Infrared Spectroscopy

with Synchrotron Sources

September 16, 2015
Cheiron 2015 School
SPring-8
Hyogo, Japan

Ferenc Borondics
SMIS beamline
Synchrotron Soleil
Gif-sur-Yvette, FranceOutline• IR spectroscopy –theory• IR instrumentation• Some IR beamlines (SOLEIL, CLS, ALS)
• Exotic techniques – recent developments• Practical things• Examples• Proposal writing tips for IR spectromicroscopy

Good reference books

IR beamlines around the world

Source: http://infrared.als.lbl.gov

Sir William Herschel (1738-1822)
Composer
Feb. 11, 1800
Astronomer
UranusOberonTitania
Mimas
Enceladus

W. Herschel, Phil. Trans. R. Soc. London, Vol 90, 284-292, (1800)

With numbers…
Near-IR

12500 - 4000 cm-1

0.8 - 2.5 µm

1.55 - 0.5 eV

Mid-IR

4000 - 500 cm-1

2.5 - 20 µm

0.5 - 0.06 eV

Far-IR

500 - 5 cm-1

20 - 2000 µm

60 - 0.6 meVWhat can we look at?
•••

Broad band electronic excitations
RotationsVibrations

Processes
I

TR• Transmission• Reflection• Absorption

SampleTransmittanceAn infrared spectrum

EnergyBasic optical functions
Goal: determine ε(ω), the dielectric function
Information about the electronic structure

Measure: reflectivity, r(ω); transmittance, T(ω)!

All of them are related

Basic optical functions
Goal: determine ε(ω), the dielectric function
Information about the electronic structure

Measure: reflectivity, r(ω); transmittance, T(ω)"!

All complex functions
Kramers Kronig transformation

Energy gaps of semiconductors
conduction bande-h+valence band
General semiconductor

-2

-1

0

Energy / eV

C-SWNT

12

Models to understand εDrude model

1.0

Reflectivity

0.8

0.6

0.4

0.2

0.0

0

1

2

E / eV3

4

Models to understand εDrude – Lorentz model

1.0

Reflectivity

0.8

0.6

0.4

0.2

0.0

0

1

2

E / eV

3

4

Molecular vibrations

Diatomic molecule, harmonic oscillator

BH 2400
2.04

m1

m2

CH 3000 NH 3400 OH 3600
2.55
3.04
3.44

FH 4000
3.98

OH 3600 OD 2600

Molecular vibrations

Intensity

Diatomic molecule, ideal case (alone)

Frequency
ocw.mit.edu – 5.61 – Physical Chemistry

Extra SlideMolecular vibrations

Intensity

Diatomic molecule, realistic case (solution)

Frequency
ocw.mit.edu – 5.61 – Physical Chemistry

Extra SlideMolecular vibrations

Intensity

Diatomic molecule, realistic case (solution)

Frequency
ocw.mit.edu – 5.61 – Physical Chemistry

Extra SlideMolecular vibrations

Quantized oscillator

Anharmonicity
Diatomic molecule, anharmonic

Intensity

0->1

1->2
2->3

Frequency
ocw.mit.edu – 5.61 – Physical Chemistry

Extra SlideAnharmonicity
Diatomic molecule, anharmonic

Intensity

0->1

0->2

1->2
2->3

1->3
2->4

Frequency
ocw.mit.edu – 5.61 – Physical Chemistry

Extra SlideMore atoms
Polyatomic molecule, ideal case, harmonic

ocw.mit.edu – 5.61 – Physical Chemistry

Extra SlideA hypotethical IR spectrum
Polyatomic molecule, real case, anharmonic
ω1

ω5

ω2+ω4−ω1Intensity

ω2

ω4

ω5−ω1

ω3

Frequency
ocw.mit.edu – 5.61 – Physical Chemistry2∗ω1

# of molecular vibrations
3N-6 degrees of freedomor
3N-5 for linear molecules
3.0

H2O

Absorbance

2.5
2.0
1.5
1.0
0.5
0.0

500

1000

1500

2000

2500

3000
-1

Wavenumber / cm

3500

H2O ➙ 3x3-6=3
CO2 ➙ 3x3-5=4

Larger molecules?

Chromophores
Holt et al. Biochem J. 314, 1035-1039 (1996)

IR active vibrations
Selection Rules IR:

Raman:

Group theory
Example: H2O

If there is an inversion symmetry IR≠RamanSimplifying factors• Chromophore groups• Selection rules• Symmetry?

