Jahn-Teller Distortions, Cation Ordering and Octahedral Tilting in Perovskites

In transition metal oxides, preferential occupation of specific d orbitals on the transition metal ion can lead to the development of a long-range ordered pattern of occupied orbitals. This phenomenon, referred to as orbital ordering, is usually observed indirectly from the cooperative Jahn-Teller distortions (CJTDs) that result as a consequence of the orbital ordering. This paper examines the interplay between orbital ordering, octahedral tilting and cation ordering in perovskites. Both ternary AMX3 perovskites containing an active Jahn-Teller (J-T) ion on the octahedral site and quaternary A2MM\u27X6 perovskites containing a J-T ion on one-half of the octahedral sites have been examined. In AMX3 perovskites, the tendency is for the occupied 3d3x2-r2 and 3d3z2-r2 orbitals to order in the ac plane, as exemplified by the crystal structures of LaMnO3 and KCuF3. This arrangement maintains a favorable coordination environment for the anion sites. In AMX3 perovskites, octahedral tilting tends to enhance the magnitude of the J-T distortions. In A2MM\u27X6 perovskites, the tendency is for the occupied 3d3z2-r2 orbitals to align parallel to the c axis. This pattern maintains a favorable coordination environment about the symmetric M\u27-cation site. The orbital ordering found in rock-salt ordered A2MM\u27X6 perovskites is compatible with octahedral rotations about the c axis (Glazer tilt system a0a0c-) but appears to be incompatible with GdFeO3-type octahedral tilting (tilt system a-b+a-)

Prediction of the Crystal Structures of Perovskites Using the Software Program SPuDS

The software program SPuDS has been developed to predict the crystal structures of perovskites, including those distorted by tilting of the octahedra. The user inputs the composition and SPuDS calculates the optimal structure in ten different Glazer tilt systems. This is performed by distorting the structure to minimize the global instability index, while maintaining rigid octahedra. The location of the A-site cation is chosen so as to maximize the symmetry of its coordination environment. In its current form SPuDS can handle up to four different A-site cations in the same structure, but only one octahedral ion. Structures predicted by SPuDS are compared with a number of previously determined structures to illustrate the accuracy of this approach. SPuDS is also used to examine the prospects for synthesizing new compounds in tilt systems with multiple A-site coordination geometries (a+a+a+, a0b+b+, a0b-c+)

MetaPOAP: Presence or Absence of Metabolic Pathways in Metagenome-Assembled Genomes

Genome-resolved metagenomics allows the construction of draft microbial genomes from short-read shotgun metagenomics (Metagenome-Assembled Genomes, or MAGs); however, even high-quality MAGs are typically somewhat incomplete and contain a small amount of contaminant sequence, making accurate prediction of metabolic potential challenging. Here, we describe MetaPOAP, an algorithm for probabalistic assessment of the statistical likelihoods for the presence or absence of metabolic pathways in MAGs

Magnetic structures of NaLMnWO_6 perovskites (L=La,Nd,Tb)

The magnetic structures of the perovskites NaLaMnWO_6, NaNdMnWO_6, and NaTbMnWO_6, with rocksalt ordering of the Mn/W ions and layered ordering of Na and the rare-earth ions, have been determined by neutron powder diffraction. The manganese moments in NaLaMnWO_6 order below 10 K with a propagation vector of k_14=(1/2,0,1/2) and a moment of 3.99μB per Mn^2+ ion. The Mn^2+ and Nd^3+ ions order simultaneously in NaNdMnWO_6 at 11 K. The resulting magnetic structure is incommensurate with the underlying crystal structure and has the propagation vector of k_5=(0,0.48,1/2). NaTbMnWO_6 undergoes two magnetic phase transitions at 15 and 9 K. The structure determined at 11 K is based on two propagation vectors of k_14=(1/2,0,1/2) and k_5=(0,0.427,1/2). Upon cooling at 6 K the incommensurate vector is no longer present and the moments order only according to k_14. The moments of the Nd and Tb ions are found to remain within the planes of the A-site cations, and in NaTbMnWO_6 the Mn moments also lie within the xy plane. This study not only reveals magnetic structures with previously unexplored topologies but it also sheds light on the intricate coupling between the two magnetic sublattices

Structure Prediction of Ordered and Disordered Multiple Octahedral Cation Perovskites using SPuDS

