Changeset 2262 for Tutorials/CFXraySingleCrystal
- Timestamp:
- May 13, 2016 9:15:26 AM (7 years ago)
- Location:
- Tutorials/CFXraySingleCrystal
- Files:
-
- 11 deleted
- 8 edited
Legend:
- Unmodified
- Added
- Removed
-
Tutorials/CFXraySingleCrystal/CFSingleCrystal.htm
- Property svn:mime-type set to text/html
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mso-level-tab-stop:none; 981 mso-level-number-position:left; 982 text-indent:-.25in;} 983 @list l1:level6 984 {mso-level-number-format:roman-lower; 985 mso-level-tab-stop:none; 986 mso-level-number-position:right; 987 text-indent:-9.0pt;} 988 @list l1:level7 989 {mso-level-tab-stop:none; 990 mso-level-number-position:left; 991 text-indent:-.25in;} 992 @list l1:level8 993 {mso-level-number-format:alpha-lower; 994 mso-level-tab-stop:none; 995 mso-level-number-position:left; 996 text-indent:-.25in;} 997 @list l1:level9 998 {mso-level-number-format:roman-lower; 999 mso-level-tab-stop:none; 1000 mso-level-number-position:right; 1001 text-indent:-9.0pt;} 1002 ol 133 ol 1003 134 {margin-bottom:0in;} 1004 135 ul … … 1006 137 --> 1007 138 </style> 1008 <!--[if gte mso 10]> 1009 <style> 1010 /* Style Definitions */ 1011 table.MsoNormalTable 1012 {mso-style-name:"Table Normal"; 1013 mso-tstyle-rowband-size:0; 1014 mso-tstyle-colband-size:0; 1015 mso-style-noshow:yes; 1016 mso-style-priority:99; 1017 mso-style-parent:""; 1018 mso-padding-alt:0in 5.4pt 0in 5.4pt; 1019 mso-para-margin:0in; 1020 mso-para-margin-bottom:.0001pt; 1021 mso-pagination:widow-orphan; 1022 font-size:10.0pt; 1023 font-family:"Calibri",sans-serif;} 1024 </style> 1025 <![endif]--><!--[if gte mso 9]><xml> 1026 <o:shapedefaults v:ext="edit" spidmax="1026"/> 1027 </xml><![endif]--><!--[if gte mso 9]><xml> 1028 <o:shapelayout v:ext="edit"> 1029 <o:idmap v:ext="edit" data="1"/> 1030 </o:shapelayout></xml><![endif]--> 139 1031 140 </head> 1032 141 1033 <body lang=EN-US style='tab-interval:.5in'>142 <body lang=EN-US> 1034 143 1035 144 <div class=WordSection1> … … 1041 150 1042 151 <p class=MsoNormal>In this exercise we will use a set of X-ray single crystal 1043 structure factors to solve the structure of <span class=SpellE>dipyridyl</span> 1044 disulfide by charge flipping and then refine the structure by least-squares. 1045 The structure will be completed by adding the requisite hydrogen atoms and by 1046 using anisotropic thermal parameters for the heavier atoms. The structure was 1047 originally solved by <span class=SpellE>Raghavan</span> & <span 1048 class=SpellE>Seff</span>, <span class=SpellE>Acta</span> <span class=SpellE>Cryst</span>. 1049 B33, 386-391 (1977) in the space group P2<sub>1</sub>/c with one disordered 1050 pyridine ring with indications that the true space group was P2<sub>1</sub>. It 1051 was subsequently reinvestigated by Young (2014 1052 .) who found that the true space 1053 group was P2<sub>1</sub> with 4 molecules in the asymmetric unit. The data used 1054 in the latter analysis is what is used here and is provided as <span 1055 class=GramE>a</span> <span class=SpellE>fcf</span> file obtained after 1056 structure analysis by Shelx-97; the structure factors are scaled to those 1057 calculated from the structure. We will solve the P 2<sub>1</sub>/c structure 1058 first.</p> 1059 1060 <p class=MsoNormal><o:p> </o:p></p> 152 structure factors to solve the structure of dipyridyl disulfide by charge flipping 153 and then refine the structure by least-squares. The structure will be completed 154 by adding the requisite hydrogen atoms and by using anisotropic thermal 155 parameters for the heavier atoms. The structure was originally solved by 156 Raghavan & Seff, Acta Cryst. B33, 386-391 (1977) in the space group P2<sub>1</sub>/c 157 with one disordered pyridine ring with indications that the true space group 158 was P2<sub>1</sub>. It was subsequently reinvestigated by Young (2014 159 .) who 160 found that the true space group was P2<sub>1</sub> with 4 molecules in the 161 asymmetric unit. The data used in the latter analysis is what is used here and 162 is provided as a fcf file obtained after structure analysis by Shelx-97; the 163 structure factors are scaled to those calculated from the structure. We will 164 solve the P 2<sub>1</sub>/c structure first.</p> 165 166 <p class=MsoNormal> </p> 1061 167 1062 168 <p class=MsoNormal>Note that menu entries and user input are shown in bold face 1063 below as <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1064 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family: 1065 Calibri;mso-bidi-theme-font:minor-latin'>Help/About GSAS-II</span></b>, which 1066 lists first the name of the menu (here <b style='mso-bidi-font-weight:normal'><span 1067 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1068 mso-hansi-theme-font:minor-latin;mso-bidi-font-family:Calibri;mso-bidi-theme-font: 1069 minor-latin'>Help</span></b>) and second the name of the entry in the menu 1070 (here <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1071 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family: 1072 Calibri;mso-bidi-theme-font:minor-latin'>About GSAS-II</span></b>). If you have 1073 not done so already, start GSAS-II</p> 169 below as <b><span style='font-family:"Calibri",sans-serif'>Help/About GSAS-II</span></b>, 170 which lists first the name of the menu (here <b><span style='font-family:"Calibri",sans-serif'>Help</span></b>) 171 and second the name of the entry in the menu (here <b><span style='font-family: 172 "Calibri",sans-serif'>About GSAS-II</span></b>). If you have not done so 173 already, start GSAS-II</p> 1074 174 1075 175 <h2>Step 1. Input phase information</h2> 1076 176 1077 <p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo1'><![if !supportLists]><span 1078 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>1.<span 1079 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]>Use 1080 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1081 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin;mso-bidi-font-family: 1082 Calibri;mso-bidi-theme-font:minor-latin'>Data/Add phase</span></b> menu item 1083 add a new phase into the current GSAS-II project. A popup window will appear 1084 asking for a phase name; I entered <b style='mso-bidi-font-weight:normal'><span 1085 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1086 mso-hansi-theme-font:minor-latin'>SS <span class=SpellE>dipyridyl</span></span></b>; 1087 press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1088 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b> 1089 when done. Select <b style='mso-bidi-font-weight:normal'><span 1090 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1091 mso-hansi-theme-font:minor-latin'>Loaded Data/Phases/SS <span class=SpellE>dipyridyl</span></span></b> 1092 from the GSAS-II Data tree window. The General tab for Phase Data will appear.</p> 1093 1094 <p class=MsoListParagraph><span style='mso-no-proof:yes'><v:shapetype id="_x0000_t75" 1095 coordsize="21600,21600" o:spt="75" o:preferrelative="t" path="m@4@5l@4@11@9@11@9@5xe" 1096 filled="f" stroked="f"> 1097 <v:stroke joinstyle="miter"/> 1098 <v:formulas> 1099 <v:f eqn="if lineDrawn pixelLineWidth 0"/> 1100 <v:f eqn="sum @0 1 0"/> 1101 <v:f eqn="sum 0 0 @1"/> 1102 <v:f eqn="prod @2 1 2"/> 1103 <v:f eqn="prod @3 21600 pixelWidth"/> 1104 <v:f eqn="prod @3 21600 pixelHeight"/> 1105 <v:f eqn="sum @0 0 1"/> 1106 <v:f eqn="prod @6 1 2"/> 1107 <v:f eqn="prod @7 21600 pixelWidth"/> 1108 <v:f eqn="sum @8 21600 0"/> 1109 <v:f eqn="prod @7 21600 pixelHeight"/> 1110 <v:f eqn="sum @10 21600 0"/> 1111 </v:formulas> 1112 <v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/> 1113 <o:lock v:ext="edit" aspectratio="t"/> 1114 </v:shapetype><v:shape id="Picture_x0020_1" o:spid="_x0000_i1042" type="#_x0000_t75" 1115 style='width:393pt;height:230.25pt;visibility:visible;mso-wrap-style:square'> 1116 <v:imagedata src="CFSingleCrystal_files/image001.png" o:title=""/> 1117 </v:shape></span></p> 1118 1119 <p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo1'><![if !supportLists]><span 1120 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>2.<span 1121 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]>Enter 1122 the space group <b style='mso-bidi-font-weight:normal'><span style='font-family: 1123 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 1124 minor-latin'>P 21/c</span></b> (dont forget the space between P & 21/c) 1125 & press <b style='mso-bidi-font-weight:normal'><span style='font-family: 1126 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 1127 minor-latin'>Enter</span></b>. A Space Group Information popup window will 1128 appear; press <b style='mso-bidi-font-weight:normal'><span style='font-family: 1129 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 1130 minor-latin'>OK</span></b>. The General window will be refreshed showing only 1131 the needed lattice <span style='mso-no-proof:yes'>parameters for P 21/c.</span></p> 1132 1133 <p class=MsoListParagraph><span style='mso-no-proof:yes'><v:shape id="Picture_x0020_3" 1134 o:spid="_x0000_i1041" type="#_x0000_t75" style='width:391.5pt;height:270.75pt; 1135 visibility:visible;mso-wrap-style:square'> 1136 <v:imagedata src="CFSingleCrystal_files/image002.png" o:title=""/> 1137 </v:shape></span></p> 1138 1139 <p class=MsoListParagraph style='text-indent:-.25in;mso-list:l0 level1 lfo1'><![if !supportLists]><span 1140 style='mso-fareast-font-family:"Times New Roman"'><span style='mso-list:Ignore'>3.