Exceptional Hydrogen Diffusion Rate over Ru Nanoparticle-Doped Polar MgO(111) Surface.

Hydrogen (H) conductivity on oxide-based materials is crucially important in fuel cells and related catalysis. Here, this work measures the diffusion rate of H generated from Ru nanoparticles loaded on polar MgO(111) facet particles under H2 at elevated temperatures without moisture and compares it to conventional nonpolar MgO(110) for the first time by in situ quasielastic neutron scattering (QENS). The QENS reveals an exceptional diffusion rate on the polar facet via a proton (H+ ) hopping mechanism, which is an order of magnitude superior to that of typical H+ -conducting oxides. This work attributes this to the unique atomic arrangement of alternate layers of Mg cations and O anions of the polar MgO(111) where the strong electrostatic field of terminal oxygen anions facilitates protonic migration with a lower degree of local covalency.

Spectroscopic Signatures of Hydrogen-Bonding Motifs in Protonic Ionic Liquid Systems: Insights from Diethylammonium Nitrate in the Solid State.

Diethylammonium nitrate, [N0 0 2 2][NO3], and its perdeuterated analogue, [N D D 2 2] [NO3], were structurally characterized and studied by infrared, Raman, and inelastic neutron scattering (INS) spectroscopy. Using these experimental data along with state-of-the-art computational materials modeling, we report unambiguous spectroscopic signatures of hydrogen-bonding interactions between the two counterions. An exhaustive assignment of the spectral features observed with each technique has been provided, and a number of distinct modes related to NH···O dynamics have been identified. We put a particular emphasis on a detailed interpretation of the high-resolution, broadband INS experiments. In particular, the INS data highlight the importance of conformational degrees of freedom within the alkyl chains, a ubiquitous feature of ionic liquid (IL) systems. These findings also enable an in-depth physicochemical understanding of protonic IL systems, a first and necessary step to the tailoring of hydrogen-bonding networks in this important class of materials.

Adsorbed States of Hydrogen on Platinum: A New Perspective.

The interaction of hydrogen with platinum is enormously important in many areas of catalysis. The most significant of these are in polymer electrolyte membrane fuel cells (PEMFC), in which carbon-supported platinum is used to dissociate hydrogen gas at the anode. The nature of adsorbed hydrogen on platinum has been studied for many years on single-crystal surfaces, on high-surface area-platinum metal (Raney platinum and platinum black), and on supported catalysts. Many forms of vibrational spectroscopy have played a key role in these studies, however, there is still no clear consensus as to the assignment of the spectra. In this work, ab initio molecular dynamics (AIMD) and lattice dynamics were used to study a 1.1 nm nanoparticle, Pt44 H80 . The results were compared to new inelastic neutron scattering spectra of hydrogen on platinum black and of a carbon-supported platinum fuel cell catalyst and an assignment scheme that rationalises all previous data is proposed.

Structural dynamics of a metal-organic framework induced by CO2 migration in its non-uniform porous structure.

Stimuli-responsive behaviors of flexible metal-organic frameworks (MOFs) make these materials promising in a wide variety of applications such as gas separation, drug delivery, and molecular sensing. Considerable efforts have been made over the last decade to understand the structural changes of flexible MOFs in response to external stimuli. Uniform pore deformation has been used as the general description. However, recent advances in synthesizing MOFs with non-uniform porous structures, i.e. with multiple types of pores which vary in size, shape, and environment, challenge the adequacy of this description. Here, we demonstrate that the CO2-adsorption-stimulated structural change of a flexible MOF, ZIF-7, is induced by CO2 migration in its non-uniform porous structure rather than by the proactive opening of one type of its guest-hosting pores. Structural dynamics induced by guest migration in non-uniform porous structures is rare among the enormous number of MOFs discovered and detailed characterization is very limited in the literature. The concept presented in this work provides new insights into MOF flexibility.

Mechanism of enhancement of ferroelectricity of croconic acid with temperature.

A detailed study of the thermal behaviour of atomic motions in the organic ferroelectric croconic acid is presented in the temperature range 5-300 K. Using high-resolution inelastic neutron scattering and first-principles electronic-structure calculations within the framework of density functional theory and a quasiharmonic phonon description of the material, we find that the frequencies of the well defined doublet in inelastic neutron scattering spectra associated with out-of-plane motions of hydrogen-bonded protons decrease monotonically with temperature indicating weakening of these bonding motifs and enhancement of proton motions. Theoretical mean-square displacements for these proton motions are within 5% of experimental values. A detailed analysis of this observable shows that it is unlikely that there is a facile proton transfer along the direction of ferroelectric polarization in the absence of an applied electric field. Calculations predict constrained thermal motion of proton along crystallographic lattice direction c retaining the hydrogen bond motif of the crystal at high temperature. Using the Berry-phase method, we have also calculated the spontaneous polarization of temperature dependent cell structures, and find that our computational model provides a satisfactory description of the anomalous and so far unexplained rise in bulk electric polarization with temperature. Correlating the thermal motion induced lattice strain with temperature dependent spontaneous polarizations, we conclude that increasing thermal strain with temperatures combined with constrained thermal motion along the hydrogen bond motif are responsible of this increase in ferroelectricity at high temperature.

