Far-IR/THz & High Spectral Resolution
Spectroscopy Using Synchrotron Radiation

Dominique Appadoo
Senior IR Beamline Scientist

CHEIRON SCHOOL OCT 5, 20081

Melbourne

CHEIRON SCHOOL OCT 5, 2008

2

Infrared beamlines worldwide
North America
ALS Berkley
CAMD Baton Rouge
CLS Saskatoon
NSLS Brookhaven
Surf III Gaithersburg
SRC Madison

Number of
beamlines

PurposeStatus

1
1
2
6
1
1

Microscopy and Far-IR
Microscopy
1 Microscopy, 1 Far-IR
3 Microscopy, 2 Far-IR, 1 THz
Microscopy
Microscopy

Operational
PlannedOperational
Operational
PlannedOperational

Asia and Australia
Australian
Synchrotron
INDUS I, India
Helios II, Singapore
NSRRC, Taiwan
NSRL, Heife
BSRF, Beijing
Spring-8, Himeji
UVSOR, Okazaki

1

Microscopy and Far-IR

Operational

1
1
1
1
1
1
1

Microscopy
Microscopy and Far-IR
Microscopy
Microscopy and Far-IR
Microscopy
Microscopy and Far-IR
Far-IR

PlannedOperational
Operational
PlannedPlannedOperational
Operational

EuropeESRF, Grenoble
Soleil, St. Aubin
ELETTRA, Trieste
DAPHNE, Frascati
SLS, Villigen
ANKA, Karlsruhe
BESSY II, Berlin
DELTA, Dortmund
MAX II, Lund
DIAMOND, Didcot

1
2
1
1
1
1
1
1
2
1

Microscopy
1 Microscopy, 1 Far-IR
Microscopy and Far-IR
Far-IR
Microscopy and Far-IR
Microscopy and Far-IR
Microscopy and Far-IR
Microscopy
Microscopy and Far-IR
Microscopy

Operational
Commissioning
Operational
Operational
Commissioning
Operational
Operational
Plannedoperational
Planned32 IR Beamlines
CHEIRON SCHOOL OCT 5, 2008

3

The far-IR/THz spectral region

Electronics

λ
ν
ν
E

= 1000 – 10 μm= 10 – 1000 cm-1
= 0.3 – 30 THz=
1 – 124 mEV

Photonics

THz Energy Gap

Far-IR/THz ≡ XSX→ eXtremely Soft X-ray- lack of adequate tunable lasers- weakness of conventional thermal sources- difficulties with far-IR detectors
wwww.lbl.gov/MicroWorlds/ALSTool/EMSpec/EMSpec2.html

CHEIRON SCHOOL OCT 5, 2008

4

The Final Frontier- cw & pulsed THz lasers are now available- Backward-wave oscillators- Accelerator-based sources …
CHEIRON SCHOOL OCT 5, 2008

5

What kind of interactions
take place in the far-IR?
van der Waals energies

H-bondingRotational manifolds
v=2
v=1
phonon modes- surface/adsorbate interactions- biological processes- chemical dynamics

PQ R

v=0

• rotation of smaller molecules• ro-vibration of larger molecules

CHEIRON SCHOOL OCT 5, 2008

6

What can we learn from these interactions?
– How does energy flow within a molecule?
– What is the nature of the weak attractive forces that exist
among atoms and molecules?
– How do metal atoms bond to other chemical groups?
– What are the structures of long carbon chain molecules?
– How do the optical properties of a material change under ultrahigh pressures?

... this is just the beginning!
CHEIRON SCHOOL OCT 5, 20087

OverviewI.

