Ab Initio Structure Solution Research Articles

Ab-initio structure solution without the use of atomicity

Ab-initio structure solution without the use of atomicity

Single-crystal characterization of Co7(OH)6(H2O)3(C4H4O4)4⋅7H2O; A new cobalt succinate identified through high-throughput synthesis

A new form of cobalt succinate has been discovered using high-throughput methods and its structure was solved by single crystal X-ray diffraction. Co7(C4H4O4)4(OH)6(H2O)3⋅7H2O crystallizes in the monoclinic space group P21/c with cell parameters: a=7.888(2) Å, b=19.082(6) Å, c=23.630(7) Å, β=91.700(5)°, V=3555(2) Å3, R1=0.0469. This complex structure, containing 55 crystallographically distinct non-hydrogen atoms, is compared to the previously reported nickel phase, characterized using ab initio structure solution from synchrotron powder diffraction data.

Structure and Luminescence of 2D Dilute Magnetic Semiconductors: Cd1-xMnxSe·L0.5 (L = Diamines)

The two-dimensional (2D) dilute magnetic semiconductors Cd1-xMnxSe·L0.5 (L = ethylenediamine, or en, and 1,6-hexanediamine, or hda, x = 0−0.8) were synthesized in an autoclave at 120 °C. Ab initio structure solution from X-ray powder diffraction reveals the host compound CdSe·hda0.5 (space group, Pbca, a = 6.8852 Å, b = 6.7894 Å, c = 27.4113 Å) is structurally analogous to CdSe·en0.5, except for a subtle difference in alignment of aliphatic diamine ligandsthe hda molecule deflects from the c axis and inclines toward the b axis. CdSe·L0.5 shows well-defined UV absorption and emission peaks, which is attributed to a 2D exciton band edge transition due to size confinement effect in the c direction and the only photoemission level is the 2D exciton ground state with a long lifetime (7 μs) and intrinsic line width (177 meV) at room temperature. When Cd2+ is partly substituted by Mn2+, a strong Mn2+-related luminescence peak at 2.12 eV (584 nm) is obtained at room temperature, which can be assigned to Mn2+ internal transition (4T1 → 6A1); its excitation peak overlaps with the photoemission peak of the 2D exciton ground state which indicates that the Mn2+ emission is driven by the 2D exciton ground-state transition. For x = 0.02, the photoluminescence intensity of Cd1-xMnxSe·hda0.5 reaches maximum and enhances 28 times compared with that of Cd1-xMnxSe·en. When x < 0.05, the Mn2+ luminescence is a characteristic single-exponential decay process with a well-defined constant lifetime of 375 μs. Electron spin resonance spectra show that Mn2+ substitutes Cd2+ ion and forms a [MnSe3N] coordination tetrahedron and that there are isolated Mn2+ luminescence centers in Cd1-xMnxSe·hda0.5 (x < 0.05), which is the key factor for their stronger luminescence character compared to Cd1-xMnxSe·en0.5.

Rationalizing the Structural Properties of Bupivacaine Base—A Local Anesthetic—Directly from Powder X-Ray Diffraction Data

Bupivacaine belongs to a family of 1-alkyl-2′,6′-pipecoloxylidides, which has shown promise as reversible action potential blockers that can introduce prolonged local anesthetic effects. The crystal structure of the free-base form of bupivacaine has been determined directly from powder X-ray diffraction data using the Genetic Algorithm technique for structure solution, followed by Rietveld refinement. This work further emphasizes the scope and utility of ab initio structure solution directly from powder X-ray diffraction data for tackling structural problems within the biomedical field, leading to opportunities for the investigation of structure–property relationships. © 2004 Wiley-Liss, Inc. and the American Pharmacists Association

Completion of Crystal Structure with Polyhedral Coordination: A New Procedure

The ab-initio crystal structure solution via powder diffraction data is often uncomplete. A recent procedure POLPO [1] aims at completing a partial structure model provided by Direct Methods by exploiting the prior information on the polyhedral coordination of the located atoms (tetrahedral or octahedral) and their connectivity has been developed. The POLPO procedure requires that all the cations are correctly labelled and rightly located. This condition does not always occur, particularly when the data quality is poor. A new method is described which is able to locate missing cations and surrounding anions when the cation coordination is tetrahedral or octahedral.

