From owner-chemistry@ccl.net Sat Sep 19 10:02:01 2009 From: "Jacco van de Streek vandestreek!=!avmatsim.de" To: CCL Subject: CCL: To determine atom type from electron density map Message-Id: <-40283-090919095841-8989-XFmqvb1kHyxRkJjJwGaucQ!A!server.ccl.net> X-Original-From: Jacco van de Streek Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Sat, 19 Sep 2009 15:05:01 +0200 MIME-Version: 1.0 Sent to CCL by: Jacco van de Streek [vandestreek_+_avmatsim.de] Yukiko Okada alchjhy,,hotmail.com wrote: > What i doubt > is when we determine atom type from electron density map, could we > distinguish magneium ion(+2) and oxygen ion from water? > > What is the diffrent point between Mg2+ electron density map and > Oxygen electron density map from water? This sounds like a crystallography question rather than a computational chemistry question. Assuming you are referring to X-ray diffraction of a crystal of a small organometallic compound, the answers to your question are roughly as follows: 1. Mg2+ and O differ by two electrons. On modern-day diffractometers, with most single-crystal experiments being performed at about 120 Kelvin these days, two electrons probably suffices that you can simply assign the correct atom type straight from the electron density. (I only solve crystal structures from powder data, so I do not know if this is true, but you can ask your local crystallographer.) 2. However, this is not how atom types are distinguished from X-ray diffraction data. The experimental data is not the electron density, but the structure factors. So what is relevant are not the number of electrons but the atomic scattering factors, and the atomic scattering factors for Mg and O are different. The most reliable way to distinguish Mg from O is to simply try all permutations and refine all models, including hydrogens. The model with the lowest R-factor and with "normal" Atomic Anisotropic Displacement Parameters is the correct model. I think it is correct when I say that because the angle dependence of scattering factors of different elements are different, even Mg(2+) and O(2-) (which are isoelectronic), can still be distinguished this way. The effective electron densities are the same, but their angle-dependences (the way the electron density is distributed over the structure factors) are not. 3. Third, there is of course the chemistry: the magnesium will be coordinated by the water molecules, so the atom "in the centre" must be the magnesium. Furthermore, the water molecules will probably form hydrogen bonds. Using the known distances for O-H...O and H2O...Mg(2+) (for O-H...O, you use the distance between the two oxygen atoms), you can probably assign the correct atom types using chemical intuition. And then there is the geometry: hydrogen bonds form tetrahedra, I do not know what the Mg coordination would look like. And there must be a counterion: the Mg(2+) is probably surrounded by two counterions with known distances and geometries. This is all a matter of looking at known crystal structures of compounds containing Mg(2+) and H2O, of which there are probably at least several dozen. I have no experience with single crystal data for organometallic compounds, so to be on the safe side you should either ask your local crystallographer or try another mailing list. Best wishes, -- Dr Jacco van de Streek Senior Scientist Avant-garde Materials Simulation Freiburg im Breisgau, Germany From owner-chemistry@ccl.net Sat Sep 19 12:40:01 2009 From: "sreelatha k. kusum.rai88(0)gmail.com" To: CCL Subject: CCL: guassian NICS calculations Message-Id: <-40284-090919022609-13799-3vvgows2zPQEkFKbLJxncQ_._server.ccl.net> X-Original-From: "sreelatha k." Date: Sat, 19 Sep 2009 02:25:58 -0400 Sent to CCL by: "sreelatha k." [kusum.rai88#,#gmail.com] how to submit NICS, HOMA calculations in guassian 03 package. From owner-chemistry@ccl.net Sat Sep 19 17:03:01 2009 From: "D. Boyd dboyd+/-iupui.edu" To: CCL Subject: CCL: Computational Materials Chemistry Message-Id: <-40285-090919152843-8523-wPFp0kz7Tk01Po4BTd6TEg() server.ccl.net> X-Original-From: "D. Boyd" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed Date: Sat, 19 Sep 2009 14:56:20 -0400 Mime-Version: 1.0 (Apple Message framework v936) Sent to CCL by: "D. Boyd" [dboyd.:.iupui.edu] Victor, In fact, there is a Journal of Computational Materials Science. http://www.elsevier.com/wps/find/journaldescription.cws_home/523412/description#description Don