From chemistry-request@server.ccl.net Wed Sep 13 03:36:18 2000 Received: from aurora.balcab.ch (aurora.balcab.ch [213.200.1.126]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA12264 for ; Wed, 13 Sep 2000 03:36:17 -0400 Received: from sigma.balcab.ch (sigma.balcab.ch [213.200.1.125]) by aurora.balcab.ch (8.9.1/8.9.1) with ESMTP id JAA00807 for ; Wed, 13 Sep 2000 09:36:09 +0200 (MET DST) Received: from ubaclu.unibas.ch ([213.200.8.206]) by sigma.balcab.ch (Netscape Messaging Server 3.6) with ESMTP id AAA389; Wed, 13 Sep 2000 09:36:08 +0200 Message-ID: <39BF2EBB.5A28BBA9@ubaclu.unibas.ch> Date: Wed, 13 Sep 2000 09:37:31 +0200 From: Shu-Kun Lin Reply-To: lin@mdpi.org Organization: MDPI (http://www.mdpi.org) X-Mailer: Mozilla 4.61 [en] (Win98; I) X-Accept-Language: en-US,zh,zh-CN MIME-Version: 1.0 To: chemistry@server.ccl.net, CHMINF-L@LISTSERV.INDIANA.EDU Subject: Chemistry librarians are also welcomed to submit papers to my session at ACS 2001 Spring Mtg Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Chemistry librarians are also welcomed to submit papers to the symposium "Electronic Chemistry Publishing" at the Spring ACS meeting in San Diego (April 1-5, 2001). I know some librarires successfully integrated primary, secondary and tertiary literature sources on the internet (intranet) in their library servers. Online publication is very convenient for this effort in libraries. Because electronic publishing is our topic, I would like to ask you to submit papers exclusively electronically at the http://oasys.acs.org/acs/221nm/cinf/papers/index.cgi website. It is a very good system. You can revise as many times as you like before the deadline of November 30. If you prefer poster presentation, you may send the paper to my session first and mark the button "Poster preferred". The Spring ACS meeting in San Diego (April 1-5, 2001) will have a poster session for all topics. Please e-mail me if you have any question. Regards, Shu-Kun -- Dr. Shu-Kun Lin Molecular Diversity Preservation International (MDPI) Saengergasse 25, CH-4054 Basel, Switzerland Tel. +41 79 322 3379, Fax +41 61 302 8918 E-mail: lin@mdpi.org http://www.mdpi.org/lin/ From chemistry-request@server.ccl.net Wed Sep 13 04:32:53 2000 Received: from cheviot3.ncl.ac.uk (root@cheviot.ncl.ac.uk [128.240.233.51]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA12719 for ; Wed, 13 Sep 2000 04:32:52 -0400 Received: from aidan.ncl.ac.uk (nbwt@aidan.ncl.ac.uk [128.240.233.1]) by cheviot3.ncl.ac.uk (8.10.1/8.10.1) with ESMTP id e8D8Wem07386; Wed, 13 Sep 2000 09:32:41 +0100 (BST) Received: from localhost (nbwt@localhost) by aidan.ncl.ac.uk (8.9.3+Sun/8.9.0) with ESMTP id JAA03590; Wed, 13 Sep 2000 09:32:40 +0100 (BST) X-Authentication-Warning: aidan.ncl.ac.uk: nbwt owned process doing -bs Date: Wed, 13 Sep 2000 09:32:40 +0100 (GMT) From: "Bruce. Tattershall" To: =?iso-8859-1?Q?Ot=E1vio=20Lu=EDs?= de Santana cc: CCL Subject: Re: CCL:Compiling the NBO program. In-Reply-To: <39BE7B1C.7B14BC3@npd.ufpe.br> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Filter-Version: 1.8 (cheviot3) Otavio: I have successfully changed MAXBAS to 999 in the NBO module of g94 and of g98, l607. One had to go through the .f source with an editor, and change every PARAMETER statement containing MAXBAS, of which there are many. We were caught out by two little traps left in the code in both versions. (a) MAXBAS is spelled with mixed upper and lower case letters in at least one routine, while it is in all upper case in others. A case-insensitive editor must be used for searching. (b) In some cases, one or two spaces have been left around the = in MAXBAS=500, so a global replacement of MAXBAS=500 is not sufficient. I have not tried to change MAXATM. Bruce Personal Email: Bruce.Tattershall@newcastle.ac.uk Dr. B.W. Tattershall Department of Chemistry, University of Newcastle, England From chemistry-request@server.ccl.net Wed Sep 13 06:57:19 2000 Received: from uscmail.usc.es (uscmail.usc.es [193.144.75.8]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA14229 for ; Wed, 13 Sep 2000 06:56:34 -0400 Received: from localhost (qflulus@localhost) by uscmail.usc.es (8.9.1/8.9.1) with ESMTP id MAA17889 for ; Wed, 13 Sep 2000 12:54:47 +0200 (MET DST) Date: Wed, 13 Sep 2000 12:54:47 +0200 (MET DST) From: Jose Luis Perez Lustres To: chemistry@ccl.net Subject: AM1 partial charges on N Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear collegues, Does anyone know any reference about the quality of partial charges on nitrogen atoms calculated by AM1 by any method (NAO, Mulliken, ...). I know that PM3 tends to do N's far too electropositive (see for example, Cramer, C. J.; Truhlar, D. G.; J. Comp. Chem., 13 (9), 1089-1097) and expect that AM1 could show the same bug, but have no reference for that. ________________________________________________________________________ Jose Luis Perez Lustres - PhD student Photochemistry Group (Physical-Chemistry Department) Santiago de Compostela University Campus Sur - 15706 Santiago de Compostela SPAIN Phone: ++81 + 563100 Ext 14300 Fax: ++81 + 595012 From chemistry-request@server.ccl.net Wed Sep 13 07:43:39 2000 Received: from bilbo.edu.uy (bilbo.edu.uy [164.73.160.