source: Tutorials/CFXraySingleCrystal/CFSingleCrystal.htm @ 3047

Last change on this file since 3047 was 3047, checked in by vondreele, 4 years ago

update to 2 frame version

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402  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 2"/>
403  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 2"/>
404  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 2"/>
405  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 2"/>
406  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 2"/>
407  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 2"/>
408  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 2"/>
409  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 2"/>
410  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 2"/>
411  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 2"/>
412  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 2"/>
413  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 3"/>
414  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 3"/>
415  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 3"/>
416  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 3"/>
417  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 3"/>
418  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 3"/>
419  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 3"/>
420  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 3"/>
421  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 3"/>
422  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 3"/>
423  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 3"/>
424  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 3"/>
425  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 3"/>
426  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 3"/>
427  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 4"/>
428  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 4"/>
429  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 4"/>
430  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 4"/>
431  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 4"/>
432  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 4"/>
433  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 4"/>
434  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 4"/>
435  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 4"/>
436  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 4"/>
437  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 4"/>
438  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 4"/>
439  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 4"/>
440  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 4"/>
441  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 5"/>
442  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 5"/>
443  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 5"/>
444  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 5"/>
445  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 5"/>
446  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 5"/>
447  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 5"/>
448  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 5"/>
449  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 5"/>
450  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 5"/>
451  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 5"/>
452  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 5"/>
453  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 5"/>
454  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 5"/>
455  <w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 6"/>
456  <w:LsdException Locked="false" Priority="61" Name="Light List Accent 6"/>
457  <w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 6"/>
458  <w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 6"/>
459  <w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 6"/>
460  <w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 6"/>
461  <w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 6"/>
462  <w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 6"/>
463  <w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 6"/>
464  <w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 6"/>
465  <w:LsdException Locked="false" Priority="70" Name="Dark List Accent 6"/>
466  <w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 6"/>
467  <w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 6"/>
468  <w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 6"/>
469  <w:LsdException Locked="false" Priority="19" QFormat="true"
470   Name="Subtle Emphasis"/>
471  <w:LsdException Locked="false" Priority="21" QFormat="true"
472   Name="Intense Emphasis"/>
473  <w:LsdException Locked="false" Priority="31" QFormat="true"
474   Name="Subtle Reference"/>
475  <w:LsdException Locked="false" Priority="32" QFormat="true"
476   Name="Intense Reference"/>
477  <w:LsdException Locked="false" Priority="33" QFormat="true" Name="Book Title"/>
478  <w:LsdException Locked="false" Priority="37" SemiHidden="true"
479   UnhideWhenUsed="true" Name="Bibliography"/>
480  <w:LsdException Locked="false" Priority="39" SemiHidden="true"
481   UnhideWhenUsed="true" QFormat="true" Name="TOC Heading"/>
482  <w:LsdException Locked="false" Priority="41" Name="Plain Table 1"/>
483  <w:LsdException Locked="false" Priority="42" Name="Plain Table 2"/>
484  <w:LsdException Locked="false" Priority="43" Name="Plain Table 3"/>
485  <w:LsdException Locked="false" Priority="44" Name="Plain Table 4"/>
486  <w:LsdException Locked="false" Priority="45" Name="Plain Table 5"/>
487  <w:LsdException Locked="false" Priority="40" Name="Grid Table Light"/>
488  <w:LsdException Locked="false" Priority="46" Name="Grid Table 1 Light"/>
489  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2"/>
490  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3"/>
491  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4"/>
492  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark"/>
493  <w:LsdException Locked="false" Priority="51" Name="Grid Table 6 Colorful"/>
494  <w:LsdException Locked="false" Priority="52" Name="Grid Table 7 Colorful"/>
495  <w:LsdException Locked="false" Priority="46"
496   Name="Grid Table 1 Light Accent 1"/>
497  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 1"/>
498  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 1"/>
499  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 1"/>
500  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 1"/>
501  <w:LsdException Locked="false" Priority="51"
502   Name="Grid Table 6 Colorful Accent 1"/>
503  <w:LsdException Locked="false" Priority="52"
504   Name="Grid Table 7 Colorful Accent 1"/>
505  <w:LsdException Locked="false" Priority="46"
506   Name="Grid Table 1 Light Accent 2"/>
507  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 2"/>
508  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 2"/>
509  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 2"/>
510  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 2"/>
511  <w:LsdException Locked="false" Priority="51"
