In this exercise we will use a set of X-ray single cry= stal structure factors to solve the structure of dipyridyl disulfide by charge flipping and then refine the structure by least-squares. The structure will= be completed by adding the requisite hydrogen atoms and by using anisotropic thermal parameters for the heavier atoms. The structure was originally solv= ed by Raghavan & Seff, Acta Cryst. B33, 386-391 (1977) in the space group = P21/c with one disordered pyridine ring with indications that the true space group was P21. It was subsequently reinvestigated by Young (2014….) who found that the true space group was P21 with 4 molecules in the asymmetric unit. The data used in the latter analysis is what is used here = and is provided as a “fcf” file obtained after structure analysis by Shelx-97; = the structure factors are scaled to those calculated from the structure. We will solve the P 21/c structure first.
Note that menu entries and user input are shown in bol= d face below as Help/About GSAS-II, whi= ch lists first the name of the menu (here Help) and second the name of the entry in the menu (here About GSAS-II). If you = have not done so already, start GSAS-II
1. Use the Data/Add phase menu item add a new phase into the current GSAS-II project. A popup window will appear asking for a phase name; I entered SS dipyridyl; press OK when done. Select Loaded Data/Phases/SS dipyridyl from the GSAS-II Data tree window. The General tab for Phase Data will appe= ar.
2. Enter the space group P 21/c (don’t forget the space between P & 21/c) & press Enter. A Space Group Information popup window will appear; press OK. The General window will be refreshed showing on= ly the needed lattice parameters for P 21/c.<= /span>
3. Enter 15.8489<= /span>, 5.5008, 23.118, and 96.9160<= /span> for a, b, c and beta, respectively; the unit cell volume will be recalculat= ed at each entry.
There are two parts to this step: one is to import the= data and the second is to connect the data with the phase within GSAS-II.
To do these, do Import/Structure factor/from CIF file
from the main GSAS-II data tree window menu. A file selection dialog will
appear; find exercises\CF Xray single crystal\S2dipyridyl.fcf and
press Open.
A popup window asking if this is the file you want; press Yes. After a pause
while the file is read a new popup will appear offering the chance to rename
the structure factor set; press
Because the fcf file has both observed and calculated structure factors, the plot shows a small R value for the layer. The observ= ed structure factors are shown as blue rings, the calculated ones as green rin= gs and a small green or red dot may appear at each ring center showing Fo= -Fc. If the reflection data file had only observed structure factors then only b= lue rings will be seen. You can explore the plot options in the ‘K= ’ box in the plot toolbar.
To solve (again) this crystal structure we will use ch=
arge
flipping. Charge flipping in GSAS-II is implemented to solve the crystal
structure without consideration of space group symmetry. To do this it oper=
ates
on the entire unit cell volume to a selected resolution (usually 0.5Å) using fast fouri=
er
transform techniques. This requires a set of structure factors in an array =
of
the same dimensions as the density array covering the unit cell (i.e. a box
bounded by ~0.5Å
resolution). The space group symmetry is applied to the observed structure
factors to create a full sphere which is then zero filled out to the 0.5
Find the Fourier map controls and change
the Peak cut=
off
% to 10; then immediately below find the Charge f=
lip
controls. Press Select reflection sets, pick HKLF
S2dipyridyl.fcf:1a from the list (the only one) and press OK.
If you had multiple data sets for this phase, you can pick more than one and
GSAS-II will use a “last one in” process for assembling the reflection set =
to
use for charge flipping. There are four more settings to consider: 1) kMax
controls the upper cutoff for charge flipping; if the density is > k-Max=
*sr (map standard deviat=
ion)
then flip the charge. This prevents the “Uranium solution” sometimes found
where all the density is concentrated in a single peak. A useful guide is to
use twice the largest atomic number of any element in your structure. For e=
qual
atom problems use 12-15; adjust upward for structures with heavy & light
atoms. In this case, set k-Max to 30.0 to allow the S
atom to appear. 2) k-Factor controls the lower level for charge flipping; if
the density is < k-Factor*s
With the controls all set you can now do charge flippi= ng; from the General<= /span> tab do Compute/= Charge flipping. A progress bar popup will appear showing the residual between the observed structure factors and those obtained from the inverse fourier transform of the last flipped density map. It should quickly decrea= se to the ~20% range and level out indicating a good charge flip solution. Whe= n it has reached this, press Cancel to stop the process.
