From NMUELLER@alijku06.edvz.uni-linz.ac.at Thu Oct 6 05:17:41 1994 Received: from alijku06.edvz.uni-linz.ac.at for NMUELLER@alijku06.edvz.uni-linz.ac.at by www.ccl.net (8.6.9/930601.1506) id EAA05724; Thu, 6 Oct 1994 04:48:46 -0400 Received: from [140.78.98.5] (nmueller.chemie.uni-linz.ac.at) by alijku06.edvz.uni-linz.ac.at with SMTP id AA08312 (5.65c/IDA-1.4.4 for ); Thu, 6 Oct 1994 09:47:40 +0100 Message-Id: <199410060847.AA08312@alijku06.edvz.uni-linz.ac.at> X-Sender: k360171@pop.edvz.uni-linz.ac.at Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 6 Oct 1994 09:48:38 +0200 To: CHEMISTRY@ccl.net From: NMUELLER@jk.uni-linz.ac.at (Norbert Mueller) Subject: Serena Software / PCMODEL Can someone please send me a fax n umber or internet address of Serena Software, the publishers of PCMODEL? Please send e-mail replies to me, not to the list. If someone else is interested I will post the answer once. Thanks for your assistance. From chiche@auvergne.cbs.univ-montp1.fr Thu Oct 6 07:17:45 1994 Received: from auvergne.cbs.univ-montp1.fr for chiche@auvergne.cbs.univ-montp1.fr by www.ccl.net (8.6.9/930601.1506) id GAA06452; Thu, 6 Oct 1994 06:50:32 -0400 Received: by auvergne.cbs.univ-montp1.fr (920330.SGI/920502.SGI.AUTO) for chemistry@ccl.net id AA03491; Thu, 6 Oct 94 07:32:56 +0200 Date: Thu, 6 Oct 94 07:32:56 +0200 From: chiche@auvergne.cbs.univ-montp1.fr (Laurent Chiche) Message-Id: <9410060532.AA03491@auvergne.cbs.univ-montp1.fr> To: chemistry@ccl.net Subject: Implicit Solvation Hi, A summary was recently posted on the list about "What people are doing to approximate solvation effects in energy calculations" Beside references by the Eisenberg and the Honig groups (deliberately ommitted), few additional references might be cited (although most are included in more recent reviews): 1 W.C. Still et al. (J. Amer. Chem. Soc 112, 6127-6129, 1990) 2 Yu, Pettitt and Karplus (J. Amer. Chem. Soc. 113, 2425-2434, 1991) 3 Cramer and Truhlar (Science 256, 213-217, 1992) 4 Holm and Sander (J. Mol. Biol. 225, 93-105, 1992) 5 Holm and Sander (Proteins, 14, 213-223, 1992) 6 Schiffer Caldwell Kollman and Stroud (Protein. Sci. 1, 396-400, 1992) 7 Schiffer Caldwell Stroud and Kollman (Molec. Simul. 10, 121, 1993) Conclusion of the summary was: > Finally, when using the "Eisenberg" approach of surface area changes and > atomic solvation parameters: > > 1) It is currently unclear as to what is the most appropriate > set of atomic solvation parameters to use for docking > or protein folding. > > 2) Given the potential benefits of such a calculation there > seem to be surprisingly few tests of this method. Reference 7 above specifically addressed these questions. I would also like to add that we applied with some success the "Eisenberg approach" of implicit solvation to NMR based structural studies: -Chiche, Gaboriaud, Heitz, Mornon, Castro and Kollman (Proteins, 6, 405-417, 1989) "Use of restrained molecular dynamics in water to determine 3D protein structure: Prediction of the 3D structure of Trypsin inhibitor EETI II" -LeNguyen, Heitz, Chiche, ElHajji and Castro (Protein. Sci. 2, 165-174, 1993) "Characterization and 2D NMR study of the stable [9-15, 21-27] 2 disulfide intermediate in the folding of the 3 disulfide trypsin inhibitor EETI II" and that we have a paper in press in which we test the usefulness of this approach for homology modeling (using atomic solvation params from ref 7 above): -Cregut, Liautard and Chiche (to appear in Prot. Engineering, vol 7 no 11, 1994) "Homology modeling of annexin I: implicit solvation improves side chain prediction, and combination of evaluation criteria allows recognition of different types of conformational errors" ********************************************************************** ** Laurent Chiche !! e-mail: ** ** !! lchiche@cbs.univ-montp1.fr ** ** Centre de Biochimie Structurale !! ** ** Faculte de Pharmacie !! Tel: 