From chemistry-request@server.ccl.net Thu Aug 5 09:38:25 1999 Received: from apollo.syrres.com (apollo.syrres.com [204.168.121.242]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA12486 for ; Thu, 5 Aug 1999 09:38:25 -0400 Received: from pc-howardp ([204.168.121.208]) by apollo.syrres.com (Netscape Messaging Server 3.62) with SMTP id 373; Thu, 5 Aug 1999 09:28:47 -0400 Message-Id: <3.0.32.19990805093210.00f577c4@apollo.syrres.com> X-Sender: howardp@apollo.syrres.com X-Mailer: Windows Eudora Pro Version 3.0 (32) Date: Thu, 05 Aug 1999 09:32:10 -0400 To: Jon Sorenson , chemistry@ccl.net From: "Phil Howard" Subject: Re: CCL:cLogP calculator Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Jon, You should check out our LOGKOW program http://esc.syrres.com/~esc1/estsoft.htm It is one of the most accurate available and does not have any missing fragment problems (see J. Pharm Sci 84:83-92,1995). The program also has a unique feature that allows the user to adjust the estimation using an experimental octanol/water partition coefficient from a structurally-related chemical compound. Batch file processing is also possible. Phil Philip H. Howard, Ph.D. Phone: 315-452-8417 Director, Environmental Sciences Center Fax: 315-452-8440 Syracuse Research Corporation Email: howardp@syrres.com 6225 Running Ridge Rd. Website http://esc.syrres.com North Syracuse, NY 13212 At 06:12 PM 8/4/1999 -0700, Jon Sorenson wrote: > >Hi netizens, > >I'm forwarding this message for a friend in the pharmaceutical >industry who's not on the list: > >> Subj: cLogP calculator > >> Hello, We have an ISIS database for our synthetic compound collection >> (>20,000 cmpds right now). We would like to add a well-validated >> computational package for determining cLogP values. Any suggestions out >> there? Thanks in advance! > >If there's interest, I'll summarize replies to the list. > >Thanks, > >Jon Sorenson > >----------------------------------------------------------------------- >Jon Sorenson JMSorenson@lbl.gov >Ph.D. Student http://www.lbl.gov/~jsorenso >Dept. of Chemistry Donner 474 >U.C. Berkeley 510.486.6933 >Berkeley, CA 94720 >----------------------------------------------------------------------- > > > >-= 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 Wed Aug 4 04:18:37 1999 Received: from office.un.md (root@office.un.md [212.0.211.34]) by server.ccl.net (8.8.7/8.8.7) with SMTP id EAA01274 for ; Wed, 4 Aug 1999 04:18:36 -0400 Received: from un.md ([212.0.205.37]) by office.un.md (8.6.13/8.6.12xla) with SMTP id LAA24004; Wed, 4 Aug 1999 11:12:14 +0300 Date: Wed, 4 Aug 1999 11:13:36 +0300 From: Mike Peleah X-Mailer: The Bat! (v1.15) S/N B6042885 Reply-To: Mike Peleah X-Priority: 3 (Normal) Message-ID: <16467.990804@mail.ru> To: Mike CC: chemistry@ccl.net Subject: Re[2]: CCL:natural internal coordinates References: +======================---------------- --- -- - - - - . | Dear Mike, : . you wrote: M> excuse my ignorance, what do you call "natural internal M> coordinates"? Are they - torsional angles, bond angles, and bond M> lengths It is a combination of torsional angles, bond angles, and bond lengths. This coordinates are described in P.Pulay, G.Fogarosi, F.Pang, J.E.Boggs // J.Am.Chem.Soc. 101, 2550-2560 (1979) and G.Fogarasi, X.Zhou, P.W.Taylor, P.Pulay // J.Am.Chem.Soc. 114, 8191-8201 (1992). These coordinates are better than cartesian and Z-matrix for my systems (multiring). Best regards, Mike mailto:MikePeleah@mail.ru : | . - - - - -- --- ----------------======================+ From chemistry-request@server.ccl.net Thu Aug 5 14:13:56 1999 Received: from mailbox.syr.edu (root@mailbox.syr.edu [128.230.18.