Modeling RNA loops using sequence homology and geometric constraints

Summary: RNA loop regions are essential structural elements of RNA molecules influencing both their structural and functional properties. We developed RLooM, a web application for homology-based modeling of RNA loops utilizing template structures extracted from the PDB. RLooM allows the insertion and replacement of loop structures of a desired sequence into an existing RNA structure. Furthermore, a comprehensive database of loops in RNA structures can be accessed through the web interface

Study of the Negative Magneto-Resistance of Single Proton-Implanted Lithium-Doped ZnO Microwires

The magneto-transport properties of single proton-implanted ZnO and of Li(7\%)-doped ZnO microwires have been studied. The as-grown microwires were highly insulating and not magnetic. After proton implantation the Li(7\%) doped ZnO microwires showed a non monotonous behavior of the negative magneto-resistance (MR) at temperature above 150 K. This is in contrast to the monotonous NMR observed below 50 K for proton-implanted ZnO. The observed difference in the transport properties of the wires is related to the amount of stable Zn vacancies created at the near surface region by the proton implantation and Li doping. The magnetic field dependence of the resistance might be explained by the formation of a magnetic/non magnetic heterostructure in the wire after proton implantation.Comment: 6 pages with 5 figure

Nitrogen transfer properties in tantalum nitride based materials

Ta3-xMxNy (M = Re, Fe, Co; x = 0, 0.25, 0.5, 1) materials with different microstructural features (e.g. surface area) were successfully prepared using different synthesis techniques. The dependence of nitrogen transfer properties upon tantalum nitride microstructure and its chemical composition was evaluated using the ammonia synthesis with a H2/Ar feedstream (a reaction involving lattice nitrogen transfer). It was shown that nitrogen reactivity for tantalum nitride is more dominated by lattice nitrogen stability rather than microstructural properties. In the case of non-doped tantalum nitride, only a limited improvement of reactivity with enhanced surface area was observed which demonstrates the limited impact of microstructure upon reactivity. However, the nature of the transition metal dopant as well as its content was observed to play a key role in the nitrogen transfer properties of tantalum nitride and to impact strongly upon its reactivity. In fact, doping tantalum nitride with low levels of Co resulted in enhanced reactivity at lower temperature

Nitrides as ammonia synthesis catalysts and as potential nitrogen transfer reagents

In this article, an overview of the application of selected metal nitrides as ammonia synthesis catalysts is presented. The potential development of some systems into nitrogen transfer reagents is also described

On the possibility of an Eley-Rideal mechanism for ammonia synthesis on Mn6N5+x (x=1)-(111) surfaces

Recently we reported an Eley–Rideal/Mars–van Krevelen mechanism for ammonia synthesis on cobalt molybdenum nitride (Co3Mo3N). In this mechanism hydrogenation of activated dinitrogen occurs directly from the gas phase in a low barrier step forming a hydrazinylidene intermediate [double bond, length as m-dash]NNH2. In this paper we study whether such a mechanism of ammonia synthesis could occur on the (111) surface of another metal nitride, Mn6N5+x (x = 1), as this would explain the low-T ammonia synthesis activity of Co3Mo3N. We find that although N2 adsorbs more strongly than H2 on the (111) surface, having also examined the (110) and the (100) surface, N2 is not significantly activated when adsorbed in an end-on configuration. The hydrogenation reactions via an Eley–Rideal mechanism are all high barrier processes (>182 kJ mol−1) and therefore an Eley–Rideal mechanism for ammonia synthesis is predicted to not occur on this material unless there are high temperatures. Our study indicates that the fact that an Eley–Rideal/Mars–van Krevelen mechanism occurs on Co3Mo3N is a result of the stronger activation of dinitrogen at nitrogen vacancies when dinitrogen is adsorbed in an end-on configuration

The integration of experiment and computational modelling in heterogeneously catalysed ammonia synthesis over metal nitrides

