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Interatomic Distances (interatomic + distance)
Selected AbstractsArtemisinin Derivatives with Antimalarial Activity against Plasmodium falciparum Designed with the Aid of Quantum Chemical and Partial Least Squares MethodsMOLECULAR INFORMATICS, Issue 8 2003Abstract Artemisinin derivatives with antimalarial activity against Plasmodium falciparum resistant to mefloquine are designed with the aid of Quantum Chemical and Partial Least Squares Methods. The PLS model with three principal components explaining 89.55% of total variance, Q2=0.83 and R2=0.92 was obtained for 14/5 molecules in the training/external validation set. The most important descriptors for the design of the model were one level above the lowest unoccupied molecular orbital energy (LUMO+1), atomic charges in atoms C9 and C11 (Q9) and (Q11) respectively, the maximum number of hydrogen atoms that might make contact with heme (NH) and RDF030,m (a radial distribution function centered at 3.0,Å interatomic distance and weighted by atomic masses). From a set of ten proposed artemisinin derivatives, a new compound (26), was predicted with antimalarial activity higher than the compounds reported in literature. Molecular graphics and modeling supported the PLS results and revealed heme-ligand and protein-ligand stereoelectronic relationships as important for antimalarial activity. The most active 26 and 29 in the prediction set possess substituents at C9 able to extend to hemoglobin exterior, what determines the high activity of these compounds. [source] Possible model of protein nucleation and crystallization on porous siliconPHYSICA STATUS SOLIDI (A) APPLICATIONS AND MATERIALS SCIENCE, Issue 8 2005S. Stolyarova Abstract The problem of macromolecular nucleation and crystallization on porous silicon surface is investigated theoretically. The fractality of the porous silicon layer is exploited. It is shown that the effective surface density of adsorbed particles on a fractal self-similar surface significantly exceeds that on a flat surface. The resulting local supersaturation explains enhanced nucleation phenomena associated with porous silicon. In addition, the self-affine fractal surface exhibits quasi-periodicity that can facilitate long-range ordering of the nucleated molecules, i.e. the crystallization process. Moreover, small elastic constants of porous silicon are favorable for the surface periodicity tuning to different lattice parameters of growing crystals. The anomalous large scaling range (from silicon interatomic distance up to 100 nm) is favorable for the crystallization of wide range of big macromolecules such as proteins. (© 2005 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Temperature-dependent crystal structure refinement and 57Fe Mössbauer spectroscopy of Cu2Fe2Ge4O13ACTA CRYSTALLOGRAPHICA SECTION B, Issue 1 2007Günther J. Redhammer The germanate compound Cu2Fe2Ge4O13, dicopper diiron germanate, was synthesized by solid-state reaction at 1403,K and ambient pressure. There is no change of space-group symmetry between 10 and 900,K. Between 40,K and room temperature the a lattice parameter shows a negative thermal expansion which can be connected to a decreasing Cu,Cu interatomic distance. Above room temperature all the lattice parameters are positively correlated with temperature. Among the structural parameters several alterations with temperature occur, which are most prominent for the distorted Fe3+ octahedral site. Besides an increase of the average bond length and of the interatomic Fe,Fe distances, distortional parameters also increase with temperature, while the average Cu,O bond length remains almost constant between 100 and 900,K, as do the average Ge,O distances. 