Changes between Version 1 and Version 2 of KEMM37/Lab1A


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Jan 25, 2018 4:04:33 AM (6 years ago)
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ajj
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  • KEMM37/Lab1A

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    173173 
    174174 
    175 == [=#section3 3. Fitting SANS data] == 
    176  
    177 This part of the exercise will use real SANS data taken from a study of surfactant self assembly in deep eutectic solvents (DES).  
    178  
     175=== [=#section24 2.4 Resolution] === 
    179176{{{ 
    180 #!div style="background: lightblue" 
    181 [=#task9 **TASK 9:**] Restart !SasView 
    182  
    183 Before starting this part of the exercise, you should have a clean !SasView instance. Quit !SasView and restart it. 
    184 }}} 
    185  
    186 === [=#section31 3.1 Background Information] === 
    187 Deep eutectic solvents are a class of ionic liquids formed from a hydrogen bond donor and a halide salt. At a certain mixture ratio, the eutectic mixture, the melting point is significantly depressed to values below room temperature. 
    188  
    189 Here we will examine the self-assembly of a [https://en.wikipedia.org/wiki/Surfactant surfactant], [https://en.wikipedia.org/wiki/Sodium_dodecyl_sulfate sodium dodecyl sulfate (SDS)] in the deep eutectic solvent formed from a 1:2 molar ratio mixture of [https://en.wikipedia.org/wiki/Choline_chloride   choline chloride] and [https://en.wikipedia.org/wiki/Urea   urea]. 
    190  
    191 ||Sodium Dodecyl Sulfate||Choline Chloride||Urea|| 
    192 ||[[Image(tartu_sds.png)]]||[[Image(tartu_choline.png)]]||[[Image(tartu_urea.png)]]|| 
    193  
    194 {{{ 
    195 #!div style="background: lightblue" 
    196 [=#task10 **TASK 10:**] Download the SANS data :  [attachment:TartuSasViewTutorialData.zip​] and unzip the file in a known location on your filesystem. Note where you have placed the data. 
    197 }}} 
    198  
    199 You should now have a folder containing a set of files named as follows: 
    200  
    201 [[Image(tartu_datafileslist.png)]] 
    202  
    203 The data are SANS curves collected on SANS2D at ISIS and D22 at ILL for samples of protonated (normal) SDS in 1:2 d9-choline chloride:d4-urea. This sample was chosen to give maximum contrast and minimum background signal from incoherent scattering. There were 7 samples with 0.2 wt%, 0.5 wt%, 1.0 wt%, 2.0 wt%, 5.0 wt%, 7.5 wt% and 10 wt% of SDS in the DES with the filenames corresponding to each sample given below: 
    204  
    205 || Surfactant Concentration (wt%) || Data File || 
    206 || 0.2 || 0p2hSDS_dChCldUrea_sub.txt || 
    207 || 0.5 || 0p5hSDS_dChCldUrea_sub.txt || 
    208 || 1.0 || 1hSDS_dChCldUrea_sub.txt || 
    209 || 2.0 || 2hSDS_dChCldUrea_sub.txt || 
    210 || 5.0 || 5hSDS_dChCldUrea_sub.txt || 
    211 || 7.5 || 7p5hSDS_dChCldUrea_sub.txt || 
    212 || 10.0 || 10hSDS_dChCldUrea_sub.txt || 
    213  
    214  
    215 All the data files have been processed to 1D scattering curves with the solvent background subtracted to leave only the coherent scattering signal on absolute scale. 
    216  
    217  
    218 === [=#section32 3.2 Calculating Scattering Length Density] === 
    219  
    220 The scattering length density is given by  
    221  
    222 [[Image(tartu_sld.png, 100px)]] 
    223  
    224 Scattering lengths of relevant elements: 
    225 ||= **Element** =||= **Scattering Length (fm)** =|| 
    226 ||C     ||6.646|| 
    227 ||H     ||-3.739|| 
    228 ||D     ||6.671|| 
    229 ||N     ||9.36|| 
    230 ||O     ||5.803|| 
    231 ||Cl    ||9.577|| 
    232  
    233  
    234 Physical properties of the DES components: 
    235 ||= **Component**       =||= **Chemical Formula** =||=  **Molecular Volume (Å3)**       =||= **Density (g/cm3)** =|| 
    236 ||d9-Choline Chloride|| C5H5D9NOCl      || 210.77 ||1.17|| 
    237 ||d4-Urea||     CD4N2O  ||.75.55 ||     1.41|| 
    238  
    239  
    240 {{{ 
    241 #!div style="background: lightblue" 
