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144 | <div class=WordSection1> |
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145 | |
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146 | <h1>Single crystal structure determination and refinement with X-ray data in |
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147 | GSAS-II</h1> |
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148 | |
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149 | <h2>Introduction</h2> |
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150 | |
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151 | <p class=MsoNormal>In this exercise we will use a set of X-ray single crystal |
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152 | structure factors to solve the structure of dipyridyl disulfide by charge flipping |
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153 | and then refine the structure by least-squares. The structure will be completed |
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154 | by adding the requisite hydrogen atoms and by using anisotropic thermal |
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155 | parameters for the heavier atoms. The structure was originally solved by |
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156 | Raghavan & Seff, Acta Cryst. B33, 386-391 (1977) in the space group P2<sub>1</sub>/c |
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157 | with one disordered pyridine ring with indications that the true space group |
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158 | was P2<sub>1</sub>. It was subsequently reinvestigated by Young (2014
.) who |
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159 | found that the true space group was P2<sub>1</sub> with 4 molecules in the |
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160 | asymmetric unit. The data used in the latter analysis is what is used here and |
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161 | is provided as a fcf file obtained after structure analysis by Shelx-97; the |
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162 | structure factors are scaled to those calculated from the structure. We will |
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163 | solve the P 2<sub>1</sub>/c structure first.</p> |
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164 | |
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165 | <p class=MsoNormal> </p> |
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166 | |
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167 | <p class=MsoNormal>Note that menu entries and user input are shown in bold face |
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168 | below as <b><span style='font-family:"Calibri",sans-serif'>Help/About GSAS-II</span></b>, |
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169 | which lists first the name of the menu (here <b><span style='font-family:"Calibri",sans-serif'>Help</span></b>) |
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170 | and second the name of the entry in the menu (here <b><span style='font-family: |
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171 | "Calibri",sans-serif'>About GSAS-II</span></b>). If you have not done so |
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172 | already, start GSAS-II</p> |
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173 | |
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174 | <h2>Step 1. Input phase information</h2> |
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175 | |
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176 | <p class=MsoListParagraph style='text-indent:-.25in'>1.<span style='font:7.0pt "Times New Roman"'> |
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177 | </span>Use the <b><span style='font-family:"Calibri",sans-serif'>Data/Add phase</span></b> |
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178 | menu item add a new phase into the current GSAS-II project. A popup window will |
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179 | appear asking for a phase name; I entered <b><span style='font-family:"Calibri",sans-serif'>SS |
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180 | dipyridyl</span></b>; press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b> |
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181 | when done. Select <b><span style='font-family:"Calibri",sans-serif'>Loaded |
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182 | Data/Phases/SS dipyridyl</span></b> from the GSAS-II Data tree window. The |
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183 | General tab for Phase Data will appear.</p> |
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184 | |
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185 | <p class=MsoListParagraph><img width=524 height=307 id="Picture 1" |
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186 | src="CFSingleCrystal_files/image001.png"></p> |
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187 | |
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188 | <p class=MsoListParagraph style='text-indent:-.25in'>2.<span style='font:7.0pt "Times New Roman"'> |
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189 | </span>Enter the space group <b><span style='font-family:"Calibri",sans-serif'>P |
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190 | 21/c</span></b> (dont forget the space between P & 21/c) & press <b><span |
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191 | style='font-family:"Calibri",sans-serif'>Enter</span></b>. A Space Group |
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192 | Information popup window will appear; press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>. |
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193 | The General window will be refreshed showing only the needed lattice parameters |
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194 | for P 21/c.</p> |
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195 | |
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196 | <p class=MsoListParagraph><img width=522 height=361 id="Picture 3" |