<span 1141 style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]>Enter 1142 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1143 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>15.8489</span></b>, 1144 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1145 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>5.5008</span></b>, 1146 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1147 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>23.118</span></b>, 1148 and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1149 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>96.9160</span></b> 1150 for a, b, c and beta, respectively; the unit cell volume will be recalculated 1151 at each entry.</p> 177 <p class=MsoListParagraph style='text-indent:-.25in'>1.<span style='font:7.0pt "Times New Roman"'> 178 </span>Use the <b><span style='font-family:"Calibri",sans-serif'>Data/Add phase</span></b> 179 menu item add a new phase into the current GSAS-II project. A popup window will 180 appear asking for a phase name; I entered <b><span style='font-family:"Calibri",sans-serif'>SS 181 dipyridyl</span></b>; press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b> 182 when done. Select <b><span style='font-family:"Calibri",sans-serif'>Loaded 183 Data/Phases/SS dipyridyl</span></b> from the GSAS-II Data tree window. The 184 General tab for Phase Data will appear.</p> 185 186 <p class=MsoListParagraph><img width=524 height=307 id="Picture 1" 187 src="CFSingleCrystal_files/image001.png"></p> 188 189 <p class=MsoListParagraph style='text-indent:-.25in'>2.<span style='font:7.0pt "Times New Roman"'> 190 </span>Enter the space group <b><span style='font-family:"Calibri",sans-serif'>P 191 21/c</span></b> (dont forget the space between P & 21/c) & press <b><span 192 style='font-family:"Calibri",sans-serif'>Enter</span></b>. A Space Group 193 Information popup window will appear; press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>. 194 The General window will be refreshed showing only the needed lattice parameters 195 for P 21/c.</p> 196 197 <p class=MsoListParagraph><img width=522 height=361 id="Picture 3" 198 src="CFSingleCrystal_files/image002.png"></p> 199 200 <p class=MsoListParagraph style='text-indent:-.25in'>3.<span style='font:7.0pt "Times New Roman"'> 201 </span>Enter <b><span style='font-family:"Calibri",sans-serif'>15.8489</span></b>, 202 <b><span style='font-family:"Calibri",sans-serif'>5.5008</span></b>, <b><span 203 style='font-family:"Calibri",sans-serif'>23.118</span></b>, and <b><span 204 style='font-family:"Calibri",sans-serif'>96.9160</span></b> for a, b, c and 205 beta, respectively; the unit cell volume will be recalculated at each entry.</p> 1152 206 1153 207 <h2>Step 2. Import structure factors </h2> … … 1156 210 and the second is to connect the data with the phase within GSAS-II.</p> 1157 211 1158 <p class=MsoNormal>To do these, do <b style='mso-bidi-font-weight:normal'><span 1159 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1160 mso-hansi-theme-font:minor-latin'>Import/Structure factor/from CIF file</span></b> 1161 from the main GSAS-II data tree window menu. A file selection dialog will 1162 appear; find <b style='mso-bidi-font-weight:normal'><span style='font-family: 1163 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 1164 minor-latin'>exercises\CF <span class=SpellE>Xray</span> single 1165 crystal\S2dipyridyl.fcf</span></b> and press <b style='mso-bidi-font-weight: 1166 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1167 minor-latin;mso-hansi-theme-font:minor-latin'>Open</span></b>. A popup window 1168 asking if this is the file you want; press <span class=GramE><b 1169 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1170 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Yes</span></b></span>. 212 <p class=MsoNormal>To do these, do <b><span style='font-family:"Calibri",sans-serif'>Import/Structure 213 factor/from CIF file</span></b> from the main GSAS-II data tree window menu. A 214 file selection dialog will appear; find <b><span style='font-family:"Calibri",sans-serif'>exercises\CF 215 Xray single crystal\S2dipyridyl.fcf</span></b> and press <b><span 216 style='font-family:"Calibri",sans-serif'>Open</span></b>. A popup window asking 217 if this is the file you want; press <b><span style='font-family:"Calibri",sans-serif'>Yes</span></b>. 1171 218 After a pause while the file is read a new popup will appear offering the 1172 chance to rename the structure factor set; press <b style='mso-bidi-font-weight: 1173 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1174 minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>. After some time a 1175 new popup will appear to <span style='mso-bidi-font-family:"Times New Roman"'>Add 1176 the new structure factor set</span> to the SS <span class=SpellE>dipyridyl</span> 1177 phase. Select the phase and press <b style='mso-bidi-font-weight:normal'><span 1178 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1179 mso-hansi-theme-font:minor-latin'>OK</span></b>. The plot will show a rectangular 1180 array of circles for the hk0 reflection layer; select the plot & press <b 1181 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1182 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>k</span></b> 219 chance to rename the structure factor set; press <b><span style='font-family: 220 "Calibri",sans-serif'>OK</span></b>. After some time a new popup will appear to 221 Add the new structure factor set to the SS dipyridyl phase. Select the phase 222 and press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>. The 223 plot will show a rectangular array of circles for the hk0 reflection layer; 224 select the plot & press <b><span style='font-family:"Calibri",sans-serif'>k</span></b> 1183 225 to get an h0l layer.</p> 1184 226 1185 <p class=MsoNormal><span style='mso-no-proof:yes'><v:shape id="Picture_x0020_2" 1186 o:spid="_x0000_i1040" type="#_x0000_t75" style='width:5in;height:309pt; 1187 visibility:visible;mso-wrap-style:square'> 1188 <v:imagedata src="CFSingleCrystal_files/image003.png" o:title=""/> 1189 </v:shape></span></p> 1190 1191 <p class=MsoNormal>Because the <span class=SpellE>fcf</span> file has both 1192 observed and calculated structure factors, the plot shows a small R value for 1193 the layer. The observed structure factors are shown as blue rings, the 1194 calculated ones as green rings and a small green or red dot may appear at each 1195 ring center showing <span class=SpellE>F<sub>o</sub></span>-F<sub>c</sub>. If 1196 the reflection data file had only observed structure factors then only blue 1197 rings will be seen. You can explore the plot options in the <b 1198 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1199 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>K</span></b> 1200 box in the plot toolbar.</p> 227 <p class=MsoNormal><img width=480 height=412 id="Picture 2" 228 src="CFSingleCrystal_files/image003.png"></p> 229 230 <p class=MsoNormal>Because the fcf file has both observed and calculated 231 structure factors, the plot shows a small R value for the layer. The observed 232 structure factors are shown as blue rings, the calculated ones as green rings 233 and a small green or red dot may appear at each ring center showing F<sub>o</sub>-F<sub>c</sub>. 234 If the reflection data file had only observed structure factors then only blue 235 rings will be seen. You can explore the plot options in the <b><span 236 style='font-family:"Calibri",sans-serif'>K</span></b> box in the plot toolbar.</p> 1201 237 1202 238 <h2>Step 3. Setup for charge flipping</h2> … … 1205 241 flipping. Charge flipping in GSAS-II is implemented to solve the crystal 1206 242 structure without consideration of space group symmetry. To do this it operates 1207 on the entire unit cell volume to a selected resolution (usually 0.5<span 1208 style='mso-bidi-font-family:"Times New Roman"'>Å</span>) using fast <span 1209 class=SpellE><span class=GramE>fourier</span></span> transform techniques. This 1210 requires a set of structure factors in an array of the same dimensions as the 1211 density array covering the unit cell (i.e. a box bounded by ~0.5<span 1212 style='mso-bidi-font-family:"Times New Roman"'>Å</span> resolution). The space 1213 group symmetry is applied to the observed structure factors to create a full 1214 sphere which is then zero filled out to the 0.5<span style='mso-bidi-font-family: 1215 "Times New Roman"'>Å</span> resolution bounded box. To be reasonably assured of 1216 success, the observed structure factors should extend to ~1<span 1217 style='mso-bidi-font-family:"Times New Roman"'>Å</span> resolution; we have 1218 that here for this example. To begin select <b style='mso-bidi-font-weight: 1219 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1220 minor-latin;mso-hansi-theme-font:minor-latin'>Phases/SS <span class=SpellE>dipyridyl</span></span></b> 1221 from the GSAS-II data tree; the General tab will be shown</p> 1222 1223 <p class=MsoNormal><span style='mso-no-proof:yes'><v:shape id="Picture_x0020_4" 1224 o:spid="_x0000_i1039" type="#_x0000_t75" style='width:468pt;height:300.75pt; 1225 visibility:visible;mso-wrap-style:square'> 1226 <v:imagedata src="CFSingleCrystal_files/image004.png" o:title=""/> 1227 </v:shape></span></p> 1228 1229 <p class=MsoNormal>Find the <b style='mso-bidi-font-weight:normal'><span 1230 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1231 mso-hansi-theme-font:minor-latin'>Fourier map controls</span></b> and change 1232 the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1233 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Peak cutoff 1234 %</span></b> to <b style='mso-bidi-font-weight:normal'><span style='font-family: 1235 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 1236 minor-latin'>10</span></b>; then immediately below find the <b 1237 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1238 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Charge flip 1239 controls</span></b>. Press <b style='mso-bidi-font-weight:normal'><span 1240 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1241 mso-hansi-theme-font:minor-latin'>Select reflection sets</span></b>, pick <b 1242 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1243 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>HKLF 1244 S2dipyridyl.fcf:1a</span></b> from the list (the only one) and press <b 1245 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1246 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>. 