Self-assembled molecular complexes and coordination polymers of CdII, hexamine, and monocarboxylates: structural analysis and theoretical studies of supramolecular interactions

Four new cadmium(II) complexes [Cd-2(bz)(4)(H2O)(4)(mu 2-hmt)]center dot Hbz center dot H2O (1), [Cd-3(bz)(6)(H2O)(6)(mu 2-hmt)(2)]center dot 6H(2)O (2), [Cd(pa)(2)(H2O)(mu(2)-hmt)](n) (3), and {[Cd-3(ac)(6)(H2O)(3)(mu(3)-hmt)(2)]center dot 6H(2)O}(n) (4) with hexamine (hmt) and monocarboxylate ions, benzoate (bz), phenylacetate (pa), or acetate (ac) have been synthesized and characterized structurally. Structure determinations reveal that 1 is dinuclear, 2 is trinuclear, 3 is a one-dimensional (1D) infinite chain, and 4 is a two-dimensional (2D) polymer with fused hexagonal rings consisting of Cd-II and hmt. All the Cd-II atoms in the four complexes (except one CdII in 2) possess seven-coordinate pentagonal bipyramidal geometry with the various chelating bidentate carboxylate groups in equatorial sites. One of the CdII ions in 2, a complex that contains two monodentate carboxylates is in a distorted octahedral environment. The bridging mode of hmt is mu 2- in complexes 1-3 but is mu 3- in complex 4. In all complexes, there are significant numbers of H-bonds, C-H/pi, and pi-pi interactions which play crucial roles in forming the supramolecular networks. The importance of the noncovalent interactions in terms of energies and geometries has been analyzed using high level ab initio calculations. The effect of the cadmium coordinated to hmt on the energetic features of the C-H/pi interaction is analyzed. Finally, the interplay between C-H/pi and pi-pi interactions observed in the crystal structure of 3 is also studied.

Proteogenomics and in silico structural and functional annotation of the barley powdery mildew Blumeria graminis f. sp. hordei

Blumeria graminis is an economically important obligate plant-pathogenic fungus, whose entire genome was recently sequenced and manually annotated using ab initio in silico predictions [7]. Employing large scale proteogenomic analysis we are now able to verify independently the existence of proteins predicted by 24% of open reading frame models. We compared the haustoria and sporulating hyphae proteomes and identified 71 proteins exclusively in haustoria, the feeding and effector-delivery organs of the pathogen. These proteins are ‘significantly smaller than the rest of the protein pool and predicted to be secreted. Most do not share any similarities with Swiss–Prot or Trembl entries nor possess any identifiable Pfam domains. We used a novel automated prediction pipeline to model the 3D structures of the proteins, identify putative ligand binding sites and predict regions of intrinsic disorder. This revealed that the protein set found exclusively in haustoria is significantly less disordered than the rest of the identified Blumeria proteins or random (and representative) protein sets generated from the yeast proteome. For most of the haustorial proteins with unknown functions no good templates could be found, from which to generate high quality models. Thus, these unknown proteins present potentially new protein folds that can be specific to the interaction of the pathogen with its host.

Assessment of the consistency of H2O line intensities over the near-infrared using sun-pointing ground-based Fourier transform spectroscopy

We report on the consistency of water vapour line intensities in selected spectral regions between 800–12,000 cm−1 under atmospheric conditions using sun-pointing Fourier transform infrared spectroscopy. Measurements were made across a number of days at both a low and high altitude field site, sampling a relatively moist and relatively dry atmosphere. Our data suggests that across most of the 800–12,000 cm−1 spectral region water vapour line intensities in recent spectral line databases are generally consistent with what was observed. However, we find that HITRAN-2008 water vapour line intensities are systematically lower by up to 20% in the 8000–9200 cm−1 spectral interval relative to other spectral regions. This discrepancy is essentially removed when two new linelists (UCL08, a compilation of linelists and ab-initio calculations, and one based on recent laboratory measurements by Oudot et al. (2010) [10] in the 8000–9200 cm−1 spectral region) are used. This strongly suggests that the H2O line strengths in the HITRAN-2008 database are indeed underestimated in this spectral region and in need of revision. The calculated global-mean clear-sky absorption of solar radiation is increased by about 0.3 W m−2 when using either the UCL08 or Oudot line parameters in the 8000–9200 cm−1 region, instead of HITRAN-2008. We also found that the effect of isotopic fractionation of HDO is evident in the 2500–2900 cm−1 region in the observations.

