Alpha.pdf

User Manual

1005541

ALPHA

2nd edition, publication date May 2011

2011 BRUKER OPTIK GmbH, Rudolf-Plank-Strae 27, D-76275 Ettlingen, www.brukerop-tics.com

All rights reserved. No part of this manual may be reproduced or transmitted in any form or by any means including printing, photocopying, microfilm, electronic systems etc. without our prior written permission. Brand names, registered trademarks etc. used in this manual, even if not explicitly marked as such, are not to be considered unprotected by trademarks law. They are the property of their respective owner.

This manual is the original documentation for the ALPHA spectrometer. The ALPHA spec-trometer is covered by one or more of the following patents: US 5,499,095; US 5,923,422; DE 19940981. Other US and international patents are pending.

B r u k e r O p t i k G m b H A L P H A U s e r M a n u a l i i i

< N u m b e r > 1

Table of Contents

1 About this Manual . . . . . . . . . . . . . . . . . . . . . . . . 1

2 ALPHA & Measurement Modules . . . . . . . . . . . . . 32.1 General Technical Features . . . . . . . . . . . . . . . . . . . . 32.2 Basic Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42.3 ALPHA-T Measurement Module . . . . . . . . . . . . . . . . . . 52.4 ALPHA-P Measurement Module . . . . . . . . . . . . . . . . . 72.5 ALPHA-E Measurement Module . . . . . . . . . . . . . . . . . 82.6 Exchanging Measurement Module . . . . . . . . . . . . . . 92.7 Operat ing Spectrometer . . . . . . . . . . . . . . . . . . . . . . 112.8 Act ivat ing Stand-by Mode . . . . . . . . . . . . . . . . . . . . 11

3 Quick User Guide . . . . . . . . . . . . . . . . . . . . . . . 133.1 Measurement . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 133.2 Qual i ty Contro l . . . . . . . . . . . . . . . . . . . . . . . . . . . . 243.3 Ident i f icat ion of an unknown Substance . . . . . . . . . . . 313.4 Quant i tat ion of a Sample Component . . . . . . . . . . . . 35

4 Sample Preparation . . . . . . . . . . . . . . . . . . . . . . 414.1 No Sample Preparat ion . . . . . . . . . . . . . . . . . . . . . . 424.2 KBr Pel let . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 424.3 Thin f i lm between two plates . . . . . . . . . . . . . . . . . . 43

5 Transmission Measuring . . . . . . . . . . . . . . . . . . 455.1 General Informat ion . . . . . . . . . . . . . . . . . . . . . . . . . 455.2 ALPHA-T . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 465.3 Posi t ioning sample in the ALPHA-T sample compart-

ment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 475.4 Measur ing Sample . . . . . . . . . . . . . . . . . . . . . . . . . . 50

6 ATR Measuring . . . . . . . . . . . . . . . . . . . . . . . . . 516.1 General Informat ion . . . . . . . . . . . . . . . . . . . . . . . . . 516.2 ATR Measurement Module . . . . . . . . . . . . . . . . . . . . 526.3 Performing Cleanness Test . . . . . . . . . . . . . . . . . . . 576.4 Placing Sample on ATR Crystal . . . . . . . . . . . . . . . . 576.5 Measur ing Sample . . . . . . . . . . . . . . . . . . . . . . . . . . 586.6 Cleaning ATR Module . . . . . . . . . . . . . . . . . . . . . . . 596.7 ATR Spectra . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60

i v A L P H A U s e r M a n u a l B r u k e r O p t i k G m b H

T a b l e o f C o n t e n t s

7 Maintenance & Repair . . . . . . . . . . . . . . . . . . . . 617.1 Replacing IR Source . . . . . . . . . . . . . . . . . . . . . . . . 627.2 Replacing Desiccant Bags . . . . . . . . . . . . . . . . . . . . 657.3 Replacing Windows . . . . . . . . . . . . . . . . . . . . . . . . . 677.4 Cleaning Windows . . . . . . . . . . . . . . . . . . . . . . . . . . 707.5 Cleaning Spectrometer Housing . . . . . . . . . . . . . . . . 70

8 Troubleshooting . . . . . . . . . . . . . . . . . . . . . . . . 718.1 General Informat ion . . . . . . . . . . . . . . . . . . . . . . . . . 718.2 Avai lable Diagnost ic Means . . . . . . . . . . . . . . . . . . . 728.3 Problem - Possible Causes - Solut ions . . . . . . . . . . . 79

A Specif ications . . . . . . . . . . . . . . . . . . . . . . . . . . 93

B Consumables . . . . . . . . . . . . . . . . . . . . . . . . . . 95

C Dimensional Drawings . . . . . . . . . . . . . . . . . . . . 97

D Glossary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107

E Service Addresses . . . . . . . . . . . . . . . . . . . . . 111

B r u k e r O p t i k G m b H A L P H A U s e r M a n u a l 1

C h a p t . 1

1 About this ManualThe ALPHA user manual contains detailed information on the single spectrometer measurement modules in chapter 2.

On the basis of different examples the Quick User Guide in chapter 3provides a step-by-step introduction into the OPUS software, and gives answers to analytical problems.

For sample preparation refer to chapter 4 which contains a short summary of the most important sample preparation methods.

Chapter 5 describes in detail the measuring in transmission modeand gives information on how to properly position the sample in the sample compartment of the transmission module.

Detailed information on what has to be considered in case of ATR measuring, what crystal types are available and how to position the sample on the ATR crystal is given in chapter 6.

Maintenance instructions and a description of the steps required when replacing the IR source, the desiccant bag as well as the KBr-window are included in chapter 7.

Chapter 8 describes possible spectrometer problems, their diagnosis as well as troubleshooting by means of the OPUS software.

The specifications of the ALPHA spectrometer are listed in appendix A, the most important customer drawings are included in appendix B.

The glossary in appendix D describes single relevant spectroscopic terms in more detail. For the worldwide Bruker service addresses refer to appendix E.

C h a p t . 1

2 A L P H A U s e r M a n u a l B r u k e r O p t i k G m b H

A b o u t t h i s M a n u a l


C h a p t . 2

2 ALPHA & Measure-ment Modules

2.1 General Technical Features

The ALPHA spectrometer is a small compact FT-IR spectrometer designed for routine applications in the laboratory. Due to its modular design ALPHA ensures highest possible flexibility during measurement. ALPHA consists of a basic module and an exchangeable measurement module. The following measurement modules are available.

Module available Type of measurement To be used for the following sample types

ALPHA-T(Universal Sampling Module)

Transmission Solids (e.g. plasic films, KBr pellets) liquids, gases

ALPHA-P(Platinum ATR Module; avail-able as high pressure module as well)

Attenuated total reflection (ATR)

Solids, liquids

ALPHA-E(Economic ATR Module)

Attenuated total reflection (ATR)

Solids, liquids

The different modules are described in the following. For further information on the single measurement modules refer to chapter 5 and 6.

Figure 1: Modular spectrometer design

Basic module

Exchangeable measurement module

C h a p t . 2


A L P H A & M e a s u r e m e n t M o d u l e s

2.2 Basic Module

The basic module contains the following optical components:

IR source low voltage, air cooledlifetime: 44,000 operating hours

Interferometer Rocksolid, permanently adjusted

Beam splitter(material)

KBr (standard)ZnSe (in case of high humidity option)

Window KBr (standard)ZnSe (in case of high humidity option)

Detector DTGS detector (room temperature)

A permanent online diagnosis of the single components (e.g. IR source, laser, detector and interferometer) facilitates troubleshooting and maintenance.

The connecting ports (e.g. power, Ethernet) and the system diagnosis LEDs are at the rear side of the basic module, see figure 2.

A

Figure 2: ALPHA rear side - Connecting ports and LEDs

B C D E F G H I J K

Type Definition

A USB port Not available.

B ETH/LAN port The ETH/LAN port is used to connect the spectrometer to a computer on which the OPUS software is installed. The ETH port is designed for RJ-45 plugs and complies with the Ethernet standard. To connect the spectrometer to the PC the supplied data cable (cross over, 10Base-T with RJ45 ports) is used. See also the ALPHA installation instructions.


C h a p t . 2A L P H A - T M e a s u r e m e n t M o d u l e

2.3 ALPHA-T Measurement Module

The ALPHA-T measurement module is designed for measurements in transmission. This measurement module allows to spectroscopically analyze both solids, liquids as well as gases.

