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Gamal A. Hamid FTIR OMNIC SOFTWARE Gamal A. Hamid

FTIR software

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Page 1: FTIR software

Gamal A. Hamid

FTIR OMNIC SOFTWAREGamal A. Hamid

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Contents

Introduction

Software

Menu bar

Tools bar

Pane

Palette

View finder

Getting started

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INTRODUCTION

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FT-IR

FT-IR stands for Fourier Transform Infrared

An infrared spectroscopic technique that uses an interferometer for data collection and a digital Fourier transformation to process the data.

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FTIR Instrumentation

1) Source (ETC EverGlo)

2) Laser (for internal calibration)

3) Interferometer

A. beam splitter semi-reflecting

B. fixed mirror

C. moving mirror

4) Detector (DTGS Deuterium tri glycine sulphate)

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1. Source ETC EverGlo

Electronically Temperature Controlled (ETC) EverGlo

The ETC EverGlo source is an efficient ceramic, refractory

composite that rapidly rises to operating temperature and is

also thermally insulated to maintain a constant operating

temperature.

provide energy for the spectral region from 7400 – 50 cm-1.

the source temperature is constantly monitored and

controlled at 1140°C by the ETC.

The temperature of the source is dropped to 900°C if the

spectrometer has been inactive for a period of time

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2. Laser

A Helium–neon laser or HeNe laser, is a type

of gas laser whose gain medium consists of a

mixture of helium and neon(10:1) inside of a

small bore capillary tube, usually excited by a DC

electrical discharge.

Laser create the drive volt for the moving mirror.

The He-Ne laser is used as an internal reference

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3. Interferometer

The interferometer produces a unique type of signal which has all of the

infrared frequencies “encoded” into it.

The signal can be measured very quickly, usually on the order of one second

or so. Thus, the time element per sample is reduced to a matter of a few

seconds rather than several minutes.

It contain:-

1. fixed mirror.

2. Moving mirror.

3. beam splitter.

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The Michelson Interferometer

Consists of a perpendicular mirrors with a beam

splitter between them. When one of the two mirrors

is translated, all optical frequencies are converted

into cosine waves of intensity; the result is the

complex time variation of intensity called the

interferogram.

An interferogram is the sum of all cosine waves for

all optical frequencies. The spectrum is calculated

from the interferogram by computing its cosine

Fourier transform. This in effect, decodes the

individual frequencies in the spectral analysis.

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Beamsplitter

Most interferometers employ a beamsplitter which takes the

incoming infrared beam and divides it into two optical beams.

One beam reflects off of a flat mirror which is fixed in place.

The other beam reflects off of a flat mirror which is on a

mechanism which allows this mirror to move a very short

distance (typically a few millimeters) away from the

beamsplitter.

The two beams reflect off of their respective mirrors and

are recombined when they meet

back at the beamsplitter.

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Interferogram

the path that one beam travels is a fixed length and the other is constantly

changing as its mirror moves, the signal which exits the interferometer is the

result of these two beams “interfering” with each other.

The resulting signal is called an interferogram which has the unique property

that every data point (a function of the moving mirror position) which makes

up the signal has information about every infrared frequency which comes

from the source.

the measured interferogram signal can not be interpreted directly.

A means of “decoding” the individual frequencies is required. This can be

accomplished via a well-known mathematical technique called the Fourier

transformation.

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4. Detector

FT-IR spectrometers use either

1. Pyroelectric ( thermal detectors ) DTGS.

2. Photoconductive detectors. (quantum detector) MCT.

Pyroelectric detectors a thin, Pyroelectric crystals such as deuterated triglycine sulfate

(DTGS) or LITA (lithium tantalate), When a pyroelectric material is polarized by an

electric field, it remains polarized after the field is removed due to an effect called

residual electric polarization. This residual polarization is sensitive to changes in

temperature.

Photoconductive detectors show an increase in electrical conductivity when

illuminated with IR radiation, They have a rapid response and high sensitivity. The most

commonly used photoconductive detector is the MCT (Mercury Cadmium Telluride),

which must be cooled to liquid nitrogen temperatures for proper operation.

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The Sample Analysis sequence

1. The Source: Infrared energy is emitted from a source.

2. The Interferometer: The beam enters the interferometer where the “spectral

encoding” takes place”.

