Soenke Seifert

Controlled Growth of Platinum Nanoparticles on Strontium Titanate Nanocubes by Atomic Layer Deposition

With an eye toward using surface morphology to enhance heterogeneous catalysis, Pt nanoparticles are grown by atomic layer deposition (ALD) on the surfaces of SrTiO(3) nanocubes. The size, dispersion, and chemical state of the Pt nanoparticles are controlled by the number of ALD growth cycles. The SrTiO(3) nanocubes average 60 nm on a side with {001} faces. The Pt loading increases linearly with Pt ALD cycles to a value of 1.1 x 10(-6) g cm(-2) after five cycles. Scanning electron microscopy images reveal discrete, well-dispersed Pt nanoparticles. Small- and wide-angle X-ray scattering show that the Pt nanoparticle spacing and size increase as the number of ALD cycles increases. X-ray absorption spectroscopy shows a progression from platinum(II) oxide to metallic platinum and a decrease in Pt--O bonding with an increase in Pt--Pt bonding as the number of ALD cycles increases.

Grazing-incidence small angle x-ray scattering studies of phase separation in hafnium silicate films

Grazing-incidence small-angle x-ray scattering (GISAXS) and high-resolution transmission electron microscopy (HRTEM) were used to investigate phase separation in hafnium silicate films after rapid thermal annealing between 700 and 1000 °C. 4-nm-thick Hf–silicate films with 80 and 40 mol % HfO2, respectively, were prepared by metalorganic vapor deposition. Films of the two compositions showed distinctly different phase-separated microstructures, consistent with two limiting cases of microstructural evolution: nucleation/growth and spinodal decomposition. Films with 40 mol % HfO2 phase separated in the amorphous by spinodal decomposition and exhibited a characteristic wavelength in the plane of the film. Decomposition with a wavelength of ∼3 nm could be detected at 800 °C. At 1000 °C the films rapidly demixed with a wavelength of 5 nm. In contrast, films with 80 mol % HfO2 phase separated by nucleation and growth of crystallites, and showed a more random microstructure. The factors determining specific film...

Assembly and organization processes in DNA-directed colloidal crystallization

We present an analysis of the key steps involved in the DNA-directed assembly of nanoparticles into crystallites and polycrystalline aggregates. Additionally, the rate of crystal growth as a function of increased DNA linker length, solution temperature, and self-complementary versus non-self-complementary DNA linker strands (1- versus 2-component systems) has been studied. The data show that the crystals grow via a 3-step process: an initial “random binding” phase resulting in disordered DNA-AuNP aggregates, followed by localized reorganization and subsequent growth of crystalline domain size, where the resulting crystals are well-ordered at all subsequent stages of growth.

Pressure-Jump Small-Angle X-Ray Scattering Detected Kinetics of Staphylococcal Nuclease Folding

The kinetics of chain disruption and collapse of staphylococcal nuclease after positive or negative pressure jumps was monitored by real-time small-angle x-ray scattering under pressure. We used this method to probe the overall conformation of the protein by measuring its radius of gyration and pair-distance-distribution function p(r) which are sensitive to the spatial extent and shape of the particle. At all pressures and temperatures tested, the relaxation profiles were well described by a single exponential function. No fast collapse was observed, indicating that the rate limiting step for chain collapse is the same as that for secondary and tertiary structure formation. Whereas refolding at low pressures occurred in a few seconds, at high pressures the relaxation was quite slow, approximately 1 h, due to a large positive activation volume for the rate-limiting step for chain collapse. A large increase in the system volume upon folding implies significant dehydration of the transition state and a high degree of similarity in terms of the packing density between the native and transition states in this system. This study of the time-dependence of the tertiary structure in pressure-induced folding/unfolding reactions demonstrates that novel information about the nature of protein folding transitions and transition states can be obtained from a combination of small-angle x-ray scattering using high intensity synchrotron radiation with the high pressure perturbation technique.

