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Crystallographic Symmetry (crystallographic + symmetry)
Selected AbstractsThree-dimensional thermoelastic stresses in off-axis oriented single crystals with hexagonal symmetryCRYSTAL RESEARCH AND TECHNOLOGY, Issue 3 2007K. Böttcher Abstract A three-dimensional (3D) thermoelastic stress analysis is carried out on a single crystal with axisymmetric geometry but with a hexagonal crystallographic symmetry. The crystallographic orientation is off-axis with respect to the cylindrical coordinate system. By applying a Fourier series expansion with respect to the rotational angle , of the cylindrical coordinates, the 3D boundary value problem is reduced to a sequence of 2D ones on the meridian plane, which are solved by the finite-element method. In our example, the off-axis orientation is towards a direction of high symmetry, and therefore only four of the six stress tensor components are non-zero. In the end, the stress tensor is projected onto the slip system of the crystal. (© 2007 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Synthesis, Characterization, and Electrochemical Properties of Dinuclear Complexes Assembled from Asymmetric CoIII Bis(dioximates) and Boronic AcidsEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 19 2005Renata Dreos Abstract Bis(methylphenylglyoximate)cobalt(III) complexes exist both as cis and trans isomers due to the asymmetry of the equatorial ligand, and, when the axial ligands are different, the trans isomer is chiral. The reaction of racemic trans -[CH3Co(mpgH)2py] (1) with either 3- or 4-pyridylboronic acid affords dimeric units arranged on a crystallographic symmetry center such that the pyridyl nitrogen of one moiety coordinates to the Co atom of the symmetry-related unit. In principle, three structurally different dimeric species (two homodimers and one heterodimer) can be obtained. Time-resolved 1H NMR spectra of a 1:1 mixture of racemic 1 and either 3- or 4-pyridylboronic acid in CDCl3/CD3OD show that the reaction does not converge toward a unique species in solution. Nevertheless, X-ray structures show that the heterochiral dimers are the only products that crystallize from the reaction mixture. The nature of the dioximate side groups does not affect the geometry of the dimeric arrangements assembled by 4-pyridylboronic acid ("molecular box"). On the contrary, the geometry of the species assembled by 3-pyridylboronic acid varies from the "molecular parallelogram" obtained from the bis(dimethylglyoximates) to the highly squeezed "molecular box" obtained from bis(methylphenylglyoximates). Cyclic voltammetry studies show that the metal centers in the dimeric species do not interact with each other and undergo a simultaneous redox process. However, depending on the geometry of the systems, the redox process involves a single four-electron reduction for 3 and 5 or two consecutive two-electron reduction steps for 4 and 6. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005) [source] Practical modeling of molecular systems with symmetriesJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 9 2010Sergei Grudinin Abstract A new method for efficient modeling of macromolecular systems with symmetries is presented. The method is based on a hierarchical representation of the molecular system and a novel fast binary tree-based neighbor list construction algorithm. The method supports all types of molecular symmetry, including crystallographic symmetry. Testing the proposed neighbor list construction algorithm on a number of different macromolecular systems containing up to about 200,000 of atoms shows that (1) the current binary tree-based neighbor list construction algorithm scales linearly in the number of atoms for the central subunit, and sublinearly for its replicas, (2) the overall computational overhead of the method for a system with symmetry with respect to the same system without symmetry scales linearly with the cutoff value and does not exceed 50% for all but one tested macromolecules at the cutoff distance of 12 Å. (3) the method may help produce optimized molecular structures that are much closer to experimentally determined structures when compared with the optimization without symmetry, (4) the method can be applied to models of macromolecules with still unknown detailed structure. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] Linear and nonlinear magneto-optical response of ultrathin Co/Au/Mo and Co/Mo films grown on sapphire substratesPHYSICA STATUS SOLIDI (A) APPLICATIONS AND MATERIALS SCIENCE, Issue 8 2008A. Stupakiewicz Abstract We report studies of the linear and nonlinear magneto-optical properties of epitaxial ultrathin Co films grown on sapphire substrates covered with Mo or Mo/Au buffers. Changes of the crystallographic symmetry and magnetization of buried interfaces were deduced from the magneto-optical Kerr effect hysteresis loops and magnetization-induced second-harmonic generation (MSHG). Depending on the buffer, two-fold (for Mo buffer) or six-fold (for Mo/Au buffer) symmetries were observed in both inplane magnetic anisotropy and MSHG intensity. (© 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Upgrading the twin variables algorithm for large structuresACTA CRYSTALLOGRAPHICA SECTION A, Issue 2 2000K. Bethanis Phase extension from lower to higher resolution by using an upgraded TWIN variables algorithm [Hountas & Tsoucaris (1995). Acta Cryst. A51, 754,763] in protein molecules with close to 1000 non-H atoms is presented. Three points of this procedure are of particular interest. (i) The use of a set of auxiliary variables providing a satisfactory fit for many kinds of constraints: the new algorithm works efficiently despite the extreme `dilution' of very limited initial phase information into a much larger set of auxiliary variables. (ii) The extension of this auxiliary variables set beyond the resolution of the observed data, which enhances the phase extension in a so-called `super-resolution' sphere. (iii) The use of the crystallographic symmetry as a new figure of merit and as a reliable test for the correctness of the phase-extension process allows an efficient screening. [source] Spatial arrangement of molecules in homomolecular Z' = 2 structuresACTA CRYSTALLOGRAPHICA SECTION B, Issue 2 2006Elna Pidcock The Box Model of crystal packing describes unit cells in terms of a limited number of arrangements of molecular building blocks. An analysis of Z,, 1 structures has shown that cell dimensions are related to molecular dimensions in a systematic way and that the spatial arrangement of molecules in crystal structures is very similar, irrespective of Z or space group. In this paper it is shown that the spatial arrangement of molecules in Z, = 2 structures are, within the context of the Box Model, very similar to that found for Z,, 1 structures. The absence of crystallographic symmetry does not appear to affect correlations between molecular dimensions and cell dimensions, or between the packing patterns and the positions of molecules in the unit cell, established from the analysis of Z,, 1 structures. The preference shown by Z, = 2 structures for low surface-area packing patterns and the observation that strong energetic interactions are most often found between the large faces of the independent molecules reaffirms the importance of molecular shape in crystal packing. [source] Automated assignment of graph-set descriptors for crystallographically symmetric moleculesACTA CRYSTALLOGRAPHICA SECTION B, Issue 3 2000W. D. Samuel Motherwell Algorithms for the automatic assignment of graph-set notation for intermolecular networks have been extended to molecules having internal crystallographic symmetry, for patterns up to the second level. This provides a means of achieving systematic and consistent assignments for networks containing symmetric molecules. These methodologies have been implemented in the program RPLUTO. Examples are given of the application of the method to a number of molecules with hydrogen-bonded and other intermolecular networks, illustrating the diversity of the patterns that occur. [source] Strong asymmetric hydrogen bonding in 2-(oxamoylamino)ethylammonium oxamate,oxamic acid (1/1)ACTA CRYSTALLOGRAPHICA SECTION C, Issue 3 2010Marta Martinez Belmonte The title compound, C4H10N3O2+·C2H2NO3,·C2H3NO3, contains at least 11 distinct hydrogen-bond interactions showing a great variety of bond strengths. The shortest and strongest hydrogen bond [O...O = 2.5004,(12),Å] is found between the uncharged oxamic acid molecule and the oxamate monoanion. The grouping formed by such a strong hydrogen bond can thus be considered as a hydrogen bis(oxamate) monoanion. It lacks crystallographic symmetry and the two oxamate groups have different conformations, showing an asymmetric hydrogen-bond interaction. Significantly, the asymmetry allows us to draw a direct