From cdac.ernet.in!gadre@parcom.ernet.in Fri May 15 02:31:04 1998 Received: from naveen.ncst.ernet.in for cdac.ernet.in!gadre@parcom.ernet.in by www.ccl.net (8.8.3/950822.1) id CAA14956; Fri, 15 May 1998 02:03:58 -0400 (EDT) Received: from iucaa (iucaa.ernet.in [202.141.155.1]) by naveen.ncst.ernet.in (8.6.12/8.6.6) with SMTP id LAA10767 for ; Fri, 15 May 1998 11:43:24 +0530 Received: from iucaa by iucaa (5.65v3.2/SMI-4.1) id AA27706; Fri, 15 May 1998 11:30:46 +0500 Received: by parcom.cdac.ernet.in (4.1/SMI-4.1) id AA09955; Fri May 15 11:07:45 1998 (GMT + 0530) Date: Fri May 15 11:07:45 1998 (GMT + 0530) From: gadre@cdac.ernet.in Message-Id: <9805150537.AA09955@parcom.cdac.ernet.in> To: CHEMISTRY@www.ccl.net Subject: SO2-CO2 complex Dear Sirs/Madams : I am interested in understanding weak interaction in the SO2...CO2 binary complex. Apart from the work of Prof. R.L. Kuczkowski regarding structure determination by FTMS, I am unaware of the literature in this area. I would appreciate any recent experimental/theoretical reports on this system. Thank you very much. Shridhar R. Gadre Department of Chemistry University of Pune, India. From chan@uni-muenster.de Fri May 15 06:31:06 1998 Received: from asterix.uni-muenster.de for chan@uni-muenster.de by www.ccl.net (8.8.3/950822.1) id FAA15587; Fri, 15 May 1998 05:58:26 -0400 (EDT) Received: from localhost (chan@localhost) by asterix.uni-muenster.de (8.8.7/8.7.5) with SMTP id JAA99964 for ; Fri, 15 May 1998 09:58:25 GMT X-Authentication-Warning: asterix.uni-muenster.de: chan owned process doing -bs Date: Fri, 15 May 1998 11:58:25 +0200 (MES) From: "Jerry C.C. Chan" To: chemistry@www.ccl.net Subject: 31P chemical shielding calculation Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi Netters, I would like to make a literature search on the 31P chemical shielding tensor calculation (DFT, ab inito). Could anyone send me pointers to the latest works or reviews? Thanks, Jerry ****************************************************************** * Jerry Chun Chung CHAN chan@moorea.uni-muenster.de * * * * Universitaet Muenster phone: 0049-251-83-29156 * * Institut fuer Physikalische Chemie fax: 0049-251-83-29159 * * Schlossplatz 4-7 * * D-48149 Muenster * * Germany * ****************************************************************** From wdi@mail2.organik.uni-erlangen.de Fri May 15 08:31:08 1998 Received: from faui45.informatik.uni-erlangen.de for wdi@mail2.organik.uni-erlangen.de by www.ccl.net (8.8.3/950822.1) id HAA15986; Fri, 15 May 1998 07:53:35 -0400 (EDT) Received: from mail2.organik.uni-erlangen.de (lesath.organik.uni-erlangen.de [131.188.128.10]) by faui45.informatik.uni-erlangen.de (8.8.8/8.1.16-FAU) with ESMTP id NAA22307 for ; Fri, 15 May 1998 13:53:23 +0200 (MET DST) Received: from wtewael.organik.uni-erlangen.de (wtewael [131.188.128.216]) by mail2.organik.uni-erlangen.de (8.8.8/8.1.4-FAU) with ESMTP id NAA20621; Fri, 15 May 1998 13:53:06 +0200 (MET DST) Received: (from wdi@localhost) by wtewael.organik.uni-erlangen.de (8.8.7/8.1.59-FAU) id LAA03536; Fri, 15 May 1998 11:52:01 GMT From: "Wolf-Dietrich Ihlenfeldt" Message-Id: <9805151352.ZM3534@torvs.ccc.uni-erlangen.de> Date: Fri, 15 May 1998 13:52:00 -0600 In-Reply-To: Rochus Schmid "CCL:molecular builder" (May 12, 18:41) References: Reply-To: Wolf-Dietrich.Ihlenfeldt@CCC.Chemie.Uni-Erlangen.DE X-Phones: +49-9131-85-6579 X-Fax: +49-9131-85-6566 X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: Rochus Schmid Subject: Re: CCL:molecular builder Cc: CHEMISTRY@www.ccl.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 8bit On May 12, 18:41, Rochus Schmid wrote: > Subject: CCL:molecular builder > > Dear Netters, > > Please forgive me for asking that question, which came up a couple of > times already, I know. But I am desperate and my question is rather > specific: > > I am searching for a (simple!!!, 3D!) molecular builder: > > - it should run under UNIX/X and be free (I know cerius2 and insightII > and and and ....) > > - it should be very simple (I don't need ruberbands, rayshading etc. and > it is only for a couple of atoms and not for > proteins) > > - it should be able to add or delete atoms by mouse and change bond > length, angles and dihedrals by selecting the atoms. > > - it should be able to read and write the stuff as pdb or xyz or whatever > > I follow this mailing list for quite a while now and similar questions > came up quite often, I know. > > So I know about gopenmol and xmol and viewmol and molden and vmd and a > couple more. But none of these programs is what I'm looking for. > > To make that more clear: > I really like xmol. It's simple and free etc. but you can't build > molecules. > > And