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA14538 for ; Wed, 13 Sep 2000 07:43:36 -0400 Received: from localhost (oscar@localhost) by bilbo.edu.uy (8.11.0/8.11.0) with SMTP id e8DBhEQ26659; Wed, 13 Sep 2000 08:43:14 -0300 Date: Wed, 13 Sep 2000 08:43:13 -0300 (GRNLNDST) From: "Oscar N. Ventura" To: Jens Spanget-Larsen cc: chemistry@ccl.net Subject: Re: CCL: HYBRIDIZATION NOT "REAL" In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Jens: Of course, you are right. I was trying to make another point and simplified too much. Actually your argument reinforces what I wanted to point out with my previous (so calld "marxist" :-) argument. Regards. Oscar ------------------------------------------------------------------------------- Prof.Dr.Oscar N. Ventura Tel.+(5982)9248396 Fax +(5982)9241906 MTC-Lab,Facultad de Quimica MTC-Lab http://bilbo.edu.uy/MTC-Lab.html Universidad de la Republica Gral.Flores 2124, C. C. 1157 All opinions are my own, and not Montevideo 11800, URUGUAY necessarily those of my employer "Violence is the last refuge of the incompetent." --- Salvor Hardin ------------------------------------------------------------------------------- From chemistry-request@server.ccl.net Wed Sep 13 03:57:48 2000 Received: from ncsbex78.ncsbe.jnj.com (smtp.be.jnj.com [194.74.108.12]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA12371 for ; Wed, 13 Sep 2000 03:57:48 -0400 Received: from smtp.jnj.com by smtp.jnj.com id e8D7vY702033; Wed, 13 Sep 2000 09:57:35 +0200 (MET DST) Received: FROM ncsbebeexh3.ncsbe.jnj.com BY ncsbebesvc06.jnjeu.jnj.com ; Wed Sep 13 09:57:33 2000 +0200 Received: by ncsbebeexh3.ncsbe.jnj.com with Internet Mail Service (5.5.2651.58) id ; Wed, 13 Sep 2000 09:57:32 +0200 Message-ID: <63575A10E3FAD1119DDC0008C7242D3E02AA9734@JANBEBEEXS3.janbe.jnj.com> From: "Langenaeker, Wilfried [JanBe]" To: "'chemistry@ccl.net'" Subject: database of pharmacokinetic properties Date: Wed, 13 Sep 2000 09:57:29 +0200 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2651.58) Content-Type: text/plain; charset="iso-8859-1" Dear CCL-er's is anyone aware of a publicly or commercially available database of pharmacokinetic properties like plasma binding, clearance, renal excretion, etc. for drug and drug-like compounds together with the structure of these compounds in machine readable format. Thanks in advance, Wilfried Dr. Wilfried Langenaeker Senior Scientist Theoretical Medicinal Chemistry Janssen Research Foundation Devision of Janssen Pharmaceutica NV Turnhoutseweg 30 B-2340 Beerse Belgium Tel. : +32(0)14/60.69.18 Fax: +32(0)14/60.25.57 e-mail: wlangena@janbe.jnj.com From chemistry-request@server.ccl.net Wed Sep 13 06:03:39 2000 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 GAA13123 for ; Wed, 13 Sep 2000 06:03:38 -0400 Received: from smtprelay.ruc.dk (smtprelay.ruc.dk [130.225.220.22]) by mel.ruc.dk (8.9.3/8.9.1) with ESMTP id MAA12882; Wed, 13 Sep 2000 12:03:28 +0200 (MET DST) Received: from virgil.ruc.dk (virgil.ruc.dk [130.225.220.110]) by smtprelay.ruc.dk (8.9.3+Sun/8.9.3) with ESMTP id LAA04055; Wed, 13 Sep 2000 11:53:54 +0200 (MEST) Received: from VIRGIL/SpoolDir by virgil.ruc.dk (Mercury 1.44); 13 Sep 00 12:03:27 +0100 Received: from SpoolDir by VIRGIL (Mercury 1.44); 13 Sep 00 12:03:24 +0100 From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter To: "Oscar N. Ventura" , chemistry@ccl.net Date: Wed, 13 Sep 2000 12:03:23 +0100 Subject: CCL: HYBRIDIZATION NOT "REAL" Priority: normal X-mailer: Pegasus Mail for Windows (v2.23) Message-ID: Oscar N. Ventura: > Total density (STM), differential density (X-ray), energies of single > electrons within a molecule (photoelectron spectroscopy) are observable. > Molecular or atomic orbitals, energies of the molecular orbitals, etc, are > constructs of the theory and are not observable. Dear Oscar, I object to the statement that "energies of single