2
$\begingroup$

This is a screenshot of a portion of a metal organic framework (MOF). These are two oxygens of two NMP solvent molecules. What I am wondering is why they are so close and overlapping like this. I checked the CIF file, and occupancy for all atoms in this structure is 1, so it doesn't seem to be the case that there is only one NMP molecule in two equally likely positions.

Could someone explain this? Thanks

Overlapping oxygens

$\endgroup$
3
$\begingroup$

It's a bit hard to answer without having coordinates file (*.res or *.xyz), but the simplest answer that I would expect is that these oxygen atoms belong to two different molecules that are disordered over the same position (i.e. they have only partial occupation on the site that in sum is 1). It's very common for f.e. thf coordinated to alkali-metals.

If you have shelx input for the structure look for the line that defines one of oxygens and see if 6th parameter is 11.0

O1    5   -0.180348    0.245831    0.298215    11.00000    0.02208    0.02526 = 
                                               ^^  

This means fixed (10) occupancy of 1.

If you have cif-file look for the atom loop

loop_ 
 _atom_site_label 
 _atom_site_type_symbol 
 _atom_site_fract_x 
 _atom_site_fract_y 
 _atom_site_fract_z 
 _atom_site_U_iso_or_equiv 
 _atom_site_adp_type 
 _atom_site_occupancy 
 _atom_site_symmetry_multiplicity 
 _atom_site_calc_flag 
 _atom_site_refinement_flags 
 _atom_site_disorder_assembly 
 _atom_site_disorder_group 
O1 O -0.18035(6) 0.24583(6) 0.29822(5) 0.02794(8) Uani 1 1 d . . .  

8th parameter is occupancy (_atom_site_occupancy).

These both examples were for not disordered atoms. If they are disordered then it looks like this:

shelx-ins/res

O1    4    0.297097   -0.198418   -0.064164    10.50000    0.34896    0.34935 =
                                                  ^ occup. 1/2  

or

FVAR       0.22777   0.51340   0.51266  
...
O1    4    0.551971    0.536866    0.295322    21.00000    0.03100    0.03031 =
                                                ^ occup. bound to 2nd free variable
                                                  here 51%

cif-file:

O1_20 O 0.6673(9) 0.3140(7) 0.1724(3) 0.0434(14) Uani 0.513(3) 1 d PDU C 1
                                                      ^
$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.