From chemistry-request@server.ccl.net Tue Aug 1 21:03:30 2000 Received: from castor.rice.edu (castor.rice.edu [128.42.81.29]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id VAA28890 for ; Tue, 1 Aug 2000 21:03:29 -0400 Received: from localhost (knk@localhost) by castor.rice.edu (AIX4.3/8.9.3/8.9.3) with ESMTP id UAA24946 for ; Tue, 1 Aug 2000 20:02:48 -0500 Date: Tue, 1 Aug 2000 20:02:47 -0500 (CDT) From: News user To: chemistry@ccl.net Subject: Re: CCL:TM force fields In-Reply-To: <3986FB1F.38006858@eeyore.cm.utexas.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Tue, 1 Aug 2000, Isaac B. Bersuker wrote: > > All this together makes imposible to get reasonable parametrization of > a force field (with transferable parameters) that could be used in > modeling similar to that of organic and/or non-TMS, in general. > > I am sorry that these important features of TMS remain unknown to > people engaged in their investigation. > While I am an outsider to this field of chemistry, I could not help but comment on the above. Dr. Bersuker states that it is not possible to design a general force field which will work equally well in all the TMS compounds. While nobody argues with this generalization, I do not think that the generalization allows one to conclude that no force field works in any class of TMS compounds no matter how small this class is. The other posters were talking exactly about such narrow class of TMS compounds, where useful parametrization was obtained, applied to other similar TMS compounds, and documented in the literature. In the light of the above, what is then the substance of Dr. Bersuker's critisism of the work that other people do ? Sincerely, Konstantin Kudin From chemistry-request@server.ccl.net Tue Aug 1 21:10:31 2000 Received: from koh13.stanford.edu (KOH13.Stanford.EDU [171.64.123.208]) by server.ccl.net (8.8.7/8.8.7) with SMTP id VAA28918 for ; Tue, 1 Aug 2000 21:10:30 -0400 Received: from eis41.stanford.edu by koh13.stanford.edu with SMTP; Tue, 1 Aug 2000 18:00:37 -0700 (PDT) Message-ID: <398774FC.F41@stanford.edu> Date: Tue, 01 Aug 2000 18:10:20 -0700 From: Robert K Szilagyi Reply-To: szilagyi@stanford.edu X-Mailer: Mozilla 3.01Gold (Win95; I) MIME-Version: 1.0 To: chemistry@ccl.net Subject: TM force fields - questions References: <39823A46.37BBE83A@studentergaarden.dk> <3985A906.DF449838@eeyore.cm.utexas.edu> <00073114171305.29864@ice> <3986FB1F.38006858@eeyore.cm.utexas.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Prof. Bersuker, as a fellow, who was quite engaged in developing molecular mechanical force fields for transition metal complexes (especially mononuclear organometallic complexes, which have well-defined structures and have catalytic importance - in my case in olefin metathesis and polymerisation) Reading your previous email, I would like to point out one important aspect of using MM model chemistries. You have listed very important features of transition metal systems (cis/trans effect; donation/back donation; JT effects), which are indisputable are the major factors determining the molecular structure and reactivity of such systems, but they all related to the electronic structure or wavefunction. In the MM models *** THERE ARE NO ELECTRONS*** and no one is expecting any insight about the electronic structure of the wavefunction, otherwise it would be a complete abuse of the method. Users of the MM methods are interested in something else. May I term this: the result of all those effect you have mentioned (and many others, of course). Their superposition, as it, is manifested in the molecular structure. During the MM parameter development, experimental steric information (internal coordinates) are given as starting point supplied with experimental force constants, which than adjusted in order to reach as good agreement as possible between the experimental and calculated structures. I would like to emphasise the word STRUCTURE quite much. How would you consider a case study of the following reaction mechanism carried out by MM? For example, asymmetric synthesis by a TM complex with huge, chiral, sterically crowded phosphine/phosphite ligands (BINAPHOS, etc.), where all the intermediates of the reaction pathway are very well understood experimentally. Each intermediate isolated and characterised separately