scholarly journals The Extended PLATON/SQUEEZE Tool in the Context of Twinning and SHELXL2014

2014 ◽  
Vol 70 (a1) ◽  
pp. C1436-C1436 ◽  
Author(s):  
Anthony Spek
Keyword(s):  
Structure Determination ◽  
Fourier Transformation ◽  
Ad Hoc ◽  
Solvent Mixtures ◽  
Density Peaks ◽  
Difference Density ◽  
Valence States ◽  
Structure Factors ◽  
Density Map ◽  
Solvent Molecules

The completion of a single crystal structure determination is often hampered by the presence of disordered solvent molecules of crystallization. The often not interesting details of that solvent disorder and its contribution to the calculated structure factors has to be modelled in some way in order to obtain publishable results. Current refinement programs include suitable constraints and restraints for a stable refinement of a discrete disorder model. This is often the preferred procedure, in particular when charge balances and valence states are relevant. Unfortunately, a discrete disorder model is not always feasible. Examples include solvent molecules in infinite channels or structures including unknown solvents or solvent mixtures. In such cases the iterative back-Fourier transformation of the content of the disordered solvent volume in a difference density map can be attempted as the contribution to the calculated structure factors. Back-Fourier transformation of disordered solvent regions was prototyped by us nearly 25 years ago (van der Sluis & Spek, 1990) around the, at that time widely used, SHELX76 refinement program. The original reason for its development was the structure determination of a pharmaceutical that contained infinite channels filled with ridges of electron density in the difference density map rather than discrete density peaks (van der Sluis & Spek, 1990). The preliminary implementation of a successful prototype procedure (called BYPASS) was complex and found not to be easily distributable due to its dependence on many (local) ad-hoc programs. A new distributable version, compatible with the next generation refinement program SHELXL97, was implemented as the SQUEEZE tool in the program package PLATON Spek, 2009). The new SHELXL2014 refinement program allows for an even more elegant implementation of the SQUEEZE tool including the possibility to apply it also for twinned structures. Examples and restrictions will be discussed.

Density-modification procedures: improving a calculated map before interpretation

2002 ◽  
Author(s):  
David Blow
Keyword(s):  
Electron Density ◽  
Uniform Density ◽  
Anomalous Scattering ◽  
Molecular Replacement ◽  
Small Proteins ◽  
Isomorphous Replacement ◽  
Structure Factors ◽  
Density Map ◽  
Solvent Molecules ◽  
Electron Density Map

Procedures to determine the phases of the structure factors, by isomorphous replacement, by anomalous scattering, or by molecular replacement, were described in the Chapters 7–9. Using one or more of these methods, phases are generated which allow an electron-density map to be calculated, at a resolution to which the phases are thought to be reliable. In many cases this electron density can be confidently interpreted in terms of atomic positions. But this is not always the case. Quite often, the procedures so far described offer a tantalizing puzzle map, with some features which I think I can interpret, but raising many questions. Before devoting effort to interpreting an unsatisfactory electron-density map, a number of procedures are available, which might make a striking improvement. Perhaps the most important strategy is to seek out more isomorphous and anomalous scattering derivatives. Before doing that, there are other possibilities which may improve an electron-density map without any more experimental data. These methods are known collectively as density modification. The first group of methods exploits features of the electron density which result from the packing of molecules into a crystal. Macromolecular crystals composed of rigid molecules have voids between the molecules filled with disordered solvent, often including the precipitants used in the crystallization process. These solvent regions present featureless density between the structured density of the macromolecules. A high-quality electron-density map will show these featureless regions clearly. In a map of poorer quality, the voids between molecules may be clearly defined, but far from featureless. This provides a method to improve the map. Although some solvent molecules are immobilized on the surface of the macromolecule, those further from the surface are in a disordered liquid-like state which presents a uniform density. Except in very small proteins, the majority of solvent is disordered. If such uniform solvent regions can be recognized, they allow surfaces to be defined which separate solvent regions from protein regions. Two procedures are described below. It has become almost a matter of routine to use one or both of these methods.

