scholarly journals WinPSSP: a revamp of the computer program PSSP and its performance solving the crystal structures of small organic compounds and solids of biological and pharmaceutical interest

2017 ◽  
Vol 50 (1) ◽  
pp. 293-303 ◽  
Author(s):  
Silvina Pagola ◽  
Alekos Polymeros ◽  
Nikolaos Kourkoumelis
Keyword(s):  
Crystal Structure ◽  
Degrees Of Freedom ◽  
Structural Parameters ◽  
Rietveld Analysis ◽  
Molecular Solids ◽  
Structure Information ◽  
Individual Solution ◽  
Structure Determinations ◽  
Definition Of ◽  
Integrated Intensities

The direct-space methods software Powder Structure Solution Program (PSSP) [Pagola & Stephens (2010). J. Appl. Cryst. 43, 370–376] has been migrated to the Windows OS and the code has been optimized for fast runs. WinPSSP is a user-friendly graphical user interface that allows the input of preliminary crystal structure information, integrated intensities of the reflections and FWHM, the definition of structural parameters and a simulated annealing schedule, and the visualization of the calculated and experimental diffraction data overlaid for each individual solution. The solutions are reported as filename.cif files, which can be used to analyze packing motifs and chemical bonding, and to input the atomic coordinates into the Rietveld analysis software GSAS. WinPSSP performance in straightforward crystal structure determinations has been evaluated using 18 molecular solids with 6–20 degrees of freedom. The free-distribution program as well as multimedia tutorials can be accessed at http://users.uoi.gr/nkourkou/winpssp/.

The effect of profile-step counting time on the determination of crystal structure parameters by X-ray Rietveld analysis

1984 ◽  
Vol 17 (5) ◽  
pp. 297-306 ◽  
Author(s):  
R. J. Hill ◽  
I. C. Madsen
Keyword(s):  
Crystal Structure ◽  
Goodness Of Fit ◽  
Structural Parameters ◽  
Rietveld Analysis ◽  
Structure Parameters ◽  
Model Errors ◽  
Diffraction Profile ◽  
X Ray ◽  
Counting Time ◽  
Step Counting

Crystal structure parameters have been obtained for α-Al2O3, β-PbO2 and (Mg, Fe)2SiO4 by Rietveld analysis of Cu Kα X-ray powder diffraction data collected on a conventional diffractometer using counting times ranging from 0.01 to 5 s per step. For all but the 0.01 s data collected on (Mg, Fe)2SiO4 the structural parameters obtained at different counting times are statistically identical at the 3 σ level, and the spread in the values is essentially the same as that obtained by sample repacking at a fixed counting time of 1 s per step. The parameter e.s.d.'s and conventional agreement indices Rwp and RB decrease to values limited by residual model errors as the counting time increases, but the goodness-of-fit parameter becomes unacceptably larger than its ideal value of unity. When more than a few thousand counts are accumulated for the maximum step intensity in the diffraction profile a weighting scheme based solely on counting variance is inappropriate and the parameter e.s.d.'s are no longer a reflection of their accuracy.

scholarly journals New refinement of the crystal structure of Zn(NH3)2Cl2 at 100 K

2019 ◽  
Vol 75 (9) ◽  
pp. 1386-1388
Author(s):  
Trpimir Ivšić ◽  
David Wenhua Bi ◽  
Arnaud Magrez
Keyword(s):  
Crystal Structure ◽  
Crystal Packing ◽  
Structural Parameters ◽  
Point Group ◽  
Three Dimensional ◽  
Group Symmetry ◽  
Hydrogen Atoms ◽  
Dimensional Network ◽  
Structure Determinations ◽  
Insight Into

The crystal structure of [ZnCl2(NH3)2], diamminedichloridozinc, was re-investigated at low temperature, revealing the positions of the hydrogen atoms and thus a deeper insight into the hydrogen-bonding scheme in the crystal packing. In comparison with previous crystal structure determinations [MacGillavry & Bijvoet (1936). Z. Kristallogr. 94, 249–255; Yamaguchi & Lindqvist (1981). Acta Chem. Scand. 35, 727–728], an improved precision of the structural parameters was achieved. In the crystal, tetrahedral [Zn(NH3)2Cl2] units (point-group symmetry mm2) are linked through N—H...Cl hydrogen bonds into a three-dimensional network.

scholarly journals PSSP, a computer program for the crystal structure solution of molecular materials from X-ray powder diffraction data