electrons within a molecule (photoelectron spectroscopy) are observable". In photoelectron spectroscopy you observe differences in energy between the ground state of the neutral molecule and the different electronic states of the molecular radical cation. That is, you observe differences in energy between many-electronic states, not single electron energies. If you assume the validity of Koopmans' approximation (briefly: adopt the MO model and assume the same set of MO functions for the neutral molecule and the radical cation), the ionization energies of a closed-shell molecule can be set equal the negative of the energies of the occupied canonical MOs. This result is usually referred to as "Koopmans' theorem", but it is only valid within the above-mentioned approximations. The errors involved in these approximations tend to cancel each other out and "Koopmans' theorem" is thus very useful in the interpretation of photoelectron spectra. But the underlying assumptions frequently break down, leading to inapplicability of the approximate one-electron picture of ionization. Yours, 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 Wed Sep 13 08:07:50 2000 Received: from hawk.dcu.ie (mail.dcu.ie [136.206.1.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA14692 for ; Wed, 13 Sep 2000 08:07:49 -0400 Received: from dcu.ie (136.206.86.63) by hawk.dcu.ie (5.0.047) id 3972E2C40009FC58; Wed, 13 Sep 2000 13:08:01 +0100 Message-ID: <39BF6E13.D3AECB37@dcu.ie> Date: Wed, 13 Sep 2000 13:07:47 +0100 From: Dermot Brougham Organization: DCU X-Mailer: Mozilla 4.73 [en] (Win95; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net, postmaster@claessen.net, han.vos@dcu.ie Subject: Summary: Calculations on quantum dots? Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit My original question was: >Have people calculated the electronic states of the interacting >electrons in a quantum dot from first principles. Or, if there have been >no ab initio calculations, other more "approximate" methods would be >interesting. A citation search throws up a lot of stuff, which as an >outsider I cannot prune down. >So my question is; what are the key papers and who are the key people, >or has the area been reviewed? I summarize the replies below: Niri Govind and Michael Nolan suggested Alex Zunger. Zunger is at the nation renewable energy lab in Colorado. He has published a lot of work using pseudopotentials on Quantum Dots. Susan Atlas suggested Das Sarma who I think is in Bangalore, India. Sarma has published a lot of work involvng spectroscopy and calculations. Guido Raos suggested J. R. Chelikowsky (University of Minnesota) and coworkers who have done first principle DFT calculations of the electronic states of large Si clusters (several hundred atoms). eg S. Ogut, J.R. Chelikowsky, and S.G. Louie: "Quantum Confinement and Optical Gaps in Si Nanocrystals," Phys. Rev. Lett. 79, 1770 (1997). These were helpful and interesting contributions, but they didn't help me cut down the search that much. Probably the most useful respense was >from Dage Sundholm, I will quote Dage directly: >We use the finite mass approximation and solve the Schrödinger equation >for electrons and holes coonfined in a QD the size (radius) of which is >about 40 nm. We have studied QDs containing up to 10 carrier pairs >using full configuration interaction and for the larger dots truncated >configuration interaction such as the all singles, doubles, triples and >quadruples (SDTQ) CI method. Our paper is enclosed in pdf format. >To my knowledge this is the most accurate method applied on this kind of >QDs. Hawrylak has also done some calculations, but not very extensive >correlation calculations. >See: L. Jacak, P. Hawrylak, and A. Wojs, > Quantum Dots (Springer, Berlin, 1998). >For smaller dots (less than 5 nm) the molecular approach has to be used. >In this context I can mention Zunger and coworkers in Boulder Colorado. >An other family of quantum dots are large QDs containing only electrons. >This kind of QDs has been studied by several groups, since the same >methods as used in atomic and molecular physics or quantum chemistry >can be applied. The only difference is that the nuclear attraction potential >is replaced by a confinement potential. For example in Finland >at least two different groups (at University of Oulu and at the >Technical University of Helsinki) have studied this kind of QDs >at ab initio level. >sundholm@chem.helsinki.fi Dage's paper was: Full configuration interaction calculations of electron-hole correlation effects in strain-induced quantum dots PHYS REV B 61: (11) 7652-7655 MAR 15 2000 I am sure he would make this available to anybody else who is interested, I didn't want to do this with somebody elses work! Many thanks again to all who replied. Dermot Dr. Dermot Brougham, School of Chemical Sciences, Dublin City University, Dublin 9, Ireland. dermot.brougham@dcu.ie From chemistry-request@server.ccl.net Wed Sep 13 09:02:18 2000 Received: from ucidoor.unitedcatalysts.com ([208.23.162.