source: Tutorials/CFXraySingleCrystal/CFSingleCrystal.htm @ 2262

Last change on this file since 2262 was 2262, checked in by vondreele, 6 years ago

make visible as html
  • Property svn:mime-type set to text/html
File size: 32.1 KB
Line 
1<html>
2
3<head>
4<meta http-equiv=Content-Type content="text/html; charset=windows-1252">
5<meta name=Generator content="Microsoft Word 15 (filtered)">
6<style>
7<!--
8 /* Font Definitions */
9 @font-face
10        {font-family:"Cambria Math";
11        panose-1:2 4 5 3 5 4 6 3 2 4;}
12@font-face
13        {font-family:Calibri;
14        panose-1:2 15 5 2 2 2 4 3 2 4;}
15@font-face
16        {font-family:Cambria;
17        panose-1:2 4 5 3 5 4 6 3 2 4;}
18 /* Style Definitions */
19 p.MsoNormal, li.MsoNormal, div.MsoNormal
20        {margin:0in;
21        margin-bottom:.0001pt;
22        font-size:12.0pt;
23        font-family:"Times New Roman",serif;}
24h1
25        {mso-style-link:"Heading 1 Char";
26        margin-right:0in;
27        margin-left:0in;
28        font-size:24.0pt;
29        font-family:"Times New Roman",serif;}
30h2
31        {mso-style-link:"Heading 2 Char";
32        margin-right:0in;
33        margin-left:0in;
34        font-size:18.0pt;
35        font-family:"Times New Roman",serif;}
36h3
37        {mso-style-link:"Heading 3 Char";
38        margin-right:0in;
39        margin-left:0in;
40        font-size:10.0pt;
41        font-family:"Times New Roman",serif;}
42h4
43        {mso-style-link:"Heading 4 Char";
44        margin-top:10.0pt;
45        margin-right:0in;
46        margin-bottom:0in;
47        margin-left:0in;
48        margin-bottom:.0001pt;
49        page-break-after:avoid;
50        font-size:10.0pt;
51        font-family:"Cambria",serif;
52        color:#4F81BD;
53        font-style:italic;}
54h5
55        {mso-style-link:"Heading 5 Char";
56        margin-right:0in;
57        margin-left:0in;
58        font-size:10.0pt;
59        font-family:"Times New Roman",serif;
60        color:#4F4FFF;}
61p.MsoTitle, li.MsoTitle, div.MsoTitle
62        {mso-style-link:"Title Char";
63        margin-top:0in;
64        margin-right:0in;
65        margin-bottom:15.0pt;
66        margin-left:0in;
67        font-size:10.0pt;
68        font-family:"Cambria",serif;
69        color:#17365D;
70        letter-spacing:.25pt;}
71p.MsoNoSpacing, li.MsoNoSpacing, div.MsoNoSpacing
72        {margin:0in;
73        margin-bottom:.0001pt;
74        font-size:12.0pt;
75        font-family:"Times New Roman",serif;}
76p.MsoListParagraph, li.MsoListParagraph, div.MsoListParagraph
77        {margin-top:0in;
78        margin-right:0in;
79        margin-bottom:0in;
80        margin-left:.5in;
81        margin-bottom:.0001pt;
82        font-size:12.0pt;
83        font-family:"Times New Roman",serif;}
84span.MsoIntenseReference
85        {font-variant:small-caps;
86        color:#C0504D;
87        letter-spacing:.25pt;
88        font-weight:bold;
89        text-decoration:underline;}
90span.Heading1Char
91        {mso-style-name:"Heading 1 Char";
92        mso-style-link:"Heading 1";
93        font-family:"Times New Roman",serif;
94        font-weight:bold;}
95span.Heading2Char
96        {mso-style-name:"Heading 2 Char";
97        mso-style-link:"Heading 2";
98        font-family:"Times New Roman",serif;
99        font-weight:bold;}
100span.Heading3Char
101        {mso-style-name:"Heading 3 Char";
102        mso-style-link:"Heading 3";
103        font-family:"Times New Roman",serif;
104        font-weight:bold;}
105span.Heading4Char
106        {mso-style-name:"Heading 4 Char";
107        mso-style-link:"Heading 4";
108        font-family:"Cambria",serif;
109        color:#4F81BD;
110        font-weight:bold;
111        font-style:italic;}
112span.Heading5Char
113        {mso-style-name:"Heading 5 Char";
