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1.  The development of Laue techniques for single-pulse diffraction of chemical complexes: time-resolved Laue diffraction on a binuclear rhodium metal-organic complex 
A modified Laue technique suitable for time-resolved diffraction is described in which profile-independent integration is used, the RATIO method is applied and multi-crystal data are normalized to a common scale. The method is applied in single-pulse pump–probe studies of a binuclear Rh complex, showing Rh—Rh bond shortening of 0.136 (8) Å on excitation.
A modified Laue method is shown to produce excited-state structures at atomic resolution of a quality competitive with those from monochromatic experiments. The much faster data collection allows the use of only one or a few X-ray pulses per data frame, which minimizes crystal damage caused by laser exposure of the samples and optimizes the attainable time resolution. The method has been applied to crystals of the α-modification of Rh2(μ-PNP)2(PNP)2 (BPh4)2 [PNP = CH3N(P(OCH3)2)2, Ph = phenyl]. The experimental results show a shortening of the Rh—Rh distance in the organometallic complex of 0.136 (8) Å on excitation and are quantitatively supported by quantum-mechanical (QM)/molecular-mechanics (MM) theoretical calculations which take into account the confining effect of the crystal environment, but not by theoretical results on the isolated complex, demonstrating the defining effect of the crystal matrix.
doi:10.1107/S0108767311011883
PMCID: PMC3121236  PMID: 21694470
Laue techniques; single-pulse diffraction; quantum-mechanical/molecular-mechanics calculations; QM/MM calculations; time-resolved X-ray crystallography
2.  Restricted Photochemistry in the Molecular Solid State: Structural changes on Photoexcitation of Cu(I) Phenanthroline metal-to-ligand-charge-transfer (MLCT) complexes by Time-Resolved Diffraction 
The journal of physical chemistry. A  2012;116(13):3359-3365.
The excited state structure of [Cu(1)[(1,10-phenanthroline-N,N’) bis(triphenylphosphine)] cations in their crystalline [BF4] salt has been determined at both 180 and 90K by single-pulse time-resolved synchrotron experiments with the modified polychromatic Laue method. The two independent molecules in the crystal show distortions on MLCT excitation which differ in magnitude and direction, a difference attributed to a pronounced difference in the molecular environment of the two complexes. As the excited states differ, the decay of the emission is bi-exponential with two strongly different lifetimes, the longer lifetime, assigned to the more restricted molecule, becoming more prevalent as the temperature increases. Standard deviations in the current Laue study are very much lower than those achieved in a previous monochromatic study of a Cu(I) 2,9 dimethyl-phenanthroline substituted complex (J. Am. Chem. Soc. 2009, 131, 6566), but the magnitude of the shifts on excitation is similar, indicating that lattice restrictions dominate over the steric effect of the methyl substitution. Above all the study illustrates emphatically that molecules in solids have physical properties different from those of isolated molecules and that their properties depend on the specific molecular environment. This conclusion is relevant for the understanding of the properties of molecular solid state devices which are increasingly used in current technology.
doi:10.1021/jp300313s
PMCID: PMC3545449  PMID: 22385365
3.  Time-resolved Laue diffraction of excited species at atomic resolution: 100 ps single-pulse diffraction of the excited state of the organometallic complex Rh2(μ-PNP)2(PNP)2 ·BPh4 
The polychromatic Laue technique has been applied in 100 ps delay synchrotron pump–probe experiments of the triplet excited state of a Rh(I) dinuclear complex. The observed contraction of the Rh–Rh distance of 0.154 (13) Å is less than predicted by a series of theoretical calculations, a difference attributed to the constraining effect of the crystal lattice.
doi:10.1039/c0cc04997b
PMCID: PMC3129623  PMID: 21210070
4.  Feasibility of one-shot-per-crystal structure determination using Laue diffraction 
Structure determination was successfully carried out using single Laue exposures from a group of lysozyme crystals. The Laue method may be a viable option for collection of one-shot-per-crystal data from microcrystals.
