Stockholm University

About: Stockholm University is a education organization based out in Stockholm, Sweden. It is known for research contribution in the topics: Population & Supernova. The organization has 21052 authors who have published 62567 publications receiving 2725859 citations. The organization is also known as: University of Stockholm & Stockholms universitet.

Quantum chemical studies of mechanisms for metalloenzymes.

Abstract: ing a hydrogen atom from substrates with relatively weak X−H bonds (Figure 56). Such a situation was found in the catalytic cycle of ACCO, where cleavage of the N−H bond is facilitated by the ferrous ion capable of (partly) reducing the resulting N-based radical to an anion. In the catalytic cycle of HEPD and in the reaction of HppE with an enantiomer of the native substrate, a C−H bond at the carbon hosting a deprotonated alcohol group is severed by the superoxide. In these cases transfer of a hydrogen atom to the superoxide is coupled to one-electron reduction of Fe(III) to Fe(II), which yields aldehyde or ketone products. In a similar way a thioaldehyde is produced during the initial steps of the IPNS catalytic cycle. Figure 53. Reaction catalyzed by NDO. Figure 54. X-ray structure of the non-heme iron cofactor in the NDO active site (PDB 1O7G). Figure 55. Reaction mechanism for the dihydroxylation reaction catalyzed by NDO suggested on the basis of the results of a DFT study. Relative energy values in kilocalories per mole are given beneath the structures shown and above the arrows for the transition states connecting them. Chemical Reviews Review dx.doi.org/10.1021/cr400388t | Chem. Rev. 2014, 114, 3601−3658 3636 The most often encountered reaction of the Fe(III)−O2 species is an electrophilic attack on an electron-rich (co)substrate that yields an Fe(II) intermediate with a peroxide bridge between the ferrous ion and an organic molecule (Figure 57). In all examples shown in the figure the reactive spin state is a quintet with high-spin Fe(III) antiferromagnetically coupled to the superoxide radical. This particular electronic structure allows for a smooth two-electron reaction, leading to a ferrous intermediate featuring a high-spin Fe(II) ion, i.e., also lying on a quintet PES. When the substrates are easily one-electron-oxidized, as, for example, carotenoids or catecholates, already the ternary enzyme−dioxygen−organic substrate complex may contain an organic radical along with the superoxide anion stabilized by coordination to the metal (Figure 58). With proper (antiferromagnetic) alignment of the spins of the unpaired electrons on the two radicals, direct coupling between them proceeds with a straightforward formation of a new C−O bond. With the O2 ligand already protonated, several different reaction scenarios are usually plausible, and one of them, arguably the simplest, involves a transfer of the HOO group from the metal ion to the organic substrate (Figure 59). In the reaction of HEPD, it is the distal, i.e., originally protonated, oxygen atom that attacks the aldehyde group and the proton is transferred to the second (proximal) oxygen atom with the help of a phosphonic group of the substrate. In this reaction HOO acts as a nucleophile. In the case of HGD, the HOO ligand has a partial radical character, and hence, in its attack on the aromatic ring, it behaves as an electrophilic reagent. Moreover, in the HGD and ACO cases, it is the proximal oxygen atom that is directly transferred from the metal ion to the organic radical, i.e., the proton remains on the same oxygen atom throughout the reaction. When a catalytic reaction involves a homolytic O−O bond cleavage, one end of the peroxo group is in contact with the metal ion, and it is reduced to HO− or RO− when the O−O bond breaks (Figure 60). The electron required for the reduction is provided usually by the ferrous ion; in intradiol dioxygenases, which host Fe(III) in the active site, a tyrosinate ligand can serve as a reductant. Heterolytic cleavage of the O−O bond typically yields highvalent iron(IV)−oxo species, and such a reaction requires Fe(II), a deprotonated proximal oxygen atom, and usually also that the distal oxygen atom has a chance to develop a second covalent bond when the O−O gets broken (Figure 61). The bonding partner for the distal oxygen can be a hydrogen (PDHs, IPNS, ACCO) or a (co)substrate’s carbon (αKAOs, ACO, Dke1) atom. Heterolysis to Fe(IV)O usually proceeds on the quintet PES. Finally, heterolytic O−O bond cleavage may proceed without changing the oxidation state of the metal but instead with coupled two-electron oxidation of an organic substrate (Figure Figure 56. Examples of Fe(II)/Fe(III)−O2 reactions involving hydrogen atom abstraction. Only the most relevant fragment of the substrate is shown. Figure 57. Examples of Fe(III)−O2 reactions involving electrophilic attack and two-electron oxidation of an organic (co)substrate. Figure 58. Examples of Fe(II)/Fe(III)−O2 reactions involving radical coupling between the superoxide and an organic radical. Only the most relevant fragment of the substrate is shown. Chemical Reviews Review dx.doi.org/10.1021/cr400388t | Chem. Rev. 2014, 114, 3601−3658 3637 62). In both cases depicted in the figure, a hydroperoxo group is bound to high-spin Fe(III), and when theO−Obond cleaves, the OH group remains on iron and the other oxygen atom forms two covalent bonds with the organic substrate. This kind of heterolytic O−O cleavage requires that the donor orbital of the organic substrate, i.e., the one that provides two electrons for reduction of the peroxo group, has a good overlap with the O−O σ* orbital. 