From owner-chemistry@ccl.net Sun Aug 10 03:01:00 2014 From: "Paul Fleurat-Lessard Paul.Fleurat-Lessard(~)ens-lyon.fr" To: CCL Subject: CCL: Computational chemistry wiki Message-Id: <-50393-140809054729-25109-+HF+lwUIQ0EtVU2c9Zvxxw#,#server.ccl.net> X-Original-From: Paul Fleurat-Lessard Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Sat, 09 Aug 2014 11:38:06 +0200 MIME-Version: 1.0 Sent to CCL by: Paul Fleurat-Lessard [Paul.Fleurat-Lessard%x%ens-lyon.fr] Hi, Some of you might be interested by Orbimol developed by P. Chaquin and Franck Fuster: http://www.lct.jussieu.fr/pagesperso/orbimol/fr/index-fr.shtml Language can be changed from French to many others. Regards, Paul. Le 06/08/2014 10:32, Jan Halborg Jensen jhjensen*chem.ku.dk a écrit : > > Sent to CCL by: Jan Halborg Jensen [jhjensen-x-chem.ku.dk] > Alan Hincliffe's Molecular Modeling for Beginners might be something you can use. There's also Heine et al.s Computational Chemistry Workbook. > > That being said, I increasingly drop textbooks and instead assign reading/videos available on the web and make my own if need be. > > Chris Cramer has lots of video lectures on Comp Chem: http://pollux.chem.umn.edu/8021/Lectures/ > > My group has developed the Molecule Calculator (http://molcalc.org) designed specifically to incorporate molecular modeling into chemistry courses. You can read more about it here: http://molecularmodelingbasics.blogspot.dk/search/label/molecule%20calculator > > Finally, I have developed some GAMESS tutorials, so it if you are interested in using GAMESS have a look at: > > http://molecularmodelingbasics.blogspot.dk/search/label/gamess > > and > > http://molecularmodelingbasics.blogspot.dk/search/label/teaching%20molecular%20modeling > > Best regards, Jan > ________________________________________ >> From: owner-chemistry+jhjensen==chem.ku.dk|ccl.net [owner-chemistry+jhjensen==chem.ku.dk|ccl.net] on behalf of rjensen ~~ ualberta.ca [owner-chemistry|ccl.net] > Sent: Wednesday, August 06, 2014 1:26 AM > To: Jan Halborg Jensen > Subject: CCL: Computational chemistry wiki > > Sent to CCL by: rjensen++ualberta.ca > I'm talking about a course where the students learn to use > computational software, not learn the underlying mathematics. In the > extreme, they would see the Schrödinger equation with an expanded > potential. > Truncation at the first term (harmonic oscillator) would approximate > molecular mechanics. There would be no solution of the SE, but > students would then learn that MM is commonly used to investigate bio > molecular systems and such things as protein binding, etc. > Estimating the next few terms would approximate semi-empirical > methods. Again, there would be no solution of this SE, but students > would learn where semi-empirical methods are commonly used. > ... > This would continue with DFT, ab initio, and up to MRCI, etc. > > Again, no mathematics, but a focus on understanding the capabilities > and limitations of the methods, the available software, and an > analysis of the results compared with experimental data. Another > emphasis will be on method validation so that students can validate > new methods when they are released and with increasing computing > power. > > With this knowledge, these skills could be applied in advanced > physical, organic, inorganic, and biochemistry courses. And of course > in their future careers. > > Students interested in the underlying mathematics could take a senior > or graduate-level course in quantum chemistry. > > I'm familiar with Hehre's book, and the examples therein would be > updated and made available on the wiki, with the permission of > Wavefunction. > > Dr. Roy Jensen > (==========)-----------------------------------------¤ > Lecturer, Chemistry > E5-33F, University of Alberta > 780.248.1808 > > > > On Tue, 5 Aug 2014 18:04:23 -0400, you wrote: > >> What do you mean by "computational chemistry"? Is this a synonym of quantum mechanics, or does it include classical mechanics and/or molecular modeling? I assume drug design/med chem/applications of modeling is taught in a separate course later in the student's progression? >> >> Leach did a book on modeling, and Cramer did one on Computational Chemistry. Looking at Amazon, there's a whole lot of looked-at books when you search for these two. Tim Clark did one back in the mid-80's which is one of the first I recall. It's an older, well-published field. >> >> If it's applied QM you're looking for, didn't Warren Hehre with Wavefunction do several books/courses on this? >> >> Joe Leonard >> On Aug 5, 2014, at 2:44 PM, rjensen .. ualberta.ca wrote: >> >>> >>> Sent to CCL by: rjensen/a\ualberta.ca >>> Colleagues >>> >>> Computational chemistry is beginning to be taught as a second year >>> course at some institutions, often as the *first* physical chemistry >>> course taken by students. Taught from a minimized-mathematical >>> perspective, this course may potentially not scare students from >>> physical chemistry AND would give students a foundation for applying >>> computational chemistry in their senior organic, inorganic, >>> biochemistry, and physical chemistry courses. >>> >>> I'm just wondering if there are any instructional resources (textbook, >>> etc.) that might be suitable for this course? If nothing is available, >>> I have discussed the idea of creating a wiki. >>> >>> Thanks, >>> Dr. Roy Jensen >>> (==========)-----------------------------------------¤ >>> Lecturer, Chemistry >>> E5-33F, University of Alberta >>> 780.248.1808http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt> > -- Fleurat-Lessard Paul, Associate Professor Laboratoire de Chimie e-mail: Paul.Fleurat-Lessard/a\ens-lyon.fr ENS de Lyon / On leave in DIJON tel: 03 80 39 37 20 ICMUB / 9 avenue Alain Savary - BP 47870 21078 DIJON Cedex - FRANCE