Manual of RAIRS Mattson Instrument
(Cygnus 100 Rev.7)
Guangming Liu
Postdoctoral researcher in Zaera's lab
Zaera's Laboratory
Department of Chemistry
University of California Riverside
Jan 26, 2004
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1. Optical Route Alignment:
I.
Press a sample as bare clean Au film onto sample holder—home made
reflectance unit.
This position of sample can be adjusted in 3 directions (X, Y,
Z), and it has already been optimized with the maximum signal intensity, try to
keep the same position for every measurement. If possible, suggest to change
another reflectance unit which can be adjusted with the incidence angle (the price
may be around thousands of bucks).
II.
Fill sufficient liquid nitrogen into the MCT detector.
Turn the MCT
preamplifier on. Remember fill this tank at least 1 hour earlier before each
measurement. For better performance, pump this detector each month if possible.
III.
Set the parameters of FTIR for RAIRS measurement in Winfirst program.
Detailed Instructions for Winfirst is written in its manual. Typically I set the
parameters as follows: gain = 4, resolution = 4, Iris = 40%, scan = 4096.
IV.
Display interferogram on the oscilloscope connected preamplifier of MCT
detector.
V.
Move mirrors for getting maximum intensity of interferogram as possible as you
can. Thermal sensitive film (IR card) can be used to track the IR beam and also
focus the beam on sample surface.
VI.
Check interferogram for both p and s polarizations.
2. Optimization of RAIRS Setting up
I. The gain of the instrument can be set to 1, 2, 4. The limit of the centerburst in the
interferogram is 9.999 V, max= 4.999 V, min= -4.999 V. Check the detector was
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saturated or not when the gain set to high values. Using a stable sample as M192/Au as
standard sample, checked the different gain values influence. The following parameters
were set to see how the spectra changing with the different gain values, scan= 1024,
Iris= 40 %, resolution= 2.0 cm-1.
Gain = 1  noise: RMS = 0.0225 (2150-2200 cm-1), p2p = 4.869 V, Signal = 15.582
(970-1040 cm-1), S/N = 692.53;
Gain = 2  noise: RMS = 0.0424 (2150-2200 cm-1), p2p = 6.301 V, Signal = 18.393
(970-1040 cm-1), S/N = 433.80;
Gain = 4  noise: RMS = 0.0410 (2150-2200 cm-1), p2p = 9.999 V, Signal = 22.358
(970-1040 cm-1), S/N = 545.32.
From these data, the best S/N can be achieved at gain= 1, but sometime if you want to
get strong signal intensity, set Gain to 4 is also necessary.
II. Using bare Au film as sample and keep the beam completely open, took back to back
spectra of the same sample and ratioing them, the measured RMS region was from 2100
to 2150 cm-1, the gain = 2, resolution = 4, Iris = 40 %.
Scan= 1  RMS= 0.0861
Scan= 4  RMS= 0.0399
Scan= 16  RMS= 0.0226
Scan= 64  RMS= 0.0111
Scan= 256  RMS= 0.0045
Scan= 1024  RMS= 0.0038
The noise level approximately goes down by a factor of 2 with increasing the scan
number from 1 to 256 except from 256 to 1024.
III. Choose a fixed scan number of 256 (Iris= 40%, Gain= 2, Resolution= 4), and run
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back to back spectra at the different mirror speeds. The velocity of mirror fwd and rev
can be selected as the following values: 80, 40, 20, 10, 5.7, 3.6, 2.6. A series of
experiments were done by choosing the value of 40, 20, 10 and 5.7, repectively.
However, the speed of 80 cannot be properly run by the Winfirst program, there is an
error signal of “laser fault” appeared in the display panel.
Speed set to 40  time= 2.13 min, RMS= 0.0059
Speed set to 20  time= 4.05 min, RMS= 0.0067
Speed set to 10  time= 7.50 min, RMS= 0.0044
Speed set to 5.7  time= 12.58 min, RMS= 0.0041
So the mirror speed of 40 is the best speed which can get with the shortest acquisition
time and the appropriate noise.
IV. To maximize the signal intensity in the interferogram by optimizing the optical route,
we can slightly change the micrometer settings in the fixed comer cube mount. The
horizontal micrometer was kept at 3.525 without change, vertical micrometer was
decreased from 4.059 to 4.025. At this position, the centerburst in the interferogram
reached the maximum intensity although the bottom part was a little clipping.
V. Took spectra versus opening of the iris by using M192/Au polymer as standard
sample. Fixed the following parameters: Resolution = 4.0, Gain = 4.0, Scan = 1024,
Mirror speed: fwd = rev = 40.0.