Characteristic frequencies

www.brukeroptics.com/downloads.html

Influencing factors
Shifts• Atomic masses• Bond order (single, double, triple)• Electronegativity• Symmetry – molecular or crystal• Solvent effects, hydrogen bonding• Conformational changes

Rotations

Criterion: molecule must havepermanent dipole moment∆j=-1 ∆j=0 ∆j=+1

Rotational spectrum example
Nitrous Oxide

P-BRANCH

R-BRANCH

Q-BRANCH
Frequency / cm-1

Note: spectral range
HR spectrum

Spectrometer designs
Dispersive

3.0
2.5

Slow, but simple
Resolution, throughput, etc…

2.0
1.5
1.0
0.5
0.0

500

1000

1500

2000

2500

3000
-1

Wavenumber / cm

3500

Spectrometer designs

Fourier Transform - Michaelson interferometerA spectrometer layout

A – source
B – beamsplitterC – sample
D - detector

Light Sources+ synchrotrons+ lasers

www.brukeroptics.com/downloads.html

Detectors

www.brukeroptics.com/downloads.html

Beamsplitterswww.brukeroptics.com/downloads.html

FT spectroscopy advantages••••

Connes advantage: internal calibration He/Ne
Jacquinot advantage: interferometer is bright
Fellgett advantage: all ν in the same time
No stray light∑: FT is 2000x more sensitive than dispersive

FT-IR
WavelengthMichaelson interferometer

3.0
2.5
2.0
1.5

FT

1.0
0.5
0.0

500

1000

1500

2000

2500

3000
-1

Wavenumber / cm

3500

Resolution
FT:
discrete

Nyquist:Resolution!

Solutions:

Zero filling – looks nicer, but uselessPathlength – real information

Size matters
Bruker AlphaA4 paper size

Bruker 125hr

Moving mirror - meters
http://infrared.als.lbl.gov

IR Sources- a comparison -Producing IR lightBlack body radiation
GLOBAR – SiC rod, resistive heating

Producing IR light

D. Attwood, UC Berkeley, http://ast.coe.berkeley.edu/srms/2007/Intro2007.pdf

Producing IR light
Moving frame of reference

Laboratory frame of reference

Synchrotron radiation
D. Attwood, UC Berkeley, http://ast.coe.berkeley.edu/srms/2007/Intro2007.pdf

IR beamlines

Insertion devices

D. Attwood, UC Berkeley, http://ast.coe.berkeley.edu/srms/2007/Intro2007.pdf

Producing IR light
Bending magnet radiation

Bendingmagnete- beam
Problem: source size, focusing

Which one is better?
GlobarSRGlobar wins

Total flux
(CLS)

Synchrotron wins

Brightness(CLS)

High spectral resolution
spectroscopy

Pathlength and resolution

Source size (pinhole)

GlobarSR

http://www.newport.com/images/web600w-EN/images/2407.gifSR advantage – “low” res…
50"
45"
40"
35"

S/N$

30"
25"
20"
15"
10"
5"

35
42
49
57
64
71
78
85
93
100
107
114
121
129
136
143
150
157
165
172
179
186
193
201
208
215
222
229
237
244
251
258
265
273
280
287
294
301
309
316
323
330
337
345

0"

Frequency (cm-1)

35-350 cm-1 | Resolution: 0.002 cm-1 | Aperture: 3.15 mm | Velocity: 30 KHz / 5KHz

Data from Brant Billinghurst, Canadian Light SourceSR advantage

Extra Slide

25"

20"

S/N$

15"

10"

5"

35
43
52
60
69
77
85
94
102
111
119
127
136
144
153
161
169
178
186
195
203
211
220
228
237
245
253
262
270
279
287
295
304
312
321
329
337
346
354
363
371
379
388
396

0"

Frequency (cm-1)

35-350 cm-1 | Resolution: 0.00096 cm-1 | Aperture: 2 mm | Velocity: 30 KHz / 5KHz

Data from Brant Billinghurst, Canadian Light SourceSR advantage

Extra Slide

80"
70"
60"

S/N$

50"
40"
30"
20"
10"

335
340
345
349
354
358
363
368
372
377
381
386
391
395
400
404
409
414
418
423
427
432
437
441
446
450
455
460
464
469
473
478
483
487
492
496
501
506
510
515
519
524
529
533

0"

Frequency (cm-1)

335-535 cm-1 | Resolution: 0.001 cm-1 | Aperture: 1.5 mm | Velocity: 40 KHz

Data from Brant Billinghurst, Canadian Light SourceSR advantage – high res
35"
30"

S/N$

25"
20"
15"
10"
5"

500
511
522
532
543
554
565
576
586
597
608
619
630
640
651
662
673
684
694
705
716
727
738
748
759
770
781
792
802
813
824
835
846
856
867
878
889
900
910
921
932
943
954
964
975
986
997

0"

500-1000 cm-1 |Frequency (cm-1)
Resolution: 0.001 cm-1 | Aperture: 1.15 mm| Velocity: 40 KHz

Data from Brant Billinghurst, Canadian Light SourceApplications
High resolution FTIR on gases– Important for Astronomy(interstellar gases, small molecules)– Atmospheric science(ozone, pollution, radicals)– Basic physical chemistry(molecular dynamics, radicals, etc…)