Crystal size is an important factor in determining the number of diffraction patterns which may be obtained from a protein crystal before severe radiation damage sets in. As crystal dimensions decrease this number is reduced, eventually falling to one, at which point a complete data set must be assembled using data from multiple crystals. When only a single exposure is to be collected from each crystal, the polychromatic Laue technique may be preferable to monochromatic methods owing to its simultaneous recording of a large number of fully recorded reflections per image. To assess the feasibility of solving structures using single Laue images from multiple crystals, data were collected using a ‘pink’ beam at the CHESS D1 station from groups of lysozyme crystals with dimensions of the order of 20–30 µm mounted on MicroMesh grids. Single-shot Laue data were used for structure determination by molecular replacement and correct solutions were obtained even when as few as five crystals were used.
doi:10.1107/S0907444909037731
PMCID: PMC2803125  PMID: 20057043
Laue diffraction; microcrystallography; X-ray optics
5.  High-resolution study of (002, 113, 11−1) four-beam diffraction in Si 
A high-resolution study of (002, 113, 11−1) four-beam diffraction in Si was performed both experimentally and theoretically. Excellent coincidence between theory and experiment was achieved. The forbidden two-beam 002 reflection was excited with the maximum reflectivity of 80%.
The results of a high-resolution study of the (002, 113, ) four-beam diffraction in Si are presented. The incident synchrotron radiation beam was highly monochromated and collimated with a multi-crystal arrangement in a dispersive setup in both vertical and horizontal planes, in an attempt to experimentally approach plane-wave incident conditions. The Renninger scheme was used with the forbidden reflection reciprocal-lattice vector 002 normal to the crystal surface. The azimuthal and polar rotations were performed in the crystal surface plane and the vertical plane correspondingly. The polar angular curves for various azimuthal angles were measured and found to be very close to theoretical computer simulations, with only a small deviation from the plane monochromatic wave. The effect of the strong two-beam 002 diffraction was observed for the first time with the maximum reflectivity close to 80%. The structure factor of the 002 reflection in Si was experimentally determined as zero.
doi:10.1107/S0108767312012305
PMCID: PMC3329769  PMID: 22514065
X-ray multiple diffraction; silicon; high resolution; forbidden reflections
6.  Time-resolved structural studies of protein reaction dynamics: a smorgasbord of X-ray approaches 
Time-resolved structural studies of proteins have undergone several significant developments during the last decade. Recent developments using time-resolved X-ray methods, such as time-resolved Laue diffraction, low-temperature intermediate trapping, time-resolved wide-angle X-ray scattering and time-resolved X-ray absorption spectroscopy, are reviewed.
Proteins undergo conformational changes during their biological function. As such, a high-resolution structure of a protein’s resting conformation provides a starting point for elucidating its reaction mechanism, but provides no direct information concerning the protein’s conformational dynamics. Several X-ray methods have been developed to elucidate those conformational changes that occur during a protein’s reaction, including time-resolved Laue diffraction and intermediate trapping studies on three-dimensional protein crystals, and time-resolved wide-angle X-ray scattering and X-ray absorption studies on proteins in the solution phase. This review emphasizes the scope and limitations of these complementary experimental approaches when seeking to understand protein conformational dynamics. These methods are illustrated using a limited set of examples including myoglobin and haemoglobin in complex with carbon monoxide, the simple light-driven proton pump bacteriorhodopsin, and the superoxide scavenger superoxide reductase. In conclusion, likely future developments of these methods at synchrotron X-ray sources and the potential impact of emerging X-ray free-electron laser facilities are speculated upon.
doi:10.1107/S0108767309054361
PMCID: PMC2824530  PMID: 20164644
time-resolved diffraction; structural biology; protein structural dynamics; Laue diffraction; kinetic crystallography; WAXS; XAS
7.  High-resolution study of (222, 113) three-beam diffraction in Ge 
Good agreement between the high-resolution experimental results for (222, 113) three-beam diffraction in Ge and computer simulations based on the dynamical multiple diffraction theory are presented.
