A theoretical study of atomic oxygen chemisorption on the Ni(100) and Ni(111) surfaces

Atomic oxygen chemisorption has been studied for the fourfold hollow site of the Ni(100) surface and for the threefold hollow site of the Ni(111) surface. To model the Ni(100) surface, 10 different clusters in the range Ni₅ to Ni₄₁ were used, and for the Ni(111) surface, 11 different clusters in the range Ni₁₃ to Ni₄₃ were used. A detailed analysis of the orbital occupations of the cluster with and without oxygen for the different clusters shows that there are three different possible bonding mechanisms. In two of these, the basic feature is that a₁ electrons of the cluster are kicked out by the oxygen 2p_z orbital and moved to holes in the 2p_{x, y} orbitals. A picture where the oxygen electrons fit into the electronic structure of the cluster is emphasized. The third mechanism, which is applicable for only one cluster, can be described as the formation of two covalent bonds of E symmetry. The final best estimate of the oxygen chemisorption energy for the Ni(100) surface is about 130 kcal/mol, and for the Ni(111) surface, about 115 kcal/mol. In particular for the Ni(111) surface, an excited oxygen state with radical character is identified, which might be a catalytically important species. The excitation energy to reach this state should be on the order of 10 kcal/mol for the Ni(111) surface.     

A hybrid density functional study of O-O bond cleavage and phenyl ring hydroxylation for a biomimetic non-heme iron complex

Density functional calculations using the B3LYP functional have been used to study the reaction mechanism of [Fe(Tp(Ph2))BF] (Tp(Ph2) = hydrotris(3,5-diphenylpyrazol-1-yl)borate; BF = benzoylformate) with dioxygen. This mononuclear non-heme iron(II) complex was recently synthesized, and it proved to be the first biomimetic complex reproducing the dioxygenase activity of alpha-ketoglutarate-dependent enzymes. Moreover, the enthalpy and entropy of activation for this biologically interesting process were derived from kinetic experiments offering a unique possibility for direct comparison of theoretical and experimental data. The results reported here support a mechanism in which oxidative decarboxylation of the keto acid is the rate-limiting step. This oxygen activation process proceeds on the septet potential energy surface through a transition state for a concerted O-O and C-C bond cleavage. In the next step, a high-valent iron-oxo species performs electrophilic attack on the phenyl ring of the Tp(Ph2) ligand leading to an iron(III)-radical sigma-complex. Subsequent proton-coupled electron-transfer yields an iron(II)-phenol intermediate, which can bind dioxygen and reduce it to a superoxide radical. Finally, the protonated superoxide radical leaves the first coordination sphere of the iron(III)-phenolate complex and dismutates to dioxygen and hydrogen peroxide. The calculated activation barrier (enthalpy and entropy) and the overall reaction energy profile agree well with experimental data. A comparison to the enzymatic process, which is suggested to occur on the quintet surface, has been made.     

X-ray emission spectra of small molecules

An instrument for X-ray emission studies of free molecules is described and electron and fluorescence excitations are discussed. The application of X-ray emission spectroscopy to free molecules is exemplified by the spectra of N₂, CO, NO and CO₂. From the spectra the core level binding energies of the molecules are deduced. For the diatomic molecules vibrational fine structure is resolved and analyzed in terms of different bond lengths in the initial and final states. The change in bond length, when the initial 1s vacancy is formed, is also discussed. The influence of the X-ray selection rules and molecular localization properties on the band intensities are discussed and exemplified by the O1s and C1s spectra of CO and CO₂. In the spectra about ten satellites are found.     