512   Name="Grid Table 6 Colorful Accent 2"/>
513  <w:LsdException Locked="false" Priority="52"
514   Name="Grid Table 7 Colorful Accent 2"/>
515  <w:LsdException Locked="false" Priority="46"
516   Name="Grid Table 1 Light Accent 3"/>
517  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 3"/>
518  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 3"/>
519  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 3"/>
520  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 3"/>
521  <w:LsdException Locked="false" Priority="51"
522   Name="Grid Table 6 Colorful Accent 3"/>
523  <w:LsdException Locked="false" Priority="52"
524   Name="Grid Table 7 Colorful Accent 3"/>
525  <w:LsdException Locked="false" Priority="46"
526   Name="Grid Table 1 Light Accent 4"/>
527  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 4"/>
528  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 4"/>
529  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 4"/>
530  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 4"/>
531  <w:LsdException Locked="false" Priority="51"
532   Name="Grid Table 6 Colorful Accent 4"/>
533  <w:LsdException Locked="false" Priority="52"
534   Name="Grid Table 7 Colorful Accent 4"/>
535  <w:LsdException Locked="false" Priority="46"
536   Name="Grid Table 1 Light Accent 5"/>
537  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 5"/>
538  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 5"/>
539  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 5"/>
540  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 5"/>
541  <w:LsdException Locked="false" Priority="51"
542   Name="Grid Table 6 Colorful Accent 5"/>
543  <w:LsdException Locked="false" Priority="52"
544   Name="Grid Table 7 Colorful Accent 5"/>
545  <w:LsdException Locked="false" Priority="46"
546   Name="Grid Table 1 Light Accent 6"/>
547  <w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 6"/>
548  <w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 6"/>
549  <w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 6"/>
550  <w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 6"/>
551  <w:LsdException Locked="false" Priority="51"
552   Name="Grid Table 6 Colorful Accent 6"/>
553  <w:LsdException Locked="false" Priority="52"
554   Name="Grid Table 7 Colorful Accent 6"/>
555  <w:LsdException Locked="false" Priority="46" Name="List Table 1 Light"/>
556  <w:LsdException Locked="false" Priority="47" Name="List Table 2"/>
557  <w:LsdException Locked="false" Priority="48" Name="List Table 3"/>
558  <w:LsdException Locked="false" Priority="49" Name="List Table 4"/>
559  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark"/>
560  <w:LsdException Locked="false" Priority="51" Name="List Table 6 Colorful"/>
561  <w:LsdException Locked="false" Priority="52" Name="List Table 7 Colorful"/>
562  <w:LsdException Locked="false" Priority="46"
563   Name="List Table 1 Light Accent 1"/>
564  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 1"/>
565  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 1"/>
566  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 1"/>
567  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 1"/>
568  <w:LsdException Locked="false" Priority="51"
569   Name="List Table 6 Colorful Accent 1"/>
570  <w:LsdException Locked="false" Priority="52"
571   Name="List Table 7 Colorful Accent 1"/>
572  <w:LsdException Locked="false" Priority="46"
573   Name="List Table 1 Light Accent 2"/>
574  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 2"/>
575  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 2"/>
576  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 2"/>
577  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 2"/>
578  <w:LsdException Locked="false" Priority="51"
579   Name="List Table 6 Colorful Accent 2"/>
580  <w:LsdException Locked="false" Priority="52"
581   Name="List Table 7 Colorful Accent 2"/>
582  <w:LsdException Locked="false" Priority="46"
583   Name="List Table 1 Light Accent 3"/>
584  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 3"/>
585  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 3"/>
586  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 3"/>
587  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 3"/>
588  <w:LsdException Locked="false" Priority="51"
589   Name="List Table 6 Colorful Accent 3"/>
590  <w:LsdException Locked="false" Priority="52"
591   Name="List Table 7 Colorful Accent 3"/>
592  <w:LsdException Locked="false" Priority="46"
593   Name="List Table 1 Light Accent 4"/>
594  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 4"/>
595  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 4"/>
596  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 4"/>
597  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 4"/>
598  <w:LsdException Locked="false" Priority="51"
599   Name="List Table 6 Colorful Accent 4"/>
600  <w:LsdException Locked="false" Priority="52"
601   Name="List Table 7 Colorful Accent 4"/>
602  <w:LsdException Locked="false" Priority="46"
603   Name="List Table 1 Light Accent 5"/>
604  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 5"/>
605  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 5"/>
606  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 5"/>
607  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 5"/>
608  <w:LsdException Locked="false" Priority="51"
609   Name="List Table 6 Colorful Accent 5"/>
610  <w:LsdException Locked="false" Priority="52"
611   Name="List Table 7 Colorful Accent 5"/>
612  <w:LsdException Locked="false" Priority="46"
613   Name="List Table 1 Light Accent 6"/>
614  <w:LsdException Locked="false" Priority="47" Name="List Table 2 Accent 6"/>
615  <w:LsdException Locked="false" Priority="48" Name="List Table 3 Accent 6"/>
616  <w:LsdException Locked="false" Priority="49" Name="List Table 4 Accent 6"/>
617  <w:LsdException Locked="false" Priority="50" Name="List Table 5 Dark Accent 6"/>
618  <w:LsdException Locked="false" Priority="51"
619   Name="List Table 6 Colorful Accent 6"/>
620  <w:LsdException Locked="false" Priority="52"
621   Name="List Table 7 Colorful Accent 6"/>
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941<body lang=EN-US style='tab-interval:.5in'>
942
943<div class=WordSection1>
944
945<h1><span style='mso-fareast-font-family:"Times New Roman"'>Single crystal
946structure determination and refinement with X-ray data in GSAS-II<o:p></o:p></span></h1>
947
948<h2><span style='mso-fareast-font-family:"Times New Roman"'>Introduction<o:p></o:p></span></h2>
949
950<p class=MsoNormal>In this exercise we will use a set of X-ray single crystal
951structure factors to solve the structure of <span class=SpellE>dipyridyl</span>
952disulfide by charge flipping and then refine the structure by least-squares.
953The structure will be completed by adding the requisite hydrogen atoms and by
954using anisotropic thermal parameters for the heavier atoms. The structure was
955originally solved by <span class=SpellE>Raghavan</span> &amp; <span
956class=SpellE>Seff</span>, <span class=SpellE>Acta</span> <span class=SpellE>Cryst</span>.