Sample preparation
IR transparent
windows

Gases

Multi-pass cells

GAS

Gas cells• 30 cm White Cell
• Ambient Temperature• Pathlength up to 12 m

• 2 m White Cell
• Coolable (down to -80 °C)• Pathlength up to 80 m

Gas cells (discharge)• 1 m White Cell
• Adjustable Power• 4 m PathHigh spatial resolution
spectroscopy(spectromicroscopy)

General IR microscope Layout

The Schwarzschild objective

Resolution
Fraunhofer diffraction
Occurs in the “far field”

W2
<<, L
λ

where W is the size of the entrance
aperture,
l is the wavelength and L is
DIFFRACTION
3.23
2
the distance from W! 2J ( x ) $I (θ ) = I 0 #
"

S

1

x

&
%

S'

L
A
FIGURE 18 Fraunhofer diffraction of an aperture A , with a converging
spherical wave. S : point source. L: converging lens. S !: image.

In an imaging situation (see Fig. 18), a diverging spherical wave is brought to a focus ine image plane. This is also an example of Fraunhofer diffraction pattern of the lighttribution in the aperture A by a converging spherical wave. To realize Fraunhofer
fraction, a similar situation is obtained when a narrow diffracting aperture is held next toe eye when it is focused on a distant point source. The diffraction pattern is observed ine plane of the source.
An optical processing setup is shown in Fig. 19 where collimated or parallel light iscident normally on plane 1. In this arrangement an inverted image of plane 1 is formedplane 3 (see Chap. 1). The imaging process may be thought of as a Fourier transform
raunhofer diffraction) of the light distribution in plane 1 onto plane 2, followed byother Fourier transform of the light distribution in plane 2 onto plane 3.
Recall our earlier discussion in relation to Eqs. (33) and (34). When the quadratic phase(In case of a circular aperture)2

2

Airy disk

Rayleigh criterion
Two objects are resolved if:

http://goo.gl/cp6WGTThe first object’s Airy disk’s maximum
coincides with the second’s firstminimum

In practiceRayleigh resolution limit:

1.22 λ
R=
NAcond + NAobj
NA = n ⋅ sin (θ )n – refractive index of the medium
the objective is looking into

But…

Beyond Rayleigh

Σ: Higher resolution possible

Image processing algorithms,
2D deconvolution techniqueswith PSF modelor Bayesian (model free)
Oversampling!

GlobarSRGlobar vs. Synchrotron

Globar vs. Synchrotron

Globar Light Spot in Plane of
Confocal Aperture

Synchrotron Light Spot inPlane of Confocal ApertureGlobar vs. Synchrotron

2x2 µm pinhole

5x5 µm pinhole

3x3 µm pinhole

10x10 µm pinholeGlobar vs. Synchrotron

AbsorbanceAbsorbance

6x6 µm aperture (single cell)

3500

3000

2500

2000

Wavenumbers / cm-1

1500

1000

3500

3000

2500

2000

Wavenumbers / cm-1

1500

1000

Beam spot in the CLSSpatial resolution…
VisibleSynchrotron Radiation

Globar

2.46 μm
3000 cm-1

2000 cm-1

1500 cm-1

2000 cm-1

Diffraction limited resolution can be achieved only by SR

…diffraction limited

Extra Slide

5000 cm-1

GlobarInfrared beamlines- some examples -Canadian Light Source Mid-IR
30

0
-50

)mm( y

-20

-60

-40

M6

0

-20

0

20

x (mm)

σy: 23.105mm Avg:-4.6752
Good:14904 σx: 6.9572mm Avg:8.3454

400

x (mm)

50

UHV Window
Focus

20

root:Mirr2G_y_1 vs. Mirr2G_x_1
Good:14904 σx: 14.725mm Avg:23.075
σy: 53.038mm Avg:3.1469

y (mm)

20

-40

10

-40

y (mm)

00y (mm)x (mm)
-10

50

M3

50

100

M4

root:Mirr4G_y_0 vs. Mirr4G_x_0

100

Good:14904 σx: 33.412mm Avg:-4.4553
σy: 32.184mm Avg:44.646
150

root:Mirr5G_y_1 vs. Mirr5G_x_1
Good:14904 σx: 16.976mm Avg:-23.986
σy: 59.41mm Avg:7.509

0

-50

0

root:Mirr7G_y_0 vs. Mirr7G_x_0
x (mm)
-2

0

2

4

-2
0
2
4

8

6

root:Mirr1G_y_0 vs. Mirr1G_x_0

8

20

4

0
5

SHADOW Beam shapes on mirror
surfaces for 25 micron wavelength.