The results of high-resolution analysis of the (222, >113) three-beam diffraction in Ge are presented. For monochromatization and angular collimation of the incident synchrotron beam a multi-crystal arrangement in a dispersive setup in both vertical and horizontal planes was used in an attempt to experimentally approach plane-wave incident conditions. Using this setup, for various azimuthal angles the polar angular curves which are very close to theoretical computer simulations for the plane monochromatic wave were measured. The effect of the strong two-beam 222 diffraction was observed for the first time with the maximum reflectivity close to 60% even though the total reflection of the incident beam into a forbidden reflection was not achieved owing to absorption. The structure factor of the 222 reflection in Ge was experimentally determined.
doi:10.1107/S0108767311015261
PMCID: PMC3121237  PMID: 21694480
dynamical diffraction; multiple diffraction; synchrotron radiation; plane waves; X-ray optics
8.  The LaueUtil toolkit for Laue photocrystallography. I. Rapid orientation matrix determination for intermediate-size-unit-cell Laue data 
Journal of Applied Crystallography  2011;44(Pt 6):1182-1189.
A new method for determination of the orientation matrix of Laue X-ray data is presented. The method is based on matching of the patterns of central reciprocal lattice rows projected on a unit sphere centered on the origin of the reciprocal lattice of the Laue data set with the corresponding pattern of a monochromatic data set on the same material.
A new method for determination of the orientation matrix of Laue X-ray data is presented. The method is based on matching of the experimental patterns of central reciprocal lattice rows projected on a unit sphere centered on the origin of the reciprocal lattice with the corresponding pattern of a monochromatic data set on the same material. This technique is applied to the complete data set and thus eliminates problems often encountered when single frames with a limited number of peaks are to be used for orientation matrix determination. Application of the method to a series of Laue data sets on organometallic crystals is described. The corresponding program is available under a Mozilla Public License-like open-source license.
doi:10.1107/S0021889811038143
PMCID: PMC3246831  PMID: 22199400
LaueUtil; Laue photocrystallography; orientation matrix determination; computer programs
9.  The RATIO method for time-resolved Laue crystallography 
Journal of Synchrotron Radiation  2009;16(Pt 2):226-230.
A RATIO method for analysis of intensity changes in time-resolved pump–probe Laue diffraction experiments is described.
A RATIO method for analysis of intensity changes in time-resolved pump–probe Laue diffraction experiments is described. The method eliminates the need for scaling the data with a wavelength curve representing the spectral distribution of the source and removes the effect of possible anisotropic absorption. It does not require relative scaling of series of frames and removes errors due to all but very short term fluctuations in the synchrotron beam.
doi:10.1107/S0909049508040892
PMCID: PMC2651764  PMID: 19240334
Laue diffraction; time-resolved diffraction; ratio method; data reduction
10.  Achromatic nested Kirkpatrick–Baez mirror optics for hard X-ray nanofocusing 
Journal of Synchrotron Radiation  2011;18(Pt 4):575-579.
A nested Kirkpatrick–Baez mirror pair has been designed, fabricated and tested for achromatic nanofocusing synchrotron hard X-rays. The prototype system achieved a FWHM focal spot of about 150 nm in both horizontal and vertical directions.
The first test of nanoscale-focusing Kirkpatrick–Baez (KB) mirrors in the nested (or Montel) configuration used at a hard X-ray synchrotron beamline is reported. The two mirrors are both 40 mm long and coated with Pt to produce a focal length of 60 mm at 3 mrad incident angle, and collect up to a 120 µm by 120 µm incident X-ray beam with maximum angular acceptance of 2 mrad and a broad bandwidth of energies up to 30 keV. In an initial test a focal spot of about 150 nm in both horizontal and vertical directions was achieved with either polychromatic or monochromatic beam. The nested mirror geometry, with two mirrors mounted side-by-side and perpendicular to each other, is significantly more compact and provides higher demagnification than the traditional sequential KB mirror arrangement. Ultimately, nested mirrors can focus larger divergence to improve the diffraction limit of achromatic optics. A major challenge with the fabrication of the required mirrors is the need for near-perfect mirror surfaces near the edge of at least one of the mirrors. Special polishing procedures and surface profile coating were used to preserve the mirror surface quality at the reflecting edge. Further developments aimed at achieving diffraction-limited focusing below 50 nm are underway.
doi:10.1107/S0909049511010995
PMCID: PMC3267635  PMID: 21685674
hard X-ray nanofocusing; achromatic; nested Kirkpatrick–Baez; Montel
11.  Structural evolution of the chromophore in the primary stages of trans/cis isomerization in photoactive yellow protein 
Journal of the American Chemical Society  2005;127(51):18100-18106.
