introduction to synchrotron infrared …
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On Leave from: Department of Physics, Faculty of Science,
Helwan University, Cairo , Egypt
Gihan kamel
SESAME Infrared Beamline Scientist
gihan.kamel@sesame.org.jo
INTRODUCTION TO SYNCHROTRON INFRARED
MICROSPECTROSCOPY
(9:00-11:00 a.m.):
Introduction to the IR Microspectroscopy: Infrared microspectroscopy
technique, instrumentation, measuring modes.
Pieces of advice on samples’ preparation and handling.
General knowledge: (data collection, processing, analysis and interpretation).
The advantages of the synchrotron-based FTIR Microspectroscopy.
(12:20 – 13:00 p.m.):
SESAME IR beamline capabilities.
Practical session: Group 1- (14:00 – 15:50 p.m.):
Practical session: Group 1I - (16:10 – 18:00 p.m.):
IR MICROSPECTROSCOPY:
THURSDAY, JUNE 26, 2019.
Questions:
What is the history of the sample?
What is the reason for the analysis?
What information is needed?
Can the sample be moved? If yes, how much (which form)? If no, other
options?
Does the sample have a single component or is it multicomponent?
Are all components original to the piece?
Has any previous analysis been done?
WHY, HOW AND WHAT?
(HISTORY, DESIGN AND RESULTS)
WHAT DO YOU NEED TO KNOW: I
Infrared Absorption Theory
Electromagnetic Radiation
Molecular Absorptions
Infrared Spectra
Infrared Regions (Near-Infrared, Mid-Infrared, Far-Infrared)
Sample Collection and Preparation
Sampling Methodology (Design, Tools, Documentation and Storage)
Avoidance of Contamination
Sample Collection and Preparation\manipulation Procedures
Infrared Analysis Methods
Infrared Transmission Measurements (Infrared Window Materials)
Infrared Reflection Measurements (Specular Reflection, Reflection-
Absorption, Diffuse Reflection, Internal Reflection, etc)
Infrared Microspectroscopy
Microspectrometer (Design and Capabilities)
Microspectroscopic Accessories
WHAT DO YOU NEED TO KNOW: 1I
WHAT DO YOU NEED TO KNOW: III
Spectral Interpretation
Instrument Configuration
Qualitative Analysis (Spectral Quality, Visual Comparison, Spectral Libraries)
Spectral Region Examination
Spectra-Structure Correlations
Mathematical Manipulations of Spectra (Subtraction Techniques, Resolution
Enhancement Methods, etc.).
TO TAKE AWAY:
Scientific approach to the environmental science field.
(Why and how?)
Introduction to the IR Microspectroscopy Basics.
(EM radiation, Absorption theory, IR spectroscopy, ...)
The advantages of the SR-based FTIR Microspectroscopy.
(IR thermal sources are still great, but sometimes NOT
great enough!)
“Ideally”, a technique for a proper analysis should be*:
• Non-destructive (non-invasive) [rare/one of a kind items]
• Fast.
• Universal: different objects may be studied with minimal or no sample pre-
treatment.
• Versatile: local information of small areas and average composition to be
obtained (spatial resolution).
• Sensitive: able to detect trace quantities.
• Multi-elemental: simultaneously detect multiple components in a single
measurement.
* Lahanier et al. Nuc. Instrum. Meth. B14 (1986) 1-9.
IR spectroscopy
A COMPARISON OF COMMONLY USED CHEMICAL ANALYSIS
TECHNIQUES.
COMMON SR TECHNIQUES EMPLOYED IN THE FIELD OF
ENVIRONMENTAL SCIENCES
L. Bertrand et al., Heritage and archaeological materials studied by synchrotron methods, DOI 10.1007/s00339-011-6686-4, Appl Phys A.
Pharmaceuticals
Cultural heritage
Food
Disciplines.. or better to say DEMANDS?!
Chemistry
Physics Forensics
Cell biology
Ecology
Biology
Mineralogy
Agriculture
Geology
Archeology
Astronomy
Art restoration
Environment
Medicine
Forensics
Data Analysis
(Imaging)
POCKET: WORK FLOW FOR FTIR MICROSPECTROSCOPY
FTIR Data CollectionSamples preparation
Powder
Cross sections
Bulk Original as it is
IR reflective slides
BaF2 or CaF2 slides Globar
SR
Others
Transmission
Reflection
Data Analysis (Diagnosis)
ELECTROMAGNETIC RADIATION SPECTRUM
Electromagnetic radiation can be characterized by the number
of waves per unit length (wavenumber (cm-1))
The science mission in all synchrotron
facilities defines performance goals
reaching from:
- the mid-IR (2.5–25μm),
- and the far-IR (25–1000μm).