957B33, 386-391 (1977) in the space group P2<sub>1</sub>/c with one disordered
958pyridine ring with indications that the true space group was P2<sub>1</sub>. It
959was subsequently reinvestigated by Young (2014….) who found that the true space
960group was P2<sub>1</sub> with 4 molecules in the asymmetric unit. The data used
961in the latter analysis is what is used here and is provided as a “<span
962class=SpellE>fcf</span>” file obtained after structure analysis by Shelx-97;
963the structure factors are scaled to those calculated from the structure. We will
964solve the P 2<sub>1</sub>/c structure first.</p>
965
966<p class=MsoNormal>&nbsp;</p>
967
968<p class=MsoNormal>Note that menu entries and user input are shown in bold face
969below as <b><span style='font-family:"Calibri",sans-serif'>Help/About GSAS-II</span></b>,
970which lists first the name of the menu (here <b><span style='font-family:"Calibri",sans-serif'>Help</span></b>)
971and second the name of the entry in the menu (here <b><span style='font-family:
972"Calibri",sans-serif'>About GSAS-II</span></b>). If you have not done so
973already, start GSAS-II</p>
974
975<h2><span style='mso-fareast-font-family:"Times New Roman"'>Step 1. Input phase
976information<o:p></o:p></span></h2>
977
978<p class=MsoListParagraph style='text-indent:-.25in'>1.<span style='font-size:
9797.0pt'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Use the <b><span style='font-family:
980"Calibri",sans-serif'>Data/Add new phase</span></b> menu item add a new phase
981into the current GSAS-II project. A popup window will appear asking for a phase
982name; I entered <b><span style='font-family:"Calibri",sans-serif'>SS <span
983class=SpellE>dipyridyl</span></span></b>; press <b><span style='font-family:
984"Calibri",sans-serif'>OK</span></b> when done. Select <b><span
985style='font-family:"Calibri",sans-serif'>Loaded Data/Phases/SS <span
986class=SpellE>dipyridyl</span></span></b> from the GSAS-II Data tree window. The
987General tab for Phase Data will appear.</p>
988
989<p class=MsoListParagraph><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shapetype
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1014
1015<p class=MsoListParagraph style='text-indent:-.25in'>2.<span style='font-size:
10167.0pt'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Enter the space group <b><span
1017style='font-family:"Calibri",sans-serif'>P 21/c</span></b> (don’t forget the
1018space between P &amp; 21/c) &amp; press <b><span style='font-family:"Calibri",sans-serif'>Enter</span></b>.
1019A Space Group Information popup window will appear; press <b><span
1020style='font-family:"Calibri",sans-serif'>OK</span></b>. The General window will
1021be refreshed showing only the needed lattice parameters for P 21/c.</p>
1022
1023<p class=MsoListParagraph><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
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1029
1030<p class=MsoListParagraph style='text-indent:-.25in'>3.<span style='font-size:
10317.0pt'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Enter <b><span style='font-family:
1032"Calibri",sans-serif'>15.8489</span></b>, <b><span style='font-family:"Calibri",sans-serif'>5.5008</span></b>,
1033<b><span style='font-family:"Calibri",sans-serif'>23.118</span></b>, and <b><span
1034style='font-family:"Calibri",sans-serif'>96.9160</span></b> for a, b, c and
1035beta, respectively; the unit cell volume will be recalculated at each entry.</p>
1036
1037<h2><span style='mso-fareast-font-family:"Times New Roman"'>Step 2. Import
1038structure factors <o:p></o:p></span></h2>
1039
1040<p class=MsoNormal>There are two parts to this step: one is to import the data
1041and the second is to connect the data with the phase within GSAS-II.</p>
1042
1043<p class=MsoNormal>To do these, do <b><span style='font-family:"Calibri",sans-serif'>Import/Structure
1044factor/from CIF file</span></b> from the main GSAS-II data tree window menu. A
1045file selection dialog will appear; find <span class=SpellE><b><span
1046style='font-family:"Calibri",sans-serif'>CFXraySingleCrystal</span></b></span><b><span
1047style='font-family:"Calibri",sans-serif'>\data\S2dipyridyl.fcf</span></b> and
1048press <b><span style='font-family:"Calibri",sans-serif'>Open</span></b>. A
1049popup window asking if this is the file you want; press <b><span
1050style='font-family:"Calibri",sans-serif'>Yes</span></b>. After a pause while
1051the file is read a new popup will appear offering the chance to rename the
1052structure factor set; press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>.
1053After some time a new popup will appear to Add the new structure factor set to
1054the SS <span class=SpellE>dipyridyl</span> phase. Select the phase and press <b><span
1055style='font-family:"Calibri",sans-serif'>OK</span></b>. The plot will show a
1056rectangular array of circles for the hk0 reflection layer; select the plot
1057&amp; press <b><span style='font-family:"Calibri",sans-serif'>k</span></b> to
1058get an h0l layer.</p>
1059
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1066
1067<p class=MsoNormal>Because the <span class=SpellE>fcf</span> file has both
1068observed and calculated structure factors, the plot shows a small R value for
1069the layer. The observed structure factors are shown as blue rings, the
1070calculated ones as green rings and a small green or red dot may appear at each
1071ring center showing <span class=SpellE>F<sub>o</sub></span>-F<sub>c</sub>. If
1072the reflection data file had only observed structure factors then only blue
1073rings will be seen. You can explore the plot options in the ‘<b><span
1074style='font-family:"Calibri",sans-serif'>K</span></b>’ box in the plot toolbar.</p>
1075
1076<h2><span style='mso-fareast-font-family:"Times New Roman"'>Step 3. Setup for
1077charge flipping<o:p></o:p></span></h2>
1078
1079<p class=MsoNormal>To solve (again) this crystal structure we will use charge
1080flipping. Charge flipping in GSAS-II is implemented to solve the crystal
1081structure without consideration of space group symmetry. To do this it operates
1082on the entire unit cell volume to a selected resolution (usually 0.5Å) using
1083fast <span class=SpellE>fourier</span> transform techniques. This requires a
1084set of structure factors in an array of the same dimensions as the density
1085array covering the unit cell (i.e. a box bounded by ~0.5Å resolution). The
1086space group symmetry is applied to the observed structure factors to create a
1087full sphere which is then zero filled out to the 0.5Å resolution bounded box.