We have studied the structural changes induced by optical excitation of the chromophore in wild type photoactive yellow protein (PYP) in liquid solution with a combined approach of polarization-sensitive ultrafast infrared spectroscopy and density functional theory calculations. We identify the νC8-C9 marker modes for solution phase PYP in the P and I0 states, from which we derive that the first intermediate state I0, that appears with a 3 ps time constant, can be characterized to have a cis geometry. This is the first unequivocal demonstration that the formation of I0 correlates with the conversion from the trans to the cis state. For the P and I0 states we compare the experimentally measured vibrational band patterns and anisotropies with calculations and find that for both trans and cis configurations the planarity of the chromophore to have a strong influence. The C7=C8-(C9=O)-S moiety of the chromophore in the dark P state has a trans geometry with the C=O group slightly tilted out-of-plane, in accordance with the earlier reported structure obtained in a X-ray diffraction study of PYP crystals. In the case of I0, experiment and theory are only in agreement when the C7=C8-(C9=O)-S moiety has a planar configuration. We find that the carboxylic side group of Glu46, that is hydrogen bonded to the chromophore phenolate oxygen, does not alter its orientation in going from the electronic ground P state, via the electronic excited P* state to the intermediate I0 state, providing conclusive experimental evidence that the primary stages of PYP photoisomerization involve flipping of the enone thioester linkage without significant relocation of the phenolate moiety.
doi:10.1021/ja051210k
PMCID: PMC2580759  PMID: 16366562
12.  Time-resolved structural studies at synchrotrons and X-ray free electron lasers: opportunities and challenges 
X-ray free electron lasers (XFELs) are potentially revolutionary X-ray sources because of their very short pulse duration, extreme peak brilliance and high spatial coherence, features that distinguish them from today’s synchrotron sources. We review recent time-resolved Laue diffraction and time-resolved wide angle X-ray scattering (WAXS) studies at synchrotron sources, and initial static studies at XFELs. XFELs have the potential to transform the field of time-resolved structural biology, yet many challenges arise in devising and adapting hardware, experimental design and data analysis strategies to exploit their unusual properties. Despite these challenges, we are confident that XFEL sources are poised to shed new light on ultrafast protein reaction dynamics.
doi:10.1016/j.sbi.2012.08.006
PMCID: PMC3520507  PMID: 23021004
13.  Spectral CT Imaging of Laryngeal and Hypopharyngeal Squamous Cell Carcinoma: Evaluation of Image Quality and Status of Lymph Nodes 
PLoS ONE  2013;8(12):e83492.
Purpose
The purpose of this study was to evaluate image quality and status of lymph nodes in laryngeal and hypopharyngeal squamous cell carcinoma (SCC) patients using spectral CT imaging.
Materials and Methods
Thirty-eight patients with laryngeal and hypopharyngeal SCCs were scanned with spectral CT mode in venous phase. The conventional 140-kVp polychromatic images and one hundred and one sets of monochromatic images were generated ranging from 40 keV to 140 keV. The mean optimal keV was calculated on the monochromatic images. The image quality of the mean optimal keV monochromatic images and polychromatic images was compared with two different methods including a quantitative analysis method and a qualitative analysis method. The HU curve slope (λHU) in the target lymph nodes and the primary lesion was calculated respectively. The ratio of λHU was studied between metastatic and non-metastatic lymph nodes group.
Results
A total of 38 primary lesions were included. The mean optimal keV was obtained at 55±1.77 keV on the monochromatic images. The image quality evaluated by two different methods including a quantitative analysis method and a qualitative analysis method was obviously increased on monochromatic images than polychromatic images (p<0.05). The ratio of λHU between metastatic and non-metastatic lymph nodes was significantly different in the venous phase images (p<0.05).
Conclusion
The monochromatic images obtained with spectral CT can be used to improve the image quality of laryngeal and hypopharyngeal SCC and the N-staging accuracy. The quantitative ratio of λHU may be helpful for differentiating between metastatic and non-metastatic cervical lymph nodes.
doi:10.1371/journal.pone.0083492
PMCID: PMC3875441  PMID: 24386214
14.  Tyrosine Deprotonation and Associated Hydrogen Bond Rearrangements in a Photosynthetic Reaction Center 
PLoS ONE  2011;6(10):e26808.
