source: Tutorials/CFXraySingleCrystal/CFSingleCrystal.htm @ 2386

Last change on this file since 2386 was 2386, checked in by vondreele, 5 years ago
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401  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 2"/>
402  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 2"/>
403  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 2"/>
404  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 2"/>
405  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 2"/>
406  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 2"/>
407  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 2"/>
408  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 2"/>
409  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 2"/>
410  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 2"/>
411  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 3"/>
412  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 3"/>
413  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 3"/>
414  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 3"/>
415  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 3"/>
416  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 3"/>
417  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 3"/>
418  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 3"/>
419  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 3"/>
420  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 3"/>
421  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 3"/>
422  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 3"/>
423  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 3"/>
424  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 3"/>
425  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 4"/>
426  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 4"/>
427  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 4"/>
428  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 4"/>
429  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 4"/>
430  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 4"/>
431  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 4"/>
432  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 4"/>
433  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 4"/>
434  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 4"/>
435  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 4"/>
436  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 4"/>
437  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 4"/>
438  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 4"/>
439  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 5"/>
440  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 5"/>
441  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 5"/>
442  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 5"/>
443  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 5"/>
444  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 5"/>
445  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 5"/>
446  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 5"/>
447  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 5"/>
448  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 5"/>
449  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 5"/>
450  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 5"/>
451  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 5"/>
452  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 5"/>
453  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 6"/>
454  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 6"/>
455  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 6"/>
456  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 6"/>
457  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 6"/>
458  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 6"/>
459  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 6"/>
460  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 6"/>
461  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 6"/>
462  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 6"/>
463  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 6"/>
464  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 6"/>
465  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 6"/>
466  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 6"/>
467  <w:LsdException Locked="false" Priority="19" QFormat="true"
468   Name="Subtle Emphasis"/>
469  <w:LsdException Locked="false" Priority="21" QFormat="true"
470   Name="Intense Emphasis"/>
471  <w:LsdException Locked="false" Priority="31" QFormat="true"
472   Name="Subtle Reference"/>
473  <w:LsdException Locked="false" Priority="32" QFormat="true"
474   Name="Intense Reference"/>
475  <w:LsdException Locked="false" Priority="33" QFormat="true" Name="Book Title"/>
476  <w:LsdException Locked="false" Priority="37" SemiHidden="true"
477   UnhideWhenUsed="true" Name="Bibliography"/>
478  <w:LsdException Locked="false" Priority="39" SemiHidden="true"
479   UnhideWhenUsed="true" QFormat="true" Name="TOC Heading"/>
480  <w:LsdException Locked="false" Priority="41" Name="Plain Table 1"/>
481  <w:LsdException Locked="false" Priority="42" Name="Plain Table 2"/>
482  <w:LsdException Locked="false" Priority="43" Name="Plain Table 3"/>
483  <w:LsdException Locked="false" Priority="44" Name="Plain Table 4"/>
484  <w:LsdException Locked="false" Priority="45" Name="Plain Table 5"/>
485  <w:LsdException Locked="false" Priority="40" Name="Grid Table Light"/>
486  <w:LsdException Locked="false" Priority="46" Name="Grid Table 1 Light"/>
487  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2"/>
488  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3"/>
489  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4"/>
490  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark"/>
491  <w:LsdException Locked="false" Priority="51" Name="Grid Table 6 Colorful"/>
492  <w:LsdException Locked="false" Priority="52" Name="Grid Table 7 Colorful"/>
493  <w:LsdException Locked="false" Priority="46"
494   Name="Grid Table 1 Light Accent 1"/>
495  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 1"/>
496  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 1"/>
497  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 1"/>
498  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 1"/>
499  <w:LsdException Locked="false" Priority="51"
500   Name="Grid Table 6 Colorful Accent 1"/>
501  <w:LsdException Locked="false" Priority="52"
502   Name="Grid Table 7 Colorful Accent 1"/>
503  <w:LsdException Locked="false" Priority="46"
504   Name="Grid Table 1 Light Accent 2"/>
505  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 2"/>
506  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 2"/>
507  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 2"/>
508  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 2"/>
509  <w:LsdException Locked="false" Priority="51"
510   Name="Grid Table 6 Colorful Accent 2"/>
