Crystal structure of copper perchlorophthalocyanine analysed by 3D electron diffraction

Copper perchlorophthalocyanine (CuPcCl16, CuC32N8Cl16, Pigment Green 7) is one of the commercially most important green pigments. The compound is a nanocrystalline fully insoluble powder. Its crystal structure was first addressed by electron diffraction in 1972 [Uyeda et al. (1972). J. Appl. Phys. 43, 5181–5189]. Despite the commercial importance of the compound, the crystal structure remained undetermined until now. Using a special vacuum sublimation technique, micron-sized crystals could be obtained. Three-dimensional electron diffraction (3D ED) data were collected in two ways: (i) in static geometry using a combined stage-tilt/beam-tilt collection scheme and (ii) in continuous rotation mode. Both types of data allowed the crystal structure to be solved by direct methods. The structure was refined kinematically with anisotropic displacement parameters for all atoms. Due to the pronounced crystal mosaicity, a dynamic refinement was not feasible. The unit-cell parameters were verified by Rietveld refinement from powder X-ray diffraction data. The crystal structure was validated by many-body dispersion density functional theory (DFT) calculations. CuPcCl16 crystallizes in the space group C2/m (Z = 2), with the molecules arranged in layers. The structure agrees with that proposed in 1972.

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Fast electron diffraction tomography

Journal of Applied Crystallography ◽

10.1107/s1600576715004604 ◽

2015 ◽

Vol 48 (3) ◽

pp. 718-727 ◽

Cited By ~ 76

Author(s):

Mauro Gemmi ◽

Maria G. I. La Placa ◽

Athanassios S. Galanis ◽

Edgar F. Rauch ◽

Stavros Nicolopoulos

Keyword(s):

Crystal Structure ◽

Electron Diffraction ◽

Direct Methods ◽

Diffraction Tomography ◽

Automatic Data ◽

Cell Parameters ◽

Continuous Rotation ◽

Fully Automatic ◽

Data Collections ◽

Tomography Data

A fast and fully automatic procedure for collecting electron diffraction tomography data is presented. In the case of a very stable goniometer it is demonstrated how, by variation of the tilting speed and the CCD detector parameters, it is possible to obtain fully automatic precession-assisted electron diffraction tomography data collections, rotation electron diffraction tomography data collections or new integrated electron diffraction tomography data collections, in which the missing wedge of the reciprocal space between the patterns is recorded by longer exposures during the crystal tilt. It is shown how automatic data collection of limited tilt range can be used to determine the unit-cell parameters, while data of larger tilt range are suitable to solve the crystal structureabinitiowith direct methods. The crystal structure of monoclinic MgMoO4has been solved in this way as a test structure. In the case where the goniometer is not stable enough to guarantee a steady position of the crystal over large tilt ranges, an automatic method for tracking the crystal during continuous rotation of the sample is proposed.

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Redefinition of satimolite

Mineralogical Magazine ◽

10.1180/minmag.2017.081.081 ◽

2018 ◽

Vol 82 (5) ◽

pp. 1033-1047 ◽

Cited By ~ 2

Author(s):

Igor V. Pekov ◽

Natalia V. Zubkova ◽

Dmitry A. Ksenofontov ◽

Nikita V. Chukanov ◽

Vasiliy O. Yapaskurt ◽

...

Keyword(s):

Crystal Structure ◽

Single Crystal ◽

Rietveld Method ◽

Three Dimensional ◽

Direct Methods ◽

Salt Dome ◽

Unit Cell ◽

Unit Cell Parameters ◽

Cell Parameters ◽

Octahedral Clusters

ABSTRACTThe borate mineral satimolite, which was first described in 1969 and remained poorly-studied until now, has been re-investigated (electron microprobe analysis, single-crystal and powder X-ray diffraction studies, crystal-structure determination, infrared spectroscopy) and redefined based on the novel data obtained for the holotype material from the Satimola salt dome and a recently found sample from the Chelkar salt dome, both in North Caspian Region, Western Kazakhstan. The revised idealized formula of satimolite is KNa2(Al5Mg2)[B12O18(OH)12](OH)6Cl4·4H2O (Z = 3). The mineral is trigonal, space group R$\bar{3}$m, unit-cell parameters are: a = 15.1431(8), c = 14.4558(14) Å and V = 2870.8(4) Å3 (Satimola) and a = 15.1406(4), c = 14.3794(9) Å and V = 2854.7(2) Å3 (Chelkar). The crystal system and unit-cell parameters are quite different from those reported previously. The crystal structure of the sample from Chelkar was solved based on single-crystal data (direct methods, R = 0.0814) and the structure of the holotype from Satimola was refined on a powder sample by the Rietveld method (Rp = 0.0563, Rwp = 0.0761 and Rall = 0.0667). The structure of satimolite is unique for minerals. It contains 12-membered borate rings [B12O18(OH)12] in which BO3 triangles alternate with BO2(OH)2 tetrahedra sharing common vertices, and octahedral clusters [M7O6(OH)18] with M = Al5Mg2 in the ideal case, with sharing of corners between rings and clusters to form a three-dimensional heteropolyhedral framework. Each borate ring is connected with six octahedral clusters: three under the ring and three over the ring. Large ellipsoidal cages in the framework host Na and K cations, Cl anions and H2O molecules.