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197 | src="CFSingleCrystal_files/image002.png"></p> |
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198 | |
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199 | <p class=MsoListParagraph style='text-indent:-.25in'>3.<span style='font:7.0pt "Times New Roman"'> |
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200 | </span>Enter <b><span style='font-family:"Calibri",sans-serif'>15.8489</span></b>, |
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201 | <b><span style='font-family:"Calibri",sans-serif'>5.5008</span></b>, <b><span |
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202 | style='font-family:"Calibri",sans-serif'>23.118</span></b>, and <b><span |
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203 | style='font-family:"Calibri",sans-serif'>96.9160</span></b> for a, b, c and |
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204 | beta, respectively; the unit cell volume will be recalculated at each entry.</p> |
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205 | |
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206 | <h2>Step 2. Import structure factors </h2> |
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207 | |
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208 | <p class=MsoNormal>There are two parts to this step: one is to import the data |
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209 | and the second is to connect the data with the phase within GSAS-II.</p> |
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210 | |
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211 | <p class=MsoNormal>To do these, do <b><span style='font-family:"Calibri",sans-serif'>Import/Structure |
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212 | factor/from CIF file</span></b> from the main GSAS-II data tree window menu. A |
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213 | file selection dialog will appear; find <b><span style='font-family:"Calibri",sans-serif'>exercises\CF |
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214 | Xray single crystal\S2dipyridyl.fcf</span></b> and press <b><span |
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215 | style='font-family:"Calibri",sans-serif'>Open</span></b>. A popup window asking |
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216 | if this is the file you want; press <b><span style='font-family:"Calibri",sans-serif'>Yes</span></b>. |
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217 | After a pause while the file is read a new popup will appear offering the |
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218 | chance to rename the structure factor set; press <b><span style='font-family: |
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219 | "Calibri",sans-serif'>OK</span></b>. After some time a new popup will appear to |
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220 | Add the new structure factor set to the SS dipyridyl phase. Select the phase |
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221 | and press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>. The |
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222 | plot will show a rectangular array of circles for the hk0 reflection layer; |
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223 | select the plot & press <b><span style='font-family:"Calibri",sans-serif'>k</span></b> |
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224 | to get an h0l layer.</p> |
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225 | |
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226 | <p class=MsoNormal><img width=480 height=412 id="Picture 2" |
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227 | src="CFSingleCrystal_files/image003.png"></p> |
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228 | |
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229 | <p class=MsoNormal>Because the fcf file has both observed and calculated |
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230 | structure factors, the plot shows a small R value for the layer. The observed |
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231 | structure factors are shown as blue rings, the calculated ones as green rings |
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232 | and a small green or red dot may appear at each ring center showing F<sub>o</sub>-F<sub>c</sub>. |
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233 | If the reflection data file had only observed structure factors then only blue |
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234 | rings will be seen. You can explore the plot options in the <b><span |
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235 | style='font-family:"Calibri",sans-serif'>K</span></b> box in the plot toolbar.</p> |
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236 | |
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237 | <h2>Step 3. Setup for charge flipping</h2> |
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238 | |
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239 | <p class=MsoNormal>To solve (again) this crystal structure we will use charge |
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240 | flipping. Charge flipping in GSAS-II is implemented to solve the crystal |
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241 | structure without consideration of space group symmetry. To do this it operates |
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242 | on the entire unit cell volume to a selected resolution (usually 0.5Å) using |
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243 | fast fourier transform techniques. This requires a set of structure factors in |
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244 | an array of the same dimensions as the density array covering the unit cell |
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245 | (i.e. a box bounded by ~0.5Å resolution). The space group symmetry is applied |
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246 | to the observed structure factors to create a full sphere which is then zero |
