From chemistry-request@server.ccl.net Fri Aug 23 04:34:33 2002 Received: from smtp2.ruc.dk ([130.225.220.70]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7N8YWQ15250 for ; Fri, 23 Aug 2002 04:34:33 -0400 Received: by smtp2.ruc.dk (Postfix, from userid 504) id 4859A43D836; Fri, 23 Aug 2002 10:34:22 +0200 (CEST) Received: from virgil.ruc.dk (virgil.ruc.dk [130.225.220.110]) by smtp2.ruc.dk (Postfix) with ESMTP id 6CF3443D833; Fri, 23 Aug 2002 10:34:21 +0200 (CEST) Received: from VIRGIL/SpoolDir by virgil.ruc.dk (Mercury 1.47); 23 Aug 02 10:34:21 +0100 Received: from SpoolDir by VIRGIL (Mercury 1.47); 23 Aug 02 10:34:16 +0100 From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter To: chemistry@ccl.net Date: Fri, 23 Aug 2002 10:34:03 +0100 Subject: CCL: History question Reply-To: spanget@ruc.dk Cc: Thorsten Thormann Priority: normal X-mailer: Pegasus Mail for Windows (v2.23) Message-ID: <38EED9506B1@virgil.ruc.dk> Dear CCL, we are occasionally told that towards the end of the 19th century, some scientists (physicists?) tended to believe that after Newton's Mechanics and Maxwell's Equations all fundamental discoveries in physics were made and that future work would only deal with details. They even discouraged young people to enter the field! But then, of course, came the turn of the century with, in 1895-1905, X-rays, Zeeman effect, radioactivity, the electron, quantum theory, and theory of relativity. I would be grateful for information on literature that documents this story. Any quotations? Yours, Jens >--< NB! Please note new mail address: =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= JENS SPANGET-LARSEN Office: +45 4674 2710 Department of Chemistry Fax: +45 4674 3011 Roskilde University (RUC) Mobile: +45 2320 6246 P.O.Box 260 E-Mail: spanget@ruc.dk DK-4000 Roskilde, Denmark http://virgil.ruc.dk/~spanget =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From chemistry-request@server.ccl.net Fri Aug 23 04:33:49 2002 Received: from chemde5.LeidenUniv.nl ([132.229.119.141]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7N8XmQ15214 for ; Fri, 23 Aug 2002 04:33:48 -0400 Received: (from aldert@localhost) by chemde5.LeidenUniv.nl (8.9.3/8.9.3) id KAA00742; Fri, 23 Aug 2002 10:25:25 +0200 (METDST) Date: Fri, 23 Aug 2002 10:25:25 +0200 (METDST) From: Aldert Westra Hoekzema Message-Id: <200208230825.KAA00742@chemde5.LeidenUniv.nl> To: chemistry@ccl.net, Thomas Exner Subject: Re: CCL:Summary of "rotating a density matrix" Reply-To: a.whoekzema@chem.LeidenUniv.nl Hi Thomas, I have not read the articles you mention, but solved the problem of rotating d-functions (6D set) myself around 1993. Below you can find the relevant comment cut from a fortran77 program. Expanding to f-functions (10F set) should be analogous, probably including the normalization pecularity (see below). Kind greetings, Aldert A.J.A. Westra Hoekzema Leiden Institue of Chemistry The Netherlands *---------------------------------------------------------------------- * ROTATE D-FUNCTIONS (LOCATED IN THE ORIGIN) * * IDENTIFY THE SET OF 6 D-FUNCTIONS WITH A TWO-DIMENSIONAL TENSOR: * D(XX) = T(1,1) D(XY) = T(1,2) + T(2,1) * D(YY) = T(2,2) D(XZ) = T(1,3) + T(3,1) * D(ZZ) = T(3,3) D(YZ) = T(2,3) + T(3,2) * WHERE T(I,J) INDICATES A 3X3 TENSOR WITH ELEMENT (I,J) EQUAL TO 1 * AND THE OTHER EIGHT ELEMENTS EQUAL TO 0 * * A ROTATED TENSOR GIVEN IN TERMS OF THE ORIGINAL TENSOR ELEMENTS * DEPENDS ON THE ROTATION-MATRIX R: * 3 3 * ROT T(I,J) = SUM SUM R(I,K) R(J,L) T(K,L) * K=1 L=1 * * WITH R(K,I) = PARTIAL DERIVATIVE OF ROTATED CARTESIAN TO OLD ONE * * AFTER ROTATION A GENERAL COMBINATION OF D-FUNCTIONS PHI RESULTS IN * A COMBINATION EXPRESSED IN TERMS OF THE ORIGINAL COEFFICIENTS: * * PHI = SUM SUM