Single-crystal quality data from polycrystalline samples: finding the needle in the haystack

Advances in X-ray hardware and software have revolutionized crystallography: now crystal structures can be routinely solved first, with publication-quality datasets collected second. This same approach now allows multi-grain crystallography to be completed in the laboratory with Cu Kα X-rays.


List of Tables
SXD data for (C6F6)3:(C4H5N)4 at 150 K Table S1a.Crystal data and structure refinement S8 Table S1b.Fractional atomic coordinates and U(eq) for all atoms S9 SXD data for phase II of p-C6H4Me2:C6F5H at 120 K Table S4a.Crystal data and structure refinement S18 Table S4b.Fractional atomic coordinates and U(eq) for all atoms S19 Table S4c.Anisotropic displacement parameters S20 Table S4d.Selected bond lengths S20 Table S4e.Selected bond angles S21

List of Figures
Subsequently, a second sample was prepared for DSC in the correct 3:4 ratio to match the co-crystal structure.

S2. Single-crystal X-ray diffraction (SXD) experiments
X−ray diffraction data on crystals of (C6F6)3:(C4H5N)4 and C6F6:C5H5N were obtained using an Agilent Oxford Diffraction SuperNova diffractometer equipped with microfocus X−ray sources, and upgraded with a Rigaku HyPix Arc-100 detector (Fig. S1).X−ray diffraction data on p-C6H4Me2:C6F5H were obtained on the Agilent Oxford Diffraction SuperNova diffractometer equipped using the older Atlas CCD detector, shortly before the installation of the new HyPix one.

S2.1. Crystal growing from equimolar mixture of C4H5N and C6F6
The flame-sealed capillary containing C6F6:C4H5N was mounted on the diffractometer and cooled rapidly in situ to 230 K resulting in the formation of numerous white crystals.The temperature was then increased to 260 K, (just below the melting point at 266 K) in order to encourage annealing of single crystals present.The sample was held at 260 K for 2 hours before cooling to 254 K for data acquisition.Post structure solution, it was found that the co−crystal from an equimolar mixture of C4H5N and C6F6 did not crystallise in a 1:1 molar ratio, but rather in a 3:4 ratio, which explained the difficulties encountered when trying to grow single crystals of this material.The use of the wrong ratio resulted in additional unwanted diffraction signal from the excess C6F6 present.After mounting on the diffractometer, the capillary containing C6F6:C5H5N was cooled rapidly in situ to 200 K resulting in the formation of numerous white crystals.The temperature was then raised to 230 K, and crystal growth was encouraged by manual slow translation of the capillary sample through the cold N2 gas stream.Data was initially acquired at 200 K, and then subsequently a full-sphere of data was measured at 150 K.

S2.3. Crystal growing from equimolar mixture of p-C6H4Me2 and C6F5H
After mounting on the diffractometer, the capillary containing p-C6H4Me2:C6F5H was cooled rapidly in situ to 200 K resulting in the formation of numerous clear/white crystals.The temperature was then raised to just below the melt at about 255 K, and crystal growth was encouraged by manual slow translation of the capillary sample through the cold N2 gas stream.A full-sphere of data was initially acquired at 230 K, and then subsequently at 160 K, 200 K, and finally at 120 K.It is noteworthy that the system underwent a phase transition between 160 K and 120 K (later confirmed by DSC), which saw a doubling of the unit cell volume on cooling.