114        mso-style-link:"Heading 5";
115        font-family:"Times New Roman",serif;
116        color:#4F4FFF;
117        font-weight:bold;}
118span.TitleChar
119        {mso-style-name:"Title Char";
120        mso-style-link:Title;
121        font-family:"Cambria",serif;
122        color:#17365D;
123        letter-spacing:.25pt;}
124.MsoChpDefault
125        {font-size:10.0pt;
126        font-family:"Calibri",sans-serif;}
127@page WordSection1
128        {size:8.5in 11.0in;
129        margin:1.0in 1.0in 1.0in 1.0in;}
130div.WordSection1
131        {page:WordSection1;}
132 /* List Definitions */
133 ol
134        {margin-bottom:0in;}
135ul
136        {margin-bottom:0in;}
137-->
138</style>
139
140</head>
141
142<body lang=EN-US>
143
144<div class=WordSection1>
145
146<h1>Single crystal structure determination and refinement with X-ray data in
147GSAS-II</h1>
148
149<h2>Introduction</h2>
150
151<p class=MsoNormal>In this exercise we will use a set of X-ray single crystal
152structure factors to solve the structure of dipyridyl disulfide by charge flipping
153and then refine the structure by least-squares. The structure will be completed
154by adding the requisite hydrogen atoms and by using anisotropic thermal
155parameters for the heavier atoms. The structure was originally solved by
156Raghavan &amp; Seff, Acta Cryst. B33, 386-391 (1977) in the space group P2<sub>1</sub>/c
157with one disordered pyridine ring with indications that the true space group
158was P2<sub>1</sub>. It was subsequently reinvestigated by Young (2014….) who
159found that the true space group was P2<sub>1</sub> with 4 molecules in the
160asymmetric unit. The data used in the latter analysis is what is used here and
161is provided as a “fcf” file obtained after structure analysis by Shelx-97; the
162structure factors are scaled to those calculated from the structure. We will
163solve the P 2<sub>1</sub>/c structure first.</p>
164
165<p class=MsoNormal>&nbsp;</p>
166
167<p class=MsoNormal>Note that menu entries and user input are shown in bold face
168below as <b><span style='font-family:"Calibri",sans-serif'>Help/About GSAS-II</span></b>,
169which lists first the name of the menu (here <b><span style='font-family:"Calibri",sans-serif'>Help</span></b>)
170and second the name of the entry in the menu (here <b><span style='font-family:
171"Calibri",sans-serif'>About GSAS-II</span></b>). If you have not done so
172already, start GSAS-II</p>
173
174<h2>Step 1. Input phase information</h2>
175
176<p class=MsoListParagraph style='text-indent:-.25in'>1.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
177</span>Use the <b><span style='font-family:"Calibri",sans-serif'>Data/Add phase</span></b>
178menu item add a new phase into the current GSAS-II project. A popup window will
179appear asking for a phase name; I entered <b><span style='font-family:"Calibri",sans-serif'>SS
180dipyridyl</span></b>; press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>
181when done. Select <b><span style='font-family:"Calibri",sans-serif'>Loaded
182Data/Phases/SS dipyridyl</span></b> from the GSAS-II Data tree window. The
183General tab for Phase Data will appear.</p>
184
185<p class=MsoListParagraph><img width=524 height=307 id="Picture 1"
186src="CFSingleCrystal_files/image001.png"></p>
187
188<p class=MsoListParagraph style='text-indent:-.25in'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
189</span>Enter the space group <b><span style='font-family:"Calibri",sans-serif'>P
19021/c</span></b> (don’t forget the space between P &amp; 21/c) &amp; press <b><span
191style='font-family:"Calibri",sans-serif'>Enter</span></b>. A Space Group
192Information popup window will appear; press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>.
