From ccchuang@gate.sinica.edu.tw Fri Jun 7 02:52:15 1996 Received: from gate.sinica.edu.tw for ccchuang@gate.sinica.edu.tw by www.ccl.net (8.7.5/950822.1) id CAA26040; Fri, 7 Jun 1996 02:46:37 -0400 (EDT) Received: from ccchuang.bc.sinica.edu.tw ([140.109.64.170]) by gate.sinica.edu.tw (5.x/SMI-SVR4) id AA27476; Fri, 7 Jun 1996 14:46:21 +0800 Message-Id: <1.5.4.32.19960607064709.006ae200@gate.sinica.edu.tw> X-Sender: ccchuang@gate.sinica.edu.tw X-Mailer: Windows Eudora Light Version 1.5.4 (32) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Fri, 07 Jun 1996 14:47:09 +0800 To: xtal-log@net.bio.net From: Chyh-Chong Chuang Subject: coordinate of ser/thr phosphatase-1 by Prof. J. Kuriyan's group Cc: molmodel@net.bio.net, CHEMISTRY@www.ccl.net, str-nmr@net.bio.net., pdb-l@pdb.pdb.bnl.gov Dear netters: Does anyony know how to contact with Prof. John Kuriyan's group at Howard Hughes Medical institutes of the rockefeller University. They had published the 3d structure of ser/thr phosphatase-1 complex with microcystin in 1995. But I still do not find the coordinate of this complex by assceesing the PDB WWW Browser and do a search. It seems that the coordinate of this complex have not been deposited to PDB. Could anyone point me how to contact with them by email or FAX. Any response will be great appreciated. Thanks all. ccchuang From 9610538n@Lv.Levels.Unisa.Edu.Au Fri Jun 7 03:05:56 1996 Received: from bROLga.Levels.UniSA.Edu.Au for 9610538n@Lv.Levels.Unisa.Edu.Au by www.ccl.net (8.7.5/950822.1) id CAA25928; Fri, 7 Jun 1996 02:17:16 -0400 (EDT) Received: from CT2114-12079.Levels.UniSA.Edu.Au ("port 1486"@CT2114-12079.Levels.UniSA.Edu.Au) by Levels.UniSA.Edu.Au (PMDF V5.0-4 #9510) id <01I5MS8RPNGW9PLSWX@Levels.UniSA.Edu.Au> for chemistry@www.ccl.net; Fri, 07 Jun 1996 15:46:42 +0930 Date: Fri, 07 Jun 1996 15:46:42 +0930 Date-warning: Date header was inserted by Levels.UniSA.Edu.Au From: 9610538n@Lv.Levels.Unisa.Edu.Au (Terri Soar) Subject: a MOPAC 93.00 problem? X-Sender: 9610538n@Lv.Levels.Unisa.Edu.Au To: chemistry@www.ccl.net Message-id: <01I5MS8RRSMQ9PLSWX@Levels.UniSA.Edu.Au> MIME-version: 1.0 X-Mailer: Windows Eudora Version 1.4.3b4 Content-type: text/plain; charset="us-ascii" Content-transfer-encoding: 7BIT Hi all! I am using MOPAC 93.00 to look at the thermodynamic data for some simple molecules (in gas phase) and have come across a problem. The Cartesian coordinates of the molecule O-Al-H (i.e. aluminium hydride oxide) in the .dat file are changed in the .out file so that the molecule is somehow transformed into Al-O-H (i.e. aluminium hydroxide). This complete rearrangement is unexpected on my behalf. Does anybody know why this has occurred?? Regards, Terri. -------------------------------------------------------------------- Terri Soar - e-mail: 9610538N@lv.levels.unisa.edu.au Ian Wark Research Institute, University of South Australia Warrendi Road, The Levels, 5095 S.A. AUSTRALIA Ph: +61 08 302 3709 Fax: +61 08 302 3668 ------------------------------------------------------------------- From Regis.Gautier@univ-rennes1.fr Fri Jun 7 05:52:15 1996 Received: from mailimailo.univ-rennes1.fr for Regis.Gautier@univ-rennes1.fr by www.ccl.net (8.7.5/950822.1) id FAA26650; Fri, 7 Jun 1996 05:28:13 -0400 (EDT) From: Received: from daniels.univ-rennes1.fr (daniels.univ-rennes1.fr [129.20.128.26]) by mailimailo.univ-rennes1.fr (8.6.10/kit5.1-0905) with SMTP id LAA18050 for ; Fri, 7 Jun 1996 11:28:12 +0200 Message-Id: <199606070928.LAA18050@mailimailo.univ-rennes1.fr> To: CHEMISTRY@www.ccl.net Subject: CCL Date: Fri, 07 Jun 96 11:28:42 +0200 Dear CCL'ers, We are looking for two things concerning K-points (for extended Huckel program in solid state). 1) a program which can generate these K-points. 