Ab-initio calculations of the proton location in topaz-OH, Al2SiO4(OH)2

The position of hydrogen in the structure of topaz-OH was determined by means of ab-initio quantum-mechanic calculations. Static lattice energy calculations predict the existence of four non-equivalent positions of protons, which are characterized by O4-H1... O1, O4-H2... O2, O4-H3... O3 and O4-H4... O4 hydrogen bonds. The distribution of the protons between positions of local equilibrium is controlled by the proton-proton avoidance rule and the strength of the hydrogen bonds. The most favourable configuration of hydrogen atoms is achieved for adjacent protons, which form O4-H3... O3 and O4-H4... O4 hydrogen bonds, respectively. The thermal excitation of atoms at a temperature of 55 K is large enough for the hydrogen atoms occasionally to change their positions to form O4-H1... O1 and O4-H2... O2 bonds. At ambient pressures and higher temperatures the protons are in a dynamic exchange between the allowed positions of local minima. As a consequence, for nearly room-temperature conditions, the dynamic change between different structural configurations leads to the violation of all possible symmetry elements and with that to space group #E5/E5#1. The flipping of the protons between different sites is achieved by simple rotation of the OH-dipole and does not produce any significant distortion of the framework of topaz, whose symmetry remains that of the space group Pbnm. Therefore, no reduction of symmetry has been observed in former X-ray studies on topaz-OH. Calculated IR absorption spectra of topaz-OH were found to be in good agreement with measured spectra. According to the calculations, the two favourable configurations of protons might correspond to the measured peak splitting within the OH-stretching range. An experimentally observed low-frequency band at 3520 cm−1 was assigned to the OH-stretching of the O4-H3... O3 bond, while the band at 3600 cm−1 was attributed to OH-stretching of the O4-H4... O4 hydrogen bond. The broad peak in FAR-IR frequency range at 100-150 cm−1 is attributed to the stretching of H3... O3 and H4... O4 contacts. The rate of proton exchange at 670 K among different sites was estimated by ab-inito molecular dynamic simulations. The calculations predict that flipping of adjacent protons between O4-H3... O3 and O4-H4... O4 bonds at 670 K occur at a rate of about 1.96 TH

Waves of genomic hitchhikers shed light on the evolution of gamebirds (Aves: Galliformes) : research article

Background The phylogenetic tree of Galliformes (gamebirds, including megapodes, currassows, guinea fowl, New and Old World quails, chicken, pheasants, grouse, and turkeys) has been considerably remodeled over the last decades as new data and analytical methods became available. Analyzing presence/absence patterns of retroposed elements avoids the problems of homoplastic characters inherent in other methodologies. In gamebirds, chicken repeats 1 (CR1) are the most prevalent retroposed elements, but little is known about the activity of their various subtypes over time. Ascertaining the fixation patterns of CR1 elements would help unravel the phylogeny of gamebirds and other poorly resolved avian clades. Results We analyzed 1,978 nested CR1 elements and developed a multidimensional approach taking advantage of their transposition in transposition character (TinT) to characterize the fixation patterns of all 22 known chicken CR1 subtypes. The presence/absence patterns of those elements that were active at different periods of gamebird evolution provided evidence for a clade (Cracidae + (Numididae + (Odontophoridae + Phasianidae))) not including Megapodiidae; and for Rollulus as the sister taxon of the other analyzed Phasianidae. Genomic trace sequences of the turkey genome further demonstrated that the endangered African Congo Peafowl (Afropavo congensis) is the sister taxon of the Asian Peafowl (Pavo), rejecting other predominantly morphology-based groupings, and that phasianids are monophyletic, including the sister taxa Tetraoninae and Meleagridinae. Conclusions The TinT information concerning relative fixation times of CR1 subtypes enabled us to efficiently investigate gamebird phylogeny and to reconstruct an unambiguous tree topology. This method should provide a useful tool for investigations in other taxonomic groups as well

Retrophylogenomics place tarsiers on the evolutionary branch of anthropoids

One of the most disputed issues in primate evolution and thus of our own primate roots, is the phylogenetic position of the Southeast Asian tarsier. While much molecular data indicate a basal place in the primate tree shared with strepsirrhines (prosimian monophyly hypothesis), data also exist supporting either an earlier divergence in primates (tarsier-first hypothesis) or a close relationship with anthropoid primates (Haplorrhini hypothesis). The use of retroposon insertions embedded in the Tarsius genome afforded us the unique opportunity to directly test all three hypotheses via three pairwise genome alignments. From millions of retroposons, we found 104 perfect orthologous insertions in both tarsiers and anthropoids to the exclusion of strepsirrhines, providing conflict-free evidence for the Haplorrhini hypothesis, and none supporting either of the other two positions. Thus, tarsiers are clearly the sister group to anthropoids in the clade Haplorrhini

Pushing the limits of energetic materials - the synthesis and characterization of dihydroxylammonium 5,5'-bistetrazole-1,1'-diolate