Photosynthetic reaction centers from Blastochloris viridis possess Tyr-L162 located mid-way between the special pair chlorophyll (P) and the heme (heme3). While mutation of the tyrosine does not affect the kinetics of electron transfer from heme3 to P, recent time-resolved Laue diffraction studies reported displacement of Tyr-L162 in response to the formation of the photo-oxidized P+•, implying a possible tyrosine deprotonation event. pKa values for Tyr-L162 were calculated using the corresponding crystal structures. Movement of deprotonated Tyr-L162 toward Thr-M185 was observed in P+• formation. It was associated with rearrangement of the H-bond network that proceeds to P via Thr-M185 and His-L168.
doi:10.1371/journal.pone.0026808
PMCID: PMC3200362  PMID: 22039551
15.  Inorganic pyrophosphatase crystals from Thermococcus thioreducens for X-ray and neutron diffraction 
Inorganic pyrophosphatase from T. thioreducans has been crystallized and the crystals were deemed to be suitable for both X-ray and neutron diffraction at room temperature.
Inorganic pyrophosphatase (IPPase) from the archaeon Thermococcus thioreducens was cloned, overexpressed in Escherichia coli, purified and crystallized in restricted geometry, resulting in large crystal volumes exceeding 5 mm3. IPPase is thermally stable and is able to resist denaturation at temperatures above 348 K. Owing to the high temperature tolerance of the enzyme, the protein was amenable to room-temperature manipulation at the level of protein preparation, crystallization and X-ray and neutron diffraction analyses. A complete synchrotron X-ray diffraction data set to 1.85 Å resolution was collected at room temperature from a single crystal of IPPase (monoclinic space group C2, unit-cell parameters a = 106.11, b = 95.46, c = 113.68 Å, α = γ = 90.0, β = 98.12°). As large-volume crystals of IPPase can be obtained, preliminary neutron diffraction tests were undertaken. Consequently, Laue diffraction images were obtained, with reflections observed to 2.1 Å resolution with I/σ(I) greater than 2.5. The preliminary crystallographic results reported here set in place future structure–function and mechanism studies of IPPase.
doi:10.1107/S1744309112032447
PMCID: PMC3509969  PMID: 23192028
inorganic pyrophosphatase; Thermococcus thioreducens; neutron diffraction
16.  Application of Polychromatic µCT for Mineral Density Determination 
Journal of Dental Research  2011;90(1):18-30.
Accurate assessment of mineral density (MD) provides information critical to the understanding of mineralization processes of calcified tissues, including bones and teeth. High-resolution three-dimensional assessment of the MD of teeth has been demonstrated by relatively inaccessible synchrotron radiation microcomputed tomography (SRµCT). While conventional desktop µCT (CµCT) technology is widely available, polychromatic source and cone-shaped beam geometry confound MD assessment. Recently, considerable attention has been given to optimizing quantitative data from CµCT systems with polychromatic x-ray sources. In this review, we focus on the approaches that minimize inaccuracies arising from beam hardening, in particular, beam filtration during the scan, beam-hardening correction during reconstruction, and mineral density calibration. Filtration along with lowest possible source voltage results in a narrow and near-single-peak spectrum, favoring high contrast and minimal beam-hardening artifacts. More effective beam monochromatization approaches are described. We also examine the significance of beam-hardening correction in determining the accuracy of mineral density estimation. In addition, standards for the calibration of reconstructed grey-scale attenuation values against MD, including K2PHO4 liquid phantom, and polymer-hydroxyapatite (HA) and solid hydroxyapatite (HA) phantoms, are discussed.
doi:10.1177/0022034510378429
PMCID: PMC3144098  PMID: 20858779
mineralized tissue/development; dentin; enamel; bone remodeling/regeneration
17.  A comparative study of high resolution cone beam X-ray tomography and synchrotron tomography applied to Fe- and Al-alloys 
Ndt & E International  2010;43(7-3):599-605.
