New Dimensions in Synchrotron Infrared Spectroscopy and Imaging Michael C. Martin, ALS MCMartin@lbl.gov
Introduction
10 7
Introduction Continuous spectrum - from infrared to hard x-rays ALS Bend Magnet Flux and Brightness Curves
The discovery of infrared lig In 1800, Herschel studied the spectrum of sunlight with a prism. He measured the temperature of each color, and found the highest temperature was just beyond the red, what we now call the infrared (‘below the red’). The Science Museum, UK F.W. Herschel, Phil. Trans. Royal Soc. London 90, 49 (1800).
Atoms vibrate with frequencies in the IR range ● Chemical Analysis: • Match spectra to known databases –  Identifying an unknown compound, Forensics, etc. •  Monitor chemical reactions in-situ ● Structural ideas: • Can determine what chemical groups are in a specific compound ● Electronic Information: • Measure optical conductivity – Determine if Metal, Insulator, Superconductor, Semiconductor –  Band Gaps, Drude model
Imagine the mass is an atom, carrying a charge. This will then couple to the electric field in light. Ball & Spring equation:  F = -k Dx Spring constants for chemical bonds: • k = 40 – 400 N/m for covalent bonds • k = 20 – 200 N/m for ionic bonds • k = 0.5 – 4 N/m for Van der Waals bonds Solution to resonance frequency for ball & spring:
A hydrogen atom has a mass of 1.6735 x 10-27 kg An oxygen atom has a mass of 2.6561 X 10-² 6 kg
ERNEST ORLANDO LAWRENCE Berkeley National Laboratory
Protein Amide I: 1690-1600 Protein Amide II:1575-1480 Typical IR absorbance Lipid =CH,: 3100-3000 Lipid -CH₂, -CH₃: 3000-2850 positions: Nucleic Acid -PO,-:1225, 1084 The peak positions of Amide I and II are sensitive to the protein secondary structure (α-helix, β-sheet, random coils, etc.) A good reference: Mantsch and Chapman, Infrared spectroscopy of biomolecules. 1996, New York: Wiley-Liss.
ERNEST ORLANDO LAWRENCE Berkeley National Laboratory
Michelson wanted to measure the speed the the earth moves through the ether (the medium in which light travels).  By measuring the interference between light paths at right angles, one could find the direction & speed of the ether. Michelson’s first interferometer (1881)
Still no fringes → No ether. The speed of light is constant. A new physics of light was needed. "My honored Dr. Michelson, it was you who led the physicists into new paths, and through your marvelous experimental work paved the way for the development of the theory of relativity.“ – Albert Einstein, 1931. Michelson-Morley interferometer (1887)
Michelson won the Nobel Prize in physics in 1907. He continued pioneering optical measurements: • The speed of light • The size of stars • Using a particular wavelength of light as a distance standard
A Simple Spectrometer Layout Pathlength difference = x The intensity detected of two plane waves: I = | Ë |² = | E 1 2 + | E 2 2 + 2 E 1 ● E 2 cos( θ ) Normal incidence, θ = kx, can simplify to: I(x) = 2[1+ cos(kx)] For non-monochromatic light: I(x) = [[1+ cos(kx)G(k)dk dk
We can rewrite this to something more familiar:
A Fourier Transform! The detected intensity as a function of moving mirror position, l(x), can therefore be converted into G(k), the intensity spectrum as a function of frequency by a simple Fourier transform.
rnest Orlando Lawren Berkeley National Laborat
· High brightness
• Essentially a point source • Can focus light to a diffraction- limited size:  Microscopy • More far-IR flux • Smaller samples • Better signal-to-noise
• Pulsed source
• Light is from electron bunches • Fast timing measurements (nsec)

Advantages
• Diffraction-limited spot sizes for microscopy (2-10 μm) Levenson, Lerch & Martin, J. Synch. Rad. (2008) • Superior collimation for high spectral resolution • Smaller samples • Better signal to noise ratios • Faster data acquisition Holman et al., Spectroscopy - An International Journal 17(2-3), 139-159 (2003).
