Pseudo-tetragonal twinning


1/6: Introduction

Not all cases of twinning by pseudo-merohedry can be handled by the TWIN command in SHELXL. This tutorial describes the crystal structure of pinacol monohydrate, which has primitive monoclinic symmetry of type P 2/n, but is four-fold twinned by virtue of a pseudo-tetragonal I-centered supercell. Unlike three-fold twinning in B21, there is no setting of the space group (conventional or otherwise) that would allow use of the TWIN/BASF approach. This means that, for refinement using SHELXL, a dataset in SHELX  'HKLF 5' format is required.

The monohydrate phase of crystalline pinacol has been known since 1922. Despite attempts to determine its structure, however, it remained unsolved until 2003. An account is given by Hao et al. (2005), Acta Cryst. B61, 689-699. An ellipsoid plot of the structure looks like this:

pinacol-monohydrate-final

To enable you to follow along, the dataset of Hao et al. (2005) is available here:

triP.hkl

At the time of the investigation in 2003, facilities within the data collection software (Nonius collect ) for handling twins were far less sophisticated than are available today (e.g. in Bruker APEX3 or Rigaku-Oxford CrysAlis ). Thus, to ensure that no experimental information was inadvertently lost or skipped, data were collected assuming a primitive triclinic unit cell. That cell allowed for integration of intensities for all the observable diffraction maxima, but without making any assumptions about crystal symmetry. The cell dimensions were:

a = 12.9001(7) Å
b = 12.8941(7) Å
c = 12.8917(9) Å
α = 107.517(3)°
β = 110.359(3)°
γ = 110.581(3)°

In this unit cell a,b,c are all about the same, as are β and γ, so we can expect it to transform to something of higher symmetry. We'll tackle the problem of structure solution and accounting for the twinning step-by-step, in small, hopefully straightforward segments. Luckily, pinacol has few atoms, so molecular complexity should not get in the way.

This tutorial uses (and assumes familiarity with) the following programs:

XPREP for analysis and file setup
SHELXD for structure solution
SHELXL for structure refinement
ShelXle for model building
Platon for structure analysis

To proceed, click on the 'Analysis and file set up with XPREP ' link below.



1: Introduction
2: Analysis and file set up with XPREP
3: Solve the structure in I2/a using SHELXD
4: Find true space group symmetry using Platon
5: Generate 'HKLF 5' format dataset
6: Complete four-fold P2/n twin refinement

Return to the main Tutorials page or to the main X-Ray Lab page