Analysis of atomic displacement parameters and molecular motion in crystals

Hummel, W.; Raselli, Andrea; Bürgi, Hans‐Beat

doi:10.1107/s0108768190006334

Cited by 63 publications

(17 citation statements)

References 5 publications

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“…Y. Fu thanks the Graduate School t Hummel et al (1990) have shown that replacement of spherical atoms with multipoles in the refinement of boron nitrilotriacetate has little effect on the out-of-plane displacement parameters for the O atoms of the carbonyl groups. ++Capelli & Buergi (1997) have analyzed our results with their new algorithm that accounts explicitly for the temperature dependence of the ADP's.…”

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confidence: 99%

Temperature Dependence of the Rigid-Body Motion of Anthraquinone

Fu¹,

Brock²

1998

Acta Crystallogr Sect B

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Anthraquinone has been studied at five temperatures between 296 and 162 K. The unsatisfactory agreement factors obtained in earlier studies probably resulted from the use of data collected from twinned crystals; needle-like crystals with approximately equidimensional cross sections are usually contact twins related by reflection across (10:2). The temperature dependence of the T and L tensors is normal. The out-of-plane displacement parameters of the O atom indicate a large-amplitude internal vibration.

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confidence: 99%

Temperature Dependence of the Rigid-Body Motion of Anthraquinone

Fu¹,

Brock²

1998

Acta Crystallogr Sect B

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“…Additional evidence for coupling of motions comes from detailed analysis of the thermal atomic displacements of the potassium-ruthenium Tutton salt X-ray diffraction patterns. 12,13 In most cases the thermal atomic displacements fit the predictions of the internal force field plus a term for the translation-rotation of the molecule as a whole. However, the potassium-ruthenium Tutton salt does not follow the general rule.…”

Section: Discussionmentioning

confidence: 90%

Transformations in Crystalline Ammonium Nickel Tutton Salt Induced by Infrared Hole Burning

Cha

Strauss

2000

J. Phys. Chem. A

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The title compound doped with a small amount of deuterium shows infrared bands due to the N-D and O-D stretching vibrations. When one of the N-D bands is irradiated with an infrared laser, holes and antiholes are produced. The pattern of these holes/anti-holes depends on the irradiation time. A ten-minute irradiation produces holes/anti-holes in the N-D bands only. A ten-second irradiation produces holes/antiholes in the O-D bands as well. The features produced by the ten-second irradiation decay during the longer irradiation. Thus, the burning and decay kinetics of the Tutton salts involve processes that occur on at least two time scales.The ammonium Tutton salts, (NH 4 ) 2 X(H 2 O) 6 (SO 4 ) 2 , with X a divalent transition metal ion, form a series of well-known isomorphous crystals. 1 Introducing a small amount of deuterium produces crystals containing some NH 3 D + ions and some HOD molecules. The Tutton salts all crystallize in the monoclinic space group P2 1 /a(#14) with the transition metal ion at a center of inversion. This ion is surrounded by the six water molecules in a distorted octahedron. The hydrogen atoms are equivalent in pairs: thus there are six distinct sets of H-atom sites. The water molecules are hydrogen bonded to the sulfate ions and these, in turn, to the ammonium ions. The ammonium ions sit in general sites, and so there are 4 distinct H positions for the ammonium hydrogen atoms.The deuterium-doped crystals show a series of 10 distinct O-D and N-D bands, one for each distinct H (D) site. The different orientations of the HOD and NH 3 D + molecules have slightly different energies since they put the D-atom in different inequivalent sites. The small energy differences determine the equilibrium distribution of the orientations at a given temperature. 2, 3 We disturb the orientational distribution by irradiating the band corresponding to a given N-D band and then watch the relaxation back to equilibrium in the dark. We have previously reported on the effect of using a hole-burning laser for a period of about 30 min on a variety of ammonium Tutton saltsscobalt, 2 nickel, and their mixed crystals, 4,5 and copper. 6 For the copper salt, we noticed that the relaxation depended strongly on the timesthat is, the relaxation was not a merely monotonic decay, but instead a result of a number of conformational processes occurring on different time scales.Consequently, we developed an irradiation-spectrometer system to examine the kinetics on the order of seconds as well as over longer intervals. In this paper, we briefly explain the new apparatus and then consider the results of irradiating the ammonium nickel Tutton salt for two different periods, 10 s and 10 min. To compare results on such different time scales using a fixed power laser it is necessary to repeat the short irradiation process and its decay many times and co-add the results, and we do just that.For the Cu salt and, to a lesser extent the Co salt, the JahnTeller effect produces a distorted octahedron of water molecules, and this distor...

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“…They are also comparable with the translation amplitudes of m-nitroaniline (Wo Â jcik & Holband, 2001). The values of the reliability index, wR, reported in Table 3 indicate that the contributions of the internal vibrations to the anisotropic displacement parameters determined by X-ray diffraction at 95 and 180 K are similar and this contribution is less at 300 K (Hummel et al, 1990). This contribution may originate from The variation of the IP lattice parameters with temperature.…”

Section: Rigid-body Analysis Of Anisotropic Displacement Parameters Wmentioning

confidence: 94%

Variable-temperature studies of the 4-isopropylphenol crystal structure from X-ray diffraction. Comparison of thermal expansion and molecular dynamics with spectroscopic results

Wójcik

Holband

2002

Acta Crystallogr Sect B

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Crystalline 4-isopropylphenol, C(9)H(12)O, an optically non-linear material, was studied by X-ray diffraction in order to determine its structure at several temperatures in the 95-300 K range. The thermal expansion coefficients have been calculated from the lattice parameters' dependence on temperature. The rigid-body analysis of the anisotropic displacement parameters including the correlation with the internal motion of large amplitude provided the values of the molecular translation and libration tensors at the temperatures studied and was used to characterize the torsional motion of the isopropyl group. The calculated normal modes and internal torsion frequency were compared with the wave numbers at the maximum of bands in the low-frequency Raman scattering, FTIR and inelastic neutron scattering spectra.

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Analysis of atomic displacement parameters and molecular motion in crystals

Cited by 63 publications

References 5 publications

Temperature Dependence of the Rigid-Body Motion of Anthraquinone

Temperature Dependence of the Rigid-Body Motion of Anthraquinone

Transformations in Crystalline Ammonium Nickel Tutton Salt Induced by Infrared Hole Burning

Variable-temperature studies of the 4-isopropylphenol crystal structure from X-ray diffraction. Comparison of thermal expansion and molecular dynamics with spectroscopic results

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