PerkinElmer HATR User manual

HATR SAMPLING ACCESSORY
User’s Guide
MOLECULAR SPECTROSCOPY

Release History
Part Number Release Publication Date
L1050081 B February 2011
Any comments about the documentation for this product should be addressed to:
User Assistance
PerkinElmer Ltd
Chalfont Road
Seer Green
Beaconsfield
Bucks HP9 2FX
United Kingdom
Or emailed to: [e-mail]
Notices
The information contained in this document is subject to change without notice.
Except as specifically set forth in its terms and conditions of sale, PerkinElmer makes no
warranty of any kind with regard to this document, including, but not limited to, the
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.
Copyright Information
This document contains proprietary information that is protected by copyright.
All rights are reserved. No part of this publication may be reproduced in any form whatsoever or
translated into any language without the prior, written permission of PerkinElmer, Inc.
Copyright © 2011 PerkinElmer, Inc.
Produced in the UK.
Trademarks
Registered names, trademarks, etc. used in this document, even when not specifically marked as such,
are protected by law.
PerkinElmer is a registered trademark of PerkinElmer, Inc.
Frontier and Spectrum 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
Introduction...................................................................................................... 7
Installing the Accessory..................................................................................... 9
Fitting the Accessory................................................................................... 9
Accessory Detection by Spectrum Software .................................................11
Contamination Check........................................................................................13
Applying Pressure.............................................................................................14
Using the Accessory with Spectrum Software .....................................................15

4 . HATR Sampling Accessory 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 exampleENTER 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 a Frontier IR System, Spectrum 400 Series or Spectrum 100
Series 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.

HATR Sampling Accessory User’s Guide . 5
Warnings and Safety Information
Before handling ZnSe (zinc selenide), Ge (germanium) 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 . HATR Sampling Accessory 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.

HATR Sampling Accessory User’s Guide . 7
Introduction
Figure 1 The HATR Sampling Accessory
What is the HATR used for?
The HATR (Horizontal Attenuated Total Reflectance) Sampling Accessory is an internal
reflection accessory used with Frontier IR System, Spectrum 100 Series or Spectrum 400
Series spectrometers for simplifying the analysis of solids, powders, pastes, gels and liquids.
The technique is non-destructive.
As the beam does not penetrate too 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 instrument. 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

8 . HATR Sampling Accessory User’s Guide
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 can be supplied with top plates fitted with zinc selenide (ZnSe), germanium (Ge)
or AMTIR-1 crystals. Consult your PerkinElmer Sales Representative for further information
about available top plates.
Choosing the correct crystal
Zinc selenide (ZnSe) crystals are most commonly used as they have a wide range
(650–17000 cm−1) and a refractive index of 2.4. However, zinc selenide is incompatible with
many acids and bases. Therefore AMTIR-1 is often used as its properties are very similar, but
it is more resistant to acids.
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 Sales Representative for advice.
Details of the top plate crystal are displayed in Spectrum software, and this information is
stored in the status information for each spectrum collected.
Figure 3 Top plate details displayed on the Setup Instrument Basic tab in
Spectrum software
Please ensure that you have read the safety information starting on page 4 of this User’s
Guide for your crystal type before continuing.
Choosing the angle of the crystal face
The number of internal reflections and depth of penetration of the beam can be decreased
and absorbance bands in the spectrum weakened by using, for instance, a 60° crystal rather
than a 45° crystal.

HATR Sampling Accessory User’s Guide . 9
Installing the Accessory
Fitting the Accessory
The HATR Sampling Accessory can be simply installed into the sample compartment of the
spectrometer, after first removing any other sampling accessory that is currently fitted.
To remove the current accessory and then install the HATR:
1. Raise the sample cover to the vertical position, press the release clip and lift the cover
upwards, clear of the instrument.
Store it in a safe place for future re-use.
2. Reach in under the base of the current accessory and pull the release handle towards
you to release the accessory.
3. Now simply slide the accessory out of the sample area (Figure 4).
Store it in a safe place for future re-use.
Figure 4 Removing the basic sample slide

10 . HATR Sampling Accessory User’s Guide
4. Slide in the HATR Sampling Accessory, rest the back of it on the ledge in the sample
area and slide it into position. Push it firmly home to ensure that the connector on the
rear of the HATR Sampling Accessory mates properly with the spectrometer connector.
Figure 5 Installing the HATR accessory
5. Place the required top plate (trough or flat plate type) on the HATR accessory, with the
arrows pointing towards the back (Figure 6).
Figure 6 HATR accessory top plate with arrows circled
The HATR Sampling Accessory is now ready for use.