1088To be reasonably assured of success, the observed structure factors should
1089extend to ~1Å resolution; we have that here for this example. To begin select <b><span
1090style='font-family:"Calibri",sans-serif'>Phases/SS <span class=SpellE>dipyridyl</span></span></b>
1091from the GSAS-II data tree; the General tab will be shown</p>
1092
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1099
1100<p class=MsoNormal>Find the <b><span style='font-family:"Calibri",sans-serif'>Fourier
1101map controls</span></b> and change the <b><span style='font-family:"Calibri",sans-serif'>Peak
1102cutoff %</span></b> to <b><span style='font-family:"Calibri",sans-serif'>10</span></b>;
1103then immediately below find the <b><span style='font-family:"Calibri",sans-serif'>Charge
1104flip controls</span></b>. Press <b><span style='font-family:"Calibri",sans-serif'>Select
1105reflection sets</span></b>, pick <b><span style='font-family:"Calibri",sans-serif'>HKLF
1106S2dipyridyl.fcf:1a</span></b> from the list (the only one) and press <b><span
1107style='font-family:"Calibri",sans-serif'>OK</span></b>. If you had multiple
1108data sets for this phase, you can pick more than one and GSAS-II will use a
1109“last one in” process for assembling the reflection set to use for charge
1110flipping. There are four more settings to consider: 1) <span class=SpellE>kMax</span>
1111controls the upper cutoff for charge flipping; if the density is &gt; k-Max*<span
1112style='font-family:Symbol'>s<sub>r</sub></span> (map standard deviation) then
1113flip the charge. This prevents the “Uranium solution” sometimes found where all
1114the density is concentrated in a single peak. A useful guide is to use twice
1115the largest atomic number of any element in your structure. For equal atom
1116problems use 12-15; adjust upward for structures with heavy &amp; light atoms.
1117In this case, set <b><span style='font-family:"Calibri",sans-serif'>k-Max</span></b>
1118to <b><span style='font-family:"Calibri",sans-serif'>30.0</span></b> to allow
1119the S atom to appear. 2) k-Factor controls the lower level for charge flipping;
1120if the density is &lt; k-Factor*<span style='font-family:Symbol'>s<sub>r</sub></span>
1121then flip the charge. The default value seems to work pretty well; I’d only
1122change it if the charge flipping is having trouble solving the structure. 3)
1123Resolution selects the spacing between map points. 0.5Å is sufficient in most
1124cases. Choosing a smaller value requires more map points (NB: GSAS-II uses the
1125entire unit cell volume for charge flipping) and thus will require more
1126structure factors since the fast <span class=SpellE>fourier</span> algorithm
1127requires the same size arrays in both real space and reciprocal space. This
1128will slow down the charge flip process. 4) Normalizing element selects a form
1129factor to rescale the structure factors thus “sharpening” the density map. I
1130suggest trying <b><span style='font-family:"Calibri",sans-serif'>None</span></b>
1131first, otherwise select a representative element (really doesn’t matter which).</p>
1132
1133<h2 style='page-break-after:avoid'><span style='mso-fareast-font-family:"Times New Roman"'>Step
11344. Charge flipping<o:p></o:p></span></h2>
1135
1136<p class=MsoNormal>With the controls all set you can now do charge flipping;
1137from the <b><span style='font-family:"Calibri",sans-serif'>General</span></b>
1138tab do <b><span style='font-family:"Calibri",sans-serif'>Compute/Charge
1139flipping</span></b>. A progress bar popup will appear showing the residual
1140between the observed structure factors and those obtained from the inverse <span
1141class=SpellE>fourier</span> transform of the last flipped density map. It
1142should quickly decrease to the ~20% range and level out indicating a good
1143charge flip solution. When it has reached this, press <b><span
1144style='font-family:"Calibri",sans-serif'>Cancel</span></b> to stop the process.</p>
1145
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1148
1149<p class=MsoNormal>The console window will show something like</p>
1150
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1157
1158<p class=MsoNormal>There may be a pause at <b><span style='font-family:"Calibri",sans-serif'>Begin
1159<span class=SpellE><span class=GramE>fourier</span></span> map search</span></b>
1160before it finishes. Provided is a summary of the charge flip calculation (time,
1161map size, density range &amp; structure factor residual). The map offset is
1162discovered by an analysis of the reflection phases with respect to how they
1163should be distributed for your chosen space group. These offsets are then
1164applied to shift the map so that the symmetry elements are properly located in
1165the unit cell. The quality of this fit (chi**2) is given. This process is not
1166necessarily perfect; you are given an opportunity to hand-tune the offset.
