From chemistry-request@server.ccl.net Mon Sep 11 08:05:02 2000 Received: from gwdu42.gwdg.de (root@gwdu42.gwdg.de [134.76.10.26]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA29401 for ; Mon, 11 Sep 2000 08:05:02 -0400 Received: from gwdu20.gwdg.de ([134.76.98.2] ident=dvainiu) by gwdu42.gwdg.de with smtp (Exim 3.14 #18) id 13YSKN-0003iA-00 for chemistry@ccl.net; Mon, 11 Sep 2000 14:04:47 +0200 Received: from localhost by gwdu20.gwdg.de (5.65v4.0/1.1.10.5/11Feb98-0154PM) id AA18056; Mon, 11 Sep 2000 14:04:46 +0200 Date: Mon, 11 Sep 2000 14:04:46 +0200 (MET DST) From: Darius Vainius To: chemistry@ccl.net Subject: Fitting the data of reaction kinetics: FACSIMILE: how do I... Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, does anybody know how to access the RSQS (Residual Sum of Squares) after the data fitting run was finished? >>>... !!!!! COMMAND INTERPRETER RE-ENTERED COMPILE INSTANT; LOCN INSTRUCTION 142:WRITE 1=6, "RSQS = ", (E10,4), RSQS %; !!!!! ILLEGAL OR UNRECOGNISED NAME WRITE 1=6, "RSQS = ", (E10,4), RSQS %; !!!!! ERROR DETECTED AT WORD: RSQS ENDING IN POSITION 35 OF ABOVE LINE !!!!! PROCEEDING BUT EXECUTION DELETED !!!!! ERROR STOP INSTRUCTION COMPILED AT LOCATION 158 159:**; ...<<< It seems that FACSIMILE compiler doesn't know RSQS, although PSTREAM puts into the output the calculated values of the RSQS during the fitting run. Then, the next thing I tried, was simply to sum the squares of the RESIDARRAY elements: (this is just a tail of the code) >>>... SETVARY ID IC ; NBEGIN 200; BEGIN; COMPILE INSTANT; RSSQR = 0.0; DO 1 FOR #1 = 0 (1) 999; RSSQR = RSSQR + RESIDARRAY<0,#1> * RESIDARRAY<0,#1>; LABEL 1; WRITE 1=6, "RSSQR = ", (E10,4), RSSQR %; **; STOP; <<< But the value of RSSQR I've got here, is about 2x highier than the RSQS value, which is putted by PSTREAM into the output: >>>... AFTER 0 ITERATIONS AND 1 RUNS, INDIVIDUAL CURVE STATISTICS ARE RSQS CORI AUCO AUCR 3.6781E+01 -0.3466 0.0431 0.0316 TOTAL RESIDUAL SUM OF SQUARES IS 3.67813E+01 MEAN ABSOLUTE CORRELATION INDEX IS 0.34656 VARY( 1):ID = 2.1650E+05 VARY( 2):IC = 1.8596E+05 1 SIMULATION RUNS COMPLETED 2 SIMULATION RUNS COMPLETED 3 SIMULATION RUNS COMPLETED PARAMETER NUMBER, TYPE, NAME, VALUE 1 PRI. ID 2.1650E+05 2 PRI. IC 1.8596E+05 RESIDUAL SUM OF SQUARES = 3.6781E+01 FOR 998 DEGREES OF FREEDOM SINGULAR VALUES OF DEPENDENCE MATRIX AND STRUCTURE OF COMPONENTS VALUES 2481.822 455.336 ID 0.11017 -0.99391 IC 0.99391 0.11017 FITTED VALUES, ACCURACIES AND CONFIDENCE LIMITS NO. NAME VALUE SDLN 5 PERCENT 95 PERCENT 1 ID 2.1650E+05 0.0004 2.1635E+05 2.1665E+05 2 IC 1.8596E+05 0.0001 1.8593E+05 1.8599E+05 CORRELATION MATRIX COMPONENTS COLUMN 1 2 ROW 1 1.000 -0.500 ROW 2 -0.500 1.000 !!!!! COMMAND INTERPRETER RE-ENTERED COMPILE INSTANT; LOCN INSTRUCTION 142:RSSQR = 0.0; 148:DO 1 FOR #1 = 0 (1) 999; 156:RSSQR = RSSQR + RESIDARRAY<0,#1> * RESIDARRAY<0,#1>; 169:LABEL 1; 196:WRITE 1=6, "RSSQR = ", (E10,4), RSSQR %; 217:**; <...> RSSQR = 6.172E+01 STOP; !!!!! STOP !!!!! FORMATTED WRITE NUMBER 1 CLEARED ...<<< So, why do these values differ? Or maybe I'm doing something wrong here? Many thanks in advance, Darius -- Darius Vainius Department of Molecular Biology Max Planck Institute for Biophysical Chemistry e-mail: dvainius@mpc186.mpibpc.gwdg.de From chemistry-request@server.ccl.net Mon Sep 11 08:50:03 2000 Received: from dsa.mpi-muelheim.mpg.de (dsa.mpi-muelheim.mpg.de [192.108.70.121]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA29967 for ; Mon, 11 Sep 2000 08:50:03 -0400 Received: from mpi-muelheim.mpg.de ([172.17.8.148]) by dsa.mpi-muelheim.mpg.de (8.11.0/8.11.0) with ESMTP id e8BCnpY353746 for ; Mon, 11 Sep 2000 14:49:51 +0200 (MEST) Message-ID: <39BC80FD.C97BB1F5@mpi-muelheim.mpg.de> Date: Mon, 11 Sep 2000 14:51:41 +0800 From: Zhongfang Chen X-Mailer: Mozilla 4.72 [en] (Win98; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: a question about computational transition chemistry Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Sir, Now I am doing calculations on transition metal complexes using Gaussian 98. I always need to check and alter the orbitals since the initial guess is too bad. Sometimes I really felt frustracted for this problem. According to the literature, EHT (Extended Hueckel Theory) has been claimed to be the only method to give exactly ligand field theory orbital ordering. Some companies claimed that their softwares such as Jaguar are more efficient to get the correct initial guess which is crutial for the convergence and finding the corrct spin state. Maybe EHT method can be embeded in Guassion and we can use EHT guess for further calculations. Any suggestions to this problem would be appreciated. Best regards, Dr. Zhongfang Chen From chemistry-request@server.ccl.net Mon Sep 11 08:44:57 2000 Received: from server.biokemi.su.se (server.biokemi.su.se [130.237.179.5]) by server.ccl.net (8.8.7/8.8.7) with