From chemistry-request@ccl.net Wed Oct 22 17:59:51 2003 Received: from antivirus2.its.rochester.edu (antivirus2.its.rochester.edu [128.151.57.53]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9MLxKMV028617 for ; Wed, 22 Oct 2003 17:59:20 -0400 Received: from antivirus2.its.rochester.edu (localhost [127.0.0.1]) by antivirus2.its.rochester.edu (8.12.9/8.12.4) with ESMTP id h9MLxIHg015196 for ; Wed, 22 Oct 2003 17:59:19 -0400 (EDT) Received: from mail.rochester.edu (mail1.ats.rochester.edu [128.151.224.31]) by antivirus2.its.rochester.edu (8.12.9/8.12.4) with SMTP id h9MLxI1R015192; Wed, 22 Oct 2003 17:59:18 -0400 (EDT) Received: from mail.rochester.edu (mail.rochester.edu [128.151.224.17]) by mail.rochester.edu (8.12.10/8.12.1) with SMTP id h9MLxHSZ006040; Wed, 22 Oct 2003 17:59:18 -0400 (EDT) Sender: weiz=at=mail.rochester.edu From: "weiz" Reply-to: weiz=at=mail.rochester.edu To: Christoph Dellago , Christoph Dellago Cc: chemistry=at=ccl.net Subject: a question about g(r) for heteroatoms X-Mailer: Quality Web Email v3.0q, http://netwinsite.com/refw.htm Date: Wed, 22 Oct 2003 17:59:17 -0400 Priority: normal Message-id: <3f96fdb5.1796.17301=at=mail.rochester.edu> X-Spam-Status: No, hits=2.6 required=7.0 tests=DEAR_SOMETHING version=2.55 X-Spam-Level: ** X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear Sir: I have a problem to calculate the g(r) for heteroatoms. the system that I am studying is a peptide in DMSO system.now I want to calculate the g(r) for the polar H of peptide (which are the ones connected to nitrogens) and the peptide Oxygen atoms ( on the C=O bond),I want to use it to check the intramolecular hydrogen bonding property of this peptide in different stages of the peptide dynamics. ok,now,what I did is based on the algorithm in frenkel's book for the homoatoms: for one specific stage during the relaxation,I sampled 4000 configurations,then I calcualte all the O-H distances and seperate them into different bins according to the lengths. when a distance falls into one specific bin [r,r+1],I add 1 to the counter GNUM ( in frenkel,it counts 2,but mine is a heteroatom system,which means I look at the hydrogen \ bonding from the oxygen side), now I calculate the condition for ideal gas, first I calculate the volume of the bin V,which is 4/3 * ((r+1)^3-r^3),then I need to calculate the number of hydrogen atoms fall into this neighbor of one oxygen in the ideal gas condition,thus I simply use the number density of hydrogen atoms rho(H) (number of polar H divided by the cell volume ) multiply the bin volume V and the number 4000,GNUM_ig=rho(H)*V*4000,then I obtain g(r) by GNUM/GNUM_ig. this method looks ok,but wait!!,if I take a look at the hydrogen bonding > from hydrogen atoms' side,then GNUM is the same but GNUM_ig will be different if the numbers of oxygen and polar hydrogen are different,then g(r) will be different,what is the problem? I know there are many references about calculating the g(r) for heteroatoms,please give me some comment and/or refer me to some references. Wei From chemistry-request@ccl.net Wed Oct 22 14:37:29 2003 Received: from sentinel.ucr.edu (sentinel.ucr.edu [138.23.226.228]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9MIauMV023409 for ; Wed, 22 Oct 2003 14:36:57 -0400 Received: from dopetec (dunn4470.ucr.edu [138.23.156.82]) by sentinel.ucr.edu (Mirapoint Messaging Server MOS 3.2.1-GA) with ESMTP id ASC07956 for ; Wed, 22 Oct 2003 11:36:51 -0700 (PDT) Reply-To: From: "Donald Keidel" To: Subject: Searchable Chemical Database - Substructures and Similarity Date: Wed, 22 Oct 2003 11:36:49 -0700 Organization: UCR Message-ID: <003b01c398cb$743ddc20$529c178a@dopetec> MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.3416 Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-Spam-Status: No, hits=0.0 required=7.0 tests=none version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hello, I am looking for a web site or program that allows an organic chemist or a biochemist looking for potential ligand candidates for a protein to search a huge chemical database of known compounds based on a substructure or similarity search. I have