PerkinElmer Spectrum Two HATR User manual

SPECTRUM TWO HATR
User’s Guide
MOLECULAR SPECTROSCOPY

Release History
Part Number Release Publication Date
L1050232 A March 2011
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United Kingdom
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Notices
The information contained in this document is subject to change without notice.
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implied warranties of merchantability and fitness for a particular purpose.
PerkinElmer shall not be liable for errors contained herein for incidental consequential damages in
connection with furnishing, performance or use of this material.
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Copyright © 2011 PerkinElmer, Inc.
Produced in the UK.
Trademarks
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are protected by law.
PerkinElmer is a registered trademark of PerkinElmer, Inc.
Spectrum and Spectrum Two are trademarks of PerkinElmer, Inc.

Contents
Conventions Used in this Manual........................................................................ 4
Notes, Cautions and Warnings..................................................................... 4
Warnings and Safety Information....................................................................... 5
ZnSe (zinc selenide) crystals........................................................................ 5
Ge (germanium) crystals............................................................................. 6
AMTIR-1 crystals ........................................................................................ 6
KRS5 (Thallium bromide/iodide) Crystals...................................................... 7
Introduction...................................................................................................... 8
Installing the Accessory....................................................................................11
Accessory Detection by Spectrum Software .................................................12
Aligning the HATR............................................................................................14
Purging the HATR.............................................................................................17
Installing the Pressure Clamp............................................................................18
Using the Accessory with Spectrum Software .....................................................20
Contamination Check........................................................................................25

4 . Spectrum Two HATR User's Guide
Conventions Used in this Manual
Normal text is used to provide information and instructions.
Bold text refers to text that is displayed on the screen.
UPPERCASE text, for example ENTER or ALT, refers to keys on the PC keyboard. '+' is
used to show that you have to press two keys at the same time, for example, ALT+F.
All eight-digit numbers are PerkinElmer part numbers unless stated otherwise.
The term ‘instrument’ refers to the Spectrum Two FT-IR spectrometer, and any sampling
accessory fitted.
Notes, Cautions and Warnings
Three terms, in the following standard formats, are also used to highlight special
circumstances and warnings.
NOTE: A note indicates additional, significant information that is provided with some
procedures.
CAUTION
We use the term CAUTION to inform you about situations that could
result in
serious damage
to the instrument
or other equipment.
Details about these circumstances are in a box like this one.
WARNING
We use the term WARNING to inform you about situations that could
result in personal injury to yourself or other persons. Details about these
circumstances are in a box like this one.

Spectrum Two HATR User's Guide . 5
Warnings and Safety Information
Before handling ZnSe (zinc selenide), Ge (germanium), KRS5 (thallium bromo-iodide) or
AMTIR-1 crystals, please ensure that you have read the appropriate Material Safety Data
Sheets (MSDS).
You can search for up-to-date copies of safety data sheets on materials used in PerkinElmer
products that are known to have safety issues from the Technical Resources section of the
PerkinElmer website. The MSDS information is available in a range of languages, and includes
data items required in specific national, supra-national and state jurisdictions.
To obtain a safety data sheet for a particular compound, follow the steps described below.
NOTE: To read MSDS .pdf files you will need Adobe Reader 5.0 or later. An installation of
this software is available on the Software Utilities CD .
1. Launch your web browser and navigate to the PerkinElmer web site:
www.perkinelmer.com
If you are not redirected automatically you may have to select the home page
appropriate to your location.
2. Search for the term MSDS using the search box located at the top of the home page.
The Search for Material Safety Data Sheets (MSDS) page is displayed.
3. Enter the key words for the compound, in the Product name box, and then click Go.
A full list of all MSDS documents that refer to the compound is displayed.
4. Select the MSDS document you want to view.
ZnSe (zinc selenide) crystals
WARNING
During routine use of your HATR Sampling Accessory the ZnSe crystal
presents no hazard, but:
DO
wear protective gloves when handling the crystal.
DO NOT
use acids to wash the crystal because they react to emit H2Se,
which is very toxic and irritating.
DO NOT
allow the crystal to come into contact with oxidizers.
The crystal is highly toxic by ingestion.