X-ray computed tomography (XCT) has become a very important method for non-destructive 3D-characterization and evaluation of materials. Due to measurement speed and quality, XCT systems with cone beam geometry and matrix detectors have gained general acceptance. Continuous improvements in the quality and performance of X-ray tubes and XCT devices have led to cone beam CT systems that can now achieve spatial resolutions down to 1 μm and even below. However, the polychromatic nature of the source, limited photon flux and cone beam artefacts mean that there are limits to the quality of the CT-data achievable; these limits are particularly pronounced with materials of higher density like metals. Synchrotron radiation offers significant advantages by its monochromatic and parallel beam of high brilliance. These advantages usually cause fewer artefacts, improved contrast and resolution.
Tomography data of a steel sample and of two multi-phase Al-samples (AlSi12Ni1, AlMg5Si7) are recorded by advanced cone beam XCT-systems with a μ-focus (μXCT) and a sub-μm (nano-focus, sub-μXCT) X-ray source with voxel dimensions between 0.4 and 3.5 μm and are compared with synchrotron computed tomography (sXCT) with 0.3 μm/voxel. CT data features like beam hardening and ring artefacts, detection of details, sharpness, contrast, signal-to-noise ratio and the grey value histogram are systematically compared. In all cases μXCT displayed the lowest performance. Sub-μXCT gives excellent results in the detection of details, spatial and contrast resolution, which are comparable to synchrotron-XCT recordings. The signal-to-noise ratio is usually significantly lower for sub-μXCT compared with the two other methods. With regard to measurement costs “for industrial users”, scanning volume, accessibility and user-friendliness sub-μXCT has significant advantages in comparison to synchrotron-XCT.
doi:10.1016/j.ndteint.2010.06.004
PMCID: PMC2947926  PMID: 20976283
X-ray computed tomography; Synchrotron tomography; High resolution tomography; 3D-characterization
18.  Preliminary neutron crystallographic study of human transthyretin 
Human transthyretin, a hormone-binding protein of high abundance in blood and cerebrospinal fluid, is intrinsically amyloidogenic. Preliminary results from a neutron diffraction analysis of this protein that may shed light on the mechanism of tetramer dissociation and successive fatal aggregation are presented.
Preliminary studies of perdeuterated crystals of human transthyretin (TTR) have been carried out using the LADI-III and D19 diffractometers at the Institut Laue–Langevin in Grenoble. The results demonstrate the feasibility of a full crystallographic analysis to a resolution of 2.0 Å using Laue diffraction and also illustrate the potential of using monochromatic instruments such as D19 for higher resolution studies where larger crystals having smaller unit cells are available. This study will yield important information on hydrogen bonding, amino-acid protonation states and hydration in the protein. Such information will be of general interest for an understanding of the factors that stabilize/destabilize TTR and for the design of ligands that may be used to counter TTR amyloid fibrillogenesis.
doi:10.1107/S1744309111036244
PMCID: PMC3212468  PMID: 22102249
transthyretin; TTR; amyloidosis; neutron crystallography; deuteration; perdeuteration
19.  Development of a bent Laue beam-expanding double-crystal monochromator for biomedical X-ray imaging 
Journal of Synchrotron Radiation  2014;21(Pt 3):479-483.
A bent Laue beam-expanding double-crystal monochromator was developed and tested at the Biomedical Imaging and Therapy beamline at the Canadian Light Source. The expander will reduce scanning time for micro-computed tomography and allow dynamic imaging that has not previously been possible at this beamline.
The Biomedical Imaging and Therapy (BMIT) beamline at the Canadian Light Source has produced some excellent biological imaging data. However, the disadvantage of a small vertical beam limits its usability in some applications. Micro-computed tomography (micro-CT) imaging requires multiple scans to produce a full projection, and certain dynamic imaging experiments are not possible. A larger vertical beam is desirable. It was cost-prohibitive to build a longer beamline that would have produced a large vertical beam. Instead, it was proposed to develop a beam expander that would create a beam appearing to originate at a source much farther away. This was accomplished using a bent Laue double-crystal monochromator in a non-dispersive divergent geometry. The design and implementation of this beam expander is presented along with results from the micro-CT and dynamic imaging tests conducted with this beam. Flux (photons per unit area per unit time) has been measured and found to be comparable with the existing flat Bragg double-crystal monochromator in use at BMIT. This increase in overall photon count is due to the enhanced bandwidth of the bent Laue configuration. Whilst the expanded beam quality is suitable for dynamic imaging and micro-CT, further work is required to improve its phase and coherence properties.
doi:10.1107/S1600577514003014
PMCID: PMC3998813  PMID: 24763635
beam expander; bent Laue diffraction; double-crystal monochromator; biomedical imaging; dynamic imaging
20.  Protein crystallography with a micrometre-sized synchrotron-radiation beam 
For the first time, protein microcrystallography has been performed with a focused synchrotron-radiation beam of 1 µm using a goniometer with a sub-micrometre sphere of confusion. The crystal structure of xylanase II has been determined with a flux density of about 3 × 1010 photons s−1 µm−2 at the sample.
