The use of restraints in Rietveld refinement of molecular compounds; a case study using the crystal structure determination of tryptamine free base

The previously unknown crystal structure of the biogenic compound tryptamine, in the form of a free base (C₁₀H₁₂N₂), has been solved from X-ray powder diffraction data using simulated annealing followed by restrained Rietveld refinement [space group P2₁2₁2₁, a = 12.28593 (6), b = 8.53351 (4), c = 8.49385 (4) Å, Z = 4, final reduced-χ² = 5.255]. A restrained Rietveld refinement was carried out in which the global weight factor, f, of the stereochemical restraints was gradually lowered. The effect of the relaxation of restraints on the crystal structure and on χ² was studied and a criterion for the final choice of f is reported. The crystal structure reported here shows efficient packing involving weak intermolecular hydrogen bonding and a herringbone-type packing pattern.

Computing details

Figures

(TRYPT_phase_1)

Crystal data

?	c = 8.49385 (4) Å
Mr = ?	V = ? Å^3
Orthorhombic, P212121	Z = ?
a = 12.28593 (6) Å	? radiation, λ = ? Å
b = 8.53351 (4) Å	?, ? × ? × ? mm

Data collection

Refinement

Rp = ?	χ^2 = NOT FOUND
Rwp = ?	? data points
Rexp = ?

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq
C1	0.2030 (4)	0.8790 (7)	1.0953 (5)	0.0464 (7)*
C2	0.3076 (4)	0.9420 (6)	1.0836 (5)	0.0464 (7)*
C3	0.3748 (4)	0.9048 (7)	0.9605 (6)	0.0464 (7)*
C4	0.1659 (4)	0.7708 (6)	0.9885 (6)	0.0464 (7)*
C5	0.2333 (3)	0.7249 (6)	0.8653 (5)	0.0464 (7)*
C6	0.3376 (3)	0.7930 (6)	0.8526 (5)	0.0464 (7)*
N7	0.3864 (3)	0.7303 (5)	0.7217 (5)	0.0507 (14)*
C8	0.3178 (4)	0.6250 (7)	0.6542 (5)	0.0464 (7)*
C9	0.2223 (3)	0.6177 (6)	0.7353 (5)	0.0464 (7)*
H10	0.4567 (13)	0.728 (3)	0.708 (3)	0.025*
C11	0.1234 (4)	0.5241 (5)	0.6943 (6)	0.0464 (7)*
C12	0.0430 (4)	0.6098 (7)	0.5890 (6)	0.0464 (7)*
N13	0.0819 (4)	0.6579 (6)	0.4376 (6)	0.0507 (14)*
H14	0.4495 (16)	0.943 (4)	0.957 (3)	0.025*
H15	0.3254 (15)	1.033 (3)	1.143 (3)	0.025*
H16	0.1661 (17)	0.885 (3)	1.195 (2)	0.025*
H17	0.3334 (17)	0.581 (4)	0.553 (3)	0.025*
H18	0.1453 (11)	0.4220 (19)	0.647 (2)	0.025*
H19	0.0863 (11)	0.4921 (19)	0.7917 (18)	0.025*
H20	0.0922 (18)	0.726 (4)	0.998 (3)	0.025*
H21	−0.0196 (13)	0.540 (2)	0.5740 (17)	0.025*
H22	0.0158 (18)	0.7059 (18)	0.6429 (18)	0.025*
H23	0.108 (3)	0.574 (2)	0.378 (3)	0.025*
H24	0.126 (3)	0.748 (3)	0.432 (3)	0.025*