Rhodium bis(quinolinyl)benzene complexes for methane activation and functionalization.

A series of rhodium(III) bis(quinolinyl)benzene (bisq(x)) complexes was studied as candidates for the homogeneous partial oxidation of methane. Density functional theory (DFT) (M06 with Poisson continuum solvation) was used to investigate a variety of (bisq(x)) ligand candidates involving different functional groups to determine the impact on Rh(III)(bisq(x))-catalyzed methane functionalization. The free energy activation barriers for methane C-H activation and Rh-methyl functionalization at 298 K and 498 K were determined. DFT studies predict that the best candidate for catalytic methane functionalization is Rh(III) coordinated to unsubstituted bis(quinolinyl)benzene (bisq). Support is also found for the prediction that the η(2)-benzene coordination mode of (bisq(x)) ligands on Rh encourages methyl group functionalization by serving as an effective leaving group for SN2 and SR2 attack.

Long-range C-H bond activation by Rh(III)-carboxylates.

Traditional C-H bond activation by a concerted metalation-deprotonation (CMD) mechanism involves precoordination of the C-H bond followed by deprotonation from an internal base. Reported herein is a "through-arene" activation of an uncoordinated benzylic C-H bond that is 6 bonds away from a Rh(III) ion. The mechanism, which was investigated by experimental and DFT studies, proceeds through a dearomatized xylene intermediate. This intermediate was observed spectroscopically upon addition of a pyridine base to provide a thermodynamic trap.

Design and validation of non-metal oxo complexes for C-H activation.

We use our recent discovery of the reduction-coupled oxo activation (ROA) principle to design a series of organometallic molecules that activate C-H bonds through this unique proton/electron-decoupled hydrogen abstraction mechanism, in which the main group oxo moiety binds to the proton while the electron is transferred to the transition metal. Here we illustrate this general class of catalyst clusters with several examples that are validated through quantum mechanics calculations.

Genomic analysis of oceanic cyanobacterial myoviruses compared with T4-like myoviruses from diverse hosts and environments.

T4-like myoviruses are ubiquitous, and their genes are among the most abundant documented in ocean systems. Here we compare 26 T4-like genomes, including 10 from non-cyanobacterial myoviruses, and 16 from marine cyanobacterial myoviruses (cyanophages) isolated on diverse Prochlorococcus or Synechococcus hosts. A core genome of 38 virion construction and DNA replication genes was observed in all 26 genomes, with 32 and 25 additional genes shared among the non-cyanophage and cyanophage subsets, respectively. These hierarchical cores are highly syntenic across the genomes, and sampled to saturation. The 25 cyanophage core genes include six previously described genes with putative functions (psbA, mazG, phoH, hsp20, hli03, cobS), a hypothetical protein with a potential phytanoyl-CoA dioxygenase domain, two virion structural genes, and 16 hypothetical genes. Beyond previously described cyanophage-encoded photosynthesis and phosphate stress genes, we observed core genes that may play a role in nitrogen metabolism during infection through modulation of 2-oxoglutarate. Patterns among non-core genes that may drive niche diversification revealed that phosphorus-related gene content reflects source waters rather than host strain used for isolation, and that carbon metabolism genes appear associated with putative mobile elements. As well, phages isolated on Synechococcus had higher genome-wide %G+C and often contained different gene subsets (e.g. petE, zwf, gnd, prnA, cpeT) than those isolated on Prochlorococcus. However, no clear diagnostic genes emerged to distinguish these phage groups, suggesting blurred boundaries possibly due to cross-infection. Finally, genome-wide comparisons of both diverse and closely related, co-isolated genomes provide a locus-to-locus variability metric that will prove valuable for interpreting metagenomic data sets.

Portal protein diversity and phage ecology.

Oceanic phages are critical components of the global ecosystem, where they play a role in microbial mortality and evolution. Our understanding of phage diversity is greatly limited by the lack of useful genetic diversity measures. Previous studies, focusing on myophages that infect the marine cyanobacterium Synechococcus, have used the coliphage T4 portal-protein-encoding homologue, gene 20 (g20), as a diversity marker. These studies revealed 10 sequence clusters, 9 oceanic and 1 freshwater, where only 3 contained cultured representatives. We sequenced g20 from 38 marine myophages isolated using a diversity of Synechococcus and Prochlorococcus hosts to see if any would fall into the clusters that lacked cultured representatives. On the contrary, all fell into the three clusters that already contained sequences from cultured phages. Further, there was no obvious relationship between host of isolation, or host range, and g20 sequence similarity. We next expanded our analyses to all available g20 sequences (769 sequences), which include PCR amplicons from wild uncultured phages, non-PCR amplified sequences identified in the Global Ocean Survey (GOS) metagenomic database, as well as sequences from cultured phages, to evaluate the relationship between g20 sequence clusters and habitat features from which the phage sequences were isolated. Even in this meta-data set, very few sequences fell into the sequence clusters without cultured representatives, suggesting that the latter are very rare, or sequencing artefacts. In contrast, sequences most similar to the culture-containing clusters, the freshwater cluster and two novel clusters, were more highly represented, with one particular culture-containing cluster representing the dominant g20 genotype in the unamplified GOS sequence data. Finally, while some g20 sequences were non-randomly distributed with respect to habitat, there were always numerous exceptions to general patterns, indicating that phage portal proteins are not good predictors of a phage's host or the habitat in which a particular phage may thrive.

A ligand field chemistry of oxygen generation by the oxygen-evolving complex and synthetic active sites.

Oxygen-oxygen bond formation and O2 generation occur from the S4 state of the oxygen-evolving complex (OEC). Several mechanistic possibilities have been proposed for water oxidation, depending on the formal oxidation state of the Mn atoms. All fall under two general classifications: the AB mechanism in which nucleophilic oxygen (base, B) attacks electrophilic oxygen (acid, A) of the Mn4Ca cluster or the RC mechanism in which radical-like oxygen species couple within OEC. The critical intermediate in either mechanism involves a metal oxo, though the nature of this oxo for AB and RC mechanisms is disparate. In the case of the AB mechanism, assembly of an even-electron count, high-valent metal-oxo proximate to a hydroxide is needed whereas, in an RC mechanism, two odd-electron count, high-valent metal oxos are required. Thus the two mechanisms give rise to very different design criteria for functional models of the OEC active site. This discussion presents the electron counts and ligand geometries that support metal oxos for AB and RC O-O bond-forming reactions. The construction of architectures that bring two oxygen functionalities together under the purview of the AB and RC scenarios are described.