Applied Topological Analysis of Crystal Structures with the Program Package ToposPro

Блатов, В. А.; Шевченко, А. П.; Proserpio, Davide M.

doi:10.1021/cg500498k

Cited by 2,645 publications

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References 86 publications

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“…The CrystalGrower growth code is written in Fortran 95. Input polyhedral units (tiles or Voronoi polyhedra) and their connectivities (partitioning) are provided via an interface with ToposPro 22 . ToposPro builds natural tiling or Voronoi partition in accordance with strict and unambiguous algorithms 21,22 .…”

Section: Methodsmentioning

confidence: 99%

“…Input polyhedral units (tiles or Voronoi polyhedra) and their connectivities (partitioning) are provided via an interface with ToposPro 22 . ToposPro builds natural tiling or Voronoi partition in accordance with strict and unambiguous algorithms 21,22 . As a result, all the information for a given polyhedral unit in terms of the initial vertex condensation is provided for CrystalGrower.…”

Section: Methodsmentioning

confidence: 99%

“…Closed cages are readily determined using the approach of 3D-tiling achieved by the ToposPro code 22 which computes natural tiles 21 . For the 299 zeolite frameworks studied, this accounts for 54 (less than one quarter) of all the structure codes that are constructed entirely from closed cages / tiles made up of Q 3 tetrahedral atoms.…”

Section: Methodsmentioning

confidence: 99%

“…Therefore, the cages become a suitable unit of growth even though they are not the growth unit. These cages are 3-dimensional spacefilling tiles that can be computed in a relatively straightforward manner using algorithms such as those implemented in ToposPro 21,22 (Figure 1). Consequently, this establishes a simplified route to coarse-grain the zeolite problem into energetically minimised, metastable, rate-determining steps that, when balanced against a potential energy driving force from the growth medium permits generation of a general kinetic Monte Carlo algorithm for zeolites.…”

mentioning

confidence: 99%

“…For complex crystal systems there could be thousands of possible surface site types although, in principle, only a fraction of these will be topologically viable during crystal growth. By interfacing our kinetic Monte Carlo code with the 3-D partitioning approach of ToposPro 22 we can compute all the possible connectivities for any partitioning pattern and, consequently, any crystal structure. Then, to a first approximation, the energies of the polyhedral units are directly related to the degree of condensation/attachment (see Figure E1 for the LTA zeolite system).…”

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Predicting crystal growth via a unified kinetic three-dimensional partition model

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Gebbie-Rayet

Hill

et al. 2017

Nature

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2017) 'Predicting crystal growth via a uni ed kinetic three-dimensional partition model. ', Nature., 544 (7651). pp. 456-459. Further information on publisher's website:https://doi.org/10.1038/nature21684Publisher's copyright statement:Additional information: Use policyThe full-text may be used and/or reproduced, and given to third parties in any format or medium, without prior permission or charge, for personal research or study, educational, or not-for-pro t purposes provided that:• a full bibliographic reference is made to the original source • a link is made to the metadata record in DRO • the full-text is not changed in any way The full-text must not be sold in any format or medium without the formal permission of the copyright holders.Please consult the full DRO policy for further details. Understanding and predicting the course of crystal growth is fundamental to the control of functionality in modern materials. Despite investigations for over one hundred years 1-5 it is only recently that the molecular intricacies of these processes have been revealed by scanning probe microscopies 6-8 . In order to bring some order and understanding to this vast amount of new information requires new rules to be developed and tested. To date, because of the complexity and variety of different crystal systems, this has relied on developing models that are usually constrained to one system only 9-11 . Such work is painstakingly slow and will not be able to achieve the wide scope of understanding in order to create a unified model across crystal types and crystal structures. Here we describe a new approach to understand and, in theory, predict the growth of crystals, including the incorporation of defect structures, by simultaneous molecular-scale simulation of crystal habit and surface topology using a unified kinetic 3-D partition model. We exemplify our approach by predicting the crystal growth of a diverse set of crystal types including zeolites, metal-organic frameworks, calcite, urea and L-cystine.By understanding crystal growth at the molecular scale we have the possibility to control crystal habit, crystal size, the elimination or incorporation of defects and the development of intergrowth structures. As crystals are used in technologies from pharmaceuticals to gas storage and separation materials, from optoelectronic devices to heterogeneous catalysts, such understanding is vital. If we take an example of a very complex and yet very important crystal type, that of zeolites 12 which form the backbone of the heterogeneous catalysis industry, then many of the problems that must be addressed in crystal growth can be illustrated. Zeolites are nanoporous materials were the framework of the material is constructed from a strong covalently bonded network of Si -O and Al -O bonds. The pores of the material are filled with water and cations that balance the negative charge on the framework. Crystals of zeolites grow from aqueous solutions at temperatures up to about 230 o C and it is well known from NMR spectroscopy that...

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

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Stability of B2‐type FeS at Earth's inner core pressures

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Using density functional theory, we investigated how substituting sulfur atoms for iron atoms affects the structure and energy of the body centered cubic and hexagonal close‐packed iron phases at 350 GPa and at 0 K. We conclude that formation of random (Fe,S) solid solutions is energetically favorable in all intermediate compositions, although the random low‐symmetry substitutions cause structural distortion. The (Fe,S) solid solution is nearly as favorable as the mechanical mixture of Fe‐hcp and FeS‐B2. This finding, in combination with dynamical stability, defines the B2 structure as a strong candidate for the sulfur‐bearing phase of the Earth's inner core.

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The Chemistry of Metal-Organic Frameworks: Synthesis, Characterization, and Applications

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Applied Topological Analysis of Crystal Structures with the Program Package ToposPro

Cited by 2,645 publications

References 86 publications

Predicting crystal growth via a unified kinetic three-dimensional partition model

Predicting crystal growth via a unified kinetic three-dimensional partition model

Stability of B2‐type FeS at Earth's inner core pressures

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