Polymorphism of naphthazarin and its relation to solid-state proton transfer. Neutron and X-ray diffraction studies on naphthazarin C

Abstract

The crystal structure of naphthazarin C has been determined by neutron diffraction at 60 and 300 K (λ ═ 0.895 Å; 1 Å ═ 10 -10 m ═ 10 -1 nm) and X-ray diffraction at 300 K. The space group is Pc at 60 K, but P 2 1 /c at 300 K. There are small but significant differences in cell dimensions at the two temperatures: a ═ 7.664 (7.915), b ═ 7.304 (7.262), c ═ 15.16 (15.284) Å; β ═ 114.60 (114.20)°; Z ═ 4; U ═ 771.6 (801.3) Å 3 (values at 300 K in parentheses). Neutron diffraction shows that the Pc and P 2 1 /c structures are related by an order-disorder transition at 110±1 K. Structure analysis (1771 reflections; R F ═ 0.035; R W ═ 0.036) showed that the hydroxyl hydrogens are largely ordered at 60 K, the appropriate molecular formula being 5, 8-dihydroxy-1, 4-naphthadione. Neutron diffraction measurements at 300 K (1769 reflections; R F ═ 0.052) indicated a disordered molecular model with one-half of an hydrogen atom attached to each oxygen. X -ray diffraction measurements on naphthazarin C at 300 K (two independent sets of intensity measurements, one with CuKα and the other with MoKα) support this disordered model. The molecular dimensions for naphthazarin A and B also fit this model. Comparison of the crystal structure of naphthazarin C with those of the A and B polymorphs shows that only the former has intermolecular O─H • • • O hydrogen bonding. The diffraction results combined with the available solid-state n. m. r. data show that there is at room temperature a rapid intramolecular exchange of hydroxylic protons between each pair of oxygen atoms in all three naphthazarin polymorphs. Many 1, 3-diketones exist in an enol form in the solid. These enol forms have been reported to be disordered for about twenty molecules at room temperature (this total includes one molecule studied at 108 K, and four amino-imino systems) and ordered systems have been reported for about fifteen molecules. Intermolecular hydrogen bonding occurs only in a few of these crystals.

Ab initio HF-SCF study of naphthazarin: Geometries, isomerism, hydrogen bonding, and vibrational spectrum

“…Some selected bond distances obtained in this work at various levels of theory, and those of previous AM 1 [1] and HF/STO-3G [10] studies are compared with the geometrical parameters derived from low-temperature neutron diffraction [4] (see Table II). Although the dependence on the basis set is appreciable, the geometries obtained from ab initio and AM 1 calculations are consistent with the experimental data, and the deviations of the theoretical bond distances from the observed ones are smaller for the HF/6-31G geometry.…”

“…On the grounds of the theoretical and experimental ge- (3) 1.577 (7) 2.620 (8) dNaphthazarin C from neutron diffraction at 60 K (Ref. 4). The least-square standard deviations are reported as units in the last digit.…”

“…1) having different point group symmetry. The X-ray results [4], combined with NMR spectroscopy data of the solid [9], indicate that there is a rapid proton exchange between the adjacent oxygen atoms at room temperature in all three polymorphs and the resulting structures are centrosymmetrical. At low temperature, naphthazarin undergoes a phase modification caused by changes in the hydrogen bond, and the molecular structure determined from 60 K neutron diffraction data shows C2v symmetry (Fig.…”

“…In spite of the fact that crystallographic information is available for some systems, such as naphthazarin [4], 9-hydroxyphenalenone [5], and 1,4-dihydroxyanthraquinone [6], studies of the structure of the isolated molecule are still limited to a few spectroscopic investigations [7]. It is therefore worthwhile to examining the structural and energetic properties of some of these molecules by theoretical and experimental approaches.…”

“…The crystal structure of naphthazarin has been the subject of numerous X-ray and neutron diffraction [4], spectroscopic [8], and NMR [9] investigations (for a summary of the structural work see ReL 4). Naphthazarin crystallizes in three polymorphic forms at room temperature, and there is a phase change at lower temperature [4]. The location of the proton between each pair of oxygen atoms gives rise to distinct configurations for this molecule ( Fig.…”