511  <w:LsdException Locked="false" Priority="52"
512   Name="Grid Table 7 Colorful Accent 2"/>
513  <w:LsdException Locked="false" Priority="46"
514   Name="Grid Table 1 Light Accent 3"/>
515  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 3"/>
516  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 3"/>
517  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 3"/>
518  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 3"/>
519  <w:LsdException Locked="false" Priority="51"
520   Name="Grid Table 6 Colorful Accent 3"/>
521  <w:LsdException Locked="false" Priority="52"
522   Name="Grid Table 7 Colorful Accent 3"/>
523  <w:LsdException Locked="false" Priority="46"
524   Name="Grid Table 1 Light Accent 4"/>
525  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 4"/>
526  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 4"/>
527  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 4"/>
528  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 4"/>
529  <w:LsdException Locked="false" Priority="51"
530   Name="Grid Table 6 Colorful Accent 4"/>
531  <w:LsdException Locked="false" Priority="52"
532   Name="Grid Table 7 Colorful Accent 4"/>
533  <w:LsdException Locked="false" Priority="46"
534   Name="Grid Table 1 Light Accent 5"/>
535  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 5"/>
536  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 5"/>
537  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 5"/>
538  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 5"/>
539  <w:LsdException Locked="false" Priority="51"
540   Name="Grid Table 6 Colorful Accent 5"/>
541  <w:LsdException Locked="false" Priority="52"
542   Name="Grid Table 7 Colorful Accent 5"/>
543  <w:LsdException Locked="false" Priority="46"
544   Name="Grid Table 1 Light Accent 6"/>
545  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 6"/>
546  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 6"/>
547  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 6"/>
548  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 6"/>
549  <w:LsdException Locked="false" Priority="51"
550   Name="Grid Table 6 Colorful Accent 6"/>
551  <w:LsdException Locked="false" Priority="52"
552   Name="Grid Table 7 Colorful Accent 6"/>
553  <w:LsdException Locked="false" Priority="46" Name="List Table 1 Light"/>
554  <w:LsdException Locked="false" Priority="47" Name="List Table 2"/>
555  <w:LsdException Locked="false" Priority="48" Name="List Table 3"/>
556  <w:LsdException Locked="false" Priority="49" Name="List Table 4"/>
557  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark"/>
558  <w:LsdException Locked="false" Priority="51" Name="List Table 6 Colorful"/>
559  <w:LsdException Locked="false" Priority="52" Name="List Table 7 Colorful"/>
560  <w:LsdException Locked="false" Priority="46"
561   Name="List Table 1 Light Accent 1"/>
562  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 1"/>
563  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 1"/>
564  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 1"/>
565  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 1"/>
566  <w:LsdException Locked="false" Priority="51"
567   Name="List Table 6 Colorful Accent 1"/>
568  <w:LsdException Locked="false" Priority="52"
569   Name="List Table 7 Colorful Accent 1"/>
570  <w:LsdException Locked="false" Priority="46"
571   Name="List Table 1 Light Accent 2"/>
572  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 2"/>
573  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 2"/>
574  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 2"/>
575  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 2"/>
576  <w:LsdException Locked="false" Priority="51"
577   Name="List Table 6 Colorful Accent 2"/>
578  <w:LsdException Locked="false" Priority="52"
579   Name="List Table 7 Colorful Accent 2"/>
580  <w:LsdException Locked="false" Priority="46"
581   Name="List Table 1 Light Accent 3"/>
582  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 3"/>
583  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 3"/>
584  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 3"/>
585  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 3"/>
586  <w:LsdException Locked="false" Priority="51"
587   Name="List Table 6 Colorful Accent 3"/>
588  <w:LsdException Locked="false" Priority="52"
589   Name="List Table 7 Colorful Accent 3"/>
590  <w:LsdException Locked="false" Priority="46"
591   Name="List Table 1 Light Accent 4"/>
592  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 4"/>
593  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 4"/>
594  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 4"/>
595  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 4"/>
596  <w:LsdException Locked="false" Priority="51"
597   Name="List Table 6 Colorful Accent 4"/>
598  <w:LsdException Locked="false" Priority="52"
599   Name="List Table 7 Colorful Accent 4"/>
600  <w:LsdException Locked="false" Priority="46"
601   Name="List Table 1 Light Accent 5"/>
602  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 5"/>
603  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 5"/>
604  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 5"/>
605  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 5"/>
606  <w:LsdException Locked="false" Priority="51"
607   Name="List Table 6 Colorful Accent 5"/>
608  <w:LsdException Locked="false" Priority="52"
609   Name="List Table 7 Colorful Accent 5"/>
610  <w:LsdException Locked="false" Priority="46"
611   Name="List Table 1 Light Accent 6"/>
612  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 6"/>
613  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 6"/>
614  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 6"/>
615  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 6"/>
616  <w:LsdException Locked="false" Priority="51"
617   Name="List Table 6 Colorful Accent 6"/>
618  <w:LsdException Locked="false" Priority="52"
619   Name="List Table 7 Colorful Accent 6"/>
620 </w:LatentStyles>
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937<body lang=EN-US style='tab-interval:.5in'>
938
939<div class=WordSection1>
940
941<h1><span style='mso-fareast-font-family:"Times New Roman"'>Single crystal
942structure determination and refinement with X-ray data in GSAS-II<o:p></o:p></span></h1>
943
944<h2><span style='mso-fareast-font-family:"Times New Roman"'>Introduction<o:p></o:p></span></h2>
945
946<p class=MsoNormal>In this exercise we will use a set of X-ray single crystal
947structure factors to solve the structure of <span class=SpellE>dipyridyl</span>
948disulfide by charge flipping and then refine the structure by least-squares.
949The structure will be completed by adding the requisite hydrogen atoms and by
950using anisotropic thermal parameters for the heavier atoms. The structure was
951originally solved by <span class=SpellE>Raghavan</span> &amp; <span
952class=SpellE>Seff</span>, <span class=SpellE>Acta</span> <span class=SpellE>Cryst</span>.