Interfacial properties of the nanostructured dye-sensitized solid heterojunction TiO(2)/RuL(2)(NCS)(2)/CuI

The interfaces of the nanostructured dye-sensitized solid heterojunction TiO(2)/Ru-dye/CuI have been studied using photoelectron spectroscopy of core and valence levels, x-ray absorption spectroscopy and atomic force microscopy. A nanostructured anatase TiO(2) film sensitized with RuL(2)(NCS)(2) [cis-bis(4,4(')-dicarboxy-2,2(')-bipyridine)-bis(isothio-cyanato)-ruthenium(II)] was prepared in a controlled way using a novel combined in-situ and ex-situ (Ar atmosphere) method. Onto this film CuI was deposited in-situ. The formation of the dye-CuI interface and the changes brought upon the dye-TiO(2) interface could be monitored in a stepwise fashion. A direct interaction between the dye NCS groups and the CuI is evident in the core level photoelectron spectra. Concerning the energy matching of the valence electronic levels, the photoelectron spectra indicate that the dye HOMO overlaps in energy with the Cu 3d-I 5p hydrid states. The CuI grow in the form of particles, which at the initial stages displace the dye molecules causing dye-TiO(2) bond breaking. Consequently, the very efficient charge injection channel provided by the dye-TiO(2) carboxylic bonding is directly affected for a substantial part of the dye molecules. This may be of importance for the functional properties of such a heterojunction.     

Mechanism and selectivity of the dinuclear iron benzoyl-coenzyme A epoxidase BoxB

Benzoyl-CoA epoxidase is a dinuclear iron enzyme that catalyzes the epoxidation reaction of the aromatic ring of benzoyl-CoA with chemo-, regio- and stereo-selectivity. It has been suggested that this enzyme may also catalyze the deoxygenation reaction of epoxide, suggesting a unique bifunctionality among the diiron enzymes. We report a density functional theory study of this enzyme aimed at elucidating its mechanism and the various selectivities. The epoxidation is suggested to start with the binding of the O₂ molecule to the diferrous center to generate a diferric peroxide complex, followed by concerted O–O bond cleavage and epoxide formation. Two different pathways have been located, leading to (2S,3R)-epoxy and (2R,3S)-epoxy products, with barriers of 17.6 and 20.4 kcal mol^–1, respectively. The barrier difference is 2.8 kcal mol^–1, corresponding to a diastereomeric excess of about 99 : 1. Further isomerization from epoxide to phenol is found to have quite a high barrier, which cannot compete with the product release step. After product release into solution, fast epoxide–oxepin isomerization and racemization can take place easily, leading to a racemic mixture of (2S,3R) and (2R,3S) products. The deoxygenation of epoxide to regenerate benzoyl-CoA by a diferrous form of the enzyme proceeds via a stepwise mechanism. The C2–O bond cleavage happens first, coupled with one electron transfer from one iron center to the substrate, to form a radical intermediate, which is followed by the second C3–O bond cleavage. The first step is rate-limiting with a barrier of only 10.8 kcal mol^–1. Further experimental studies are encouraged to verify our results.     

Computational analysis of the autocatalytic posttranslational cyclization observed in histidine ammonia-lyase. A comparison with green fluorescent protein.

Density functional calculations using hybrid functionals (B3LYP) have been performed to study the mechanism of the autocatalytic posttranslational cyclization observed in histidine ammonia-lyase. Two mechanisms were analyzed, the commonly accepted mechanism in which cyclization precedes dehydrogenation (reduced mechanism) and a mechanism in which dehydrogenation precedes cyclization (oxidized mechanism). The reduced pathway is not supported by the calculations, while the alternative oxidized mechanism where a dehydration occurs prior to the formation of the ring yields reasonable energetics for the system. Database searches showed that the oxidative mechanism in which the formation of the dehydro amino acids in residue i + 1 precedes the cyclization is also structurally advantageous as it results in shorter distances between the carbonyl carbon of residue i and the amide nitrogen of residue i + 2 and, therefore, preorganizes the protein for cyclization. Conformational searches showed that these distances were also unusually short and exhibited very little variation in the Delta-Ala143 HAL tetramer, indicating that like GFP the tetrameric form of HAL is rigidly preorganized for cyclization. The monomeric form of HAL is less preorganized than the tetrameric form of HAL. Dehydro amino acids aid in the preorganization, but the main driving force in the rigid tight turn formation is the influence of the surrounding protein.