From rochus@felix.anorg.chemie.tu-muenchen.de Tue Oct 31 03:16:05 1995 Received: from felix.anorg.chemie.tu-muenchen.de for rochus@felix.anorg.chemie.tu-muenchen.de by www.ccl.net (8.6.10/950822.1) id DAA03071; Tue, 31 Oct 1995 03:14:09 -0500 Received: by felix.anorg.chemie.tu-muenchen.de (940816.SGI.8.6.9/930416.SGI) id JAA03117; Tue, 31 Oct 1995 09:13:00 +0100 From: "Rochus Schmid" Message-Id: <9510310913.ZM3115@felix> Date: Tue, 31 Oct 1995 09:12:59 +0100 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@www.ccl.net Subject: Loewdin charges/ DFT Cc: rochus@felix.anorg.chemie.tu-muenchen.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear Netters, Recently I've optimized a number of low valent Rhodium (I) complexes with DGauss on the LDA level (DZVP basis). The Loewdin charges of the metal atom calculated by the program show a reasonable tendency for the different complexes, but the absolute values are always negative (down to -1), which I didn't expect. Others (they do a lot of TM ab initio calculations) told me, that they never get negative values in any charge analysis for TM atoms. My questions are: - is this something to worry about? (I want to discuss the tendency only) - if it is something unusual, what is the origin: DFT or the Loewdin charge analysis? I would be very happy about any hints/ comments on this matter. I will summarize to the net. Thanks in advance. Rochus -- ******************************************************************************** Rochus Schmid Technische Universitaet Muenchen Tel. ++49 89 3209 3140 Anorganisch Chemisches Institut 1 Fax. ++49 89 3209 3473 Prof. W. A. Herrmann E-mail: Lichtenbergstrasse 4 rochus@felix.anorg.chemie.tu-muenchen.de 85747 Garching ******************************************************************************** From eldbjorg@chem.uit.no Tue Oct 31 05:16:06 1995 Received: from kvikk.uit.no for eldbjorg@chem.uit.no by www.ccl.net (8.6.10/950822.1) id FAA04612; Tue, 31 Oct 1995 05:06:32 -0500 Received: from trypsin.chem.uit.no by kvikk.uit.no (8.6.12/MLH-1.2(V8)) id LAA02391 ; Tue, 31 Oct 1995 11:06:31 +0100 Received: by trypsin.chem.uit.no (911016.SGI/ABaa-2.0mini) id AA00005; Tue, 31 Oct 95 11:31:47 +0100 Date: Tue, 31 Oct 95 11:31:47 +0100 From: eldbjorg@chem.uit.no (Eldbjoerg S. Heimstad) Message-Id: <9510311031.AA00005@trypsin.chem.uit.no> To: chemistry@www.ccl.net Subject: Cavities within proteins Does anyone of you have a way to calculate cavities within proteins ? All replies will be appreciated - Regards, ####################################################### # Eldbjoerg Sofie Heimstad # # Protein Crystallography Group # # University Of Tromsoe, IMR # # 9037 Tromsoe, NORWAY phone: +47-776-45706 # # 44737 # # fax : +47-776-44765 # # E-mail: eldbjorg@chem.uit.no # # Web: http://www.chem.uit.no # ####################################################### From laaksone@csc.fi Tue Oct 31 06:46:07 1995 Received: from finsun.csc.fi for laaksone@csc.fi by www.ccl.net (8.6.10/950822.1) id GAA05547; Tue, 31 Oct 1995 06:38:45 -0500 Received: (from laaksone@localhost) by finsun.csc.fi (8.6.9/8.6.9+CSC-2.0) id NAA05435; Tue, 31 Oct 1995 13:38:42 +0200 Content-Transfer-Encoding: 8bit Date: Tue, 31 Oct 1995 13:38:41 +0200 (EET) From: Leif Laaksonen Subject: Re: CCL:Cavities within proteins To: "Eldbjoerg S. Heimstad" cc: chemistry@www.ccl.net In-Reply-To: <9510311031.AA00005@trypsin.chem.uit.no> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, You should be able to calculate them in much the same way as we did it for cavities in polyisobutylene (PIB): http://www.csc.fi/lul/chem/movies/pib/pib_movies.html Regards, -leif laaksonen On Tue, 31 Oct 1995, Eldbjoerg S. Heimstad wrote: > > Does anyone of you have a way to calculate cavities within > proteins ? > > All replies will be appreciated - > > Regards, > > > ####################################################### > # Eldbjoerg Sofie Heimstad # > # Protein Crystallography Group # > # University Of Tromsoe, IMR # > # 9037 Tromsoe, NORWAY phone: +47-776-45706 # > # 44737 # > # fax : +47-776-44765 # > # E-mail: eldbjorg@chem.uit.no # > # Web: http://www.chem.uit.no # > ####################################################### > > > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: eldbjorg@chem.uit.no > -- Original Sender From: Address: eldbjorg@chem.uit.no > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > > ------------------------------------------------------------------- Leif Laaksonen | Center for Scientific Computing | Phone: 358 0 4572378 P.O. Box 405 | Mobile: 358 400425203 FIN-02101 Espoo | Telefax: 358 0 4572302 FINLAND | Mail: Leif.Laaksonen@csc.fi ---------URL: http://laaksonen.csc.fi/leif.laaksonen.html---------- Tried to save the trees. Bought a plastic bag. The bottom fell out. It was a piece of crap. N. Young ------------------------------------------------------------------- From owner-chemistry@ccl.net Tue Oct 31 08:16:10 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id IAA06879; Tue, 31 Oct 1995 08:04:23 -0500 Received: from styx.iqm.unicamp.br for anderson@IQM.Unicamp.BR by bedrock.ccl.net (8.6.10/950822.1) id IAA13999; Tue, 31 Oct 1995 08:04:11 -0500 Received: (anderson@localhost) by styx.iqm.unicamp.br (8.6.10/IQM-ANSP1.5) id LAA23490; Tue, 31 Oct 1995 11:00:48 -0200 From: Anderson Coser Gaudio Posted-Date: Tue, 31 Oct 1995 11:00:48 -0200 Message-Id: <199510311300.LAA23490@styx.iqm.unicamp.br> Subject: Fukui indices and molecular geometry To: CHEMISTRY@ccl.net Date: Tue, 31 Oct 1995 11:00:46 -0200 (EDT) X-Mailer: ELM [version 2.4 PL23] Content-Type: text Content-Length: 1393 Dear netters, I am interested in one aspect of the calculation of the Fukui indices frontier electron density (FED), frontier orbital density (FOD), and frontier radical density (FRD). Does anyone know a paper that deals with the dependence of these indices with the molecular geometry ? Please write answers to my personal address. I will resume them later in the list. Anderson | O | | O | | | | | +---+--------------------------------------------------------+---+ | | | | | O | | O | | | Anderson Coser Gaudio | | | O | | O | | | Inst. Quimica - Unicamp anderson@iqm.unicamp.br | | | O | CP 6154 - Cid. Universitaria Phone: 55-0192-39 8413 | O | | | Campinas - SP - Brazil Fax: 55-0192-39 3805 | | | O | CEP 13 081-970 | O | | | | | +---+--------------------------------------------------------+---+ | | | | | O | | O | From owner-chemistry@ccl.net Tue Oct 31 10:01:11 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id JAA09443; Tue, 31 Oct 1995 09:54:11 -0500 Received: from nuhub.dac.neu.edu for MARYJO@neu.edu by bedrock.ccl.net (8.6.10/950822.1) id JAA15129; Tue, 31 Oct 1995 09:54:09 -0500 From: Received: from neu.edu by neu.edu (PMDF V4.3-7 #11963) id <01HX33RM1TS093FSFB@neu.edu>; Tue, 31 Oct 1995 09:56:24 EST Date: Tue, 31 Oct 1995 09:56:24 -0500 (EST) Subject: size limits in MOPAC To: chemistry@ccl.net Message-id: <01HX33RM48KY93FSFB@neu.edu> X-Envelope-to: chemistry@ccl.net X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-transfer-encoding: 7BIT Hello Everybody. I am asking this question on behalf of a colleague who is running MOPAC 6 (vintage 1993). In this version, the maximum number of heavy atoms is 24. His molecule is bigger by a couple of atoms. Is there a version of MOPAC that will take a slightly bigger molecule, and that runs on a 486? If so, where can we get a copy? Thanks very much, Mary j.o. From owner-chemistry@ccl.net Tue Oct 31 11:16:12 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id LAA11295; Tue, 31 Oct 1995 11:05:02 -0500 Received: from nomad.holonet.net for BOBS@MDLI.COM by bedrock.ccl.net (8.6.10/950822.1) id LAA15891; Tue, 31 Oct 1995 11:04:58 -0500 Received: from jubal.mdli.com by nomad.holonet.net (BOBS@mdli.com) id HAA19515; Tue, 31 Oct 1995 07:49:36 -0800 Received: from gimli.mdli.com by jubal.mdli.com (AIX 4.1/UCB 5.64/9393.1) id AA30570; Tue, 31 Oct 1995 07:49:02 -0800 Received: from mdli.com by mdli.com (PMDF V4.3-10 #6626) id <01HX2ZFV8608HXIX1B@mdli.com>; Tue, 31 Oct 1995 07:49:29 -0800 (PST) Date: Tue, 31 Oct 1995 07:49:29 -0800 (PST) From: "Bob Snyder, x1162" Subject: CINF New Orleans talk deadline is November 1, 1995 To: chemistry@ccl.net Message-Id: <01HX2ZFV860AHXIX1B@mdli.com> X-Vms-To: IN%"chemistry@ccl.net" X-Vms-Cc: BOBS Mime-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Content-Transfer-Encoding: 7BIT This is a reminder that the deadline for CINF talks in New Orleans is coming up November 1st. ------------------------------------------------------------------------ Symposium: Utilization of Information in Databases of Biologically Active Compounds Location: American Chemical Society 211th National Meeting Division of Chemical Information (CINF) New Orleans, Louisiana USA Date: March 24-28, 1996 This symposium will focus on information requirements during drug discovery and how information about biologically active compounds can be used at all levels of the drug discovery process. Several invited speakers have been confirmed for the symposium. If you are interested in contributing to this symposium, please send a summary of about 200 words describing your presentation by November 1, 1995 to: Robert W. Snyder MDL Information Systems, Inc. 14600 Catalina Street San Leandro, CA 94577 USA Phone: (510) 895-1313 Fax: (510) 614-3652 Email: bobs@mdli.com Abstracts for accepted papers must be submitted by November 15, 1995 on official ACS abstract forms. For those wishing to attend, I look forward to seeing you in New Orleans. [This message has been posted to: CHEMIND-L, CHMINF-L, ACSMEDI, CCL, ISISforum-L, and MOL-DIVERSITY lists] From owner-chemistry@ccl.net Tue Oct 31 12:01:13 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id LAA12899; Tue, 31 Oct 1995 11:51:53 -0500 Received: from pnl.gov for ma_thompson@ccmail.pnl.gov by bedrock.ccl.net (8.6.10/950822.1) id LAA16563; Tue, 31 Oct 1995 11:51:51 -0500 From: Received: from ccmail.pnl.gov by pnl.gov (PMDF V4.3-13 #6012) id <01HX31MAXZPC8Y4WPY@pnl.gov>; Tue, 31 Oct 1995 08:51:43 -0800 (PST) Date: Tue, 31 Oct 1995 08:48 -0800 (PST) Subject: Re: CCL:M:size limits in MOPAC To: chemistry@ccl.net, chemistry-request@www.ccl.net Message-id: <01HX31MB06TE8Y4WPY@pnl.gov> MIME-version: 1.0 Content-transfer-encoding: 7BIT Regarding: M:size limits in MOPAC A couple of solutions that I know of exist. 1). Walter Thiel's MNDO program will certainly handle very large systems. I believe it's distributed with a nominal charge. I don't know if it will run on a PC. 2). HyperChem: certainly does MOPAC type stuff and obviously runs on a PC. 3). CAChe: supports MOPAC, though I'm not sure if they have the same size limits. 4). We are working very hard to finish preparing for a source-code distribution of Argus 3.0. Argus does implement the MNDO methods (MNDO, AM1, and PM3), has no size limits, and does run on an PC (as well as Unix platforms). For relevant details see the below references: Thompson, Mark A. Molecular Dynamics Study of Li and Still's New Rigidified 18-Crown-6 Derivative Using a QM/MM Method. Int. J. Quantum Chemistry, 1995 (in press). Thompson, Mark A. Studies of Molecular Recognition Using QM/MM Methods. The Potential of Mean Force for the Association of K+ with Dimethylether in Aqueous Solution. J. Am. Chem. Soc., 1995 (in press, out in Nov). Thompson, Mark A. and Gregory K. Schenter. Excited States of the Bacteriochlorophyllb Dimer of Rhodopseudomonas viridis: A QM/MM Study of the Photosynthetic