I really liked the UNICHEM interface by Cray. This was perfect to me > but it is not free ;-) > > Is there anything on this beautifull world like that?? > I can't believe, that I'm the only one who needs that kind of software. > > Thanks in advance for any comment or hint. > Happy computing, > > Rochus Have your tried the free WWW- or Email-based CORINA service? http://www2.ccc.uni-erlangen.de/corina/ > >-- End of excerpt from Rochus Schmid -- Dr. Wolf-D. Ihlenfeldt Computer Chemistry Center, University of Erlangen-Nuernberg Naegelsbachstrasse 25, D-91052 Erlangen (Germany) Tel (+49)-(0)9131-85-6579 Fax (+49)-(0)9131-85-6566 From brupalf@umich.edu Fri May 15 09:31:09 1998 Received: from berzerk.rs.itd.umich.edu for brupalf@umich.edu by www.ccl.net (8.8.3/950822.1) id JAA16374; Fri, 15 May 1998 09:13:29 -0400 (EDT) Received: from seawolf.rs.itd.umich.edu (smtp@seawolf.rs.itd.umich.edu [141.211.63.88]) by berzerk.rs.itd.umich.edu (8.8.8/4.3-mailhub) with ESMTP id JAA22542 for ; Fri, 15 May 1998 09:13:25 -0400 (EDT) Received: from localhost (brupalf@localhost) by seawolf.rs.itd.umich.edu (8.8.8/5.1-client) with SMTP id JAA16835 for ; Fri, 15 May 1998 09:13:24 -0400 (EDT) Precedence: first-class Date: Fri, 15 May 1998 09:13:24 -0400 (EDT) From: Bruce Allan Palfey X-Sender: brupalf@seawolf.rs.itd.umich.edu To: chemistry@www.ccl.net Subject: LBHBs Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Status: RO Content-Length: 11061 Thanks to all of you who replied concerning my question on simulating Low Barrier Hydrogen Bonds (LBHB) by MM methods. It seems that the majority of those responding don't expect good results, and that nothing short of ab initio calculations will do the job. Several people expressed interest in references on LBHBs. A heated debate has been in progress in enzymology over the past several years. A good, concise overview of the field, with lots of leading references, can be found in Pan & McAllister (1997) Journal of Organic Chemistry, 62, 8171-8176. The inability of MM methods to handle LBHBs raises a (potentially) bothersome point. The refinement of macromolecular structures in X-ray crystallography and NMR generally uses an MM force field, e.g., the CHARMm force field in the ubiquitous X-plor. Can structures of molecules that contain LBHBs determined this way be considered accurate if the force field used in solving the structure is not accurate? Perhaps this only leads to errors localized to the region of the LBHB, but since these generally occur at the enzyme active site (the region where the highest accuracy is desirable), this situation may not be satisfactory. Any comments? ciao, Bruce ***************************************************************************** My original post: Over the past few years, low barrier hydrogen bonds (LBHB for short) have received a fair amount of attention in enzymology. They are characterized by being short, having low isotopic fractionation factors, and very large proton NMR chemical shifts. Some say that they are extremely favorable energetically and hence an important "tool" used by enzymes in catalysis, while others disagree. I was wondering if anyone could tell me whether the common molecular mechanics force fields could be expected to properly model LBHB. Can one expect AMBER, CHARMm, etc., to accurately predict the LBHB lengths and frequencies? Or are these bonds unusual enough that new terms need to be included? ***************************************************************************** From: "Samuel A. Abrash" To: 'Bruce Allan Palfey' Subject: RE: low barrier hydrogen bonds Dear Dr. Palfey, I am very interested in the responses to your question, because I was under the impression that MM models could not accurately predict any bond lengths and frequencies involving weak intermolecular forces. I know that these can be obtained with reasonable accuracy using medium sized gaussian basis sets and hybrid density functional theories, but was not aware that any degree of accuracy could be obtained with lower levels of theory. However, my expertise tends toward either ab initio work or experiment, so I may be sadly misinformed about the state of the art in molecular mechanics calculations. If I am correct, though, one thing that might interest you is a new option within Gaussian 98 which allows you to use different levels of theory on different portions of a molecule (ONIOM). This method was developed by the group of Keiji Morokuma at Emory, and would allow you to use a relatively high level of theory to treat the low barrier hydrogen bonds, while using successively lower levels of theory to treat the rest of the molecule. Thank you for tolerating