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Crystal structure determination of karibibite, an Fe3+ arsenite, using electron diffraction tomography

Mineralogical Magazine ◽

10.1180/minmag.2016.080.159 ◽

2017 ◽

Vol 81 (5) ◽

pp. 1191-1202 ◽

Cited By ~ 5

Author(s):

Fernando Colombo ◽

Enrico Mugnaioli ◽

Oriol Vallcorba ◽

Alberto García ◽

Alejandro R. Goñi ◽

...

Keyword(s):

Crystal Structure ◽

Electron Diffraction ◽

Dft Calculations ◽

Density Functional ◽

Weak Interactions ◽

Diffraction Tomography ◽

X Ray Diffraction ◽

Orthorhombic Space Group ◽

X Ray ◽

Cell Parameters

AbstractThe crystal structure of karibibite, Fe33+(As3+O2)4(As23+O5)(OH), from the Urucum mine (Minas Gerais, Brazil), was solved and refined from electron diffraction tomography data [R1 = 18.8% for F > 4σ(F)] and further confirmed by synchrotron X-ray diffraction and density functional theory (DFT) calculations. The mineral is orthorhombic, space group Pnma and unit-cell parameters (synchrotron X-ray diffraction) are a = 7.2558(3), b = 27.992(1), c = 6.5243 (3) Å, V = 1325.10(8) Å3, Z = 4. The crystal structure of karibibbite consists of bands of Fe3+O6 octahedra running along a framed by two chains of AsO3 trigonal pyramids at each side, and along c by As2O5 dimers above and below. Each band is composed of ribbons of three edge-sharing Fe3+O6 octahedra, apex-connected with other ribbons in order to form a kinked band running along a. The atoms As(2) and As(3), each showing trigonal pyramidal coordination by O, share the O(4) atom to form a dimer. In turn, dimers are connected by the O(3) atoms, defining a zig-zag chain of overall (As3+O2)n-n stoichiometry. Each ribbon of (Fe3+O6) octahedra is flanked on both edges by the (As3+O2)n-n chains. The simultaneous presence of arsenite chains and dimers is previously unknown in compounds with As3+. The lone-electron pairs (4s2) of the As(2) and As(3) atoms project into the interlayer located at y = 0 and y = ½, yielding probable weak interactions with the O atoms of the facing (AsO2) chain.The DFT calculations show that the Fe atoms have maximum spin polarization, consistent with the Fe3+ state.

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Ab initiostructure determination of nanocrystals of organic pharmaceutical compounds by electron diffraction at room temperature using a Timepix quantum area direct electron detector

Acta Crystallographica Section A Foundations and Advances ◽

10.1107/s2053273315022500 ◽

2016 ◽

Vol 72 (2) ◽

pp. 236-242 ◽

Cited By ~ 73

Author(s):

E. van Genderen ◽

M. T. B. Clabbers ◽

P. P. Das ◽

A. Stewart ◽

I. Nederlof ◽

...

Keyword(s):

Electron Diffraction ◽

Room Temperature ◽

Dynamic Range ◽

Signal To Noise Ratio ◽

Three Dimensional ◽

Direct Methods ◽

Liquid Nitrogen Temperature ◽

High Dynamic Range ◽

Electron Diffraction Data ◽

High Signal

Until recently, structure determination by transmission electron microscopy of beam-sensitive three-dimensional nanocrystals required electron diffraction tomography data collection at liquid-nitrogen temperature, in order to reduce radiation damage. Here it is shown that the novel Timepix detector combines a high dynamic range with a very high signal-to-noise ratio and single-electron sensitivity, enablingab initiophasing of beam-sensitive organic compounds. Low-dose electron diffraction data (∼0.013 e− Å−2 s−1) were collected at room temperature with the rotation method. It was ascertained that the data were of sufficient quality for structure solution using direct methods using software developed for X-ray crystallography (XDS,SHELX) and for electron crystallography (ADT3D/PETS,SIR2014).