6 . Spectrum Two HATR User's Guide
Cleaning ZnSe crystals
Avoid contact of the crystal with oxidizers and acids. ZnSe can be cleaned in pure dry acetone
or methanol using a soft, lint-free cloth. Dry in a current of warm air so that there is no
possibility of condensation forming on the crystal. Other suitable solvents are petroleum ether
and hexane. It may also be cleaned in some commercial laboratory detergents, but they
must be neutral. Alkaline solutions will slightly etch the surface, and acids will severely attack
the material. A final rinse in distilled water and then drying in a current of warm air is
recommended.
Ge (germanium) crystals
WARNING
During routine use of your HATR Sampling Accessory the Ge crystal
presents no hazard, but:
DO
wear protective gloves when handling the crystal.
May be harmful if ingested in quantity, and may irritate or cause
physical damage to eyes.
DO NOT
use acids to wash the crystal.
Ge can react violently with oxidizers, and can ignite in contact with
chlorine and bromine.
Cleaning Ge crystals
Clean the crystal using an organic solvent; do not use acids or oxidizers.
AMTIR-1 crystals
WARNING
During routine use of your HATR Sampling Accessory the
AMTIR-1 crystal presents no hazard, but:
DO
wear protective gloves when handling the crystal.
DO NOT
use strong acids, strong bases or strong oxidizers with
the AMTIR-1 crystal.
Cleaning AMTIR-1 Crystals
Use an organic solvent to clean the crystal.

Spectrum Two HATR User's Guide . 7
KRS5 (Thallium bromo-iodide) Crystals
WARNING
During routine use of your HATR, the KRS5 crystal presents no hazard,
but:
DO
wear protective gloves when handling the crystal.
DO NOT
allow
the crystal to come into contact with oxidizers.
We recommend that you
DO NOT
wash the crystal with water.
The crystal is extremely toxic by ingestion, and is harmful in contact with
skin. May evolve toxic fumes in a fire.
Cleaning KRS5 Crystals
Clean the crystal using an organic solvent; do not use an oxidizer.

8 . Spectrum Two HATR User's Guide
Introduction
The Horizontal Attenuated Total Reflectance (HATR) Accessory is an internal reflection
accessory used for simplifying the analysis of solids, powders, pastes, gels and liquids
(Figure 1). The technique is non-destructive.
Figure 1 The Horizontal Attenuated Total Reflectance (HATR) Accessory
As the beam does not penetrate far into the sample, this technique is ideal for analyzing
strong infrared absorbing solutions, such as emulsions or aqueous solutions. The technique
can also prove useful in measuring homogenous solid samples, solid surfaces and coatings on
solid samples.
How it works
The technique involves placing a sample on top of a crystal with a high refractive index. An
infrared beam from the instrument is passed into the accessory and up into the crystal. It is
then reflected internally along the crystal, and back towards the detector that is housed
within the spectrometer. Each time the beam is reflected within the crystal, it penetrates into
the sample by a few microns. Figure 2 illustrates this process.
Figure 2 Principle of HATR operation