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA14899 for ; Wed, 13 Sep 2000 09:02:17 -0400 Received: by ucidoor.unitedcatalysts.com; (8.8.8/1.3/10May95) id JAA24879; Wed, 13 Sep 2000 09:02:04 -0400 (EDT) Received: from 10.1.0.50 by ucismtp02.unitedcatalysts.com (InterScan E-Mail VirusWall NT); Wed, 13 Sep 2000 09:01:49 -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 <0G0T00IQ9TE342@lvlmail.unitedcatalysts.com>; Wed, 13 Sep 2000 08:58:51 -0400 (EDT) Received: by lvlxch01.unitedcatalysts.com with Internet Mail Service (5.5.2650.21) id ; Wed, 13 Sep 2000 09:00:31 -0400 Content-return: allowed Date: Wed, 13 Sep 2000 09:00:30 -0400 From: "Shobe, Dave" Subject: RE: Deduction of electronic properties from Gaussian output. To: "'Roy Jensen'" , CHEMISTRY@ccl.net Message-id: <157A51F55AAAD3119CD70008C7B1629D63855A@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 JAA14900 > 1. How can I tell if I need to use guess=alter? I don't know of a way to test a "stable" wavefunction to see if it's the lowest energy state, anymore than I know of a way to test if a particular geometry is the lowest energy for the system. It's the "a local minimum is not necessarily the global minimum" problem. You could try switching the HOMO and LUMO (especially if they have different symmetries) and seeing what happens. One thing I haven't tried but might work: if you do a CIS calculation, maybe it will show a negative excitation energy if you don't start with a ground state. (Reading below, it sounds like you'd like to do a CIS calc. anyway if you can afford it). Also, if you're calculating a series of similar complexes, you might see whether the orbitals (especially the SOMOs) are similar. You wouldn't expect NiCl2(NH3)2 and NiCl2(ethylenediamine) to have wildly different electron configurations for example. > 2. Is it reasonable to run the same complex as a singlet, triplet, > quintet, and septet and determine the ground state multiplicity as the > job that has the lowest energy? That's basically what you have to do, although you may be able to rule some of these out by chemical intuition. Be careful, though: the HF method heavily favors high-spin states. (I.e. there's more correlation energy within electron pairs than between unpaired electrons). I don't know if that applies to B3LYP or not. > 3. I generally run NBO analysis on these complexes. How do I determine > the electronic angular momentum? Can't help with this one. > 4. Is it reasonable to _estimate_ allowed and forbidden electronic > transitions by using the orbital energy levels provided from the > optimized geometries? I understand that CIS and CASSCF calculations > would provide better results. I imagine the trends within a series of similar complexes would be useful information. > I have been using the UB3LYP/LANL2DZ basis set for the calculations; > MP2/anything takes too long to converge. > > Roy Jensen CIS will take even longer. :-( But at least you only have to do it at a single point, and if my answer to #4 is correct, you won't have to do it for every molecule. --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 Wed Sep 13 09:44:45 2000 Received: from host23.lctn.u-nancy.fr (host23.lctn.u-nancy.fr [192.54.210.30]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA15256 for ; Wed, 13 Sep 2000 09:44:44 -0400 From: assfeld@host23.lctn.u-nancy.fr Received: (from assfeld@localhost) by host23.lctn.u-nancy.fr (AIX4.3/8.9.3/8.9.3) id PAA21112 for CHEMISTRY@ccl.net; Wed, 13 Sep 2000 15:44:08 +0200 Date: Wed, 13 Sep 2000 15:44:08 +0200 Message-Id: <200009131344.PAA21112@host23.lctn.u-nancy.fr> Subject: Kato's reference To: CHEMISTRY@ccl.net Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-MD5: 9tP3JcmqJbT4Qtp2RaHmjQ== Dear CCLers, sorry to bother you with a library problem. After some searches (not exhaustive) I give up. I am looking for a paper of Kato (don't even know the first name!) dealing with the first derivative of a wavefunction with respect to interelectronic distance, when this distance goes to zero, which must be proportional of half the wavefunction. I think that people having interest in explicit-r12 methods know what I mean. I had just eard about it and I don't have further details! I hope that someone could help me. Thanx for your leniency. ...Xav Ast. Pr. Xavier Assfeld Xavier.Assfeld@lctn.u-nancy.fr Laboratoire de Chimie theorique (T) 33 3 83 91 21 49 Universite Henri Poincare (F) 33 3 83 91 25 30 F-54506 Nancy BP 239 http://www.lctn.u-nancy.fr From chemistry-request@server.ccl.net Wed Sep 13 10:32:58 2000 Received: from silver.ch.unito.it (silver.ch.unito.it [130.192.118.