my ignorance of MM methods. Best regards, Sam Abrash sabrash@richmond.edu ***************************************************************************** Date: Fri, 8 May 1998 19:04:21 +0200 (MET DST) From: "J.Lin" To: brupalf@umich.edu Subject: Re: CCL:low barrier hydrogen bonds Dear Bruce, > Over the past few years, low barrier hydrogen bonds (LBHB for short) have ^^^^^^^^^^^^^^^^^^^^^^^^^^ Could you give some references? > received a fair amount of attention in enzymology. They are characterized > by being short, having low isotopic fractionation factors, and very large ^^^^^ shorter than normal hydrogen bond? > proton NMR chemical shifts. Some say that they are extremely favorable > energetically and hence an important "tool" used by enzymes in catalysis, > while others disagree. I was wondering if anyone could tell me whether > the common molecular mechanics force fields could be expected to properly > model LBHB. Can one expect AMBER, CHARMm, etc., to accurately predict the > LBHB lengths and frequencies? Or are these bonds unusual enough that new > terms need to be included? In AMBER '91 parameters set, there are still hydrogen bond parameters with 12-10 functional form, but in new AMBER '94 and '96 parameters they are already absorbed into electrostatic and Lennard-Jones (12-6) interactions. It means, the direction of force field development of AMBER is trying to avoid unnecessary functional terms and parameters. Sorry that I'm not an expert on LBHB and could not tell you if AMBER can do this job. In my personal speculation I would say if the LBHB effect is not very quantum-mechanical, one can try to optimize the parameters to describe his system. regards, Jung-hsin -- -------------------------------------------------------------------------------- Jung-hsin Lin Forum Modellierung und Institut fuer Festkoerperforschung Forschungszentrum Juelich GmbH. D-52425 Juelich. Germany Phone (Office): +49-2461-61-2515; Fax: - 2983; email: j.lin@fz-juelich.de Phone/Fax (Home): +49-2461-54419; Addr: Muenchener Str. 5, D-52428 Juelich, Germany ------------------------------------------------------------------------------ ***************************************************************************** Date: Fri, 08 May 98 14:24:47 EDT From: Janet Del Bene To: brupalf@UMICH.EDU Subject: Low-barrier hydrogen bonds Hi, Bruce, Realistic descriptions of "normal" hydrogen bonds are often lacking using the empirical/semi-empirical levels of theory, and even low-levels of ab initio theory. So, I do not think that these methods could give consistently reliable descriptions of the so-called "LBHB". I am actually looking into this area, motivated primarily by one of the biochemists at this University. Janet E. Del Bene ***************************************************************************** Date: Fri, 8 May 1998 13:55:44 -0500 (CDT) From: Michael A McAllister To: Bruce Allan Palfey Subject: Re: CCL:low barrier hydrogen bonds Hello Brian, I was very interested to see your message on CCL. We have been interested in LBHBs from a computational standpoint for a few years now, mostly at the non-empirical level. There is no doubt that current force fields would NOT be able to accurately model any kind of strong H-bond interaction. We have looked at some semi-empirical models and even these are substantially lacking in accuracy. One of our current interests/projects is to actually incorporate some decent force field parameters for "LBHB" type hydrogens into common FFs. As far as I know, this has not been done yet. Mike M. ************************************************************************** Michael A. McAllister Assistant Professor of Chemistry voice: 940-565-4584 University of North Texas fax: 940-565-4318 P.O. Box 305070 email: McAllister@unt.edu Denton, TX 76203 www: http://people.unt.edu/~mam0008 ************************************************************************** ***************************************************************************** Date: Sat, 9 May 1998 01:20:23 -0700 From: Jiangang Chen To: Bruce Allan Palfey Cc: Achim Kless Subject: Re: CCL:low barrier hydrogen bonds Dear Bruce, Common force field methods model the hydrogen bonding with classical electrostatical method. However, Low barrier hydorgen bond has large covalent character. I doubt that calculation with existing force field parameters could capture the correct energetics of low barrier hydorgen bond. Jiangang Chen UCLA ***************************************************************************** Date: Mon, 11 May 1998 09:28:17 +0010 From: Andrey Bliznyuk To: brupalf@umich.edu Cc: Andrey.Bliznyuk@anu.edu.au Subject: Re: CCL:low barrier hydrogen bonds