The resulting interferogram signal then exits the interferometer to the sample.

3. The Sample: The beam is transmitted through or reflected off of the surface of

the sample, where specific frequencies of energy, which are uniquely

characteristic of the sample bonds are absorbed, the rest go to the detector.

4. The Detector: The beam finally passes to the detector for final measurement

5. The Computer: The measured signal is digitized and sent to the computer

where the Fourier transformation takes place.

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Sequence

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SOFTWARE

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Software Starting

Open OMNIC

Double-click the OMNIC program icon on

your computer desktop.

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Omnic window

I. Menu bar.

II. Tools bar.

III. Pane “Spectrum window.

IV. Palette.

V. View finder.

VI. Bench status indicator.

VII. Information button.

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Menu Bar

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I. Menu Bar

The Edit menu allows you to enable, disable, hide, add, delete and

modify items in the menus.

The menu bar contains the OMNIC menu names. The menus are

arranged in an order that is convenient for collecting and processing

data.

Within each menu, the commands are grouped according to their

related functions.

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1. Edit menu

Options to customize OMNIC for the way you prefer

to use the software. You can set options that affect

how spectra are collected, displayed, processed,

saved and printed.

The Edit Menu command allows you to customize the

contents of the OMNIC menus for the way each

person prefers to use the software.

You can disable, but not hide.

You can hide all of the menus by turning on Hide All

OMNIC Menus in the Edit Toolbar dialog box.

Edit Toolbar lets you create custom toolbars

containing buttons for quickly initiating commands.

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2. Collect menu

Experiment setup

Collect sample

Collect background

All of above commands will discuss later in

details in the toolbar section.

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3. View menu

Display Setup to specify how spectra are to be displayed in pane

Stacking spectra is useful when you are comparing spectra that

are significantly different.

Hide Spectra to hide the selected spectra from view.

Full Scale to adjust the vertical scale of the spectra .

Common Scale to display all the spectra using the same Y-axis

Match Scale ,All the spectra in the window are displayed using

the Y-axis limits of the selected spectrum.

Offset Scale to display the spectra vertically offset from each

other, Separating the spectra.

Display Limits to specify the X-axis and Y-axis display limits.

Automatic Full Scale automatically displays the spectra full.

Roll/Zoom lets you access a set of symbols that you can use to

adjust the display of spectra.

Toolbar , select or deselect the appearance of it.

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System Status

The System Suitability features, let you

check the suitability of your

spectrometer for use in your particular

application.

The tests can be performed with your

sample or automatically using a

validation wheel, if installed.

Run the test, get the report including

FAILED, or PASSED.

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4. Process menu

All the spectrum related commands.

Final Format parameter determines the units used

for the collected data. A, T, or others.

Correction parameter to select the type of

correction to use when collected spectra are

processed.

Subtract and remove parameters for spectrum or

a part of it.

smoothing and drawing parameters

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Process 1

Transmittance IR energy transmitted through the sample.

%T = (S/B)*100 where S is IR intensity

B is IR intensity without a sample in place (background).

Absorbance at a frequency is defined by the equation

A = log(100/%T)

Reprocess to transform the interferogram data for the

selected spectra using different transformation parameter

settings or ratio the spectra against a different background

to improve the final data.

Retrieve Interferogram to display the interferogram for the

selected spectrum in the active spectral window.

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Process 2

Baseline Correct to correct a sloping, curving, shifted or

otherwise undesirable baseline of a spectrum so that the

baseline appears flat and near zero absorbance.

Automatic Baseline Correct lets you automatically correct

the baseline of the selected spectra.

Advanced ATR Correction to correct (ATR) spectra for the

shifting of infrared absorption bands and the effects of

variation in depth of penetration.

PAS Linearize lets you correct photoacoustic data to

enhance the infrared signal at the sample surface or

improve quantitative linearity.

Interactive Kramers-Kronig to convert a specular

reflection (SR) spectrum to a transmission.

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Process 3

Blank to delete the data points in the selected

spectral region.

Straight Line lets you replace the selected region

of the selected spectra with data points that form

a straight line.

Subtract whenever you want to subtract one

spectrum from another.

Automatic Region Subtract to let you quickly

subtract from a mixture or sample spectrum the

spectral data due to a particular component or

contaminant.

