AU Biomaterials Design Lab:Protocols/Ocean Optics Absorbance

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Description

The Ocean Optics spectrometer allows for full spectral acquisition over a broad time range. These full spectra allow us to observe, in a more total way, what is happening during a chemical reaction in which there are important absorbance features that change during the course of the reaction. This instrumentation is found in Beeghly 203B and is maintained by Dr. Hartings.

Protocol

  1. Extra Steps
    1. Do you need temperature control or need stirring?
      1. See the protocol for controlling the cuvette controller Quantum Northwest Cuvette Holder
  2. Turn on the jaz spectrophotometer (red on-off button)
  3. Turn on the Lamps (Ocean Optics DH-2000)
    1. Turn on the switch in the back of the controller box
    2. Press the blue "Deuterium" button and wait for the light to stay on
    3. Press the red "Halogen" button
    4. The lamps need 15 minutes to warm up before you are ready to proceed to the next step.
  4. Starting the software
    1. Open the OceanView software.
      1. Click on the "Create New Spectroscopy Application" icon (looks like a bunch of shark fins stacked on one another)
        1. Click on "Spectroscopy"
        2. Select JAZA1666 and click "Next"
        3. Select "Absorbance" and click "Next"
        4. Set Acquisition Parameters
          1. Set "Integration Time" to 1 ms
          2. Set "Scans to Average" to 100
          3. Click "Next"
        5. Store Reference Spectrum
          1. Make sure that the toggle on the light source is switched to "Open"
          2. Click on the light bulb icon
            1. A spectrum should appear in the middle display
          3. Click "Next"
        6. Store Background Spectrum
          1. Make sure that the toggle on the light source is switched to "Closed"
          2. Click on the light bulb icon
            1. A spectrum should appear in the middle display
          3. Click "Finish"
        7. Make sure that the toggle on the light source is switched to "On"
  5. Set up your data acquisition schedule
    1. Click on the "Save graph to file/files" icon (the floppy disc icon on the lower icon panel)
    2. Click "Yes" for "You must configure save parameters first. Do you want to configure now?"
    3. Set Save Options
      1. Choose the "Between saved scans, wait at least" option
      2. Set the time to whatever the experiment requires
        1. For most nanoparticle syntheses, this will be 2 minutes
      3. Choose the "Stop after this amount of time" option
        1. For most nanoparticle syntheses, this will be 3 hours
    4. Set File Options
      1. Save to Directory: C:\Users\Lab Admin\DropBox\CHEM471 2016\Ocean Optics\Year\Month\Date
      2. Select Open
      3. Set Basename to something that will be descriptive of your data for example Lysozyme_AuNP_Ratio45_80C
      4. Click "Apply"
      5. Click "Exit"
  6. Start data collection
    1. After you have your sample, cuvette, and cuvette holder properly prepared perform the following:
      1. Click the "Save graph to file/files" icon (the floppy disc icon on the lower icon panel)
      2. Data files should be showing up in your selected folder. If it isn't, you have done something wrong.
  7. Shutting down
    1. When your data collection is finished, perform the following steps
      1. Shut down the OceanView software
      2. Turn off the jaz spectrophotometer
      3. Turn off the lamps (main switch in the back)
      4. Shut down the Quantum Northwest Cuvette Holder if necessary
  8. Analyzing Data
    1. Open data compilation folder.
    2. Open copy command.txt document.
    3. In data compilation folder shift right click and choose open command window here.
    4. Copy the first line from the copy command.txt document and paste into the command window. Hit enter.
    5. It will prompt “location?” Copy the location of the saved scans, paste it into the command window, and hit enter.
    6. It will prompt "new file name?" Choose a name for the data.
    7. Then copy the second line from the copy command.txt document, paste into the command window, and hit enter.
    8. It will prompt “number of files.” Enter the number of files that it has copied which will be immediately above the prompt.
    9. It will prompt “number of lines per file.” Enter 2048.
    10. It will prompt “number of lines before data.” Enter 17.
    11. It will prompt “Are you sure (Y/N)?” Enter Y.
    12. Data will be saved as the name you gave it.txt in the correct folder.

Notes

References