    242 [=#task11 **TASK 11:**] Calculate the scattering length density (SLD) of a 1:2 mole ratio mixture of choline chloride and urea. 
    243  
    244 Use the information in the table above to calculate the SLD. There are multiple ways to do so, including: 
    245 * Calculating by hand 
    246 * Using a spreadsheet 
    247 * Using the SLD calculator built in to !SasView (in the Tools menu). 
    248 * Using online calculators e.g. [https://www.ncnr.nist.gov/resources/activation/] 
    249  
    250 Try multiple ways and see if you get the same answer! 
    251 }}} 
    252  
    253  
    254 === [=#section33 3.3 Loading and Plotting the data] === 
    255  
    256 You will now load the data into !SasView and make a plot in order to visually inspect the scattering curves. 
    257  
    258 {{{ 
    259 #!div style="background: lightblue" 
    260 [=#task12 **TASK 12:**] Click on the "Load Data" button in the Data Explorer 
    261  
    262 Locate the folder where you placed the data, select all the files in that folder and click "Open" in the dialog. 
    263 }}} 
    264  
    265 The Available Data section of the Data Explorer should look something like: 
    266  
    267 [[Image(tartu_loaddata.png)]] 
    268  
    269  
    270 {{{ 
    271 #!div style="background: lightblue" 
    272 [=#task13 **TASK 13:**] Plot the loaded data 
    273  
    274 Make sure that all the datasets have check marks next to them in the Available Data section of the Data Explorer, as shown above. 
    275  
    276 Click the "New Plot" button in the Data Explorer. 
    277 }}} 
    278  
    279 A new window should appear with a plot of the data that looks something like: 
    280  
    281 [[Image(tartu_dataplot.png)]] 
    282  
    283 {{{ 
    284 #!div style="background: lightblue" 
    285 [=#task14 **TASK 14:**] Examining the Data. 
    286  
    287 Visually inspect the data, zooming in and making additional plots as needed. 
    288  
    289 * What trends do you notice? 
    290 * What can you say about the possible solution structure from looking at the data? 
    291  
    292 }}} 
    293  
    294  
    295 === [=#section34 3.4 Fitting the data] === 
    296 {{{ 
    297 #!div style="background: lightblue" 
    298 [=#task15 **TASK 15:**] Fitting the lowest concentration data. 
    299  
    300 Select the lowest concentration data only in the data explorer by ensuring only 0p2hSDS_dChCldUrea_sub.txt has a check mark next to it and click “Send to" fitting. 
    301  
    302 * Select the model for the structure you predicted for this dataset.  
    303   * How does it compare to the data? 
    304 * Fill in parameters you know and adjust the others to see how close you get to the data. 
    305 * Select parameters to fit and run the fit by clicking "Fit" at the bottom of the fitting panel. 
    306   * Do you get a good fit? 
    307   * Are the parameters you get physically reasonable? 
    308  
    309 }}} 
    310  
    311  
    312 {{{ 
    313 #!div style="background: lightblue" 
    314 [=#task16 **TASK 16:**] Fitting the other data, starting with the 7.5 wt% data set. 
    315  
    316 Repeat for other concentrations 
    317 * Does the same model fit all data? 
    318 * What is consistent between datasets? What is different?  
     177#!div style="background: light blue" 
     178[=#task9 **TASK 9:**] Apply resolution functions to your model 
    319179 
    320180 
     
    322182 
    323183 
    324  
    325 == [=#resources Resources] == 
    326  
    327 * The original [attachment:MicelleStructureinDeepEutecticSolvents.pdf paper] and [attachment:MicelleStructureinDeepEutecticSolventsSupplementaryInformation.pdf​ supplementary information] 
    328 * NIST SLD calculator [https://www.ncnr.nist.gov/resources/activation/] 
    329 * NIST Scattering Length and Scattering Cross Section Database [https://www.ncnr.nist.gov/resources/n-lengths/] 
     184== What's Next? == 
     185You can now move on to the second lab session looking at fitting of data : [wiki:KEMM37/Lab1B Lab 1B Data Fitting]