C TKD LED The green TKD LED indicates that the interferometer mir-ror is within the data acquisition range. When data acquisi-tion actually takes place the light intensity changes to bright green. The TKD abbreviation means Take Data.

D ACC LED The yellow ACC LED indicates that the network accesses the optics. During transition of measuring data the LED will be light yellow. The ACC abbreviation means Access.

E DIR/ERR LED In normal operation mode the DIR/ERR LED flashes slightly red and indicates the scanner movement. If the LED lights permanently bright red, there must be an inter-ferometer problem, e.g. missing laser signal. As long as this LED lights permanently red no data acquisition is pos-sible. The DIR abbreviation means Direction, ERR means Error.

F Ext. Accessory port This port can be used to connect external optional acces-sories, e.g. detector, remote trigger etc.

G TAP port The TAP male connector includes 10 socket contacts and is used for service and diagnostics only. The TAP abbrevi-ation means Test Access Port.

H CFG switch CFG is a fourfold DIP switch: #1 ON and #2 OFF: DHCP mode - use last DHCP

address #1 OFF and #2 ON: use ON-IP address 10.10.0.1 #3: stay in boot loader, do not load the application pro-

gram #4: reservedThe CFG abbreviation means Configuration.

I SBY/RES button Depending on how long you press this button you either activate/deactivate the stand-by mode or reset the spec-trometer (i.e. restore the initial spectrometer state). If you press this button about 2 seconds, you activate/deactivate the stand-by mode. If you press this button more than 6 seconds, the spectrometer will be reset. The abbreviation SBY means Standby, RES means Reset.

J POWER port This port is used to connect the spectrometer to the power supply. Use the supplied power cord with mains adapter. The POWER port is suited for extra low-voltage connec-tors. Only use power cords which have been approved by Bruker. See also the ALPHA installation instructions.

K Kensington lock This optional lock is a kind of safety (anti-theft) lock for mobile hardware.

Type Definition

C h a p t . 2



In case of measuring liquid and gaseous samples optional liquid and gas cells are available. These gas cells can be mounted into the sample compartment of the transmission measurement module. For further details on this subject see also chapter 5.

Figure 3: ALPHA-T

A

B

C

D

E

Definition

A Basic module (with integrated electronics and optics)

B Lock/release

C ALPHA measurement module (for spectroscopic trans-mission measurements

D Sample compartment lid

E Status indicator

2.3.1 ALPHA-T sample compartment

The ALPHA-T sample compartment is behind the blue cover (D in figure 3) and can be accessed from the front side.

To open the sample compartment. . .

...reach under the bottom edge of the sample compartment lid and lift it up.

Figure 4: ALPHA-T - Sample compartment open

A

B

C

Definition

A Sample compartment lid

B Sample holder

C Ports for the IR beam passing the sample compartment


C h a p t . 2A L P H A - P M e a s u r e m e n t M o d u l e

For detailed information on how to prepare and insert samples refer to chapter 4 and 5.

2.4 ALPHA-P Measurement Module

The ALPHA-P measurement module is designed for measurements in attenuated total reflection (ATR). This measurement module allows to spectroscopically analyze both solids (e.g. paste, powder) as well as liquids.

The following ATR crystal types are available:

Diamond Germanium (Ge)

For further information on this measurement module refer to chapter 6.

Figure 5: ALPHA-P

A

B

C

D

E

F

G

H

I

Definition

A Lever to move the anvil up and down

B Pressure control spot (round recess)

C Anvil

D ATR crystal

E ALPHA-P measurement module for ATR

F Height adjustment for pressure arm

G Basic module

H Status indicator

I Crystal plate with integrated ATR crystal

C h a p t . 2



2.5 ALPHA-E Measurement Module

The ALPHA-E measurement module is designed for measurements in attenuated total reflection (ATR). This measurement module allows to spectroscopically analyze both solids (e.g. paste, powder) as well as liquids.


C h a p t . 2E x c h a n g i n g M e a s u r e m e n t M o d u l e

The following ATR crystal types are available:

Germanium (Ge) Zinc selenide (ZnSe)

For further information on this measurement module refer to chapter 6.

Figure 6: ALPHA-E

A

B

C

D

E

F

Definition

A Knob to press and release the anvil

B Anvil

C Crystal plate with integrated ATR crystal

D ALPHA-P measurement module for ATR

E Basic module

F Status indicator

2.6 Exchanging Measurement Module

The three different measurement modules available (ALPHA-T, ALPHA-P and ALPHA-E) can be exchanged. The procedure is the same for all three measurement modules. See the following figure:

C h a p t . 2

1 0 A L P H A U s e r M a n u a l B r u k e r O p t i k G m b H


Figure 7: Procedure when exchanging the measurement module

Step 1: Press the lock on the basic module right down.Note: The measurement module is released from the basic module and the lock stops at half-height.

Step 2: Pull out the measurement module from the basic module.

Step 3: Push the new measurement module right against the basic module.

Step 4: Press the lock on the basic module once again right down.Note: The measurement module engages into the basic module, and the lock snaps right up.


C h a p t . 2O p e r a t i n g S p e c t r o m e t e r

What happens after exchanging the measure-ment module?

OPUS automatically recognizes the newly inserted measurement module and starts a performance test (accessory test). For more detailed information refer to the OPUS/MENTOR manual.

2.7 Operating Spectrometer

The spectrometer is operated by means of the OPUS software. For detailed information on the OPUS software refer to the OPUS/MENTOR manual and chapter 3.

2.8 Activating Stand-by Mode

Basically, you can either set the spectrometer to stand-by mode or completely disconnect it from the mains supply by unplugging the power cord.

It is recommended to set the spectrometer to stand-by mode overnight. Only in case of longer shut-down periods (e.g. several days) is it advisable to completely disconnect the spectrometer from the mains supply.

If the spectrometer is in stand-by mode, it is not switched off completely. There is still some power consumption which is, however, significantly lower than in operation mode as the IR source, laser and detector are switched off.

How to set ALPHA into stand-by mode?

1 Press the SBY/RES button (A in figure 8) at the spectrometer rear side for a short time (about 1 to 2 seconds).

Figure 8: ALPHA rear side - Stand-by/Reset key

A

C h a p t . 2



2 Now, the spectrometer beeps and the green status indicator on the spectrometer top side begins to flash in short intervals. The OPUS status light becomes gray.

How to set ALPHA into operation mode again?

1 Press again the SBY/RES button at the spectrometer rear side only for a short time (about 1 to 2 seconds).

2 Now, the spectrometer beeps and the laser, IR source and detec-tor are switched on again.

3 As the IR source warm-up takes about 7 minutes, the spectrome-ter status indicator is yellow during this period.

4 As soon as the IR source has reached its operating temperature, the spectrometer status indicator permanently lights green.


C h a p t . 3

3 Quick User GuideThe purpose of this quick user guide is to enable you to familiarize yourself with the OPUS software within a short period of time and to learn how to perform the most relevant analytical tasks on your own. This chapter describes the procedures for realizing the following analytical task definitions:

Sample Measurement - How to perform a spectroscopic mea-surement? How to manipulate a sample spectrum? How to save and/or print a spectrum?

Quality Control - Are the delivered goods or the self-made products consistent with the specified quality criteria?

Identification of an unknown substance - What substance is it?

Quantitative Analysis - How much of a certain component does the sample contain?

3.1 Measurement

3.1.1 General Information

It is recommended to perform a measurement using the factory parameter settings. In this case, you can start with the measurement immediately. See the following descriptions General Measurement Procedure.

In addition, OPUS offers you also the possibility to adapt the measurement parameter settings (e.g. the parameter value Scan Time) to your special demands. To do this, click in the OPUS wizard with the left mouse button next to the Measurement button and select the option Setup "Measurement"... (see figure 9). As a result, the Setup Measurement Parameters dialog opens. For a detailed description of this dialog window refer to the OPUS/MENTOR manual.

Figure 9: OPUS Wizard - Opening the Setup Measurement Parameters dialog

C h a p t . 3


Q u i c k U s e r G u i d e

When measuring a sample, always pay attention to the fol lowing issues:

If the sample needs to be prepared, due to its composition, prepare it carefully and avoid preparation errors. For informa-tion about sample preparation refer to chapter 4.

Avoid measurement errors (e.g. the ATR crystal is not covered completely with the sample).