and all the transition states (at least the activation barriers) are established by kinetical measurement. As far as I know in most cases the rate determining step is the substrate coordination, which is allowed in certain orientation. This specificity is the origin of any stereo-/regio-/enantio-selectivity. Let's be honest, in such an ideal case, doing quantum chemical calculation does not give more insight, other than a nice way of method calibration. BUT, if we would like to optimise the catalyst system - that is a different story: design of new phosphine ligands and study the effect of various substitutions of quite a few variation (referring here to combinatorical chemistry approaches, structural libraries, etc). Cannot we use a very precisely parameterised MM force field of an intermediate and compare the relative energies of various derivatives STRICKLY KEEPING THE SAME SET OF ATOM AND BOND TYPES around the TM centre? What would be your reaction as a referee of such a research paper or research proposal? I hope I'm not going to offend you by my lines and sorry for the long email, but I wanted to be very clear! I very much interested in your reply! Best wishes from Stanford, Robert ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Robert K. SZILAGYI, PhD postdoctoral fellow Department of Chemistry (Solomon Group-Room OC105) Phone: +1 650 723 0041 Stanford University Fax: +1 650 725 0259 333 Campus Drive Email: szilagyi@stanford.edu Stanford CA 94305-5080 ICQ: 16833945@pager.icq.com ====================================================================== ********** All opinions are my own, NOT my employer's ! ********** ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From chemistry-request@server.ccl.net Wed Aug 2 04:05:13 2000 Received: from vytautas.vdu.lt (mail@vytautas.vdu.lt [193.219.38.33]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA30789 for ; Wed, 2 Aug 2000 04:05:05 -0400 Received: from vaidila.vdu.lt ([193.219.38.52] ident=root) by vytautas.vdu.lt with esmtp for chemistry@ccl.net id 13JtVy-000233-00; Wed, 02 Aug 2000 10:04:34 +0200 Received: from vaidila.vdu.lt (vejas.vdu.lt [193.219.38.82]) by vaidila.vdu.lt (8.9.3/8.9.3) with ESMTP id KAA16016 for ; Wed, 2 Aug 2000 10:04:33 +0200 (GMT) Message-ID: <39885619.249374E8@vaidila.vdu.lt> Date: Wed, 02 Aug 2000 10:10:50 -0700 From: "art'" X-Mailer: Mozilla 4.7 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 CC: Computational Chemistry List Subject: CCL: Atomic charges References: Content-Type: text/plain; charset=koi8-r Content-Transfer-Encoding: 7bit Hi CCLers, Your opinion is interesting about what method from Gaussian is the best to reproduce atomic charges. Does anybody knows, how sensitive atomic charges are to geometry optimisation? I know that Mulliken routin is very basis set sensitive and the best it is use with minimal basis sets (Mulliken). How about other methods? Best wishes to all A.Ziemys *Vytautas Magnus Universitu Ins. of Biochemistry Dept. of Biology Lab. of Enzymatic chemistry Vileikos 8 Mokslininku 12 LT-3035, Kaunas Vilnius Lithuania Lithuania From chemistry-request@server.ccl.net Wed Aug 2 05:55:48 2000 Received: from avfw98.lundbeck.com (firewall.lundbeck.com [130.227.160.11]) by server.ccl.net (8.8.7/8.8.7) with SMTP id FAA31248 for ; Wed, 2 Aug 2000 05:55:48 -0400 Received: from firewall.lundbeck.com [130.227.160.11] (HELO localhost) by avfw98.lundbeck.com (AltaVista Mail V2.0J/2.0J BL25J listener) id 0000_005d_3987_fbd5_8944; Wed, 02 Aug 2000 11:45:41 +0100 Received: from somewhere by smtpxd Message-ID: From: Jan Torleif Pedersen To: "'chemistry@ccl.net'" Subject: Ab-initio charges for blocked amino-acids Date: Wed, 2 Aug 2000 11:55:24 +0200 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-Type: text/plain; charset="iso-8859-1" Greetings CCLers, I am looking for a set of state-of-the-art partial charges for blocked amino-acids, derived using ab-initio methods. That is N-acetyl-C-aminomethyl-amino-acids. Preferentially for a number of low energy conformations. If anybody is in possession of such a database for the 20 aminoacids or could point me in the direction of some recent publication I would be greaful. Also I would be interested in knowing what the best type of ab-initio method would give me the best answer in case I should attempt to make