tried the Aldrich one, SciFinder Scholar, and the one that comes with Chem Office (ACX), but I was wondering if there are more that might be more comprehensive and might have links to the manufacturer of the chemical so that it can be purchased. We would like to bind these chemical directly or use them as synthons in organic synthesis reactions. Thank you in advance for all help. Don ------------------------------------------------------------------------ --------------------------------------- Donald J. Keidel University of California, Riverside Department of Biochemistry and Molecular Biology Riverside, CA 92521 phone: (909) 787-5493 fax: (909) 787-4434 dopetec=at=dslextreme.com webpage: www.biochemistry.ucr.edu/gru/gradstudents/don_keidel/index.htm From chemistry-request@ccl.net Wed Oct 22 12:46:49 2003 Received: from mr1.cc.ic.ac.uk (mr1.cc.ic.ac.uk [155.198.5.111]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9MGkIMV017789 for ; Wed, 22 Oct 2003 12:46:18 -0400 Received: from rzepa-g5.ch.ic.ac.uk ([155.198.36.88]) by mr1.cc.ic.ac.uk with esmtp (Exim 3.36 #1) id 1ACM7m-0002vM-01 for chemistry~at~ccl.net; Wed, 22 Oct 2003 17:46:18 +0100 Mime-Version: 1.0 X-Sender: rzepa~at~argon.ch.ic.ac.uk Message-Id: In-Reply-To: References: Date: Wed, 22 Oct 2003 17:46:12 +0100 To: chemistry~at~ccl.net From: "Rzepa, Henry" Subject: Re: CCL:XDfile format Reviews Content-Type: text/plain; charset="us-ascii" X-Spam-Status: No, hits=-1.0 required=7.0 tests=IN_REP_TO,REFERENCES version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) >MDL is not working on converting the structure data into XML format. Much >work has been done by the CML group and we see no need to repeat their work. >Our focus in on high volume structural data processing and compact >representations are required to give the best performance. The XDfile can >accommodate any structural data format and we believe that a CML >representation can be used in the file. And just to remind people that information about CML can be found at http://cml.sourceforge.net/, including how to subscribe to cml-discuss (where the current topic is CMLComp, as I believe Peter has already posted to this list). -- Henry Rzepa. +44 (020) 7594 5774 (Voice); +44 (0870) 132 3747 (eFax) http://www.ch.ic.ac.uk/rzepa/ Dept. Chemistry, Imperial College London, SW7 2AZ, UK. From chemistry-request@ccl.net Thu Oct 23 09:29:30 2003 Received: from casbah.it.northwestern.edu (casbah.it.northwestern.edu [129.105.16.52]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9NDSxMV014081 for ; Thu, 23 Oct 2003 09:28:59 -0400 Received: (from mailnull@localhost) by casbah.it.northwestern.edu (8.12.10/8.12.10) id h9NDSwET021036 for ; Thu, 23 Oct 2003 08:28:58 -0500 (CDT) Received: from chief (chief.chem-eng.northwestern.edu [129.105.205.171]) by casbah.it.northwestern.edu via smap (V2.0) id xma020482; Thu, 23 Oct 03 08:28:46 -0500 From: "Jim Pfaendtner" To: Subject: Help With Gaussian 98 Hindered Rotor Calculations Date: Thu, 23 Oct 2003 08:28:47 -0500 Message-ID: <000201c39969$968ee9b0$abcd6981@chief> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0003_01C3993F.ADB8E1B0" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.2627 Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-Spam-Status: No, hits=0.6 required=7.0 tests=HTML_70_80,HTML_MESSAGE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) This is a multi-part message in MIME format. ------=_NextPart_000_0003_01C3993F.ADB8E1B0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Hello, I am trying to use the hindered rotor approximation for frequency calculations on benzyl radicals such as styrene radicals. I am using Gaussian 98 with G3//B3LYP level of theory. When using the command freq=hindrot after geometry optimization is complete, Gaussian crashes with the error message "problem with the number of degrees of freedom". If I replace the radical with a hydrogen (e.g. toluene or styrene) I have no problems completing the calculations. Does anyone have any suggestions/experience with this? Thanks much ------=_NextPart_000_0003_01C3993F.ADB8E1B0 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Hello,