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The crystal structure of gatehouseite

Mineralogical Magazine ◽

10.1180/minmag.2011.075.6.2823 ◽

2011 ◽

Vol 75 (6) ◽

pp. 2823-2832

Author(s):

P. Elliott ◽

A. Pring

Keyword(s):

Crystal Structure ◽

Hydrogen Bonding ◽

Three Dimensional ◽

Direct Methods ◽

Chemical Analyses ◽

X Ray Diffraction ◽

X Ray ◽

Manganese Phosphate ◽

Phosphate Mineral ◽

Unit Formula

AbstractThe crystal structure of the manganese phosphate mineral gatehouseite, ideally Mn52+(PO4)2(OH)4, space group P212121, a = 17.9733(18), b = 5.6916(11), c = 9.130(4) Å, V= 933.9(4) Å3, Z = 4, has been solved by direct methods and refined from single-crystal X-ray diffraction data (T = 293 K) to an R index of 3.76%. Gatehouseite is isostructural with arsenoclasite and with synthetic Mn52+(PO4)2(OH)4. The structure contains five octahedrally coordinated Mn sites, occupied by Mn plus very minor Mg with observed <Mn—O> distances from 2.163 to 2.239 Å. Two tetrahedrally coordinated P sites, occupied by P, Si and As, have <P—O> distances of 1.559 and 1.558 Å. The structure comprises two types of building unit. A strip of edge-sharing Mn(O,OH)6 octahedra, alternately one and two octahedra wide, extends along [010]. Chains of edge- and corner-shared Mn(O,OH)6 octahedra coupled by PO4 tetrahedra extend along [010]. By sharing octahedron and tetrahedron corners, these two units form a dense three-dimensional framework, which is further strengthened by weak hydrogen bonding. Chemical analyses by electron microprobe gave a unit formula of (Mn4.99Mg0.02)Σ5.01(P1.76Si0.07(As0.07)Σ2.03O8(OH)3.97.

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Synthesis, Crystal Structure, DFT studies, Docking Studies and Fluorescent Properties of 2-(Adamantan-1-yl)-2H-isoindole-1-carbonitrile

10.20944/preprints201812.0173.v1 ◽

2018 ◽

Author(s):

Jacques Joubert

Keyword(s):

Crystal Structure ◽

Binding Affinity ◽

Active Site ◽

Density Functional ◽

Protein Crystal ◽

Frontier Molecular Orbital ◽

Biological Interactions ◽

Fluorescent Properties ◽

Orthorhombic Space Group ◽

Cell Parameters

2-(Adamantan-1-yl)-2H-isoindole-1-carbonitrile (1) has been identified as a neurobiological fluorescent ligand that may be used to develop receptor and enzyme binding affinity assays. Compound 1 was synthesised using an optimised microwave irradiation reaction and crystallised from ethanol. Crystallization occurred in the orthorhombic space group P212121 with unit cell parameters: a = 6.4487(12) Å, b = 13.648(3) Å, c = 16.571(3) Å, V = 1458(5) Å3, Z = 4. Density functional theory (DFT) (B3LYP/6-311++G (d,p)) calculations of 1 were carried out. Results showed that the optimised geometry is similar to the crystal structure parameters with a root-mean-squared deviation of 0.143 Å. Frontier molecular orbital energies and net atomic charges are discussed with a focus on potential biological interactions. Docking experiments within the active site of the neuronal nitric oxide synthase (nNOS) protein crystal structure were carried out and analysed. Important binding interactions between the DFT optimised structure and amino acids within the nNOS active site were identified that explain the strong NOS binding affinity reported. Fluorescent properties of 1 were studied using aprotic solvents of different polarities. Compound 1 showed the highest fluorescence intensity in polar solvents with excitation and emission values of 336 nm and 380 nm, respectively.

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Crystal structure of vyacheslavite, U(PO4)(OH), solved from natural nanocrystal: a precession electron diffraction tomography (PEDT) study and DFT calculations

RSC Advances ◽

10.1039/c9ra03694f ◽

2019 ◽

Vol 9 (34) ◽

pp. 19657-19661 ◽

Cited By ~ 3

Author(s):

Gwladys Steciuk ◽

Seyedayat Ghazisaeed ◽

Boris Kiefer ◽

Jakub Plášil

Keyword(s):

Crystal Structure ◽

Density Functional Theory ◽

Electron Diffraction ◽

Dft Calculations ◽

Density Functional ◽

Diffraction Tomography ◽

Functional Theory ◽

Phosphate Mineral ◽

Precession Electron Diffraction ◽

Nano Crystal

The crystal structure of the U(iv)-phosphate mineral vyacheslavite has been solved from precession electron diffraction tomography (PEDT) data from the natural nano-crystal and further refined using density-functional theory (DFT) calculations.

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A novel representative in the rare family of trivanadates, KMn2V3O10: synthesis, crystal structure and magnetic properties

Acta Crystallographica Section B Structural Science Crystal Engineering and Materials ◽

10.1107/s205252061701811x ◽

2018 ◽

Vol 74 (1) ◽

pp. 97-103 ◽

Cited By ~ 5

Author(s):

Olga Yakubovich ◽

Larisa Shvanskaya ◽

Zlata Pchelkina ◽

Olga Dimitrova ◽

Anatoliy Volkov ◽

...