IR BEAMLINES UTILIZE THE INFRARED REGION ON THE
ELECTROMAGNETIC SPECTRUM
INTRODUCTION TO SR-IR BASICS
EFFECT OF ELECTROMAGNETIC RADIATION ON MOLECULES
Molecular spectroscopy uses EM energy, or radiation, as the physical stimulus
Infrared radiation is largely thermal energy. It induces stronger molecular
vibrations in covalent bonds as springs holding together two masses..
THE ORIGINS OF THE INFRARED SPECTRUM
The IR spectrum is formed as a consequence of the absorption of EM
radiation at frequencies that correlate to the vibration of specific
sets of chemical bonds within a molecule.
The energy distribution possessed by a molecule at any given moment, is
defined as the sum of the contributing energy terms.
Etotal = Eelectronic + Evibrational + Erotational + Etranslational (Eq. 1)
The vibrational energy: corresponds to the absorption of energy by
a molecule as the component atoms vibrate about the mean center
of their chemical bonds.
DO ALL MOLECULES INTERACT WITH IR-EM
FIELD?
Fundamental rule: “There MUST be a
net change in dipole moment
during the vibration for the
molecule or the functional group
under study.”
• Not all covalent bonds display bands in the IR
spectrum. Only polar bonds do so. These are
referred to as IR active.
• The intensity of the bands depends on the
magnitude of the dipole moment associated
with the bond in question:
• Strongly polar bonds such as carbonyl groups
(C=O) produce strong bands.
• Medium polarity bonds and asymmetric bonds
produce medium bands.
• Weakly polar bond and symmetric bonds
produce weak or non observable bands.
DEGREES OF FREEDOM IN A MOLECULE
The atoms are constrained by molecular bonds to move together in certainspecified ways: Degrees of Freedom (DoF).
For a molecule with N atoms, the total number of coordinates specified will be 3N.These 3N coordinates are the maximum number of potential transitionspossessed by that molecule. (assigned to the translational, rotational, andvibrational motions of the molecule.):
- All molecules have 3 translational DoF.- Nonlinear molecules have 3 rotational DoF and linear molecules have only 2.- The total of translational and rotational degrees of freedom is 6 (or 5 forlinear molecules).- All remaining motions are vibrational (3N-6) DoF for nonlinear and (3N -5) forlinear molecules. All vibrational motions of the atoms can be described completelyas 3N-6 or 3N-5 fundamental vibrations (normal modes of vibration) for themolecule.
POCKET:
NORMAL MODES
EXAMPLE...
The typical IR absorption range
for covalent bonds is 600 - 4000
cm-1. The graph shows the
regions of the spectrum where
the following types of bonds
normally absorb.
IR ABSORPTION RANGE
Two types of interactions- absorption and transmission- are
important in the typical IR experiment:
When the molecule in the sample compartment of the spectrometer
is exposed to a source of continuous IR radiation, the photons of
discrete energy units that are absorbed by the molecule do not reach
the detector. Photons that are not absorbed by the sample are
transmitted to the detector essentially unaltered.
The IR spectrum reveals these “missing photons”, or absorptions,
as a series of well-defined, characteristic, and reproducible
absorption bands.
For a given wavelength or frequency of IR radiation striking a
sample, these two interactions are inversely related where: A:
absorbance and T: transmittance (% T/l00).
The presence or the absence of specific functional groups.
The molecular fingerprint that can be used when comparing samples. (If two pure
samples display the same IR spectrum it can be argued that they are the same
compound.)
The molecular information on both organic and inorganic species without inducing
any beam damage nor suffering from fluorescence effects often encountered with the
UV/visible excitation in Raman spectroscopy.
The information regarding the chemical structure, as well as, quantitative information
in specific conditions.
INFORMATION OBTAINED FROM IR SPECTRA
POCKET: FTIR SPECTROSCOPY
Alvise Vianello, Jes Vollertsen Aalborg University, Denmark
Fourier Transform Infrared Spectroscopy (FT-IR)
Michelson Interferometer
Michelson interferometerPractical sessions
cooled or RT detectors
TE Cooled DLaTGS Detector with KBr Window (12,500-350 cm-1)
DLaTGS Detector with Polyethylene Window (700-50 cm-1)
Room Temperature InGaAs Detector for NIR (12,000-3,800 cm-1)
50um MCT-A Detector (11,400-700 cm-1)
MCT-B Detector (11,700-450 cm-1)
IR DETERCTORS
SAMPLING TECHNIQUES
Depends on:
- Sample form (solid, liquid, powder, film),
- what to mantain? (it is possible to use different sampling techniques,
destructive or non destructive?)
- Transmission: liquids, powders, thin sections...
- Specular reflection: crystals, polished sections...
- Diffuse reflectance: powders...
- Attenuated Total Reflection (ATR): thick samples, non reflecting surfaces...