10y (mm)

-8

-6

-4

0

2

-2

y (mm)

4

-2

0

2

root:Star3G_x_1 vs. Star3G_z_1

x (mm)

6

Good:14904 σx: 20.126mm Avg:-1.5859
σy: 11.053mm Avg:0.066009

Good:14904 σx: 1.7001mm Avg:-1.0273
σy: 3.3622mm Avg:1.5963

root:Star6G_x_0 vs. Star6G_z_0-4-5x (mm)

root:Star8G_x_0 vs. Star8G_z_0-10

Good:14904 σx: 4.7954mm Avg:-1.5743
σy: 2.8756mm Avg:-5.8612

0

-5

-10

-15

Good:14904 σx: 3.2889mm Avg:1.4637
σy: 1.7268mm Avg:-1.0759-6

y (mm)

M5

60

M2

-8

M7

RV Target
Focus

40

y (mm)FTIR

20
x (mm)

0
-10
-20
-20

0

20

x (mm)

M1

Canadian Light Source Mid-IR

Advanced Light Source, Bl 5.4~10 m+ Beamline 1.4, under construction: 2.4

Focusing problem
Bending magnet radiation

Bendingmagnete- beam
Problem: source size, focusing

acceptance angle of 36.5(horizontal) ! 12.6(vertical) mrad2. Since the radius of the electron beam orbit
39.3 m at the bending magnet, the emission length is 1.44 m. To focus the light from this long source, w
employed a perfect focusing mirror for the circular orbit, a so-called ‘‘magic mirror’’ proposed by Lope
Delgado and Szwarc [2]. The magic mirror not only focuses the source but also reduces the time delay dto the large acceptance: the summation of the optical path length and the electron orbital length is the samfor each emitting position. We have expanded the formula to include the vertical direction. The vertic
direction is approximated by a spherical curve using the distance between the emission and focusing poinand the incident angle to the magic mirror. The formula of the coordinates of the surface of the mag
mirror (M) is

Solution 1: magic mirror
Spring-8
Perfect solution.

1
fðd0 % ryÞ2 % r2 % a2 g þ ar sin y;AMðyÞ ¼ 2
d0 % ry % a cos y
qﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃ
MI ðyÞ ¼ r2 þ AMðyÞ2 þ a2 % 2aðr sin y þ AMðyÞ cos yÞ ;Fig. 1. Schematic figure of the optical system of the infrared beamline at SPring-8. PM, MM and PrM indicate plane, magic and oﬀ$"#%
axis parabolic mirrors, respectively. W is an2AMðyÞðd
optical window,
which separates upstream
area and downstream low1 ultrahigh-vacuum
0 % ry % AMðyÞÞ
%1 AMðyÞ % a cos y
cos andcos
RðyÞ(wedged-diamond¼; vacuum.
vacuum one. The two optical windows
and BaF2) are installed
can be changed without breaking

Complicated surface!!!
Not cheap.
Difficult.

d0 % ry2

MI ðyÞ

and&'8jRðyÞj sin y % ðrcos y % AMðyÞ sin yÞ=MI ðyÞ>>>
qﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃ
xðy; vÞ ¼ r cos y % AMðyÞ sin y þ>>>>
2 þ 2ðAMðyÞ % a cos yÞ=MI ðyÞ
>
>
>
(
"
#)
>
>
>
v
>
>
! 1 % cos tan%1
;
>
>
RðyÞ
>
>
>
&
'
<
jRðyÞj %cos y þ ða % r sin y % AMðyÞ cos yÞ=MI ðyÞ
M yðy; vÞ ¼ r sin y þ AMðyÞ cos y þ
qﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃﬃ>>>
2 þ 2ðAMðyÞ % a cos yÞ=MI ðyÞ
>
>
>
(
"
#)
>
>
>
v
>
>
! 1 % cos tan%1
;
>
>
RðyÞ
>
>
>
"
#
>
>
v
>
>
: zðy; vÞ ¼ RðyÞ sin tan%1:
RðyÞHere, r is the radius of the electron orbit, a the length between the center of the electron orbit and the foc
point, d0 the optical pass from a standard point, y the acceptance angle of SR from electron orbit and v t
vertical size of the magic mirror. The parameters for BL43IR are r ¼ 39271:8 mm, a ¼ 46025:4 mm
d0 ¼ 69807:4 mm, y¼ 1:480421:5169 rad and v¼ %22222 mm. AM, MI and R have the same meanings
in ref. [2].
The schematic figure of the BL43IR optical system is shown in Fig. 1. The magic mirror (M1) is locat
at 4.37 m from the center of the emission point. The focal point is located at 11.32 m from the center of temission point. The result of the ray trace at the focusing point is shown in Fig. 2(a). The beam size at t
focal point depends on the electron beam size (s: 200(h) ! 20(v) mm2 was assumed) and the emission angof the IRSR. The emission angle also depends on photon energy. Fig. 2(a) is the result at hn ¼ 0:5 e(s0 ' 2:5 mrad). The energy is at the center of the range covered by a HgCdTe detector, which is used in t
beam size measurement. The beam size (s) at the focal point is 0.63 (h) ! 0.37 (v) mm2. In the calculatio
the diﬀraction eﬀect was not included because the diﬀraction eﬀect is negligible at hn50:04 eV.
Fig. 2. Calculated photon beam image of hv ¼ 0:5 eV (s1 ¼ 2:5 mrad) (a) and measured beam profile by a HgCdTe detector (b) at the
Nuclear Instruments and Methods in Physics Research A 467–468 (2001) 437–4
focal point in Fig. 1.

