scholarly journals PLATONSQUEEZE: a tool for the calculation of the disordered solvent contribution to the calculated structure factors

2015 ◽  
Vol 71 (1) ◽  
pp. 9-18 ◽  
Author(s):  
Anthony L. Spek
Keyword(s):  
Crystal Structure ◽  
Least Squares ◽  
Electron Density ◽  
Structure Refinement ◽  
Acta Cryst ◽  
Reflection Data ◽  
Structure Factors ◽  
Current Implementation ◽  
Alternative Means ◽  
Solvent Molecules

The completion of a crystal structure determination is often hampered by the presence of embedded solvent molecules or ions that are seriously disordered. Their contribution to the calculated structure factors in the least-squares refinement of a crystal structure has to be included in some way. Traditionally, an atomistic solvent disorder model is attempted. Such an approach is generally to be preferred, but it does not always lead to a satisfactory result and may even be impossible in cases where channels in the structure are filled with continuous electron density. This paper documents the SQUEEZE method as an alternative means of addressing the solvent disorder issue. It conveniently interfaces with the 2014 version of the least-squares refinement programSHELXL[Sheldrick (2015).Acta Cryst.C71. In the press] and other refinement programs that accept externally provided fixed contributions to the calculated structure factors. ThePLATONSQUEEZE tool calculates the solvent contribution to the structure factors by back-Fourier transformation of the electron density found in the solvent-accessible region of a phase-optimized difference electron-density map. The actual least-squares structure refinement is delegated to, for example,SHELXL. The current versions ofPLATONSQUEEZE andSHELXLnow address several of the unnecessary complications with the earlier implementation of the SQUEEZE procedure that were a necessity because least-squares refinement with the now supersededSHELXL97program did not allow for the input of fixed externally provided contributions to the structure-factor calculation. It is no longer necessary to subtract the solvent contribution temporarily from the observed intensities to be able to useSHELXLfor the least-squares refinement, since that program now accepts the solvent contribution from an external file (.fab file) if the ABIN instruction is used. In addition, many twinned structures containing disordered solvents are now also treatable by SQUEEZE. The details of a SQUEEZE calculation are now automatically included in the CIF archive file, along with the unmerged reflection data. The current implementation of the SQUEEZE procedure is described, and discussed and illustrated with three examples. Two of them are based on the reflection data of published structures and one on synthetic reflection data generated for a published structure.

scholarly journals Crystal structure of (methanol-κO)[5,10,15,20-tetrakis(2-aminophenyl)porphyrinato-κ4 N]zinc(II)–chloroform–methanol (1/1/1)

2018 ◽  
Vol 74 (9) ◽  
pp. 1285-1289 ◽  
Author(s):  
Lisa Leben ◽  
Christian Näther ◽  
Rainer Herges
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Electron Density ◽  
Solvent Molecule ◽  
Methanol Molecule ◽  
Acta Cryst ◽  
Picket Fence ◽  
Phenyl Rings ◽  
Residual Electron Density ◽  
Solvent Molecules

In the crystal structure of the title compound, [Zn(C44H32N8)(CH3OH)]·CHCl3·CH3OH, the ZnII cation is coordinated by four porphyrin N and one methanol O atom within a slightly distorted square-pyramidal environment and is shifted out of the porphyrin plane towards the direction of the methanol molecule. The methyl group of the coordinating methanol molecule is disordered over two sets of sites. The porphyrin backbone is nearly planar and the phenyl rings are almost perpendicular to the porphyrin plane. As is typical for picket-fence porphyrins, all four ortho substituents of the meso-phenyl groups (here the amino groups) are facing to the same side of the porphyrin molecule. In the crystal structure, two neighbouring porphyrin complexes form centrosymmetric dimers that are connected via O—H...N hydrogen bonding. With the aid of additional N—H...N and C—H...N hydrogen bonding, these dimers are stacked into columns parallel to [010] that are finally arranged into layers parallel to (001). Between these layers channels are formed where chloroform solvent molecules are located that are connected to the porphyrin complexes by weak C—H...Cl hydrogen bonding. There are additional cavities in the structure where some small residual electron density is found, indicating the presence of disordered methanol molecules, but a reasonable model could not be refined. Therefore the contribution of the electron density associated with the methanol solvent molecule was removed with the SQUEEZE procedure [Spek (2015). Acta Cryst. C71, 9–18] in PLATON. Nevertheless, the given chemical formula and other crystal data take into account the methanol solvent molecule.

scholarly journals Crystal structure of bis{1-[(E)-(2-methoxyphenyl)diazenyl]naphthalen-2-olato-κ3O,N2,O′}copper(II) containing an unknown solvate