57Fe Mössbauer spectroscopy was used to detect long-range magnetic ordering in Cu2Fe2Ge4O13. While around 100,K, which is the temperature at which a broad maximum is observed in the magnetic susceptibility, no magnetic ordering was detected in the Mössbauer spectrum, below 40,K a narrow split sextet is developed which is indicative of a three-dimensional magnetic ordering of the sample. [source] Tetrakis(tetramethylammonium) dodeca-,-chloro-hexachloro- octahedro -hexatantalate chlorideACTA CRYSTALLOGRAPHICA SECTION C, Issue 1 2004Marija Vojnovi The title compound, (C4H12N)4[Ta6Cl18]Cl, crystallizes in the cubic space group . The crystal structure contains two different types of coordination polyhedra, i.e. four tetrahedral [(CH3)4N]+ cations and one octahedral [(Ta6Cl12)Cl6]3, cluster anion, and one Cl, ion. The presence of three different kinds of Cl atoms [bridging (,2), terminal and counter-anion] in one molecule makes this substance unique in the chemistry of hexanuclear halide clusters of niobium and tantalum. The Ta6 octahedron has an ideal Oh symmetry, with a Ta,Ta interatomic distance of 2.9215,(7),Å. [source] Determination of intermolecular distance for a model peptide of Bombyx mori silk fibroin, GAGAG, with rotational echo double resonanceBIOPOLYMERS, Issue 2 2002Tsunenori Kameda Abstract Rotational echo double resonance NMR spectroscopy is applied for the determination of the distance of intermolecular chains of pentapeptide, GAGAG (G: Gly, A: Ala), a model typical of the crystalline domain in Bombyx mori silk fibroin. 1:4 mixture of G[1- 13C]AGAG and GAG[15N]AG with antiparallel ,-sheet structure was used to determine the distance of intermolecular hydrogen bonding between adjacent molecules within pleated sheet and the 13C,15N interatomic distance was determined to be 4.3 Å. On the other hand, 1:4 mixture of GAG[1- 13C]AG and GAG[15N]AG gave information on the interpleated sheet arrangement. When we assumed the same distances between two interpleated sheets, the distance was calculated to be 5.3 Å and the angle 15N,13C,15N was 180°. © 2002 Wiley Periodicals, Inc. Biopolymers 64: 80,85, 2002 [source] Self-Assembled Monolayers of Alkoxy-Substituted Octadehydrodibenzo[12]annulenes on a Graphite Surface: Attempts at peri -Benzopolyacene Formation by On-Surface PolymerizationCHEMISTRY - A EUROPEAN JOURNAL, Issue 28 2010Kazukuni Tahara Dr. Abstract Self-assembled monolayers of a series of tetraalkoxy-substituted octadehydrodibenzo[12]annulene (DBA) derivatives 1,c,g possessing butadiyne linkages were studied at the 1,2,4-trichlorobenzene (TCB) or 1-phenyloctane/graphite interface by scanning tunneling microscopy (STM). The purpose of this research is not only to investigate the structural variation of two-dimensional (2D) monolayers, but also to assess a possibility for peri -benzopolyacene formation by two-dimensionally controlled polymerization on a surface. As a result, the formation of three structures, porous, linear, and lamella structures, were observed by changing the alkyl chain length and the solute concentration. The formation of multilayers of the lamella structure was often observed for all compounds. The selection of molecular networks is basically ascribed to intermolecular and molecule,substrate interactions per unit area and network density. The selective appearance of the linear structure of 1,d is attributed to favorable epitaxial registry matching between the substrate lattice and the overlayer lattice. Even though the closest interatomic distance between the diacetylenic units of the DBAs in the lamella structure (,0.6,nm) is slightly larger compared to the typical distances necessary for topochemical polymerization, the reactivity toward external stimuli (electronic-pulse irradiation from an STM tip and UV irradiation) was investigated. Unfortunately, no evidence for polymerization of the DBAs on the surface was observed. The present results indicate the necessity for further designing a suitable system for the on-surface construction of structurally novel conjugated polymers, which are otherwise difficult to prepare. [source] High-precision measurement of internuclear distances using solid-state NMRCONCEPTS IN MAGNETIC RESONANCE, Issue 1 2008Jae-Seung Lee Abstract Today, nuclear magnetic resonance (NMR) is among the most efficient tools in structural studies. Measurement of interatomic distances is the most common way of determining high-resolution structures of molecules using NMR techniques. In this article, we describe NMR techniques for static powder samples, based on a two-dimensional single-echo scheme, enhanced