The safe preparation and characterization (XRD, NMR and vibrational spectroscopy, DSC, mass spectrometry, sensitivities) of a new explosive dihydroxylammonium 5,5'-bistetrazole-1,1'-diolate (TKX-50) that outperforms all other commonly used explosive materials is detailed. While much publicized high-performing explosives, such as octanitrocubane and CL-20, have been at the forefront of public awareness, this compound differs in that it is simple and cheap to prepare from commonly available chemicals. TKX-50 expands upon the newly exploited field of tetrazole oxide chemistry to produce a material that not only is easily prepared and exceedingly powerful, but also possesses the required thermal insensitivity, low toxicity, and safety of handling to replace the most commonly used military explosive, RDX (1,3,5-trinitro-1,3,5-triazacyclohexane). In addition, the crystal structures of the intermediates 5,5'-bistetrazole-1,1'-diol dihydrate, 5,5'-bistetrazole-1,1'-diol dimethanolate and dimethylammonium 5,5'-bistetrazole-1,1'-diolate were determined and presented

Structure, bonding and morphology of hydrothermally synthesised xonotlite

The authors have systematically investigated the role of synthesis conditions upon the structure and morphology of xonotlite. Starting with a mechanochemically prepared, semicrystalline phase with Ca/Si=1, the authors have prepared a series of xonotlite samples hydrothermally, at temperatures between 200 and 250 degrees C. Analysis in each case was by X-ray photoelectron spectroscopy, environmental scanning electron microscopy and X-ray diffraction. The authors’ use of a much lower water/solid ratio has indirectly confirmed the ‘through solution’ mechanism of xonotlite formation, where silicate dissolution is a key precursor of xonotlite formation. Concerning the role of temperature, too low a temperature (~200 degrees C) fails to yield xonotlite or leads to increased number of structural defects in the silicate chains of xonotlite and too high a temperature (>250 degrees C) leads to degradation of the xonotlite structure, through leaching of interchain calcium. Synthesis duration meanwhile leads to increased silicate polymerisation due to diminishing of the defects in the silicate chains and more perfect crystal morphologies

Coalescent-based genome analyses resolve the early branches of the euarchontoglires

Despite numerous large-scale phylogenomic studies, certain parts of the mammalian tree are extraordinarily difficult to resolve. We used the coding regions from 19 completely sequenced genomes to study the relationships within the super-clade Euarchontoglires (Primates, Rodentia, Lagomorpha, Dermoptera and Scandentia) because the placement of Scandentia within this clade is controversial. The difficulty in resolving this issue is due to the short time spans between the early divergences of Euarchontoglires, which may cause incongruent gene trees. The conflict in the data can be depicted by network analyses and the contentious relationships are best reconstructed by coalescent-based analyses. This method is expected to be superior to analyses of concatenated data in reconstructing a species tree from numerous gene trees. The total concatenated dataset used to study the relationships in this group comprises 5,875 protein-coding genes (9,799,170 nucleotides) from all orders except Dermoptera (flying lemurs). Reconstruction of the species tree from 1,006 gene trees using coalescent models placed Scandentia as sister group to the primates, which is in agreement with maximum likelihood analyses of concatenated nucleotide sequence data. Additionally, both analytical approaches favoured the Tarsier to be sister taxon to Anthropoidea, thus belonging to the Haplorrhine clade. When divergence times are short such as in radiations over periods of a few million years, even genome scale analyses struggle to resolve phylogenetic relationships. On these short branches processes such as incomplete lineage sorting and possibly hybridization occur and make it preferable to base phylogenomic analyses on coalescent methods

Classification of perovskite structural types with dynamical octahedral tilting.

Perovskites ABX3 with delocalized positions of the X atoms represent a distinct class of dynamically distorted structures with peculiar structural relations and physical properties. The delocalization originates from atoms crossing shallow barriers of the potential energy surface. Quantum mechanically, they can be treated similar to light atoms in diffusive states. Many of these perovskite structures are widely used functional materials thanks to their particular physical properties, such as superconductivity, ferroelectricity and photo-activity. A number of these properties are related to static or dynamic motion of octahedral units. Yet, a full understanding of the relationships between perovskite crystal structure, chemical bonding and physical properties is currently missing. Several studies indicate the existence of dynamic disorder generated by anharmonic motion of octahedral units, e.g. in halide perovskite structures. To simplify structural analysis of such systems we derive a set of space groups for simple perovskites ABX3 with dynamical octahedral tilting. The derived space groups extend the well established space group tables for static tiltings by Glazer [Acta Cryst. B (1972). 28, 3384-3392], Aleksandrov [Ferroelectrics (1976). 24, 801-805] and Howard & Stokes [Acta Cryst. B (1998). 54, 782-789]. Ubiquity of dynamical tilting is demonstrated by an analysis of the structural data for perovskites reported in recent scientific publications and the signature of dynamic tilting in the corresponding structures is discussed, which can be summarized as follows: (a) volume increase upon a lowering of temperature, (b) apparent distortion of octahedra (where Jahn-Teller distortions can be ruled out), (c) mismatch between observed instantaneous symmetry and average symmetry, (d) deviation of the experimental space group from the theoretically predicted structures for static tilting, (e) inconsistency of lattice parameters with those suggested by the theory of static tilts, and (f) large displacement parameters for atoms at the X and B sites. Finally, the possible influence of dynamic disorder on the physical properties of halide perovskites is discussed