source: Tutorials/CFXraySingleCrystal/CFSingleCrystal.htm @ 4752

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add data link to tutorials
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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><BL>
951  <LI>Exercise files are found <A href="./data/" target="_blank">here</a>
952</BL></P><P></P>
953
954  <p class=MsoNormal>In this exercise we will use a set of X-ray single crystal
955structure factors to solve the structure of <span class=SpellE>dipyridyl</span>
956disulfide by charge flipping and then refine the structure by least-squares.
957The structure will be completed by adding the requisite hydrogen atoms and by
958using anisotropic thermal parameters for the heavier atoms. The structure was
959originally solved by <span class=SpellE>Raghavan</span> &amp; <span
960class=SpellE>Seff</span>, <span class=SpellE>Acta</span> <span class=SpellE>Cryst</span>.
961B33, 386-391 (1977) in the space group P2<sub>1</sub>/c with one disordered
962pyridine ring with indications that the true space group was P2<sub>1</sub>. It
963was subsequently reinvestigated by Young (2014….) who found that the true space
964group was P2<sub>1</sub> with 4 molecules in the asymmetric unit. The data used
965in the latter analysis is what is used here and is provided as a “<span
966class=SpellE>fcf</span>” file obtained after structure analysis by Shelx-97;
967the structure factors are scaled to those calculated from the structure. We will
968solve the P 2<sub>1</sub>/c structure first.</p>
969
970<p class=MsoNormal>&nbsp;</p>
971
972<p class=MsoNormal>Note that menu entries and user input are shown in bold face
973below as <b><span style='font-family:"Calibri",sans-serif'>Help/About GSAS-II</span></b>,
974which lists first the name of the menu (here <b><span style='font-family:"Calibri",sans-serif'>Help</span></b>)
975and second the name of the entry in the menu (here <b><span style='font-family:
976"Calibri",sans-serif'>About GSAS-II</span></b>). If you have not done so
977already, start GSAS-II</p>
978
979<h2><span style='mso-fareast-font-family:"Times New Roman"'>Step 1. Input phase
980information<o:p></o:p></span></h2>
981
982<p class=MsoListParagraph style='text-indent:-.25in'>1.<span style='font-size:
9837.0pt'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Use the <b><span style='font-family:
984"Calibri",sans-serif'>Data/Add new phase</span></b> menu item add a new phase
985into the current GSAS-II project. A popup window will appear asking for a phase
986name; I entered <b><span style='font-family:"Calibri",sans-serif'>SS <span
987class=SpellE>dipyridyl</span></span></b>; press <b><span style='font-family:
988"Calibri",sans-serif'>OK</span></b> when done. Select <b><span
989style='font-family:"Calibri",sans-serif'>Loaded Data/Phases/SS <span
990class=SpellE>dipyridyl</span></span></b> from the GSAS-II Data tree window. The
991General tab for Phase Data will appear.</p>
992
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1018
1019<p class=MsoListParagraph style='text-indent:-.25in'>2.<span style='font-size:
10207.0pt'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Enter the space group <b><span
1021style='font-family:"Calibri",sans-serif'>P 21/c</span></b> (don’t forget the
1022space between P &amp; 21/c) &amp; press <b><span style='font-family:"Calibri",sans-serif'>Enter</span></b>.
1023A Space Group Information popup window will appear; press <b><span
1024style='font-family:"Calibri",sans-serif'>OK</span></b>. The General window will
1025be refreshed showing only the needed lattice parameters for P 21/c.</p>
1026
1027<p class=MsoListParagraph><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
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1033
1034<p class=MsoListParagraph style='text-indent:-.25in'>3.<span style='font-size:
10357.0pt'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>Enter <b><span style='font-family:
1036"Calibri",sans-serif'>15.8489</span></b>, <b><span style='font-family:"Calibri",sans-serif'>5.5008</span></b>,
1037<b><span style='font-family:"Calibri",sans-serif'>23.118</span></b>, and <b><span
1038style='font-family:"Calibri",sans-serif'>96.9160</span></b> for a, b, c and
1039beta, respectively; the unit cell volume will be recalculated at each entry.</p>
1040
1041<h2><span style='mso-fareast-font-family:"Times New Roman"'>Step 2. Import
1042structure factors <o:p></o:p></span></h2>
1043
1044<p class=MsoNormal>There are two parts to this step: one is to import the data
1045and the second is to connect the data with the phase within GSAS-II.</p>
1046
1047<p class=MsoNormal>To do these, do <b><span style='font-family:"Calibri",sans-serif'>Import/Structure
1048factor/from CIF file</span></b> from the main GSAS-II data tree window menu. A
1049file selection dialog will appear; find <span class=SpellE><b><span
1050style='font-family:"Calibri",sans-serif'>CFXraySingleCrystal</span></b></span><b><span
1051style='font-family:"Calibri",sans-serif'>\data\S2dipyridyl.fcf</span></b> and
1052press <b><span style='font-family:"Calibri",sans-serif'>Open</span></b>. A
1053popup window asking if this is the file you want; press <b><span
1054style='font-family:"Calibri",sans-serif'>Yes</span></b>. After a pause while
1055the file is read a new popup will appear offering the chance to rename the
1056structure factor set; press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>.