with adiabatic cross-polarization. They can significantly increase the accuracy of measuring internuclear distances and turn NMR into a high-precision crystallographic technique, complementing the X-ray, and neutron-scattering methods. Experimental examples are presented for intramolecular CN and CC distances in ,-crystalline form of glycine. © 2008 Wiley Periodicals, Inc. Concepts Magn Reson Part A 32A: 56,67, 2008. [source] A Multiscale Description of the Electronic Transport within the Hierarchical Architecture of a Composite Electrode for Lithium BatteriesADVANCED FUNCTIONAL MATERIALS, Issue 17 2009Jean-Claude Badot Abstract The broadband dielectric spectroscopy technique is applied, for the first time, to a composite material used as an electrode for lithium battery. The electrical properties (permittivity and conductivity) are measured from low (a few Hz) to microwave (a few GHz) frequencies. The results demonstrate that the broadband dielectric spectroscopy technique is very sensitive to the different scales of the electrode architecture involved in electronic transport, from interatomic distances to macroscopic sizes, as well as to the morphology at these scales, coarse or fine distribution of the constituents. This work opens up new prospects for a more fundamental understanding and more rational optimization of the electronic transport in composite electrodes for lithium batteries and other electrochemical energy storage technologies (including other batteries, supercapacitors, low- and medium-temperature fuel cells), electrochemical sensors and conductor,insulator composite materials. [source] Unusual Lattice-Magnetism Connections in MnBi NanorodsADVANCED FUNCTIONAL MATERIALS, Issue 7 2009Kyongha Kang Abstract Lattice parameter, particle size, and thermal expansion results obtained from high-temperature synchrotron transmission X-ray diffraction are reported for magnetostructual NiAs-type MnBi nanorods embedded in a Bi matrix. The structural data are consistent with elevated-temperature magnetic measurements that indicate a first-order nanorod Curie transition at 520,K, significantly depressed from the bulk MnBi Curie temperature of 633,K. The data suggest that the unit cell volume dependence of the magnetic behavior,also known as the volume exchange striction,of the MnBi compound is the determining factor underlying this phenomenon. The results imply that materials with magnetostructural transitions of technological interest may be altered by strain effects to tailor the interatomic distances towards the critical transition values. [source] Aspects of the modelling of the radial distribution function for small nanoparticlesJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 6 2007Vladimir I. Korsunskiy An approach to modelling radial distribution functions (RDFs) of nanoparticle samples over a wide range of interatomic distances is presented. Two different types of contribution to the model RDF are calculated. The first explicitly reflects the structure of the nanoparticle parts with more or less crystalline atomic structure. It can be calculated precisely and contains comparatively sharp peaks, which are produced by the set of discrete interatomic distances. The second includes RDF contributions from distances between weakly correlated atoms positioned within different nanoparticles or within different parts of a nanoparticle model. The calculation is performed using the approximation of a uniform distribution of atoms and utilizes the ideas of the characteristic functions of the particle shape known in small-angle scattering theory. This second RDF contribution is represented by slowly varying functions of interatomic distance r. The relative magnitude of this essential part of the model RDF increases with increasing r compared with the part that represents the ordered structure. The method is applied to test several spherical and core/shell models of semiconductor nanoparticles stabilized with organic ligands. The experimental RDFs of ZnSe and CdSe/ZnS nanoparticle samples were obtained by high-energy X-ray diffraction at beamline BW5, HASYLAB, DESY. The ZnSe nanoparticles have a spherical core with