1167Finally the number of peaks found in the map is listed, the structure is drawn
1168(I’ve made the view down the b-axis)</p>
1169
1170<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1171 id="Picture_x0020_24" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:450pt;
1172 height:387.75pt;visibility:visible;mso-wrap-style:square'>
1173 <v:imagedata src="CFSingleCrystal_files/image011.png" o:title=""/>
1174</v:shape><![endif]--><![if !vml]><img width=600 height=517
1175src="CFSingleCrystal_files/image012.gif" v:shapes="Picture_x0020_24"><![endif]></span></p>
1176
1177<p class=MsoNormal>&nbsp;<span class=GramE>and</span> the Phase data window
1178will show the map peaks tab</p>
1179
1180<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1181 id="Picture_x0020_25" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:450pt;
1182 height:219.75pt;visibility:visible;mso-wrap-style:square'>
1183 <v:imagedata src="CFSingleCrystal_files/image013.png" o:title=""/>
1184</v:shape><![endif]--><![if !vml]><img width=600 height=293
1185src="CFSingleCrystal_files/image014.gif" v:shapes="Picture_x0020_25"><![endif]></span></p>
1186
1187<p class=MsoNormal>These are listed in order of magnitude; a double click on
1188any of the table headings will sort the list according to that parameter. My
1189list has 112 entries; <span class=SpellE>dipyridyl</span> disulfide has 14 C
1190&amp; S atoms so this list is appropriate for 8 molecules in the unit cell and
1191thus all atoms were found in this charge flipping result.</p>
1192
1193<p class=MsoNormal>If all went well then the drawing should nicely show all the
1194atoms in the structure placed properly with respect to the locations of the
1195inversion centers (they are at all the corners, edge centers, face centers and
1196cell center). If not then you can shift the map &amp; peaks with the <b><span
1197style='font-family:"Calibri",sans-serif'>L</span></b>, <b><span
1198style='font-family:"Calibri",sans-serif'>R</span></b>, <b><span
1199style='font-family:"Calibri",sans-serif'>U</span></b> &amp; <b><span
1200style='font-family:"Calibri",sans-serif'>D</span></b> keys (NB: rotate the
1201drawing so the axes are ~horizontal/vertical); the map/peaks will move in
1202resolution steps (0.5A). The table is also updated with new peak positions. You
1203could also just repeat the charge flipping and hope to get a better map offset
1204solution (examine the map offset chi**2 to get a sense of this). You can also
1205show the map density (highest point is shown as a green dot somewhere in the
1206map – on a S-atom position); select the <b><span style='font-family:"Calibri",sans-serif'>Draw
1207Options</span></b> tab and use the <b><span style='font-family:"Calibri",sans-serif'>Contour
1208level</span></b> slider. The drawing will show green dots at each set map point
1209with size in proportion to the density. The mouse <b><span style='font-family:
1210"Calibri",sans-serif'>RB</span></b> can be used to slide the structure around;
1211the density is always drawn in a space surrounding the view point (multicolored
1212cross at the center). While here you can also change the <b><span
1213style='font-family:"Calibri",sans-serif'>Bond search factor</span></b> to <b><span
1214style='font-family:"Calibri",sans-serif'>0.90</span></b> to ensure all S-C
1215bonds are shown.</p>
1216
1217<p class=MsoNormal>If the charge flipping has failed (high residual &amp; no
1218recognizable structure) the process should be just repeated. This gives it a
1219new random start for the structure factor phases which may lead to a good
1220solution. After a few attempts, you can try different control settings to see
1221if that will coax out a good solution; first be sure <b><span style='font-family:
1222"Calibri",sans-serif'>k-Max</span></b> is properly set and then perhaps try
1223different <b><span style='font-family:"Calibri",sans-serif'>k-Factors</span></b>
1224and do <b><span style='font-family:"Calibri",sans-serif'>Normalizing</span></b>
1225by some element form factor. If it seemed to work but very few peaks were
1226found, make sure <b><span style='font-family:"Calibri",sans-serif'>Peak cutoff</span></b>
1227was properly set; you can then repeat the peak search by doing <b><span
1228style='font-family:"Calibri",sans-serif'>Compute/Search map</span></b>.</p>
1229
1230<h2><span style='mso-fareast-font-family:"Times New Roman"'>Step 5. Extract
1231solution and make molecules<o:p></o:p></span></h2>
1232
1233<p class=MsoNormal>Assuming that the map &amp; peak positions are properly
1234placed with respect to the symmetry elements of the space group, we can now
1235select those peaks which describe the structure. Select the <b><span
1236style='font-family:"Calibri",sans-serif'>Map peaks</span></b> tab and double LB
1237click the blank upper left corner of the table; all entries will be highlighted
1238in blue. Then do <b><span style='font-family:"Calibri",sans-serif'>Map
1239peaks/Unique peaks</span></b>; after a bit of time 1/4 of the peaks in the list
1240will be highlighted and the corresponding peaks in the drawing will be green
1241(NB: if you navigate away from this tab, this selection will be lost and you’ll
1242have to repeat it!). The console will show a summary giving the number &amp;
1243fraction of unique peaks found; in this case 28 &amp; 0.25 are the correct
1244values. Next, do <b><span style='font-family:"Calibri",sans-serif'>Map
1245peaks/Move peaks</span></b>; these peaks will be transferred to the <b><span
1246style='font-family:"Calibri",sans-serif'>Atoms</span></b> list as H-atoms named
1247according to their position in the magnitude column.</p>
1248
1249<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1250 id="Picture_x0020_26" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:468pt;
1251 height:198.75pt;visibility:visible;mso-wrap-style:square'>
1252 <v:imagedata src="CFSingleCrystal_files/image015.png" o:title=""/>
1253</v:shape><![endif]--><![if !vml]><img width=624 height=265
1254src="CFSingleCrystal_files/image016.gif" v:shapes="Picture_x0020_26"><![endif]></span></p>
1255
1256<p class=MsoNormal>The drawing will show white balls at the atom positions
1257scattered over several molecules.</p>
1258
1259<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1260 id="Picture_x0020_27" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:468pt;
1261 height:405pt;visibility:visible;mso-wrap-style:square'>
1262 <v:imagedata src="CFSingleCrystal_files/image017.png" o:title=""/>
1263</v:shape><![endif]--><![if !vml]><img width=624 height=540
1264src="CFSingleCrystal_files/image018.gif" v:shapes="Picture_x0020_27"><![endif]></span></p>
