From glee@calstatela.edu Tue Nov 28 00:08:33 1995 Received: from eagle.calstatela.edu for glee@calstatela.edu by www.ccl.net (8.6.10/950822.1) id XAA14559; Mon, 27 Nov 1995 23:57:47 -0500 Received: from mars.calstatela.edu (mars.calstatela.edu [130.182.5.1]) by eagle.calstatela.edu (8.6.12/8.6.12) with ESMTP id VAA25890 for ; Mon, 27 Nov 1995 21:01:22 -0800 Received: (from glee@localhost) by mars.calstatela.edu with id UAA01020 for CHEMISTRY@www.ccl.net; Mon, 27 Nov 1995 20:58:54 -0800 Date: Mon, 27 Nov 1995 20:58:54 -0800 From: Ging Lee Message-Id: <199511280458.UAA01020@mars.calstatela.edu> To: CHEMISTRY@www.ccl.net Subject: hydrogel materials Content-Length: 376 Hello people, I would like to know if anyone out there who can give me a pointer to find information about a class of material call "hydrogel". They can come from either theory or synthese work. I have looked in out library and not even one book was on this subject, so that's why I need your help. Thank you very much in advance. Ging Lee glee@chem0sun.calstatela.edu From ipcakc@ipc.iisc.ernet.in Mon Nov 27 03:23:20 1995 Received: from soochak.ncst.ernet.in for ipcakc@ipc.iisc.ernet.in by www.ccl.net (8.6.10/950822.1) id DAA25652; Mon, 27 Nov 1995 03:22:58 -0500 Received: from postoffice.iisc.ernet.in (twisha.ece.iisc.ernet.in [144.16.64.4]) by soochak.ncst.ernet.in (8.6.8.1/8.6.6) with ESMTP id NAA19429 for ; Mon, 27 Nov 1995 13:52:03 +0530 Received: by postoffice.iisc.ernet.in (ERNET-IISc/SMI-4.1) id NAA10226; Mon, 27 Nov 1995 13:52:59 +0500 Date: Mon, 27 Nov 1995 13:52:59 +0500 From: ipcakc@ipc.iisc.ernet.in (Dr.A.K.Chandra) Message-Id: <199511270852.NAA10226@postoffice.iisc.ernet.in> To: CHEMISTRY@www.ccl.net Subject: INTRAMOLECULAR H-ABSTRACTION IN ENES Status: RO dear netters, Are there any reports on INTRA-MOLECULAR (NOT INTERMOLECULAR) H-ABSTRACTION IN EXCITED STATES (LIKE LOWEST TRIPLET STATES) OF OLEFINIC COMPOUNDS? I HAVE FOUND ONLY INTER-MOLECULAR REACTIONS (LIKE RADICAL ADDITIONS TO OLEFINS IN GROUND STATES.) EVEN IN GROUND STATE (I.E. LOWEST SINGLET STATE) REACTIONS ARE ALSO WELCOMED. Thanks in advance. Sridhar E-mail : ipcakc@postoffice.iisc.ernet.in (or) akc@hamsadvani.serc.iisc.ernet.in From owner-chemistry@ccl.net Mon Nov 27 19:56:03 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id TAA12526; Mon, 27 Nov 1995 19:56:01 -0500 Received: from criba.edu.ar for rvgloss@criba.edu.ar by bedrock.ccl.net (8.7.1/950822.1) id TAA25553; Mon, 27 Nov 1995 19:55:54 -0500 (EST) Received: by criba.edu.ar (4.1/SMI-4.1) id AA09564; Mon, 27 Nov 95 21:56:25 WDT Date: Mon, 27 Nov 95 21:56:25 WDT From: rvgloss@criba.edu.ar (Daniel Glossman) Message-Id: <9511280056.AA09564@criba.edu.ar> To: chemistry@ccl.net Subject: reduction potentials and energy differences Status: RO Dear netters: Is it possible to establish any relationship between the differences in energy of the anion and the neutral molecule and the experimental reduction potential for organic molecules? Thank in advance Daniel Glossman ************************************************************************** Dr. Daniel Glossman Programa QUINOR - CONICET Universidad Nacional de Lujan Departamento de Quimica Departamento de Ciencias Basicas Universidad Nacional de La Plata Division Quimica Casilla de Correo 962 Casilla de Correo 221 (1900) La Plata (6700) Lujan Republica Argentina Republica Argentina Phone/FAX: (54 21) 259485 FAX: (54 323) 25795 E-mail: rvgloss@criba.edu.ar E-mail: glossman@unlu01.edu.ar *************************************************************************** From smori@chem.s.u-tokyo.ac.jp Mon Nov 27 23:29:41 1995 Received: from utsc.s.u-tokyo.ac.jp for smori@chem.s.u-tokyo.ac.jp by www.ccl.net (8.6.10/950822.1) id XAA14321; Mon, 27 Nov 1995 23:29:36 -0500 Received: from [133.11.6.112] (smori.chem.s.u-tokyo.ac.jp) by utsc.s.u-tokyo.ac.jp (5.67+1.6W/TISN-1.3/R2) id AA02822; Tue, 28 Nov 95 13:29:07 JST Message-Id: <9511280429.AA02822@utsc.s.u-tokyo.ac.jp> Date: Tue, 28 Nov 1995 13:33:48 +0900 To: chemistry@www.ccl.net From: smori@chem.s.u-tokyo.ac.jp (Mori Seiji) X-Sender: smori@chem.s.u-tokyo.ac.jp (Unverified) Subject: NMR calculation-ISOTROPIC and ANITROSOPY Cc: smori@utsc.s.u-tokyo.ac.jp, help@gaussian.com Mime-Version: 1.0 Content-Type: text/plain; charset=iso-2022-jp X-Mailer: Eudora-J(1.3.8.5-J13) Status: RO Dear Sirs, I posted to CCL about the methods of NMR calculation a fey days ago , and had an other question. In G94, I tried to calculate the chemical shifts , there are magnetic shieldings in the output, however, no chemical shift but isotropic and anitrosopy. I examine meaning of these terms in the user's manual of Gaussian 94 and several original papers,for example, M. Schindler, et al. JCP, 1982, 76, 1919 and Pulay et al. JACS, 1990, 112, 8251, and so on which there is replies of my previous questions , but I only know that isotropic terms is "likely" to be corresponding to the chemical shifts which was experimentally observed. I had had experiments in organic chemistry, and I am now carrying out the ab initio calculations but I amn't much familiar to know the theory of NMR spectroscopy. Would you please tell me the physical meaning of isotropic and anitrosopy, and which is an equivalent of the experimental chemical shift? It is better that you show the references. Sincerely yours, Seiji Mori #################################################### Seiji Mori Graduate student in Nakamura Laboratory Department of Chemistry The University of Tokyo Hongo 7-3-1, Bunkyou-ku, Tokyo 113, JAPAN. email:smori@chem.s.u-tokyo.ac.jp #################################################### From owner-chemistry@ccl.net Tue Nov 28 05:38:40 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id FAA19419; Tue, 28 Nov 1995 05:25:44 -0500 Received: from earth.ox.ac.uk for Keith.Refson@earth.ox.ac.uk by bedrock.ccl.net (8.7.1/950822.1) id FAA29210; Tue, 28 Nov 1995 05:25:39 -0500 (EST) Received: from rahman.earth.ox.ac.uk by earth.ox.ac.uk; Tue, 28 Nov 1995 10:24:48 GMT Date: Tue, 28 Nov 95 10:24:46 GMT Message-Id: <7673.9511281024@rahman.earth.ox.ac.uk> From: Keith Refson Subject: Re: CCL:statistical error in simulations To: chemistry@ccl.net Organisation: Earth Sciences Department, Oxford University. Dear Rafael, > I'm looking for references about calculation of errors in quantities > like RDF, running integration numbers,... obtained by means of MD/MC > simulations. Take a look at Allen and Tildesley, p191 onwards. Also worth a look is @Article{schiferl:85, author = {S. K. Schiferl and D. C. Wallace}, title = {Statistical Errors in Molecular Dynamics Averages}, journal = jcp, year = 1985, volume = 83, number = 10, pages = {5203-5209} } Keith Refson ------------------------------------------------------------------------------ | Email : keith@earth.ox.ac.uk | Dr Keith Refson, Dept of Earth Sciences| | TEL(FAX): +44 1865 272026 (272072)| Parks Road, Oxford OX1 3PR, UK | ------------------------------------------------------------------------------ From separk@cs.usc.edu Tue Nov 28 07:38:45 1995 Received: from pollux.usc.edu for separk@cs.usc.edu by www.ccl.net (8.6.10/950822.1) id HAA20457; Tue, 28 Nov 1995 07:37:28 -0500 Received: (separk@localhost) by pollux.usc.edu (8.7.1/8.6.4) id EAA22743; Tue, 28 Nov 1995 04:37:28 -0800 (PST) Date: Tue, 28 Nov 95 4:37:27 PST From: "S. Park" To: CHEMISTRY@www.ccl.net Cc: separk@pollux.usc.edu Subject: Questions about the docking problem Message-ID: Hello, I have been studying the rigid molecular docking problem and have several questions about the assumptions typically made. Since my major is computer science, I lack lots of basic knowledge on the subject and I wonder if anyone could kindly tell me about your opinion and give me any references that I could use for the study. I would really appreciate it ! Here are my questions: It seems to me that there are three assumptions for the molecular docking problem: 1. Rigidity 2. Availability of the atomic coordinates 3. Solvent effects related assumption First of all, I would like to know how "accurate" the results we have with the assumptions above. For example, I understand that the answers are "approximate" solutions for the real answer. But how reliable (or, exact, valid ?) are they ? Can we quantify this ? Secondly, it seems to me that most of the automated docking procedures make use of the atomic coordinates of the molecules. But what if we don't have their crystal structures ? How could we find the mode of binding in these cases ? Thirdly, I wonder how much information could we glean from the geometric complementarity based approach. I understand that this is a sort of "screening" process for later "energy minimization". It seems to me that geometric complementarity serves as a necessary condition for the real answer. But what if we miss the real "answer" in this "screening" step ? Finally, I wonder how reliable the result that comes from without considering the surrounding solvent is. It seems to me that one of the reasons that we don't consider the solvent effect is due to the expensive computational cost. But then how "accurate" is the result ? Thank you very much for your time ! Regards, Seongbin Park (separk@pollux.usc.edu) From owner-chemistry@ccl.net Tue Nov 28 07:42:41 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id HAA20373; Tue, 28 Nov 1995 07:29:25 -0500 Received: from monge.brunel.ac.uk for Jeffrey.Gosper@brunel.ac.uk by bedrock.ccl.net (8.7.1/950822.1) id HAA29559; Tue, 28 Nov 1995 07:29:15 -0500 (EST) From: Received: from loki.brunel.ac.uk by monge.brunel.ac.uk with SMTP (PP) id <16406-0@monge.brunel.ac.uk>; Tue, 28 Nov 1995 12:05:31 +0000 Message-Id: <20944.9511281205@loki.brunel.ac.uk> Subject: Early termination of IRC calculations To: chemistry@ccl.net Date: Tue, 28 Nov 1995 12:05:26 +0000 (GMT) X-Mailer: ELM [version 2.4 PL24] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Dear compuational colleagues, I have been performing a number of IRC calculations using Mopac 6 on an VAXstation 3520 and I have had a problem with the early termination of the IRC calculation, which was due to MOPAC running out of time. However I have provided enough time for the calculation to run to completeion and placed it on a parasitic queue that has an infinite time allowance. (See below) Also in DIMSIZES.DAT I have given the following MAXTIM=1000000, MAXDMP=21000 Also I have failed to RESTART any of these IRC calculations. If anyone has a solution please advise me ASAP. Thanks in advance Jeff Gosper ******************************************************************************* ** FRANK J. SEILER RES. LAB., U.S. AIR FORCE ACADEMY, COLO. SPGS., CO. 80840 ** ******************************************************************************* AM1 CALCULATION RESULTS ******************************************************************************* * MOPAC: VERSION 6.00 CALC'D. 27-NOV-95 * LARGE - EXPANDED OUTPUT TO BE PRINTED * X-PRIOR - GEOMETRY CHANGES TAKE PRIORITY IN DRC * RESTART - CALCULATION RESTARTED * IRC=N - INTRINSIC REACTION COORDINATE 1 DEFINED * T= - A TIME OF 0.100E+07 SECONDS REQUESTED * DUMP=N - RESTART FILE WRITTEN EVERY 25000.0 SECONDS * AM1 - THE AM1 HAMILTONIAN TO BE USED * PRECISE - CRITERIA TO BE INCREASED BY 100 TIMES * ISOTOPE - FORCE MATRIX WRITTEN TO DISK (CHAN. 9 ) ***********************************************************************043BY043 AM1 PRECISE ISOTOPE T=1000000 IRC=1 LARGE X-PRIO RESTART TS optimized FINAL HEAT OF FORMATION = -57.83639 KCAL ......Z-matrix cut from here ......output for numerous cycles appears then RUNNING OUT OF TIME, RESTART FILE WRITTEN GEOMETRY AND VELOCITY ARE IN RESTART FILE IN ASCII TOTAL CPU TIME: 75008.92 SECONDS == MOPAC DONE == From andreas@majestix.msp.univie.ac.at Tue Nov 28 08:38:41 1995 Received: from majestix.msp.univie.ac.at for andreas@majestix.msp.univie.ac.at by www.ccl.net (8.6.10/950822.1) id IAA21301; Tue, 28 Nov 1995 08:28:11 -0500 Received: by majestix.msp.univie.ac.at (940816.SGI.8.6.9/940406.SGI.AUTO) id OAA11413; Tue, 28 Nov 1995 14:26:40 +0100 From: "Andreas Parusel" Message-Id: <9511281426.ZM11411@majestix.msp.univie.ac.at> Date: Tue, 28 Nov 1995 14:26:36 +0100 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@www.ccl.net, pm@katz.cc.univie.ac.at Subject: Excited States with