approximately 26,Å diameter and zincblende structure. The RDF of the CdSe/ZnS nanoparticle sample shows resolved peaks of the first- and the second-neighbour distances characteristic for CdSe (2.62 and 4.27,Å) and for ZnS (2.33 and 3.86,Å) and for the first time clearly confirms the presence of CdSe and ZnS nanophases in such objects. The diameters of the CdSe and ZnS spherical cores are estimated as 27 and 15,Å. CdSe and ZnS are present in the sample for the most part as independent nanoparticles. A smaller amount of ZnS forms an irregularly shaped shell around the CdSe cores, which consists of small independently oriented ZnS particles. [source] Investigation of nanocrystalline CdS,glutathione particles by radial distribution functionJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 6 2003V. I. Korsounski Using high-energy synchrotron radiation, powder diffraction experiments were carried out on CdS nanocrystals stabilized with glutathione. The radial distribution function was calculated from the data and analysed. The nanoparticle core, of diameter estimated as 15,20,Å, consists of Cd and S atoms in the proportion 1:1. Inside the core, both Cd and S atoms coordinate each other approximately tetrahedrally. The surface S atoms are connected to just two or three Cd atoms of the core and belong to the glutathione molecules of the particle shell. These S atoms are also a part of the core structure and contribute about one half of the total number of S atoms per particle. First-neighbour Cd,S distances are 2.523,Å with a narrow distance distribution. No difference is observed between the lengths of Cd,S bonds involving the sulfur of the glutathione molecules and the sulfur atoms which are solely bound to Cd. The bond angle Cd,S,Cd at the surface bridging S atoms of glutathione is ca 99.5°, i.e. significantly smaller than an average one of 109.5° characteristic of the Cd and S atom packing inside the core. Beyond the range of the near interatomic distances, the influence of the surface and the defects cause a significant distinction of the particle core structure from those of zincblende and wurtzite, characteristic of bulk CdS. [source] On the efficient evaluation of Fourier patterns for nanoparticles and clustersJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 9 2006Antonio Cervellino Abstract Samples made of an isotropically oriented ensemble of atomic clusters or structures that are not large crystals (i.e. extended less than 10 periods in each direction) are at the frontier of today's material science and chemistry. Examples are nanoparticles, nanotubes, amorphous matter, polymers, and macromolecules in suspension. For such systems the computation of powder diffraction patterns (which may provide an efficient characterization) is to be performed the hard way, by summing contributions from each atom pair. This work deals with performing such computation in the most practical and efficient way. Three main points are developed: how to encode the enormous array of interatomic distances (which increase as the square or higher powers of the cluster diameter) to a much smaller array of equispaced values on a coarse grid (whose size increases linearly with the diameter); how to perform a fast computation of the diffraction pattern from this equispaced grid; how to optimize the grid step to obtain an arbitrarily small error on the computed diffraction pattern. Theory and examples are jointly developed and presented. © 2006 Wiley Periodicals, Inc. J Comput Chem 27: 995,1008, 2006 [source] Electronic structure, chemical bonding, and finite-temperature magnetic properties of full Heusler alloysJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 1 2006Yasemin Kurtulus Abstract The electronic structure, chemical bonding, and magnetic properties of 15 full Heusler alloys X2MnZ have been studied on the basis of density-functional theory using the TB-LMTO-ASA approach and the local-density (LDA), as well as the generalized-gradient approximation (GGA). Correlations between the chemical bondings derived from crystal orbital Hamilton population (COHP) analysis and magnetic phenomena are obvious, and different mechanisms leading to spin