193The General window will be refreshed showing only the needed lattice parameters
194for P 21/c.</p>
195
196<p class=MsoListParagraph><img width=522 height=361 id="Picture 3"
197src="CFSingleCrystal_files/image002.png"></p>
198
199<p class=MsoListParagraph style='text-indent:-.25in'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
200</span>Enter <b><span style='font-family:"Calibri",sans-serif'>15.8489</span></b>,
201<b><span style='font-family:"Calibri",sans-serif'>5.5008</span></b>, <b><span
202style='font-family:"Calibri",sans-serif'>23.118</span></b>, and <b><span
203style='font-family:"Calibri",sans-serif'>96.9160</span></b> for a, b, c and
204beta, respectively; the unit cell volume will be recalculated at each entry.</p>
205
206<h2>Step 2. Import structure factors </h2>
207
208<p class=MsoNormal>There are two parts to this step: one is to import the data
209and the second is to connect the data with the phase within GSAS-II.</p>
210
211<p class=MsoNormal>To do these, do <b><span style='font-family:"Calibri",sans-serif'>Import/Structure
212factor/from CIF file</span></b> from the main GSAS-II data tree window menu. A
213file selection dialog will appear; find <b><span style='font-family:"Calibri",sans-serif'>exercises\CF
214Xray single crystal\S2dipyridyl.fcf</span></b> and press <b><span
215style='font-family:"Calibri",sans-serif'>Open</span></b>. A popup window asking
216if this is the file you want; press <b><span style='font-family:"Calibri",sans-serif'>Yes</span></b>.
217After a pause while the file is read a new popup will appear offering the
218chance to rename the structure factor set; press <b><span style='font-family:
219"Calibri",sans-serif'>OK</span></b>. After some time a new popup will appear to
220Add the new structure factor set to the SS dipyridyl phase. Select the phase
221and press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>. The
222plot will show a rectangular array of circles for the hk0 reflection layer;
223select the plot &amp; press <b><span style='font-family:"Calibri",sans-serif'>k</span></b>
224to get an h0l layer.</p>
225
226<p class=MsoNormal><img width=480 height=412 id="Picture 2"
227src="CFSingleCrystal_files/image003.png"></p>
228
229<p class=MsoNormal>Because the fcf file has both observed and calculated
230structure factors, the plot shows a small R value for the layer. The observed
231structure factors are shown as blue rings, the calculated ones as green rings
232and a small green or red dot may appear at each ring center showing F<sub>o</sub>-F<sub>c</sub>.
233If the reflection data file had only observed structure factors then only blue
234rings will be seen. You can explore the plot options in the ‘<b><span
235style='font-family:"Calibri",sans-serif'>K</span></b>’ box in the plot toolbar.</p>
236
237<h2>Step 3. Setup for charge flipping</h2>
238
239<p class=MsoNormal>To solve (again) this crystal structure we will use charge
240flipping. Charge flipping in GSAS-II is implemented to solve the crystal
241structure without consideration of space group symmetry. To do this it operates
242on the entire unit cell volume to a selected resolution (usually 0.5Å) using
243fast fourier transform techniques. This requires a set of structure factors in
244an array of the same dimensions as the density array covering the unit cell
245(i.e. a box bounded by ~0.5Å resolution). The space group symmetry is applied
246to the observed structure factors to create a full sphere which is then zero
247filled out to the 0.5Å resolution bounded box. To be reasonably assured of
248success, the observed structure factors should extend to ~1Å resolution; we
249have that here for this example. To begin select <b><span style='font-family:
250"Calibri",sans-serif'>Phases/SS dipyridyl</span></b> from the GSAS-II data
251tree; the General tab will be shown</p>
252
253<p class=MsoNormal><img width=624 height=401 id="Picture 4"
254src="CFSingleCrystal_files/image004.png"></p>
255
256<p class=MsoNormal>Find the <b><span style='font-family:"Calibri",sans-serif'>Fourier
257map controls</span></b> and change the <b><span style='font-family:"Calibri",sans-serif'>Peak
258cutoff %</span></b> to <b><span style='font-family:"Calibri",sans-serif'>10</span></b>;
259then immediately below find the <b><span style='font-family:"Calibri",sans-serif'>Charge
260flip controls</span></b>. Press <b><span style='font-family:"Calibri",sans-serif'>Select
261reflection sets</span></b>, pick <b><span style='font-family:"Calibri",sans-serif'>HKLF