Better Signal-to-Noise and Faster Collection Globar: 6x6 μm² 1000 scans = 500s Synchrotron: 6x6 μm² 32 scans = 16 s From Paul Dumas, SOLEIL High Brightness = Better for small sam Better Signal-to-Noise and Faster Collection Mineral sample (ocean basalt) in diamond anvil cell at high pressure Lab FTIR: 60,000 scans averaged (~ 16 hours averaging!) Panero, Benedetti, Jeanloz
one usions • High-impact science with a cost-effective beamline. • Diffraction-limited spot size: analysis of micron-scale cells, tissues, particles, novel materials, fibers, heterogeneity, etc. Science and Applications of SR Beamtime allocated for the ALS IR Beamlines Physics 20% Biology 36% Applied( 15% Environ- mental 29%
(1999) o
Prof, Feng Wang, Yuanbo Zhang, Tsung-Ta Tung, Cheol-Hwan Park, Baisong Geng, Caglar Girif Profs. Mike Crommie, Steve Louie, Ron Shen, and Alex Zettl, UC Berkeley Dimitri Basov, Zhiqiang Li, UC San Diego E. A. Henriksen, Z. Jiang, P Colombia Kimi Hi INIVERSITY Michael C. Martin, Hans Bechtel, ALS, I Zhao Hao, Earth Sciences Division, LBNL Synchrotron ' Infrared Beamlines
E = V F ・P Attractive for both fundamental physics Massless Dirac fermion. and technological Ballistic Transport. applications. Tunable via: Electrical Field Layer-Layer interactions Nanopatterning Field effect devices Bilayer
SR-FTIR spectromicroscopy with Oxford microstat for samples at 4 - 400 Kelvin at ALS beamline 1.4.4.
Top View Side View
Dual-gated bilayer graphene is a remarkably flexible tool for nanoscale electronic devices. A bandgap over 250 meV can be achieved. Zhang, Tang, Girit, Hao, Martin, Zettl, Crommie, Shen, and Wang, Nature, 459, 820-823 (2009). irrently the highest cited paper from our beamline with >1200 citations) Science and Applications of SR Beamtime allocated for the ALS IR Beamlines Physics 20% Biology 36% Applied( 15% Environ- mental 29%
•On April 20, 2010 the Deepwater Horizon exploded. •The floating rig burned for 2 days then sank, shearing the 21-inch riser pipe 600 ft above the BOP. •Leak estimated at ~65,000 barrels per day •87 days of flow into Gulf until containment. •Largest offshore oil spill in history.
•Scientific Response:
•Measurements revealed a large lens of oil •Deepest and largest lens was at 1,200m and measured approx. 15 km long •Oil aggregates and mousse floated
Cell Density [log cells/ml] 3.5 4.0 4.5 5.0      5.5 Cell Density [log cells/ml] 3.5      4.0      4.5 3.0 5.5 5.0 3.0 bm58 10.08 km Cell Density [log cells/ml] 3.5 4.0      4.5      5.0      5.5 bm61 Outside Plume 5.06 km A significant plume of oil was found at a depth of 1200 m. Fluorescence [mg/m³] 0 0 5 10　 15　 20　 25　 30　 35 10　15　20　25　30　35 10  15  20  25  30  35 5 Fluorescence [mg/m³] Fluorescence [mg/m³] Fluorescence [mg/m³]
SR-FTIR analysis of Sample # OV01105 Floc riched in oil degradation products Microbe-rich floc with oil degradation products malized intens 0.0 Hazen, et al., Science 330(6001), 204-208 (2010). Scale bars = 10 micrometers Science and Applications of SR Beamtime allocated for the ALS IR Beamlines Physics 20% Applied( 15% Biology 36% Environ- mental 29%
STARDUST flew threw comet WILD-2’s tail… …and landed January 15, 2006.