 

I am trying to use the hindered rotor approximation = for frequency calculations on benzyl radicals such as styrene radicals.  I am using Gaussian 98 with = G3//B3LYP level of theory.  When = using the command freq=3Dhindrot after geometry = optimization is complete, Gaussian crashes with the error message “problem with = the number of degrees of freedom”.  If I replace the radical with a = hydrogen (e.g. toluene or styrene) I have no problems completing the calculations. =

 

Does anyone have any suggestions/experience with = this?

 

Thanks much

 

------=_NextPart_000_0003_01C3993F.ADB8E1B0-- From chemistry-request@ccl.net Thu Oct 23 08:59:33 2003 Received: from sun-blade.cnrs-orleans.fr (sun-blade.cnrs-orleans.fr [163.9.1.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9NCx1MV013498 for ; Thu, 23 Oct 2003 08:59:02 -0400 Received: from chinon (chinon.cnrs-orleans.fr [163.9.6.107]) by sun-blade.cnrs-orleans.fr (8.12.10/jtpda-5.4) with ESMTP id h9NCtOkW028770 ; Thu, 23 Oct 2003 14:55:24 +0200 (MEST) Content-Type: text/plain; charset="us-ascii" From: Konrad Hinsen To: "chemistry{at}ccl.net" Subject: Announcement: new FSAtom work group on open standards for Molecular Mechanics Date: Thu, 23 Oct 2003 14:59:09 +0200 User-Agent: KMail/1.4.3 MIME-Version: 1.0 Message-Id: <200310231459.09542.hinsen{at}cnrs-orleans.fr> X-MailScanner: Found to be clean X-Spam-Status: No, hits=0.0 required=7.0 tests=USER_AGENT_KMAIL version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h9NCxXMV013517 The FSatom Work Group on "Open Standards for Molecular Mechanics" aims to bring open standards to the molecular simulation community, in order to facilitate the exchange of information, to eliminate duplicate work. and to aid in the comparison of results between different molecular simulation codes. The initial aim of the group is to develop open standards for describing structural information about molecular systems and for storing simulated trajectories. Such standardized file formats would facilitate the combined use of different simulation and analysis codes as well as the creation of archives that are useful to the whole community. Additionally, it would eliminate the need for the time- consuming and error-prone process of file conversion. Standards are useful only if they are accepted by a sufficiently large number of programs. The work group currently includes developers working on the simulation packages AMBER, CHARMM, GROMACS, MMTK, and TINKER. Sufficient support of the newly developed standards can therefore be expected. The work group is open to all interested scientists and program developers. For more information, see http://dirac.cnrs-orleans.fr/fsatom_wiki/MolecularMechanicsOpenStandards About FSAtom: The Free Software project for Atomic-scale Simulation (FSAtom) has the aim to spread the use of the ``Free Software'' concept in the community of Atomic-scale Simulation software developers, to improve the awareness of modern software engineering concepts, and to constitute the natural place for interactions between different groups of developers in this field. For more information, see www.fsatom.org. -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen{at}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@ccl.net Thu Oct 23 04:03:42 2003 Received: from exchangesrv01.nuevolution.com ([80.196.27.25]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9N839MV005967 for ; Thu, 23 Oct 2003 04:03:10 -0400 X-MimeOLE: Produced By Microsoft Exchange V6.0.5762.3 content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Subject: RE: Searchable Chemical Database - Substructures and Similarity Date: Thu, 23 Oct 2003 10:06:48 +0200 Message-ID: X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: Searchable Chemical Database - Substructures and Similarity Thread-Index: AcOZKbE7GR5HbNsVSam+dBTmEak6MgAEj79Q From: =?iso-8859-1?Q?Mads_N=F8rregaard-Madsen?= To: "Donald Keidel" , X-Spam-Status: No, hits=0.0 required=7.0 tests=none version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h9N83gMV005992 Hi Donald, I recall receiving a free CD from MDD with a database of virtually available compounds collected from hundreds of companies and universities around the world - maybe it could be of use? Their website is www.worldmolecules.com /Mads ------------------------------------------ Mads Nxrregaard-Madsen, PhD. Director of Molecular Design Nuevolution A/S Rxnnegade 8 DK2100 Copenhagen www.nuevolution.com -----Original Message----- From: Donald Keidel [mailto:dopetec{at}dslextreme.com] Sent: Wednesday, October 22, 2003 8:37 PM To: chemistry{at}ccl.net Subject: CCL:Searchable Chemical Database - Substructures and Similarity Hello, I am looking for a web site or program that allows an organic chemist or a biochemist looking for potential ligand candidates for a protein to search a huge chemical database of known compounds based on a substructure or similarity search. I have tried the Aldrich one, SciFinder Scholar, and the one that comes with Chem Office (ACX), but I was wondering if there are more