PubMed Journal Database | Acta crystallographica. Section B, Structural science 
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Showing PubMed Articles, all 21 from Acta crystallographica. Section B, Structural science
The charge-flipping algorithm in crystallography.
The charge-flipping algorithm (CFA) is a member of the diverse family of dual-space iterative phasing algorithms. These algorithms use alternating modifications in direct and reciprocal space to find a solution to the phase problem. The current state-of-the-art CFA is reviewed and it is put in the context of related dual-space algorithms with relevance for crystallography. The CFA has found applications in many crystallographic problems. The principal applications in various fields are described with sectio...
The various superstructure phases that occur with the anion-deficient compositions of binary oxides MO(2 - x) with the fluorite structure as parent are explored here in terms of the original `coordination defect' (or CD) concept in which each vacant oxygen site, □, is `coordinated' by six O atoms thereby creating the octahedral `structure-determining' entity [M(3.5)□O(6)]. It emerges that the structure and composition of each anion-deficient (polymorph) phase can be described in terms of crystallogr...
The structure of low-temperature grown GaAs with equidistant δ-layers of Sb and P was studied by analysis of the X-ray curves, which was supported by optical absorption measurements and transmission electron microscopy. The simultaneous fitting of the X-ray reflectivity curve and diffraction ones for GaAs (004) and GaAs (115) crystallographic planes provided reliable information about the period of δ-layer superlattice, thickness of the Sb and P δ-layers, and amount of excess As. Variation of these param...
A range of single-crystal structures of the type [Pd(cod)(LL'-Bid)]A, where LL'-Bid = acetylacetonato (acac), thenoyltrifluoroactetonato (thtfac) and hexafluoroacetylacetonato (hfacac), and A = tetrafluoroborate (BF(4)(-)) and hexafluorophosphate (PF(6)(-)), are reported. The complexes [Pd(cod)(acac)]PF(6) (I), [Pd(cod)(thtfac)]PF(6) (III), [Pd(cod)(thtfac)]BF(4) (IV) and [Pd(cod)(hfacac)]PF(6) (V) are isostructural in the monoclinic space group P2(1)/c. The influence of the variation of the β-diketonato-t...
The synthesis and characterization of a series of halogen-substituted pseudoterpyridine Zn(II) homoleptic mononuclear complexes, based on ligands L(11)-L(44) [2,6-pyridinedicarboxaldehydebis(p-R-phenylimines), R = F, Cl, Br, I] are reported. Neither of the structures contain relatively strong classical hydrogen bonds (OH...O, NH...O, OH...N, NH...N) and the structure packing is thus determined by a subtle interplay of weaker interactions. Isostructurality of the four halogen analogues is very rare, and in t...
The bisphosphoramidate (C(6)H(5)O)(2)P(O)NH(CH(2))(4)NHP(O)(OC(6)H(5))(2) crystallizes in two polymorphs, one (ndl) with a needle habit from tetrahydrofuran (THF)/ethanol and another (prm) which forms prisms from H(2)O/ethanol. The molecules in the two forms differ from each other in some torsion angles and the orientation of the diaminobutane bridge, although the differences between the similar bond lengths are not significant for the two polymorphs. The geometry optimizations at the B3LYP/6-31+G* level fo...
The one-step reaction of isophthaloyl dichloride with the 2-aminopyridine derivative (methyl 6-aminonicotinate) yields (i) a trimer-based macrocycle (EsIO)(3) and (ii) a tetramer-based macrocycle (EsIO)(4) in modest isolated synthetic yields (total of 25%), together with (iii) longer open-chain oligomers. The macrocyclization relies on the semi-flexible imide hinge formed by reaction of the 2-amino(pyridine) functional group with two acyl chloride functional groups. The determining factors in macrocycle syn...
Thermodynamic and structural relationships between the two polymorphs of 1,3-dimethylurea.
The title compound exists as polymorph (I), Fdd2 with Z = 8 [Pérez-Folch et al. (1997). J. Chem. Cryst. 27, 367-369; Marsh (2004). Acta Cryst. B60, 252-253], and as polymorph (II), P2(1)2(1)2 with Z = 2 [Martins et al. (2009). J. Phys. Chem. A, 113, 5998-6003]. We have redetermined both structures at somewhat lower temperatures [(I) at 180 K rather than room temperature; (II) at 100 K rather than 150 K]. For polymorph (I) the space group Fdd2 is confirmed rather than the original choice of Cc. The mo...
The crystal structure of the high-pressure polymorph (α') of an antidiabetic drug, chlorpropamide [4-chloro-N-(propylaminocarbonyl)benzenesulfonamide, C(10)H(13)ClN(2)O(3)S], which is formed at ∼ 2.8 GPa from the α-polymorph (P2(1)2(1)2(1)) on hydrostatic compression in saturated ethanol solution, has been determined. As a result of the phase transition, the a, c and α parameters change jumpwise, whereas the changes in b parameter are continuous through the phase transition point. The high-pressure...
On the shortest B(III)-O bonds.
For the crystal structures of oxoborates, the value of ∼ 1.2 Å can be regarded as the lower physical limit for B(III)-O bond lengths. The oxoborate crystal structures with B(III)-O bond lengths shorter than ∼ 1.2 Å have been found to be either doubtful or clearly erroneous.
