I11-High Resolution Powder Diffraction
I19-Small Molecule Single Crystal Diffraction
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Abstract: A novel open-framework germanate, denoted as SU-74-MPMD, was prepared by hydrothermal synthesis using 2-methylpentamethylenediamine (MPMD) as the organic structure directing agent (SDA). The structure of SU-74-MPMD was determined from synchrotron X-ray powder diffraction (XRPD) data using the charge-flipping algorithm, and is one of the most complicated germanates solved from X-ray powder diffraction. The structure is built of layers of Ge10O26(OH)2 (Ge10) clusters that are connected by additional GeO4 tetrahedra to form a three-dimensional (3D) framework with 10- and 12-rings. The organic structure directing agent MPMD in the pores was located by simulated annealing. SU-74-MPMD: space group P21/c, a = 12.62726(4) Å, b = 17.35186 (5) Å, c = 16.17343(5) Å, β = 115.5509(2)° and Z = 4. SU-74 was later synthesized using 1-(2-aminoethyl)piperazine (AEP) as the SDA (denoted as SU-74-AEP), and its structure was solved by single crystal synchrotron X-ray diffraction. The framework structure of SU-74-AEP is the same as that of SU-74-MPMD. The locations of the organic SDAs in the pores are different for SU-74-MPMD and SU-74-AEP, suggesting a space-filling role of the SDAs. The Ge10 clusters follow the fcu-11-P21/c net. The underlying topology of SU-74 is compared to those of other Ge10 structures containing additional GeO4 tetrahedra. The presence of additional tetrahedra can significantly affect the framework topology through the addition of edges between the Ge10 nodes.
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Sep 2012
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I11-High Resolution Powder Diffraction
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Diamond Proposal Number(s):
[6357]
Abstract: Given the importance of the phenomenon of polymorphism from both fundamental and applied perspectives, there is considerable interest in the discovery of new systems that exhibit abundant polymorphism. In the present article, the preparation strategies and structural properties of three new polymorphs (denoted Forms III, IV, and V) of m-aminobenzoic acid (m-ABA) are reported, elevating this system to the rare class of polymorphic systems with at least five known polymorphs. The crystal structures of the three new polymorphs have been determined directly from powder X-ray diffraction data, using the direct-space genetic algorithm technique for structure solution followed by Rietveld refinement, demonstrating the opportunities that now exist for determining crystal structures when crystals of sufficient size and quality for single-crystal X-ray diffraction are not available. In two of the new polymorphs (Forms III and IV), the m-ABA molecules exist in the zwitterionic form (as in the previously known Form I), while the m-ABA molecules in the other new polymorph (Form V) are nonzwitterionic (as in the previously known Form II). Furthermore, disorder of the molecular orientation, and hence disorder in the intermolecular hydrogen-bonding arrangement, is revealed in Form V. The assignment of the tautomeric form in each polyinorph is confirmed by X-ray photoelectron spectroscopy. Issues relating to the relative stabilities of the five polymorphs of m-ABA are discussed.
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Jun 2012
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I22-Small angle scattering & Diffraction
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Diamond Proposal Number(s):
[57701]
Abstract: Many organisms use amorphous calcium carbonate (ACC) during crystalline calcium carbonate biomineralization, as a means to control particle shape/size and phase stability. Here, we present an in situ small- and wide-angle X-ray scattering (SAXS/WAXS) study of the mechanisms and kinetics of ACC crystallization at rapid time scales (seconds). Combined with offline solid and solution characterization, we show that ACC crystallizes to vaterite via a three-stage process. First, hydrated and disordered ACC forms, then rapidly transforms to more ordered and dehydrated ACC; in conjunction with this, vaterite forms via a spherulitic growth mechanism. Second, when the supersaturation of the solution with respect to vaterite decreases sufficiently, the mechanism changes to ACC dissolution and vaterite crystal growth. The third stage is controlled by Ostwald ripening of the vaterite particles. Combining this information with previous studies, allowed us to develop a mechanistic understanding of the abiotic crystallization process from ACC to vaterite and all the way to calcite. We propose this is the underlying abiotic mechanism for calcium carbonate biomineralization from ACC. This process is then augmented or altered by organisms (e.g., using organic compounds) to form intricate biominerals. This study also highlights the applicability of in situ time-resolved SAXS/WAXS to study rapid crystallization reactions.
