Systematic intensity errors caused by spectral truncation: origin and remedy

Three L-hydroxylysine structures have been determined at 100 K by single-crystal X-ray diffraction. High-resolution data using either a laboratory or synchrotron source were collected and subjected to invariom- and independent atom-model (IAM) refinements. Anisotropic displacement parameters (ADPs) obtained from invariom refinement were compared (i) with results from a full multipole and (ii) with an IAM high-order refinement. Differences were visualized with the program PEANUT and were complemented by quantitative results from a Hirshfeld test. Influences of scale factor differences, and of refinement against F;2 versus F, have been investigated. Systematic errors were observed in the IAM, especially when only low-order data were available. Although these errors were reduced in high-order IAM refinements, they only disappeared in charge density--and likewise--invariom refinements.

Section: The Influence Of Data Resolutionmentioning

confidence: 99%

Improvement of anisotropic displacement parameters from invariom-model refinements for three L-hydroxylysine structures

Dittrich

McKinnon

Warren

2008

“…When analysing X-ray diffraction data and modelling electron density deformations due to bonding, the motions and positions of heavier atoms can be determined with similar accuracy and greater precision than from neutron diffraction data. However, spectral truncation of the reflection profile due to the effects of K 1 , 2 splitting can systematically affect the ADPs obtained from X-ray diffraction data (Lenstra et al, 2001;Rousseau et al, 2000). With all these possible effects able to compromise the results obtained, it is not uncommon to find significant differences for heavy-atom ADPs between X-ray and neutron diffraction experiments, sometimes by as much as 50% (Coppens et al, 1984).…”

Section: Introductionmentioning

confidence: 99%

Anisotropic displacement parameters for H atoms using an ONIOM approach

Whitten

Spackman

2006

X-ray diffraction data cannot provide anisotropic displacement parameters (ADPs) for H atoms, a major outstanding problem in charge-density analysis of molecular crystals. Although neutron diffraction experiments are the preferred source of this information, for a variety of reasons they are possible only for a minority of materials of interest. To date, approximate procedures combine rigid-body analysis of the molecular heavy-atom skeleton, based on ADPs derived from the X-ray data, with estimates of internal motion provided by spectroscopic data, analyses of neutron diffraction data on related compounds, or ab initio calculations on isolated molecules. Building on these efforts, an improved methodology is presented, incorporating information on internal vibrational motion from ab initio cluster calculations using the ONIOM approach implemented in GAUSSIAN03. The method is tested by comparing model H-atom ADPs with reference values, largely from neutron diffraction experiments, for a variety of molecular crystals: benzene, 1-methyluracil, alpha-glycine, xylitol and 2-methyl-4-nitroaniline. The results are impressive and, as the method is based on widely available software, and is in principle widely applicable, it offers considerable promise in future charge-density studies of molecular crystals.

“…The refined anisotropic displacement parameters from Xray data are considerably larger than those from neutron data. This may be explained by scan truncation errors in the X-ray data which may be even larger than postulated in Lenstra et al (2001) Thermal displacement tensors of red HgI 2 as functions of the temperature T, refined from the powder neutron intensities and single-crystal X-ray data.…”

Section: Figurementioning

confidence: 98%

“…(2) The use of graphite-monochromated radiation in singlecrystal studies always results in scan-truncation errors (Rousseau et al, 2000;Lenstra et al, 2001), in particular for the high-order reflections which are indispensible for a precise determination of displacement parameters.…”

Section: Introductionmentioning

confidence: 99%

“…Absorption effects in HgI 2 are small. The wavelength dispersion in a monochromated neutron beam is much better defined than in a graphite-monochromated X-ray beam; it is well known that displacement parameters measured with neutrons are in general more trustworthy, while those from graphite-mono-chromated X-rays are most often too large (Lenstra et al, 2001). The sample can be enclosed in a solid container that is transparent to neutrons.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Neutron diffraction investigation of the temperature dependence of crystal structure and thermal motions of red HgI₂

Schwarzenbach

Birkedal

Hostettler

et al. 2007

The structure of, and anisotropic thermal motions in, the red semiconductor tetrahedral layer structure of HgI(2) have been studied with neutron powder diffraction as a function of temperature from 10 to 293 K. Average thermal displacement parameters U(eq) of the two atoms are comparable in size at 10 K, but U(eq)(Hg) increases considerably faster with temperature than U(eq)(I), the Hg-I bond being highly non-rigid. The anisotropic displacement tensor U(I) is strongly anisotropic with one term about twice as large as the others, while U(Hg) is nearly isotropic. All displacement tensor elements, except U(22)(I), increase faster with temperature than harmonic quantum oscillator curves indicating a softening of the isolated-atom potentials at large amplitudes. A lattice dynamical model provides arguments that the anisotropic thermal motions of I are dominated by a soft mode with a wavevector at the [(1/2) (1/2) 0] boundary of the Brillouin zone consisting essentially of coupled librations of the HgI(4) tetrahedra, and by translations of the entire layer. The large vibration amplitudes of Hg suggest weak Hg-I force constants compared with the I-I force constants, allowing Hg to move quite freely inside the tetrahedra. The libration mode induces dynamic deformations of the Hg-I bond with twice its frequency. This provides a mechanism for the anharmonicity and may explain the lightening of the color from red to orange upon cooling at ca 80 K.