Detecting Molecular Rotational Dynamics Complementing the Low-Frequency Terahertz Vibrations in a Zirconium-Based Metal-Organic Framework.

We show clear experimental evidence of cooperative terahertz (THz) dynamics observed below 3 THz (∼100 cm^{-1}), for a low-symmetry Zr-based metal-organic framework structure, termed MIL-140A [ZrO(O_{2}C-C_{6}H_{4}-CO_{2})]. Utilizing a combination of high-resolution inelastic neutron scattering and synchrotron radiation far-infrared spectroscopy, we measured low-energy vibrations originating from the hindered rotations of organic linkers, whose energy barriers and detailed dynamics have been elucidated via ab initio density functional theory calculations. The complex pore architecture caused by the THz rotations has been characterized. We discovered an array of soft modes with trampolinelike motions, which could potentially be the source of anomalous mechanical phenomena such as negative thermal expansion. Our results demonstrate coordinated shear dynamics (2.47 THz), a mechanism which we have shown to destabilize the framework structure, in the exact crystallographic direction of the minimum shear modulus (G_{min}).

Heads or tails: how do chemically substituted fullerenes melt?

We address the question as to whether the melting of chemically substituted fullerenes is driven by the dynamics of the fullerene moiety (the head) or the substituted sub-unit (the tail). To this end, we have performed quasielastic neutron-scattering experiments and classical molecular-dynamics simulations as a function of temperature on the prototypical fullerene derivative phenyl-C61-butyric acid methyl ester. To enable a direct and quantitative comparison between experimental and simulation data, dynamic structure factors for the latter have been calculated from atomic trajectories and further convolved with the known instrument response. A detailed analysis of the energy- and momentum-transfer dependence of this observable in the quasielastic regime shows that melting is entirely driven by temperature-activated tail motions. We also provide quantitative estimates of the activation energy for this process as the material first enters a plastic-crystalline phase, followed by the emergence of a genuine liquid at higher temperatures.

Computation of diffuse scattering arising from one-phonon excitations in a neutron time-of-flight single-crystal Laue diffraction experiment.

Direct phonon excitation in a neutron time-of-flight single-crystal Laue diffraction experiment has been observed in a single crystal of NaCl. At room temperature both phonon emission and excitation leave characteristic features in the diffuse scattering and these are well reproduced using abinitio phonons from density functional theory (DFT). A measurement at 20 K illustrates the effect of thermal population of the phonons, leaving the features corresponding to phonon excitation and strongly suppressing the phonon annihilation. A recipe is given to compute these effects combining DFT results with the geometry of the neutron experiment.

Hydrogen-bond structure and anharmonicity in croconic acid.

First-principles molecular dynamics simulations and neutron-scattering experiments have been employed to investigate the structure and underlying vibrational motions in croconic acid as a function of temperature over the range 4-400 K. Calculated hydroxyl-bond distances were within 4% of the experimentally determined bond lengths. Temperature-dependent structures have been explored using large-scale molecular dynamics simulations. From the calculated radial distribution functions, it is found that medium-range order associated with O···H and O···O correlations are affected by an increase in temperature, yet the characteristic long-range layered structure of this material remains unaltered. Hydrogen-bond anharmonicity has been assessed from the molecular dynamics simulations, showing a red shift of ca. 50 cm(-1) of the O-H stretch frequency relative to quasi-harmonic results. This shift shows the importance of anharmonic corrections on hydrogen bonds in solid croconic acid.

High-redundancy draft sequencing of 15 clinical and environmental Burkholderia strains.

The Gram-negative Burkholderia genus includes several species of intracellular bacterial pathogens that pose substantial risk to humans. In this study, we have generated draft genome sequences of 15 strains of B. oklahomensis, B. pseudomallei, B. thailandensis, and B. ubonensis to an average sequence read coverage of 25- to 40-fold.

Electronic structure of Lewis acid sites on high surface area aluminium fluorides: a combined XPS and ab initio investigation.