Reaction Center That Includes MM Polarization. J. Phys. Chem. 1995, 99, 6374-6386. Thompson, Mark A. Hybrid Quantum Mechanical/Molecular Mechanical Force Field Development for Large Flexible Molecules: A Molecular Dynamics Study of 18-Crown-6. J. Phys. Chem. 1995, 99, 4794-4804. Thompson, Mark, A.; Glendening, Eric, D. and David Feller. The Nature of K+/Crown-Ether Interactions: A Hybrid Quantum Mechanical/Molecular Mechanical Study. J. Phys. Chem. 1994, 98, 10465. Hope this helps. Mark Thompson Environmental Molecular Sciences Laboratory Pacific Northwest National Laboratory Richland, Wa. 99352 ma_thompson@pnl.gov _______________________________________________________________________________ Subject: CCL:M:size limits in MOPAC From: chemistry-request@www.ccl.net at -SMTPlink Date: 10/31/95 6:56 AM Hello Everybody. I am asking this question on behalf of a colleague who is running MOPAC 6 (vintage 1993). In this version, the maximum number of heavy atoms is 24. His molecule is bigger by a couple of atoms. Is there a version of MOPAC that will take a slightly bigger molecule, and that runs on a 486? If so, where can we get a copy? Thanks very much, Mary j.o. -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: owner-chemistry@ccl.net -- Original Sender From: Address: MARYJO@neu.edu CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search Web: http://www.ccl.net/chemistry.html From mcgsw@cotton.vislab.olemiss.edu Tue Oct 31 12:16:13 1995 Received: from sun1.mcsr.olemiss.edu for mcgsw@cotton.vislab.olemiss.edu by www.ccl.net (8.6.10/950822.1) id MAA13553; Tue, 31 Oct 1995 12:14:06 -0500 Received: from cotton.vislab.olemiss.edu by sun1.mcsr.olemiss.edu (4.1/SMI-4.1) id AA29373; Tue, 31 Oct 95 11:17:39 CST Received: by cotton.vislab.olemiss.edu (4.1/SMI-4.1) id AA15127; Tue, 31 Oct 95 11:14:03 CST Date: Tue, 31 Oct 1995 11:14:00 -0600 (CST) From: Scott Weston To: "Eldbjoerg S. Heimstad" Cc: chemistry@www.ccl.net Subject: Re: CCL:Cavities within proteins In-Reply-To: <9510311031.AA00005@trypsin.chem.uit.no> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Eldbjoerg, Depending on what your exact needs are, one good approach to the isolation and visualization of protein cavities is the one encoded in the CAVITY SEARCH program by Chris Ho and Garland Marshall at the Center for Molecular Design (J Comput Aided Mol Des (JCB), 1990 Dec; 4 (4): 337-54. More information is available at their Web site at http://wucmd.wustl.edu. Good luck, Scott ================================================================= Scott Weston Lab Phone: (601) 232-7187 Grad. Student Lab FAX: (601) 232-5118 Dept. of Medicinal Chemistry Home Phone: (601) 234-0067 University of Mississippi mcgsw@cotton.vislab.olemiss.edu University, MS 38677 ================================================================= On Tue, 31 Oct 1995, Eldbjoerg S. Heimstad wrote: > > Does anyone of you have a way to calculate cavities within > proteins ? > > All replies will be appreciated - > > Regards, > > > ####################################################### > # Eldbjoerg Sofie Heimstad # > # Protein Crystallography Group # > # University Of Tromsoe, IMR # > # 9037 Tromsoe, NORWAY phone: +47-776-45706 # > # 44737 # > # fax : +47-776-44765 # > # E-mail: eldbjorg@chem.uit.no # > # Web: http://www.chem.uit.no # > ####################################################### > > > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: eldbjorg@chem.uit.no > -- Original Sender From: Address: eldbjorg@chem.uit.no > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > > From owner-chemistry@ccl.net Tue Oct 31 12:46:12 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id MAA14263; Tue, 31 Oct 1995 12:37:30 -0500 Received: from rani.chem.yale.edu for lim@rani.chem.yale.edu by bedrock.ccl.net (8.6.10/950822.1) id MAA17224; Tue, 