IR Spectroscopy

II. Synchrotron IR Radiation
III. The IR Beamline at the Australian Synchrotron
IV. FT Spectroscopy
V. Applications of Far-IR & High Resolution
Synchrotron Spectroscopy
VI. Coherent Synchrotron Radiation
CHEIRON SCHOOL OCT 5, 20088

I. Introduction to IR spectroscopy

CHEIRON SCHOOL OCT 5, 2008

9

Fingerprint spectral region

http://www.brukeroptics.com/downloads.html
CHEIRON SCHOOL OCT 5, 200810

IR spectroscopy of condensed samples:
Vibrational Spectroscopy → spatial resolution

ν-shifts
relative intensities
Spatial resolution required
Amide I
C=O

0.8
0.7

Absorbance

0.6
0.5

Amide II
C-N and N-H

Broad O-H and N-H
Stretching
CH2 and CH3
stretching

0.4

CH3 bending
PO2- stretching

0.3

PO32- stretching

0.2
CO2

0.1

C-O stretch
4000

3500

3000

2500
2000
Wavenumbers (cm-1)

1500

1000

CHEIRON SCHOOL OCT 5, 200811

IR spectroscopy of gas-phase samples:
Ro-Vibrational Spectroscopy → Spectral Resolution

Diatomic molecules

Polyatomic molecules: linear 3N-5 modes
non-linear 3N-6 modes

CHEIRON SCHOOL OCT 5, 200812

Potential energy curve ofa diatomic molecule in its
ground electronic state.

Manifold of rotational states
within each vibrational level

Rotational manifolds
v=2

De
v=1
V = 1

ωe
J=5

re

P Q R

J=0

CHEIRON SCHOOL OCT 5, 2008

v=0

13

Diatomic Model
E(v,J) = Te + G(v) + Fv(J)
whereG(v) = ωe(v+ ½ ) – ωexe(v+ ½ )2 + ωeye (v+ ½ )3 + …
Fv(J) = Bv J(J+1) – Dv (J(J+1))2 + Hv (J(J+1))3 + …
where

Bv = Be – αe(v+ ½ ) + βe(v+ ½ )2 + …
2Be α 1/μre
De ~ Σ ΔGv
V=0

ωe is the fundamental frequency (α μ-1/2)
re is the bond length
De is the dissociation energy CHEIRON SCHOOL OCT 5, 200814

Absorption Spectroscopy…
I0

I1

CHEIRON SCHOOL OCT 5, 200815

Rotational, vibrational and electronic Transitions

v=2

v=1

J=5

P Q R

ΔErot

J=0

v=0

ΔEvib

ΔEelecCHEIRON SCHOOL OCT 5, 200816

IR emission spectrum of ZnD (2Σ)

CHEIRON SCHOOL OCT 5, 200817

Life can get complicated even for diatomics

IR spectrum of MnH (7Σ)Δν= 0.006 cm-1

CHEIRON SCHOOL OCT 5, 200818

IR spectrum of MnH (7Σ)
1122.6639
1122.6580

Δν~0.006 cm-1

CHEIRON SCHOOL OCT 5, 2008

19

Simply put, spectra for diatomic molecules canbe complicated and congested!
- Heavy molecules: closely-spaced transitions,overlapping bands, and narrow linewidths- Presence of naturally occurring isotopomers inmeasurable quantities- High-spin electronic states due to open-shells: spinsplitting… Need high spectral resolution!

CHEIRON SCHOOL OCT 5, 2008

20

F

H

H

C

Polyatomics:
Asymmetric Top Molecule

C

F

H

H
0.30

IR Spectrum of R152a at low resolution
CF2 ν8

0.25

C-C

0.20

ν5

CH3 rockν16

CH3 def.