comparison of site basicity for the two inequivalent carboxylate O atoms in the planar oxamate anion. The constituent molecular ions of (I) form ribbons, where all amide and carboxylate groups are coplanar. Graph-set analysis of the hydrogen-bonded networks reveals the R22(10) and R22(9) homodromic nets as important structure-directing motifs, which appear to be a common feature of many oxamate-containing compounds. [source] Rock salt,urea,water (1/1/1) at 293 and 117,KACTA CRYSTALLOGRAPHICA SECTION C, Issue 8 2008S. Müller The crystal structure of NaCl·CH4N2O·H2O has been determined at 117,K and redetermined at room temperature. It can be described as consisting of alternating `organic' and `inorganic' planar layers. While at room temperature the structure belongs to the space group I2, the low-temperature structure belongs to the space group Pn21m. All water O atoms are located on positions with crystallographic symmetry 2 (m) in the room-temperature (low-temperature) structure, which means that the water molecules belong, in both cases, to point group mm2. During the phase transition, half of the urea molecules per unit cell perform a 90° rotation about their respective C,O axes. The other half and the inorganic parts of the structure remain unaltered. The relationship between the two phases is remarkable, inasmuch as no obvious reason for the transition to occur could be found; the internal structures of all components of the two phases remain unaltered and even the interactions between the different parts seem to be the same before and after the transition (at least when looked at from an energetic point of view). [source] Three substituted (Z)-5-benzylidene-2-thioxothiazolidin-4-ones: hydrogen-bonded dimers that can be effectively isolated or linked into chains either by aromatic ,,, stacking interactions or by dipolar carbonyl,carbonyl interactionsACTA CRYSTALLOGRAPHICA SECTION C, Issue 7 2006Paula Delgado In each of the isomeric compounds (Z)-5-(2-fluorobenzylidene)-2-thioxothiazolidin-4-one, C10H6FNOS2, (I), and (Z)-5-(4-fluorobenzylidene)-2-thioxothiazolidin-4-one, C10H6FNOS2, (II), there is a very wide C,C,C angle (ca 130°) at the methine C atom linking the two rings. In each isomer, paired N,H,O hydrogen bonds link the molecules into centrosymmetric R22(8) dimers; the hydrogen-bonded dimers are linked into chains by an aromatic ,,, stacking interaction in isomer (I) and by an antiparallel dipolar carbonyl,carbonyl interaction in isomer (II). (Z)-5-(3,4,5-Trimethoxybenzylidene)-2-thioxothiazolidin-4-one, C13H13NO4S2, (III), which crystallizes with Z, = 2 in the space group P, shows the same very wide angle at the bridging methine C atom; the two independent molecules are linked into an isolated dimer having no crystallographic symmetry. [source] ,-Rubidium antimonide, Rb4Sb4ACTA CRYSTALLOGRAPHICA SECTION C, Issue 5 2001Christian Hirschle ,-RbSb crystallizes with the LiAs structure type. As in the , phase (NaP type), Sb, forms approximate 41 helical chains (21 crystallographic symmetry), with Sb,Sb distances of 2.838,(1) and 2.862,(1),Å. In contrast to the , phase, the helices have different chirality. [source] Detection and correction of underassigned rotational symmetry prior to structure depositionACTA CRYSTALLOGRAPHICA SECTION D, Issue 5 2010Billy K. Poon Up to 2% of X-ray structures in the Protein Data Bank (PDB) potentially fit into a higher symmetry space group. Redundant protein chains in these structures can be made compatible with exact crystallographic symmetry with minimal atomic movements that are smaller than the expected range of coordinate uncertainty. The incidence of problem cases is somewhat difficult to define precisely, as there is no clear line between underassigned symmetry, in which the subunit differences are unsupported by the data, and pseudosymmetry, in which the subunit differences rest on small but significant intensity differences in the diffraction pattern. To help catch symmetry-assignment problems in the future, it is useful to add a validation step that operates on the refined coordinates just prior to structure deposition. If redundant symmetry-related chains can be removed at this stage, the resulting model (in a higher symmetry space group) can readily serve as an isomorphous replacement starting point for re-refinement using re-indexed and re-integrated raw data. These ideas are implemented in new software tools available at