1247 If you had multiple data sets for this phase, you can pick more than one and 1248 GSAS-II will use a last one in process for assembling the reflection set to 1249 use for charge flipping. There are four more settings to consider: 1) <span 1250 class=SpellE>kMax</span> controls the upper cutoff for charge flipping; if the 1251 density is > k-Max*<span style='font-family:Symbol'>s</span><sub><span 1252 style='font-family:Symbol;mso-bidi-font-family:"Times New Roman"'>r</span></sub> 243 on the entire unit cell volume to a selected resolution (usually 0.5Å) using 244 fast fourier transform techniques. This requires a set of structure factors in 245 an array of the same dimensions as the density array covering the unit cell 246 (i.e. a box bounded by ~0.5Å resolution). The space group symmetry is applied 247 to the observed structure factors to create a full sphere which is then zero 248 filled out to the 0.5Å resolution bounded box. To be reasonably assured of 249 success, the observed structure factors should extend to ~1Å resolution; we 250 have that here for this example. To begin select <b><span style='font-family: 251 "Calibri",sans-serif'>Phases/SS dipyridyl</span></b> from the GSAS-II data 252 tree; the General tab will be shown</p> 253 254 <p class=MsoNormal><img width=624 height=401 id="Picture 4" 255 src="CFSingleCrystal_files/image004.png"></p> 256 257 <p class=MsoNormal>Find the <b><span style='font-family:"Calibri",sans-serif'>Fourier 258 map controls</span></b> and change the <b><span style='font-family:"Calibri",sans-serif'>Peak 259 cutoff %</span></b> to <b><span style='font-family:"Calibri",sans-serif'>10</span></b>; 260 then immediately below find the <b><span style='font-family:"Calibri",sans-serif'>Charge 261 flip controls</span></b>. Press <b><span style='font-family:"Calibri",sans-serif'>Select 262 reflection sets</span></b>, pick <b><span style='font-family:"Calibri",sans-serif'>HKLF 263 S2dipyridyl.fcf:1a</span></b> from the list (the only one) and press <b><span 264 style='font-family:"Calibri",sans-serif'>OK</span></b>. If you had multiple 265 data sets for this phase, you can pick more than one and GSAS-II will use a 266 last one in process for assembling the reflection set to use for charge 267 flipping. There are four more settings to consider: 1) kMax controls the upper 268 cutoff for charge flipping; if the density is > k-Max*<span 269 style='font-family:Symbol'>s</span><sub><span style='font-family:Symbol'>r</span></sub> 1253 270 (map standard deviation) then flip the charge. This prevents the Uranium 1254 271 solution sometimes found where all the density is concentrated in a single 1255 272 peak. A useful guide is to use twice the largest atomic number of any element 1256 273 in your structure. For equal atom problems use 12-15; adjust upward for 1257 structures with heavy & light atoms. In this case, set <b style='mso-bidi-font-weight: 1258 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1259 minor-latin;mso-hansi-theme-font:minor-latin'>k-Max</span></b> to <b 1260 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1261 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>30.0</span></b> 1262 to allow the S atom to appear. 2) k-Factor controls the lower level for charge 1263 flipping; if the density is < k-Factor*<span style='font-family:Symbol'>s</span><sub><span 1264 style='font-family:Symbol;mso-bidi-font-family:"Times New Roman"'>r</span></sub><span 1265 style='mso-bidi-font-family:"Times New Roman"'> then flip the charge. The 1266 default value seems to work pretty well; Id only change it if the charge 1267 flipping is having trouble solving the structure. 3) Resolution selects the 1268 spacing between map points. 0.5Å is sufficient in most cases. Choosing a 1269 smaller value requires more map points (NB: GSAS-II uses the entire unit cell 1270 volume for charge flipping) and thus will require more structure factors since 1271 the fast <span class=SpellE>fourier</span> algorithm requires the same size 1272 arrays in both real space and reciprocal space. This will slow down the charge 1273 flip process. 4) Normalizing element selects a form factor to rescale the 1274 structure factors thus sharpening the density map. I suggest trying </span><span 1275 class=GramE><b style='mso-bidi-font-weight:normal'><span style='font-family: 1276 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 1277 minor-latin;mso-bidi-font-family:"Times New Roman"'>None</span></b></span><span 1278 style='mso-bidi-font-family:"Times New Roman"'> first, otherwise select a 1279 representative element (really doesnt matter which).<o:p></o:p></span></p> 274 structures with heavy & light atoms. In this case, set <b><span 275 style='font-family:"Calibri",sans-serif'>k-Max</span></b> to <b><span 276 style='font-family:"Calibri",sans-serif'>30.0</span></b> to allow the S atom to 277 appear. 2) k-Factor controls the lower level for charge flipping; if the 278 density is < k-Factor*<span style='font-family:Symbol'>s</span><sub><span 279 style='font-family:Symbol'>r</span></sub> then flip the charge. The default 280 value seems to work pretty well; Id only change it if the charge flipping is 281 having trouble solving the structure. 3) Resolution selects the spacing between 282 map points. 0.5Å is sufficient in most cases. Choosing a smaller value requires 283 more map points (NB: GSAS-II uses the entire unit cell volume for charge 284 flipping) and thus will require more structure factors since the fast fourier 285 algorithm requires the same size arrays in both real space and reciprocal 286 space. This will slow down the charge flip process. 4) Normalizing element 287 selects a form factor to rescale the structure factors thus sharpening the 288 density map. I suggest trying <b><span style='font-family:"Calibri",sans-serif'>None</span></b> 289 first, otherwise select a representative element (really doesnt matter which).</p> 1280 290 1281 291 <h2 style='page-break-after:avoid'>Step 4. Charge flipping</h2> 1282 292 1283 293 <p class=MsoNormal>With the controls all set you can now do charge flipping; 1284 from the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1285 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>General</span></b> 1286 tab do <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1287 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Compute/Charge 294 from the <b><span style='font-family:"Calibri",sans-serif'>General</span></b> 295 tab do <b><span style='font-family:"Calibri",sans-serif'>Compute/Charge 1288 296 flipping</span></b>. A progress bar popup will appear showing the residual 1289 between the observed structure factors and those obtained from the inverse <span 1290 class=SpellE><span class=GramE>fourier</span></span> transform of the last 1291 flipped density map. It should quickly decrease to the ~20% range and level out 1292 indicating a good charge flip solution. When it has reached this, press <span 1293 class=GramE><b style='mso-bidi-font-weight:normal'><span style='font-family: 1294 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 1295 minor-latin'>Cancel</span></b></span> to stop the process.</p> 1296 1297 <p class=MsoNormal><span style='mso-no-proof:yes'><v:shape id="Picture_x0020_6" 1298 o:spid="_x0000_i1038" type="#_x0000_t75" style='width:274.5pt;height:135pt; 1299 visibility:visible;mso-wrap-style:square'> 1300 <v:imagedata src="CFSingleCrystal_files/image005.png" o:title=""/> 1301 </v:shape></span></p> 297 between the observed structure factors and those obtained from the inverse 298 fourier transform of the last flipped density map. It should quickly decrease 299 to the ~20% range and level out indicating a good charge flip solution. When it 300 has reached this, press <b><span style='font-family:"Calibri",sans-serif'>Cancel</span></b> 301 to stop the process.