From SUNDIUS@phcu.helsinki.fi Thu Mar 10 05:40:20 1994 Received: from fltc.helsinki.fi for SUNDIUS@phcu.helsinki.fi by www.ccl.net (8.6.4/930601.1506) id FAA04345; Thu, 10 Mar 1994 05:01:39 -0500 Received: from phcu.helsinki.fi by phcu.helsinki.fi (PMDF V4.2-14 #4706) id <01H9T0HEI2I8C6A2F4@phcu.helsinki.fi>; Thu, 10 Mar 1994 12:01:54 EET Date: Thu, 10 Mar 1994 12:01:54 +0200 (EET) From: Tom Sundius U of Helsinki +358 0 1918339 Subject: Checking for matrix non-singularity To: chemistry@ccl.net Message-id: <01H9T0HEJEQQC6A2F4@phcu.helsinki.fi> X-VMS-To: IN%"chemistry@ccl.net" X-VMS-Cc: SUNDIUS MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Recently there has been some discussion about how to check if a matrix is non-singular. According to definition, a (square) matrix is non-singular if it has an inverse, but there are several other definitions, which are equivalent (a non-zero determinant and linearly independent rows or columns). The determinant can be used to check for singularity, but a direct calculation of the determinant is often unstable (and timeconsuming). Using the LU decomposition method, the determinant can be calculated as the product of the diagonal element of the U-matrix (but one has to arrange the calculation to avoid over- or underflow). A better method to check the condition of a matrix is to use the "condition number", which is discussed (for instance) in the book by Kahaner, Moler & Nash : Numerical methods and software. The condition number of a matrix can be defined as the ratio of the norm of the matrix and the norm of its inverse. If one performs a singular value decomposition (SVD) of the matrix, the condition number can be calculated as the ratio of the largest and the smallest singular value. Since a singular matrix will have (at least) one singular value = 0, it follows that the condition number of a matrix close to singularity will be very large. From OLIVER@psipsy.uct.ac.za Thu Mar 10 07:40:15 1994 Received: from ucthpx.uct.ac.za for OLIVER@psipsy.uct.ac.za by www.ccl.net (8.6.4/930601.1506) id HAA05323; Thu, 10 Mar 1994 07:10:03 -0500 Received: by ucthpx.uct.ac.za (/\==/\ Smail3.1.28.1 #28.8) id m0pejWa-000KSrC; Thu, 10 Mar 94 14:07 SAST Received: From ITS/WORKQ3 by charongw3.uct.ac.za via Charon-4.0A-VROOM with IPX id 100.940310140639.352; 10 Mar 94 14:09:49 -0200 Message-ID: To: chemistry@ccl.net From: "Hill, RO, Oliver, HLLROB010" Date: Thu, 10 Mar 1994 14:00:12 SAST-2 Subject: PRDDO Method ?? Return-receipt-to: "Hill, RO, Oliver, HLLROB010" Priority: normal X-mailer: WinPMail v1.0 (R1) Dear Modellers I have recently started using GAMESS (US) to study organometallic systems. I have been digging out various papers and have found one which refers to the PRDDO method (Partial Retention of Diatomic Differential Overlap). The authors use the method for geometry optimization and transition state location, followed by GAMESS for single points. The results look pretty good and the speed is especially impressive. My question is what do people "in the know" think of this method and how many people are using it? Also how does it compare with methods such as ZINDO (INDO/1 & INDO/S)? (It's supposed to extend the approach taken in the CNDO, INDO and NDDO methods by allowing PRDDO). I'd very much like to get hold of the program, so if anyone has that information I'd appreciate that as well. I have tried without success to find the E-Mail address of the authors of the paper I have (Dennis Marynick et al at Univ. of Texas at Arlington). The paper I have is "Potential Energy Surface for Methyl Migration in Tetracarbonylmethylcobalt(I) and Dicarbonylcyclopentadienylmethyliron(II)", Jimmy