2015 ◽  
Vol 71 (11) ◽  
pp. m207-m208 ◽  
Author(s):  
Souheyla Chetioui ◽  
Noudjoud Hamdouni ◽  
Djamil-Azzeddine Rouag ◽  
Salah Eddine Bouaoud ◽  
Hocine Merazig
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Electron Density ◽  
Title Complex ◽  
Unit Cell ◽  
Asymmetric Unit ◽  
Acta Cryst ◽  
Coordination Environment ◽  
Independent Molecules ◽  
Solvent Molecules

The title complex, [Cu(C17H13N2O2)2], crystallizes with two independent molecules in the asymmetric unit. Each CuIIatom has a distorted ocahedral coordination environment defined by two N atoms and four O atoms from two tridentate 1-[(E)-(2-methoxyphenyl)diazenyl]naphthalen-2-olate ligands. In the crystal, the two molecules are linkedviaweak C—H...O hydrogen bonds which in turn stack parallel to [010]. A region of disordered electron density, most probably disordered methanol solvent molecules, was corrected for using the SQUEEZE routine inPLATON[Spek (2015).Acta Cryst.C71, 9–18]. Their formula mass and unit-cell characteristics were not taken into account during refinement.

scholarly journals Polder maps: improving OMIT maps by excluding bulk solvent

2017 ◽  
Vol 73 (2) ◽  
pp. 148-157 ◽  
Author(s):  
Dorothee Liebschner ◽  
Pavel V. Afonine ◽  
Nigel W. Moriarty ◽  
Billy K. Poon ◽  
Oleg V. Sobolev ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Cell Volume ◽  
Electron Density ◽  
Unit Cell Volume ◽  
Model Building ◽  
Unit Cell ◽  
Structure Factors ◽  
Structure Solution ◽  
Solvent Model ◽  
Solvent Molecules

The crystallographic maps that are routinely used during the structure-solution workflow are almost always model-biased because model information is used for their calculation. As these maps are also used to validate the atomic models that result from model building and refinement, this constitutes an immediate problem: anything added to the model will manifest itself in the map and thus hinder the validation. OMIT maps are a common tool to verify the presence of atoms in the model. The simplest way to compute an OMIT map is to exclude the atoms in question from the structure, update the corresponding structure factors and compute a residual map. It is then expected that if these atoms are present in the crystal structure, the electron density for the omitted atoms will be seen as positive features in this map. This, however, is complicated by the flat bulk-solvent model which is almost universally used in modern crystallographic refinement programs. This model postulates constant electron density at any voxel of the unit-cell volume that is not occupied by the atomic model. Consequently, if the density arising from the omitted atoms is weak then the bulk-solvent model may obscure it further. A possible solution to this problem is to prevent bulk solvent from entering the selected OMIT regions, which may improve the interpretative power of residual maps. This approach is called a polder (OMIT) map. Polder OMIT maps can be particularly useful for displaying weak densities of ligands, solvent molecules, side chains, alternative conformations and residues both in terminal regions and in loops. The tools described in this manuscript have been implemented and are available inPHENIX.

scholarly journals Crystal structure refinement withSHELXL

2015 ◽  
Vol 71 (1) ◽  
pp. 3-8 ◽  
Author(s):  
George M. Sheldrick
Keyword(s):  
Crystal Structure ◽  
Structure Refinement ◽  
Crystal Structure Refinement ◽  
Disordered Structures ◽  
Reflection Data ◽  
Structure Factors ◽  
Recent Developments ◽  
Information Framework ◽  
Absolute Structure

The improvements in the crystal structure refinement programSHELXLhave been closely coupled with the development and increasing importance of the CIF (Crystallographic Information Framework) format for validating and archiving crystal structures. An important simplification is that now only one file in CIF format (for convenience, referred to simply as `a CIF') containing embedded reflection data andSHELXLinstructions is needed for a complete structure archive; the programSHREDCIFcan be used to extract the .hkl and .ins files required for further refinement withSHELXL. Recent developments inSHELXLfacilitate refinement against neutron diffraction data, the treatment of H atoms, the determination of absolute structure, the input of partial structure factors and the refinement of twinned and disordered structures.SHELXLis available free to academics for the Windows, Linux and Mac OS X operating systems, and is particularly suitable for multiple-core processors.