67.04.34.32 ** ** 15 Ave. Charles Flahault !! ** ** 34060 Montpellier - France !! Fax: 67.52.96.23 ** ********************************************************************** From jlabanow@magnus.acs.ohio-state.edu Thu Oct 6 05:17:41 1994 Received: from alijku06.edvz.uni-linz.ac.at for NMUELLER@alijku06.edvz.uni-linz.ac.at by www.ccl.net (8.6.9/930601.1506) id EAA05724; Thu, 6 Oct 1994 04:48:46 -0400 Received: from [140.78.98.5] (nmueller.chemie.uni-linz.ac.at) by alijku06.edvz.uni-linz.ac.at with SMTP id AA08312 (5.65c/IDA-1.4.4 for ); Thu, 6 Oct 1994 09:47:40 +0100 Message-Id: <199410060847.AA08312@alijku06.edvz.uni-linz.ac.at> X-Sender: jlabanow@magnus.acs.ohio-state.edu Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 6 Oct 1994 09:48:38 +0200 To: CHEMISTRY@ccl.net From: jabanow@magnus.acs.ohio-stat.edu Subject: Serena Software / PCMODEL Can someone please send me a fax n umber or internet address of Serena Software, the publishers of PCMODEL? Please send e-mail replies to me, not to the list. If someone else is interested I will post the answer once. Thanks for your assistance. From VENEGAS_R@fisons.com Thu Oct 6 10:17:43 1994 Received: from CASPER.FISONS.COM for VENEGAS_R@fisons.com by www.ccl.net (8.6.9/930601.1506) id KAA09164; Thu, 6 Oct 1994 10:07:37 -0400 Date: Thu, 6 Oct 1994 10:06:27 -0400 (EDT) From: "RUBEN E. VENEGAS" To: chemistry@ccl.net Message-Id: <941006100627.24a09d87@fisons.com> Subject: Quantum Chemist in Chile. Dr. Ramiro Arratia-Perez writes: > this letter may shock you. Last Friday >September 1 (16:30 hrs) the Personnel Officer >(non-academic) send me a letter comunicating >that the Pontificia Universidad Catolica de >Chile decided to cancel my academic position. Although I think everybody will sympathize with you I think nobody will be shocked (in USA). At this moment, job security means nothing for thousand of chemists working for private institutions in this country (I don't know about academic or government positions). I know many people who have lost their job just like you, but with only five minutes of notification and having to walk out of the premises immediately. Like you, they are very good scientists, never did anything wrong, always on time to work, good performance, etc., but everything comes down to one thing: CUT COSTS FOR THE COMPANY AND IMPROVE PROFITS. Ruben Venegas Sr. Research Scientist Fisons Pharmaceuticals e-mail : venegas_r@casper.fisons.com **All official and unofficial disclaimers apply** From jlabanow@magnus.acs.ohio-state.edu Thu Oct 6 05:17:41 1994 Received: from alijku06.edvz.uni-linz.ac.at for NMUELLER@alijku06.edvz.uni-linz.ac.at by www.ccl.net (8.6.9/930601.1506) id EAA05724; Thu, 6 Oct 1994 04:48:46 -0400 Received: from [140.78.98.5] (nmueller.chemie.uni-linz.ac.at) by alijku06.edvz.uni-linz.ac.at with SMTP id AA08312 (5.65c/IDA-1.4.4 for ); Thu, 6 Oct 1994 09:47:40 +0100 Message-Id: <199410060847.AA08312@alijku06.edvz.uni-linz.ac.at> X-Sender: jlabanow@magnus.acs.ohio-state.edu Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 6 Oct 1994 09:48:38 +0200 To: CHEMISTRY@ccl.net From: jabanow@magnus.acs.ohio-state.edu Subject: Serena Software / PCMODEL Can someone please send me a fax n umber or internet address of Serena Software, the publishers of PCMODEL? Please send e-mail replies to me, not to the list. If someone else is interested I will post the answer once. Thanks for your assistance. From YQIN@aardvark.ucs.uoknor.edu Thu Oct 6 11:06:24 1994 Received: from aardvark.ucs.uoknor.edu for YQIN@aardvark.ucs.uoknor.edu by www.ccl.net (8.6.9/930601.1506) id KAA10069; Thu, 6 Oct 1994 10:52:30 -0400 From: Message-Id: <199410061452.KAA10069@www.ccl.net> Date: Thu, 6 Oct 94 09:53 CDT Subject: Explorer manual To: chemistry@ccl.net X-VMS-To: IN%"chemistry@ccl.net" Dear netters: Can someone please tell me how and where to get the manual of Explorer for SGI. We apparently try to run Eyechem in