From owner-chemistry@ccl.net Sun Jul 26 10:40:01 2009 From: "William F. Coleman wcoleman ~~ wellesley.edu" To: CCL Subject: CCL: bridge bond Message-Id: <-39850-090726103732-3826-VWKuqX6h0j14HwZeBT0pzw:_:server.ccl.net> X-Original-From: "William F. Coleman" Content-Type: multipart/alternative; boundary="--=_--1deecf17.1deecd96.c6921a9c" Date: Sun, 26 Jul 2009 10:37:16 -0400 MIME-Version: 1.0 Sent to CCL by: "William F. Coleman" [wcoleman^wellesley.edu] This is a multi-part message in MIME format. ----=_--1deecf17.1deecd96.c6921a9c Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Bridge bonds are quite common in transition metal complexes, both in organometallic complexes and traditional Werner complexes. Common bridging ligands are chloride and hydroxide ions, and using different atoms for the two ends of the bridge, cyanide and thiocyanate ions. Any advanced inorganic chemistry text will show a number of such examples. Aluminum chemistry shows some bridges that are similar to those found in the boranes, for example, in Al2Cl6. The BHB feature is found throughout borane chemistry. The formation of bridged complexes leads to the transtition state in so-called inner spehere electron transfer process. Cheers, Flick _______________ William F. Coleman Professor of Chemistry Wellesley College Wellesley MA 02481 www.wellesley.edu/Chemistry/colemanw.html Editor, JCE WebWare and JCE Featured Molecules http://www.jce.divched.org/JCEDLib/WebWare/ http://jchemed.chem.wisc.edu/JCEWWW/Features/MonthlyMolecules/index.html ----=_--1deecf17.1deecd96.c6921a9c Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable <=21DOCTYPE HTML PUBLIC =22-//W3C//DTD HTML 4.0 Transitional//EN=22>

Bridge bonds are quite common in tran= sition metal complexes, both in organometallic complexes and traditional We= rner complexes. Common bridging ligands are chloride and hydroxide io= ns, and using different atoms for the two ends of the bridge, cyanide and t= hiocyanate ions. Any advanced inorganic chemistry text will show a nu= mber of such examples. Aluminum chemistry shows some bridges that are similar to those found in the boranes, for example, in Al2= Cl6. The BHB feature is found throughout borane chemistry. The = formation of bridged complexes leads to the transtition state in so-called = inner spehere electron transfer process.

Cheers,

Flick

_______________

William F. Coleman

Professor of Chemistry

Wellesley College

Wellesley MA 02481

www.wellesley.edu/Chemist= ry/colemanw.html

Editor, JCE WebWare and JCE Featured = Molecules

http://www.jce.divched.org/JCE= DLib/WebWare/

h= ttp://jchemed.chem.wisc.edu/JCEWWW/Features/MonthlyMolecules/index.html=

----=_--1deecf17.1deecd96.c6921a9c-- From owner-chemistry@ccl.net Sun Jul 26 13:14:00 2009 From: "aps1968,googlemail.com" To: CCL Subject: CCL: QSAR for algae toxicity Message-Id: <-39851-090725023901-30655-2X83GAVIEedvRl+Xn+blrQ-.-server.ccl.net> X-Original-From: aps1968###googlemail.com Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Sat, 25 Jul 2009 08:33:32 +0200 MIME-Version: 1.0 Sent to CCL by: aps1968[A]googlemail.com Dear colleagues, has anybody seen any QSAR equation for *polar* narcosis in green algae? I mean, a simple linear function of logKow. Could be 72 or 96 hours. Regards, Andrzej Szymoszek From owner-chemistry@ccl.net Sun Jul 26 14:57:00 2009 From: "Kalju Kahn kalju**chem.ucsb.edu" To: CCL Subject: CCL: Scientific coding Message-Id: <-39852-090726145428-12334-wlC+xf0E2JVOpE7UF0Tl4g|-|server.ccl.net> X-Original-From: "Kalju Kahn" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Sun, 26 Jul 2009 11:54:11 -0700 MIME-Version: 1.0 Sent to CCL by: "Kalju Kahn" [kalju-.-chem.ucsb.edu] Syed, As someone with limited formal programming experience I have found that Mathematica by Wolfram Research is very helpful when I need to figure out how to go from theory to equation ... it also allows you to try out some possible ways of laying down possible algorithms ... of course you shall not read much into performance numbers at this stage. For something like an MD simulation trajectory analysis, it may be easier to work out your algorithm first in a high-level language, like python (esp. if you are not sure about nuances of c / java implementation). With modules such numpy it is surprisingly capable, and if you don't need numpy, Psyco may offers a nice performance boost. Once you understand the algorithm but feel that speed is critical, consider how to code it efficiently in c. My 0.02$, Kalju > > Sent to CCL by: "Syed Tarique Moin" [tarisyed,+,yahoo.com] > Hello, CCl users, > > I am a student of theoretical chemistry. I do md simulation "classical > mechanical and quantum mechanical". I am interested to develop a analysis > tool for the trajectory analysis using c programming and java like rdf > (radial distribution function) and many others. Can any body guide me how > to start from theory to equation, then algorithm and then coding and so > on. > > Regards> > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr. Kalju Kahn Department of Chemistry and Biochemistry UC Santa Barbara, CA 93106 From owner-chemistry@ccl.net Sun Jul 26 16:51:01 2009 From: "m.somers^chem.leidenuniv.nl" To: CCL Subject: CCL: Scientific coding Message-Id: <-39853-090726075955-20474-T08lkNJdpyCC7L2T68jD7A!=!server.ccl.net> X-Original-From: m.somers-x-chem.leidenuniv.nl Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Sun, 26 Jul 2009 13:21:11 +0200 MIME-Version: 1.0 Sent to CCL by: m.somers- -chem.leidenuniv.nl Hi, then you perhaps want to take a look at http://boinc.gorlaeus.net. Especially at http://boinc.gorlaeus.net/ClassicalBuilder.php. Here you also can have access to a desktop grid of 50K+ computers for doing md simulations yourself. m. > Sent to CCL by: "Syed Tarique Moin" [tarisyed,+,yahoo.com] > Hello, CCl users, > > I am a student of theoretical chemistry. I do md simulation > "classical mechanical and quantum mechanical". I am interested to > develop a analysis tool for the trajectory analysis using c > programming and java like rdf (radial distribution function) and > many others. Can any body guide me how to start from theory to > equation, then algorithm and then coding and so on. > > Regards