EPR spectroscopy of iron- and nickel-doped [ZnAl]-layered double hydroxides: modeling active sites in heterogeneous water oxidation catalysts

Iron-doped nickel layered double hydroxides (LDHs) are among the most active heterogeneous water oxidation catalysts. Due to inter-spin interactions, however, the high density of magnetic centers results in line-broadening in magnetic resonance spectra. As a result, gaining atomic-level insight into the catalytic mechanism via electron paramagnetic resonance (EPR) is not generally possible. To circumvent spin-spin broadening, iron and nickel atoms were doped into non-magnetic [ZnAl]-LDH materials and the coordination environments of the isolated Fe(III) and Ni(II) sites were characterized. Multifrequency EPR spectroscopy identified two distinct Fe(III) sites (S = 5/2) in [Fe:ZnAl]-LDH. Changes in zero field splitting (ZFS) were induced by dehydration of the material, revealing that one of the Fe(III) sites is solvent-exposed (i.e. at an edge, corner, or defect site). These solvent-exposed sites feature an axial ZFS of 0.21 cm⁻¹ when hydrated. The ZFS increases dramatically upon dehydration (to -1.5 cm⁻¹), owing to lower symmetry and a decrease in the coordination number of iron. The ZFS of the other (“inert”) Fe(III) site maintains an axial ZFS of 0.19-0.20 cm⁻¹ under both hydrated and dehydrated conditions. We observed a similar effect in [Ni:ZnAl]-LDH materials; notably, Ni(II) (S = 1) atoms displayed a single, small ZFS (±0.30 cm⁻¹) in hydrated material, whereas two distinct Ni(II) ZFS values (±0.30 and ±1.1 cm⁻¹) were observed in the dehydrated samples. Although the magnetically-dilute materials were not active catalysts, the identification of model sites in which the coordination environments of iron and nickel were particularly labile (e.g. by simple vacuum drying) is an important step towards identifying sites in which the coordination number may drop spontaneously in water, a probable mechanism of water oxidation in functional materials

EPR spectroscopy of iron- and nickel-doped [ZnAl]-layered double hydroxides: modeling active sites in heterogeneous water oxidation catalysts

Iron-doped nickel layered double hydroxides (LDHs) are among the most active heterogeneous water oxidation catalysts. Due to inter-spin interactions, however, the high density of magnetic centers results in line-broadening in magnetic resonance spectra. As a result, gaining atomic-level insight into the catalytic mechanism via electron paramagnetic resonance (EPR) is not generally possible. To circumvent spin-spin broadening, iron and nickel atoms were doped into non-magnetic [ZnAl]-LDH materials and the coordination environments of the isolated Fe(III) and Ni(II) sites were characterized. Multifrequency EPR spectroscopy identified two distinct Fe(III) sites (S = 5/2) in [Fe:ZnAl]-LDH. Changes in zero field splitting (ZFS) were induced by dehydration of the material, revealing that one of the Fe(III) sites is solvent-exposed (i.e. at an edge, corner, or defect site). These solvent-exposed sites feature an axial ZFS of 0.21 cm⁻¹ when hydrated. The ZFS increases dramatically upon dehydration (to -1.5 cm⁻¹), owing to lower symmetry and a decrease in the coordination number of iron. The ZFS of the other (“inert”) Fe(III) site maintains an axial ZFS of 0.19-0.20 cm⁻¹ under both hydrated and dehydrated conditions. We observed a similar effect in [Ni:ZnAl]-LDH materials; notably, Ni(II) (S = 1) atoms displayed a single, small ZFS (±0.30 cm⁻¹) in hydrated material, whereas two distinct Ni(II) ZFS values (±0.30 and ±1.1 cm⁻¹) were observed in the dehydrated samples. Although the magnetically-dilute materials were not active catalysts, the identification of model sites in which the coordination environments of iron and nickel were particularly labile (e.g. by simple vacuum drying) is an important step towards identifying sites in which the coordination number may drop spontaneously in water, a probable mechanism of water oxidation in functional materials

