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Atomic Positions (atomic + position)
Selected AbstractsSyntheses, Structures and Theoretical Investigations of [Li(thf)4]2[Ti2Cu8S4(SPh)10] and [Ti2Ag6S6Cl2(PPhiPr2)6]EUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 28 2009Heino Sommer Abstract The reaction of CuOAc (OAc = acetate) with TiCl4·2thf and LiSPh in thf leads to the formation of tiny deep-red crystals of [Li(thf)4]2[Ti2Cu8S4(SPh)10]. The silver/titanium cluster complex [Ti2Ag6S6Cl2(PPhiPr2)6] was synthesized by the reaction of TiCl4·2thf with AgPhCO2 and S(SiMe3)2 in the presence of PPhiPr2. The crystal structures of the compounds were determined by X-ray analysis of single crystals. Additionally, theoretical investigations were performed to assign the proper chlorine/sulfur atomic positions and to rationalize the bonding situation in 1 and 2. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2009) [source] Direct methods and the solution of organic structures from powder dataJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 2 2007Angela Altomare The electron density map produced after the application of direct methods to powder diffraction data of organic compounds is usually very approximated: some atoms are missed, other atoms are in false positions, some atoms are imperfectly located and the connectivity is quite low. A new procedure able to recover the complete structure model is described. In this procedure, a better interpretation of the map is combined with geometrical techniques for generating new atomic positions. The application of the new procedure may lead to the recovery of the complete crystal structure. [source] MDLab: A molecular dynamics simulation prototyping environmentJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 7 2010Trevor Cickovski Abstract Molecular dynamics (MD) simulation involves solving Newton's equations of motion for a system of atoms, by calculating forces and updating atomic positions and velocities over a timestep ,t. Despite the large amount of computing power currently available, the timescale of MD simulations is limited by both the small timestep required for propagation, and the expensive algorithm for computing pairwise forces. These issues are currently addressed through the development of efficient simulation methods, some of which make acceptable approximations and as a result can afford larger timesteps. We present MDLab, a development environment for MD simulations built with Python which facilitates prototyping, testing, and debugging of these methods. MDLab provides constructs which allow the development of propagators, force calculators, and high level sampling protocols that run several instances of molecular dynamics. For computationally demanding sampling protocols which require testing on large biomolecules, MDL includes an interface to the OpenMM libraries of Friedrichs et al. which execute on graphical processing units (GPUs) and achieve considerable speedup over execution on the CPU. As an example of an interesting high level method developed in MDLab, we present a parallel implementation of the On-The-Fly string method of Maragliano and Vanden-Eijnden. MDLab is available at http://mdlab.sourceforge.net. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] Electronic Structure and Bonding of All Crystalline Phases in the Silica,Yttria,Silicon Nitride Phase Equilibrium DiagramJOURNAL OF THE AMERICAN CERAMIC SOCIETY, Issue 11 2004Wai-Yim Ching This paper reviews the structures and properties of 10 binary, ternary, and quaternary crystals within the equilibrium phase diagram of the SiO2,Y2O3,Si3N4 system. They are binary compounds SiO2, Y2O3, Si3N4; ternary compounds Si2N2O, Y2Si2O7, and YSi2O5; and quaternary crystals Y2Si3N4O3 (M-melilite), Y4Si2O7N2, (N-YAM), YSiO2N (wallastonite), and Y10(SiO4)6N2 (N-apatite, N-APT). Although the binary compounds are well-known and extensively studied, the ternary and the quaternary crystals are not. Most of the ternary and the quaternary crystals simply have been referenced as secondary phases in the processing of nitrogen ceramics. Their crystal structures are complex and not precisely determined. In the quaternary crystals, there exists O/N disorder in that the exact atomic positions of the anions cannot be uniquely determined. It is envisioned that a variety of cation,anion bonding configurations exist in these complex crystals. The electronic structure and bonding in these crystals are, therefore, of great interest and are indispensable for a fundamental understanding of structural ceramics. We have used ab initio methods to study the structure and bonding properties of these 10 crystals. For crystals with unknown or incomplete structural information, we use an accurate total