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247 | filled out to the 0.5Å resolution bounded box. To be reasonably assured of |
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248 | success, the observed structure factors should extend to ~1Å resolution; we |
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249 | have that here for this example. To begin select <b><span style='font-family: |
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250 | "Calibri",sans-serif'>Phases/SS dipyridyl</span></b> from the GSAS-II data |
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251 | tree; the General tab will be shown</p> |
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252 | |
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253 | <p class=MsoNormal><img width=624 height=401 id="Picture 4" |
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254 | src="CFSingleCrystal_files/image004.png"></p> |
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255 | |
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256 | <p class=MsoNormal>Find the <b><span style='font-family:"Calibri",sans-serif'>Fourier |
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257 | map controls</span></b> and change the <b><span style='font-family:"Calibri",sans-serif'>Peak |
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258 | cutoff %</span></b> to <b><span style='font-family:"Calibri",sans-serif'>10</span></b>; |
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259 | then immediately below find the <b><span style='font-family:"Calibri",sans-serif'>Charge |
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260 | flip controls</span></b>. Press <b><span style='font-family:"Calibri",sans-serif'>Select |
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261 | reflection sets</span></b>, pick <b><span style='font-family:"Calibri",sans-serif'>HKLF |
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262 | S2dipyridyl.fcf:1a</span></b> from the list (the only one) and press <b><span |
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263 | style='font-family:"Calibri",sans-serif'>OK</span></b>. If you had multiple |
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264 | data sets for this phase, you can pick more than one and GSAS-II will use a |
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265 | last one in process for assembling the reflection set to use for charge |
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266 | flipping. There are four more settings to consider: 1) kMax controls the upper |
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267 | cutoff for charge flipping; if the density is > k-Max*<span |
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268 | style='font-family:Symbol'>s</span><sub><span style='font-family:Symbol'>r</span></sub> |
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269 | (map standard deviation) then flip the charge. This prevents the Uranium |
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270 | solution sometimes found where all the density is concentrated in a single |
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271 | peak. A useful guide is to use twice the largest atomic number of any element |
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272 | in your structure. For equal atom problems use 12-15; adjust upward for |
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273 | structures with heavy & light atoms. In this case, set <b><span |
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274 | style='font-family:"Calibri",sans-serif'>k-Max</span></b> to <b><span |
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275 | style='font-family:"Calibri",sans-serif'>30.0</span></b> to allow the S atom to |
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276 | appear. 2) k-Factor controls the lower level for charge flipping; if the |
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277 | density is < k-Factor*<span style='font-family:Symbol'>s</span><sub><span |
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278 | style='font-family:Symbol'>r</span></sub> then flip the charge. The default |
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279 | value seems to work pretty well; Id only change it if the charge flipping is |
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280 | having trouble solving the structure. 3) Resolution selects the spacing between |
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281 | map points. 0.5Å is sufficient in most cases. Choosing a smaller value requires |
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282 | more map points (NB: GSAS-II uses the entire unit cell volume for charge |
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283 | flipping) and thus will require more structure factors since the fast fourier |
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284 | algorithm requires the same size arrays in both real space and reciprocal |
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285 | space. This will slow down the charge flip process. 4) Normalizing element |
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286 | selects a form factor to rescale the structure factors thus sharpening the |
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287 | density map. I suggest trying <b><span style='font-family:"Calibri",sans-serif'>None</span></b> |
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288 | first, otherwise select a representative element (really doesnt matter which).</p> |
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289 | |
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290 | <h2 style='page-break-after:avoid'>Step 4. Charge flipping</h2> |
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291 | |
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292 | <p class=MsoNormal>With the controls all set you can now do charge flipping; |
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293 | from the <b><span style='font-family:"Calibri",sans-serif'>General</span></b> |
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294 | tab do <b><span style='font-family:"Calibri",sans-serif'>Compute/Charge |