ν7

ν

0.10

0.15

3N-6 modes where N=8 ≡ 18 modes

ν6

0.05

4

0.00

Absorbance Units

Normal modes of vibration of R152a

1 5 00

14 0 0

13 0 01 2 001 1 00

10 0 0W a v e n u m b e r cm -1

CHEIRON SCHOOL OCT 5, 200821

Part of the IR spectrum of R152a
ν7 ν15

ν16

0.35

0.40

ν5

ν14 ν

0.15

0.20

6

ν8

0.10

Absorbance Units

0.25

0.30

ν4

0.00

0.05

ν9+ν17 ?
1500

1400

1300

1200

1100

1000

Wavenumber cm-1

Low resolution EFC spectrum

CHEIRON SCHOOL OCT 5, 2008

22

Asymmetric Rotor Model__<v:J,K|H| v:J,K> = v +B J(J+1) + ( A - B) K2- ΔJJ [J(J+1)]2 - ΔJK J(J+1) K2 - ΔKK K4+ ΦJJJ [J(J+1)]3 + ΦJJK [J(J+1)]2 K2 + ΦJKK [J(J+1)] K4 + ΦKKK K6- ΛJJJJ [J(J+1)]4 - ΛJJJK [J(J+1)]3 K2 - ΛJJKK [J(J+1)]2 K4 - ΛJKKK J(J+1) K6 ΛKKKK K8 ….
_<v:J,K|H| v:J,K ± 2> = [ ½B - δJJ(J+1) - δK{(K ± 2)2 + K2}+ φJJ [J(J+1)]2 + 1/2φJK [J(J+1)] {(K ± 2)2 + K2} + 1/2φKK {(K ± 2)4 + K4}- λJJJ [J(J+1)]3 - λJJK [J(J+1)]2 {(K ± 2)2 + K2} - λJKK [J(J+1)] {(K ± 2)4 + K4}- λKKK {(K ± 2)6 + K6} … ] F± (J,K) F± (J,K ± 1)
where

1/2

F ±(J,K) = { J(J+1) - K(K ± 1) }_B = 1/2 (B-C)

CHEIRON SCHOOL OCT 5, 200823

Pyrrole at 0.00096 cm-1(~0.1 μeV)Δ = 0.01 cm-1

δ = 0.00107 cm-1

-1
wavenumbers / cmCHEIRONSCHOOL OCT 5, 200824

Spectroscopic issues to contend with
•
•
•
•
•

Overlapping & Hot bands
Coupling of vibrational modes: Coriolis and Fermi resonnances
Closely spaced lines & Narrow linewidths as the MW increases
Isotope splitting
Hyperfine structure.... Clearly we need high spectral resolution in order toresolve these narrow spectral lines!
How high a resolution is required?
CHEIRON SCHOOL OCT 5, 200825

Observed Linewidth: ΔνObs ~ √ ΔνDop2 + Δνcol2 + ΔνILW2
Different factors contribute to the width of an observed transition
Doppler width, ΔνD = 2ν √ 2ln2k/c2 √ T/M~ 7.16E-7 ν √ Τ/Μ

Pressure broadening, Δνcol = 16pr2/√πMkT ~ 3Ε-4 cm-1 / Torr
Instrument linewidth ≡ ΔνILW dictated by apodisation function

Therefore, the observed linewidth can be minimised by reducing
the Temperature and Pressure!
CHEIRON SCHOOL OCT 5, 200826

Spectroscopic issues to contend with
• Small quantity of sample to minimize Pressure
broadening effects or hard to synthesize• Isotopologues with low natural abundance• Weak absorbers.... Need bright source!

CHEIRON SCHOOL OCT 5, 200827

II. SYNCHROTRON INFRARED LIGHTCHEIRON SCHOOL OCT 5, 200828

Infrared mission from a synchrotron bending magnet
Edge Radiation and Bending Magnet Radiation

Large vertical divergence
Relative to X-ray beam

• Bright• Broadband• Pulsed• Polarized

CHEIRON SCHOOL OCT 5, 200829

Port 02B1-1 @ CLS: Far-IRē beam~ 40 cm

55×37 mrad2

SH

2.0

1.5

2
4

λ

0

X-Rays-2ΘV = 37 mrad

Θv

Mirror length (mm)λΘH = 55 mrad

1.0

IR

-4

ΘH

0.5

SV

2

-6

SV = 13 μm

0.0

SH = 480 μm-3Power density (x10 W/mm )6

IR

CHEIRON SCHOOL OCT 5, 200830

Is thesynchrotronbrightness
IR beam very that
intense?
It’s thesynchrotron
counts1
SOLEIL
20x78
mrad
I= 5000.8 GeV,
90x90
mrad,
800 mAmA
BlackBody 2000°K