energy relaxation scheme to obtain the most likely atomic positions. Based on the theoretically modeled structures, the electronic structure and bonding in these crystals are investigated and related to various local cation,anion bonding configurations. These results are presented in the form of atom-resolved partial density of states, Mulliken effective charges, and bond order values. It is shown that Y,O and Y,N bonding are not negligible and should be a part of the discussion of the overall bonding schemes in these crystals. Spectroscopic properties in the form of complex, frequency-dependent dielectric functions, X-ray absorption near-edge structure (XANES), and the electron energy-loss near-edge structure (ELNES) spectra in these crystals also are calculated and compared. These results are discussed in the context of specific bonding configurations between cations (silicon and yttrium) and anions (oxygen and nitrogen) and their implications on intergranular thin films in polycrystalline Si3N4 containing rare-earth elements. [source] Magnetic semiconductors in ternary Cd,Mn,Te compoundsPHYSICA STATUS SOLIDI (B) BASIC SOLID STATE PHYSICS, Issue 5 2008Yong Liu Abstract Since Mn-doped CdTe in zincblende structure has been fabricated for Mn concentrations from 0 to 0.5, we use a first-principles full-potential method to study CdTe-based ternary Cd,Mn,Te compounds for possible magnetic semiconductors. The compounds are constructed by substituting Mn for some Cd atoms in zincblende CdTe. We optimize fully their geometric structures and internal atomic positions, and then study their electronic and magnetic properties. We find that the stable CdMnTe2 and Cd3MnTe4 are antiferromagnetic semiconductors with space groups 160 and 111, and the stable Cd7MnTe8 is a layered ferromagnetic semiconductor with space group 115. Their real lattice constants are a little smaller than CdTe's and an Mn atom contributes 5 Bohr magnetons to their total magnetic moments. The antiferromagnetism for the CdMnTe2 is attributed to the Te-based superexchange of Mn spins. For the other two, the MnMn spin interactions are dependent on the MnMn distance and the environment. The antiferromagnetism for the Cd3MnTe4 and the layered ferromagnetism for the Cd7MnTe8 can be attributed to two weaker indirect exchange interactions based on both Cd and Te. The Kohn,Sham gaps of the three magnetic semiconductors are 0.52 eV, 0.80 eV, and 1.23 eV, respectively. The real semiconductor gaps may be larger than 1 eV considering the fact that the Kohn,Sham gap of CdTe is 0.55 eV but the experimental semiconductor gap is 1.56 eV at 300 K. These magnetic semiconductors, compatible with semiconductors such as CdTe, could be useful in spintronics applications. (© 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Raman scattering of vanadium ladder compounds from first principlesPHYSICA STATUS SOLIDI (C) - CURRENT TOPICS IN SOLID STATE PHYSICS, Issue 11 2004J. Spitaler Abstract We investigate phonon Raman scattering of the Ag modes in NaV2O5 and CaV2O5. We perform firstprinciples calculations within density functional theory (DFT) to obtain the ground state with relaxed atomic positions. Thereupon we determine eigenvectors and frequencies of the 8 Ag modes within the frozen phonon approach and compute the dielectric functions ,(,) for structures distorted according to the phonon eigenvectors. Raman intensities are obtained using the derivatives of ,(,) with respect to the normal coordinates Q taken at the incident photon energy ,I. For NaV2O5 the peak positions and the relative intensities of the theoretical results for the experimentally used frequency ,I = 2.5 eV excellently agree with measured data. Moreover, for the three different scattering geometries a strong dependency of the Raman intensity on ,I is revealed. (© 2004 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Non-equilibrium phonon dynamics studied by grazing-incidence femtosecond X-ray crystallographyACTA CRYSTALLOGRAPHICA SECTION A, Issue 2 2010S. L. Johnson The timescales for structural changes in a single crystal of bismuth after excitation with an intense near-infrared laser pulse are studied with femtosecond pump-probe X-ray diffraction. Changes in the intensity and reciprocal-lattice vector of several reflections give quantitative information on the structure factor and lattice strain as a function of time, with a resolution of 200,fs. The results indicate that the majority of excess carrier energy that remains near the surface is transferred to vibrational modes on a timescale of about 10,ps, and that the resultant increase in the variance of the atomic positions at these times is consistent with the overall magnitude of lattice strain that develops. [source] Correcting electron-density