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295 | flipping</span></b>. A progress bar popup will appear showing the residual |
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296 | between the observed structure factors and those obtained from the inverse |
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297 | fourier transform of the last flipped density map. It should quickly decrease |
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298 | to the ~20% range and level out indicating a good charge flip solution. When it |
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299 | has reached this, press <b><span style='font-family:"Calibri",sans-serif'>Cancel</span></b> |
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300 | to stop the process.</p> |
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301 | |
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302 | <p class=MsoNormal><img width=366 height=180 id="Picture 6" |
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303 | src="CFSingleCrystal_files/image005.png"></p> |
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304 | |
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305 | <p class=MsoNormal>The console window will show something like</p> |
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306 | |
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307 | <p class=MsoNormal><img width=624 height=166 id="Picture 7" |
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308 | src="CFSingleCrystal_files/image006.png"></p> |
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309 | |
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310 | <p class=MsoNormal>There may be a pause at <b><span style='font-family:"Calibri",sans-serif'>Begin |
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311 | fourier map search</span></b> before it finishes. Provided is a summary of the |
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312 | charge flip calculation (time, map size, density range & structure factor |
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313 | residual). The map offset is discovered by an analysis of the reflection phases |
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314 | with respect to how they should be distributed for your chosen space group. |
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315 | These offsets are then applied to shift the map so that the symmetry elements |
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316 | are properly located in the unit cell. The quality of this fit (chi**2) is |
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317 | given. This process is not necessarily perfect; you are given an opportunity to |
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318 | hand-tune the offset. Finally the number of peaks found in the map is listed, |
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319 | the structure is drawn (Ive made the view down the b-axis)</p> |
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320 | |
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321 | <p class=MsoNormal><img width=478 height=402 id="Picture 11" |
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322 | src="CFSingleCrystal_files/image007.jpg"></p> |
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323 | |
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324 | <p class=MsoNormal> and the Phase data window will show the map peaks tab</p> |
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325 | |
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326 | <p class=MsoNormal><img width=500 height=300 id="Picture 12" |
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327 | src="CFSingleCrystal_files/image008.png"></p> |
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328 | |
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329 | <p class=MsoNormal>These are listed in order of magnitude; a double click on |
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330 | any of the table headings will sort the list according to that parameter. My |
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331 | list has 112 entries; dipyridyl disulfide has 14 C & S atoms so this list |
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332 | is appropriate for 8 molecules in the unit cell and thus all atoms were found |
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333 | in this charge flipping result.</p> |
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334 | |
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335 | <p class=MsoNormal>If all went well then the drawing should nicely show all the |
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336 | atoms in the structure placed properly with respect to the locations of the |
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337 | inversion centers (they are at all the corners, edge centers, face centers and |
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338 | cell center). If not then you can shift the map & peaks with the <b><span |
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339 | style='font-family:"Calibri",sans-serif'>L</span></b>, <b><span |
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340 | style='font-family:"Calibri",sans-serif'>R</span></b>, <b><span |
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341 | style='font-family:"Calibri",sans-serif'>U</span></b> & <b><span |
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342 | style='font-family:"Calibri",sans-serif'>D</span></b> keys (NB: rotate the |
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343 | drawing so the axes are ~horizontal/vertical); the map/peaks will move in |
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344 | resolution steps (0.5A). The table is also updated with new peak positions. You |
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345 | could also just repeat the charge flipping and hope to get a better map offset |
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346 | solution (examine the map offset chi**2 to get a sense of this). You can also |