R. Rogers, Ojin Kwon and Dennis S. Marynick*, Organometallics, 1991, 10, 2816-2823. The original paper for the method is "Self-consistent- field wavefunctions for complex molecules. The approximation of partial retention of diatomic differential overlap", Thomas A. Halgren* and William N. Lipscomb, J. Chem. Phys., Vol 58, No 4, 1973, 1569-1591. Information on any other papers on (or using) the method would be welcomed. Please E-mail me direct (to save bandwidth) and I will summerize to the list. ANY and ALL comments welcome. Thanks in Advance Oliver ______________________________________________________________________ | Oliver Hill | | | Department of Chemistry | "The true scientist never | | University of Cape Town | loses the faculty of | | Rondebosch, 7700 | amazement. It is the essence | | SOUTH AFRICA | of his being." | | OLIVER@PSIPSY.UCT.AC.ZA (internet) | - HANS SELYE | | | | | Tel. +27-21-650-2527 | | | Fax. +27-21-650-3788 | | |____________________________________|_______________________________| From bbendik@telerama.lm.com Thu Mar 10 08:41:36 1994 Received: from telerama.lm.com for bbendik@telerama.lm.com by www.ccl.net (8.6.4/930601.1506) id IAA05996; Thu, 10 Mar 1994 08:35:56 -0500 From: Received: from localhost (bbendik@localhost) by telerama.lm.com (8.6.5/8.6.5) id IAA28158; Thu, 10 Mar 1994 08:34:59 -0500 Date: Thu, 10 Mar 1994 08:34:57 +0500 (EST) Subject: Re: CCL:Program for pKa determination To: CHAMANKHAH@sask.usask.ca cc: chemistry@ccl.net In-Reply-To: <01H9RY642C2A9LZUO2@SKYCAT.USask.CA> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Mahmood - Molecular Simulations offers a program that calculates .delta.G of solvation, from which some pK values can be obtained. The package is called Polaris (ref. by author Arieh Warshel). It lies somewhere between an atomistic approach and a continuum approach. It's worth looking into, as long as you apply it to molecules that are "reasonably" similar in structure. Regards, Bev Beverly Bendiksen Research Associate Calgon Corporation Pittsburgh, PA (412)7778862 voice (412)7778714 fax From cooksj@ttown.apci.com Thu Mar 10 10:40:53 1994 Received: from ttown.apci.com for cooksj@ttown.apci.com by www.ccl.net (8.6.4/930601.1506) id JAA06726; Thu, 10 Mar 1994 09:48:06 -0500 Received: by ttown.apci.com (5.57/Ultrix3.0-C) id AA21425; Thu, 10 Mar 94 09:49:54 -0500 Date: Thu, 10 Mar 94 09:49:54 -0500 From: cooksj@ttown.apci.com (Stephen J. Cook) Message-Id: <9403101449.AA21425@ttown.apci.com> To: chemistry@ccl.net Subject: Program for calculating accessible surface area Reply-To: cooksj@ttown.apci.com Folks, I'm looking for a program to calculate the accessible surface area available to a penetrant molecule in some well-defined molecular space. Although I'm specifically interested in the ACCESSIBLE surface area of a molecular sieve, I suspect that similar programs written for drug or polymer applications would work just as well. Thanks. Steve Cook ********************************************************************* * Steve Cook cooksj@ttown.apci.com * * Air Products and Chemicals, Inc. Tel. (610) 481-2135 * * 7201 Hamilton Blvd. FAX (610) 481-2446 * * Allentown, PA 18195 * * USA * ********************************************************************* * Emacs - the choice of a GNU generation * ********************************************************************* From cqsimpson@halnet.com Thu Mar 10 10:43:44 1994 Received: from interlock.halnet.com for cqsimpson@halnet.com by www.ccl.net (8.6.4/930601.1506) id KAA06971; Thu, 10 Mar 1994 10:07:20 -0500 Received: by interlock.halnet.com id AA09370 (InterLock SMTP Gateway 1.1 