resolution bias in reciprocal spaceACTA CRYSTALLOGRAPHICA SECTION A, Issue 3 2009Angela Altomare Fourier syntheses are always affected by series-termination errors, which generate sets of positive and negative ripples around each main peak in the map. The interaction among the ripples distorts the profile of the map and moves peaks away from their correct positions. In a previous paper [Altomare et al. (2008). Acta Cryst. A64, 326,336] an algorithm was described which reduces the resolution bias by removing the effects of the ripples in direct space. In this paper the correction is performed in reciprocal space: the effect of the ripples on the atomic scattering factors is calculated and subtracted from the usual atomic scattering factors. The modified scattering factors are used to calculate new structure factors, from which more accurate electron-density maps may be obtained. The experimental tests show that the procedure minimizes the effects of the resolution bias and provides atomic positions that are more accurate than those provided by traditional approaches. [source] Introduction to a general crystallographyACTA CRYSTALLOGRAPHICA SECTION A, Issue 4 2001A. Janner The definition of an extended crystallographic group is given, based on an -dimensional Euclidean space, carrier of a faithful integral representation of a permutation group of atomic positions. The Euclidean crystallography of normal crystals and the higher-dimensional one applied to incommensurately modulated crystals, intergrowth crystals and quasicrystals are special cases of a general crystallography. The same is true for the multimetrical crystallographic characterization of ice and of snow crystals. This approach can also be applied to single molecules, leading to what may be denoted as molecular crystallography. It possibly allows non-trivial structural relations between atomic positions belonging to the asymmetric unit of the molecular point group to be obtained. Two simple molecules, polycyclic aromatic hydrocarbons, are treated as illustrative examples. [source] Modulation of atomic positions in CaCuxMn7,xO12 (x, 0.1)ACTA CRYSTALLOGRAPHICA SECTION B, Issue 5 2009The modulation of atomic positions in CaCuxMn7,xO12 (x = 0 and 0.1) was studied using synchrotron radiation powder diffraction below 250 and 220,K, respectively. The copper-rich member CaCuxMn7,xO12 (x = 0.23) does not show any modulation of the atomic positions at temperatures as low as 10,K. Using low-temperature neutron powder diffraction the modulation of the magnetic moments of Mn ions in CaCuxMn7,xO12 (x = 0, 0.1 and 0.23) has been investigated. Long-range modulated magnetic ordering in CaCuxMn7,xO12 (x = 0, 0.1 and 0.23) is observed below 90.4, 89.2 and 78.1,K. (0,0,qp) and (0,0,qm) are the propagation vectors describing the modulations of the atomic positions and the magnetic moments. For CaCuxMn7,xO12 (x = 0 and 0.1) the magnetic modulation and atomic modulation lengths are related by a factor of 2 satisfying the relation (1 ,qp) = 2(1 ,qm). [source] Revision of pyrrhotite structures within a common superspace modelACTA CRYSTALLOGRAPHICA SECTION B, Issue 5 2007Zunbeltz Izaola The structure of pyrrhotite (Fe1,,,xS with 0.05 ,x, 0.125) has been reinvestigated in the framework of the superspace formalism. A common model with a centrosymmetric superspace group is proposed for the whole family. The atomic domains in the internal space representing the Fe atoms are parametrized as crenel functions that fulfil the closeness condition. The proposed model explains the x -dependent space groups observed and the basic features of the structures reported up to now. Our model yields for any x value a well defined ordered distribution of Fe vacancies in contrast to some of the structural models proposed in the literature. A new (3,+,1)-dimensional refinement of Fe0.91S using the deposited dataset [Yamamoto & Nakazawa (1982). Acta Cryst. A38, 79,86] has been performed as a benchmark of the model. The consistency of the proposed superspace symmetry and its validity for other compositions has been further checked by means of ab initio calculations of both atomic forces and equilibrium atomic positions in non-relaxed and relaxed structures, respectively. [source] Superspace description of the crystal structures of Can(Nb,Ti)nO3n,+,2 (n = 5 and 6)ACTA CRYSTALLOGRAPHICA SECTION B, Issue 2 2007Jonathan Guevarra The crystal structures of two members of the homologous series Can(Nb,Ti)nO3n,+,2, with n = 5 and 6, are presented within the superspace formalism. A common (3,+,1)-dimensional superspace model is used to describe the crystal structures of both compositions within a particular homologous series, where the primary modulation wavevector and the width of the atomic domains