The crystal structure of dizinc trimolybdenum(IV) octaoxide, Zn2Mo3O8, has been redetermined from single-crystal X-ray data. The structure has been reported previously based on neutron powder diffraction data [Hibble et al. (1999 ▶). Acta Cryst. B55, 683-697] and single-crystal data [McCarroll et al. (1957 ▶). J. Am. Chem. Soc.
79, 5410–5414; Ansell & Katz (1966 ▶) Acta Cryst.
21, 482–485]. The results of the current redetermination show an improvement in the precision of the structural and geometric parameters with all atoms refined with anisotropic displacement parameters. The crystal structure consists of distorted hexagonal-close-packed oxygen layers with stacking sequence abac along  and is held together by alternating zinc and molybdenum layers. The Zn atoms occupy both tetrahedral and octahedral interstices with a ratio of 1:1. The Mo atoms occupy octahedral sites and form strongly bonded triangular clusters involving three MoO6 octahedra that are each shared along two edges, forming a Mo3O13 unit. All atoms lie on special positions. The Zn atoms are in 2b Wyckoff positions with 3m. site symmetry, the Mo atoms are in 6c Wyckoff positions with . m. site symmetry and the O atoms are in 2a, 2b and 6c Wyckoff positions with 3m. and . m. site symmetries, respectively.
The crystal structure of the title compound, 4-hydroxy-2-pyridone, C5H5NO2, which has been the subject of several determinations using X-rays and neutron diffraction, was first reported by Low & Wilson [Acta Cryst. (1983). C39, 1688–1690]. It has been redetermined, providing a significant increase in the precision of the derived geometric parameters. The asymmetric unit comprises a planar 4-enol tautomer having some degree of delocalization of π-electron density through the molecule. In the crystal structure, the molecules are connected into chains by two strong O—H⋯O and N—H⋯O hydrogen bonds between the OH and NH groups and the carbonyl O atom.
Single crystals of silver(I) polyphosphate(V), AgPO3, were prepared via a phosphoric acid melt method using a solution of Ag3PO4 in H3PO4. In comparison with the previous study based on single-crystal Weissenberg photographs [Jost (1961 ▶). Acta Cryst. 14, 779–784], the results were mainly confirmed, but with much higher precision and with all displacement parameters refined anisotropically. The structure is built up from two types of distorted edge- and corner-sharing [AgO5] polyhedra, giving rise to multidirectional ribbons, and from two types of PO4 tetrahedra linked into meandering chains (PO3)n spreading parallel to the b axis with a repeat unit of four tetrahedra. The calculated bond-valence sum value of one of the two AgI ions indicates a significant strain of the structure.
Goethite is a common and reactive mineral in the environment. The transport of contaminants and anaerobic respiration of microbes are significantly affected by adsorption and reduction reactions involving goethite. An understanding of the mineral-water interface of goethite is critical for determining the molecular-scale mechanisms of adsorption and reduction reactions. In this study, periodic density functional theory (DFT) calculations were performed on the mineral goethite and its (010) surface, using the Vienna Ab Initio Simulation Package (VASP).
Calculations of the bulk mineral structure accurately reproduced the observed crystal structure and vibrational frequencies, suggesting that this computational methodology was suitable for modeling the goethite-water interface. Energy-minimized structures of bare, hydrated (one H2O layer) and solvated (three H2O layers) (010) surfaces were calculated for 1 × 1 and 3 × 3 unit cell slabs. A good correlation between the calculated and observed vibrational frequencies was found for the 1 × 1 solvated surface. However, differences between the 1 × 1 and 3 × 3 slab calculations indicated that larger models may be necessary to simulate the relaxation of water at the interface. Comparison of two hydrated surfaces with molecularly and dissociatively adsorbed H2O showed a significantly lower potential energy for the former.
Surface Fe-O and (Fe)O-H bond lengths are reported that may be useful in surface complexation models (SCM) of the goethite (010) surface. These bond lengths were found to change significantly as a function of solvation (i.e., addition of two extra H2O layers above the surface), indicating that this parameter should be carefully considered in future SCM studies of metal oxide-water interfaces.
