'D' is now an alias for 'H' The fact that it came in as a 'D' is completely lost and within Jmol it is an 'H'. So, for example, if you turn on the element symbol labels they will be identified as 'H'.
> There really is no size issue with respect to isotopes. Although the > nuclear mass of H doubles in going to D, the nuclear mass does not > determine atomic size. Atomic sizes are determined by the radial > distribution of the electrons around the nucleus. That is determined by > the > number of electrons, their orbital disposition, and the charge of the > nucleus. None of these changes when you go to an isotope of the same atom. > In summary, an isotope of an atom has essentially the same size as that > atom. OK > But size can change dramatically with changes in ionization state. For > example Mg (radius=160 pm) is much larger than Mg2+ (radius=79 pm). This > has to do with "filling the next shell" - ie., what orbital the outermost > electron is in. This is too much for Jmol to worry about. Any magnesium > found in protein structures will be Mg2+, so I would stay with that size. > An inorganic chemist, presenting packing in solid Mg, however, will want a > larger size - he or she can adjust accordingly. Jmol has support for different ionic radii. However, it is rarely used since most files do not have ionic data. Q: Are 'ionization state' and 'ionic charge' and 'formal charge' all exactly the same thing (for my purposes) ? > Also remember that atoms are NOT hard spheres. "Size" really reflects a > probability distribution of the electrons. There are different ways of > "determining" size - imagine that you might say it's the radius within > which the electron is found 80% of the time, but I might say it's the > radius within which the electron if found 95% of the time. My "size" would > be bigger than your size. A Gen Chem text can tell you of the different > measuring schemes. > > So in the end, don't get too hung up on size. Hmmm ... as I recall my therapist told me the same thing ;-) > As for funny symbols, I think that "D" is the only commonly used > alphabetic > symbol for an isotope. Others are usually presented as 13C, 15N, etc (in > this case, D would 2H). I don't think you'll find 13C, et al. in > structures. So you can add "D" to your table, with the size of "H" and > probably stop there. Done. Miguel ----- Open Source Molecular Visualization www.jmol.org [EMAIL PROTECTED] ----- ------------------------------------------------------- This SF.Net email is sponsored by: InterSystems CACHE FREE OODBMS DOWNLOAD - A multidimensional database that combines robust object and relational technologies, making it a perfect match for Java, C++,COM, XML, ODBC and JDBC. www.intersystems.com/match8 _______________________________________________ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