the calculations myself. Regards Dr. Jan Torleif Pedersen Dep. Computational Chemistry H. Lundbeck A/S Ottiliavej 9 DK-2000 Valby - Copenhagen DENMARK phone : +45 36 44 24 25 ext 2887 FAX : +45 36 30 13 85 email : jatp@lundbeck.com From chemistry-request@server.ccl.net Wed Aug 2 05:55:55 2000 Received: from smtp.csc.fi (pobox5.csc.fi [193.166.0.99]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA31254 for ; Wed, 2 Aug 2000 05:55:52 -0400 Received: from voxopm.csc.fi (voxopm.csc.fi [128.214.248.23]) by smtp.csc.fi (8.9.3/8.9.3/CSC) with ESMTP id MAA22571 for ; Wed, 2 Aug 2000 12:55:39 +0300 Date: Wed, 2 Aug 2000 12:55:39 +0300 From: "Dr. T. Raaska" To: chemistry@ccl.net Subject: Third call:Minisymposium on DFT methods (ADF) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Just a reminder... the registration is still open for =================================================================== Minisymposium on Density Functional Theory ( Amsterdam Density Functional Code ) 5-6th October, 2000 Espoo, FINLAND """"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" Please have a look at http://www.csc.fi/chem/adf_symposium for the latest information. The quest speakers of the minisymposium are Dr. Bert te Velde and Dr. F. Matthias Bickelhaupt Scientific Computing and Modeling NV Vrije Universiteit, the Netherlands In addition to invited lectures, the program will include a number of oral communications by participants, and a poster session. It is our intention to make this symposium a memorable event, both scientifically and socially. If you have never been in Scandinavia, the meeting gives you a perfect opportunity for that. Even though the meeting is subtitled Amsterdam Density Functional Code, any presentation or poster describing the application of any density functional code besides ADF is more than welcome. For registration and more information, please visit the minisymposium www-pages at http://www.csc.fi/chem/adf_symposium We look forward to meet you in October! On behalf of the organizing team Tuija Raaska Organizing committee: Drs. Maija Lahtela-Kakkonen, Tuija Raaska, Juha Fagerholm and Juha Haataja Professor, Scientific Director Kari Laasonen Please use my address below for further inquieries. =================================================== Dr. Tuija Raaska CSC-Scientific Computing Ltd. Tekniikantie 15 a D 02101 Espoo, Finland tel.+358-(09)-457 2713 Tuija.Raaska@csc.fi http://www.csc.fi/chem/adf_symposium =================================================== From chemistry-request@server.ccl.net Wed Aug 2 05:23:56 2000 Received: from dire.bris.ac.uk (dire.bris.ac.uk [137.222.10.60]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA31084 for ; Wed, 2 Aug 2000 05:23:56 -0400 Received: from sis.bris.ac.uk by dire.bris.ac.uk with SMTP-PRIV with ESMTP; Wed, 2 Aug 2000 10:23:29 +0100 Received: from localhost (localhost [127.0.0.1]) by sis.bris.ac.uk (8.9.3/8.9.3) with SMTP id KAA18475; Wed, 2 Aug 2000 10:21:34 +0100 (BST) Date: Wed, 2 Aug 2000 10:21:34 +0100 (BST) From: BK Szefczyk X-Sender: bs9814@sis To: Tarek Mamoun El-Gogary cc: "'CHEMISTRY@ccl.net'" Subject: Re: CCL:Gamess question In-Reply-To: <4EF2E03A9B67D2119E2E0000F8053499427422@mum.mans.eun.eg> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id FAA31085 The keywords for 6-31G** basis set are: $BASIS GBASIS=N31 NGAUSS=6 NDFUNC=1 NPFUNC=1 $END ^ ^ | | This is the first star | (d type functions) | | This is the second star (p type functions) Borys. On Tue, 1 Aug 2000, Tarek Mamoun El-Gogary wrote: > Dear ccl’s, > Could any Gamess users, kindly, let me know what is the key word for the > basis set HF/6-31G** to be inserted in the input file. > Thanks > Tarek El-gogary > Ddept of Chem. > Fac. of Sci. > Mans. Univ. > Egypt. > From chemistry-request@server.ccl.net Wed Aug 2 05:31:38 2000 Received: from info.human.nagoya-u.ac.jp (gshi1.info.human.nagoya-u.ac.jp [133.6.48.