Spectrum Two HATR User's Guide . 9
Choosing the top plate
The HATR can be used to analyze powders, pastes, gels and liquids using a trough top plate,
where the sample is poured into the trough. Alternatively, a flat plate may be used for
homogenous solid samples, solid surfaces, or coatings on solid samples. Force may be
applied to ensure good contact between the sample and the crystal. The flat plate can also
be used to analyze gels and pastes, by spreading them on the surface of the plate.
The HATR is supplied with a top plate fitted with a ZnSe crystal. Top plates fitted with
germanium (Ge), KRS5 or AMTIR-1 crystals (Table 1) are available.
Table 1 HATR top plates
Sample trough Flat sampling plate
ZnSe L1360266 L1360267
Ge L1360268 L1360269
AMTIR-1 L1360270 L1360271
KRS5 L1360272 L1360273
Choosing the correct crystal
For most applications involving organic materials, ZnSe is the most useful HATR crystal
material. It combines a relatively wide transmission range (17 000–650 cm−1), a high
refractive index (2.4) and hardness, and is insoluble in distilled water. ZnSe is, however,
incompatible with many acids and bases.
AMTIR-1 has a similar hardness and refractive index to ZnSe, so absorption bands will be of
similar intensity to within approximately 10%. The transmission range is slightly narrower
than ZnSe (11 000–700 cm−1). AMTIR-1 is more resistant than ZnSe to acids (to
approximately 6 N), and is therefore more appropriate for use with some acidic solutions. We
recommend that you DO NOT use AMTIR-1 with strong acids, strong bases and strong
oxidizers.
Germanium (Ge) crystals have a high refractive index of 4.0 and are used for highly
absorbing samples such as carbon-filled polymers and rubbers, and samples with a high
water content. These crystals are also resistant to strong acids and bases.
NOTE: Derivative-shaped bands can be observed in the spectrum if the refractive index of
the sample is too close to the refractive index of the crystal. For this reason,
alternative crystal types may be required for specific sample types. Consult your
PerkinElmer Customer Care Representative for advice.
You must verify that the sampling crystal is not soluble or otherwise damaged by the sample.
A summary of the physical properties of commonly used crystal materials is provided in
Table 2.
NOTE: We recommend that you remove the sample plate from the HATR when you clean the
crystal.

10 . Spectrum Two HATR User's Guide
Table 2 Properties of crystal materials
ZnSe Ge KRS5 AMTIR-1
ATR range (cm−1) 17 000–650 5500–600 14 000–400 11 000–700
Refractive index at
1000 cm−1 2.4 4.0 2.37 2.50
Density (g/cm3) 5.27 5.32 7.37 4.4
Max. useful temp.
in air (°C) 300 270 200 300
Hardness
(Knoop #) 150 1150 40.2 170
Cleaning agents acetone, water toluene, water MEK organic solvents
Solvents that
attack material acids, strong alkalis hot H2SO4, aqua regia complexing agents strong acids, strong bases,
strong oxidizers
Remarks hard,
easily cracked hard and brittle, high reflection
loss
deforms under
pressure, toxic,
does not cleave
hard and brittle
NOTE: The ATR crystal is bonded to the sample plate with an adhesive, we therefore
recommend that you do not leave the crystal in contact with solvents, particularly
chlorinated solvents, for long periods.
Please ensure that you have read the safety information starting on page 4 of this User’s
Guide for your crystal type before continuing.

Spectrum Two HATR User's Guide . 11
Installing the Accessory
CAUTION
The mirrors in the HATR are aluminum-coated and, although they are
durable, their surfaces are relatively soft and difficult to clean without
scratching. Therefore, take care to avoid dropping materials on the
mirrors when you are handling the unit and placing samples on the
sampling surface.
The HATR is pre-mounted on the Spectrum Two baseplate for quick installation into the
sample compartment of the spectrometer.
To remove the current accessory and then install the HATR:
1. Open the sample cover of the Spectrum Two, if fitted.
2. Pull the baseplate of the current sample accessory towards you, and slide the accessory
out of the sample area (Figure 3).
Store it in a safe place for future re-use.
Figure 3 Removing the sampling accessory
3. Start Spectrum software and connect to the instrument.
4. Select Monitor from the Measurement menu in Spectrum software and record the
energy throughput of the open beam.
When you have finished, click Halt.
5. If you are using the flat sampling plate or analyzing powder samples using the trough
sampling plate, ensure that the pressure clamp is fitted before you install and align the
HATR.
If required, follow the instructions to install the pressure clamp in
Installing the Pressure
Clamp
on page 17.
Accessory baseplate with
sample holder fitted

12 . Spectrum Two HATR User's Guide
6. Slide in the HATR accessory baseplate (Figure 4). Push it in firmly to ensure that the
connector on the rear of the baseplate connects properly with the spectrometer
connector.
Figure 4 Installing the HATR accessory
7. Place the required top plate (trough or flat plate type) on the HATR accessory.
Although the HATR is pre-mounted on the baseplate, we recommended that you maximize
the energy throughput of the system as described in
Aligning the HATR on page 14 after
installing the accessory, or after changing between top plates with crystals of very different
refractive index.
Accessory detection by Spectrum software
When the accessory is installed in the sample compartment, Spectrum software detects it,
and the Setup Instrument Basic (Figure 5) and Setup Instrument BeamPath (Figure 6) tabs
are updated to show that the HATR Accessory is in position. The Accessory toolbar displays
the HATR icon .
Figure 5 Setup Instrument Basic tab with HATR