scholarly journals A complicated quasicrystal approximant ∊16 predicted by the strong-reflections approach

2010 ◽  
Vol 66 (1) ◽  
pp. 17-26 ◽  
Author(s):  
Mingrun Li ◽  
Junliang Sun ◽  
Peter Oleynikov ◽  
Sven Hovmöller ◽  
Xiaodong Zou ◽  
...  
Keyword(s):  
Electron Diffraction ◽  
Unit Cell ◽  
Space Groups ◽  
Inverse Fourier Transformation ◽  
Transmission Electron ◽  
Structure Factors ◽  
Precession Electron Diffraction ◽  
Density Map ◽  
Electron Density Map ◽  
Good Agreement

The structure of a complicated quasicrystal approximant ∊16 was predicted from a known and related quasicrystal approximant ∊6 by the strong-reflections approach. Electron-diffraction studies show that in reciprocal space, the positions of the strongest reflections and their intensity distributions are similar for both approximants. By applying the strong-reflections approach, the structure factors of ∊16 were deduced from those of the known ∊6 structure. Owing to the different space groups of the two structures, a shift of the phase origin had to be applied in order to obtain the phases of ∊16. An electron-density map of ∊16 was calculated by inverse Fourier transformation of the structure factors of the 256 strongest reflections. Similar to that of ∊6, the predicted structure of ∊16 contains eight layers in each unit cell, stacked along the b axis. Along the b axis, ∊16 is built by banana-shaped tiles and pentagonal tiles; this structure is confirmed by high-resolution transmission electron microscopy (HRTEM). The simulated precession electron-diffraction (PED) patterns from the structure model are in good agreement with the experimental ones. ∊16 with 153 unique atoms in the unit cell is the most complicated approximant structure ever solved or predicted.

scholarly journals 1,1′,3,3′-Tetramesitylquinobis(imidazole)-2,2′-dithione

IUCrData ◽  
2019 ◽  
Vol 4 (9) ◽  
Author(s):  
Jayaraman Selvakumar ◽  
Kuppuswamy Arumugam
Keyword(s):  
Crystal Structure ◽  
Molecular Weight ◽  
Solid State ◽  
Structural Analysis ◽  
Hydrogen Bonds ◽  
Cell Volume ◽  
Title Compound ◽  
Unit Cell Volume ◽  
Density Peaks ◽  
Solvent Molecules

The solid-state structural analysis of the title compound [systematic name: 5,11-disulfanylidene-4,6,10,12-tetrakis(2,4,6-trimethylphenyl)-4,6,10,12-tetraazatricyclo[7.3.0.03,7]dodeca-1(9),3(7)-diene-2,8-dione], C44H44N4O2S2 [+solvent], reveals that the molecule crystallizes in a highly symmetric cubic space group so that one quarter of the molecule is crystallographically unique, the molecule lying on special positions (two mirror planes, two twofold axes and a center of inversion). The crystal structure exhibits large cavities of 193 Å3 accounting for 7.3% of the total unit-cell volume. These cavities contain residual density peaks but it was not possible to unambiguously identify the solvent therein. The contribution of the disordered solvent molecules to the scattering was removed using a solvent mask and is not included in the reported molecular weight. No classical hydrogen bonds are observed between the main molecules.

Neutron diffraction investigation of copper tellurite glasses with high real-space resolution

2021 ◽  
Vol 54 (6) ◽  
Author(s):  
Navjot Kaur ◽  
Atul Khanna ◽  
Alex C. Hannon
Keyword(s):  
Neutron Diffraction ◽  
Coordination Number ◽  
Diffraction Data ◽  
Fourier Transformation ◽  
Short Range ◽  
Real Space ◽  
Tellurite Glasses ◽  
Space Resolution ◽  
Bond Lengths ◽  
Structure Factors