2) and maybe, a database where we can found different sets of K-points (for the different lattices) and the representation of the Brillouin zones. Could you send us directly your message, we will do a summary for the CCL readers. Thanks for your help Best regards Regis Gautier (Regis.Gautier@univ-rennes1.fr) From ferenc@rchsg8.chemie.uni-regensburg.de Fri Jun 7 06:05:21 1996 Received: from comsun.rz.uni-regensburg.de for ferenc@rchsg8.chemie.uni-regensburg.de by www.ccl.net (8.7.5/950822.1) id FAA26639; Fri, 7 Jun 1996 05:19:38 -0400 (EDT) Received: from rchsg8.chemie.uni-regensburg.de by comsun.rz.uni-regensburg.de with SMTP id AA02733 (5.65c/IDA-1.4.4 for ); Fri, 7 Jun 1996 11:19:29 +0200 Received: by rchsg8.chemie.uni-regensburg.de (931110.SGI/URRZ-Sub-1.5-irix) (for CHEMISTRY@www.ccl.net) id AA20993; Fri, 7 Jun 96 11:17:41 +0200 Date: Fri, 7 Jun 96 11:17:41 +0200 From: ferenc@rchsg8.chemie.uni-regensburg.de (Ferenc Molnar) Message-Id: <9606070917.AA20993@rchsg8.chemie.uni-regensburg.de> To: CHEMISTRY@www.ccl.net Subject: Q:INDY R5000 benchmarks? Dear Netters: Has anybody out there performed benchmark calculations with comp. chem. software on an SGI-INDY with R5000 CPU. I would be interested especially in a comparison: Intel Pentium - R5000 Thanx, Ferenc Ferenc Molnar --------------------------------------------------------------------------- Institut fuer Physikalische und Theoretische Chemie - Lehrstuhl Prof. Dick - Tel.: (+49) 941 943-4466 /-4486 Universitaet Regensburg Fax.: (+49) 941 943-4488 Universitaetsstrasse 31 D-93053 Regensburg Deutschland / Germany --------------------------------------------------------------------------- EMail (SMTP): Ferenc.Molnar@chemie.uni-regensburg.de --------------------------------------------------------------------------- Those who do not archive the past are condemned to retype it! -- Garfinkel & Spafford, Practical Unix Security --------------------------------------------------------------------------- From toukie@zui.unizh.ch Fri Jun 7 11:52:20 1996 Received: from rzusuntk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.7.5/950822.1) id KAA28270; Fri, 7 Jun 1996 10:58:21 -0400 (EDT) From: Received: from rzurs3.unizh.ch by rzusuntk.unizh.ch (4.1/SMI-4.1.9) id AA28536; Fri, 7 Jun 96 16:58:15 +0200 Received: by rzurs3.unizh.ch (AIX 3.2/UCB 5.64/4.03) id AA84382; Fri, 7 Jun 1996 16:58:10 +0200 Message-Id: <9606071458.AA84382@rzurs3.unizh.ch> Subject: Seeking neutron diffraction data To: chemistry@www.ccl.net Date: Fri, 7 Jun 1996 16:58:10 +0200 (MEST) X-Mailer: ELM [version 2.4 PL24 PGP2] Content-Type: text Dear Colleagues; I am seeking neutron diffraction data for phenols with intramolecular hydrogen bonds _other than salicylic acid_, e.g., catechol, o-methoxyphenol, o-ethoxyphenol, o-propoxyphenol, o-phenoxyphenol, etc. If anyone knows of any references to published works on the above, kindly share them with me. Thanks in advance to all responders. Sincerely, S. Shapiro ZH, CH toukie@zui.unizh.ch From owner-chemistry@ccl.net Fri Jun 7 12:24:22 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.5/950822.1) id LAA28290; Fri, 7 Jun 1996 11:01:31 -0400 (EDT) Received: from gaia.msicam.co.uk for rnobes@msicam.co.uk by bedrock.ccl.net (8.7.5/950822.1) id LAA05796; Fri, 7 Jun 1996 11:01:30 -0400 (EDT) Received: by gaia.msicam.co.uk (940816.SGI.8.6.9/SMI-4.1 (MSI-Cambridge)) id PAA17101; Fri, 7 Jun 1996 15:52:45 +0100 From: rnobes@msicam.co.uk (Ross Nobes) Message-Id: <199606071452.PAA17101@gaia.msicam.co.uk> Subject: CCL:M:M: esp failure To: chemistry@ccl.net Date: Fri, 7 Jun 1996 15:52:45 +0100 (BST) Reply-To: rnobes@msi.com X-Mailer: ELM [version 2.4 PL23] Content-Type: text A J Turner writes: > I have been approached by a couple of people over this mopac deck > that caused some problems for me. I include the .dat and .out files. > My concern is that the C to which the Cl is bonded has a