I have resolved several aromatic compounds' absolute structures in single-crystal x-ray, and all of them showed cofacial/slipped close-packing/stacking of the aromatic rings.
Later, I used VESTA to visualize the PXRD spectra, hoping to grab a quantitative value for the d-spacing of the close-packed aromatic rings:
1. Generate PXRD spectrum from single crystal .cif data in VESTA.
2. From the PXRD list, I identify the (hkl) of d-spacing around 3.6~3.1 Ang., with moderate~strong PXRD intensity
3.Visualizing the (hkl) on the absolute structures and confirm the miller plane is parallel/overlapping with planar aromatic molecules.
The d-spacing I have identified in my compounds were as small as 3.14, 3.15, 3.20, etc. The values seem quite small compared to those reported ones, 3.3~3.6. I want to confirm if my way of grabbing d-spacing is correct?
Thanks in advance.
See first of all you cannot call the powder diffraction spectrum, it is a powder diffraction pattern. There is plenty of software available using crystallographic parameters like lattice parameters, space group, and atomic position one can generate the powder XRD pattern. If you want to make it send me the data I will make it and send it to you.
See first of all you cannot call the powder diffraction spectrum, it is a powder diffraction pattern. There is plenty of software available using crystallographic parameters like lattice parameters, space group, and atomic position one can generate the powder XRD pattern. If you want to make it send me the data I will make it and send to you.
you need to use any gui for single crystal structure viewing like: Mercury, Vesta, crystal maker etc and then simulate PXRD pattern. Later you can index that data to get desired information
@Ahmad Husain Irrespective of the single crystal form or powder form unit cell structure is going to be the same. So once you have the crystallographic parameters like, lattice parameters a, b, c, Alpha, Beta, Gamma, Space Group, and atomic positions one cane generate the powder diffraction pattern easily. If the questioner could not make the theoretical powder XRD pattern, let him send me all the above parameters, I will make the pattern and send to him.
Hi Bryan,
I personally would recommend measuring the distance between the phenyl-rings using your single crystal structure instead of converting it into a powder diffraction pattern and then using the reflection positions to calculate a d-spacing. The problem with your approach is that the diffraction planes are not necessarily identical to the planes of the phenyl-rings.
I would suggest to use the atomic coordinates from your single crystal structure to measure the distance between phenyl-rings:
1) convert the (xyz) coordinates of 3 atoms in a ring into Angstroms
2) use the 3 sets of coordinates to define a plane of the form Ax+By+Cz+D = 0
3) repeat 1) and 2) for a parallel aromatic ring to get A'x+B'y+C'z+D' = 0
If the two rings are truely parallel, A=A', B=B' and C=C'.
4) The distance d between the planes is then d = |D-D'| / √(A^2 + B^2 + C^2)
To Jan P Scheifers:
Thanks for the suggestion on calculating interplanar spacing.
I guess calculating d-d from XRD could be a reason why they are slightly smaller than the reported ones.
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