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Process 4

Fourier Self-Deconvolution to reveal overlapping

spectral features that cannot be resolved by

collecting data at a higher resolution setting.

Smooth to improve the appearance of the selected

spectra by preferentially smoothing the high-

frequency component of the spectral data.

Derivative to convert the selected spectra to their

first or second derivatives.

Multiply to multiply each data point in a spectrum

by a number of your choice.

Spectral Math to perform arithmetic operations on

one or two selected spectra.

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5. Analyze menu

Find Peaks to identify peak locations in a

spectrum.

Send To OMNIC Specta If you have installed

OMNIC SpectaTM software, you can export the

selected spectra to that program. The spectra

are added to the data tray.

Average to find the average Y value of the data

points in the selected spectral region .

Statistical Spectra lets you perform statistical

calculations on two or more selected spectra.

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Analyze

Library Setup to specify how to perform a spectral search of one or more search

libraries to identify an unknown spectrum, or a QC comparison of one or more QC

libraries to verify the composition of a sample.

To add and remove libraries.

IR Spectral Interpretation to help you determine which chemical functional groups

may be present in an FT-IR spectrum.

Library Manager gives you the ability to view the spectra and related information

contained in commercial and user libraries of spectra.

QCheck Before comparing spectra with in the Analyze menu, use QCheck Setup in

the Analyze menu to set up the comparison.

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Noise

The noise level of a spectrum depends on many factors, including

the hardware being used, the experiment parameter settings and

the physical surroundings of the system.

Use Noise in the Analyze menu to measure the noise in the

selected spectral region of a spectrum, Both peak-to-peak and root

mean square (rms) noise are measured.

Peak-to-peak noise

is the difference between the highest and lowest noise peaks in the

selected spectral region.

RMS (root mean square) noise

A measure of the statistical analysis of the noise variation in a

spectral region.

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6. Report menu

Template, to select , edit or create a report

template.

Preview/Print Report to view a report as it

would appear on paper and print it.

New Notebook to create a new report

notebook to which you can add reports.

Auto Report Options to specify headers

and footers that will appear on each page

of any reports you display or print using

Preview/Print Auto Report in the Report

menu.

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Tool bar

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II. Toolbar

the Edit menu allows you to enable, disable, hide,

add, delete and modify items in the menus.

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Experiment Setup

The Experiment Setup features:

1. Collect

2. Bench

3. Quality

4. Advanced

5. Diagnostic

6. Configure

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1. Collect Parameters

Collection parameters

File handling

Background handling

Experimental description

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Number of scan

How many Scans are performed during a sample or

background data collection.

Increasing the number of scans reduces the noise level

of the data (increases the signal-to-noise ratio) and

increases the sensitivity .

The smaller the Resolution value, the higher (better) is

the resolution

Typically resolutions of 8 or 4 wavenumbers are used

for solid and liquid samples. Gas samples normally

require a resolution of 2 wavenumbers or better (lower

setting of Resolution).

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a. Collect a Background Spectrum

Acquire a Background Scan

Before a sample can be acquired, a

background scan must be

obtained. Water vapor and carbon

dioxide in the air will produce

interfering bands which must be

subtracted from the spectrum.

Select Collect – Collect

Background. The instrument will

begin collecting a background

spectrum.

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Background interferences

Spectral Range (wavenumbers) Interference

5580-5500 NIR range, water vapor

3950-3500 Water vapor

2400-2270 Carbon dioxide

2670-1800 Diamond bands (diamond ATR)

2000-1290 Water vapor

700-400 Carbon dioxide

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b. Collect a Sample Spectrum

Once you have a background prepared,

Select Collect – Collect Sample from the

menu above,

The instrument will ask for a spectrum

title.

Name the sample, Click OK and the

instrument will begin collecting a

spectrum in scout scan mode.

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2. Bench Features

Detector Type of detector used.

Beamsplitter Type of beamsplitter used.

Source Type of source used.

Gain Gain used to amplify the detector signal.

Optical Velocity

A value that is twice the velocity of the moving mirror.

Aperture Relative size of the aperture expressed as a percent of maximum area.