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA31132 for ; Wed, 2 Aug 2000 05:31:37 -0400 Received: from 614DELL..info.human.nagoya-u.ac.jp ([133.6.49.29]) by info.human.nagoya-u.ac.jp (8.9.3/3.7W-00060513) with ESMTP id SAA20790 for ; Wed, 2 Aug 2000 18:31:22 +0900 (JST) (envelope-from suresh@info.human.nagoya-u.ac.jp) Message-Id: <4.3.0.20000802182753.00a83e20@133.6.48.1> X-Sender: suresh@133.6.48.1 X-Mailer: QUALCOMM Windows Eudora Version 4.3 Date: Wed, 02 Aug 2000 18:37:44 +0900 To: chemistry@ccl.net From: sureshch Subject: Lanthanoids & Actinoids Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Dear CCL-ers: What is the best method currently available for the compounds of Lanthanoids & Actinoids? Is it B3LYP/SDD ? Any useful references? Thanks in advance. Suresh CH Nagoya University From chemistry-request@server.ccl.net Wed Aug 2 05:41:02 2000 Received: from mail1.uniroma1.it (mail1.uniroma1.it [151.100.4.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA31177 for ; Wed, 2 Aug 2000 05:41:01 -0400 From: molbeam@uniroma1.it Received: from chilasdue.uniroma1.it ([151.100.52.3]) by mail1.uniroma1.it (Lotus Domino Release 5.0.4) with ESMTP id 2000080211433969:143866 ; Wed, 2 Aug 2000 11:43:39 +0200 Message-Id: <4.3.1.0.20000802113609.00a7ce00@mail.uniroma1.it> X-Sender: molbeam@mail.uniroma1.it X-Mailer: QUALCOMM Windows Eudora Version 4.3.1 Date: Wed, 02 Aug 2000 11:41:00 +0200 To: giardini@uniroma1.it Subject: XIX MOLBEAMS Mime-Version: 1.0 X-MIMETrack: Itemize by SMTP Server on mail1/Uniroma1/it(Release 5.0.4 |June 8, 2000) at 02/08/2000 11.43.40, Serialize by Router on mail1/Uniroma1/it(Release 5.0.4 |June 8, 2000) at 02/08/2000 11.47.28, Serialize complete at 02/08/2000 11.47.28 Content-Type: text/plain; charset="us-ascii"; format=flowed Dear Collegue, to receive the 2nd announcement and further informations about the meeting please send your complete address (not only e.mail) to: Mrs. Patrizia BONADIES e.mail bonadies@caspur.it fax: +39 06 490324 Hoping to see you next year during the Meeting Sincerely Yours on the behalf of the Organizing Committee (Prof. Anna Giardini) From chemistry-request@server.ccl.net Wed Aug 2 07:13:49 2000 Received: from balder.nilu.no (balder.nilu.no [128.39.104.34]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA32549 for ; Wed, 2 Aug 2000 07:13:47 -0400 Received: from afrodite.no. (afrodite.nilu.no) by balder.nilu.no (Sun Internet Mail Server sims.3.5.2000.01.05.12.18.p9) with ESMTP id <0FYN00KCMWII98@balder.nilu.no> for chemistry@ccl.net; Wed, 2 Aug 2000 13:13:30 +0200 (MET DST) Received: from eshpc (eshpc.nilu.no. [128.39.66.15]) by afrodite.no. (8.9.1b+Sun/8.9.1) with SMTP id NAA15230 for ; Wed, 02 Aug 2000 13:13:24 +0200 (MET DST) Date: Wed, 02 Aug 2000 13:13:23 +0200 From: =?iso-8859-1?Q?Eldbj=F8rg_Sofie_Heimstad?= Subject: Autodock: allosteric sites in proteins To: chemistry@ccl.net Reply-to: =?iso-8859-1?Q?Eldbj=F8rg_Sofie_Heimstad?= Message-id: <013c01bffc72$ac5fe420$0f422780@nilu.no> MIME-version: 1.0 X-Mailer: Microsoft Outlook Express 5.00.2314.1300 Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: 8BIT X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 X-Priority: 3 Dear Colleagues, Have any of you experience with use of the program Autodock to locate allosteric binding sites in proteins or know about references to such work? Thanks in advance, ######################################### Eldbjørg S. Heimstad NILU Norwegian Institute for Air Research The Polar Environmental Centre N-9296 Tromsø, Norway Tel. +47-77 75 03 75 Fax. +47-77 75 03 76 E-mail: Eldbjorg.Sofie.Heimstad@nilu.no Web: http://www.nilu.no ######################################### From chemistry-request@server.ccl.net Wed Aug 2 08:59:47 2000 Received: from mail-f.bcc.ac.uk (mail-f.bcc.ac.uk [128.40.23.81]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA00230 for ; Wed, 2 Aug 2000 08:59:46 -0400 Received: from pat.biochem.ucl.ac.uk by mail-f.bcc.ac.uk with SMTP (XT-PP) with ESMTP; Wed, 2 Aug 2000 13:59:11 +0100 Received: from bsmir18 (bsmir18 [128.40.46.21]) by pat.biochem.ucl.ac.uk (8.9.3/8.9.3) with SMTP id NAA11897 for ; Wed, 2 Aug 2000 13:58:49 +0100 Date: Wed, 2 Aug 2000 13:58:46 +0100 (BST) From: Irilenia Nobeli X-Sender: nobeli@bsmir18 To: Computational Chemistry List Subject: Software for databases of chemical information? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, We are planning to build a database of molecules. The database will contain both chemical structures and text. The database itself will probably be based on Oracle. We are looking for software that will allow us to access, search and retrieve data, eventually through a web interface. I have found a lot of commercial software that seems capable of performing this task (MDL, Daylight, Tripos and Synopsys all have such tools available I believe), but I would like to hear from people who have actually used such software and had hands-on experience. I would be particularly interested in software used by academic institutions (as it is likely that this will be more affordable...or even free!). If anyone knows of any non-commercial software, even if they have not used it, I'd be very interested to hear from them. Many thanks in advance. Irilenia ------------------------------------------------ Irene (Irilenia) Nobeli Biomolecular Structure and Modelling Unit Department of Biochemistry and Molecular Biology University College London Darwin Building Gower Street London WC1E 6BT nobeli@biochem.ucl.ac.uk tel. 020 7679 2171 fax. 020 7679 7193 >>> The greatest proof of the existence of intelligent life outside Earth is that they haven't contacted us yet. <<<< From chemistry-request@server.ccl.net Wed Aug 2 05:33:03 2000 Received: from mserv.rug.ac.be (mserv.rug.ac.be [157.193.40.37]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA31145 for ; Wed, 2 Aug 2000 05:33:02 -0400 Received: from hartree4.rug.ac.be (hartree4.rug.ac.be [157.193.91.12]) by mserv.rug.ac.be (8.9.3/8.9.3) with ESMTP id LAA09630 for ; Wed, 2 Aug 2000 11:32:51 +0200 (MET DST) Received: from hartree6.rug.ac.be (hartree6.rug.ac.be [157.193.91.27]) by hartree4.rug.ac.be (AIX4.2/UCB 8.7/8.7) with ESMTP id LAA09422 for ; Wed, 2 Aug 2000 11:36:55 +0100 (NFT) Message-Id: <4.3.2.7.2.20000802110418.00a93880@hartree4.rug.ac.be> X-Sender: patrick@hartree4.rug.ac.be X-Mailer: QUALCOMM Windows Eudora Version 4.3.2 Date: Wed, 02 Aug 2000 11:25:22 +0200 To: chemistry@ccl.net From: Patrick Bultinck Subject: mixing entropies for a molecule with multiple minima Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1"; format=flowed Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id FAA31146 Dear, I would like to calculate thermodynamical parameters (Delta-H°, Delta-S° and Delta-G°) for an ensemble of conformations of a molecule. DH° etc. can easily be calculated for each conformation by calculating the hessian. DG° is also easily calculated of course. Using Boltzmann's law, one can calculate the mole fractions of each conformation you would have for one mole of the molecule. DH° is easily calculated for the ensemble using the individual mole fractions and DH° values for each conformation. DS° also in first approximation, but... should DS° not be augmented with a mixing entropy term because you are mixing different conformations, which you all treat separately as ideal gases ? I think you would need to add a term DS°(mix)=sum(x_i*ln(x_i)), where x_i is the mole fraction for conformation i. Since you treat them as ideal gases, nothing changes in DH° for the ensemble (they do not interact). Using the mixing-corrected DS°, a new DG° can be calculated. So I am using the following steps to calculate DG° for an ensemble of conformations of the same molecule : - Calculate DH°, DS° and DG° for each conformation separately - Correct where necessary for chiral degeneracy of each conformation, and obtain (for some conformations) chiral corrected values (not every ab initio program does this on the fly). - Calculate Boltzmann determined occupations for all conformations. - Calculate DH° for the ensemble of conformations, as well as DS° from individual DH° and DS° values of all conformations - Correct DS° with a mixing term, accounting for the fact that each conformation is an ideal gas, and that mixing ideal gases brings about a mixing entropy. - Calculate a new DG° value from DH° and the corrected DS° value. In my opinion, only then can I calculate the DG° value in a reaction : metal + ligand -> complex. I would very much appreciate your opinions on this. I am not ignorant in thermodynamics, but I would like to have more experienced people to comment on my way to calculate DG° for an ensemble of conformations of the same molecule. Especially for the fact that Boltzmann is used to calculate mole fractions for each conformation, based on individual values for each conformation, and that then later on, a term is added to DS° which can only be calculated for an ensemble (but to calculate S_mix, you need the mole fractions first)... Thanks, Patrick Bultinck Ghent University