3.1.2 General Measurement Procedure

Generally, the measurement procedure can be subdivided into the following steps:

1 Measuring a background spectrum2 Preparing the sample, if required3 Measuring the sample spectrum4 Manipulating the sample spectrum5 Performing a peak pick, if required6 Saving and / or printing the manipulated spectrum7 Measuring the next sample, if required

How to perform a measurement:

1 Click in the OPUS Wizard on the Measurement button (see figure 10).

Figure 10: OPUS Wizard - Starting a measurement

2 The following dialog window opens:

Figure 11: Measurement dialog - Starting a Background/Sample Measurement


C h a p t . 3M e a s u r e m e n t

3 First, perform a background measurement (i.e. a measurement without a sample in the spectrometer sample compartment or without a sample on the ATR crystal) by clicking on the Start Background Measurement button.

Note: When you acquire a background spectrum using the ATR module, first check whether the ATR crystal is really clean, i.e. it is absolutely free from residuals of the previous sample. If your sample needs to be prepared using a solvent acquire the background spectrum of the pure solvent (i.e. solvent without sample).

4 The background measurement takes a few seconds. The mea-surement progress is shown in the lower status bar.

5 Put the sample in the spectrometer sample compartment or on the ATR crystal.

Note: Depending on the composition of the sample (solid, powdery, paste-like, liquid etc.), the sample may need to be prepared before you can put it in measurement position of the spec-trometer. For detailed information about sample preparation refer to chapter 4.

6 Then click on the Start Sample Measurement button (see figure 11).

7 The sample measurement takes a few seconds. The measure-ment progress is shown in the lower status bar. Afterwards, the acquired sample spectrum is displayed in the OPUS spectrum window.

Note: If you use the factory parameter settings, the spectrum is stored by default under OPUS path/meas. The file name is identical to the sample name you have entered in the Mea-surement dialog (see figure 11). If you do not enter a different sample name the file name is incremented with any further measurement.

Immediately after the sample measurement, the OPUS Wizard switches automatically to the Manipulate level (see the following section).

C h a p t . 3



3.1.3 Manipulating a Sample Spectrum

After the sample measurement, a spectrum postprocessing may be required to ensure that OPUS yields acceptable evaluation results, for example when you intend to perform a substance identification or a quantitative analysis. For this purpose, OPUS offers a number of manipulation commands. Manipulating in this context means "optimizing" the measured sample spectrum. This section describes the following manipulation commands:

Baseline Correction Atmospheric Compensation

For information about additional manipulation commands refer to the OPUS/MENTOR manual.

A Baseline Correction is always highly advisable if the spectrum baseline deviates strongly from a theoretical horizontal line. This phenomenon may occur, for example, when you measure a sample prepared as a KBr pellet. (See also chapter 4, Sample Preparation.) Figure 12 illustrates the effect of a baseline correction. For detailed information about this command refer to the OPUS/MENTOR manual.

Figure 12: Baseline Correction

Spectrum before a baseline correction

Spectrum after a baseline correction

How to perform a baseline correction:

1 Measure a spectrum or load the file of the spectrum you intend to manipulate by clicking on the corresponding button in the OPUS wizard (see figure 10). Thereupon, the sample spectrum is displayed in the spectrum window and OPUS switches automatically to the Manipulate level.

2 Click in the OPUS Wizard on the Baseline Correction button (see figure 13).

Figure 13: OPUS Wizard - Performing a Baseline Correction



3 Thereupon, OPUS performs a baseline correction and displays automatically the corrected spectrum in the OPUS spectrum win-dow.

Note: To undo a baseline correction, select the Undo Changes com-mand in the OPUS File menu.

The OPUS Atmospheric Compensation command eliminates H2O and/or CO2 bands from a sample spectrum. These bands result from the ambient air and occur if there is a difference in the H2O and/or CO2 concentration between the moment of the background measurement and the moment of the sample measurement. Figure 14 illustrates the effect of an atmospheric compensation. For detailed information about this command refer to the OPUS/MENTOR manual.

Figure 14: Atmospheric Compensation

Spectrum beforean atmosphericcompensation

Spectrum after an atmospheric compensation

C h a p t . 3



How to perform an atmospheric compensation:

1 Measure a spectrum or load the file of the spectrum you intend to manipulate by clicking on the corresponding button in the OPUS wizard (see figure 10). Thereupon, the sample spectrum is displayed in the spectrum window (as shown in figure 15) and OPUS switches automatically to the Manipulate level.

Figure 15: Spectrum before an atmospheric compensation

OPUS Browser with a loaded spectrum file.This file contains, amongst others, a SSC data block and a RSC data block.

Note: The Atmospheric Compensation command requires a spec-trum file that includes, amongst others, the data blocks SSC (Sample Single Channel) and RSC (Reference Single Chan-nel). (See figure 15.) Otherwise, an atmospheric compensa-tion cannot be performed.

2 Click on the Atmospheric Compensation button in the OPUS Wiz-ard.

3 Thereupon, OPUS performs an atmospheric compensation and displays automatically the atmospherically compensated spec-trum in the OPUS spectrum window (see figure 16).

Note: To undo an atmospheric compensation, select the Undo Changes command in the OPUS File menu.

Figure 16: Spectrum after an atmospheric compensation



3.1.4 Peak Picking

The Peak Picking allows you a prompt determination of the exact spectrum peak positions, i.e. the exact frequency values (x-values) at which maxima (in case of an absorption spectrum) or minima (in case of an transmission spectrum) occur in the spectrum.

How to perform a peak pick:1 Measure a spectrum or load the file of the spectrum you intend to

manipulate by clicking on the corresponding button in the OPUS wizard (see figure 10). Thereupon, the sample spectrum is displayed in the spectrum window and OPUS switches automatically to the Manipulate level. Depending on the measurement method, the displayed spectrum is either an absorption spectrum or a transmission spectrum or an ATR spectrum.

2 Manipulate the spectrum, if required. Otherwise, click on the Eval-uate tab and then on the Peak Picking button in the OPUS wizard.

3 Thereupon, the exact frequency values, at which maxima or min-ima occur, are displayed in the spectrum window. See figure 17a and 17b.

Figure 17: a)Peak pick result in case of absorption b) Peak pick result in case of transmission

C h a p t . 3



How to perform an interactive peak pick:

1 Alternatively, you can pick peak(s) also interactively by clicking with the left mouse button next to the Peak Picking button and selecting the option Interactive Peak Picking. Thereupon, the following view appears:

Figure 18: Interactive peak picking

Line

2 Using the line in the spectrum window, you can select interac-tively the peaks of which the frequency value is of interest to you. To do this, place the cursor on the symbol and move the line with pressed left mouse button up- or downwards. The frequency values of all peaks above this line are displayed (see figure 18).

3 Click on the Save button to save the currently displayed peak position values. Thereupon, a PEAK data block is added to the spectrum file in the OPUS browser.

4 Alternatively, you can view the peak picking result in form of a report. The report is displayed below the spectrum window. See figure 19. For information about the permanent display of the information view, refer to the OPUS/MENTOR manual.

Figure 19: Peak picking report

Peak picking report

Peak pick-ing result displayed in the spec-trum window



How to perform a single peak pick:

Besides the Peak Picking command in the OPUS wizard, OPUS offers you also the possibility to pick specifically a single peak (i.e. to have the frequency value of a certain peak displayed) which is of interest to you. To do this, proceed as follows:

1 The spectrum in question is displayed in the spectrum window. Click with the right mouse button on the spectrum window and select in the context menu the Single Peak Pick command (see figure 20).

Figure 20: Single peak pick - Step 1

C h a p t . 3



2 As a result, the cursor changes its appearance as follows: 3 Place the cursor on the peak which is of special interest to you

and press the left mouse button. Thereupon, the frequency value of the peak in question is displayed above the peak (see figure 21). You can repeat a single peak pick as often as you like.

Figure 21: Single peak pick - Step 2

Position of an individually selected peak

3.1.5 Defining the next procedures

After OPUS has performed a spectrum manipulation, the wizard switches automatically to the Evaluate level. Depending on your particular analytical task (quality control, substance identification quantitative analysis etc.) you can now evaluate your sample spectrum using the corresponding OPUS evaluation command. The following sections 3.2, 3.3 and 3.4 provide a detailed description of the most relevant evaluation commands (Quick Compare, Spectrum Search and Quantitative Analysis). For information about all available evaluation commands refer to the OPUS/MENTOR manual.

After OPUS has performed an evaluation (e.g. Spectrum Search) the wizard switches automatically to the Report level. On this level, you decide how to deal with the current spectrum file. OPUS offers the following options:

saving the processed spectrum and/or printing the processed spectrum and/or unloading the spectrum file and/or measuring the next sample.

