Hello Tao Zeng.

Determine the hydrogen positions is very challenging. A regular XRD analysis with copper radiation may not be able to generate a result that can be used to determine them. What analysis are you using?

Best regards,

Ricardo Tadeu

Hello, Ricardo Tadeu Maia.

I wanna use the neutron powder diffraction to dertermine the position without deuteration. Ricardo Tadeu Maia

It's posible, but not easy anyway. If you want help, we can try to use GSAS-II and EXPO to try to solve the structure

Dear Tao Zeng,

I have not worked much with neutron diffraction patterns.

What kind of sample do you have, organic or inorganic?

Has the structure already been reported or has it already been determined?

As Ricardo Tadeu Maia mentioned, it is challenging. With X-ray diffraction data, if it is an organic compound and the structure of the non-hydrogen atoms is known, either from a previously reported structure or from a structural determination. In Rietveld refinement by refining the atomic coordinates of the non-hydrogen atoms, the positions of the hydrogens are recalculated each time they are refined. The hydrogen positions can be calculated using programs such as Mercury (https://www.ccdc.cam.ac.uk/solutions/software/free-mercury/), EXPO2 (https://www.ba.ic.cnr.it/softwareic/expo2014/), or Sir2019 (https://www.ba.ic.cnr.it/softwareic/sir2014/). EXPO2 has the advantage of being able to optimize the geometry of the molecule or selected atoms using Open Babel's force fields (http://dx.doi.org/10.1017/S088571561700015X). Therefore, it is possible to optimize the positions of the hydrogen atoms, not only to calculate them, but also to obtain the best position where the energy is minimized.

Another option available for TOPAS-Academic (http://www.topas-academic.net/) is to use distance and bond angle restraints on the hydrogen atoms and refine the hydrogen coordinates as well. The TOPAS algorithm is powerful enough to produce good results with hydrogen refinement. I think this type of refinement can also be used with the GSASII software.

For powder neutron data you have to have a good starting point. Typically, before you measure the neutron diffraction pattern, you record the X-ray diffraction pattern. Do a Rietveld refinement of the x-ray diffraction data using the procedure mentioned above. With this initial model with hydrogen atoms, it can perform the new refinement on this neutron data. Check the Fourier map with the program GFourier and see if the hydrogen positions are correct, in the case of Fullprof. Since you have neutron data, you can also refine the coordinates of the hydrogen atoms without the above restraints and check again in the Fourier map.

Best regards

Analio Dugarte-Dugarte

If you are using laboratory based X-rays, the ability to “see” light elements is improved by using a Variable Counting Time (VCT)* regime. This results in data with more uniform peak intensities over the pattern.

The Bruker data collection software has VCT built in and the data can be analysed using TOPAS.

* "Collection and analysis of powder diffraction data with near-constant counting statistics", I. C. Madsen and R. J. Hill, J. Appl. Cryst. (1994). 27, 385-392, http://www.iucr.org/cgi-bin/paper?hz0014 I. C. Madsen and R. J. Hill, Adv. X-ray Anal. (1992), 35, 39-47