953B33, 386-391 (1977) in the space group P2<sub>1</sub>/c with one disordered
954pyridine ring with indications that the true space group was P2<sub>1</sub>. It
955was subsequently reinvestigated by Young (2014….) who found that the true space
956group was P2<sub>1</sub> with 4 molecules in the asymmetric unit. The data used
957in the latter analysis is what is used here and is provided as a “<span
958class=SpellE>fcf</span>” file obtained after structure analysis by Shelx-97;
959the structure factors are scaled to those calculated from the structure. We
960will solve the P 2<sub>1</sub>/c structure first.</p>
961
962<p class=MsoNormal>&nbsp;</p>
963
964<p class=MsoNormal>Note that menu entries and user input are shown in bold face
965below as <b><span style='font-family:"Calibri",sans-serif'>Help/About GSAS-II</span></b>,
966which lists first the name of the menu (here <b><span style='font-family:"Calibri",sans-serif'>Help</span></b>)
967and second the name of the entry in the menu (here <b><span style='font-family:
968"Calibri",sans-serif'>About GSAS-II</span></b>). If you have not done so
969already, start GSAS-II</p>
970
971<h2><span style='mso-fareast-font-family:"Times New Roman"'>Step 1. Input phase
972information<o:p></o:p></span></h2>
973
974<p class=MsoListParagraph style='text-indent:-.25in'>1.<span style='font-size:
9757.0pt'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Use the <b><span style='font-family:
976"Calibri",sans-serif'>Data/Add phase</span></b> menu item add a new phase into
977the current GSAS-II project. A popup window will appear asking for a phase
978name; I entered <b><span style='font-family:"Calibri",sans-serif'>SS <span
979class=SpellE>dipyridyl</span></span></b>; press <b><span style='font-family:
980"Calibri",sans-serif'>OK</span></b> when done. Select <b><span
981style='font-family:"Calibri",sans-serif'>Loaded Data/Phases/SS <span
982class=SpellE>dipyridyl</span></span></b> from the GSAS-II Data tree window. The
983General tab for Phase Data will appear.</p>
984
985<p class=MsoListParagraph><span style='mso-no-proof:yes'><img width=524
986height=307 id="_x0000_i1042" src="CFSingleCrystal_files/image001.png"></span></p>
987
988<p class=MsoListParagraph style='text-indent:-.25in'>2.<span style='font-size:
9897.0pt'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Enter the space group <b><span
990style='font-family:"Calibri",sans-serif'>P 21/c</span></b> (don’t forget the
991space between P &amp; 21/c) &amp; press <b><span style='font-family:"Calibri",sans-serif'>Enter</span></b>.
992A Space Group Information popup window will appear; press <b><span
993style='font-family:"Calibri",sans-serif'>OK</span></b>. The General window will
994be refreshed showing only the needed lattice parameters for P 21/c.</p>
995
996<p class=MsoListParagraph><span style='mso-no-proof:yes'><img width=522
997height=361 id="_x0000_i1041" src="CFSingleCrystal_files/image002.png"></span></p>
998
999<p class=MsoListParagraph style='text-indent:-.25in'>3.<span style='font-size:
10007.0pt'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Enter <b><span style='font-family:
1001"Calibri",sans-serif'>15.8489</span></b>, <b><span style='font-family:"Calibri",sans-serif'>5.5008</span></b>,
1002<b><span style='font-family:"Calibri",sans-serif'>23.118</span></b>, and <b><span
1003style='font-family:"Calibri",sans-serif'>96.9160</span></b> for a, b, c and
1004beta, respectively; the unit cell volume will be recalculated at each entry.</p>
1005
1006<h2><span style='mso-fareast-font-family:"Times New Roman"'>Step 2. Import
1007structure factors <o:p></o:p></span></h2>
1008
1009<p class=MsoNormal>There are two parts to this step: one is to import the data
1010and the second is to connect the data with the phase within GSAS-II.</p>
1011
1012<p class=MsoNormal>To do these, do <b><span style='font-family:"Calibri",sans-serif'>Import/Structure
1013factor/from CIF file</span></b> from the main GSAS-II data tree window menu. A
1014file selection dialog will appear; find <b><span style='font-family:"Calibri",sans-serif'>CF
1015<span class=SpellE>Xray</span> single crystal\data\S2dipyridyl.fcf</span></b>
1016and press <b><span style='font-family:"Calibri",sans-serif'>Open</span></b>. A
1017popup window asking if this is the file you want; press <b><span
1018style='font-family:"Calibri",sans-serif'>Yes</span></b>. After a pause while
1019the file is read a new popup will appear offering the chance to rename the
1020structure factor set; press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>.
1021After some <span class=GramE>time</span> a new popup will appear to Add the new
1022structure factor set to the SS <span class=SpellE>dipyridyl</span> phase.
1023Select the phase and press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>.
1024The plot will show a rectangular array of circles for the hk0 reflection layer;
1025select the plot &amp; press <b><span style='font-family:"Calibri",sans-serif'>k</span></b>
1026to get an h0l layer.</p>
1027
1028<p class=MsoNormal><span style='mso-no-proof:yes'><img width=480 height=412
1029id="_x0000_i1040" src="CFSingleCrystal_files/image003.png"></span></p>
1030
1031<p class=MsoNormal>Because the <span class=SpellE>fcf</span> file has both
1032observed and calculated structure factors, the plot shows a small R value for
1033the layer. The observed structure factors are shown as blue rings, the
1034calculated ones as green rings and a small green or red dot may appear at each
1035ring center showing <span class=SpellE>F<sub>o</sub></span>-F<sub>c</sub>. If
1036the reflection data file had only observed structure <span class=GramE>factors</span>
1037then only blue rings will be seen. You can explore the plot options in the ‘<b><span
1038style='font-family:"Calibri",sans-serif'>K</span></b>’ box in the plot toolbar.</p>
1039
1040<h2><span style='mso-fareast-font-family:"Times New Roman"'>Step 3. Setup for
1041charge flipping<o:p></o:p></span></h2>
1042
1043<p class=MsoNormal>To solve (again) this crystal structure we will use charge
1044flipping. Charge flipping in GSAS-II is implemented to solve the crystal
1045structure without consideration of space group symmetry. To do this it operates
1046on the entire unit cell volume to a selected resolution (usually 0.5Å) using
1047fast <span class=SpellE>fourier</span> transform techniques. This requires a
1048set of structure factors in an array of the same dimensions as the density
1049array covering the unit cell (i.e. a box bounded by ~0.5Å resolution). The
1050space group symmetry is applied to the observed structure factors to create a
1051full sphere which is then zero filled out to the 0.5Å resolution bounded box.