SMTP id IAA29920 for ; Mon, 11 Sep 2000 08:44:56 -0400 Received: from mail.biokemi.su.se (unverified [130.237.179.175]) by server.biokemi.su.se (EMWAC SMTPRS 0.83) with SMTP id ; Mon, 11 Sep 2000 14:46:25 +0200 Sender: zhang@ccl.net Message-ID: <39BCD2BC.A320E60@mail.biokemi.su.se> Date: Mon, 11 Sep 2000 14:40:28 +0200 From: Xiao-Ping Zhang Reply-To: zhang@biokemi.su.se X-Mailer: Mozilla 4.72 [en] (X11; U; Linux 2.2.14-12 i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: autodock 3 - what's new in the latest release Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, Does any one know the difference between the autodock 3.0.3, 3.0.5 and the first release 3.00? Thank you for your information. Sincerely, Xiao-Ping Zhang ****************************** Xiao-Ping Zhang Department of Biochemistry Arrhenius Laboratories of Natural Sciences Stockholm Universities 106 91 Stockholm Sweden Phone: 046-08-162472 /162582 Fax: 046-08-153679 e-mail: zhang@biokemi.su.se From chemistry-request@server.ccl.net Mon Sep 11 10:25:08 2000 Received: from ne059.cm.utexas.edu (ne059.cm.utexas.edu [146.6.145.59]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA30337 for ; Mon, 11 Sep 2000 10:25:07 -0400 Received: from eeyore.cm.utexas.edu (ne057.cm.utexas.edu [146.6.145.57]) by ne059.cm.utexas.edu (8.10.2/8.10.2) with ESMTP id e8BEIZ506914; Mon, 11 Sep 2000 09:18:36 -0500 Message-ID: <39BD05DE.2A4DFC2C@eeyore.cm.utexas.edu> Date: Mon, 11 Sep 2000 09:18:38 -0700 From: "Isaac B. Bersuker" X-Mailer: Mozilla 4.7 [en] (WinNT; I) X-Accept-Language: en MIME-Version: 1.0 To: elewars CC: chemistry@ccl.net Subject: Re: CCL:HYBRIDIZATION NOT "REAL";V. FOCK References: <39BC0884.4ADBB8E@trentu.ca> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I believe that you are wrong in your statement that hybridization is a mathematical procedure. The point is that there is no hybridization in free atoms, but it takes place UNDER THE INFLUENCE OF THE ENVIRONMENT, THE BONDING. In this formulation hybridization is quite a legitimate physical phenomenom (see, e.g., my latest book >from Wiley, New York, 1996) Bersuker elewars wrote: > 2000 Sun Sept 10 > > Hello, > > We know that hybridization is a mathematical procedure and not an actual > physical process; for example, an s and a p orbital > (orbital=one-electron function) are vectors in Hilbert space, which can > be mathematically combined to give two new orbitals (two sp orbitals). > > QUESTIONS: > > (1) Did Linus Pauling _invent_ hybridization? He certainly popularized > it. > > (2) Did Pauling accept that hybridization is "only" a mathematical > procedure? > > ----- > By the way, does anyone know where Vladimer Fock got his Ph.D., and > where and when he died? I think he worked at the University of St. > Petersburg/Leningrad. > > Thanks. > > E. Lewars > ========== > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net -- Dr. Isaac B. Bersuker Institute for Theoretical Chemistry Department of Chemistry & Biochemistry The University of Texas at Austin Austin, TX 78712, USA Ph: (512) 471-4671 Fax: (512) 471-8696 Email: bersuker@eeyore.cm.utexas.edu From chemistry-request@server.ccl.net Mon Sep 11 11:25:06 2000 Received: from junco.tcc ([193.137.208.70]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA30746 for ; Mon, 11 Sep 2000 11:25:04 -0400 Received: from qta.qui.uc.pt (IDENT:paulo@localhost.localdomain [127.0.0.1]) by junco.tcc (8.9.3/8.9.3) with ESMTP id QAA13354 for ; Mon, 11 Sep 2000 16:23:34 +0100 Sender: paulo@junco.tcc Message-ID: <39BCF8F6.F79F85FD@qta.qui.uc.pt> Date: Mon, 11 Sep 2000 16:23:34 +0100 From: "Paulo E. Abreu" X-Mailer: Mozilla 4.75 [en] (X11; U; Linux 2.2.17 i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Re: CCL:HYBRIDIZATION NOT "REAL";V. FOCK References: <39BC0884.4ADBB8E@trentu.ca> <39BD05DE.2A4DFC2C@eeyore.cm.utexas.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit "Isaac B. Bersuker" wrote: > I believe that you are wrong in your statement that hybridization is a mathematical > procedure. The point is that there is no hybridization in free atoms, but it takes > place UNDER THE INFLUENCE OF THE ENVIRONMENT, THE BONDING. In this formulation > hybridization is quite a legitimate physical phenomenom (see, e.g., my latest book > >from Wiley, New York, 1996) What do you mean by a legitimate physical phenomenom ? Can you detect it experimentally ? I thought it was a way to explain chemical bonding in the VB approach. Like for instances in CH4, where the the bonds are made of orbitals with the suitable symmentry and not a priori with a recipe. I dont know your book, but I would like to read very much. Can you provide more details ? Paulo E. Abreu -- Departamento de Quimica e-mail:qtabreu@ci.uc.pt Universidade de Coimbra TEL:351 239 852080 3049 Coimbra Codex FAX:351 239 827703 Portugal From chemistry-request@server.ccl.net Mon Sep 11 12:38:27 2000 