1057After some time a new popup will appear to Add the new structure factor set to
1058the SS <span class=SpellE>dipyridyl</span> phase. Select the phase and press <b><span
1059style='font-family:"Calibri",sans-serif'>OK</span></b>. The plot will show a
1060rectangular array of circles for the hk0 reflection layer; select the plot
1061&amp; press <b><span style='font-family:"Calibri",sans-serif'>k</span></b> to
1062get an h0l layer.</p>
1063
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1070
1071<p class=MsoNormal>Because the <span class=SpellE>fcf</span> file has both
1072observed and calculated structure factors, the plot shows a small R value for
1073the layer. The observed structure factors are shown as blue rings, the
1074calculated ones as green rings and a small green or red dot may appear at each
1075ring center showing <span class=SpellE>F<sub>o</sub></span>-F<sub>c</sub>. If
1076the reflection data file had only observed structure factors then only blue
1077rings will be seen. You can explore the plot options in the ‘<b><span
1078style='font-family:"Calibri",sans-serif'>K</span></b>’ box in the plot toolbar.</p>
1079
1080<h2><span style='mso-fareast-font-family:"Times New Roman"'>Step 3. Setup for
1081charge flipping<o:p></o:p></span></h2>
1082
1083<p class=MsoNormal>To solve (again) this crystal structure we will use charge
1084flipping. Charge flipping in GSAS-II is implemented to solve the crystal
1085structure without consideration of space group symmetry. To do this it operates
1086on the entire unit cell volume to a selected resolution (usually 0.5Å) using
1087fast <span class=SpellE>fourier</span> transform techniques. This requires a
1088set of structure factors in an array of the same dimensions as the density
1089array covering the unit cell (i.e. a box bounded by ~0.5Å resolution). The
1090space group symmetry is applied to the observed structure factors to create a
1091full sphere which is then zero filled out to the 0.5Å resolution bounded box.
1092To be reasonably assured of success, the observed structure factors should
1093extend to ~1Å resolution; we have that here for this example. To begin select <b><span
1094style='font-family:"Calibri",sans-serif'>Phases/SS <span class=SpellE>dipyridyl</span></span></b>
1095from the GSAS-II data tree; the General tab will be shown</p>
1096
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1103
1104<p class=MsoNormal>Find the <b><span style='font-family:"Calibri",sans-serif'>Fourier
1105map controls</span></b> and change the <b><span style='font-family:"Calibri",sans-serif'>Peak
1106cutoff %</span></b> to <b><span style='font-family:"Calibri",sans-serif'>10</span></b>;
1107then immediately below find the <b><span style='font-family:"Calibri",sans-serif'>Charge
1108flip controls</span></b>. Press <b><span style='font-family:"Calibri",sans-serif'>Select
1109reflection sets</span></b>, pick <b><span style='font-family:"Calibri",sans-serif'>HKLF
1110S2dipyridyl.fcf:1a</span></b> from the list (the only one) and press <b><span
1111style='font-family:"Calibri",sans-serif'>OK</span></b>. If you had multiple
1112data sets for this phase, you can pick more than one and GSAS-II will use a
1113“last one in” process for assembling the reflection set to use for charge
1114flipping. There are four more settings to consider: 1) <span class=SpellE>kMax</span>
1115controls the upper cutoff for charge flipping; if the density is &gt; k-Max*<span
1116style='font-family:Symbol'>s<sub>r</sub></span> (map standard deviation) then
1117flip the charge. This prevents the “Uranium solution” sometimes found where all
1118the density is concentrated in a single peak. A useful guide is to use twice
1119the largest atomic number of any element in your structure. For equal atom
1120problems use 12-15; adjust upward for structures with heavy &amp; light atoms.
