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Journal ArticleDOI

J. Appl. Cryst.の発刊に際して

10 Mar 1970-Vol. 12, Iss: 1, pp 1-1
About: The article was published on 1970-03-10 and is currently open access. It has received 8159 citations till now.
Citations
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Journal ArticleDOI
TL;DR: Quantitative analysis of the X-ray pair distribution function collected on calcium silicate hydrates having Ca/Si ratios ranging between 0.57 and 1.47 found that with increasing Ca/ Si ratio, Si bridging tetrahedra are omitted and Ca(OH)2 is detected at the highest ratios.
Abstract: The structural evolution of nanocrystalline calcium silicate hydrate (C–S–H) as a function of its calcium to silicon (Ca/Si) ratio has been probed using qualitative and quantitative X-ray atomic pair distribution function analysis of synchrotron X-ray scattering data. Whatever the Ca/Si ratio, the C–S–H structure is similar to that of tobermorite. When the Ca/Si ratio increases from ∼0.6 to ∼1.2, Si wollastonite-like chains progressively depolymerize through preferential omission of Si bridging tetrahedra. When the Ca/Si ratio approaches ∼1.5, nanosheets of portlandite are detected in samples aged for 1 d, while microcrystalline portlandite is detected in samples aged for 1 year. High-resolution transmission electron microscopy imaging shows that the tobermorite-like structure is maintained to Ca/Si > 3.

63 citations

Journal ArticleDOI
TL;DR: In this paper, an increase of the X-ray diffraction line broadening with increasing diffraction angle was observed experimentally in nanocrystalline thin films, which contradicts the assumptions that the micro-strain is relatively low in the sample and is caused mainly by small crystallite size.
Abstract: An increase of the X-ray diffraction line broadening with increasing diffraction angle was observed experimentally in nanocrystalline thin films. Such a change of the line width is usually related to the microstrain in the sample, which, however, contradicts the assumptions that the microstrain is relatively low in nanocrystalline materials and that the line broadening is caused mainly by small crystallite size. For nanocrystalline thin films, the observed changes in the diffraction line broadening are explained by a partial coherence of adjacent crystallites, which is stronger at low diffraction angles than at high diffraction angles. Furthermore, it is found that the degree of coherence of the adjacent crystallites depends on their size and preferred orientation. Smaller crystallites show better coherence, because the corresponding reciprocal-lattice points are broadened compared with those related to large crystallites. A strong preferred orientation improves further the coherence of the adjacent crystallites. Theoretical results are confirmed by experimental data obtained on nanocrystalline (Ti,Al)N thin films using a combination of glancing-angle X-ray diffraction, high-resolution transmission electron microscopy and X-ray texture analysis.

63 citations


Additional excerpts

  • ...…made by van Berkum et al. (1996), who introduced a model of general defects characterized by a strain ®eld and a distribution of the defects, and by Breuer et al. (2000), who suggested a method for separation of the effects related to the so-called second-kind stresses from those related to…...

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Journal ArticleDOI
TL;DR: The novel complex cis-[(ITMe)2Pd(SiMe3)2 (ITMe=1,3,4,5-tetramethylimidazol-2-ylidene) has been synthesized by mild oxidative cleavage of Me3SiSiMe 3 using [(ITMe).
Abstract: The novel complex cis-[(ITMe)2Pd(SiMe3)2 (ITMe=1,3,4,5-tetramethylimidazol-2-ylidene) has been synthesized by mild oxidative cleavage of Me3SiSiMe3 using [(ITMe)2Pd0]. The use of this complex as precatalyst for the cis-bis(silyl)ation of alkynes using unactivated disilanes is reported.

63 citations

Journal ArticleDOI
Giovanna Scapin1
TL;DR: A brief overview, with examples, of the evolution of molecular-replacement methods and models over the past few years is presented.
Abstract: The `phase problem' in crystallography results from the inability to directly measure the phases of individual diffracted X-ray waves. While intensities are directly measured during data collection, phases must be obtained by other means. Several phasing methods are available (MIR, SAR, MAD, SAD and MR) and they all rely on the premise that phase information can be obtained if the positions of marker atoms in the unknown crystal structure are known. This paper is dedicated to the most popular phasing method, molecular replacement (MR), and represents a personal overview of the development, use and requirements of the methodology. The first description of noncrystallographic symmetry as a tool for structure determination was explained by Rossmann and Blow [Rossmann & Blow (1962), Acta Cryst. 15, 24–31]. The term `molecular replacement' was introduced as the name of a book in which the early papers were collected and briefly reviewed [Rossmann (1972), The Molecular Replacement Method. New York: Gordon & Breach]. Several programs have evolved from the original concept to allow faster and more sophisticated searches, including six-dimensional searches and brute-force approaches. While careful selection of the resolution range for the search and the quality of the data will greatly influence the outcome, the correct choice of the search model is probably still the main criterion to guarantee success in solving a structure using MR. Two of the main parameters used to define the `best' search model are sequence identity (25% or more) and structural similarity. Another parameter that may often be undervalued is the quality of the probe: there is clearly a relationship between the quality and the correctness of the chosen probe and its usefulness as a search model. Efforts should be made by all structural biologists to ensure that their deposited structures, which are potential search probes for future systems, are of the best possible quality.