for chemistry@ccl.net); Thu, 10 Mar 1994 09:07:15 -0600 Received: by interlock.halnet.com (Internal Mail Agent-1); Thu, 10 Mar 1994 09:07:15 -0600 Date: Thu, 10 Mar 1994 09:06:50 -0600 From: cqsimpson@halnet.com (Charlie Simpson) Message-Id: <9403101506.AA20340@cre2> To: chemistry@ccl.net Subject: Fe Basis Set & Surface Cc: mf10110@sc.msc.edu Fellow Netters: I am interested in the interaction of organic molecules with Fe surfaces using a MM/MD approach. This project requires that the Fe atom charges be as realistic as possible. Currently, my approach is to calculate the electrostatic potential of my Fe surface and then fit charges to it. Three questions come to my mind I would like your opinions on: 1) Can anyone recceommend a suitable Fe basis set for this sort of calculation? My Fe surface could potentially have up 3000 atoms. Soo,...the smallest basis set I could get away with would be great. 2) What level of theory, beyond HF, would be reasonable to go to considering the number of atoms I might be considering? 3) Finally, has anyone else looked at this type of problem before? Are there Fe surfaces with fitted charges in the literature that any of you know of? Any comments or suggestions you may have are welcome. I'll summarize the responses early next week. Many thanks in advance! Respectfully, Charlie Simpson ================================================================================ Charlie Simpson Ph.D. cqsimpson@halnet.com Halliburton Energy Services P.O. Box 1431 Phone 405/251-4564 Duncan, OK 73536-0438 Fax 405/251-3218 We have staked the whole future of the American civilization, not upon the power of government, far from it. We have staked the future...upon the capacity of each and all of us to govern ourselves, to control ourselves, to sustain ourselves, according to the Ten Commandments of God. James Madison ================================================================================ From markus@link.sunet.se Thu Mar 10 11:40:16 1994 Received: from decnet.sunet.se for markus@link.sunet.se by www.ccl.net (8.6.4/930601.1506) id LAA07915; Thu, 10 Mar 1994 11:20:10 -0500 Received: from LINK.DECnet MAIL11D_V3 by decnet.sunet.se (5.57/2.01) id AA29754; Thu, 10 Mar 94 17:19:11 +0100 Date: Thu, 10 Mar 94 17:19:11 +0100 Message-Id: <9403101619.AA29754@decnet.sunet.se> From: markus@ccl.net (Markus Haeberlein ) To: "chemistry@ccl.net"@kth.sunet.se Cc: MARKUS@decnet.sunet.se Subject: Summer schools in quantum chemistry Dear Netters, I would appreciate information about summer schools in quantum chemistry that will be held in the summer of 1994. Please reply directly to me and I will compile and post the summary. Thanks. Markus Haeberlein From Don_Gregory@MSI.COM Thu Mar 10 11:46:11 1994 Received: from schizoid.msi.com for Don_Gregory@MSI.COM by www.ccl.net (8.6.4/930601.1506) id LAA08028; Thu, 10 Mar 1994 11:30:03 -0500 Received: from msi.com (qmail-gw.msi.com) by schizoid.msi.com (4.1/SMI-4.1) id AA01993; Thu, 10 Mar 94 11:29:32 EST Message-Id: <9403101629.AA01993@schizoid.msi.com> Date: 10 Mar 1994 11:30:53 +0000 From: "Don Gregory" Subject: Re: CCL-Program for pKa dete To: chemistry@ccl.net Reply to: RE>CCL:Program for pKa determi I'd like to address one fine point in Beverly's response to Mamhood's pKa question. Polaris calculates the *delta*pKa as a function of environmental change. A small distinction, but quite an important one. For example, should one wish to know how a mutated residue affects the pKa of a wild-type histidine in an active-side, knowing the wild-type pKa, *as a reference*, one can calculate the delta-pKa as a function of the environment change caused by the