31 Oct 1995 12:37:27 -0500 Received: by rani.chem.yale.edu; Tue, 31 Oct 95 12:37:28 -0500 From: Dongchul Lim Message-Id: <9510311737.AA28985@rani.chem.yale.edu> Subject: Standard orientation in Gaussian To: chemistry@ccl.net (Computational Chemistry) Date: Tue, 31 Oct 95 12:37:27 EST X-Mailer: ELM [version 2.3 PL11] How does one get the standard orientation from a Z-matrix (or input) orientation without running Gaussian? -D. Lim, lim@rani.chem.yale.edu From owner-chemistry@ccl.net Tue Oct 31 13:31:13 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id NAA15404; Tue, 31 Oct 1995 13:24:35 -0500 Received: from olimp.irb.hr for kiralj@olimp.irb.hr by bedrock.ccl.net (8.6.10/950822.1) id NAA17820; Tue, 31 Oct 1995 13:24:23 -0500 From: Received: by olimp.irb.hr (MX V4.1 VAX) id 52; Tue, 31 Oct 1995 19:23:15 MET-DST Date: Tue, 31 Oct 1995 19:23:14 MET-DST To: CHEMISTRY@ccl.net Message-ID: <00998B4E.CA06E9D6.52@olimp.irb.hr> Subject: pi stacking area calculations again Dear CCL Netters, Last week I posted to the CCL inquiring with the following problem: Does anybody know for some program applicable to crystals or molecules with pi stacking interactions, that calculate area of the aromatic molecule or fragment covered by the neighbour aromatic molecule or fragment? Since I have no answers to summarize the subject, and supposing my question was not precise enough, I am asking for help on the pi stacking area calculations: Suppose one have several solved crystal structures or extracted from Cambridge Structural Database, or molecules are built and optimized by molecular mechanics or quantum mechanics programs. If these molecules are partially or completely aromatic, then it is possible that neighbour molecules or aromatic fragments are mutually parallel and on the distance approximately 3.5 A. If one can find a suitable view normal to the aromatic planes, stacking could be observed as covering of one aromatic system by one or two neighbour system. By changing the relative positional parameters of the neighbour aromatic systems this covering is changed. In the first approximation it could be taken that measure of this covering is area of the observed aromatic system (the system is taken as planar hexagons) or surface area (the system is supposed to be three-dimensional in pi interactions, and the interacting surface is not a plane containing the hexagons). The question is: Is there any program or appropriate reference dealing with such or similar calculations of the covering (pi stacking) areas or surface areas for a specified set of relative positional parameters? Any information or suggestion is welcome. Thanks in advance. Rudolf ------------- Rudolf Kiralj Department of Materials Science and Electronics Rudjer Boskovic Institute Bijenicka 54 10 000 Zagreb Croatia e-mail: kiralj@olimp.irb.hr From smb@smb.chem.niu.edu Tue Oct 31 14:16:13 1995 Received: from mp.cs.niu.edu for smb@smb.chem.niu.edu by www.ccl.net (8.6.10/950822.1) id OAA17000; Tue, 31 Oct 1995 14:15:55 -0500 Received: from cz2.chem.niu.edu by mp.cs.niu.edu with SMTP id AA22750 (5.67b/IDA-1.5 for <@mp.cs.niu.edu.chem.niu.edu:chemistry@www.ccl.net>); Tue, 31 Oct 1995 13:15:57 -0600 Received: from smb.chem.niu.edu by cz2.chem.niu.edu via SMTP (920330.SGI/890607.SGI) (for @mp.cs.niu.edu.chem.niu.edu:chemistry@www.ccl.net) id AA20461; Tue, 31 Oct 95 13:34:16 -0600 Received: by smb.chem.niu.edu (920330.SGI/890607.SGI) (for @cz2.chem.niu.edu:chemistry@www.ccl.net) id AA08577; Tue, 31 Oct 95 13:34:10 -0600 Date: Tue, 31 Oct 95 13:34:10 -0600 From: smb@smb.chem.niu.edu (Steven Bachrach) Message-Id: <9510311934.AA08577@smb.chem.niu.edu> To: chemistry@www.ccl.net Subject: ECCC2 Starts Tomorrow A reminder to all that the Second Electronic Computational Chemistry Conference begins tomorrow. You can register at