1121In this case, set <b><span style='font-family:"Calibri",sans-serif'>k-Max</span></b>
1122to <b><span style='font-family:"Calibri",sans-serif'>30.0</span></b> to allow
1123the S atom to appear. 2) k-Factor controls the lower level for charge flipping;
1124if the density is &lt; k-Factor*<span style='font-family:Symbol'>s<sub>r</sub></span>
1125then flip the charge. The default value seems to work pretty well; I’d only
1126change it if the charge flipping is having trouble solving the structure. 3)
1127Resolution selects the spacing between map points. 0.5Å is sufficient in most
1128cases. Choosing a smaller value requires more map points (NB: GSAS-II uses the
1129entire unit cell volume for charge flipping) and thus will require more
1130structure factors since the fast <span class=SpellE>fourier</span> algorithm
1131requires the same size arrays in both real space and reciprocal space. This
1132will slow down the charge flip process. 4) Normalizing element selects a form
1133factor to rescale the structure factors thus “sharpening” the density map. I
1134suggest trying <b><span style='font-family:"Calibri",sans-serif'>None</span></b>
1135first, otherwise select a representative element (really doesn’t matter which).</p>
1136
1137<h2 style='page-break-after:avoid'><span style='mso-fareast-font-family:"Times New Roman"'>Step
11384. Charge flipping<o:p></o:p></span></h2>
1139
1140<p class=MsoNormal>With the controls all set you can now do charge flipping;
1141from the <b><span style='font-family:"Calibri",sans-serif'>General</span></b>
1142tab do <b><span style='font-family:"Calibri",sans-serif'>Compute/Charge
1143flipping</span></b>. A progress bar popup will appear showing the residual
1144between the observed structure factors and those obtained from the inverse <span
1145class=SpellE>fourier</span> transform of the last flipped density map. It
1146should quickly decrease to the ~20% range and level out indicating a good
1147charge flip solution. When it has reached this, press <b><span
1148style='font-family:"Calibri",sans-serif'>Cancel</span></b> to stop the process.</p>
1149
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1152
1153<p class=MsoNormal>The console window will show something like</p>
1154
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1161
1162<p class=MsoNormal>There may be a pause at <b><span style='font-family:"Calibri",sans-serif'>Begin
1163<span class=SpellE><span class=GramE>fourier</span></span> map search</span></b>
1164before it finishes. Provided is a summary of the charge flip calculation (time,
1165map size, density range &amp; structure factor residual). The map offset is
1166discovered by an analysis of the reflection phases with respect to how they
1167should be distributed for your chosen space group. These offsets are then
1168applied to shift the map so that the symmetry elements are properly located in
1169the unit cell. The quality of this fit (chi**2) is given. This process is not
1170necessarily perfect; you are given an opportunity to hand-tune the offset.
1171Finally the number of peaks found in the map is listed, the structure is drawn
1172(I’ve made the view down the b-axis)</p>
1173
1174<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1175 id="Picture_x0020_24" o:spid="_x0000_i1036" type="#_x0000_t75" style='width:450pt;
1176 height:387.75pt;visibility:visible;mso-wrap-style:square'>
1177 <v:imagedata src="CFSingleCrystal_files/image011.png" o:title=""/>
1178</v:shape><![endif]--><![if !vml]><img width=600 height=517
1179src="CFSingleCrystal_files/image012.gif" v:shapes="Picture_x0020_24"><![endif]></span></p>
1180
1181<p class=MsoNormal>&nbsp;<span class=GramE>and</span> the Phase data window
1182will show the map peaks tab</p>
1183
1184<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1185 id="Picture_x0020_25" o:spid="_x0000_i1035" type="#_x0000_t75" style='width:450pt;
1186 height:219.75pt;visibility:visible;mso-wrap-style:square'>
1187 <v:imagedata src="CFSingleCrystal_files/image013.png" o:title=""/>
1188</v:shape><![endif]--><![if !vml]><img width=600 height=293
1189src="CFSingleCrystal_files/image014.gif" v:shapes="Picture_x0020_25"><![endif]></span></p>
1190
1191<p class=MsoNormal>These are listed in order of magnitude; a double click on
1192any of the table headings will sort the list according to that parameter. My
1193list has 112 entries; <span class=SpellE>dipyridyl</span> disulfide has 14 C
1194&amp; S atoms so this list is appropriate for 8 molecules in the unit cell and
1195thus all atoms were found in this charge flipping result.</p>
1196
1197<p class=MsoNormal>If all went well then the drawing should nicely show all the
1198atoms in the structure placed properly with respect to the locations of the
1199inversion centers (they are at all the corners, edge centers, face centers and