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2. Bench Features

Detector Pyroelectric ( thermal detectors ) DTGS

Beamsplitter K Br beamsplitter

Source IR source

Gain 1, 2, 4, 8, Auto gain. for ATR and diffuse reflection typically use a Gain setting of 2 or 4. OMNIC automatically adjust the gain to maximize the signal by setting Gain to Autogain

Optical Velocity Using a faster velocity lets you collect more scans in a given amount of time, The stronger signal obtained at the slower velocity,

Aperture The larger the aperture, the better is the signal to noise ratio of the collected data. The smaller the aperture, the better the stability and accuracy will be. Small apertures are needed for high-resolution experiments

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3. Quality Checks

OMNIC offers four categories of

spectral quality checks:

Spectrum checks

Parameter checks

Background checks

Interferogram checks

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4. Advanced Parameters

The Advanced tab in the

Experiment Setup dialog box

contains parameters drawing

the spectrum.

Automatic Blanking Of

Regions box specifies spectral

regions to be blanked so that

they contain no data points in

the collected spectrum.

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5. Diagnostic

Note: The availability of the indicators depends

on the spectrometer model you have.

Power supply

HeNe laser

Light source

Electronics

Beamsplitter and detector

Align

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Align the spectrometer

It is also a good idea to align the interferometer if the

signal intensity has dropped significantly from its usual

level.

The spectrometer power should be on for at least 15

minutes (1 hour or longer for best results) before you

perform an alignment.

Set Gain to 1 before clicking the Align button.

Remove any accessories or samples from the sample

compartment before aligning the spectrometer.

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6. Configure

You can use the Source

Rest Mode features to

extend the life of the

infrared source.

(A white light source

cannot be placed into Rest

mode.)

The table below describes

what Rest mode does

when you are not using

the source.

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Bench configuration

You can configure the system for the

hardware you are using or perform

other tasks described below by

clicking the Configure Bench button.

You must configure the system after

you install:-

Source

Beamsplitter

Detector

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Processing Tools

Stack spectra

Full scale

Common scale

Automatic baseline correction

Advances ATR

Subtract spectrum

Find peaks

Select all

clear

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Library Tools

Add to library

Library setup

Search

QC compare

Library manager

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Report Tools

Template

Preview / print report

View notebook

Add to notebook

Preview / print auto report

Auto report options

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Pane and Palette

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III. Pane

A pane is an area of the spectral window

used to display a spectrum along with

associated information and software

features.

A spectral window can contain one or

several panes, as specified by Display Setup

and the Window options (available through

Options in the Edit menu).

You can display spectra in overlaid or

stacked panes, depending on how you

want to view the data.

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Pane “Spectrum window”

Four regions of Chart

3700 – 2500 cm-1 Single bonds to hydrogen

2300 – 2000 cm-1 Triple bonds

1900 - 1500 cm-1 Double bonds

1400 - 650 cm-1 Single bonds (other than hydrogen)

Fingerprint region

1- The region to the right-hand side of the diagram (from about 1650 to 500 cm-1)

2- Usually contains a very complicated series of absorptions

3- Contains peaks due to bending vibrations

4- It is rarely possible to assign a specific peak to a specific group.

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IV. Palette

The Palette of the spectral window contain six tools to

performing some operation on the spectrum.

The names and appearances of the palette indicates

their functions

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View and others

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V. View Finder

The view finder lets you adjust the display of all the spectra in a spectral

window or task window to show a larger or smaller spectral region or a

different region of the same size.

You can also adjust the vertical scale of the selected spectra.

If more than one spectrum is selected in a spectral window, an image of the

first spectrum selected appears in the view finder.

If no spectrum is selected, the view finder is empty.

The currently displayed spectral region is indicated by the region markers, the

blue vertical lines within the view finder.

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V. View finders

Expand the spectra horizontally about the center.

Contract the spectra horizontally about the center.

To roll the spectra to right.

To roll the spectrum to lift.

Expand the spectra vertically .

To contract the spectra vertically.

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VI. Bench status indicator.

If the spectrometer has passed all of its tests, the System Status indicator

shows a green check mark.

If the System Status indicator shows a yellow icon containing an

exclamation mark, a cooled detector has become warm or data cannot be

collected because the printer port is being used to print information (on

some systems).

If the System Status indicator shows red "X," the spectrometer has failed a

test and requires corrective action or the computer cannot communicate

with the spectrometer.

For help with solving the problem, click the indicator, click Instrument

Status in the System Status Overview dialog box and click the Explain Error

button.

