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
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.
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.