our SGI/indigo, but we have some difficulty to make it. Please send e-mail replies to me, not to the list. If someone else is interested I centainly will post the answer. Thanks for your assistance. with my best regards yue qin yqin@aardvark.ucs.ouknor.edu From biosym.com!tony@biosym.com Thu Oct 6 11:06:34 1994 Received: from bioc1.biosym.com for biosym.com!tony@biosym.com by www.ccl.net (8.6.9/930601.1506) id KAA09733; Thu, 6 Oct 1994 10:24:38 -0400 Received: from biosym.com by bioc1.biosym.com (5.64/0.0) id AA19568; Thu, 6 Oct 94 07:09:25 -0700 Received: by east1.biosym.com (920330.SGI/920502.SGI) for bioc1!ccl.net!chemistry id AA11236; Thu, 6 Oct 94 09:58:59 -0400 Date: Thu, 6 Oct 94 09:58:59 -0400 From: biosym.com!tony@biosym.com (Tony Schmidt) Message-Id: <9410061358.AA11236@east1.biosym.com> To: chemistry@ccl.net Subject: CCL: implicit solvation Cc: tony@biosym.com, lchiche@cbs.univ-montp1.fr Reply-To: biosym.com!tony@biosym.com Laurent Chiche writes: ... >Beside references by the Eisenberg and the Honig groups (deliberately ommitted), >few additional references might be cited (although most are included in more >recent reviews): >1 W.C. Still et al. (J. Amer. Chem. Soc 112, 6127-6129, 1990) >2 Yu, Pettitt and Karplus (J. Amer. Chem. Soc. 113, 2425-2434, 1991) >3 Cramer and Truhlar (Science 256, 213-217, 1992) >4 Holm and Sander (J. Mol. Biol. 225, 93-105, 1992) >5 Holm and Sander (Proteins, 14, 213-223, 1992) >6 Schiffer Caldwell Kollman and Stroud (Protein. Sci. 1, 396-400, 1992) >7 Schiffer Caldwell Stroud and Kollman (Molec. Simul. 10, 121, 1993) >Conclusion of the summary was: >> Finally, when using the "Eisenberg" approach of surface area changes and >> atomic solvation parameters: >> >> 1) It is currently unclear as to what is the most appropriate >> set of atomic solvation parameters to use for docking >> or protein folding. >> >> 2) Given the potential benefits of such a calculation there >> seem to be surprisingly few tests of this method. ... The paper "A CFF91-based continuum solvation model: solvation free energies of small molecules and conformations of the alanine dipeptide in solution" by A.B.Schmidt and R.M.Fine to be published in Molecular Simulation, 1994. In particular, we have shown that the Wesson-Eisenberg model used in [7] provides the differences in the solvation energies of the alanine dipeptide within the full Ramachandran map not exceeding 4 kcal/mol while the Poisson- Boltzmann approach exhibits the difference between C7 axial and alpha L minima of about 9 kcal/mol (not to mention energy maxima). Anatoly B. Schmidt, Ph.D Delphi Project Manager email: tony@biosym.com Biosym Technologies, Inc. tel: (201)267-4476 4 Century Dr., Parsippany, fax: (201)267-9648 NJ 07054 Tony Schmidt tony@biosym.com From toukie@zui.unizh.ch Thu Oct 6 12:17:45 1994 Received: from rzusuntk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.6.9/930601.1506) id MAA11546; Thu, 6 Oct 1994 12:16:16 -0400 Received: by rzusuntk.unizh.ch (4.1/SMI-4.1.9) id AA06334; Thu, 6 Oct 94 17:16:12 +0100 X-Nupop-Charset: British Date: Thu, 6 Oct 1994 17:11:04 +0100 (MET) From: "Hr Dr. S. Shapiro" Sender: toukie@zui.unizh.ch Reply-To: toukie@zui.unizh.ch Message-Id: <61864.toukie@zui.unizh.ch> To: chemistry@ccl.net Subject: Energetics of Walden inversions Dear Colleagues; Recently I had a dicussion with an associate regarding the stereo- chemistry of enzymic hydroxylations at position C-14 of steroidal molecules. Most such substrates have a 14-alpha-H configuration, whereas many products have a 14-beta-OH configuration. The question arose as to whether this could be due to a simple Walden inversion. I opined that whilst a simple Walden inversion, in which the departing hydrogen leaves on the alpha-side opposite to the trajectory of the incoming hydroxyl group, might sound rea- sonable, upon reflection it might not be such a feasible mechanism because in