For the first time, protein microcrystallography has been performed with a focused synchrotron-radiation beam of 1 µm using a goniometer with a sub-micrometre sphere of confusion. The crystal structure of xylanase II has been determined with a flux density of about 3 × 1010 photons s−1 µm−2 at the sample. Two sets of diffraction images collected from different sized crystals were shown to comprise data of good quality, which allowed a 1.5 Å resolution xylanase II structure to be obtained. The main conclusion of this experiment is that a high-resolution diffraction pattern can be obtained from 20 µm3 crystal volume, corresponding to about 2 × 108 unit cells. Despite the high irradiation dose in this case, it was possible to obtain an excellent high-resolution map and it could be concluded from the individual atomic B-factor patterns that there was no evidence of significant radiation damage. The photoelectron escape from a narrow diffraction channel is a possible reason for reduced radiation damage as indicated by Monte Carlo simulations. These results open many new opportunities in scanning protein microcrystallography and make random data collection from microcrystals a real possibility, therefore enabling structures to be solved from much smaller crystals than previously anticipated as long as the crystallites are well ordered.
doi:10.1107/S090744490705812X
PMCID: PMC2467531  PMID: 18219115
microcrystallography; xylanase II
21.  Night Myopia Studied with an Adaptive Optics Visual Analyzer 
PLoS ONE  2012;7(7):e40239.
Purpose
Eyes with distant objects in focus in daylight are thought to become myopic in dim light. This phenomenon, often called “night myopia” has been studied extensively for several decades. However, despite its general acceptance, its magnitude and causes are still controversial. A series of experiments were performed to understand night myopia in greater detail.
Methods
We used an adaptive optics instrument operating in invisible infrared light to elucidate the actual magnitude of night myopia and its main causes. The experimental setup allowed the manipulation of the eye's aberrations (and particularly spherical aberration) as well as the use of monochromatic and polychromatic stimuli. Eight subjects with normal vision monocularly determined their best focus position subjectively for a Maltese cross stimulus at different levels of luminance, from the baseline condition of 20 cd/m2 to the lowest luminance of 22×10−6 cd/m2. While subjects performed the focusing tasks, their eye's defocus and aberrations were continuously measured with the 1050-nm Hartmann-Shack sensor incorporated in the adaptive optics instrument. The experiment was repeated for a variety of controlled conditions incorporating specific aberrations of the eye and chromatic content of the stimuli.
Results
We found large inter-subject variability and an average of −0.8 D myopic shift for low light conditions. The main cause responsible for night myopia was the accommodation shift occurring at low light levels. Other factors, traditionally suggested to explain night myopia, such as chromatic and spherical aberrations, have a much smaller effect in this mechanism.
Conclusions
An adaptive optics visual analyzer was applied to study the phenomenon of night myopia. We found that the defocus shift occurring in dim light is mainly due to accommodation errors.
doi:10.1371/journal.pone.0040239
PMCID: PMC3388063  PMID: 22768343
22.  Singlet excited-state dynamics of 5-fluorocytosine and cytosine: An experimental and computational study 
The journal of physical chemistry. A  2005;109(20):4431-4436.