polarization and ferromagnetism are derived. As long as a magnetically active metal atom X is present, antibonding XX and XMn interactions at the Fermi level drive the systems into the ferromagnetic ground state; only if X is nonmagnetic (such as in Cu2MnZ), antibonding MnMn interactions arise, which again lead to ferromagnetism. Finite-temperature effects (Curie temperatures) are analyzed using a mean-field description, and a surprisingly simple (or, trivial) relationship between structural properties (MnMn interatomic distances) and TC is found, being of semiquantitative use for the prediction of the latter. © 2005 Wiley Periodicals, Inc. J Comput Chem 27: 90,102, 2006 [source] Determination of the local structure of the first and second shells in ordered and disordered Ni,Mn alloysJOURNAL OF SYNCHROTRON RADIATION, Issue 2 2001A. V. Ryazhkin The coordination numbers and the interatomic distances for 50, 75 and 80 at.% Ni-Mn alloys in ordered and disordered states are presented. A new method for determining the first and second nearest neighbor coordination numbers in a binary alloy is applied. It is shown that magnetic properties of these alloys depend on short range order in atomic arrangement. [source] Temperature-induced phase transition in simulated amorphous Al2O3PHYSICA STATUS SOLIDI (B) BASIC SOLID STATE PHYSICS, Issue 2 2006Vo Van Hoang Abstract Our previous simulation studies indicated the existence of pressure-induced phase transition in liquid and amorphous Al2O3. In the current paper, we present the structural transformation of simulated amorphous Al2O3 from an octahedral to a tetrahedral network structure by heating from the high-density amorphous (hda) model at constant pressure P = 0 GPa. The structure of the models was analyzed through the partial radial distribution functions (PRDFs), coordination number distributions, bond-angle distributions and interatomic distances. Furthermore, significant differences in structural characteristics of low-density amorphous (lda) models obtained by heating from the hda one and by cooling from the low-density melt have been found and are presented. (© 2006 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] The structure of short-lived excited states of molecular complexes by time-resolved X-ray diffractionACTA CRYSTALLOGRAPHICA SECTION A, Issue 2 2005Philip Coppens Experimental and computational methods for time-resolved (TR) diffraction now allow the determination of geometry changes on molecular excitation. The first results indicate significant changes in the interatomic distances and molecular shape on photo-excitation, but also a dependence of the induced changes on the molecular environment. Though the use of high-brightness synchrotron sources is essential, it limits the time resolution to the width of the synchrotron pulse which is currently 70,100,ps. The experiments discussed fall into two categories: (i) picosecond powder diffraction experiments on the molecular excitation to a singlet state, and (ii) microsecond experiments on the excited states of inorganic complexes. Both involve reversible processes for which a stroboscopic technique can be applied. [source] Single-crystal structure refinement of NaTiSi2O6 clinopyroxene at low temperatures (298,<,T,<,100,K)ACTA CRYSTALLOGRAPHICA SECTION B, Issue 6 2003Günther J. Redhammer The alkali-metal clinopyroxene NaTi3+Si2O6, one of the rare compounds with trivalent titanium, was synthesized at high temperature/high pressure and subsequently investigated by single-crystal X-ray diffraction methods between 298 and 100,K. One main difference between the high- and the low-temperature form is the sudden appearance of two different Ti3+,Ti3+ interatomic distances within the infinite chain of the TiO6 octahedra just below 197 K. This change can be seen as direct evidence for the formation of Ti,Ti singlet pairs in the low-temperature phase. Mean Ti,O bond lengths smoothly decrease with decreasing temperature and the phase transition is associated with a slight jump in the Ti,O bond length. The break in symmetry, however, causes distinct variations, especially with respect to the two Ti,Oapex bond lengths, but also with