Keyword(s):

Crystal Structure ◽

Three Dimensional ◽

Exchange Interactions ◽

Potassium Ions ◽

The Novel ◽

First Principles Calculations ◽

X Ray Diffraction ◽

Magnetic Exchange ◽

Cell Parameters ◽

Magnetic Couplings

Potassium dimanganese trivanadate, KMn2V3O10, was synthesized hydrothermally and its crystal structure was determined from single-crystal X-ray diffraction data. The novel phase crystallizes with triclinic symmetry in space group P\bar 1 with unit-cell parameters of a = 6.912 (5), b = 6.993 (5), c = 9.656 (5) Å, α = 101.858 (5), β = 102.627 (5), γ = 100.669 (5)°, Z = 2 and V = 432.6 (5) Å3. Its structure is built from tetramers of MnO6 octahedra sharing edges and trimers of VO4 tetrahedra sharing vertices. These main structural fragments are linked in a three-dimensional framework with channels occupied by potassium ions. The transformation of this structure to that of interconnected NaCa3Mn(V3O10)(V2O7) is discussed. The title compound orders antiferromagnetically at T N = 8.2 K due to the magnetic exchange interactions between tetramers of Mn octahedra through VO4 tetrahedra. First-principles calculations show the magnetic couplings via Mn—O—Mn and Mn—O—V—O—Mn pathways.

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Synthesis, Characterization, and Crystal Structure Determination of a New Lithium Zinc Iodate Polymorph LiZn(IO3)3

Crystals ◽

10.3390/cryst9090464 ◽

2019 ◽

Vol 9 (9) ◽

pp. 464 ◽

Cited By ~ 5

Author(s):

Hebboul ◽

Galez ◽

Benbertal ◽

Beauquis ◽

Mugnier ◽

...

Keyword(s):

Crystal Structure ◽

Density Functional Theory ◽

Density Functional ◽

Second Harmonic ◽

Infrared Absorption Spectrum ◽

Density Functional Theory Calculations ◽

Functional Theory ◽

Space Group ◽

X Ray ◽

Cell Parameters

Synthesis and characterization of anhydrous LiZn(IO3)3 powders prepared from an aqueous solution are reported. Morphological and compositional analyses were carried out by using scanning electron microscopy and energy-dispersive X-ray measurements. The synthesized powders exhibited a needle-like morphology after annealing at 400 °C. A crystal structure for the synthesized compound was proposed from powder X-ray diffraction and density-functional theory calculations. Rietveld refinements led to a monoclinic structure, which can be described with space group P21, number 4, and unit-cell parameters a = 21.874(9) Å, b = 5.171(2) Å, c = 5.433(2) Å, and  = 120.93(4)°. Density-functional theory calculations supported the same crystal structure. Infrared spectra were also collected, and the vibrations associated with the different modes were discussed. The non-centrosymmetric space group determined for this new polymorph of LiZn(IO3)3, the characteristics of its infrared absorption spectrum, and the observed second-harmonic generation suggest it is a promising infrared non-linear optical material.

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Crystal structure of (Z)-cefprozil monohydrate, C18H19N3O5S(H2O)

Powder Diffraction ◽

10.1017/s0885715619000666 ◽

2019 ◽

Vol 34 (4) ◽

pp. 379-388

Author(s):

Zachary R. Butler ◽

James A. Kaduk ◽

Amy M. Gindhart ◽

Thomas N. Blanton

Keyword(s):

Crystal Structure ◽

Powder Diffraction ◽

Density Functional ◽

Three Dimensional ◽

Ion Pair ◽

Powder Diffraction Data ◽

Powder Diffraction File ◽

X Ray ◽

Dimensional Network ◽

Acid Proton

The crystal structure of cefprozil monohydrate has been solved and refined using synchrotron X-ray powder diffraction data and optimized using density functional techniques. Cefprozil monohydrate crystallizes in space group P21 (#4) with a = 11.26513(6), b = 11.34004(5), c = 14.72649(11) Å, β = 90.1250(4)°, V = 1881.262(15) Å3, and Z = 4. Although a reasonable fit was obtained using an orthorhombic model, closer examination showed that many peaks were split and/or had shoulders, and thus the true symmetry was monoclinic. DFT calculations revealed that one carboxylic acid proton moved to an amino group. The structure thus contains one ion pair and one pair of neutral molecules. This protonation was confirmed by infrared spectroscopy. There is an extensive array of hydrogen bonds resulting in a three-dimensional network. The powder pattern has been submitted to ICDD® for inclusion in the Powder Diffraction File™.

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