Crystal Structures of Polymerized Fullerides AC60, A=K, Rb, Cs and Alkali-mediated Interactions

Starting from a model of rigid interacting C60 polymer chains on an orthorhombic lattice, we study the mutual orientation of the chains and the stability of the crystalline structures Pmnn and I2/m. We take into account i) van der Waals interactions and electric quadrupole interactions between C60 monomers on different chains as well as ii) interactions of the monomers with the surrounding alkali atoms. The direct interactions i) always lead to an antiferrorotational structure Pmnn with alternate orientation of the C60 chains in planes (001). The interactions ii) with the alkalis consist of two parts: translation-rotation (TR) coupling where the orientations of the chains interact with displacements of the alkalis, and quadrupolar electronic polarizability (ep) coupling, where the electric quadrupoles on the C60 monomers interact with induced quadrupoles due to excited electronic d states of the alkalis. Both interactions ii) lead to an effective orientation-orientation interaction between the C60 chains and always favor the ferrorotational structure I2/m where C60 chains have a same orientation. The structures Pmnn for KC60 and I2/m for Rb- and CsC60 are the result of a competition between the direct interaction i) and the alkali-mediated interactions ii). In Rb- and CsC60 the latter are found to be dominant, the preponderant role being played by the quadrupolar electronic polarizability of the alkali ions.Comment: J.Chem.Phys., in press, 14 pages, 3 figures, 8 table

Isoprene oxidation by the gram-negative model bacterium variovorax sp. WS11

Plant-produced isoprene (2-methyl-1,3-butadiene) represents a significant portion of global volatile organic compound production, equaled only by methane. A metabolic pathway for the degradation of isoprene was first described for the Gram-positive bacterium Rhodococcus sp. AD45, and an alternative model organism has yet to be characterised. Here, we report the characterisation of a novel Gram-negative isoprene-degrading bacterium, Variovorax sp. WS11. Isoprene metabolism in this bacterium involves a plasmid-encoded iso metabolic gene cluster which differs from that found in Rhodococcus sp. AD45 in terms of organisation and regulation. Expression of iso metabolic genes is significantly upregulated by both isoprene and epoxyisoprene. The enzyme responsible for the initial oxidation of isoprene, isoprene monooxygenase, oxidises a wide range of alkene substrates in a manner which is strongly influenced by the presence of alkyl side-chains and differs from other well-characterised soluble diiron monooxygenases according to its response to alkyne inhibitors. This study presents Variovorax sp. WS11 as both a comparative and contrasting model organism for the study of isoprene metabolism in bacteria, aiding our understanding of the conservation of this biochemical pathway across diverse ecological niches

Regulation of plasmid-encoded isoprene metabolism in Rhodococcus, a representative of an important link in the global isoprene cycle

Emissions of biogenic volatile organic compounds (VOCs) form an important part of the global carbon cycle, comprising a significant proportion of net ecosystem productivity. They impact atmospheric chemistry and contribute directly and indirectly to greenhouse gases. Isoprene, emitted largely from plants, comprises one third of total VOCs, yet in contrast to methane, which is released in similar quantities, we know little of its biodegradation. Here, we report the genome of an isoprene degrading isolate, Rhodococcus sp. AD45, and, using mutagenesis shows that a plasmid-encoded soluble di-iron centre isoprene monooxygenase (IsoMO) is essential for isoprene metabolism. Using RNA sequencing (RNAseq) to analyse cells exposed to isoprene or epoxyisoprene in a substrate-switch time-course experiment, we show that transcripts from 22 contiguous genes, including those encoding IsoMO, were highly upregulated, becoming among the most abundant in the cell and comprising over 25% of the entire transcriptome. Analysis of gene transcription in the wild type and an IsoMO-disrupted mutant strain showed that epoxyisoprene, or a subsequent product of isoprene metabolism, rather than isoprene itself, was the inducing molecule. We provide a foundation of molecular data for future research on the environmental biological consumption of this important, climate-active compound

A tight binding model for water

We demonstrate for the first time a tight binding model for water incorporating polarizable anions. A novel aspect is that we adopt a "ground up" approach in that properties of the monomer and dimer only are fitted. Subsequently we make predictions of the structure and properties of hexamer clusters, ice-XI and liquid water. A particular feature, missing in current tight binding and semiempirical hamiltonians, is that we reproduce the almost two-fold increase in molecular dipole moment as clusters are built up towards the limit of bulk liquid. We concentrate on properties of liquid water which are very well rendered in comparison with experiment and published density functional calculations. Finally we comment on the question of the contrasting densities of water and ice which is central to an understanding of the subtleties of the hydrogen bond

Editorial: The Impact of Microorganisms on Consumption of Atmospheric Trace Gases

Editorial on the Research Topic: The Impact of Microorganisms on Consumption of Atmospheric Trace Gase

Extended Huckel theory for bandstructure, chemistry, and transport. II. Silicon

In this second paper, we develop transferable semi-empirical parameters for the technologically important material, silicon, using Extended Huckel Theory (EHT) to calculate its electronic structure. The EHT-parameters areoptimized to experimental target values of the band dispersion of bulk-silicon. We obtain a very good quantitative match to the bandstructure characteristics such as bandedges and effective masses, which are competitive with the values obtained within an $sp^3 d^5 s^*$ orthogonal-tight binding model for silicon. The transferability of the parameters is investigated applying them to different physical and chemical environments by calculating the bandstructure of two reconstructed surfaces with different orientations: Si(100) (2x1) and Si(111) (2x1). The reproduced $\pi$- and $\pi^*$-surface bands agree in part quantitatively with DFT-GW calculations and PES/IPES experiments demonstrating their robustness to environmental changes. We further apply the silicon parameters to describe the 1D band dispersion of a unrelaxed rectangular silicon nanowire (SiNW) and demonstrate the EHT-approach of surface passivation using hydrogen. Our EHT-parameters thus provide a quantitative model of bulk-silicon and silicon-based materials such as contacts and surfaces, which are essential ingredients towards a quantitative quantum transport simulation through silicon-based heterostructures.Comment: 9 pages, 9 figure

