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Crystallography
Kinds of Crystallography Terms modified by Crystallography Selected AbstractsMacrocyclic Cyclo[n]malonates , Synthetic Aspects and Observation of Columnar Arrangements by X-ray CrystallographyEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 10 2006Nikos Chronakis Abstract A variety of achiral and chiral macrocyclic oligomalonates were synthesised in a one-step procedure through condensation of malonyl dichloride with ,,,-diols. We have investigated the applicability of this method by varying the length and type of the spacers in the diol. Product distribution analysis revealed that the preferential formation of monomeric, dimeric, or trimeric macrocyclic malonates can be controlled by choosing diols with specific spacers connecting the hydroxy groups. Of special interest are the macrocyclic bismalonates, as they show pronounced crystallisability and arrange into columnar motifs in the solid state. They feature distinctive dihedral angles: all ester moieties adopt anti conformations whereas the planes of the carboxy moieties of each malonate residue arrange in an approximately orthogonal fashion. The latter geometry is enforced by the macrocyclic structures, as revealed by a conformational search in the Cambridge Structural Database. The X-ray diffraction data show that C=O···H,C, and C,O···H,C hydrogen bonds stabilise the columnar arrangement of the dimeric rings with formation of tubular assemblies. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006) [source] Solid-State Structure and Tautomerism of 2-Aminotroponimines Studied by X-ray Crystallography and Multinuclear NMR SpectroscopyEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 21 2004Rosa M. Claramunt Abstract Structural studies in the solid state by X-ray crystallography and by 13C and 15N CPMAS NMR spectroscopy carried out on a series of 2-aminotroponimine derivatives 2,5 has allowed to establish the existence of hydrogen bonding and to determine the most stable tautomer. Almost all the structures reflect the classical double-well potential function for the N,H···N hydrogen bonds. Only in the case of the compound N -(pyrrol-1-yl)-2-(pyrrol-1-ylamino)troponimine (5) the crystal structure shows two independent molecules, one with a classical hydrogen bond and another with either a single-well or a low-barrier hydrogen bond. The structure of this compound is discussed with the use of the solid-state NMR spectroscopic data. 2-Aminotropones, as intermediates to the 2-aminotroponimines, show the oxo-tautomer as the stable form. B3LYP/6-31G* calculations are used to rationalise the experimental results. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004) [source] New Editor of Journal of Applied CrystallographyJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 4 2007Gernot Kostorz First page of article [source] Outcomes of the International Union of Crystallography Commission on Powder Diffraction Round Robin on Quantitative Phase Analysis: samples 2, 3, 4, synthetic bauxite, natural granodiorite and pharmaceuticalsJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 4 2002Nicola V. Y. Scarlett The International Union of Crystallography (IUCr) Commission on Powder Diffraction (CPD) has sponsored a round robin on the determination of quantitative phase abundance from diffraction data. The aims of the round robin have been detailed by Madsen et al. [J. Appl. Cryst. (2001), 34, 409,426]. In summary, they were (i) to document the methods and strategies commonly employed in quantitative phases analysis (QPA), especially those involving powder diffraction, (ii) to assess levels of accuracy, precision and lower limits of detection, (iii) to identify specific problem areas and develop practical solutions, (iv) to formulate recommended procedures for QPA using diffraction data, and (v) to create a standard set of samples for future reference. The first paper (Madsen et al., 2001) covered the results of sample 1 (a simple three-phase mixture of corundum, fluorite and zincite). The remaining samples used in the round robin covered a wide range of analytical complexity, and presented a series of different problems to the analysts. These problems included preferred orientation (sample 2), the analysis of amorphous content (sample 3), microabsorption (sample 4), complex synthetic and natural mineral suites, along with pharmaceutical mixtures with and without an amorphous component. This paper forms the second part of the round-robin study and reports the results of samples 2 (corundum, fluorite, zincite, brucite), 3 (corundum, fluorite, zincite, silica flour) and 4 (corundum, magnetite, zircon), synthetic bauxite, natural granodiorite and the synthetic pharmaceutical mixtures (mannitol, nizatidine, valine, sucrose, starch). The outcomes of this second part of the round robin support the findings of the initial study. The presence of increased analytical problems within these samples has only served to exacerbate the difficulties experienced by many operators with the sample 1 suite. The major difficulties are caused by lack of operator expertise, which becomes more apparent with these more complex samples. Some of these samples also introduced the requirement for skill and judgement in sample preparation techniques. This second part of the round robin concluded that the greatest physical obstacle to accurate QPA for X-ray based methods is the presence of absorption contrast between phases (microabsorption), which may prove to be insurmountable in some circumstances. [source] Outcomes of the International Union of Crystallography Commission on Powder Diffraction Round Robin on Quantitative Phase Analysis: samples 1a to 1hJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 4 2001Ian C. Madsen The International Union of Crystallography (IUCr) Commission on Powder Diffraction (CPD) has sponsored a round robin on the determination of quantitative phase abundance from diffraction data. Specifically, the aims of the round robin were (i) to document the methods and strategies commonly employed in quantitative phase analysis (QPA), especially those involving powder diffraction, (ii) to assess levels of accuracy, precision and lower limits of detection, (iii) to identify specific problem areas and develop practical solutions, (iv) to formulate recommended procedures for QPA using diffraction data, and (v) to create a standard set of samples for future reference. Some of the analytical issues which have been addressed include (a) the type of analysis (integrated intensities or full-profile, Rietveld or full-profile, database of observed patterns) and (b) the type of instrument used, including geometry and radiation (X-ray, neutron or synchrotron). While the samples used in the round robin covered a wide range of analytical complexity, this paper reports the results for only the sample 1 mixtures. Sample 1 is a simple three-phase system prepared with eight different compositions covering a wide range of abundance for each phase. The component phases were chosen to minimize sample-related problems, such as the degree of crystallinity, preferred orientation and microabsorption. However, these were still issues that needed to be addressed by the analysts. The results returned indicate a great deal of variation in the ability of the participating laboratories to perform QPA of this simple three-component system. These differences result from such problems as (i) use of unsuitable reference intensity ratios, (ii) errors in whole-pattern refinement software operation and in interpretation of results, (iii) operator errors in the use of the Rietveld method, often arising from a lack of crystallographic understanding, and (iv) application of excessive microabsorption correction. Another major area for concern is the calculation of errors in phase abundance determination, with wide variations in reported values between participants. Few details of methodology used to derive these errors were supplied and many participants provided no measure of error at all. [source] A new format and overall appearance for Journal of Applied CrystallographyJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 1 2000G. Kostorz First page of article [source] Quantum chemical geometry optimizations in proteins using crystallographic raw dataJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 11 2002Ulf Ryde Abstract A method is developed for the combination of quantum chemical geometry optimizations and crystallographic structure refinement. The method is implemented by integrating the quantum chemical software Turbomole with the crystallographic software Crystallography and NMR System (CNS), using three small procedures transferring information between the two programs. The program (COMQUM-X)is used to study the binding of the inhibitor N -methylmesoporphyrin to ferrochelatase, and we show that the method behaves properly and leads to an improvement of the structure of the inhibitor. It allows us to directly quantify in energy terms how much the protein distort the structure of the bound inhibitor compared to the optimum vacuum structure (4,6 kJ/mol). The approach improves the standard combined quantum chemical and molecular mechanics (QC/MM) approach by guaranteeing that the final structure is in accordance with experimental data (the reflections) and avoiding the risk of propagating errors in the crystal coordinates. The program can also be seen as an improvement of standard crystallographic refinement, providing an accurate empirical potential function for any group of interest. The results can be directly interpreted in standard crystallographic terms (e.g., R factors or electron density maps). The method can be used to interpret crystal structures (e.g., the protonation status of metal-bound water molecules) and even to locally improve them. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 1058,1070, 2002 [source] Structure Determination by X-ray Crystallography.JOURNAL OF SYNCHROTRON RADIATION, Issue 3 2006By Mark Ladd, Rex Palmer. First page of article [source] Opechowski,Guccione-like symbols labelling magnetic space groups independent of tabulated (0, 0, 0)+ setsACTA CRYSTALLOGRAPHICA SECTION A, Issue 3 2010Hans Grimmer For the magnetic space-group types with a black and white lattice two sets of symbols have been proposed: the BNS symbols [Belov et al. (1957). Sov. Phys. Crystallogr.2, 311,322] and the OG symbols [Opechowski & Guccione (1965). Magnetism, edited by G. T. Rado & H. Suhl, Vol. II, Part A, pp. 105,165. New York: Academic Press]. Whereas generators of the group can be read off the BNS symbol, International Tables for X-ray Crystallography (1952) must be consulted to interpret the OG symbols. In the cases where the black and white lattice is centred, it is shown how the OG symbols can be modified so that generators of the group can be deduced directly from the symbol. [source] The application of eigensymmetries of face forms to anomalous scattering and twinning by merohedry in X-ray diffractionACTA CRYSTALLOGRAPHICA SECTION A, Issue 3 2010H. Klapper The face form (crystal form) {hkl} which corresponds to an X-ray reflection hkl is considered. The eigensymmetry (inherent symmetry) of such a face form can be used to derive general results on the intensities of the corresponding X-ray reflections. Two cases are treated. (i) Non-centrosymmetric crystals exhibiting anomalous scattering: determination of reflections hkl for which Friedel's rule is strictly valid, i.e.I(hkl) = I() (Friedel pair, centric reflection), or violated, i.e.I(hkl) , I() (Bijvoet pair, acentric reflection). It is shown that those reflections hkl strictly obey Friedel's rule, for which the corresponding face form {hkl} is centrosymmetric. If the face form {hkl} is non-centrosymmetric, Friedel's rule is violated due to anomalous scattering. (ii) Crystals twinned by merohedry: determination of reflections hkl, the intensities of which are affected (or not affected) by the twinning. It is shown that the intensity is affected if the twin element is not a symmetry element of the eigensymmetry of the corresponding face form {hkl}. The intensity is not affected if the twin element belongs to the eigensymmetry of {hkl} (`affected' means that the intensities of the twin-related reflections are different for different twin domain states owing to differences either in geometric structure factors or in anomalous scattering or in both). A simple procedure is presented for the determination of these types of reflections from Tables 10.1.2.2 and 10.1.2.3 of International Tables for Crystallography, Vol. A [Hahn & Klapper (2002). International Tables for Crystallography, Vol. A, Part 10, edited by Th. Hahn, 5th ed. Dordrecht: Kluwer]. The application to crystal-structure determination of crystals twinned by merohedry (reciprocal space) and to X-ray diffraction topographic mapping of twin domains (direct space) is discussed. Relevant data and twinning relations for the 63 possible twin laws by merohedry in the 26 merohedral point groups are presented in Appendices A to D. [source] Foundations of Crystallography with Computer Applications.ACTA CRYSTALLOGRAPHICA SECTION A, Issue 6 2009By Maureen M. Julian. First page of article [source] Gjřnnes Medal in Electron Crystallography , call for nominationsACTA CRYSTALLOGRAPHICA SECTION A, Issue 6 2009DOI: 10.1107/S010876730904244 First page of article [source] International Union of Crystallography Twenty-First General Assembly and International Congress of Crystallography, Osaka, Japan, 23,31 August 2008ACTA CRYSTALLOGRAPHICA SECTION A, Issue 5 2009DOI: 10.1107/S010876730803364 First page of article [source] 60 years of IUCr journalsACTA CRYSTALLOGRAPHICA SECTION A, Issue 3 2009André Authier In the 60 years since its birth in 1948, the