63 citations


Cites background from "J. Appl. Cryst.の発刊に際して"

  • ...Paula Fitzgerald’s MERLOT (Fitzgerald, 1988) was the first program to provide most of the necessary features in one program suite, including rapid screening of a large number of potential MR solutions generated, for example, by noisy rotation-function results....

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  • ...MERLOT included two programs for calculating the rotation (including Crowther’s fast rotation function; Crowther, 1972), three methods for solving the translation problem [the Lattman translation function, a packing function (Hendrickson & Ward, 1976) and an R-value mapping program] and a program for optimizing a potential solution....

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  • ...AMoRe extended the MERLOT idea of allowing the rapid screening of a large number of potential MR solutions generated, for example, by noisy rotation-function results....

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  • ...Although MERLOT lacks automation to the same degree as found in more modern programs, it has been used well into the 21st century (for example, for PDB entry 4dne; Panwar et al., 2012)....

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Journal ArticleDOI
TL;DR: The interweaving of two identical acyclic positively charged anion recognizing units around a chloride anion template leads to the formation of an orthogonal supramolecular ensemble which upon subsequent double ring cyclization gives a chloride selective [2]catenane in very high yield.

63 citations

References
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Journal ArticleDOI
TL;DR: The goals of the PDB are described, the systems in place for data deposition and access, how to obtain further information and plans for the future development of the resource are described.
Abstract: The Protein Data Bank (PDB; http://www.rcsb.org/pdb/ ) is the single worldwide archive of structural data of biological macromolecules. This paper describes the goals of the PDB, the systems in place for data deposition and access, how to obtain further information, and near-term plans for the future development of the resource.

34,239 citations

Journal ArticleDOI
TL;DR: New features added to the refinement program SHELXL since 2008 are described and explained.
Abstract: The improvements in the crystal structure refinement program SHELXL have been closely coupled with the development and increasing importance of the CIF (Crystallographic Information Framework) format for validating and archiving crystal structures. An important simplification is that now only one file in CIF format (for convenience, referred to simply as `a CIF') containing embedded reflection data and SHELXL instructions is needed for a complete structure archive; the program SHREDCIF can be used to extract the .hkl and .ins files required for further refinement with SHELXL. Recent developments in SHELXL facilitate refinement against neutron diffraction data, the treatment of H atoms, the determination of absolute structure, the input of partial structure factors and the refinement of twinned and disordered structures. SHELXL is available free to academics for the Windows, Linux and Mac OS X operating systems, and is particularly suitable for multiple-core processors.

28,425 citations

Journal ArticleDOI
TL;DR: CCP4mg is a project that aims to provide a general-purpose tool for structural biologists, providing tools for X-ray structure solution, structure comparison and analysis, and publication-quality graphics.
Abstract: CCP4mg is a project that aims to provide a general-purpose tool for structural biologists, providing tools for X-ray structure solution, structure comparison and analysis, and publication-quality graphics. The map-fitting tools are available as a stand-alone package, distributed as `Coot'.

27,505 citations

Journal ArticleDOI
TL;DR: The PHENIX software for macromolecular structure determination is described and its uses and benefits are described.
Abstract: Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. How­ever, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics. PHENIX has been developed to provide a comprehensive system for macromolecular crystallo­graphic structure solution with an emphasis on the automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a tight integration between the algorithms.

18,531 citations

Journal ArticleDOI
TL;DR: A description is given of Phaser-2.1: software for phasing macromolecular crystal structures by molecular replacement and single-wavelength anomalous dispersion phasing.
Abstract: Phaser is a program for phasing macromolecular crystal structures by both molecular replacement and experimental phasing methods. The novel phasing algorithms implemented in Phaser have been developed using maximum likelihood and multivariate statistics. For molecular replacement, the new algorithms have proved to be significantly better than traditional methods in discriminating correct solutions from noise, and for single-wavelength anomalous dispersion experimental phasing, the new algorithms, which account for correlations between F+ and F−, give better phases (lower mean phase error with respect to the phases given by the refined structure) than those that use mean F and anomalous differences ΔF. One of the design concepts of Phaser was that it be capable of a high degree of automation. To this end, Phaser (written in C++) can be called directly from Python, although it can also be called using traditional CCP4 keyword-style input. Phaser is a platform for future development of improved phasing methods and their release, including source code, to the crystallographic community.

17,755 citations