respect to the four Ti,O bonds in the equatorial plane of the octahedron. The TiO6 octahedron appears to be stretched in the chain direction with a slightly larger elongation in the P low-temperature phase compared with the C2/c high-temperature phase. Polyhedral distortion parameters such as bond-length distortion and octahedral angle variance suggest the TiO6 octahedron in P to be closer to the geometry of an ideal octahedron than in C2/c. Mean Na,O bond lengths decrease with decreasing temperature and the variations in individual Na,O bond lengths are the result of variations in the geometry of the octahedral site. The tetrahedral site acts as a rigid unit, which does not show pronounced changes upon cooling and through the phase transitions. There are neither large changes in bond lengths and angles nor in polyhedral distortion parameters, for the tetrahedral site, when they are plotted. In contrast with the C2/c,P21/c phase transition, found especially in LiMSi2O6 clinopyroxenes, no very large variations are found for the tetrahedral bridging angle. Thus, it is concluded that the main factor inducing the phase transition and controlling the structural variations is the M1 octahedral site. [source] X-ray study and structure simulation of amorphous tungsten oxideACTA CRYSTALLOGRAPHICA SECTION B, Issue 4 2002L. A. Lugovskaya In this work, X-ray studies of the amorphous oxide films obtained by thermal evaporation of WO3 powder in a vacuum and by anodic oxidation were carried out. X-ray diffraction patterns were obtained in the symmetric reflection geometry on a DRON-4 diffractometer (Mo K, radiation, LiF monochromator) in automatic mode. Molecular dynamics simulation of amorphous tungsten oxide atomic configurations has been carried out in the micro-canonical ensemble (NVE) for N,=,208 atoms and N,=,624 atoms, in a cubic cell, using pairwise Born,Mayer interaction potentials and periodic boundary conditions. One of the purposes of the present work is to analyze the influence of the parameters and the cutoff of the interaction potentials on the interatomic distances. The values obtained in the molecular dynamics simulation for the pair functions D(r) are compared with the experimental data for amorphous oxides in order to choose the most convenient aforesaid values. The values of the average interatomic distances and the coordination numbers obtained by both methods are also compared. The result shows that the tungsten subsystem can be well reproduced using the potential cutoff radius of about 4,Å, but the oxygen subsystem can be well reproduced when the cutoff of the potential for the W,O pairs is equal to 2.8,Å. The configuration built during the molecular dynamics experiment consists of distorted octahedra. These octahedra form chains, as in the WO3 phases of type ReO3, and hexagonal rings, of the same type as in the WO3(1/3)H2O phase, when we extract (1/3)O at every WO3 unit. The pair function D(r) and scattering intensity I(s) distribution curves calculated for simulation configurations show a satisfactory agreement with experiment. [source] Five-dimensional structure refinement of natural melilite, (Ca1.89Sr0.01Na0.08K0.02)(Mg0.92Al0.08)(Si1.98Al0.02)O7ACTA CRYSTALLOGRAPHICA SECTION B, Issue 6 2001Luca Bindi The structure of a crystal of natural melilite from San Venanzo, Umbria (Italy) of the general formula X2T1(T2)2O7, where X = Ca0.945Sr0.005Na0.04K0.01, T1 = Mg0.92Al0.08 and T2 = Si0.99Al0.01, has been solved and refined as an incommensurate structure in five-dimensional superspace. The structure is tetragonal, superspace group P21m:p4mg, cell parameters a = 7.860,(1), c = 5.024,(1),Å, modulation vectors q1 = 0.2815,(3)(a* + b*), q2 = 0.2815,(3)(,a* + b*). The data collection was performed on a KumaCCD diffractometer. The structure was refined from 7606 reflections to final R = 0.0481. A special modification of the refinement program Jana2000 was necessary to take into account overlapping of satellite reflections m×n = ±1, which could not be properly separated in the integration procedure. The final model includes modulations of the atomic positions as well as modulations of the thermal parameters. The latter are