Belgium From chemistry-request@server.ccl.net Wed Aug 2 10:47:01 2000 Received: from mcmail.cis.McMaster.CA (mattacf@mcmail.CIS.McMaster.CA [130.113.64.66]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA01195 for ; Wed, 2 Aug 2000 10:47:01 -0400 Received: from localhost (mattacf@localhost) by mcmail.cis.McMaster.CA with ESMTP id KAA00044; Wed, 2 Aug 2000 10:46:40 -0400 (EDT) Date: Wed, 2 Aug 2000 10:46:39 -0400 (EDT) From: "C.F. Matta" To: Jan Torleif Pedersen cc: "'chemistry@ccl.net'" Subject: Re: CCL:Ab-initio charges for blocked amino-acids In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi Dr. Pedersen, Have a look to our recent publication (which will be followed by 2 papers probably this year): Matta,C.F. and Bader, R.F.W. "An Atoms-In-Molecules Study of the Genetically-Encoded Amino Acids: I. Effects of Conformation and of Tautomerization on Geometric, Atomic, and Bond Properties". PROTEINS: Structure, Function and Genetics Vol.40: 310-329 (2000). You may find answers to your questions. Take care. Cherif ___________________________________________________________________________ Cherif F. Matta tel. (905) 525-9140 ext. 22502 Chemistry Department fax (905) 522-2509 McMaster University _______________________ Hamilton, Ontario, CANADA L8S 4M1. | "Choice not chance ....................................................| determines one's Member of the Board of Governors of the University | destiny". Anonymous ___________________________________________________________________________ From chemistry-request@server.ccl.net Wed Aug 2 10:29:57 2000 Received: from coltrane.dichi.unina.it (cavallo@coltrane.dichi.unina.it [192.135.165.154]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA01037 for ; Wed, 2 Aug 2000 10:29:57 -0400 Received: from localhost (cavallo@localhost) by coltrane.dichi.unina.it (8.8.7/8.8.7) with ESMTP id PAA01244 for ; Wed, 2 Aug 2000 15:43:00 GMT X-Authentication-Warning: coltrane.dichi.unina.it: cavallo owned process doing -bs Date: Wed, 2 Aug 2000 15:43:00 +0000 (GMT) From: Luigi Cavallo X-Sender: cavallo@coltrane.dichi.unina.it To: chemistry@ccl.net Subject: Re: CCL:TM force fields - questions In-Reply-To: <398774FC.F41@stanford.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, just to add my 2 cents to the discussion. I substantially agree with P-O Norrby and with R K Szilagy. I have been working many years with pure MM methods on the stereo- and regioselectivity in the polymerization of 1-alkenes with heterogeneous and homogeneous Ziegler-Natta catalysts. A few years ago, to make such calculations you had to "guess" several force field parameters, or just fix some internal coordinates to "reasonable" values. Although quite rude, the approach has worked. In the last few years, however, several research groups developed MM force fields for metallocenes, and now the MM calculations on these systems can be done without any "guess" or fixing of internal coordinates. Force fields for metallocenes can be found in: Doman et al JACS 1992, 114, 7264 Hollis et al Organometallics 1993, 12, 3385 Doman et al JACS 1995, 117, 1352 Howler et al Organometallics 1994, 13, 2380 Good resumes on the applications can be found in: Resconi et al Chem Rev 2000, 100, 1253 Angermund et al Chem Rev 2000, 100, 1457 The improvements of MM force fields for TM complexes has been rather good in the last years. And the results obtained with such developments are there to witness the validity of such approaches. Clearly, people have to know what CAN be done and what CANNOT be done with MM. In the post of Szilagy, the applicability of such methods is briefly but correctly reviewed. Regards, Luigi -------------------------------------------------------------------------- | Dr. Luigi Cavallo Dept. of Chemistry | | Ph: ++39-81-2536635 Univ. of Naples | | Fax: ++39-81-5527771 Via Mezzocannone 4 | | Email cavallo@chemistry.unina.it I-80134 Napoli, ITALY | -------------------------------------------------------------------------- From chemistry-request@server.ccl.net Wed Aug 2 10:36:32 2000 Received: from vytautas.vdu.lt (mail@vytautas.vdu.lt [193.219.38.33]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA01118 for ; Wed, 2 Aug 2000 10:36:22 -0400 Received: from vaidila.vdu.lt ([193.219.38.52] ident=root) by vytautas.vdu.lt with esmtp id 