0.1
0.01

Watts/cm-1/mm2sr

1 E16

1E-4
1E-5
1E-6

Far- IR

Mid- IR

1E-7

1 E15

1E-8
1E-9

1 E14

1E-10
1E-11

1

10

100

1000

Wavenumbers / cm-1

Flux ( in Photons/s/0.1% bw)

1E-3

10000
I=800 mA

CHEIRON SCHOOL OCT 5, 2008

31

SR Advantages over thermal sources• Brightness: better S/N• Small source: better throughput with small
samples• Highly collimated: higher resolution achievable• Polarized: ellispsometry• Pulsed: pump & probe experiments

CHEIRON SCHOOL OCT 5, 200832

Far-IR SR wavelength limits• Height of dipole chamber:λo = 2h√h/Rwhere h is the height of the dipole chamber and R theradius of the bend magnet• Extraction aperture:λc = R(ΘNat/1.66188)3
where ΘNat represents the vertical angle in radians

CHEIRON SCHOOL OCT 5, 2008

33

EXTRACTION OF SYNCHROTRON IR RADIATIONCHEIRON SCHOOL OCT 5, 200834

2. Mirror M1 inserted into dipole “crotch” from above or below
Optical Layout at the CLS
M2

M4

DW
M3

M6
M5

Ge:Cu

M8

M1
M7

CHEIRON SCHOOL OCT 5, 200835

2. Mirror M1 inserted into dipole “crotch” from above or below
e.g. Soleil, ESRF…

M2
M1 Mirror with thermocouple wires

DipoleMultipole

M1

Images courtesy of Paul Dumas, Soleil.

Top view of mirror insertion port
CHEIRON SCHOOL OCT 5, 200836

3. Mirror inserted into dipole chamber from sidee.g. Australian Synchrotron

Zero degree line
-14 mrad +44 mrad

Mirrorinsertion port

Beam extraction port

Which brings us to…
CHEIRON SCHOOL OCT 5, 200837

III. The Australian SYNCHROTRONINFRARED BEAMLINECHEIRON SCHOOL OCT 5, 2008

38

Adapted Infrared Dipole Chamber at Australian Synchrotron

Electron beam

Mirror in
IR beam out

CHEIRON SCHOOL OCT 5, 200839

Beamsplitter
optics

M1 mirror
mechanism
Diamond Window andGate Valves

Matching optics forHigh Resolution FTIR

Matching optics for
IR Microscope

Storage ring wall

Focusing andSteering mirrors

Infrared beamline showing (from right) synchrotron beam entering front end optics (M1, M2,
M3, M3a), diamond exit window, beamsplitter optics vessel and matching optics boxes forthe two endstation instruments.

CHEIRON SCHOOL OCT 5, 200840

Microscope beamline

Far-IR & High-Res Beamline

SR beamsplitter
vacuum chamber

CHEIRON SCHOOL OCT 5, 200841

Visible light in the beamsplitter vessel at theAustralian Synchrotron Infrared beamline

Edge & Bend Magnet radiation to“THz & high resolution” spectrometer

Bending magnet
radiation to “microscope”

CHEIRON SCHOOL OCT 5, 200842

Vertical position / mm60

λ = 100 µm

40
20
0
-20
-40

Vertical position / mm

-80
30

Bending Magnet
Radiation

Edge Radiation

-60

-60

-40

-20

0

20

40

60

80

λ = 10 µm

20
10
0
-10
-20
-30

Edge Radiation-40

Bending Magnet
Radiation-20
0
20
Horizontal position / mm

40

CHEIRON SCHOOL OCT 5, 200843

IR beam profile – comparison with SRW

CHEIRON SCHOOL OCT 5, 2008

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INFRARED BEAMLINE INSTRUMENTATIONCHEIRON SCHOOL OCT 5, 200845

Infrared Beamline at the Australian Synchrotron
Microscope Branch
Confocal point scanning - current technology
Transmission
Trans-Reflection
Grazing Incidence Angle
Attenuated Total Reflectance
Bruker V80v with Hyperion 3000 microscope

50×50 μm2 Narrow-Band MCT
250×250 μm2 Wide- Band MCT
Option for bolometer

CHEIRON SCHOOL OCT 5, 200846

Microscope Branch
Focal Plane Array - next technology
64x64 photovoltaic MCT Focal Plane Array