To do this, activate the corresponding checkbox(es) and click on the Gobutton. As a result, OPUS performs automatically the selected action(s). See figure 22.

Figure 22: OPUS Wizard - Report level



How to save a processed spectrum:1 Activate the Save Changes checkbox.2 Click on the Go button. As a result, OPUS saves the processed

spectrum with the same file name and under the same path as the original spectrum, i.e. the original spectrum is overwritten by the processed one.

Note: If you want to preserve the original spectrum select the Save File As command in the OPUS File menu and define a different file name and/or path for saving the processed spectrum.

How to print a spectrum:1 Activate the Print checkbox.2 Click on the Go button. As a result, the spectrum currently dis-

played in the spectrum window is printed.

How to unload a spectrum fi le:1 Activate the Unload checkbox.

Note: If you want to unload a processed spectrum, it is advisable also to save it. To do this, also activate the Save Changescheckbox. (See section How to save a processed spectrum.)

2 Click on the Go button. As a result, the current spectrum file is unloaded from the OPUS browser.

How to start the next sample measurement:1 Activate the Measure Next Sample checkbox.

Note: If you want to measure the next sample after having processed a spectrum it is advisable to save this spectrum. To do this, also activate the Save Changes checkbox. (See section How to save a processed spectrum.)

2 Click on the Go button. As a result, the Measurement dialog win-dow (figure 10) opens again allowing you to start the next sample measurement by clicking on the corresponding button (see section 3.1.2.)

C h a p t . 3



3.2 Quality Control


The Quick Compare evaluation command allows to check whether the delivered goods or the self-made products are consistent with the specified quality criteria. For realizing this task, there are the following two OPUS commands:

Quick Compare Setup - This command allows to setup a quick compare method. The method setup has to be done prior to the actual Quick Compare.

Quick Compare - This command allows to perform a Quick Compare using the method you have set up in advance. (Quick Compare implies the comparison of a sample spectrum with one or several reference spectra.)

3.2.2 The general course of quality control

Generally, quality control can be subdivided into the following steps:

1 Measuring reference sample(s) and storing the spectrum (spectra)

2 Setting up a quick compare method and saving method file3 Measuring the sample to be analyzed4 Performing a quick compare5 Interpreting the quick compare result

How to choose and measure a reference sam-ple:

For setting up a quick compare method, you first need to measure at least one or more reference spectra. In this case, reference spectra are spectra of samples of which you know for certain that they are absolutely consistent with the specified quality criteria. These samples are also called reference standards.

When choosing and measuring reference sample(s), pay attention to the following aspects:

Use only pure samples as reference standard (i.e. samples that are free of unwanted contaminants).

Prepare the reference standards carefully (see chapter 4, Sample Preparation).

Avoid measurement errors (e.g. the ATR crystal is not com-pletely covered with the sample).

For detailed information about how to perform a measurement refer to section 3.1.


C h a p t . 3Q u a l i t y C o n t r o l

How to setup a new Quick Compare method:

1 Click on the Evaluate tab and then on the Quick Compare button in the OPUS wizard. Thereupon, the following OPUS message appears:

Figure 23: OPUS Message

Note: This message appears only when you click on the Quick Com-pare button for the very first time because at this stage a quick compare method has not yet be set up. Otherwise, the quick compare method set up or loaded at last is used automatically.

2 Click on the OK button. Thereupon, the Quick Compare Setup dialog window opens. See figure 24.

Figure 24: Quick Compare Setup - Load/Store Method

Click on this button if you want to modify an existing method file (*.QCM).

If you want to set up a new method, click on the other two tabs (fig. 25 and 26) and enter the desired parameter values. Then, return to this page of the dialog window and click on the Store Method button.

Note: In the upper part of this page, an overview of the parameter values you have specified on the other pages of this dialog window is shown.

3 Click on the Reference Files tab and select reference spectrum file(s) in question (see figure 25).

Figure 25: Quick Compare Setup - Reference Files

On this page, you select the ref-erence spectrum/reference spec-tra for Quick Compare.

You can select either:

- only one reference spectrum or

- all reference spectra that are stored in a certain directory (In this case, the reference spectra can originate from the different sample materials.) or

- the average spectrum of all ref-erence spectra stored in a cer-tain directory. (In this case, the reference spectra must origi-nate from the same sample material!)

C h a p t . 3



4 Click on the Parameters tab and enter the desired parameter val-ues (see figure 26).

Figure 26: Quick Compare Setup - Parameters

The entry of a comment is optional.

The threshold value has an influ-ence on the quick compare result.a) You can either set this value (in %) using the slider or enter it manually.

When defining the frequency region for the quick compare, you can either:

- use the file limits or,- enter the values for one or

more regions manually or - select one or more frequency

regions interactively. (See fig. 27.)

a) With the threshold value, you determine the degree of similarity between the reference spec-trum and the sample spectrum. In other words, you determine how similar reference spec-trum and sample spectrum need to be in order that the quick compare result is OK. As a general guideline: The higher the threshold value is the higher the similarity between the ref-erence and the sample spectrum needs to be in order to get an OK result.

If required, you can also define a data preprocessing method (first or second derivative) and you can exclude those spectral regions from the Quick Compare in which CO2 bands occur (between 2400 ... 2275 and 680 ... 660cm-1) by activating the corresponding checkbox.



We recommend the interactive selection of the frequency region. Select those regions in which are the most relevant spectral information of the substance to be analyzed. To define further regions, click with the right mouse button on the Select Frequency Region(s) dialog and select the option Add Regions in the popup menu (see figure 27). Then, put the cursor on a boundary line of the newly added frequency region and move it with pressed left mouse button to the desired position. After having defined all relevant frequency regions, click on the OK button.

Figure 27: Interactive selection of the frequency region

5 To store the newly set-up method, click again on the Load/Store Method tab an then on the Store Method button. See figure 24.

For detailed information about this dialog window refer to the OPUS/MENTOR manual.

How to perform Quick Compare:

1 Measure the sample of which you want to test the quality and manipulate the sample spectrum, if required. See section 3.1. (Do not unload the spectrum yet!)

2 Click on the Evaluate level in the OPUS wizard.3 Click on the Quick Compare button. As a result, OPUS performs

automatically a Quick Compare using the method you have set up before or the method which has been loaded last.

4 Immediately after OPUS has executed a Quick Compare evalua-tion, the result is displayed automatically. (See figure 29, for example.)

Note: Alternatively, you can start a quick compare evaluation using the Quick Compare dialog window. To do this, click on the Evaluate level in the OPUS wizard. Then, click with the left mouse button next to the Quick Compare button and select the option Select "Quick Compare" method.... Thereupon, the Quick Compare dialog window opens (see figure 28).

Figure 28: Starting a Quick Compare

Spectrum file of the sample to be analyzed (path and file name)

Click on this button if you want to use a different method.

You can decide whether the result is to be displayed immediately after the execution of the Quick Compare and/or printed automati-cally by activating the correspond-ing checkbox(es).

Path and file name of the cur-rently loaded method Note: Nor-mally, it is the method you have set up or used at last.

C h a p t . 3



How to interpret a Quick Compare result:

The Quick Compare result is OK if the correlation value is higher than the threshold value you have determined. Analogous to this, the Quick Compare result is not OK if the correlation value is lower than the threshold value. In case of a Quick Compare evaluation, the correlation coefficient1 r is a measure for the similarity between the two items "reference spectrum" and "sample spectrum".

Depending on what you have selected as reference for the Quick Compare (a single reference spectrum, an average spectrum or all spectra of a certain directory), keep in mind the following when interpreting the result:

If you have selected a single file or an average as reference, you will get either an OK or Not OK as result (see figure 29, 30and 31). In both cases, the displayed result allows you to see at first sight whether the analyzed sample meets the specified quality criteria or not (see figure 29 and 30).

If you have selected all spectrum files of a certain directory as reference, you will not get a simply OK or Not OK as result. In this case, only those reference spectra which have a sufficient similarity with the sample spectrum, due to the threshold value you have entered and the correlation value OPUS has calcu-lated, are displayed black. All other reference spectra which do not show a sufficient similarity with your sample spectrum are displayed gray (see figure 32)-

1. Normally, the correlation coefficient values can range from -1,0 (i.e. no similarity between the reference spectrum and sample spectrum at all) to +1,0 (i.e. absolutely identical spectra). For the quick compare result, this value is converted into percentage with the range 1 r 0being mapped to 0% and the range 0 r 1 being mapped linearly to 0% ... 100%.