induced by strong differences in the neighbourhood of the actual modulated positions. The occupational modulation was neither significant for X nor for T1 sites and the sites were supposed to be occupied only by Ca and Mg, respectively. As a consequence of the Ca and O positional modulations six-, seven- and eightfold Ca coordination occur throughout the structure and the thermal ellipsoid changes its shape correspondingly. The positional modulation of the atoms causes variations in the interatomic distances which, however, do not affect bond-valence sums considerably, but induce flattening and rotation in T1 and T2 tetrahedra, respectively. [source] Hydrated metal complexes of N -(6-amino-3,4-dihydro-3-methyl-5-nitroso-4-oxopyrimidin-2-yl)glycinate: interplay of molecular, molecular,electronic and supramolecular structuresACTA CRYSTALLOGRAPHICA SECTION B, Issue 3 2001John N. Low The title anion, (C7H8N5O4),, L,, forms hydrated metal complexes with a range of metal ions M+ and M2+. Lithium and manganese(II) form finite molecular aggregates [Li(L)(H2O)3] (1) and [Mn(L)2(H2O)4].6H2O (4) in which the molecular aggregates are linked into three-dimensional frameworks by extensive hydrogen bonding. The sodium and potassium derivatives, [Na2(L)2(H2O)3] (2) and [K(L)(H2O)] (3) both form organic,inorganic hybrid sheets in which metal,oxygen ribbons are linked by strips containing only organic ligands: these sheets are linked by hydrogen bonds into three-dimensional frameworks. In (2) the metal,oxygen ribbon is built from pairs of edge-shared trigonal bipyramids linked by water molecules, while in (3) it consists of a continuous chain of vertex-sharing octahedra. The nitroso group in the anion acts as an ,1 ligand towards Na+ and as an ,2 ligand towards K+. In all cases the anion L, shows the same unusual pattern of interatomic distances as the neutral parent LH. [source] A hydrogen-bonded ribbon in 6-amino-3-methyl-5-nitroso-2-(pyrrolidin-1-yl)pyrimidin-4(3H)-one monohydrate and hydrogen-bonded sheets in 6-amino-2-dimethylamino-3-methyl-5-nitrosopyrimidin-4(3H)-one monohydrateACTA CRYSTALLOGRAPHICA SECTION C, Issue 11 2009Fabían Orozco In each of 6-amino-3-methyl-5-nitroso-2-(pyrrolidin-1-yl)pyrimidin-4(3H)-one monohydrate, C9H13N5O2·H2O, (I), and 6-amino-2-dimethylamino-3-methyl-5-nitrosopyrimidin-4(3H)-one monohydrate, C7H11N5O2·H2O, (II), the interatomic distances indicate significant polarization of the electronic structures of the pyrimidinone molecules. In each compound, the organic component contains an intramolecular N,H...O hydrogen bond. The molecular components in (I) are linked by a combination of two-centre O,H...O, O,H...N and N,H...O hydrogen bonds and a three-centre O,H...(NO) hydrogen bond to form a broad ribbon containing five distinct ring motifs. In compound (II), three intermolecular hydrogen bonds, one each of the O,H...O, O,H...N and N,H...O types, link the molecules into sheets containing equal numbers of centrosymmetric R44(10) and R108(34) rings. [source] Weak intermolecular interactions in isomorphous 5-(2-chloroethoxy)-2,3-dihydro-1,4-benzodioxine and 5-(2-bromoethoxy)-2,3-dihydro-1,4-benzodioxine: bonding or nonbonding interactionsACTA CRYSTALLOGRAPHICA SECTION C, Issue 8 2009Rafal Kruszynski The title compounds, C10H11ClO3, (I), and C10H11BrO3, (II), are isomorphous and effectively isostructural; all of the interatomic distances and angles are normal. The structures exhibit long intermolecular C,H...O and C,H..., contacts with attractive energies ranging from 1.17 to 2.30,kJ,mol,1. Weak C,H...O hydrogen bonds form C(3) and C(4) motifs, combining to form a two-dimensional R34(12) net. No face-to-face stacking interactions are observed. [source] Structural effects on the solid-state photodimerization of 2-pyridone derivatives in inclusion compoundsACTA CRYSTALLOGRAPHICA SECTION C, Issue 7 2009Marina Telzhensky The structures of six crystalline inclusion compounds between various host molecules and three guest molecules based on the 2-pyridone skeleton are described. The six compounds are 1,1,-biphenyl-2,2,-dicarboxylic acid,2-pyridone (1/2), C14H10O4·2C5H5NO, (I,a), 1,1,-biphenyl-2,2,-dicarboxylic