Iris = 100%  RMS = 0.0574 (2150-2200 cm-1), signal = 18.77 (970-1040 cm-1),
centerburst: p2p = 9.842 V (Min= -4.842 V, Max= 4.999 V); S/N= 327.00
Iris = 80%  RMS = 0.0574 (2150-2200 cm-1), signal = 18.76 (970-1040 cm-1),
centerburst: p2p = 9.771 V (Min= -4.772 V, Max= 4.999 V); S/N= 326.83
Iris = 60%  RMS = 0.0560 (2150-2200 cm-1), signal = 18.66 (970-1040 cm-1),
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centerburst: p2p = 9.652 V (Min= -4.660 V, Max= 4.999 V); S/N= 333.21
Iris = 40%  RMS = 0.0366 (2150-2200 cm-1), signal = 17.52 (970-1040 cm-1),
centerburst: p2p = 8.408 V (Min= -3.408 V, Max= 4.999 V); S/N= 478.69
Iris = 30%  RMS = 0.0377 (2150-2200 cm-1), signal = 16.804 (970-1040 cm-1),
centerburst: p2p = 8.072 V (Min= -3.072 V, Max= 4.999 V); S/N= 445.73
Iris = 20%  RMS = 0.0351 (2150-2200 cm-1), signal = 15.1465 (970-1040 cm-1),
centerburst: p2p = 7.658 V (Min= -2.658 V, Max= 4.999 V); S/N= 431.52
Iris = 10%  RMS = 0.0248 (2150-2200 cm-1), signal = 11.63 (970-1040 cm-1),
centerburst: p2p = 5.097 V (Min= -1.826 V, Max= 3.276 V); S/N= 468.95
Both of the signal intensity and the noise level increased with the opening of the iris
size, the best S/N was found at the iris size of 40% opening.
VI. Using mask to define beam at different size of 1.2, 1.0, 0.5 (diameter), checked
the size of the centerburst, the noise level, and the actual size of the strongest peaks, for
each beam size spectra were measured by using two iris sizes of 40% and 100%,
respectively.
A. Beam size= 1.2 ,
Iris= 40%  RMS= 0.0322 (2150-2200 cm-1), signal= 6.70 (970-1040 cm-1),
centerburst: p2p=6.656 V (Min= -2.355 V, Max= 4.340 V)
Iris= 100%  RMS= 0.0347 (2150-2200 cm-1), signal= 6.75 (970-1040 cm-1),
centerburst: p2p=7.187 V (Min= -2.522 V, Max= 4.750 V)
B. Beam size= 1.0 ,
Iris= 40%  RMS= 0.0256 (2150-2200 cm-1), signal= 4.15 (970-1040 cm-1),
centerburst: p2p=5.797 V (Min= -2.149 V, Max= 3.685 V)
Iris= 100%  RMS= 0.0260 (2150-2200 cm-1), signal= 4.18 (970-1040 cm-1),
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centerburst: p2p=6.333 V (Min= -2.002 V, Max= 4.335 V)
C. Beam size= 0.5 ,
Iris= 40%  RMS= 0.0082 (2150-2200 cm-1), signal= 1.0512 (970-1040 cm-1),
centerburst: p2p=2.569 V (Min= -0.925 V, Max= 1.660 V)
Iris= 100%  RMS= 0.0090 (2150-2200 cm-1), signal= 1.0521 (970-1040 cm-1),
centerburst: p2p=2.568 V (Min= -0.936 V, Max= 1.645 V)
D. Beam size= 3.0  (without mask),
Iris= 40%  RMS= 0.0496 (2150-2200 cm-1), signal= 18.61 (970-1040 cm-1),
centerburst: p2p=8.880 V (Min= -3.880 V, Max= 4.999 V)
Iris= 100%  RMS= 0.0570 (2150-2200 cm-1), signal= 18.60 (970-1040 cm-1),
centerburst: p2p=4.176 V (Min= -4.187 V, Max= 4.999 V)
VII. Test the quality of the spectra taken at different resolutions. There are several
options for the resolution of this instrument, such as 0.5, 1.0, 2.0, 4.0, 8.0, 16.0, 32.0,
64.0, 128.0, cm-1, higher resolution does increase the sensitivity of the spectra, make it
easier to find the peak we want, however, it also means more acquisition time and much
more noise. Using the stable M192/Au as standard sample, checked the spectra quality
with the different resolution (1,2, 4, 8 cm-1), as shown in the figure below.
Resolution = 8 cm-1  t = 5.12 min, RMS = 0.0252 (2150-2200 cm-1), signal = 18.865
(970-1040 cm-1);
Resolution = 4 cm-1  t = 8.51 min, RMS = 0.0332 (2150-2200 cm-1), signal = 21.93
(970-1040 cm-1);
Resolution = 2 cm-1  t = 15.36 min, RMS = 0.0529 (2150-2200 cm-1), signal = 22.857
(970-1040 cm-1);
Resolution = 1 cm-1  t = 29.01 min, RMS = 0.0536 (2150-2200 cm-1), signal = 22.77
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(970-1040 cm-1);
So the resolution 2 or 4 cm-1 is the desirable resolution we can select in the experiments.
VIII.
Optimize the incidence angle:
The incidence angle was optimized to set around 83. If the incident angle was set near
85, the signal intensity was very small at this position; most of the beam was directly
transmitted while not reflected to the mirror. This means much signal intensity was lost,
so it is very difficult to set the angle over 85, 83 is probably the most incident angle we
can reach with high intensity.