CHEIRON SCHOOL OCT 5, 2008

47

Infrared Beamline at the Australian SynchrotronHigh Resolution branch
Sample compartment:
cells ≤ 30×20×10 cm3

Beamsplitters• Multi/Mylar
30 – 630 & 12 – 35 cm-1
• Ge/KBr
450 – 4 800 cm-1

IR Detectors• Si bolometer 10 – 370 cm-1
• Si:B bolometer 300 – 1850 cm-1
100 – 3000 cm-1
• DTGS
700 – 5 000 cm-1
• MCTN
600 – 5 000 cm-1
• MCTM

OPD: 942 cm→ resolution ≥ 0.00096 cm-1 (0.1 μeV)
Optics: f/6.5
Bruker IFS 125HR FTIR Spectrometer

Sources• Synchrotron mw – vis• Hg-Arc lamp
5 – 1 000 cm-1
• Globar
10 – 13 000 cm-1
• Tunsten lamp 1 000 – 25 000 cm-1
Optical Filters• series of narrow band pass IR filters
Apertures• 0.5 – 12.5 mm
CHEIRON SCHOOL OCT 5, 200848

Recall …
Observed Linewidth: ΔνObs ~ √ ΔνDop2 + Δνcol2 + ΔνILW2

Therefore, the observed linewidth can be minimised by reducing
the Pressure and Temperature!

CHEIRON SCHOOL OCT 5, 200849

50 cm Multipass gas cell for high resolution
spectroscopy of room temperature samples
Small quantity of sample to minimize Pressure broadening effects

Recall that Absorbance α εclwhere c is the concentrationand l the interaction path.

CHEIRON SCHOOL OCT 5, 200850

MCT detector
Enclosive Flow Coolingmultipass cell for gas-phasestudies at cryogenic
temperatures.
N2 gasCEP

sample165

colanderflow ofcold N2
liq. N2
vacuum495
insulation
evacuation
portheatedmirror300

CHEIRON SCHOOL OCT 5, 2008

51

N2O mid-IR spectrum ( 0.002 cm-1 )Trot = 112 K

Clusterformation

0.2

0.4

0.6

0.8

1.0

0.00

0.05

0.10

Trot = 112 K

0.0

Absorbance Units

0.0

0.2

0.4

0.6

0.8

1.0

Trot = 302 K

2250

2220

wavenumber / cm-1

2190

CHEIRON SCHOOL OCT 5, 200852

More Scientific Apparatus
Grazing Incidence Angle Cell

Diamond Anvil Cell
< 100 μm

Metal foil gasket

Supersonic Jet Expansion chamber

CHEIRON SCHOOL OCT 5, 2008

53

IR Cryostat for matrix isolation studies
Low freq. vibrations of biological samples

Down to 10 K!

Minimise H2O interference
Increase Absorption coefficient for a range of substances
CHEIRON SCHOOL OCT 5, 200854

Assessing beamline performance

CHEIRON SCHOOL OCT 5, 200855

Performance of the microscope beamline
Synchrotron infrared beam focused on sample

Beamline 11 at SRS - unapertured beam profile at sample stage.
Area mapped = 30x30 µm. Beam halfwidth = 8x8 µm.

CHEIRON SCHOOL OCT 5, 200856

Advantage of using a synchrotron seen in spectra…
CH stretch absorption bands from 5
micron spot in tissue sample.
Equivalent spectra recorded usingsynchrotron
(top)
and
Globar(bottom).

Absorbance spectra of tissue sample recorded at 10µm spatial resolution under identical collection
conditions using a Globar™ infrared source andsynchrotron radiation.