Consequently, a pair of conical and cylindrical mirrors, both working in tangent
replaces the toroid mirror of Fig.1.
Fig.3 gives the optical layout proposed for the infrared beamline at LNLS. The
Fig.1 has been replaced by a M2 conical mirror with radii varying between 4.922
positioned at 3.1 m from the source, followed by a cylindrical M3 mirror with a radiu
positioned at 3.7 m from the source (Fig.3).

Solution 2: LNLS II

Decouplethe problem…
Variablefocus
the previous
layout (Fig.2). Table 2 compares the properties of the beam between the typical andproposed optical layouts. We can see that, thanks to the conical shape mirror M , the new opticalstrongly remove
the horizontal beam aberrations. Nevertheless, the vertical beam divergence
conicallayout
mirror(M2)
remains non-negligible due to the fact that the cylindrical M mirror cannot be placed in the best2

3

position to remove the COMA aberrations of the electrons trajectory.

Figure 3: Optical layout proposed for the infrared beamline at LNLS

+ cylindrical M3.

were initially impos
Because the position of the M1 flat mirror and the focal plane
ADD measurements
cannot be placed in the optimum position to remove completely the COMA aberrati
emission. Consequently, the resulting vertical beam divergence remains significant (to the close distance between the focal plane and the vertical collimating M5, this mparabolic shape (with radii ranging from 1.083 – 1.682 m) unlike the horizontal one
2013 J. Phys.: Conf. Ser. 425 142003
cylindricala radiusof 2.444
Figure 4: (withRay-tracing
simulations@ λ = 10m).
µm with the optimized optical layout: a) beam size ond) beamthe exit ofthethe focal
plane,b) beam divergenceafter
the last mirror (MWe
have
simulated,
at thewavelengthof6), λc) and= 10µm,imagetheatbeam
propertiesof thIR spectroscopy- samples and measurement
techniques -Sample forms
Gases

IR transparent
windows

Multi-pass cells

GASSample forms
Liquids

SampleSpacerIR transparent
windows

Sample forms
SolidsSampleTransmission

SampleSubstrate

SampleReflection

Reflection-absorption
Transflecion

Self supporting
Lying on substrate
Suspended in carrier (KBr, CsI, Nujol, etc.)

Reflection setups
RegularConvenient
SampleSubstrate

Very thin samples
Grazing angle incidence

SampleSubstrate

Special microscope objectives
Increases optical pathlength
Monolayers

Reflection setups

We are happy

DRIFTS
Diffuse reflection
Integrating sphere

Not so lucky

Application:- Powders- Catalysis

Reflection setups
Total internal reflection< micronReflection setups
Attenuated total internal reflection
Multiple reflection
Very sensitive

Number of reflections:

SMIS multireflection ATR setup
ATR Crystal

SMIS multireflection ATR setup

ATR Crystal(71 bounces)Reflection setups
ATR for microscopy

Single reflection
ATR Microscopy

SMIS inverted ATR microscope

SMIS inverted ATR microscope
Semi-hemisphere
The slide “extends” it.
Resolution enhancement ~ nGravity helps to keep things on.

Possible problems

Artifacts?
Samples are not ideal…thickness/roughness

Life gets very complicatedArtifacts?
Samples are not ideal…
Mie Scattering

Mohlenhoff et al., Biophysical Journal 88, 3635-3640, (2005)

Artifacts?
Samples are not ideal…scattering.

Mohlenhoff et al., Biophysical Journal 88, 3635-3640, (2005)

Artifacts? – solutions…
• Second derivatives• EMSC (extended multiplicative scattering correction)• Mie Scattering corr., Resonant Mie Scattering corr.

How to differentiate spectra?
• Statistical analysis– Cluster analysis– Principal Component Analysis– Partial Least Squares regression

Cytospec
R, Matlab,
Eigenvetcor
The Unscrambler

Artifacts? – RMieSc
Samples are not ideal…
resonant scattering.
Amide I – 1641 cm-1
b-sheet, random

Amide I – 1650 cm-1
random, turns

Amide I – 1654 cm-1
a-helix
Bassan et al., The Analyst 135, 268-277, (2010)

Artifacts? – RMieSc…
Samples are not ideal…resonant scattering.
Input

Output“When you have a big hammer, everything looks like a nail…”
Bassan et al., The Analyst 135, 268-277, (2010)

Artifacts? – RMieSc…
Samples are not ideal…resonant scattering.