</p> 302 303 <p class=MsoNormal><img width=366 height=180 id="Picture 6" 304 src="CFSingleCrystal_files/image005.png"></p> 1302 305 1303 306 <p class=MsoNormal>The console window will show something like</p> 1304 307 1305 <p class=MsoNormal><span style='mso-no-proof:yes'><v:shape id="Picture_x0020_7" 1306 o:spid="_x0000_i1037" type="#_x0000_t75" style='width:468pt;height:124.5pt; 1307 visibility:visible;mso-wrap-style:square'> 1308 <v:imagedata src="CFSingleCrystal_files/image006.png" o:title=""/> 1309 </v:shape></span></p> 1310 1311 <p class=MsoNormal>There may be a pause at <b style='mso-bidi-font-weight:normal'><span 1312 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1313 mso-hansi-theme-font:minor-latin'>Begin <span class=SpellE><span class=GramE>fourier</span></span> 1314 map search</span></b> before it finishes. Provided is a summary of the charge 1315 flip calculation (time, map size, density range & structure factor 308 <p class=MsoNormal><img width=624 height=166 id="Picture 7" 309 src="CFSingleCrystal_files/image006.png"></p> 310 311 <p class=MsoNormal>There may be a pause at <b><span style='font-family:"Calibri",sans-serif'>Begin 312 fourier map search</span></b> before it finishes. Provided is a summary of the 313 charge flip calculation (time, map size, density range & structure factor 1316 314 residual). The map offset is discovered by an analysis of the reflection phases 1317 315 with respect to how they should be distributed for your chosen space group. … … 1322 320 the structure is drawn (Ive made the view down the b-axis)</p> 1323 321 1324 <p class=MsoNormal><span style='mso-no-proof:yes'><v:shape id="Picture_x0020_11" 1325 o:spid="_x0000_i1036" type="#_x0000_t75" style='width:358.5pt;height:301.5pt; 1326 visibility:visible;mso-wrap-style:square'> 1327 <v:imagedata src="CFSingleCrystal_files/image007.png" o:title="" croptop="12490f" 1328 cropbottom="16795f" cropleft="47577f" cropright="3045f"/> 1329 </v:shape></span></p> 1330 1331 <p class=MsoNormal><span style='mso-spacerun:yes'> </span><span class=GramE>and</span> 1332 the Phase data window will show the map peaks tab</p> 1333 1334 <p class=MsoNormal><span style='mso-no-proof:yes'><v:shape id="Picture_x0020_12" 1335 o:spid="_x0000_i1035" type="#_x0000_t75" style='width:375pt;height:225pt; 1336 visibility:visible;mso-wrap-style:square'> 1337 <v:imagedata src="CFSingleCrystal_files/image008.png" o:title=""/> 1338 </v:shape></span></p> 1339 1340 <p class=MsoNormal>These are listed in order of magnitude; a double click on any 1341 of the table headings will sort the list according to that parameter. My list 1342 has 112 entries; <span class=SpellE>dipyridyl</span> disulfide has 14 C & S 1343 atoms so this list is appropriate for 8 molecules in the unit cell and thus all 1344 atoms were found in this charge flipping result.</p> 322 <p class=MsoNormal><img width=478 height=402 id="Picture 11" 323 src="CFSingleCrystal_files/image007.jpg"></p> 324 325 <p class=MsoNormal> and the Phase data window will show the map peaks tab</p> 326 327 <p class=MsoNormal><img width=500 height=300 id="Picture 12" 328 src="CFSingleCrystal_files/image008.png"></p> 329 330 <p class=MsoNormal>These are listed in order of magnitude; a double click on 331 any of the table headings will sort the list according to that parameter. My 332 list has 112 entries; dipyridyl disulfide has 14 C & S atoms so this list 333 is appropriate for 8 molecules in the unit cell and thus all atoms were found 334 in this charge flipping result.</p> 1345 335 1346 336 <p class=MsoNormal>If all went well then the drawing should nicely show all the 1347 atoms in the structure placed properly with respect to the locations of the inversion 1348 centers (they are at all the corners, edge centers, face centers and cell 1349 center). If not then you can shift the map & peaks with the <b 1350 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1351 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>L</span></b>, 1352 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1353 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>R</span></b>, 1354 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1355 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>U</span></b> 1356 & <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1357 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>D</span></b> 1358 keys (NB: rotate the drawing so the axes are ~horizontal/vertical); the 1359 map/peaks will move in resolution steps (0.5A). The table is also updated with 1360 new peak positions. You could also just repeat the charge flipping and hope to 1361 get a better map offset solution (examine the map offset chi**2 to get a sense 1362 of this). You can also show the map density (highest point is shown as a green 1363 dot somewhere in the map on <span class=GramE>a</span> S-atom position); 1364 select the <b style='mso-bidi-font-weight:normal'><span style='font-family: 1365 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 1366 minor-latin'>Draw Options</span></b> tab and use the <b style='mso-bidi-font-weight: 1367 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1368 minor-latin;mso-hansi-theme-font:minor-latin'>Contour level</span></b> slider. 1369 The drawing will show green dots at each set map point with size in proportion 1370 to the density. The mouse <b style='mso-bidi-font-weight:normal'><span 1371 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1372 mso-hansi-theme-font:minor-latin'>RB</span></b> can be used to slide the 1373 structure around; the density is always drawn in a space surrounding the view 1374 point (multicolored cross at the center). While here you can also change the <b 1375 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1376 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Bond search 1377 factor</span></b> to <b style='mso-bidi-font-weight:normal'><span 1378 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1379 mso-hansi-theme-font:minor-latin'>0.90</span></b> to ensure all S-C bonds are 1380 shown.</p> 337 atoms in the structure placed properly with respect to the locations of the 338 inversion centers (they are at all the corners, edge centers, face centers and 339 cell center). If not then you can shift the map & peaks with the <b><span 340 style='font-family:"Calibri",sans-serif'>L</span></b>, <b><span 341 style='font-family:"Calibri",sans-serif'>R</span></b>, <b><span 342 style='font-family:"Calibri",sans-serif'>U</span></b> & <b><span 343 style='font-family:"Calibri",sans-serif'>D</span></b> keys (NB: rotate the 344 drawing so the axes are ~horizontal/vertical); the map/peaks will move in 345 resolution steps (0.5A). The table is also updated with new peak positions. You 346 could also just repeat the charge flipping and hope to get a better map offset 347 solution (examine the map offset chi**2 to get a sense of this). You can also 348 show the map density (highest point is shown as a green dot somewhere in the 349 map on a S-atom position); select the <b><span style='font-family:"Calibri",sans-serif'>Draw 350 Options</span></b> tab and use the <b><span style='font-family:"Calibri",sans-serif'>Contour 351 level</span></b> slider. The drawing will show green dots at each set map point 352 with size in proportion to the density. The mouse <b><span style='font-family: 353 "Calibri",sans-serif'>RB</span></b> can be used to slide the structure around; 354 the density is always drawn in a space surrounding the view point (multicolored 355 cross at the center). While here you can also change the <b><span 356 style='font-family:"Calibri",sans-serif'>Bond search factor</span></b> to <b><span 357 style='font-family:"Calibri",sans-serif'>0.90</span></b> to ensure all S-C 358 bonds are shown.</p> 1381 359 1382 360 <p class=MsoNormal>If the charge flipping has failed (high residual & no … … 1384 362 new random start for the structure factor phases which may lead to a good 1385 363 solution. After a few attempts, you can try different control settings to see 1386 if that will coax out a good solution; first be sure <b style='mso-bidi-font-weight: 1387 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1388 minor-latin;mso-hansi-theme-font:minor-latin'>k-Max</span></b> is properly set 1389 and then perhaps try different <b style='mso-bidi-font-weight:normal'><span 1390 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1391 mso-hansi-theme-font:minor-latin'>k-Factors</span></b> and do <b 1392 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1393 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Normalizing</span></b> 364 if that will coax out a good solution; first be sure <b><span style='font-family: 365 "Calibri",sans-serif'>k-Max</span></b> is properly set and then perhaps try 366 different <b><span style='font-family:"Calibri",sans-serif'>k-Factors</span></b> 367 and do <b><span style='font-family:"Calibri",sans-serif'>Normalizing</span></b> 1394 368 by some element form factor. If it seemed to work but very few peaks were 1395 found, make sure <b style='mso-bidi-font-weight:normal'><span style='font-family: 1396 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 1397 minor-latin'>Peak cutoff</span></b> was properly set; you can then repeat the 1398 peak search by doing <b style='mso-bidi-font-weight:normal'><span 1399 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1400 mso-hansi-theme-font:minor-latin'>Compute/Search map</span></b>.