vary systematically with composition. The two crystal structures are characterized as commensurately modulated structures consisting of discontinuous atomic domains described by occupational crenel functions. The displacive modulation functions for the two compounds exhibit similarities, but they also show that the idea of a unified superspace model does not extend toward the precise atomic positions. For n = 6, the centrosymmetric (3,+,1)-dimensional superspace symmetry provides a natural explanation for the pseudo-symmetries that are present in the non-centrosymmetric (three-dimensional) superstructure of this compound. The efficiency of the superspace approach is demonstrated by structure refinements in (3,+,1)-dimensional superspace and by comparing these results with the refinements in their three-dimensional superstructures. [source] Structure,property correlation over five phases and four transitions in Pb5Al3F19ACTA CRYSTALLOGRAPHICA SECTION B, Issue 5 2003S. C. Abrahams The calorimetric and dielectric properties of Pb5Al3F19 in the five phases stable under ambient pressure are correlated with structure for fuller characterization of each phase. The first-order transition between ferroelectric phase V and antiferroelectric phase IV at TV,IV = 260,(5),K exhibits a thermal hysteresis of 135,(5),K on heating, with a maximum atomic displacement ,(xyz)max = 1.21,(6),Å; the transition from phase IV to ferroelastic phase III at 315,(5),K is also first order but with a thermal hysteresis of 10,(5),K and ,(xyz)max = 0.92,(7) ,Å; that from phase III to paraelastic phase II at 360,(5),K is second order without hysteresis and has ,(xyz)max = 0.69,(4),Å; and the transition from phase II to paraelectric phase I at 670,(5),K is second or higher order, with ,(xyz)max = 0.7,(4),Å. The measured entropy change ,S at TV,IV agrees well with ,S as derived from the increased configurational energy by Stirling's approximation. For all other phase transitions, 0.5 ,,S > 0,J,mol,1,K,1 is consistent with an entropy change caused primarily by the changes in the vibrational energy. The structure of phase III is determined both by group theoretical/normal mode analysis and by consideration of the structures of phases II, IV and V reported previously; refinement is by simultaneous Rietveld analysis of the X-ray and neutron diffraction powder profiles. The structure of prototypic phase I is predicted on the basis of the atomic arrangement in phases II, III, IV and V. The introduction of 3d electrons into the Pb5Al3F19 lattice disturbs the structural equilibrium, the addition of 0.04% Cr3+ causing significant changes in atomic positions and increasing TIV,III by ,15,K. Substitution of Al3+ by 20% or more Cr3+ eliminates the potential minima that otherwise stabilize phases IV, III and II. [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] Li12Cu16+xAl26,x (x = 3.2): a new intermetallic structure typeACTA CRYSTALLOGRAPHICA SECTION C, Issue 8 2008Volodymyr Pavlyuk The new ternary lithium copper aluminide, Li12Cu16+xAl26,x (x = 3.2), dodecalithium nonadecacopper tricosaaluminide, crystallizes in a new structure type with space group P4/mbm. Among nine independent atomic positions, two Al (one of which is statistically disordered with Cu) and three Li atoms have point symmetry m.2m, two statistically disordered Al/Cu atoms are in m.. sites, one Al atom is in a 4/m.. site and one Cu atom occupies a general site. The framework of Li12Cu16+xAl26,x consists of pseudo-Frank,Kasper polyhedra enclosing channels of hexagonal prisms occupied by Li atoms. The crystallochemical peculiarity of this new structure type is discussed in relation to the derivatives from Laves phases (LiCuAl2 and Li8Cu12+xAl6,x) and to the well known CaCu5 structure. [source] Unambiguous determination of H-atom positions: comparing results from neutron and high-resolution X-ray crystallographyACTA CRYSTALLOGRAPHICA SECTION D, Issue 5 2010Anna S. Gardberg The locations of H atoms in biological structures can be difficult to determine using X-ray diffraction methods. Neutron diffraction offers a relatively greater scattering magnitude from H and D atoms. Here, 1.65,Å resolution neutron diffraction studies of fully perdeuterated and selectively CH3 -protonated perdeuterated crystals of Pyrococcus furiosus rubredoxin (D-rubredoxin and HD-rubredoxin, respectively) at room temperature (RT) are described, as well as 1.1,Å resolution X-ray diffraction studies of the same protein at both RT and 100,K. The two techniques are quantitatively compared in terms of their power to directly provide atomic positions for D atoms and analyze the role played by atomic thermal motion by computing the , level at the D-atom coordinate in simulated-annealing composite D-OMIT maps. It is