mutation. People have also used this capability to determine the change in metal-clusters as a function of explicit counter-ion, etc. Beverly is also correct in stating that Prof. Warshal's approach (using Langevin dipoles) is somewhere between atomistic and continum,inthat one may as as many explicit waters as one wishes, and they, as well as the solute (even protein for deltaG-binding calculations) are treated explicitly. Over that, one may impose quite large volumes of grid points, each representing the position of a Langevin dipole. Thus, one can mix explicit & Langevin regions as one wishes. A final note, these are delta-G's, NOT delta-delta's! And the Langevin approach results in delta-G calculations that take 10's of minutes at most. I don't really want to turn this into a sales/marketing tirade; I'm very much a believer that this isn't the place for that sort of thing, but I thought some technical clarity might be useful. Don Gregory Mgr. Application Science MSI -------------------------------------- From: bbendik@telerama.lm.com Date: Thu, 10 Mar 1994 08:34:57 +0500 (EST) Subject: CCL:Program for pKa determination Mahmood - Molecular Simulations offers a program that calculates .delta.G of solvation, from which some pK values can be obtained. The package is called Polaris (ref. by author Arieh Warshel). It lies somewhere between an atomistic approach and a continuum approach. It's worth looking into, as long as you apply it to molecules that are "reasonably" similar in structure. Regards, Bev Beverly Bendiksen Research Associate Calgon Corporation Pittsburgh, PA (412)7778862 voice (412)7778714 fax ---Administrivia: This message is automatically appended by the mail exploder: CHEMISTRY@ccl.net -- everyone | CHEMISTRY-REQUEST@ccl.net -- coordinator MAILSERV@ccl.net: HELP CHEMISTRY | Gopher: www.ccl.net (port 70 or 73) Anon. ftp www.ccl.net | CHEMISTRY-SEARCH@ccl.net -- archive search From marshall@mcs.anl.gov Thu Mar 10 12:40:18 1994 Received: from antares.mcs.anl.gov for marshall@mcs.anl.gov by www.ccl.net (8.6.4/930601.1506) id LAA08310; Thu, 10 Mar 1994 11:49:00 -0500 Received: from mcs.anl.gov (clyde.mcs.anl.gov [140.221.11.2]) by antares.mcs.anl.gov (8.6.4/8.6.4) with ESMTP id KAA06311; Thu, 10 Mar 1994 10:48:46 -0600 Message-Id: <199403101648.KAA06311@antares.mcs.anl.gov> To: cooksj@ttown.apci.com cc: chemistry@ccl.net, marshall@antares.mcs.anl.gov Subject: Re: CCL:Program for calculating accessible surface area In-reply-to: Your message of "Thu, 10 Mar 1994 09:49:54 EST." <9403101449.AA21425@ttown.apci.com> Date: Thu, 10 Mar 1994 10:48:44 -0600 From: ""Chris Marshall (Argonne Nat. Laboratory)"" Steve, I would be very interested in hearing what you get back on this note. I am involved in zeolite and amorphous catalyst synthesis and characterization so this type of software would be of interest to me. Would you please forward anything pertinent to me at the address below. Thanks. Chris ********************************************************************** * __________________________________________________________________ * *| |* *| Christopher L. Marshall |* *| Research Scientist, Coal Chemistry Group |* *| |* *| Argonne National Laboratory Phone: (708) 252-4310 |* *| Building 200; Room L-121 FAX: (708) 252-9288 |* *| 9700 South Cass Avenue Internet: marshall@mcs.anl.gov |* *| Argonne, IL 60439-4831 |* *|__________________________________________________________________|* * * ********************************************************************** From hreese@alchemy.chem.utoronto.ca Thu Mar 10 13:40:19 1994 Received: from alchemy.chem.utoronto.ca for hreese@alchemy.chem.utoronto.ca