Organics Captured from Comet Wild 2 by the Stardust Spacecraft Sandford et al. Science, 314, 1720-1724 (December 2006) Fig. 2. IR transmittance spectra obtained along a line perpendic- ular to cometary impact tracks (A) track 59 and (B) track 61. In addition to aerogel features, the spectra of track 59 (A) display peaks at 3322 (broad), 2968, 2923, 2855, and 1706 cm-1 (not shown), both inside the track and extending outward into the aerogel. (B) track 61 exhibits only the aliphatic CH stretching feature dominated by the 2968 cm¯¹ peak and (Si-O) bands (not shown) characteristic of the flight aerogel. The optical images of the same tracks, with corre- sponding maps to the same scale showing the intensity distribution of the 2923 cm-¹ peak (—CH 2 —), are displayed in (C) and (D). The false-color image scale shown at the bottom is used in both maps, and the black scale bars correspond to 100 μm. In both cases, the entrance of the cometary particle is on the left side. The false-color map in (C) shows an increase in intensity of the 2923 cm¯¹ —CH₂— peak in and near the track. The distributions of other organics peaks are similar. In contrast, the second track shown in (D) shows almost uniform distribution of the peak area centered at 2923 cm-1; that is, the track shows only the features of aerogel.

Assessment and control of organic and other contaminants associated with
the Stardust sample return from comet 81P/Wild 2
Scott A. Sandford, Sasa Bajt, Simon J. Clemett, George Cody, Bradley T. Degregorio, Vanessa De Vera, Jason P. Dworkin, Jamie E. Elsila, George J. Flynn, Daniel P. Glavin, Antonio Lanzirotti, Thomas Limero, Mildred P. Martin, Christopher J. Snead, Maegan K. Spencer, Thomas Stephan, Andrew J. Westphal, Sue Wirick, Richard N. Zare, Michael Zolensky Meteoritics & Planetary Science, 45(3), 406-433 (March 2010). Fig. 1. Infrared spectrum of an approximately 10 μm × 10 μm spot on C2115,23,21, a keystone extracted from the C2115, Stardust aerogel flight cell. The strong Si-O, C = O, aliphatic ; -CH2- and -CH3, structural -OH, and adsorbed H2O absorption features were seen at all the spots examined and a their presence is typical of Stardust flight aerogels. Next Challenges for SRIR How can we go beyond diffraction-limited spectro-microscopy? > 3D FTIR Spectro-Microtomography Martin et al., Nature Methods 10, 861-864 (2013) ▷ Synchrotron Infrared Nano Spectroscopy Bechtel et al., PNAS 111(20), 7191–7196 ( 2014). 3D Imaging with Infrared Spectral Microtomography Michael C. Martin, Charlotte Dabat-Blondeau, Hans A. Bechtel, Dula Parkinson Advanced Light Source, Lawrence Berkeley National Laboratory Carol Hirschmugl, Miriam Unger Physics Department, University of Wisconsin-Milwaukee Julia Sedlmair, Barbara IIIman Forrest Products Laboratory and SRC, Madison Jonathan M. Castro, Institute of Geosciences, University of Mainz Marco Keiluweit, Lawrence Livermore National Laboratory
FPA detector systems can be used for faster full-field imaging. IRENI (Nasse, Hirschmugl, et al.)
Measure projected transmission image: In a single 2D projection, cannot tell the depth or 3D extent of each object. Rotate sample and measure many projection images. Then computed tomography algorithms reconstruct slices through the sample, revealing the 3D nature. 3D picture remains gray scale: can observe different densities. b. Using many views
Can we do this in “Full-Color”?? Use the power of FTIR spectroscopy to provide meaningful colors based on full spectral identification.
What’s needed:
1.   A fast FTIR imaging instrument with complete spectral images obtained in ~1 minute so a full 180 degrees of sample rotation can be measured within a reasonable time. 2.  A sample rotation stage. 3. Tomography reconstruction algorithms that are spectroscopy aware.
Proof of principle experiments, 2012 We removed the x-y sample stage at the IRENI beamline and installed a test sample rotation stage. The combination of the tip-tilt stage and the x-y-z stage allows us to place the center of rotation at any sample location of interest.
x 1.1 microns per pixel at the sample. Diffraction-limit still applies.