5.2. Dinuclear Non-Heme Iron Enzymes 5.2.1. Methane Monooxygenase. MMO is an enzyme which inserts one oxygen from O2 into methane to form methanol. The active site of the soluble form of MMO is shown in Figure 63. It contains an iron dimer complex linked by oxygen-derived ligands and has four glutamates and two histidines. Due to the presence of a well-resolved X-ray structure, and the technical importance of the reaction catalyzed, this was actually the first redox-active enzymemechanism that was treated with the cluster model using modern DFT functionals in 1997. Several groups were active at an early stage, and the most essential parts of the reaction mechanism were determined more than a decade ago. A comprehensive review of this development was written by Friesner et al. In short, the active species (compound Q) has a diamond core structure with two bridging oxo groups and is in an Fe2(IV,IV) state, one of themost oxidized species in nature. One of the oxo groups of compound Q activates nethane by an abstraction of one hydrogen atom. The TS is linear in C···H···O to form an Fe2(III,IV) state and amethyl radical. The loss of entropy at the TS is a large part of the barrier. In the second step, the methyl radical recombines with the bridging hydroxide formed in the first step. The TS for this step was first located by Basch et al. This rebound mechanism was criticized by interpretations of radical clock experiments, which appeared to show that there could not be a sufficiently long-lived alkyl radical to be consistent with a two-step mechanism. A concerted mechanism with simultaneous cleavage of the C−H bond and formation of the C−O bond was therefore suggested. Several explanations were suggested to resolve this apparent discrepancy between experiment and theory. In one of them, it was concluded that the radical clock probe molecules Figure 59. Examples of HOO transfer reactions. Only the most relevant fragment of the substrate is shown. Figure 60. Examples of O−O bond homolysis facilitated by oneelectron reduction of the proximal oxygen atom. Only the most relevant fragment of the substrate is shown. Figure 61. Examples of heterolytic O−O bond cleavage yielding iron(IV)−oxo species. Figure 62. Examples of heterolytic O−Obond cleavage proceeding with direct two-electron oxidation of the organic molecule. Chemical Reviews Review dx.doi.org/10.1021/cr400388t | Chem. Rev. 2014, 114, 3601−3658 3638 were chemically so different from methane that different mechanisms were likely. The probes are much easier to ionize and could form cations instead of radicals. Another suggestion was a so-called two-channel mechanism of the dynamics involving a bound radical intermediate. A third possibility could be something analogous to the two-state reactivity mechanism suggested for P450 to explain similar discrepancies in that case, but this has not been tested. In summary, a concerted mechanism, as suggested by the experiments, has never been found in DFT modeling calculations for methane hydroxylation by MMO, at least when reasonable models have been tried, and the suggestion has therefore not survived. In the initial phase of the MMO studies, there were problems converging to proper electronic states. These problems were solved by Friesner et al., who were able to obtain the correct antiferromagnetic coupling of compound Q with two high-spin irons. A state of key importance is also the first intermediate after Q, with an electronic structure characterized as Fe2(III,IV)− O•, discussed further below in connection with mixedMn−Fe dimers. It was found that already at the TS for hydrogen abstraction the iron dimer is in an Fe2(III,IV) state as it is in the product of this step. The bridging oxygen radical would then act as a hydrogen atom abstractor. At the TS, the spins are divided between a bridging oxo ligand and the methyl, while the iron spins stay essentially constant from the Fe2(III,IV)−O state to the product. The O−O bond cleavage to reach compound Q is also a significant step in the catalytic cycle. Again, several groups were involved in studying this step at an early stage. There was essential agreement among these studies on the mechanism. First, a peroxide (compound P) is formed between the two irons in an Fe2(III,III) state. Several different structures of P are nearly degenerate. In the TS for the O−O cleavage, the oxygens are symmetric, but only one of the irons is redox-active. In the final Figure 63. Active site of methane monooxygenase. Figure 64. R1 and R2 proteins in RNR. Chemical Reviews Review dx.doi.org/10.1021/cr400388t | Chem. Rev. 2014, 114, 3601−3658 3639 stage, the other iron also changes its oxidation state to IV, and compound Q is formed. In the study by Friesner et al.,