number of journals published by the International Union of Crystallography has risen from one to eight. A brief account of the history of the forerunner of the IUCr journals, Zeitschrift für Kristallographie, is given. The context of the birth of the IUCr and the first of its journals, Acta Crystallographica, is recalled. The circumstances which led to the growth of Acta into several sections, at first A and B then, successively, C, D, E and F, and the launch of two new journals, the Journal of Applied Crystallography and the Journal of Synchrotron Radiation, are described. The transition from print-on-paper to electronic journals is also remembered. [source] Comments on tables of magnetic space groupsACTA CRYSTALLOGRAPHICA SECTION A, Issue 2 2009Hans Grimmer Litvin [Acta Cryst. (2008), A64, 419,424 and supplementary material] extends much of the information contained in Volume A of International Tables for Crystallography for the 230 space-group types to the 1651 types of Shubnikov space groups, using Opechowski,Guccione (OG) notation for the space groups with a black,white lattice. It is pointed out that OG notation has crucial disadvantages compared to Belov,Neronova,Smirnova (BNS) notation. It is shown how Litvin's diagrams of symmetry elements for the orthorhombic Shubnikov space groups can be interpreted in terms of BNS symbols and how those containing e -glides can be simplified. A number of mistakes in the diagrams of Litvin are corrected. [source] Crystallography and the World of Symmetry.ACTA CRYSTALLOGRAPHICA SECTION A, Issue 2 2009By Sanat K. Chatterjee. First page of article [source] Crystallography Across the Sciences 2ACTA CRYSTALLOGRAPHICA SECTION A, Issue 1 2008Henk Schenk First page of article [source] A systematic approach to the derivation of standard orientation-location parts of symmetry-operation symbolsACTA CRYSTALLOGRAPHICA SECTION A, Issue 6 2007Kazimierz Stró Automatically generated orientation-location parts, or coordinate triplets describing the geometric elements, differ frequently from the corresponding parts of the symmetry-operation symbols listed in International Tables for Crystallography [(1983), Vol. A, Space-Group Symmetry, edited by Th. Hahn. Dordrecht: Reidel]. An effective algorithm enabling the derivation of standard orientation-location parts from any symmetry matrix is described and illustrated. The algorithm is based on a new concept alternative to the `invariant points of reduced operation'. First, the geometric element that corresponds to a given symmetry operation is oriented and located in a nearly convention free manner. The application of the direction indices [uvw] or Miller indices (hkl) gives a unique orientation provided the convention about the positive direction is defined. The location is fixed by the specification of a unique point on the geometric element, i.e. the point closest to the origin. Next, both results are converted into the standard orientation-location form. The standardization step can be incorporated into other existing methods of derivation of the symmetry-operation symbols. A number of standardization examples are given. [source] Combinatorial construction of tilings by barycentric simplex orbits (D symbols) and their realizations in Euclidean and other homogeneous spacesACTA CRYSTALLOGRAPHICA SECTION A, Issue 6 2005Emil Molnár A new method, developed in previous works by the author (partly with co-authors), is presented which decides algorithmically, in principle by computer, whether a combinatorial space tiling (,,) is realizable in the d -dimensional Euclidean space Ed (think of d = 2, 3, 4) or in other homogeneous spaces, e.g. in Thurston's 3-geometries: Then our group , will be an isometry group of a projective metric 3-sphere , acting discontinuously on its above tiling . The method is illustrated by a plane example and by the well known rhombohedron tiling , where , = Rm is the Euclidean space group No. 166 in International Tables for Crystallography. [source] Quantum Crystallography: Electron Density and Bonding, a MicrosymposiumACTA CRYSTALLOGRAPHICA SECTION A, Issue 2 2004Seppo Manninen First page of article [source] Form factors for core electrons useful for the application of quantum crystallography (QCr) to organic moleculesACTA CRYSTALLOGRAPHICA SECTION A, Issue 4 2002Lulu Huang Form factors are calculated for the core electrons of the first-row atoms B, C, N, O and F. The form factors are presented in an analytical form, as appears in International Tables for X-ray Crystallography [Ibers & Hamilton (1974), Vol. IV, pp. 103,145. Birmingham: Kynoch Press; present