S2.4. Data acquisition, reduction, and structure solution and refinement
Full spheres of X-ray diffraction data were collected to 0.84 Å resolution using 0.5° ω scan frames; 6124 frames at 2 s per frame for (C6F6)3:(C4H5N)4 and 6496 frames at 0.75 s per frame for C6F6:C5H5N.This corresponds to a total collection time of under 4 hrs for (C6F6)3:(C4H5N)4 and about At 120 K, a triclinic cell was identified from 45% of the visible spots with a = 8.567 Å, b = 8.779 Å, c = 9.371 Å, α = 79.94°,β = 69.33°,γ = 70.14°,and V = 619.0Å 3 , for which the volume is roughly double that observed at higher temperatures.However, this unit cell does not easily relate to that of phase I. Subsequently, a larger I-centred triclinic unit cell was chosen such that the molecular column axis in both phases is in the same direction along c.The refined parameters for this cell are: The structures of phases I and II of p-C6H4Me2:C6F5H were refined by least−squares using the refinement program SHELXL 2 within the Olex2 program suite. 3 The positions of all atoms were refined freely, with isotropic displacement parameters used for H atoms.In phase I of p-C6H4Me2:C6F5H, the centre of mass of both rings sit on a point of inversion within space group P1.
Refinement of the fluorine occupancy for F(1), F(2), and F(3) indicated that the single H atom in C6F5H was unevenly distributed across all three possible positions (see Fig. S17).In the least-squares refinement, the total occupancy of the fluorine sites was tightly restrained to 5 per molecule such that the molecular formula is exactly C6F5H.It is not possible to locate the single H atom of C6F5H in phase I and so its electron density was constrained to be at the same position as the F atoms.In phase I, the methyl group of p-C6H4Me2 was assumed to be disordered and is modelled with 6 positions for the three H atoms.In phase II of p-C6H4Me2:C6F5H, there are two crystallographicallydistinct p-C6H4Me2 molecules, both of which sit on a point of inversion within space group I1.The methyl group was modelled as ordered using the AFIX 137 instruction.For C6F5H, the site occupancy of all 6 possible F positions were refined: one fluorine showed a low occupancy while the occupancy of sites F(1) and F(4) refined to nearly 100%.The latter were therefore fixed as fully occupied.In this phase, the H atom is mainly located on one site but there is still some residual disorder, possible due to the fact that the measurement was unwittingly made close to the phase-transition temperature.
The position of H(2) was refined to be co-axial with the residual fluorine density on this site, but residual H scattering was distributed on to the F(3), F(5) and F(6) sites (see Fig. S18).As with phase I, the total occupancy of the fluorine sites was heavily restrained to maintain the correct molecular formula of C6F5H.CIF files have been uploaded to the Cambridge Crystallographic Data Centre with deposition numbers 2287264-2287267.

S3. Powder X-ray diffraction (PXRD) experiments
A small amount of the liquid mixture of p-C6H4Me2:C6F5H was pipetted into the end of a 1.0 mm Xray capillary, shaken to the closed end, and then carefully flame-sealed to prevent sample loss, particularly of the more volatile component.The flame-sealed end was checked visually for integrity and the sample was used immediately in the PXRD experiment.Variable temperature powder X-ray diffraction (VT-PXRD) measurements were performed using a Stoe Stadi-P diffractometer equipped with a Cu anode, Ge<111> monochromator, a restricted height collimator to limit axial divergence, a Dectris Mythen 1K detector, and an Oxford Instruments CryojetHT (90-500 K) with an in-house modified sample setup to discourage the formation of ice on the goniometer head at low temperature.
The sample was flash-frozen by placing the capillary directly into the cold jet N2 gas of the CryojetHT precooled to 100 K to encourage formation of a crystalline powder.The temperature was raised from 100 K to room temperature in 10 K increments.At each temperature, the detector was scanned in 2θ from 2° to 60° in steps of 0.5° at 10 s per step, a complete scan lasting approx.30 min; each 10 K temperature change took approx.7-10 min and the sample was kept at the set temperature for 5 min before starting the next scan.
The primary purpose of our VT-PXRD analysis is the identification of phase transitions and the determination of lattice parameters and unit cell volume as a function of temperature as data collected for this purpose are not of sufficient statistical quality for structure analysis using the Rietveld method.Le Bail whole pattern fitting5 using the program Rietica6 (version 1.7.7) was used to refine the cell parameters from the data shown in Fig. S14.The results are tabulated in Table S5.It is noteworthy that large errors on the lattice parameters are likely to be obtained when the crystal system is triclinic, when a second impurity phase is present, and when the sample is not an ideal powder due to large crystallites as observed here; consequently, on several occasions inaccurate lattice parameters were obtained due to the presence of false minima and these fits had to be repeated.The variation in molecular volume (obtained by dividing the unit-cell volume by the number of molecules per cell, Z) with temperature is plotted in Fig. S15.

