Frode Mo

Existence of two crystal structures of the complex α-D-glucose . NaCl . H2O (2 :1:1) verified by three-beam diffraction experiments

Triplet phases from three-beam interference measurements have been used to resolve a case of apparent structural ambiguity. 13 crystals, all cut from one large single crystal of the complex α-d-glucose · NaCl · H2O (2:1:1) were subjected to physical measurements of triplet phases, which involved studies of a set of model-sensitive triplets being particularly sensitive to the differences in structure between the two models. From 8 to 43 triplets were examined for each crystal specimen. The estimated phases have been compared with the corresponding quantities calculated for the refined structure models. A statistical analysis of the results provides highly significant evidence that both structure models are present, but do not coexist in the same crystal. One possible explanation for this apparent anomaly is that a phase transition may be induced by the mechanical stress applied during cutting of the hard and nearly perfect crystals. Triplet phases for structure verification and discrimination between similar structure models, as demonstrated in the present work, appears to be a novel and potentially powerful application of three-beam interference measurements.

X-Ray induced radiation damage in taurine: a combined X-ray diffraction and Raman study

The impact of X-radiation on crystalline taurine has been investigated by time resolved synchrotron X-ray powder and single crystal diffraction and Raman spectroscopy. Multiple data sets have been collected at 120 and 296 K. All the observed effects of radiation, i.e. broadening and shifts of Raman and diffraction lines, a dose dependent irreversible increase in the atomic displacement parameters (ADPs) as well as in one of the unit-cell axes, and an apparent enhancement of electron density in the SO(3) group can be tentatively attributed to primary radical formation predominantly involving the SO(3) group. In secondary reactions molecular species that are distinct from taurine are created in minute quantities, thereby introducing local departure from crystalline order, i.e. enhanced static disorder and a build-up of local strain. Our study provides evidence for ascribing the linear increase in ADPs as well as the expansion of the c axis to the accumulation of foreign species in the crystal, and not to a thermal effect. Once initiated, this process appears to continue also without radiation, however, then at a much reduced rate.

Physical estimation of triplet phases from two new proteins

Three-beam interference experiments have been performed with crystals of two glycosidases: guinea-fowl hexagonal lysozyme, MW 14.3 kDa, and C. thermocellum endoglucanase CelA, MW 40 kDa. In both cases triplet phases could be estimated. Experimental parameters and details of the procedure are presented along with some examples of the results. The average differences between the estimated phases and those calculated from the crystallographic refinements were 17.9 and 15.9 degrees, respectively. A brief discussion of alternative methods for physical phase acquisition is given, including possible strategies for the measurement and application of experimental phases in macromolecular crystallography.

A sample cell for diffraction studies with control of temperature, relative humidity and applied electric field

Sample cells for applying an electric field on the sample during synchrotron X-ray diffraction experiments have been designed and built, both for small single crystals in an arbitrary orientation and for thin films. For the former type of sample, the cell also includes equipment for control of relative humidity and temperature. Cells of different design have been used successfully with single crystals of two distinct phases of the organic ferroelectric Rochelle salt and in studies of epitaxial thin films of ferroelectric PbTiO3 on a SrTiO3 substrate under weak electric fields.

Three-beam interference measurements with a six-circle κ diffractometer

A procedure for calculating the correct angle setting for a specific three-beam situation on a six-circle κ diffractometer is outlined. It is experimentally shown that interference profiles can be recorded using this approach. Limitations owing to mechanical constraints, with particular emphasis on the ability to measure Friedel-related triplets, are discussed.

Application of Known X-ray Phases in the Crystallographic Study of a Small Protein

Phase information, assumed known from three-beam diffraction experiments, has been used successfully as input to direct methods to re-determine the crystal structure of rubredoxin. With data at 1.54 A resolution, starting sets containing 26 single phases, or alternatively 45 triplet phases, in both cases known with a mean error of +/-22.5 degrees, were sufficient to initiate solution of the structure. Conventional figures of merit were employed in the early stages to reject the majority of the incorrect phase models. The presence of a FeS(4) cluster in the structure was used in the interpretation of the initial maps. Phase sets including 2500 Es with a mean single phase error approximately 70 degrees or a mean triplet phase error approximately 80 degrees, both relative to the model from the crystallographic refinement, could be refined and expanded by Fourier recycling using the SAYTAN formalism. Several parameters have been varied to study their influence on phase expansion and refinement.

