Research at ABEX

What is ABEX?
ABEX is a OBER DOE funded program which aims to provide a better understanding of chemical reactions that play key roles in biological and environmental chemistry. Specifically it is providing a new user resource to use novel x-ray spectroscopies, such as soft x-ray absorption and x-ray magnetic circular dichroism, to study metal centers in biological and bioenvironmental systems. These exploit the availability of high brightness, circularly polarized soft x-rays at the Advanced Light Source (ALS) beamline 4.0.2.

Why use Soft X-rays?
The Soft X-ray region (50 - 2000 eV) contains the first transition metal L-edges which are dominated by allowed 2p -> 3d transitions, as well as the light element (Boron to Fluorine) K-edge with 1s -> 2p transitions. All these transitions are allowed and involve valence orbitals, and the resulting spectra are intense and comprise a direct probe of bonding of the element under study. Analysis yields information such as ligand field structure, spin-state, oxidation state and so forth.

Soft X-rays thus offer unique advantages in analyzing the detailed electronic and magnetic structure of biological metal sites, often providing information that is difficult or impossible to obtain through other techniques.

What Research does ABEX do?
ABEX has an active research program which addresses fundamental biological questions, such as:

• how can you break nature’s strongest chemical bond (the N-N triple bond) at room temperature and atmospheric pressure?
• how does nature catalyze rapid formation of the simplest molecule (H2) with Fe instead of expensive Pt?
• how do microorganisms produce and consume greenhouse gases or toxins such as CH4 and CO?

as well as difficult environmental issues, such as:

• what are the chemical forms of U and mechanisms involved in the conversion of a water-soluble U(VI) form to an insoluble U(IV) species during bioremediation?
• how do oxidized Mn minerals interact with Cr and other metals in aquifers?
• how are As and Se metabolized in living organisms, and how do they interact to become poisons or antidotes under different circumstances?

What are the Technical Problems?
Soft X-rays are readily absorbed, even by air, and they only penetrate a few micron depth of a sample. Hence there is a need to work in high vacuum, using frozen concentrated samples.

Much of ABEXs development program is designed to minimize these limitations with highly sensitive, state of the art detectors, novel chambers and sample cells.

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Current User Research and Collaborations

Nickel and Iron L-edge XAS and XMCD of NiFe CO dehydrogenase:
James Ferry
Pennsylvania State University

Nickel L-Edge X-Ray Absorption & XMCD of [NiFe] Hydrogenases – What is the True Spin State of Nickel?
Hideaki Ogata and Wolfgang Lubitz
Max Planck Institute for Bioinorganic Chemistry, Germany

Nitrogen K-edge XAS of functional nitrogenase mimics
Jonas Peters
California Institute of Technology

Direct demonstration of a tyrosyl radical in intermediate state PM of ubiquinol oxidase by XMCD: relevance for the catalytic cycle of cytochrome c oxidase.
Edward Solomon and Matthew Kieber-Emmons
Stanford University

Nickel L-edge XAS Acetyl CoA Synthase
Stephen W. Ragsdale
University of Michigan Ann Arbor

Novel detector materials for detector development
Stephan Friedrich
Lawrence Livermore National Laboratory

X-ray Magnetic Circular Dichroism of Gadolinium In Nephrogenic Systemic Fibrosis
Simon J. George
University of California, Davis