262S2dipyridyl.fcf:1a</span></b> from the list (the only one) and press <b><span
263style='font-family:"Calibri",sans-serif'>OK</span></b>. If you had multiple
264data sets for this phase, you can pick more than one and GSAS-II will use a
265“last one in” process for assembling the reflection set to use for charge
266flipping. There are four more settings to consider: 1) kMax controls the upper
267cutoff for charge flipping; if the density is &gt; k-Max*<span
268style='font-family:Symbol'>s</span><sub><span style='font-family:Symbol'>r</span></sub>
269(map standard deviation) then flip the charge. This prevents the “Uranium
270solution” sometimes found where all the density is concentrated in a single
271peak. A useful guide is to use twice the largest atomic number of any element
272in your structure. For equal atom problems use 12-15; adjust upward for
273structures with heavy &amp; light atoms. In this case, set <b><span
274style='font-family:"Calibri",sans-serif'>k-Max</span></b> to <b><span
275style='font-family:"Calibri",sans-serif'>30.0</span></b> to allow the S atom to
276appear. 2) k-Factor controls the lower level for charge flipping; if the
277density is &lt; k-Factor*<span style='font-family:Symbol'>s</span><sub><span
278style='font-family:Symbol'>r</span></sub> then flip the charge. The default
279value seems to work pretty well; I’d only change it if the charge flipping is
280having trouble solving the structure. 3) Resolution selects the spacing between
281map points. 0.5Å is sufficient in most cases. Choosing a smaller value requires
282more map points (NB: GSAS-II uses the entire unit cell volume for charge
283flipping) and thus will require more structure factors since the fast fourier
284algorithm requires the same size arrays in both real space and reciprocal
285space. This will slow down the charge flip process. 4) Normalizing element
286selects a form factor to rescale the structure factors thus “sharpening” the
287density map. I suggest trying <b><span style='font-family:"Calibri",sans-serif'>None</span></b>
288first, otherwise select a representative element (really doesn’t matter which).</p>
289
290<h2 style='page-break-after:avoid'>Step 4. Charge flipping</h2>
291
292<p class=MsoNormal>With the controls all set you can now do charge flipping;
293from the <b><span style='font-family:"Calibri",sans-serif'>General</span></b>
294tab do <b><span style='font-family:"Calibri",sans-serif'>Compute/Charge
295flipping</span></b>. A progress bar popup will appear showing the residual
296between the observed structure factors and those obtained from the inverse
297fourier transform of the last flipped density map. It should quickly decrease
298to the ~20% range and level out indicating a good charge flip solution. When it
299has reached this, press <b><span style='font-family:"Calibri",sans-serif'>Cancel</span></b>
300to stop the process.</p>
301
302<p class=MsoNormal><img width=366 height=180 id="Picture 6"
303src="CFSingleCrystal_files/image005.png"></p>
304
305<p class=MsoNormal>The console window will show something like</p>
306
307<p class=MsoNormal><img width=624 height=166 id="Picture 7"
308src="CFSingleCrystal_files/image006.png"></p>
309
310<p class=MsoNormal>There may be a pause at <b><span style='font-family:"Calibri",sans-serif'>Begin
311fourier map search</span></b> before it finishes. Provided is a summary of the
312charge flip calculation (time, map size, density range &amp; structure factor
313residual). The map offset is discovered by an analysis of the reflection phases
314with respect to how they should be distributed for your chosen space group.
315These offsets are then applied to shift the map so that the symmetry elements
316are properly located in the unit cell. The quality of this fit (chi**2) is
317given. This process is not necessarily perfect; you are given an opportunity to
318hand-tune the offset. Finally the number of peaks found in the map is listed,
319the structure is drawn (I’ve made the view down the b-axis)</p>
320
321<p class=MsoNormal><img width=478 height=402 id="Picture 11"
322src="CFSingleCrystal_files/image007.jpg"></p>
323
324<p class=MsoNormal> and the Phase data window will show the map peaks tab</p>
325
326<p class=MsoNormal><img width=500 height=300 id="Picture 12"
327src="CFSingleCrystal_files/image008.png"></p>
328
329<p class=MsoNormal>These are listed in order of magnitude; a double click on