2010 ◽  
Vol 43 (2) ◽  
pp. 370-376 ◽  
Author(s):  
Silvina Pagola ◽  
Peter W. Stephens
Keyword(s):  
Crystal Structure ◽  
Computer Program ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Degrees Of Freedom ◽  
Space Structure ◽  
Molecular Solids ◽  
Powder Diffraction Data ◽  
X Ray ◽  
Structure Solution

This work describes the computer programPSSP(powder structure solution program) for the crystal structure solution of molecular solids from X-ray powder diffraction data. This direct-space structure solution program uses the simulated annealing global optimization algorithm to minimize the difference between integrated intensities calculated from trial models and those extracted in a Le Bail fit of the experimental pattern, using a cost function for dealing with peak overlap through defined intensity correlation coefficients, computationally faster to calculate thanRwp. The methodology outlined is applicable to organic solids composed of moderately complex rigid and flexible molecules, using diffraction data up to relatively low resolution.PSSPperformance tests using 11 molecular solids with six to 20 degrees of freedom are analyzed.

Combination of energy minimizations and rigid-body Rietveld refinement: the structure of 2,5-dihydroxybenzo[de]benzo[4,5]imidazo[2,1-a]isoquinolin-7-one

1999 ◽  
Vol 32 (2) ◽  
pp. 178-186 ◽  
Author(s):  
Martin U. Schmidt ◽  
Robert E. Dinnebier
Keyword(s):  
Crystal Structure ◽  
Rigid Body ◽  
Degrees Of Freedom ◽  
Three Dimensional ◽  
Rietveld Analysis ◽  
Hydrogen Bond Network ◽  
Intermolecular Energy ◽  
Planar Molecules ◽  
Bond Network ◽  
Random Packings

The crystal structure of the yellow pigment 2,5-dihydroxybenzo[de]benzo[4,5]imidazo[2,1-a]isoquinolin-7-one (C18H10N2O3) was determined from powder data. The crystal structure was solved by minimizing the intermolecular energy starting from random packings. Subsequently, the structure was refined by rigid-body Rietveld analysis, using synchrotron powder data. The refinement included several intramolecular degrees of freedom. The compound crystallizes inPna21,Z\,=\,4, with lattice parametersa\,=\,13.2759 (3),b\,=\,20.9561 (5),c\,=\,4.7798 (1) Å, andV\,=\,1329.79 (5) Å3. The crystal consists of planar molecules, connected by hydrogen bonds of the types O–H...OH and O–H...N, which form a three-dimensional hydrogen-bond network.

Least-square refinement of structure parameters from CBED integrated intensities: application to determination of temperature factors in Y BA2CU3O7

1992 ◽  
Vol 50 (2) ◽  
pp. 1456-1457
Author(s):  
Kjersti Gjønnes ◽  
Jon Gjønnes
Keyword(s):  
Least Square ◽  
Measured Intensity ◽  
Structure Information ◽  
Accurate Temperature ◽  
Least Square Fit ◽  
Case Application ◽  
Integrated Intensities ◽  
Temperature Factors ◽  
Narrow Bands

Electron diffraction intensities can be obtained at large scattering angles (sinθ/λ ≥ 2.0), and thus structure information can be collected in regions of reciprocal space that are not accessable with other diffraction methods. LACBED intensities in this range can be utilized for determination of accurate temperature factors or for refinement of coordinates. Such high index reflections can usually be treated kinematically or as a pertubed two-beam case. Application to Y Ba2Cu3O7 shows that a least square refinememt based on integrated intensities can determine temperature factors or coordinates.LACBED patterns taken in the (00l) systematic row show an easily recognisable pattern of narrow bands from reflections in the range 15 < l < 40 (figure 1). Integrated intensities obtained from measured intensity profiles after subtraction of inelastic background (figure 2) were used in the least square fit for determination of temperature factors and refinement of z-coordinates for the Ba- and Cu-atoms.

Shape Dynamics and the Linking Theory

2018 ◽  
Author(s):  
Flavio Mercati
Keyword(s):  
Phase Space ◽  
Degrees Of Freedom ◽  
Line Element ◽  
Hamiltonian Formulation ◽  
Operational Definition ◽  
Extended Phase Space ◽  
Extended Phase ◽  
Problem Of Time ◽  
Definition Of ◽  
Matter Fields

This chapter explains in detail the current Hamiltonian formulation of SD, and the concept of Linking Theory of which (GR) and SD are two complementary gauge-fixings. The physical degrees of freedom of SD are identified, the simple way in which it solves the problem of time and the problem of observables in quantum gravity are explained, and the solution to the problem of constructing a spacetime slab from a solution of SD (and the related definition of physical rods and clocks) is described. Furthermore, the canonical way of coupling matter to SD is introduced, together with the operational definition of four-dimensional line element as an effective background for matter fields. The chapter concludes with two ‘structural’ results obtained in the attempt of finding a construction principle for SD: the concept of ‘symmetry doubling’, related to the BRST formulation of the theory, and the idea of ‘conformogeometrodynamics regained’, that is, to derive the theory as the unique one in the extended phase space of GR that realizes the symmetry doubling idea.