FTIR SAMPLES HANDLING (SAMPLE TYPE, METHOD, RATING)
WHAT IF THE SAMPLE IS REALLY REALLY SMALL?!
MICROSCOPE
IR Microspectroscopy
WHY SR-IR BEAMLINES?
• Non-destructive technique that exhibits a strong interest at various worldwide
synchrotron facilities.
• Combining the spatial resolution of a the IR-visible microscope with the high chemical
sensitivity of the FTIR spectrometer.
• SR-IR source broad spectral emission and wavelength characteristics,
• SR-IR sources provide extremely valuable information in its brightness/brilliance (about
1000 times brighter) with a signal-to-noise ratio that cannot be achieved by the
conventional sources.
• The mid-infrared region (2.5-25 µm) is very informative on the microscopic scale (a few
tens of micron resolution). The spatial resolution is no longer controlled by the
geometrical aperture size, but rather by the numerical aperture of the optical system and
the wavelength of the light. Therefore, the spot size is set to diffraction limit (3 to 10 µm)
in confocal geometry.
The high brightness of the SR-IR enables rapid acquisition of spectra at
high spatial resolution for static or time-resolved measurements of
dynamic properties.
The high degree of the SR optical polarization makes it the perfect tool for
many customized/tailored industrial applications.
Small samples studies are accessible thanks to SR-IR microscopic power.
Hot filament
Flux: radiated in all directions
Flux ∝Temperature
Accelerated charged particles
Flux: radiated in a tangential, well
defined cone
Flux ∝ beam current
Conventional IR SR-IR
IR SOURCES (LAB-BASED)
Adapted from S. Lupi
IR MICROSPECTROSCOPY BASICS
MS: coupling of a microscope to the IR spectrometer.
First made commercially in the 1950s. (satisfactory design, but
costly, limited by the low energy throughput and
corresponding low signal-to-noise ratios)
FT-IR advantages + advances in IR detector technology fueled
the reemergence in 1983.
Recent success in application of this instrumentation to many
areas of research has established the technique of IR
microspectroscopy as a powerful tool in the analysis of small
samples in so many applications..
The microscope contained all the necessary transfer optics to
direct the IR beam from the spectrometer source to the sample
positioned on the stage of the microscope.
The optics used in IR microspectrometers are reflecting
optics. Since both glass and quartz absorb IR light over much of
the region of interest, the IR microspectrometers are unable to
employ standard, visible-light refracting (lens) optics but rather
must use reflecting (mirror) optics.
MICROSPECTROMETER DESIGN
The next wave of improvements came when IR spectrometers were built
with the ability to direct the IR source beam external to the instrument.
This flexibility allowed modifications, redesign, and production of new
spectrometers with optimal geometry for coupling to IR microscopes.
Since the IR microscope had its own onboard detector, it was a complete
system, minus the IR source and data processing/computer
system. With this new design, the microscope no longer occupied the
sample compartment of the spectrometer, so that conventional methods
could still be used to analyze macro samples.
OPTIMUM COUPLING
The detector of choice is (MCT) detector.
The MCT detector element is cryogenically cooled to liquid
nitrogen temperature, thus providing high sensitivity and signal-to-
noise values necessary for the low energy levels and small
sampling areas.
As the microscope designs changed, a major improvement in
signal-to-noise levels was achieved when the MCT
detector was repositioned from the spectrometer bench
to the microscope apparatus.
IR SIGNAL DETECTION
Minimizing the IR beam path after interaction with the sample..
MICROSPECTROMETER VS. OPTICAL MICROSCOPE
First: All IR microspectrometers have visible-light imaging
available. Provide photomicroscopy and/or videomicroscopy.
Second: the ability to isolate a particular area of the sample
optically by the use of movable apertures [fixed-diameter-circle or
a variable-circle iris, or an adjustable knife-edge rectangle.].
Heterogeneous samples
Third: all IR microspectrometers have the ability to collect IR
reflectance spectra. Reflection IR is useful for highly absorbing
samples that do not transmit IR well, as well as, for providing
information on the surface composition of a material. >> the
ability to perform reflection analysis increases the versatility of the
IR microspectrophotometer. Practical sessions
POCKET: FTIR MICRSCOPE IS BEAM CONDENSER
AlviseVianello, JesVollertsen Aalborg University, Denmark
Optical lens that renders a divergent beam from a point source into a parallel or
converging beam to illuminate an obejct.
Upper Aperturesize settings
Lower Aperturesize settings
Lateral resolution ~l/2
SR-IR MICROSCOPE WORKS IN CONFOCAL GEOMETRY
Adapted from P. Dumas
TRANSMISSION MODE
Sample must be thin.
Embedding (the medium may contribute to the spectra)
Requires IR transparent windows ( CaF2, BaF2, ZnSe, ZnS, diamond!)
