From chemistry-request@server.ccl.net Sun Feb 11 12:08:12 2001 Received: from mailgate.ice.mpg.de (IDENT:root@mailgate.ice.mpg.de [195.37.47.9]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1BH8Bw09871 for ; Sun, 11 Feb 2001 12:08:11 -0500 Received: from ice.mpg.de (relax.ice.mpg.de [195.37.47.207]) by mailgate.ice.mpg.de (8.9.3/8.9.3) with ESMTP id SAA21784; Sun, 11 Feb 2001 18:06:48 +0100 Message-ID: <3A86C6FA.6EA7F0CB@ice.mpg.de> Date: Sun, 11 Feb 2001 18:08:10 +0100 From: Christoph Steinbeck Reply-To: steinbeck@ice.mpg.de Organization: Max-Planck-Institute of Chemical Ecology X-Mailer: Mozilla 4.75 [en] (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: ccl , "CHMINF-L@LISTSERV.INDIANA.EDU" , "jchempaint-devel@lists.sourceforge.net" , "compchem-cdk-dev@lists.sourceforge.net" Subject: ANNOUNCEMENT: JChemPaint 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit It is our pleasure to announce the release 1.0 of JChemPaint. JChemPaint is a Java 2 program for drawing 2D chemical structures like those found in most chemistry textbooks. The program is developed as an Open Source Project and released under GNU Lesser General Public License (LGPL). Since written in Java, the program should run under Win32, Linux, Solaris, AIX and all others OS's for which Java 2 is available. JChemPaint is developed by Christop Steinbeck, Egon Willighagen, Martin Schild, Stefan Krause and others and hosted by SourceForge (http://jchempaint.sourceforge.net and http://sourceforge.net/projects/jchempaint) Version 1.0 is a feature-freeze and bug-fix release. We are now going to move JChemPaint to a new base library, the Chemistry Development Kit (CDK). The CDK (http://compchem.sourceforge.net) is a rewrite of the old compchem library with clear object-oriented design and full documentation. Changes in version 1.0: - bugfixes for: #127756, #131892, #131898 and #128070 - New features in version 0.8: - Clean up of multiple molecules in one document now works. - Colouring of substructures. - Now possible to assign charges to atoms. - Drawing of implicit hydrogens. - Structures can now be accompanied with some properties: Generator, Software, CAS-number and generation date. - Insert SMILES functionality (By entering them in a pop-up window) - Help functionality with complete user manual. - Greatly improved website - Export filter for SVG. - Print capabilities. For those who just want to run the program, we recommend the binary version. More information as well as a download option can be found on http://jchempaint.sourceforge.net. JChemPaint is associated with the OpenScience project (www.openscience.org) and the 3D molecular viewer Jmol (http://www.openscience.org/jmol/), both initiated by Dan Gezelter at the University of Notre Dame (http://www.nd.edu/~gezelter/) We would be happy to get some feedback from people who have downloaded and tested the program. Also people who want to join the development of JChemPaint or want to contribute code are welcome. -- Dr. Christoph Steinbeck (http://www.ice.mpg.de/departments/ChemInf) MPI of Chemical Ecology, Carl-Zeiss-Promenade 10, 07745 Jena, Germany Tel: +49(0)3641 643644 - Fax: +49(0)3641 643665 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. From chemistry-request@server.ccl.net Sun Feb 11 12:51:21 2001 Received: from mserv.itpa.lt (mserv.itpa.lt [193.219.53.20]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1BHm2w10057 for ; Sun, 11 Feb 2001 12:50:10 -0500 Received: from localhost (tamulis@localhost) by mserv.itpa.lt (8.11.1/8.11.0) with ESMTP id f1BHlOi19478; Sun, 11 Feb 2001 19:47:27 +0200 (EET) (envelope-from tamulis@itpa.lt) Date: Sun, 11 Feb 2001 19:47:23 +0200 (EET) From: Arvydas Tamulis To: cc: Jelena Tamuliene Subject: Paramagnetically shifted 1H NMR spectra Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters, We did not succeeded to calculate paramagnetically shifted 1H NMR spectrum of biliverdin molecule CuOEB using Gaussian 98 (see experimental data in J. Am. Chem.Soc., vol. 115, p. 12206 (1993)). We have optimized geometry of TeMeSilane molecule and obtained from NMR calculation the Isotropic Shielding values for H atoms (in ppm): H Isotropic = 31.9027 Anisotropy = 9.6413 XX= 29.4642 YX= 0.2951 ZX= -0.7329 XY= 0.4642 YY= 32.9871 ZY= -5.1492 XZ= -0.8947 YZ= -5.1015 ZZ= 33.2567 Eigenvalues: 27.9348 29.4430 38.3302 We have used Density Functional Theory B3PW91/6-311G** We have taken geometry of CuOEB from X-Ray experiment. Our B3PW91\6-311G** calculated CuOEB NMR Hm shielding values (ppm): 23 H Isotropic = 28.4781 Anisotropy = 10.0683 XX= 24.0637 YX= -1.2135 ZX= -.8179 XY= -.0906 YY= 35.1141 ZY= -2.2717 XZ= 9.0739 YZ= 1.6948 ZZ= 26.2566 Eigenvalues: 20.8808 29.3633 35.1904 60 H Isotropic = 27.5216 Anisotropy = 12.3793 XX= 22.4061 YX= 2.7621 ZX= -1.0495 XY= -.3733 YY= 35.4454 ZY= 2.7019 XZ= 10.0293 YZ= -6.4196 ZZ= 24.7134 Eigenvalues: 18.6646 28.1258 35.7745 and shielding Hm' value: 24 H Isotropic = 25.8868 Anisotropy = 16.3237 XX= 36.5750 YX= -.6396 ZX= 4.7813 XY= -.0379 YY= 23.9614 ZY= .1694 XZ= -.9100 YZ= 2.3766 ZZ= 17.1241 Eigenvalues: 16.7005 24.1907 36.7693 It means that our calculated chemical shifts for Hm and Hm' are equal to few ppm while CuOEB experimental NMR chemical shift values for Hm and Hm' in J. Am. Chem.Soc., vol 115, p. 12206 are equal approximately to 135 ppm and -100 ppm. Why so badly we have calculated paramagnetically shifted 1H NMR spectrum for CuOEB molecule? Maybe GAUSSIAN is not able to calculate paramagnetically shifted 1H NMR spectra? Which program is suitable for calculations of paramagnetically shifted 1H NMR spectra? Thanking your in advance. With best regards, Arvydas Tamulis & Jelena Tamuliene ******************************************************* Arvydas Tamulis Doctor of Natural Sciences, senior research fellow Institute of Theoretical Physics and Astronomy, 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 Phone: +(370-2)-778743