S4. Differential scanning calorimetry (DSC) experiments
37.4 mg of C6F6:C4H5N (prepared as 0.01 mol to 0.013 mol, 3:4 ratio) was loaded into an Al pan, covered with an Al lid, and crimped.The sample pan was then loaded into a PerkinElmer DSC8000 calorimeter at +20 °C.A helium purge gas was used (40 mL min −1 ).The sample was initially warmed to 30 °C (heating rate 10 °C min −1 ) and held at this temperature for 1 min.It was then cooled to −180 °C at 10 °C min −1 , held at low temperature for 1 min, and then heated back to 30 °C.The data is shown in Fig. S10.Subsequent data analysis to determine both peak maxima and peak area used the Pyris Thermal Analysis software (version 11.1.1.0492)from PerkinElmer.The data showed a sharp single exothermic peak at 240.2 K on cooling due to freezing of the liquid and a broader endothermic peak at 266.4 K on the return heating cycle due to melting of the solid.The enthalpy of fusion is S7 48 kJ mol −1 .It is noteworthy that an additional small exothermic peak observed at 233.3 K on cooling and the equivalent endothermic peak observed at 246.8 K on heating are attributed to a slight excess of C4H5N in the mixture from a handling loss of the more highly volatile C6F6.
As there was no suggestion of a phase transition in the SXD experiments on C6F6:C5H5N, no DSC data was obtained on this system.DSC data was obtained on p-C6H4Me2:C6F5H using the same protocol as for C6F6:C4H5N.The data is shown in Fig. S16.The mass of sample used was 18.930 mg with a similar scan to that used for C6F6:C5H5N, but with the final temperature limited to 20 °C.The DSC shows a sharp exothermic peak at 248.7 K on cooling due to freezing of the liquid and a broader endothermic peak at 256.5 K on the return heating cycle due to melting of the solid.The enthalpy of fusion is 20 kJ mol −1 .In addition, and in agreement with VT-PXRD, a solid-state phase transition was observed at low temperature.The enthalpy change on heating was 0.3 kJ mol −1 .On cooling, the observed transition temperature was at 125.8 K while on heating the transition was at 128.7 K.

S5. Hirshfeld surface calculations
Hirshfeld and electron density surfaces were calculated in the CrystalExplorer 7 software by selecting the desired fragment and using the "Generate Surface" function.

Table S2b
Fractional atomic coordinates and equivalent isotropic displacement parameters for C6F6:C5H5N at 150 K. Ueq is defined as ⅓ of the trace of the orthogonalised Uij tensor.

Table S3c
Anisotropic displacement parameters for phase I of p-C6H4Me2:C6F5H at 160 K.The anisotropic displacement factor exponent has the form:  16)

Table S3d
Selected bond lengths for phase I of p-C6H4Me2:C6F5H at 160 K.

Table S3e
Selected bond angles for phase I of p-C6H4Me2:C6F5H at 160 K.

Table S4b
Fractional atomic coordinates and equivalent isotropic displacement parameters for phase II of p-C6H4Me2:C6F5H at 120 K. Ueq is defined as ⅓ of the trace of the orthogonalised Uij tensor.

Table S4c
Anisotropic displacement parameters for phase II of p-C6H4Me2:C6F5H at 120 K.The anisotropic displacement factor exponent has the form:

Table S4e
Selected bond angles for phase II of p-C6H4Me2:C6F5H at 120 K.

Table S5
Lattice parameters and unit cell volume of p-C6H4Me2:C6F5H obtained from Le Bail fits to the VT-PXRD data shown in Fig. S14.Note that the fits for the unit cell of phase II used a unit cell with Z = 4 (as the cell is doubled along c and is I centred) where phase I is primitive triclinic with Z = 1.S5.

Figure S1
Figure S1 Photograph showing the experimental setup for the X−ray diffraction measurements.Microfocus X−ray sources (Cu and Mo) are seen on the left−hand side, the sample capillary (which is cooled with an Oxford Instruments Cryojet5) is seen mounted in a brass stub on the goniometer head, and the Rigaku HyPix−Arc 100° curved Hybrid Photon Counting (HPC) X−ray detector with "go−faster" blue lights is seen on the right−hand side of the image.

Figure
Figure S2 (a) An exemplar frame of raw X-ray data from one crystallisation attempt on (C6F6)3:(C4H5N)4 demonstrating that the sample in the beam is not suitable for crystal structure solution.There is no sign of diffraction spots at small d-spacings (rings of constant d with valuesshown in black).Secondly, the data at low angle shows poorly resolved spots lying on rings, behaviour that is typical of many small crystallites in the beam.(b) By contrast, another exemplar frame of raw X-ray data.The raw data seen here shows clean spots out to small d-spacing value even though some spots from different largish crystals are accidentally overlapped.

Figure S3 A
Figure S3 A subset of peak search data with a possible unit cell with the associated lattice for it highlighted in red and blue shown using the Ewald Explorer option within the CrysAlis PRO software from Rigaku.The genuine periodicity in reciprocal space is demonstrated from the sharp peaks seen in the distribution histograms along a*, b*, and c* directions on the right-hand side, which are shown in an enlarged format in the lower figure.

Figure S4
Figure S4This shows the same data as in Fig.S3but with the unindexed spots hidden to the viewer.The lattice formed by the diffraction spots is now more evident.

