JHU CORE FACILITIES  1  Dr. Joel A. Tang 

1.0 ThermoNicolet Nexus 670 FTIR Spectrometer Instructions

1.1 Click on the OMNIC icon to open the software.

1.2 Check that a signal is being measured by opening the “Experiment Setup” menu under the “Collect” tab and go to the “Bench” tab. You should see a peak centered in the left window with a Max value around between 9 and 10.

1.3 If you have problems seeing a signal, or

the signal is low, you can realign the mirrors to obtain an optimum signal. Go into the “Diagnostic” tab and click on the “Align…” button.

1.4 Click on the “Collect” tab and setup the experiment

1. No. of scans: Number of scans to acquire background and spectrum. Default is 64.

2. Resolution: Resolution of the spectrum can be adjusted for course or fine details. Resolution range is between 32 and 0.125. Default value is 4.

3. Experiment title: This is required and used to identify the experiment

4. Background Handling: Recommend to select “Collect background before every sample”. This will prompt the user to collect a background spectrum before each sample.

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1.5 Go back to the “Bench” tab to adjust the spectral window. Max range is between 4000 and 400 cm-1.

Click “OK” button to exit the Experiment setup.

1.6 On the left side of the window, there are two buttons: Collect background, Collect Sample

If the option to “Collect background before every sample” is selected, you can just click on collect Sample button.

1.7 It will first ask to prepare sample chamber for background

collection.

1.8 Select proper sample assembly and place in sample chamber.

(a) (b) There many types of sample holders such as (right) for slides (KBr disk, glass slide etc.) or (left) for liquids/solutions. The sample holder slides into the sample chamber support with the sample facing the right. There is also an ATR attachment (see below) for both solutions and solid samples.

1.9 Place background material into the sample chamber (KBr disk, solvent etc…) and click “OK”.

1.10 Once the background is collected, you can insert your

sample. A prompt will show and you can enter a title for your spectrum. Click “OK” when ready to collect sample.

1.11 During acquisition, you can select which window to add the spectrum to when completed. If you want to put

them in separate windows select “Add to new window” in the drop down menu above the spectrum.

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1.12 Peak positions can be determined through the “Analyze” menu and “Find Peaks…” option.

1.13 In the spectrum window you can adjust the peak picking threshold by clicking on the spectrum and adjusting the location of the horizontal line.

The sensitivity of the peak picking can be adjusted by the siding bar on the left of the spectrum.

1.14 Once peaks are selected you can choose to replace the original spectrum, or add it to a different window. To avoid confusion, select “Replace the original spectrum” and click on “Replace” button.

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1.15 You can save your data on the local hard drive C:\IR data\“Group”\“User Name” where Group is your PI name and User Name is your JHED id. The file can be saved under different formats:

Spectra (*.spa) – Standard spectra file format, read in by OMNIC CSV Text (*.csv) – Comma-separated values, text file containing data points to be read in by a spreadsheet program (e.g. Excel, Origin). Does not save peak labels. Windows Metafile (*.WMF) / TIFF (*.TIF) – image file format. Saves what is seen in the spectrum window.

JHU CORE FACILITIES  5  Dr. Joel A. Tang 

2.0 Nicolet Smart Golden Gate, KRS-5 ATR Accessory

2.1 The ATR accessory is in a black plastic case under the counter in the cabinet. Take it out carefully and lay it on the counter.

2.2 Remove the sample support platform from the FTIR. There is a small peg in the back restricting it to slide forward. Use the hole in the front to lift the plate up. The software will detect that the plate has been removed.

2.3 Take out the ATR and insert into the FTIR from the top. The round openings on the side of the ATR, under the case, will align with the open slots for the laser/detector of the sample chamber.

2.4 The software will automatically detect that the ATR was installed and read in default experiment settings. Go

back under the “Collect” menu -> “Experiment Setup…” -> “Bench” tab and a peak should again be detected, but at a lower level (should be around 2). If you have problems seeing a signal you can realign the mirrors to obtain an optimum signal. Go into the “Diagnostic” tab and click on the “Align…” button.

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2.5 Lift up the “golden gate” by unscrewing the left latch. Clean the crystals on the platform and the tip with methanol.

2.6 Lower the arm and re-latch in place. Turn the top knob to compress the two crystals together. ONLY TURN

UNTIL FINGER TIGHT. Collect a background spectrum.

2.7 Turn the knob to loosen the compression and lift the arm to place your sample. Directly place the solid or liquid sample onto the crystal on the platform.

For solids: lower arm and turn the knob again until

finger tight. For liquids: Place cap on top to prevent

evaporation of volatile solutions. DO NOT COMPRESS THE ARM ON TOP OF CAP.

 

2.8 Collect data by following steps 10 to 15 in Section 1.

2.9 When you are finished clean the crystals carefully and put the disassembled apparatus back in the case. Replace

the standard cell holder.