This example uses example Cimetidine data from the EXPO software
At present (September 2000) Rietveld programs are not as powerful for calculating
hydrogen positions and setting found and calculated hydrogens refining as riding atoms.
Thus it can be easier to use a single crystal program to provide calculated hydrogen
(This is most reliable if you know where the hydrogens are located. Care - and some confirming NMR spectra may be required)
Having refined the structure using a Rietveld program (such as LHPM-Rietica, Fullprof, GSAS, etc), it would be a good idea to add calculated hydrogens where possible as this is part of the total scattering intensity you are trying to model.
In the following case, it will be assumed that the structure has been refined in LHPM-Rietica (though it is the same procedure if this was a Fullprof or GSAS file).
Obtain a dummy Shelx HKL fileObtain a dummy HKL file in Shelx format (using the Le Bail extracted HKL file would be OK but any HKL file will do). Shelx will want to see an HKL file when it is run to generate the hydrogens.
If you don't have a dummy Shelx HKL file click here to obtain one.
Shelx Home Site - George Sheldrick
WinGX and Ortep-3 for MS Windows - Louis J. Farrugia
The Shelx file probably does not have the SFAC for Hydrogen so it would be good to add this in now. Manually edit the Shelx file and change:
SFAC S N C UNIT 1 6 10to:
SFAC S N C H UNIT 1 6 10 9
Also if a L.S. command is present, make sure it is set to zero (0). The L.S. 0 command which tells Shelxl97 to allow refinement cycles but to do zero (0) cycles of refinement (effectively telling it to do calculations - not refinement).
You may like to rename the Shelx001.ins file to match the name of the dummary HKL file and copy these files into a new directory before running WinGX (or any other single crystal suite). Also copy the *.INS file to *.RES as by default SXGRAPH like to open the *.RES file.
Run WinGX and go through the Model, Prelim, Auto-start procedure to generate the struc.cif file.
Don't over write the *.INS file created by GUi WinORTEP. Going through this is described in
Using WinGX with Powder Diffraction Extracted Intensities.
Now run SXGRAPH (3rd ICON from the left) and open the Shelx *.ins file.
SXGRAPH will allow you to graphically select atoms of interest, then apply the Hydrogen
addition commands. Shelxl97 is then run with zero (0) cycles to generate the hydrogens.
Refer: Perils of automatic hydrogen placement on powder refined structuresA note from David Watkin on this (in the context of Rietveld refinement before placing the hydrogens):
More information on "To restrain - or not to restrain"
Date: Wed, 13 Sep 2000 11:18:59 +0100 (BST) From: David Watkin [email@example.com] To: Lachlan Cranswick [L.M.D.Cranswick@dl.ac.uk] This is a deep philisophical problem, and draws in the Bayesian/non-Bayesian people. The non-Bayesians say that each experinent should be treated as separate from any other, so you just refine as best you can with the x-ray data you have. The Baysians say that this is daft. If some other good experiment has given good values for something, you should include this knowlwdge in the current process. The trick is to know what weight to give this external information. A weight of zero makes it a non-Baysian calculation. A weight of infinity makes it a constrained calculation. Other weights lead to restraints. Im a Bayesian myself. If a bond length is weird, either its a fantastic discovery, or its wrong. If it's wrong - what's the point in publishing it? Put it right. If the Rfactor goes up, then the data is rubbish and needs improving. If it stays about the same, then the data doesn't define the parameter - but it may also fall showing that the trial model was poor. If one parameter is left at a poor value, others may take on incorrect values to try to compensate - this is because the parameters are always correllated! Best wishes David
In the case of the Methyl Carbons, select these carbons by clicking on them with the mouse (selected atoms have a yellow dot on them).
Select Model, Add Hydrogen, Methyl Group and select the default
calculated, unrefined hydrogen placement where the hydrogens ride
off their bonded atoms.
Select OK followed by File, Save INS File and then Refinement, Run Shelxl-97.
This will now produce an updated structure with the placed Methyl hydrogens.
Repeat this for the other atoms (it can be very dodgy attempting to calculate hydrogens for Oxygen atoms).
If you make a mistake, use SXGRAPH to delete the offending Hydrogen atoms and try again. (Not all of
the Hydrogen placement options for certain atom types are offered in SXGRAPH so you may have to
read the relevant part of the Shelx manual to find the instruction codes).
(As mentioned above, this is most reliable if you know where the hydrogens are located. Care - and some confirming NMR spectra may be required to be confident about where hydrogens are placed.)
After defining all the hydrogen placement HFIX commands; select File, Save INS File and then run Shelxl 97 using Refinement, Run Shelxl-97.
Please note that all the HFIX options are not defined in SXGRAPH so you may have to
read the Shelxl 97 manual and put these in your self. The manual also mentions
that m = 4 will handled "Aromatic C-H or amide N-H"
Thus, this reading this information in the Shelxl97 manual gives us the information to add hydrogens to the "relevant" Nitrogen in this example.
However, it should be noted that the information from the ICDD database implies we have added hydrogen to the wrong Nitrogen. Shelx in this case will obey your command as it assumes you know what you are doing in this regard.
(Again, as mentiond above, this is most reliable if you know where the hydrogens are located. Care - and some confirming NMR spectra may be required to be confident about where hydrogens are placed.)