Figure 29: Result of a Quick Compare using one Reference - Sample Spectrum is OK

Figure 30: Result of a Quick Compare using one Reference - Sample Spectrum is not OK



Figure 31: Result of a Quick Compare using an average as reference - Sample spectrum is OK

Figure 32: Result of a Quick Compare using several references - 1 hit has been found

C h a p t . 3




C h a p t . 3I d e n t i f i c a t i o n o f a n u n k n o w n S u b s t a n c e

3.3 Identif ication of an unknown Substance


The Spectrum Search evaluation command allows to identify an unknown substance on the basis of its IR spectrum by comparing this spectrum with the spectra of a library. Those library spectra which show an obvious similarity with the spectrum of the unknown substance are listed in a search report.

As already mentioned, a spectrum search is only possible if at least one spectra library is available. By default, the two non-commercial spectra libraries (with 350 and 200 entries, respectively) are delivered together with the OPUS programme (see figure 33). Both libraries contain spectra of a number of classes of substances (e.g. polymers, pharmaceuticals etc.).

Figure 33: Available spectra libraries

Note: Besides the two libraries delivered with the OPUS software, Bruker also offers a number of additional spectra libraries which you can purchase.

A decisive factor for a successful substance identification is the appropriateness of the available spectra libraries, i.e. a spectrum search can yield only acceptable results if the selected library (libraries) contain(s) entries (i.e. spectra plus additional information) of the classes of substances (e.g. polymers, pharmaceuticals etc.) that you actually analyze.

C h a p t . 3



In addition, OPUS offers you also the possibility to create your own spectra library which is adapted to your special needs regarding the substances you intend to identify. See section 3.3.3 Creating, building up and maintaining your own spectra library.

3.3.2 The general course of a substance iden-t i f ication

Generally, a spectrum search in a library can be subdivided into the following steps:

1 Measuring the sample of an unknown substance and manipulating the sample spectrum, if required.

2 Starting the spectrum search.3 Interpreting the result of a spectrum search.

How to perform a spectrum search in a l ibrary: Measure the sample of an unknown substance and manipulate

the sample spectrum, if required (see section 3.1). After having executed a manipulation command, OPUS

switches to the Evaluate level. In case you did not manipulate the spectrum, click on the Evaluate tab in the OPUS wizard.

Click on the Spectrum Search button. Thereupon, OPUS starts the spectrum search using the factory-set search parameters. In this case, all spectra libraries that are in the directory OPUS path/Data/Library are searched.

Note: OPUS offers you also the possibility to change the factory-set search parameters and/or to select different libraries. For detailed information about this topic refer to the OPUS/MEN-TOR manual.

Immediately after OPUS has completed the spectrum search, the search report is shown (see figure 34).

How to interpret a spectrum search result:

The search report consists of 4 sub-windows (see figure 34). The lower sub-window shows the list of all hits found in the selected library (libraries). By default, the first hit in the hit list is marked and its information (spectrum, structural formula and compound information, e.g. compound name, molecular formula, molecular weight etc.) are displayed in the upper three sub-windows. To see this kind of information for another hit, click in the hit list of the hit of which you want to see more information.

Figure 34: Spectrum Search report

Hit list

Structural formula

Library spec-trum and query spec-trum

Substance information

Hit quality value


C h a p t . 3I d e n t i f i c a t i o n o f a n u n k n o w n S u b s t a n c e

The hit quality value in the hit list gives you a general clue to what extent the spectrum of the unknown substance (also called query spectrum) resembles the library spectrum.

The hit quality value can range from 0 (i.e. no resemblance at all) to 1000 (i.e. absolute conformity of the library spectrum with the query spectrum). The hit list is sorted according the hit quality value, i.e. the hit with the highest quality value ranks first in the hit list.

Moreover, you can compare visually the query spectrum with the library spectrum to find out whether there is a certain resemblance between the two spectra.

3.3.3 Creating, building up and maintaining your own spectra l ibrary

Besides the usage of the delivered and/or commercial spectra libraries, OPUS offers you the possibility to create your own library that suits your specific analytical needs.

For creating, building up and maintaining your own spectra library, the following OPUS commands are available:

Initialize Library Store Spectrum in Library Library Editor Library Browser

For detailed information about these commands refer to the OPUS/MENTOR manual.

C h a p t . 3



When creating your own spectra library, pay attention to following aspects:

When choosing the samples for the library, try to cover the hole range of the class(es) of substances you want to analyze with this library in the future. Keep in mind the following: The more extensive and diverse the library is, the better the search result will be.

Use only pure substances (i.e. substance that are free of unwanted contaminants).

Prepare these samples carefully (see chapter 4, Sample Prep-aration.)

Avoid measurement errors (e.g. the ATR crystal is not covered completely with the sample).

Before adding the measured sample spectra to the library, opti-mize them adequately using the available manipulation com-mands.

Add preferably absorption spectra1 to the library. Think already in advance of the additional information you

want to include in the library and make sure that they are avail-able.

The above mentioned aspects are crucial preconditions for the creation of a library that is to yield acceptable search results for future analyses.

1. In an IR spectrum, the position and intensity of the absorption bands are very substance-spe-cific. Similar to a human fingerprint, the absorption spectrum of a substance is well-suited for the identification of it.


C h a p t . 3Q u a n t i t a t i o n o f a S a m p l e C o m p o n e n t

3.4 Quantitation of a Sample Compo-nent

3.4.1 General InformationIf your sample is a mixture of several components (e.g. a tablet containing several active agents) OPUS allows you to quantitate one of these components which is of special interest to you (e.g. the quantity of active agent A contained in the tablet). For realizing this task, there are the following two OPUS commands:

Quant Builder - for setting up a QUANT method and Quantitative Analysis - for performing the actual quantitative

analysis

When you perform a quantitative analysis, it is highly recommended that you normalize all spectra (i.e. both the calibration spectra and the spectra of the sample(s) you intend to analyze) before the evaluation. Spectra normalization is an OPUS manipulation command. Normalizing means that the spectra are scaled to that effect that the minimum and/or maximum of the spectra assume the same value. In doing so, the spectra can better be compared with each other. Especially in case of ATR spectra, a normalization is highly recommended. For detailed information about this command refer to the OPUS/MENTOR manual.

3.4.2 The general course of a quantitat ive analysis

Generally, a quantitative analysis can be subdivided into the following steps:

1 Getting a set of about 5 samples and determining the exact concentration values of the sample component in question using a different technique (e.g. weighing). These samples are also called calibration samples. They are required for setting up the QUANT method.

2 Setting up a QUANT method using the OPUS command Quant builder and the calibration samples.

3 Performing a quantitative analysis using the QUANT method you have set up before and the OPUS command Quantitative Analy-sis.

4 Interpreting the analysis.

C h a p t . 3



When choosing the calibration samples, pay attention to the fol lowing aspects:

Ideally, the calibration sample set should contain at least 5 samples.

Make sure that the concentration value of the component in question differs from calibration sample to calibration sample.

How to setup a QUANT method:

1 Measure one of the calibration samples and manipulate the sample spectrum, if required (see section 3.1). Keep the spectrum file loaded in the OPUS browser.

2 Click on the Evaluate tab in the OPUS wizard, select the option Quant Builder in the drop-down list and click on the Go button. Thereupon, the Quant Builder - New dialog window opens (see figure 35). The dialog window already includes the path and the file name of the currently loaded spectrum file.

3 Enter the name of the component to be analyzed.4 Specify the unit of the measurement (e.g. mg, ml, %) for the con-

centration value. Note: The unit of measurement you enter in this dialog depends on the unit in which you have deter-mined the concentration values of the calibration sample before. And the result of the quantitative analysis is dis-played in this unit as well.

5 Enter the exact component concentration value for the calibration sample in question. Note: You need to have determined this value before using a different analytical technique.

Figure 35: Dialog Window Quant Builder

Calibration line

Enter the exact concentration value of the component in question. Note: This value needs to be deter-mined before by a different tech-nique.

Path and file name of the current spectrum file

Enter the component name

Enter the unit of mea-surement



Already at this stage (i.e. on the basis of one calibration spectrum and its corresponding concentration value), OPUS calculates a calibration line1(see figure 35). In the further course of the QUANT method setup, this calibration line will be improved by adding the data of the other calibration samples.