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA14294 for ; Thu, 5 Aug 1999 14:13:56 -0400 Received: from syr.edu (curie.syr.edu [128.230.187.116]) by mailbox.syr.edu (8.9.2/8.9.2) with ESMTP id OAA12674 for ; Thu, 5 Aug 1999 14:07:16 -0400 (EDT) Sender: desingh@mailbox.syr.edu Message-ID: <37A9D3F4.42C9E763@syr.edu> Date: Thu, 05 Aug 1999 14:12:04 -0400 From: Deepak Singh Organization: Dept. of Chem & Biochem, Syracuse University X-Mailer: Mozilla 4.61C-SGI [en] (X11; I; IRIX64 6.5 IP30) X-Accept-Language: en MIME-Version: 1.0 To: Computational Chemistry List Subject: MOPAC2000 and MOLZYME Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi everyone, Does anyone have experience with the MOLZYME module of MOPAC2000. We have been running it of a DELL XPS-T500 and it requires a LOT of memory for minimizing a 28 kDa protein. Does anyone have a memory requirement for something like a SGI Octane? Thanks Deepak. -- ********************************************************************** Deepak Singh Tel : (315)443 1739 (w) Graduate Student (315)472 9659 (h) Dept. of Chemistry Fax : (315)443 4070 Syracuse University email : desingh@syr.edu 1-014 CST, Syracuse URL : http://web.syr.edu/~desingh NY 13244 "Violence is the last refuge of the incompetent." --- Salvor Hardin ********************************************************************** From chemistry-request@server.ccl.net Wed Aug 4 10:38:36 1999 Received: from mel.ruc.dk (mel.ruc.dk [130.225.220.27]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA04099 for ; Wed, 4 Aug 1999 10:38:35 -0400 Received: from virgil.ruc.dk (virgil.ruc.dk [130.225.220.110]) by mel.ruc.dk (8.9.3/8.9.1) with ESMTP id QAA07877 for ; Wed, 4 Aug 1999 16:32:11 +0200 (MET DST) Received: from VIRGIL/SpoolDir by virgil.ruc.dk (Mercury 1.40); 4 Aug 99 16:34:05 +0100 Received: from SpoolDir by VIRGIL (Mercury 1.40); 4 Aug 99 16:34:00 +0100 From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter To: chemistry@ccl.net Date: Wed, 4 Aug 1999 16:33:46 +0100 Subject: CCL: Time-Dependent-DFT Oscillator Strengths Priority: normal X-mailer: Pegasus Mail for Windows (v2.23) Message-ID: <1CF95034FA5@virgil.ruc.dk> CCL: TD-DFT theory appears to provide a useful approach to the electronic spectra of many molecules. In our lab, TD-B3LYP calculations (Gaussian98w, vs. 5.0) have satisfactorily reproduced transition energies and relative intensities for several organic chromophores. However, the absolute intensities are much too low: The predicted oscillator strengths are one order of magnitude too small, compared with data derived from experimental spectra. The discrepancy does not seem to depend significantly on basisset. Is this a problem intrinsic to TD-DFT? What is the explanation? Thank you, Jens >--< =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= JENS SPANGET-LARSEN Phone: +45 4674 2000 (RUC) Department of Chemistry +45 4674 2710 (direct) Roskilde University (RUC) Fax: +45 4674 3011 P.O.Box 260 E-Mail: JSL@virgil.ruc.dk DK-4000 Roskilde, Denmark http://www.rub.ruc.dk/dis/chem/psos/ =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From chemistry-request@server.ccl.net Thu Aug 5 09:59:13 1999 Received: from server.nybc.org (server.nybc.org [192.94.249.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA12613 for ; Thu, 5 Aug 1999 09:59:13 -0400 Received: from iris.nybc.org ([192.94.249.42]) by server.nybc.org (Netscape Mail Server v2.0) with ESMTP id AAA1640; Thu, 5 Aug 1999 09:52:33 -0400 Received: by iris.nybc.org (980427.SGI.8.8.8/940406.SGI.AUTO) id JAA11366; Thu, 5 Aug 1999 09:52:49 -0400 (EDT) From: "Asim Kumar Debnath" Message-Id: <9908050952.ZM11106@iris.nybc.org> Date: Thu, 5 Aug 1999 09:52:49 -0400 X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: jsorenso@water.lbl.gov, chemistry@ccl.net Subject: clogP Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear Jon: Please check the clogP method, most widely used and verified on a large dataset of experimental logP, by Dr. Albert Leo and Dr. Corwin Hansch's group at Pomona College, California. The web address is http://www.biobyte.com. Hope this helps. Asim -- ======================================================================= *** *** **** Asim K. Debnath, Ph.D. **** Lindsley F. Kimball Research Institute **** *** The New York Blood Center **** **** 310 E 67 Th Street **** ** **** New York, NY 10021 **** **** **** Tel. (212) 570-3373 **** ** **** Fax. (212) 570-3299 **************** E-mail: adebnath@nybc.org ************** ======================================================================== From chemistry-request@server.ccl.net Wed Aug 4 22:41:35 1999 Received: from plmsc.psu.edu (kotelyan@raman.plmsc.psu.edu [128.118.156.124]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id WAA07992 for ; Wed, 4 Aug 1999 22:41:34 -0400 Received: from localhost (kotelyan@localhost) by plmsc.psu.edu (8.8.7/8.8.7) with SMTP id WAA11419; Wed, 4 Aug 1999 22:31:18 GMT Date: Wed, 4 Aug 1999 22:31:18 +0000 (GMT) From: Mike To: Mike Peleah cc: chemistry@ccl.net Subject: Re: Re[2]: CCL:natural internal coordinates In-Reply-To: <16467.990804@mail.ru> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id WAA07993 > M> excuse my ignorance, what do you call "natural internal > M> coordinates"? Are they - torsional angles, bond angles, and bond > M> lengths > It is a combination of torsional angles, bond angles, and bond > lengths. This coordinates are described in P.Pulay, G.Fogarosi, > F.Pang, J.E.Boggs // J.Am.Chem.Soc. 101, 2550-2560 (1979) and > G.Fogarasi, X.Zhou, P.W.Taylor, P.Pulay // J.Am.Chem.Soc. 114, > 8191-8201 (1992). > > These coordinates are better than cartesian and Z-matrix for my > systems (multiring). Well, these coordinates have been used "since day 1" in polymer simulations (and small molecules also", given cartesian coordinates and connectivity of the atoms (list of bonds, angles, and torsions) calculating bond lengths should be trivial, first: calculate the vectors for all bonds: l=r_i-r_j, bond length - is it's length , angle between two bonds is calculated from the scalar product of two bond vectors: cos(phi) = l_i*l_(i+1)/|l_i||l_(i+1)| torsions are a little trickier, but also not hard: torsional angle is an angle between the planes made up by three successuve bonds l_(i-1), l_i, l_(i+1), normals to the planes are a=[l_i x l_(i-1)] and b=[l_(i+1) x l_i] ([ x ] - stands for the cross-product of two vectors. Torsional angle can be determined as angle between a and b, I hope it will not take you long to write a simple program to implement these calculations. More details can be found in any simulation text of which the standard is M.P.Allen and D.J.Tildesley "Computer Simulations of liquids" or in a series of papers from group of prof. Ueli Suter, Doros N. Theodorou and others from that group from 1985 and later, they are all published in Macromolecules >from that time. For instance: @incollection{Ludovice92, author="Ludovice,P.J. and Suter,U.W.", title="Detailed Molecular Structure of a Polar Vinyl Polymer Glass", booktitle="Computational Modeling of Polymers", editor="J.Bicerano", publisher="Marcel Dekker", address="New York", year="1992", pages="401"} @article{The85, author="Theodorou, D.N. and Suter, U.W.", title="Detailed Molecular Structure of a Vinyl Polymer Glass", journal="Macromolecules", year="1985", volume="18", pages="1467-1478" } @Book{SuterMattice, author = {Mattice,W. and Suter,U.W.