The console window will show something like
There may be a pause at Begin fourier map search befor= e it finishes. Provided is a summary of the charge flip calculation (time, map s= ize, density range & structure factor residual). The map offset is discovere= d by an analysis of the reflection phases with respect to how they should be distributed for your chosen space group. These offsets are then applied to shift the map so that the symmetry elements are properly located in the unit cell. The quality of this fit (chi**2) is given. This process is not necessarily perfect; you are given an opportunity to hand-tune the offset. Finally the number of peaks found in the map is listed, the structure is dr= awn (I’ve made the view down the b-axis)
and the Phase= data window will show the map peaks tab
These are listed in order of magnitude; a double click= on any of the table headings will sort the list according to that parameter. My li= st has 112 entries; dipyridyl disulfide has 14 C & S atoms so this list is appropriate for 8 molecules in the unit cell and thus all atoms were found = in this charge flipping result.
If all went well then the drawing should nicely show a= ll the atoms in the structure placed properly with respect to the locations of the= inversion centers (they are at all the corners, edge centers, face centers and cell center). If not then you can shift the map & peaks with the L= , R= , U= & D= keys (NB: rotate the drawing so the axes are ~horizontal/vertical); the map/peaks will move in resolution steps (0.5A). The table is also updated w= ith new peak positions. You could also just repeat the charge flipping and hope= to get a better map offset solution (examine the map offset chi**2 to get a se= nse of this). You can also show the map density (highest point is shown as a gr= een dot somewhere in the map – on a S-atom position); select the Draw Opt= ions tab and use the Contour level slider. The drawing will show green d= ots at each set map point with size in proportion to the density. The mouse RB can be used to slide the structure around; the density is always drawn in a space surrounding the view point (multicolored cross at the center). While = here you can also change the Bond search factor to 0.90 to ensure all S-C bonds are shown.
If the charge flipping has failed (high residual &=
no
recognizable structure) the process should be just repeated. This gives it a
new random start for the structure factor phases which may lead to a good
solution. After a few attempts, you can try different control settings to s=
ee
if that will coax out a good solution; first be sure k-Max is properly =
set
and then perhaps try different
Assuming that the map & peak positions are properly placed with respect to the symmetry elements of the space group, we can now select those peaks which describe the structure. Select the Map peak= s tab and double LB click the blank upper left corner of the table; all entri= es will be highlighted in blue. Then do Map peaks/Unique peaks; after a bit of time 1/4 of the peaks in the list will be highlighted and the corresponding peaks in the drawing will be green (NB: if you navigate away = from this tab, this selection will be lost and you’ll have to repeat it!). Next,= do Map peaks/Move peaks; these peaks will be transferred to the Atoms list as H-atoms named according to their position in the magnitude column.<= /p>
The drawing will show white balls at the atom positions scattered over several molecules.
Notice that 4 atoms have magnitudes ~90+, these are th= e S atoms. The rest are C & N atoms. In the Atoms tab select t= he first 4 atoms (press LB on the 1st & shift LB on the 4t= h one). Then do Edit/Modify atom parameters; a popup window will appear. Select Type & press OK; a Periodic Table will appe= ar. Select S= ; the atoms will be renames and their Type changed to S. Next select the rema= ining H atoms (a quick way it to double LB click the Type column heading and select H from the popup window). Then do Edit/Modify atom parameters and Type from the popup; select C from the Periodic Table as we don’t know which ones are N. The drawing will change (you may have to wiggl= e it a bit to force the update).
Notice that the atoms are scattered over several molec= ules; we want to assemble them into 2 conveniently placed ones. Begin by selectin= g an atom (make sure the Atom tab is displayed & do shift LB on an atom in the drawing – I chose the S atom near the upper midd= le); it will turn green and a line in the Atom table will be highlighted. Next d= o Edit/Ass= emble molecule; a popup window will appear. Change the Bond sea= rch factor to 0.90 to be sure all S-C bonds = are found.
Press OK; atoms will be collected in= to a well positioned group, but others are not. Next select one of the unassembl= ed atoms (I chose a C-atom in a nearby SS-dipyridyl) and do Edit/Assemble molecule= ; there will be two nicely assembled SS-dipyridyls.
You should probably save this project as it contains y= our solved crystal structure.
Since we now have a structural model, we can do the in= itial structure refinement. By default this will only refine the scale factor; do= Calculat= e/Refine from the main GSAS-II data tree window. Convergence will quickly occur with= Rw ~35%. More useful is to refine the atom positions and isotropic thermal parameters. Select the Atoms tab from the Phase windo= w. Then LB double click the refine column heading; a popup window will appear. Select X and U and press OK. The Atoms window will show XU for each atom in the refine column. Then do Calculat= e/Refine (twice to get convergence) and the Rw ~12%.
