A one-pot, water compatible synthesis of pyrimidine nucleobases under plausible prebiotic conditions

Herein, we report a new prebiotically plausible pathway towards a pyrimidine nucleobase in continuous manner. The route involves simultaneous methylation and carbamoylation of cyanoacetylene-derived alpha,beta-unsaturated thioamide with N-methyl-N-nitrosourea (MNU) in aqueous media. This provides S-methylpyrimidinone in one-pot, which can be converted into a variety of 4-substituted pyrimidine nucleobases including cytosine and uracil

Retrieval of vegetative fluid resistance terms for rigid stems using airborne lidar.

Hydraulic resistance of riparian forests is an unknown but important term in flood conveyance modeling. Lidar has proven to be a very important new data source to physically characterize floodplain vegetation. This research outlines a recent campaign that aims to retrieve vegetation fluid resistance terms from airborne laser scanning to parameterize trunk roughness. Information on crown characteristics and vegetation spacing can be extracted for individual trees to aid in the determining of trunk stem morphology. Airborne lidar data were used to explore the potential to characterize some of the prominent tree morphometric properties from natural and planted riparian poplar zones such as tree position, tree height, trunk location, and tree spacing. Allometric equations of tree characteristics extrapolated from ground measurements were used to infer below-canopy morphometric variables. Results are presented from six riparian-forested zones on the Garonne and Allier rivers in southern and central France. The tree detection and crown segmentation (TDCS) method identified individual trees with 85% accuracy, and the TreeVaW method detected trees with 83% accuracy. Tree heights were overall estimated at both river locations with an RMSE error of around 19% for both methods, but crown diameter at the six sites produced large deviations from ground-measured values of above 40% for both methods. Total height-derived trunk diameters using the TDCS method produced the closest roughness coefficient values to the ground-derived roughness coefficients. The stem roughness values produced from this method fell within guideline values

Electron Paramagnetic Resonance Characterization of the Triheme Cytochrome from <i>Geobacter sulfurreducens</i>

Periplasmic cytochrome A (PpcA) is a representative of a broad class of multiheme cytochromes functioning as protein “nanowires” for storage and extracellular transfer of multiple electrons in the δ-proteobacterium <i>Geobacter sulfurreducens</i>. PpcA contains three bis-His coordinated hemes held in a spatial arrangement that is highly conserved among the multiheme cytochromes c₃ and c₇ families, carries low potential hemes, and is notable for having one of the lowest number of amino acids utilized to maintain a characteristic protein fold and site-specific heme function. Low temperature X-band electron paramagnetic resonance (EPR) spectroscopy has been used to characterize the electronic configuration of the Fe­(III) and the ligation mode for each heme. The three sets of EPR signals are assigned to individual hemes in the three-dimensional crystal structure. The relative energy levels of the Fe­(III) 3d orbitals for individual hemes were estimated from the principal <i>g</i>-values. The observed <i>g</i>-tensor anisotropy was used as a probe of electronic structure of each heme, and differences were determined by specifics of axial ligation. To ensure unambiguous assignment of highly anisotropic low-spin (HALS) signal to individual hemes, EPR analyses of iron atom electronic configurations have been supplemented with investigation of porphyrin macrocycles by one-dimensional ¹H NMR chemical shift patterns for the methyl substituents. Within optimized geometry of hemes in PpcA, the magnetic interactions between hemes were found to be minimal, similar to the c₃ family of tetraheme cytochromes

Artificial Hydrogenases Based on Cobaloximes and Heme Oxygenase

International audienceThe insertion of cobaloxime catalysts in the heme-binding pocket of heme oxygenase (HO) yields artificial hydrogenases active for H-2 evolution in neutral aqueous solutions. These novel biohybrids have been purified and characterized by using UV/visible and EPR spectroscopy. These analyses revealed the presence of two distinct binding conformations, thereby providing the cobaloxime with hydrophobic and hydrophilic environments, respectively. Quantum chemical/molecular mechanical docking calculations found open and closed conformations of the binding pocket owing to mobile amino acid residues. HO-based biohybrids incorporating a {Co(dmgH)(2)} (dmgH(2)=dimethylglyoxime) catalytic center displayed up to threefold increased turnover numbers with respect to the cobaloxime alone or to analogous sperm whale myoglobin adducts. This study thus provides a strong basis for further improvement of such biohybrids, using well-designed modifications of the second and outer coordination spheres, through site-directed mutagenesis of the host protein