High surface area (HS) A1F3 samples have been examined by X-ray photoelectron spectroscopy (XPS). The experimentally observed binding energy (BE) shifts were analysed by reference to core level BEs obtained from ab initio total energy calculations on a range of different, clean and hydroxylated alpha- and beta-A1F3 surfaces. Examination of the two components visible in the A1 2p emission indicates that surface A13+ sites can, depending on the local geometric structure, contribute to both a high BE peak at 77.0 eV and a low BE peak at 76.1 eV. Consequently, the areas under the peaks do not quantitatively correlate with surface area or Lewis acidity. However, a significant correlation between the number of surface A1 centres with dangling F or OH groups and the appearance of an A1 2p emission component at a BE lower than in the alpha-A1F3 bulk is predicted. The experimental F 1s emission data indicate that dangling F species are essentially absent. Examination of the O 1s emission suggests that HS A1F3 handled at room temperature under any practical laboratory conditions, including glovebox environments, probably contains intrinsically a significant amount of OH groups and adsorbed water, which results in the covering of A1F3 surfaces by dangling or bridging OH groups. These Bronsted acid species must be removed by treatment at higher temperature before HS A1F3 reagents can fully develop their Lewis acidity.

Differential transcriptional responses between the interferon-gamma-induction and iron-limitation models of persistence for Chlamydia pneumoniae.

BACKGROUND AND PURPOSE: Chlamydia spp. are important pathogens of humans and animals that cause a wide range of acute and chronic infections. A persistence model has been developed in which Chlamydia spp. do not complete their developmental cycle, have significantly reduced infectivity for new host cells, and exhibit abnormal inclusion and reticulate body morphology. This study was performed to compare the interferon-gamma (IFN-gamma) induction and iron-limitation models of persistence for Chlamydia spp. to investigate the common and unique transcriptional pathways involved. METHODS: A quantitative real time-polymerase chain reaction approach was used to compare the IFN-gamma induction and iron-limitation models of Chlamydia pneumoniae persistence at the transcriptional level by analyzing selected genes in each of 5 distinct, functionally relevant subcategories. RESULTS: The models showed minimal evidence of a general transcriptional stress response in persistence, with only 1 of the 7 genes analyzed in the IFN-gamma induction model (htrA) and 4 of the genes in the iron-limitation model (htrA, clpB, clpP1, ahpC) showing increased mRNA levels. Both models showed similar responses in relation to the genes associated with lack of reticulate body to elementary body conversion (ctcB, lcrH1, and hctB levels were all unchanged or downregulated). The models also showed similar responses to the key cell wall/envelope genes, ompA, omcB, and crpA, exhibiting lower mRNA levels in both models. CONCLUSIONS: These data show that several key transcriptional pathways (lack of late developmental cycle completion, key cell wall components) respond similarly between the models. However, other pathways appear to differ depending on the persistence-inducing mechanism. This result suggests that Chlamydia spp. have evolved more than 1 mechanism to respond to different persistence-inducing conditions, but ultimately the pathways probably converge through a common persistence regulon.

Identification of Bacillus anthracis spore component antigens conserved across diverse Bacillus cereus sensu lato strains.

We sought to identify proteins in the Bacillus anthracis spore, conserved in other strains of the closely related Bacillus cereus group, that elicit an immune response in mammals. Two high throughput approaches were used. First, an in silico screening identified 200 conserved putative B. anthracis spore components. A total of 192 of those candidate genes were expressed and purified in vitro, 75 of which reacted with the rabbit immune sera generated against B. anthracis spores. The second approach was to screen for cross-reacting antigens in the spore proteome of 10 diverse B. cereus group strains. Two-dimensional electrophoresis resolved more than 200 protein spots in each spore preparation. About 72% of the protein spots were found in all the strains. 18 of these conserved proteins reacted against anti-B. anthracis spore rabbit immune sera, two of which (alanine racemase, Dal-1 and the methionine transporter, MetN) overlapped the set of proteins identified using the in silico screen. A conserved repeat domain protein (Crd) was the most immunoreactive protein found broadly across B. cereus sensu lato strains. We have established an approach for finding conserved targets across a species using population genomics and proteomics. The results of these screens suggest the possibility of a multiepitope antigen for broad host range diagnostics or therapeutics against Bacillus spore infection.

Evidence for persistent Chlamydia pneumoniae infection of human coronary atheromas.

