The atomic structure of protons and hydrides in Sm1.92Ca0.08Sn2O7-δ pyrochlore from DFT calculations and FTIR spectroscopy

A combined density functional theory and Fourier transform infrared spectroscopy study of the structure and specific site preference of protons and hydrides in the pyrochlore Sm1.92Ca0.08Sn2O7-delta is presented. Two protonic sites of particular high stability are identified, both located on O(1) oxygen atoms closely associated with a Ca dopant. Further, the unexpected presence of Ho hydride defects in undoped, oxygen deficient Sm2Sn2O7 is reported. Finally, the stretching frequencies and relative intensities for these and other sites are calculated. The main features of the Fourier transform infrared spectra are hereby resolved. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4737786

Structures and reaction rates of the gaseous oxidation of SO₂ by an O₋₃ (H₂O)₀₋₅ cluster – a density functional theory investigation

Based on density functional theory calculations we present a study of the gaseous oxidation of SO₂ to SO₃ by an anionic O₃^&minus;(H₂O)_<i>n</i> cluster, <i>n</i> = 0–5. The configurations of the most relevant reactants, transition states, and products are discussed and compared to previous findings. Two different classes of transition states have been identified. One class is characterised by strong networks of hydrogen bonds, very similar to the reactant complexes. The other class is characterised by sparser structures of hydration water and is stabilised by high entropy. At temperatures relevant for atmospheric chemistry, the most energetically favourable class of transition states vary with the number of water molecules attached. A kinetic model is utilised, taking into account the most likely outcomes of the initial SO₂ O₃^&minus;(H₂O)_<i>n</i> collision complexes. This model shows that the reaction takes place at collision rates regardless of the number of water molecules involved. A lifetime analysis of the collision complexes supports this conclusion. Hereafter, the thermodynamics of water and O₂ condensation and evaporation from the product SO₃^&minus;O₂(H₂O)_<i>n</i> cluster is considered and the final products are predicted to be O₂SO₃^&minus; and O₂SO₃^&minus;(H₂O)₁. The low degree of hydration is rationalised through a charge analysis of the relevant complexes. Finally, the thermodynamics of a few relevant reactions of the O₂SO₃^&minus; and O₂SO₃^&minus;(H₂O)₁ complexes are considered

Ab initio studies of O2-(H2O)n and O3-(H2O)n anionic molecular clusters, n≤12

An ab initio study of gaseous clusters of O₂^&minus; and O₃^&minus; with water is presented. Based on thorough scans of configurational space, we determine the thermodynamics of cluster growth. The results are in good agreement with benchmark computational methods and existing experimental data. We find that anionic O₂^&minus;(H₂O)_<i>n</i> and O₃^&minus;(H₂O)_<i>n</i> clusters are thermally stabilized at typical atmospheric conditions for at least <i>n</i> = 5. The first 4 water molecules are strongly bound to the anion due to delocalization of the excess charge while stabilization of more than 4 H₂O is due to normal hydrogen bonding. Although clustering up to 12 H₂O, we find that the O₂ and O₃ anions retain at least ca. 80 % of the charge and are located at the surface of the cluster. The O₂^&minus; and O₃^&minus; speicies are thus accessible for further reactions. We consider the distributions of cluster sizes as function of altitude before finally, the thermodynamics of a few relevant cluster reactions are considered

An isotopic analysis of ionising radiation as a source of sulphuric acid

Sulphuric acid is an important factor in aerosol nucleation and growth. It has been shown that ions enhance the formation of sulphuric acid aerosols, but the exact mechanism has remained undetermined. Furthermore some studies have found a deficiency in the sulphuric acid budget, suggesting a missing source. In this study the production of sulphuric acid from SO&lt;sub&gt;2&lt;/sub&gt; through a number of different pathways is investigated. The production methods are standard gas phase oxidation by OH radicals produced by ozone photolysis with UV light, liquid phase oxidation by ozone, and gas phase oxidation initiated by gamma rays. The distributions of stable sulphur isotopes in the products and substrate were measured using isotope ratio mass spectrometry. All methods produced sulphate enriched in &lt;sup&gt;34&lt;/sup&gt;S and we find an enrichment factor (&amp;delta;&lt;sup&gt;34&lt;/sup&gt;S) of 8.7 ± 0.4&amp;permil; (1 standard deviation) for the UV-initiated OH reaction. Only UV light (Hg emission at 253.65 nm) produced a clear non-mass-dependent excess of &lt;sup&gt;33&lt;/sup&gt;S. The pattern of isotopic enrichment produced by gamma rays is similar, but not equal, to that produced by aqueous oxidation of SO&lt;sub&gt;2&lt;/sub&gt; by ozone. This, combined with the relative yields of the experiments, suggests a mechanism in which ionising radiation may lead to hydrated ion clusters that serve as nanoreactors for S(IV) to S(VI) conversion

proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes

The interpretation of genomic, transcriptomic and other microbial 'omics data is highly dependent on the availability of well-annotated genomes. As the number of publicly available microbial genomes continues to increase exponentially, the need for quality control and consistent annotation is becoming critical. We present proGenomes3, a database of 907 388 high-quality genomes containing 4 billion genes that passed stringent criteria and have been consistently annotated using multiple functional and taxonomic databases including mobile genetic elements and biosynthetic gene clusters. proGenomes3 encompasses 41 171 species-level clusters, defined based on universal single copy marker genes, for which pan-genomes and contextual habitat annotations are provided. The database is available at http://progenomes.embl.de/

Density functional theory based screening of ternary alkali-transition metal borohydrides: A computational material design project

The dissociation of molecules, even the most simple hydrogen molecule, cannot be described accurately within density functional theory because none of the currently available functionals accounts for strong on-site correlation. This problem led to a discussion of properties that the local Kohn-Sham potential has to satisfy in order to correctly describe strongly correlated systems. We derive an analytic expression for the nontrivial form of the Kohn-Sham potential in between the two fragments for the dissociation of a single bond. We show that the numerical calculations for a one-dimensional two-electron model system indeed approach and reach this limit. It is shown that the functional form of the potential is universal, i.e., independent of the details of the two fragments.We acknowledge funding by the Spanish MEC (Grant No. FIS2007-65702-C02-01), “Grupos Consolidados UPV/EHU del Gobierno Vasco” (Grant No. IT-319-07), and the European Community through e-I3 ETSF project (Grant Agreement No. 211956).Peer reviewe