Hydrogenase biomimetics with redox-active ligands: Electrocatalytic proton reduction by [Fe2(CO)4(κ2-diamine)(μ-edt)] (diamine = 2,2′-bipy, 1,10-phen)

Diiron complexes bearing redox active diamine ligands have been studied as models of the active site of [FeFe]-hydrogenases. Heating [Fe2(CO)6(μ-edt)] (edt = 1,2-ethanedithiolate) with 2,2′-bipyridine (2,2′-bipy) or 1,10-phenanthroline (1,10-phen) in MeCN in the presence of Me3NO leads to the formation of [Fe2(CO)4(κ2-2,2′-bipy)(μ-edt)] (1-edt) and [Fe2(CO)4(κ2-1,10-phen)(μ-edt)] (2-edt), respectively, in moderate yields. In the solid state the diamine resides in dibasal sites, while both dibasal and apical–basal isomers are present in solution. Both stereoisomers protonate readily upon addition of strong acids. Cyclic voltammetry in MeCN shows that both complexes undergo irreversible oxidation and reduction, proposed to be a one- and two-electron process, respectively. The structures of neutral 2-edt and its corresponding one- and two-electron reduced species have been investigated by DFT calculations. In 2-edt− the added electron occupies a predominantly ligand-based orbital, and the iron–iron bond is maintained, being only slightly elongated. Addition of the second electron affords an open-shell triplet dianion where the second electron populates an Fe–Fe σ* antibonding orbital, resulting in effective scission of the iron–iron bond. The triplet state lies 4.2 kcal mol−1 lower in energy than the closed-shell singlet dianion whose HOMO correlates nicely with the LUMO of the neutral species 2-edt. Electrocatalytic proton reduction by both complexes has been studied in MeCN using CF3CO2H as the proton source. These catalysis studies reveal that while at high acid concentrations the active catalytic species is [Fe2(CO)4(μ-H)(κ2-diamine)(μ-edt)]+, at low acid concentrations the two complexes follow different catalytic mechanisms being associated with differences in their relative rates of protonation

DNA looping: the consequences and its control

The formation of DNA loops by proteins and protein complexes is ubiquitous to many fundamental cellular processes, including transcription, recombination, and replication. Here we review recent advances in understanding the properties of DNA looping in its natural context and how they propagate to the cellular behavior through gene regulation. The results of connecting the molecular properties with cellular physiology indicate that looping of DNA in vivo is much more complex and easier than predicted from current models and reveals a wealth of previously unappreciated details

Mixed main group transition metal clusters: Reactions of [Ru 3 (CO) 10 (μ-dppm)] with Ph 3 SnH

Novel dppm-ligated ruthenium-tin clusters have been prepared from the reaction of [Ru3(CO)10(μ-dppm)] with Ph3SnH. At room temperature and in the presence of Me3NO, [Ru3(CO)9(SnPh3) (μ-dppm) (μ-H)] (1) is produced from the formal loss of CO and Sn-H bond oxidative-addition. Treatment of 1 with a further two equivalents of Ph3SnH (in the presence of Me3NO) gave [Ru3(CO)7(SnPh3)2(μ-SnPh2)(μ-dppm)(μ-H)(μ3-H)] (2) which results from both Sn–H and Sn–C bond scission and contains two different hydride environments (μ and μ3) and a μ-SnPh2 moiety. Cluster 2 has 48 CVE (cluster valence electron) with three formal ruthenium-ruthenium bonds; two of those are very long and fall at the extreme end of distances attributed to ruthenium-ruthenium bonds. Thermolysis of 2 at 66 °C liberates benzene to give [Ru3(CO)8(SnPh3)(μ-SnPh2)(μ3-SnPh2)(μ-dppm)(μ-H)] (3). DFT calculations confirm that the hydride bridges one of the Ru-μ-SnPh2 bonds in 3. The solid-state structures of 2 and 3 have been determined by X-ray crystallography, and the bonding and ligand distribution have been investigated by DFT studies. The geometry-optimized structures are consistent with the solid-state structures

Alkyne activation and polyhedral reorganization in benzothiazolate-capped osmium clusters on reaction with diethyl acetylenedicarboxylate (DEAD) and ethyl propiolate

