Problem Solving with the TOPAS Macro Language: Corrections and Constraints in Simulated Annealing and Rietveld Refinement

Whitfield, Pamela S.; Davidson, Isobel; Mitchell, Laura E.; Wilson, Siobhan A.; Mills, Stuart J.

doi:10.4028/www.scientific.net/msf.651.11

Cited by 8 publications

(6 citation statements)

References 19 publications

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“…At Mount Keith, a complete solid-solution series was shown to exist between woodallite and stichtite (e.g. Woodhouse, 2006;Mills et al, 2012c), and Rietveld analysis was employed to model the 3R structure at various points in the series (Whitfield et al, 2010;Mills et al, 2012c).…”

Section: Woodallitementioning

confidence: 99%

Nomenclature of the hydrotalcite supergroup: natural layered double hydroxides

Mills¹,

Christy²,

Génin³

et al. 2012

Mineral. mag.

367

325

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Layered double hydroxide (LDH) compounds are characterized by structures in which layers with a brucite-like structure carry a net positive charge, usually due to the partial substitution of trivalent octahedrally coordinated cations for divalent cations, giving a general layer formula [(M1–x2+M3+x)(OH)2]x+. This positive charge is balanced by anions which are intercalated between the layers. Intercalated molecular water typically provides hydrogen bonding between the brucite layers. In addition to synthetic compounds, some of which have significant industrial applications, more than 40 mineral species conform to this description. Hydrotalcite, Mg6Al2(OH)16[CO3]·4H2O, as the longest-known example, is the archetype of this supergroup of minerals. We review the history, chemistry, crystal structure, polytypic variation and status of all hydrotalcite-supergroup species reported to date. The dominant divalent cations,M2+, that have been reported in hydrotalcite supergroup minerals are Mg, Ca, Mn, Fe, Ni, Cu and Zn; the dominant trivalent cations,M3+, are Al, Mn, Fe, Co and Ni. The most common intercalated anions are (CO3)2–, (SO4)2–and Cl–; and OH–, S2–and [Sb(OH)6]– have also been reported. Some species contain intercalated cationic or neutral complexes such as [Na(H2O)6]+or [MgSO4]0. We define eight groups within the supergroup on the basis of a combination of criteria. These are (1) the hydrotalcite group, withM2+:M3+= 3:1 (layer spacing ∼7.8 Å); (2) the quintinite group, withM2+:M3+= 2:1 (layer spacing ∼7.8 Å); (3) the fougèrite group, withM2+= Fe2+,M3+= Fe3+in a range of ratios, and with O2– replacing OH– in the brucite module to maintain charge balance (layer spacing ∼7.8 Å); (4) the woodwardite group, with variableM2+:M3+and interlayer [SO4]2 –, leading to an expanded layer spacing of ∼8.9 Å; (5) the cualstibite group, with interlayer [Sb(OH)6]– and a layer spacing of ∼9.7 Å; (6) the glaucocerinite group, with interlayer [SO4]2– as in the woodwardite group, and with additional interlayer H2O molecules that further expand the layer spacing to ∼11 Å; (7) the wermlandite group, with a layer spacing of ∼11 Å, in which cationic complexes occur with anions between the brucite-like layers; and (8) the hydrocalumite group, withM2+= Ca2+andM3+= Al, which contains brucite-like layers in which the Ca:Al ratio is 2:1 and the large cation, Ca2+, is coordinated to a seventh ligand of 'interlayer' water.The principal mineral status changes are as follows. (1) The names manasseite, sjögrenite and barbertonite are discredited; these minerals are the 2H polytypes of hydrotalcite, pyroaurite and stichtite, respectively. Cyanophyllite is discredited as it is the 1M polytype of cualstibite. (2) The mineral formerly described as fougèrite has been found to be an intimate intergrowth of two phases with distinct Fe2+:Fe3+ratios. The phase with Fe2+:Fe3+= 2:1 retains the name fougèrite; that with Fe2+:Fe3+= 1:2 is defined as the new species trébeurdenite. (3) The new minerals omsite (IMA2012-025), Ni2Fe3+(OH)6[Sb(OH)6], and mössbauerite (IMA2012-049), Fe3+6O4(OH)8[CO3]·3H2O, which are both in the hydrotalcite supergroup are included in the discussion. (4) Jamborite, carrboydite, zincaluminite, motukoreaite, natroglaucocerinite, brugnatellite and muskoxite are identified as questionable species which need further investigation in order to verify their structure and composition. (5) The ranges of compositions currently ascribed to motukoreaite and muskoxite may each represent more than one species. The same applies to the approved species hydrowoodwardite and hydrocalumite. (6) Several unnamed minerals have been reported which are likely to represent additional species within the supergroup.This report has been approved by the Commission on New Minerals, Nomenclature and Classification (CNMNC) of the International Mineralogical Association, voting proposal 12-B.We also propose a compact notation for identifying synthetic LDH phases, for use by chemists as a preferred alternative to the current widespread misuse of mineral names.