3100

3000

2900

2800

Wavenumbers / cm-1

CHEIRON SCHOOL OCT 5, 2008

57

Testing the IR Beamline Performance with
Custom Resolution targets

CHEIRON SCHOOL OCT 5, 200858

WAVELENGTH DEPENDENCE OF MICROSCOPE SPATIALRESOLUTION DEMONSTRATED AT INFRARED BEAMLINE

20µm

Polymer pattern on CaF2
produced byphotolithography

IR absorbance image
At 2935 ±125 cm-1
CH band region

IR absorbance image
At 1701 ±59 cm-1
C=O band region

CHEIRON SCHOOL OCT 5, 200859

Performance of the far-IR beamline
Bolometer / 6μm Mylar

Ge:Cu / KBr

40

Ratio of Intensities

1.3 mmIII

2.0 mmSR / Hg

30

10-13 × Photons/s/0.1%BW

I
SR

4

15
3
10

20

SR /GB2

100 × SR
SR

1

5

5

200

GB

100 × GB

Hg
100

600

500

300

700

800

900

1000

SR 200mA, (57×35) mrad2~4 ×

3~4.4 ×~7.2 ×2
1

1.15mmII

SR /GB

10

4

MCTn / KBr

20

~18 ×

~5 ×

~8 ×

1475 K Blackbody
200

600

400

800

Energy / cm-1
CHEIRON SCHOOL OCT 5, 2008

1000

60

Spectrum of Pyrrole at 0.001 cm-1 resolution
GLOBAR

40 days

SYNCHROTRONCHEIRON SCHOOL OCT 5, 2008

10 hrs61

IV. Introduction to Fourier transform
Infrared spectroscopy

CHEIRON SCHOOL OCT 5, 200862

Fourier transform spectroscopy
Brüker IFS120HR
AC
BS

S3
S2
S1

M1

FC
AC

samplefront
channelInterferogram
FT spectrum

Amplitude

M2

S1-S3 Internal Sources
S4
External Source
AC
Aperture Changer
FC
Filter ChangerBS
Beamsplitter
M1-M2 Retroreflectors
D1-D6 Detectors

Frequency componentsof the interferogram

S4

back
channelcompartment

sca
nne
r di
stan

ce

Res = 0.9/OPD

D3

D4

D1

D2

D5

D6

OPD = SCL/2
CHEIRON SCHOOL OCT 5, 200863

Many frequencies are present in the infrared beam

Position of “zero path difference”
CHEIRON SCHOOL OCT 5, 200864

Summing of all frequencies for each position of the mirror

CHEIRONSCHOOLOCT 5,
2008difference”
Positionof “zeropath
65Data output from FTIR system

4
3
2
1
0
-1
-2
-3
-4
-5

Single Beam

Volts

“Centre burst” at Zero Path Difference

200

400

600

800

1000

Data points

Interferogram

Fourier

11
10
9
8
7
6
5
4
3
2
1
4000 3500 3000 2500 2000 1500 1000 500
Wavenumbers (cm-1)

Single Beam Spectrum

Transform

CHEIRON SCHOOL OCT 5, 2008

66

A

A

11
10
9
8
7
6
5
4
3
2
Sample Single Beam Spectrum
14000 3500 3000 2500 2000 1500 1000 500
Wavenumbers (cm-1)

Single Beam

B

Sample Absorbance Spectrum

0.60
AbsorbanceSingle Beam

Data output from FTIR system

11
10
9
8
7
6
5
4
3
2
Background Single Beam Spectrum
14000 3500 3000 2500 2000 1500 1000 500
Wavenumbers (cm-1)

Log(A/B)

0.50
0.40
0.30
0.20
0.10
4000 3500 3000 2500 2000 1500 1000 500
Wavenumbers (cm-1)

CHEIRON SCHOOL OCT 5, 200867

Pros and Cons of Fourier transform spectrometry
Advantages over grating spectrometers
•
•
•
•
•

Felgett or Multiplex
Jacquinot or throughput: apertures instead of slits
High wavenumber accuracy: sampling λHeNe/2
High resolving power: ~ 106
Fast

Disadvantages• Complex system (but can be used as a black box by Users)• Expensive ....
• Can take a lot of room!
CHEIRON SCHOOL OCT 5, 2008

68

V. APPLICATIONS OFSYNCHROTRON INFRARED LIGHTCHEIRON SCHOOL OCT 5, 200869

Applications of synchrotron IR radiation with a microscope
ATR objective
2790-2989 cm-1