Hi, > Over the past few years, low barrier hydrogen bonds (LBHB for short) > have received a fair amount of attention in enzymology. They are > characterized by being short, having low isotopic fractionation > factors, and very large proton NMR chemical shifts. Some say that > they are extremely favorable energetically and hence an important > "tool" used by enzymes in catalysis, while others disagree. The name low barrier hydrogen bonds appeared simply because some people did not know what they are talking about and jumped to discover the wonders of enzyme catalysis. The proper name for these bonds is charged H-bonds, which are known to be strong and there have been plenty on literature on this subject both experimental and theoretical (for somewhat outdated review see, for example, A.A. Voityuk & A.A. Bliznyuk, Zh. Struct. Khim, 1992, 33(6), pp. 157-183). The physical chemist community was simply stunned by ignorance of published articles and did not respond immediately. However, two paper seems to close the subject: JACS, 1995, 117, pp.6970-6975 Chemistry and Biology, 1996, 3, pp.163-170. > I was > wondering if anyone could tell me whether the common molecular > mechanics force fields could be expected to properly model LBHB. > Can one expect AMBER, CHARMm, etc., to accurately predict the LBHB > lengths and frequencies? Or are these bonds unusual enough that new > terms need to be included? There is nothing unusual about these bonds from the computational point of view, and all MM force fields would treat the energy of these bonds more or less correctly. Of course, the charge transfer will not be taken into account, and hence the results will not be exceptionally good, but it is well known problem with MM approaches. And if the total energy or geometry is what you are looking for, then it is not too bad. Andrey Dr. Andrey Bliznyuk ANU Supercomputer Facility IT services The Australian National University Canberra, ACT 0200 Australia Email: Andrey.Bliznyuk@anu.edu.au ***************************************************************************** Date: Wed, 13 May 1998 10:19:33 -0700 (MST) From: Soaring Bear To: chemistry@www.ccl.net Subject: CCL:CCL:low barrier hydrogen bonds Considering how variable crystal hydrogen bonds are [see Gilli in "Fund Princ of Molec Modeling" ed W Gans 1996 and GA Jeffrey & W Saenger "Hydrogen Bonding in Biol. Structures" 1991] modeling forcefields can only be expected to be an approximation. ^[[7m^[[5mSOARING BEAR^[[0m PhD bear@pharmacy.arizona.edu Computational Medicinal Chemistry; Molecular Modeling; Pharmacognosy Protein & DNA Structural Biology; Cancer Biochemistry; Informatics; QSAR http://ellington.pharmacy.arizona.edu/~bear/resume.html currently seeking employment From hyzhang@carb.nist.gov Fri May 15 14:31:11 1998 Received: from tabasco.carb.nist.gov for hyzhang@carb.nist.gov by www.ccl.net (8.8.3/950822.1) id OAA18178; Fri, 15 May 1998 14:09:37 -0400 (EDT) Received: from localhost (hyzhang@localhost) by tabasco.carb.nist.gov (8.7.5/8.7.3) with SMTP id OAA07673 for ; Fri, 15 May 1998 14:11:03 -0400 (EDT) X-Authentication-Warning: tabasco.carb.nist.gov: hyzhang owned process doing -bs Date: Fri, 15 May 1998 14:11:03 -0400 (EDT) From: Hongyu Zhang To: COMP_CHEM_LIST Subject: Threading template from SCOP Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Status: RO Content-Length: 706 Dear all, We want to build a threading template set from SCOP, i.e., each template is a representative structure of a SCOP family or superfamily. Does anyone know if there is such a set somewhere, so I would not reinvent the wheel? Appreciate your time ! --Hongyu ------------------------------------------------------------------ Hongyu Zhang, Ph.D. | Tel: (301) 738-6117 (w) ^/..\^ CARB, University of Maryland | (301) 987-0179 (h) -m( 00 )m- 9600 Gudelsky Drive | Fax: (301) 738-6255 Rockville, Maryland 20850 | Email: hyzhang@carb.nist.gov URL: http://indigo5.carb.nist.gov/~hyzhang ------------------------------------------------------------------ From pang@iris.chem.cuhk.edu.hk Sat May 16 03:31:18 1998 Received: from iris.chem.cuhk.edu.hk for pang@iris.chem.cuhk.edu.hk by www.ccl.net (8.8.3/950822.1) id DAA23746; Sat, 16 May 1998 03:25:06 -0400 (EDT) Received: by iris.chem.cuhk.edu.hk (940816.SGI.8.6.9/940406.SGI.AUTO) id PAA01631; Sat, 16 May 1998 15:26:28 +0800 Date: Sat, 16 May 1998 15:26:24 +0800 (HKT) From: Pang Siu Kwong To: chemistry@www.ccl.net Subject: Full Linear Search and Maximum Rotation Gradient Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello! In Guaussian 94, there are three techniques, SD, SSD and QC, for convergence. How does the "Full Linear Search" affect the convergence