The phase problem and electron-density maps

2010 ◽  
Author(s):  
Jenny Pickworth Glusker ◽  
Kenneth N. Trueblood
Keyword(s):  
Crystal Structure ◽  
Fourier Series ◽  
Diffraction Pattern ◽  
Electron Density ◽  
Bragg Reflection ◽  
Three Dimensional ◽  
Density Maps ◽  
Structure Factors ◽  
Unit Cells ◽  
Phase Angles

In order to obtain an image of the material that has scattered X rays and given a diffraction pattern, which is the aim of these studies, one must perform a three-dimensional Fourier summation. The theorem of Jean Baptiste Joseph Fourier, a French mathematician and physicist, states that a continuous, periodic function can be represented by the summation of cosine and sine terms (Fourier, 1822). Such a set of terms, described as a Fourier series, can be used in diffraction analysis because the electron density in a crystal is a periodic distribution of scattering matter formed by the regular packing of approximately identical unit cells. The Fourier series that is used provides an equation that describes the electron density in the crystal under study. Each atom contains electrons; the higher its atomic number the greater the number of electrons in its nucleus, and therefore the higher its peak in an electrondensity map.We showed in Chapter 5 how a structure factor amplitude, |F (hkl)|, the measurable quantity in the X-ray diffraction pattern, can be determined if the arrangement of atoms in the crystal structure is known (Sommerfeld, 1921). Now we will show how we can calculate the electron density in a crystal structure if data on the structure factors, including their relative phase angles, are available. The Fourier series is described as a “synthesis” when it involves structure amplitudes and relative phases and builds up a picture of the electron density in the crystal. By contrast, a “Fourier analysis” leads to the components that make up this series. The term “relative” is used here because the phase of a Bragg reflection is described relative to that of an imaginary wave diffracted in the same direction at a chosen origin of the unit cell.

scholarly journals Crystal structure of pentakis(ethylenediamine-κ2N,N′)lanthanum(III) trichloride–ethylenediamine–dichloromethane (1/1/1)

2014 ◽  
Vol 70 (11) ◽  
pp. 424-426 ◽  
Author(s):  
Hope T. Sartain ◽  
Richard J. Staples ◽  
Shannon M. Biros
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Electron Density ◽  
Inversion Center ◽  
Asymmetric Unit ◽  
Acta Cryst ◽  
Bypass Procedure ◽  
Hydrogen Bonding Network ◽  
Additional Hydrogen

We report here the crystal structure of a ten-coordinate lanthanum(III) metal coordinated by five bidentate ethylenediamine ligands, [La(C2H8N2)5]Cl3·C2H8N2·CH2Cl2. One free ethylenediamine molecule and three Cl−anions are also located in the asymmetric unit. The overall structure is held together by an extensive hydrogen-bonding network between the Cl−anions and the NH groups on the metal-bound ethylenediamine ligands. The free ethylenediamine molecule is held in an ordered position by additional hydrogen bonds involving both the chlorides and –NH groups on the metal-bound ligands. One highly disordered molecule of dichloromethane is located on an inversion center; however, all attempts to model this disorder were unsuccessful. The electron density in this space was removed using the BYPASS procedure [van der Sluis & Spek (1990).Acta Cryst.A46, 194–201].

Multipole electron densities and atomic displacement parameters in urea from accurate powder X-ray diffraction

2019 ◽  
Vol 75 (4) ◽  
pp. 600-609 ◽  
Author(s):  
Bjarke Svane ◽  
Kasper Tolborg ◽  
Lasse Rabøl Jørgensen ◽  
Martin Roelsgaard ◽  
Mads Ry Vogel Jørgensen ◽  
...  
Keyword(s):  
Electron Density ◽  
Molecular System ◽  
Atomic Displacement ◽  
High Symmetry ◽  
X Ray Diffraction ◽  
High Quality ◽  
Acta Cryst ◽  
X Ray ◽  
Density Determination ◽  
Structure Factors

Electron density determination based on structure factors obtained through powder X-ray diffraction has so far been limited to high-symmetry inorganic solids. This limit is challenged by determining high-quality structure factors for crystalline urea using a bespoke vacuum diffractometer with imaging plates. This allows the collection of data of sufficient quality to model the electron density of a molecular system using the multipole method. The structure factors, refined parameters as well as chemical bonding features are compared with results from the high-quality synchrotron single-crystal study by Birkedalet al.[Acta Cryst.(2004), A60, 371–381] demonstrating that powder X-ray diffraction potentially provides a viable alternative for electron density determination in simple molecular crystals where high-quality single crystals are not available.

scholarly journals The Crystal Structure and Chemical Properties of U2Al3C4 and Structure Refinement of Al4C3

1995 ◽  
Vol 50 (2) ◽  
pp. 196-200 ◽  
Author(s):  
Thorsten M. Gesing ◽  
Wolfgang Jeitschko
Keyword(s):  
Crystal Structure ◽  
Single Crystal ◽  
Structure Refinement ◽  
Chemical Properties ◽  
Variable Parameters ◽  
Higher Symmetry ◽  
Structure Factors ◽  
Hydrolysis Of ◽  
Symmetry Space ◽  
Symmetry Space Group