19th century parchment sample

100 μmForensic examination of paper documents
837-1165 cm-1

Cross sections ofagricultural soils: analysis
of distribution and forms ofcarbon functional groups

Cellulose

Ink

CaCO3

2850 - 3023 cm-1

1580 - 1600 cm-1

856 – 897 cm-1

100 μm

10 microns aperture, 5 microns steps

Peter Fisher, Matt Kitching (DPI Victoria) / Simon Lewis, Bill van Bronswijk (Curtin University)
Kenneth Paul Kirkbride, Vincent Otieno-Alego (AFP) / Alana Treasure, Dudley
Creagh(Uni Canberra)
CHEIRONSCHOOLOCT 5, 200870

Grazing angle objective

Protein resistant plasma polymer thin films
Ether/hydrocarbon ratio of
DGpp gradient films

Diethylene glycol dimethyl ether (DG)

distance fromrazor (mm)

2.4
2.35

COC ether

2.3
2.25
2.2
2.15
2.1
2.05
-2

-1.5

-1

-0.5

0

0.5

1

1.5

2

COC/CH

CH2
OH

Plasma polimerisation technique used to
produce high throughput gradient PEG(poly (ethylene glycol) based films on ananometer scale.

CO

Systematically varied chemistry byaltering the plasma processing conditions.
Study the mechanism of protein repellant
properties of PEG coatings.

Donna Menzies, Thomas Gengenbach, Celesta Fong, John Forsythe, Ben
Muir – CSIRO/ Monash
CHEIRONSCHOOLOCT 5, 2008

71

SINGLE CELL WORKLive Human
Mesenchymal Stem Cells

Live Leukaemia Cells

70 μm

10 μm

10 × 10 µm aperture

Fixed mouse Oocyte Cell

8 x 8 μm

Fixed Malaria infected RBCs

CHEIRON SCHOOL OCT 5, 200872

Response of single living phytoplankton cells to changes
in the environment
Lipid concentration FTIR maps

Control

Nitrogen starved cell
Re-supplied with nitrogen

Freshwater alga Micrasterias hardyi.

Phil Heraud, Sally Cane, Anthony Eden, Don McNaughton, CHEIRON
Bayden Wood,MonashSCHOOLOCT 5,University
2008

73

Applications of synchrotron IR radiation with a
High-Resolution FT spectrometer

Molecular species of Astrophysical interest
Ethane- prototype system for torsional motion- Intramolecular Vibl Redistribution- Earth and Jovian atmospheres- Pluto: clues to evolution
early solar system

Titan

SaturnMethyl Silane

CHEIRON SCHOOL OCT 5, 200874

Molecular species of Astrophysical interest
Telescope missions in the submillimeter region for the study of star formation-

Herschel Space Observatory (2008, 3-4 years)
Stratospheric Observatory for Infrared Astronomy: SOFIA (2010, 20 years)
Atacama Large Millimeter Array: ALMA (2011, decades)

Astrophysical weed-molecules & their isotopologues-Class I: CH3OH, HCOOCH3, CH3OCH3, C2H5CN

CH3-18OH

Recorded at the CLS

13CH -OH
3

WAVENUMBER / CM-1

CHEIRON SCHOOL OCT 5, 200875

Far-IR spectroscopy of aromatic cycles containing heteroatoms
Dennis Tokaryk (U. of New Brunswick) & Jen van Winjgaarden (U. of Manitoba)

H
N

O

S

pyrrolefuran

thiophene

These heterocycles and their derivatives are:• building blocks of organic chemistry-pharmaceuticals, agrochemicals, dyes

• constituents of biologically active molecule
such as heme and chlorophyll• byproducts of combustion processes• candidates for interstellar detection• solvents/additives in industrial processes• naturally found in wood, petroleum

CHEIRON SCHOOL OCT 5, 200876

Samples of Environmental interest
Spotted Tiger Muscovite – self supported crystal: Mylar multilayer beamsplitter, Si Bolometer
SR
50o
35o
20o
10o
0o

