Structures of endothiapepsin-fragment complexes from crystallographic fragment screening using a novel, diverse and affordable 96-compound fragment library.

Crystallographic screening of the binding of small organic compounds (termed fragments) to proteins is increasingly important for medicinal chemistry-oriented drug discovery. To enable such experiments in a widespread manner, an affordable 96-compound library has been assembled for fragment screening in both academia and industry. The library is selected from already existing protein-ligand structures and is characterized by a broad ligand diversity, including buffer ingredients, carbohydrates, nucleotides, amino acids, peptide-like fragments and various drug-like organic compounds. When applied to the model protease endothiapepsin in a crystallographic screening experiment, a hit rate of nearly 10% was obtained. In comparison to other fragment libraries and considering that no pre-screening was performed, this hit rate is remarkably high. This demonstrates the general suitability of the selected compounds for an initial fragment-screening campaign. The library composition, experimental considerations and time requirements for a complete crystallographic fragment-screening campaign are discussed as well as the nine fully refined obtained endothiapepsin-fragment structures. While most of the fragments bind close to the catalytic centre of endothiapepsin in poses that have been observed previously, two fragments address new sites on the protein surface. ITC measurements show that the fragments bind to endothiapepsin with millimolar affinity.

Proton ordering in (NH4)3H(SO4)2 at low-temperature phase transitions.

Single-crystal neutron diffraction was used to investigate the H-atom disorder in triammonium hydrogen disulfate (TAHS), (NH4)3H(SO4)2, below room temperature. Crystal structure analysis of the monoclinic phase III shows an increase of proton ordering with decreasing temperature in the (SO4)H(SO4) dimer. Moreover, the NH4(+) groups on a general position begin ordering in this phase. The monoclinic unit cell of TAHS-IV doubles in the b direction and a slight distortion of SO4(2-) and NH4(+) tetrahedra is observed. The order parameter introduced by Landau was determined for the second-order II/III and III/IV phase transitions from the intensities of the superstructure reflections. TAHS-V has a triclinic space group and the crystal structure seems to be completely ordered according to a structure analysis by single-crystal X-ray diffraction measurements. In addition, the decisive role of the dynamical disorder of different ammonium groups on successive phase transitions is discussed. Additional peaks were observed by X-ray powder diffraction measurements at ∼ 70 K on cooling, which refers to the V/VII phase transition. These additional peaks remained up to ∼ 85 K on heating. They were described with a doubling of the unit cell along all three principal crystallographic directions.

Disorder of (NH4)3H(SO4)2 in the high-temperature phase I.

The highly disordered crystal structure of triammonium hydrogen disulfate, (NH(4))(3)H(SO(4))(2), in the high-temperature phase I was studied using single-crystal neutron diffraction. It is known that the O atom involved in hydrogen bonding between neighbouring SO(4) tetrahedra is disordered and takes a split-atom position, building a two-dimensional hydrogen-bond network in the (001) plane. The H atoms in these SO(4)-H-SO(4) hydrogen bonds are disordered and hence refined with a split-atom model. Moreover, from the much larger anisotropic mean-square displacements of ammonium protons the NH(4)(+) groups were refined with a reasonable split-atom model, and their motional behaviour was also analysed by rigid-body treatment. Finally, careful consideration was given to show possible supplementary proton migration between the ammonium protons and those of the hydrogen bonds in this high-temperature phase.

Dynamic proton disorder and the II-I structural phase transition in (NH(4))(3)H(SO(4))(2).

X-ray powder diffraction, differential scanning calorimetry (DSC)/thermogravimetry (TG) and single-crystal neutron diffraction methods were used to investigate triammonium hydrogen disulfate (NH(4))(3)H(SO(4))(2) (TAHS) in the temperature range between 293 and 493 K. The temperature-dependent X-ray powder diffraction measurements show a clear hysteresis of the I <-->II phase transition of TAHS with transition temperatures of T(up) = 412.9 (1) K on heating and of T(down) = 402.6 (1) K on cooling. From the existence of hysteresis and from the jump-like changes of the lattice parameters, the I <--> II phase transition of TAHS is considered to be first order. With DSC/TG measurements we confirmed that there is only one phase transition between 293 and 493 K. Through careful investigation on single crystals of TAHS using neutron diffraction, the correct space group (C2/c) of room-temperature TAHS-II phase was confirmed. Crystal structure analysis by single-crystal neutron diffraction showed a strongly elongated displacement ellipsoid of the proton which lies in the middle of the (SO(4))H(SO(4)) dimer with \bar 1 local symmetry. The protons of the NH(4) groups also show strongly enlarged anisotropic mean-square displacements. These findings are interpreted in terms of a characteristic proton disorder in the TAHS-II phase.

The new pentaborate Na3SrB5O10.

Sodium strontium pentaborate, Na(3)SrB(5)O(10), maintains the same, previously unobserved, structure type at 200, 250 and 293 K. The fundamental building units are anionic [B(5)O(10)](5-) groups distorted from mm2 point symmetry. The Sr atoms are eightfold coordinated by O atoms, forming trigonal dodecahedra. The Na atoms appear in three crystallographically different environments. The present single-crystal results correct a previous report in which a monoclinic cell was deduced for this compound on the basis of powder diffraction data. The structure of the title compound is discussed in the crystalochemical context of other borates with the same formula type. Although the unit cell of the present compound is similar to that determined in a previous study of the analogous Ca-containing compound, this study demonstrates that the structures of the two are different. These novel alkali-alkaline earth borates are considered as potential host materials for optical applications (fluorescence materials or phosphors).