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Section: Woodallitementioning

confidence: 99%

Nomenclature of the hydrotalcite supergroup: natural layered double hydroxides

Mills¹,

Christy²,

Génin³

et al. 2012

Mineral. mag.

367

325

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“…That leaves the additional scattering from the water O atoms the only freely refined occupancy variable. Details of the structure refinement strategy employed are given by Whitfield et al (2010). There have been few previous Rietveld refinements of similar materials, and these have mostly been conducted on Cl --dominant synthetic hydrotalcites (e.g., Ennadi et al 2000;Roussel et al 2000;Simon et al 2003), while Bellotto et al (1996) Note: H2 fixed at sof = 0.5.…”

Section: Sa M P L E D E S C R I P T I O N a N D S T R U C T U R E Stimentioning

confidence: 99%

The crystal structure of stichtite, re-examination of barbertonite, and the nature of polytypism in MgCr hydrotalcites

Mills

Whitfield

Wilson

et al. 2010

American Mineralogist

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The crystal structure of stichtite, re-examination of barbertonite and the nature of polytypism in MgCr hydrotalcites Mills, Stuart J.; Whitfield, Pamela S.; Wilson, Siobhan A.; Woodhouse, Joanne N.; Dipple, Gregory M.; Raudsepp, Mati; Francis, Carl A. American Mineralogist, Volume 96, pages 179-187, 2011 AB S T R A C TStichtite, ideally Mg 6 Cr 2 CO 3 (OH) 16 •4H 2 O, from Stichtite Hill, Tasmania, Australia, and barbertonite, also ideally Mg 6 Cr 2 CO 3 (OH) 16 •4H 2 O, from the Kaapsehoop asbestos mine, South Africa, have been studied by powder X-ray diffraction and their structures have been refined using the Rietveld method. Stichtite from Stichtite Hill crystallizes in the rhombohedral space group R3m, with unitcell parameters a = 3.09575(3) and c = 23.5069(6) Å, V = 195.099(6) Å 3 , with Z = 3/8. Barbertonite from the Kaapsehoop asbestos mine crystallizes in the hexagonal space group P6 3 /mmc. The co-type specimens of barbertonite were found to be intergrown mixtures consisting of barbertonite and stichtite. Unit-cell parameters of barbertonite from the co-type specimens were a = 3.09689(6), c = 15.6193(8) Å, and V = 129.731(8) Å 3 and a = 3.09646(6), c = 15.627(1) Å V = 129.76(1) Å 3 , and Z = ¼. Rietveld refinements of both stichtite and barbertonite show that they are polytypes rather than polymorphs and do not represent distinct mineral species. Several possible nomenclature systems are discussed for the naming of hydrotalcite minerals and groups. Raman band assignments are also presented for stichtite from Stichtite Hill.Stichtite and hydrotalcite minerals make up a large proportion of the ore at the Mount Keith nickel mine in Western Australia. Bulk powder diffraction shows the ore contains 6.1 wt% stichtite and 5.6 wt% iowaite. Hydrotalcite group minerals provide an important potential reservoir of CO 2 . At Mount Keith, the amount of CO 2 mined as stichtite could exceed 45 000 metric tons per year, while exchange of Cl for CO 3 could fix in excess of 40 000 metric tons CO 2 per year if end-member iowaite is reacted to form pyaroaurite.

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“…Direct space methods for solving crystal structures using powder diffraction data started to be developed due to the appearance of high-speed personal computers in 1990s and are based on the Monte-Carlo method [1,2], genetic algorithms [3,4], and simulated annealing [5,6]. At present, the FOX [7], DASH [8], and TOPAS [9] programs based on simulated annealing are used. Genetic algorithms have been implemented in the well-known EAGER [10], GEST [11], and MAUD programs [12].…”

Section: Introductionmentioning

confidence: 99%

Multipopulation Genetic Algorithm for Determining Crystal Structures Using Powder Diffraction Data

Zaloga

Yakimov

Dubinin

2018

J. Synch. Investig.

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A method for the automatic determination of crystal structures using powder diffraction data by the multipopulation genetic algorithm is proposed. The advantage of using coevolution with exchange by better individuals over using evolution within a single genetic algorithm without interpopulation exchange is demonstrated. The process of searching for a structural solution using the multipopulation genetic algorithm is illustrated and analyzed by the example of the known Ca 2 Al 3 O 6 F crystal structure (sp. gr. R , a = 17.3237(1) Å, c = 7.0002(0) Å, Z = 6, and V = 1819.38(1) Å 3 ). The fitness functions for the best structural models and atomic position maps at different algorithm operation stages are plotted.

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Problem Solving with the TOPAS Macro Language: Corrections and Constraints in Simulated Annealing and Rietveld Refinement

Cited by 8 publications

References 19 publications

Nomenclature of the hydrotalcite supergroup: natural layered double hydroxides

Nomenclature of the hydrotalcite supergroup: natural layered double hydroxides

The crystal structure of stichtite, re-examination of barbertonite, and the nature of polytypism in MgCr hydrotalcites

Multipopulation Genetic Algorithm for Determining Crystal Structures Using Powder Diffraction Data

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