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From: Fco. Javier Modrego <modrego@un...> - 2004-11-29 15:49:29
Just my two (euro)cents about this issue.
I have recently moved from JMolAppletPre10 to pre 20. An .xyz
animation which previously was fine now show some bonds broken.
The animation should show Berry's pseudorotation using a sequence of
coordinates of AsF5 in .xyz format as a model of fluxional behaviour.
For example the first step is:
F 0.0000 0.0000 -0.9570
As 0.0000 0.0000 0.7034
F -1.4343 -0.0001 1.5387
F 1.4343 0.0001 1.5387
F -0.0001 1.6817 0.7002
F 0.0001 -1.6817 0.7004
The problem is that only three As-F bond are shown instead of five,
just the three F which are closer to As. As the animation advances
the bonding changes but it keeps showing just three bonds. I guess
that some internal parameters (either the minimum bond distance, the
covalent radii or the coordination number...) in JMolApplet have been
changed in recent releases.
I have been reading this post about "atom types" and I have found
also that there was an "autobonding of oxygen" thread in the
developers' list which discuss around a similar question. I have read
in some post about a pathological case of hundred of bonds around an
atom. Obviously there is some chemical problem which such a model, I
cannot think about any sensible structure of this kind. Only in
strongly dissordered X-Ray structural data this kind of things could
have any meaning (I think).
My personal view is that everything should be kept as simple as
posible and the autobonding feature should be based just in the sum
of covalent radii. For inorganic and organometallic chemistry
structures it is not very convenient to limit the number of
coordination based on the type of atom. For example, more than
4-coordinate carbon atom is no such rare beast in inorganic chemistry
either in solid state carbides, in organometalic compounds carbide
ligands or in carbon monoxide acting as a bridge between metal atoms,
not to speak about bridging halides, bridging hydrides and so on.
Dr. F.J. Modrego
Department of Inorganic Chemistry
Facultad de Ciencias
University of Zaragoza
Francisco en Espana escribio:
> Just my two (euro)cents about this issue.
> I have recently moved from JMolAppletPre10 to pre 20. An .xyz
> animation which previously was fine now show some bonds broken.
> The problem is that only three As-F bond are shown instead of five,
> just the three F which are closer to As.
> I guess that some internal parameters (either the minimum
> bond distance, the covalent radii or the coordination
> number...) in JMolApplet have been changed in recent releases.
I recently *enhanced* the bonding table by introducing maximum limits on
the number of bonds in the autobonding algorithm. I took the numbers from=
Indeed, 'As' has a limit of 3.
This *enhancement* has caused a number of difficulties. It will be remove=
in the next release.
> I have read in some post about a pathological case of
> hundred of bonds around an atom.
To minimize the impact caused by this type of pathological problem the
modified code will have an upper limit of 20 bonds per atom in the