1200cell center). If not then you can shift the map &amp; peaks with the <b><span
1201style='font-family:"Calibri",sans-serif'>L</span></b>, <b><span
1202style='font-family:"Calibri",sans-serif'>R</span></b>, <b><span
1203style='font-family:"Calibri",sans-serif'>U</span></b> &amp; <b><span
1204style='font-family:"Calibri",sans-serif'>D</span></b> keys (NB: rotate the
1205drawing so the axes are ~horizontal/vertical); the map/peaks will move in
1206resolution steps (0.5A). The table is also updated with new peak positions. You
1207could also just repeat the charge flipping and hope to get a better map offset
1208solution (examine the map offset chi**2 to get a sense of this). You can also
1209show the map density (highest point is shown as a green dot somewhere in the
1210map – on a S-atom position); select the <b><span style='font-family:"Calibri",sans-serif'>Draw
1211Options</span></b> tab and use the <b><span style='font-family:"Calibri",sans-serif'>Contour
1212level</span></b> slider. The drawing will show green dots at each set map point
1213with size in proportion to the density. The mouse <b><span style='font-family:
1214"Calibri",sans-serif'>RB</span></b> can be used to slide the structure around;
1215the density is always drawn in a space surrounding the view point (multicolored
1216cross at the center). While here you can also change the <b><span
1217style='font-family:"Calibri",sans-serif'>Bond search factor</span></b> to <b><span
1218style='font-family:"Calibri",sans-serif'>0.90</span></b> to ensure all S-C
1219bonds are shown.</p>
1220
1221<p class=MsoNormal>If the charge flipping has failed (high residual &amp; no
1222recognizable structure) the process should be just repeated. This gives it a
1223new random start for the structure factor phases which may lead to a good
1224solution. After a few attempts, you can try different control settings to see
1225if that will coax out a good solution; first be sure <b><span style='font-family:
1226"Calibri",sans-serif'>k-Max</span></b> is properly set and then perhaps try
1227different <b><span style='font-family:"Calibri",sans-serif'>k-Factors</span></b>
1228and do <b><span style='font-family:"Calibri",sans-serif'>Normalizing</span></b>
1229by some element form factor. If it seemed to work but very few peaks were
1230found, make sure <b><span style='font-family:"Calibri",sans-serif'>Peak cutoff</span></b>
1231was properly set; you can then repeat the peak search by doing <b><span
1232style='font-family:"Calibri",sans-serif'>Compute/Search map</span></b>.</p>
1233
1234<h2><span style='mso-fareast-font-family:"Times New Roman"'>Step 5. Extract
1235solution and make molecules<o:p></o:p></span></h2>
1236
1237<p class=MsoNormal>Assuming that the map &amp; peak positions are properly
1238placed with respect to the symmetry elements of the space group, we can now
1239select those peaks which describe the structure. Select the <b><span
1240style='font-family:"Calibri",sans-serif'>Map peaks</span></b> tab and double LB
1241click the blank upper left corner of the table; all entries will be highlighted
1242in blue. Then do <b><span style='font-family:"Calibri",sans-serif'>Map
1243peaks/Unique peaks</span></b>; after a bit of time 1/4 of the peaks in the list
1244will be highlighted and the corresponding peaks in the drawing will be green
1245(NB: if you navigate away from this tab, this selection will be lost and you’ll
1246have to repeat it!). The console will show a summary giving the number &amp;
1247fraction of unique peaks found; in this case 28 &amp; 0.25 are the correct
1248values. Next, do <b><span style='font-family:"Calibri",sans-serif'>Map
1249peaks/Move peaks</span></b>; these peaks will be transferred to the <b><span
1250style='font-family:"Calibri",sans-serif'>Atoms</span></b> list as H-atoms named
1251according to their position in the magnitude column.</p>
1252
1253<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1254 id="Picture_x0020_26" o:spid="_x0000_i1034" type="#_x0000_t75" style='width:468pt;
1255 height:198.75pt;visibility:visible;mso-wrap-style:square'>
1256 <v:imagedata src="CFSingleCrystal_files/image015.png" o:title=""/>
1257</v:shape><![endif]--><![if !vml]><img width=624 height=265
1258src="CFSingleCrystal_files/image016.gif" v:shapes="Picture_x0020_26"><![endif]></span></p>
1259
1260<p class=MsoNormal>The drawing will show white balls at the atom positions
1261scattered over several molecules.</p>
1262
1263<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1264 id="Picture_x0020_27" o:spid="_x0000_i1033" type="#_x0000_t75" style='width:468pt;
1265 height:405pt;visibility:visible;mso-wrap-style:square'>
1266 <v:imagedata src="CFSingleCrystal_files/image017.png" o:title=""/>
1267</v:shape><![endif]--><![if !vml]><img width=624 height=540
1268src="CFSingleCrystal_files/image018.gif" v:shapes="Picture_x0020_27"><![endif]></span></p>