}, ALTeditor = {}, title = {Conformational theory of large molecules, the rotational isomeric state model in macromolecular systems}, publisher = {J.Wiley}, year = {1994}, OPTkey = {}, OPTvolume = {}, OPTnumber = {}, OPTseries = {}, address = {New York}, OPTedition = {}, OPTmonth = {}, OPTnote = {}, OPTannote = {} } Hope it helps Michael > > > Best regards, > Mike mailto:MikePeleah@mail.ru > > ... Если голова болит, значит она есть . > : > | > . - - - - -- --- ----------------======================+ > > From chemistry-request@server.ccl.net Thu Aug 5 16:05:10 1999 Received: from ml.wpafb.af.mil (firewall-user@ml-firewall.ml.wpafb.af.mil [134.131.90.33]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA15335 for ; Thu, 5 Aug 1999 16:05:10 -0400 Received: by ml.wpafb.af.mil; id PAA14147; Thu, 5 Aug 1999 15:58:26 -0400 (EDT) Received: from fszhtv48.ml.wpafb.af.mil(134.131.37.142) by ml-firewall.ml.wpafb.af.mil via smap (V5.0) id xmaa14013; Thu, 5 Aug 99 15:57:49 -0400 Received: by fszhtv48.ml.wpafb.af.mil with Internet Mail Service (5.5.2448.0) id ; Thu, 5 Aug 1999 15:56:58 -0400 Message-ID: <0163F33EE074D211810C0000F8CD2354B7166F@fszhtv48.ml.wpafb.af.mil> From: Nguyen Kiet A Contr AFRL/MLPJ To: chemistry@ccl.net, "'Jens Spanget-Larsen'" Subject: RE: Time-Dependent-DFT Oscillator Strengths Date: Thu, 5 Aug 1999 15:56:50 -0400 X-Mailer: Internet Mail Service (5.5.2448.0) I am not sure about the window versions of G98. For the unix releases, TD-DFT oscillator strength was not implemented (even though the numbers appear in the print out) until release A7. However, I don't think the present implementation is correct. I have tried to contact Gaussian but got no response. It is unfortunate that Gaussian did not mention this in their release notes. Kiet > ---------- > From: Jens Spanget-Larsen > Sent: Wednesday, August 4, 1999 11:33 AM > To: chemistry@ccl.net > Subject: CCL:Time-Dependent-DFT Oscillator Strengths > > CCL: > > TD-DFT theory appears to provide a useful approach to the electronic > spectra of many molecules. In our lab, TD-B3LYP calculations > (Gaussian98w, vs. 5.0) have satisfactorily reproduced transition > energies and relative intensities for several organic chromophores. > However, the absolute intensities are much too low: The predicted > oscillator strengths are one order of magnitude too small, compared > with data derived from experimental spectra. The discrepancy does > not seem to depend significantly on basisset. > > Is this a problem intrinsic to TD-DFT? What is the > explanation? > > Thank you, Jens >--< > > =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= > JENS SPANGET-LARSEN Phone: +45 4674 2000 (RUC) > Department of Chemistry +45 4674 2710 (direct) > Roskilde University (RUC) Fax: +45 4674 3011 > P.O.Box 260 E-Mail: JSL@virgil.ruc.dk > DK-4000 Roskilde, Denmark http://www.rub.ruc.dk/dis/chem/psos/ > =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= > > -= 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 Thu Aug 5 17:26:11 1999 Received: from mx.seanet.com (dns2.seanet.com [199.181.164.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA16123 for ; Thu, 5 Aug 1999 17:26:11 -0400 Received: from biggeek ([150.215.141.174]) by mx.seanet.com (8.9.3/Seanet-8.7.3) with SMTP id OAA26218 for ; Thu, 5 Aug 1999 14:19:29 -0700 (PDT) Message-ID: <000b01bedf88$34285f80$ae8dd796@biggeek.wrq.com> From: "Mark Thompson" To: "Computational Chemistry List" Subject: Beautifying geometry Date: Thu, 5 Aug 1999 14:19:29 -0700 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 I would appreciate hearing from people who can suggest good sources of information on rule-based "beautify" or "clean" geometry; journal articles, personal experience, etc. In particular, I'm interested in various approaches that have been tried for ring-systems. (As usual, a summary of responses will follow.) Thanks in advance, Mark