such a rigid polycyclic structure as a steroid the tertiary carbon atom C-14 occupies a keystone position and that it might be energetically too unfavourable for such a Walden inversion to occur at C-14, at least not without affecting more distal positions in the molecule. It later occurred to me that perhaps the C-14 position might also be too sterically hindered for a Walden inversion to readily occur there. With that introduction, my questions are: (1) does anyone have hay definitive information or references re the the mechanism of enzymic hydroxylation of steroidal substrates at C-14 (or tertiary carbons in other rigid polycyclic molecules) with net inversion of configuration? (2) would anyone care to comment on the arguments I put forth against hydroxylation proceeding by a simple Walden inversion at C-14 of steroidal-type molecules? (3) can the unsubstituted C-14 position (with an alpha-H atom) be re- garded as a hindered position? (4) does anyone have any information on the energetics of Walden inver- sions at primary vs. secondary vs. tertiary carbon atoms? If so, could you please share your information with me, and send me rele- vant references? I thank all responders in advance for their generous cooperation in the above matter. Yours sincerely, (Dr.) S. Shapiro Institut fuer orale Mikrobiologie und allgemeine Immunologie Zentrum fuer Zahn-, Mund-, und Kieferheilkunde der Universitaet Zuerich Plattenstrasse 11 Postfach CH-8028 Zuerich, Switzerland Internet: toukie@zui.unizh.ch FAX-nr: ( ... + 1) 261'56'83 From jkl@ccl.net Thu Oct 6 12:33:02 1994 Received: for jkl@ccl.net by www.ccl.net (8.6.9/930601.1506) id MAA11883; Thu, 6 Oct 1994 12:32:09 -0400 Date: Thu, 6 Oct 1994 12:32:09 -0400 From: Jan Labanowski Message-Id: <199410061632.MAA11883@www.ccl.net> To: chemistry@ccl.net Subject: this is a test Cc: jkl@ccl.net This is a test to chem list This is a test to chem list This is a test to chem list This is a test to chem list This is a test to chem list This is a test to chem list This is a test to chem list This is a test to chem list This is a test to chem list This is a test to chem list This is a test to chem list This is a test to chem list This is a test to chem list This is a test to chem list This is a test to chem list This is a test to chem list This is a test to chem list This is a test to chem list This is a test to chem list This is a test to chem list This is a test to chem list This is a test to chem list From doherty@msc.edu Thu Oct 6 14:17:47 1994 Received: from noc.msc.edu for doherty@msc.edu by www.ccl.net (8.6.9/930601.1506) id NAA13588; Thu, 6 Oct 1994 13:56:00 -0400 Received: from uh.msc.edu by noc.msc.edu (5.65/MSC/v3.0.1(920324)) id AA00954; Thu, 6 Oct 94 12:55:50 -0500 Received: from mac3.msc.edu by uh.msc.edu (5.65/MSC/v3.1r(920220)) id AA04194; Thu, 6 Oct 94 12:55:47 -0500 Message-Id: <9410061755.AA04194@uh.msc.edu> X-Sender: doherty@uh.msc.edu Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 6 Oct 1994 12:56:05 -0500 To: chemistry@ccl.net From: doherty@msc.edu (David C. Doherty) Subject: HF treatment of ester hydrolysis? Can someone please point me in the direction of references related to (preferably) Hartree-Fock treatments of (isodesmic) ester hydroylsis reactions? Thanks in advance, Dave Doherty --- David C. Doherty Minnesota Supercomputer Center, Inc. doherty@msc.edu From wiesiek@phys.uni.torun.pl Thu Oct 6 14:18:00 1994 Received: from sunic.sunet.se for wiesiek@phys.uni.torun.pl by www.ccl.net (8.6.9/930601.1506) id NAA13610; Thu, 6 Oct 1994 13:56:45 -0400 Received: from class1.phys.uni.torun.pl by sunic.sunet.se (8.6.8/2.03) id SAA15587; Thu, 6 Oct 1994 18:56:35 +0100 Received: by class1.phys.uni.torun.pl (5.0/SMI-SVR4) id AA08021; Thu, 6 Oct 94 18:54:58 +0100 From: wiesiek@phys.uni.torun.pl (Wieslaw Nowak) Message-Id: <9410061754.AA08021@class1.phys.uni.torun.pl> Subject: question:acetoxy group