A simple refinement of density distributions of bonding electrons. IX. Bond electron density distribution in thiourea, CS(NH₂)₂, at 123K

Abstract

A model for thiourea is described in which valence electrons are included separately in the refinement. A :significantly better R value is obtained for this model (0.017) compared with the usual spherical atom refinement (0.025). Core parameters agree within 2.5o with those from the neutron diffraction study [Elcombe & Taylor (1968). Acta Cryst. A24, 410-4201. Bond population parameters are given, and a dynamic valence density based on the refined model is presented. This density is compared with the valence density of urea . Acta Cryst. B34, 1624-16271. REFINEMENT OF DENSITY DISTRIBUTIONS OF BONDING ELECTRONS. IX Introduction Refinement of a model including valence electronsThis study of thiourea represents a continuation of the work in which a model describing valence density distributions is refined (HeUner, 1977;Mullen & Hellner, 1977). In a previous paper , the same valence density model was applied to urea, and a comparison of the two molecules is given below.Thiourea has been studied by X-ray diffraction (Truter, 1967), by neutron diffraction (Elcombe & Taylor, 1968, hereafter ET) and by electron diffraction (Dvoryankina & Vainshtein, 1960). Thiourea undergoes a series of phase changes on cooling below room temperature (Goldsmith & White, 1959). While at room temperature there is only one molecule in the asymmetric unit, at 123 K there are two independent molecules. ExperimentalA crystal of thiourea was ground to a sphere of 0.50 mm diameter. Three-dimensional X-ray data at 123 _+ 2 K were collected on a Philips (PW 1100) four-circle diffractometer equipped with a Heraeus-Leybold liquid nitrogen cryostat. Four symmetry-equivalent octants were measured to sin 0/2 = 0.90 /~-l using graphite monochromated Mo Ktt radiation. Agreement between symmetry-equivalent reflections was 2.8%. A total of 1142 independent reflections were obtained, of which 21 had F _< 2tr(F) and were designated as unobserved. The averaged data were corrected for Lorentz and polarization effects and for absorption (# = 6.29 cm-m). An isotropic extinction correction was applied using Finger's (1972) program. The highest extinction correction factor (applied to F 2) was 0.63.Cell dimensions at 123 K were measured as a = 7-487 (3), b = 8.536 (3) and c = 5.474 (3) A. At this temperature thiourea crystallizes in the orthorhombic space group P2 lma [Pmc21, International Tables for X-ray Crystallography (1952)]. For the starting model in the refinement, core parameters were taken from the neutron diffraction investigation of ET at 115 K. Bond charges were placed at the mid-points of bonds. The lone pairs on S and N were placed at the respective core positions, but allowed to move from these positions on refinement.For the cores, form factors were taken from International Tables for X-ray Crystallography (1974).Bond charges were given Gaussian form factors described by flu tensors. The C=S bonds were given populations of 4 electrons, the C-N bonds 2 e and the N-H bonds 1.5 e in the starting model. The H atoms were allocated 0-5 e.In the f...

A critical analysis of dipole-moment calculations as obtained from experimental and theoretical structure factors

“…A similar point-charge model has already been applied in a few cases in the literature: it was reported for urea (Scheringer, Kutoglu et al, 1978;Mullen & Hellner, 1978a), thiourea (Scheringer, Kutoglu et al, 1978;Mullen & Hellner, 1978b), diborane (Mullen & Hellner, 1977;, decaborane (Dietrich et al, 1979), cyanuric acid (Dietrich et al, 1979) and silicon (Scheringer, 1980). More recently, a bond scatterers model was applied by Afonine et al (2004Afonine et al ( , 2007 for ultra-high-resolution protein refinement.…”

Aminoguanidinium nitrate

“…Several guanidinium salts have been studied over the last two decades (Adams & Small, 1974) and the chloride (Bryden, 1957), dihydrogenphosphate (Adams, 1977) and sulfate (Mullen & Hellner, 1978) salts have been structurally characterized. In the oxoanion salts, multiple hydrogen bonds to O atoms are present, each O atom accepting three H atoms.…”

Structure and charge density of the 1:1 complex of thiourea with parabanic acid at 298 K

“…Thus the region near the S atom is almost featureless for both molecules A and B in the crystal structure ofthiourea. To enable more direct comparisons to be made, we have carried out new refinements based on the X-ray data for thiourea collected at 123 K by Mullen & Hellner (1978) and subsequently revised by Kutoglu et al (1982). We assumed the same pseudoatom structure model that was used for TUPA.…”