To date, structures representing developmental stages of Chlamydia pneumoniae, especially persistent forms of this intracellular bacteria, have not been described in human atherosclerotic tissues using specific antibody labeling and transmission electron microscopy. Staining of atherosclerotic tissue from five patients seeking heart transplantation with gold-labeled antibodies specific for up-regulated chlamydial heat shock proteins, GroEL and GroES, and visualisation via transmission electron microscopy revealed intracellular, atypical, round to oval structures of variable diameter. These structures resembled reticulate bodies of Chlamydia, were surrounded by membranes and were located within smooth muscle cells, macrophages or fibroblasts. By using double immunogold electron microscopy technique (GroEL and GroES in combination with chlamydial LPS/MOMP antibodies), we demonstrated these structures were of chlamydial origin. In the current study, we demonstrated the presence of aberrant bodies of C. pneumoniae in vivo in archival coronary atheromatous heart tissues by the immunogold electron microscopy technique.

Vibrational analysis study of aluminum trifluoride phases.

The vibrational modes of three solid AlF3 phases (alpha, beta, and amorphous high surface area AlF3) are investigated. Calculations have been performed using hybrid exchange correlation functionals to determine the equilibrium geometries and Gamma-point phonon frequencies for the alpha-AlF3 and beta-AlF3 phases. The calculated optical modes are in excellent agreement with experiment. The IR absorption of the amorphous, glasslike high surface area (HS)-AlF3 is also discussed. Deconvolution of the broad envelope of IR stretches and bending vibrations identifies the components of the observed broad band. From the IR vibrational spectrum it has been shown that both short-range and medium-range disorder are present within HS-AlF3. Structural phase transitions are identified by their phase transition temperature Tc, measured by thermal analysis.

Tissue MicroArray (TMA) analysis of normal and persistent Chlamydophila pneumoniae infection.

BACKGROUND: Chlamydophila pneumoniae infection has been implicated as a potential risk factor for atherosclerosis, however the mechanism leading to persistent infection and its role in the disease process remains to be elucidated. METHODS: We validated the use of tissue microarray (TMA) technology, in combination with immunohistochemistry (IHC), to test antibodies (GroEL, GroES, GspD, Ndk and Pyk) raised against differentially expressed proteins under an interferon-gamma (IFN-gamma) induced model of chlamydial persistence. RESULTS: In the cell pellet array, we were able to identify differences in protein expression patterns between untreated and IFN-gamma treated samples. Typical, large chlamydial inclusions could be observed in the untreated samples with all antibodies, whereas the number of inclusions were decreased and were smaller and atypical in shape in the IFN-gamma treated samples. The staining results obtained with the TMA method were generally similar to the changes observed between normal and IFN-gamma persistence using proteomic analysis. Subsequently, it was shown in a second TMA including archival atheromatous heart tissues from 12 patients undergoing heart transplantation, that GroEL, GroES, GspD and Pyk were expressed in atheromatous heart tissue specimens as well, and were detectable morphologically within lesions by IHC. CONCLUSION: TMA technology proved useful in documenting functional proteomics data with the morphologic distribution of GroEL, GroES, GspD, Ndk and Pyk within formalin-fixed, paraffin-embedded cell pellets and tissues from patients with severe coronary atherosclerosis. The antibodies GroEL and GroES, which were upregulated under persistence in proteomic analysis, displayed positive reaction in atheromatous heart tissue from 10 out of 12 patients. These may be useful markers for the detection of persistent infection in vitro and in vivo.

Identification of Chlamydia pneumoniae proteins in the transition from reticulate to elementary body formation.

Chlamydia pneumoniae is an important human respiratory pathogen that is responsible for an estimated 10% of community-acquired pneumonia and 5% of bronchitis and sinusitis cases. We examined changes in global protein expression profiles associated with the redifferentiation of reticulate body (RB) to elementary body (EB) as C. pneumoniae cells progressed from 24 to 48 h postinfection in HEp2 cells. Proteins corresponding to those showing the greatest changes in abundance in the beginning of the RB to EB transition were then identified from purified EBs. Among the 300 spots recognized, 35 proteins that were expressed at sufficiently high levels were identified by mass spectrometry. We identified C. pneumoniae proteins that showed more than 2-fold increases in abundance in the early stages of RB to EB transition, including several associated with amino acid and cofactor biosynthesis (Ndk, TrxA, Adk, PyrH, and BirA), maintenance of cytoplasmic protein function (GroEL/ES, DnaK, DksA, GrpE, HtrA, ClpP, ClpB, and Map), modification of the bacterial cell surface (CrpA, OmpA, and OmcB), energy metabolism (Tal and Pyk), and the putative transcriptional regulator TctD. This study identified C. pneumoniae proteins involved in the process of redifferentiation into mature, infective EBs and indicates bacterial metabolic pathways that may be involved in this transition. The proteins involved in RB to EB transition are key to C. pneumoniae infection and are perhaps suitable targets for therapeutic intervention.