HATR Sampling Accessory User’s Guide . 11
Figure 7 HATR installed in a Frontier IR System
NOTE: When the HATR is installed, a connection is made between the accessory and the
purge system used in the instrument. To purge the accessory, use the left-hand
(Sample) purge connector on the rear of the instrument. The right-hand purge
connector purges the instrument.
Accessory Detection by Spectrum Software
NOTE: If you do not have an instrument installed, see the Administrator’s Guide for your
software for details of the Instrument Install Wizard.
The Spectrum software detects the presence of the accessory, and the HATR icon is
added to the toolbar. The Setup Instrument Basic (Figure 8) and Setup Instrument BeamPath
(Figure 9) tabs are updated to show that the HATR Accessory is in position.
Figure 8 Setup Instrument Basic tab with HATR

12 . HATR Sampling Accessory User’s Guide
Figure 9 Setup Instrument BeamPath tab with HATR icon circled

HATR Sampling Accessory User’s Guide . 13
Contamination Check
The surface of the crystal must be clean before a measurement is taken. The contamination
check can be used to ensure this. If the crystal is not properly cleaned, you may observe
negative bands in the spectra.
Cleaning the crystal
Once data has been collected, clean the crystal using a cotton bud or cotton wool moistened
with water or an organic solvent. Take care not to scratch the surface of the crystal. Ensure
the crystal is completely dry before re-use.
Top plates can be cleaned at the same time as the crystal. However, we recommend that you
remove the top plate from the accessory before cleaning, as a safeguard against spillage.
Do not leave the top of the accessory uncovered for long periods of time. Always place the
dust cover over the accessory when the top plate is removed.
Contamination Ready Check
NOTE: For information about setting up Ready Checks see the Spectrum on-screen Help. The
following description assumes that Ready Checks are already set up and enabled.
To perform a Ready Check:
1. From the Measurement menu, select the Instrument Checks sub-menu and then
Contamination from the Ready Checks available.
The Ready Checks dialog is displayed.
2. Make sure that you have removed your sample and cleaned the top plate, and then click
Scan.
A new background spectrum is collected, compared to the reference background
spectrum and the result of the test is displayed.
3. If required, click the link that enables you to see a print preview of the Instrument
Ready Checks Report.

14 . HATR Sampling Accessory User’s Guide
Applying Pressure
Good contact between the sample and the surface of the crystal is important to prevent loss
of beam penetration. To aid this, a pressure arm can be used to apply controlled force to the
sample to make better contact with the crystal. The pressure arm is used in conjunction with
either a volatiles cover (part number L1205436) or a powder press (part number L1201944),
as described in Table 1.
Table 1 Use of volatiles cover and powder press
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 arm).
Powder press Not applicable. Used to apply pressure to ensure
good contact when analyzing
powders.

HATR Sampling Accessory User’s Guide . 15
Using the Accessory with Spectrum Software
The following pages outline the procedure for obtaining a sample spectrum using a Frontier
instrument fitted with an HATR and running Spectrum software.
For further information on how to use Spectrum software, see the on-screen help provided.
1. Enter the required scan and instrument parameters in the Instrument Settings toolbar.
When your accessory is installed in the instrument, Spectrum will default to the
instrument settings last used to perform a successful scan with that accessory.
Figure 10 The Instrument Settings toolbar
If you want to set instrument parameters that are not displayed in the Instrument
Settings toolbar, select Instrument from the Setup menu. The Setup Instrument pages
are then displayed in the Dialog Pane at the bottom of the workspace.
Figure 8 on page 11 shows the Setup Instrument Basic tab.
2. If you need to collect a background spectrum, ensure that the top plate is clean and
then click on the Measurement toolbar.
Spectrum automatically alerts you when you need a new background, and can be
configured to request a new background at set intervals (on the Setup Instrument Data
Collection tab).
NOTE: If you want to collect a background that will be added to the Sample View and can be
saved separately, then select Background as the Scan type on the Setup Instrument
Basic tab.
3. Place your sample on the top plate.
4. If appropriate, place a powder press or volatiles cover over the sample.

16 . HATR Sampling Accessory User’s Guide
5. If you are using a powder press swing the pressure arm round from the docked position
until it is above the center of the cover as shown in Figure 11.
Figure 11 Pressure arm in operating position, over a powder press
CAUTION
The pressure arm must NOT be used without a volatiles cover or powder
press, as this will result in damage to the top plate.
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 analyzed using a
trough top plate.
6. Screw down the pressure pin to apply force to the sample.
CAUTION
Excessive force can crack and permanently damage the crystal in the top
plate or damage the pressure arm. Be careful not to apply too much
force.
7. Enter a suitable Sample ID and Description in the toolbar, and then click to
enter Preview mode.
The Live tab is displayed.
NOTE: If you have deselected the Preview checkbox on the toolbar, you should select the
Monitor option from the Measurement menu in order to enter Preview mode.

HATR Sampling Accessory User’s Guide . 17
8. Screw down the pressure pin to apply the minimum force to the sample required to give
a good spectrum, as shown on the Live tab.
If an adequate spectrum, with a transmission level of between 40 and 80%, cannot be
achieved, the pressure should be released and a new sample prepared with an
increased or decreased amount of material.
The Force Gauge area of the dialog will display the force being applied. If the indicator
bar turns red, then so much force is being applied that the pressure arm and/or the
crystal is in danger of being damaged.
NOTE: The Force Gauge area is not displayed when the HATR is used in conjunction with a
Spectrum 65 spectrometer.
NOTE: If you want to compare various samples, or use quantitative techniques, ensure you use
the same amount of force each time.
Figure 12 Force Gauge indication in Spectrum software
You are now ready to collect data.
9. Click to obtain the sample spectrum.
The History settings of your sample will contain information about the HATR accessory
type.
The Spectrum Help file describes how to format, process and report your results. To
open the Help file, select Contents from the Help menu.

18 . HATR Sampling Accessory User’s Guide