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We propose a method for determining the projected electron density of an individual molecule from diffraction patterns of many such simultaneously illuminated molecules, randomly oriented about an axis parallel to an incident x-ray beam. We illustrate the idea with a simulation of a structure determination of a K-channel membrane protein in situ.
Following structural dynamics in real time is a fundamental goal towards a better understanding of chemical reactions. Recording snapshots of individual molecules with ultrashort exposure times is a key ingredient towards this goal, as atoms move on femtosecond (10 -15 s) timescales. For condensed-phase samples, ultrafast, atomically resolved structure determination has been demonstrated using X-ray and electron diffraction. Pioneering experiments have also started addressing gaseous samples. However, they face the problem of low target densities, low scattering cross sections and random spatial orientation of the molecules. Therefore, obtaining images of entire, isolated molecules capturing all constituents, including hydrogen atoms, remains challenging. Here we demonstrate that intense femtosecond pulses from an X-ray free-electron laser trigger rapid and complete Coulomb explosions of 2-iodopyridine and 2-iodopyrazine molecules. We obtain intriguingly clear momentum images depicting ten or eleven atoms, including all the hydrogens, and thus overcome a so-far impregnable barrier for complete Coulomb explosion imaging—its limitation on molecules consisting of three to five atoms. In combination with state-of-the-art multi-coincidence techniques and elaborate theoretical modelling, this allows tracing ultrafast hydrogen emission and obtaining information on the result of intramolecular electron rearrangement. Our work represents an important step towards imaging femtosecond chemistry via Coulomb explosion.
Systematic synthesis studies of the formation of tetrahedral FeS-ethylenediamine intercalates resulted in the synthesis of a new compound, [Fe 9.4(2) S 10 ][Fe(en) 3 ] 0.6(1) ·en 0.9 ( 3 ). The composition and complex crystal structure were determined based on a synergistic combination of elemental composition, decomposition behavior, high-resolution synchrotron X-ray diffraction and total scattering, 57 Fe Mössbauer spectroscopy, and electron diffraction. The structural model was derived based on a systematic comparison to the previously reported structures [Fe 8 S 10 ][Fe(en) 3 ] 1 ·en 0.5 and tetragonal FeS. The new compound has flat Fe 9.4 S 10 layers, analogous to those in superconducting binary FeS. In the crystal structure of [Fe 9.4 S 10 ][Fe(en) 3 ] 0.6 ·en 0.9 , the interlayer space is occupied by [Fe(en) 3 ] 2+ complexes and neutral ethylenediamine molecules in a ~2:3 ratio. Interlayer species are not randomly oriented but ordered as evidenced by superstructural diffraction peaks in both high-resolution X-ray diffraction and electron diffraction patterns. Magnetic studies reveal no superconducting transition down to 2 K, indicating that the presence of minute amounts (~6%) of iron vacancies at the Fe-S layer in [Fe 9.4 S 10 ][Fe(en) 3 ] 0.6 ·en 0.9 is still sufficient to shift the position of the Fermi level resulting in an adjustment of the properties. Here, our work shows the importance of detailed characterization of the crystal structure of intercalated compounds to understand the origin of the observed properties and develop proper structure–property relationships.
This Final report summarizes progress under this award for the final reporting period 2002 - 2013 in our development of quantitive electron nanodiffraction to materials problems, especially devoted to atomistic processes in semiconductors and electronic oxides such as the new artificial oxide multilayers, where our microdiffraction is complemented with energy-loss spectroscopy (ELNES) and aberration-corrected STEM imaging (9). The method has also been used to map out the chemical bonds in the important GaN semiconductor (1) used for solid state lighting, and to understand the effects of stacking sequence variations and interfaces in digital oxide superlattices (8). Other projects include the development of a laser-beam Zernike phase plate for cryo-electron microscopy (5) (based on the Kapitza-Dirac effect), work on reconstruction of molecular images using the scattering from many identical molecules lying in random orientations (4), a review article on space-group determination for the International Tables on Crystallography (10), the observation of energy-loss spectra with millivolt energy resolution and sub-nanometer spatial resolution from individual point defects in an alkali halide, a review article for the Centenary of X-ray Diffration (17) and the development of a new method of electron-beam lithography (12). We briefly summarize here the work on GaN, on oxide superlattice ELNES, and on lithography by STEM.
