Synchrotron Based Scanning Transmission X-ray Microscopy and Microspectroscopy (C-, N-, O-XANES)


Recent advances in X-ray micro-focusing techniques coupled with brilliant, synchrotron derived X-ray sources have lead to the development of Scanning Transmission (Soft) X-ray Microscopy (STXM) (e.g. Jacobsen and Kirz, 1998); a technology that allows the quantitative analysis of bio-organic structure for functional group distributions at spatial resolutions approaching 50 nm. The particular STXM I have used most extensively was designed and built by Chris Jacobsen and the X-ray Optics group of the Department of Physics, SUNY Stony Brook and resides at the X1A beam line at the National Synchrotron Light Source, a 2.8 GeV electron storage ring.  Harald Ade (NCSU-Physics) has built a new STXM (beamline 5.3.2) located on a bending magnet at the Advanced Light Source, Lawrence Berkeley Laboratory.  Aside from ALS 5.3.2 there exist several other “Soft” X-ray beam lines at ALS.  New STXM instruments have been installed or will soon be at synchrotrons in in Europe, Canada, and Australia; as far as I know there are plans for such instruments to be installed at synchtrons in Japan, Korea, China


Figure LeftThis is a STXM image of a very intriguing 45 million year old sample of wood from the Canadian Arctic “Fossil Forest”.  The image was acquired at 285 eV. Dark =strong absorption, Light = weak absorption.  Absorption intensity at this energy corresponds to aromatic carbon, e.g. in the biopolymer lignin.  Note that the sample was embedded in epoxy, hence the deep blue intercellular carbon is epoxy. The contrast reflects differences in lignin-polysaccharide abundances. The intriguing structure shown here records an as yet unknown degradation mechanism that may not have involved fungal and/or bacteria.  For scale, the width of narrowest region of the middle lamellae is ~ 50 nm.


Soft X-rays are generated via perturbation of the synchrotron electron beam by an undulator, i.e. imagine a series of opposed dipolar magnets placed on either side of the electron storage ring. By varying the undulator gap X-rays in the soft X-ray range ~ 150 – 800 eV are generated.  The effective energy bandwidth of the X-ray beam at X1A is on the order of 40 eV, allowing complete access to a given absorption edge region at a given undulator gap setting.  Energy selection is obtained via a series of order sorting mirrors, exit and entrance slits, and a spherical grating monochromator with an energy resolution on the order of 0.03 eV (see discussions and references in Jacobsen and Kirz, 1998).

Figure Above: This awesome image is of compression wood from red spruce. Note that the darker (purple) regions correspond to increased lignin content. This image shows that in compression wood lignin accumulates in the secondary cell wall next to the primary cell wall at concentrations as high as observed in the compound middle lamellae. The finest scale features in this image are on the order of 50 nm.


The power of soft x-ray microscopy is that image contrast is derived from chemistry by exploiting various absorption bands that exist in the pre-edge region of carbon 1s absorption edge, e.g. Carbon X-ray Absorption Near Edge Spectroscopy (C-XANES). X-rays with sufficient energy are capable of promoting core level electrons completely far from any columbic interaction with the core hole, i.e., ionization.  For carbon the ionization energy threshold occurs at ~ 292-295 eV. X-rays with slightly lower energy are capable of promoting 1s electrons up to various “bound” states, i.e., unoccupied molecular and/or atomic levels.  Electrons in these bound states are strongly connected to the core hole through columbic forces.  The unoccupied π orbitals (π* states) of unsaturated carbon containing functional groups provide particularly intense absorption bands.  These bands are shifted in energy by the electronic perturbation of neighboring atoms, e.g. the electron withdrawing nature of oxygen will impart significant energy shifts of 1s-π* transitions.  Aliphatic or sp3 carbon also exhibit absorption bands corresponding (approximately) to 1s-s* transitions; these absorption bands are also shifted by electron withdrawing substituents. 


Figure Above:  Note that the spatial distribution of lignin and polysaccharides can be revealed by imaging at different energies.

Figure Above:  This image reveals a thin band of cutinite in a ~ 300 My old organic sediment.  Cutinite is derived from the waxy outer coating of leaves.  At 285 eV the cutinite is weakly absorbing due to the low concentration of aromatic carbon.  At 288.1 eV (corresponding to the relatively strong 1s-3p/s*transition of aliphatic carbon) the cutin absorbs strongly relative to the surrounding vitrinite.

Figure Above:  In collaboration with others we have been using STXM to explore the microbial degradation of lingo-cellulosic materials.  This series of micro C-XANES spectra clearly reveal the selective degradation of polysaccharides relative to lignin after months of inoculation with the brown rot fungus P. placenta.


STXM is extremely powerful analytical instrumentation.  As a component of my research I continue to apply STXM to a variety of scientific questions in fields such as paleobotany, organic geochemistry (kerogen evolution), cosmochemistry, and biogeochemistry.  See research projects for details or call/email me.


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