shown that 1.65,Å resolution RT neutron data for perdeuterated rubredoxin are ,8 times more likely overall to provide high-confidence positions for D atoms than 1.1,Å resolution X-ray data at 100,K or RT. At or above the 1.0, level, the joint X-ray/neutron (XN) structures define 342/378 (90%) and 291/365 (80%) of the D-atom positions for D-rubredoxin and HD-rubredoxin, respectively. The X-ray-only 1.1,Å resolution 100,K structures determine only 19/388 (5%) and 8/388 (2%) of the D-atom positions above the 1.0, level for D-rubredoxin and HD-rubredoxin, respectively. Furthermore, the improved model obtained from joint XN refinement yielded improved electron-density maps, permitting the location of more D atoms than electron-density maps from models refined against X-ray data only. [source] A comparison of refined X-ray structures of hydrogenated and perdeuterated rat ,E-crystallin in H2O and D2OACTA CRYSTALLOGRAPHICA SECTION D, Issue 11 2005Jean-Baptiste Artero Rat ,E-crystallin was overexpressed, purified under different labelling conditions and crystallized and X-ray data were collected at resolutions between 1.71 and 1.36,Å. The structures were determined by molecular replacement. In these structures, the cd loop of the Greek-key motif 3, which is the major structural key motif of the two phase-transition groups of ,-crystallins, presents a double conformation. The influence of the perdeuteration on the protein structure was determined by comparison of the atomic positions and temperature factors of the different models. The perdeuterated proteins have a similar structure to their hydrogenated counterparts, but partial or full deuteration may have some effect on the atomic B -factor values. [source] The structure of uracil-DNA glycosylase from Atlantic cod (Gadus morhua) reveals cold-adaptation featuresACTA CRYSTALLOGRAPHICA SECTION D, Issue 8 2003Ingar Leiros Uracil-DNA glycosylase (UDG; EC 3.2.2.3) is a DNA-repair protein that catalyses the hydrolysis of promutagenic uracil residues from single- or double-stranded DNA, generating free uracil and abasic DNA. The crystal structure of the catalytic domain of cod uracil-DNA glycosylase (cUDG) has been determined to 1.9,Å resolution, with final R factors of 18.61 and 20.57% for the working and test sets of reflections, respectively. This is the first crystal structure of a uracil-DNA glycosylase from a cold-adapted species and a detailed comparison with the human enzyme is performed in order to rationalize the cold-adapted behaviour of the cod enzyme at the structural level. The catalytic domain of cUDG comprises 223 residues, with a sequence identity to the human UDG of 75%. The tertiary structures of the two enzymes are also similar, with an overall displacement in main-chain atomic positions of 0.63,Å. The amino-acid substitutions and the differences in intramolecular hydrogen bonds, hydrophobic interactions, ion-pair interactions and electrostatic potentials are compared and discussed in order to gain insight into the factors that cause the increased activity and reduced thermostability of the cod enzyme. In particular, the reduced number of strong ion-pair interactions in the C-terminal half of cUDG is believed to greatly affect the flexibility and/or stability. Increased positive electrostatic surface potential on the DNA-facing side of cUDG seems to be responsible for increasing the affinity for the negatively charged DNA compared with that of hUDG. [source] A systematic case study on using NMR models for molecular replacement: p53 tetramerization domain revisitedACTA CRYSTALLOGRAPHICA SECTION D, Issue 12 2000Yu Wai Chen Molecular replacement using search models derived from nuclear magnetic resonance (NMR) spectroscopy has often proved problematic. It has been known for some time that the overall differences in atomic positions (r.m.s.d.) between the crystalline and the solution states of the same protein are of the order of 1,2,Å and approach the limit of molecular replacement. In most cases, this structural difference is a result of calculating the NMR structure with insufficient data, yielding an NMR structure of limited accuracy. A systematic case study was performed to investigate the use of NMR models for molecular replacement on the p53 tetramerization domain: NMR search models of varying degrees of accuracy were employed to solve phases for the 1.5,Å X-ray diffraction data. An approximate correlation was found between the accuracy of the NMR search model and the clarity and quality of the molecular-replacement solution. It was found that ensemble models perform better than single averaged models and have a larger tolerance in model inaccuracy. Also, distance-derived B factors can improve the performance of single models. [source] | |||||||||||||