A destabilized bacterial luciferase for dynamic gene expression studies

Fusions of genetic regulatory elements with reporter genes have long been used as tools for monitoring gene expression and have become a major component in synthetic gene circuit implementation. A major limitation of many of these systems is the relatively long half-life of the reporter protein(s), which prevents monitoring both the initiation and the termination of transcription in real-time. Furthermore, when used as components in synthetic gene circuits, the long time constants associated with reporter protein decay may significantly degrade circuit performance. In this study, short half-life variants of LuxA and LuxB from Photorhabdus luminescens were constructed in Escherichia coli by inclusion of an 11-amino acid carboxy-terminal tag that is recognized by endogenous tail-specific proteases. Results indicated that the addition of the C-terminal tag affected the functional half-life of the holoenzyme when the tag was added to luxA or to both luxA and luxB, but modification of luxB alone did not have a significant effect. In addition, it was also found that alteration of the terminal three amino acid residues of the carboxy-terminal tag fused to LuxA generated variants with half-lives of intermediate length in a manner similar to that reported for GFP. This report is the first instance of the C-terminal tagging approach for the regulation of protein half-life to be applied to an enzyme or monomer of a multi-subunit enzyme complex and will extend the utility of the bacterial luciferase reporter genes for the monitoring of dynamic changes in gene expression

Grand Challenges for Biological and Environmental Research: A Long-Term Vision

The interactions and feedbacks among plants, animals, microbes, humans, and the environment ultimately form the world in which we live. This world is now facing challenges from a growing and increasingly affluent human population whose numbers and lifestyles are driving ever greater energy demand and impacting climate. These and other contributing factors will make energy and climate sustainability extremely difficult to achieve over the 20-year time horizon that is the focus of this report. Despite these severe challenges, there is optimism that deeper understanding of our environment will enable us to mitigate detrimental effects, while also harnessing biological and climate systems to ensure a sustainable energy future. This effort is advanced by scientific inquiries in the fields of atmospheric chemistry and physics, biology, ecology, and subsurface science - all made possible by computing. The Office of Biological and Environmental Research (BER) within the Department of Energy's (DOE) Office of Science has a long history of bringing together researchers from different disciplines to address critical national needs in determining the biological and environmental impacts of energy production and use, characterizing the interplay of climate and energy, and collaborating with other agencies and DOE programs to improve the world's most powerful climate models. BER science focuses on three distinct areas: (1) What are the roles of Earth system components (atmosphere, land, oceans, sea ice, and the biosphere) in determining climate? (2) How is the information stored in a genome translated into microbial, plant, and ecosystem processes that influence biofuel production, climate feedbacks, and the natural cycling of carbon? (3) What are the biological, geochemical, and physical forces that govern the behavior of Earth's subsurface environment? Ultimately, the goal of BER science is to support experimentation and modeling that can reliably predict the outcomes and behaviors of complex biological and environmental systems, leading to robust solutions for DOE missions and strategic goals. In March 2010, the Biological and Environmental Research Advisory Committee held the Grand Challenges for Biological and Environmental Research: A Long-Term Vision workshop to identify scientific opportunities and grand challenges for BER science in the coming decades and to develop an overall strategy for drafting a long-term vision for BER. Key workshop goals included: (1) Identifying the greatest scientific challenges in biology, climate, and the environment that DOE will face over a 20-year time horizon. (2) Describing how BER should be positioned to address those challenges. (3) Determining the new and innovative tools needed to advance BER science. (4) Suggesting how the workforce of the future should be trained in integrative system science. This report lays out grand research challenges for BER - in biological systems, climate, energy sustainability, computing, and education and workforce training - that can put society on a path to achieve the scientific evidence and predictive understanding needed to inform decision making and planning to address future energy needs, climate change, water availability, and land use

Frustrated tunnelling ionization during strong-field fragmentation of D3+

We reveal surprisingly high kinetic energy release in the intense-field fragmentation of D[subscript 3][superscript +] to D[superscript +] + D[superscript +] + D with 10[superscript 16]Wcm[superscript −2], 790 nm, 40 fs (and 7 fs) laser pulses. This feature strongly mimics the behaviour of the D[superscript +] + D[superscript +] + D[superscript +] channel. From the experimental evidence, we conclude that the origin of the feature is due to frustrated tunnelling ionization, the first observation of this mechanism in a polyatomic system. Furthermore, we unravel evidence of frustrated tunnelling ionization in dissociation, both two-body breakup to D + D[subscript 2][superscript +] and D[superscript +] + D[subscript 2], and three-body breakup to D[superscript +] + D + D

Quantification of Nitrosomonas oligotropha and Nitrospira spp. Using Competitive Polymerase Chain Reaction in Bench-Scale Wastewater Treatment Reactors Operating at Different Solids Retention Times