when using these techniques? If the convergence problem encounters, does the "Full Linear Search" help? Furthermore, how does the Maximum Rotation Gradient affect the QC? If the convergence problem encounters, does change the value of "Maximum Rotation Gradient" for solving this problem? Thank your for your attention. P. Pang From A_SALEM@FRCU.EUN.EG Sat May 16 05:31:18 1998 Received: from FRCU.EUN.EG for A_SALEM@FRCU.EUN.EG by www.ccl.net (8.8.3/950822.1) id FAA23929; Sat, 16 May 1998 05:03:19 -0400 (EDT) From: Received: from FRCU.EUN.EG by FRCU.EUN.EG (PMDF V5.1-9 #20502) id <01IX3MQG2AVK000LVQ@FRCU.EUN.EG> for chemistry@www.ccl.net; Sat, 16 May 1998 12:02:55 +0200 Date: Sat, 16 May 1998 12:02:54 +0200 Subject: Chemistry Courses To: chemistry@www.ccl.net Message-id: <01IX3MQG9SXU000LVQ@FRCU.EUN.EG> X-VMS-To: IN%"chemistry@www.ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Dear CCl collegues I am doing a comparative study about teaching Chemistry for pre- and post-graduate level. This is in the frame of our university effort for developing University education. All Chemistry topics including Computational, Analytical, Organic, Physical and Inorganic,....etc are required. Therefore, I would be so grateful for all who will reply me with chemistry syllabus at their universities. Data from Europe, USA, Cnada, ...other places are required. I aslo would be so grateful for reffering me to any site at the internet where one can find such information. REsults will be statistically treated, summarized and posted to the CCL. Yours sincerely Dr. Alaa Salem Depart. Chemistry Faculty of Science Cairo University Egypt. From arno@almaak.usc.edu Mon May 18 15:33:23 1998 Received: from almaak.usc.edu (almaak.usc.edu [128.125.253.166]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id PAA07312 for ; Mon, 18 May 1998 15:33:22 -0400 (EDT) Received: from localhost (arno@localhost) by almaak.usc.edu (8.8.8/8.8.8/usc) with SMTP id MAA22080; Mon, 18 May 1998 12:33:22 -0700 (PDT) Date: Mon, 18 May 1998 12:33:22 -0700 (PDT) From: Arno Papazyan Reply-To: Arno Papazyan To: Bruce Allan Palfey cc: chemistry@www.ccl.net Subject: Re: CCL:low barrier hydrogen bonds In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Sorry for jumping into the LBHB thread so late. I have been away for a CECAM workshop, and now I am writing this message from a yet another country. In order to ask meaningful questions on LBHBs, we first have to know what they are. Perhaps surprisingly, not all "low-barrier" hydrogen bonds are "low-barrier hydrogen bonds" !! The original LBHB hypothesis in enzyme catalysis was not clear about the distinction between "regular" or "ordinary" HBs and LBHBs, other than the fact that LBHBs had a low barrier for proton motion in the HB. However, since the barrier itself is basically irrelevant to enzyme catalysis other than as a rough correlator of bond energy (but not even as an indicator of relative stabilities of alternative HB+environment configurations), and using the bond energy or relative stability would be circular, one has to define LBHBs in terms of their source of stabilization. We can decompose an HB into its "electrostatic" and "covalent" contributions. An "ordinary" HB (OHB) has both electrostatic and covalent components, although it can be reasonably modelled by classical force fields by dumping everything into electrostatic parameters. An OHB can be neutral or charged. A charged HB is often stronger than the neutral variety, and this difference can often be explained electrostatically. So, usually there is nothing unusual or non-"ordinary" about a strong, short HB (very often with little or no barrier to proton motion). The only true distinction would come from an unusually large "covalent" or "purely quantum mechanical" contribution to the bond energy. Thus one should understand that most (if not the vast majority) of the so-called "LBHB"s are plain, old, mundane, ordinary HBs! ;-) And therefore somewhat modellable by classical force fields to the same extent that they have been until now ;-) Of course, why anyone would get excited over an already-well-known effect in enzyme catalysis is another matter! ;-) As for catching anomalously high covalent contributions, obviously something quantum mechanical should be done. My humble opinion on this is that a well-calibrated Empirical Valence Bond approach would be a natural choice. A super- duper hyper-expensive "traditional" quantum calculation need not be used directly, but rather as a calibration for the EVB description, which may then be used quite reliably to your hearts content. This makes catching a true LBHB "almost" accessible to force-field