A. polyphaga mimivirus, the largest known double-stranded DNA virus, is the first virus to exhibit a nucleoside diphosphate kinase gene. The expression and crystallization of the viral NDK are reported.
The complete sequence of the largest known double-stranded DNA virus, Acanthamoeba polyphaga mimivirus, has recently been determined [Raoult et al. (2004 ▶), Science, 306, 1344–1350] and revealed numerous genes not expected to be found in a virus. A comprehensive structural and functional study of these gene products was initiated [Abergel et al. (2005 ▶), Acta Cryst. F61, 212–215] both to better understand their role in the virus physiology and to obtain some clues to the origin of DNA viruses. Here, the preliminary crystallographic analysis of the viral nucleoside diphosphate kinase protein is reported. The crystal belongs to the cubic space group P213, with unit-cell parameter 99.425 Å. The self-rotation function confirms that there are two monomers per asymmetric unit related by a twofold non-crystallographic axis and that the unit cell thus contains four biological entities.
nucleocytoplasmic large DNA virus; NCLDV; nucleoside diphosphate kinase; structural genomics
In this work, we make use of a model chemistry within Density Functional Theory (DFT) recently presented, which is called M05-2X, to calculate the molecular structure of the flavonoid Rutin, as well as to predict the infrared (IR) and ultraviolet (UV-Vis) spectra, the dipole moment and polarizability, the free energy of solvation in different solvents as an indication of solubility, the HOMO and LUMO orbitals, and the chemical reactivity parameters that arise from Conceptual DFT. The calculated values are compared with the available experimental data for this molecule as a means of validation of the used model chemistry.
To understand the role of the conjugate bridge in modifying the properties of organic dye sensitizers in solar cells, the computations of the geometries and electronic structures for 10 kinds of tetrahydroquinoline dyes were performed using density functional theory (DFT), and the electronic absorption and fluorescence properties were investigated via time dependent DFT. The population analysis, molecular orbital energies, radiative lifetimes, exciton binding energies (EBE), and light harvesting efficiencies (LHE), as well as the free energy changes of electron injection (ΔGinject ) and dye regeneration (
ΔGdyeregen ) were also addressed. The correlation of charge populations and experimental open-circuit voltage (Voc) indicates that more charges populated in acceptor groups correspond to larger Voc. The elongating of conjugate bridge by thiophene units generates the larger oscillator strength, higher LHE, larger absolute value of ΔGinject, and longer relative radiative lifetime, but it induces the decreasing of EBE and
ΔGdyeregen. So the extending of conjugate bridge with thiopene units in organic dye is an effective way to increase the harvest of solar light, and it is also favorable for electron injection due to their larger ΔGinject. While the inversely correlated relationship between EBE and LHE implies that the dyes with lower EBE produce more efficient light harvesting.
tetrahydroquinoline dyes; electronic structure; density functional theory; absorption spectra; dye sensitized solar cells
The crystal structure of the title compound [systematic name: 5,6,10-trihydroxy-7-isopropyl-1,1,4a-trimethyl-2,3,4,4a-tetrahydrophenanthren-9(1H)-one], C20H26O4, has been reported previously [Salae et al. (2009 ▶). Acta Cryst. E65, o2379–o2380], but the absolute configuration could not be determined as there was no significant anomalous dispersion using data collected with Mo radiation. The absolute configuration has now been determined by refinement of the Flack parameter with data collected using Cu radiation. The absolute configuration at position 4a of the diterpenoid is (R)-methyl; other features of the molecule and its crystal packing are similar to those previously described.