Spectrum Two HATR User's Guide . 13
Figure 6 Setup Instrument BeamPath tab with HATR icon circled

14 . Spectrum Two HATR User's Guide
Aligning the HATR
Make sure that the sample trough or the flat sampling plate and, if applicable, the pressure
clamp are properly mounted on the base assembly before aligning the HATR.
1. In Spectrum software, select Monitor from the Measurement menu.
The Live tab is displayed.
2. Record the energy throughput of the HATR.
3. Compare this value with the value for the energy throughput of the open beam
(recorded at the beginning of the installation procedure – Step 4 on page 11).
If you did not record the value, remove the HATR from the spectrometer and then
measure the value.
If you do not observe an energy throughput, or if you are aligning your accessory for
the first time, continue at Step 4.
If you do observe an energy throughput, and your accessory has been aligned
previously, continue at Step 15.
4. Click Halt to exit the Live tab.
5. Insert the alignment tool in position on the baseplate (Figure 7).
Press the alignment tool mount firmly to locate the two pins on the base of the
alignment tool into the holes on the baseplate.
Figure 7 Alignment tool in position on the HATR baseplate
6. Connect the 15-way connector on the cable of the alignment tool into the EXT
DETECTOR port on the rear of the spectrometer (Figure 8).
The white LED on the alignment tool should be lit.

Spectrum Two HATR User's Guide . 15
Figure 8 Alignment tool connected to EXT DETECTOR port
7. Make sure that mirrors 1 and 4 (Figure 9) are against their alignment pins, using the
wrench supplied.
The top plate of the accessory can be removed to confirm this. Figure 9 shows the
mirrors and the corresponding adjustment nuts on the rear of the HATR are shown.
Mirror 1 should be rotated fully clockwise and mirror 4 should be rotated fully
counterclockwise, looking from the front of the sample compartment.
Figure 9 HATR with top plate removed (viewed from rear to show the adjustment
nuts)
Figure 10 shows the optical path of the accessory, viewed from the rear as in Figure 9.
Figure 10 Optical path of the accessory
Mirror 2
Mirror 4
Mirror 1
Mirror 3
Mirror 2
Crystal
Mirror 1
Mirror 3
Mirror 4
Alignment pin
Alignment pin
IR beam (from left of
sample compartment)

16 . Spectrum Two HATR User's Guide
NOTE: Take care when adjusting mirrors 2 and 3. They are very sensitive to rotational
adjustment.
8. Place the top plate on the accessory.
9. Look at the crystal from above, and gently adjust mirror 2 until the crystal is illuminated
as brightly as possible.
10. Place a card between the exit port of the HATR and the window on the right of the
sample compartment.
11. Adjust mirror 3 until the movable part of the beam is centered on the exit window.
12. Remove the card from the HATR.
13. Remove the white-light alignment tool from the baseplate.
14. Select Monitor from the Measurement menu.
The Live tab is displayed.
15. Gently adjust mirror 2, using a wrench, until you obtain an energy maximum.
16. Repeat for mirror 3.
NOTE: You may need to adjust mirror 2 and mirror 3 several times to find the optimum
position.
17. Record the maximum throughput energy and then click Halt.
18. Compare the maximum energy with that recorded at the beginning of the installation
procedure (Step 4 on page 11).
If the energy throughput of the HATR is 15–25% of the energy throughput of the open
beam, no further adjustments are needed.
If the energy throughput of the HATR is lower than 15% of the energy throughput of
the open beam, repeat the alignment procedure.