Steric effects on uranyl complexation: synthetic, structural, and theoretical studies of carbamoyl pyrazole compounds of the uranyl(VI) ion

New bifunctional pyrazole based ligands of the type [C3HR2N2CONR'] (where R = H or CH3; R' = CH3, C2H5, or (C3H7)-C-i) were prepared and characterized. The coordination chemistry of these ligands with uranyl nitrate and uranyl bis(dibenzoyl methanate) was studied with infrared (IR), H-1 NMR, electrospray-mass spectrometry (ES-MS), elemental analysis, and single crystal X-ray diffraction methods. The structure of compound [UO2(NO3)(2)(C3H3N2CON{C2H5}(2))] (2) shows that the uranium(VI) ion is surrounded by one nitrogen atom and seven oxygen atoms in a hexagonal bipyramidal geometry with the ligand acting as a bidentate chelating ligand and bonds through both the carbamoyl oxygen and pyrazolyl nitrogen atoms. In the structure of [UO2(NO3)(2)(H2O)(2)(C5H7N2CON {C2H5}(2))(2)], (5) the pyrazole figand acts as a second sphere ligand and hydrogen bonds to the water molecules through carbamoyl oxygen and pyrazolyl nitrogen atoms. The structure of [UO2(DBM)(2)C3H3N2CON{C2H5}(2)] (8) (where DBM = C6H5COCHCOC6H5) shows that the pyrazole ligand acts as a monodentate ligand and bonds through the carbamoyl oxygen to the uranyl group. The ES-MS spectra of 2 and 8 show that the ligand is similarly bonded to the metal ion in solution. Ab initio quantum chemical studies show that the steric effect plays the key role in complexation behavior.

Global warming potentials and radiative efficiencies of halocarbons and related compounds: a comprehensive review

In the mid-1970s it was recognized that, as well as being substances that deplete stratospheric ozone, chlorofluorocarbons (CFCs) were strong greenhouse gases that could have substantial impacts on radiative forcing of climate change. Around a decade later, this group of radiatively active compounds was expanded to include a large number of replacements for ozone-depleting substances such as chlorocarbons, hydrochlorocarbons, hydrochlorofluorocarbons (HCFCs), hydrofluorocarbons (HFCs), perfluorocarbons (PFCs), bromofluorocarbons, and bromochlorofluorocarbons. This paper systematically reviews the published literature concerning the radiative efficiencies (REs) of CFCs, bromofluorocarbons and bromochlorofluorocarbons (halons), HCFCs, HFCs, PFCs, SF6, NF3, and related halogen containing compounds. In addition we provide a comprehensive and self-consistent set of new calculations of REs and global warming potentials (GWPs) for these compounds, mostly employing atmospheric lifetimes taken from the available literature. We also present Global Temperature change Potentials (GTPs) for selected gases. Infrared absorption spectra used in the RE calculations were taken from databases and individual studies, and from experimental and ab initio computational studies. Evaluations of REs and GWPs are presented for more than 200 compounds. Our calculations yield REs significantly (> 5%) different from those in the Intergovernmental Panel on Climate Change Fourth Assessment Report (AR4) for 49 compounds. We present new RE values for more than 100 gases which were not included in AR4. A widely-used simple method to calculate REs and GWPs from absorption spectra and atmospheric lifetimes is assessed and updated. This is the most comprehensive review of the radiative efficiencies and global warming potentials of halogenated compounds performed to date.

Band gap control via tuning of inversion degree in CdIn2S4 spinel

Based on theoretical arguments we propose a possible route for controlling the band-gap in the promising photovoltaic material CdIn2S4. Our ab initio calculations show that the experimental degree of inversion in this spinel (fraction of tetrahedral sites occupied by In) corresponds approximately to the equilibrium value given by the minimum of the theoretical inversion free energy at a typical synthesis temperature. Modification of this temperature, or of the cooling rate after synthesis, is then expected to change the inversion degree, which in turn sensitively tunes the electronic band-gap of the solid, as shown here by Heyd-Scuseria-Ernzerhof screened hybrid functional calculations.

Dopant-vacancy binding effects in Li-doped magnesium hydride

We use a combination of ab initio calculations and statistical mechanics to investigate the substitution of Li+ for Mg2+ in magnesium hydride (MgH2) accompanied by the formation of hydrogen vacancies with positive charge (with respect to the original ion at the site). We show that the binding energy between dopants and vacancy defects leads to a significant fraction of trapped vacancies and therefore a dramatic reduction in the number of free vacancies available for diffusion. The concentration of free vacancies initially increases with dopant concentration but reaches a maximum at around 1 mol % Li doping and slowly decreases with further doping. At the optimal level of doping, the corresponding concentration of free vacancies is much higher than the equilibrium concentrations of charged and neutral vacancies in pure MgH2 at typical hydrogen storage conditions. We also show that Li-doped MgH2 is thermodynamically metastable with respect to phase separation into pure magnesium and lithium hydrides at any significant Li concentration, even after considering the stabilization provided by dopant-vacancy interactions and configurational entropic effects. Our results suggest that lithium doping may enhance hydrogen diffusion hydride but only to a limited extent determined by an optimal dopant concentration and conditioned to the stability of the doped phase.

Independence referendums: who should vote and who should be offered citizenship?

