Two new soft X-ray scanning transmission microscopes located at the Advanced Light Source (ALS) have been designed, built and commissioned. Interferometer control implemented in both microscopes allows the precise measurement of the transverse position of the zone plate relative to the sample. Long-term positional stability and compensation for transverse displacement during translations of the zone plate have been achieved. The interferometer also provides low-distortion orthogonal x, y imaging. Two different control systems have been developed: a digital control system using standard VXI components at beamline 7.0, and a custom feedback system based on PC AT boards at beamline 5.3.2. Both microscopes are diffraction limited with the resolution set by the quality of the zone plates. Periodic features with 30 nm half period can be resolved with a zone plate that has a 40 nm outermost zone width. One microscope is operating at an undulator beamline (7.0), while the other is operating at a novel dedicated bending-magnet beamline (5.3.2), which is designed speci®cally to illuminate the microscope. The undulator beamline provides count rates of the order of tens of MHz at highenergy resolution with photon energies of up to about 1000 eV. Although the brightness of a bending-magnet source is about four orders of magnitude smaller than that of an undulator source, photon statistics limited operation with intensities in excess of 3 MHz has been achieved at high energy resolution and high spatial resolution. The design and performance of these microscopes are described.
Oscillator strengths for C 1s, N 1s, and O 1s excitation spectra of gaseous glycine and the dipeptide, glycylglycine, have been derived from inner-shell electron energy-loss spectroscopy recorded under scattering conditions where electric dipole transitions dominate (2.5 keV residual energy, θ ≈ 2°). X-ray absorption spectra of solid glycine, glycyl-glycine, glycyl-glycyl-glycine, and a large protein, fibrinogen, were recorded in a scanning transmission X-ray microscope. The experimental spectra are assigned through interspecies comparisons and by comparison to ab initio computed spectra of various conformations of glycine and glycylglycine. Inner-shell excitation spectral features characteristic of the peptide bond are readily identified by comparison of the spectra of gas-phase glycine and glycyl-glycine. They include a clear broadening and a ∼0.3 eV shift of the C 1s f π* CdO peak and introduction of a new pre-edge feature in the N 1s spectrum. These effects are due to 1s f π* amide transitions introduced with formation of the peptide bond. Similar changes occur in the spectra of the solids. The computational results support the interpretation of the experimental inner-shell spectra and provide insight into electron density distributions in the core excited states. Possible conformational dependence of the inner-shell excitation spectra was explored by computing the spectra of neutral glycine in its four most common conformations, and of glycyl-glycine in planar and two twisted conformations. A strong dependence of the computed C 1s, N 1s, and O 1s spectra of glycylglycine on the conformation about the amide linkage was confirmed by additional ab initio calculations of the conformational dependence of the spectra of formamide.
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