Design and performance of a ASAXS instrument at the Advanced Photon Source

The SAXS instrument on the high brilliance undulator beam line (ID12, BESSRC-CAT) at APS has been designed to produce high-resolution scattering patterns in the millisecond time domain. This instrument is equipped with a 18 cm x 18 cm position sensitive gas detector and a 15 cm x 15 cm high-resolution position sensitive CCD mosaic detector. A photodiode detector mounted on a 3.7 mm diameter beam stop permits quick alignment of the instrument as well as precise measurement of the transmitted beam intensity. The exposure time with the CCD detector varies from 0.1 to 10 seconds depending on the scattering cross-section of the samples. Techniques to interface ancillary equipment for time-resolved studies and software for faster online analysis of the data have also been developed. We have obtained data on the unfolding of proteins in the millisecond time domain and ASAXS of metallic alloys using this instrument.

Carbon Dioxide Conversion to Methanol over Size-Selected Cu4 Clusters at Low Pressures

The activation of CO2 and its hydrogenation to methanol are of much interest as a way to utilize captured CO2. Here, we investigate the use of size-selected Cu4 clusters supported on Al2O3 thin films for CO2 reduction in the presence of hydrogen. The catalytic activity was measured under near-atmospheric reaction conditions with a low CO2 partial pressure, and the oxidation state of the clusters was investigated by in situ grazing incidence X-ray absorption spectroscopy. The results indicate that size-selected Cu4 clusters are the most active low-pressure catalyst for catalytic CO2 conversion to CH3OH. Density functional theory calculations reveal that Cu4 clusters have a low activation barrier for conversion of CO2 to CH3OH. This study suggests that small Cu clusters may be excellent and efficient catalysts for the recycling of released CO2.

Solution structure of copper ion-induced molecular aggregates of tyrosine melanin.

Melanin, the ubiquitous biological pigment, provides photoprotection by efficient filtration of light and also by its antioxidant behavior. In solutions of synthetic melanin, both optical and antioxidant behavior are affected by the aggregation states of melanin. We have utilized small-angle x-ray and neutron scattering to determine the molecular dimensions of synthetic tyrosine melanin in its unaggregated state in D(2)O and H(2)O to study the structure of melanin aggregates formed in the presence of copper ions at various copper-to-melanin molar ratios. In the absence of copper ions, or at low copper ion concentrations, tyrosine melanin is present in solution as a sheet-like particle with a mean thickness of 12.5 A and a lateral extent of approximately 54 A. At a copper-to-melanin molar ratio of 0.6, melanin aggregates to form long, rod-like structures with a radius of 32 A. At a higher copper ion concentration, with a copper-to-melanin ratio of 1.0, these rod-like structures further aggregate, forming sheet-like structures with a mean thickness of 51 A. A change in the charge of the ionizable groups induced by the addition of copper ions is proposed to account for part of the aggregation. The data also support a model for the copper-induced aggregation of melanin driven by pi stacking assisted by peripheral Cu(2+) complexation. The relationship between our results and a previous hypothesis for reduced cellular damage from bound-to-melanin redox metal ions is also discussed.

High performance aliphatic-heterocyclic benzyl-quaternary ammonium radiation-grafted anion-exchange membranes