GAUSSIAN Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear Sirs! I am posting here just for an information. If anybody is working with the GAUSSIAN94 programm and its use for calculation of excited states and/or the fluorescence, i'd be glad if he could contact me for some questions! Thanks a lot for everybody in advance! Andreas Parusel, Vienna -- ======================================================================= _/_/ _/_/ andreas@majestix.msp.univie.ac.at = _/ _/_/ _/ andreas@phys-chemie.uni-wuerzburg.de = _/ _/_/ _/ parusel@aries.scs.uiuc.edu = _/_/ _/_/ = = Andreas Parusel Institut fuer Theoretische Chemie = Drorygasse 15/27 Althanstr. 14 = A-1030 Wien A-1030 Wien = +43 1 7519244 Tel +43 1 31336 1572 = ======================================================================= From bernhard@quant1.chemie.uni-leipzig.de Tue Nov 28 08:53:42 1995 Received: from quant1.chemie.uni-leipzig.de for bernhard@quant1.chemie.uni-leipzig.de by www.ccl.net (8.6.10/950822.1) id IAA21526; Tue, 28 Nov 1995 08:40:26 -0500 From: Received: by quant1.chemie.uni-leipzig.de (AIX 3.2/UCB 5.64/4.03) id AA15346; Tue, 28 Nov 1995 13:20:51 +0100 Message-Id: <9511281220.AA15346@quant1.chemie.uni-leipzig.de> To: Uli Salzner Cc: ccl , bernhard@quant1.chemie.uni-leipzig.de Subject: Re:DFT/spurious integrated densities In-Reply-To: (Your message of Fri, 24 Nov 95 13:22:28 -0330.) Date: Tue, 28 Nov 95 13:20:51 +0100 Hi, few weeks ago i struggle over the same problem. I got the tip to add the keywords SCF=NoVarACC INT=FineGrid which work in ca. 90% of all cases (using B3LYP). The first is not fully known to me (didn't find the keyword in the g92 manual), but i think it enhance the accuracy of the integrals or is related to this point, the second point results in better numerics while integration. Don't take it for good, i'm just a starter... If this doesn't work, then a slight alteration of the geometry helps sometime (nearly in all remaining cases). Bernhard Eck From moshe_o@VNET.IBM.COM Tue Nov 28 10:08:42 1995 Received: from VNET.IBM.COM for moshe_o@VNET.IBM.COM by www.ccl.net (8.6.10/950822.1) id JAA23211; Tue, 28 Nov 1995 09:55:50 -0500 Message-Id: <199511281455.JAA23211@www.ccl.net> Received: from HAIFASC3 by VNET.IBM.COM (IBM VM SMTP V2R3) with BSMTP id 4117; Tue, 28 Nov 95 09:55:42 EST Date: Tue, 28 Nov 95 16:36:37 IST From: "Moshe Olshansky" To: chemistry@www.ccl.net Subject: combining different basis sets - an addition Dear netters! After posting the summary of the responses I got an additional note which may be of interest to some of you. Here it is: - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Date: Mon, 27 Nov 1995 16:23:15 -0330 (NST) From: Uli Salzner Subject: basis set mixing Dear Moshe, I just read read the answers you received according basis set mixing and I think one important point was not addressed. It is definetly important that a basis set has to be balanced but that does not mean that you have to use the same basis set for each atom. In fact, to use the "same" basis set for different atoms may be the perfect way to get an unbalanced basis set. For example: consider the calculation of an ionic compound such as LiF. If you use 6-31G* on both atoms, you have a very good basis set for Li. Since Li looses about 90% of its 2s electron (maybe even more) when bound to F, it has almost no electrons in the 2s and 2p. For such a cation a valence double zeta basis set is very good. On the other hand fluorine is an anion with a diffuse charge distribution. For an anion the 6-31G* basis set quite bad. What you get is spurious charge transfer >from F to Li. Thus, one uses different basis sets for different atoms all the time even if they have the same name. What you have to figure out is how to combine different basis sets in the right way. For the above example it would be a improvement to use 6-31+G* on F. This gives a better balanced basis set than 6-31G* on both atoms. Similar arguments hold for polarization functions. You have to decide which atoms need them and which don't. For instance for third row systems you definetely need d-functions. But there is no