</p> 369 found, make sure <b><span style='font-family:"Calibri",sans-serif'>Peak cutoff</span></b> 370 was properly set; you can then repeat the peak search by doing <b><span 371 style='font-family:"Calibri",sans-serif'>Compute/Search map</span></b>.</p> 1401 372 1402 373 <h2>Step 5. Extract solution and make molecules</h2> … … 1404 375 <p class=MsoNormal>Assuming that the map & peak positions are properly 1405 376 placed with respect to the symmetry elements of the space group, we can now 1406 select those peaks which describe the structure. Select the <b 1407 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1408 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map peaks</span></b> 1409 tab and double LB click the blank upper left corner of the table; all entries 1410 will be highlighted in blue. Then do <b style='mso-bidi-font-weight:normal'><span 1411 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1412 mso-hansi-theme-font:minor-latin'>Map peaks/Unique peaks</span></b>; after a 1413 bit of time 1/4 of the peaks in the list will be highlighted and the 1414 corresponding peaks in the drawing will be green (NB: if you navigate away from 1415 this tab, this selection will be lost and youll have to repeat it!). Next, do <b 1416 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1417 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map 1418 peaks/Move peaks</span></b>; these peaks will be transferred to the <b 1419 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1420 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Atoms</span></b> 1421 list as H-atoms named according to their position in the magnitude column.</p> 1422 1423 <p class=MsoNormal><span style='mso-no-proof:yes'><v:shape id="Picture_x0020_13" 1424 o:spid="_x0000_i1034" type="#_x0000_t75" style='width:468pt;height:200.25pt; 1425 visibility:visible;mso-wrap-style:square'> 1426 <v:imagedata src="CFSingleCrystal_files/image009.png" o:title=""/> 1427 </v:shape></span></p> 377 select those peaks which describe the structure. Select the <b><span 378 style='font-family:"Calibri",sans-serif'>Map peaks</span></b> tab and double LB 379 click the blank upper left corner of the table; all entries will be highlighted 380 in blue. Then do <b><span style='font-family:"Calibri",sans-serif'>Map 381 peaks/Unique peaks</span></b>; after a bit of time 1/4 of the peaks in the list 382 will be highlighted and the corresponding peaks in the drawing will be green 383 (NB: if you navigate away from this tab, this selection will be lost and youll 384 have to repeat it!). Next, do <b><span style='font-family:"Calibri",sans-serif'>Map 385 peaks/Move peaks</span></b>; these peaks will be transferred to the <b><span 386 style='font-family:"Calibri",sans-serif'>Atoms</span></b> list as H-atoms named 387 according to their position in the magnitude column.</p> 388 389 <p class=MsoNormal><img width=624 height=267 id="Picture 13" 390 src="CFSingleCrystal_files/image009.png"></p> 1428 391 1429 392 <p class=MsoNormal>The drawing will show white balls at the atom positions 1430 393 scattered over several molecules.</p> 1431 394 1432 <p class=MsoNormal><span style='mso-no-proof:yes'><v:shape id="Picture_x0020_14" 1433 o:spid="_x0000_i1033" type="#_x0000_t75" style='width:355.5pt;height:306.75pt; 1434 visibility:visible;mso-wrap-style:square'> 1435 <v:imagedata src="CFSingleCrystal_files/image010.png" o:title="" croptop="9479f" 1436 cropbottom="18319f" cropleft="42631f" cropright="7857f"/> 1437 </v:shape></span></p> 395 <p class=MsoNormal><img width=474 height=409 id="Picture 14" 396 src="CFSingleCrystal_files/image010.jpg"></p> 1438 397 1439 398 <p class=MsoNormal>Notice that 4 atoms have magnitudes ~90+, these are the S 1440 atoms. The rest are C & N atoms. In the <b style='mso-bidi-font-weight: 1441 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1442 minor-latin;mso-hansi-theme-font:minor-latin'>Atoms</span></b> tab select the 1443 first 4 atoms (press LB on the 1<sup>st</sup> & shift LB on the 4<sup>th</sup> 1444 one). Then do <b style='mso-bidi-font-weight:normal'><span style='font-family: 1445 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 1446 minor-latin'>Edit/Modify atom parameters</span></b>; a popup window will 1447 appear. Select <b style='mso-bidi-font-weight:normal'><span style='font-family: 1448 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 1449 minor-latin'>Type</span></b> & press <b style='mso-bidi-font-weight:normal'><span 1450 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1451 mso-hansi-theme-font:minor-latin'>OK</span></b>; a Periodic Table will appear. 1452 Select <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1453 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>S</span></b>; 1454 the atoms will be renames and their Type changed to S. Next select the remaining 1455 H atoms (a quick way it to double LB click the <b style='mso-bidi-font-weight: 1456 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1457 minor-latin;mso-hansi-theme-font:minor-latin'>Type</span></b> column heading 1458 and select <b style='mso-bidi-font-weight:normal'><span style='font-family: 1459 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 1460 minor-latin'>H</span></b> from the popup window). Then do <b style='mso-bidi-font-weight: 1461 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1462 minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Modify atom parameters</span></b> 1463 and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1464 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Type</span></b> 1465 from the popup; select <b style='mso-bidi-font-weight:normal'><span 1466 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1467 mso-hansi-theme-font:minor-latin'>C</span></b> from the Periodic Table as we 1468 dont know which ones are N. The drawing will change (you may have to wiggle it 1469 a bit to force the update).</p> 1470 1471 <p class=MsoNormal><span style='mso-no-proof:yes'><v:shape id="Picture_x0020_17" 1472 o:spid="_x0000_i1032" type="#_x0000_t75" style='width:5in;height:292.5pt; 1473 visibility:visible;mso-wrap-style:square'> 1474 <v:imagedata src="CFSingleCrystal_files/image011.png" o:title="" croptop="12086f" 1475 cropbottom="17505f" cropleft="42193f" cropright="8105f"/> 1476 </v:shape></span></p> 399 atoms. The rest are C & N atoms. In the <b><span style='font-family:"Calibri",sans-serif'>Atoms</span></b> 400 tab select the first 4 atoms (press LB on the 1<sup>st</sup> & shift LB on 401 the 4<sup>th</sup> one). Then do <b><span style='font-family:"Calibri",sans-serif'>Edit/Modify 402 atom parameters</span></b>; a popup window will appear. Select <b><span 403 style='font-family:"Calibri",sans-serif'>Type</span></b> & press <b><span 404 style='font-family:"Calibri",sans-serif'>OK</span></b>; a Periodic Table will 405 appear. Select <b><span style='font-family:"Calibri",sans-serif'>S</span></b>; 406 the atoms will be renames and their Type changed to S. Next select the 407 remaining H atoms (a quick way it to double LB click the <b><span 408 style='font-family:"Calibri",sans-serif'>Type</span></b> column heading and 409 select <b><span style='font-family:"Calibri",sans-serif'>H</span></b> from the 410 popup window). Then do <b><span style='font-family:"Calibri",sans-serif'>Edit/Modify 411 atom parameters</span></b> and <b><span style='font-family:"Calibri",sans-serif'>Type</span></b> 412 from the popup; select <b><span style='font-family:"Calibri",sans-serif'>C</span></b> 413 from the Periodic Table as we dont know which ones are N. The drawing will 414 change (you may have to wiggle it a bit to force the update).</p> 415 416 <p class=MsoNormal><img width=480 height=390 id="Picture 17" 417 src="CFSingleCrystal_files/image011.jpg"></p> 1477 418 1478 419 <p class=MsoNormal>Notice that the atoms are scattered over several molecules; 1479 420 we want to assemble them into 2 conveniently placed ones. Begin by selecting an 1480 atom (make sure the <b style='mso-bidi-font-weight:normal'><span 1481 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1482 mso-hansi-theme-font:minor-latin'>Atom</span></b> tab is displayed & do 1483 shift LB on an atom in the drawing I chose the S atom near the upper middle); 1484 it will turn green and a line in the Atom table will be highlighted. Next do <b 1485 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1486 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Assemble 1487 molecule</span></b>; a popup window will appear. Change the <b 1488 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1489 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Bond search 1490 factor</span></b> to <b style='mso-bidi-font-weight:normal'><span 1491 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1492 mso-hansi-theme-font:minor-latin'>0.90</span></b> to be sure all S-C bonds are 1493 found.