Crystal structure of indole under ambient conditions (orthorhombic, Pna21). (a) Viewing down c-axis, the two sets of molecules are at different viewing depths, grey is closer to viewer. The green vectors are perpendicular to the average molecular plane and define the interplanar angle. (b) Viewing down b-axis where the coloring is the same as in (a). Grey/taupe: carbon, white: hydrogen, and blue: nitrogen.
Indole molecule and the bicyclic angle. (a) Calculated indole molecular structure at ambient pressure. The bicyclic angle is defined by a torsion angle (blue dotted lines and arc), which begins at one ring's center of mass, passes through the molecular hinge (C8 and C9), and ends at the second center of mass. (b) Absolute value of the bicyclic angle as a function of pressure. Open symbols indicate the pyrrole moiety is bent towards molecule 6 of Figure 3 (positive angle value); solid symbols the pyrrole moiety is bent away (negative angle value). Blue vertical line represents symmetry changes in the crystal. Red lines indicate notable discontinuities.
Nearest neighbor centers of mass in crystalline indole at (a) ambient pressure and (b) as a function of pressure. In (a), red molecules (inequivalent) have both N–H···π and C–H···π interactions with the central green molecule. Turquoise molecules (inequivalent) have only C–H···π interactions with the central green molecule. Purple molecules (equivalent) have π···π interactions with the green central molecule. In b, nearest neighbor COM distances as a function of pressure for molecules 1 and 4 are represented by purple diamonds, for molecules 2 and 6, red triangles and those involving molecules 3 and 5 are represented as turquoise squares. Blue vertical lines represent symmetry changes in the crystal. Red lines indicate notable discontinuities.
Simulated powder XRD patterns of crystalline indole at selected isostatic pressures, using Cu Kα1 radiation.
Relative contributions to the Hirshfeld surface area for the intermolecular close contacts as a function of pressure. In c, the N···H contacts are on the secondary axis (3.5%–6%). Blue vertical lines represent symmetry changes in the crystal. Red lines indicate notable discontinuities.
Unit cell parameters (a, b, c) and density as a function of isostatic pressure of indole. Blue vertical lines represent symmetry changes in the crystal. Red lines indicate notable discontinuities.
Motif assignment via classical (see Ref. 15 and 16) and π° parameters (see Ref. 19) for the calculated structures. (a) Classical motif categorization. Red circles are in order of increasing pressure from right to left; black rectangle represents the “forbidden zone.” Blue vertical lines represent symmetry changes in the crystal. Red lines indicate notable discontinuities. (b) Motif categorization via π°. Numbers on plot represent pressures (GPa).
Hirshfeld surfaces mapped with D norm and corresponding fingerprint plots as a function of pressure. The first two rows demonstrate the Hirshfeld surface with respect to the molecular orientations (both the front and back of the molecule are shown as the environment is anisotropic). D norm coloring scheme is standardized (color scale min: −0.68; max: 0.38). Fingerprint plots correspond to the above Hirshfeld surfaces. Red circles in the fingerprint plots represent π···π contacts, black ovals represent H···π contacts, and orange circles represent H···H contacts.
Closest contact patterns in crystalline indole under representative isostatic pressures (measurements in Å): (a) ambient condition (b) 5 GPa and (c) 25 GPa. Supercells of 1 × 2 × 1 are used to demonstrate intermolecular relationships. Looking down c-axis where the ball and stick molecules are layered in front of the wire structures. H-atoms are omitted from the structures for clarity.
Reaction of indole molecules when the molecules approach each other along the long molecular axis. Only the reacting molecules are shown for clarity. Corresponding electron density isosurfaces, at the isovalue of 1 electron, are shown to demonstrate bonding. (a) Equilibrium structure under 25 GPa. (b) Transition state. (c) Equilibrium structure when the molecules reacted.
Experimental and calculated unit cell parameters, densities, and bicyclic angles for crystalline indole.
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