Uncorrected

Mie scatteringcorrected

Resonant
Mie scatteringcorrected

Bassan et al., The Analyst 135, 268-277, (2010)

Artifacts?
Does the synchrotron light heat the sample?
Synchrotron source:
Measured 1 mW focused onto ~10 X 10 μm2

DPPC = dipalmitoylphosphatidylcholine,
a phospholipid bilayer
Undergoes a gel to liquid-crystalline phasetransition at T= 316 K

Less than 0.5˚ C temp rise on sample
Important: No Evidence for Cytotoxic Effects on Living Cells

M.C. Martin et al., Applied Spectroscopy 55, 111 (2001)

SR IR spectroscopy- applications -Beating the diffraction limit - SNOM

SNOM = Scanning Near-field Optical Microscopy

Photothermal

Scattering

Two distinct principles

Basic principles - differences

αexp
S≈⋅Uabs ⋅z 3,
ηαexp − thermal expansion coefficientη − thermal conductivity
Uabs − absorbed energy per unit areaz − sample thickness

Es is a complex function…

www.anasysinstruments.com
A. Centrone, Annu. Rev. Anal. Chem. , 8 101–126 (2015).

Scattering SNOMs in SR facilities
Fully home built

Semi-home built

Commercial

From basic parts

Commercial FTIR
Commercial AFM
Home built combination

Commercial SNOM
Only interfacing to SR

Why synchrotrons?
Narrow band:
IR lasers
Supercontinuum lasers
Quantum cascade lasers

Broad band:(Globar – highly questionable – very low brightness!)
Synchrotrons – high brightness !

General setup
Lock-in amplifier
AFM
sampleStoragering

Interferometry
Measure amplitude and phase
Calculate absorbance
H.A. Bechtel et al. PNAS 111, 7191-7196 (2014)

Scattering SNOM

H.A. Bechtel et al. PNAS 111, 7191-7196 (2014)

Approach curves

H.A. Bechtel et al. PNAS 111, 7191-7196 (2014)

Broadband nano-imaging

Spatial Resolution ~ < 50 nm, better than λ/200!

H.A. Bechtel et al. PNAS 111, 7191-7196 (2014)

Broadband nano-spectroscopy:
interferograms

SiO2

1 µm

Si

H.A. Bechtel et al. PNAS 111, 7191-7196 (2014)

Broadband nano-spectroscopy

FFT

H.A. Bechtel et al. PNAS 111, 7191-7196 (2014)

Linescans

Extra Slide

H.A. Bechtel et al. PNAS 111, 7191-7196 (2014)

Biological Samples

H.A. Bechtel et al. PNAS 111, 7191-7196 (2014)

Photothermal Imaging

Absorbance
response

Frequency
Analysis

Dazzi, A.; Prazeres, R.; Glotin, F.; Ortega, J.M.; Opt. Lett. 2005, 30, 2388-2390.

Absorbance / a.u.

Getting the absorbance spectrum
Easy to interpret

Frequency / cm-1

Excellent correlation with bulk techniques

Single point spectroscopy

0
3400

3200

3000

2800

0

7.5
(µm)

The band intensity at 3300 cm-1 increases as tip approaches the
Sharp transition within 100 – 200 nm

15

-250

(nm)

250

AFM image(µm)

Normalized amplitude(2956 cm-1)

10

Blend of nylon and natural rubber

Chemical imaging
AFM image (15 μm x 10 μm)

3300 cm-1

3300 cm-1 / 2956 cm-1

2956 cm-1

Contrast is enhanced in ratio image

Plasmonic enhancement

AFM-IR provides nanoscale spatial
resolution on mid-IR resonators
Polarization control allows
polarization dependentmeasurements

B. Lahiri, et al Nano Letters, 2013, 13 (7), pp 3218–3224

Resonance enhancement
New feature in Analysis Studio in ‘14
Pulse IR source at resonant frequency of cantileverContinuous oscillation, precise magnitudeSample thickness down to single monolayers
Conventional AFM-IR
Quantum
Cascade Laser

Resonance enhanced

F. Lu and M. A. Belkin, Opt. Express 29, 19942–19947 (2011).

Spectroscopy of 20 nm PMMA

AFM Image
10 x 15 μm scan sizeSelf assembled monolayers

Highly engineered experiment…

F. Lu, M. Jin, and M.A. Belkin, Nat. Photonics 8, 307–312 (2014).

Recent developments

NanoIR 2-s
2-in-1 instrument
Photothermal
Scattering
There is no best technique…
Great potential: combination of methods!

Extra Slide

Spectroelectrochemistry
kinetics at the diffraction limit
Kinetics: problem RC time constant of the electrodesolution: decrease size
Small electrode size ~ 10 mm
Need for SR

Flow Through Holes

CE

WE

1.0
0.15

0.8
i / µA

0.10

0.00
-0.05
-0.10
-0.4

-0.2

0.0

0.2

0.4

0.6

E vs Ag wire

0.4

0.6
0.4

0.2

E / V vs Ag

q / µC

0.6

0.05

0.2
0.0
-0.2

0.0

0

30

32

34

36

38

time / s

0

1

2

3

4

time / s

5

6

7

8

RE

Rosendahl SM; Borondics F; May T; Pedersen T; Burgess I, Anal. Chem. 83 (10), 3632-3639, 2011.