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA15564 for ; Wed, 13 Sep 2000 10:32:57 -0400 Received: (from milanesi@localhost) by silver.ch.unito.it (8.9.3/8.9.3) id QAA17479; Wed, 13 Sep 2000 16:47:50 +0200 (MET DST) Date: Wed, 13 Sep 2000 16:47:50 +0200 (MET DST) From: Marco Milanesio To: "Bruce. Tattershall" cc: =?iso-8859-1?Q?Ot=E1vio=20Lu=EDs?= de Santana , CCL Subject: Re: CCL:Compiling the NBO4.0 program in G98 In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all, I am sorry I can not give any answer to your question, because I have a problem compiling the original version of NBO4.0 In fact I'm trying to substituite the original l607.exe in g98A7 with the NBO4.0 (october 1999 version) on a SGI with 4 procs and 7.3.0 fortran compiler. I was not able to build the new l607.exe. AT first I enabled the UNIX version following the instructions at page A10 of NBO4.0 manual and all worked well and I've got my new l607.F After this I tried to build the new l607.exe with "bsd/bldg98 linkrest l607.exe" as described in appendix 2.2 of the NBO4.0 manual, but if finished with this error: a - ihtyp.o a -initwt.o a - intrn.o a - ioinqr.o a - ionic.o a - iontst.o a - iwprj.o a -jacobi.o a - jobopt.o a - kekule.o a - keyerr.o a - keypar.o a - [l-zL-Z]*.o rm -f -r temp-l607 bsd/fixlib l607.a `main.a' is up to date. f77 -nocpp -w -i8 -r8 -mips4 -64 -align64 -r10000 -mp -G 0 -O3 -LNO:blocking=OFF:prefetch=1 -r8const -OPT:roundoff=3:IEEE_arithmetic=3:IEEE_comparisons=1:liberal_ivdep=TRUE:Olimit=0:reorg_common=OFF -o l607.exe ml607.o l607.a util.so -mp -lblas_mp -lfastm *** Error code 2 (ignored) rm -f ml607.o Could anyone help me in solving this problem? Thank you so much Marco Marco Milanesio milanesi@ch.unito.it From chemistry-request@server.ccl.net Wed Sep 13 10:36:53 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 KAA15618 for ; Wed, 13 Sep 2000 10:36:52 -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 e8DEacY447172 for ; Wed, 13 Sep 2000 16:36:38 +0200 (MEST) Message-ID: <39BF3D06.3AC6CF5E@mpi-muelheim.mpg.de> Date: Wed, 13 Sep 2000 16:38:30 +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: How to study the effect of external electric field using Gaussian Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear colleages, I hope to study the effect of external electric field on the molecular geometres using Gaussian, would you like to give me some suggestions here? Thanks in advance!! Dr. Z. Chen From chemistry-request@server.ccl.net Wed Sep 13 11:48:20 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 LAA15983 for ; Wed, 13 Sep 2000 11:48:19 -0400 Received: from [128.97.147.216] (ch-16.psnet.ucla.edu [128.97.147.216]) by carbon.chem.ucla.edu (8.9.1a/8.9.1) with ESMTP id IAA01750 for ; Wed, 13 Sep 2000 08:48:02 -0700 (PDT) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Message-Id: Date: Wed, 13 Sep 2000 08:47:09 -0800 To: chemistry@ccl.net From: Eric Scerri Subject: Pauling and orbitals THe original question which started this thread was partly about Pauling's OWN views about hybridization and orbitals. I think Pauling was surprisingly naive philosophically when it came to interpretation of what he was doing. I base this on the following personal anecdote. When the debate with Ogilvie was taking place in J. Chem. Ed. the same issue that carried the Pauling response also included three other reponses including a brief piece by myself. I used this as an excuse to get in touch with Pauling to try to explore his view further. In his reply he said almost verbatim, "Orbitals clearly exist since Mulliken and I have been writing about them for the past 60 years" I could not resist replying that storytellers have also been writing about unicorns for many years. Dr. Eric R. Scerri Department of Chemistry & Biochemistry, UCLA, 607 Charles E. Young Drive East, Los Angles, CA 90095-1569, USA tel: 310 206 3708 -------------------------------------------------------------------------- Editor: Foundations of Chemistry, An Interdisciplinary journal for Philosophical, Historical and Educational Aspects of Chemistry. http://www.wkap.nl/journals/foch See also International Society for the Philosophy of Chemistry (ISPC) http://www.georgetown.edu/earleyj/ISPC.html From chemistry-request@server.ccl.net Wed Sep 13 11:58:50 2000 Received: from rzumail2.unizh.ch (rzumail2.unizh.ch [130.60.128.10]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA16065 for ; Wed, 13 Sep 2000 11:58:49 -0400 Received: from zisgi.unizh.ch (zisgi.unizh.ch [130.60.19.17]) by rzumail2.unizh.ch (8.9.3/8.9.3/07) with ESMTP id RAA12624 for ; Wed, 13 Sep 2000 17:58:36 +0200 (MET DST) Date: Wed, 13 Sep 2000 17:58:36 +0200 From: "Dr. Peter Burger" To: CHEMISTRY@ccl.net Subject: dipole moment of charged molecule Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, somehow I got stuck. I want to calculate and compare (DFT) the dipole moments for a series of charged molecules (monocations). Is this possible? I noticed a severe problem, so far, which I believe is in part due to the choice of reference point (so far center of mass). Any pointer is highly appreciated. Peter From chemistry-request@server.ccl.net Wed Sep 13 15:03:28 2000 Received: from Mercury.acs.unt.edu (mercury.acs.unt.edu [129.120.220.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA16834 for ; Wed, 13 Sep 2000 15:03:27 -0400 Received: from jove.acs.unt.edu (10759@jove.acs.unt.edu [129.120.220.41]) by Mercury.acs.unt.edu (8.8.8/8.8.8) with ESMTP id OAA21015; Wed, 13 Sep 2000 14:03:13 -0500 (CDT) Received: from localhost (tdp0006@localhost) by jove.acs.unt.edu (8.8.8/8.8.8) with ESMTP id OAA16127; Wed, 13 Sep 2000 14:03:12 -0500 (CDT) Date: Wed, 13 Sep 2000 14:03:11 -0500 (CDT) From: TREVOR D POWER To: Zhongfang Chen cc: chemistry@ccl.net Subject: Re: CCL:How to study the effect of external electric field using Gaussian In-Reply-To: <39BF3D06.3AC6CF5E@mpi-muelheim.mpg.de> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Zhongfang, My collegues and I published a paper: J. Phys. Chem. 1996, 100, 18875-18881. In this article, we calculated electric properties of nucleic acid bases with Sadlej's basis set from optimizations with MP2/6-31G(d,p). Although the paper may not be of interest to you, the procedure for setting this up is either in the paper or in the list of references. Regards, David Power Department of Chemistry University of North Texas NT Station, Box 305070 Denton, TX 76203-5070 tdp0006@unt.edu On Wed, 13 Sep 2000, Zhongfang Chen wrote: > Dear colleages, > > I hope to study the effect of external electric field on the molecular > geometres using Gaussian, would you like to give me some suggestions > here? > > Thanks in advance!! > > Dr. Z. Chen > > > -= 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 Sep 13 10:16:38 2000 Received: from mail1.mclink.it (net128-007.mclink.it [195.110.128.7]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA15500 for ; Wed, 13 Sep 2000 10:16:34 -0400 Received: from k7 (net138-059.mclink.it [195.110.138.59]) by mail1.mclink.it (8.9.1/8.9.0) with SMTP id QAA07650 for ; Wed, 13 Sep 2000 16:16:17 +0200 (CEST) Message-ID: <004c01c01d8d$3339e3c0$070000c0@k7> From: "Elena Fioravanzo" To: "CCL" Subject: docking tools Date: Wed, 13 Sep 2000 16:16:16 +0200 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0049_01C01D9D.F1B7CF00" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2615.200 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 This is a multi-part message in MIME format. ------=_NextPart_000_0049_01C01D9D.F1B7CF00 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi CCLers, could you please point me to softwares for docking studies? I know some of them but I would like to check if there is something new = to use. I thank everyone in advance Elena --------------------------------------------------------- dott. Elena Fioravanzo - Consultant S.IN - Soluzioni Informatiche S.a.s. Via Salvemini 9 I-36100 Vicenza Italy - Europe Voice ++39 0444 240341 Mobile ++39 0347 4054991 Fax ++39 0444 533954 E-mail s.in-support@mclink.it Web http://www.goldnet.it/sin/ ------=_NextPart_000_0049_01C01D9D.F1B7CF00 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi CCLers,
 
could you please point me to softwares = for docking=20 studies?
I know some of them but I would like to = check if=20 there is something new to use.
I thank everyone in = advance
 
Elena
---------------------------------------------------------
dot= t. Elena=20 Fioravanzo - Consultant
S.IN - Soluzioni Informatiche S.a.s.
