Re: [Jmol-users] No bonds drawn to metals from shelxl .res file

[<rg...@el...>]

On Fri, March 11, 2005 1:06 pm, Bob Hanson said:
> The problem is in the RES file decoder not recognizing "EU1" as europium.

The shelx atom name is an arbitrary string that matches a corresponding
string in its scattering-factor definitions. To be perfectly general the
reader would need to parse the SFAC instruction and match atom-type (given
by the table number in the ATOM info) to the element designator label in
the SFAC instruction and, potentially, decode the general SFAC instruction
to determine the closest neutral atom-type.

>
>
> But Pat is right that there is also another issue. The Li-O distances here
> are
> about 1.9 A. This compares well with others I know (listed in pm):
>
> http://www.stolaf.edu/depts/chemistry/mo/struc/explore.htm?bond=Li-O
>
> In this data set, the Li-O bond ranges in length between 188.3 and 249.4
> pm.
>
> Li-O 188 tetrahedral (C4H8O)4Li+ tetrakis(tetrahydrofuran)lithium cation
> Li-O 196 square pyramidal (C18H32O4)Li(NCS)
> Li-O 213 square pyramidal (C8H16O4)LiCl  (12- crown- 4)- chloro- lithium
> Li-O 222 square antiprism (C8H16O4)2Li+  bis(12- crown- 4)- lithium cation
>
A histogram of all Li-O distances in the Cambridge Database shows an
interesting bell curve with a max. at ~1.9 and a long tail up to 2.6'ish
and a shorter tail to 1.7. The real question comes down to are there Li-O
distances less than 2.6 that *aren't* bonds?

Rich