acid,4-methyl-2-pyridone (1/2), C14H10O4·2C6H7NO, (I,c), 1,1,-biphenyl-2,2,-dicarboxylic acid,6-methyl-2-pyridone (1/2), C14H10O4·2C6H7NO, (I,d), 1,1,6,6-tetraphenyl-2,4-hexadiyne-1,6-diol,1-methyl-2-pyridone (1/2), C30H22O2·2C6H7NO, (II,b), 1,1,6,6-tetraphenyl-2,4-hexadiyne-1,6-diol,4-methy-2-pyridone (1/2), C30H22O2·2C6H7NO, (II,c), and 4,4,,4,,-(ethane-1,1,1-triyl)triphenol,6-methyl-2-pyridone,water (1/3/1), C20H18O3·3C6H7NO·H2O, (III,d). In two of the compounds, (I,a) and (I,d), the host molecules lie about crystallographic twofold axes. In two other compounds, (II,b) and (II,c), the host molecules lie across inversion centers. In all cases, the guest molecules are hydrogen bonded to the host molecules through O,H...O=C hydrogen bonds [the range of O...O distances is 2.543,(2),2.843,(2),Å. The pyridone moieties form dimers through N,H...O=C hydrogen bonds in five of the compounds [the range of N...O distances is 2.763,(2),2.968,(2),Å]. In four compounds, (I,a), (I,c), (I,d) and (II,c), the molecules are arranged in extended zigzag chains formed via host,guest hydrogen bonding. In five of the compounds, the guest molecules are arranged in parallel pairs on top of each other, related by inversion centers. However, none of these compounds underwent photodimerization in the solid state upon irradiation. In one of the crystalline compounds, (III,d), the guest molecules are arranged in stacks with one disordered molecule. The unsuccessful dimerization is attributed to the large interatomic distances between the potentially reactive atoms [the range of distances is 4.027,(4),4.865,(4),Å] and to the bad overlap, expressed by the lateral shift between the orbitals of these atoms [the range of the shifts from perfect overlap is 1.727,(4),3.324,(4),Å]. The bad overlap and large distances between potentially photoreactive atoms are attributed to the hydrogen-bonding schemes, because the interactions involved in hydrogen bonding are stronger than those in ,,, interactions. [source] Ce20Mg19Zn81: a new structure type with a giant cubic cellACTA CRYSTALLOGRAPHICA SECTION C, Issue 7 2008Volodymyr Pavlyuk Icosacerium nonadecamagnesium henoctacontazinc, Ce20Mg19Zn81, synthesized by fritting of the pure elements with subsequent arc melting, crystallizes with an unusually large cubic unit cell [space group F3m, a = 21.1979,(8),Å] and represents a new structure type among the technologically important family of ternary rare earth,transition metal,magnesium intermetallics. The majority of atoms (two Ce and five Zn) display .3m site symmetry, two Ce and one Mg atom occupy three 2.mm positions, one Mg and one Zn have 3m site symmetry, one Mg and three Zn atoms sit in ..m positions, and one Zn atom is in a general position. The Ce20Mg19Zn81 structure can be described using the geometric concept of nested polyhedral units, by which it consists of four different polyhedral units, viz. A (Zn+Zn4+Zn4+Zn12+Ce6), B (Mg+Zn12+Ce4+Zn24+Ce4), C (Zn4+Zn12+Mg6) and D (Zn4+Zn4+Mg12+Ce6), with the outer construction unit being an octahedron or tetrahedron. All interatomic distances in the structure indicate metallic-type bonding. [source] WHEATSHEAF: an algorithm to average protein structure ensemblesACTA CRYSTALLOGRAPHICA SECTION D, Issue 1 2005David Thomas A new algorithm is described that forms a single structure representative of ensembles of structures from files in the format used by the Protein Data Bank. A first attempt is made by averaging in the space spanned by bond lengths, inter-bond rotations and symmetry-multiplied dihedral rotations. This normally produces well formed regular secondary-structure elements, but the intervening less well ordered regions are often distorted because of the invalidity of averaging large rotations about divergent axes. For this reason, the algorithm includes a second stage that pulls the interatomic distances towards more fully representative values. Results produced by this method have proved better as judged by conventional quality checks than any input structure in nearly all cases tested so far, especially for the backbone, and much better than those produced by commonly used alternative methods. [source] | |||||||||||||