In this perspective we present recent experimental and computational progress in catalytic ammonia synthesis research on metal nitrides involving a combined approach. On this basis, it suggested that the consideration of nitrogen vacancies in the synthesis of ammonia can offer new low energy pathways that were previously unknown. We have shown that metal nitrides that are also known to have high activity for ammonia synthesis can readily form nitrogen vacancies on their surfaces. These vacancies adsorb dinitrogen much more strongly than the defect-free surfaces and can efficiently activate the strong N–N triple bond. These fundamental studies suggest that heterogeneously catalysed ammonia synthesis over metal nitrides is strongly affected by bulk and surface defects and that further progress in the discovery of low temperature catalysts relies on more careful consideration of nitrogen vacancies. The potential occurrence of an associative pathway in the case of the Co3Mo3N catalytic system provides a possible link with enzymatic catalysis, which will be of importance in the design of heterogeneous catalytic systems operational under process conditions of reduced severity which are necessary for the development of localised facilities for the production of more sustainable “green” ammonia

Sound comparisons: a new online database and resource for research in phonetic diversity

Sound Comparisons hosts over 90,000 individual word recordings and 50,000 narrow phonetic transcriptions from 600 language varieties from eleven language families around the world. This resource is designed to serve researchers in phonetics, phonology and related fields. Transcriptions follow new initiatives for standardisation in usage of the IPA and Unicode. At soundcomparisons.com, users can explore the transcription datasets by phonetically-informed search and filtering, customise selections of languages and words, download any targeted data subset (sound files and transcriptions) and cite it through a custom URL. We present sample research applications based on our extensive overage of regional and sociolinguistic variation within major languages, and also of endangered languages, for which Sound Comparisons provides a rapid first documentation of their diversity in phonetics. The multilingual interface and user-friendly, ‘hover-tohear’ maps likewise constitute an outreach tool, where speakers can instantaneously hear and compare the phonetic diversity and relationships of their native languages

Sound comparisons: A new online database and resource for research in phonetic diversity

Sound Comparisons hosts over 90,000 individual word recordings and 50,000 narrow phonetic transcriptions from 600 language varieties from eleven language families around the world. This resource is designed to serve researchers in phonetics, phonology and related fields. Transcriptions follow new initiatives for standardisation in usage of the IPA and Unicode. At soundcomparisons.com, users can explore the transcription datasets by phonetically-informed search and filtering, customise selections of languages and words, download any targeted data subset (sound files and transcriptions) and cite it through a custom URL. We present sample research applications based on our extensive overage of regional and sociolinguistic variation within major languages, and also of endangered languages, for which Sound Comparisons provides a rapid first documentation of their diversity in phonetics. The multilingual interface and user-friendly, ‘hover-tohear’ maps likewise constitute an outreach tool, where speakers can instantaneously hear and compare the phonetic diversity and relationships of their native languages

A computational study of the heterogeneous synthesis of hydrazine on Co3Mo3N

Periodic and molecular density functional theory calculations have been applied to elucidate the associative mechanism for hydrazine and ammonia synthesis in the gas phase and hydrazine formation on Co3Mo3N. We find that there are two activation barriers for the associative gas phase mechanism with barriers of 730 and 658 kJ/mol, corresponding to a hydrogenation step from N2 to NNH2 and H2NNH2 to H3NNH3, respectively. The second step of the mechanism is barrierless and an important intermediate, NNH2, can also readily form on Co3Mo3N surfaces via the Eley–Rideal chemisorption of H2 on a pre-adsorbed N2 at nitrogen vacancies. Based on this intermediate a new heterogeneous mechanism for hydrazine synthesis is studied. The highest relative barrier for this heterogeneous catalysed process is 213 kJ/mol for Co3Mo3N containing nitrogen vacancies, clearly pointing towards a low-energy process for the synthesis of hydrazine via a heterogeneous catalysis route

Binding MOAD, a high-quality protein–ligand database

Binding MOAD (Mother of All Databases) is a database of 9836 protein–ligand crystal structures. All biologically relevant ligands are annotated, and experimental binding-affinity data is reported when available. Binding MOAD has almost doubled in size since it was originally introduced in 2004, demonstrating steady growth with each annual update. Several technologies, such as natural language processing, help drive this constant expansion. Along with increasing data, Binding MOAD has improved usability. The website now showcases a faster, more featured viewer to examine the protein–ligand structures. Ligands have additional chemical data, allowing for cheminformatics mining. Lastly, logins are no longer necessary, and Binding MOAD is freely available to all at http://www.BindingMOAD.org