1052To be reasonably assured of success, the observed structure factors should
1053extend to ~1Å resolution; we have that here for this example. To begin select <b><span
1054style='font-family:"Calibri",sans-serif'>Phases/SS <span class=SpellE>dipyridyl</span></span></b>
1055from the GSAS-II data tree; the General tab will be shown</p>
1056
1057<p class=MsoNormal><span style='mso-no-proof:yes'><img width=624 height=401
1058id="_x0000_i1039" src="CFSingleCrystal_files/image004.png"></span></p>
1059
1060<p class=MsoNormal>Find the <b><span style='font-family:"Calibri",sans-serif'>Fourier
1061map controls</span></b> and change the <b><span style='font-family:"Calibri",sans-serif'>Peak
1062cutoff %</span></b> to <b><span style='font-family:"Calibri",sans-serif'>10</span></b>;
1063then immediately below find the <b><span style='font-family:"Calibri",sans-serif'>Charge
1064flip controls</span></b>. Press <b><span style='font-family:"Calibri",sans-serif'>Select
1065reflection sets</span></b>, pick <b><span style='font-family:"Calibri",sans-serif'>HKLF
1066S2dipyridyl.fcf:1a</span></b> from the list (the only one) and press <b><span
1067style='font-family:"Calibri",sans-serif'>OK</span></b>. If you had multiple
1068data sets for this phase, you can pick more than one and GSAS-II will use a
1069“last one in” process for assembling the reflection set to use for charge
1070flipping. There are four more settings to consider: 1) <span class=SpellE>kMax</span>
1071controls the upper cutoff for charge flipping; if the density is &gt; k-Max*<span
1072style='font-family:Symbol'>s<sub>r</sub></span> (map standard deviation) then
1073flip the charge. This prevents the “Uranium solution” sometimes found where all
1074the density is concentrated in a single peak. A useful guide is to use twice
1075the largest atomic number of any element in your structure. For equal atom
1076problems use 12-15; adjust upward for structures with heavy &amp; light atoms.
1077In this case, set <b><span style='font-family:"Calibri",sans-serif'>k-Max</span></b>
1078to <b><span style='font-family:"Calibri",sans-serif'>30.0</span></b> to allow
1079the S atom to appear. 2) k-Factor controls the lower level for charge flipping;
1080if the density is &lt; k-Factor*<span style='font-family:Symbol'>s<sub>r</sub></span>
1081then flip the charge. The default value seems to work pretty well; I’d only
1082change it if the charge flipping is having trouble solving the structure. 3)
1083Resolution selects the spacing between map points. 0.5Å is sufficient in most
1084cases. Choosing a smaller value requires more map points (NB: GSAS-II uses the
1085entire unit cell volume for charge flipping) and thus will require more
1086structure factors since the fast <span class=SpellE>fourier</span> algorithm
1087requires the same size arrays in both real space and reciprocal space. This
1088will slow down the charge flip process. 4) Normalizing element selects a form
1089factor to rescale the structure factors thus “sharpening” the density map. I
1090suggest trying <b><span style='font-family:"Calibri",sans-serif'>None</span></b>
1091first, otherwise select a representative element (really doesn’t matter which).</p>
1092
1093<h2 style='page-break-after:avoid'><span style='mso-fareast-font-family:"Times New Roman"'>Step
10944. Charge flipping<o:p></o:p></span></h2>
1095
1096<p class=MsoNormal>With the controls all set you can now do charge flipping;
1097from the <b><span style='font-family:"Calibri",sans-serif'>General</span></b>
1098tab do <b><span style='font-family:"Calibri",sans-serif'>Compute/Charge
1099flipping</span></b>. A progress bar popup will appear showing the residual
1100between the observed structure factors and those obtained from the inverse <span
1101class=SpellE>fourier</span> transform of the last flipped density map. It
1102should quickly decrease to the ~20% range and level out indicating a good
1103charge flip solution. When it has reached this, press <b><span
1104style='font-family:"Calibri",sans-serif'>Cancel</span></b> to stop the process.</p>
1105
1106<p class=MsoNormal><span style='mso-no-proof:yes'><img width=366 height=180
1107id="_x0000_i1038" src="CFSingleCrystal_files/image005.png"></span></p>
1108
1109<p class=MsoNormal>The console window will show something like</p>
1110
1111<p class=MsoNormal><span style='mso-no-proof:yes'><img width=624 height=166
1112id="_x0000_i1037" src="CFSingleCrystal_files/image006.png"></span></p>
1113
1114<p class=MsoNormal>There may be a pause at <b><span style='font-family:"Calibri",sans-serif'>Begin
1115<span class=SpellE>fourier</span> map search</span></b> before it finishes.