Note: When you add the first calibration spectrum to a new QUANT method, make sure that the New option button is activated.

6 Click on the Set Integration Area button. Thereupon, the window shown in figure 36 appears allowing you to set an integration area and select an integration method.

Figure 36: Defining the Integration Area and the Integration Method

Spectral band resulting from agent A

Note: You can change the integration area bound-aries interactively by placing the cursor on a boundary and shifting it with pressed left mouse button.

Note: Set the integration area in such a way that the spectral band resulting from the component in question is within integration area. For this reason, it is recommended to set the integration area not until at least 3 or 4 calibration spectra have been added to the QUANT method because only at this stage you can recognize clearly the spectral band resulting from the component in question (see figure 37).

7 Now click on the Go to Quant button in order to return to the Quant Builder dialog window.

8 Click on the Save button. As you are setting up a new QUANT method, OPUS prompts you to enter file name and path under which the method file is to be saved. Enter a file name, specify the path and click on the Save button.

9 Thereupon, the Quant Builder dialog window disappears.10 Measure the next calibration sample by clicking on the Measure

Next Sample... button in the OPUS wizard (see section 3.1).

1.The calibration line visualizes the relation between the calibration spectra and the correspond-ing concentration values of the component in question. For the quantitation of a certain com-ponent, OPUS calculates the quantity of this component on the basis of the spectrum of the sample to be analyzed and the calibration line.

C h a p t . 3



11 Open the Quant Builder dialog again by clicking in the OPUS wiz-ard on the Evaluate tab, selecting in the drop-down list the option Quant Builder and clicking on the Go button.

12 Enter the component concentration value of the calibration sam-ple in question.

Note: For the second and every following calibration sample, you donot need to enter component name and unit again.

13 When adding the second or any further calibration spectrum to the existing QUANT method, make sure that the Add spectrumoption button is activated.

14 To add the data of the second calibration sample to the QUANT method, click on the Save button. Thereupon, the Quant Builder dialog window disappears.

15 Repeat step 10 to 14 for the remaining calibration samples.

Only after you have added 3 or 4 calibration spectra to the QUANT method is it recommended to set the integration area. To do this, activate the Change option button and click on the Set Integration Areabutton. Thereupon, the window shown in figure 37 appears.

Figure 37: Defining the integration area on the basis of several calibration spectra

At this stage, the window includes all calibration spectra added to the QUANT method so far. The display of several calibration spectra enables you to set the integration area because now the band resulting from the component to be quantified is clearly recognizable due to differences in the band height because the band height is quantity-dependent.

For detailed information about the Quant Builder command refer to the OPUS/MENTOR manual.



How to perform a quantitative analysis:

1 Measure a sample of which you want to quantitate a certain component. For information about how to perform a measurement refer to section 3.1.

2 Click on the Evaluate tab an then on the Quantitative Analysisbutton in the OPUS wizard. Thereupon, the Quantitative Analysisdialog window opens. See figure 38.

Figure 38: Quantitative Analysis dialog

Spectrum file of the sample to be analyzed (path and file name)

Click on this button if you want to use a different QUANT method.

Path and file name of the cur-rently loaded QUANT method Note: Normally, it is the method you have set up or used at last.

3 The sample spectrum file is already included in the File(s) for Quantitative Analysis field.

4 The QUANT method you have set up or used at last is already loaded. In case you want to use a different method click on the Load Quant Method button and select the QUANT method file (*.q1) you intend to use.

Note: You can perform a quantitative analysis using either: a newly set-up method or an existing method you have modified or an existing method you select explicitly or the method which has been loaded last.

5 Make sure that the Show results immediately button is activated (see figure 38). In this case, the result is shown immediately after OPUS has completed the evaluation. The result is displayed in form of a report (see figure 39).

Note: In case this check box has not been activated double-click on the QUANT data block of the spectrum file in order to display the quantitative analysis result.

6 Finally, click on the Analyze button.

C h a p t . 3



How to interpret a quantitative analysis result:

Figure 39: QUANT Report - Result of a quantitative analysis

The QUANT report delivers the following information:

name of the component that has been quantitated concentration value (prediction) of the component in question

calculated by OPUS standard deviation (sigma1) of the calculated prediction value unit in which the calculated concentration value is given

Note: You have specified this unit when setting up the QUANT method.

the integration result for the spectral band which results from the component to be quantitated.

1. Sigma is the standard deviation of the calculated concentration value. The sigma value is de-termined by the quality of the QUANT method you have set up. Ideally, the sigma value should be as small as possible.


C h a p t . 4

4 Sample PreparationProper sample preparation is crucial to obtain good and meaningful spectra. This chapter describes the most important sample preparation methods1. Useful information will give you some help in selecting the most suitable sample preparation method for a given sample.

How must the sam-ple be like?

homogeneous (constant concentration or composition within the sample area to be analyzed)

Disadvantages of a non-homogeneous sample

misleading or erroneous measuring data

What has to be considered when selecting a sample preparation method?

aggregation state of the sample absorptivity of the sample

What has to be considered in case of a strongly absorbing sample?

sample has to be very thin sample has to be diluted by a solvent or powder that is not

strongly absorbing(otherwise the spectrum is not meaningful)

What kind of sol-vents can be used?

Carbon tetrachloride Carbon disulphide Chloroform Cyclohexane Acetonitrile Tetrachloroethylene

ALPHA allows to measure both solids and liquids. The most common sample preparation methods include:

No sample preparation (e.g. self-supporting film or measure-ment using an ATR unit)

Preparing a KBr pellet (for solids) Preparing thin film of liquid sample solution between two trans-

parent plates (for liquids)

Caution: Most of the described sample preparation methods involve the use of hygroscopic materials (such as NaCl or KBr). If these materials come in contact with water or alcoholic sol-vents, they begin to dissolve or become cloudy and thus, impair the measurement results. Therefore, avoid all sources of water and even alcohol (ethanol and methanol).

1. For more detailed information about the different sample preparation methods refer to the rel-evant specialist literature.

C h a p t . 4


S a m p l e P r e p a r a t i o n

4.1 No Sample Preparation

Type of sample films and polymers (with a thickness of less than approx. 100m)

Advantage enables fast sample measurements

Disadvantage sometimes the samples are too thick

Tip A large number of solid and liquid samples can also be analyzed by using an ATR unit. In this case a sample preparation is not required either.

4.2 KBr Pellet

Type of sample solids

Advantages meaningful IR spectrum KBr shows no absorption in the wavenumber area 4000cm-1 to

250cm-1 this prevents the sample spectrum from containing any disturb-

ing absorption bands

Disadvantages time-consuming sample preparation method interference of water bands (3,960 to 3,480cm-1 and 1,950 to

1,300cm-1 and below 500cm-1) in same cases there may be structural changes caused by high

pressure applied to the KBr/sample mixture

What has to be considered during sample prepara-tion?

grind the sample as fine as possible to minimize the infrared light scattering on the particle surface, and the portion of the reflected light

keep everything moisture free as the KBr material is hygro-scopic, otherwise the pellets become cloudy

it would be best to keep the KBr material in a drying oven at a temperature of 50 to 60C

Tip A common mistake is to use too much sample material. The con-centration of the sample in KBr should be between 0.2% and 1% (i.e. typically a mixing ratio of 300:1).


C h a p t . 4T h i n f i l m b e t w e e n t w o p l a t e s

4.3 Thin f i lm between two plates

Type of sample liquids (e.g. oils)

Advantages easy sample preparation method small amount of sample material required

Disadvantages not suitable for samples which include water the material of the plates (NaCl or KBr) are extremely moisture

sensitive frequently there are air bubbles between the plates

What has to be considered during sample prepara-tion?

pipette one drop of the sample on one of the plates to avoid air bubbles the liquid sample between the two plates

has to be a uniform film

Tips do not use the plates in case of samples that contain water as the plate material (NaCl or KBr) is extremely moisture sensitive

keep the plates always dry (e.g. in an exicator) clean the plates only by using chloroform or high purity acetone

and polish them carefully after each use

C h a p t . 4


S a m p l e P r e p a r a t i o n


C h a p t . 5

5 Transmission Measur-ing

5.1 General Information

To perform transmission measurements the ALPHA-T module is available, see chapter 5.2. More information on the principle of transmission measurements is provided in the glossary in appendix D.

Measuring in transmission is suited for the fol-lowing samples:

Solids, in the form of powder as well (except for highly absorb-ing substances)

Liquids Gases

Depending on the sample material, sample preparation can be very complex in case of measuring in transmission mode, see chapter 4.