C(IJ) D(IJ) * I <= J * * PHI' = ROT PHI = ROT SUM SUM C(IJ) D(IJ) = SUM SUM C(IJ) D(IJ)' = * I <= J I <= J * * SUM SUM C(IJ) SUM SUM R(I,K) R(J,L) T(K,L) = * I <= J K L * * SUM SUM SUM SUM C(IJ) { R(I,K) R(J,L) + { DELTA(K,L) - 1 } * K <= L I <= J R(I,L) R(J,K) } D(KL) * * WITH DELTA THE KRONECKER DELTA * * USING THE 6-D SET OF D-FUNCTIONS THERE IS ANOTHER PECULARITY. THE * NORMALIZATION FACTORS DIFFER BETWEEN D(XX/YY/ZZ) AND D(XY/XZ/YZ): * * N(II) = (1/9) TO THE POWER (1/4) TIMES N(IJ) , J /= I * * THIS INTRODUCES A FACTOR IN THE ROTATED COMBINATION: * * PHI' = SUM SUM SUM SUM C(IJ) { R(I,K) R(J,L) + { DELTA(K,L) - 1 } * K <= L I <= J R(I,L) R(J,K) } D(KL) F(IJ,KL) * * WITH F: II --> KK = 1 , II --> KL = SQRT(3) , * IJ --> KL = 1 , IJ --> KK = 1 / SQRT(3) , FOR EXAMPLE: * * ROT DIJ <=> ROT ( N(IJ) IJ EXP ) = .. + N(IJ) KK EXP <=> * * SQRT(3) / SQRT(3) N(IJ) KK EXP <=> SQRT(3) N(KK) KK EXP * * A GENERAL EXPRESSION: * * F(IJ,KL) = 1 + DELTA(I,J) { 1 - DELTA(K,L) } { 1 / SQRT(3) - 1 } * * + DELTA(K,L) { 1 - DELTA(I,J) } { SQRT(3) - 1 } * * REFERENCES: -D.E. BOURNE AND P.C. KENDALL, * VECTOR ANALYSIS AND CARTESIAN TENSORS, 2ND ED., * NELSON, 1980 * -GEORGE ARFKEN, * MATHEMATICAL METHODS FOR PHYSICISTS, 2ND ED., * ACADEMIC PRESS, 1970 * -W.J. HEHRE, L. RADOM, P.V.R. SCHLEYER & J.A. POPLE, * AB INITIO MOLECULAR ORBITAL THEORY, 1986, P19 *---------------------------------------------------------------------- > From chemistry-request@ccl.net Fri Aug 23 09:10:08 2002 > From: Thomas Exner > > Hi CCLers, > > I have an additional question to the rotation of the density matrix. I > accounted some difficulties while implementing the rotation of the d > orbitals as discribed by Ferre et al. (J.Comp.Chem. 23(6) 2002, 610-624) > and Philipp and Friesner (J.Comp.Chem. 20(14) 1999, 1468-1494). I think > I found one error in the equation in the second paper. But because I > don't really understand how the rotation matrix is affiliated, it is > impossible for me to figure out if there are any other errors in the > equation or if it is a problem with my implementation. I would > appriciate if someone could give me some hints how the rotation matrix > has to be constructed. Perhaps, this could also help me to construct a > rotation matrix for f orbital. Thank you very much. > > Best wishes, > Thomas > > -- > ____________________________________________________________________ > > Dr. Thomas Exner > Computational, Theoretical & Mathematical Chemistry > Department of Chemistry > University of Saskatchewan > 110 Science Place 431 Edmund Park > Saskatoon, SK, S7N 5C9 Saskatoon, SK, S7H 0Z4 > Canada Canada > > phone: +1-306-966-5357 +1-306-382-5397 > fax: +1-306-966-4730 > > > Department of Physical Chemistry > Physical Chemistry I > Darmstadt University of Technology (TUD) > Petersenstr. 20 Auf der Marienhoehe 5 > 64287 Darmstadt 64297 Darmstadt > Germany Germany > > phone: +49-6151-16 2398 +49-6151-537165 > fax: +49-6151-16 4298 > e-mail: exner@pc.chemie.tu-darmstadt.de texner@gmx.net > WWW: http://www.pc.chemie.tu-darmstadt.de/staff/exner/ > ____________________________________________________________________ > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Fri Aug 23 10:14:13 2002 Received: from ws0e.pc.chemie.tu-darmstadt.de ([130.83.242.14]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7NEECr00971 for ; Fri, 23 Aug 2002 10:14:12 -0400 Received: from localhost (hatice@localhost) by ws0e.pc.chemie.tu-darmstadt.de (SGI-8.9.3/8.9.3) with ESMTP id QAA02590 for ; Fri, 23 Aug 2002 16:14:11 +0200 (CDT) Date: Fri, 23 Aug 2002 16:14:11 +0200 From: "Dr. Hatice Can" To: chemistry@ccl.net Subject: Summary:Convert G98 output file to pdb Message-ID: MIME-Version: 1.0 Content-Type: MULTIPART/MIXED; BOUNDARY="-2108427762-767610079-1030112051=:2172" This message is in MIME format. The first part should be readable text, while the remaining parts are likely unreadable without MIME-aware tools. Send mail to mime@docserver.cac.washington.edu for more info. ---2108427762-767610079-1030112051=:2172 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear All, I would like to thank you so much for quick and kindly attention to my question which was about convertion of Gaussian 98 output to pdb file. All the responses were summarised in the attachment file. 