Via = Salvemini=20 9
I-36100 Vicenza
Italy - Europe
 
Voice   ++39 0444 = 240341
Mobile =20 ++39 0347 4054991
Fax      ++39 0444=20 533954
E-mail  s.in-support@mclink.it
Web&= nbsp;   =20 http://www.goldnet.it/sin/=
------=_NextPart_000_0049_01C01D9D.F1B7CF00-- From chemistry-request@server.ccl.net Wed Sep 13 11:58:10 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 LAA16061 for ; Wed, 13 Sep 2000 11:58:09 -0400 Received: from mail.biokemi.su.se (unverified [130.237.179.175]) by server.biokemi.su.se (EMWAC SMTPRS 0.83) with SMTP id ; Wed, 13 Sep 2000 18:00:18 +0200 Sender: zhang@ccl.net Message-ID: <39BFA307.3468CE5@mail.biokemi.su.se> Date: Wed, 13 Sep 2000 17:53:43 +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: Hetenyi Csaba , garrett@scripps.edu, chemistry@ccl.net Subject: Re: CCL:Reusing autogrid maps in autodock References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Csaba and Dr. Morris, Thank you for your e-mails to correct my mistake. Although I am ashamed for my ignorance on the autodock theory, your information might be useful for autodock novices. Therefore, I post it to the net. Hope everyone can forgive me. Sincerely, Xiao-Ping Zhang Csaba wrote: > > Dear Xiao-Ping, > > The grid maps are specific only for the ligand ATOM TYPES and not for the > ligands, itself. > So, it is possible to use the same map files for different ligands with > the same atom types. /if spacing, No. of grid points, target etc. are the > same/ > > Regards, > Csaba. > _______________________________________ > Csaba Hetenyi, M.Sc., Ph.D. student > University of Szeged > Dept. of Medical Chemistry > Addr.:H-6720 Szeged, Dom ter 8, Hungary > Tel.: +36-62545147 or +36-62545136 > Fax.: +36-62545971 > > On Tue, 12 Sep 2000, Xiao-Ping Zhang wrote: > > > Dear Trevor, > > > > If you run autogrid for your ligands against one > > macromolecule separately, you will get different map files > > for different ligands. As I understand, the map files should > > be ligand specific, otherwise the program may not > > discriminate good and bad ligand. > > > > Sincerely, > > > > Xiao-Ping Zhang > > "Garrett M. Morris" wrote: > > Dear Zhang, > > The grid maps can be reused. The only thing that AutoGrid > cares about in the ligand are the atom types. If you calculate > a set of maps, one for each atom type in all of your ligands, > then you have everything you need. > > If you have 2000 ligands, and all have C, N, O, and H, but some > also have S, then you would calculated C, N, O, S, and H maps, > once and once only, then you are done. > > On Tue, 12 Sep 2000, Xiao-Ping Zhang wrote: > > > Dear Trevor, > > > > If you run autogrid for your ligands against one > > macromolecule separately, you will get different map files > > for different ligands. As I understand, the map files should > > be ligand specific, otherwise the program may not > > discriminate good and bad ligand. > > This is wrong. AutoDock discriminates based on the topology and > atom types in the ligand. > > The maps are specific only to the protein or macromolecule. > > > > > Sincerely, > > > > Xiao-Ping Zhang > > > > > > Best wishes, > > Garrett > > ___ > Dr Garrett M. Morris, MA, DPhil > The Scripps Research Institute, tel: (858) 784-2292 > Dept. Molecular Biology, MB-5, fax: (858) 784-2860 > 10550 North Torrey Pines Road, email: garrett@scripps.edu > La Jolla, CA 92037-1000, USA. www.scripps.edu/pub/olson-web/gmm ****************************** 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 Wed Sep 13 11:51:37 2000 Received: from abacus.ac.BrockU.CA (abacus.ac.BrockU.CA [139.57.65.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA16040 for ; Wed, 13 Sep 2000 11:51:37 -0400 Received: from localhost (srothste@localhost) by abacus.ac.BrockU.CA (8.9.3/8.9.3) with SMTP id LAA150644; Wed, 13 Sep 2000 11:48:48 -0400 (EDT) Date: Wed, 13 Sep 2000 11:48:48 -0400 (EDT) From: "Stuart M. Rothstein" To: assfeld@host23.lctn.u-nancy.fr cc: CHEMISTRY@ccl.net Subject: Re: CCL:Kato's reference In-Reply-To: <200009131344.PAA21112@host23.lctn.u-nancy.fr> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Xav: The Kato reference is as follows: T. Kato, Commun. Pure Appl. Math. 10, 151 (1957). Among other work on this topic I suggest you look at: M. Hoffmann-Ostenhof, T. Hoffmann-Ostenhof, and H. Stremnitzer, Phys. Rev. Lettr. 68, 3857 (1992) and R.T. Pack and W.B. Brown, J. Chem. Phys. 45, 556 (1966). Stuart M. Rothstein, Professor of Chemistry and Physics, Brock University, St. Catharines, Ontario, L2S 3A1 CANADA srothste@abacus.ac.brocku.ca http://chemiris.labs.brocku.ca/~chemweb/faculty/rothstein/ On Wed, 13 Sep 2000 assfeld@host23.lctn.u-nancy.fr wrote: > Dear CCLers, > > sorry to bother you with a library problem. > After some searches (not exhaustive) I give up. > I am looking for a paper of Kato (don't even know the first name!) > dealing with the first derivative of a wavefunction with > respect to interelectronic distance, when this distance > goes to zero, which must be proportional of half the wavefunction. > I think that people having interest in explicit-r12 methods know > what I mean. > I had just eard about it and I don't have further details! > I hope that