</p> 1494 1495 <p class=MsoNormal><span style='mso-no-proof:yes'><v:shape id="Picture_x0020_16" 1496 o:spid="_x0000_i1031" type="#_x0000_t75" style='width:198.75pt;height:167.25pt; 1497 visibility:visible;mso-wrap-style:square'> 1498 <v:imagedata src="CFSingleCrystal_files/image012.png" o:title=""/> 1499 </v:shape></span><span style='mso-spacerun:yes'> </span></p> 1500 1501 <p class=MsoNormal>Press <b style='mso-bidi-font-weight:normal'><span 1502 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1503 mso-hansi-theme-font:minor-latin'>OK</span></b>; atoms will be collected into a 1504 <span class=SpellE>well positioned</span> group, but others are not. Next 1505 select one of the unassembled atoms (I chose a C-atom in a nearby SS-<span 1506 class=SpellE>dipyridyl</span>) and do <b style='mso-bidi-font-weight:normal'><span 1507 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1508 mso-hansi-theme-font:minor-latin'>Edit/Assemble molecule</span></b>; there will 1509 be two nicely assembled SS-<span class=SpellE>dipyridyls</span>.</p> 1510 1511 <p class=MsoNormal><span style='mso-no-proof:yes'><v:shape id="Picture_x0020_5" 1512 o:spid="_x0000_i1030" type="#_x0000_t75" style='width:5in;height:4in; 1513 visibility:visible;mso-wrap-style:square'> 1514 <v:imagedata src="CFSingleCrystal_files/image013.png" o:title="" croptop="11447f" 1515 cropbottom="19102f" cropleft="41491f" cropright="8984f"/> 1516 </v:shape></span></p> 421 atom (make sure the <b><span style='font-family:"Calibri",sans-serif'>Atom</span></b> 422 tab is displayed & do shift LB on an atom in the drawing I chose the S 423 atom near the upper middle); it will turn green and a line in the Atom table 424 will be highlighted. Next do <b><span style='font-family:"Calibri",sans-serif'>Edit/Assemble 425 molecule</span></b>; a popup window will appear. Change the <b><span 426 style='font-family:"Calibri",sans-serif'>Bond search factor</span></b> to <b><span 427 style='font-family:"Calibri",sans-serif'>0.90</span></b> to be sure all S-C 428 bonds are found.</p> 429 430 <p class=MsoNormal><img width=265 height=223 id="Picture 16" 431 src="CFSingleCrystal_files/image012.png"> </p> 432 433 <p class=MsoNormal>Press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>; 434 atoms will be collected into a well positioned group, but others are not. Next 435 select one of the unassembled atoms (I chose a C-atom in a nearby SS-dipyridyl) 436 and do <b><span style='font-family:"Calibri",sans-serif'>Edit/Assemble molecule</span></b>; 437 there will be two nicely assembled SS-dipyridyls.</p> 438 439 <p class=MsoNormal><img width=480 height=384 id="Picture 5" 440 src="CFSingleCrystal_files/image013.jpg"></p> 1517 441 1518 442 <p class=MsoNormal>You should probably save this project as it contains your … … 1522 446 1523 447 <p class=MsoNormal>Since we now have a structural model, we can do the initial 1524 structure refinement. By default this will only refine the scale factor; do <b 1525 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1526 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> 1527 from the main GSAS-II data tree window. Convergence will quickly occur with <span 1528 class=SpellE>Rw</span> ~35%. More useful is to refine the atom positions and 1529 isotropic thermal parameters. Select the <b style='mso-bidi-font-weight:normal'><span 1530 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1531 mso-hansi-theme-font:minor-latin'>Atoms</span></b> tab from the Phase window. 1532 Then LB double click the <b style='mso-bidi-font-weight:normal'><span 1533 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1534 mso-hansi-theme-font:minor-latin'>refine</span></b> column heading; a popup 1535 window will appear. Select <b style='mso-bidi-font-weight:normal'><span 1536 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1537 mso-hansi-theme-font:minor-latin'>X</span></b> and <b style='mso-bidi-font-weight: 1538 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1539 minor-latin;mso-hansi-theme-font:minor-latin'>U</span></b> and press <b 1540 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1541 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>. 1542 The <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1543 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Atoms</span></b> 1544 window will show <b style='mso-bidi-font-weight:normal'><span style='font-family: 1545 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 1546 minor-latin'>XU</span></b> for each atom in the refine column. Then do <b 1547 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1548 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b> 1549 (twice to get convergence) and the <span class=SpellE>Rw</span> ~12%.</p> 448 structure refinement. By default this will only refine the scale factor; do <b><span 449 style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b> from the 450 main GSAS-II data tree window. Convergence will quickly occur with Rw ~35%. 451 More useful is to refine the atom positions and isotropic thermal parameters. 452 Select the <b><span style='font-family:"Calibri",sans-serif'>Atoms</span></b> 453 tab from the Phase window. Then LB double click the <b><span style='font-family: 454 "Calibri",sans-serif'>refine</span></b> column heading; a popup window will 455 appear. Select <b><span style='font-family:"Calibri",sans-serif'>X</span></b> 456 and <b><span style='font-family:"Calibri",sans-serif'>U</span></b> and press <b><span 457 style='font-family:"Calibri",sans-serif'>OK</span></b>. The <b><span 458 style='font-family:"Calibri",sans-serif'>Atoms</span></b> window will show <b><span 459 style='font-family:"Calibri",sans-serif'>XU</span></b> for each atom in the 460 refine column. Then do <b><span style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b> 461 (twice to get convergence) and the Rw ~12%.</p> 1550 462 1551 463 <h2>Step 7. Determine C/N choice</h2> 1552 464 1553 465 <p class=MsoNormal>We know from the chemistry that the N atom is in the 2 1554 position of the pyridine ring, i.e. next to the point of attachment to the 1555 S-atom. However, we dont know which one that is and we have 8 atoms of which 4 1556 a re C and 4 are N.</p>466 position of the pyridine ring, i.e. next to the point of attachment to the S-atom. 467 However, we dont know which one that is and we have 8 atoms of which 4 are C 468 and 4 are N.</p> 1557 469 1558 470 <p class=MsoNormal>To work out the C/N problem above we need the atoms to be in 1559 471 a chemically sensible order. The assemble molecule routine did construct chains 1560 472 of atoms but this ordering is not really satisfactory. The ordering can quickly 1561 be done by hand by following a labelled drawing. First go to the <b 1562 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1563 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Draw Atoms</span></b> 1564 tab and double LB click the <b style='mso-bidi-font-weight:normal'><span 1565 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1566 mso-hansi-theme-font:minor-latin'>Style</span></b> column; select <b 1567 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1568 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>balls & 1569 sticks</span></b> from the popup box. Press <b style='mso-bidi-font-weight: 1570 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1571 minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>. Next, double LB 1572 click the <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1573 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Label</span></b> 1574 column and select <b style='mso-bidi-font-weight:normal'><span 1575 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1576 mso-hansi-theme-font:minor-latin'>name</span></b> from the popup box; press <b 1577 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1578 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>. 1579 Then go to the <b style='mso-bidi-font-weight:normal'><span style='font-family: 1580 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 1581 minor-latin'>Draw options</span></b> tab and adjust the <b style='mso-bidi-font-weight: 1582 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1583 minor-latin;mso-hansi-theme-font:minor-latin'>Ball scale</span></b> & <b 1584 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1585 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Bond radius </span></b>to 473 be done by hand by following a labelled drawing. First go to the <b><span 474 style='font-family:"Calibri",sans-serif'>Draw Atoms</span></b> tab and double 475 LB click the <b><span style='font-family:"Calibri",sans-serif'>Style</span></b> 476 column; select <b><span style='font-family:"Calibri",sans-serif'>balls & 477 sticks</span></b> from the popup box. Press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>. 478 Next, double LB click the <b><span style='font-family:"Calibri",sans-serif'>Label</span></b> 479 column and select <b><span style='font-family:"Calibri",sans-serif'>name</span></b> 480 from the popup box; press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>. 