From chemistry-request@server.ccl.net Fri May 31 05:14:22 2002 Received: from resu1.ulb.ac.be ([164.15.59.200]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4V9ELC05455 for ; Fri, 31 May 2002 05:14:21 -0400 Received: from resu1.ulb.ac.be (resu1.ulb.ac.be [164.15.59.200]) by resu1.ulb.ac.be (8.8.8/3.17.1.ap (resu)) id LAA18106; Fri, 31 May 2002 11:11:49 +0200 (MEST) for chemistry@ccl.net Date: Fri, 31 May 2002 11:11:49 +0200 (MEST) Message-Id: <200205310911.LAA18106@resu1.ulb.ac.be> From: Pierre Mignon To: chemistry@ccl.net Subject: PM3 parameterization i X-Mailer: Webmail ULB v2.1 Hello all, A collegue of mine gets in trouble in optimizing a peptide chain in PM3. The problem arising is that the peptide bond (O=C-N-H) is not planar in the optimized geometry. I don't mean a small deviation but the hybridation is not sp2. Does anyone has allready met this problem or has any information upon this feature ??? Thank's in advance. Mignon Pierre PhD student Free University of Brussel (VUB) Dienst Algemene Chemie (ALGC) Pleinlaan, 2 1050 Brussels Belgium Tel + 32 2 629 35 16 Fax + 32 2 629 33 17 e-mail pmignon@vub.ac.be From chemistry-request@server.ccl.net Fri May 31 05:41:12 2002 Received: from mserv.itpa.lt ([193.219.53.20]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4V9fBC06119 for ; Fri, 31 May 2002 05:41:11 -0400 Received: from localhost (tamulis@localhost) by mserv.itpa.lt (8.11.6/8.11.0) with ESMTP id g4V9f7I97803 for ; Fri, 31 May 2002 11:41:11 +0200 (EET) (envelope-from tamulis@itpa.lt) Date: Fri, 31 May 2002 11:41:07 +0200 (EET) From: Arvydas Tamulis To: Subject: One molecule spin flip Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Colleagues, I would like to ask you advise how to find researchers dealing with one (or few) molecule spin flips. Do you know any laboratory which can by constant magnetic field prepare quantum state of one molecule with all protons spins oriented down and then by changing magnetic field to flip one by one all protons spins oriented up of this single molecule (in my case elements of molecular quantum computers - see our website: www.itpa.lt/~tamulis/). Thanking your in advance. With best reagards, Arvydas Tamulis ******************************************************************* Arvydas Tamulis Doctor of Natural Sciences, senior research fellow Institute of Theoretical Physics and Astronomy, Vilnius University, Theoretical Molecular Electronics Research Group, A. Gostauto 12, Vilnius 2600, Lithuania e-mail: TAMULIS@ITPA.lt; WEBsite: http://www.itpa.lt/~tamulis/ fax: +(370-2)-225361 or +(370-2)-224694 Phone: +(370-2)-620861 Home address: Didlaukio 27-40, Vilnius 2057, Lithuania Mobile phone: +370-9919397 ******************************************************************* From chemistry-request@server.ccl.net Fri May 31 05:52:39 2002 Received: from roche.bath.ac.uk (IDENT:h0rmwb7gfo4h4mi7y6sp@[138.38.32.21]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4V9qdC06454 for ; Fri, 31 May 2002 05:52:39 -0400 Received: from mmdf by roche.bath.ac.uk with pleasure id 17Dj5J-0005Cx-02 for chemistry@ccl.net; Fri, 31 May 2002 10:52:37 +0100 Received: from amos.bath.ac.uk ([138.38.32.36] ident=mmdf) by roche.bath.ac.uk with smtp id 17Dj5I-00023d-02; Fri, 31 May 2002 10:52:36 +0100 Received: from prpcn144 ( prpc-n144.bath.ac.uk [138.38.128.144] ) by amos.bath.ac.uk id aa22349 ; 31 May 2002 10:52 +0100 From: James Robinson To: Pierre Mignon , chemistry@ccl.net Subject: RE: PM3 parameterization i Date: Fri, 31 May 2002 10:53:34 +0100 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2911.0) X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 In-Reply-To: <200205310911.LAA18106@resu1.ulb.ac.be> Importance: Normal Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g4V9qdC06455 PM3 and AM1 treat amide bonds poorly. Have low rotational barriers. With Mopac93 need to add kewords MMOK to add a correction for amide bonds. James -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request@ccl.net]On Behalf Of Pierre Mignon Sent: 31 May 2002 10:12 To: chemistry@ccl.net Subject: CCL:PM3 parameterization i Hello all, A collegue of mine gets in trouble in optimizing a peptide chain in PM3. The problem arising is that the peptide bond (O=C-N-H) is not planar in the optimized geometry. I don't mean a small deviation but the hybridation is not sp2. Does anyone has allready met this problem or has any information upon this feature ??? Thank's in advance. Mignon Pierre PhD student Free University of Brussel (VUB) Dienst Algemene Chemie (ALGC) Pleinlaan, 2 1050 Brussels Belgium Tel + 32 2 629 35 