http://cci.lbl.gov/labelit. [source] Type II dehydroquinase: molecular replacement with many copiesACTA CRYSTALLOGRAPHICA SECTION D, Issue 1 2008Kirsty Anne Stewart Type II dehydroquinase is a small (150-amino-acid) protein which in solution packs together to form a dodecamer with 23 cubic symmetry. In crystals of this protein the symmetry of the biological unit can be coincident with the crystallographic symmetry, giving rise to cubic crystal forms with a single monomer in the asymmetric unit. In crystals where this is not the case, multiple copies of the monomer are present, giving rise to significant and often confusing noncrystallographic symmetry in low-symmetry crystal systems. These different crystal forms pose a variety of challenges for solution by molecular replacement. Three examples of structure solutions, including a highly unusual triclinic crystal form with 16 dodecamers (192 monomers) in the unit cell, are described. Four commonly used molecular-replacement packages are assessed against two of these examples, one of high symmetry and the other of low symmetry; this study highlights how program performance can vary significantly depending on the given problem. In addition, the final refined structure of the 16-dodecamer triclinic crystal form is analysed and shown not to be a superlattice structure, but rather an F -centred cubic crystal with frustrated crystallographic symmetry. [source] Structure of Escherichia coli uridine phosphorylase at 2.0,ÅACTA CRYSTALLOGRAPHICA SECTION D, Issue 1 2003F. Temple Burling The 2.0,Å crystal structure has been determined for Escherichia coli uridine phosphorylase (UP), an essential enzyme in nucleotide biosynthesis that catalyzes the phosphorolytic cleavage of the C,N glycosidic bond of uridine to ribose-1-phosphate and uracil. The structure determination of two independent monomers in the asymmetric unit revealed the residue composition and atomic details of the apo configurations of each active site. The native hexameric UP enzyme was revealed by applying threefold crystallographic symmetry to the contents of the asymmetric unit. The 2.0,Å model reveals a closer structural relationship to other nucleotide phosphorylase enzymes than was previously appreciated. [source] Crystallization and preliminary crystallographic studies of a new crystal form of Escherichia colil -asparaginase II (Ser58Ala mutant)ACTA CRYSTALLOGRAPHICA SECTION D, Issue 4 2000Maciej Kozak Periplasmic Escherichia colil -asparaginase II with an Ser58Ala mutation in the active-site cavity has been crystallized in a new orthorhombic form (space group P21212). Crystals of this polymorph suitable for X-ray diffraction have been obtained by vapour diffusion using two sets of conditions: (i) 1% agarose gel using MPD as precipitant (pH 4.8) and (ii) liquid droplets using PEG-MME 550 (pH 9.0). The crystals grown in agarose gel are characterized by unit-cell parameters a = 226.9, b = 128.4, c = 61.9,Å and diffract to 2.3,Å resolution. The asymmetric unit contains six protein molecules arranged into one pseudo-222-symmetric homotetramer and an active-site competent dimer from which another homotetramer is generated by crystallographic symmetry. [source] A New Hydroxo-bridged Chromium(III) Dimer [Cr(saltn)OH]2·4H2O: Synthesis, Crystal Structure and Magnetic PropertiesCHINESE JOURNAL OF CHEMISTRY, Issue 6 2005Ni Zhong-Hai Abstract A new hydroxo-bridged dimeric Cr(III) complex [Cr(saltn)OH]2·4H2O [H2saltn=N,N,-bis(salicylidene)trimethylenediamine] has been synthesized and its structural and magnetic properties have been investigated. The complex crystallizes in the triclinic space group P -1 with one dimeric formula unit in a cell of dimensions a=0.95828(19) nm, b=0.95926(19) nm, c=1.0437(2) nm, ,=86.77(3)°, ,=82.48(3)°, and ,=64.93(3)°. The geometry around each chromium(III) center is six-coordinate, distorted-octahedral. The bridging Cr2O2 unit is strictly planar, as required by the crystallographic symmetry. The CrOCr, bridging angle is 99.94(16)°, and the distance between Cr,Cr, is 0.3019 nm. The magnetic susceptibility of the complex has been examined in the range of 2-300 K. By using the spin-spin coupled model for an S1=S2=3/2 dimeric system , the magnetic data were fitted to give the parameters of g=2.01(1), J=-0.85(2) cm -1, and zJ' =0.18(3)cm -1, indicating the presence of a weak antiferromagnetic spin-exchange interaction between the Cr(III) ions in the binuclear complex. [source] | |||||||||||||