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May 2012
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I19-Small Molecule Single Crystal Diffraction
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Abstract: Two families of halopyridnium hexacyanometallate salts, (3-XpyMe)3[M(CN)6] and (3,5-X2pyMe)3[M(CN)6] (X = I, Br; 3-XpyMe = N-methyl-3-halopyridinium; 3,5-XpyMe = N-methyl-3,5-dihalopyridinium; M = Cr, Fe, Co), have been synthesized and characterized by single crystal X-ray diffraction. Five of the six members of each family are characterized as isostructural compounds, two structures are reported as solvates, (3-IpyMe)3[Fe(CN)6]·2MeCN (2·2MeCN) and (3,5-Br2pyMe)3[Cr(CN)6]·4H2O (10·4H2O), and the solvate (3-IpyMe)3[Co(CN)6]·2MeCN (3·2MeCN) has been characterized in addition to the unsolvated 3. All halogens participate in halogen bonding, forming C–X···NC(M) halogen bonds and in one case a C–Br···O halogen bond (in 10·4H2O). The halogen bond distances are shorter than the corresponding sum of van der Waals radii, and stronger interactions are formed by iodine than bromine (I···N 2.789(7)–3.116(7), RIN 0.790–0.883; Br···N 2.884(3)–3.166(2), RBrN 0.848–0.931). Longer halogen bonds are formed in 10·4H2O (Br···N 3.041(6)–3.380(6), RBrN 0.894–0.994) due to competition from O–H···N hydrogen bonding. All halogen bonds have interaction geometries at the halogen close to linearity (most have C–X···N > 165°; smallest angle is 154.1(3)°). The geometry of interaction of the halogen bond donor (C–X) with the cyanide ligand either suggests interaction predominantly with the exo lone pair of the nitrogen atom (C≡N···X > 145°) or predominant involvement of the C≡N π-bond in the halogen bond (C≡N···X < 105°) acceptor role. The former are shorter interactions than the latter. Halogen bonds become shorter across each isostructural series for Cr > Fe > Co, and this is discussed in the context of metal-to-cyanide π-back-donation.
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Dec 2011
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I19-Small Molecule Single Crystal Diffraction
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Diamond Proposal Number(s):
[987]
Abstract: Four new layered phases have been synthesized by the hydrothermal reactions of zinc and magnesium salts with fenbufen (γ-oxo-(1,10-biphenyl)-4-butanoic acid) as a result of the oxidation of fenbufen at the ketone forming biphenylcarboxylate. Reactions with zinc nitrate give different degrees of oxidation, yielding Zn(C16H13O3)(C13H9O2)(H2O) (1) and Zn5(OH)6(C13H9O2)4 (2), depending on the reaction temperature. Compound 2 has an unusual zinc hydroxide layer structure which contains hydroxide-centered Zn4OH(OH)4 units where the central hydroxide has two long and two short bonds to the Zn atoms. The mechanism for the ketone oxidation has been investigated by a series of DFT calculations which indicate that a concerted, metalmediated pathway is lower in energy than a two-step process. The importance of the metal cation in this oxidation reaction has been shown by demonstrating that oxidation of fenbufen also occurs during reactions with magnesium nitrate and zinc chloride. These reactions yielded fully oxidized Mg(C13H9O2)2(H2O)2 (3) and half-oxidized Zn(C16H13O3)(C13H9O2)(H2O) (4), a polymorph of 1. Reactions with ammonium salts gave only recrystallized fenbufen, providing further evidence for the role of the metal cation in these oxidation reactions.
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Jul 2011
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I11-High Resolution Powder Diffraction
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Abstract: Pyroglutamic acid (P) racemised spontaneously when heated above its melting temperature, ~162 °C. No catalysts or solvents were involved in the racemisation and the rate is very temperature-dependent, requiring e.g. > 24.5 h at 160 °C but ~1.5 h at 210 °C. The degree of racemisation was studied indirectly by both X-ray powder diffraction and IR spectroscopy on samples that had been crystallised after melting for various times; the occurrence of racemisation was also confirmed by HPLC analysis. The time spent in the molten state controlled the enantiomeric composition of the liquid and this had a major effect on the subsequent composition-dependent crystallisation kinetics. Thus, crystallisation of P from undercooled melt was particularly slow if the enantiomeric compositions of the melt and the crystallising phase(s) were significantly different; crystallisation then required long-range counter-diffusion of P molecules in the viscous, hydrogen-bonded melt. On crystallisation of P from melt, evidence was obtained for metastable L, D and DL polymorphs, labelled as γ. The binary phase diagram L-DL-D for P has been determined experimentally and compares well with a calculated phase diagram.
