Chemical Crystallography (Structure Determination) Using the STOE IPDS 2T Diffractometer

Table of Contents

Data Collection on YLID (C11H10O2S)
Data Collection on Zeolite LTA {Na12 [Al12Si12O48] . 27 H2O}8


Although Mo Kα radiation is typically utilized to determine the structure of small molecules, Cu Kα radiation is considered to be more ideal for treating a number of applications in chemical crystallography. These include studies on small and weakly diffracting crystals, measurements on fibrous or partly disordered samples, absolute structure determination, etc.

Trial measurements were carried out on two samples, which are often utilized for testing purposes. This was done to assess the appropriateness of the STOE IPDS 2T image-plate system equipped with XENOCS’ GeniX Cu Kα microbeam delivery system (Figure 1) for use in chemical crystallography.

Figure 1. IPDS 2T-GeniX setup at the EPF

Data Collection on YLID (C11H10O2S)

YLID is a small-molecule standard widely used in the single-crystal diffraction. It is part of the orthorhombic system so that the modification of the cell angles guarantees a proper assessment of the geometric precision, general performance, and alignment of a laboratory diffractometer setup.

The GeniX microbeam delivery system was operated at 50 kV, 1 mA, and the circular image plate was positioned 40 mm away from the sample and was offset in 2Θ by 60°. Data to minimum Bragg spacings of 0.83 Å was acquired with the help of this set up. A redundant data set was obtained that contained three 0–180° omega-scans taken at three different phi angles, i.e. 0°, 45° and 90°. The data included 540 frames, with each corresponding to an omega rotation of 1° and an exposure of 60 seconds. The frames were indexed and then integrated with STOE’s X-Area software. The STOE XRed program was used to perform data reduction i.e. scaling and merging.

In order to make a comparison, STOE’s IPDS 2 diffractometer was used for gathering reference data from the same sample on a Mo Kα source in the laboratory. Structure refinement was performed using SHELXL.

The refined cell parameters for both measurements, along with the available reference data are shown in Table 1. Structure refinement and data reduction statistics are depicted in Table 2.

Table 1. Cell parameter refinement of YLID. nc: non constrained refinement, c: constrained refinement (i.e. cell angles are fixed at 90°)

Data   a [Å] b [Å] c [Å] α [Å] β [Å] γ [Å]
IPDS 2T + GeniX Cu Kα nc 5.9603(5) 9.0354(5) 18.3859(12) 90.036(5) 90.033(6) 90.036(6)
  c 5.9677(4) 9.0336(5) 18.3883(11)
IPDS 2 + sealed tube Mo Kα nc 5.9606(5) 9.0337(7) 18.3818(15) 90.014(7) 90.010(6) 90.027(6)
  c 5.9606(3) 9.0338(5) 18.3796(15)
Reference (Bryant) Cu Kα c 5.96260(10) 9.03940(10) 18.3890(2)      


Table 2. Data reduction and structure refinement statistics for Ylid. SAV: Systematic absence violations, IEq: Inconsistent Equivalents

Data dmin / Å Rint Rσ SAV IEq R1 Flack par.
IPDS2T + GeniX Cu Kα 0.8354 0.0629 0.0362 0 291 0.0292 -0.019(21)
  0.9020 0.0627 0.0353 0 285 0.0240 -0.011(18)
IPDS2 + sealed tube Mo Kα 0.5717 0.0255 0.0242 0 3 0.0363 -0.005(61)
Reference (Bryant et al.) Cu Kα 0.9020 0.0644 0.0343 13 218 0.0277 -0.022(19)


The data obtained on the STOE IPDS 2T/Xenocs–GeniX system were better to a certain extent when compared to the literature values obtained from a popular Cu Kα instrument. However, they would have been a lot better if a test-crystal with an enhanced mount and shape had been used. The extraordinary intensity of the Xenocs/GeniX source was established by comparing the two measurements. For about the same Rs value, the exposure time with Mo Kα radiation (53kV, 43mA) should be five times greater when compared to the microbeam delivery system.

Data Collection on Zeolite LTA {Na12 [Al12Si12O48] . 27 H2O}8

Zeolites are microporous, alumino-silicate minerals. The porous molecular structures of these minerals make them ideal for many industrial applications, such as molecular sieves, catalysts and detergents, to mention a few. Zeolite A has a Linde Type A (LTA) structure. The chemical partition between aluminum (Al) and silicon (Si) (Figure 2) doubles the unit cell of symmetry, leading to a supercell comprising of unit-cell parameters of 24.572Å.

Figure 2. The framework structure Zeolite A with Si-O and Al-O bonds colored respectively in blue and red.

Weak superlattice reflections are produced because of the doubling of the unit-cell. Diffraction data on a small zeolite A crystal was acquired using STOE’s IPDS 2T image plate system equipped with XENOCS’ GeniX microbeam delivery system.

The GeniX microbeam delivery system was run at 50 kV, 1 mA, and an exposure time of 90 seconds for each 1° omega-rotation helped in recording data with good statistics (Figure 3).

Figure 3. Diffraction frame recorded on a crystal of Zeolite A, Scan width 1° (omega), exposure time 90s. Crystal-detector distance 70mm, 2Θ offset 45°.

The image plate was placed 70 mm away from the sample and was offset in 45° 2Θ. Three omega scans were recorded at varied phi angles, producing highly redundant data. Data collection parameters and data reduction statistics are shown in Table 3, and data quality indicators for Zeolite A are shown in Table 4.

Table 3. Data collection and reduction statistics for Zeolite A

Refined unit cell parameter: a / Å 24.5719 (0.0009)
Space group F m -3 c
Number of measured reflections 16249
Number of unique reflections 881
Rint 0.0575
Absorption correction transmission factors Face-indexed 0.41 0.51
Rint after absorption correction 0.0545


Table 4. Data quality indicators for Zeolite A

dmin / Å 14.19 2.60 1.90 1.62 1.42 1.31 1.21 1.13 1.06 0.99 0.93
Mean I/sd(I) 28.12 12.48 16.43 18.12 15.40 15.01 7.11 5.34 5.76 3.25
Rint 28.12 0.076 0.068 0.054 0.043 0.040 0.050 0.054 0.072 0.152
Completeness / % 98 100 100 100 100 100 100 100 100 100


The superlattice reflections can be seen clearly in a mutual lattice reconstruction from the experimental data (Figure 4), confirming the data quality. The framework structure shown in Figure 2 can be resolved with the help of SHELXS with default parameters.

Figure 4. Reciprocal lattice reconstruction of the ((hk0) layer from experimental data. The weak superlattice reflections are clearly visible.


Precise data were acquired on samples obtained from complex inorganic structures as well as organic molecules by using the IPDS 2T-GeniX setup at the EPFL-Lausanne laboratory.

This information has been sourced, reviewed and adapted from materials provided by STOE.

For more information on this source, please visit STOE.

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