Anion-exchange membranes (AEM) containing saturated-heterocyclic benzyl-quaternary ammonium (QA) groups synthesised by radiation-grafting onto poly(ethylene-co-tetrafluoroethylene) (ETFE) films are reported. The relative properties of these AEMs are compared with the benchmark radiation-grafted ETFE-g-poly(vinylbenzyltrimethylammonium) AEM. Two AEMs containing heterocyclic-QA head groups were down-selected with higher relative stabilities in aqueous KOH (1 mol dm−3) at 80 °C (compared to the benchmark): these 100 μm thick (fully hydrated) ETFE-g-poly(vinylbenzyl-N-methylpiperidinium)- and ETFE-g-poly(vinylbenzyl-N-methylpyrrolidinium)-based AEMs had as-synthesised ion-exchange capacities (IEC) of 1.64 and 1.66 mmol g−1, respectively, which reduced to 1.36 mmol dm−3 (ca. 17–18% loss of IEC) after alkali ageing (the benchmark AEM showed 30% loss of IEC under the same conditions). These down-selected AEMs exhibited as-synthesised Cl− ion conductivities of 49 and 52 mS cm−1, respectively, at 90 °C in a 95% relative humidity atmosphere, while the OH− forms exhibited conductivities of 138 and 159 mS cm−1, respectively, at 80 °C in a 95% relative humidity atmosphere. The ETFE-g-poly(vinylbenzyl-N-methylpyrrolidinium)-based AEM produced the highest performances when tested as catalyst coated membranes in H2/O2 alkaline polymer electrolyte fuel cells at 60 °C with PtRu/C anodes, Pt/C cathodes, and a polysulfone ionomer: the 100 μm thick variant (synthesised from 50 μm thick ETFE) yielded peak power densities of 800 and 630 mW cm−2 (with and without 0.1 MPa back pressurisation, respectively), while a 52 μm thick variant (synthesised from 25 μm thick ETFE) yielded 980 and 800 mW cm−2 under the same conditions. From these results, we make the recommendation that developers of AEMs, especially pendent benzyl-QA types, should consider the benzyl-N-methylpyrrolidinium head-group as an improvement to the current de facto benchmark benzyltrimethylammonium head-group.

The Ligand-Free State of the TPP Riboswitch: A Partially Folded RNA Structure

Riboswitches are elements of mRNA that regulate gene expression by undergoing structural changes upon binding of small ligands. Although the structures of several riboswitches have been solved with their ligands bound, the ligand-free states of only a few riboswitches have been characterized. The ligand-free state is as important for the functionality of the riboswitch as the ligand-bound form, but the ligand-free state is often a partially folded structure of the RNA, with conformational heterogeneity that makes it particularly challenging to study. Here, we present models of the ligand-free state of a thiamine pyrophosphate riboswitch that are derived from a combination of complementary experimental and computational modeling approaches. We obtain a global picture of the molecule using small-angle X-ray scattering data and use an RNA structure modeling software, MC-Sym, to fit local structural details to these data on an atomic scale. We have used two different approaches to obtaining these models. Our first approach develops a model of the RNA from the structures of its constituent junction fragments in isolation. The second approach treats the RNA as a single entity, without bias from the structure of its individual constituents. We find that both approaches give similar models for the ligand-free form, but the ligand-bound models differ for the two approaches, and only the models from the second approach agree with the ligand-bound structure known previously from X-ray crystallography. Our models provide a picture of the conformational changes that may occur in the riboswitch upon binding of its ligand. Our results also demonstrate the power of combining experimental small-angle X-ray scattering data with theoretical structure prediction tools in the determination of RNA structures beyond riboswitches.

Solution structures of DEAD-box RNA chaperones reveal conformational changes and nucleic acid tethering by a basic tail

The mitochondrial DEAD-box proteins Mss116p of Saccharomyces cerevisiae and CYT-19 of Neurospora crassa are ATP-dependent helicases that function as general RNA chaperones. The helicase core of each protein precedes a C-terminal extension and a basic tail, whose structural role is unclear. Here we used small-angle X-ray scattering to obtain solution structures of the full-length proteins and a series of deletion mutants. We find that the two core domains have a preferred relative orientation in the open state without substrates, and we visualize the transition to a compact closed state upon binding RNA and adenosine nucleotide. An analysis of complexes with large chimeric oligonucleotides shows that the basic tails of both proteins are attached flexibly, enabling them to bind rigid duplex DNA segments extending from the core in different directions. Our results indicate that the basic tails of DEAD-box proteins contribute to RNA-chaperone activity by binding nonspecifically to large RNA substrates and flexibly tethering the core for the unwinding of neighboring duplexes.