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347 | show the map density (highest point is shown as a green dot somewhere in the |
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348 | map on a S-atom position); select the <b><span style='font-family:"Calibri",sans-serif'>Draw |
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349 | Options</span></b> tab and use the <b><span style='font-family:"Calibri",sans-serif'>Contour |
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350 | level</span></b> slider. The drawing will show green dots at each set map point |
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351 | with size in proportion to the density. The mouse <b><span style='font-family: |
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352 | "Calibri",sans-serif'>RB</span></b> can be used to slide the structure around; |
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353 | the density is always drawn in a space surrounding the view point (multicolored |
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354 | cross at the center). While here you can also change the <b><span |
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355 | style='font-family:"Calibri",sans-serif'>Bond search factor</span></b> to <b><span |
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356 | style='font-family:"Calibri",sans-serif'>0.90</span></b> to ensure all S-C |
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357 | bonds are shown.</p> |
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358 | |
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359 | <p class=MsoNormal>If the charge flipping has failed (high residual & no |
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360 | recognizable structure) the process should be just repeated. This gives it a |
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361 | new random start for the structure factor phases which may lead to a good |
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362 | solution. After a few attempts, you can try different control settings to see |
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363 | if that will coax out a good solution; first be sure <b><span style='font-family: |
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364 | "Calibri",sans-serif'>k-Max</span></b> is properly set and then perhaps try |
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365 | different <b><span style='font-family:"Calibri",sans-serif'>k-Factors</span></b> |
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366 | and do <b><span style='font-family:"Calibri",sans-serif'>Normalizing</span></b> |
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367 | by some element form factor. If it seemed to work but very few peaks were |
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368 | found, make sure <b><span style='font-family:"Calibri",sans-serif'>Peak cutoff</span></b> |
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369 | was properly set; you can then repeat the peak search by doing <b><span |
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370 | style='font-family:"Calibri",sans-serif'>Compute/Search map</span></b>.</p> |
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371 | |
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372 | <h2>Step 5. Extract solution and make molecules</h2> |
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373 | |
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374 | <p class=MsoNormal>Assuming that the map & peak positions are properly |
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375 | placed with respect to the symmetry elements of the space group, we can now |
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376 | select those peaks which describe the structure. Select the <b><span |
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377 | style='font-family:"Calibri",sans-serif'>Map peaks</span></b> tab and double LB |
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378 | click the blank upper left corner of the table; all entries will be highlighted |
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379 | in blue. Then do <b><span style='font-family:"Calibri",sans-serif'>Map |
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380 | peaks/Unique peaks</span></b>; after a bit of time 1/4 of the peaks in the list |
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381 | will be highlighted and the corresponding peaks in the drawing will be green |
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382 | (NB: if you navigate away from this tab, this selection will be lost and youll |
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383 | have to repeat it!). Next, do <b><span style='font-family:"Calibri",sans-serif'>Map |
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384 | peaks/Move peaks</span></b>; these peaks will be transferred to the <b><span |
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385 | style='font-family:"Calibri",sans-serif'>Atoms</span></b> list as H-atoms named |
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386 | according to their position in the magnitude column.</p> |
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387 | |
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388 | <p class=MsoNormal><img width=624 height=267 id="Picture 13" |
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389 | src="CFSingleCrystal_files/image009.png"></p> |
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390 | |
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391 | <p class=MsoNormal>The drawing will show white balls at the atom positions |
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392 | scattered over several molecules.</p> |
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393 | |
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394 | <p class=MsoNormal><img width=474 height=409 id="Picture 14" |
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395 | src="CFSingleCrystal_files/image010.jpg"></p> |
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396 | |