simulations. To end this note, let me re-emphasize that without distinguishing charged HBs from LBHBs, and without representing the solvation of the system accurately, One should not even try working on this question. Regards to all, Arno Papazyan From David.DeVito@chiphy.unige.ch Tue May 19 02:45:30 1998 Received: from sc2a.unige.ch (sc2a.unige.ch [129.194.48.4]) by ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id CAA11879 for ; Tue, 19 May 1998 02:45:29 -0400 (EDT) Received: from PCC2340E.unige.ch ([129.194.52.14]) by sc2a.unige.ch (PMDF V5.1-10 #10385) with SMTP id <01IX7MQ21TM2000O69@sc2a.unige.ch> for chemistry@www.ccl.net; Tue, 19 May 1998 08:45:27 MET Date: Tue, 19 May 1998 08:45:05 +0200 From: David De Vito Subject: Question about CERIUS 2 To: CCL Message-id: <003d01bd82f1$a8e43820$0e34c281@PCC2340E.unige.ch> MIME-version: 1.0 X-Mailer: Microsoft Outlook Express 4.72.2106.4 Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: 7bit X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 X-Priority: 3 We have purchased the Cerius 2 programm package and I have a little question about it. I tried to use the 'free volume' calculation option and I'd like to know how the programm make this evaluation since I don't find any information about it in the help and manuals. The help support said me since we don't have any "maintenance" we can't obtain any answer in case of problems... That's a pity, really ! Thanks in advance for the very helpfully explanations and best regards. Nice day for all the CCL people, D. De Vito. **************************************************************** D. De Vito Department of Physical Chemistry Group of Prof. Weber (Computational Chemistry) University of Geneva Office 106 - Sciences II 30, Quai Ernest-Ansermet 1211 Geneva 4 / Switzerland +4122 / 702.65.35 (Office) +4179 / 310.05.76 (Mobile) +4122 / 733.38.35 (Home) http://lcta.unige.ch/~devito (Personal Page) http://www.unige.ch/sciences/chimie (Web Master) **************************************************************** From spoel@xray.bmc.uu.se Tue May 19 03:57:58 1998 Received: from hermes.bmc.uu.se (hermes.bmc.uu.se [130.238.39.159]) by ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id DAA12268 for ; Tue, 19 May 1998 03:57:57 -0400 (EDT) Received: from alpha2.bmc.uu.se ([130.238.37.65]) by hermes.bmc.uu.se (post.office MTA v2.0 0813 ID# 0-17733) with SMTP id AAA18788; Tue, 19 May 1998 09:55:56 +0200 Received: from munch.bmc.uu.se by alpha2.bmc.uu.se; (5.65v3.2/1.1.8.2/30Jan97-1111AM) id AA04502; Tue, 19 May 1998 09:57:53 +0200 Date: Tue, 19 May 1998 09:57:53 +0200 (MET DST) From: David van der Spoel X-Sender: spoel@munch To: Bruce Allan Palfey Cc: chemistry@www.ccl.net Subject: Re: CCL:LBHBs In-Reply-To: Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Fri, 15 May 1998, Bruce Allan Palfey wrote: > >Thanks to all of you who replied concerning my question on simulating >Low Barrier Hydrogen Bonds (LBHB) by MM methods. It seems that the >majority of those responding don't expect good results, and that nothing >short of ab initio calculations will do the job. Several people >expressed interest in references on LBHBs. A heated debate has been in >progress in enzymology over the past several years. A good, concise >overview of the field, with lots of leading references, can be found in >Pan & McAllister (1997) Journal of Organic Chemistry, 62, 8171-8176. > >The inability of MM methods to handle LBHBs raises a (potentially) >bothersome point. The refinement of macromolecular structures in X-ray >crystallography and NMR generally uses an MM force field, e.g., the >CHARMm force field in the ubiquitous X-plor. Can structures of >molecules that contain LBHBs determined this way be considered accurate >if the force field used in solving the structure is not accurate? >Perhaps this only leads to errors localized to the region of the LBHB, >but since these generally occur at the enzyme active site (the region >where the highest accuracy is desirable), this situation may not be >satisfactory. Any comments? > >ciao, >Bruce > You are probably aware that the force field is only an aid in structure determination, in that it provides bond lengths, angles etc. Often nonbonded interactions are discarded in the final stages of refinement. Furthermore X-ray can not see protons unless the resolution is well under one Angstrom. NMR does see protons, but the accuracy is not of the order of a few tenths of an Angstrom. In other words, I don't think that force fields devaluate the accuracy of structures, this is entirely determined by the accuracy of the experimental data (and the skills of the experimentalist). Finally I would like to add (like