1116Provided is a summary of the charge flip calculation (time, map size, density
1117range &amp; structure factor residual). The map offset is discovered by an
1118analysis of the reflection phases with respect to how they should be
1119distributed for your chosen space group. These offsets are then applied to
1120shift the map so that the symmetry elements are properly located in the unit
1121cell. The quality of this fit (chi**2) is given. This process is not
1122necessarily perfect; you are given an opportunity to hand-tune the offset. <span
1123class=GramE>Finally</span> the number of peaks found in the map is listed, the
1124structure is drawn (I’ve made the view down the b-axis)</p>
1125
1126<p class=MsoNormal><span style='mso-no-proof:yes'><img width=478 height=402
1127id="_x0000_i1036" src="CFSingleCrystal_files/image007.jpg"></span></p>
1128
1129<p class=MsoNormal>&nbsp;and the Phase data window will show the map peaks tab</p>
1130
1131<p class=MsoNormal><span style='mso-no-proof:yes'><img width=500 height=300
1132id="_x0000_i1035" src="CFSingleCrystal_files/image008.png"></span></p>
1133
1134<p class=MsoNormal>These are listed in order of magnitude; a double click on
1135any of the table headings will sort the list according to that parameter. My
1136list has 112 entries; <span class=SpellE>dipyridyl</span> disulfide has 14 C
1137&amp; S atoms so this list is appropriate for 8 molecules in the unit cell and
1138thus all atoms were found in this charge flipping result.</p>
1139
1140<p class=MsoNormal>If all went well then the drawing should nicely show all the
1141atoms in the structure placed properly with respect to the locations of the
1142inversion centers (they are at all the corners, edge centers, face centers and
1143cell center). If not then you can shift the map &amp; peaks with the <b><span
1144style='font-family:"Calibri",sans-serif'>L</span></b>, <b><span
1145style='font-family:"Calibri",sans-serif'>R</span></b>, <b><span
1146style='font-family:"Calibri",sans-serif'>U</span></b> &amp; <b><span
1147style='font-family:"Calibri",sans-serif'>D</span></b> keys (NB: rotate the
1148drawing so the axes are ~horizontal/vertical); the map/peaks will move in
1149resolution steps (0.5A). The table is also updated with new peak positions. You
1150could also just repeat the charge flipping and hope to get a better map offset
1151solution (examine the map offset chi**2 to get a sense of this). You can also
1152show the map density (highest point is shown as a green dot somewhere in the
1153map – on a S-atom position); select the <b><span style='font-family:"Calibri",sans-serif'>Draw
1154Options</span></b> tab and use the <b><span style='font-family:"Calibri",sans-serif'>Contour
1155level</span></b> slider. The drawing will show green dots at each set map point
1156with size in proportion to the density. The mouse <b><span style='font-family:
1157"Calibri",sans-serif'>RB</span></b> can be used to slide the structure around;
1158the density is always drawn in a space surrounding the view point (multicolored
1159cross at the center). While here you can also change the <b><span
1160style='font-family:"Calibri",sans-serif'>Bond search factor</span></b> to <b><span
1161style='font-family:"Calibri",sans-serif'>0.90</span></b> to ensure all S-C
1162bonds are shown.</p>
1163
1164<p class=MsoNormal>If the charge flipping has failed (high residual &amp; no
1165recognizable structure) the process should be just repeated. This gives it a
1166new random start for the structure factor phases which may lead to a good
1167solution. After a few attempts, you can try different control settings to see
1168if that will coax out a good solution; first be sure <b><span style='font-family:
1169"Calibri",sans-serif'>k-Max</span></b> is properly set and then perhaps try
1170different <b><span style='font-family:"Calibri",sans-serif'>k-Factors</span></b>
1171and do <b><span style='font-family:"Calibri",sans-serif'>Normalizing</span></b>
1172by some element form factor. If it seemed to work but very few peaks were
1173found, make sure <b><span style='font-family:"Calibri",sans-serif'>Peak cutoff</span></b>
1174was properly set; you can then repeat the peak search by doing <b><span
1175style='font-family:"Calibri",sans-serif'>Compute/Search map</span></b>.</p>
1176
1177<h2><span style='mso-fareast-font-family:"Times New Roman"'>Step 5. Extract
1178solution and make molecules<o:p></o:p></span></h2>
1179
1180<p class=MsoNormal>Assuming that the map &amp; peak positions are properly
1181placed with respect to the symmetry elements of the space group, we can now
1182select those peaks which describe the structure. Select the <b><span
1183style='font-family:"Calibri",sans-serif'>Map peaks</span></b> tab and double LB
1184click the blank upper left corner of the table; all entries will be highlighted
1185in blue. Then do <b><span style='font-family:"Calibri",sans-serif'>Map
1186peaks/Unique peaks</span></b>; after a bit of time 1/4 of the peaks in the list
1187will be highlighted and the corresponding peaks in the drawing will be green
1188(NB: if you navigate away from this tab, this selection will be lost and you’ll
1189have to repeat it!). Next, do <b><span style='font-family:"Calibri",sans-serif'>Map
1190peaks/Move peaks</span></b>; these peaks will be transferred to the <b><span
1191style='font-family:"Calibri",sans-serif'>Atoms</span></b> list as H-atoms named
1192according to their position in the magnitude column.</p>
1193
1194<p class=MsoNormal><span style='mso-no-proof:yes'><img width=624 height=267
1195id="_x0000_i1034" src="CFSingleCrystal_files/image009.png"></span></p>
1196
1197<p class=MsoNormal>The drawing will show white balls at the atom positions
1198scattered over several molecules.</p>
1199
1200<p class=MsoNormal><span style='mso-no-proof:yes'><img width=474 height=409
1201id="_x0000_i1033" src="CFSingleCrystal_files/image010.jpg"></span></p>
1202
1203<p class=MsoNormal>Notice that 4 atoms have magnitudes ~90+, these are the S
1204atoms. The rest are C &amp; N atoms. In the <b><span style='font-family:"Calibri",sans-serif'>Atoms</span></b>
1205tab select the first 4 atoms (press LB on the 1<sup>st</sup> &amp; shift LB on
1206the 4<sup>th</sup> one). Then do <b><span style='font-family:"Calibri",sans-serif'>Edit/Modify
1207atom parameters</span></b>; a popup window will appear. Select <b><span
1208style='font-family:"Calibri",sans-serif'>Type</span></b> &amp; press <b><span
1209style='font-family:"Calibri",sans-serif'>OK</span></b>; a Periodic Table will
1210appear. Select <b><span style='font-family:"Calibri",sans-serif'>S</span></b>;
1211the atoms will be <span class=GramE>renames</span> and their Type changed to S.