Spectral estimation for spatial point patterns

This article determines how to implement spatial spectral analysis of point processes (in two dimensions or more), by establishing the moments of raw spectral summaries of point processes. We establish the first moments of raw direct spectral estimates such as the discrete Fourier transform of a point pattern. These have a number of surprising features that departs from the properties of raw spectral estimates of random fields and time series. As for random fields, the special case of isotropic processes warrants special attention, which we discuss. For time series and random fields white noise plays a special role, mirrored by the Poisson processes in the case of the point process. For random fields bilinear estimators are prevalent in spectral analysis. We discuss how to smooth any bilinear spectral estimator for a point process. We also determine how to taper this bilinear spectral estimator, how to calculate the periodogram, sample the wavenumbers and discuss the correlation of the periodogram. In parts this corresponds to recommending suitable separable as well as isotropic tapers in d dimensions. This, in aggregation, establishes the foundations for spectral analysis of point processes.Comment: 29 pages + 23 pages of supplements, 6 figure

Human cytomegalovirus: taking the strain

In celebrating the 60th anniversary of the first isolation of human cytomegalovirus (HCMV), we reflect on the merits and limitations of the viral strains currently being used to develop urgently needed treatments. HCMV research has been dependent for decades on the high-passage strains AD169 and Towne, heavily exploiting their capacity to replicate efficiently in fibroblasts. However, the genetic integrity of these strains is so severely compromised that great caution needs to be exercised when considering their past and future use. It is now evident that wild-type HCMV strains are not readily propagated in vitro. HCMV mutants are rapidly selected during isolation in fibroblasts, reproducibly affecting gene RL13, the UL128 locus (which includes genes UL128, UL130 and UL131A) and often the UL/b′ region. As a result, the virus becomes less cell associated, altered in tropism and less pathogenic. This problem is not restricted to high-passage strains, as even low-passage strains can harbour biologically significant mutations. Cloning and manipulation of the HCMV genome as a bacterial artificial chromosome (BAC) offers a means of working with stable, genetically defined strains. To this end, the low-passage strain Merlin genome was cloned as a BAC and sequentially repaired to match the viral sequence in the original clinical sample from which Merlin was derived. Restoration of UL128L to wild type was detrimental to growth in fibroblasts, whereas restoration of RL13 impaired growth in all cell types tested. Stable propagation of phenotypically wild-type virus could be achieved only by placing both regions under conditional expression. In addition to the development of these tools, the Merlin transcriptome and proteome have been characterized in unparalleled detail. Although Merlin may be representative of the clinical agent, high-throughput whole-genome deep sequencing studies have highlighted the remarkable high level of interstrain variation present in circulating virus. There is a need to develop systems capable of addressing the significance of this diversity, free from the confounding effects of genetic changes associated with in vitro adaptation. The generation of a set of BAC clones, each containing the genome of a different HCMV strain repaired to match the sequence in the clinical sample, would provide a pathway to address the biological and clinical effects of natural variation in wild-type HCMV

Electronic structure and the glass transition in pnictide and chalcogenide semiconductor alloys. Part I: The formation of the ppσpp\sigma-network

Semiconductor glasses exhibit many unique optical and electronic anomalies. We have put forth a semi-phenomenological scenario (J. Chem. Phys. 132, 044508 (2010)) in which several of these anomalies arise from deep midgap electronic states residing on high-strain regions intrinsic to the activated transport above the glass transition. Here we demonstrate at the molecular level how this scenario is realized in an important class of semiconductor glasses, namely chalcogen and pnictogen containing alloys. Both the glass itself and the intrinsic electronic midgap states emerge as a result of the formation of a network composed of $\sigma$-bonded atomic $p$-orbitals that are only weakly hybridized. Despite a large number of weak bonds, these $pp\sigma$-networks are stable with respect to competing types of bonding, while exhibiting a high degree of structural degeneracy. The stability is rationalized with the help of a hereby proposed structural model, by which $pp\sigma$-networks are symmetry-broken and distorted versions of a high symmetry structure. The latter structure exhibits exact octahedral coordination and is fully covalently-bonded. The present approach provides a microscopic route to a fully consistent description of the electronic and structural excitations in vitreous semiconductors.Comment: 22 pages, 17 figures, revised version, final version to appear in J. Chem. Phy

State-to-State Differential and Relative Integral Cross Sections for Rotationally Inelastic Scattering of H2O by Hydrogen

State-to-state differential cross sections (DCSs) for rotationally inelastic scattering of H2O by H2 have been measured at 71.2 meV (574 cm-1) and 44.8 meV (361 cm-1) collision energy using crossed molecular beams combined with velocity map imaging. A molecular beam containing variable compositions of the (J = 0, 1, 2) rotational states of hydrogen collides with a molecular beam of argon seeded with water vapor that is cooled by supersonic expansion to its lowest para or ortho rotational levels (JKaKc= 000 and 101, respectively). Angular speed distributions of fully specified rotationally excited final states are obtained using velocity map imaging. Relative integral cross sections are obtained by integrating the DCSs taken with the same experimental conditions. Experimental state-specific DCSs are compared with predictions from fully quantum scattering calculations on the most complete H2O-H2 potential energy surface. Comparison of relative total cross sections and state-specific DCSs show excellent agreement with theory in almost all detailsComment: 46 page