Ab Initio Structure Solution of Icosahedral Cd-Yb Quasicrystals by a Density Modification Method

The six-dimensional (6D) low density elimination method has been applied to solve an icosahedral Cd-Yb quasicrystal. It shows that i-Cd-Yb is composed of similar atomic clusters that exist in the cubic approximant crystals, but the inner most shell is highly disordered. A construction of the 6D cluster model of i-Cd-Yb is outlined.

Direct structure determination of a multicomponent molecular crystal prepared by a solid-state grinding procedure.

A three-component molecular cocrystal material has been prepared by a solvent-free route involving mechanical grinding of the pure phases of the individual components. This material is not accessible from conventional solution-state crystallization procedures. Due to the fact that the grinding procedure intrinsically leads to a microcrystalline powder sample, the use of powder X-ray diffraction data is essential for structure determination. This work emphasizes the scope and utility of ab initio structure solution directly from powder X-ray diffraction data for carrying out structural characterization of new materials prepared via the solid-state grinding route, leading to the opportunity to establish structure-property relationships for such materials.

Polymorphism of a Novel Sodium Ion Channel Blocker

2‐{[4‐(4‐Fluorophenoxy)phenyl]‐methylene}‐hydrazinecarboxamide, a member of the semicarbazone family which has shown potential therapeutic use as anticonvulsants, has been found to exist in two polymorphic forms denoted A and B. In addition to reporting aspects of the physical characterization of both forms, the crystal structure of polymorph A has been determined directly from powder X‐ray diffraction data using the Genetic Algorithm technique for structure solution, followed by Rietveld refinement. This structure is compared with that of polymorph B, which was determined previously from single crystal X‐ray diffraction data. Knowledge of the crystal structures of the two polymorphs provides the opportunity for establishing structure‐property relationships. This work further emphasizes the scope and utility of ab initio structure solution from powder X‐ray diffraction data in the pharmaceuticals field. © 2003 Wiley‐Liss, Inc. and the American Pharmacists Association J Pharm Sci 92:2017–2026, 2003

Ab initio protein phasing at 1.4 A resolution.

All the techniques today available for the ab initio crystal structure solution of proteins require that the atomicity condition is satisfied. Accordingly, diffraction data at resolution equal or better than 1.2 A are necessary. This condition reduces the role of the ab initio techniques in macromolecular crystallography. The computer program SIR2002 has been modified in such a way that it may succeed also with 1.4 A resolution diffraction data. The modifications concern all the modules of the program: the modified program also benefits by the efficiency of a figure of merit.

Ab initio structure study from in-house powder diffraction of a novel ZnS(EN)0.5 structure with layered wurtzite ZnS fragment.

The solvothermal reaction of elemental zinc with sulfur in ethylenediamine (en) as solvent yields [ZnS-0.5(NH2CH2CH2NH2)], 1, an unprecedented ethylenediamine pillared ZnS layered compound, containing two dimensional (2-D) boat-type 6-membered rings, which was characterized by ab initio structure solution from powder diffraction data (SDPD).

The Solid State Structures of Potassium and Rubidium Salicylate by High Resolution X-Ray Powder Diffraction

We report the ab initio structure solution of rubidiumsalicylate C7H5O3Rb and the crystal packing of potassium-salicylate C7H5O3K by high resolution X-ray powder diffraction. The compounds are of interest for the understanding of the mechanism of Kolbe-Schmitt type reactions. C7H5O3Rb (I) crystallizes in space group P21/n, Z = 4, with unit cell parameters a = 7.2110(1) Å, b = 26.5258(3) Å, c = 4.23110(6) Å, β = 106.843(1)?, and V = 774.60(2) Å3. C7H5O3K (II) crystallizes in space group P&1macr;, Z = 2, with unit cell parameters a = 7.3575(2), b = 13.6399(3), c = 3.8622(1) Å, α = 95.955(4)?, β = 103.326(2)?, γ = 92.994(4)?, and V = 373.95(2) Å3. Both compounds exhibit similar crystal packing schemes and consist of layers of distorted RbO8 resp. KO7 polyhedra perpendicular to the b-axis and phenol rings almost perpendicular to the layers pointing up and down. The molecular structure is held together by van der Waals forces between the phenyl groups of different layers. The sample of C7H5O3K shows extremely anisotropic peak broadening and stacking faults which could not be satisfactory modeled by the available models.