1265
1266<p class=MsoNormal>Notice that 4 atoms have magnitudes ~90+, these are the S
1267atoms. The rest are C &amp; N atoms. In the <b><span style='font-family:"Calibri",sans-serif'>Atoms</span></b>
1268tab select the first 4 atoms (press LB on the 1<sup>st</sup> &amp; shift LB on
1269the 4<sup>th</sup> one). Then do <b><span style='font-family:"Calibri",sans-serif'>Edit
1270Atoms/On selected atoms…/Modify parameters</span></b>; a popup window will
1271appear. Select <b><span style='font-family:"Calibri",sans-serif'>Type</span></b>
1272&amp; press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>; a
1273Periodic Table will appear. Select <b><span style='font-family:"Calibri",sans-serif'>S</span></b>;
1274the atoms will be renamed and their Type changed to S. The structure will be
1275redrawn with yellow balls for the S atoms. Next select the remaining H atoms (a
1276quick way it to double LB click the <b><span style='font-family:"Calibri",sans-serif'>Type</span></b>
1277column heading and select <b><span style='font-family:"Calibri",sans-serif'>H</span></b>
1278from the popup window). Then do <b><span style='font-family:"Calibri",sans-serif'>Edit
1279Atoms/On selected atoms…/Modify parameters</span></b> and <b><span
1280style='font-family:"Calibri",sans-serif'>Type</span></b> from the popup; select
1281<b><span style='font-family:"Calibri",sans-serif'>C</span></b> from the
1282Periodic Table as we don’t know which ones are N. The drawing will change (you
1283may have to wiggle it a bit to force the update).</p>
1284
1285<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1286 id="Picture_x0020_28" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:468pt;
1287 height:405pt;visibility:visible;mso-wrap-style:square'>
1288 <v:imagedata src="CFSingleCrystal_files/image019.png" o:title=""/>
1289</v:shape><![endif]--><![if !vml]><img width=624 height=540
1290src="CFSingleCrystal_files/image020.gif" v:shapes="Picture_x0020_28"><![endif]></span></p>
1291
1292<p class=MsoNormal>Notice that the atoms are scattered over several molecules;
1293we want to assemble them into 2 conveniently placed ones. Begin by selecting an
1294atom (make sure the <b><span style='font-family:"Calibri",sans-serif'>Atom</span></b>
1295tab is displayed &amp; do <b style='mso-bidi-font-weight:normal'><span
1296style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1297mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>shift LB</span></b>
1298on an atom in the drawing – I chose the S atom on the left side of the drawing);
1299it will turn green and a line in the Atom table will be highlighted. Next do <b><span
1300style='font-family:"Calibri",sans-serif'>Edit Atoms/Assemble molecule</span></b>;
1301a popup window will appear. Change the <b><span style='font-family:"Calibri",sans-serif'>Bond
1302search factor</span></b> to <b><span style='font-family:"Calibri",sans-serif'>0.90</span></b>
1303to be sure all S-C bonds are found.</p>
1304
1305<p class=MsoNormal><span style='mso-no-proof:yes'><img width=265 height=223
1306id="_x0000_i1031" src="CFSingleCrystal_files/image012.png"></span>&nbsp;</p>
1307
1308<p class=MsoNormal>Press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>;
1309atoms will be collected into a <span class=SpellE>well positioned</span> group,
1310but others are not. Next select one of the unassembled atoms (I chose a C-atom
1311in a nearby SS-<span class=SpellE>dipyridyl</span>) and do <b><span
1312style='font-family:"Calibri",sans-serif'>Edit Atoms/Assemble molecule</span></b>;
1313there will be two nicely assembled SS-<span class=SpellE>dipyridyls</span>.</p>
1314
1315<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1316 id="Picture_x0020_29" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:468pt;
1317 height:405pt;visibility:visible;mso-wrap-style:square'>
1318 <v:imagedata src="CFSingleCrystal_files/image021.png" o:title=""/>
1319</v:shape><![endif]--><![if !vml]><img width=624 height=540
1320src="CFSingleCrystal_files/image022.gif" v:shapes="Picture_x0020_29"><![endif]></span></p>
1321
1322<p class=MsoNormal>You should probably save this project as it contains your
1323solved crystal structure.</p>
1324
1325<h2><span style='mso-fareast-font-family:"Times New Roman"'>Step 6. Initial
1326refinement<o:p></o:p></span></h2>
1327
1328<p class=MsoNormal>Since we now have a structural model, we can do the initial
1329structure refinement. By default this will only refine the scale factor; do <b><span
1330style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b> from the
1331main GSAS-II data tree window. Convergence will quickly occur with <span
1332class=SpellE>Rw</span> ~35%. More useful is to refine the atom positions and
1333isotropic thermal parameters. Select the <b><span style='font-family:"Calibri",sans-serif'>Atoms</span></b>
1334tab from the Phase window. Then LB double click the <b><span style='font-family:
1335"Calibri",sans-serif'>refine</span></b> column heading; a popup window will
1336appear. Select <b><span style='font-family:"Calibri",sans-serif'>X</span></b>
1337and <b><span style='font-family:"Calibri",sans-serif'>U</span></b> and press <b><span
1338style='font-family:"Calibri",sans-serif'>OK</span></b>. The <b><span
1339style='font-family:"Calibri",sans-serif'>Atoms</span></b> window will show <b><span
1340style='font-family:"Calibri",sans-serif'>XU</span></b> for each atom in the
1341refine column. Then do <b><span style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b>
1342(2-3 times to get convergence) and the <span class=SpellE>Rw</span> ~12%.</p>
1343
1344<h2><span style='mso-fareast-font-family:"Times New Roman"'>Step 7. Determine
1345C/N choice<o:p></o:p></span></h2>
1346
1347<p class=MsoNormal>We know from the chemistry that the N atom is in the 2
1348position of the pyridine ring, i.e. next to the point of attachment to the
1349S-atom. However, we don’t know which one that is and we have 8 atoms of which 4
1350are C and 4 are N.</p>
1351
1352<p class=MsoNormal>To work out the C/N problem above we need the atoms to be in
1353a chemically sensible order. The assemble molecule routine did construct chains
1354of atoms but this ordering is not really satisfactory. The ordering can quickly
1355be done by hand by following a labelled drawing. First go to the <b><span
1356style='font-family:"Calibri",sans-serif'>Draw Atoms</span></b> tab and double
1357LB click the <b><span style='font-family:"Calibri",sans-serif'>Style</span></b>
1358column; select <b><span style='font-family:"Calibri",sans-serif'>balls &amp;
1359sticks</span></b> from the popup box. Press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>.