481 Then go to the <b><span style='font-family:"Calibri",sans-serif'>Draw options</span></b> 482 tab and adjust the <b><span style='font-family:"Calibri",sans-serif'>Ball scale</span></b> 483 & <b><span style='font-family:"Calibri",sans-serif'>Bond radius </span></b>to 1586 484 allow the labels to be easily seen. After shifting the view point the drawing 1587 485 should look something like</p> 1588 486 1589 <p class=MsoNormal><o:p> </o:p></p> 1590 1591 <p class=MsoNormal><span style='mso-no-proof:yes'><v:shape id="Picture_x0020_9" 1592 o:spid="_x0000_i1029" type="#_x0000_t75" style='width:355.5pt;height:289.5pt; 1593 visibility:visible;mso-wrap-style:square'> 1594 <v:imagedata src="CFSingleCrystal_files/image014.png" o:title="" croptop="11765f" 1595 cropbottom="18146f" cropleft="38895f" cropright="11572f"/> 1596 </v:shape></span></p> 1597 1598 <p class=MsoNormal>Now go to the <b style='mso-bidi-font-weight:normal'><span 1599 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1600 mso-hansi-theme-font:minor-latin'>Atoms</span></b> tab. If you look carefully, 1601 you can see that the atoms in each SS-<span class=SpellE>dipyridyl</span> are 1602 grouped together in the table but they are not in chemically sensible order. The 1603 atoms can be reordered by selecting one row with the <b style='mso-bidi-font-weight: 1604 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1605 minor-latin;mso-hansi-theme-font:minor-latin'>Alt</span></b> key down (the 1606 status line will tell which atom is selected to move) and then with the <b 1607 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1608 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Alt</span></b> 1609 key still down pick a row below where you want to insert it. I ordered them so 1610 each S-atom was followed by the C-atoms in order around the ring; my list 1611 looked like (I show just the 1<sup>st</sup> SS <span class=SpellE>dipyridyl</span> 1612 molecule)</p> 1613 1614 <p class=MsoNormal><span style='mso-no-proof:yes'><v:shape id="Picture_x0020_10" 1615 o:spid="_x0000_i1028" type="#_x0000_t75" style='width:468pt;height:306pt; 1616 visibility:visible;mso-wrap-style:square'> 1617 <v:imagedata src="CFSingleCrystal_files/image015.png" o:title=""/> 1618 </v:shape></span></p> 487 <p class=MsoNormal> </p> 488 489 <p class=MsoNormal><img width=474 height=386 id="Picture 9" 490 src="CFSingleCrystal_files/image014.jpg"></p> 491 492 <p class=MsoNormal>Now go to the <b><span style='font-family:"Calibri",sans-serif'>Atoms</span></b> 493 tab. If you look carefully, you can see that the atoms in each SS-dipyridyl are 494 grouped together in the table but they are not in chemically sensible order. 495 The atoms can be reordered by selecting one row with the <b><span 496 style='font-family:"Calibri",sans-serif'>Alt</span></b> key down (the status 497 line will tell which atom is selected to move) and then with the <b><span 498 style='font-family:"Calibri",sans-serif'>Alt</span></b> key still down pick a 499 row below where you want to insert it. I ordered them so each S-atom was 500 followed by the C-atoms in order around the ring; my list looked like (I show 501 just the 1<sup>st</sup> SS dipyridyl molecule)</p> 502 503 <p class=MsoNormal><img width=624 height=408 id="Picture 10" 504 src="CFSingleCrystal_files/image015.png"></p> 1619 505 1620 506 <p class=MsoNormal>Once you have reordered the atoms to your satisfaction they 1621 507 can be renamed to be in order. To do this select all the atoms (double LB click 1622 the empty corner box) and then do <b style='mso-bidi-font-weight:normal'><span 1623 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1624 mso-hansi-theme-font:minor-latin'>Edit/Modify atom parameters</span></b>. 1625 Select <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1626 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Name</span></b> 1627 and press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1628 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>; 1629 press <span class=GramE><b style='mso-bidi-font-weight:normal'><span 1630 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1631 mso-hansi-theme-font:minor-latin'>Yes</span></b></span> to the popup question. 1632 The atoms will be renamed in numerical order. Do <b style='mso-bidi-font-weight: 1633 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1634 minor-latin;mso-hansi-theme-font:minor-latin'>Edit/Reload draw atoms</span></b>; 1635 the labels will change. In my numbering scheme, half of the C3, C7, C10, C14, 1636 C17, C21, C24 and C28 carbon atoms are really nitrogen (if they are ordered). 1637 Select these and do <b style='mso-bidi-font-weight:normal'><span 1638 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1639 mso-hansi-theme-font:minor-latin'>Edit/Set atom refinement flags</span></b>; 1640 select <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1641 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>F</span></b>, 1642 <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1643 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>X</span></b> 1644 & <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1645 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>U</span></b> 1646 for these. Do <b style='mso-bidi-font-weight:normal'><span style='font-family: 1647 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 1648 minor-latin'>Calculate/Refine</span></b>; the <span class=SpellE>Rw</span> will 1649 drop to ~10% and 4 of the atom <span class=SpellE><b style='mso-bidi-font-weight: 1650 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1651 minor-latin;mso-hansi-theme-font:minor-latin'>frac</span></b></span> values 1652 will be ~1.25 while the others are ~1.0. The former are N-atoms and the latter 1653 are C-atoms. Change the <b style='mso-bidi-font-weight:normal'><span 1654 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1655 mso-hansi-theme-font:minor-latin'>Type</span></b> for the N-atoms and repeat <b 1656 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1657 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; 1658 the <span class=SpellE>Rw</span> will be high to start, but immediately fall to 1659 ~10%. In the Atom table all 8 refined <span class=SpellE>frac</span> values are 1660 be now ~1.0. To finish this part of the refinement, set all <span class=SpellE><b 1661 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1662 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>frac</span></b></span> 1663 values to <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1664 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>1.0</span></b> 1665 and all refine flags to <b style='mso-bidi-font-weight:normal'><span 1666 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1667 mso-hansi-theme-font:minor-latin'>XU</span></b>. Do <b style='mso-bidi-font-weight: 1668 normal'><span style='font-family:"Calibri",sans-serif;mso-ascii-theme-font: 1669 minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; the 1670 final <span class=SpellE>Rw</span> ~10.5%</p> 508 the empty corner box) and then do <b><span style='font-family:"Calibri",sans-serif'>Edit/Modify 509 atom parameters</span></b>. Select <b><span style='font-family:"Calibri",sans-serif'>Name</span></b> 510 and press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>; 511 press <b><span style='font-family:"Calibri",sans-serif'>Yes</span></b> to the 512 popup question. The atoms will be renamed in numerical order. Do <b><span 513 style='font-family:"Calibri",sans-serif'>Edit/Reload draw atoms</span></b>; the 514 labels will change. In my numbering scheme, half of the C3, C7, C10, C14, C17, 515 C21, C24 and C28 carbon atoms are really nitrogen (if they are ordered). Select 516 these and do <b><span style='font-family:"Calibri",sans-serif'>Edit/Set atom 517 refinement flags</span></b>; select <b><span style='font-family:"Calibri",sans-serif'>F</span></b>, 518 <b><span style='font-family:"Calibri",sans-serif'>X</span></b> & <b><span 519 style='font-family:"Calibri",sans-serif'>U</span></b> for these. Do <b><span 520 style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b>; the Rw 521 will drop to ~10% and 4 of the atom <b><span style='font-family:"Calibri",sans-serif'>frac</span></b> 522 values will be ~1.25 while the others are ~1.0. The former are N-atoms and the 523 latter are C-atoms. Change the <b><span style='font-family:"Calibri",sans-serif'>Type</span></b> 524 for the N-atoms and repeat <b><span style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b>; 525 the Rw will be high to start, but immediately fall to ~10%. In the Atom table 526 all 8 refined frac values are be now ~1.0. To finish this part of the 527 refinement, set all <b><span style='font-family:"Calibri",sans-serif'>frac</span></b> 528 values to <b><span style='font-family:"Calibri",sans-serif'>1.0</span></b> and 529 all refine flags to <b><span style='font-family:"Calibri",sans-serif'>XU</span></b>. 