Ab initio structure solutions of quasicrystals by a density modification method

A unique and powerful density modification method for solving multi-dimensional crystal structures has been developed. The method is an extension of the Low Density Elimination (LDE) method1,2,3. The LDE method was made applicable to multi-dimensional crystal structures and applied to several quasicrystals including an unknown structure. Tests on the X-ray single crystal data of icosahedral AlPdMn4 and synthetic data of decagonal AlNiCo quasicrystals suggests that the multi-dimensional LDE method can easily solve quasicrystal structures starting from completely random phases. The procedure has also been applied to an unknown structure of icosahedral ZnMgHo quasicrystal. Multi-solution strategy was employed and 28 resultant maps clearly showed the positions and shapes of occupation domains. We were convinced by analyzing the map that the 28 results were the solutions.

Tetracycline hydrochloride: a synchrotron microcrystal study.

The title compound, [(4S,4aS,5aS,6S,12aS)-2-aminohydroxymethylene-1, 2,3,4,4a,5,5a,6,11,12a-decahydro-6,10,12,12a-tetrahydroxy-6-methyl -1, 3,11-trioxonaphthacen-4-yl]dimethylammonium chloride, C(22)H(25)N(2)O(8)(+).Cl(-), a well known antibiotic, has been structurally characterized from an individual coarse powder grain by use of high-intensity synchrotron radiation, in conjunction with an exercise in ab initio powder diffraction structure solution. Free refinement of all H atoms establishes the major tautomeric form of the protonated tetracycline molecule without prejudice. The molecule has extensive intramolecular hydrogen bonding involving most of the potential donors and acceptors, and all intermolecular hydrogen bonding uses the chloride anion as acceptor.

Anomalous scattering for small-molecule crystallography

Anomalous dispersion techniques in small-molecule crystallography have been used in recent years with the advent of intense tunable X-radiation from synchrotron X-ray sources. By tuning the wavelength of the radiation close to the absorption edges of specific elements, it is possible to identify and distinguish between atoms which are close together in atomic number, even when two or more such atoms occupy a single site. Anomalous dispersion techniques can also be used to distinguish between valence states of different sites of an element by the valence contrast method or to determine the coordination geometry of an atom. In some cases, when the coordination of an atom is asymmetric, the absorption-edge position may depend on the orientation of the crystal. Finally, anomalous dispersion techniques can be used for ab initio structure solution from powder diffraction data. The properties of microporous materials often depend on the incorporation of metal atoms into the framework. Two or more metal atoms close together in atomic number may be incorporated, sometimes occupying a single site. In one study the site of an Ni atom in the aluminophosphate NiAPO was determined by anomalous dispersion techniques and data from the NSLS. Also, the location of the isomorphously substituted cobalt over two crystallographically different zinc sites was determined in the zincophosphate CoZnPO-CZP, in a five-wavelength study using data from ELETTRA.

Crystal structures and phase behaviour of acetaldehyde- d4: a study by high-resolution neutron powder diffraction and calorimetry

High-resolution neutron powder diffraction is particularly suited for structure solution and refinement of low-melting point organic crystals of moderate complexity. Here we present the ab initio structure solution and refinement of stable-phase and metastable-phase perdeuterated acetaldehyde (m.p.: 151 K). In the stable phase, the molecule crystallises in the space group P2 1/c (no. 14) with a=3.9069(1) A ̊ , b=5.4224(1) A ̊ , c=12.1868(1) A ̊ , β=94.2970(2)° at 5 K, Z=4. In the metastable phase, the molecule crystallises in the space group Pna2 1 (no. 33) with a=5.1973(1) A ̊ , b=6.9791(1) A ̊ , c=6.9712(1) A ̊ at 5 K, Z=4. The metastable to stable phase transition is characterised by heat capacity measurements.