The reactivity of the face-capped benzothiazolate clusters HOs3(CO)9[μ3-C7H3(R)NS] (1a, R = H; 1b, R = 2-CH3) with alkynes has been investigated. 1a reacts with DEAD at 67 °C to furnish the isomeric alkenyl clusters Os3(CO)9(μ-C7H4NS)(μ3-EtO2CCCHCO2Et) (2a and 3a). X-ray crystallographic analyses of 2a and 3a have confirmed the stereoisomeric relationship of these products and the regiospecific polyhedral expansion that follows the formal transfer of the hydride to the coordinated alkyne ligand in HOs3(CO)9(μ-C7H4NS)(2-DEAD). The significant structural differences between the two isomers, as revealed by the solid-state structures, derives from the regiospecific cleavage of one of the three Os-Os bonds in the intermediate alkenyl cluster Os3(CO)9(μ-C7H4NS)(1-EtO2CCCHCO2Et), which follows hydride transfer to the coordinated alkyne ligand in the pi compound HOs3(CO)9(μ-C7H4NS)(2-DEAD). Control experiments confirm the reversibility of the reaction leading to the formation of 2a and 3a. Whereas heating either isomer in refluxing THF or benzene affords a binary mixture containing 2a and 3a, thermolysis in refluxing toluene leads to the activation of the alkenyl ligand and formation of the new cluster Os3(CO)9(μ-C7H4NS)(μ3-EtO2CCCH2) (4). 4 was independently synthesized from 1a and ethyl propiolate at room temperature. The computed mechanisms that account for the formation of 2a and 3a are presented, along with the mechanism for the reaction of 1a with ethyl propiolate to give 4

Reactions of Ru3(CO)10(μ-dppm) with Ph3GeH: Ge–H and Ge–C bond cleavage in Ph3GeH at triruthenium clusters

The activation of Ph3GeH at the dppm-bridged cluster Ru3(CO)10(μ-dppm) [dppm = bis(diphenylphosphino)methane] has been investigated. Ru3(CO)10(μ-dppm) reacts with Ph3GeH at room temperature in the presence of Me3NO to give the new cluster products Ru3(CO)9(GePh3)(μ-dppm)(μ-H) (1) and Ru3(CO)8(GePh3)2(μ-dppm)(μ-H)2 (2) via successive oxidation-addition of two Ge–H bonds. Refluxing 1 in THF furnishes the diruthenium complex Ru2(CO)6(μ-GePh2)(μ-dppm) (3) as the major product (44%), in addition to Ru3(CO)7(μ-CO)(GePh3){μ3-PhPCH2P(Ph)C6H4}(μ-H) (4) and the known cluster Ru3(CO)9(μ-H)(μ3-Ph2PCH2PPh) (5) in 7 and 8% yields, respectively. Heating samples of cluster 2 also afforded 3 as the major product together with a small amount of Ru3(CO)7(GePh3)(μ-OH)(μ-dppm)(μ-H)2 (6). DFT calculations establish the stability of the different possible isomers for clusters 1, 2, and 6, in addition to providing insight into the mechanism for hydride fluxionality in 2. All new compounds have been characterized by analytical and spectroscopic methods, and the molecular structures of 1, 3, and 6 have been established by single-crystal X-ray diffraction analyses

Reversible C-H bond activation at a triosmium centre: A comparative study of the reactivity of unsaturated triosmium clusters Os3(CO)8(μ-dppm)(μ-H)2 and Os3(CO)8(μ-dppf)(μ-H)2 with activated alkynes

Heating a benzene solution of the unsaturated cluster Os3(CO)8(μ-dppm)(μ-H)2 (1) [dppm = bis(diphenylphosphino)methane] with MeO2CCtriple bond; length of mdashCCO2Me (DMAD) or EtO2CCtriple bond; length of mdashCCO2Et (DEAD) at 80 °C furnished the dinuclear compounds Os2(CO)4(μ-dppm)(μ-η2;η1;к1-RO2CCCHCO2R)(μ-H) (3a, R = Me, 3b, R = Et) and the saturated trinuclear complexes Os3(CO)7(μ-dppm)(μ3-η2;η1;η1-RO2CCCCO2R)(μ-H)2 (4a, R = Me, 4b, R = Et). In contrast, similar reactions using unsaturated Os3(CO)8(μ-dppf)(μ-H)2 (2) [dppf = bis(diphenylphosphino)ferrocene] afforded only the trinuclear complexes Os3(CO)8(μ-dppf)(μ-η2;η1-RO2CCHCCO2R)(μ-H) (5a, R = Me; 5b, R = Et) and Os3(CO)7(μ-dppf)(μ3-η2;η1;η1-RO2CCCCO2R)(μ-H)2 (6a, R = Me; 6b, R = Et). Control experiments confirm that 5a and 5b decarbonylate at 80 °C to give 6a and 6b, respectively. Both 5a and 5b exist as a pair of isomers in solution, as demonstrated by 1H NMR and 31P{1H} NMR spectroscopy. DFT calculations on cluster 5a (as the dppf-Me4 derivative) indicate that the isomeric mixture derives from a torsional motion that promotes the conformational flipping of the cyclopentadienyl groups of the dppf-Me4 ligand relative to the metallic plane. VT NMR measurements on clusters 6a and 6b indicate that while the hydride ligand associated with the dppf-bridged Os-Os bond is nonfluxional at room temperature, the second hydride rapidly oscillates between the two non-dppf-bridged Os-Os edges. DFT examination of this hydride fluxionality confirms a “windshield wiper” motion for the labile hydride that gives rise to a time-average coupling of this hydride to both phosphorus centers of the dppf ligand. Thermolysis of 6a and 6b in refluxing toluene yielded Os3(CO)7(μ-dppf)(μ-η2;η1;к1-CCHCO2R) (7a, R=Me; 7b, R=Et). The vinylidene moieties in 7a and 7b derive from the carbon-carbon bond cleavage of coordinated alkyne ligands, and these two products exhibit high thermal stability in refluxing toluene