Presented is an extension of the CHARMM General force field (CGenFF) to enable the modeling of sulfonyl-containing compounds. Model compounds containing chemical moieties such as sulfone, sulfonamide, sulfonate and sulfamate were used as the basis for the parameter optimization. Targeting high-level quantum mechanical and experimental crystal data, the new parameters were optimized in a hierarchical fashion designed to maintain compatibility with the remainder of the CHARMM additive force field. The optimized parameters satisfactorily reproduced equilibrium geometries, vibrational frequencies, interactions with water, gas phase dipole moments and dihedral potential energy scans. Validation involved both crystalline and liquid phase calculations showing the newly developed parameters to satisfactorily reproduce experimental unit cell geometries, crystal intramolecular geometries and pure solvent densities. The force field was subsequently applied to study conformational preference of a sulfonamide based peptide system. Good agreement with experimental IR/NMR data further validated the newly developed CGenFF parameters as a tool to investigate the dynamic behavior of sulfonyl groups in a biological environment. CGenFF now covers sulfonyl group containing moieties allowing for modeling and simulation of sulfonyl-containing compounds in the context of biomolecular systems including compounds of medicinal interest.
empirical force field; molecular mechanics; molecular dynamics; molecular modeling; potential energy function; sulfonamide; β-strand mimetic; peptidomimetic; medicinal chemistry; drug design
The title compound, C10H12FN3S, crystallizes in the same space group (P21/c) as two polymorphic forms of 4-phenyl-1-(propan-2-ylidene)thiosemicarbazone [Jian et al. (2005). Acta Cryst. E61, o653–o654; Venkatraman et al. (2005). Acta Cryst. E61, o3914–o3916]. The arrangement of molecules relative to the twofold screw axes is similar to that in the crystal structure of the lower density polymorph. In the solid state, the molecular conformation is stabilized by an intramolecular N—H⋯N hydrogen bond. The molecules form centrosymmetric R
2(8) dimers in the crystal through pairs of N—H⋯S hydrogen bonds.
The title Schiff base compound, C25H19NO2S, crystallizes in a statistically disordered structure comprising keto and enol tautomeric forms. In the enol form, the benzenoid arrangment is promoted by a strong intramolecular O—H⋯N hydrogen bond and adopts an E conformation about the imine bond. In the keto form there is an intramolecular N—H⋯O hydrogen bond. In the crystal, an extended network of C—H⋯O hydrogen bonds stabilizes columns parallel to the c axis, forming large voids (there are four cavities of 108 Å3 per unit cell) with highly disordered residual electron density. The SQUEEZE procedure in PLATON [Spek (2009 ▶). Acta Cryst. D65, 148–155] was used to eliminate the contribution of this electron density from the intensity data, and the solvent-free model was employed for the final refinement. The contribution of this undetermined solvent was ignored in the calculation of the unit-cell characteristics.
Corrigendum to Acta Cryst. (2009), E65, o301.
Consideration of a previous unrecognized twinning of the original investigated crystal of the title compound [Kia et al. (2009 ▶). Acta Cryst. E65, o301] led to improved reliability factors and to a slightly higher precision for all geometric parameters. The crystal under investigation was twinned by pseudo-merohedry with [100, 00, 00] as the twin matrix and a refined twin domain fraction of 0.9610 (5):0.0390 (5). The results of the new crystal structure refinement are given here.
The redetermined structure of title chalcone derivative, C23H16O2, corrects errors in the title, scheme and synthesis in the previous report of the same structure [Jasinski et al. (2011 ▶). Acta Cryst. E67, o795]. There are two independent molecules in the asymmetric unit with slight differences in bond lengths and angles. The dihedral angle between the benzene ring and the anthracene ring system is 73.30 (4)° in one molecule and 73.18 (4)° in the other. Both molecules feature an intramolecular O—H⋯O hydrogen bond, which generates an S(6) ring. In the crystal, molecules are arranged into sheets lying parallel to the ac plane and further stacked along the b axis by π–π interactions with centroid–centroid distances in the range 3.6421 (6)–3.7607 (6) Å. The crystal structure is further stabilized by C—H⋯π interactions. There are also C⋯O [3.2159 (15) Å] short contacts.
The crystal structure of the 37.2 kDa At3g21360 gene product from A. thaliana was determined at 2.4 Å resolution. The structure establishes that this protein binds a metal ion and is a member of a clavaminate synthase-like superfamily in A. thaliana.