that might be more comprehensive and might have links to the manufacturer of the chemical so that it can be purchased. We would like to bind these chemical directly or use them as synthons in organic synthesis reactions. Thank you in advance for all help. Don ------------------------------------------------------------------------ --------------------------------------- Donald J. Keidel University of California, Riverside Department of Biochemistry and Molecular Biology Riverside, CA 92521 phone: (909) 787-5493 fax: (909) 787-4434 dopetec{at}dslextreme.com webpage: www.biochemistry.ucr.edu/gru/gradstudents/don_keidel/index.htm -= This is automatically added to each message by the mailing script =- To send e-mail to subscribers of CCL put the string CCL: on your Subject: line and send your message to: CHEMISTRY{at}ccl.net Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST{at}ccl.net HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs If your mail is bouncing from CCL.NET domain send it to the maintainer: Jan Labanowski, jkl{at}ccl.net (read about it on CCL Home Page) -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@ccl.net Thu Oct 23 02:44:12 2003 Received: from sesosn01.astrazeneca.com (sesosn01.astrazeneca.com [212.209.42.131]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9N6heMV004308 for ; Thu, 23 Oct 2003 02:43:41 -0400 Received: from sesosn11.seso.astrazeneca.net (sesosn11.seso.astrazeneca.net [192.168.199.18]) by sesosn01.astrazeneca.com (8.12.10/8.12.10) with ESMTP id h9N6hX8V015818; Thu, 23 Oct 2003 08:43:39 +0200 (MET DST) Received: from sesosn21.seso.astrazeneca.net (sesosn21.seso.astrazeneca.net [192.71.145.181]) by sesosn11.seso.astrazeneca.net (8.12.10/8.12.10/AZ-def_main_in.12.10.0) with ESMTP id h9N6gvpM008295; Thu, 23 Oct 2003 08:42:57 +0200 (MET DST) Received: from astra-cdc-x03.seso.astrazeneca.net (astra-cdc-x03.seso.astrazeneca.net [192.71.145.48]) by sesosn21.seso.astrazeneca.net (8.12.10/8.12.10) with ESMTP id h9N6gvHq018080; Thu, 23 Oct 2003 08:42:57 +0200 (MET DST) Received: by astra-cdc-x03.seso.astrazeneca.net with Internet Mail Service (5.5.2650.21) id <47G60XQT>; Thu, 23 Oct 2003 08:42:56 +0200 Message-ID: <710925AD6A27D6118B050002A5F0889301D79150{at}semldsntmsx205.seml.astrazeneca.net> From: Sorel.Muresan{at}astrazeneca.com To: dopetec{at}dslextreme.com Cc: chemistry{at}ccl.net Subject: RE: Searchable Chemical Database - Substructures and Similarity Date: Thu, 23 Oct 2003 08:39:25 +0200 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-Type: text/plain; charset="iso-8859-1" X-Spam-Status: No, hits=1.0 required=7.0 tests=MSG_ID_ADDED_BY_MTA_3,NO_REAL_NAME,ORIGINAL_MESSAGE version=2.55 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h9N6iCMV004320 Hi Don, Try ChemNavigator at www.chemnavigator.com (you have to register). You'll get access to more than 12 million chemical samples, a search interface, and all info to order compounds. Cheers, Sorel. Sorel Muresan, PhD AstraZeneca R&D Mvlndal EST Chemical Computing Pepparedsleden 1, 431 83 Mvlndal, Sweden Tel: +46-31-7065283 Fax: +46-31-7763792 sorel.muresan{at}astrazeneca.com -----Original Message----- From: Donald Keidel [mailto:dopetec{at}dslextreme.com] Sent: torsdag, oktober 23, 2003 07:17 To: chemistry{at}ccl.net Subject: CCL:Searchable Chemical Database - Substructures and Similarity Hello, I am looking for a web site or program that allows an organic chemist or a biochemist looking for potential ligand candidates for a protein to search a huge chemical database of known compounds based on a substructure or similarity search. I have tried the Aldrich one, SciFinder Scholar, and the one that comes with Chem Office (ACX), but I was wondering if there are more that might be more comprehensive and might have links to the manufacturer of the chemical so that it can be purchased. We would like to bind these chemical directly or use them as synthons in organic synthesis reactions. Thank you in advance for all help. Don ------------------------------------------------------------------------ --------------------------------------- Donald J. Keidel University of California, Riverside Department of Biochemistry and Molecular Biology Riverside, CA 92521 phone: (909) 787-5493 fax: (909) 787-4434 dopetec{at}dslextreme.com webpage: www.biochemistry.ucr.edu/gru/gradstudents/don_keidel/index.htm -= This is automatically added to each message by the mailing script =- To send e-mail to subscribers of CCL put the string CCL: on your Subject: line and send your message to: CHEMISTRY{at}ccl.net Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST{at}ccl.net HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs If your mail is bouncing from CCL.NET domain send it to the maintainer: Jan Labanowski, jkl{at}ccl.net (read about it on CCL Home Page) -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@ccl.net Thu Oct 23 10:52:52 2003 Received: from mercury.chem.pitt.edu (mercury.chem.pitt.edu [136.142.60.100]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9NEqKMV016365 for ; Thu, 23 Oct 2003 10:52:21 -0400 Received: from ringo.chem.pitt.edu (localhost.localdomain [127.0.0.1]) by mercury.chem.pitt.edu (Postfix) with SMTP id 5AEDB483D for ; Thu, 23 Oct 2003 10:20:37 -0400 (EDT) Received: from 150.161.200.40 (SquirrelMail authenticated user gustavo) by mercury.chem.pitt.edu with HTTP; Thu, 23 Oct 2003 10:20:37 -0400 (EDT) Message-ID: <1500.150.161.200.40.1066918837.squirrel~at~mercury.chem.pitt.edu> Date: Thu, 23 Oct 2003 10:20:37 -0400 (EDT) Subject: Summary: Absorption Cross Section From: To: X-Priority: 3 Importance: Normal X-Mailer: SquirrelMail (version 1.2.11) MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Spam-Status: No, hits=0.8 required=7.0 tests=NO_REAL_NAME version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear CCL readers, here you have the summary to my question about absorption cross sections. I thank Prof. Egbert Zojer for his answer. Basically, he too is looking for a reference describing the derivation of the equation that relates the two-photon absorption cross section to Im[gamma]. sincerely yours, Gustavo L.C. Moura gustavo~at~mercury.chem.pitt.edu Original question: Dear CCL readers, I have read several papers about the calculation of the cross sections for two-photon absorption (d). The value of d as a function of the frequency of the incident photon (w) is related to the imaginary part of the second hyperpolarizability gamma(-w;w,w,-w) through d=(8*pi^2*hbar*w^2)/(n*c)^2*Im[gamma(-w;w,w,-w)] where n is a refractive index and c is the speed of light. None of the papers I have read so far say where the equation above came from. So my question is: Does anybody on this list know the origin of the equation above? Reference? I am also curious to know if there is a similar equation relating the imaginary part of the polarizability alpha(-w;w) to a cross section for one-photon absorption. Is this cross section simply the oscillator strength for the one photon transition? Thank you very much in advance. I will summarize if I receive any answer. Gustavo Moura gustavo~at~mercury.chem.pitt.edu Answer: Dear Gustavo, You can, e.g., get this equation by solving the wave equations for a damped non-linear medium. I am pretty sure that it has to be somewhere in the literature, but I also could not find it, so I did the derivation myself starting from the un-damped equations as you can find them e.g. in Boyd "Nonlinear Optics". The linear absorption coefficient is proportional to Energy times Im(alpha). This you should, however, find in most textbooks about electrodynamics and you can simply get it from the linear damped wave equations - just include a complex k-vector in your plane wave, put it into the wave equations and you will see that the amplitude decreases. regards, egbert P.S.: If anyone can point you to a derivation of delta prop. Im(gamma) in the literature, would be very interested to know it. At 10:28 PM 10/19/2003 -0400, you wrote: --------------------------------------------------------------------------- A.o. Univ.-Prof. Dr. Egbert Zojer Tel.:++43/316/873-8475 Advanced Materials Division Fax.:++43/316/873-8478 Institute of Solid State Physics Graz University of Technology e-mail.: egbert.zojer~at~tugraz.at Petersgasse 16, 8010 Graz, AUSTRIA http://www.cis.TUGraz.at/if/egbert.htm --------------------------------------------------------------------------- currently at the School of Chemistry and Biochemistry Georgia Institute of Technology Atlanta, GA 30332-0400 Tel.: ++1/404/385-4984 FAX.: ++1/404/894-7452 --------------------------------------------------------------------------- From chemistry-request@ccl.net Thu Oct 23 19:44:42 2003 Received: from red.CACheSoftware.com ([12.17.172.66]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9NNi9MV031286 for ; Thu, 23 Oct 2003 19:44:09 -0400 Received: from DAVEG-LIFEBOOK.cachesoftware.com (netscreen.cachesoftware.com [12.17.172.74]) by red.CACheSoftware.com (8.11.6/8.9.3/3) with ESMTP id h9NNn5Y07909; Thu, 23 Oct 2003 16:49:05 -0700 Message-Id: <5.2.1.1.0.20031023162230.03174f70|at|mail.cachesoftware.com> X-Sender: daveg|at|mail.cachesoftware.com (Unverified) X-Mailer: QUALCOMM Windows Eudora Version 5.2.1 Date: Thu, 23 Oct 2003 16:36:35 -0700 To: chemistry|at|ccl.net From: David Gallagher Subject: FREE 3D Auto-stereoscopic Laptop with CAChe Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====================_20959408==.ALT" X-Spam-Status: No, hits=2.0 required=7.0 tests=HTML_20_30,HTML_MESSAGE,SUBJ_FREE_CAP version=2.55 X-Spam-Level: ** X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) --=====================_20959408==.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed The new Sharp 3D Auto-stereoscopic Windows Laptop is being offered free of charge with qualifying commercial orders for CAChe & BioMedCAChe software packages. 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The Sharp laptop can also show movies and PowerPoint presentations in 3D stereo and you can convert your photos to display in 3D stereo with an optional application. The brief laptop specifications are as follows:

          Sharp Actius RD3D Laptop Computer:
     Screen: 15" 3D-LCD XGA switchable auto-stereoscopic (no glasses required)
     2.8GHz Pentium 4 with 512 MB DDR266 SDRAM (Max: 1GB)
     Video: nVidia GeHForce4 440 Go with 64MB DDR VRAM
     DVD-R/RW/RAM and CD-R/RW (CD & DVD writer)
     60GB Hard drive, Windows XP

For full details and limitations of this offer or a demonstration of CAChe, please contact sales|at|CACheSoftware.com.

CAChe Group, Fujitsu
Tel: 1 503 746 3602
Email: sales|at|CACheSoftware.com
http://www.cachesoftware.com/



==============================================
  David A. Gallagher, C. Chem.
  Vice President, Sales and Marketing
  CAChe Group
  Fujitsu America, Inc.
  15244 NW Greenbrier Parkway
  Beaverton, OR 97006-5733, USA
  Direct dial:          503 746 3607
  Main Switchboard:     503 746 3600
  Fax:                  503 531 9966
  email: dgallagher|at|cachesoftware.com
  http://www.cachesoftware.com
  http://www.cachesoftware.com/staff/dg.shtml
============================================== --=====================_20959408==.ALT-- From chemistry-request@ccl.net Thu Oct 23 18:18:02 2003 Received: from red.CACheSoftware.com ([12.17.172.66]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9NMHUMV030170 for ; Thu, 23 Oct 2003 18:17:31 -0400 Received: from DAVEG-LIFEBOOK.cachesoftware.com (netscreen.cachesoftware.com [12.17.172.74]) by red.CACheSoftware.com (8.11.6/8.9.3/3) with ESMTP id h9NMMXY05247; Thu, 23 Oct 2003 15:22:33 -0700 Message-Id: <5.2.1.1.0.20031023141121.032efb60_at_mail.cachesoftware.com> X-Sender: daveg_at_mail.cachesoftware.com (Unverified) X-Mailer: QUALCOMM Windows Eudora Version 5.2.1 Date: Thu, 23 Oct 2003 15:09:19 -0700 To: chemistry_at_ccl.net From: David Gallagher Subject: CCL: New FastDock & ActiveSite tools Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====================_15768594==.ALT" X-Spam-Status: No, hits=1.5 required=7.0 tests=HTML_10_20,HTML_MESSAGE version=2.55 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) --=====================_15768594==.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed The new ActiveSite(TM) module for BioMedCAChe 6.11, incorporating FastDock(TM), has just been released for Windows. FastDock(TM) automatically docks rigid or flexible ligands into proteins with rigid or flexible side chains, and uses a lamarckian genetic algorithm for docking and an enhanced PMF method for scoring. To request a demonstration or more information please contact sales_at_CACheSoftware.com . CAChe Group, Fujitsu Tel: 1 503 746 3602 Email: sales_at_CACheSoftware.com http://www.cachesoftware.com/ --=====================_15768594==.ALT Content-Type: text/html; charset="us-ascii" The new ActiveSite(TM) module for BioMedCAChe 6.11, incorporating FastDock(TM), has just been released for Windows. FastDock(TM) automatically docks rigid or flexible ligands into proteins with rigid or flexible side chains, and uses a lamarckian genetic algorithm for docking and an enhanced PMF method for scoring. To request a demonstration or more information please contact sales_at_CACheSoftware.com .