Detector
REFLECTION MODE
Sample must be flat or flattened
Signal is weaker
Adapted from P. DumasPractical sessions
POCKET: FTIR SPECTROSCOPY
Adapted from: AlviseVianello, JesVollertsen Aalborg University, Denmark
POCKET: FTIR MICROSPECTROSCOPY
cooled or RT detectors
cooled or RT detectors
The heterogeneity and low amount of cultural heritage materials led to
seeking to attain higher lateral resolution with imaging capabilities. >>
Microscopy + SR.
Synchrotron-based FT-IR microscopy with a confocal arrangement made it
possible to analyse and even map very small samples with high signal-to-
noise ratio (S/N) at the diffraction limit. The diffraction limit is proportional
to the wavelength and inversely proportional to the numerical aperture of
the optics.
Q: Definition of: Diffraction limit?
Q: Definition of the Lateral resolution?
Q:What is the highest lateral resolution obtainable at 1000cm−1
and at 3000cm−1 in reflection and transmission?
WHY SR-BASED FTIR MICROSPECTROSCOPY?
SESAME SR-IR Emission Source: Bending magnet
Edge Radiation (ER): Emitted at the
entrance (exit) of the bending
magnet (BM) due to the rapid
variation of the magnetic field (B)
Standard Bending Magent Radiation:
Emitted during the circular trajectory
in the bending magnet (BM) due to the
constant magnetic field (B)
Vertical collection angle = 15 mrad
Horizontal collection angle = 39 mrad
Opening angles require
modifying the dipole chamber! More on the IR beamline.. Later today
Beginning of 1990 : 5 facilities
Beginning of 2000 : 14 facilities
In 2017: 30+ facilities
The high brightness of the synchrotron IR light (100–1000 times > conventional
sources) has allowed important development in both the mid- and far-IR regions.
S/N RATIO? INFORMATION?
P. Dumas
The coupling of SR-FT-IR microspectroscopy with other synchrotron-based
techniques (XRF, XRD, ...) or laboratory FT-IR imaging techniques (Globar) is
an interesting approach that is increasingly evolving.
The combination of SR-FTIR microspectroscopy with FT-IR imaging: provides
respectively the very high signal-to-noise ratio data on local areas together
with the spatial distribution of species over large areas in a short time.
Mid-IR microspectroscopy together with Raman spectroscopy is commonly
applied to identify the compounds or at least the functional groups present.
SR-IR MICROSPECTROSCOPY +
Synchrotron and thermal IR sources play complementary roles
• With the thermal source: many millimeters can be surveyed
quickly and offer excellent performance down to about 10μm
spatial resolution.
• With the synchrotron: the resolution limit may be extended
down to around 1μm, but over a much more limited area.
Something to remember..
POCKET: ADVANTAGES OF SR-FTIR MICROSPECTROSCOPY
(MICROSCOPY + SPECTROSCOPY)
Broadband
Brightness
Linear & Circular
Polarization
Pulsed Emission
Diffraction limited
spatial resolution
Better S/N ratio
Faster Data Collection
Spectroscopy
Polarized
Microspectroscopy
Time resolved
Studies
Microscopy
Broadband
Brightness
Adapted from Lisa Miller
Dr. MARTIN, Michael (Lawrence Berkeley National Laboratory)
While using FTIR spectroscopy appears straightforward for well handled samples,
the evaluation becomes significantly more complicated when probing very
small and/or heterogeneous samples.
: because it monitors the global chemical composition in the probed volume, the
vibrational signatures recorded are a superposition of the spectra of thousands
of constituents.
.. Yet despite the complexity, it has been demonstrated that the technique is highly
sensitive to slight changes in the composition. The interpretation of these
composite spectra requires sophisticated data analysis, which is still evolving
through the continued development of multivariate methods.
THE COMPLEXITY OF THE FTIR
MICROSPECTROSCOPIC DATA
These approaches are based on the principle that there
exist small, but reproducible changes in the spectra that
can be associated with the variations in sample properties
that are investigated.
There exist several known statistical approaches for
infrared data analysis, but the most frequently used is
principal components analysis (PCA).
It aims at determining if the variance in the spectral pattern
of all the individual entities studied is correlated, or due to
random fluctuations.
Diletta Ami, Paolo Mereghetti and Silvia Maria Doglia, http://dx.doi.org/10.5772/53850
Regression and classification techniques
MULTIVARIATE ANALYSIS FOR FTIR SPECTRA OF
COMPLEX CHEMICAL/BIOLOGICAL SYSTEMS AND PROCESSES
Visual effect of different pre-processing sets on a set of spectra
Some existing FTIR spectroscopy data analysis software
Available at SESAME
Available at SESAME
Available at SESAME
Remote Access authorization for data processing and
analysis for EXPERIENCED USERS
THANK YOU!
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