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397 | <p class=MsoNormal>Notice that 4 atoms have magnitudes ~90+, these are the S |
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398 | atoms. The rest are C & N atoms. In the <b><span style='font-family:"Calibri",sans-serif'>Atoms</span></b> |
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399 | tab select the first 4 atoms (press LB on the 1<sup>st</sup> & shift LB on |
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400 | the 4<sup>th</sup> one). Then do <b><span style='font-family:"Calibri",sans-serif'>Edit/Modify |
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401 | atom parameters</span></b>; a popup window will appear. Select <b><span |
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402 | style='font-family:"Calibri",sans-serif'>Type</span></b> & press <b><span |
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403 | style='font-family:"Calibri",sans-serif'>OK</span></b>; a Periodic Table will |
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404 | appear. Select <b><span style='font-family:"Calibri",sans-serif'>S</span></b>; |
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405 | the atoms will be renames and their Type changed to S. Next select the |
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406 | remaining H atoms (a quick way it to double LB click the <b><span |
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407 | style='font-family:"Calibri",sans-serif'>Type</span></b> column heading and |
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408 | select <b><span style='font-family:"Calibri",sans-serif'>H</span></b> from the |
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409 | popup window). Then do <b><span style='font-family:"Calibri",sans-serif'>Edit/Modify |
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410 | atom parameters</span></b> and <b><span style='font-family:"Calibri",sans-serif'>Type</span></b> |
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411 | from the popup; select <b><span style='font-family:"Calibri",sans-serif'>C</span></b> |
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412 | from the Periodic Table as we dont know which ones are N. The drawing will |
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413 | change (you may have to wiggle it a bit to force the update).</p> |
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414 | |
---|
415 | <p class=MsoNormal><img width=480 height=390 id="Picture 17" |
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416 | src="CFSingleCrystal_files/image011.jpg"></p> |
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417 | |
---|
418 | <p class=MsoNormal>Notice that the atoms are scattered over several molecules; |
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419 | we want to assemble them into 2 conveniently placed ones. Begin by selecting an |
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420 | atom (make sure the <b><span style='font-family:"Calibri",sans-serif'>Atom</span></b> |
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421 | tab is displayed & do shift LB on an atom in the drawing I chose the S |
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422 | atom near the upper middle); it will turn green and a line in the Atom table |
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423 | will be highlighted. Next do <b><span style='font-family:"Calibri",sans-serif'>Edit/Assemble |
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424 | molecule</span></b>; a popup window will appear. Change the <b><span |
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425 | style='font-family:"Calibri",sans-serif'>Bond search factor</span></b> to <b><span |
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426 | style='font-family:"Calibri",sans-serif'>0.90</span></b> to be sure all S-C |
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427 | bonds are found.</p> |
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428 | |
---|
429 | <p class=MsoNormal><img width=265 height=223 id="Picture 16" |
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430 | src="CFSingleCrystal_files/image012.png"> </p> |
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431 | |
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432 | <p class=MsoNormal>Press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>; |
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433 | atoms will be collected into a well positioned group, but others are not. Next |
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434 | select one of the unassembled atoms (I chose a C-atom in a nearby SS-dipyridyl) |
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435 | and do <b><span style='font-family:"Calibri",sans-serif'>Edit/Assemble molecule</span></b>; |
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436 | there will be two nicely assembled SS-dipyridyls.</p> |
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437 | |
---|
438 | <p class=MsoNormal><img width=480 height=384 id="Picture 5" |
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439 | src="CFSingleCrystal_files/image013.jpg"></p> |
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440 | |
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441 | <p class=MsoNormal>You should probably save this project as it contains your |
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442 | solved crystal structure.</p> |
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443 | |
---|
444 | <h2>Step 6. Initial refinement</h2> |
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445 | |
---|
446 | <p class=MsoNormal>Since we now have a structural model, we can do the initial |
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447 | structure refinement. By default this will only refine the scale factor; do <b><span |
---|
448 | style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b> from the |
---|
449 | main GSAS-II data tree window. Convergence will quickly occur with Rw ~35%. |
---|
450 | More useful is to refine the atom positions and isotropic thermal parameters. |
---|
451 | Select the <b><span style='font-family:"Calibri",sans-serif'>Atoms</span></b> |
