E. J. Sonneveld

Application of simulated annealing approach for structure solution of molecular crystals from X-ray laboratory powder data

Abstract Simulated annealing approach was successfully applied to solve three unknown molecular structures from X-ray laboratory powder data using a priory known structural fragments. Some possible developments of the method are discussed.

Crystal structure determination of a series of small organic compounds from powder data

Abstract The crystal structures of 2,4-di-bromo-aniline (A; C6H5NBr2 ), 4-iodo-anisole (B; C7H7OI), 2-iodo-benzenemethanol (C; C7H7OI), 2-amino-benzothiazole (D; C7H6N2S) and 2-amino, 5-bromo-pyridine (E; C5H5N2Br) have been determined from X-ray powder diffraction data. Grid search and Rietveld refinement have been used to determine the structures. The crystals of (A) and (B) are orthorhombic, the crystals of (C), (D) and (E) are monoclinic. (A): Space group P212121, Z=4 with cell parameters a = 11.18(1), b = 16.17(1), c = 4.110(3)Å; (B): Space group Pca21, Z = 4, a = 6.288(4), b = 7.361(4), c = 16.93(1)Å; (C): Space group P21/n, Z = 4, a = 13.23(1), b = 4.652(3), c = 12.82(1)Å, β = 109.69(4)°; (D): Space group P21/c, Z = 4, a = 14.58(2), b = 4.094(4), c = 11.62(1)Å, β = 94.12(6)°; (E): Space group P21/c, Z = 4, a = 13.80(1), b = 5.839(5), c = 7.687(7)Å, β = 106.04(5)°. Chemical diagrams of all five compounds are depicted in Fig. 1. Soft constraints have been applied to the molecules during Rietveld refinement. The final Rp values obtained were 7.3 (A), 2.9 (B), 11.1 (C), 16.4 (D) and 7.9% (E) respectively. All compounds were measured on a Guinier camera. In addition, the structure of compound (A) was confirmed by single-crystal structure determination.

Visible spectra of crystalline anthraquinone colorants: the impact of crystal packing

Abstract The crystal structures of purpurin monohydrate and 1,4-dihydroxy-5,8-di-p-toluidinoanthraquinone were determined from single-crystal and powder X-ray diffraction data, respectively, and the visible reflection spectra of 18 crystalline colorants, (anthraquinones and related compounds) were obtained. Twelve of the compounds showed moderate (440–1090 cm−1) bathochromic shifts of their absorption maxima, compared to the solutions; other compounds exhibited greater bathochromic (up to 2900 cm−1) or hypsochromic (up to −1130 cm−1) shifts. For some of the compounds, the differences in colour between crystals and solutions are ascribable to the changes in molecular conformations or to the impact of hydrogen bonds.

Structures of tetrabromothiophene and tetrabromoselenophene: the influence of the heteroatom on the heterophene packing

The crystal structures of C(4)Br(4)S and C(4)Br(4)Se have been determined from X-ray powder diffraction data, using direct-space search techniques. In the case of C(4)Br(4)S two crystalline phases occur, a stable orthorhombic and a metastable monoclinic phase. For the orthorhombic phase two different structural models were found that fit the experimental data equally well. The diversity in crystal structure models and packings of C(4)Br(4)S is explained.

The crystal structure of sodium selenite Na2SeO3 from powder diffraction data

The crystal structure of sodium selenite, Na 2 SeO 3 , has been determined from X-ray powder diffraction data. The direct method package POWSIM has been used to determine the structure. The crystal structure is monoclinic, P2 1 /c, Z = 4, a = 4.8963(2) A, b = 9.9849(4) A, c = 6.8391(3) A, β = 91.994(3)° and V = 334.3 A 3 . The final R Bragg value obtained with Rietveld refinement was 3.3%. The structure consists of [NaO 6 ] octahedra and [SeO 3 ] pyramids which are linked together through their edges.

Metabolic pathways of dithiocarbamates from laboratory powder diffraction data.

In order to correlate the reactivity and molecular structures of dithiocarbamates, the crystal structures of 6-dimethylamino-5-nitropyrimidin-4-yl N,N-diethyldithiocarbamate, C11H17N5O2S2, (Ia), and 6-methylamino-5-nitropyrimidin-4-yl N,N-diethyldithiocarbamate, C10H15N5O2S2, (Ib), and of the product of thermolysis of (Ib), namely 4-diethylamino-6-methylamino-5-nitropyrimidinium chloride monohydrate, C9H16N5(O2)(+).Cl(-).H2O, (II), have been determined from X-ray laboratory powder diffraction data. Conformational preferences in (Ia) and (Ib) were studied on the density functional theory (DFT) level. Deviation of the reaction centre of the molecule from planarity and breakage of the secondary S...O contact cause switching between two alternative pathways of thermolysis.

Study of the reaction of 3,5-diamino-4-carbomethoxypyrazole with acetoacetic ester. Synthesis of pyrazolo[1,5-a]pyrimidine

X-Ray structural analysis has shown that condensation of 3,5-diamino-4-carbomethoxypyrazole with acetoacetic ester occurs to give derivatives of 7-oxopyrazolo[1,5-a]pyrimidine (rather than 5-oxo as proposed previously).

Intermolecular —CH3⋯O2N— contacts in two polymorphic modifications of (1E)-N'-[(E)-2-cyano-1-(dimethylamino)-2-nitrovinyl]-N,N-dimethyl­ethanimidamide

The title compound was synthesized and isolated in two crystal modifications. The structure of the orthorhombic modification was determined by the X-ray powder diffraction method and the structure of the monoclinic modification was determined using the X-ray single-crystal diffraction technique. The molecules in both polymorphs are E,E isomers. Intermolecular H(3)C....NO(2) contacts and their role in the formation of the polymorphic modifications are analyzed.

X-ray mapping in heterocyclic design: IV. Crystal structure determination of 3-(p-nitrobenzoyl)-2-oxooxazolo[3,2-a]pyridine from powder diffraction data.

The structure of 3-(p-nitrobenzoyl)-2-oxooxazolo[3,2-a]pyridine is determined by the powder diffraction technique. The crystals are monoclinic, a = 13.642(2) Å, b = 22.278(3) Å, c = 3.917(1) Å, β = 90.63(2)°, Z = 4, and space group P21/n. The structure is solved by a modified Monte Carlo method and refined by the Reitveld method. The six-membered heterocycle is characterized by the alternation of partially single and partially double bonds. The system of two conjugated heterocycles is planar and forms a dihedral angle of 46.1(1)° with the plane of the phenyl ring. The nitro group is virtually coplanar with the phenyl fragment. An extensive system of intramolecular and intermolecular contacts involving hydrogen, oxygen, and nitrogen atoms is observed in the crystal.

3,12-diaza-6,9-diazoniadispiro[5.2.5.2]hexadecane dichloride from X-ray powder data

The crystal structure of the title compound, C 12 H 26 N 2+ 4 .-2Cl - , was determined from X-ray laboratory powder data. All three rings adopt a chair conformation. Hydrogen bonds involving NH groups are absent from this structure.