Ba3Li2V2O7Cl4, a new vanadate with a channel structure.

The tribarium dilithium divanadate tetrachloride Ba(3)Li(2)V(2)O(7)Cl(4) is a new vanadate with a channel structure and the first known vanadate containing both Ba and Li atoms. The structure contains four non-equivalent Ba(2+) sites (two with m and two with 2/m site symmetry), two Li(+) sites, two nonmagnetic V(5+) sites, five O(2-) sites (three with m site symmetry) and four Cl(-) sites (m site symmetry). One type of Li atom lies in LiO(4) tetrahedra (m site symmetry) and shares corners with VO(4) tetrahedra to form eight-tetrahedron Li(3)V(5)O(24) rings and six-tetrahedron Li(2)V(4)O(18) rings; these rings are linked within porous layers parallel to the ab plane and contain Ba(2+) and Cl(-) ions. The other Li atoms are located on inversion centres and form isolated chains of face-sharing LiCl(6) octahedra.

The diphyllosilicate Rb2(VO)2[Si8O19].

Dirubidium divanadyl phyllooctasilicate, Rb(2)(VO)(2)[Si(8)O(19)], is the first known anhydrous diphyllosilicate containing V(IV). The structure consists of silicate double layers which are separated by [V(2)O(8)](8-) dimers and is related to that of the compounds A(2)Cu(2)[Si(8)O(19)] (A = Rb or Cs), although the title compound crystallizes in a noncentrosymmetric orthorhombic space group. The silicate double layers contain four tetrahedrally coordinated Si sites in general positions and 12 O sites, nine in general positions and the other three on mirror planes. The vanadyl dimers have two square-pyramidally coordinated V sites (site symmetry m). There are two different 10- and 12-fold coordinated Rb sites with site symmetry m, one of which is a split position located between the dimers in the interlayer space, while the other is in a channel within the silicate layer.

Temperature dependence of the AV3O7 (A = Ca, Sr) structure.

The V(4+) (spin (1/2)) oxovanadates AV(3)O(7) (A = Ca, Sr) were synthesized and studied by means of single-crystal X-ray diffraction. The room-temperature structures of both compounds are orthorhombic and their respective space groups are Pnma and Pmmn. The previously assumed structure of SrV(3)O(7) has been revised and the temperature dependence of both crystal structures in the temperature ranges 297-100 K and 315-100 K, respectively, is discussed for the first time.

Synthesis and structural characterization of BaV4O9.

The new spin (1/2) V(4+) barium oxovanadate BaV(4)O(9) was synthesized and studied by means of single-crystal X-ray diffraction. Its room-temperature structure is monoclinic, space group P2/c. We discuss the temperature evolution of the crystal structure and thermal expansion tensor of the material between 293 and 100 K.

Temperature-dependent crystal structure refinement and 57Fe Mössbauer spectroscopy of Cu2Fe2Ge4O13.

The germanate compound Cu2Fe2Ge4O13, dicopper diiron germanate, was synthesized by solid-state reaction at 1403 K and ambient pressure. There is no change of space-group symmetry between 10 and 900 K. Between 40 K and room temperature the a lattice parameter shows a negative thermal expansion which can be connected to a decreasing Cu-Cu interatomic distance. Above room temperature all the lattice parameters are positively correlated with temperature. Among the structural parameters several alterations with temperature occur, which are most prominent for the distorted Fe3+ octahedral site. Besides an increase of the average bond length and of the interatomic Fe-Fe distances, distortional parameters also increase with temperature, while the average Cu-O bond length remains almost constant between 100 and 900 K, as do the average Ge-O distances. 57Fe Mössbauer spectroscopy was used to detect long-range magnetic ordering in Cu2Fe2Ge4O13. While around 100 K, which is the temperature at which a broad maximum is observed in the magnetic susceptibility, no magnetic ordering was detected in the Mössbauer spectrum, below 40 K a narrow split sextet is developed which is indicative of a three-dimensional magnetic ordering of the sample.

Modulated corrugations in the crystal structure of the superconductor CaAlSi.

We report the crystal structure analyses of CaAlSi from single-crystal and powder X-ray diffraction and the existence of two commensurately modulated phases, a sixfold and a fivefold modulated structure. This polymorphism seems to be correlated to the thermal history of the sample. We describe both modulated structures using a three-dimensional and a (3 + 1)-dimensional formalism.

Reinvestigation of the structure of BaCuSi(2)O(6) -- evidence for a phase transition at high temperature.

Superstructure reflections have been observed in the room-temperature X-ray diffraction pattern of BaCuSi(2)O(6), barium copper disilicate. The tetragonal structure has a fourfold unit-cell volume compared with the original structure determined by Finger et al. At T(s) = 610 K BaCuSi(2)O(6) undergoes a structural phase transition upon which the superstructure reflections disappear. The description of the structure in the larger cell removes the crystal-chemical inconsistencies observed for the original structure.