Rhodium complexes have potential uses in both catalysis and promoting the cleavage of C-C bonds. In order to further our understanding of these species and their potential applications, it is vital to obtain insight into the bonding within the species, particularly the Rh-C interactions, and to this end experimental charge-density studies have been undertaken on the title complexes. High-resolution single-crystal datasets to sin θ/λ = 1.06 Å(-1) were obtained at 100 K and analysed using Bader's `At...
The crystal structures of 4,10-dibromo-anthanthrone (Pigment Red 168; 4,10-dibromo-dibenzo[def,mno]chrysene-6,12-dione), 4,10-dichloro- and 4,10-diiodo-anthanthrone have been determined by single-crystal X-ray analyses. The dibromo and diiodo derivatives crystallize in P2(1)/c, Z = 2, the dichloro derivative in P\bar 1, Z = 1. The molecular structures are almost identical and the unit-cell parameters show some similarities for all three compounds, but the crystal structures are neither isotypic to another n...
Polymorphism in the highly flexible organic Schiff-base macrocycle ligand 3,6,9,17,20,23-hexa-azapentacyclo(23.3.1.1(11,15).0(2,6).0(16,20))triaconta-1(29),9,11,13,15(30),23,25,27-octaene (DIEN, C(24)H(30)N(6)) has been studied by single-crystal X-ray diffraction and both solid-state and gas-phase density functional theory (DFT) calculations. In the literature, only solvated structures of the title compound are known. Two new polymorphs and a new solvated form of DIEN, all obtained from the same solvent wit...
This paper describes the validation of a dispersion-corrected density functional theory (d-DFT) method for the purpose of assessing the correctness of experimental organic crystal structures and enhancing the information content of purely experimental data. 241 experimental organic crystal structures from the August 2008 issue of Acta Cryst. Section E were energy-minimized in full, including unit-cell parameters. The differences between the experimental and the minimized crystal structures were subjected to...
The crystal structures of GeSb(6)Te(10) and GeBi(6)Te(10) were scrutinized using an X-ray powder diffraction method, which revealed that these compounds crystallize in trigonally distorted cubic close-packed structures with a 51-layer period (R\bar 3m). Each layer consists of a triangular atomic net; Te atoms occupy their own specific layers, whereas Ge, Sb and Bi atoms are located in the other layers. In these pseudobinary compounds, random atomic occupations of Ge and Sb/Bi are observed and the layers for...
Polymorphism and piezochromicity in the three-dimensional network-based phosphate RbCuPO(4).
Rubidium copper phosphate, RbCuPO(4), forms two room-temperature polymorphs that have been investigated with neutron powder diffraction. Polymorph (II) can be converted quantitatively into (I) by grinding the material or by pelletization, and the phase transition is accompanied by a significant colour change from very pale green to sky blue. Polymorph (II) can be obtained essentially free of (I) by quenching from 723 K. Each polymorph shows two unique Cu atoms: in (I) both sites are four-coordinate in a 2:1...
Attempts to prepare the compound [Ni(H(2)O)(2)(15-crown-5)](X)(2) were eventually successful with X = NO_3;- provided that a synthetic route aimed at restricting water was followed. Application of this method was extended to make the analogous compound with X = HSO_4;-, for which three symmetry-related phases were isolated between 295 and 110 K: a room-temperature phase with Z' = (1/2) [phase (I)], an intermediate-temperature phase with Z' = 1 [phase (II)] and a low-temperature phase with Z' = 2 [phase (III...
Two polymorphs (alpha, beta) of pyrazinium hydrogen sulfate (pyzH(+)HSO_4;-, abbreviated as PHS) with distinctly different hydrogen-bond types and topologies but close electronic energies have been synthesized and characterized for the first time. The alpha-polymorph (P2(1)2(1)2(1)) forms distinct blocks in which the pyzH(+) and HSO_4;- ions are interconnected through a network of NH...O and OH...O hydrogen bonds. The beta-form (P\bar 1) consists of infinite chains of alternating pyzH(+) and HSO_4;- ions co...
Pressure-induced phase transitions in L-alanine, revisited.
The effect of pressure on L-alanine has been studied by X-ray powder diffraction (up to 12.3 GPa), single-crystal X-ray diffraction, Raman spectroscopy and optical microscopy (up to approximately 6 GPa). No structural phase transitions have been observed. At approximately 2 GPa the cell parameters a and b become accidentally equal to each other, but without a change in space-group symmetry. Neither of two transitions reported by others (to a tetragonal phase at approximately 2 GPa and to a monoclinic phase...
Crystal structures of Tröger's base (5,11-methano-2,8-dimethyl-5,6,11,12-tetrahydrodibenzo[b,f][1,5]diazocine) analogues with the methyl groups replaced by ethyl, iso-propyl and tert-butyl groups were studied. The incidence of Z' > 1 structures increases to rather conspicuous levels. The reasons behind this trend are expanded upon, and a possible explanation is given in the flexibility of the alkyl substituents and van der Waals stabilization. In combination these effects allow for an additional stabilizat...
An experimental charge density of HEPES.
We report the experimental charge density of HEPES [4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid], which is a common buffering agent. The structure was refined using the Hansen-Coppens formalism. The ability of the HEPES molecule to form stable intermolecular interactions and intermolecular hydrogen bonds in the crystal structure is discussed in terms of its buffering properties. The protonation mode observed in the crystal structure is different from that expected in solution, suggesting that additio...