In this EUDO CITIZENSHIP Forum Debate, several authors consider the interrelations between eligibility criteria for participation in independence referendum (that may result in the creation of a new independent state) and the determination of putative citizenship ab initio (on day one) of such a state. The kick-off contribution argues for resemblance of an independence referendum franchise and of the initial determination of the citizenry, critically appraising the incongruence between the franchise for the 18 September 2014 Scottish independence referendum, and the blueprint for Scottish citizenship ab initio put forward by the Scottish Government in its 'Scotland's Future' White Paper. Contributors to this debate come from divergent disciplines (law, political science, sociology, philosophy). They reflect on and contest the above claims, both generally and in relation to regional settings including (in addition to Scotland) Catalonia/Spain, Flanders/Belgium, Quebec/Canada, Post-Yugoslavia and Puerto-Rico/USA.

New opportunities for secure communication networks using shaped femtosecond laser pulses inducing filamentation processes in the atmosphere

The current study discusses new opportunities for secure ground to satellite communications using shaped femtosecond pulses that induce spatial hole burning in the atmosphere for efficient communications with data encoded within super-continua generated by femtosecond pulses. Refractive index variation across the different layers in the atmosphere may be modelled using assumptions that the upper strata of the atmosphere and troposphere behaving as layered composite amorphous dielectric networks composed of resistors and capacitors with different time constants across each layer. Input-output expressions of the dynamics of the networks in the frequency domain provide the transmission characteristics of the propagation medium. Femtosecond pulse shaping may be used to optimize the pulse phase-front and spectral composition across the different layers in the atmosphere. A generic procedure based on evolutionary algorithms to perform the pulse shaping is proposed. In contrast to alternative procedures that would require ab initio modelling and calculations of the propagation constant for the pulse through the atmosphere, the proposed approach is adaptive, compensating for refractive index variations along the column of air between the transmitter and receiver.

Methane in the atmosphere of the transiting hot Neptune GJ436b?

We present an analysis of seven primary transit observations of the hot Neptune GJ436b at 3.6, 4.5, and 8 μm obtained with the Infrared Array Camera on the Spitzer Space Telescope. After correcting for systematic effects, we fitted the light curves using the Markov Chain Monte Carlo technique. Combining these new data with the EPOXI, Hubble Space Telescope, and ground-based V, I, H, and Ks published observations, the range 0.5-10 μm can be covered. Due to the low level of activity of GJ436, the effect of starspots on the combination of transits at different epochs is negligible at the accuracy of the data set. Representative climate models were calculated by using a three-dimensional, pseudospectral general circulation model with idealized thermal forcing. Simulated transit spectra of GJ436b were generated using line-by-line radiative transfer models including the opacities of the molecular species expected to be present in such a planetary atmosphere. A new, ab-initio-calculated, line list for hot ammonia has been used for the first time. The photometric data observed at multiple wavelengths can be interpreted with methane being the dominant absorption after molecular hydrogen, possibly with minor contributions from ammonia, water, and other molecules. No clear evidence of carbon monoxide and carbon dioxide is found from transit photometry. We discuss this result in the light of a recent paper where photochemical disequilibrium is hypothesized to interpret secondary transit photometric data. We show that the emission photometric data are not incompatible with the presence of abundant methane, but further spectroscopic data are desirable to confirm this scenario.

Mode-specific reactivity of CH4 on Pt(110)-(1Ã2): The concerted role of stretch and bend excitation

The state-resolved reaction probability of CH4 on Pt�110-�1�2 was measured as a function of CH4 translational energy for four vibrational eigenstates comprising different amounts of C-H stretch and bend excitation. Mode-specific reactivity is observed both between states from different polyads and between isoenergetic states belonging to the same polyad of CH4. For the stretch/bend combination states, the vibrational efficacy of reaction activation is observed to be higher than for either pure C-H stretching or pure bending states, demonstrating a concerted role of stretch and bend excitation in C-H bond scission. This concerted role, reflected by the nonadditivity of the vibrational efficacies, is consistent with transition state structures found by ab initio calculations and indicates that current dynamical models of CH4 chemisorption neglect an important degree of freedom by including only C-H stretching motion.

Intensities and self-broadening coefficients of the strongest water vapour lines in the 2.7 and 6.25μm absorption bands

Intensities and self-broadening coefficients are presented for about 460 of the strongest water vapour lines in the spectral regions 1400–1840 cm−1 and 3440–3970 cm−1 at room temperature, obtained from rather unique measurements using a 5-mm-path-length cell. The retrieved spectral line parameters are compared with those in the HITRAN database ver. 2008 and 2012 and with recent ab-initio calculations. Both the retrieved intensities and half-widths are on average in reasonable agreement with those in HITRAN-2012. Maximum systematic differences do not exceed 4% for intensities (1600 cm−1 band) and 7% for self-broadening coefficients (3600 cm−1 band). For many lines however significant disagreements were detected with the HITRAN-2012 data, exceeding the average uncertainty of the retrieval. In addition, water vapour line parameters for 5300 cm−1 (1.9 μm) band reported by us in 2005 were also compared with HITRAN-2012, and show average differences of 4–5% for both intensities and half-widths.