hubertc
Dear All,
I'm actually working on a structure containing benzene rings but the material being poorly crystalline, I have to constrain the carbon atoms defining the benzene ring. The most suitable option seems to be the following command:
rigid
Hexagon_sitting_on_side_in_xy_plane(C12, C13, C16, C15, C11, C14, 1.4)
Rotate_about_axies( @ 55.30755`, @ 117.44639`, @ 356.92214`)
Translate( @ 0.63680`, @ 0.48817`, @ 0.58321`)
where C12, C13, C16, C15, C11, C14 define the benzene ring and will allow the benzene ring to translate and rotate.
Nevertheless, in the asymmetric unit, some of the benzene rings are defined by2 or 4 carbon atoms only, which exclude the use of the previous command as we can’t use equivalent positions with this command.
I have 2 options in mind, either strong distance and angle restrain but it could lead to benzene ring with variation in distance and angle (they are supposed to be exactly the same) or create the equivalent position as a new atom in the input file and divide the occupancy by the number of created atoms.
Are there others possibilities that could be more suitable?
Thank you
Hubert
johnsoevans
Hubert,
The other option is to define a smaller rigid body and just let symmetry create the rest of it. Depending on symmetry you may then need to think about which angles/centre of mass coordinates for the rigid body can actually be refined freely without breaking symmetry of the ring.
John
hubertc
Thank you.
(For information, the space group is Fd-3m (n°227))
I had a go using the equivalent position with a divided occupancy to define a full benzene ring in order to use the keyword:
rigid
Hexagon_sitting_on_side_in_xy_plane(C95, C96, C95m, C96m, C119, C120, 1.4)
Rotate_about_axies( @ 7.37201`, @ -5.42500`, @ 344.90466`)
Translate( @ 0.83123`, @ -0.20964`, @ 1.03639`)
Whereas C95, C96 are in position 192 (C95m and C96m, being the new atoms I created with Occ=0.5, I also changed the one of C95, C96 to 0.5) and C119, C120 are in position 96g.
But the symmetry of the benzene ring was broken, which means C119, C120 should be maintain in position 96g, thus I must constrain the rigid body in a way to allow C119, C120 to translate along C119C120 axis (as well as C95, C96) and C95, C96 to rotate along C119C120 axis (but not C119, C120 as they must remain on position 96g). I’m not sure if my explanation is clear or not, let me know.
I’m not really familiar with rigid body define by a z-matrix, but it seems I’ll have the same issue apart if we can constrain the mass centre (in the middle of the benzene ring) as well as C119, C120 to remain on position 96g.
An alternative could be to use distance/angle restrain and the keyword “Flatten” for C95, C96, C119, C120 (without creating C95m, C96m) and introduce distance restrain between C95 and its equivalent position in this ring (as well as C96), can we use distance restrain between equivalent position? Or certainly better to create C95m, C96m and to “Flatten” C95, C95m, C96, C96m, C119, C120.