530 Do <b><span style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b>; 531 the final Rw ~10.5%</p> 1671 532 1672 533 <h2>Step 8. Anisotropic thermal motion refinement</h2> 1673 534 1674 535 <p class=MsoNormal>Given reasonable measured structure factors one can improve 1675 a crystal model by using anisotropic thermal motion models for all the <span 1676 class=SpellE>nonhydrogen</span> atoms. To convert all the atoms here select the 1677 Atoms tab and then do a double LB click on <span class=GramE>the I</span>/A 1678 column heading. Select Anisotropic from the popup and press OK; the Atom table 1679 will be redrawn with <span class=SpellE>Uij</span> values equivalent to the 1680 corresponding <span class=SpellE>Uiso</span> (now hidden). Do <b 1681 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1682 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; 1683 the final <span class=SpellE>Rw</span> ~8.2%</p> 536 a crystal model by using anisotropic thermal motion models for all the 537 nonhydrogen atoms. To convert all the atoms here select the Atoms tab and then 538 do a double LB click on the I/A column heading. Select Anisotropic from the 539 popup and press OK; the Atom table will be redrawn with Uij values equivalent 540 to the corresponding Uiso (now hidden). Do <b><span style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b>; 541 the final Rw ~8.2%</p> 1684 542 1685 543 <h2 style='page-break-after:avoid'>Step 9. H-atom placement & final … … 1688 546 <p class=MsoNormal>This structure can be completed by adding the 4 H-atoms per 1689 547 pyridine ring (16 in all). One could do this (painfully) by hand by looking for 1690 them in <span style='font-family:Symbol'>D</span>F maps, but it is simpler to 1691 just place them knowing the bonding chemistry of the rings. To start this 1692 select the <b style='mso-bidi-font-weight:normal'><span style='font-family: 1693 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 1694 minor-latin'>Atoms</span></b> tab for the phase. Then select the C-atoms by a 1695 double LB click on the <b style='mso-bidi-font-weight:normal'><span 1696 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1697 mso-hansi-theme-font:minor-latin'>Type</span></b> column heading and select <b 1698 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1699 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>C</span></b> 1700 from the popup; press <b style='mso-bidi-font-weight:normal'><span 1701 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1702 mso-hansi-theme-font:minor-latin'>OK</span></b>. The C-atoms will be 1703 highlighted. Next do <b style='mso-bidi-font-weight:normal'><span 1704 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1705 mso-hansi-theme-font:minor-latin'>Edit/Insert H atoms</span></b>; a <b 1706 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1707 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Distance 548 them in <span style='font-family:Symbol'>D</span>F maps, but it is simpler to just 549 place them knowing the bonding chemistry of the rings. To start this select the 550 <b><span style='font-family:"Calibri",sans-serif'>Atoms</span></b> tab for the 551 phase. Then select the C-atoms by a double LB click on the <b><span 552 style='font-family:"Calibri",sans-serif'>Type</span></b> column heading and 553 select <b><span style='font-family:"Calibri",sans-serif'>C</span></b> from the 554 popup; press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>. 555 The C-atoms will be highlighted. Next do <b><span style='font-family:"Calibri",sans-serif'>Edit/Insert 556 H atoms</span></b>; a <b><span style='font-family:"Calibri",sans-serif'>Distance 1708 557 Angle Controls</span></b> popup will appear; the numbers should be as before. 1709 Press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1710 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>OK</span></b>; 1711 a new popup will appear</p> 1712 1713 <p class=MsoNormal><span style='mso-no-proof:yes'><v:shape id="Picture_x0020_8" 1714 o:spid="_x0000_i1027" type="#_x0000_t75" style='width:300pt;height:363.75pt; 1715 visibility:visible;mso-wrap-style:square'> 1716 <v:imagedata src="CFSingleCrystal_files/image016.png" o:title=""/> 1717 </v:shape></span></p> 558 Press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>; a new 559 popup will appear</p> 560 561 <p class=MsoNormal><img width=400 height=485 id="Picture 8" 562 src="CFSingleCrystal_files/image016.png"></p> 1718 563 1719 564 <p class=MsoNormal>This is the hydrogen add control; it shows both the expected … … 1721 566 determine the geometry of the C-H bond. Check to make sure that 4 H-atoms will 1722 567 be added for each ring. Note that C2, C9, C16 & C23 will not have an H-atom 1723 added as these are the S-atom attachment points in SS-<span class=SpellE>dipyridyl</span>. 1724 Press <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1725 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Ok</span></b>; 1726 the H-atoms will be inserted immediately after the corresponding C-atoms and 1727 the drawing is updated showing van der Waals spheres for all atoms.</p> 1728 1729 <p class=MsoNormal><span style='mso-no-proof:yes'><v:shape id="Picture_x0020_15" 1730 o:spid="_x0000_i1026" type="#_x0000_t75" style='width:468pt;height:297pt; 1731 visibility:visible;mso-wrap-style:square'> 1732 <v:imagedata src="CFSingleCrystal_files/image017.png" o:title=""/> 1733 </v:shape></span></p> 1734 1735 <p class=MsoNormal><o:p> </o:p></p> 1736 1737 <p class=MsoNormal><span style='mso-no-proof:yes'><v:shape id="Picture_x0020_18" 1738 o:spid="_x0000_i1025" type="#_x0000_t75" style='width:362.25pt;height:295.5pt; 1739 visibility:visible;mso-wrap-style:square'> 1740 <v:imagedata src="CFSingleCrystal_files/image018.png" o:title="" croptop="12402f" 1741 cropbottom="17514f" cropleft="39344f" cropright="11175f"/> 1742 </v:shape></span></p> 1743 1744 <p class=MsoNormal>Next, do <b style='mso-bidi-font-weight:normal'><span 1745 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1746 mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; there will be an 1747 immediate drop in <span class=SpellE>Rw</span> ~3.2%. Note that we did not 1748 refine the H-atom positions or thermal parameters. The H-atom insertion process 1749 retains the mechanisms for creating them in the first place and these tools can 1750 be used to move them to reflect the changes in the C-atom parameters thus 1751 forcing them to ride on the C-atoms. Do <b style='mso-bidi-font-weight:normal'><span 1752 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1753 mso-hansi-theme-font:minor-latin'>Edit/Update H atoms</span></b>; the H-atom 1754 positions & <span class=SpellE>Uisos</span> will be <span class=GramE>revised.</span> 1755 Repeat <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1756 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Calculate/Refine</span></b>; 1757 there will be a slight improvement in <span class=SpellE>Rw</span>. Repeat 1758 these two steps (twice); <span class=SpellE>Rw</span> should not change on the 1759 last round. This completes the refinement of the SS-<span class=SpellE>dipyridyl</span> 568 added as these are the S-atom attachment points in SS-dipyridyl. Press <b><span 569 style='font-family:"Calibri",sans-serif'>Ok</span></b>; the H-atoms will be 570 inserted immediately after the corresponding C-atoms and the drawing is updated 571 showing van der Waals spheres for all atoms.</p> 572 573 <p class=MsoNormal><img width=624 height=396 id="Picture 15" 574 src="CFSingleCrystal_files/image017.png"></p> 575 576 <p class=MsoNormal> </p> 577 578 <p class=MsoNormal><img width=483 height=394 id="Picture 18" 579 src="CFSingleCrystal_files/image018.jpg"></p> 580 581 <p class=MsoNormal>Next, do <b><span style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b>; 582 there will be an immediate drop in Rw ~3.2%. Note that we did not refine the 583 H-atom positions or thermal parameters. The H-atom insertion process retains 584 the mechanisms for creating them in the first place and these tools can be used 585 to move them to reflect the changes in the C-atom parameters thus forcing them 586 to ride on the C-atoms. Do <b><span style='font-family:"Calibri",sans-serif'>Edit/Update 587 H atoms</span></b>; the H-atom positions & Uisos will be revised. Repeat <b><span 588 style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b>; there 589 will be a slight improvement in Rw. Repeat these two steps (twice); Rw should 590 not change on the last round. This completes the refinement of the SS-dipyridyl 1760 591 structure. You can generate a final <span style='font-family:Symbol'>D</span>F 1761 map from the <b style='mso-bidi-font-weight:normal'><span style='font-family: 1762 "Calibri",sans-serif;mso-ascii-theme-font:minor-latin;mso-hansi-theme-font: 1763 minor-latin'>General</span></b> tab; in <b style='mso-bidi-font-weight:normal'><span 1764 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1765 mso-hansi-theme-font:minor-latin'>Fourier map controls</span></b> select the <b 1766 style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1767 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Map type</span></b> 1768 and <b style='mso-bidi-font-weight:normal'><span style='font-family:"Calibri",sans-serif; 1769 mso-ascii-theme-font:minor-latin;mso-hansi-theme-font:minor-latin'>Reflection 1770 sets</span></b>, then do <b style='mso-bidi-font-weight:normal'><span 1771 style='font-family:"Calibri",sans-serif;mso-ascii-theme-font:minor-latin; 1772 mso-hansi-theme-font:minor-latin'>Compute/Fourier map</span></b>. The <span 1773 style='font-family:Symbol'>r</span><sub>max</sub> (=0.33) and <span 592 map from the <b><span style='font-family:"Calibri",sans-serif'>General</span></b> 593 tab; in <b><span style='font-family:"Calibri",sans-serif'>Fourier map controls</span></b> 594 select the <b><span style='font-family:"Calibri",sans-serif'>Map type</span></b> 595 and <b><span style='font-family:"Calibri",sans-serif'>Reflection sets</span></b>, 596 then do <b><span style='font-family:"Calibri",sans-serif'>Compute/Fourier map</span></b>. 597 The <span style='font-family:Symbol'>r</span><sub>max</sub> (=0.33) and <span 1774 598 style='font-family:Symbol'>r</span><sub>min</sub> (=-0.31) are listed on the 1775 599 console; these seem to be concentrated around the S-atoms.</p>
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