calcs. To: chemistry@ccl.net Date: Thu, 6 Oct 1994 18:54:57 +0100 (MET) Cc: wiesiek@phys.uni.torun.pl (Wieslaw Nowak) X-Mailer: ELM [version 2.4 PL22] Content-Type: text Content-Length: 704 Dear Netters, I am interesting in electronic structure and conformations of acetoxy (CH3-CO-O-, ester group) derivatives of benzene and anthracene. Any references to semiempirical (ZDO type) or ab inito calculations done for such compounds would be the most appreciated. I will summarize responses. Greetings, Wieslaw Nowak. ========================================================= Dr. Wieslaw Nowak Molecular Biophysics Group Intitute of Physics N.Copernicus University ul. Grudziadzka 5 PL-87-100 Torun, Poland tel. (48-56) 210-65 ext. 213, 216 fax. (48-56) 253-97 telex 055412 umk pl e-mail: wiesiek@phys.uni.torun.pl (internet) ----------------------------------------------------------- From NMUELLER@alijku06.edvz.uni-linz.ac.at Thu Oct 6 17:17:48 1994 Received: from alijku06.edvz.uni-linz.ac.at for NMUELLER@alijku06.edvz.uni-linz.ac.at by www.ccl.net (8.6.9/930601.1506) id RAA18764; Thu, 6 Oct 1994 17:01:36 -0400 Received: from [140.78.98.5] (nmueller.chemie.uni-linz.ac.at) by alijku06.edvz.uni-linz.ac.at with SMTP id AA24239 (5.65c/IDA-1.4.4 for ); Thu, 6 Oct 1994 22:00:13 +0100 Message-Id: <199410062100.AA24239@alijku06.edvz.uni-linz.ac.at> X-Sender: k360171@pop.edvz.uni-linz.ac.at Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 6 Oct 1994 22:01:17 +0200 To: CHEMISTRY@ccl.net From: NMUELLER@jk.uni-linz.ac.at (Norbert Mueller) Subject: Summary: Serena Software / PCMODEL I have received a large number of replies concerning Serena Software and PCMODEL. Thanks to everyone who helped. Since I have also received some requests to post the answers I got, here's a short summary: Serena Software PO Box 3076 Bloomington, IN 47402-3076 e-mail: GILBERT@ucs.indiana.edu (I got a reply from Kevin Gilbert, president of Serena soft) maybe also: gilbert@iubacs.bitnet fax: 812-332-0877 (USA) tel: 812-333-0823 (USA) It seems another company also sells PCMODEL: ARSoftware 8201 Corporate Drive, Suite 1110 Landover, Maryland 20785 Phone: (800) 257-0073 (301) 459-3773 Fax: (301) 459-3776 e-mail: arsoftware@arclch.com -- Norbert Mueller Assoc. Prof. of Physical Organic Chemistry Institut fuer Chemie, Johannes Kepler Universitaet A-4040 Linz, Austria e-mail: NMUELLER@jk.uni-linz.ac.at (preferred) Norbert@soft.uni-linz.ac.at (private messages) NorbertM@AMDA.UNI-LINZ.AC.AT (AmdaLink-LINZ via Internet) From eslone@mason1.gmu.edu Thu Oct 6 23:17:54 1994 Received: from mason1.gmu.edu for eslone@mason1.gmu.edu by www.ccl.net (8.6.9/930601.1506) id WAA21692; Thu, 6 Oct 1994 22:36:28 -0400 Received: by mason1.gmu.edu (5.65/DEC-Ultrix/4.3/GMUv3) id AA24162; Thu, 6 Oct 1994 22:36:08 -0400 Message-Id: <9410070236.AA24162@mason1.gmu.edu> Subject: A question regarding INORGANIC structure To: chemistry@ccl.net Date: Thu, 6 Oct 1994 22:36:08 -0400 (EDT) From: "J. Eric Slone" X-Mailer: ELM [version 2.4 PL23] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 1004 Could anyone advise me as to why ReO3 assumes the structure that it does? A unit cell (viewed with Re in the corner positions) has a higher lattice energy than if the Re were in tetrahedral sites. Obviously, there is no change in the coordination numbers, and I cannot find any reason as to why the structure "naturally" assumes one with a higher lattice energy. Responses, both factual and theoretical are appreciated. Eric ________________________________________________________________________________ J. Eric Slone Scientific Consulting Services Serving Government & Industry Since 1982 Internet: eslone@mason1.gmu.edu Compuserve: 73757,2776 "True science teaches, above all, to Fax: (703) 751-6639 doubt, and to be ignorant." Voice: (703) 461-7078 Miguel do Unamuno ________________________________________________________________________________