by www.ccl.net (8.6.4/930601.1506) id NAA09148; Thu, 10 Mar 1994 13:00:11 -0500 Received: from localhost (hreese@localhost) by alchemy.chem.utoronto.ca (8.6.4/8.6.4) id MAA20314 for chemistry@ccl.net; Thu, 10 Mar 1994 12:56:00 -0500 Date: Thu, 10 Mar 1994 12:56:00 -0500 From: Howard Reese Message-Id: <199403101756.MAA20314@alchemy.chem.utoronto.ca> To: chemistry@ccl.net Subject: Labeling of CERIUS models Fellow CERIUS users, Lately, I've been using Molecular Simulations CERIUS package to make slides of molecules that are of interest to our group. I would like to add titles and a few lines of data to the models, but there doesn't seem to be any way to annotate a CERIUS model. Does anybody have any suggestions on how to do this? Thanks Howie Reese From AHOLDER@VAX1.UMKC.EDU Thu Mar 10 13:41:34 1994 Received: from VAX1.UMKC.EDU for AHOLDER@VAX1.UMKC.EDU by www.ccl.net (8.6.4/930601.1506) id MAA09011; Thu, 10 Mar 1994 12:42:34 -0500 From: Received: from VAX1.UMKC.EDU by VAX1.UMKC.EDU (PMDF V4.2-11 #4431) id <01H9T0QCII1I9BWG4L@VAX1.UMKC.EDU>; Thu, 10 Mar 1994 11:42:22 CST Date: Thu, 10 Mar 1994 11:42:22 -0600 (CST) Subject: Announcing the IBM/PC version of AMPAC To: CHEMISTRY@ccl.net Message-id: <01H9T0QCII1K9BWG4L@VAX1.UMKC.EDU> X-VMS-To: IN%"CHEMISTRY@ccl.net" MIME-version: 1.0 Content-transfer-encoding: 7BIT Dear Netters, Semichem is pleased to announce AMPAC 5.0PC for use on IBM/PC and comp- atible computers to be released May 2, 1994. AMPAC 5.0PC features MJS Dewar's new SAM1 semiempirical method and now includes parameters for iron (Fe). All of the power of AMPAC 5.0 for small and medium-sized molec- ules is now available on the desktop and in instructional environments. We will demonstrate the new version of AMPAC at the American Chemical Society Meeting in San Diego next week in Booth 1008 and will be happy to talk with you about your needs. =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- DR. ANDREW HOLDER President, Semichem Semichem, Inc. || Internet Addr: aholder@vax1.umkc.edu 7128 Summitt || Phone Number: (913) 268-3271 Shawnee, KS 66216 || FAX Number: (913) 268-3445 =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- From AHOLDER@VAX1.UMKC.EDU Thu Mar 10 13:42:30 1994 Received: from VAX1.UMKC.EDU for AHOLDER@VAX1.UMKC.EDU by www.ccl.net (8.6.4/930601.1506) id MAA09008; Thu, 10 Mar 1994 12:42:30 -0500 From: Received: from VAX1.UMKC.EDU by VAX1.UMKC.EDU (PMDF V4.2-11 #4431) id <01H9T0PRBHV49BWG4L@VAX1.UMKC.EDU>; Thu, 10 Mar 1994 11:41:57 CST Date: Thu, 10 Mar 1994 11:41:57 -0600 (CST) Subject: Announcing AMPAC 5.0 with Graphical User Interface To: CHEMISTRY@ccl.net Message-id: <01H9T0PRC15U9BWG4L@VAX1.UMKC.EDU> X-VMS-To: IN%"CHEMISTRY@ccl.net" MIME-version: 1.0 Content-transfer-encoding: 7BIT Dear Netters, Semichem is pleased to announce AMPAC 5.0 with Graphical User Interface to be released May 2, 1994. AMPAC 5.0 features MJS Dewar's new SAM1 semi- empirical method and now includes parameters for iron (Fe). Our program offers state-of-the-art semiempirical methodology in an easily accessible format, supported by Semichem's expert customer service. We will demon- strate the new version of AMPAC at the American Chemical Society Meeting in San Diego next week in Booth 1008. AMPAC runs on virtually every plat- form and our Graphical User Interface uses the popular X-Windows/Motif protocol for compatibility and seamless network access. =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- DR. ANDREW HOLDER President, Semichem Semichem, Inc. || Internet Addr: aholder@vax1.umkc.edu 7128 Summitt || Phone Number: (913) 268-3271 Shawnee, KS 66216 || FAX Number: (913) 268-3445 =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- From DSMITH@uoft02.utoledo.edu Thu Mar 10 14:40:15 1994 Received: from uoft02.utoledo.edu for DSMITH@uoft02.utoledo.edu by www.ccl.net (8.6.4/930601.1506) id OAA10198; Thu, 10 Mar 1994 14:28:58 -0500 Received: from UOFT02.UTOLEDO.EDU by UOFT02.UTOLEDO.EDU (PMDF V4.2-10 #3438) id <01H9T6F1NO640046HE@UOFT02.UTOLEDO.EDU>; Thu, 10 Mar 1994 14:27:35 EST Date: Thu, 10 Mar 1994 14:27:35 -0500 (EST) From: "DR. DOUGLAS A. SMITH, UNIVERSITY OF TOLEDO" Subject: The AVS Chemistry Viewer To: chemistry@ccl.net Message-id: <01H9T6F1NO660046HE@UOFT02.UTOLEDO.EDU> X-Envelope-to: chemistry@ccl.net X-VMS-To: CHEMISTRY MIME-version: 1.0 Content-transfer-encoding: 7BIT The AVS Chemistry Viewer, a graphical interface to quantum chemistry and molecular modeling codes, will be on display at the ACS meeting in San Diego at the DEC and IBM booths at the exposition. Stop by and learn more about the functionality of this package. The AVS Chemistry Viewer is sold and supported by The DASGroup, Inc. Douglas A. Smith, Ph.D. President The DASGroup, Inc. voice: 419-537-2116 or 419-472-9160 fax: 419-472-4757 email: dsmith@uoft02.utoledo.edu mailing address: 3807 Elmhurst Road Toledo, OH 43613-4209 From david@iris.claremont.edu Thu Mar 10 15:42:00 1994 Received: from iris.claremont.edu for david@iris.claremont.edu by www.ccl.net (8.6.4/930601.1506) id OAA10781; Thu, 10 Mar 1994 14:58:09 -0500 Received: from localhost (david@localhost) by iris.claremont.edu (8.6.4/8.6.4) id MAA14108 for CHEMISTRY@ccl.net; Thu, 10 Mar 1994 12:01:51 -0800 From: "David H." Message-Id: <199403102001.MAA14108@iris.claremont.edu> Subject: HOMO values from AM1 To: CHEMISTRY@ccl.net Date: Thu, 10 Mar 1994 12:01:50 -0800 (PST) X-Mailer: ELM [version 2.4 PL20] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 403 I'm posting this question for a colleague; please reply to this list, or directly to her at "litai@qsar.claremont.edu". ------ Can anyone explain why the HOMO calculated for hydroquinone is higher than that for resorcinol? The results (from AM1, version 6.0) I obtained were: -8.74 hydroquinone -8.99 resorcinol Litai Zhang ------ -- David Hoekman Pomona College 909-624-5509 (phone & fax) From PHYSPLMP@MIZZOU1.missouri.edu Thu Mar 10 16:40:18 1994 Received: from MIZZOU1.missouri.edu for PHYSPLMP@MIZZOU1.missouri.edu by www.ccl.net (8.6.4/930601.1506) id QAA11613; Thu, 10 Mar 1994 16:25:19 -0500 From: Message-Id: <199403102125.QAA11613@www.ccl.net> Received: from MIZZOU1 by MIZZOU1.missouri.edu (IBM VM SMTP V2R2) with BSMTP id 9598; Thu, 10 Mar 94 15:26:03 CST Received: by MIZZOU1 (Mailer R2.10 ptf000) id 9348; Thu, 10 Mar 94 15:26:03 CST Date: Thu, 10 Mar 94 15:23:26 CST To: chemistry@ccl.net Subject: XXVII Midwest Theoretical Chemistry Conference The 1994 conference will be held on the campus of the University of Missouri in Columbia, MO and May 19-21. The co-organizers for this year's conference are Pat Plummer and John Adams. As has been the practice in past years, the conference will open with a reception on Thursday evening, and papers(in either oral or poster format) will be presented all day Friday and on Saturday morning The conference banquet will be held on Friday evening. In order to keep expens es down and thus to encourage the maximum amount of student participation (an important tradition of thi meeting), accommondations during the conference will available in University dormitories at a very reasonable price. Details con- cerning registration, accommondations, abstract format, etc., will be supplied in the second announcement and call for papers which will be mailed at the