The effect of solids retention time (SRT) on ammonia and nitrite‐oxidizing bacteria was measured by Nitrosomonas oligotropha‐like ammonia monooxygenase A and Nitrospira 16S rDNA competitive polymerase chain reaction assays in a complete‐mix, bench‐scale, activated‐sludge system. During steady‐state operation, nitrification was complete in the 20‐ and 10‐day SRT reactors, nearly complete in the 5‐day SRT reactor, and incomplete in the 2‐day SRT reactor (76% ammonia oxidation and 85% nitrite oxidation). Total microbes, measured by dot‐blot hybridizations, ranged from 3 × 1011 to 3 × 1012 cells/L, and increased with increasing SRTs. The concentration of the ammonia‐oxidizer N. oligotropha dropped 100‐fold from the 20‐day SRT (5 × 109 cells/L) to the 2‐day SRT (≤4 × 107 cells/L). Thus, N. oligotropha became a much smaller fraction of the total biomass in the poorly performing 2‐day SRT reactor. The concentration of Nitrospira cells also decreased (10‐fold) as the SRT was reduced from 20 days to 2 days. However, the number of Nitrospira cells was always greater than the number of N. oligotropha cells measured in each reactor (10‐ to 60‐fold). While Nitrospira comprised 1 to 2% of the biomass, N. oligotropha represented only 0.04 to 0.27% of the total population. This low percentage suggests that N. oligotropha was not a dominant ammonia oxidizer in the bench‐scale systems.Fil: Dionisi, Hebe Monica. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Nacional Patagónico; ArgentinaFil: Layton, A. C.. University of Tennessee; Estados UnidosFil: Robinson, K. G.. University of Tennessee; Estados UnidosFil: Brown, J. R.. University of Tennessee; Estados UnidosFil: Gregory, I. R.. University of Tennessee; Estados UnidosFil: Parker, J. J.. University of Tennessee; Estados UnidosFil: Sayler, G. S.. University of Tennessee; Estados Unido

Dissociative Ligand Exchange at Identical Molecular and Carbon Nanoparticle Binding Sites

Department of Energy (DOE)National Institutes of Health (NIH)National Science Foundation (NSF

Trapping and Electron Paramagnetic Resonance Characterization of the 5'dAdo• Radical in a Radical S-Adenosyl Methionine Enzyme Reaction with a Non-Native Substrate.

S-Adenosyl methionine (SAM) is employed as a [4Fe-4S]-bound cofactor in the superfamily of radical SAM (rSAM) enzymes, in which one-electron reduction of the [4Fe-4S]-SAM moiety leads to homolytic cleavage of the S-adenosyl methionine to generate the 5'-deoxyadenosyl radical (5'dAdo•), a potent H-atom abstractor. HydG, a member of this rSAM family, uses the 5'dAdo• radical to lyse its substrate, tyrosine, producing CO and CN that bind to a unique Fe site of a second HydG Fe-S cluster, ultimately producing a mononuclear organometallic Fe-l-cysteine-(CO)2CN complex as an intermediate in the bioassembly of the catalytic H-cluster of [Fe-Fe] hydrogenase. Here we report the use of non-native tyrosine substrate analogues to further probe the initial radical chemistry of HydG. One such non-native substrate is 4-hydroxy phenyl propanoic acid (HPPA) which lacks the amino group of tyrosine, replacing the CαH-NH2 with a CH2 at the C2 position. Electron paramagnetic resonance (EPR) studies show the generation of a strong and relatively stable radical in the HydG reaction with natural abundance and 13C2-HPPA, with appreciable spin density localized at C2. These results led us to try parallel experiments with the more oxidized non-native substrate coumaric acid, which has a C2=C3 alkene substitution relative to HPPA's single bond. Interestingly, the HydG reaction with the cis-p-coumaric acid isomer led to the trapping of a new radical EPR signal, and EPR studies using cis-p-coumaric acid along with isotopically labeled SAM reveal that we have for the first time trapped and characterized the 5'dAdo• radical in an actual rSAM enzyme reaction, here by using this specific non-native substrate cis-p-coumaric acid. Density functional theory energetics calculations show that the cis-p-coumaric acid has approximately the same C-H bond dissociation free energy as 5'dAdo•, providing a possible explanation for our ability to trap an appreciable fraction of 5'dAdo• in this specific rSAM reaction. The radical's EPR line shape and its changes with SAM isotopic substitution are nearly identical to those of a 5'dAdo• radical recently generated by cryophotolysis of a prereduced [4Fe-4S]-SAM center in another rSAM enzyme, pyruvate formate-lyase activating enzyme, further supporting our assignment that we have indeed trapped and characterized the 5'dAdo• radical in a radical SAM enzymatic reaction by appropriate tuning of the relative radical free energies via the judicious selection of a non-native substrate