The enhancement of the x-ray scattering signal from partially aligned molecular samples is investigated. The alignment properties of the studied molecular system are modeled based on the method of laser alignment. With the advances in the area of laser alignment of molecules, the application of this sample manipulation technique promises a great potential for x-ray scattering measurements. Preferential alignment of molecules in an otherwise amorphous sample leads to constructive interference and thus increases the scattering intensity. This enhances the structural information encoded in the scattering images and enables improved resolution in studies of reaction dynamics, as in this work is shown for the example of the photo-isomerization of stilbene. We demonstrate that the scattering signal is strongly influenced by the alignment axis. Even the most basic one-dimensional alignment offers significant improvement compared to the structural information provided by a randomly oriented sample. Although the signal is sensitive to the uncertainty in the alignment angle, it offers encouraging results even at realistic alignment uncertainties.
Here we present a sub-picosecond resolved investigation of the structural solvent reorganization and geminate recombination dynamics following 400 nm two-photon excitation and photodetachment of a valence p electron from the aqueous atomic solute, I–(aq). The measurements utilized time-resolved X-ray Absorption Near Edge Structure (TR-XANES) spectroscopy and X-ray Solution Scattering (TR-XSS) at the Linac Coherent Light Source x-ray free electron laser in a laser pump/x-ray probe experiment. The XANES measurements around the L 1 -edge of the generated nascent iodine atoms (I 0 ) yield an average electron ejection distance from the iodine parent of 7.4 ± 1.5 Å with an excitation yield of about 1/3 of the 0.1M NaI aqueous solution. The kinetic traces of the XANES measurement are in agreement with a purely diffusion-driven geminate iodine–electron recombination model without the need for a long-lived (I 0 :e–) contact pair. Nonequilibrium classical molecular dynamics simulations indicate a delayed response of the caging H 2 O solvent shell and this is supported by the structural analysis of the XSS data: We identify a two-step process exhibiting a 0.1 ps delayed solvent shell reorganization time within the tight H-bond network and a 0.3 ps time constant for the mean iodine–oxygen distance changes. The results indicate that most of the reorganization can be explained classically by a transition from a hydrophilic cavity with a well-ordered first solvation shell (hydrogens pointing toward I–) to an expanded cavity around I 0 with a more random orientation of the H 2 O molecules in a broadened first solvation shell.
X-ray free-electron lasers have enabled femtosecond protein nanocrystallography, a novel method to determine the structure of proteins. It allows time-resolved imaging of nanocrystals that are too small for conventional crystallography. The short pulse duration helps in overcoming the detrimental effects of radiation damage because x rays are scattered before the sample has been significantly altered. It has been suggested that, fortuitously, the diffraction process self-terminates abruptly once radiation damage destroys the crystalline order. Our calculations show that high-intensity x-ray pulses indeed trigger a cascade of damage processes in ferredoxin crystals, a particular metalloprotein of interest. However, we found that the damage process is initially not completely random. Correlations exist among the protein monomers, so that Bragg diffraction still occurs in the damaged crystals, despite significant atomic displacements. Our results show that the damage process is reproducible to a certain degree, which is potentially beneficial for the orientation step in single-molecule imaging.
It has been suggested that the three-dimensional structure of one particle may be reconstructed using the scattering from many identical, randomly oriented copies ab initio, without modeling or a priori information. This may be possible if these particles are frozen in either space or time, so that the conventional two-dimensional small-angle x-ray scattering (SAXS) distribution contains fluctuations and is no longer isotropic. We consider the magnitude of the correlated fluctuation SAXS (CFSAXS) signal for typical x-ray free-electron laser (XFEL) beam conditions and compare this against the errors derived with the inclusion of Poisson photon counting statistics. The resulting signal-to-noise ratio (SNR) is found to rapidly approach a limit independent of the number of particles contributing to each diffraction pattern, so that the addition of more particles to a ''single-particle-per-shot'' experiment may be of little value, apart from reducing solvent background. When the scattering power is significantly less than one photon per particle per Shannon pixel, the SNR grows in proportion to incident flux. We provide simulations for protein molecules in support of these analytical results, and discuss the effects of solvent background scatter. We consider the SNR dependence on resolution and particle size, and discuss the application of the method to glasses and liquids, and the implications of more powerful XFELs, smaller focused beams, and higher pulse repetition rates for this approach. We find that an accurate CFSAXS measurement may be acquired to subnanometer resolution for protein molecules if a 9-keV beam containing 10{sup 13} photons is focused to a {approx}100-nm spot diameter, provided that the effects of solvent background can be reduced sufficiently.