XFEL Microcrystallography of Self-Assembling Silver n-Alkanethiolates

Abstract

New synthetic hybrid materials and their increasing complexity have placed growing demands on crystal growth for single-crystal X-ray diffraction analysis. Unfortunately, not all chemical systems are conducive to the isolation of single crystals for traditional characterization. Here, small-molecule serial femtosecond crystallography (smSFX) at atomic resolution (0.833 Å) is employed to characterize microcrystalline silver n-alkanethiolates with various alkyl chain lengths at X-ray free electron laser facilities, resolving long-standing controversies regarding the atomic connectivity and odd-even effects of layer stacking. smSFX provides high-quality crystal structures directly from the powder of the true unknowns, a capability that is particularly useful for systems having notoriously small or defective crystals. We present crystal structures of silver n-butanethiolate (C4), silver n-hexanethiolate (C6), and silver n-nonanethiolate (C9). We show that an odd-even effect originates from the orientation of the terminal methyl group and its role in packing efficiency. We also propose a secondary odd-even effect involving multiple mosaic blocks in the crystals containing even-numbered chains, identified by selected-area electron diffraction measurements. We conclude with a discussion of the merits of the synthetic preparation for the preparation of microdiffraction specimens and compare the long-range order in these crystals to that of self-assembled monolayers.

Figure 1:

a) Illustration of the synthetic approach used to prepare alkanethiolates. b) Schematic of smSFX experiment showing how randomly oriented microcrystals interact with the XFEL pulse for the collection of partial diffraction frames recorded on the detector (blue). (c) Alkyl chain lengths studied range from two (2) to twelve (12). d) A space-filling perspective model of the C9 crystal structure depicting the general organization of the silver n-alkanethiolates. The silver atoms (blue) are in a nominally 2D layer, coordinated by the sulfur atoms. Note that alkyl chains are packed end-to-end.

Figure 2:

Example morphologies of the various silver n-alkanethiolates over the range of chain length 4-12. For this work, C2, C3, and C12 morphologies proved a poor match for smSFX characterization because of a lack of single microcrystals in the residue. All examples have nominally similar habits and there are examples of long and short crystals of most in the series.

Figure 3:

A) Atomic force topography of a C12 crystal terraces with well-defined molecular step edges and its rendering in 3D. Each terrace presents the methyl terminus of the layers. Surfaces are largely featureless over many microns with no clear evidence of corrugation, vacancies, or domain boundaries. B) An assortment of aggregated crystals from C9-C12. Each is largely featureless on its outermost surface and isolated step edges (as in A) were rare in these samples.

Figure 4:

a,c,e) Cross-sectional views of the C4, C6, and C9 smSFX crystal structures down the c axis. The unit cell dimensions are outlined in black. The 22° tilt of the chains from the surface normal direction is conserved across all chain lengths. b,d,f) Viewing the crystals down the b axis (view is towards the crystal basal plane) shows the conservation of azimuthal angle and its offset from the principal lattice directions. The purple arrows give the relative orientation of the alkyl chains determined analytically by projecting a vector passing between first and last pairs of carbon atoms onto the ca plane. It is approximately parallel to a*.

Figure 5:

a-d) Brightfield TEM micrographs and schematics depict the orientation of the principal lattice vectors with the crystal (a and c: real space vectors, a* and c*: reciprocal space vectors. a and a* do not align due to monoclinic symmetry). Assignments were made based on the C9 unit cell. The area in each overlain circle was used for selected-area electron diffraction measurements. e-h) The SAED patterns were indexed using the C9 unit cell as a guide. Both allowed and forbidden reflections are observed in the SAED (e.g. 1 0 0 is forbidden in space group P 2₁/n). For C10 and C12 (f and h), additional Bragg spots are observed that may be explained by reticular twinning, involving a two-fold rotation about the a axis, generating the blue model with primed axes and Miller index numbering (supplemental Fig. S5b). Also, white rectangles highlight extremely faint spots that might indicate c-axis doubling (supplemental Fig. S5c).

Figure 6:

The odd-even effect in interfacial packing is attributed to differences in packing efficiency at the methyl-methyl interface between layers. Packing patterns are visualized by modeling terminal methyl groups as spheres having a radius of 2 Å that are color-coded by sub-layer. a) Even-numbered alkyl chains in C4 and C6 have a slightly expanded unit cell along the b axis relative to the b) odd-numbered C9 system, which is slightly contracted. c) All atoms are hidden except the color-coded methyl groups. Van der Waals contact between a given methyl group and three methyl groups in the next layer creates an effective three-fold hollow (eg. the D/A interface, labeled red and black respectively. The next interface is the B/C interface, labeled purple and blue, respectively. A section of the D/A interface is cut away to reveal B/C. These two interfaces are non-superimposable and there is a small offset between the two interfaces reducing registry. The white arrows indicate the gaps opened by shifting into the 3-fold hollow. d) The methyl groups are well-registered between layers in C9, and the methyl groups are more centered in a 4-fold hollow. Unit cell dimensions are noted as black (even) and red (odd) boxes. Arrows are meant to show the tilt of the various molecules making up each sub-layer.