Figure S5
Figure S5 Peak search result from a full-sphere of data with unindexed spots hidden to the viewer.The distribution histograms along a*, b*, and c* directions on the right-hand side now show a clean and symmetric distribution about the mid-point.

Figure S6
Figure S6 Asymmetric unit from the refined crystal structure of (C6F6)3:(C4H5N)4 in space group P21/n at 150 K showing the crystallographic labelling of the atoms.H atoms are numbered according to the label of the atom to which they are bonded.The labels of a few H atoms are omitted for clarity.

Figure S7
Figure S7 Using the Olex2 program suite 3 , a view of the asymmetric unit of the crystal structure of (C6F6)3:(C4H5N)4 in space group P21/n at 150 K showing the refined positions and thermal displacements of the C, N, and F atoms.Positions of highest residual electron density are shown in brown and correspond to the 10 expected positions of the hydrogen atoms.

Figure
Figure S8 (a) View of the head to tail zig-zag arrangement formed by the molecules in the crystal structure of solid pyrrole as determined by Goddard et al. (1997) 8 with close contacts between rings shown as dashed cyan lines; (b) the contrasting tetramer unit formed by the pyrrole molecules in the asymmetric unit of the crystal structure of (C6F6)3:(C4H5N)4.

Figure
Figure S9 (a) Calculated electron density map for two molecules in (C6F6)3:(C4H5N)4 with areas of higher electron density presented in red and lower electron density in blue, and green is the neutral point; (b) the Hirshfeld surface for the same two molecules.For the Hirshfeld surface, closest contacts to atoms from other molecules are seen in red and voids between are shown in blue; white is the neutral point.

Figure S10
Figure S10 DSC data (shown as "endo up") on (C6F6)3:(C4H5N)4 prepared as a 3:4 molar ratio sample.The sample exhibits a sharp freezing point at 240.2 K on cooling (blue line) and no other solid−solid phase transitions down to 95 K. On heating (red line), the sample showed a broad melting transition at 266.4 K.The black vertical arrows show a transition due to the presence of a slight excess of pyrrole as a result of the high volatility of C6F6.

Figure S12
Figure S12 Refined crystal structure of C6F6:C5H5N in space group P212121 at 150 K viewed down a showing the crystallographic labelling of the atoms.H atoms are numbered according to the label of the atom to which they are bonded.

Figure
Figure S13 (a) Calculated electron density map for two molecules in C6F6:C5H5N; (b) the Hirshfeld surface for the same two molecules.The colour schemes are the same as those described in the caption to Fig. S9.

Figure S15
Figure S15Change in molecular volume relative to 100 K of p-C6H4Me2:C6F5H obtained by Le Bail fits to the VT-PXRD data shown in Fig.S14; the data is presented in TableS5.There is no noticeable change in the volume of p-C6H4Me2:C6F5H on passing through the phase transition, the only slight change is a very small expansion along the column axis c.The thermal expansion is mainly due to the increase in the distance between the columns of molecules with increasing temperature as evidenced by the change in the a and b values given in TableS5.

Figure S16 Figure S17 Figure S18
Figure S16 The curves show DSC data obtained on cooling (in blue) and heating (in red) for a sample of p-C6H4Me2:C6F5H.A single solid-state phase transition is observed on cooling (126 K) and heating (129 K).The DSC curves for this phase transition are shown on an expanded (×10) scale given the intensity of the peaks due to the freezing and melting transitions at 249 K and 257 K, respectively.

Table S2a .
Crystal data and structure refinement S12

Table S2b .
Fractional atomic coordinates and U(eq) for all atoms S13

SXD data for phase I of p-C6H4Me2:C6F5H at 160 KTable S3a .
Crystal data and structure refinement S15

Table S3b .
Fractional atomic coordinates and U(eq) for all atoms S16

S2.2. Crystal growing from equimolar mixture of C5H5N and C6F6
Ueq is defined as ⅓ of the trace of the orthogonalised Uij tensor.

Table S2a
Crystal data and structure refinement for C6F6:C5H5N at 150 K.

Table S3a
Crystal data and structure refinement for phase I of p-C6H4Me2:C6F5H at 160 K.

Table S3b
Fractional atomic coordinates and equivalent isotropic displacement parameters for phase I of p-C6H4Me2:C6F5H at 160 K. Ueq is defined as ⅓ of the trace of the orthogonalised Uij tensor.

Table S4a
Crystal data and structure refinement for phase II of p-C6H4Me2:C6F5H at 120 K.