one of the last contributors) that the concept of "LBHB" is not well defined, as there is a continuous range in hydrogen bond lengths and energies, and besides that, at a given temperature there are fluctuations in these properties as well. Groeten, David. ________________________________________________________________________ Dr. David van der Spoel Biomedical center, Dept. of Biochemistry s-mail: Husargatan 3, Box 576, 75123 Uppsala, Sweden e-mail: spoel@xray.bmc.uu.se www: http://zorn.bmc.uu.se/~spoel phone: 46 18 471 4205 fax: 46 18 511 755 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From Robert.S.DeWitte@abbott.com Tue May 19 09:26:14 1998 Received: from host241.abbott.com (host241.abbott.com [207.140.194.241]) by ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id JAA15010 for ; Tue, 19 May 1998 09:26:14 -0400 (EDT) Received: by host241.abbott.com id AA23934 (InterLock SMTP Gateway 3.0 for chemistry@www.ccl.net); Tue, 19 May 1998 08:26:14 -0500 Received: by host241.abbott.com (Internal Mail Agent-2); Tue, 19 May 1998 08:26:14 -0500 Received: by host241.abbott.com (Internal Mail Agent-1); Tue, 19 May 1998 08:26:14 -0500 From: "DeWitte,Robert" To: Subject: Java Beans/Classes for Chemical Computation Message-Id: <0017000007534450000002L002*@MHS> Date: Tue, 19 May 1998 08:26:12 -0500 Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by ccl.net id JAA15010 Hi CCL List, We are currently trying to design/build a seamless environment for chemical computation in pharmaceutical discovery using modern distributed object technology (Java, Beans, CORBA, ...) and would like to avoid reinventing any wheels that we could acquire through vendors. Does anyone have any experience with Vendor supplied Java Beans and/or Classes for Chemical Computation and/or Data Visualization? If you are a vendor with something to offer, please contact me. If you are a vendor looking for a client to drive an internal project in the above direction, please contact me. Thanks, Robert S. DeWitte, Ph.D. Computer Aided Molecular Design Pharmaceutical Discovery Abbott Labs robert.s.dewitte@abbott.com (847)937-4036 From pang@dft.chem.cuhk.edu.hk Tue May 19 09:30:28 1998 Received: from dft.chem.cuhk.edu.hk (dft.chem.cuhk.edu.hk [137.189.38.216]) by ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id JAA15079 for ; Tue, 19 May 1998 09:30:26 -0400 (EDT) Received: (from pang@localhost) by dft.chem.cuhk.edu.hk (8.9.0.Beta3/8.9.0.Beta3) id VAA09301; Tue, 19 May 1998 21:27:00 +0800 (HKT) Date: Tue, 19 May 1998 21:26:59 +0800 (HKT) From: patrick To: chemistry@www.ccl.net Subject: convergence criterion in SCF for calculation of polarizability Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello! In Gaussian 94, the SCF convergence will be finished when a specific density-based convergence criterion (10^-N) is met. What is the convergence criterion suitable for calculation of polarizability? Of course, 10^-8 is the best. However, it will be paid much computational time. Is it suitable for choosing 10^-4? Thank you for your attention. Patrick Pang From h.rzepa@ic.ac.uk Tue May 19 13:25:21 1998 Received: from romeo.ic.ac.uk (romeo.ic.ac.uk [155.198.5.9]) by ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id NAA18007 for ; Tue, 19 May 1998 13:25:06 -0400 (EDT) Received: from oban.cc.ic.ac.uk [155.198.5.28] by romeo.ic.ac.uk with smtp (Exim 1.62 #1) id 0ybq86-0001Nk-00; Tue, 19 May 1998 18:24:46 +0100 Received: from sg1.cc.ic.ac.uk ([155.198.63.8] helo=cscmgb.cc.ic.ac.uk) by oban.cc.ic.ac.uk with smtp (Exim 1.90 #1) for CHEMISTRY@www.ccl.net id 0ybq85-0000hM-00; Tue, 19 May 1998 18:24:45 +0100 Received: from [155.198.224.86] by cscmgb.cc.ic.ac.uk (940816.SGI.8.6.9/4.0) id SAA03074; Tue, 19 May 1998 18:24:44 +0100 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" X-Sender: rzepa@155.198.63.8 Message-Id: Date: Tue, 19 May 1998 18:29:49 +0100 To: CHEMISTRY@www.ccl.net From: "Rzepa, Henry" Subject: DNA Base Pairing: Watson-Crick/Hoogsteen/"Curtis" A recent "popular" article in the New Scientist magazine (May 16) suggests that Watson-Crick might have been wrong, and that the DNS bases pair up differently. The suggestion comes from an artist called Curtis, who built geometric models to come up with the theory, and apparently got Maurice Wilkins interested. The article interestingly fails to mention energetics at all, and does not note the curious similarity of the Curtis proposal to Hoogsteen's pairing for AT. Curtis proposes a similar pairing for CG (which Hoogsteen never did). Apart from the fact that the geometries Curtis assumed for his model are quantitatively wrong, does/has anyone had the energy/inclination to try to build