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ZnJlZSANCiAgZm9yIGFjYWRlbWljIHVzZS4gSnVzdCBzZWFyY2ggZm9yIE1P TERFTiBvbiBnb29nbGUuY29tLiBNT0xERU4gcmVhZHMgDQogIGdhdXNzaWFu IG91dHB1dHMgYW5kIGNvbnZlcnRzIHN0cnVjdHVyZXMgaW50byBwZGIsIG1v bDIgZXRjLiANCg0KICAvcGV0ZXIgDQoNCg0KDQoNCg0K ---2108427762-767610079-1030112051=:2172-- From chemistry-request@server.ccl.net Fri Aug 23 10:30:47 2002 Received: from carbon.chem.ucla.edu ([128.97.35.55]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7NEUlr06719 for ; Fri, 23 Aug 2002 10:30:47 -0400 Received: from chem.ucla.edu (dserv3.chem.ucla.edu [169.232.135.20]) by carbon.chem.ucla.edu (8.11.4/8.11.4) with SMTP id g7NEUZR21438; Fri, 23 Aug 2002 07:30:35 -0700 (PDT) Message-Id: <200208231430.g7NEUZR21438@carbon.chem.ucla.edu> Date: Fri, 23 Aug 2002 14:30:35 -0000 To: "Jens Spanget-Larsen" , Subject: Re: CCL:History question From: X-Mailer: TWIG 2.7.5 In-Reply-To: <38EED9506B1@virgil.ruc.dk> Cc: "Thorsten Thormann" A book "The End of Science" written by John Horgan and published a few years ago begins with the quotation in question and goes on to argue that although science did not in fact end around 1900 we have reached the point at which it is now more or less over. As you may suppose, the arguments are not exactly compelling but you might get the backgound to the 1900 situation from the notes and references. regards, eric scerri Jens Spanget-Larsen said: > Dear CCL, > > we are occasionally told that towards the end of the 19th century, > some scientists (physicists?) tended to believe that after Newton's > Mechanics and Maxwell's Equations all fundamental discoveries in > physics were made and that future work would only deal with details. > They even discouraged young people to enter the field! But then, of > course, came the turn of the century with, in 1895-1905, X-rays, > Zeeman effect, radioactivity, the electron, quantum theory, and > theory of relativity. > > I would be grateful for information on literature that documents this > story. Any quotations? > > Yours, Jens >--< > > > NB! Please note new mail address: > =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= > JENS SPANGET-LARSEN Office: +45 4674 2710 > Department of Chemistry Fax: +45 4674 3011 > Roskilde University (RUC) Mobile: +45 2320 6246 > P.O.Box 260 E-Mail: spanget@ruc.dk > DK-4000 Roskilde, Denmark http://virgil.ruc.dk/~spanget > =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > -- From chemistry-request@server.ccl.net Fri Aug 23 19:45:53 2002 Received: from adenine.cgl.ucsf.edu ([128.218.27.3]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7NNjrr29999 for ; Fri, 23 Aug 2002 19:45:53 -0400 Received: from localhost (socrates.cgl.ucsf.edu [128.218.27.3]) by adenine.cgl.ucsf.edu (8.12.3/8.12.3/GSC1.16) with ESMTP id g7NNjlNf553283 for ; Fri, 23 Aug 2002 16:45:53 -0700 (PDT) Date: Fri, 23 Aug 2002 16:45:47 -0700 (PDT) From: Pradipta Bandyopadhyay To: chemistry@ccl.net Subject: Compilation of charges! Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Is there any compilation of charges calculated by different methods (RESP, CHELPG, CM2, CM3) for a wide variety of molecules? Any pointer would be appreciated. Pradipta