1212Next select the remaining H atoms (a quick way it to double LB click the <b><span
1213style='font-family:"Calibri",sans-serif'>Type</span></b> column heading and
1214select <b><span style='font-family:"Calibri",sans-serif'>H</span></b> from the
1215popup window). Then do <b><span style='font-family:"Calibri",sans-serif'>Edit/Modify
1216atom parameters</span></b> and <b><span style='font-family:"Calibri",sans-serif'>Type</span></b>
1217from the popup; select <b><span style='font-family:"Calibri",sans-serif'>C</span></b>
1218from the Periodic Table as we don’t know which ones are N. The drawing will
1219change (you may have to wiggle it a bit to force the update).</p>
1220
1221<p class=MsoNormal><span style='mso-no-proof:yes'><img width=480 height=390
1222id="_x0000_i1032" src="CFSingleCrystal_files/image011.jpg"></span></p>
1223
1224<p class=MsoNormal>Notice that the atoms are scattered over several molecules;
1225we want to assemble them into 2 conveniently placed ones. Begin by selecting an
1226atom (make sure the <b><span style='font-family:"Calibri",sans-serif'>Atom</span></b>
1227tab is displayed &amp; do shift LB on an atom in the drawing – I chose the S
1228atom near the upper middle); it will turn green and a line in the Atom table
1229will be highlighted. Next do <b><span style='font-family:"Calibri",sans-serif'>Edit/Assemble
1230molecule</span></b>; a popup window will appear. Change the <b><span
1231style='font-family:"Calibri",sans-serif'>Bond search factor</span></b> to <b><span
1232style='font-family:"Calibri",sans-serif'>0.90</span></b> to be sure all S-C
1233bonds are found.</p>
1234
1235<p class=MsoNormal><span style='mso-no-proof:yes'><img width=265 height=223
1236id="_x0000_i1031" src="CFSingleCrystal_files/image012.png"></span>&nbsp;</p>
1237
1238<p class=MsoNormal>Press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>;
1239atoms will be collected into a <span class=SpellE>well positioned</span> group,
1240but others are not. Next select one of the unassembled atoms (I chose a C-atom
1241in a nearby SS-<span class=SpellE>dipyridyl</span>) and do <b><span
1242style='font-family:"Calibri",sans-serif'>Edit/Assemble molecule</span></b>;
1243there will be two nicely assembled SS-<span class=SpellE>dipyridyls</span>.</p>
1244
1245<p class=MsoNormal><span style='mso-no-proof:yes'><img width=480 height=384
1246id="_x0000_i1030" src="CFSingleCrystal_files/image013.jpg"></span></p>
1247
1248<p class=MsoNormal>You should probably save this project as it contains your
1249solved crystal structure.</p>
1250
1251<h2><span style='mso-fareast-font-family:"Times New Roman"'>Step 6. Initial
1252refinement<o:p></o:p></span></h2>
1253
1254<p class=MsoNormal>Since we now have a structural model, we can do the initial
1255structure refinement. By <span class=GramE>default</span> this will only refine
1256the scale factor; do <b><span style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b>
1257from the main GSAS-II data tree window. Convergence will quickly occur with <span
1258class=SpellE>Rw</span> ~35%. More useful is to refine the atom positions and
1259isotropic thermal parameters. Select the <b><span style='font-family:"Calibri",sans-serif'>Atoms</span></b>
1260tab from the Phase window. Then LB double click the <b><span style='font-family:
1261"Calibri",sans-serif'>refine</span></b> column heading; a popup window will
1262appear. Select <b><span style='font-family:"Calibri",sans-serif'>X</span></b>
1263and <b><span style='font-family:"Calibri",sans-serif'>U</span></b> and press <b><span
1264style='font-family:"Calibri",sans-serif'>OK</span></b>. The <b><span
1265style='font-family:"Calibri",sans-serif'>Atoms</span></b> window will show <b><span
1266style='font-family:"Calibri",sans-serif'>XU</span></b> for each atom in the
1267refine column. Then do <b><span style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b>
1268(twice to get convergence) and the <span class=SpellE>Rw</span> ~12%.</p>
1269
1270<h2><span style='mso-fareast-font-family:"Times New Roman"'>Step 7. Determine
1271C/N choice<o:p></o:p></span></h2>
1272
1273<p class=MsoNormal>We know from the chemistry that the N atom is in the 2
1274position of the pyridine ring, i.e. next to the point of attachment to the
1275S-atom. However, we don’t know which one that is and we have 8 atoms of which 4
1276are C and 4 are N.</p>
1277
1278<p class=MsoNormal>To work out the C/N problem above we need the atoms to be in
1279a chemically sensible order. The assemble molecule routine did construct chains
1280of atoms but this ordering is not really satisfactory. The ordering can quickly
1281be done by hand by following a labelled drawing. First go to the <b><span
1282style='font-family:"Calibri",sans-serif'>Draw Atoms</span></b> tab and double
1283LB click the <b><span style='font-family:"Calibri",sans-serif'>Style</span></b>
1284column; select <b><span style='font-family:"Calibri",sans-serif'>balls &amp;
1285sticks</span></b> from the popup box. Press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>.