1269
1270<p class=MsoNormal>Notice that 4 atoms have magnitudes ~90+, these are the S
1271atoms. The rest are C &amp; N atoms. In the <b><span style='font-family:"Calibri",sans-serif'>Atoms</span></b>
1272tab select the first 4 atoms (press LB on the 1<sup>st</sup> &amp; shift LB on
1273the 4<sup>th</sup> one). Then do <b><span style='font-family:"Calibri",sans-serif'>Edit
1274Atoms/On selected atoms…/Modify parameters</span></b>; a popup window will
1275appear. Select <b><span style='font-family:"Calibri",sans-serif'>Type</span></b>
1276&amp; press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>; a
1277Periodic Table will appear. Select <b><span style='font-family:"Calibri",sans-serif'>S</span></b>;
1278the atoms will be renamed and their Type changed to S. The structure will be
1279redrawn with yellow balls for the S atoms. Next select the remaining H atoms (a
1280quick way it to double LB click the <b><span style='font-family:"Calibri",sans-serif'>Type</span></b>
1281column heading and select <b><span style='font-family:"Calibri",sans-serif'>H</span></b>
1282from the popup window). Then do <b><span style='font-family:"Calibri",sans-serif'>Edit
1283Atoms/On selected atoms…/Modify parameters</span></b> and <b><span
1284style='font-family:"Calibri",sans-serif'>Type</span></b> from the popup; select
1285<b><span style='font-family:"Calibri",sans-serif'>C</span></b> from the
1286Periodic Table as we don’t know which ones are N. The drawing will change (you
1287may have to wiggle it a bit to force the update).</p>
1288
1289<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1290 id="Picture_x0020_28" o:spid="_x0000_i1032" type="#_x0000_t75" style='width:468pt;
1291 height:405pt;visibility:visible;mso-wrap-style:square'>
1292 <v:imagedata src="CFSingleCrystal_files/image019.png" o:title=""/>
1293</v:shape><![endif]--><![if !vml]><img width=624 height=540
1294src="CFSingleCrystal_files/image020.gif" v:shapes="Picture_x0020_28"><![endif]></span></p>
1295
1296<p class=MsoNormal>Notice that the atoms are scattered over several molecules;
1297we want to assemble them into 2 conveniently placed ones. Begin by selecting an
1298atom (make sure the <b><span style='font-family:"Calibri",sans-serif'>Atom</span></b>
1299tab is displayed &amp; do <b style='mso-bidi-font-weight:normal'><span
1300style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin;
1301mso-hansi-theme-font:minor-latin;mso-bidi-theme-font:minor-latin'>shift LB</span></b>
1302on an atom in the drawing – I chose the S atom on the left side of the drawing);
1303it will turn green and a line in the Atom table will be highlighted. Next do <b><span
1304style='font-family:"Calibri",sans-serif'>Edit Atoms/Assemble molecule</span></b>;
1305a popup window will appear. Change the <b><span style='font-family:"Calibri",sans-serif'>Bond
1306search factor</span></b> to <b><span style='font-family:"Calibri",sans-serif'>0.90</span></b>
1307to be sure all S-C bonds are found.</p>
1308
1309<p class=MsoNormal><span style='mso-no-proof:yes'><img width=265 height=223
1310id="_x0000_i1031" src="CFSingleCrystal_files/image012.png"></span>&nbsp;</p>
1311
1312<p class=MsoNormal>Press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>;
1313atoms will be collected into a <span class=SpellE>well positioned</span> group,
1314but others are not. Next select one of the unassembled atoms (I chose a C-atom
1315in a nearby SS-<span class=SpellE>dipyridyl</span>) and do <b><span
1316style='font-family:"Calibri",sans-serif'>Edit Atoms/Assemble molecule</span></b>;
1317there will be two nicely assembled SS-<span class=SpellE>dipyridyls</span>.</p>
1318
1319<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1320 id="Picture_x0020_29" o:spid="_x0000_i1030" type="#_x0000_t75" style='width:468pt;
1321 height:405pt;visibility:visible;mso-wrap-style:square'>
1322 <v:imagedata src="CFSingleCrystal_files/image021.png" o:title=""/>
1323</v:shape><![endif]--><![if !vml]><img width=624 height=540
1324src="CFSingleCrystal_files/image022.gif" v:shapes="Picture_x0020_29"><![endif]></span></p>
1325
1326<p class=MsoNormal>You should probably save this project as it contains your
1327solved crystal structure.</p>
1328
1329<h2><span style='mso-fareast-font-family:"Times New Roman"'>Step 6. Initial
1330refinement<o:p></o:p></span></h2>
1331
1332<p class=MsoNormal>Since we now have a structural model, we can do the initial
1333structure refinement. By default this will only refine the scale factor; do <b><span
1334style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b> from the
1335main GSAS-II data tree window. Convergence will quickly occur with <span
1336class=SpellE>Rw</span> ~35%. More useful is to refine the atom positions and
1337isotropic thermal parameters. Select the <b><span style='font-family:"Calibri",sans-serif'>Atoms</span></b>