someone could help me. > Thanx for your leniency. > > ...Xav > > Ast. Pr. Xavier Assfeld Xavier.Assfeld@lctn.u-nancy.fr > Laboratoire de Chimie theorique (T) 33 3 83 91 21 49 > Universite Henri Poincare (F) 33 3 83 91 25 30 > F-54506 Nancy BP 239 http://www.lctn.u-nancy.fr > > -= 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 Sep 13 13:15:43 2000 Received: from cheetah.it.wsu.edu (root@cheetah.it.wsu.edu [134.121.1.8]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA16417 for ; Wed, 13 Sep 2000 13:15:43 -0400 Received: from ucis (ucis.chem.wsu.edu [134.121.41.180]) by cheetah.it.wsu.edu (8.9.3/8.9.3) with SMTP id KAA01442; Wed, 13 Sep 2000 10:15:26 -0700 (PDT) Message-ID: <008101c01da6$34b6b660$b4297986@chem.wsu.edu> From: "Phillip Matz" To: "Zhongfang Chen" , References: <39BF3D06.3AC6CF5E@mpi-muelheim.mpg.de> Subject: Re: CCL:How to study the effect of external electric field using Gaussian Date: Wed, 13 Sep 2000 10:15:25 -0700 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit 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 Hello Dr Z. Chen! The keyword you are looking for is Field. I like to use this keyword when optimizing geometries in an electric dipole field when modeling molecular interactions in IMS (ion mobility spectrometry). For me the use of the keyword simply involves placing the keyword Field = Z + 1000 into to route line of an optimization job, or any job for that matter. My example choice of 1000 simply means Gaussian is applying an electric dipole field in the Z direction of 0.1 a.u. This is of course a rather large field but it is just an example. Look at the Gaussian manual for your options with field, here is a clip though: - from Gaussian manual ....the field can either involve electric multipoles (through hexadecapoles) or a Fermicontact term. Field requires a parameter in one of these two formats: M±N or F(M)N where M designates a multipole, and F(M) designates a Fermi contact perturbation for atom M (following the ordering in the molecule specification section of the input file). N*0.0001 specifies the magnitude of the field in atomic units in the first format, and specifies the magnitude of the Fermi contact perturbation in the second format. - from Gaussian manual Respectfully, Phillip Matz matz@wsunix.wsu.edu ----- Original Message ----- From: "Zhongfang Chen" To: Sent: Wednesday, September 13, 2000 1:38 AM Subject: CCL:How to study the effect of external electric field using Gaussian > Dear colleages, > > I hope to study the effect of external electric field on the molecular > geometres using Gaussian, would you like to give me some suggestions > here? > > Thanks in advance!! > > Dr. Z. Chen > > > -= 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 Sep 13 15:35:06 2000 Received: from mail.chem.tamu.edu (mail.chem.tamu.edu [165.91.176.8]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA17173 for ; Wed, 13 Sep 2000 15:35:06 -0400 Received: from mail.chem.tamu.edu ([165.91.177.236]) by mail.chem.tamu.edu (Post.Office MTA v3.5.3 release 223 ID# 0-64333U1000L100S0V35) with ESMTP id edu for ; Wed, 13 Sep 2000 14:45:06 -0500 Sender: fan@mail.chem.tamu.edu (Huajun Fan) Message-ID: <39BFD723.51D56F36@mail.chem.tamu.edu> Date: Wed, 13 Sep 2000 14:36:03 -0500 From: Huajun Fan X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 CC: chemistry@ccl.net Subject: DFT methods References: <39BF3D06.3AC6CF5E@mpi-muelheim.mpg.de> <008101c01da6$34b6b660$b4297986@chem.wsu.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers I would like to find any articles, which study the difference results (geometry, energy etc.) between the difference DFT methods, such as b3lyp, b3p86, b3pw91, bp86, blyp... ... Any suggestion will be highly appreciated. Thanks in advance. Huajun From chemistry-request@server.ccl.net Wed Sep 13 16:17:18 2000 Received: from email.nist.gov (email.nist.gov [129.6.2.7]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA17425 for ; Wed, 13 Sep 2000 16:17:18 -0400 Received: from silyl (silyl.nist.gov [129.6.194.163]) by email.nist.gov (8.9.3/8.9.3) with SMTP id QAA07975 for ; Wed, 13 Sep 2000 16:17:18 -0400 (EDT) Message-Id: <3.0.5.32.20000913161633.009cf4f0@mailserver.nist.gov> X-Sender: rdj3@mailserver.nist.gov X-Mailer: QUALCOMM Windows Eudora Pro Version 3.0.5 (32) Date: Wed, 13 Sep 2000 16:16:33 -0400 To: CHEMISTRY@ccl.net From: Russ Johnson Subject: Re: DFT methods In-Reply-To: <39BFD723.51D56F36@mail.chem.tamu.edu> References: <39BF3D06.3AC6CF5E@mpi-muelheim.mpg.de> <008101c01da6$34b6b660$b4297986@chem.wsu.edu> Mime-Version: 1.0 Content-Type: text/enriched; charset="us-ascii" Hello, The NIST Computational Chemistry Comparison and Benchmark Database allows the comparison of geometries, reaction energies, atomization energies and a few other properties. It includes BLYP, B3LYP, B3PW91 with nine different basis sets. The site includes about 600 species. The URL is: http://srdata.nist.gov/cccbdb 0000,0000,ffffDr. Russell D. Johnson III Research Chemist National Institute of Standards and Technology Computational Chemistry Group 100 Bureau Drive, Stop 8380 Gaithersburg, MD 20899-8380 voice 301+975-2513 fax 301+869-4020 email: russell.johnson@nist.gov