Advantages:

Almost all kinds of samples can be analyzed. Measurement represents the entire sample.

Disadvantages:

Depending on the sample material a complex and sometimes difficult sample preparation is required. A successful transmis-sion measurement substantially depends on how carefully the sample has been prepared.

Depending on the sample preparation method required, mea-suring in transmission may sometimes destroy the sample.

Too much a sample quantity can cause total absorption. Additional accessories (e.g. liquid and gas cells) are required.

C h a p t . 5


T r a n s m i s s i o n M e a s u r i n g

5.2 ALPHA-T

The ALPHA-T measurement module is designed for measurements in transmission. This measurement module allows to spectroscopically analyze both solids, liquids as well as gases.

Figure 40: ALPHA-T

A

B

C

Definition

A Sample compartment lid

B Sample holder

C Ports for the IR beam passing the sample com-partment


C h a p t . 5P o s i t i o n i n g s a m p l e i n t h e A L P H A - T s a m p l e c o m p a r t m e n t

5.3 Posit ioning sample in the ALPHA-T sample compartment

Depending on the type of sample used (solid, liquid or gas) you can position the sample into the ALPHA-T sample compartment by means of different measurement accessories:

sample holder supplied by default; especially suited for KBr pellets or a thin film between two IR-transparent plates

plastic film holder (optional) liquid cell (optional) gas cell (optional)

5.3.1 Sample Holder

By default, the sample holder is mounted in the middle of the sample compartment. On the left side of the sample holder there is a fixture to insert the sample.

Figure 41: ALPHA-T - Sample compartment

Fixture Sample holder

5.3.2 Plastic Fi lm Holder

The plastic film holder is put into the fixture of the sample holder (figure 41).

5.3.3 Liquid Cell

To spectroscopically analyze liquid samples optional liquid cells are available. The liquid cells are inserted into the sample holder (see chapter 5.3.1) supplied by default.

C h a p t . 5



When analyzing the sample in a l iquid cell observe the fol lowing:

Avoid any air bubbles when filling in the sample into the liquid cell.

Thoroughly empty and clean the liquid cell after each measure-ment.

Clean the liquid cell using an appropriate solvent.

Note: The solvent to be used for cleaning depends on the window material of the cell. Do not use water for cleaning in case of KBr windows. Do not use acidic solvents for cleaning in case of ZnSe windows.

5.3.4 Gas Cell

To spectroscopically analyze gaseous samples optional gas cells are available. The gas cell (B in figure 42) is supplied with a special gas cell holder (A in figure 42).

Figure 42: Delivery content in case of a gas cell

A

B

To insert the gas cell into the ALPHA-T sample compartment you first have to displace the sample holder in the sample compartment, see figure 43a and b.

Figure 43: a) Standard position of sample holder b) Right sample holder position (for gas cell)


C h a p t . 5P o s i t i o n i n g s a m p l e i n t h e A L P H A - T s a m p l e c o m p a r t m e n t

To displace the sample holder in the ALPHA-T sample compartment. . .

1 ...you have to use the supplied TORX screw driver TX20.2 Lift up the sample compartment lid.3 Remove the detachable blue casing at the front side of the sam-

ple compartment, see figure 44.

Figure 44: Removing the casing at the front of the sample compartment

TORX screw

Detachable casing

4 Loosen the two TORX screws which fix the sample holder, see figure 44.

5 Mount the sample holder into the right position, see figure 43b.6 Put the detachable blue casing to the front of the sample compart-

ment again.

To insert the gas cell into the sample compart-ment. . .

1 ...put the special gas cell holder into the fixture of the sample holder, see figure 45a.

2 Position the gas cell on the sample holder as shown in figure 45b.

Figure 45: a) Insert gas cell holder b) Gas cell on sample holder

C h a p t . 5



5.4 Measuring Sample

Use the OPUS software to measure the sample. Information on measuring the sample can be obtained from the Quick User Guide in chapter 3. For detailed information on the OPUS software refer to the OPUS/MENTOR manual.

As OPUS automatically recognizes the measurement module you work with, the software can automatically load the right experiment file supplied (i.e. Trans.XPM in case of transmission measurement). Thus, you can immediately start to measure.

The experiment file supplied includes the default parameters set by Bruker. These parameters allow to perform a transmission measurement. For information on how to set up measurement parameters refer to the OPUS/MENTOR manual.

Note: Keep the sample compartment closed during measurement.


C h a p t . 6

6 ATR Measuring6.1 General Information

ATR is the abbreviation of Attenuated Total Reflection. To perform ATR measurements three different modules are available, see chapter 6.2. For more information on the principle of ATR measurements refer to the glossary in appendix D.

Measuring in ATR is suited for the fol lowing sample type:

Liquid Powder Paste Gel and cream Polymer film Surface coating

Advantages:

Non-destructive analysis method, i.e. the sample has not to be destructed for analysis

No sample preparation required Only a small number of sample quantity required Suited for samples which are actually too thick or highly

absorbing for transmission measurement Due to the multiple reflection of the IR light, the sample

absorbs more light than in case of transmission measurement

Disadvantages:

Falsified measurement result due to possible contaminations caused by previous sample material, solvents or fingerprints.

In case of multi-layer materials only the first layer will be spec-troscopically analyzed.

The quality of the measurement result substantially depends on the contact pressure between sample and ATR crystal dur-ing measurement.

C h a p t . 6


A T R M e a s u r i n g

6.2 ATR Measurement Module

6.2.1 Overview

To perform ATR measurements by using ALPHA, the following ATR modules are available:

ALPHA-E ALPHA-P ALPHA-P High Pressure variant

Figure 46: a) ALPHA-E b) ALPHA-P c) ALPHA-P High Pressure variant

These modules differ from each other in the following technical features:

ATR-Module Crystal material available

Actual sampling surface on ATR crystal

Moving pressure arm by means of a

ALPHA-E Ge, ZnSe 5mm knob

ALPHA-P Diamond, Ge Diamond:2 x 2mmGe: 2mm

lever

ALPHA-PHigh Pressureoption

Diamond 2 x 2mm knob


C h a p t . 6A T R M e a s u r e m e n t M o d u l e

6.2.2 ATR Crystal Types

The crystal types available have the following technical features:

Crystal type To be used for Spectral range (cm-1) Refraction index

Diamond all kinds of sample material, includ-ing hard and sharp-edged samples

covers the complete spectral range speci-fied for ALPHA, see appendix A

n = 2.43

Ge (Germanium) samples with a high absorptivity, especially carbon-filled samples (e.g. O-rings, polymer)

5,000 - 550 n = 4.01

ZnSe (Zinc Selenide)CAUTION - TOXIC!

all kinds of sample material, except for acids (pH -value 8) and sharp-edged samples

>500 n = 2.43

Caution: Zinc selenide is a toxic material. During normal spectrome-ter operation the material does not pose a health risk. Be careful, however, if the crystal is broken. Avoid generating dust. The dust is harmful by inhalation, ingestion or skin absorption.

6.2.3 Exchanging ATR Crystal Plate

The ATR crystal plates can include one of the following crystal material: ZnSe, Ge and diamond. The color of the crystal indicates which crystal material is used.

Crystal material Crystal color

Diamond transparent

Ge (Germanium) silver-gray

ZnSe (Zinc selenide) yellow

It is not easy to rotate the crystal plate manually. Therefore, it is recommended to use the stick supplied. The leverage effect of the stick facilitates rotating the crystal plate.

C h a p t . 6



1 Put the stick into the bore of the crystal plate, see figure 47.

Figure 47: Exchanging crystal plate

Rotating counterclockwise releases the crystal plate

Rotating clockwise locks the crystal plate

2 Rotate the crystal plate counterclockwise by means of the pin as far as it will go (approx. 20).

3 Remove the crystal plate.4 Place the new plate onto the ATR measurement module and put

the pin into bore of the crystal plate.5 The stick helps to tighten the crystal plate again, by rotating the

plate clockwise as far as it will go.6 Remove the pin from the crystal plate bore.

6.2.4 Moving Pressure Application Device

Depending on the measurement module used the pressure application device can be moved in different ways.

ALPHA-E

The pressure application device is moved upwards or downwards by means of a knob (figure 48):

upwards - you have to rotate the knob counterclockwise downwards - you have to rotate the knob clockwise

The inner part of the pressure arm is equipped with a slip-clutch mechanism which is activated as soon as the optimal contact pressure between sample and anvil has been applied. Further rotating the knob, which is only possible by substantial force, would not have any effect on the contact pressure already applied.