CAChe Group, Fujitsu
Tel: 1 503 746 3602
Email: sales_at_CACheSoftware.com
http://www.cachesoftware.com/

 --=====================_15768594==.ALT-- From chemistry-request@ccl.net Thu Oct 23 20:43:34 2003 Received: from pado.krict.re.kr (pado.krict.re.kr [203.250.27.9]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9O0h1MV032038 for ; Thu, 23 Oct 2003 20:43:02 -0400 Received: from anakin (localhost.localdomain [127.0.0.1]) by pado.krict.re.kr (8.11.6/8.11.6) with ESMTP id h9O0hsu13095 for ; Fri, 24 Oct 2003 09:43:54 +0900 From: =?ks_c_5601-1987?B?sejA5bno?= To: Subject: anisotropic effect calculation Date: Fri, 24 Oct 2003 09:43:02 +0900 Message-ID: <000001c399c7$c8a760e0$7004facb@anakin> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0001_01C39A13.38921620" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.2627 Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-Spam-Status: No, hits=4.2 required=7.0 tests=HTML_70_80,HTML_COMMENT_8BITS,HTML_FONT_FACE_BAD, HTML_FONT_FACE_ODD,HTML_MESSAGE version=2.55 X-Spam-Level: **** X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) This is a multi-part message in MIME format. ------=_NextPart_000_0001_01C39A13.38921620 Content-Type: text/plain; charset="ks_c_5601-1987" Content-Transfer-Encoding: quoted-printable Dear CCL readers, =20 I'm trying to find how to interpret output of gaussian 98 when calculating theoretical NMR chemical shift of transition metal=20 complexes(Cobalt complexes) with axial ligand connected vertically in a somewhat looks like a porphyrin ring. I do know how to calculate NMR chemical shift(Proton and Carbon NMR chemical shifts) using isotopic result.=20 However, since my complexes has axial ligand that should be considered with anisotropic effect from whole metal complexes I do believe that I cannot calculate NMR chemical shift with isotropic result from G98 output.=20 Also, if anyone who have had made an input file of transition metal(Cobalt or any other metals) complexes,=20 may I see an example of it so that I can get a hang of how I should make an input file when dealing with Metal Complexes.=20 I would really like to hear from any of you soon. You can reach me at wjlee_at_guanine.hanyang.ac.kr=20 =20 Thank you for spending your precious time to read this note. =20 =20 Regards, =20 Jangbae * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * =BE=EE=B6=B2 =C0=CF=C0=BB =C7=CF=B1=E2=BF=A1 =B0=A1=C0=E5 =C1=C1=C0=BA, = =BF=CF=BA=AE=C7=D1 =B1=E2=C8=B8=B4=C2 =BE=F8=BD=C0=B4=CF=B4=D9. =BF=CF=C0=FC=C7=D1 =BC=F8=B0=A3=B5=B5 =BE=F8=BD=C0=B4=CF=B4=D9. =B1=D7 = =BF=CF=BA=AE=C7=D1 =B1=E2=C8=B8, =BF=CF=C0=FC=C7=D1 =BC=F8=B0=A3=B8=B8=C0=BB = =B1=E2=B4=D9=B8=B0=B4=D9=B8=E9 =C6=F2=BB=FD =B1=E2=B4=D9=B8=AE=B4=D9 = =B3=A1=C0=CC =B3=B3=B4=CF=B4=D9. =BF=EB=B1=E2, =B8=F0=C7=E8=BD=C9, =B0=E1=B4=DC=B7=C2=C0=CC = =BF=EC=B8=AE=B8=A6 =BB=F5=B7=CE=BF=EE =BA=AF=C8=AD, =BB=F5=B7=CE=BF=EE =B1=E2=C8=B8=C0=C7 =C1=D6=C0=CE=B0=F8=C0=CC = =B5=C7=B0=D4 =C7=D5=B4=CF=B4=D9. =B1=E2=C8=B8=B4=C2 =B8=B8=B5=E5=B4=C2 =B0=CD=C0=CC=C1=F6 = =C1=D6=BE=EE=C1=F6=B4=C2 =B0=CD=C0=CC =BE=C6=B4=D5=B4=CF=B4=D9. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Jangbae Kim Researcher Bio-Organic Science Division Korea Research Institute of Chemical Technology (KRICT) P.O.Box 107, Yuseong, Taejeon, 305-600, Korea TEL. : +82-42-860-7067 FAX. : +82-42-861-0307 E-mail : jbkim_at_krict.re.kr * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * =20 ------=_NextPart_000_0001_01C39A13.38921620 Content-Type: text/html; charset="ks_c_5601-1987" Content-Transfer-Encoding: quoted-printable