Protein Delivery of a Ni Catalyst to Photosystem I for Light-Driven Hydrogen Production

The direct conversion of sunlight into fuel is a promising means for the production of storable renewable energy. Herein, we use Nature’s specialized photosynthetic machinery found in the Photosystem I (PSI) protein to drive solar fuel production from a nickel diphosphine molecular catalyst. Upon exposure to visible light, a self-assembled PSI-[Ni­(P₂^PhN₂^Ph)₂]­(BF₄)₂ hybrid generates H₂ at a rate 2 orders of magnitude greater than rates reported for photosensitizer/[Ni­(P₂^PhN₂^Ph)₂]­(BF₄)₂ systems. The protein environment enables photocatalysis at pH 6.3 in completely aqueous conditions. In addition, we have developed a strategy for incorporating the Ni molecular catalyst with the native acceptor protein of PSI, flavodoxin. Photocatalysis experiments with this modified flavodoxin demonstrate a new mechanism for biohybrid creation that involves protein-directed delivery of a molecular catalyst to the reducing side of Photosystem I for light-driven catalysis. This work further establishes strategies for constructing functional, inexpensive, earth-abundant solar fuel-producing PSI hybrids that use light to rapidly produce hydrogen directly from water

The Hydrogen Catalyst Cobaloxime: A Multifrequency EPR and DFT Study of Cobaloxime’s Electronic Structure

Solar fuels research aims to mimic photosynthesis and devise integrated systems that can capture, convert, and store solar energy in the form of high-energy molecular bonds. Molecular hydrogen is generally considered an ideal solar fuel because its combustion is essentially pollution-free. Cobaloximes rank among the most promising earth-abundant catalysts for the reduction of protons to molecular hydrogen. We have used multifrequency EPR spectroscopy at X-band, Q-band, and D-band combined with DFT calculations to reveal electronic structure and establish correlations among the structure, surroundings, and catalytic activity of these complexes. To assess the strength and nature of ligand cobalt interactions, the BF₂-capped cobaloxime, Co­(dmgBF₂)₂, was studied in a variety of different solvents with a range of polarities and stoichiometric amounts of potential ligands to the cobalt ion. This allows the differentiation of labile and strongly coordinating axial ligands for the Co­(II) complex. Labile, or weakly coordinating, ligands such as methanol result in larger <i>g</i>-tensor anisotropy than strongly coordinating ligands such as pyridine. In addition, a coordination number effect is seen for the strongly coordinating ligands with both singly ligated LCo­(dmgBF₂)₂ and doubly ligated L₂Co­(dmgBF₂)₂ . The presence of two strongly coordinating axial ligands leads to the smallest <i>g</i>-tensor anisotropy. The relevance of the strength of the axial ligand(s) to the catalytic efficiency of Co­(dmgBF₂)₂ is discussed. Finally, the influence of molecular oxygen and formation of Co­(III) superoxide radicals LCo­(dmgBF₂)₂O₂^• is studied. The experimental results are compared with a comprehensive set of DFT calculations on Co­(dmgBF₂)₂ model systems with various axial ligands. Comparison with experimental values for the “key” magnetic parameters such as <i>g</i>-tensor and ⁵⁹Co hyperfine coupling tensor allows the determination of the conformation of the axially ligated Co­(dmgBF₂)₂ complexes. The data presented here are vital for understanding the influence of solvent and ligand coordination on the catalytic efficiency of cobaloximes

The Hydrogen Catalyst Cobaloxime: A Multifrequency EPR and DFT Study of Cobaloxime’s Electronic Structure

