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1.  Interfacial Electron Transfer into Functionalized Crystalline Polyoxotitanate Nanoclusters 
Interfacial electron transfer (IET) between a chromophore and a semi-conductor nanoparticle is one of the key processes in a dye sensitized solar cell. Theoretical simulations of the electron transfer in polyoxotitanate nanoclusters Ti17O24(OPri)20 (Ti17) functionalized with four para-nitrophenyl acetylacetone (NPA-H) adsorbates, of which the atomic structure has been fully established by X-ray diffraction measurements, are presented. Complementary experimental information showing IET has been obtained by EPR spectroscopy. Evolution of the time-dependent photoexcited electron during the initial 5 fs after instantaneous excitation to the NPA LUMO+1 has been evaluated. Evidence for delocalization of the excitation over multiple chromophoresafter excitation to the NPA LUMO+2 state on a 15 fs timescale is also obtained. While chromophores are generally considered electronically isolated with respect to neighboring sensitizers, our calculations show that this is not necessarily the case. The present work is the most comprehensive study to date of a sensitized semiconductor nanoparticle in which the structure of the surface and the mode of molecular adsorption are precisely defined.
doi:10.1021/ja301238t
PMCID: PMC4040533  PMID: 22548416
2.  The LaueUtil toolkit for Laue photocrystallography. II. Spot finding and integration 
Journal of Synchrotron Radiation  2012;19(Pt 4):637-646.
A spot-integration method is described which does not require prior indexing of the reflections. It is based on statistical analysis of the values from each of the pixels on successive frames, followed for each frame by morphological analysis of initial masks to identify appropriate reflection footprints. The results are compared with those of the seed-skewness method which is based on minimizing the skewness of the intensity distribution within a peak’s integration box.
A spot-integration method is described which does not require prior indexing of the reflections. It is based on statistical analysis of the values from each of the pixels on successive frames, followed for each frame by morphological analysis to identify clusters of high value pixels which form an appropriate mask corresponding to a reflection peak. The method does not require prior assumptions such as fitting of a profile or definition of an integration box. The results are compared with those of the seed-skewness method which is based on minimizing the skewness of the intensity distribution within a peak’s integration box. Applications in Laue photocrystallography are presented.
doi:10.1107/S0909049512022637
PMCID: PMC3380659  PMID: 22713901
photocrystallography; X-ray diffraction; X-ray detection; CCD; Laue method; spot integration; background estimate; statistical analysis; image filtering
3.  Ultrafast spin-state photoswitching in a crystal and slower consecutive processes investigated by femtosecond optical spectroscopy and picosecond X-ray diffraction 
We report the spin state photo-switching dynamics in two polymorphs of a spin-crossover molecular complex triggered by a femtosecond laser flash, as determined by combining femtosecond optical pump-probe spectroscopy and picosecond X-ray diffraction techniques,. The light-driven transformations in the two polymorphs are compared. Combining both techniques and tracking how the X-ray data correlate with optical signals allows understanding of how electronic and structural degrees of freedom couple and play their role when the switchable molecules interact in the active crystalline medium. The study sheds light on crossing the border between femtochemistry at the molecular scale and femtoswitching at the material scale
doi:10.1039/c2cp23587k
PMCID: PMC3463002  PMID: 22294040
4.  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
5.  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
6.  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
7.  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
8.  Optimizing the accuracy and precision of the single-pulse Laue technique for synchrotron photo-crystallography 
Journal of Synchrotron Radiation  2010;17(Pt 4):479-485.
The accuracy achieved in single-pulse pump-probe Laue experiments at beamline 14-ID at APS is estimated to be 3–4%.
The accuracy that can be achieved in single-pulse pump-probe Laue experiments is discussed. It is shown that with careful tuning of the experimental conditions a reproducibility of the intensity ratios of equivalent intensities obtained in different measurements of 3–4% can be achieved. The single-pulse experiments maximize the time resolution that can be achieved and, unlike stroboscopic techniques in which the pump-probe cycle is rapidly repeated, minimize the temperature increase due to the laser exposure of the sample.
doi:10.1107/S0909049510019710
PMCID: PMC2891491  PMID: 20567080
single-pulse diffraction; accuracy; Laue method; RATIO method; photo-crystallography
9.  Time-resolved synchrotron diffraction and theoretical studies of very short-lived photo-induced molecular species 
Excited-state geometries determined by time-resolved synchrotron diffraction are summarized with emphasis on their comparison with a series of theoretical results. The relative merits of monochromatic and polychromatic (Laue) techniques are discussed.