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May 2011
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I03-Macromolecular Crystallography
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Abstract: A new strategy is proposed for batch crystallization of proteins in solution-growth or gel-growth by using the batch method inside capillary tubes applying magnetic fields. Four proteins with differing proportions of alpha-helices and beta-sheets and crystallized in five different crystallographic space groups are studied, allowing an analysis of the anisotropy of the diamagnetic susceptibility of the peptide bond its well as the polarity of the space groups in the presence of a strong magnetic field of 11.75 T. The crystal quality is shown to be improved by using a strong magnetic field to orient protein molecules, and gel-growth (high concentrations of agar) to control the transport phenomena as well as crystal growth. Sonic advantages to increase the crystal quality for crystals from marginal conditions for X-ray diffraction, and disadvantages of the use of solution- and gel-growth (low concentration of agar) in magnetic Fields, and their plausible applications to high resolution X-ray crystallography are discussed.
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Dec 2009
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NONE-No attached Diamond beamline
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Abstract: The latent pigment 1,4-diketo-2,5-di-t-butoxycarbonyl-3,6-diphenylpyrrolo[3,4-c]pyrrole (DPP-Boc) has three well-characterized polymorphic forms (denoted ?, ?, and ?) in the solid state, although some confusion exists in the literature concerning the assignment of these polymorphs. This paper clarifies the assignment of the three polymorphs of DPP-Boc, discusses various issues concerning the polymorphism of this material, and highlights several general issues regarding the characterization, discovery, and assignment of polymorphic systems.
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Jan 2009
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NONE-No attached Diamond beamline
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Abstract: Detailed analysis of X-ray diffraction data from four single crystals of eniluracil, prepared under different crystallization conditions, confirms a picture in which the crystals exhibit different degrees of disorder, which is also suggested by the computed low energy crystal structures. Since several of these crystal structures that effectively differ by an interchange of the oxygen and hydrogen atoms on C(4) and C(6) are essentially equi-energetic, growth errors that may be difficult to reverse are practically inevitable. The structural variations observed for the crystals of eniluracil studied are more appropriately described in terms of variable degrees of disorder rather than polymorphism. Analysis of the computed crystal energy landscape for interchangeable hydrogen-bonded (or other strong) motifs is, therefore, shown to be a valuable complement to X-ray diffraction and solid-state NMR for understanding and characterizing disorder in organic solid state systems. In the case of eniluracil, this detailed picture probably accounts for the challenges in devising a robust production process for this anticancer agent in the 1990s. The specific nature of the disorder accounts for different structures being obtained from powder X-ray diffraction data of different samples, and the possibility of publishable single crystal X-ray refinements also being interpreted as polymorphism rather than disorder.
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Aug 2008
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Abstract: Experimental and computational searches for the crystal structures of the five commercially available isomers of dichloronitrobenzene and 3,4-dinitrochlorobenzene were performed to assess the relationship between functional group interactions and steric requirements in determining the solid forms. Experimentally, this resulted in the first crystal structure determination of 2,4-dichloronitrobenzene, two solvates of 3,4-dichloronitrobenzene and one of 3,4-dinitrochlorobenzene. Additionally, low temperature redeterminations of the crystal structures were obtained for 2,5-dichloronitrobenzene, 3,4-dichloronitrobenzene, and both the ?- and ?-forms of 3,4-dinitrochlorobenzene. The searches for energetically feasible structures of each of these compounds showed a wide variety of distributions leading to varying degrees of clarity of prediction of the solid state behavior. These range from 2,3-dichloronitrobenzene, which only adopts the crystal structure that was clearly the most thermodynamically stable of all five isomers, through complex systems, which show a range of low energy minima indicating possible polymorphism and solvate formation, to 2,4-dichloronitrobenzene, which can conformationally distort and adopts a complicated Z? = 2 crystal structure.
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Jan 2008
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