Solar fuels research aims to mimic photosynthesis and devise integrated systems that can capture, convert, and store solar energy in the form of high-energy molecular bonds. Molecular hydrogen is generally considered an ideal solar fuel because its combustion is essentially pollution-free. Cobaloximes rank among the most promising earth-abundant catalysts for the reduction of protons to molecular hydrogen. We have used multifrequency EPR spectroscopy at X-band, Q-band, and D-band combined with DFT calculations to reveal electronic structure and establish correlations among the structure, surroundings, and catalytic activity of these complexes. To assess the strength and nature of ligand cobalt interactions, the BF₂-capped cobaloxime, Co­(dmgBF₂)₂, was studied in a variety of different solvents with a range of polarities and stoichiometric amounts of potential ligands to the cobalt ion. This allows the differentiation of labile and strongly coordinating axial ligands for the Co­(II) complex. Labile, or weakly coordinating, ligands such as methanol result in larger <i>g</i>-tensor anisotropy than strongly coordinating ligands such as pyridine. In addition, a coordination number effect is seen for the strongly coordinating ligands with both singly ligated LCo­(dmgBF₂)₂ and doubly ligated L₂Co­(dmgBF₂)₂ . The presence of two strongly coordinating axial ligands leads to the smallest <i>g</i>-tensor anisotropy. The relevance of the strength of the axial ligand(s) to the catalytic efficiency of Co­(dmgBF₂)₂ is discussed. Finally, the influence of molecular oxygen and formation of Co­(III) superoxide radicals LCo­(dmgBF₂)₂O₂^• is studied. The experimental results are compared with a comprehensive set of DFT calculations on Co­(dmgBF₂)₂ model systems with various axial ligands. Comparison with experimental values for the “key” magnetic parameters such as <i>g</i>-tensor and ⁵⁹Co hyperfine coupling tensor allows the determination of the conformation of the axially ligated Co­(dmgBF₂)₂ complexes. The data presented here are vital for understanding the influence of solvent and ligand coordination on the catalytic efficiency of cobaloximes

Cobaloxime-based artificial hydrogenases.

International audienceCobaloximes are popular H2 evolution molecular catalysts but have so far mainly been studied in nonaqueous conditions. We show here that they are also valuable for the design of artificial hydrogenases for application in neutral aqueous solutions and report on the preparation of two well-defined biohybrid species via the binding of two cobaloxime moieties, {Co(dmgH)2} and {Co(dmgBF2)2} (dmgH2 = dimethylglyoxime), to apo Sperm-whale myoglobin (SwMb). All spectroscopic data confirm that the cobaloxime moieties are inserted within the binding pocket of the SwMb protein and are coordinated to a histidine residue in the axial position of the cobalt complex, resulting in thermodynamically stable complexes. Quantum chemical/molecular mechanical docking calculations indicated a coordination preference for His93 over the other histidine residue (His64) present in the vicinity. Interestingly, the redox activity of the cobalt centers is retained in both biohybrids, which provides them with the catalytic activity for H2 evolution in near-neutral aqueous conditions

Cobaloxime-Based Artificial Hydrogenases

Cobaloximes are popular H₂ evolution molecular catalysts but have so far mainly been studied in nonaqueous conditions. We show here that they are also valuable for the design of artificial hydrogenases for application in neutral aqueous solutions and report on the preparation of two well-defined biohybrid species via the binding of two cobaloxime moieties, {Co­(dmgH)₂} and {Co­(dmgBF₂)₂} (dmgH₂ = dimethylglyoxime), to apo <i>Sperm-whale</i> myoglobin (<i>Sw</i>Mb). All spectroscopic data confirm that the cobaloxime moieties are inserted within the binding pocket of the <i>Sw</i>Mb protein and are coordinated to a histidine residue in the axial position of the cobalt complex, resulting in thermodynamically stable complexes. Quantum chemical/molecular mechanical docking calculations indicated a coordination preference for His93 over the other histidine residue (His64) present in the vicinity. Interestingly, the redox activity of the cobalt centers is retained in both biohybrids, which provides them with the catalytic activity for H₂ evolution in near-neutral aqueous conditions