An empirical method for correcting diffractometer data for absorption effects
01 Jan 1983-Acta Crystallographica Section A (International Union of Crystallography)-Vol. 39, Iss: 1, pp 158-166
TL;DR: In this article, a Fourier series in the polar angles of the incident and diffracted beam paths is used to model an absorption surface for the difference between the observed and calculated structure factors.
Abstract: Absorption effects usually present the most serious source of systematic error in the determination of structure factors from single-crystal X-ray diffraction measurements if the crystal is not ground to a sphere or cylinder. A novel method is proposed for the correction of these effects for data collected on a diffractometer. The method works from the premise that the manifestation of systematic errors due to absorption, unlike most other sources of systematic error, will not be evenly distributed through reciprocal space, but will be localized. A Fourier series in the polar angles of the incident and diffracted beam paths is used to model an absorption surface for the difference between the observed and calculated structure factors. Knowledge of crystal dimensions or linear absorption coefficient is not required, and the method does not necessitate the measurement of azimuthal scans or any extra data beyond the unique set. Moreover, application of the correction is not dependent upon the Laue symmetry of the crystal or the geometry of the diffractometer. The method is compared with other commonly used corrections and results are presented which demonstrate its potential.
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TL;DR: The methods presented in the chapter have been applied to solve a large variety of problems, from inorganic molecules with 5 A unit cell to rotavirus of 700 A diameters crystallized in 700 × 1000 × 1400 A cell.
Abstract: Publisher Summary X-ray data can be collected with zero-, one-, and two-dimensional detectors, zero-dimensional (single counter) being the simplest and two-dimensional the most efficient in terms of measuring diffracted X-rays in all directions. To analyze the single-crystal diffraction data collected with these detectors, several computer programs have been developed. Two-dimensional detectors and related software are now predominantly used to measure and integrate diffraction from single crystals of biological macromolecules. Macromolecular crystallography is an iterative process. To monitor the progress, the HKL package provides two tools: (1) statistics, both weighted (χ2) and unweighted (R-merge), where the Bayesian reasoning and multicomponent error model helps obtain proper error estimates and (2) visualization of the process, which helps an operator to confirm that the process of data reduction, including the resulting statistics, is correct and allows the evaluation of the problems for which there are no good statistical criteria. Visualization also provides confidence that the point of diminishing returns in data collection and reduction has been reached. At that point, the effort should be directed to solving the structure. The methods presented in the chapter have been applied to solve a large variety of problems, from inorganic molecules with 5 A unit cell to rotavirus of 700 A diameters crystallized in 700 × 1000 × 1400 A cell.
31,667 citations
TL;DR: The category Computer Program Abstracts provides a rapid means of communicating up-to-date information concerning both new programs or systems and signi®cant updates to existing ones.
Abstract: The category Computer Program Abstracts provides a rapid means of communicating up-to-date information concerning both new programs or systems and signi®cant updates to existing ones. Following normal submission, a Computer Program Abstract will be reviewed by one or two members of the IUCr Commission on Crystallographic Computing. It should not exceed 500 words in length and should follow the standard format given on page 189 of the June 1985 issue of the Journal [J. Appl. Cryst. (1985). 18, 189± 190] and on the World Wide Web at http://www.iucr. org/journals/jac/software/. Lists of software presented and/or reviewed in the Journal of Applied Crystallography are available on the World Wide Web at the above address, together with information about the availability of the software where this is known.
18,151 citations
Cites methods from "An empirical method for correcting ..."
...Several absorption correction methods are available, e.g. analytical, Gaussian grid, scans, multiscan (Blessing, 1995), DIFABS (Walker & Stuart, 1983)....
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TL;DR: The WinGX suite provides a complete set of programs for the treatment of small-molecule single-crystal diffraction data, from data reduction and processing, structure solution, model refinement and visualization, and metric analysis of molecular geometry and crystal packing, to final report preparation in the form of a CIF.
Abstract: The WinGX suite provides a complete set of programs for the treatment of small-molecule single-crystal diffraction data, from data reduction and processing, structure solution, model refinement and visualization, and metric analysis of molecular geometry and crystal packing, to final report preparation in the form of a CIF. It includes several well known pieces of software and provides a repository for programs when the original authors no longer wish to, or are unable to, maintain them. It also provides menu items to execute external software, such as the SIR and SHELX suites of programs. The program ORTEP for Windows provides a graphical user interface (GUI) for the classic ORTEP program, which is the original software for the illustration of anisotropic displacement ellipsoids. The GUI code provides input capabilities for a wide variety of file formats, and extra functionality such as geometry calculations and ray-traced outputs. The programs WinGX and ORTEP for Windows have been distributed over the internet for about 15 years, and this article describes some of the more modern features of the programs.
9,479 citations
Cites background from "An empirical method for correcting ..."
...A number of absorption corrections are maintained in WinGX, of varying rigour from empirical ( scan) and semi-empirical (DIFABS; Walker & Stuart, 1983) to fully accurate analytical or Gaussian methods....
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TL;DR: Inductive coupled plasma spectroscopy reveals that the presence of the coordinating nitrile moiety in the ionic liquid leads to a significant decrease in palladium leaching relative to simple N-alkylpyridinium ionic liquids.
Abstract: A series of relatively low-cost ionic liquids, based on the N-butyronitrile pyridinium cation [C(3)CNpy](+), designed to improve catalyst retention, have been prepared and evaluated in Suzuki and Stille coupling reactions. Depending on the nature of the anion, these salts react with palladium chloride to form [C(3)CNpy](2)[PdCl(4)] when the anion is Cl(-) and complexes of the formula [PdCl(2)(C(3)CNpy)(2)][anion](2) when the anion is PF(6)(-), BF(4)(-), or N(SO(2)CF(3))(2)(-). The solid-state structures of [C(3)CNpy]Cl and [C(3)CNpy](2)[PdCl(4)] have been established by single-crystal X-ray diffraction. The catalytic activity of these palladium complexes following immobilization in both N-butylpyridinium and nitrile-functionalized ionic liquids has been evaluated in Suzuki and Stille coupling reactions. All of the palladium complexes show good catalytic activity, but recycling and reuse is considerably superior in the nitrile-functionalized ionic liquid. Inductive coupled plasma spectroscopy reveals that the presence of the coordinating nitrile moiety in the ionic liquid leads to a significant decrease in palladium leaching relative to simple N-alkylpyridinium ionic liquids. Palladium nanoparticles have been identified as the active catalyst in the Stille reaction and were characterized using transmission electron microscopy.
339 citations
TL;DR: In this paper, the trinuclear unit is held together by bridging deprotonated phenolic oxygen atoms from the Schiff base and acetate groups, and the structures of the three synthesised complexes have been determined by single-crystal X-ray diffraction.
338 citations
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