Received: from ne059.cm.utexas.edu (ne059.cm.utexas.edu [146.6.145.59]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA31142 for ; Mon, 11 Sep 2000 12:38:27 -0400 Received: from eeyore.cm.utexas.edu (ne057.cm.utexas.edu [146.6.145.57]) by ne059.cm.utexas.edu (8.10.2/8.10.2) with ESMTP id e8BGVi506116; Mon, 11 Sep 2000 11:31:44 -0500 Message-ID: <39BD2513.9E11C49E@eeyore.cm.utexas.edu> Date: Mon, 11 Sep 2000 11:31:47 -0700 From: "Isaac B. Bersuker" X-Mailer: Mozilla 4.7 [en] (WinNT; I) X-Accept-Language: en MIME-Version: 1.0 To: "Paulo E. Abreu" CC: chemistry@ccl.net Subject: Re: CCL:HYBRIDIZATION NOT "REAL";V. FOCK References: <39BC0884.4ADBB8E@trentu.ca> <39BD05DE.2A4DFC2C@eeyore.cm.utexas.edu> <39BCF8F6.F79F85FD@qta.qui.uc.pt> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit "Paulo E. Abreu" wrote: > > What do you mean by a legitimate physical phenomenom ? Can you detect it > experimentally ? Yes, you can: hybridization changes the charge distribution which is, in principle observable I. B. -- Dr. Isaac B. Bersuker Institute for Theoretical Chemistry Department of Chemistry & Biochemistry The University of Texas at Austin Austin, TX 78712, USA Ph: (512) 471-4671 Fax: (512) 471-8696 Email: bersuker@eeyore.cm.utexas.edu From chemistry-request@server.ccl.net Mon Sep 11 12:42:33 2000 Received: from lulu.it.northwestern.edu (lulu.acns.nwu.edu [129.105.16.54]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA31159 for ; Mon, 11 Sep 2000 12:42:33 -0400 Received: from localhost (far482@localhost) by lulu.it.northwestern.edu (8.8.7/8.8.7) with ESMTP id LAA08507 for ; Mon, 11 Sep 2000 11:42:19 -0500 (CDT) Date: Mon, 11 Sep 2000 11:42:19 -0500 (CDT) From: Fred Arnold To: chemistry@ccl.net Subject: Molden Quirk Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, Has anyone else tried to use Molden 3.6 to view recent files generated by GAMESS-US Mar-25-2000 or later, on an Alpha-Linux system? I get strange errors finding the wrong input to a floating point number, and then it dumps core. If you export the files to any other architecture I've tried, they load and visualize without a hitch. (I can't guarantee that on DEC/OSF-1 since we don't have any, but RS/6000, Sun, Linux-Intel) It seems to be a bug in the search routine on those systems, but I haven't been able to track it down yet. Thanks. -Fred From chemistry-request@server.ccl.net Mon Sep 11 12:59:52 2000 Received: from junco.tcc ([193.137.208.70]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA31349 for ; Mon, 11 Sep 2000 12:59:50 -0400 Received: from qta.qui.uc.pt (IDENT:paulo@localhost.localdomain [127.0.0.1]) by junco.tcc (8.9.3/8.9.3) with ESMTP id RAA13596; Mon, 11 Sep 2000 17:58:14 +0100 Sender: paulo@junco.tcc Message-ID: <39BD0F25.AA9F5F67@qta.qui.uc.pt> Date: Mon, 11 Sep 2000 17:58:13 +0100 From: "Paulo E. Abreu" X-Mailer: Mozilla 4.75 [en] (X11; U; Linux 2.2.17 i686) X-Accept-Language: en MIME-Version: 1.0 To: "Isaac B. Bersuker" CC: chemistry@ccl.net Subject: Re: CCL:HYBRIDIZATION NOT "REAL";V. FOCK References: <39BC0884.4ADBB8E@trentu.ca> <39BD05DE.2A4DFC2C@eeyore.cm.utexas.edu> <39BCF8F6.F79F85FD@qta.qui.uc.pt> <39BD2513.9E11C49E@eeyore.cm.utexas.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit "Isaac B. Bersuker" wrote: > Yes, you can: hybridization changes the charge distribution which is, in principle > observable Sorry to disagree (again) with you but I dont think that is a correct answer. Bonding changes the charge distribution not hybridization. Besides what do you mean by changing the charge distribution ? Comparing it with to the free atoms ? Orbital are models, and within these models we can describe chemical bonding with various approaches (MO or VB). Hybridization is only used in VB theory, because in MO the symmetry of the molecule plays an important role in determining the coefficients of the orbitals. Remember that to use hybrid-orbitals you must a priori know the geometry of the molecule. Paulo E. Abreu -- Departamento de Quimica e-mail:qtabreu@ci.uc.pt Universidade de Coimbra TEL:351 239 852080 3049 Coimbra Codex FAX:351 239 827703 Portugal From chemistry-request@server.ccl.net Mon Sep 11 13:50:30 2000 Received: from puck.reed.edu (puck.reed.edu [134.10.2.8]) by server.ccl.net (8.8.7/8.8.7) with SMTP id NAA31601 for ; Mon, 11 Sep 2000 13:50:30 -0400 Received: (qmail 16080 invoked from network); 11 Sep 2000 17:48:58 -0000 Received: from isis.reed.edu (134.10.2.1) by puck.reed.edu with SMTP; 11 Sep 2000 17:48:58 -0000 Message-id: <12978376@isis.reed.edu> Date: 11 Sep 2000 10:50:14 PDT From: Alan.Shusterman@directory.reed.edu (Alan Shusterman) Subject: Re: CCL:HYBRIDIZATION NOT "REAL";V. FOCK To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/enriched Content-Disposition: inline Before people get too worked up about the "reality" of hybridization, they might pause and enjoy this quote from Coulson's "Valence", p. 219, section 8.14 Status of hybridization: "The previous discussion has brought out clearly the very wide context in which hybridization seems to be relevant. We must not, however, allow ourselves to believe that it represents any real 'phenomenon', any more than resonance between different structures such as the covalent and ionic ones of a polar bond may be called a 'phenomenon'. But we can at least say: (a) that hybridization is the most efective way of preserving the concept of a localized bond with perfect pairing of orbitals on the two atoms of the bond; (b) that it is a restricted form of resonance, so that a residual resonance, due to alternative schemes of pairing, still exists." I don't see anything here to disagree with. -Alan ==== Alan Shusterman Department of Chemistry Reed College Portland, OR 97202 From chemistry-request@server.ccl.net Mon Sep 11 13:35:52 2000 Received: from ne059.cm.utexas.edu (ne059.cm.utexas.edu [146.6.145.59]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA31525 for ; Mon, 11 Sep 2000 13:35:51 -0400 Received: from eeyore.cm.utexas.edu (ne057.cm.utexas.edu [146.6.145.57]) by ne059.cm.utexas.edu (8.10.2/8.10.2) with ESMTP id e8BHMA510566; Mon, 11 Sep 2000 12:22:10 -0500 Message-ID: <39BD30E5.D6BC4D5C@eeyore.cm.utexas.edu> Date: Mon, 11 Sep 2000 12:22:13 -0700 From: "Isaac B. Bersuker" X-Mailer: Mozilla 4.7 [en] (WinNT; I) X-Accept-Language: en MIME-Version: 1.0 To: "Paulo E. Abreu" CC: "Isaac B. Bersuker" , chemistry@ccl.net Subject: Re: CCL:HYBRIDIZATION NOT "REAL";V. FOCK References: <39BC0884.4ADBB8E@trentu.ca> <39BD05DE.2A4DFC2C@eeyore.cm.utexas.edu> <39BCF8F6.F79F85FD@qta.qui.uc.pt> <39BD2513.9E11C49E@eeyore.cm.utexas.edu> <39BD0F25.AA9F5F67@qta.qui.uc.pt> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hybridization is present in any theory (VB, MO, etc.), it reflects the redistribution of charge by bonding (the mixing of orbitals of different symmetry takes place under the influence of the bonding field). Sorry, I cannot continue this discussion until you read the basics that I cannot repeat here... Regards I. B. "Paulo E. Abreu" wrote: > "Isaac B. Bersuker" wrote: > > > Yes, you can: hybridization changes the charge distribution which is, in principle > > observable > > Sorry to disagree (again) with you but I dont think that is a correct answer. Bonding > changes the charge > distribution not hybridization. Besides what do you mean by changing the charge > distribution ? > Comparing it with to the free atoms ? Orbital are models, and within these models we > can describe > chemical bonding with various approaches (MO or VB). Hybridization is only used in VB > theory, because > in MO the symmetry of the molecule plays an important role in determining the > coefficients of the orbitals. > Remember that to use hybrid-orbitals you must a priori know the geometry of the > molecule. > Paulo E. Abreu > > -- > Departamento de Quimica e-mail:qtabreu@ci.uc.pt > Universidade de Coimbra TEL:351 239 852080 > 3049 Coimbra Codex FAX:351 239 827703 > Portugal -- Dr. Isaac B. Bersuker Institute for Theoretical Chemistry Department of Chemistry & Biochemistry The University of Texas at Austin Austin, TX 78712, USA Ph: (512) 471-4671 Fax: (512) 471-8696 Email: bersuker@eeyore.cm.utexas.edu From chemistry-request@server.ccl.net Mon Sep 11 14:26:52 2000 Received: from prserv.net (out2.prserv.net [32.97.166.32]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA31763 for ; Mon, 11 Sep 2000 14:26:51 -0400 From: jmmckel@attglobal.net Received: from attglobal.net ([32.101.104.129]) by prserv.net (out2) with SMTP id <2000091118265022900pri06e>; Mon, 11 Sep 2000 18:26:51 +0000 Message-ID: <39BD2361.1174024A@attglobal.net> Date: Mon, 11 Sep 2000 13:24:33 -0500 Reply-To: jmmckel@attglobal.net X-Mailer: Mozilla 4.51 [en]C-CCK-MCD (Win95; I) X-Accept-Language: en MIME-Version: 1.0 To: "Isaac B. Bersuker" CC: "Paulo E. Abreu" , chemistry@ccl.net Subject: Re: CCL:HYBRIDIZATION NOT "REAL";V. FOCK References: <39BC0884.4ADBB8E@trentu.ca> <39BD05DE.2A4DFC2C@eeyore.cm.utexas.edu> <39BCF8F6.F79F85FD@qta.qui.uc.pt> <39BD2513.9E11C49E@eeyore.cm.utexas.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit My $0.02: Perturbations on a system that change electronic distribution can be _rationalized_ post-facto in terms of changes in [presumed] hybridization....