Stringy gravity, interacting tensionless strings and massless higher spins

Abstract: Consequences of a strong version of the AdS/CFT correspondence for extremely stringy physics are examined. In particular, properties of N = 4 supersymmetric Yang-Mills theory are used to extract results about interacting tensionless strings and massless higher spin fields in an AdS5 × S5 background. Furthermore, the thermodynamics of this model signals the presence of a Hawking-Page phase transition between AdS5 space and a “black hole”-like high temperature configuration even in the extreme string limit.

Connecting dopant bond type with electronic structure in N-doped graphene.

Abstract: Robust methods to tune the unique electronic properties of graphene by chemical modification are in great demand due to the potential of the two dimensional material to impact a range of device applications. Here we show that carbon and nitrogen core-level resonant X-ray spectroscopy is a sensitive probe of chemical bonding and electronic structure of chemical dopants introduced in single-sheet graphene films. In conjunction with density functional theory based calculations, we are able to obtain a detailed picture of bond types and electronic structure in graphene doped with nitrogen at the sub-percent level. We show that different N-bond types, including graphitic, pyridinic, and nitrilic, can exist in a single, dilutely N-doped graphene sheet. We show that these various bond types have profoundly different effects on the carrier concentration, indicating that control over the dopant bond type is a crucial requirement in advancing graphene electronics.

Super-luminous Type Ic Supernovae: Catching a Magnetar by the Tail

Abstract: We report extensive observational data for five of the lowest redshift Super-Luminous Type Ic Supernovae (SL-SNe Ic) discovered to date, namely PTF10hgi, SN2011ke, PTF11rks, SN2011kf and SN2012il. Photometric imaging of the transients at +50 to +230 days after peak combined with host galaxy subtraction reveals a luminous tail phase for four of these SL-SNe. A high resolution, optical and near infrared spectrum from xshooter provides detection of a broad He I �10830 emission line in the spectrum (+50d) of SN2012il, revealing that at least some SL-SNe Ic are not completely helium free. At first sight, the tail luminosity decline rates that we measure are consistent with the radioactive decay of 56 Co, and would require 1-4 M⊙ of 56 Ni to produce the luminosity. These 56 Ni masses cannot be made consistent with the short diffusion times at peak, and indeed are insufficient to power the peak luminosity. We instead favour energy deposition by newborn magnetars as the power source for these objects. A semi-analytical diffusion model with energy input from the spindown of a magnetar reproduces the extensive lightcurve data well. The model predictions of ejecta velocities and temperatures which are required are in reasonable agreement with those determined from our observations. We derive magnetar energies of 0.4 . E(10 51 erg) . 6.9 and ejecta masses of 2.3 . Mej(M⊙) . 8.6. The sample of five SL-SNe Ic presented here, combined with SN 2010gx - the best sampled SL-SNe Ic so far - point toward an explosion driven by a magnetar as a viable explanation for all SL-SNe Ic. Subject headings: supernovae: general - supernovae: individual (PTF10hgi, SN 2011ke, PTF11rks, SN 2011kf, SN 2012il) - stars: magnetars