---|
452 | tab from the Phase window. Then LB double click the <b><span style='font-family: |
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453 | "Calibri",sans-serif'>refine</span></b> column heading; a popup window will |
---|
454 | appear. Select <b><span style='font-family:"Calibri",sans-serif'>X</span></b> |
---|
455 | and <b><span style='font-family:"Calibri",sans-serif'>U</span></b> and press <b><span |
---|
456 | style='font-family:"Calibri",sans-serif'>OK</span></b>. The <b><span |
---|
457 | style='font-family:"Calibri",sans-serif'>Atoms</span></b> window will show <b><span |
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458 | style='font-family:"Calibri",sans-serif'>XU</span></b> for each atom in the |
---|
459 | refine column. Then do <b><span style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b> |
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460 | (twice to get convergence) and the Rw ~12%.</p> |
---|
461 | |
---|
462 | <h2>Step 7. Determine C/N choice</h2> |
---|
463 | |
---|
464 | <p class=MsoNormal>We know from the chemistry that the N atom is in the 2 |
---|
465 | position of the pyridine ring, i.e. next to the point of attachment to the S-atom. |
---|
466 | However, we dont know which one that is and we have 8 atoms of which 4 are C |
---|
467 | and 4 are N.</p> |
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468 | |
---|
469 | <p class=MsoNormal>To work out the C/N problem above we need the atoms to be in |
---|
470 | a chemically sensible order. The assemble molecule routine did construct chains |
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471 | of atoms but this ordering is not really satisfactory. The ordering can quickly |
---|
472 | be done by hand by following a labelled drawing. First go to the <b><span |
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473 | style='font-family:"Calibri",sans-serif'>Draw Atoms</span></b> tab and double |
---|
474 | LB click the <b><span style='font-family:"Calibri",sans-serif'>Style</span></b> |
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475 | column; select <b><span style='font-family:"Calibri",sans-serif'>balls & |
---|
476 | sticks</span></b> from the popup box. Press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>. |
---|
477 | Next, double LB click the <b><span style='font-family:"Calibri",sans-serif'>Label</span></b> |
---|
478 | column and select <b><span style='font-family:"Calibri",sans-serif'>name</span></b> |
---|
479 | from the popup box; press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>. |
---|
480 | Then go to the <b><span style='font-family:"Calibri",sans-serif'>Draw options</span></b> |
---|
481 | tab and adjust the <b><span style='font-family:"Calibri",sans-serif'>Ball scale</span></b> |
---|
482 | & <b><span style='font-family:"Calibri",sans-serif'>Bond radius </span></b>to |
---|
483 | allow the labels to be easily seen. After shifting the view point the drawing |
---|
484 | should look something like</p> |
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485 | |
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486 | <p class=MsoNormal> </p> |
---|
487 | |
---|
488 | <p class=MsoNormal><img width=474 height=386 id="Picture 9" |
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489 | src="CFSingleCrystal_files/image014.jpg"></p> |
---|
490 | |
---|
491 | <p class=MsoNormal>Now go to the <b><span style='font-family:"Calibri",sans-serif'>Atoms</span></b> |
---|
492 | tab. If you look carefully, you can see that the atoms in each SS-dipyridyl are |
---|
493 | grouped together in the table but they are not in chemically sensible order. |
---|
494 | The atoms can be reordered by selecting one row with the <b><span |
---|
495 | style='font-family:"Calibri",sans-serif'>Alt</span></b> key down (the status |
---|
496 | line will tell which atom is selected to move) and then with the <b><span |
---|
497 | style='font-family:"Calibri",sans-serif'>Alt</span></b> key still down pick a |
---|
498 | row below where you want to insert it. I ordered them so each S-atom was |
---|
499 | followed by the C-atoms in order around the ring; my list looked like (I show |
---|
500 | just the 1<sup>st</sup> SS dipyridyl molecule)</p> |
---|
501 | |
---|
502 | <p class=MsoNormal><img width=624 height=408 id="Picture 10" |
---|
503 | src="CFSingleCrystal_files/image015.png"></p> |
---|
504 | |
---|
505 | <p class=MsoNormal>Once you have reordered the atoms to your satisfaction they |
---|
506 | can be renamed to be in order. To do this select all the atoms (double LB click |
---|
507 | the empty corner box) and then do <b><span style='font-family:"Calibri",sans-serif'>Edit/Modify |
---|
508 | atom parameters</span></b>. Select <b><span style='font-family:"Calibri",sans-serif'>Name</span></b> |
---|
509 | and press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>; |
---|
510 | press <b><span style='font-family:"Calibri",sans-serif'>Yes</span></b> to the |
---|
511 | popup question. The atoms will be renamed in numerical order. Do <b><span |
---|
512 | style='font-family:"Calibri",sans-serif'>Edit/Reload draw atoms</span></b>; the |
---|
513 | labels will change. In my numbering scheme, half of the C3, C7, C10, C14, C17, |
---|
514 | C21, C24 and C28 carbon atoms are really nitrogen (if they are ordered). Select |
---|
515 | these and do <b><span style='font-family:"Calibri",sans-serif'>Edit/Set atom |
---|
516 | refinement flags</span></b>; select <b><span style='font-family:"Calibri",sans-serif'>F</span></b>, |
---|
517 | <b><span style='font-family:"Calibri",sans-serif'>X</span></b> & <b><span |
---|
518 | style='font-family:"Calibri",sans-serif'>U</span></b> for these. Do <b><span |
---|
519 | style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b>; the Rw |
---|
520 | will drop to ~10% and 4 of the atom <b><span style='font-family:"Calibri",sans-serif'>frac</span></b> |
---|
521 | values will be ~1.25 while the others are ~1.0. The former are N-atoms and the |
---|
522 | latter are C-atoms. Change the <b><span style='font-family:"Calibri",sans-serif'>Type</span></b> |
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523 | for the N-atoms and repeat <b><span style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b>; |