1338tab from the Phase window. Then LB double click the <b><span style='font-family:
1339"Calibri",sans-serif'>refine</span></b> column heading; a popup window will
1340appear. Select <b><span style='font-family:"Calibri",sans-serif'>X</span></b>
1341and <b><span style='font-family:"Calibri",sans-serif'>U</span></b> and press <b><span
1342style='font-family:"Calibri",sans-serif'>OK</span></b>. The <b><span
1343style='font-family:"Calibri",sans-serif'>Atoms</span></b> window will show <b><span
1344style='font-family:"Calibri",sans-serif'>XU</span></b> for each atom in the
1345refine column. Then do <b><span style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b>
1346(2-3 times to get convergence) and the <span class=SpellE>Rw</span> ~12%.</p>
1347
1348<h2><span style='mso-fareast-font-family:"Times New Roman"'>Step 7. Determine
1349C/N choice<o:p></o:p></span></h2>
1350
1351<p class=MsoNormal>We know from the chemistry that the N atom is in the 2
1352position of the pyridine ring, i.e. next to the point of attachment to the
1353S-atom. However, we don’t know which one that is and we have 8 atoms of which 4
1354are C and 4 are N.</p>
1355
1356<p class=MsoNormal>To work out the C/N problem above we need the atoms to be in
1357a chemically sensible order. The assemble molecule routine did construct chains
1358of atoms but this ordering is not really satisfactory. The ordering can quickly
1359be done by hand by following a labelled drawing. First go to the <b><span
1360style='font-family:"Calibri",sans-serif'>Draw Atoms</span></b> tab and double
1361LB click the <b><span style='font-family:"Calibri",sans-serif'>Style</span></b>
1362column; select <b><span style='font-family:"Calibri",sans-serif'>balls &amp;
1363sticks</span></b> from the popup box. Press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>.
1364Next, double LB click the <b><span style='font-family:"Calibri",sans-serif'>Label</span></b>
1365column and select <b><span style='font-family:"Calibri",sans-serif'>name</span></b>
1366from the popup box; press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>.
1367Then go to the <b><span style='font-family:"Calibri",sans-serif'>Draw options</span></b>
1368tab and adjust the <b><span style='font-family:"Calibri",sans-serif'>Ball scale</span></b>
1369&amp; <b><span style='font-family:"Calibri",sans-serif'>Bond radius </span></b>to
1370allow the labels to be easily seen. After shifting the view point the drawing
1371should look something like</p>
1372
1373<p class=MsoNormal>&nbsp;</p>
1374
1375<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1376 id="Picture_x0020_30" o:spid="_x0000_i1029" type="#_x0000_t75" style='width:453pt;
1377 height:393pt;visibility:visible;mso-wrap-style:square'>
1378 <v:imagedata src="CFSingleCrystal_files/image023.png" o:title=""/>
1379</v:shape><![endif]--><![if !vml]><img width=604 height=524
1380src="CFSingleCrystal_files/image024.gif" v:shapes="Picture_x0020_30"><![endif]></span></p>
1381
1382<p class=MsoNormal>Now go to the <b><span style='font-family:"Calibri",sans-serif'>Atoms</span></b>
1383tab. If you look carefully, you can see that the atoms in each SS-<span
1384class=SpellE>dipyridyl</span> are grouped together in the table but they are
1385not in chemically sensible order. The atoms can be reordered by selecting one
1386row with the <b><span style='font-family:"Calibri",sans-serif'>Alt</span></b> key
1387down (the status line will tell which atom is selected to move) and then with
1388the <b><span style='font-family:"Calibri",sans-serif'>Alt</span></b> key still
1389down pick a row below where you want to insert it. I ordered them so each
1390S-atom was followed by the C-atoms in order around the ring; my list looked
1391like (I show just the 1<sup>st</sup> SS <span class=SpellE>dipyridyl</span>
1392molecule)</p>
1393
1394<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1395 id="Picture_x0020_31" o:spid="_x0000_i1028" type="#_x0000_t75" style='width:468pt;
1396 height:248.25pt;visibility:visible;mso-wrap-style:square'>
1397 <v:imagedata src="CFSingleCrystal_files/image025.png" o:title=""/>
1398</v:shape><![endif]--><![if !vml]><img width=624 height=331
1399src="CFSingleCrystal_files/image026.gif" v:shapes="Picture_x0020_31"><![endif]></span></p>
1400
1401<p class=MsoNormal>Once you have reordered the atoms to your satisfaction they
1402can be renamed to be in order. To do this select all the atoms (double LB click
1403the empty corner box) and then do <b><span style='font-family:"Calibri",sans-serif'>Edit
1404Atoms/On selected atoms…/Modify atom parameters</span></b>. Select <b><span
1405style='font-family:"Calibri",sans-serif'>Name</span></b> and press <b><span
1406style='font-family:"Calibri",sans-serif'>OK</span></b>; press <b><span
1407style='font-family:"Calibri",sans-serif'>Yes</span></b> to the popup question.