Rochelle salt - a structural reinvestigation with improved tools. I. The high-temperature para- electric phase at 308 K

A novel sample cell with control of temperature and relative humidity permitted collection of data of excellent quality, enabling unrestrained refinement of all atomic parameters. One of the K atoms in the structure is disordered; very strong anisotropy in three of the four water O atoms indicates partial static disorder which does not involve the bonded H atoms.

o-Quinonoid heterocycles: synthesis and crystal structure of 2,3-dicyano-5,7-bismethylthieno[3,4-b]pyrazine.

2,3-Dicyano-5,7-bismethylthieno[3,4-b]pyrazine (5), has been obtained as a minor product from reactions of S-nucleophiles with 5,6-di(1-bromoethyl)pyrazine-2,3-dicarbonitrile (3), or from a condensation of 4-hydroxy-2,5-dimethyl-2,3-dihydrothiophen-3-one (4) with diaminomaleonitrile. The molecular structure of compound 5 has been confirmed by X-ray diffraction. A partial separation of charge causes a donor-acceptor type arrangement of the planar molecules in uniform parallel stacks with an interplanar spacing of 3.334(2) A at 100 K.

Physical Estimation of Triplet Phases – Effects of Different Radiation Sources and Modes for Profile Scans

A comparative study has been made of the intensity profiles from three-beam experiments to estimate triplet phases using radiation from a conventional sealed-tube X-ray source and two different synchrotron sources. Synchrotron radiation, with its much smaller angular divergence, narrower spectral bandwidth and higher flux, distinctly improves the experimental conditions for physical phase estimation. Pure psi scans about the primary diffraction vector, such as can be made with a six-circle diffractometer, further improve the conditions compared with combined omega/psi scans with a four-circle instrument, where the rotation in psi is accomplished by combining rotations about the three axes omega, chi and varphi. Interference profiles collected by pure psi scans and unfocused synchrotron radiation have FWHM values reduced by factors in the range 20-35 relative to those obtained with combined omega-2theta/psi scans and radiation from a conventional source. As a consequence of these changes, which also involve greatly increased peak amplitudes, the 0/pi-type asymmetry of the profiles is exposed much more pronounced closer to the three-beam point, enabling unambiguous phase assignment for all triplets that were studied. The superiority of the pure psi scan will be even more important in studies of general phases for which the phase information lies also in the relative heights of the (sharp) interference maxima for a triplet and the Friedel-related triplet.

Structure ofN, N′-diphenyl-N-(2-pyridmyl)urea hemihydrate: A crystallographic and spectroscopic investigation

N,N′-diphenyl-N-(2-pyridinyl)urea hemihydrate (C18H15N3O·1/2H2O) has been studied by crystallographic and NMR-spectroscopic methods. The crystals are monoclinic,I2/a with unit-cell parameters at 86K,a=17.820(1),b=14.857(1),c=11.299(1) Å,β=99.17(1)° andZ=8. The structure was solved by direct methods which involved the use of seventeenmeasured triplet phases in the starting set. This appears to be the first centrosymmetric structure solution being based extensively on physically acquired X-ray phases. Refinement was by full-matrix least-squares involving 3843Fo and yieldedR∼Rw=0.042. The shape of the molecules can be described approximately by two, nearly orthogonal planes, one containing pyridine, the urea group and the NH-bonded phenyl ring, the other containing the second phenyl ring. Both the X-ray and the NMR studies show that there is an intramolecular H-bond between the urea N and the pyridine N atoms. When pH is lowered, this H-bond is weakened, and eventually breaks due to protonation of the pyridine ring. The X-ray study indicates that about 20% of the pyridine rings in the crystal are protonated. The structure details of the rings, in particular the valency angles, have been analyzed in relation to the orientation of the rings relative to the main molecular plane, and the electronic effects of the substituants.