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VII. Information button.

COLLECTION , PROCESSING INFORMATION

Title ,Collected time, Accessory,

Correction parameters.

DATA COLLECTION INFORMATION

Number of sample scans: 128

Collection length: 152.2 sec

Resolution: 4.000

Number of background scans: 128

Background gain: 8.0

DATA DESCRIPTION

SPECTROMETER DESCRIPTION

Spectrometer, Source: IR

Detector: DTGS KBr

Smart Accessory ID: Unknown

Beamsplitter: KBr

Optical velocity: 0.6329

Aperture: 100.00

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GETTING STARTED

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Turn on the spectrometer

Turn on the spectrometer, the system status and system scan

LEDs next to the power switch flash in various sequences as the

system performs its diagnostic routines.

When the routines are finished, the system status LED stops

flashing and remains lit.

The system scan LED will intermittently blink, indicating that the

interferometer is scanning and working properly.

If the system status LED continues to flash or does not light at all,

turn the spectrometer power off and then back on.

If this does not resolve the problem, see Troubleshooting for

possible causes and solutions.

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Getting started

Turn on the computer. The spectrometer should be on the entire time line

Launch OMNIC on the desktop.

Make sure the bench Status is √ on the top right corner of the window.

Make sure that there isn’t anything left on the crystal.

Click on Col Bkg to take a background of air. When the confirmation window

pops up, click YES.

When the confirmation window pops up to ask to add Window 1, click NO.

Place your sample on the crystal- Liquids -place a drop of sample on the

crystal with a medicine dropper. Solids – place a small neat sample on the

crystal with a spatula.

Dial the knob of the ATR until the pressure .

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Click on Col sample, Collect Sample Window pops up, type in “sample name” and

enter, confirmation window pops up, click YES.

When the confirmation window pops up to add Window 1, click YES.

To have peaks labeled, Click Find Pks. Adjust the threshold by clicking on the window

with the left mouse button. When peaks are selected, Click on “Replace”.

If for some reason some of the peaks are not labeled, extra peaks can be manually

labeled by clicking on the “T” on the bottom left corner.

Use the “Text” too to select and or write a label or description.

If satisfied with the information on the computer displaced spectrum, then can be

printed by clicking on Print icon and then print again in the print window.

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Applications

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Applications

FTIR spectra reveal the composition of solids, liquids, and gases. The most common use

is in the identification of unknown materials and confirmation of production materials -

The areas where FTIR is applicable are listed below:

Environmental

Forensic

pharmaceutical

Polymer

Quality

Others

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Environment

Infrared spectroscopy is a valuable technique for

monitoring :-

Air quality,

Testing water quality,

Analyzing soil

to address environmental and health concerns

caused by increasing pollution levels.

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Forensics

FTIR, FT-Raman, GC-IR, and IR microscopy techniques

build a complete understanding of evidence samples

and allow forensic scientists to confidently give expert

testimony in court. These techniques can provide fast,

easy and consistent analysis for:

Seized drugs: controlled substances and cutting agents

Clandestine labs: chemical evaluation

Hit and run: paint and materials

Textile identification: fibers, coatings, and residues

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Pharmaceuticals

FTIR is an excellent technique for pharmaceutical

analysis because it is easy to use, sensitive, fast, and

helps ensure regulatory compliance through

validation protocols. Applications include:

Basic drug research and structural elucidation

Formulation development and validation

Quality control processes for incoming and

outgoing materials

Packaging testing

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Polymers & Plastics

FTIR spectroscopy is used to quickly and definitively identify

compounds such as compounded plastics, blends, fillers,

paints, rubbers, coatings, resins, and adhesives.

Key areas where infrared analysis adds value include:

Material identification and verification

Copolymer and blend assessment

Additive identification and quantification

Contaminant identification - bulk and surface

Molecular degradation assessment.

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Quality Control

Infrared spectroscopy is an ideal analytical tool

for both routine quality control (QC) analysis to

verify if materials meet specification, and

analytical investigations to identify the causes of

failures when they occur.

FTIR instrumentation can be located in the

analytical laboratory or near the production line.

With its low cost, speed, and ease of analysis,

FTIR is a method of choice for many industrial

applications.

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THANKS

Gamal A. Hamid