330any of the table headings will sort the list according to that parameter. My
331list has 112 entries; dipyridyl disulfide has 14 C &amp; S atoms so this list
332is appropriate for 8 molecules in the unit cell and thus all atoms were found
333in this charge flipping result.</p>
334
335<p class=MsoNormal>If all went well then the drawing should nicely show all the
336atoms in the structure placed properly with respect to the locations of the
337inversion centers (they are at all the corners, edge centers, face centers and
338cell center). If not then you can shift the map &amp; peaks with the <b><span
339style='font-family:"Calibri",sans-serif'>L</span></b>, <b><span
340style='font-family:"Calibri",sans-serif'>R</span></b>, <b><span
341style='font-family:"Calibri",sans-serif'>U</span></b> &amp; <b><span
342style='font-family:"Calibri",sans-serif'>D</span></b> keys (NB: rotate the
343drawing so the axes are ~horizontal/vertical); the map/peaks will move in
344resolution steps (0.5A). The table is also updated with new peak positions. You
345could also just repeat the charge flipping and hope to get a better map offset
346solution (examine the map offset chi**2 to get a sense of this). You can also
347show the map density (highest point is shown as a green dot somewhere in the
348map – on a S-atom position); select the <b><span style='font-family:"Calibri",sans-serif'>Draw
349Options</span></b> tab and use the <b><span style='font-family:"Calibri",sans-serif'>Contour
350level</span></b> slider. The drawing will show green dots at each set map point
351with size in proportion to the density. The mouse <b><span style='font-family:
352"Calibri",sans-serif'>RB</span></b> can be used to slide the structure around;
353the density is always drawn in a space surrounding the view point (multicolored
354cross at the center). While here you can also change the <b><span
355style='font-family:"Calibri",sans-serif'>Bond search factor</span></b> to <b><span
356style='font-family:"Calibri",sans-serif'>0.90</span></b> to ensure all S-C
357bonds are shown.</p>
358
359<p class=MsoNormal>If the charge flipping has failed (high residual &amp; no
360recognizable structure) the process should be just repeated. This gives it a
361new random start for the structure factor phases which may lead to a good
362solution. After a few attempts, you can try different control settings to see
363if that will coax out a good solution; first be sure <b><span style='font-family:
364"Calibri",sans-serif'>k-Max</span></b> is properly set and then perhaps try
365different <b><span style='font-family:"Calibri",sans-serif'>k-Factors</span></b>
366and do <b><span style='font-family:"Calibri",sans-serif'>Normalizing</span></b>
367by some element form factor. If it seemed to work but very few peaks were
368found, make sure <b><span style='font-family:"Calibri",sans-serif'>Peak cutoff</span></b>
369was properly set; you can then repeat the peak search by doing <b><span
370style='font-family:"Calibri",sans-serif'>Compute/Search map</span></b>.</p>
371
372<h2>Step 5. Extract solution and make molecules</h2>
373
374<p class=MsoNormal>Assuming that the map &amp; peak positions are properly
375placed with respect to the symmetry elements of the space group, we can now
376select those peaks which describe the structure. Select the <b><span
377style='font-family:"Calibri",sans-serif'>Map peaks</span></b> tab and double LB
378click the blank upper left corner of the table; all entries will be highlighted
379in blue. Then do <b><span style='font-family:"Calibri",sans-serif'>Map
380peaks/Unique peaks</span></b>; after a bit of time 1/4 of the peaks in the list
381will be highlighted and the corresponding peaks in the drawing will be green
382(NB: if you navigate away from this tab, this selection will be lost and you’ll
383have to repeat it!). Next, do <b><span style='font-family:"Calibri",sans-serif'>Map
384peaks/Move peaks</span></b>; these peaks will be transferred to the <b><span
385style='font-family:"Calibri",sans-serif'>Atoms</span></b> list as H-atoms named
386according to their position in the magnitude column.</p>
387
388<p class=MsoNormal><img width=624 height=267 id="Picture 13"
389src="CFSingleCrystal_files/image009.png"></p>
390
391<p class=MsoNormal>The drawing will show white balls at the atom positions
392scattered over several molecules.</p>
393
394<p class=MsoNormal><img width=474 height=409 id="Picture 14"
395src="CFSingleCrystal_files/image010.jpg"></p>
396