[ I can't get away from the fact that eigenvalues SCF canonical orbitals are the ones that best correlate with experiment, not the _attendant_ ones derived from a hybridization process. They render the Fock matrix non-diagonal] John McKelvey "Isaac B. Bersuker" wrote: > "Paulo E. Abreu" wrote: > > > > > What do you mean by a legitimate physical phenomenom ? Can you detect it > > experimentally ? > > Yes, you can: hybridization changes the charge distribution which is, in principle > observable > I. B. > > -- > Dr. Isaac B. Bersuker > Institute for Theoretical Chemistry > Department of Chemistry & Biochemistry > The University of Texas at Austin > Austin, TX 78712, USA > Ph: (512) 471-4671 > Fax: (512) 471-8696 > Email: bersuker@eeyore.cm.utexas.edu > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Mon Sep 11 15:41:09 2000 Received: from trifid.u.arizona.edu (root@trifid.U.Arizona.EDU [128.196.137.197]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA32206 for ; Mon, 11 Sep 2000 15:41:09 -0400 Received: from u.arizona.edu (mcafiero@lapc2.chem.Arizona.EDU [128.196.184.158]) by trifid.u.arizona.edu (8.8.8/8.8.8) with ESMTP id MAA37054 for ; Mon, 11 Sep 2000 12:41:08 -0700 Sender: mcafiero@u.arizona.edu Message-ID: <39BD3554.404D072C@u.arizona.edu> Date: Mon, 11 Sep 2000 19:41:08 +0000 From: maurice cafiero Organization: University Of Arizona Dept. Of Chemistry X-Mailer: Mozilla 4.61 [en] (X11; I; Linux 2.2.13-7mdk i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Re: CCL:HYBRIDIZATION NOT "REAL";V. FOCK References: <39BC0884.4ADBB8E@trentu.ca> <39BD05DE.2A4DFC2C@eeyore.cm.utexas.edu> <39BCF8F6.F79F85FD@qta.qui.uc.pt> <39BD2513.9E11C49E@eeyore.cm.utexas.edu> <39BD0F25.AA9F5F67@qta.qui.uc.pt> <39BD30E5.D6BC4D5C@eeyore.cm.utexas.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit > Hello: A proccess called Hybridization does not occur. No atom other than hydrogen has the familiar s,p,d, etc orbitals. A molecule is characterized by a molecular wave function that can be poorly approximated by a linear combination of atomic orbitals. It seems really silly that we are arguing over bad approximations.... mauricio cafiero From chemistry-request@server.ccl.net Mon Sep 11 16:33:43 2000 Received: from ucidoor.unitedcatalysts.com ([208.23.162.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA32532 for ; Mon, 11 Sep 2000 16:33:43 -0400 Received: by ucidoor.unitedcatalysts.com; (8.8.8/1.3/10May95) id QAA06697; Mon, 11 Sep 2000 16:33:41 -0400 (EDT) Received: from 10.1.0.50 by ucismtp02.unitedcatalysts.com (InterScan E-Mail VirusWall NT); Mon, 11 Sep 2000 16:33:32 -0400 (Eastern Daylight Time) Received: from lvlxch01.unitedcatalysts.com (lvlxch01.unitedcatalysts.com [10.1.0.88]) by lvlmail.unitedcatalysts.com (PMDF V6.0-24 #41777) with ESMTP id <0G0Q007JNOYSID@lvlmail.unitedcatalysts.com> for chemistry@ccl.net; Mon, 11 Sep 2000 16:30:28 -0400 (EDT) Received: by lvlxch01.unitedcatalysts.com with Internet Mail Service (5.5.2650.21) id ; Mon, 11 Sep 2000 16:32:08 -0400 Content-return: allowed Date: Mon, 11 Sep 2000 16:31:58 -0400 From: "Shobe, Dave" Subject: RE: HYBRIDIZATION NOT "REAL";V. FOCK To: chemistry@ccl.net Message-id: <157A51F55AAAD3119CD70008C7B1629D638546@lvlxch01.unitedcatalysts.com> MIME-version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id QAA32533 In my opinion, orbitals, hybridization, etc. are auxiliary constructs to help us think about what is really a complicated wavefunction (itself a mathematical construction to explain the behavior of waves/particles). As for which of these are "real", that discussion goes back to Plato at least... --David Shobe Süd-Chemie Inc. phone (502) 634-7409 fax (502) 634-7724 email dshobe@sud-chemieinc.com Any opinions herein are not necessarily representative of Süd-Chemie. From chemistry-request@server.ccl.net Mon Sep 11 17:13:41 2000 Received: from trifid.u.arizona.edu (root@trifid.U.Arizona.EDU [128.196.137.197]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA32652 for ; Mon, 11 Sep 2000 17:13:41 -0400 Received: from u.arizona.edu (mcafiero@lapc2.chem.Arizona.EDU [128.196.184.158]) by trifid.u.arizona.edu (8.8.8/8.8.8) with ESMTP id OAA22678 for ; Mon, 11 Sep 2000 14:13:39 -0700 Sender: mcafiero@u.arizona.edu Message-ID: <39BD4B04.4A8EB107@u.arizona.edu> Date: Mon, 11 Sep 2000 21:13:40 +0000 From: maurice cafiero Organization: University Of Arizona Dept. Of Chemistry X-Mailer: Mozilla 4.61 [en] (X11; I; Linux 2.2.13-7mdk i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Re: CCL:HYBRIDIZATION NOT "REAL";V. FOCK References: <39BC0884.4ADBB8E@trentu.ca> <39BD05DE.2A4DFC2C@eeyore.cm.utexas.edu> <39BCF8F6.F79F85FD@qta.qui.uc.pt> <39BD2513.9E11C49E@eeyore.cm.utexas.edu> <39BD0F25.AA9F5F67@qta.qui.uc.pt> <39BD30E5.D6BC4D5C@eeyore.cm.utexas.edu> <39BD3554.404D072C@u.arizona.edu> Content-Type: multipart/alternative; boundary="------------3DD7395AC462E09F82834A5D" --------------3DD7395AC462E09F82834A5D Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit > True enough, I may have been a bit rash... But I was trying to address the original question, that hybridization is not `physical, ' but theoretical and mathematical. As far as science goes, quantum mechanics is the model most removed from anything `physical.' mauricio cafiero --------------3DD7395AC462E09F82834A5D Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit
 
True enough, I may have been a bit rash...