problem to combine a sulfer basis set with d-functions with hydrogen basis set that contains only s-functions because hydrogen d-orbitals are so high in energy that the effect would be negligible. Bets wishes, Uli Salzner uli@smaug.physics.mun.ca - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - P.S. and now I have an additional question: I am a mathematician, not a chemist, so let me look at the basis sets purely mathematically. If one has a complete (and hence necessarily infinite) basis set, he/she gets a limit of Hartree-Fock model. Otherwise (with limited basis set) one gets some approximation to this limit and the more complete the basis set is the better is the approximation. Now assume one uses a certain "standard" basis set and gets some result (from Hartree-Fock model). And now we add ANY additional function to this basis set. This does not make the basis set less complete and so it should lead to at least as good (or even better) an approximation as the original basis did (it is also possible to get the original solution by taking that additional function with zero coefficient for every electron). Is there anything wrong with this statement? Moshe Olshansky IBM Israel Science & Technology From WILLSD@conrad.appstate.edu Tue Nov 28 11:08:42 1995 Received: from listserv.appstate.edu for WILLSD@conrad.appstate.edu by www.ccl.net (8.6.10/950822.1) id KAA23965; Tue, 28 Nov 1995 10:53:46 -0500 Received: from VX8550.APPSTATE.EDU ([152.10.1.2]) by listserv.appstate.edu with ESMTP id <10464-3>; Tue, 28 Nov 1995 10:53:42 -0500 Received: from conrad.appstate.edu by conrad.appstate.edu (PMDF V5.0-3 #8642) id <01HY69Y44PY894DPHX@conrad.appstate.edu>; Tue, 28 Nov 1995 10:51:16 -0400 (EDT) Date: Tue, 28 Nov 1995 10:51:13 -0400 (EDT) From: willsd@conrad.appstate.edu Subject: Re: CCL:NMR calculation-ISOTROPIC and ANITROSOPY In-reply-to: <9511280429.AA02822@utsc.s.u-tokyo.ac.jp> Sender: WILLSD@conrad.appstate.edu To: Mori Seiji Cc: chemistry@www.ccl.net, smori@utsc.s.u-tokyo.ac.jp, help@gaussian.com Message-id: MIME-version: 1.0 Content-type: TEXT/PLAIN; charset=US-ASCII Content-transfer-encoding: 7BIT On Tue, 28 Nov 1995, Mori Seiji wrote: > Dear Sirs, > > I posted to CCL about the methods of NMR calculation a fey days ago , and > had an other question. > In G94, I tried to calculate the chemical shifts , there are magnetic > shieldings snip... > Would you please tell me the physical meaning of isotropic and anitrosopy, > and which is an equivalent of the experimental chemical shift? It is better > that > you show the references. > > Sincerely yours, > Seiji Mori > #################################################### > snip... > email:smori@chem.s.u-tokyo.ac.jp Seiji: I ran into this proble recently and have a suggestion: 1) You need the isotropic part of the shielding tensor. 2) Chemical shifts can be calculated from this isotropic part using some simple theory: I recommend the information in chapter 2 of : Multinuclear NMR, J. Mason Ed., Plenum Press, New York, 1987. You will also need the isotropic shielding for the chemical shift standard for your nucleus. (In my case it was (EtO)2.BF3 for 11B NMR). Steve Williams Chemistry Appalachian State University Boone, NC 28608 willsd@appstate.edu From Yue@biotech.lan.nrc.ca Tue Nov 28 11:53:57 1995 Received: from nrcnet0.nrc.ca for Yue@biotech.lan.nrc.ca by www.ccl.net (8.6.10/950822.1) id LAA25240; Tue, 28 Nov 1995 11:53:13 -0500 Received: from coursmtp.nrc.ca by nrcnet0.nrc.ca with SMTP id AA18680 (5.67b/IDA-1.5 for ); Tue, 28 Nov 1995 11:53:12 -0500 Received: by coursmtp.nrc.ca with Microsoft Mail id <30BB3E8A@coursmtp.nrc.ca>; Tue, 28 Nov 95 11:53:30 EST From: "Yue, Shi-Yi (*ASTRA)" To: ccl Subject: MD trajectory presentation on Mac Date: Tue, 28 Nov 95 11:51:00 EST Message-Id: <30BB3E8A@coursmtp.nrc.ca> Encoding: 14 TEXT X-Mailer: Microsoft Mail V3.0 Hello everybody, I am looking a software on Mac which can be used to present trajectory files of molecular dynamics simulation >from Unix systems. Any comments and suggestions are welcome. Thank you in advance! shiyi yue yue@biotech.lan.nrc.ca