1360Next, double LB click the <b><span style='font-family:"Calibri",sans-serif'>Label</span></b>
1361column and select <b><span style='font-family:"Calibri",sans-serif'>name</span></b>
1362from the popup box; press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>.
1363Then go to the <b><span style='font-family:"Calibri",sans-serif'>Draw options</span></b>
1364tab and adjust the <b><span style='font-family:"Calibri",sans-serif'>Ball scale</span></b>
1365&amp; <b><span style='font-family:"Calibri",sans-serif'>Bond radius </span></b>to
1366allow the labels to be easily seen. After shifting the view point the drawing
1367should look something like</p>
1368
1369<p class=MsoNormal>&nbsp;</p>
1370
1371<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1372 id="Picture_x0020_30" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:453pt;
1373 height:393pt;visibility:visible;mso-wrap-style:square'>
1374 <v:imagedata src="CFSingleCrystal_files/image023.png" o:title=""/>
1375</v:shape><![endif]--><![if !vml]><img width=604 height=524
1376src="CFSingleCrystal_files/image024.gif" v:shapes="Picture_x0020_30"><![endif]></span></p>
1377
1378<p class=MsoNormal>Now go to the <b><span style='font-family:"Calibri",sans-serif'>Atoms</span></b>
1379tab. If you look carefully, you can see that the atoms in each SS-<span
1380class=SpellE>dipyridyl</span> are grouped together in the table but they are
1381not in chemically sensible order. The atoms can be reordered by selecting one
1382row with the <b><span style='font-family:"Calibri",sans-serif'>Alt</span></b> key
1383down (the status line will tell which atom is selected to move) and then with
1384the <b><span style='font-family:"Calibri",sans-serif'>Alt</span></b> key still
1385down pick a row below where you want to insert it. I ordered them so each
1386S-atom was followed by the C-atoms in order around the ring; my list looked
1387like (I show just the 1<sup>st</sup> SS <span class=SpellE>dipyridyl</span>
1388molecule)</p>
1389
1390<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1391 id="Picture_x0020_31" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:468pt;
1392 height:248.25pt;visibility:visible;mso-wrap-style:square'>
1393 <v:imagedata src="CFSingleCrystal_files/image025.png" o:title=""/>
1394</v:shape><![endif]--><![if !vml]><img width=624 height=331
1395src="CFSingleCrystal_files/image026.gif" v:shapes="Picture_x0020_31"><![endif]></span></p>
1396
1397<p class=MsoNormal>Once you have reordered the atoms to your satisfaction they
1398can be renamed to be in order. To do this select all the atoms (double LB click
1399the empty corner box) and then do <b><span style='font-family:"Calibri",sans-serif'>Edit
1400Atoms/On selected atoms…/Modify atom parameters</span></b>. Select <b><span
1401style='font-family:"Calibri",sans-serif'>Name</span></b> and press <b><span
1402style='font-family:"Calibri",sans-serif'>OK</span></b>; press <b><span
1403style='font-family:"Calibri",sans-serif'>Yes</span></b> to the popup question.
1404The atoms will be renamed in numerical order. Do <b><span style='font-family:
1405"Calibri",sans-serif'>Edit/Reload draw atoms</span></b>; the labels will
1406change. In my numbering scheme, half of the C3, C7, C10, C14, C17, C21, C24 and
1407C28 carbon atoms are really nitrogen (if they are ordered). Select these and do
1408<b><span style='font-family:"Calibri",sans-serif'>Edit Atoms/On selected atoms…/Refine
1409selected</span></b>; select <b><span style='font-family:"Calibri",sans-serif'>F</span></b>,
1410<b><span style='font-family:"Calibri",sans-serif'>X</span></b> &amp; <b><span
1411style='font-family:"Calibri",sans-serif'>U</span></b> for these. Do <b><span
1412style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b>; the <span
1413class=SpellE>Rw</span> will drop to ~10% and 4 of the atom <span class=SpellE><b><span
1414style='font-family:"Calibri",sans-serif'>frac</span></b></span> values will be
1415~1.25 while the others are ~1.0. The former are N-atoms and the latter are
1416C-atoms. Change the <b><span style='font-family:"Calibri",sans-serif'>Type</span></b>
1417for the N-atoms and repeat <b><span style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b>;
1418the <span class=SpellE>Rw</span> will be high to start, but immediately fall to
1419~10%. In the Atom table all 8 refined <span class=SpellE>frac</span> values are
1420be now ~1.0. To finish this part of the refinement, set all <span class=SpellE><b><span
1421style='font-family:"Calibri",sans-serif'>frac</span></b></span> values to <b><span
1422style='font-family:"Calibri",sans-serif'>1.0</span></b> and all refine flags to
1423<b><span style='font-family:"Calibri",sans-serif'>XU</span></b>. Do <b><span
1424style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b>; the final
1425<span class=SpellE>Rw</span> ~10.5%</p>
1426
1427<h2><span style='mso-fareast-font-family:"Times New Roman"'>Step 8. Anisotropic
1428thermal motion refinement<o:p></o:p></span></h2>
1429
1430<p class=MsoNormal>Given reasonable measured structure factors one can improve a
1431crystal model by using anisotropic thermal motion models for all the <span
1432class=SpellE>nonhydrogen</span> atoms. To convert all the atoms here select the
1433Atoms tab and then do a double LB click on the I/A column heading. Select
1434Anisotropic from the popup and press OK; the Atom table will be redrawn with <span
1435class=SpellE>Uij</span> values equivalent to the corresponding <span
1436class=SpellE>Uiso</span> (now hidden). Do <b><span style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b>;
1437the final <span class=SpellE>Rw</span> ~8.2%</p>
1438
1439<h2 style='page-break-after:avoid'><span style='mso-fareast-font-family:"Times New Roman"'>Step
14409. H-atom placement &amp; final refinement<o:p></o:p></span></h2>
1441
1442<p class=MsoNormal>This structure can be completed by adding the 4 H-atoms per
1443pyridine ring (16 in all). One could do this (painfully) by hand by looking for
1444them in <span style='font-family:Symbol'>D</span>F maps, but it is simpler to
1445just place them knowing the bonding chemistry of the rings. To start this
1446select the <b><span style='font-family:"Calibri",sans-serif'>Atoms</span></b>
1447tab for the phase. Then select the C-atoms by a double LB click on the <b><span
1448style='font-family:"Calibri",sans-serif'>Type</span></b> column heading and
1449select <b><span style='font-family:"Calibri",sans-serif'>C</span></b> from the
1450popup; press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>.