the double helix proposed using "Curtis pairing", but using the "accepted" geometries for his version of the pairing? On this point, are there any unequivocal pdb structures showing Hoogsteen pairing? I thought I found some, but they do not show it. I wrote a "letter to the New Scientist editor" in the form of the following web page http://www.ch.ic.ac.uk/newscientist/curtis/ I await the outcome. However, in the past, I have found these popular science magazines tend not to want to confuse their readers with difficult arguments (such as the difference between C-H...O and N-H...O bonding, leaving aside the fluoro-toluene results reported by Kool and commented upon by Seddon). Dr Henry Rzepa, Dept. Chemistry, Imperial College, LONDON SW7 2AY; mailto:rzepa@ic.ac.uk; Tel (44) 171 594 5774; Fax: (44) 171 594 5804. URL: http://www.ch.ic.ac.uk/rzepa/ From h.rzepa@ic.ac.uk Tue May 19 13:25:52 1998 Received: from romeo.ic.ac.uk (romeo.ic.ac.uk [155.198.5.9]) by ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id NAA18012 for ; Tue, 19 May 1998 13:25:19 -0400 (EDT) Received: from oban.cc.ic.ac.uk [155.198.5.28] by romeo.ic.ac.uk with smtp (Exim 1.62 #1) id 0ybq86-0001Nm-00; Tue, 19 May 1998 18:24:46 +0100 Received: from sg1.cc.ic.ac.uk ([155.198.63.8] helo=cscmgb.cc.ic.ac.uk) by oban.cc.ic.ac.uk with smtp (Exim 1.90 #1) for CHEMISTRY@www.ccl.net id 0ybq86-0000hO-00; Tue, 19 May 1998 18:24:46 +0100 Received: from [155.198.224.86] by cscmgb.cc.ic.ac.uk (940816.SGI.8.6.9/4.0) id SAA03076; Tue, 19 May 1998 18:24:45 +0100 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" X-Sender: rzepa@155.198.63.8 Message-Id: In-Reply-To: <0017000007534450000002L002*@MHS> Date: Tue, 19 May 1998 18:31:19 +0100 To: CHEMISTRY@www.ccl.net From: "Rzepa, Henry" Subject: Re: CCL:Java Beans/Classes for Chemical Computation >Hi CCL List, > >We are currently trying to design/build a seamless environment for chemical >computation in pharmaceutical discovery using modern distributed object >technology (Java, Beans, CORBA, ...) and would like to avoid reinventing any >wheels that we could acquire through vendors. > >Does anyone have any experience with Vendor supplied Java Beans and/or >Classes for Chemical Computation and/or Data Visualization? Apologies for not being a vendor!! http://www.ch.ic.ac.uk/java/applets/jspec/spectra/ which is a J-CAMP/SPC data visualiser. We are in the process of building beans from these classes, and they might even become "vendor supported"! We also have chemical classes for our chemical object store; http://www.ch.ic.ac.uk/vchemlab/cos/ I will be bold and venture to suggest the latter is the World's first pure object oriented molecule database, but no doubt will be deluged by emails saying these have been around for years. Certainly, not as vended by MDL via Oracle etc. Vendor supplied ChemSymphony by Toly Krassavine of course is entirely built of beans; http://www.cherwell.com/chemsymphony/ and must be the most impressive beans collection thus far. We are evaluating the beans and the BDK. One must also note JUMBO, Peter Murray-Rust's hugely impressive collection of classes for XML/CML support http://www.vsms.nottingham.ac.uk/vsms/java/jumbo/jan9801/jumbo9801a1.zip Dr Henry Rzepa, Dept. Chemistry, Imperial College, LONDON SW7 2AY; mailto:rzepa@ic.ac.uk; Tel (44) 171 594 5774; Fax: (44) 171 594 5804. URL: http://www.ch.ic.ac.uk/rzepa/ From echamorr@pregrado.ciencias.uchile.cl Tue May 19 18:52:16 1998 Received: from pregrado.ciencias.uchile.cl (echamorr@[146.83.21.47]) by ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id SAA20575 for ; Tue, 19 May 1998 18:52:09 -0400 (EDT) Received: (from echamorr@localhost) by pregrado.ciencias.uchile.cl (8.6.12/8.6.9) id SAA21987; Tue, 19 May 1998 18:55:38 -0400 Date: Tue, 19 May 1998 18:55:38 -0400 (CST) From: "Eduardo Chamorro J." To: Computational Chemistry List Subject: ESIPT reactions 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 ccl.net id SAA20575 Dear CCLers, I am very interested in the Excited State Intramolecular Proton Transfer Reactions, particulary kinetic experiments and theoretical calculations on anils systems. I would appreciate any help that CCL could supply on recent reviews or any information about research groups that are working in this area. Best regards, Eduardo Chamorro _____________________________________________________________________ Eduardo E. Chamorro J. Departamento de Quimica Facultad de Ciencias. Programa de Doctorado en Quimica. Centro de Mecanica Cuantica Aplicada Universidad de Chile Las Palmeras No. 3425. Ņuņoa. Santiago de Chile Tel: (56-2) 6787261 Fax: (56-2) 239-2755, Casilla 653 e-mail: echamorr@pregrado.ciencias.uchile.cl