C h a p t . 6A T R M e a s u r e m e n t M o d u l e

However, the contact pressure actually applied (i.e. how much the anvil presses the sample against the ATR crystal) depends on how far you rotate the pressure arm down.

Figure 48: ALPHA-E - Pressure application device

Knob

Pressure arm

Anvil

You can swing away the pressure arm and the anvil from the sampling surface. The pressure arm is rotatable by 360. If you swing the pressure arm towards the sampling surface again, it snaps into place exactly above the ATR crystal.

ALPHA-P

The pressure application device is moved upwards or downwards by means of a lever (figure 49).

lever in back position - moves the anvil up lever in front position - moves the anvil down

Figure 49: ALPHA-P - Pressure application device

Lever to move the anvil

Height adjusting knob to move the com-plete pressure application device

Red control spot indicates optimal con-tact pressure

Anvil

C h a p t . 6



The optimal contact pressure applied on the sample is ensured if the red control spot (figure 50) is exactly in the middle of the round recess.

Figure 50: ALPHA-P - Indication of the optimal contact pressure

The red spot in the mid-dle of the round recess indicates an optimal con-tact pressure applied on the sample.

To adjust the height of the complete pressure application device is required if . . .

1 ...the lever is right in the front position but the anvil has not any contact with the sample. In this case use the height adjusting knob (see figure 51) and move the complete pressure application device downwards until the red control spot is exactly in the middle of the round recess.

2 You cannot move the lever right to the front position as the sam-ple is too thick. In this case use the height adjusting knob (see figure 51) and move the complete pressure application device upwards, until the lever can be moved right to the front position and the red control spot is exactly in the middle of the round recess.

Turning the height adjusting knob to the right, moves the complete pressure application device downwards.

Turning the height adjusting knob to the left, moves the com-plete pressure application device upwards.

Figure 51: ALPHA-P - Height adjustment knob


C h a p t . 6P e r f o r m i n g C l e a n n e s s T e s t

You can swing away the pressure application device from the sampling surface. The pressure application device is rotatable by 360. If you swing the pressure application device towards the sampling surface again, it snaps into place exactly above the ATR crystal.

Note: For ALPHA-P as High-Pressure option refer to ALPHA-E.

6.3 Performing Cleanness Test

Before you start measuring perform a cleanness test by means of the OPUS software. This kind of test is a reference measurement of the ATR crystal and defines the maximum allowed limit of the crystal contamination. For further details refer to the OPUS/MENTOR manual.

6.4 Placing Sample on ATR Crystal

1 Make sure that the sampling surface, ATR crystal and anvil are clean, see chapter 6.6.

2 Place the sample on the middle of the sampling surface. Use a small amount of sample, only enough to cover the ATR crystal.

Caution: When using flammable and/or explosive materials, always wear eye protection and use a very small amount of the material. In case of extremely volatile materials do not inhale the vapor and observe the safety requirements.

C h a p t . 6



Note: If the sample cannot be placed onto the ATR crystal as the dis-tance between the ATR crystal and anvil is too small, move the pressure application device upwards (see chapter 6.2.4).

3 Press the anvil against the sample (see chapter 6.2.4). Make sure that the optimum contact pressure is used to press the sample against the ATR crystal.

4 Acquire a sample spectrum (see chapter 6.5). For detailed infor-mation to perform a measurement refer to chapter 3.

5 Move the pressure application device up again and remove the sample.

Note: Samples should not be left in contact with the crystal for an extended period of time as some samples may degrade the crystal material, and discoloration of the metal plate may occur. Once the measurement has been made, remove the sample from the crystal.

6 Thoroughly clean the sampling surface, ATR crystal and anvil (see chapter 6.6).

6.5 Measuring Sample

Use the OPUS software to measure the sample. Information on measuring the sample can be obtained from the Quick User Guide in chapter 3. For detailed information on the OPUS software refer to the OPUS/MENTOR manual.

As OPUS automatically recognizes the measurement module and the ATR crystal you work with, the software can automatically load the right experiment file supplied. Thus, you can immediately start to measure. Depending on the ATR crystal used, the following experiment files are supplied:

ATR_Di.XPM ATR_Ge.XPM ATR_ZnSE.XPM

The experiment files supplied include the default parameters set by Bruker. These parameters allow to perform an ATR measurement. For information on how to set up measurement parameters refer to the OPUS/MENTOR manual.


C h a p t . 6C l e a n i n g A T R M o d u l e

6.6 Cleaning ATR Module

When performing one measurement after the other it is important to clean all remains of the previous sample from the sampling surface and crystal, as well as from the anvil. Otherwise, you may get falsified measurement results.

Cleaning solvents:

Alcohol Acetone

Note: When using solvents inspect the materials safety data sheets associated with the solvents you are using and observe any recommended handling procedure.

The solvent used for cleaning depends on the sample that has been analyzed. In all cases it is best to try to clean the sampling surface by the mildest solvent possible.

Before cleaning.. .

...swing away the pressure application device from the sam-pling surface.

When cleaning.. .

...apply the solvent to the ATR sampling surface using a Q-tip. Gently remove the solvent using a Q-tip or lint-free cloth. Clean the anvil as well. Repeat the cleaning procedure until all sample remains have

been removed.

Caution: Never use caustic or abrasive substances or strong acids. These substances can damage the ATR sampling surface. Never rub with paper products as they may be abrasive and could cause scratches on the crystal surface, especially with Ge and ZnSe.

C h a p t . 6



6.7 ATR Spectra

Similar to transmission spectraIntensities of the spectral features are of lower absorbance than the corresponding features in a transmission spectrum, especially, in the high wavenumber (short wavelength) region of the spectrum.

IntensityIs related to the penetration depth of the evanescent wave into the sample. This depth depends on the refractive index of the crystal and sample, and on the wavelength of the IR radiation.

Main benefitThe relatively thin depth of penetration of the IR beam into the sample creates the main benefit of ATR sampling. This is in contrast to traditional FT-IR sampling by transmission where the sample must be diluted with IR transparent salt, pressed into a pellet or pressed to a thin film, prior to analysis to pre-vent totally absorbing IR bands.


C h a p t . 7

7 Maintenance & RepairALPHA is a low-maintenance instrument, i.e. the operator can replace components with a limited service life (e.g. IR source). The following maintenance procedures are described in this chapter:

Replacing IR source Replacing desiccant Replacing windows Cleaning windows Cleaning spectrometer housing

General Instructions

Perform only the maintenance procedures described in this manual. Strictly observe the relevant safety precautions. Any failure to do so may cause property damage or personal injury. In this particular case Bruker does not assume any liability. Maintenance or repair procedures not described in this manual should only be performed by a Bruker service engineer. For service assistance, see appendix E.

Depending on the degree of hazard the safety instructions to be observed in case of spectrometer maintenance or repair are classified as follows:

Caution indicates that minor personal injury or property damage CAN result if proper precautions are not taken.

Note draws your attention to particularly important information on the product, or to the product operation.

The safety instruction Caution is indicated by triangular warning label.

C h a p t . 7


M a i n t e n a n c e & R e p a i r

7.1 Replacing IR Source

ALPHA is equipped with a highly-efficient, low-power, air-cooled infrared source.

When do you have to replace the IR source?

The average IR source lifetime is specified with about 44.000 operating hours. Before this period has been expired the following message pops up in OPUS: End of average lifetime is nearly reached, spare part will be

required. In this case the OPUS status light ( ) is yellow. A yellow status light allows to continue measuring.

Order a replacement source (order no: 1005855). As soon as you have received the replacement, the existing source should be replaced.

Note: To allow the status light become green again, you have to click on the Ignore button in the Instrument Status Message dialog (see figure 65 on page 76).

The End of average lifetime is nearly reached, spare part will be required message will be displayed in regular intervals.

If the source is defective, the OPUS status light becomes red. The following message pops up in OPUS: Source is broken. A red status light does not allow to continue measuring. The source must be replaced.

How do you have to replace the IR source?

1 Switch off the power plug.2 The source is accessible from the rear side of the spectrometer.

Make sure that you have access to the rear side.3 Remove the cover plate at the rear side by loosening the 4 TORX

screws (A in figure 52). To loosen the screws use the TORX TX20 screw driver supplied.

4 Take off the cover plate.

Figure 52:

Alpha.pdf

Documents

Transcript of Alpha.pdf