1408The atoms will be renamed in numerical order. Do <b><span style='font-family:
1409"Calibri",sans-serif'>Edit/Reload draw atoms</span></b>; the labels will
1410change. In my numbering scheme, half of the C3, C7, C10, C14, C17, C21, C24 and
1411C28 carbon atoms are really nitrogen (if they are ordered). Select these and do
1412<b><span style='font-family:"Calibri",sans-serif'>Edit Atoms/On selected atoms…/Refine
1413selected</span></b>; select <b><span style='font-family:"Calibri",sans-serif'>F</span></b>,
1414<b><span style='font-family:"Calibri",sans-serif'>X</span></b> &amp; <b><span
1415style='font-family:"Calibri",sans-serif'>U</span></b> for these. Do <b><span
1416style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b>; the <span
1417class=SpellE>Rw</span> will drop to ~10% and 4 of the atom <span class=SpellE><b><span
1418style='font-family:"Calibri",sans-serif'>frac</span></b></span> values will be
1419~1.25 while the others are ~1.0. The former are N-atoms and the latter are
1420C-atoms. Change the <b><span style='font-family:"Calibri",sans-serif'>Type</span></b>
1421for the N-atoms and repeat <b><span style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b>;
1422the <span class=SpellE>Rw</span> will be high to start, but immediately fall to
1423~10%. In the Atom table all 8 refined <span class=SpellE>frac</span> values are
1424be now ~1.0. To finish this part of the refinement, set all <span class=SpellE><b><span
1425style='font-family:"Calibri",sans-serif'>frac</span></b></span> values to <b><span
1426style='font-family:"Calibri",sans-serif'>1.0</span></b> and all refine flags to
1427<b><span style='font-family:"Calibri",sans-serif'>XU</span></b>. Do <b><span
1428style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b>; the final
1429<span class=SpellE>Rw</span> ~10.5%</p>
1430
1431<h2><span style='mso-fareast-font-family:"Times New Roman"'>Step 8. Anisotropic
1432thermal motion refinement<o:p></o:p></span></h2>
1433
1434<p class=MsoNormal>Given reasonable measured structure factors one can improve a
1435crystal model by using anisotropic thermal motion models for all the <span
1436class=SpellE>nonhydrogen</span> atoms. To convert all the atoms here select the
1437Atoms tab and then do a double LB click on the I/A column heading. Select
1438Anisotropic from the popup and press OK; the Atom table will be redrawn with <span
1439class=SpellE>Uij</span> values equivalent to the corresponding <span
1440class=SpellE>Uiso</span> (now hidden). Do <b><span style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b>;
1441the final <span class=SpellE>Rw</span> ~8.2%</p>
1442
1443<h2 style='page-break-after:avoid'><span style='mso-fareast-font-family:"Times New Roman"'>Step
14449. H-atom placement &amp; final refinement<o:p></o:p></span></h2>
1445
1446<p class=MsoNormal>This structure can be completed by adding the 4 H-atoms per
1447pyridine ring (16 in all). One could do this (painfully) by hand by looking for
1448them in <span style='font-family:Symbol'>D</span>F maps, but it is simpler to
1449just place them knowing the bonding chemistry of the rings. To start this
1450select the <b><span style='font-family:"Calibri",sans-serif'>Atoms</span></b>
1451tab for the phase. Then select the C-atoms by a double LB click on the <b><span
1452style='font-family:"Calibri",sans-serif'>Type</span></b> column heading and
1453select <b><span style='font-family:"Calibri",sans-serif'>C</span></b> from the
1454popup; press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>.