3. Measurements
I. Preparation of the Pr SAMS: SAMs of porphyrins were prepared by immersing the
freshly deposited Au coated substrates into 1 mM deoxygenated solutions of the desired
porphyrin in CH2Cl2 at room temperature for 1-7 days (the deposition time was varied
to reach the desired SAM surface concentration and to ensure the formation of well
organized SAMs). Upon removal from the solution, the samples were then rinsed
thoroughly with CH2Cl2 and ethanol, to remove physisorbed species and blown dry with
a steam of argon. They were used immediately for spectral measurements.
II.
Before testing, flow the purging gas liquid nitrogen with appropriate time, the
longer time maybe reduce the water noise, but the integrity of the sample would be less,
so make sure the stability of your sample, then decide how much time you may require
(typically 1-2 hours for porphyrin molecules).
III. Press the sample to the optimized position on the sample holder surface, try to keep
the sample at the same position at each measurement.
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IV. After a certain time, start background spectral measurement at s-polarizer position.
After that, immediately start-acquiring p polarized spectra.
V. After the measurement, the sample should be pulled up from the sample holder and
make ready for the next sample.
4. Maintenance
Checking Laser Signals on Rev. 7 Polaris Benches
1. Disconnect the voice coil drive cable from P 7 (the black an white wire pair) located
just below the heat sinks on the center right side of the main control board.
2. Record the micrometer settings for the fixed corner cube mount. These numbers will
be necessary if the micrometers are changed inadvertently during this procedure.
Horizontal Micrometer 3.525
Vertical Micrometer 4.059
3. Connect the two oscilloscope input probes to TP 1 and TP 21 on the main control
board. The test pints are located 2 inches to the left of the beamsplitter under the
front lip of the touch panel display. Connect the grounds to the ground loop near P 4.
Set the oscilloscope as follows:
Channel A input
Connect to TP 1
Channel B input
Connect to TP 21
Ground Lead
Connect to ground pin
Channels A & B input coupling: Set both to ac
Vertical gain
Set to 1.0 volt/cm
Set to 20 Sec/cm
Horizontal gain
Trigger source
Channel A
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Trigger mode
Auto
Adjust the position, brightness, etc., controls until the signals are displayed. They should
be DC signals with varying voltages (close to noise until the mirror is moved by hand).
Adjust the vertical position controls on the oscilloscope so that the grounded signal from
TP 1 and TP 21 are overlapping on the center of the screen. Set the scope inputs back to
AC. Move the mirror and observe the phase difference of the signals. The phase of the
signal from TP 21 should change; (The signal from TP 1 should not change because it is
the trigger source).
Move the linear bearing slowly back and forth at about 1 to 2 cm/sec. The two signals
being displayed should appear as sine waves with a frequency, which varies with the
velocity of the mirror. Set the trigger level control on the scope to stabilize the display.
The peak-to-peak voltage of the signals should be between 2 and 4 volts. Carefully adjust
the two micrometer handles while continuing to move the bearing. Set the micrometers to
the point, which produces the maximum laser signal voltage. If the sine waves do not
appear when you move the mirror, check the micrometer setting by referring to the
numbers you recorded above.
Adjusting the amplitude of the laser signals:
If the signal intensity is low, check where the laser is striking the diode. The brightest dot
should strike the center of the diode window. If not, loosen the diode arm with a 3/32” hex
wrench, adjust and re-tighten. You can remove the diode from the holder and place a
piece of tape over the hole to see the laser’s path. At the same time check the optical
quality of the beamsplitter, is it starting to fog?
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If you cannot increase the laser-signal by optical alignment then you can adjust the
amplification of the signals on the control board. The gain pots in the circuit are R 26 for
TP 21 and R 25 for TP 1. If adjusting gain, makes sure that the signal is not clipping
(flattening off the bottom of the signals). It is better to have a 1 to 2 volt signal, than a
signal that is clipping.
The proper phase of the two signals is shown. The TP 21 signal should lead the TP1 signal
by 90 degrees when the mirror is moving towards the Beamsplitter, and should lag by 90
degrees when the mirror is moving away from the Beamsplitter. The phase angle should
be 90 degrees +/- 10 degrees. If the phase is inaccurate, the reliability of the scanning of
the mirror may be affected, or the mirror may not scan at all.
5. Typical conditions of FTIR-RAIRS
Mattson Cygnus 100
Scan speed
40
Number of scan
1024 or 4096
Aperture
25-40%
Amplifier Gain
4
Others
factory setting
Interferogram intensity
3-6 V peak-peak
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11
IR B ench Plate of C Y G N U S R ev7
29.5 c m
24 c m
2.0 cm
17.0 c m
25.5 c m
6.5 cm
D = 1.25 c m
47.0 c m
１２
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Tp 3
Le ft p in P1
R11
R12
2
1
R8
R7
Tp 1
2nd left P1
Sche m a tic e lec tro nic d ia g ra m o f sm a llc ontro lb o a rd
１３
M a ttso n FT-IR C yg nus 100
Foc us m irror
IR b e a m
W ire g rid
p o la rize r
M C T d e te ctor
Sa m p le
 

Pa ra b o lic m irro r
Pa ra b o lic m irro r
１４
１５