charge (in > the esp calc) which is highly negative whilst the Cl has a small > positive charge. > Using Alex's final structure, I find the following ESP charges: Ab initio HF/6-311+G(d) CHelpG CHelp Merz-Singh-Kollman C 0.17 0.54 -0.07 Cl -0.23 -0.28 -0.20 Semiempirical AM1 AM1 PM3 MNDO (dipole cons.) C -0.74 -0.54 -0.44 -0.31 Cl 0.00 -0.08 -0.05 -0.09 So, depending on which method one uses, the charge on C can range from +0.5 to -0.7! Could anyone please tell me whther there have been any recent reviews on determining "good" ESP-derived charges for use in, for example, force-field based methods? Cheers, Ross Nobes -- +----------------------------------------------------------------+ | Dr Ross Nobes | | Senior Scientist, Quantum Mechanics ! | | | Molecular Simulations | | 240/250 The Quorum Phone: + 44 1223 413300 | | Barnwell Road Fax: + 44 1223 413301 | | Cambridge CB5 8RE, UK E-mail: rnobes@msicam.co.uk | +----------------------------------------------------------------+ From Jeffrey.Gosper@brunel.ac.uk Fri Jun 7 12:52:26 1996 Received: from etamin.brunel.ac.uk for Jeffrey.Gosper@brunel.ac.uk by www.ccl.net (8.7.5/950822.1) id LAA28578; Fri, 7 Jun 1996 11:57:25 -0400 (EDT) Received: from chem-pc-18 (actually chem-pc-18.brunel.ac.uk) by etamin.brunel.ac.uk with SMTP (PP); Fri, 7 Jun 1996 16:57:02 +0100 Date: Fri, 7 Jun 1996 16:56:58 BST From: Jeffrey J Gosper Reply-To: Jeffrey.Gosper@brunel.ac.uk Subject: IUPAC Colors for atoms To: chemistry@www.ccl.net Message-ID: Priority: Normal MIME-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII I was told the other day that the color used to represent atoms have been defined by IUPAC. Does anyone know a source of information on this topic? /\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\ Dr. Jeff Gosper Dept. of Chemistry BRUNEL University Uxbridge Middx UB8 3PH, UK internet/WWW: http://http1.brunel.ac.uk:8080/~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 bij1slm@uxa.ecn.bgu.edu Fri Jun 7 13:52:20 1996 Received: from uxa.ecn.bgu.edu for bij1slm@uxa.ecn.bgu.edu by www.ccl.net (8.7.5/950822.1) id MAA29265; Fri, 7 Jun 1996 12:58:05 -0400 (EDT) Received: from [143.43.136.150] (tty050.gsu.bgu.edu [143.43.136.150]) by uxa.ecn.bgu.edu (8.7.3/8.7.3) with SMTP id LAA28112 for ; Fri, 7 Jun 1996 11:58:14 -0500 (CDT) Message-Id: <199606071658.LAA28112@uxa.ecn.bgu.edu> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Fri, 7 Jun 1996 12:12:43 -0600 To: chemistry@www.ccl.net From: bij1slm@uxa.ecn.bgu.edu (Sharon Lee McCarthy) Subject: Crystal Structure Data Dear Netters, Can anyone tell me where I could access crystal structure data, (ie simple salts etc) via the internet? I am interested in modeling the crystal structures in my chemistry courses. Thank you in advance for your information. Dr. Sharon Lee McCarthy Department of Chemistry and Physics Chicago State University 9501 S. King Drive Chicago, Il 60628 Work: 312-995-3892 FAX: 312-995-3809 bij1slm@bgu.edu From owner-chemistry@ccl.net Fri Jun 7 14:06:22 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.5/950822.1) id MAA29284; Fri, 7 Jun 1996 12:59:42 -0400 (EDT) Received: from msuvx1.memphis.edu for CUNDARIT@MSUVX1.MEMPHIS.EDU by bedrock.ccl.net (8.7.5/950822.1) id MAA06969; Fri, 7 Jun 1996 12:59:41 -0400 (EDT) From: Received: from MSUVX1.MEMPHIS.EDU by MSUVX1.MEMPHIS.EDU (PMDF V5.0-3 #7188) id <01I5MHVC7D1C9C9S4S@MSUVX1.MEMPHIS.EDU> for chemistry@ccl.net; Fri, 07 Jun 1996 11:58:34 -0600 (CST) Date: Fri, 07 Jun 1996 11:58:34 -0600 (CST) Subject: MM calculations on cyclopropylamines and aziridines To: chemistry@ccl.net Message-id: <01I5MHVC85YQ9C9S4S@MSUVX1.MEMPHIS.EDU> X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Hello, A student of mine is modeling amine complexes and two of the ligands we are interested in are cyclopropylamine and aziridine (sometimes, it seems, also referred as ethyleneimine). We looked in the MM2 & MM3 papers from the Allinger group and found only data for "normal" aliphatic amines; two electronic literature searches have also come up empty. Any information, published or unpublished, regarding the application of molecular mechanics to these species would be most welcome. Sincerely, Tom Cundari Associate Professor of Chemistry +===+===+===+===+===+===+===+===+===+===+===+===+===+===+===+===+===+===+===+=== Thomas R. Cundari Associate Professor of Chemistry Computational Inorganic Chemistry Lab University of Memphis Memphis, TN 38152 phone: 901-678-2629 fax: 901-678-3447 e-mail: cundarit@cc.memphis.edu http://www.chem.memphis.edu/compchem.html +===+===+===+===+===+===+===+===+===+===+===+===+===+===+===+===+===+===+===+=== From gford@post.smu.edu Fri Jun 7 14:17:42 1996 Received: from post.cis.smu.edu for gford@post.smu.edu by www.ccl.net (8.7.5/950822.1) id NAA29412; Fri, 7 Jun 1996 13:28:31 -0400 (EDT) Received: by post.cis.smu.edu (/\==/\ Smail3.1.28.1 #28.3) id ; Fri, 7 Jun 96 12:28 CDT Message-Id: Date: Fri, 7 Jun 96 12:28 CDT From: "George P. Ford" Reply-To: "George P. Ford" To: CHEMISTRY@www.ccl.net Subject: fast esp charges from AM1 calculations Dear netters: Alex Turner (University of Bath) recently posted the details of an AM1 esp calculation on a singly hydrated chloromethoxymethane using mopac93. The input file is reproduced below AM1 esp C 0.00000000 0 0.0000000 0 0.0000000 0 0 0 0 H 1.11678955 1 0.0000000 0 0.0000000 0 1 0 0 H 1.11860861 1 110.5001057 1 0.0000000 0 1 2 0 H 1.11804978 1 111.0078215 1 124.1366815 1 1 2 3 O 1.42977966 1 109.6919909 1 -121.1538376 1 1 2 3 C 1.39974700 1 114.4456389 1 68.8811837 1 5 1 2 H 1.11840798 1 106.4911216 1 161.8104747 1 6 5 1 H 1.11884361 1 112.9830933 1 35.3301012 1 6 5 1 Cl 1.80283055 1 111.4239110 1 -83.0814824 1 6 5 1 O 3.42808614 1 97.1266757 1 20.8564401 1 6 5 1 H 0.96400805 1 126.7099492 1 68.1397632 1 10 6 5 H 0.96345463 1 101.2179497 1 -48.2960684 1 10 6 5 Alex wrote: >My concern is that the C to which the Cl is bonded has a charge (in >the esp calc) which is highly negative whilst the Cl has a small >positive charge. > >It has been brought to my attention that Mopac93 _revision_2_ should >have a bug fix (Dr J Stuart - thanks), But I have not had time to >check this out yet. > Given the arbitrary nature of any definition of atomic charge differences are bound to occur. However, from the out file Alex posted it's obvious his calculation has a much more serious problem. The dipole moment given by the esp charge distribution is a ridiculous 37.2 D! I donÕt know whether this is a bug in mopac or not. (Any body have any info on this?) However, quite apart from this possibility, there is an important reason to be distrustful of the standard approach to the calculation of esp's based on AM1 and related wavefunctions (deorthogonalized or not). We have made the point before (B.Wang; G.P. Ford, J. Comput. Chem, 1994, 15, 200-207), but itÕs worth reiterating here. The standard approach is inherently inconsistent since the electronic contibution to the esp is computed using a wave function based on semiempirical values of the integrals, while the nuclear contribution is appropriate to an exact calculation. This problem doesnÕt arise in an AM1 energy calculation because the necessary balance is restored through parameterization of the core repulsion function. We have used the same philosophy to restore the balance in AM1 esp calculations (see JCC paper cited above) by parametrizing the nuclear contribution to reproduce the results of HF/6-31G* espÕs. We dubbed this approach the Parameterized Molecular Electrostatic Potential (PMEP). The resulting PMEP-derived charges are much closer to the ab initio esp charges. Because the electronic