1286Next, double LB click the <b><span style='font-family:"Calibri",sans-serif'>Label</span></b>
1287column and select <b><span style='font-family:"Calibri",sans-serif'>name</span></b>
1288from the popup box; press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>.
1289Then go to the <b><span style='font-family:"Calibri",sans-serif'>Draw options</span></b>
1290tab and adjust the <b><span style='font-family:"Calibri",sans-serif'>Ball scale</span></b>
1291&amp; <b><span style='font-family:"Calibri",sans-serif'>Bond radius </span></b>to
1292allow the labels to be easily seen. After shifting the view point the drawing
1293should look something like</p>
1294
1295<p class=MsoNormal>&nbsp;</p>
1296
1297<p class=MsoNormal><span style='mso-no-proof:yes'><img width=474 height=386
1298id="_x0000_i1029" src="CFSingleCrystal_files/image014.jpg"></span></p>
1299
1300<p class=MsoNormal>Now go to the <b><span style='font-family:"Calibri",sans-serif'>Atoms</span></b>
1301tab. If you look carefully, you can see that the atoms in each SS-<span
1302class=SpellE>dipyridyl</span> are grouped together in the table but they are
1303not in chemically sensible order. The atoms can be reordered by selecting one
1304row with the <b><span style='font-family:"Calibri",sans-serif'>Alt</span></b>
1305key down (the status line will tell which atom is selected to move) and then
1306with the <b><span style='font-family:"Calibri",sans-serif'>Alt</span></b> key
1307still down pick a row below where you want to insert it. I ordered them so each
1308S-atom was followed by the C-atoms in order around the ring; my list looked
1309like (I show just the 1<sup>st</sup> SS <span class=SpellE>dipyridyl</span>
1310molecule)</p>
1311
1312<p class=MsoNormal><span style='mso-no-proof:yes'><img width=624 height=408
1313id="_x0000_i1028" src="CFSingleCrystal_files/image015.png"></span></p>
1314
1315<p class=MsoNormal>Once you have reordered the atoms to your satisfaction they
1316can be renamed to be in order. To do this select all the atoms (double LB click
1317the empty corner box) and then do <b><span style='font-family:"Calibri",sans-serif'>Edit/Modify
1318atom parameters</span></b>. Select <b><span style='font-family:"Calibri",sans-serif'>Name</span></b>
1319and press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>;
1320press <b><span style='font-family:"Calibri",sans-serif'>Yes</span></b> to the
1321popup question. The atoms will be renamed in numerical order. Do <b><span
1322style='font-family:"Calibri",sans-serif'>Edit/Reload draw atoms</span></b>; the
1323labels will change. In my numbering scheme, half of the C3, C7, C10, C14, C17,
1324C21, C24 and C28 carbon atoms are really nitrogen (if they are ordered). Select
1325these and do <b><span style='font-family:"Calibri",sans-serif'>Edit/Set atom
1326refinement flags</span></b>; select <b><span style='font-family:"Calibri",sans-serif'>F</span></b>,
1327<b><span style='font-family:"Calibri",sans-serif'>X</span></b> &amp; <b><span
1328style='font-family:"Calibri",sans-serif'>U</span></b> for these. Do <b><span
1329style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b>; the <span
1330class=SpellE>Rw</span> will drop to ~10% and 4 of the atom <span class=SpellE><b><span
1331style='font-family:"Calibri",sans-serif'>frac</span></b></span> values will be
1332~1.25 while the others are ~1.0. The former are N-atoms and the latter are
1333C-atoms. Change the <b><span style='font-family:"Calibri",sans-serif'>Type</span></b>
1334for the N-atoms and repeat <b><span style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b>;
1335the <span class=SpellE>Rw</span> will be high to start, but immediately fall to
1336~10%. In the Atom table all 8 refined <span class=SpellE>frac</span> values are
1337be now ~1.0. To finish this part of the refinement, set all <span class=SpellE><b><span
1338style='font-family:"Calibri",sans-serif'>frac</span></b></span> values to <b><span
1339style='font-family:"Calibri",sans-serif'>1.0</span></b> and all refine flags to
1340<b><span style='font-family:"Calibri",sans-serif'>XU</span></b>. Do <b><span
1341style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b>; the final
1342<span class=SpellE>Rw</span> ~10.5%</p>
1343
1344<h2><span style='mso-fareast-font-family:"Times New Roman"'>Step 8. Anisotropic
1345thermal motion refinement<o:p></o:p></span></h2>
1346
1347<p class=MsoNormal>Given reasonable measured structure factors one can improve
1348a crystal model by using anisotropic thermal motion models for all the <span
1349class=SpellE>nonhydrogen</span> atoms. To convert all the atoms here select the
1350Atoms tab and then do a double LB click on the I/A column heading. Select
