Re: [Jmol-users] Default settings

[C Martin]

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.

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.

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.
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.

Hope this helps,
Craig
Message: 3
Date: Thu, 18 Nov 2004 08:00:43 -0500 (EST)
Subject: Re: [Jmol-users] Default settings
From: "Miguel" <[EMAIL PROTECTED]>
To: [EMAIL PROTECTED]
Reply-To: [EMAIL PROTECTED]
Anthony wrote:
I have been using JMol to display xyz files, and I have found that
deuterium (element =22D=22) is set to have a much larger covalent radiu=
s
than H.

.....
In the meantime, tell me some more about 'deuterium'.
Q: Is 'D' the accepted element symbol.
Q: What other elements have common 'alternate elements' for isotopes?
Implementing support for isotopes like this may not be straightforward.
Miguel

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