397<p class=MsoNormal>Notice that 4 atoms have magnitudes ~90+, these are the S
398atoms. The rest are C &amp; N atoms. In the <b><span style='font-family:"Calibri",sans-serif'>Atoms</span></b>
399tab select the first 4 atoms (press LB on the 1<sup>st</sup> &amp; shift LB on
400the 4<sup>th</sup> one). Then do <b><span style='font-family:"Calibri",sans-serif'>Edit/Modify
401atom parameters</span></b>; a popup window will appear. Select <b><span
402style='font-family:"Calibri",sans-serif'>Type</span></b> &amp; press <b><span
403style='font-family:"Calibri",sans-serif'>OK</span></b>; a Periodic Table will
404appear. Select <b><span style='font-family:"Calibri",sans-serif'>S</span></b>;
405the atoms will be renames and their Type changed to S. Next select the
406remaining H atoms (a quick way it to double LB click the <b><span
407style='font-family:"Calibri",sans-serif'>Type</span></b> column heading and
408select <b><span style='font-family:"Calibri",sans-serif'>H</span></b> from the
409popup window). Then do <b><span style='font-family:"Calibri",sans-serif'>Edit/Modify
410atom parameters</span></b> and <b><span style='font-family:"Calibri",sans-serif'>Type</span></b>
411from the popup; select <b><span style='font-family:"Calibri",sans-serif'>C</span></b>
412from the Periodic Table as we don’t know which ones are N. The drawing will
413change (you may have to wiggle it a bit to force the update).</p>
414
415<p class=MsoNormal><img width=480 height=390 id="Picture 17"
416src="CFSingleCrystal_files/image011.jpg"></p>
417
418<p class=MsoNormal>Notice that the atoms are scattered over several molecules;
419we want to assemble them into 2 conveniently placed ones. Begin by selecting an
420atom (make sure the <b><span style='font-family:"Calibri",sans-serif'>Atom</span></b>
421tab is displayed &amp; do shift LB on an atom in the drawing – I chose the S
422atom near the upper middle); it will turn green and a line in the Atom table
423will be highlighted. Next do <b><span style='font-family:"Calibri",sans-serif'>Edit/Assemble
424molecule</span></b>; a popup window will appear. Change the <b><span
425style='font-family:"Calibri",sans-serif'>Bond search factor</span></b> to <b><span
426style='font-family:"Calibri",sans-serif'>0.90</span></b> to be sure all S-C
427bonds are found.</p>
428
429<p class=MsoNormal><img width=265 height=223 id="Picture 16"
430src="CFSingleCrystal_files/image012.png"> </p>
431
432<p class=MsoNormal>Press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>;
433atoms will be collected into a well positioned group, but others are not. Next
434select one of the unassembled atoms (I chose a C-atom in a nearby SS-dipyridyl)
435and do <b><span style='font-family:"Calibri",sans-serif'>Edit/Assemble molecule</span></b>;
436there will be two nicely assembled SS-dipyridyls.</p>
437
438<p class=MsoNormal><img width=480 height=384 id="Picture 5"
439src="CFSingleCrystal_files/image013.jpg"></p>
440
441<p class=MsoNormal>You should probably save this project as it contains your
442solved crystal structure.</p>
443
444<h2>Step 6. Initial refinement</h2>
445
446<p class=MsoNormal>Since we now have a structural model, we can do the initial
447structure refinement. By default this will only refine the scale factor; do <b><span
448style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b> from the
449main GSAS-II data tree window. Convergence will quickly occur with Rw ~35%.
450More useful is to refine the atom positions and isotropic thermal parameters.
451Select the <b><span style='font-family:"Calibri",sans-serif'>Atoms</span></b>
452tab from the Phase window. Then LB double click the <b><span style='font-family:
453"Calibri",sans-serif'>refine</span></b> column heading; a popup window will
454appear. Select <b><span style='font-family:"Calibri",sans-serif'>X</span></b>
455and <b><span style='font-family:"Calibri",sans-serif'>U</span></b> and press <b><span
456style='font-family:"Calibri",sans-serif'>OK</span></b>. The <b><span
457style='font-family:"Calibri",sans-serif'>Atoms</span></b> window will show <b><span
458style='font-family:"Calibri",sans-serif'>XU</span></b> for each atom in the
459refine column. Then do <b><span style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b>
460(twice to get convergence) and the Rw ~12%.</p>
461
462<h2>Step 7. Determine C/N choice</h2>
463
464<p class=MsoNormal>We know from the chemistry that the N atom is in the 2
465position of the pyridine ring, i.e. next to the point of attachment to the S-atom.