Strong positive pleochroism at 146 cm-1 – implies out-of-plane mode
Slight negative at 167,189, 264 cm-1 – implies in-plane mode
No change at 110 cm-1 – expected if interlayer cation ‘rattle’To better understand the dynamics of cation exchange reactions of important minerals,commonly used as environmental barriers to contaminated wastes such as radionuclides
CHEIRON SCHOOL OCT 5, 200877

VI. COHERENTSYNCHROTRON RADIATIONCHEIRON SCHOOL OCT 5, 200878

Incoherent Synchrotron < 100 cm-1
Bolometer / 6μm Mylar40

SR / Hg

Ratio of Intensities

Apt=2.0 mm
30

20

SR

10
5

Hg
50

100

Energy / cm-1

CHEIRON SCHOOL OCT 5, 200879

Coherent Synchrotron Radiation
PSR

2
σ
2
-(ω
/c)
αN+N e z

BESSY
websiteCHEIRON SCHOOL OCT 5, 2008

80

CSR at the CLS

81
CHEIRON SCHOOL OCT 5, 200881

Period ~ 0.0731 cm-1

recorded with the Coherent SR at a resolution of 0.025 cm-1

10

12

14

N2O THz absorption spectrum

0

2

4

6

8

46 scans co-added

J”=9
6

8

10

11
10

12

13

14

15

12

wavenumber / cm-1

16
14

17

18
16

19

20
18

CHEIRON SCHOOL OCT 5, 2008

20

82
82

Summary• Synchrotrons provide intense beams at long wavelengths into the
Far-IR• IR spectroscopy is used to provide information on the chemicalcomposition of materials based on the vibration of the bonds
present.
• Synchrotron IR allows these measurements to be made rapidly
at a few microns dimension (micoscope), or at low concentration(and high SPECTRAL resolution).
• Synchrotron IR has applications in a diverse range of research areas.
• Future developments in the field will allow imaging below thediffraction limit and the use of intense Far-IR and Terahertz beams
CHEIRON SCHOOL OCT 5, 200883

Acknowledgements
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Dudley Creagh – Canberra University
Don McNaughton – Monash Univerrsity
Phil Heraud – Monash Immunology and Stem Cell Laboratories
Bayden Wood – Monash University
Liz Carter – University of SydneyPeter Lay – University of Sydney
Mark Hackett – University of Sydney
Sally Caine - Monash Immunology and Stem Cell Laboratories
Vivienne Juan - Monash Immunology and Stem Cell Laboratories
Alice Brandli – Monash University
Cassie Jean – Monash University
Alana Treasure – Univerrsity of CanberraBill van Bronswijk – Curtin University
Evan Robertson – Monash University
Ljiljana Puskar – Monash University
Tarekegn Chimdi – Monash University
Paul Dumas – Soleil
Mike Martin – ALS
Ulli Schade - BESSY IIDavid Moss – ANKA
Yves-Laurant Mathis – ANKA
Jonathan McKinlay – Australian Synchrotron
Nati Salvado – University of Barcelona
Azzedine Hammiche – University of LancasterJohn Prag – Manchester Museum
FMB – Berlin
Biolab/Bruker Instruments
CHEIRON SCHOOL OCT 5, 200884

Thanks…
Dominique Appadoo
Australian Synchrotron
800 Blackburn Road
Clayton 3168 VIC
AUSTRALIA
Tel: (03) 8540 4127
Email: dominique.appadoo@synchrotron.vic.gov.au
CHEIRON SCHOOL OCT 5, 200885

Infrared Spectroscopy
Energy range
0.001 eV to 1 eV (10 cm-1 to 10,000 cm-1)
Property accessible
molecular vibrations & rotations
Measurements
vibrational & rotational spectra
Information
molecular structure, chemical analysis
Synchrotron Benefits
signal to noise, spatial resolution(down to the diffraction limit)
AS Contact Scientists
Dr Mark Tobin, 613 8540 4172
Dr Dominique Appadoo, +613 8540 4127
Dr Lillijana Puskar, 613 8540 4185
CHEIRON SCHOOL OCT 5, 200886