The crystal structure of the gene product of At3g21360 from Arabidopsis thaliana was determined by the single-wavelength anomalous dispersion method and refined to an R factor of 19.3% (R
free = 24.1%) at 2.4 Å resolution. The crystal structure includes two monomers in the asymmetric unit that differ in the conformation of a flexible domain that spans residues 178–230. The crystal structure confirmed that At3g21360 encodes a protein belonging to the clavaminate synthase-like superfamily of iron(II) and 2-oxoglutarate-dependent enzymes. The metal-binding site was defined and is similar to the iron(II) binding sites found in other members of the superfamily.
A correction is made to the article by Kefala & Weiss [(2006), Acta Cryst. F62, 1116–1119].
A correction is made to the Experimental methods section of the article by Kefala & Weiss [(2006), Acta Cryst. F62, 1116–1119].
dihydrodipicolinate synthase; Mycobacterium tuberculosis; Rv2753c
In the title compound, C20H25NO5, the dihydropyridine ring adopts a flattened boat conformation. The methoxyphenyl ring is almost perpendicular to the mean plane of the pyridine ring [dihedral angle = 88.42 (3)°]. The two carbonyl units adopt a synperiplanar conformation with respect to the double bonds in the dihydropyridine ring. In the crystal, molecules are connected by N—H⋯O hydrogen bonds into R
4(24) tetrameric rings. A region of disordered electron density, located at the center of four adjacent molecules, was treated with the SQUEEZE routine in PLATON [Spek (2009 ▶). Acta Cryst. D65, 148–155]. It is probably the result of traces of the solvent of crystallization and was not taken into account during the structure refinement.
The crystal structure of the title compound, C28H18O2, was originally determined by Ehrenberg [(1967 ▶). Acta Cryst. 22, 482–487] using intensity data obtained from Weissenberg photographs. The current determination provides a crystal and molecular structure with a significantly higher precision and presents standard uncertainties on geometric parameters which are not available from the original work. The molecule lies on a crystallographic twofold rotation axis which bisects the C—C bond [1.603 (3) Å] which joins the two anthracen-9(10H)-one units.
The angle τ (backbone N—Cα—C) is the most contested Engh and Huber refinement target parameter. It is shown that this parameter is ‘correct’ as a PDB-wide average, but can be improved by taking into account residue types, secondary structures and many other aspects of our knowledge of the biophysical relations between residue type and protein structure.
The Engh and Huber parameters for bond lengths and bond angles have been used uncontested in macromolecular structure refinement from 1991 until very recently, despite critical discussion of their ubiquitous validity by many authors. An extensive analysis of the backbone angle τ (N—Cα—C) illustrates that the Engh and Huber parameters can indeed be improved and a recent study [Tronrud et al. (2010 ▶), Acta Cryst. D66, 834–842] confirms these ideas. However, the present study of τ shows that improving the Engh and Huber parameters will be considerably more complex than simply making the parameters a function of the backbone ϕ, ψ angles. Many other aspects, such as the cooperativity of hydrogen bonds, the bending of secondary-structure elements and a series of biophysical aspects of the 20 amino-acid types, will also need to be taken into account. Different sets of Engh and Huber parameters will be needed for conceptually different refinement programs.
protein structure; protein geometry; stereochemical parameters; restraints; N—Cα—C bond angle
The crystal structure of the title compound, C9H10O4, was first reported by Swaminathan, Vimala & Lotter [Acta Cryst. (1976), B32, 1897–1900]. It has been re-examined, improving the precision of the derived geometric parameters. The asymmetric unit comprises a non-planar independent molecule, as the methoxy substituents force the carboxy group to be twisted away from the plane of the aromatic ring by 56.12 (9)°. Due to the antiplanar conformation adopted by the OH group, the molecular components do not form the conventional dimeric units, but are associated in the crystal in chains stabilized by linear O—H⋯O hydrogen bonds, involving the OH groups and the carbonyl O atoms, which form C(3) motifs.