The software package SPuDS has previously been shown to accurately predict crystal structures of AMX3 and A1 - xA\u27xMX3 perovskites that have undergone octahedral tilting distortions. This paper describes the extension of this technique and its accuracy for A2MM\u27X6 ordered double perovskites with the aristotype Fm3̄m cubic structure, as well as those that have undergone octahedral tilting distortions. A survey of the literature shows that roughly 70% of all ordered double perovskites undergo octahedral tilting distortions. Of the 11 distinct types of octahedral tilting that can occur in ordered perovskites, five tilt systems account for ~97% of the reported structures. SPuDS can calculate structures for the five dominant tilt systems, Fm3̄m (a0a0a0), I4/m (a0a0c-), R3̄ (a-a-a-), I2/m (a0b-b-) and P21/n (a-a-b+), as well as two additional tilt systems, Pn3̄ (a+a+a+) and P4/mnc (a0a0c+). Comparison with reported crystal structures shows that SPuDS is quite accurate at predicting distortions driven by octahedral tilting. The favored modes of octahedral tilting in ordered double perovskites are compared and contrasted with those in AMX3 perovskites. Unit-cell pseudosymmetry in Sr- and Ca-containing double perovskites is also examined. Experimentally, Sr2MM\u27O6 compounds show a much stronger tendency toward pseudosymmetry than do Ca2MM\u27O6 compounds with similar tolerance factors

Structure Determination of A2M3+TaO6 and A2M3+NbO6 Ordered Perovskites: Octahedral Tilting and Pseudosymmetry

The room-temperature crystal structures of six A2M3+M5+O6 ordered perovskites have been determined from neutron and X-ray powder diffraction data. Ba2YNbO6 adopts the aristotype high-symmetry cubic structure (space group Fm3̄m, Z = 4). The symmetries of the remaining five compounds were lowered by octahedral tilting distortions. Out-of-phase rotations of the octahedra about the c axis were observed in Sr2CrTaO6 and Sr2GaTaO6, which lowers the symmetry to tetragonal (space group = I4/m, Z = 2, Glazer tilt system = a0a0c-). Octahedral tilting analogous to that seen in GdFeO3 occurs in Sr2ScNbO6, Ca2AlNbO6 and Ca2CrTaO6, which lowers the symmetry to monoclinic (space group P21/n, Z = 2, Glazer tilt system = a-a-c+). The Sr2MTaO6 (M = Cr, Ga, Sc) compounds have unit-cell dimensions that are highly pseudo-cubic. Ca2AlNbO6 and Ca2CrTaO6 have unit-cell dimensions that are strongly pseudo-orthorhombic. This high degree of pseudosymmetry complicates the space-group assignment and structure determination. The space-group symmetries, unit-cell dimensions and cation ordering characteristics of an additional 13 compositions, as determined from X-ray powder diffraction data, are also reported. An analysis of the crystal structures of 32 A2MTaO6 and A2MNbO6 perovskites shows that in general the octahedral tilt system strongly correlates with the tolerance factor

Structural distortions, phase transitions, and cation ordering in the perovskite and tungsten trioxide structures

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Evolution of Phototrophy in the Chloroflexi Phylum Driven by Horizontal Gene Transfer

The evolutionary mechanisms behind the extant distribution of photosynthesis is a point of substantial contention. Hypotheses range from the presence of phototrophy in the last universal common ancestor and massive gene loss in most lineages, to a later origin in Cyanobacteria followed by extensive horizontal gene transfer into the extant phototrophic clades, with intermediate scenarios that incorporate aspects of both end-members. Here, we report draft genomes of 11 Chloroflexi: the phototrophic Chloroflexia isolate Kouleothrix aurantiaca as well as 10 genome bins recovered from metagenomic sequencing of microbial mats found in Japanese hot springs. Two of these metagenome bins encode photrophic reaction centers and several of these bins form a metabolically diverse, monophyletic clade sister to the Anaerolineae class that we term Candidatus Thermofonsia. Comparisons of organismal (based on conserved ribosomal) and phototrophy (reaction center and bacteriochlorophyll synthesis) protein phylogenies throughout the Chloroflexi demonstrate that two new lineages acquired phototrophy independently via horizontal gene transfer (HGT) from different ancestral donors within the classically phototrophic Chloroflexia class. These results illustrate a complex history of phototrophy within this group, with metabolic innovation tied to HGT. These observations do not support simple hypotheses for the evolution of photosynthesis that require massive character loss from many clades; rather, HGT appears to be the defining mechanic for the distribution of phototrophy in many of the extant clades in which it appears