But I was trying to address the original question, that
hybridization is not `physical, ' but theoretical
and mathematical.

As far as science goes, quantum mechanics is the model
most removed from anything `physical.'

mauricio cafiero --------------3DD7395AC462E09F82834A5D-- From chemistry-request@server.ccl.net Mon Sep 11 18:33:44 2000 Received: from stout.hampshire.edu (stout.hampshire.edu [192.33.12.80]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA00336 for ; Mon, 11 Sep 2000 18:33:44 -0400 Received: from marbles.dhcp.hampshire.edu (dhcppcc250.hampshire.edu [172.20.26.250]) by stout.hampshire.edu (8.9.3+Sun/8.9.1) with SMTP id SAA20645 for ; Mon, 11 Sep 2000 18:27:40 -0400 (EDT) To: chemistry@ccl.net Subject: Reusing autogrid maps in autodock From: "Trevor Kramer" Reply-To: tkramer@hampshire.edu Date: Mon, 11 Sep 2000 18:31:53 -0400 Content-Type: text/plain; charset="ISO-8859-1" Message-ID: <968711513_PM_BeOS.tkramer@hampshire.edu> MIME-Version: 1.0 X-Mailer: Postmaster 1.1.1 for BeOS Hello, I am currently using autodock3 for a research project and have a question regarding its relation to autogrid. I have setup autodock to automatically screen a large library of molecules by seting up the parameter files for each ligand and then running autogrid3 and then autodock3. Since autogrid takes a significant period of time I was wandering of it was possible to reuse the grid maps it generates for all the runs. The same macomolecule is used in each case and the size and position of the grid is the same. I know I would have to run autogrid once so it would generate grid maps for all supported atom types but would this work? The dpf file also mentions the maps.fld file which may need to be created for each run. Any help would be appreciated. Thank you. Trevor Kramer Hampshire College From chemistry-request@server.ccl.net Mon Sep 11 19:27:07 2000 Received: from carbon.chem.ucla.edu (carbon.chem.ucla.edu [128.97.35.55]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id TAA00565 for ; Mon, 11 Sep 2000 19:27:07 -0400 Received: from [128.97.45.51] ([128.97.45.51]) by carbon.chem.ucla.edu (8.9.1a/8.9.1) with ESMTP id QAA18312 for ; Mon, 11 Sep 2000 16:27:04 -0700 (PDT) Mime-Version: 1.0 Message-Id: Date: Mon, 11 Sep 2000 16:27:02 -0700 To: chemistry@ccl.net From: Eric Scerri Subject: CCL:HYBRIDIZATION NOT "REAL";V. FOCK Content-Type: text/plain; charset="us-ascii" ; format="flowed" > QUESTIONS: > > (1) Did Linus Pauling _invent_ hybridization? He certainly popularized > it. > I believe that hybridization was introduced independently and at around the same time by Slater. > (2) Did Pauling accept that hybridization is "only" a mathematical > procedure? > Pauling's views on hybridization and resonance have been much debated. Among other things his writings were the cause of the "ban" on quantum mechanics which occurred in the 1950's in the former Soviet Union. Articles dealing with the reality or otherwise of Pauling's concepts include, Vermeeren, 1986, Controversies and Existence Claims in Chemistry, The Theory of Resonance, Synthese, 69, 273-90. Pauling himself debated the reality of orbitals, and hybridization with Ogilvie among others in the pages of Journal of Chemical Education. see Ogilvie, J, 1990, The Nature of the Chemical Bond-1990, Journal of Chemical Education, 67, 280-90. and follow up letters to the editor and a full article reponse by pauling. Pauling, L. 1992, The nature of the Chemical Bond- 1992, Journal of Chemical Education, 65, 519-21. > ----- > By the way, does anyone know where Vladimer Fock got his Ph.D., and > where and when he died? I think he worked at the University of St. > Petersburg/Leningrad. > A recent article on the life and work of Fock appeared in Chemical Intelligencer. >regards, eric scerri -- Dr. Eric Scerri , Department of Chemistry & Biochemistry, UCLA. Los Angeles, CA 90095 USA E-mail : scerri@chem.ucla.edu tel: 310 206 3708 fax: Editor of Foundations of Chemistry http://www.wkap.nl/journalhome.htm/1386-4238 Also see International Society for the Philosophy of Chemistry http://www.georgetown.edu/earleyj/ISPC.html From chemistry-request@server.ccl.net Mon Sep 11 20:12:55 2000 Received: from post1.inre.asu.edu (post1.inre.asu.edu [129.219.13.100]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id UAA00786 for ; Mon, 11 Sep 2000 20:12:55 -0400 Received: from smtp.asu.edu (smtp.asu.edu [129.219.13.92]) by asu.edu (PMDF V5.2-33 #46068) with ESMTP id <0G0Q0091LZ7S93@asu.edu> for CHEMISTRY@ccl.net; Mon, 11 Sep 2000 17:11:53 -0700 (MST) Received: from gw185k04.asu.edu (gw185k04.inre.asu.edu [129.219.71.88]) by smtp.asu.edu (8.9.3/8.9.3) with ESMTP id RAA28391 for ; Mon, 11 Sep 2000 17:11:53 -0700 (MST) Date: Mon, 11 Sep 2000 17:11:50 -0700 From: "Benjamin J. Moritz" Subject: SIESTA X-Sender: bmoritz@imap4.asu.edu To: CHEMISTRY@ccl.net Message-id: <4.3.2.7.0.20000911170910.00b07760@imap4.asu.edu> MIME-version: 1.0 X-Mailer: QUALCOMM