High real-space resolution neutron diffraction measurements up to 34 Å−1 were performed on a series of xCuO–(100 − x)TeO2 (x = 30, 40 and 50 mol%) glasses that were synthesized by the melt-quenching technique. The Fourier transformation of neutron diffraction structure factors was used to generate the pair distribution functions, with the first peak at 1.90 Å due to the overlapping Te–O and Cu–O atomic pairs. Reverse Monte Carlo (RMC) simulations were performed on the structure factors and the six partial atomic pair distributions of Cu–Cu, Cu–Te, Cu–O, Te–Te, Te–O and O–O were calculated. The Te–O and Cu–O distributions are very similar and asymmetrical, which revealed that there is a significant short-range disorder in the tellurite network due to the existence of a wide range of Te—O and Cu—O bond lengths. A high-Q (magnitude of momentum transfer function) neutron diffraction study revealed that the average Te–O coordination number decreases steadily from 3.45 to 3.18 with an increase in CuO concentration from 30 to 50 mol% in the glass network. Similar coordination number modifications were earlier found by the RMC analysis of neutron diffraction data sets of copper tellurite glasses that were performed up to lower Q maximum values of 9.5 Å−1. The comparison of high-Q and low-Q neutron diffraction studies reveals that RMC is a powerful and possibly the only technique that is available to elucidate the glass short-range and medium-range structural properties when diffraction data are available up to low Q values of, say, 9.5 Å−1, and when cation–oxygen bond lengths are strongly overlapping and cannot be resolved by Fourier transformation. In situ high-temperature (473 K) neutron diffraction studies of 50CuO–50TeO2 glass revealed that significant distortion of the tellurite network occurs with heating.

Übergangsmetallkomplexe mit Schwefelliganden, LXXXV. / Transition-Metal Complexes with Sulfur Ligands, LXXXV.

1992 ◽  
Vol 47 (5) ◽  
pp. 645-655 ◽  
Author(s):  
D. Sellmann ◽  
H. Schillinger ◽  
F. Knoch
Keyword(s):  
Transition Metal ◽  
Transition Metal Complexes ◽  
Structure Determination ◽  
Spectroscopic Methods ◽  
Apical Position ◽  
Tetragonal Pyramid ◽  
X Ray ◽  
Thiolate Ligand ◽  
Solvent Molecules

Ni(II) salts and the tetradentate thioether-thiolate ligand ′S4-C2′2- (= 1,2-bis(2-mercaptophenylthio)ethane(2-)) yield [Ni(′S4-C2′)]x (1), that also forms when Na2[Ni(′S2′ )2] (′S22-′ = o-benzenedithiolate(2-)) is alkylated by 1,2-dibromoethane. In boiling pyridine 1 adds two solvent molecules and gives pseudooctahedral [Ni(pyr)2(′S4-C2′ )] (2) which was characterized by X-ray structure determination. Reaction of 1 with PMe3 yields [Ni(PMe3)(′S4-C2′)] (4). X-ray structure determination of 4 showed that the Ni center is surrounded by one P and four S atoms in a distorted tetragonal pyramid in which the P atom, one thioether S atom and both of the thiolate S atoms form the base while the second thioether S atom occupies the apical position. Reaction of 1 with n-BuLi leads to removal of the C2H4 bridge of the ′S4-C2′2- ligand and formation of Li2[Ni(′S2′)2].When [Ni(acac)2]3 is reacted with ′buS4-C2′2 (= 1,2-bis(3,5-ditertiarybutyl-2-mercaptophenylthio)ethane(2-)) which is analogous to ′S4-C2′2-, the trinuclear [Ni(′buS4-C2′)]3 (3) forms. 3 · THF was characterized by X-ray structure determination. It contains one tetrahedrally distorted and two planar [NiS4] cores that are connected via the C2H4 groups of the ligands such that a macrocycle forms. PMe3 cleaves 3 to give mononuclear [Ni(PMe3)(′buS4-C2′)] (5). Due to its lability, it was characterized only by spectroscopic methods.

