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Methods, Problems and Solutions

Powder Diffraction Structure Solution Pathways

Solving an Organic Structure (Cimetidine - C 10 H 16 N6 S) from Powder Diffraction Data

Add Calculated Hydrogens to Cimetidine using Shelxl97 via SXGRAPH and the WinGX Single Crystal Suite

The CCP14 Homepage is at http://www.ccp14.ac.uk

[Back to: Problems and Solutions] | [Back to: Tutorials]
[Back to: Powder Diffraction Structure Solution Pathways Index]
[Back to: Solving an Organic Structure (Cimetidine) from Powder Diffraction Data]

[Back to: Initial Connectivity Searching of the Cambridge database for Cimetidine like molecules using CORINA, Platon and Quest/CSD]
[Back to: Peak Profiling of Cimetidine using XFIT]
[Back to: Powder Indexing and Spacegroup Assignment of Cimetidine using the Crysfire and Chekcell combination of programs]
[Back to: CELL Searching the Cambridge database via Platon and Quest]
[Back to: Le Bail fitting and generating an EXPO starting file using LHPM-Rietica]
[Back to: Solve the structure of Cimetidine using the Sireware EXPO direct methods software]
[Back to: Finding possibly missing Symmetry in cimetidine using the Platon ADDSYM option]
[Back to: Searching the Cambridge database via Platon and Quest for related strutures]
[Back to: Generating a 2D to 3D fragement for fragment searching using the web based CORINA; then getting into a Shelx format using Ortep-3]
[Back to: Solve the structure of Cimetidine using Sir97 Single Crystal Direct Methods Software]
[Back to: Solve the structure of Cimetidine using Dirdif fragment searching]
[Back to: Solve the structure of Cimetidine using ESPOIR with no restraints]
[Back to: Solve the structure of Cimetidine using ESPOIR with bond restraints]
[Back to: Solve the structure of Cimetidine using ESPOIR with a combination of rigid bodies freely moving atoms]
[Back to: Add Calculated Hydrogens using the Crystals Single Crystal Suite]
[Back to: Add Calculated Hydrogens using Shelxl-97 via SXGRAPH and WinGX]

[To: Xfit-Koalariet Peak Profiling Software] | [To: Crysfire Powder Indexing Suite] | [To: Chekcell Powder Indexing Helper Tool] | [To: Platon/System S Crystallographic Toolset] | [To: LHPM-Rietica Rietveld for Win95/NT] | [To: EXPO Directory Methods Structure Solution from Powder Data] | [To: Sir97 Single Crystal Structure Solution Software] | [To: WinGX Single Crystal Suite] | [To: Crystals Single Crystal Suite] | [To: Espoir Monte Carlo Structure Solution Software]

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 positions.

(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 file

Obtain 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

Run Louis Farrugia's Ortep-3 and load the LHPM-Rietica input file (or Fullprof or GSAS), then save it as a Shelx INS file using the File, Write Shelx File menu option. This will create a file named Shelx001.ins.

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  10
to:
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.

Converting LHPM input file into Shelx format


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.

Opening up the structure in SXGRAPH via WinGX


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 structures

A note from David Watkin on this (in the context of Rietveld refinement before placing the hydrogens):

Date: Mon, 11 Sep 2000 13:46:27 +0100 (BST)
From: David Watkin [david.watkin@chemistry.oxford.ac.uk]
To: Lachlan Cranswick [L.M.D.Cranswick@dl.ac.uk]

I've looked at the cimetidine structure. Instead of trying to put H atoms
on just now, you would be better off using restraints to get the bond
lengths correct.  The C4-C17 bond on 1.7 A cannot be right - ie it is
wrong, so should be put right.  The C-Cmeth is short, so CRYSTALS thinks it
is SP2, as is the N-Cmeth.  A student last year wrote code to put H on N,
which will go into some future release, but guessing N hybridisatioon from
bond lengths is even more risky than C.

More information on "To restrain - or not to restrain"

Date: Wed, 13 Sep 2000 11:18:59 +0100 (BST)
From: David Watkin [david.watkin@chemistry.oxford.ac.uk]
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).

Selecting atoms in SXGRAPH


Select Model, Add Hydrogen, Methyl Group and select the default calculated, unrefined hydrogen placement where the hydrogens ride off their bonded atoms.

Hydrogen addition menu

Hydrogen addition menu options


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.

Updated structure with Methyl Hydrogens added


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.

Carbon bonded Hydrogens are placed


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.)

Placing an Aromatic amide N-H

Molecular Connectivity from the ICDD Database


[Back to: Problems and Solutions] | [Back to: Tutorials]
[Back to: Powder Diffraction Structure Solution Pathways Index]
[Back to: Solving an Organic Structure (Cimetidine) from Powder Diffraction Data]

[Back to: Initial Connectivity Searching of the Cambridge database for Cimetidine like molecules using CORINA, Platon and Quest/CSD]
[Back to: Peak Profiling of Cimetidine using XFIT]
[Back to: Powder Indexing and Spacegroup Assignment of Cimetidine using the Crysfire and Chekcell combination of programs]
[Back to: CELL Searching the Cambridge database via Platon and Quest]
[Back to: Le Bail fitting and generating an EXPO starting file using LHPM-Rietica]
[Back to: Solve the structure of Cimetidine using the Sireware EXPO direct methods software]
[Back to: Finding possibly missing Symmetry in cimetidine using the Platon ADDSYM option]
[Back to: Searching the Cambridge database via Platon and Quest for related strutures]
[Back to: Generating a 2D to 3D fragement for fragment searching using the web based CORINA; then getting into a Shelx format using Ortep-3]
[Back to: Solve the structure of Cimetidine using Sir97 Single Crystal Direct Methods Software]
[Back to: Solve the structure of Cimetidine using Dirdif fragment searching]
[Back to: Solve the structure of Cimetidine using ESPOIR with no restraints]
[Back to: Solve the structure of Cimetidine using ESPOIR with bond restraints]
[Back to: Solve the structure of Cimetidine using ESPOIR with a combination of rigid bodies freely moving atoms] [Back to: Add Calculated Hydrogens using the Crystals Single Crystal Suite]
[Back to: Add Calculated Hydrogens using Shelxl-97 via SXGRAPH and WinGX]

[To: Xfit-Koalariet Peak Profiling Software] | [To: Crysfire Powder Indexing Suite] | [To: Chekcell Powder Indexing Helper Tool] | [To: Platon/System S Crystallographic Toolset] | [To: LHPM-Rietica Rietveld for Win95/NT] | [To: EXPO Directory Methods Structure Solution from Powder Data] | [To: Sir97 Single Crystal Structure Solution Software] | [To: WinGX Single Crystal Suite] | [To: Crystals Single Crystal Suite] | [To: Espoir Monte Carlo Structure Solution Software]

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