From peeter@chem.ut.ee Wed Mar 9 11:40:46 1994 Received: from giga.chem.ut.ee for peeter@chem.ut.ee by www.ccl.net (8.6.4/930601.1506) id LAA26424; Wed, 9 Mar 1994 11:16:31 -0500 Received: by giga.chem.ut.ee (Linux Smail3.1.28.1 #14) id m0peRDm-00023yC; Wed, 9 Mar 94 17:34 MET Message-Id: From: peeter@chem.ut.ee (Peeter Burk) Subject: Ab initio bond orders/valencies To: chemistry@ccl.net Date: Wed, 9 Mar 1994 17:34:58 +0100 (MET) X-Mailer: ELM [version 2.4 PL21] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 1288 Dear netters, In order to estimate the aromaticity of some little cyclic compounds I would like to calculate the bond orders and bond valences at ab initio level using methods proposed by K.Jug (K.Jug, J.Am.Chem.Soc., 99, 7800 , 1977; M.S.Gopinathan and K.Jug, Theor.Chim.Acta, 63, 497, 511, 1983). As much as I understand, the calculation of above mentioned parameters from ab initio calculation results is quite straightforward, if you have the density matrix, corresponding to orthonormal set of atomic orbitals. The problem is, that the density matrix you can get from routine ab initio calculations (Gaussian, etc.) to my best knowledge does not correspond to orthonormal atomic orbitals. So my question is how can I get from my Gaussian92 calculation results the density matrix corresponding to orthonormal atomic orbitals? Is there any program, which can do the trick? Or even better, calculate for me directly the bond orders and valencies? Thanking you in advance, Peeter Burk -- Peeter Burk Jakobi 2, EE2400 Tartu, Estonia Institute of Chemical Physics Phone (372-34) 31-263 Tartu University Fax (372-72) 41-453 Estonia E-mail peeter@chem.ut.ee From gmeier@ncsa.uiuc.edu Wed Mar 9 15:40:01 1994 Received: from newton.ncsa.uiuc.edu for gmeier@ncsa.uiuc.edu by www.ccl.net (8.6.4/930601.1506) id OAA28459; Wed, 9 Mar 1994 14:50:55 -0500 Received: from [128.254.136.231] by newton.ncsa.uiuc.edu with SMTP id AA17551 (5.65a/IDA-1.4.2 for CHEMISTRY@ccl.net); Wed, 9 Mar 94 13:50:50 -0600 Message-Id: <9403091950.AA17551@newton.ncsa.uiuc.edu> X-Sender: u34065@141.142.2.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Wed, 9 Mar 1994 14:55:04 -0600 To: CHEMISTRY@ccl.net From: gmeier@ncsa.uiuc.edu (Gary Meier) Subject: Pharmacophore prediction software I'm interested in hearing people's opinions about software packages for pharmacophore prediction. I'm familiar with Catalyst(tm) Disco(tm) and Apex(tm) and don't need descriptions of these programs, but I would like to hear what people who have used them think about their relative strengths and weaknesses. Also, if I have overlooked other packages that serve a similar purpose, I'd like to hear about them as well. Replies by direct e-mail are encouraged. Thanks. Gary Meier (gmeier@ncsa.uiuc.edu) FMC Corporation, Agricultural Chemical Group Box 8 Princeton, NJ 08543 (609) 951-3448 From 6031SCHRADER@vms.csd.mu.edu Wed Mar 9 15:47:58 1994 Received: from VMSF.CSD.MU.EDU for 6031SCHRADER@vms.csd.mu.edu by www.ccl.net (8.6.4/930601.1506) id PAA28562; Wed, 9 Mar 1994 15:03:13 -0500 Received: from vms.csd.mu.edu by vms.csd.mu.edu (PMDF V4.2-15 #6292) id <01H9RRGR9C348WWF9Q@vms.csd.mu.edu>; Wed, 9 Mar 1994 14:06:31 CST Date: Wed, 09 Mar 1994 14:06:31 -0600 (CST) From: "David M. Schrader" <6031SCHRADER@vms.csd.mu.edu> Subject: Linear independence of a basis set To: chemistry@ccl.net Message-id: <01H9RRGR9LQA8WWF9Q@vms.csd.mu.edu> X-Envelope-to: chemistry@ccl.net X-VMS-To: IN%"chemistry@ccl.net" X-VMS-Cc: 6031SCHRADER MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Netters: I am looking for a numerical test for linear independence of a basis set. I know that the overlap matrix S is singular for a linearly dependent basis set, and that det(S) = 1 for an orthonormal basis set. Is det(S) a good criterion for linear independence? I am sure many people have thought and written about this, and that there is a better criterion. This comes up for me because I am trying to expand some first-order decay kinetics data in a basis set which is the eigenfunctions of the Laplace transform, convoluted by the instrumental resolution function. This is a long way from quantum chemistry, my usual research area, but the problem comes up there too, of course, in the expansion of molecular orbitals in an basis of atomic orbitals. I will appreciate hearing from anyone who can help me. Dave Schrader Marquette