---|
524 | the Rw will be high to start, but immediately fall to ~10%. In the Atom table |
---|
525 | all 8 refined frac values are be now ~1.0. To finish this part of the |
---|
526 | refinement, set all <b><span style='font-family:"Calibri",sans-serif'>frac</span></b> |
---|
527 | values to <b><span style='font-family:"Calibri",sans-serif'>1.0</span></b> and |
---|
528 | all refine flags to <b><span style='font-family:"Calibri",sans-serif'>XU</span></b>. |
---|
529 | Do <b><span style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b>; |
---|
530 | the final Rw ~10.5%</p> |
---|
531 | |
---|
532 | <h2>Step 8. Anisotropic thermal motion refinement</h2> |
---|
533 | |
---|
534 | <p class=MsoNormal>Given reasonable measured structure factors one can improve |
---|
535 | a crystal model by using anisotropic thermal motion models for all the |
---|
536 | nonhydrogen atoms. To convert all the atoms here select the Atoms tab and then |
---|
537 | do a double LB click on the I/A column heading. Select Anisotropic from the |
---|
538 | popup and press OK; the Atom table will be redrawn with Uij values equivalent |
---|
539 | to the corresponding Uiso (now hidden). Do <b><span style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b>; |
---|
540 | the final Rw ~8.2%</p> |
---|
541 | |
---|
542 | <h2 style='page-break-after:avoid'>Step 9. H-atom placement & final |
---|
543 | refinement</h2> |
---|
544 | |
---|
545 | <p class=MsoNormal>This structure can be completed by adding the 4 H-atoms per |
---|
546 | pyridine ring (16 in all). One could do this (painfully) by hand by looking for |
---|
547 | them in <span style='font-family:Symbol'>D</span>F maps, but it is simpler to just |
---|
548 | place them knowing the bonding chemistry of the rings. To start this select the |
---|
549 | <b><span style='font-family:"Calibri",sans-serif'>Atoms</span></b> tab for the |
---|
550 | phase. Then select the C-atoms by a double LB click on the <b><span |
---|
551 | style='font-family:"Calibri",sans-serif'>Type</span></b> column heading and |
---|
552 | select <b><span style='font-family:"Calibri",sans-serif'>C</span></b> from the |
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553 | popup; press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>. |
---|
554 | The C-atoms will be highlighted. Next do <b><span style='font-family:"Calibri",sans-serif'>Edit/Insert |
---|
555 | H atoms</span></b>; a <b><span style='font-family:"Calibri",sans-serif'>Distance |
---|
556 | Angle Controls</span></b> popup will appear; the numbers should be as before. |
---|
557 | Press <b><span style='font-family:"Calibri",sans-serif'>OK</span></b>; a new |
---|
558 | popup will appear</p> |
---|
559 | |
---|
560 | <p class=MsoNormal><img width=400 height=485 id="Picture 8" |
---|
561 | src="CFSingleCrystal_files/image016.png"></p> |
---|
562 | |
---|
563 | <p class=MsoNormal>This is the hydrogen add control; it shows both the expected |
---|
564 | number of H-atoms to add to each C-atom and the neighboring atoms used to |
---|
565 | determine the geometry of the C-H bond. Check to make sure that 4 H-atoms will |
---|
566 | be added for each ring. Note that C2, C9, C16 & C23 will not have an H-atom |
---|
567 | added as these are the S-atom attachment points in SS-dipyridyl. Press <b><span |
---|
568 | style='font-family:"Calibri",sans-serif'>Ok</span></b>; the H-atoms will be |
---|
569 | inserted immediately after the corresponding C-atoms and the drawing is updated |
---|
570 | showing van der Waals spheres for all atoms.</p> |
---|
571 | |
---|
572 | <p class=MsoNormal><img width=624 height=396 id="Picture 15" |
---|
573 | src="CFSingleCrystal_files/image017.png"></p> |
---|
574 | |
---|
575 | <p class=MsoNormal> </p> |
---|
576 | |
---|
577 | <p class=MsoNormal><img width=483 height=394 id="Picture 18" |
---|
578 | src="CFSingleCrystal_files/image018.jpg"></p> |
---|
579 | |
---|
580 | <p class=MsoNormal>Next, do <b><span style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b>; |
---|
581 | there will be an immediate drop in Rw ~3.2%. Note that we did not refine the |
---|
582 | H-atom positions or thermal parameters. The H-atom insertion process retains |
---|
583 | the mechanisms for creating them in the first place and these tools can be used |
---|
584 | to move them to reflect the changes in the C-atom parameters thus forcing them |
---|
585 | to ride on the C-atoms. Do <b><span style='font-family:"Calibri",sans-serif'>Edit/Update |
---|
586 | H atoms</span></b>; the H-atom positions & Uisos will be revised. Repeat <b><span |
---|
587 | style='font-family:"Calibri",sans-serif'>Calculate/Refine</span></b>; there |
---|
588 | will be a slight improvement in Rw. Repeat these two steps (twice); Rw should |
---|
589 | not change on the last round. This completes the refinement of the SS-dipyridyl |
---|
590 | structure. You can generate a final <span style='font-family:Symbol'>D</span>F |
---|
591 | map from the <b><span style='font-family:"Calibri",sans-serif'>General</span></b> |
---|
592 | tab; in <b><span style='font-family:"Calibri",sans-serif'>Fourier map controls</span></b> |
---|
593 | select the <b><span style='font-family:"Calibri",sans-serif'>Map type</span></b> |
---|
594 | and <b><span style='font-family:"Calibri",sans-serif'>Reflection sets</span></b>, |
---|
595 | then do <b><span style='font-family:"Calibri",sans-serif'>Compute/Fourier map</span></b>. |
---|
596 | The <span style='font-family:Symbol'>r</span><sub>max</sub> (=0.33) and <span |
---|
597 | style='font-family:Symbol'>r</span><sub>min</sub> (=-0.31) are listed on the |
---|
598 | console; these seem to be concentrated around the S-atoms.</p> |
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599 | |
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600 | </div> |
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601 | |
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602 | </body> |
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603 | |
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604 | </html> |
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