13Jzcn-0002kI-00; Wed, 02 Aug 2000 16:36:01 +0200 Received: from vaidila.vdu.lt (vejas.vdu.lt [193.219.38.82]) by vaidila.vdu.lt (8.9.3/8.9.3) with ESMTP id QAA22011; Wed, 2 Aug 2000 16:36:01 +0200 (GMT) Message-ID: <3988B1DC.50AA480D@vaidila.vdu.lt> Date: Wed, 02 Aug 2000 16:42:20 -0700 From: "art'" X-Mailer: Mozilla 4.7 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 To: sureshch CC: chemistry@ccl.net Subject: Re: CCL:Lanthanoids & Actinoids References: <4.3.0.20000802182753.00a83e20@133.6.48.1> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, My collegues had some dificulties using SDD with Eu in a very small system of atoms. Best regards A.Ziemys sureshch wrote: > Dear CCL-ers: > What is the best method currently available for the compounds of > Lanthanoids & Actinoids? Is it B3LYP/SDD ? Any useful references? > Thanks in advance. > Suresh CH > Nagoya University > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Wed Aug 2 19:03:01 2000 Received: from comm1.umaryland.edu (comm1.umaryland.edu [134.192.1.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id TAA03474 for ; Wed, 2 Aug 2000 19:03:01 -0400 Received: from ocracoke.umaryland.edu (ocracoke.umaryland.edu [134.192.72.34]) by comm1.umaryland.edu (8.9.3/8.9.3) with ESMTP id TAA15647 for ; Wed, 2 Aug 2000 19:02:59 -0400 (EDT) Received: from ocracoke (localhost [127.0.0.1]) by ocracoke.umaryland.edu (8.9.3/8.9.3) with SMTP id TAA02554 for ; Wed, 2 Aug 2000 19:04:33 -0400 (EDT) Sender: ijen@outerbanks.umaryland.edu Message-ID: <3988A900.167E@outerbanks.umaryland.edu> Date: Wed, 02 Aug 2000 19:04:32 -0400 From: I-Jen Chen Organization: University of Maryland, Baltimore X-Mailer: Mozilla 3.0Gold (X11; I; IRIX 5.3 IP20) MIME-Version: 1.0 To: chemistry@ccl.net Subject: Reviews of De novo drug design Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers, Could someone enlighten me with some review articles about de novo drug design? If anyone could suggest some packages for de novo drug design, that would be great, too. I will summarize the results. Best regards, I-Jen -- ______________________________________________________________________ I-Jen Chen Department of Pharmaceutical Sciences University of Maryland, Baltimore Phone : US-410-706-7441 Fax : US-410-706-0346 E-mail: ichen002@umaryland.edu ______________________________________________________________________ From chemistry-request@server.ccl.net Wed Aug 2 13:38:12 2000 Received: from ne059.cm.utexas.edu (ne059.cm.utexas.edu [146.6.145.59]) by server.ccl.net (8.8.7/8.8.7) with SMTP id NAA02156 for ; Wed, 2 Aug 2000 13:38:12 -0400 Received: from ne057.cm.utexas.edu by ne059.cm.utexas.edu (AIX 3.2/UCB 5.64/4.03) id AA14124; Wed, 2 Aug 2000 12:33:10 -0500 Message-Id: <3988778D.E6A96179@eeyore.cm.utexas.edu> Date: Wed, 02 Aug 2000 12:33:33 -0700 From: "Isaac B. Bersuker" X-Mailer: Mozilla 4.7 [en] (WinNT; I) X-Accept-Language: en,zh,zh-CN,zh-TW Mime-Version: 1.0 To: Robert K Szilagyi Cc: chemistry@ccl.net Subject: Re: CCL:TM force fields - questions References: <39823A46.37BBE83A@studentergaarden.dk> <3985A906.DF449838@eeyore.cm.utexas.edu> <00073114171305.29864@ice> <3986FB1F.38006858@eeyore.cm.utexas.edu> <398774FC.F41@stanford.edu> Content-Type: text/plain; charset=koi8-r Content-Transfer-Encoding: 7bit Dear Dr Szilagyi: Thank you for your message. Your statements seem to be correct except in one point: you miss the NONTRANSFERABILITY (NT) of the force field parameters (FFP) from one compound to another which deprives the whole approach of its heuristic value. The NT emerges from the fact that in TMS the parameters for the M-L1 bond depend very strongly on the presence of other M-L2, M-L3,..., bonds. For instance, the Cu-O bond length varies between 1.8 A and 3.0 A dependent on other bonds and the next coordination sphere in the TMS (see my 1996 book). What bond length Cu-O would you take as a FFP? I also state in the book above that in very LIMITED CASES when all the bonds remain the same (and the next coordination sphere is not very intrusive) some versions of MM modeling may be useful. These special conditions should be carefully specified and checked. Unfortunately, people use the MM scheme without any discussion of these important limitations. I understand that you ask me what to do with large TMS if not modeling by means of MM. My