Definitive experimental results on the geometry of fleeting species are at the time of writing still limited to monochromatic data collection, but methods for modifications of the polychromatic Laue data to increase their accuracy and their suitability for pump–probe experiments have been implemented and are reviewed. In the monochromatic experiments summarized, excited-state conversion percentages are small when neat crystals are used, but are higher when photoactive species are embedded in an inert framework in supramolecular crystals. With polychromatic techniques and increasing source brightness, smaller samples down to tenths of a micrometre or less can be used, increasing homogeneity of exposure and the fractional population of the excited species. Experiments described include a series of transition metal complexes and a fully organic example involving excimer formation. In the final section, experimental findings are compared with those from theoretical calculations on the isolated species. Qualitative agreement is generally obtained, but the theoretical results are strongly dependent on the details of the calculation, indicating the need for further systematic analysis.
doi:10.1107/S0108767309055342
PMCID: PMC2824528  PMID: 20164641
pump–probe experiments; time-resolved diffraction; excited-state molecular geometries; excimers
10.  Direct Observation of a Photo-Induced Non-Stabilized Nitrile Imine Structure in the Solid State 
Journal of the American Chemical Society  2009;131(50):18036-18037.
We report the direct observation of a bent geometry for a non-stabilized nitrile imine in a metal-coordination crystal. The photoinduced tetrazole ring rupture to release N2 appears to depend on the size of voids around the N3-N4 bond in the crystal lattice. We further observed the selective formation of 1,3-addition product when a reactive nitrile imine was photo-generated in water. Taken together, the bent nitrile imine geometry agrees with the 1,3-dipolar structure, a transient reactive species that mediates the photoinduced 1,3-dipolar cycloaddition in the aqueous medium.
doi:10.1021/ja9094523
PMCID: PMC2797338  PMID: 19928921
11.  Combining crystallographic information and an aspherical-atom data bank in the evaluation of the electrostatic interaction energy in an enzyme–substrate complex: influenza neuraminidase inhibition 
The electrostatic component of the enzyme/inhibitor interaction of a wide range influenza neuraminidases and inhibitors has been analyzed using transferable aspherical-atom densities from a recently compiled databank. Results are subdivided into the contributions of individual active-site residues and different functional groups of the inhibitors, and the effect of the Arg292→Lys mutation is considered.
Although electrostatic interactions contribute only a part of the interaction energies between macromolecules, unlike dispersion forces they are highly directional and therefore dominate the nature of molecular packing in crystals and in biological complexes and contribute significantly to differences in inhibition strength among related enzyme inhibitors. In the reported study, a wide range of complexes of influenza neuraminidases with inhibitor molecules (sialic acid derivatives and others) have been analyzed using charge densities from a transferable aspherical-atom data bank. The strongest interactions of the residues are with the acidic group at the C2 position of the inhibitor (∼−300 kJ mol−1 for —COO− in non-aromatic inhibitors, ∼−120–210 kJ mol−1 for —­COO− in aromatic inhibitors and ∼−450 kJ mol−1 for —­PO3 2−) and with the amino and guanidine groups at C4 (∼−250 kJ mol−1). Other groups contribute less than ∼100 kJ mol−1. Residues Glu119, Asp151, Glu227, Glu276 and Arg371 show the largest variation in electrostatic energies of interaction with different groups of inhibitors, which points to their important role in the inhibitor recognition. The Arg292→Lys mutation reduces the electrostatic interactions of the enzyme with the acidic group at C2 for all inhibitors that have been studied (SIA, DAN, 4AM, ZMR, G20, G28, G39 and BCZ), but enhances the interactions with the glycerol group at C6 for inhibitors that contain it. This is in agreement with the lower level of resistance of the mutated virus to glycerol-containing in­hibitors compared with the more hydrophobic derivatives.
doi:10.1107/S0907444909009433
PMCID: PMC2672818  PMID: 19390154
electrostatic interaction energy; aspherical-atom databank; enzyme–substrate complexes; influenza neuraminidase
12.  Di-μ-nitrosyl-bis­[(η5-penta­methyl­cyclo­penta­dien­yl)ruthenium(0)](Ru—Ru). Corrigendum 
Corrigendum to Acta Cryst. (2007), E63, m2596.
The acknowledgement in the paper by Pearsal, Gembicky, Dominiak, Larsen & Coppens [Acta Cryst. (2007), E63, m2596] is extended and an omitted reference is added.
doi:10.1107/S1600536810011980
PMCID: PMC2979091  PMID: 21578980
13.  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

Results 1-13 (13)