Dear CCL readers,

 

I'm trying to find how to interpret output of gaussian 98 = when calculating theoretical NMR chemical shift of transition metal =

complexes(Cobalt complexes) with axial ligand connected vertically in a somewhat looks like a porphyrin ring.

I do know how to calculate NMR chemical shift(Proton and = Carbon NMR chemical shifts) using isotopic result. =

However, since my complexes has axial ligand that = should be considered with anisotropic effect from whole metal complexes I do = believe that I cannot calculate NMR chemical shift with isotropic result from G98 = output.

Also, if anyone who have had made an input file of transition metal(Cobalt or any other metals) complexes,

may I see an example of it so that I can get a hang of how I = should make an input file when dealing with = Metal Complexes. 

I would really like to hear from any of you soon. You can reach me at wjlee:at:guanine.hanyang.ac.kr

 

Thank you for spending your precious time to read this note. =  

 

Regards,

 

Jangbae

* * * * * * * * * * * * * * * * * * * = * = * * * = * * * * * * * * * * *     

=BE=EE=B6=B2 =C0=CF=C0=BB = =C7=CF=B1=E2=BF=A1 =B0=A1=C0=E5 =C1=C1=C0=BA, = =BF=CF=BA=AE=C7=D1 =B1=E2=C8=B8=B4=C2 = =BE=F8=BD=C0=B4=CF=B4=D9.

=BF=CF=C0=FC=C7=D1 = =BC=F8=B0=A3=B5=B5 =BE=F8=BD=C0=B4=CF=B4=D9. =B1=D7 = =BF=CF=BA=AE=C7=D1 =B1=E2=C8=B8,

=BF=CF=C0=FC=C7=D1 = =BC=F8=B0=A3=B8=B8=C0=BB =B1=E2=B4=D9=B8=B0=B4=D9=B8=E9 =C6=F2=BB=FD = =B1=E2=B4=D9=B8=AE=B4=D9 =B3=A1=C0=CC =B3=B3=B4=CF=B4=D9.

=BF=EB=B1=E2, =B8=F0=C7=E8=BD=C9, =B0=E1=B4=DC=B7=C2=C0=CC = =BF=EC=B8=AE=B8=A6 =BB=F5=B7=CE=BF=EE = =BA=AF=C8=AD,

=BB=F5=B7=CE=BF=EE = =B1=E2=C8=B8=C0=C7 =C1=D6=C0=CE=B0=F8=C0=CC =B5=C7=B0=D4 = =C7=D5=B4=CF=B4=D9.

=B1=E2=C8=B8=B4=C2 = =B8=B8=B5=E5=B4=C2 =B0=CD=C0=CC=C1=F6 =C1=D6=BE=EE=C1=F6=B4=C2 = =B0=CD=C0=CC =BE=C6=B4=D5=B4=CF=B4=D9.

* * * * * * * * * * * * * * * * * * = * = * * * = * * * * * * * * * * * *

<= font size=3D2 face=3D=B9=D9=C5=C1>Jangbae = Kim

Researcher

Bio-Organic Science Division

Korea Research Institute of Chemical Technology (KRICT)

P.O= .Box 107,  Yuseong, Taejeon, 305-600, = Korea

TEL. : +82-42-860-7067

FAX. : +82-42-861-0307

E-mail : jbkim:at:krict.re.kr<= /font>

* * * * * * * * * * * * * * * * * * * = * = * * * = * * * * * * * * * * *

 

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