part is computed strictly within the simplified integral scheme of the AM1 formalism the method is EXTREMELY FAST. The results for AlexÕs molecule are shown below (all refer to the optimized AM1 geometry). The first set of charges is from Alex's out file. The negatively charged carbon he referred to is atom No. 6. The next column shows the AM1 (PMEP) charges and the last shows the HF/6-31G* values (g94 with POP=MK). The two latter sets are qualitatively much closer to one another than either is to the standard mopac esp calculation. All methods still make C6 slightly negative, although the CH2 group as a whole in positive in the latter methods which also make the Cl markedly more negative. ATOM NO. TYPE CHARGE (esp) (qpmep) HF/6-31G* 1 C -0.4073 -0.1113 -0.021124 2 H 0.1575 0.0952 0.085615 3 H 0.1508 0.0919 0.055452 4 H 0.1626 0.1040 0.072576 5 O 0.0241 -0.2437 -0.312698 6 C -0.7417 -0.1549 -0.027673 7 H 0.3030 0.1783 0.140668 8 H 0.3827 0.1615 0.205274 9 Cl -0.0028 -0.1407 -0.206185 10 O -0.5600 -0.5888 -0.841931 11 H 0.2721 0.3114 0.430359 12 H 0.2590 0.2970 0.419665 total dipole 37.2 4.04 4.97 The QPMEP calculation required only 0.2 sec. on an SGI Indigo2 compared to the 217 secs. required for the full HF/6-31G* calculation in g94. The QPMEP calculations are available in the most recent release of moapc93 using the QPMEP keyword. Users of mopac6 can obtain the necessary subroutines via anonymous ftp from: ftp.seas.smu.edu. ============================================================================ George P. Ford | email: gford@smu.edu Department of Chemistry | web: http://www.smu.edu/~gford/ Southern Methodist University | telephone: (214)768-2479 Dallas, Texas 75275 | fax: (214)768-4089 ============================================================================ From dsmith@debye.dasgroup.com Fri Jun 7 22:52:25 1996 Received: from cool95.third-wave.com for dsmith@debye.dasgroup.com by www.ccl.net (8.7.5/950822.1) id WAA01447; Fri, 7 Jun 1996 22:21:34 -0400 (EDT) Received: from hartree ([206.31.47.69]) by cool95.third-wave.com (Netscape Mail Server v1.1) with SMTP id AAA140 for ; Fri, 7 Jun 1996 22:21:22 +0000 X-Sender: dsmith@pop.dasgroup.com X-Mailer: Windows Eudora Version 1.4.4 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" X-Priority: 1 (Highest) To: CHEMISTRY@www.ccl.net From: dsmith@debye.dasgroup.com (Doug Smith) Subject: AM1 vs PM3 vs RHF/6-31G* for isocyanates Date: Fri, 7 Jun 1996 22:21:22 +0000 Message-ID: <19960607222120482.AAA140@hartree> Dear All: We are using PM3 to calculate several compounds, including some which contain one or more isocyanate (R-N=C=O) functional groups. The choice of PM3 is dictated by a number of factors which do not bear going into here. However, the results are not intuitively obvious. For example, using H-N=C=O as a test case, the bond angles and distances are as given in the table. distance angle N-C C-O N-C-O ------- ------- --------- AM1 1.23 A 1.20 A 166.7 PM3 1.25 A 1.18 A 166.7 RHF/6-31G* 1.20 A 1.15 A 174.2 Similar deviations from linearity are seen in the angles of substituted isocyanates. What is the expected N-C-O angle based on experiment and/or higher levels of theory? Why do the semiempirical methods fail to reproduce the expected and observed linearity of the N-C-O bond? Is it appropriate to fix the N-C-O angle at a linear or near-linear value for these semiempirical studies, and if so, at what angle? Thanks for the help and advice in advance. Douglas Smith -- Dr. Douglas A. Smith, President and CEO | voice: (814) 262-9091 The DASGroup, Inc. | fax: (814) 262-9337 P.O. Box 5428 | email: dsmith@dasgroup.com Johnstown, PA 15904-5428 | Contract R&D specialists in computational chemistry, process modeling, synthesis and design of novel compounds for chemistry, materials science, and biotechnology.