1451The C-atoms will be highlighted. Next do <b><span style='font-family:"Calibri",sans-serif'>Edit
1452Atoms/On selected atoms…/<span class=SpellE>Calc</span> H atoms</span></b>; a <b><span
1453style='font-family:"Calibri",sans-serif'>Distance Angle Controls</span></b>
1454popup will appear; the numbers should be as before. Press <b><span
1455style='font-family:"Calibri",sans-serif'>OK</span></b>; a new popup will appear</p>
1456
1457<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1458 id="Picture_x0020_32" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:300pt;
1459 height:187.5pt;visibility:visible;mso-wrap-style:square'>
1460 <v:imagedata src="CFSingleCrystal_files/image027.png" o:title=""/>
1461</v:shape><![endif]--><![if !vml]><img width=400 height=250
1462src="CFSingleCrystal_files/image028.gif" v:shapes="Picture_x0020_32"><![endif]></span></p>
1463
1464<p class=MsoNormal>This is the hydrogen add control; it shows both the expected
1465number of H-atoms to add to each C-atom and the neighboring atoms used to
1466determine the geometry of the C-H bond. Check to make sure that 4 H-atoms will
1467be added for each ring. Note that C2, C9, C16 &amp; C23 will not have an H-atom
1468added as these are the S-atom attachment points in SS-<span class=SpellE>dipyridyl</span>.
1469Press <b><span style='font-family:"Calibri",sans-serif'>Ok</span></b>; the
1470H-atoms will be inserted immediately after the corresponding C-atoms and the
1471drawing is updated showing van der Waals spheres for all atoms.</p>
1472
1473<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1474 id="Picture_x0020_33" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:430.5pt;
1475 height:249pt;visibility:visible;mso-wrap-style:square'>
1476 <v:imagedata src="CFSingleCrystal_files/image029.png" o:title=""/>
1477</v:shape><![endif]--><![if !vml]><img width=574 height=332
1478src="CFSingleCrystal_files/image030.gif" v:shapes="Picture_x0020_33"><![endif]></span></p>
1479
1480<p class=MsoNormal>&nbsp;</p>
1481
1482<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1483 id="Picture_x0020_34" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:430.5pt;
1484 height:373.5pt;visibility:visible;mso-wrap-style:square'>
1485 <v:imagedata src="CFSingleCrystal_files/image031.png" o:title=""/>
1486</v:shape><![endif]--><![if !vml]><img width=574 height=498
1487src="CFSingleCrystal_files/image032.gif" v:shapes="Picture_x0020_34"><![endif]></span></p>
1488
1489<p class=MsoNormal>Next, do <b><span style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b>;
1490there will be an immediate drop in <span class=SpellE>Rw</span> ~3.2%. Note
1491that we did not refine the H-atom positions or thermal parameters. The H-atom
1492insertion process retains the mechanisms for creating them in the first place
1493and these tools can be used to move them to reflect the changes in the C-atom
1494parameters thus forcing them to ride on the C-atoms. Do <b><span
1495style='font-family:"Calibri",sans-serif'>Edit Atoms/Update H atoms</span></b>;
1496the H-atom positions &amp; <span class=SpellE>Uisos</span> will be <span
1497class=GramE>revised.</span> Repeat <b><span style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b>;
1498there will be a slight improvement in <span class=SpellE>Rw</span>. Repeat
1499these two steps (twice); <span class=SpellE>Rw</span> should not change on the
1500last round. This completes the refinement of the SS-<span class=SpellE>dipyridyl</span>
1501structure. You can generate a final <span style='font-family:Symbol'>D</span>F
1502map from the <b><span style='font-family:"Calibri",sans-serif'>General</span></b>
1503tab; in <b><span style='font-family:"Calibri",sans-serif'>Fourier map controls</span></b>
1504select the <b><span style='font-family:"Calibri",sans-serif'>Map type</span></b>
1505and <b><span style='font-family:"Calibri",sans-serif'>Reflection sets</span></b>,
1506then do <b><span style='font-family:"Calibri",sans-serif'>Compute/Fourier map</span></b>.
1507The <span style='font-family:Symbol'>r</span><sub>max</sub> (=0.33) and <span
1508style='font-family:Symbol'>r</span><sub>min</sub> (=-0.31) are listed on the
1509console; these seem to be concentrated around the S-atoms.</p>
1510
1511</div>
1512
1513</body>
1514
1515</html>
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