University Milwaukee, WI, USA 6031schrader@vms.csd.mu.edu From schneid@TC.Cornell.EDU Wed Mar 9 16:40:03 1994 Received: from theory.TC.Cornell.EDU for schneid@TC.Cornell.EDU by www.ccl.net (8.6.4/930601.1506) id QAA29177; Wed, 9 Mar 1994 16:28:48 -0500 Received: by theory.TC.Cornell.EDU id AA22391 (5.65c/IDA-1.4.4 for chemistry@ccl.net); Wed, 9 Mar 1994 16:28:35 -0500 Date: Wed, 9 Mar 1994 16:28:35 -0500 From: "David J. Schneider" Message-Id: <199403092128.AA22391@theory.TC.Cornell.EDU> To: 6031SCHRADER@vmsf.csd.mu.edu Cc: chemistry@ccl.net In-Reply-To: "David M. Schrader"'s message of Wed, 09 Mar 1994 14:06:31 -0600 (CST) <01H9RRGR9LQA8WWF9Q@vms.csd.mu.edu> Subject: CCL:Linear independence of a basis set David, Direct computation of determinants should usually be avoided because of numerical instability problems. A much better test is a singular value decomposition of the overlap (Gram) matrix. Small singular values indicate "near" linear dependence in a sense that can be made mathematically precise. For example, see "Matrix Computations" (G. Golub and C. Van Loan, Johns Hopkins Univ. Press, 1983) or "Matrix Analysis" (R. Horn and C. Johnson, Cambridge Univ. Press, 1985). You should be able to obtain free, high quality, general purpose SVD codes >from netlib. Both C and F77 are available. Good luck. Dave Schneider 626 Engineering and Theory Center Cornell University Ithaca, NY 14853 phone : (607) 254-4510 fax: (607) 254-8888 E-mail: schneid@tc.cornell.edu ======================================================================== Date: Wed, 09 Mar 1994 14:06:31 -0600 (CST) From: "David M. Schrader" <6031SCHRADER@vmsf.csd.mu.edu> Netters: I am looking for a numerical test for linear independence of a basis set. I know that the overlap matrix S is singular for a linearly dependent basis set, and that det(S) = 1 for an orthonormal basis set. Is det(S) a good criterion for linear independence? I am sure many people have thought and written about this, and that there is a better criterion. This comes up for me because I am trying to expand some first-order decay kinetics data in a basis set which is the eigenfunctions of the Laplace transform, convoluted by the instrumental resolution function. This is a long way from quantum chemistry, my usual research area, but the problem comes up there too, of course, in the expansion of molecular orbitals in an basis of atomic orbitals. I will appreciate hearing from anyone who can help me. Dave Schrader Marquette University Milwaukee, WI, USA 6031schrader@vms.csd.mu.edu ---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 zdenko@masc1.rice.edu Wed Mar 9 17:40:01 1994 Received: from moe.rice.edu for zdenko@masc1.rice.edu by www.ccl.net (8.6.4/930601.1506) id RAA29846; Wed, 9 Mar 1994 17:10:26 -0500 Received: from masc1.rice.edu by moe.rice.edu (AA12328); Wed, 9 Mar 94 16:10:23 CST Received: by masc1.rice.edu (AA22103); Wed, 9 Mar 94 16:10:19 CST Date: Wed, 9 Mar 94 16:10:19 CST From: zdenko@masc1.rice.edu (Zdenko Tomasic) Message-Id: <9403092210.AA22103@masc1.rice.edu> To: 6031SCHRADER@vmsf.csd.mu.edu Cc: chemistry@ccl.net In-Reply-To: "David M. Schrader"'s message of Wed, 09 Mar 1994 14:06:31 -0600 (CST) <01H9RRGR9LQA8WWF9Q@vms.csd.mu.edu> Subject: CCL:Linear independence of a basis set SVD(Singular Value Decomposition) is the way to go, see e.g. Golub, Van Loan: Matrix Computations. There are LAPACK drivers in netlib for it too. Det(S) is totally unreliable, as it can be tiny even though there is good linear independence. The above book is quite clear on that point. ZT From CHAMANKHAH@sask.usask.ca Wed Mar 9 18:40:10 1994 Received: from skycat.usask.ca for CHAMANKHAH@sask.usask.ca by www.ccl.net (8.6.4/930601.1506) id SAA00573; Wed, 9 Mar 1994 18:20:22 -0500 From: Received: from SKYCAT.USask.CA by SKYCAT.USask.CA (PMDF V4.2-14 #5952) id <01H9RY63X8TC9LZUO2@SKYCAT.USask.CA>; Wed, 9 Mar 1994 17:19:43 CST Date: Wed, 09 Mar 1994 17:19:42 -0600 (CST) Subject: Program for pKa determination To: chemistry@ccl.net Message-id: <01H9RY642C2A9LZUO2@SKYCAT.USask.CA> X-Envelope-to: chemistry@ccl.net X-VMS-To: IN::"chemistry@ccl.net" MIME-version: 1.0 Content-transfer-encoding: 7BIT Hi netters' I'm just wondering if anybody out there is aware of a program capable of calculating and predicting the pKa values of a series of compounds, e.g. amines or so. Your responses are greately appreciated. Yours all Mahmood