http://hackberry.chem.niu.edu/cgi-bin/discuss.cgi Registration is open to all and there is no fee. Steve Steven Bachrach Department of Chemistry Northern Illinois University DeKalb, Il 60115 Phone: (815)753-6863 smb@smb.chem.niu.edu Fax: (815)753-4802 From owner-chemistry@ccl.net Tue Oct 31 14:25:35 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id OAA16741; Tue, 31 Oct 1995 14:07:39 -0500 Received: from ucsub.colorado.edu for garciae@ucsub.colorado.edu by bedrock.ccl.net (8.6.10/950822.1) id OAA18757; Tue, 31 Oct 1995 14:07:36 -0500 Received: (from garciae@localhost) by ucsub.colorado.edu (8.6.12/8.6.12/CNS-3.6) id MAA16377; Tue, 31 Oct 1995 12:07:12 -0700 Date: Tue, 31 Oct 1995 12:07:07 -0700 (MST) From: Garcia Edgardo To: chemistry@ccl.net Subject: CCL: BSSE safe zone Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Does anybody know which would be a good safe minimum distance to possition two small molecules so that the resultant intermolecular energy, from ab initio and/or AM1 calculations, is free from BSSE ? The distance can be considered to be from the center of mass of small molecules or minimum distance for two atoms one from each molecule. Thanks for any hints. Edgardo Garcia Cristol Chem & Biochem University of Colorado BOULDER CO USA From ccl@cric.chemres.hu Tue Oct 31 15:16:15 1995 Received: from cric.chemres.hu for ccl@cric.chemres.hu by www.ccl.net (8.6.10/950822.1) id PAA18544; Tue, 31 Oct 1995 15:12:42 -0500 From: Received: by cric.chemres.hu (AIX 3.2/UCB 5.64/4.03) id AA12900; Tue, 31 Oct 1995 20:40:00 +0100 Date: Tue, 31 Oct 1995 20:40:00 +0100 (NFT) To: Mike Peterson Cc: CHEMISTRY@www.ccl.net Subject: Re: CCL:BOND ORDERS In-Reply-To: <199509291850.OAA28935@alchemy.chem.utoronto.ca> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Sory, I have not followed CCL for some time. Mike is correct: diffuse orbitals are not of really atomic character, so the indices may go wrong. In such cases one may try to turn to a Lowdin-orthogonalized basis (which I do not recommend for basis sets of "atomic" type). I am working towards a scheme combining the merits of these without their drawbacks, but this may require a while. Regards to all, Istvan Mayer e-mail: mayer@cric.chemres.hu ----------------------------------------------------------------------- On Fri, 29 Sep 1995, Mike Peterson wrote: > Errol Lewars wrote: > > >Re the question about algorithms for bond orders: Dr Istvan Mayer (Central > >Research Institute, Hungarian Acad. of Sciences) argues that only his > >algorithm really gives correct (sensible?) bond orders. Thus the > >Mayer bond order of H2+ is 0.5 (a 1-electron bond), but (all?) other > >approaches give 0.25. > > Although there is a theoretical basis for the Mayer method given > in the papers, and it gives very sensible bond orders for a wide > range of molecules and basis sets, including the * basis sets, > it can be made to fail. For example, using 3-21+G, you will > get C-C "bond order" results like: > > Molecule Mulliken Mayer > --------------- -------- ----- > Ethane -0.328 0.566 > Benzene -5.008 2.179 > Ethylene 1.169 2.480 > Acetylene -0.109 4.496 > > I suspect almost any basis set containing diffuse functions will cause > the Mayer method to fail similarly, though it at least still produces > ascending numbers. Note that the Mayer scheme can not produce negative > bond orders due to its formulation. > > For 3-21G, you get almost exactly 1.0, 1.5, 2.0 and 3.0 respectively > with the Mayer method, and pretty close to that for 6-31G* as I recall. > > Mike. > -- > When the chips are down, switch to pretzels. | Mike Peterson, SysAdmin > | U/Toronto Chemistry > E-mail: system@alchemy.chem.utoronto.ca Tel: (416)978-7094 > WWW: http://www.chem.utoronto.ca/ Fax: (416)978-8775 > --------------------------------------------------------------------------