distributor Kluwer Academic Publishers, Dordrecht]. Having such form factors for the core electrons reduces the number of parameters to be determined by the methods of quantum crystallography (QCr). It is shown that the form factors obtained are quite accurate. Thus, when they are used in QCr, they are expected to be consistent with accurate charge densities. [source] Structural Crystallography of Inorganic Oxysalts.ACTA CRYSTALLOGRAPHICA SECTION B, Issue 3 2009By S. V. Krivovichev. First page of article [source] Crystallography of Modular Materials.ACTA CRYSTALLOGRAPHICA SECTION B, Issue 5 2008First page of article [source] CIF: the computer language of crystallographyACTA CRYSTALLOGRAPHICA SECTION B, Issue 3-1 2002I. David Brown The Crystallographic Information File (CIF) was adopted in 1990 by the International Union of Crystallography as a file structure for the archiving and distribution of crystallographic information. The CIF standard is now well established and is in regular use for reporting crystal structure determinations to Acta Crystallographica and other journals. The structure of CIF is flexible and extensible and is compatible with other evolving standards. It is well suited to relational and object-oriented models, and is being adopted by the crystallographic databases. This paper reviews the development of CIF and describes its salient features. Future extension of the standard to include implementation of methods will allow CIF to exploit the potential of advanced information-handling software. [source] Biomolecular Crystallography: Principles, Practice, and Applications to Structural Biology.ACTA CRYSTALLOGRAPHICA SECTION D, Issue 5 2010By Bernhard Rupp. First page of article [source] Protein Crystallography , A Concise Guide.ACTA CRYSTALLOGRAPHICA SECTION D, Issue 9 2009By Eaton E. Lattman, Patrick J. Loll. First page of article [source] Structure Determination by X-ray Crystallography.ACTA CRYSTALLOGRAPHICA SECTION D, Issue 3 2006By Mark Ladd, Rex Palmer. First page of article [source] Refinement of protein crystal structures using energy restraints derived from linear-scaling quantum mechanicsACTA CRYSTALLOGRAPHICA SECTION D, Issue 3 2005Ning Yu A novel method is proposed in which combined restraints derived from linear-scaling semiempirical quantum-mechanical (QM) calculations and X-ray diffraction data are combined to refine crystal structures of proteins. Its performance has been tested on a small protein molecule, bovine pancreatic trypsin inhibitor (BPTI). The refinement involves minimization of the sum of a geometric energy function and an X-ray target function based on either the least-squares residual or the maximum-likelihood formalism. For comparison, similar refinement runs have also been performed using energy restraints derived from the force field available in the Crystallography & NMR System (CNS) program. The QM refinements were carried out with weights that were varied by several orders of magnitude and the optimal weights were identified by observing the trend in the final free R values, QM heats of formation and coordinate root-mean-square deviations (r.m.s.d.s) from the crystal structure. It is found that the QM weights are typically smaller but generally on the same scale as the molecular-mechanics (MM) weights for the respective X-ray target functions. The crystallographic R, free R, real-space R values and correlation coefficients based on the structures refined with the energy restraints derived from our QM calculations and Engh and Huber parameters are comparable, suggesting that the QM restraints are capable of maintaining reasonable stereochemistry to a similar degree as the force-field parameters. A detailed inspection of the structures refined with the QM and MM energy restraints reveals that one of the common differences between them and the crystal structure is that the strained bond angles in the crystal structure are corrected after energetically restrained refinements. Systematic differences in certain bond lengths between the QM-refined structures and the statistical averages of experimental structures have also been observed and discussed. [source] Biological Crystallography goes onlineACTA CRYSTALLOGRAPHICA SECTION D, Issue 1 2000Jenny P. Glusker First page of article [source] 1,3-Alternate Calix[4]arene Nitronyl Nitroxide Tetraradical and Diradical: Synthesis, X-Ray Crystallography, Paramagnetic NMR Spectroscopy, EPR Spectroscopy, and Magnetic Studies.CHEMINFORM, Issue 49 2007Andrzej Rajca Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. 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