Extra Slidee-chem cell
Ecell/I
DAQ
Computerpotentiostat

FTIR
MicroscopeLet’s roll!
Get ready…

3.8
3.6

Signal (V)Apply Estep
rest
ref

1.0
0.5
0.0
-0.5
0.00

SpectraDirect detector signal

0.05

0.10

0.15

time / s

Rosendahl SM; Borondics F; May T; Pedersen T; Burgess I, Anal. Chem. 83 (10), 3632-3639, 2011.

Extra Slide

Rosendahl SM; Borondics F; May T; Pedersen T; Burgess I, Anal. Chem. 83 (10), 3632-3639, 2011.

Extra Slide

Results

2
0

Fe(CN)64- = Fe(CN)63- + eFe(CN)64loss

0.03

-4
-6
-8
-10
-12
0

0.02

1

2

3

4

5

6

7

time / s
1.2

0.01

0.8

0.00

creationFe(CN)63-

-0.01
1900

2000

2100

2200

Wavenumber / cm

-1

2300

ΔConcentration (mM)

ΔS/S

Δ(abs) x 1000

0.04

-2

0.4
0.0
-0.4
-0.8
-1.2

0

1

2

3

time / s

Rosendahl SM; Borondics F; May T; Pedersen T; Burgess I, Anal. Chem. 83 (10), 3632-3639, 2011.

High-pressure studies
Pressure is created with diamond anvils
Max pressure depends on- gasket hardness- hole size
- thickness- diamond culet size
Important- pressure medium (hydrostatic?)

“Low” – HP studies
Most organics are interesting up to max. 20 Gpa
Practically: 100-120 µm diameter hole – what is the need for SR?

Ruby sphere

Three measurementsin the same volume- background- sample (<50 µm)- pressure (ruby FL)

Sample

The ultimate HP IR experiment

Intensity / V

Absorbance / a.u.

Hydrogen metallization
Predicted ~450 GPa (4.5 Mbar)

Frequency / cm-1

Frequency / cm-1

Diamond culet 20 µm, gasket hole ~6 µm

DIFFRACTION LIMIT!

P. Loubeyre, et al., Phys. Rev. B Condens. Matter, 87 [13] 134101 (2013).

Biology
Ideal size range for resolution
Cells, tissues, bacteria, fungi

0.8
0.7
0.6
0.5
0.4
0.3
0.2
0.1

globar source
AbsorbanceAbsorbance

SR source

4000 3500 3000 2500 2000 1500 1000
Wavenumbers (cm-1)

3500

3000

2500

2000

Wavenumbers (cm-1)

1500

1000

Extra Slide

Spectromicroscopy of Rod Cells

Lipid distribution at 2925 cm-1

Measurement of molecular orientation in a subcellularcompartment by synchrotron infrared spectromicroscopy
Quaroni et al., ChemPhysChem 9 (10) 1380-1382, 2008

crystallo
The aresiduement oband cexpecte[14]
An appwe derive hgi from the crystal structure of rhodopsin
a helicetein data bank (PDB) entry 1F88; see the SupportingInfotainedtion], thereby obtaining a value of hgi = 248, which
is in
Dichr
agreement with our spectroscopic results. The orientatio
rhodopsin a helices relative to the normal of the1740–1
memb
bonyl
o
has been previously measured by means of FTIR VLD
usinfor thiso
constituted disks or ensembles of fractured ROS. Values
thusin pr
ranging between 38 and 518 were reported
678, relworks.[12, 15] To date, our results—obtained in vivo—provid
carbony
best agreement between the spectroscopic measureme
measurthe hgi value of rhodopsin a helices and the correspon
entatiocrystallographic value.
The amide-II band overlaps with bands assignedneverto tyrb
partic aa
residues in rhodopsin,[12] which prevents a quantitative
same rement of polarization ratios by curve fitting. Nonethelessisband clearly displays opposite dichroism to that ofance
amide
ence
in
expected
based
the absorption
orientationof with
its transition
mom
Figure 1. a) ROS spectra
recordedin the on
carbonyl
regionlight polarized perpendicular(g) and parallel
the
ROScanaxis,be calculatedband,fot
An approximate
value (c)of hgtoi =338b) ROS spectra recorded in the methyl absorption region with light polarizeda helices, in fair agreement with the more accurate Band
valu
perpendicular (g) and parallel (c) to the ROS axis.
tained from the analysis of the amide-I absorption.
Dichroism is also observed for the absorption ban
1740–1720 cm!1, which is tentatively assigned to the acyli
Table 1. Band frequencies for selected ROS spectral bands measured with polarized lig
bonyl ofthe phospholipid
headgroups.
The transitionmoQuaroniet al., ChemPhysChem
9 (10)
2008 structurpolarization ratio (R), averagetransition
moment orientation(hq1380-1382,i), and average
this(hgi) relative to thefor
ROS
axis.vibration is taken to be aligned with the C=O g
thus providing an average orientation of hgi = 728 andExtra Slide

Results – polarization studies

The measurement confirmed previous results
obtained by crystallography on model systems.