The asymmetric unit of the title compound, C8H8O2, contains two crystallographically independent molecules, which form dimers linked by O⋯H—O hydrogen bonds. The benzene rings in the dimers are inclined at a dihedral angle of 7.30 (8)° and both methyl groups display rotational disorder. This redetermination results in a crystal structure with significantly higher precision than the original determination [Ellas & García-Blanco (1963 ▶). Acta Cryst. 16, 434], in which the authors reported only the unit-cell parameters and space group, without any detailed information on the atomic arrangement. In the crystal, dimers are connected by weak C—H⋯O interactions, forming R
2(10) and R
4(18) rings along  and an infinite zigzag chain of dimers along the  direction also occurs.
Crystals of the title compound, C16H12N2O4, were obtained accidentally by the hydrothermal reaction of 5-[(1H-benzo[d]imidazol-1-yl)methyl]isophthalic acid with manganese chloride tetrahydrate in the presence of KOH as alkaline reagent for the deprotonation. A triclinic polymorph of this structure has been reported previously from a similar reaction [Cheng (2011 ▶). Acta Cryst. E67, o3299]. The benzimidazole ring system is almost planar, with a maximum deviation from the mean plane of 0.020 (4) Å. The benzimidazole unit and benzene ring are inclined at a dihedral angle of 68.17 (4)°, reflecting the axial rotation of the flexible benzimidazolyl arm. In the crystal, pairs of O—H⋯O hydrogen bonds link adjacent molecules into inversion dimers. O—H⋯N contacts connect these dimers into zigzag chains along .
The title ferrocene derivative, [Fe(C5H5)(C14H13FNO)], crystallizes in the same space group with similar unit-cell parameters as the derivatives 3-anilino-1-ferrocenylpropan-1-one [Leka et al. (2012 ▶). Acta Cryst. E68, m229] and 1-ferrocenyl-3-(4-methylanilino)propan-1-one [Leka et al. (2012 ▶). Acta Cryst. E68, m230]. The dihedral angle between the best planes of the benzene ring and the substituted cyclopentadienyl ring is 83.4 (1)°. The presence of the electronegative fluoro substituent in the meta position of the aniline group does not alter the crystal packing compared to the other two derivatives. The molecules are connected into centrosymmetric dimers via N—H⋯O hydrogen bonds. In addition, C—H⋯O and C—H⋯N contacts stabilize the crystal packing.
In this work, we studied a copper complex-based dye, which is proposed for potential photovoltaic applications and is named Cu (I) biquinoline dye. Results of electron affinities and ionization potentials have been used for the correlation between different levels of calculation used in this study, which are based on The Density Functional Theory (DFT) and time-dependent (TD) DFT. Further, the maximum absorption wavelengths of our theoretical calculations were compared with the experimental data. It was found that the M06/LANL2DZ + DZVP level of calculation provides the best approximation. This level of calculation was used to find the optimized molecular structure and to predict the main molecular vibrations, the molecular orbitals energies, dipole moment, isotropic polarizability and the chemical reactivity parameters that arise from Conceptual DFT.
molecular structure; absorption spectra; polarizability; chemical reactivity; dipole moment; copper complex; dye-sensitized
The structure of the title compound, C19H28O2, has been redermined at 295 (2) K, with much improved precision. The structure and molecular packing of the title compound was first reported by Coiro et al. [Acta Cryst. (1973). B29, 1404–1409] by means of potential-energy calculations. The cell parameters in this study differ considerably in space group C2. It is a derivative of testosterone and consists of a cyclopentanone ring (A) fused to to successive cyclohexane (B and C) and cyclohexanone (D) rings. The three cyclohexanone rings are in slightly distorted boat configurations and the cyclopentanone ring is a distorted half-chair. The crystal packing is stabilized by weak intermolecular C—H⋯O interactions involving O atoms from each of the cyclohexanone and cyclopentanone rings and H atoms from each of their respective rings.
The crystal structure of the title compound, [Sn(C5H10NS2)4], was originally determined by Harreld & Schlemper [Acta Cryst. (1971), B27, 1964–1969] using intensity data estimated from Weissenberg films. In comparison with the previous refinement, the current redetermination reveals anisotropic displacement parameters for all non-H atoms, localization of the H atoms, and higher precision of lattice parameters and interatomic distances. The complex features a distorted S6 octahedral coordination geometry for tin and a cis disposition of the monodentate dithiocarbamate ligands.