Windows Eudora Version 4.3.2 Content-type: text/plain; charset="us-ascii"; format=flowed I was wondering if anyone could elaborate on an error message I'm receiving while running SIESTA. I'm trying to relax a Si(OH)4 molecule, but keep on getting an error message that states my DHSCF.h file has BAD DIMENSIONS. Does anyone have any suggestions on how to resolve his error so that the program will optimize my molecule. Thank you. **************************************************************** Benjamin J. Moritz home (602) 453-9411 Dept. of Chemistry & Biochemistry work (480) 965-8509 Arizona State University Mailto:bmoritz@asu.edu P. O. Box 871604 Tempe, AZ 85287-1604 **************************************************************** From chemistry-request@server.ccl.net Mon Sep 11 21:55:06 2000 Received: from arbornet.org (m-net.arbornet.org [209.142.209.161]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id VAA01239 for ; Mon, 11 Sep 2000 21:55:06 -0400 Received: from localhost (mrdonkey@localhost) by arbornet.org (8.10.2/8.10.2) with ESMTP id e8C1eHj28007 for ; Mon, 11 Sep 2000 21:40:17 -0400 (EDT) Date: Mon, 11 Sep 2000 21:40:17 -0400 (EDT) From: Mr Donkey To: chemistry@ccl.net Subject: Genetic Algorithms in QSAR Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII CCLers, could you please point me to open-source implementations of GA for QSAR analysis The only actual implementation I found was that of Genetic Function Approximation in MSI's Cerius. I don't want to purchase a whole modeling environment just for the GFA piece. In addition, I would like to be able to look at the source, to better understand the algorithm. Thanks. - Don From chemistry-request@server.ccl.net Mon Sep 11 19:09:00 2000 Received: from server3.safepages.com (server3.safepages.com [216.127.146.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id TAA00496 for ; Mon, 11 Sep 2000 19:08:59 -0400 Received: from quantumnt (5131-196-251.008.popsite.net [209.69.196.251]) by server3.safepages.com (Postfix) with SMTP id B762D22F3B for ; Mon, 11 Sep 2000 19:08:41 -0400 (EDT) Message-ID: <001801c01c45$39ad6540$0300a8c0@quantumnt> From: "Jim Kress" To: References: <39BC0884.4ADBB8E@trentu.ca> <39BD05DE.2A4DFC2C@eeyore.cm.utexas.edu> <39BCF8F6.F79F85FD@qta.qui.uc.pt> <39BD2513.9E11C49E@eeyore.cm.utexas.edu> <39BD0F25.AA9F5F67@qta.qui.uc.pt> <39BD30E5.D6BC4D5C@eeyore.cm.utexas.edu> <39BD3554.404D072C@u.arizona.edu> <39BD4B04.4A8EB107@u.arizona.edu> Subject: Re: CCL:HYBRIDIZATION NOT "REAL";V. FOCK Date: Mon, 11 Sep 2000 19:08:40 -0400 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0015_01C01C23.B2222870" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 This is a multi-part message in MIME format. ------=_NextPart_000_0015_01C01C23.B2222870 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Quantum Mechanics is a mathematical methodology which best (at this = time) reproduces existing knowledge. As such it is an approach that we = can use to understand our physical universe. While it describes what we = perceive as reality, it is no more "real" than the theory of phlogiston = nor are its constructs (i.e orbitals - hybridized or not) any more real = than the billiard ball representation of atomic structure. =20 These are all artificial constructs that help us humans find a frame of = reference in which we can understand the reality in which we are = immersed. They have no 'reality' beyond that we assign them to enhance = our understanding ... Jim Kress ----- Original Message -----=20 From: maurice cafiero=20 To: chemistry@ccl.net=20 Sent: Monday, September 11, 2000 5:13 PM Subject: CCL:HYBRIDIZATION NOT "REAL";V. FOCK True enough, I may have been a bit rash...=20 But I was trying to address the original question, that=20 hybridization is not `physical, ' but theoretical=20 and mathematical.=20 As far as science goes, quantum mechanics is the model=20 most removed from anything `physical.'=20 mauricio cafiero=20 ------=_NextPart_000_0015_01C01C23.B2222870 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Quantum Mechanics is a mathematical = methodology=20 which best (at this time) reproduces existing knowledge.  As such = it is an=20 approach that we can use to understand our physical universe.  = While it=20 describes what we perceive as reality, it is no more "real" than the = theory of=20 phlogiston nor are its constructs (i.e orbitals - hybridized or not) any = more=20 real than the billiard ball representation of atomic structure. =20
 
These are all artificial constructs = that help us=20 humans find a frame of reference in which we can understand the reality = in which=20 we are immersed.  They have no 'reality' beyond that we assign them = to=20 enhance our understanding ...
 
Jim Kress
----- Original Message -----
From:=20 maurice=20 cafiero
Sent: Monday, September 11, = 2000 5:13=20 PM
Subject: CCL:HYBRIDIZATION NOT = "REAL";V.=20 FOCK

 True=20 enough, I may have been a bit rash...