Evolution of cell wall composition during
enzymatic biomass hydrolysis
Goal : obtain time-lapse information of the evolution of several types of cell wallcomposition during enzymatic degradation

Microfluidic device

Enzyme circulation setup

Maize stem section

Results
phl"

scl"

pb1"

No degradation ofcell wall components

Differential degradation ofcell wall components

Spatial resolution 12 µm
Data acquisition rate : 1 min/sp
Flow rate 2 µL/min
Cell volume 1µL
Spacer thickness : 20 µm
Section thickness : 16 µm
Enzyme: cellulase

Simultaneous degradation of
all cell wall components

At SMIS in 2015 MF. Devaux et al.

Courtesy of M. J. Hackett

Stroke research with IR spectromicroscopy#The loss of blood supply to all or part of the brain (ischemia)$ Lack of O2 (hypoxia)$ Lack of glucose (energy)$

Third leading cause of death in Canada, $3.6 Billion per Year!!

Healthy Brain

Global Ischemia(i.e., cardiac arrest)

Focal Ischemia
Haemorrhagic Stroke

The “window of opportunity”

Although “stroke” (ischemic insult) occurs over a period of minutes,
neurodegeneration often occurs over a period of weeks

Courtesy of M. J. Hackett

FPA imaging of brain samples
for stroke research
Healthy

5days After Stroke
Cell types: CA1,CA3500 μmCresyl violet stained
sections

100 μmCourtesy of M. J. Hackett

Lipid

Aggregated Proteins
Cytoplasm

SingleNeuronNucleus

10 μm
Lipid
(C=O)

Nucleus
Aggregated Proteins(CH3): s(CH2)1627 : 1656 cm-1

Imaging Total Protein in Cerebellum
Purkinje Neurons
Histochemistry  Purkinje neurons have low protein content
Fixation/staining influences protein content!!!
FTIR imaging at the cellular level revealed that the Purkinje neuron is rich in Protein.
(A) Bright Field image of unstained tissue.
(B) Bright field image of cresyl violet stained tissue showing neuron body(C) FTIR image protein (amide I band, 1690 – 1610 cm-1)

M.J. Hackett, et al. ACS Chem. Neurosci., 4 [7] 1071–1080 (2013).

Courtesy of M. J. Hackett

Subcellular imaging with SR/FPA

Lipid

NucleusCourtesy of M. J. Hackett

FPA imaging of brain samples
for stroke research

52x objective high res imaging.
single pixel (512 scans) spectrum
10 minute image time (20minutes with BG).
180 mA beam current

Extra SlideAn exotic technique: IR tomograpy
Routine hospital techniqueSingle wavelength illumination
X-ray tomography
Object shape can bereconstructed in 3D via
computed tomography

An exotic technique: IR tomograpy
Multi wavelength illumination

Object shape can bereconstructed in 3D via
computed tomography
At every wavelength!
M.C. Martin, et al., Nat. Methods, 10 [9] 861–864 (2013).

Courtesy of M.C. Martin

absorbance [a.u.]

Cellulose composite sample

3600

PVOH: 2928-2966 cm-1

3300

PAA: 1684-1759 cm-1

3000

2700 2400 2100 1800
-1
wavenumber [cm ]

1500

1200

900

NFC: 1151-1181 cm-1

Courtesy of M.C. Martin

Possible with Globar source too!

L. Quaroni, et al., Angew. Chem. Int. Ed Engl., 54 [1] 318–322 (2015).

Proposal writing tips
Needs good science – obviously!
Justify the need for a synchrotron:
Remember, FTIR spectromicroscopy is NOT inherently an SR technique. You
need to justify why you can’t do your research on a lab based system.

Ask for the right amount of time:
Give a reasonably accurate estimate how many days your experiment will
take. If it is very long, find ways to reduce it.

Something to remember
Synchrotron = high brightness
Diffraction limited resolution
Small samples!
High spectral resolution
Data processing…pay attention!

Resources
•
•
•
•
•
•
•
•

Extra Slide

SMIS webpage http://www.synchrotron-soleil.fr/Recherche/LignesLumiere/SMISCLS Mid-IR webpage http://midir.lightsource.ca
ALS Infrared beamlines http://infrared.als.lbl.gov
SPring-8 publications website https://user.spring8.or.jp/uisearch/publication2/
William Reusch: Virtual Textbook of Organic Chemistry http://goo.gl/NEUWDavid Attwood SR course (EE290f) at UC Berkeley(http://www.youtube.com/watch?v=1WWnxA6odso)
Wolfram Demonstrations Project (http://demonstrations.wolfram.com)
Synchrotron Simulator
T. Shintake, Nuclear Instruments and Methods in Physics, 507 (1-2), 89-92 (2003)(http://www-xfel.spring8.or.jp/dlmonitor.html)

Thank you for your attention!

Ferenc Borondics

SMIS beamline
Synchrotron SOLEIL
ferenc.borondics@synchrotron-soleil.fr