The photophysics of singlet excited 5-fluorocytosine (5FC) was studied in steady-state and time-resolved experiments and theoretically by quantum chemical calculations. Femtosecond transient absorption measurements show that replacement of the C5 hydrogen of cytosine by fluorine increases the excited-state lifetime by two orders of magnitude from 720 fs to 73 ± 4 ps. Experimental evidence indicates that emission in both compounds originates from a single tautomeric form. The lifetime of 5FC is the same within experimental uncertainty in the solvents ethanol and dimethylsulfoxide. The insensitivity of the S1 lifetime to the protic nature of the solvent suggests that proton transfer is not the principal quenching mechanism for the excited state. Excited state calculations were carried out for the amino-keto tautomer of 5FC, the dominant species in polar environments, in order to understand its longer excited-state lifetime. CASSCF and CAS-PT2 calculations of the excited states show that the minimum energy path connecting the minimum of the 1π, π* state with the conical intersection responsible for internal conversion has essentially the same energetics for cytosine and 5FC, suggesting that both bases decay nonradiatively by the same mechanism. The dramatic difference in lifetimes may be due to subtle changes along the decay coordinate. A possible reason may be differences in the intramolecular vibrational redistribution rate from the Franck-Condon active, in-plane modes to the out-of-plane modes that must be activated to reach the conical intersection region.
doi:10.1021/jp045614v
PMCID: PMC1660529  PMID: 16833777
23.  The kinetic dose limit in room-temperature time-resolved macromolecular crystallography 
Journal of Synchrotron Radiation  2012;19(Pt 2):264-273.
The effect of the X-ray dose on room-temperature time-resolved Laue data is discussed.
Protein X-ray structures are determined with ionizing radiation that damages the protein at high X-ray doses. As a result, diffraction patterns deteriorate with the increased absorbed dose. Several strategies such as sample freezing or scavenging of X-ray-generated free radicals are currently employed to minimize this damage. However, little is known about how the absorbed X-ray dose affects time-resolved Laue data collected at physiological temperatures where the protein is fully functional in the crystal, and how the kinetic analysis of such data depends on the absorbed dose. Here, direct evidence for the impact of radiation damage on the function of a protein is presented using time-resolved macromolecular crystallography. The effect of radiation damage on the kinetic analysis of time-resolved X-ray data is also explored.
doi:10.1107/S090904951105549X
PMCID: PMC3284346  PMID: 22338689
radiation damage; X-ray dose; room temperature; time-resolved crystallography; Laue crystallography
24.  Performance of single-photon-counting PILATUS detector modules 
Journal of Synchrotron Radiation  2009;16(Pt 3):368-375.
Characterization of PILATUS single-photon-counting X-ray detector modules regarding charge sharing, energy resolution and rate capability is presented. The performance of the detector was tested with surface diffraction experiments at the synchrotron.
PILATUS is a silicon hybrid pixel detector system, operating in single-photon-counting mode, that has been developed at the Paul Scherrer Institut for the needs of macromolecular crystallography at the Swiss Light Source (SLS). A calibrated PILATUS module has been characterized with monochromatic synchrotron radiation. The influence of charge sharing on the count rate and the overall energy resolution of the detector were investigated. The dead-time of the system was determined using the attenuated direct synchrotron beam. A single module detector was also tested in surface diffraction experiments at the SLS, whereby its performance regarding fluorescence suppression and saturation tolerance were evaluated, and have shown to greatly improve the sensitivity, reliability and speed of surface diffraction data acquisition.
doi:10.1107/S0909049509009911
PMCID: PMC2678015  PMID: 19395800
hybrid pixel detector; single photon counting; energy resolution; charge sharing; dead-time; surface X-ray diffraction
25.  Development of a soft X-ray angle-resolved photoemission system applicable to 100 µm crystals 
Journal of Synchrotron Radiation  2011;18(Pt 6):879-884.
A soft X-ray angle-resolved photoemission system applicable to 100 µm crystals has been developed.
A system for angle-resolved photoemission spectroscopy (ARPES) of small single crystals with sizes down to 100 µm has been developed. Soft X-ray synchrotron radiation with a spot size of ∼40 µm × 65 µm at the sample position is used for the excitation. Using this system an ARPES measurement has been performed on a Si crystal of size 120 µm × 100 µm × 80 µm. The crystal was properly oriented on a sample stage by measuring the Laue spots. The crystal was cleaved in situ with a microcleaver at 100 K. The cleaved surface was adjusted to the beam spot using an optical microscope. Consequently, clear band dispersions along the Γ–X direction reflecting the bulk electronic states were observed with a photon energy of 879 eV.
doi:10.1107/S0909049511034418
PMCID: PMC3286358  PMID: 21997912
angle-resolved photoemission spectroscopy (ARPES); soft X-ray; small crystal; microcleaving; micropositioning

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