Test sample:  MiTeGen protein crystallography microloop holder. 1574-1655 cm-1 Polyimide absorption 2287-2415 cm-1 Edge scattering
Better automation at IRENI, 2013 Programmed macro automates tomographic data acquisition. Reconstruction programs coded to be spectroscopy aware.
Paul Dumas, et al., SOI Can we get similar information from an intact human hair? 1640 cm-1 Protein absorption
Paul Dumas, et al., SOLEIL 1640 cm-1 1705 cm-1 + Protein absorption Phospholipid absorption
Volcanic glass filament from the Puyehue volcano, Chile. Sample collected by Jon Castro, Jan 2012. IR image shows density variations and water concentration changes along darker stripes relevant to mechanism of eruption.
Brown = 1789 cm -1 = Silicate glass Blue = 3495 cm -1 = Water O-H Correlation between glass and water can be seen well.
2800 – 3000 cm -1 C-H region 1524 – 1628 cm-1 region: Shows channels made of lignin
1689 – 1782 cm-¹ region (red) Hemicellulose: Outlines channels 1524 – 1628 cm -1 region (blue) Lignin: Fills channels
Cellulose microfibrils arranges in a parallel orientation. 2360 cm-1 region (red) Scatter outline of holder 3330 cm-1 region (blue-green): Shows water in Zinnia
1650 cm-1 region (red-blue) Proteins 2850 cm-1 region (yellow-orange): Lipids
PVOH: 2928-2966 cm-1 NFC: 1151-1181 cm-1
PVOH: 2928-2966 cm PAA: 1684-1759 cm-1 NFC: 1151-1181 cm 1
4D spectral hypercube: 1.6 Million voxels, each with a fully reconstructed FTIR spectrum = 1.3 Billion datapoints Fast data pipeline to super computer center Web portal to reconstructed spectral 3D data 3D Data Visualization and Analysis room at the ALS Broadband vibrational nano-spectroscopy with a synchrotron infrared source Hans A. Bechtel and Michael C. Martin Advanced Light Source Robert L. Olmon, Eric A. Muller, Benjamin Pollard, and Markus B. Raschke University of Colorado, Boulder Beating the diffraction limit

Advantages
Nanometer spatial resolution . . Wavelength independent Soft and hard matter . . Amplitude and phase of optical field 65
S. Berweger, D.M. Nguyen, E. A. Muller, H. A. Bechtel, T. T. Perkins, and M. B. Raschke, JACS 135, 18292 (2013).

Broadband sources
• More efficient spectral collection • Improved spectral accuracy
Synchrotron IR
• Ultra-broadband • High spectral irradiance • Spatially coherent • Good spectral stability ectral Irradiance (W/cm²/cm
Synchrotron Infrared Nano-Spectroscopy Bechtel et al., PNAS 111(20), 7191–7196 (2014).

Key Components
•Floating table •Modified Bruker Innova AFM •Zurich Instruments lock-in amplifier •Commercial Thermo FTIR •Kolmar MCT (100 um)
Spatial Resolution  < 45 nm better than λ/200!
Optical Path Difference (μm)
Optical Path Difference
Samples: Sun Choi and Hoi-Ying Holman (ESD, LBNL) Topography
Samples: Gloria Olivier and Ron Zuckermann (Molecular Foundry, LBNL
Topography 150.0 130.0 120.0 110.0 90.0 80.0 70.0 60.0 50.0 40.0 30.0 20.0 10.0 0.7
168.6 nm 150.0 140.0 130.0 120.0 110.0 100.0 90.0 80.0 70.0 60.0 50.0 40.0 30.0 20.0 10.0 0.7 5.9 V 5.0 4.5 4.0 3.5 3.0 2.5 2.0 1.5 1.0 0.5 _0.0 istance (μη
S. Dai et al., Science 343 , 1125-1129 (2014)
Surface Phonon Polaritons in Boron Nitride Zhiwen Shi and Feng Wang (UC Berkeley) 40 nm Summary