466However, we don’t know which one that is and we have 8 atoms of which 4 are C
467and 4 are N.</p>
468
469<p class=MsoNormal>To work out the C/N problem above we need the atoms to be in
470a chemically sensible order. The assemble molecule routine did construct chains
471of atoms but this ordering is not really satisfactory. The ordering can quickly
472be done by hand by following a labelled drawing. First go to the <b><span
473style='font-family:"Calibri",sans-serif'>Draw Atoms</span></b> tab and double
474LB click the <b><span style='font-family:"Calibri",sans-serif'>Style</span></b>
475column; select <b><span style='font-family:"Calibri",sans-serif'>balls &amp;
476sticks</span></b> from the popup box. Press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>.
477Next, double LB click the <b><span style='font-family:"Calibri",sans-serif'>Label</span></b>
478column and select <b><span style='font-family:"Calibri",sans-serif'>name</span></b>
479from the popup box; press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>.
480Then go to the <b><span style='font-family:"Calibri",sans-serif'>Draw options</span></b>
481tab and adjust the <b><span style='font-family:"Calibri",sans-serif'>Ball scale</span></b>
482&amp; <b><span style='font-family:"Calibri",sans-serif'>Bond radius </span></b>to
483allow the labels to be easily seen. After shifting the view point the drawing
484should look something like</p>
485
486<p class=MsoNormal>&nbsp;</p>
487
488<p class=MsoNormal><img width=474 height=386 id="Picture 9"
489src="CFSingleCrystal_files/image014.jpg"></p>
490
491<p class=MsoNormal>Now go to the <b><span style='font-family:"Calibri",sans-serif'>Atoms</span></b>
492tab. If you look carefully, you can see that the atoms in each SS-dipyridyl are
493grouped together in the table but they are not in chemically sensible order.
494The atoms can be reordered by selecting one row with the <b><span
495style='font-family:"Calibri",sans-serif'>Alt</span></b> key down (the status
496line will tell which atom is selected to move) and then with the <b><span
497style='font-family:"Calibri",sans-serif'>Alt</span></b> key still down pick a
498row below where you want to insert it. I ordered them so each S-atom was
499followed by the C-atoms in order around the ring; my list looked like (I show
500just the 1<sup>st</sup> SS dipyridyl molecule)</p>
501
502<p class=MsoNormal><img width=624 height=408 id="Picture 10"
503src="CFSingleCrystal_files/image015.png"></p>
504
505<p class=MsoNormal>Once you have reordered the atoms to your satisfaction they
506can be renamed to be in order. To do this select all the atoms (double LB click
507the empty corner box) and then do <b><span style='font-family:"Calibri",sans-serif'>Edit/Modify
508atom parameters</span></b>. Select <b><span style='font-family:"Calibri",sans-serif'>Name</span></b>
509and press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>;
510press <b><span style='font-family:"Calibri",sans-serif'>Yes</span></b> to the
511popup question. The atoms will be renamed in numerical order. Do <b><span
512style='font-family:"Calibri",sans-serif'>Edit/Reload draw atoms</span></b>; the
513labels will change. In my numbering scheme, half of the C3, C7, C10, C14, C17,
514C21, C24 and C28 carbon atoms are really nitrogen (if they are ordered). Select
515these and do <b><span style='font-family:"Calibri",sans-serif'>Edit/Set atom
516refinement flags</span></b>; select <b><span style='font-family:"Calibri",sans-serif'>F</span></b>,
517<b><span style='font-family:"Calibri",sans-serif'>X</span></b> &amp; <b><span
518style='font-family:"Calibri",sans-serif'>U</span></b> for these. Do <b><span
519style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b>; the Rw
520will drop to ~10% and 4 of the atom <b><span style='font-family:"Calibri",sans-serif'>frac</span></b>
521values will be ~1.25 while the others are ~1.0. The former are N-atoms and the
522latter are C-atoms. Change the <b><span style='font-family:"Calibri",sans-serif'>Type</span></b>
523for the N-atoms and repeat <b><span style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b>;
524the Rw will be high to start, but immediately fall to ~10%. In the Atom table
525all 8 refined frac values are be now ~1.0. To finish this part of the
526refinement, set all <b><span style='font-family:"Calibri",sans-serif'>frac</span></b>
527values to <b><span style='font-family:"Calibri",sans-serif'>1.0</span></b> and
528all refine flags to <b><span style='font-family:"Calibri",sans-serif'>XU</span></b>.
