT X-Mailer: Elm [revision: 109.14] Does anyone have potential energy derivatives (parameters) for formaldehyde in mass weighted normal coordinates that they would like to share? Thanks, -- Lawrence S. Norris ________________________________________________________________________ Departments of Biomedical Engineering |http://www.chem.nwu.edu/~lnorris/ and Chemistry |e-mail address: "lnorris@nwu.edu" Northwestern University |Phone: 708-491-5635 2145 Sheridan |Phone2: 312-784-7380 Evanston, IL 60208 |Fax: 708-491-4928 ------------------------------------------------------------------------ From owner-chemistry@ccl.net Tue Aug 8 13:32:34 1995 Received: from mmlds1.pha.unc.edu for iiv@mmlds1.pha.unc.edu by www.ccl.net (8.6.10/930601.1506) id NAA21218; Tue, 8 Aug 1995 13:18:31 -0400 Received: by mmlds1.pha.unc.edu (5.57/TAS/11-16-88) id AA20780; Tue, 8 Aug 95 13:26:56 -0400 Date: Tue, 8 Aug 1995 13:26:55 -0400 (EDT) From: Iosif Vaisman To: chemistry@ccl.net Subject: Computational Molecular Biology Workshop Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII CAROLINA WORKSHOPS Computational Molecular Biology October 22 -- October 27, 1995 University of North Carolina at Chapel Hill This course is designed for scientists with limited prior experience in computational molecular biology. The topics to be covered include: biomolecular informatics and computer networks, protein and nucleic acid databases, protein and nucleic acid sequence analysis and alignment, 3D protein structure analysis and prediction, molecular modeling and dynamic simulations of proteins and nucleic acids, and structure-based drug design. The workshop will consist of the in-depth theoretical lectures and intensive hands-on laboratory sessions. The course will be taught at the training facility of the North Carolina Supercomputing Center, Research Triangle Park, North Carolina. CAROLINA WORKSHOPS are intensive hands-on courses designed to teach cutting edge methods in molecular biology and biotechnology. Four or five courses on different topics in molecular biology and/or biotechnology are offered each year. The courses are designed for novice students as well as for individuals with prior experience. All students benefit from in-depth interaction with instructors. To apply, send a curriculum vitae and a brief letter describing your research interests and their relevance to the Workshop. Applicants should contact the program office as soon as possible. Please indicate your complete mailing address and telephone/fax number. Application Deadline-September 7, 1995. Tuition - $ 1,200.00. Participation is limited to 15 people, please apply early. COURSE DIRECTOR: Alexander Tropsha, University of North Carolina at Chapel Hill INSTRUCTORS: Frank K. Brown (Glaxo-Wellcome) Wayne Litaker (UNC-Chapel Hill) Michael Mitchell (Becton-Dickinson) David C. Richardson (Duke University) Alexander Tropsha (UNC-Chapel Hill) Iosif Vaisman (UNC-Chapel Hill) For further information or to apply, contact: Dr. Wayne Litaker, Facility Director University of North Carolina at Chapel Hill Program in Molecular Biology & Biotechnology 402 Taylor Hall, CB 7100 Chapel Hill, North Carolina 27599-7100 TELEPHONE (919) 966-1730, FAX (919) 966-6821 Email Address: litaker@med.unc.edu From owner-chemistry@ccl.net Tue Aug 8 16:02:35 1995 Received: from sangam.ncst.ernet.in for mrigank@imtech.ernet.in by www.ccl.net (8.6.10/930601.1506) id PAA25206; Tue, 8 Aug 1995 15:54:56 -0400 Received: (from uucp@localhost) by sangam.ncst.ernet.in (8.6.12/8.6.6) with UUCP id BAA22569 for chemistry@ccl.net; Wed, 9 Aug 1995 01:25:23 +0530 Received: from imtech.UUCP by doe.ernet.in (4.1/SMI-4.1-MHS-7.0) id AA15588; Wed, 9 Aug 95 01:23:52+050 Message-Id: <9508082023.AA15588@doe.ernet.in> Received: by imtech.ernet.in (DECUS UUCP w/Smail); Sat, 5 Aug 95 17:09:14 +0530 Date: Sat, 5 Aug 95 17:09:14 +0530 From: Mrigank To: chemistry@ccl.net Subject: GA WORKBENCH Hi! I have been involved in development of some GA based methods for protein folding predictions. I have seen a GA Workbench which is easy to demonstarte certain concepts of GA on pc. I need it for a workshop. Can any one send any pointers to this. Thanks Mrigank ---- /Mrigank \/ Phone +91 172 690557 \ \Institute of Microbial Technology /\ Email: mrigank@imtech.ernet.in / /Sector 39A, \/ FAX: +91 172 690585 \ \Chandigarh 160 014 India. /\ / \//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\// -- When I feed the poor, they call me saint. When I ask why the poors do not have food, they call me communist - Archbishop Camaran