On the use of crystal vibrational modes in the estimation of the anisotropic displacement parameters of hydrogen atoms in molecular crystals: para-Nitroaniline as a test case

Can we trust the experiment? Anisotropic displacement parameters in 1-(halomethyl)-3-nitrobenzene (halogen = Cl or Br)

1-(Chloromethyl)-3-nitrobenzene, C7H6NClO2, and 1-(bromomethyl)-3-nitrobenzene, C7H6NBrO2, were chosen as test compounds for benchmarking anisotropic displacement parameters (ADPs) calculated from first principles in the harmonic approximation. Crystals of these compounds are isomorphous, and theory predicted similar ADPs for both. In-house diffraction experiments with Mo Kα radiation were in apparent contradiction to this theoretical result, with experimentally observed ADPs significantly larger for the bromo derivative. In contrast, the experimental and theoretical ADPs for the lighter congener matched reasonably well. As all usual quality indicators for both sets of experimental data were satisfactory, complementary diffraction experiments were performed at a synchrotron beamline with shorter wavelength. Refinements based on these intensity data gave very similar ADPs for both compounds and were thus in agreement with the earlier in-house results for the chloro derivative and the predictions of theory. We speculate that strong absorption by the heavy halogen may be the reason for the observed discrepancy.

A new tool for validating theoretically derived anisotropic displacement parameters with experiment: directionality of prolate displacement ellipsoids

How well do anisotropic displacement parameters from theory match experiment? The orientation of prolate ellipsoids contributes to the answer!

Dynamic quantum crystallography: lattice-dynamical models refined against diffraction data. I. Theory

This study demonstrates and tests the refinement of a lattice-dynamical model derived from periodic ab initio calculations at the Γ point against elastic diffraction data (X-ray or neutron). Refinement of only a handful of parameters is sufficient to obtain a similar agreement with the data as the conventional crystallographic model using anisotropic displacement parameters. By refinement against X-ray data, H displacement parameters are obtained which compare favourably with those from neutron diffraction experiments. The approach opens the door for evaluating thermodynamic properties, and for refinement against multi-temperature data, against inelastic diffraction data, spectroscopic information and thermal diffuse scattering data.

Anisotropic thermal motion in transition-metal carbonyls from experiments and ab initio theory

This proof-of-concept study extends the ab initio computation of anisotropic displacement parameters to complexes with transition metal centres.

SHADE3server: a streamlined approach to estimate H-atom anisotropic displacement parameters using periodicab initiocalculations or experimental information

A major update of theSHADEserver (http://shade.ki.ku.dk) is presented. In addition to all of the previous options for estimating H-atom anisotropic displacement parameters (ADPs) that were offered bySHADE2, the newest version offers two new methods. The first method combines the original translation–libration–screw analysis with input from periodicab initiocalculations. The second method allows the user to input experimental information from spectroscopic measurements or from neutron diffraction experiments on related structures and utilize this information to evaluate ADPs of H atoms. Tools are provided to set up theab initiocalculations and to derive the internal motion from the calculations. The new server was tested on a range of compounds where neutron diffraction data were available. In most cases, the results are significantly better than previous estimates, and for strong hydrogen bonds in proton sponges, theab initiocalculations become crucial.