A well crystallized sample of U2Al3C4 was obtained by melting the elemental components in a carbon crucible in a high frequency furnace. The crystal structure of this compound was determined from single-crystal diffractometer data of a twinned crystal: P63mc, a = 342.2(1) pm. c = 2323.0(3) pm. Z = 2 , R = 0.030 for 537 structure factors and 18 variable parameters. The structure can also be described in the higher symmetry space group P63/mmc with one split aluminum position. It consists of close packed layers of uranium and aluminum atoms with carbon atoms at interstitial sites. The structure is closely related to that of Al4C3, which was refined from single-crystal X-ray data to a residual of R = 0.033 for 135 F-values and 11 variables. The hydrolysis of U2Al3C4 with diluted hydrochloric acid resulted in about 74 (wt-)% methane, 8% ethane and ethylene, and 18% saturated and unsaturated higher hydrocarbons.

scholarly journals Crystal structure of (15,20-bis(2,3,4,5,6-pentafluorophenyl)-5,10-{(pyridine-3,5-diyl)bis[(sulfanediylmethylene)[1,1′-biphenyl]-4′,2-diyl]}porphyrinato)nickel(II) dichloromethane x-solvate (x > 1/2) showing a rare CN5 coordination

2019 ◽  
Vol 75 (8) ◽  
pp. 1180-1184 ◽  
Author(s):  
Florian Gutzeit ◽  
Christian Näther ◽  
Rainer Herges
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Title Compound ◽  
Apical Position ◽  
Acta Cryst ◽  
Solvent Molecules ◽  
Hydrogen Bonded

The crystal structure of the title compound, [Ni(C63H31F10N5S2)]·xCH2Cl2 (x > 1/2), consists of Ni–porphyrin complexes that are located in general positions and dichloromethane solvent molecules that are disordered around centers of inversion. The NiII ions are in a square-pyramidal (CN5) coordination, with four porphyrin N atoms in the equatorial and a pyridine N atom in the apical position and are shifted out of the porphyrine N4 plane towards the coordinating pyridine N atom. The pyridine substituent is not exactly perpendicular to the N4 plane with an angle of intersection between the planes planes of 80.48 (6)°. The dichloromethane solvent molecules are hydrogen bonded to one of the four porphyrine N atoms. Two complexes are linked into dimers by two symmetry-equivalent C—H...S hydrogen bonds. These dimers are closely packed, leading to cavities in which additional dichloromethane solvent molecules are embedded. These solvent molecules are disordered and because no reasonable split model was found, the data were corrected for disordered solvent using the PLATON SQUEEZE routine [Spek (2015). Acta Cryst. C71, 9–18].

scholarly journals Crystal structure of bis[cis-diaquabis(phenanthroline)cobalt(II)] bis(citrato)germanate(IV) dinitrate

2021 ◽  
Vol 77 (9) ◽  
Author(s):  
Olha Buchko ◽  
Viktoriya Dyakonenko ◽  
Elena Martsinko ◽  
Elena Chebanenko
Keyword(s):  
Crystal Structure ◽  
Solvent Molecule ◽  
Crystal Data ◽  
Chemical Formula ◽  
Asymmetric Unit ◽  
Acta Cryst ◽  
Water Oxygen ◽  
Solvent Molecules ◽  
The Given ◽  
Oxygen Atoms

The asymmetric unit of the title compound, [Co(C12H8N2)2(H2O)2]2[Ge(C6H5O7)2](NO3)2, features two complex [(C12H8N2)2(H2O)2Co]2+ cations, two NO3 − anions as well as one centrosymmetric [(C6H5O7)2Ge]2− anion. Two HCit ligands (Cit = citrate, C6H4O7) each coordinate via three different oxygen atoms (hydroxylate, α-carboxylate, β-carboxylate) to the Ge atom, forming a slightly distorted octahedron. The coordination polyhedron of the Co atom is also octahedral, formed by coordination of four nitrogen atoms from two phenanthroline molecules and two water oxygen atoms. In the crystal, the cations and anions are linked by hydrogen bonds and form layers parallel to the bc plane. The structure exhibits disorder of the NO3 − anion [disorder ratio 0.688 (9) to 0.312 (9)]. There are also highly disordered solvent molecules (presumably water and/or ethanol) in the crystal structure; explicit refinement of these molecules was not possible, and the content of the voids was instead taken into account using reverse Fourier transform methods [SQUEEZE procedure in PLATON; Spek (2015). Acta Cryst. C71, 9–18]. The given chemical formula and other crystal data do not take into account the unknown solvent molecule(s).

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