1351Anisotropic from the popup and press OK; the Atom table will be redrawn with <span
1352class=SpellE>Uij</span> values equivalent to the corresponding <span
1353class=SpellE>Uiso</span> (now hidden). Do <b><span style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b>;
1354the final <span class=SpellE>Rw</span> ~8.2%</p>
1355
1356<h2 style='page-break-after:avoid'><span style='mso-fareast-font-family:"Times New Roman"'>Step
13579. H-atom placement &amp; final refinement<o:p></o:p></span></h2>
1358
1359<p class=MsoNormal>This structure can be completed by adding the 4 H-atoms per pyridine
1360ring (16 in all). One could do this (painfully) by hand by looking for them in <span
1361style='font-family:Symbol'>D</span>F maps, but it is simpler to just place them
1362knowing the bonding chemistry of the rings. To start <span class=GramE>this</span>
1363select the <b><span style='font-family:"Calibri",sans-serif'>Atoms</span></b>
1364tab for the phase. Then select the C-atoms by a double LB click on the <b><span
1365style='font-family:"Calibri",sans-serif'>Type</span></b> column heading and
1366select <b><span style='font-family:"Calibri",sans-serif'>C</span></b> from the
1367popup; press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>.
1368The C-atoms will be highlighted. Next do <b><span style='font-family:"Calibri",sans-serif'>Edit/Insert
1369H atoms</span></b>; a <b><span style='font-family:"Calibri",sans-serif'>Distance
1370Angle Controls</span></b> popup will appear; the numbers should be as before.
1371Press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>; a new
1372popup will appear</p>
1373
1374<p class=MsoNormal><span style='mso-no-proof:yes'><img width=400 height=485
1375id="_x0000_i1027" src="CFSingleCrystal_files/image016.png"></span></p>
1376
1377<p class=MsoNormal>This is the hydrogen add control; it shows both the expected
1378number of H-atoms to add to each C-atom and the neighboring atoms used to
1379determine the geometry of the C-H bond. Check to make sure that 4 H-atoms will
1380be added for each ring. Note that C2, C9, C16 &amp; C23 will not have an H-atom
1381added as these are the S-atom attachment points in SS-<span class=SpellE>dipyridyl</span>.
1382Press <b><span style='font-family:"Calibri",sans-serif'>Ok</span></b>; the
1383H-atoms will be inserted immediately after the corresponding C-atoms and the
1384drawing is updated showing van der Waals spheres for all atoms.</p>
1385
1386<p class=MsoNormal><span style='mso-no-proof:yes'><img width=624 height=396
1387id="_x0000_i1026" src="CFSingleCrystal_files/image017.png"></span></p>
1388
1389<p class=MsoNormal>&nbsp;</p>
1390
1391<p class=MsoNormal><span style='mso-no-proof:yes'><img width=483 height=394
1392id="_x0000_i1025" src="CFSingleCrystal_files/image018.jpg"></span></p>
1393
1394<p class=MsoNormal>Next, do <b><span style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b>;
1395there will be an immediate drop in <span class=SpellE>Rw</span> ~3.2%. Note
1396that we did not refine the H-atom positions or thermal parameters. The H-atom
1397insertion process retains the mechanisms for creating them in the first place
1398and these tools can be used to move them to reflect the changes in the C-atom
1399parameters thus forcing them to ride on the C-atoms. Do <b><span
1400style='font-family:"Calibri",sans-serif'>Edit/Update H atoms</span></b>; the
1401H-atom positions &amp; <span class=SpellE>Uisos</span> will be revised. Repeat <b><span
1402style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b>; there
1403will be a slight improvement in <span class=SpellE>Rw</span>. Repeat these two
1404steps (twice); <span class=SpellE>Rw</span> should not change on the last
1405round. This completes the refinement of the SS-<span class=SpellE>dipyridyl</span>
1406structure. You can generate a final <span style='font-family:Symbol'>D</span>F
1407map from the <b><span style='font-family:"Calibri",sans-serif'>General</span></b>
1408tab; in <b><span style='font-family:"Calibri",sans-serif'>Fourier map controls</span></b>
1409select the <b><span style='font-family:"Calibri",sans-serif'>Map type</span></b>
1410and <b><span style='font-family:"Calibri",sans-serif'>Reflection sets</span></b>,
1411then do <b><span style='font-family:"Calibri",sans-serif'>Compute/Fourier map</span></b>.
1412The <span style='font-family:Symbol'>r</span><sub>max</sub> (=0.33) and <span
1413style='font-family:Symbol'>r</span><sub>min</sub> (=-0.31) are listed on the
1414console; these seem to be concentrated around the S-atoms.</p>
1415
1416</div>
1417
1418</body>
1419
1420</html>
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