Iron carbonyl complexes bearing phenazine and acridine ligands: X-ray structures of Fe(CO)(3)(eta(4)-C12H8N2), Fe(CO)(2){P(OMe)(3)}(eta(4)-C12H8N2), Fe(CO)(2)(PPh3) (eta(4)-C13H9N), and Fe(CO)(2)(kappa(1)-dppm) (eta(4)-C12H8N2)

Reactions of Fe3(CO)12 with the heterocycles phenazine and acridine in refluxing benzene afforded the mononuclear complexes Fe(CO)3(η4-C12H8N2) (1a) and Fe(CO)3(η4-C13H9N) (1b), respectively. Treatment of 1a with P(OMe)3 and PPh3 in the presence of Me3NO at room temperature yielded the carbonyl substitution products Fe(CO)2{P(OMe)3}(η4-C12H8N2) (2a) and Fe(CO)2(PPh3) (η4-C12H8N2) (3a), respectively. Similar reactions of 1b yielded Fe(CO)2{P(OMe)3}(η4-C13H9N) (2b) and Fe(CO)2(PPh3) (η4-C13H9N) (3b). Treatment of 1a with the diphosphines dppm and dppf under similar conditions afforded the mononuclear compounds Fe(CO)2(κ1-dppm) (η4-C12H8N2) (4a) and Fe(CO)2(κ1-dppf) (η4-C12H8N2) (4b). Compounds 1a, 2a, 3b, and 4a have been structurally characterized by X-ray crystallography. The ancillary phenazine and acridine ligands in these products adopt an η4-coordination mode by using only the peripheral carbon atoms in one of the carbocyclic rings. Given the rarity of this coordination mode in metal carbonyl complexes, we have performed electronic structure calculations on 1a, and these data are discussed relative to the solid-state structur

Structural constraints revealed in consistent nucleosome positions in the genome of S. cerevisiae

<p>Abstract</p> <p>Background</p> <p>Recent advances in the field of high-throughput genomics have rendered possible the performance of genome-scale studies to define the nucleosomal landscapes of eukaryote genomes. Such analyses are aimed towards providing a better understanding of the process of nucleosome positioning, for which several models have been suggested. Nevertheless, questions regarding the sequence constraints of nucleosomal DNA and how they may have been shaped through evolution remain open. In this paper, we analyze in detail different experimental nucleosome datasets with the aim of providing a hypothesis for the emergence of nucleosome-forming sequences.</p> <p>Results</p> <p>We compared the complete sets of nucleosome positions for the budding yeast (<it>Saccharomyces cerevisiae</it>) as defined in the output of two independent experiments with the use of two different experimental techniques. We found that < 10% of the experimentally defined nucleosome positions were consistently positioned in both datasets. This subset of well-positioned nucleosomes, when compared with the bulk, was shown to have particular properties at both sequence and structural levels. Consistently positioned nucleosomes were also shown to occur preferentially in pairs of dinucleosomes, and to be surprisingly less conserved compared with their adjacent nucleosome-free linkers.</p> <p>Conclusion</p> <p>Our findings may be combined into a hypothesis for the emergence of a weak nucleosome-positioning code. According to this hypothesis, consistent nucleosomes may be partly guided by nearby nucleosome-free regions through statistical positioning. Once established, a set of well-positioned consistent nucleosomes may impose secondary constraints that further shape the structure of the underlying DNA. We were able to capture these constraints through the application of a recently introduced structural property that is related to the symmetry of DNA curvature. Furthermore, we found that both consistently positioned nucleosomes and their adjacent nucleosome-free regions show an increased tendency towards conservation of this structural feature.</p

Accelerating Policy Decisions to Adopt Haemophilus influenzae Type b Vaccine: A Global, Multivariable Analysis

Jessica Shearer and colleagues analyze data from 147 countries to identify factors that influence the time taken to introduce routine vaccination against Haemophilus influenzae type b (Hib)