# Changeset 1941

Ignore:
Timestamp:
Jul 21, 2015 12:38:59 PM (8 years ago)
Message:

Location:
Tutorials/CFsucrose
Files:
14 edited

Unmodified
Removed
• ## Tutorials/CFsucrose/Charge Flipping - sucrose.htm

 r1937 Von DreeleVon Dreele31991421012015-07-20T18:13:00Z2015-07-20T18:37:00Z2015-07-21T17:36:00Z1346019722352320087Argonne National Laboratory1644623136167472356315.00 href="Charge%20Flipping%20-%20sucrose_files/item0054.xml" target="Charge%20Flipping%20-%20sucrose_files/props055.xml"> Calculate/Refine to make sure it has essentially minimized. My refinement completed with Rwp ~25%; a dialog box appears asking if you wish to load the result. Press OK. To see the plot select the PWDR line in the GSAS-II data tree (Ive adjusted the width and height).

class=SpellE>Rwp ~25% (NB: here and after succeeding refinements your Rwp values may be slightly different from what I show here); a dialog box appears asking if you wish to load the result. Press OK. To see the plot select the PWDR line in the GSAS-II data tree (Ive adjusted the width and height).

src="Charge%20Flipping%20-%20sucrose_files/image013.jpg" v:shapes="Picture_x0020_11">

The result looks very promising! Charge flipping operates should select (grey) 23 out of 46 peak positions in the table and all should be near the top of the list. The console displays this as both the number of unique peaks and the fraction found (the ideal value for the latter is easily inferred from the space group). Given the formula for sucrose is C12H22O11 that would be all the C & O atoms! They will be colored green in the plot. If more are selected then check the map offset  it may need a slight correction.

peaks and the fraction found (the ideal value,0.5, for the latter is easily inferred from the space group). Given the formula for sucrose is C12H22O11 that would be all the C & O atoms! They will be colored green in the plot. If more are selected then check the map offset  it may need a slight correction.

src="Charge%20Flipping%20-%20sucrose_files/image021.png" v:shapes="_x0000_i1047">

The atom names indicate the peak magnitude to aid src="Charge%20Flipping%20-%20sucrose_files/image022.png" v:shapes="Picture_x0020_17">

Notice that in this case the atom list is neatly sorted out into two groups with a clear gap between M79 and M64. The higher ones are likely to be the 11 O-atoms and the rest are the 12 C-atoms. There may be a bit of

Notice that in this case the atom list is neatly sorted out into two groups with a clear gap between M79 and M64. The higher ones are likely to be the 11 O-atoms and the rest are the 12 C-atoms. There may be a bit of ambiguity in the middle, but just assign the top 11 as O and the rest as C and see what happens. You can do this by selecting a block of atoms, go to

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The original charge flipping solution is still visible and

Now one can safely remove the map peaks (do General tab). The atom positions I obtained in this charge flipping run have the sucrose molecule fragmented over several neighboring molecules. We need assemble these into a single molecule. Follow the steps:

sucrose molecule fragmented over several neighboring molecules. We need assemble these into a single molecule. Follow the steps:

If it happens that the Assemble molecule routine leaves one or two atoms out, rerun it adjusting the Bond search factor to a slightly larger value (e.g. 0.9 vs 0.85). That should pick up the outliers.

To rename the atoms, select all the atoms (double click in

You can also reorder the atoms to make the connectivity mso-hansi-theme-font:minor-latin'>Calculate/Refine from the main GSAS-II data tree menu; only scale and background are refined. I got a Rwp ~20%. The plot shows clear intensity differences; the atom positions obviously need refinement.

class=SpellE>Rwp ~20%. The plot shows clear intensity differences; the atom positions obviously need refinement.

src="Charge%20Flipping%20-%20sucrose_files/image031.png" v:shapes="Picture_x0020_48">

To deal with the warning we need to set a Hold on one atom y-coordinate. Select Constraints in the main GSAS-II data tree.

mso-hansi-theme-font:minor-latin'>Constraints in the main GSAS-II data tree.

Press Ok. A new popup window will appear.

src="Charge%20Flipping%20-%20sucrose_files/image035.png" v:shapes="Picture_x0020_50">
This offers the choice of how many H-atoms to be added for each atom in the table; the maximum is chosen for each atom. If the bonds are sufficiently short normal'>Ok. The structure will be redrawn with H-atoms shown as van der Waals spheres; they are appended to the end of the Atom list.

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These hydrogen atoms will better describe the scattering

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Because the C-atoms have probably moved; the H-atoms (which Recall that the refinement was just done without any H-atoms on the oxygen atoms; it will make the best fit compensating for the missing H-atoms by displacing the O atoms in the direction of the missing H-atoms. To add the OH atoms do the following:

displacing the O atoms in the direction of the missing H-atoms. To add the OH atoms do the following:

2.      Select all O-atoms in the table (double click the Type column heading & select These OH hydrogens are found by finding the highest point in the delta-F map for all possible orientations of this bond at a fixed angle (109.5°). The new hydrogen atoms are named in sequence and are appended to the end of the Atom list.

this bond at a fixed angle (109.5°). The new hydrogen atoms are named in sequence and are appended to the end of the Atom list.

style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; mso-hansi-theme-font:minor-latin'> model
; this is the Stephens phenomenological model for microstrain which has 9 terms for monoclinic structures. Check all the boxes for it and press microstrain which has 9 terms for monoclinic structures. Check all the boxes for it and press Reset.
• ## Tutorials/CFsucrose/Charge Flipping - sucrose_files/filelist.xml

 r1937
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