For those of you interested in the vdw radius question ... I posted an inquiry to the Open Babel mailing list asking about the source of the vdw radius values that are in the Open Babel source code.
Geoff Hutchison replied with the message below. Thoughts? Comments? Miguel ---------------------------- Mensaje original ---------------------------- Asunto: Re: [Open Babel] vdw radii in openbabel (long reply) De: "Geoff Hutchison" <[EMAIL PROTECTED]> Fecha: Vie, 21 de Enero de 2005, 18:12 Para: "Miguel" <[EMAIL PROTECTED]> Cc: [EMAIL PROTECTED] -------------------------------------------------------------------------- On Jan 21, 2005, at 8:39 AM, Miguel wrote: > Q: Are the van der Waals radius values even used in OpenBabel? No, the VdW radii are not used directly in Open Babel--but that doesn't mean we're suddenly going to get rid of them. There is code and data in Open Babel that's intended for others to use, which goes along with the spirit of the project and the fact that Open Babel is a library for building chemistry applications. I like having a good set of chemical data for other programs. > My question relates to the van der Waals radii values in OpenBabel. webelements says that their reference for vdw radii is: > A. Bondi, J. Phys. Chem., 1964, 68, 441. > Q: What is the source of the vdw radii values in OpenBabel? Now you want to know where the VdW radii come from for Open Babel. Therein lies a story. See, the problem is that lots of people say they use Bondi's paper from JPC 1964. Then they go off and quote VdW radii that aren't in the paper. Bondi doesn't cover the whole periodic table (only 38 elements by my count)--so if you want the vdW radius for Fe, you're outof luck. Somehow WebElements and others give values and don't usually say where they come from. (I can't say that I've gone through everything on the WebElements site -- he's usually pretty good about giving citations.) Worse, there are a lot of inconsistent sets of VdW radii--some may look like Bondi's values for a few elements, but then *wham* they've changed a few elements with no explanations. Part of the problem is that "van der Waals radius" sounds like such a nice simple value in intro chemistry class. But then you realize that people have defined it for crystals (supposedly why people use Bondi's radii), gas phase (for the van der Waals equation), or equilibrium calculations (i.e., conformation, molecular mechanics) and a few other areas. And these don't always match: Zefirov YV RUSSIAN JOURNAL OF INORGANIC CHEMISTRY 46 (4): 568-572 APR 2001 (quite a readable article if you have the time -- it's in English) I've really hunted and hunted to find an actual academic source for a consistent set of VdW radii across the periodic table. The closest I came (besides Bondi's incomplete set): Batsanov SS, INORGANIC MATERIALS 37 (9): 871-885 SEP 2001 Now there's also this Chinese paper that looks somewhat interesting, but I can't get it (or read it): Hu SZ, Zhou ZH, Tsai KR, ACTA PHYSICO-CHIMICA SINICA 19 (11): 1073-1077 NOV 2003 Batsanov gives some fairly reasonable numbers, IMHO, and defines them for 65 elements--basically everything except the lanthanides and actinides and the nobel gases. So I used the nobel gas values from Bondi and generally the rest of them from Batsanov. I'm open to other suggestions. -Geoff ----- Open Source Molecular Visualization www.jmol.org [EMAIL PROTECTED] ----- ------------------------------------------------------- This SF.Net email is sponsored by: IntelliVIEW -- Interactive Reporting Tool for open source databases. Create drag-&-drop reports. Save time by over 75%! Publish reports on the web. Export to DOC, XLS, RTF, etc. Download a FREE copy at http://www.intelliview.com/go/osdn_nl _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