Ab initio structural approach on polycrystalline Y2 – x Ca x BaNiO5 (0 ≤ x ≤ 0.33) compounds

Abstract The procedure of ab initio structure solution from conventional X-ray powder diffraction data is successfully applied to a series of Y2–x Ca x BaNiO5 compounds (0 ≤ x ≤ 0.33). The study aimed at understanding if the presence of dopants in polycrystalline Y2BaNiO5 compound can influence the success of the structure determination process and at quantifying the substitutional defect. The new code EXPO has been used to obtain the most accurate set of structure factor moduli and to perform the direct methods procedure. It is demonstrated that the substitution on a crystallographic site, as for the above mentioned compound, does not compromise the performance of direct methods. The structural parameters obtained for samples with different x values are compared with those reported in the literature. It is pointed out that the knowledge of the dependence of lattice parameter and cell volume values on the cation site occupancy factors allows the direct determination of the degree of substitution of calcium on yttrium site of the sample.

Powder Structure Solutions of the Compounds Potassium Phenoxide-Phenol: C(6)H(5)OK.xC(6)H(5)OH (x = 2, 3).

We report the ab initio structure solutions of two solvent containing potassium phenoxides by high-resolution powder X-ray diffraction. Both compounds are of interest for the classification of the mechanism of Kolbe-Schmitt type reactions. C(6)H(5)OK.2C(6)H(5)OH crystallizes in space group Abm2, Z = 4, with unit cell parameters a = 10.12458(4) Å, b = 21.2413(1) Å, c = 7.89784(3) Å. C(6)H(5)OK.3C(6)H(5)OH crystallizes in space group Pbca, Z = 8, with unit cell parameters a = 22.7713(1) Å, b = 25.4479(2) Å, c = 7.75549(4) Å. Both compounds show polymeric zigzag chains [K([6])O(2)([2])O([1])pi(phenyl)([1])] aligned along the c-axis. The coordination of the potassium ions is similar for both compounds. They lie at the center of distorted octahedra of five oxygen atoms and one phenyl ring, which donates its pi electrons. The distortion decreases as the number of free phenol increases.

A simplified, texture-based method for intensity determination of overlapping reflections in powder diffraction

Powder diffraction intensities are almost always affected by texture (preferred orientation) and overlapping of the maxima, which make phase analysis or ab initio structure solution and refinement difficult or even impossible. An attempt at partial elimination of the problem of overlapping reflections using texture as an intensity-separating `device' is described.

Structure of ITQ-4, a New Pure Silica Polymorph Containing Large Pores and a Large Void Volume

The new pure silica polymorph ITQ-4, structure code IFR, Si32O64, monoclinic I2/m a = 18.65243(13), b = 13.49597(8), c = 7.63109(6) Å, β = 101.9781(5)°, is a zeolitic material containing a large sinusoidal channel with 12-member ring windows as minimum apertures. Its void volume (0.21 cm3/g) is surpassed only by that of pure silica Beta among the known pure silica polymorphs. The success of the ab initio structure solution from synchrotron powder diffraction data was greatly assisted by the absence of Al and Si−OH defect groups, which generates a very high degree of crystallographic order.

Novel Alkali-Metal Coordination in Phenoxides: Powder Diffraction Results on C(6)H(5)OM (M = Li, Na, K, Rb, Cs).

We report the ab initio structure solutions of C(6)H(5)OM (M = K, Rb, Cs) by high-resolution powder X-ray diffraction. The compounds, which are of interest for reactions of the Kolbe-Schmitt type, are isostructural. The crystal structures are orthorhombic, space group Pna2(1), Z = 12, with lattice parameters (a, b, c in Å) 14.1003(1), 17.9121(1), and 7.16475(1) for the K compound, 14.4166(2), 18.2028(2), and 7.4009(1) for the Rb compound, and 14.8448(2), 18.5070(2), and 7.6306(1) for the Cs compound. They have a chain structure [M([6])] along the crystallographic c axis. This is a very unusual arrangement in which two different alkali-metal coordination spheres are observed: a distorted octahedron and a 3-fold oxygen coordination. In the latter, the 3-fold-coordinated unsaturated alkali metals additionally show weak interactions with phenyl rings. We also give powder patterns for the compounds with M = Li, Na. The former crystallizes in the monoclinic space group P2(1)/a with lattice parameters a = 22.594 Å, b = 4.7459 Å, c= 10.053 Å, and beta = 97.82 degrees with Z = 8, but no structure solution was possible. The powder pattern for the Na phenolate is in agreement with the earlier single-crystal structure.