Spectrum Two HATR User's Guide . 17
Purging the HATR
With the Spectrum Two spectrometer, you can purge the HATR rather than the sample
compartment. In this way the purge is maintained when you change sample (provided that
you do not remove the top plate) and the purge volume is less.
Use polyethylene tubing with a 6 mm external diameter and a 4 mm internal diameter to
carry the gas to the purge inlet on the HATR.
1. Loosen the knurled nut on the HATR (Figure 11).
Figure 11 The purge connection on the HATR
2. Push the tube through the nut until it rests against the interior connector.
3. Tighten the nut to clamp the tube in place.
4. Purge the HATR using a flow rate of approximately 1 or 2 l/min.
5. Monitor the baseline until H2O/CO2vapor is reduced or negligible.
You should turn off the atmospheric correction in Spectrum software, by deselecting the
CO2/H2O check box on the Setup Instrument Advanced tab.
Knurled nut

18 . Spectrum Two HATR User's Guide
Installing the Pressure Clamp
CAUTION
When using a flat top plate and a solid sample, the surface of the
sample must be flat. You must not try to correct for uneven surfaces
by applying extra force as you may damage the crystal. Samples with
uneven surfaces should be ground to a powder and used on a trough
top plate.
It is important to have good contact between the sample and the surface of the crystal to
prevent loss of beam penetration. To aid this, an optional pressure clamp can be used to
apply controlled force to the sample to make better contact with the crystal.
The pressure clamp enables you to improve the contact between a film sample and the
sample plate. When analyzing powder samples, it can also be used to apply pressure to
powder in the sample trough. The pressure clamp is used in conjunction with either a
volatiles cover (L1205436) or a powder spacer (L1362431), as described in Table 3.
Table 3 Use of volatiles cover and powder spacer
Item Flat top plate Trough top plate
Volatiles cover Used to apply pressure to polymer
films or laminates. Used to prevent evaporation (without use of pressure clamp).
Powder spacer Not applicable. Used to apply pressure to ensure
good contact when analyzing
powders.
Your accessory may have been supplied with the pressure clamp installed. If, however, you
need to fit the pressure clamp, refer to the following procedure.
1. Attach the clamp to the body of the HATR using the two screws provided (Figure 12).
Figure 12 Installing the pressure clamp
Sample plate
Pressure pad
Clamp
Securing
screws

Spectrum Two HATR User's Guide . 19
2. Place the pressure pad on the sample plate, in the V-shaped slot in the clamp, so that
the graduated scale on the pressure plate faces toward you.
3. Push the lever of the clamp into position so that pressure is applied to the sample plate.
Adjusting the pressure
The clamp is supplied pre-set to apply approximately 50 newtons of pressure to a flat crystal
assembly (45° ZnSe). This is a satisfactory setting for most applications.
1. Read the scale on the pressure pad and use Figure 13 to calculate the approximate
pressure being applied.
Figure 13 Pressure as a function of the spring height of the clamp
2. To adjust the pressure, turn the screw on the top of the clamp.
CAUTION
Excessive pressures can crack and permanently damage the ATR crystal.
Do not use the pressure clamp to crush the sample, and do not apply
pressure to the crystal for extended periods of time.

20 . Spectrum Two HATR User's Guide
Using the Accessory with Spectrum Software
CAUTION
Excessive pressures can crack and permanently damage the ATR crystal.
Do not use the pressure clamp to crush the sample, and do not apply
pressure to the crystal for extended periods of time.
The Measurement bar (Figure 14) displayed by default at the top of the workspace includes
the tools you need to collect a spectrum from a sample. You can also select these commands
from the Measurement menu.
Figure 14 Spectrum Two Measurement bar
To perform a scan:
1. Ensure that the required scan and instrument parameters have been set.
When you first fit the accessory, the software automatically sets default scan
parameters to values that are appropriate to the HATR.
If you want to set any of the instrument parameters that are not included on the
toolbars, select Instrument from the Setup menu to display the Setup Instrument tabs.
2. If you want, enter a unique Sample ID and Description for the sample on the
Measurement bar.
3. Ensure that the top plate is clean and then click to collect a background spectrum.
4. Place your sample on the top plate and, if appropriate, place a powder spacer or
volatiles cover over the sample.
Refer to
Sample Preparation on page 22 for more details of how to prepare your sample
for analysis.
5. If Preview is selected on the Measurement bar, click to view the spectrum.
NOTE: If Preview is not selected, you can preview the spectrum by selecting Monitor from
the Measurement menu.
The Live tab is displayed. The spectrum is displayed, but no data is recorded.