end of March. Questions may directed to either of the organizers c/o Chemistry Department University of Missouri-Columbia, Columbia, MO 65211, FAX 314-882- 2754 or Prof. Patricia Plummer, physplmp@mizzou1.missouri.edu, (314) 882-3053 Prof. John Adams, chem1059@mizzou1.missouri.edu, (314) 882-3245 To insure that you receive the 2nd announcement and call for papers, please drop a note to one of the organizers(e-mail preferred) indicating your interest From AMS%NPD1@itep.itep.br Thu Mar 10 16:41:26 1994 Received: from fpsp.fapesp.br for AMS%NPD1@itep.itep.br by www.ccl.net (8.6.4/930601.1506) id PAA11309; Thu, 10 Mar 1994 15:48:27 -0500 From: Received: from itep.itep.br by fpsp.fapesp.br with PMDF#10108; Thu, 10 Mar 1994 17:46 BSC (-0300 C) Received: from DECNET-MAIL (AMS@NPD1) by itep.itep.br (PMDF V4.2-11 #3257) id <01H9TD7H1CSG00075B@itep.itep.br>; Thu, 10 Mar 1994 17:44:05 -0300 Date: Thu, 10 Mar 1994 17:44:04 -0300 Subject: Bond breaking predicted by semiempirical methods To: CHEMISTRY@ccl.net Message-id: <01H9TD7H53TE00075B@itep.itep.br> X-Envelope-to: CHEMISTRY@ccl.net X-VMS-To: ITEP::IN%"CHEMISTRY@ccl.net" MIME-version: 1.0 Content-transfer-encoding: 7BIT Dear Netters, Sometimes when I try to fully optimize the geometry of an organic molecule using AM1, PM3 or any other semiempirical method, a situation arises where a particular bond distance in the molecule is optimized to a very large value. At first, one would be inclined to say that a case of structural instability is at hand and that such a molecule could not possibly exist. However, when I perform the same calculation using almost any ab-initio technique, a very stable and nice structure is predicted. That happens even with molecules that have been synthesized, are well known and whose x-ray structures have been determined. I would like to know if any of you can send me some references on that. I will summarize the results to the net for the benefit of all. ************************************************************************ * * * Alfredo Mayall Simas e-mail: AMS@npd1.ufpe.br * * Departamento de Quimica Fundamental Fax: (081) 271-8442 * * Universidade Federal de Pernambuco Office: (081) 271-8440 x 37 * * 50.739-000 Recife, PE CCEN: (081) 271-8400 * * Brasil * * * ************************************************************************ From elewars@alchemy.chem.utoronto.ca Thu Mar 10 17:44:07 1994 Received: from alchemy.chem.utoronto.ca for elewars@alchemy.chem.utoronto.ca by www.ccl.net (8.6.4/930601.1506) id RAA12450; Thu, 10 Mar 1994 17:36:41 -0500 Received: from localhost (elewars@localhost) by alchemy.chem.utoronto.ca (8.6.4/8.6.4) id RAA15631 for chemistry@ccl.net; Thu, 10 Mar 1994 17:32:28 -0500 Date: Thu, 10 Mar 1994 17:32:28 -0500 From: "E. Lewars" Message-Id: <199403102232.RAA15631@alchemy.chem.utoronto.ca> To: chemistry@ccl.net Subject: calculating pKa's Mahmood asks how to calculate pK's. I don't know if there is a program that will take the structure of an acid and spew out the pKa, but pKa's can be estimated in at least two ways. One can calculate the energy of the acid and its conjugate base, or do an isodesmic reaction calc and get the pK from the deltaE. A simpler method is based on the correlation of maximum calc electrostatic potential with pKa. For examples, get hold of "Experiments in Computational Organic Chemistry" by Hehre, Burke, Shusterman and Pietro (Wavefunction Inc, 1993; (714)955-2120)). See also Dewar and Dieter, JACS 1986 108 8075-86. ==== From JARRINM%AM.mrgate@woods.uml.edu Thu Mar 10 18:40:19 1994 Received: from willow.uml.edu for JARRINM%AM.mrgate@woods.uml.edu by www.ccl.net (8.6.4/930601.1506) id