16 Fax + 32 2 629 33 17 e-mail pmignon@vub.ac.be -= 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 Fri May 31 07:01:55 2002 Received: from mail.kemi.dtu.dk (IDENT:root@[130.225.67.150]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4VB1tC08019 for ; Fri, 31 May 2002 07:01:55 -0400 Received: from [192.38.70.75] (pon.ok.dtu.dk [192.38.70.75]) by mail.kemi.dtu.dk (8.11.6/8.11.4) with ESMTP id g4VB1nJ31715; Fri, 31 May 2002 13:01:50 +0200 Mime-Version: 1.0 X-Sender: pon@mail.kemi.dtu.dk Message-Id: In-Reply-To: <200205310911.LAA18106@resu1.ulb.ac.be> References: <200205310911.LAA18106@resu1.ulb.ac.be> Date: Fri, 31 May 2002 13:01:51 +0200 To: Pierre Mignon From: Per-Ola Norrby Subject: Re: CCL:PM3 parameterization i Cc: chemistry@ccl.net Content-Type: text/plain; charset="us-ascii" ; format="flowed" Hi, >A collegue of mine gets in trouble in optimizing a peptide chain in >PM3. The problem arising is that the peptide bond (O=C-N-H) is not >planar in the optimized geometry. I don't mean a small deviation but >the hybridation is not sp2. Does anyone has allready met this >problem or has any information upon this feature ??? This is well known. You can get around it by adding a molecular mechanics term to PM3, but in fact, unless you really need the orbitals, almost every property is more accurately calculated if you use well-parameterized molecular mechanics. There are several dozen methods out there that are more accurate than PM3 for peptides, not to mention about 3 orders of magnitude faster... /Per-Ola Norrby -- ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Per-Ola Norrby, Assoc. Professor, http://compchem.dfh.dk/PeO/ Technical University of Denmark, Dept. of Chem., Org. Chem. Building 201, Kemitorvet, DK-2800 Kgs. Lyngby, Denmark Email: pon@kemi.dtu.dk tel +45-45252123, fax +45-45933968 From chemistry-request@server.ccl.net Fri May 31 07:42:32 2002 Received: from chinon.cnrs-orleans.fr ([163.9.6.107]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4VBgVC08826 for ; Fri, 31 May 2002 07:42:31 -0400 Received: (from hinsen@localhost) by chinon.cnrs-orleans.fr (8.11.2/8.11.2) id g4VBeCf00575; Fri, 31 May 2002 13:40:12 +0200 X-Authentication-Warning: chinon.cnrs-orleans.fr: hinsen set sender to hinsen@cnrs-orleans.fr using -f Sender: hinsen@chinon.cnrs-orleans.fr To: Hannes Loeffler Cc: chemistry@CCL.net Subject: Re: CCL:summary: diffusion coefficient from MSD References: <1022743262.3cf5d2de65e32@web-mail1.uibk.ac.at> From: Konrad Hinsen Date: 31 May 2002 13:40:12 +0200 In-Reply-To: <1022743262.3cf5d2de65e32@web-mail1.uibk.ac.at> Message-ID: Lines: 25 User-Agent: Gnus/5.0808 (Gnus v5.8.8) Emacs/20.7 MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hannes Loeffler writes: > 2) Statistics is considerably improved if multiple time origins are > taken into account. Here's a trick that is not as widely known as it should be: You can do an average over all possible time origins with little effort by 1) Expanding the square in the MSD expression. 2) Calculate the correlation function term in the expansion by Fourier transforms (FFT). Although an average over all possible time origins is exaggerated (the corresponding subtrajectories are not all independent), this procedure is much faster than averaging over a moderate amount of time origins in the standard way, due to the efficiency of the FFT algorithm. -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@cnrs-orleans.fr Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.56.24 Rue Charles Sadron | Fax: +33-2.38.63.15.17 45071 Orleans Cedex 2 | Deutsch/Esperanto/English/ France | Nederlands/Francais ------------------------------------------------------------------------------- From chemistry-request@server.ccl.net Fri May 31 02:35:23 2002 Received: from hamlin.cc.boun.edu.tr ([193.140.192.230]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4V6ZMC01715 for ; Fri, 31 May 2002 02:35:22 -0400 Received: by hamlin.cc.boun.edu.tr (Postfix, from userid 757) id 056DE1F8E; Fri, 31 May 2002 09:29:01 +0300 (EET DST) Received: from localhost (localhost [127.0.0.1]) by hamlin.cc.boun.edu.tr (Postfix) with ESMTP id EBA401C0D for ; Fri, 31 May 2002 09:29:01 +0300 (EET DST) Date: Fri, 31 May 2002 09:29:01 +0300 (EET DST) From: Nurcan Senyurt X-Sender: senyurtn@hamlin.cc.boun.edu.tr To: chemistry@ccl.net Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers I am trying to find how much two atoms in a transition state overlap with the Gaussian 98 programme. (These atoms are the reacting sites in the TS). Does anybody know any keyword? Thanks in advance. Best Regards