answer is to use combined QM/MM methods in which the metal site is treated by QM, while the huge environment is modeled by MM. Of course, this approach is not simple and not strightforward (no serious science is strightforward), see, e.g., in Combined QM/MM Methods, Gao and Thompson, Eds., ACS Series 712, Washington 1998. Best Regards Isaac Robert K Szilagyi wrote: > Dear Prof. Bersuker, > as a fellow, who was quite engaged in developing molecular mechanical > force fields for transition metal complexes (especially mononuclear > organometallic complexes, which have well-defined structures and have > catalytic importance - in my case in olefin metathesis and > polymerisation) > Reading your previous email, I would like to point out one important > aspect of using MM model chemistries. > > You have listed very important features of transition metal systems > (cis/trans effect; donation/back donation; JT effects), which are > indisputable are the major factors determining the molecular structure > and reactivity of such systems, but they all related to the electronic > structure or wavefunction. > In the MM models *** THERE ARE NO ELECTRONS*** and no one is expecting > any insight about the electronic structure of the wavefunction, > otherwise it would be a complete abuse of the method. > > Users of the MM methods are interested in something else. May I term > this: the result of all those effect you have mentioned (and many > others, of course). Their superposition, as it, is manifested in the > molecular structure. > > During the MM parameter development, experimental steric information > (internal coordinates) are given as starting point supplied with > experimental force constants, which than adjusted in order to reach as > good agreement as possible between the experimental and calculated > structures. I would like to emphasise the word STRUCTURE quite much. > > How would you consider a case study of the following reaction mechanism > carried out by MM? For example, asymmetric synthesis by a TM complex > with huge, chiral, sterically crowded phosphine/phosphite ligands > (BINAPHOS, etc.), where all the intermediates of the reaction pathway > are very well understood experimentally. Each intermediate isolated and > characterised separately and all the transition states (at least the > activation barriers) are established by kinetical measurement. As far as > I know in most cases the rate determining step is the substrate > coordination, which is allowed in certain orientation. This specificity > is the origin of any stereo-/regio-/enantio-selectivity. > Let's be honest, in such an ideal case, doing quantum chemical > calculation does not give more insight, other than a nice way of method > calibration. BUT, if we would like to optimise the catalyst system - > that is a different story: design of new phosphine ligands and study the > effect of various substitutions of quite a few variation (referring here > to combinatorical chemistry approaches, structural libraries, etc). > > Cannot we use a very precisely parameterised MM force field of an > intermediate and compare the relative energies of various derivatives > STRICKLY KEEPING THE SAME SET OF ATOM AND BOND TYPES around the TM > centre? > What would be your reaction as a referee of such a research paper or > research proposal? > > I hope I'm not going to offend you by my lines and sorry for the long > email, but I wanted to be very clear! > > I very much interested in your reply! > Best wishes from Stanford, > Robert > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > Robert K. SZILAGYI, PhD postdoctoral fellow > Department of Chemistry > (Solomon Group-Room OC105) Phone: +1 650 723 0041 > Stanford University Fax: +1 650 725 0259 > 333 Campus Drive Email: szilagyi@stanford.edu > Stanford CA 94305-5080 ICQ: 16833945@pager.icq.com > ====================================================================== > ********** All opinions are my own, NOT my employer's ! ********** > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > -= 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 -- Isaac B. Bersuker Institute for Theoretical Chemistry Department of Chemistry & Biochemistry The University of Texas at Austin Austin, TX 78712, USA Ph: (512) 471-4671 Fax: (512) 471-8696 Email: bersuker@eeyore.cm.utexas.edu