SAA13124; Thu, 10 Mar 1994 18:32:02 -0500 Received: by woods.uml.edu (MX V3.3 VAX) id 326; Thu, 10 Mar 1994 18:30:07 EST Date: Thu, 10 Mar 1994 18:29:38 EST From: JARRINM%AM.mrgate@woods.uml.edu To: cooksj@ttown.apci.com, CHEMISTRY@ccl.net X-VMSmail-To: MX%"cooksj@ttown.apci.com",CHEMISTRY@ccl.net Message-ID: <0097B3CB.E52D6700.326@woods.uml.edu> Subject: RE: CCL:Program for calculating accessible surface area From: NAME: JARRINM TEL: N/A ADDR: STUDENT To: NAME: MX%"cooksj@ttown.apci.com" CC: chemistry@ccl.net@INTERNET With CHARMm it si possible to calulate both accessible and contact surface areas. The algorithm used calculates the Lee and Richards surface. Look up these two papers to get a better idea: Lee, B.; Richards, F. M. "The interpretation of Protein Structures: Estimation of Static Accessibility"; J. Mol. Biol. 1971, 55, 379. Richrds, F. M. "Areas, Volumes, Packing, and Protein Structure" Ann. Rev. Biophys. Bioeng. 1977, 6, 151-176. I belive there is a program available from QCPE that uses the Lee and Richards method. Good Luck. Mario A. Jarrin Chemistry Department U. of Massachusetts at Lowell Lowell, MA 02148 From NRICHAR@uoft02.utoledo.edu Thu Mar 10 20:40:19 1994 Received: from uoft02.utoledo.edu for NRICHAR@uoft02.utoledo.edu by www.ccl.net (8.6.4/930601.1506) id UAA13804; Thu, 10 Mar 1994 20:26:32 -0500 From: Received: from UOFT02.UTOLEDO.EDU by UOFT02.UTOLEDO.EDU (PMDF V4.2-10 #3438) id <01H9TIZ6KZF4003WL2@UOFT02.UTOLEDO.EDU>; Thu, 10 Mar 1994 20:25:15 EST Date: Thu, 10 Mar 1994 20:25:15 -0500 (EST) Subject: ESR Spectra To: CHEMISTRY@ccl.net Message-id: <01H9TIZ6MLAQ003WL2@UOFT02.UTOLEDO.EDU> X-Envelope-to: CHEMISTRY@ccl.net X-VMS-To: CHEMISTRY@ccl.net MIME-version: 1.0 Content-transfer-encoding: 7BIT We need to interpret the ESR spectrum of a highly twisted olefinic system, C22H28. I realize that planar pi systems can be approximated by noting the unpaired spin density in the SOMO. Spin contamination creates serious problems when attempting to calculate ESR spectra of other systems. Does anyone have a reasonable suggestion? Thanks. Jim Gano Department of Chemistry University of Toledo Toledo, Ohio 43606 From mes@atlas.chemistry.uakron.edu Thu Mar 10 21:40:20 1994 Received: from atlas.chemistry.uakron.edu for mes@atlas.chemistry.uakron.edu by www.ccl.net (8.6.4/930601.1506) id UAA14261; Thu, 10 Mar 1994 20:56:11 -0500 Received: by atlas.chemistry.uakron.edu (4.1/SMI-4.1) id AA21540; Thu, 10 Mar 94 21:00:09 EST Date: Thu, 10 Mar 1994 20:59:09 -0500 (EST) From: Mary Ellen Scott Sender: Mary Ellen Scott Reply-To: Mary Ellen Scott Subject: pKa prediction To: chemistry@ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Text: pKa Prediction for organic Acids and Bases D.D. Perrin, Boyd Dempsey & E.P. Serjeant From JKONG@ac.dal.ca Thu Mar 10 21:43:26 1994 Received: from SYSWRK.UCIS.DAL.CA for JKONG@ac.dal.ca by www.ccl.net (8.6.4/930601.1506) id UAA14223; Thu, 10 Mar 1994 20:49:55 -0500 Received: from AC.Dal.Ca by SYSWRK.UCIS.DAL.CA (PMDF V4.2-14 #2545) id <01H9TLXB7V4W002EUB@SYSWRK.UCIS.DAL.CA>; Thu, 10 Mar 1994 21:49:26 -0400 Received: from AC.DAL.CA by AC.DAL.CA (PMDF V4.2-14 #2545) id <01H9TLQL1ZC000024H@AC.DAL.CA>; Thu, 10 Mar 1994 21:47:36 -0400 Date: Thu, 10 Mar 1994 21:47:36 -0400 From: JING KONG Subject: H-bonds To: chemistry@ccl.net Message-id: <01H9TLQL4XFM00024H@AC.DAL.CA> X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Dear netters, I would like to know the bond-lengths and directions of as many H-bonds as possible. Where or how can I get them? Are there any reviews on that topic? Thank you in advance. I will give a summary if there is enough interest. Jing