1455The C-atoms will be highlighted. Next do <b><span style='font-family:"Calibri",sans-serif'>Edit
1456Atoms/On selected atoms…/<span class=SpellE>Calc</span> H atoms</span></b>; a <b><span
1457style='font-family:"Calibri",sans-serif'>Distance Angle Controls</span></b>
1458popup will appear; the numbers should be as before. Press <b><span
1459style='font-family:"Calibri",sans-serif'>OK</span></b>; a new popup will appear</p>
1460
1461<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1462 id="Picture_x0020_32" o:spid="_x0000_i1027" type="#_x0000_t75" style='width:300pt;
1463 height:187.5pt;visibility:visible;mso-wrap-style:square'>
1464 <v:imagedata src="CFSingleCrystal_files/image027.png" o:title=""/>
1465</v:shape><![endif]--><![if !vml]><img width=400 height=250
1466src="CFSingleCrystal_files/image028.gif" v:shapes="Picture_x0020_32"><![endif]></span></p>
1467
1468<p class=MsoNormal>This is the hydrogen add control; it shows both the expected
1469number of H-atoms to add to each C-atom and the neighboring atoms used to
1470determine the geometry of the C-H bond. Check to make sure that 4 H-atoms will
1471be added for each ring. Note that C2, C9, C16 &amp; C23 will not have an H-atom
1472added as these are the S-atom attachment points in SS-<span class=SpellE>dipyridyl</span>.
1473Press <b><span style='font-family:"Calibri",sans-serif'>Ok</span></b>; the
1474H-atoms will be inserted immediately after the corresponding C-atoms and the
1475drawing is updated showing van der Waals spheres for all atoms.</p>
1476
1477<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1478 id="Picture_x0020_33" o:spid="_x0000_i1026" type="#_x0000_t75" style='width:430.5pt;
1479 height:249pt;visibility:visible;mso-wrap-style:square'>
1480 <v:imagedata src="CFSingleCrystal_files/image029.png" o:title=""/>
1481</v:shape><![endif]--><![if !vml]><img width=574 height=332
1482src="CFSingleCrystal_files/image030.gif" v:shapes="Picture_x0020_33"><![endif]></span></p>
1483
1484<p class=MsoNormal>&nbsp;</p>
1485
1486<p class=MsoNormal><span style='mso-no-proof:yes'><!--[if gte vml 1]><v:shape
1487 id="Picture_x0020_34" o:spid="_x0000_i1025" type="#_x0000_t75" style='width:430.5pt;
1488 height:373.5pt;visibility:visible;mso-wrap-style:square'>
1489 <v:imagedata src="CFSingleCrystal_files/image031.png" o:title=""/>
1490</v:shape><![endif]--><![if !vml]><img width=574 height=498
1491src="CFSingleCrystal_files/image032.gif" v:shapes="Picture_x0020_34"><![endif]></span></p>
1492
1493<p class=MsoNormal>Next, do <b><span style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b>;
1494there will be an immediate drop in <span class=SpellE>Rw</span> ~3.2%. Note
1495that we did not refine the H-atom positions or thermal parameters. The H-atom
1496insertion process retains the mechanisms for creating them in the first place
1497and these tools can be used to move them to reflect the changes in the C-atom
1498parameters thus forcing them to ride on the C-atoms. Do <b><span
1499style='font-family:"Calibri",sans-serif'>Edit Atoms/Update H atoms</span></b>;
1500the H-atom positions &amp; <span class=SpellE>Uisos</span> will be <span
1501class=GramE>revised.</span> Repeat <b><span style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b>;
1502there will be a slight improvement in <span class=SpellE>Rw</span>. Repeat
1503these two steps (twice); <span class=SpellE>Rw</span> should not change on the
1504last round. This completes the refinement of the SS-<span class=SpellE>dipyridyl</span>
1505structure. You can generate a final <span style='font-family:Symbol'>D</span>F
1506map from the <b><span style='font-family:"Calibri",sans-serif'>General</span></b>
1507tab; in <b><span style='font-family:"Calibri",sans-serif'>Fourier map controls</span></b>
1508select the <b><span style='font-family:"Calibri",sans-serif'>Map type</span></b>
1509and <b><span style='font-family:"Calibri",sans-serif'>Reflection sets</span></b>,
1510then do <b><span style='font-family:"Calibri",sans-serif'>Compute/Fourier map</span></b>.
1511The <span style='font-family:Symbol'>r</span><sub>max</sub> (=0.33) and <span
1512style='font-family:Symbol'>r</span><sub>min</sub> (=-0.31) are listed on the
1513console; these seem to be concentrated around the S-atoms.</p>
1514
1515</div>
1516
1517</body>
1518
1519</html>
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