From owner-chemistry@ccl.net Tue Nov 13 04:40:01 2007 From: "Jia Hu hujia02+/-gmail.com" To: CCL Subject: CCL: Question about the Hirshfield charge analysis Message-Id: <-35597-071113043639-17601-lYbOOKSZP67eF+mz2IbF+A:-:server.ccl.net> X-Original-From: "Jia Hu" Date: Tue, 13 Nov 2007 04:36:35 -0500 Sent to CCL by: "Jia Hu" [hujia02() gmail.com] Dear CCLers, Recently I did Hirshfield charge analysis for a bunch of compounds in a 3D periodic table, all of them successfully optimized.BUT unfortunately,the resulting charge is rather too small: NaCl: +/- 0.2117; CaO: +/- 0.4243; Cu2O: +/-0.1686; CuO: +/-0.3273; ZnO: +/-0.3482 Even with the most ionic ones, such as NaCl or CaO, the data is no more than 0.5, which should have a normal charge +/- 1 and +/- 2 respectively and without much polarization.So question raises for How could I handle these results? It can be seen that the charge for CaO and CuO are namely about just 2 times large than NaCl and Cu2O respectively, fits weel about one's chemical imagination, but why is these charge so small? Do I need any re'evaluation? P.S.: My software is CASTEP and DMol3 in Accelrys' Material Studio package. Thanks for any reply! Jia Hu PhD student Lanzhou University China hujia02%gmail.com From owner-chemistry@ccl.net Tue Nov 13 08:58:01 2007 From: "Shaillay Dogra shaillay-$-strandls.com" To: CCL Subject: CCL: contribute to QSAR-World Message-Id: <-35598-071113011352-22891-CWjJuFNrIM0vTRYF8TofBw**server.ccl.net> X-Original-From: Shaillay Dogra Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Tue, 13 Nov 2007 11:12:58 +0530 (IST) MIME-Version: 1.0 Sent to CCL by: Shaillay Dogra [shaillay{=}strandls.com] Dear Colleague, I believe you are aware of this web-resource called QSAR-World (www.qsarworld.com) that we have put together for the benefit of the QSAR community. We have noticed that, primarily, it has been of use to students and researchers getting on to this field and looking for learning resources. Also, I believe some of the datasets we have provided here have been valuable (http://www.qsarworld.com/qsar-datasets.php?mm=5). I request you to kindly contribute to this effort by providing us with articles that you could write, pre-prints of your papers and conference posters that we could upload, datasets that you can share, or anything else in and around QSAR! Such a contribution should help us take this effort forward and make it a whole lot more meaningful. Please feel free to write to me for any clarifications. Hoping to hear from you soon! With best regards, Shaillay ----- Shaillay Kumar Dogra Senior Scientist & Scientific Editor (QSARWorld) Strand Life Sciences Pvt. Ltd. 237, Sir C. V. Raman Avenue, RMV, Sadashivnagar, Bangalore 560080 INDIA Phone: +91 80 2361 8992 | Facsimile: +91 80 2361 8996 Website: www.strandls.com | www.qsarworld.com ---- From owner-chemistry@ccl.net Tue Nov 13 09:34:00 2007 From: "Victor Bernshtein chr21vb||technion.ac.il" To: CCL Subject: CCL: FORTRAN code for building Gold lattice Message-Id: <-35599-071113005851-21955-bPdEiyivBuvN12kTtlHXrA/./server.ccl.net> X-Original-From: "Victor Bernshtein" Date: Tue, 13 Nov 2007 00:58:46 -0500 Sent to CCL by: "Victor Bernshtein" [chr21vb###technion.ac.il] Dear CCL Subscribers, I'm looking for a FORTRAN code for building Gold and Silicon PBC lattices. I would like to attach the code to the MD code employed for the fullerene surface impact calculations. Kind regards, Victor Bernshtein Technion-Israel Institute of Technology, Technion City, Haifa, 32000 From owner-chemistry@ccl.net Tue Nov 13 11:13:00 2007 From: "may abdelghani may01dz- -yahoo.fr" To: CCL Subject: CCL: Cp ring by simple atoms like H and Cl??? Message-Id: <-35600-071113094430-6269-bPdEiyivBuvN12kTtlHXrA*_*server.ccl.net> X-Original-From: may abdelghani Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-2133739111-1194961304=:48626" Date: Tue, 13 Nov 2007 14:41:44 +0100 (CET) MIME-Version: 1.0 Sent to CCL by: may abdelghani [may01dz\a/yahoo.fr] --0-2133739111-1194961304=:48626 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit dear CCLers Somme people replace, in you molecule models, the Cp ring by simple atoms like H and Cl. I not understand how, this atoms, can accommodate the very huge size of this ring, and in what extent this replacement give a reasonable results. --------------------------------- Ne gardez plus qu'une seule adresse mail ! Copiez vos mails vers Yahoo! Mail --0-2133739111-1194961304=:48626 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
dear CCLers
Somme people replace, in you molecule models, the Cp ring by simple atoms like H and Cl. I not understand how, this atoms, can accommodate the very huge size of this ring, and in what extent this replacement give a reasonable results.

Ne gardez plus qu'une seule adresse mail ! Copiez vos mails vers Yahoo! Mail --0-2133739111-1194961304=:48626-- From owner-chemistry@ccl.net Tue Nov 13 21:50:00 2007 From: "Hua Li pebblepeddle*gmail.com" To: CCL Subject: CCL: Alpha helix stability correlate with circumstance Message-Id: <-35601-071113214805-13947-B9IqUzRrEs1IkdhyOR9K/A++server.ccl.net> X-Original-From: "Hua Li" Date: Tue, 13 Nov 2007 21:48:01 -0500 Sent to CCL by: "Hua Li" [pebblepeddle]~[gmail.com] Hello, everyone. I may ask a question. The alpha helix structure is a stability structure of a protein chain. However, there are some other stable conformations like beta sheet, gama or epsilon conformation. My question is in which circumstance, the alpha helix will be the most stable conformation than other types? Add a metal cation? Protonated? Deprotonated or some other? Some references correlated to these are welcomed. Many thanks to all.