We know from the chemistry that the N atom is in the 2 position of the pyridine ring, i.e. next to the point of attachment to the S-atom. However, we don’t know which one that is and we have 8 atoms of whi= ch 4 are C and 4 are N.
To work out the C/N problem above we need the atoms to= be in a chemically sensible order. The assemble molecule routine did construct ch= ains of atoms but this ordering is not really satisfactory. The ordering can qui= ckly be done by hand by following a labelled drawing. First go to the Draw Ato= ms tab and double LB click the Style column; select balls &a= mp; sticks from the popup box. Press OK. Next, double LB click the Label column and select name from the popup box; press= OK. Then go to the Draw options tab and adjust the Ball scale & Bond rad= ius to allow the labels to be easily seen. After shifting the view point the drawi= ng should look something like
Now go to the Atoms tab. If you look careful= ly, you can see that the atoms in each SS-dipyridyl are grouped together in the table but they are not in chemically sensible order. The atoms can be reord= ered by selecting one row with the Alt key down (the status line = will tell which atom is selected to move) and then with the Alt key still down pick a row below where you want to insert it. I ordered them so each S-atom= was followed by the C-atoms in order around the ring; my list looked like (I sh= ow just the 1st SS dipyridyl molecule)
Once you have reordered the atoms to your satisfaction=
they
can be renamed to be in order. To do this select all the atoms (double LB c=
lick
the empty corner box) and then do =
Edit/Modify atom parameters.
Select Name
and press OK;
press Yes
to the popup question. The atoms will be renamed in numerical order. Do Edit/Rel=
oad
draw atoms; the labels will change. In my numbering scheme, half=
of
the C3, C7, C10, C14, C17, C21, C24 and C28 carbon atoms are really nitrogen
(if they are ordered). Select these and do Edit/Set atom refinement flags;
select F=
,
X=
& U=
for these. Do Calculate/Refine; the Rw will drop to ~10% and 4 of=
the
atom frac
values will be ~1.25 while the others are ~1.0. The former are N-atoms and =
the
latter are C-atoms. Change the
Given reasonable measured structure factors one can im= prove a crystal model by using anisotropic thermal motion models for all the nonhydrogen atoms. To convert all the atoms here select the Atoms tab and t= hen do a double LB click on the I/A column heading. Select Anisotropic from the popup and press OK; the Atom table will be redrawn with Uij values equivale= nt to the corresponding Uiso (now hidden). Do Calculate/Refine; the final Rw ~8.2%
This structure can be completed by adding the 4 H-atom= s per pyridine ring (16 in all). One could do this (painfully) by hand by looking= for them in DF maps, but it is simple= r to just place them knowing the bonding chemistry of the rings. To start this select the Atoms tab for the phase. Then select the C-atoms by= a double LB click on the Type column heading and select= C= from the popup; press OK. The C-atoms will be highlighted. Next do Edit/Insert H atoms; a Distance Angle Controls popup will appear; the numbers should be as befor= e. Press OK; a new popup will appear
This is the hydrogen add control; it shows both the ex= pected number of H-atoms to add to each C-atom and the neighboring atoms used to determine the geometry of the C-H bond. Check to make sure that 4 H-atoms w= ill be added for each ring. Note that C2, C9, C16 & C23 will not have an H-= atom added as these are the S-atom attachment points in SS-dipyridyl. Press Ok; the H-atoms will be inserted immediately after the corresponding C-atoms and the drawing is updated showing van der Waals spheres for all atoms.
Next, do Calculate/Refine; there will b=
e an
immediate drop in Rw ~3.2%. Note that we did not refine the H-atom position=
s or
thermal parameters. The H-atom insertion process retains the mechanisms for
creating them in the first place and these tools can be used to move them to
reflect the changes in the C-atom parameters thus forcing them to ride on t=
he
C-atoms. Do Edit/Update H atoms; the H-atom positions & Uis=
os
will be revised. Repeat Calculate/Refine; there will b=
e a
slight improvement in Rw. Repeat these two steps (twice); Rw should not cha=
nge
on the last round. This completes the refinement of the SS-dipyridyl struct=
ure.
You can generate a final DF map f=
rom
the General<=
/span>
tab; in Fourier =
map
controls select the