scholarly journals Crystal structure of d(CCGGGGTACCCCGG)2at 1.4 Å resolution

2017 ◽  
Vol 73 (5) ◽  
pp. 259-265
Author(s):  
Selvam Karthik ◽  
Arunachalam Thirugnanasambandam ◽  
Pradeep Kumar Mandal ◽  
Namasivayam Gautham
Keyword(s):  
Crystal Structure ◽  
Metal Ion ◽  
Double Helix ◽  
Barium Chloride ◽  
Base Pairs ◽  
X Ray ◽  
Density Map ◽  
Solvent Molecules ◽  
Electron Density Map ◽  
Phosphate Groups

The X-ray crystal structure of the DNA tetradecamer sequence d(CCGGGGTACCCCGG)2is reported at 1.4 Å resolution in the tetragonal space groupP41212. The sequence was designed to fold as a four-way junction. However, it forms an A-type double helix in the presence of barium chloride. The metal ion could not be identified in the electron-density map. The crystallographic asymmetric unit consists of one A-type double helix with 12 base pairs per turn, in contrast to 11 base pairs per turn for canonical A-DNA. A large number of solvent molecules have been identified in both the grooves of the duplex and around the backbone phosphate groups.

109Ag NMR-Study of the Selective Solvation of the Ag+ Ion in Solvent Mixtures of Water and the Organic Solvents: Pyridine, Acetonitrile, and Dimethyl Sulfoxide

1984 ◽  
Vol 39 (1) ◽  
pp. 83-94 ◽  
Author(s):  
L. Guinand. K. L. Hobt. E. Mittermaier ◽  
E. Rößler ◽  
A. Schwenk ◽  
H. Schneider
Keyword(s):  
Chemical Shift ◽  
Dimethyl Sulfoxide ◽  
Organic Solvents ◽  
Mole Fraction ◽  
Chemical Exchange ◽  
Chemical Shifts ◽  
Equilibrium Constants ◽  
Solvent Mixtures ◽  
Nmr Study ◽  
Solvent Molecules

In mixtures of water (W) and one of the organic solvents pyridine, acetonitrile, and dimethyl sulfoxide (O), the silver ion forms the following solvate complexes: AgW2, AgWO, and Ag02. The chemical shift of 109Ag is strongly affected by the ligating solvent molecules, and replacing the ligand W by one of the three organic ligands yields a higher Larmor frequency. In solvent mixtures, only a single resonance line has been observed because of rapid chemical exchange. The measured chemical shifts in the range up to 400 ppm are mean values of the chemical shifts of the different solvate species in a given mixture, weighted with their relative concentrations. The 109Ag chemical shifts were determined for 0.05 to 0.15 molal solutions of AgNO3, as functions of the mole fractions of the solvent components. Using a Gaussian least squares fitting routine, the individual chemical shifts of the Ag+ solvate complexes and the corresponding equilibrium constants were determined. This fit was successful for the whole mole fraction range of DMSO, while in the solvent systems with acetonitrile and with pyridine at higher concentrations of the organic component the chemical shift is influenced by more than two solvent molecules. In these cases equilibrium constants were calculated from chemical shift data for solutions of low mole fraction of acetonitrile and pyridine.

scholarly journals Lattice filter for processing image data of three-dimensional protein nanocrystals

2016 ◽  
Vol 72 (1) ◽  
pp. 34-39 ◽  
Author(s):  
E. van Genderen ◽  
Y.-W. Li ◽  
I. Nederlof ◽  
J. P. Abrahams
Keyword(s):  
Maximum Likelihood ◽  
High Resolution ◽  
Structure Determination ◽  
Fourier Transformation ◽  
Three Dimensional ◽  
Image Data ◽  
Crystalline Lattice ◽  
Dimensional Structure ◽  
Lattice Filter ◽  
Wiener Type

When 300 kV cryo-EM images at Scherzer focus are acquired from ∼100 nm thick three-dimensional protein nanocrystals using a Falcon 2 direct electron detector, Fourier transformation can reveal the crystalline lattice to surprisingly high resolutions, even though the images themselves seem to be devoid of any contrast. Here, it is reported how this lattice information can be enhanced by means of a wave finder in combination with Wiener-type maximum-likelihood filtering. This procedure paves the way towards full three-dimensional structure determination at high resolution for protein crystals.

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