529Do <b><span style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b>;
530the final Rw ~10.5%</p>
531
532<h2>Step 8. Anisotropic thermal motion refinement</h2>
533
534<p class=MsoNormal>Given reasonable measured structure factors one can improve
535a crystal model by using anisotropic thermal motion models for all the
536nonhydrogen atoms. To convert all the atoms here select the Atoms tab and then
537do a double LB click on the I/A column heading. Select Anisotropic from the
538popup and press OK; the Atom table will be redrawn with Uij values equivalent
539to the corresponding Uiso (now hidden). Do <b><span style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b>;
540the final Rw ~8.2%</p>
541
542<h2 style='page-break-after:avoid'>Step 9. H-atom placement &amp; final
543refinement</h2>
544
545<p class=MsoNormal>This structure can be completed by adding the 4 H-atoms per
546pyridine ring (16 in all). One could do this (painfully) by hand by looking for
547them in <span style='font-family:Symbol'>D</span>F maps, but it is simpler to just
548place them knowing the bonding chemistry of the rings. To start this select the
549<b><span style='font-family:"Calibri",sans-serif'>Atoms</span></b> tab for the
550phase. Then select the C-atoms by a double LB click on the <b><span
551style='font-family:"Calibri",sans-serif'>Type</span></b> column heading and
552select <b><span style='font-family:"Calibri",sans-serif'>C</span></b> from the
553popup; press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>.
554The C-atoms will be highlighted. Next do <b><span style='font-family:"Calibri",sans-serif'>Edit/Insert
555H atoms</span></b>; a <b><span style='font-family:"Calibri",sans-serif'>Distance
556Angle Controls</span></b> popup will appear; the numbers should be as before.
557Press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>; a new
558popup will appear</p>
559
560<p class=MsoNormal><img width=400 height=485 id="Picture 8"
561src="CFSingleCrystal_files/image016.png"></p>
562
563<p class=MsoNormal>This is the hydrogen add control; it shows both the expected
564number of H-atoms to add to each C-atom and the neighboring atoms used to
565determine the geometry of the C-H bond. Check to make sure that 4 H-atoms will
566be added for each ring. Note that C2, C9, C16 &amp; C23 will not have an H-atom
567added as these are the S-atom attachment points in SS-dipyridyl. Press <b><span
568style='font-family:"Calibri",sans-serif'>Ok</span></b>; the H-atoms will be
569inserted immediately after the corresponding C-atoms and the drawing is updated
570showing van der Waals spheres for all atoms.</p>
571
572<p class=MsoNormal><img width=624 height=396 id="Picture 15"
573src="CFSingleCrystal_files/image017.png"></p>
574
575<p class=MsoNormal>&nbsp;</p>
576
577<p class=MsoNormal><img width=483 height=394 id="Picture 18"
578src="CFSingleCrystal_files/image018.jpg"></p>
579
580<p class=MsoNormal>Next, do <b><span style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b>;
581there will be an immediate drop in Rw ~3.2%. Note that we did not refine the
582H-atom positions or thermal parameters. The H-atom insertion process retains
583the mechanisms for creating them in the first place and these tools can be used
584to move them to reflect the changes in the C-atom parameters thus forcing them
585to ride on the C-atoms. Do <b><span style='font-family:"Calibri",sans-serif'>Edit/Update
586H atoms</span></b>; the H-atom positions &amp; Uisos will be revised. Repeat <b><span
587style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b>; there
588will be a slight improvement in Rw. Repeat these two steps (twice); Rw should
589not change on the last round. This completes the refinement of the SS-dipyridyl
590structure. You can generate a final <span style='font-family:Symbol'>D</span>F
591map from the <b><span style='font-family:"Calibri",sans-serif'>General</span></b>
592tab; in <b><span style='font-family:"Calibri",sans-serif'>Fourier map controls</span></b>
593select the <b><span style='font-family:"Calibri",sans-serif'>Map type</span></b>
594and <b><span style='font-family:"Calibri",sans-serif'>Reflection sets</span></b>,
595then do <b><span style='font-family:"Calibri",sans-serif'>Compute/Fourier map</span></b>.
596The <span style='font-family:Symbol'>r</span><sub>max</sub> (=0.33) and <span
597style='font-family:Symbol'>r</span><sub>min</sub> (=-0.31) are listed on the
598console; these seem to be concentrated around the S-atoms.</p>
599
600</div>
601
602</body>
603
604</html>
Note: See TracBrowser for help on using the repository browser.