Wechselwirkungen in Molekülkristallen, 160 [1,2]. Kristallzüchtung und Strukturbestimmung der verschiedenartigen Polyphenyl-Kontaktionenmultipel [p-Quaterphenylee⊖⊖][Na⊕(DME)3]2, [p-Quaterphenyl⊖⊖(Na⊕(THF)3)2] und [p-Terphenyl⊖⊖Na⊕(DME)2Na⊕(DME)]2 / Interaction in Molecular Crystals, 160 [1, 2]. Crystallization and Structure Determination of the Different Polyphenyl Contact Ion Multiples [p-Quaterphenylee⊖⊖][Na⊕(DME)3]2, [p-Quaterphenyl⊖⊖(Na⊕(THF)3)2] und [p-Terphenyl⊖⊖Na⊕(DME)2Na⊕(DME)]2

2000 ◽  
Vol 55 (12) ◽  
pp. 1103-1113 ◽  
Author(s):  
Hans Bock ◽  
K. Gharagozloo-Hubmann ◽  
M. Sievert
Keyword(s):  
Crystal Structure ◽  
Single Crystal ◽  
Sodium Salt ◽  
Structure Determination ◽  
Metal Cation ◽  
Molecular Crystals ◽  
Sodium Salts ◽  
Structure Determinations ◽  
Cation Coordination

The π-hydrocarbons p-terphenyl and p-quaterphenyl are reduced to their dianions in aprotic solutions of different ethers at sodium metal mirrors. Single crystal structure determinations of the solvent-separated or solvens-shared contact ion multiples, [p-terphenyl⊖⊖ Na⊕(DME)2Na⊕DME]2, p-quaterphenyl⊖⊖ ][Na⊕(DME)3]2 and [p-quaterpheny⊖⊖( Na⊕(THF)3)2], prove the essential cation solvation by the chelating dimethoxyethane (DME) versus the bulky tetrahydrofuran (THF) ligands: The solution network of equilibria between solvent separated and solvent shared ion aggregates can be considerably and transparently modified by the ether solvent selected. In addition, the structures of the monomeric sodium salts reveal partly novel details of metal cation coordination by contacts Na⊕ ··· O as well as Na⊕ ··· Cπ such as in the dimeric sodium salt of p-terphenyl dianion, [(DME)2Na⊕ (terphenyl⊖⊖)(Na⊕ DME)(terphenyl⊖⊖)Na⊕ (DME)2].

Influence of Clearances and Thermal Effects on the Dynamic Behavior of Gear-Hydrodynamic Journal Bearing Systems

2013 ◽  
Vol 135 (6) ◽  
Author(s):  
R. Fargère ◽  
P. Velex
Keyword(s):  
Degrees Of Freedom ◽  
Integration Scheme ◽  
Time Step ◽  
Specific Element ◽  
Normal Contact ◽  
Contact Algorithm ◽  
Gear Teeth ◽  
Proposed Model ◽  
Elastic Couplings ◽  
Definition Of

A global model of mechanical transmissions is introduced which deals with most of the possible interactions between gears, shafts, and hydrodynamic journal bearings. A specific element for wide-faced gears with nonlinear time-varying mesh stiffness and tooth shape deviations is combined with shaft finite elements, whereas the bearing contributions are introduced based on the direct solution of Reynolds' equation. Because of the large bearing clearances, particular attention has been paid to the definition of the degrees-of-freedom and their datum. Solutions are derived by combining a time step integration scheme, a Newton–Raphson method, and a normal contact algorithm in such a way that the contact conditions in the bearings and on the gear teeth are simultaneously dealt with. A series of comparisons with the experimental results obtained on a test rig are given which prove that the proposed model is sound. Finally, a number of results are presented which show that parameters often discarded in global models such as the location of the oil inlet area, the oil temperature in the bearings, the clearance/elastic couplings interactions, etc. can be influential on static and dynamic tooth loading.

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