But I was trying to address = the=20 original question, that
hybridization is not `physical, ' but = theoretical=20
and mathematical.=20

As far as science goes, quantum mechanics is the model
most = removed=20 from anything `physical.'=20

mauricio cafiero

------=_NextPart_000_0015_01C01C23.B2222870-- From chemistry-request@server.ccl.net Mon Sep 11 20:50:15 2000 Received: from web2104.mail.yahoo.com (web2104.mail.yahoo.com [128.11.68.248]) by server.ccl.net (8.8.7/8.8.7) with SMTP id UAA00974 for ; Mon, 11 Sep 2000 20:50:14 -0400 Received: (qmail 26451 invoked by uid 60001); 12 Sep 2000 00:50:09 -0000 Message-ID: <20000912005009.26450.qmail@web2104.mail.yahoo.com> Received: from [63.97.7.140] by web2104.mail.yahoo.com; Mon, 11 Sep 2000 17:50:09 PDT Date: Mon, 11 Sep 2000 17:50:09 -0700 (PDT) From: Jianxin Guo Subject: alignment and QSAR? To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi, CCLers, Most of commercial software for 3D or 4D QSAR required for alignment of the molecules. Which is necessary for the field analysis (especially for CoMFA) and 3D descriptors. However, we know the tooplogy of the molecules structure determine the possibility of the alignment.so there must be some mothods to avoid the slow alignment. Are there any good papers for discussing this issue? Even for the alignment, the so-called pharmacophore or template should be used. The idea is similar, which is better? The pharmacophore asked information about the docking packet. so template is simpler as a starting point? Thanks, Jianxin __________________________________________________ Do You Yahoo!? Yahoo! Mail - Free email you can access from anywhere! http://mail.yahoo.com/ From chemistry-request@server.ccl.net Mon Sep 11 20:58:57 2000 Received: from email.guomai.sh.cn (unldvnanbe@e4000.guomai.sh.cn [202.96.206.72]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id UAA01000 for ; Mon, 11 Sep 2000 20:58:47 -0400 Received: from guomai.sh.cn ([202.101.13.140]) by email.guomai.sh.cn (Sun Internet Mail Server sims.3.5.1999.07.30.00.05.p8) with ESMTP id <0G0R00LG721YGA@email.guomai.sh.cn> for CHEMISTRY@ccl.net; Tue, 12 Sep 2000 09:13:12 +0800 (CST) Date: Tue, 12 Sep 2000 09:00:31 +0800 From: Yubo Fan Subject: ECP basis set for Samarium To: CHEMISTRY@ccl.net Message-id: <39BD802F.4C909AC9@guomai.sh.cn> Organization: Fudan University MIME-version: 1.0 X-Mailer: Mozilla 4.75 [en] (Win98; U) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en Hi, Everyone, I have got an ECP basis set for Samarium recently. I don't know how to use it in G98 input files. Could someone give me some help? Especially the ECP part. The basis set is: Basis functions for Sm S 3 1.0 6.477588000 -.563323000 5.791813000 .961496000 2.412584000 -1.349481000 S 1 1.0 .606601000 1.000000000 S 1 1.0 .300832000 1.000000000 S 1 1.0 .055202000 1.000000000 S 1 1.0 .025731000 1.000000000 P 3 1.0 4.026092000 .405992000 3.045263000 -.822491000 .720567000 1.215545000 P 1 1.0 .313021000 1.000000000 P 1 1.0 .097310000 1.000000000 P 1 1.0 .033798000 1.000000000 D 3 1.0 2.176192000 -.076284000 .778621000 .385532000 .323910000 .715687000 D 1 1.0 .131924000 1.000000000 D 1 1.0 .051322000 1.000000000 **** ECP for Sm SM 4 51 SM FIT G ECP 1 1 1.0 0.0 SM FIT S-G ECP 2 2 4.4735 125.808087 2 2.2368 -6.169188 SM FIT P-G ECP 2 2 3.8294 86.294826 2 1.9147 -1.686917 SM FIT D-G ECP 2 2 2.6882 40.149862 2 1.3441 -0.140083 SM FIT F-G ECP 1 2 1.1741 8.925543 Sincerely Y. Fan -- ============================================================= Yubo Fan Email: yubofan@guomai.sh.cn Organic Synthesis Lab The Department of Chemistry Fudan University Phone: 8621-65648139 No. 220 Handan Road Fax: 8621-65641740 Shanghai, 200433 P. R. China ============================================================= From chemistry-request@server.ccl.net Mon Sep 11 23:29:48 2000 Received: from shardagate.mahindrabt.com (root@[206.102.1.162]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id XAA01807 for ; Mon, 11 Sep 2000 23:29:46 -0400 Received: (from uucp@localhost) by shardagate.mahindrabt.com (8.9.3/8.9.3/SuSE Linux 8.9.3-0.1) id IAA25670 for ; Tue, 12 Sep 2000 08:59:37 +0530 Received: from UNKNOWN(10.5.0.15), claiming to be "intranet.sharda.mahindrabt.com" via SMTP by shardagate, id smtpdOgLZUH; Tue Sep 12 08:59:31 2000 Received: from mahindrabt.com ([10.5.2.73]) by intranet.sharda.mahindrabt.com (8.9.3/8.9.3) with ESMTP id IAA08522 for ; Tue, 12 Sep 2000 08:59:31 +0530 Message-ID: <39BDA149.C2BD8915@mahindrabt.com> Date: Tue, 12 Sep 2000 08:51:45 +0530 From: vijay pargaonkar X-Mailer: Mozilla 4.7 [en] (Win95; I) X-Accept-Language: en MIME-Version: 1.0 To: "CHEMISTRY@ccl.net" Subject: HYBRIDIZATION made easy Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear cclers, The topic discussed on hybridization is put on http://www.science.domainvalet.com Go to ONLINE DISCUSSION FORUM FOR COMPUTATIONAL CHEMISTRY The discussion so far is already put on the site. You can post your arguments, comments, views, explainations on the discussion board. with regards pargaonkar vijay