Visualization and analysis of crystal structures using CrystalMaker software

Palmer, David C.

doi:10.1515/zkri-2015-1869

Cited by 173 publications

(147 citation statements)

References 6 publications

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“…Atomic coordinates, equivalent atomic displacement parameters, as well as the selected bond distances and angles are shown in Tables S1-S3. All crystal structure figures were generated using CrystalMaker® [18]. ToposPro [19] was used to analyze the topologies of the anionic nets within the structure of Li 2 CoGeS 4 , as well as Li 2 MnGeS 4 and Li 2 CdGeS 4 .…”

Section: Single Crystal X-ray Diffractionmentioning

confidence: 99%

A new class of lithium ion conductors with tunable structures and compositions: Quaternary diamond-like thiogermanates

et al. 2015

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The new Li 2 CoGeS 4 compound crystallizes in the Pn space group with the wurtz-kesterite structure, according to single crystal X-ray diffraction. The structure of Li 2 CoGeS 4 and the high degree of phase-purity in which it is prepared are supported by high-resolution synchrotron X-ray powder diffraction. Varying the divalent ion in Li 2 -II-GeS 4 materials yields three different structure types, all of which are derived from hexagonal diamond. These structural variations give rise to Li + -encompassing [II-GeS 4 ] 2− nets with different topologies that offer diversity in lithium ion diffusion pathways. In the first systematic study of the lithium ion conductivity in quaternary diamond-like materials, wurtz-kesterite-type Li 2 CoGeS 4 and Li 2 FeGeS 4 (Pn), lithium cobalt(II) silicate-type Li 2 MnGeS 4 (Pna2 1 ), and wurtz-stannite-type Li 2 CdGeS 4 (Pmn2 1 ) are presented as environmentally stable lithium ion conductors. These materials are comprised of cubic diamond-like [CoGeS 4 ] 2− and [FeGeS 4 ] 2− anionic frameworks, ABW-like [MnGeS 4 ] 2− , and square lattice-like [CdGeS 4 ] 2− . As assessed using impedance spectroscopy, Li 2 FeGeS 4 exhibits the most promising Li + ion conductivity of 1.8(3) × 10 −4 S/cm at 100°C, while Li 2 CdGeS 4 shows the lowest activation energy for lithium ion conduction, E A = 0.74(2) eV.

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Section: Single Crystal X-ray Diffractionmentioning

confidence: 99%

A new class of lithium ion conductors with tunable structures and compositions: Quaternary diamond-like thiogermanates

et al. 2015

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“…Kozlikova et al reviewed the state of the art of visualisation of biomolecular structures [4]. Some examples of molecular viewers are pyMol [5], VMD [6], Chimera [7], JMOL [8], Mercury [9], RASMOL [10], Materials Studio [11], Crystalmaker [12], Avogadro [13], VESTA [14], cellVIEW [15], MegaMol [16], and Qutemol [17]. Most visualisation packages are crossplatform.…”

Section: Introductionmentioning

confidence: 99%

iRASPA: GPU-accelerated visualization software for materials scientists

Dubbeldam

Calero

Vlugt

2018

Molecular Simulation

133

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A new macOS software package, iRASPA, for visualisation and editing of materials is presented. iRASPA is a document-based app that manages multiple documents with each document containing a unique set of data that is stored in a file located either in the application sandbox or in iCloud drive. The latter allows collaboration on a shared document (on High Sierra). A document contains a gallery of projects that show off the main features, a CloudKit-based access to the CoRE MOF database (approximately 8000 structures), and local projects of the user. Each project contains a scene of one or more structures that can initially be read from CIF, PDB or XYZ-files, or made from scratch. Main features of iRASPA are: structure creation and editing, pictures and movies, ambient occlusion and high-dynamic range rendering, collage of structures, (transparent) adsorption surfaces, cell replicas and supercells, symmetry operations like space group and primitive cell detection, screening of structures using user-defined predicates, and GPU-computation of helium void fraction and surface areas in a matter of seconds. Leveraging the latest graphics technologies like Metal, iRASPA can render hundreds of thousands of atoms (including ambient occlusion) with stunning performance. The software is freely available from the Mac App Store. ARTICLE HISTORY

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“…Non-H atoms were refined anisotropically and hydrogen atoms were treated as riding atoms. CrystalMaker [28] 3$ The bond length distortion of the octahedra in each composition at both 173 and 298 K was calculated using Equation (1) [31], where d is the average Pb-I bond distance and dn are the six individual bond distances. The bond angle variance of each octahedron from the ideal 90° of an undistorted structure was calculated using Equation (2) [32], where θi is the individual I-Pb-I angle.…”

Section: Characterizationmentioning

confidence: 99%

Three New Lead Iodide Chain Compounds, APbI3, Templated by Molecular Cations

2019

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The crystal structures of three new hybrid organic-inorganic lead halide compounds [IqH]PbI3, [4MiH]PbI3, and [BzH]PbI3 ([IqH+] = isoquinolinium, [4MiH+] = 4-methylimidazolium, [BzH+] = benzotriazolium) have been determined by single crystal x-ray diffraction. All three compounds have the same generic formula as perovskite, ABX3, but adopt a rare non-perovskite structure built from one dimensional (1D) edge-sharing octahedral chains. The bandgap of each compound was investigated by solid UV-Vis spectra. In comparison with previously reported hybrid compounds containing the same type of octahedral chains, [C10H7CH2NH3]Pbl3 and (C7H7N2)PbI3, all three new compounds have lower bandgaps (<2.4 ev), indicating that they may be promising for photovoltaic application.

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Visualization and analysis of crystal structures using CrystalMaker software

Cited by 173 publications

References 6 publications

A new class of lithium ion conductors with tunable structures and compositions: Quaternary diamond-like thiogermanates

A new class of lithium ion conductors with tunable structures and compositions: Quaternary diamond-like thiogermanates

iRASPA: GPU-accelerated visualization software for materials scientists

Three New Lead Iodide Chain Compounds, APbI3, Templated by Molecular Cations

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