Oxidation of nitrided si(100) by gaseous atomic and molecular oxygen

The nitridation of Si(100) by ammonia and the subsequent oxidation of the nitrided surface by both gaseous atomic and molecular oxygen was investigated under ultrahigh vacuum (UHV) conditions using X-ray photoelectron spectroscopy (XPS). Nitridation of Si(100) by the thermal decomposition of NH3 results in the formation of a subsurface nitride and a decrease in the concentration of surface dangling bond sites. On the basis of changes in the N1s spectra obtained after NH3 adsorption and decomposition, we estimate that the nitride resides about four to five layers below the vacuum-solid interface and that the concentration of surface dangling bonds after nitridation is only 59% of its value on Si(100)-(2 x 1). Oxidation of the nitrided surface is found to produce an oxide phase that remains in the outer layers of the solid and interacts only weakly with the underlying nitride for oxygen coverages up to 2.5 ML. Slight changes in the N1s spectra observed after oxidizing at 300 K are suggested to arise primarily from the introduction of strain within the nitride, and by the formation of a small amount of Si2=N-O species near the nitride-oxide interface. The nitrogen bonding environment changes negligibly after oxidizing at 800 K, which is indicative of greater phase separation at elevated surface temperature. Nitridation is also found to significantly reduce the reactivity of the Si(100) surface toward both atomic and molecular oxygen. A comparison of the oxygen uptake on the clean and nitrided surfaces shows quantitatively that the decrease in dangling bond concentration is responsible for the reduced activity of the nitrided surface toward oxidation, and therefore that dangling bonds are the initial adsorption site for both gaseous oxygen atoms and molecules. Increasing the surface temperature is found to promote the uptake of oxygen when O2 is used as the oxidant, but brings about only a small enhancement in the uptake of gaseous O-atoms. The different effects of surface temperature on the uptake of O versus O2 are interpreted in terms of the efficiency at which dangling bond pairs are regenerated on the surface at elevated temperature and the different site requirements for the adsorption of O and O2.     

Reactions of N-heterocyclic carbenes (NHCs) with one-electron oxidants: possible formation of a carbene cation radical

One-electron oxidation of N-heterocyclic carbenes (NHCs) has been carried out using oxidising agents such as tetracyanoethylene (TCNE) and ferrocenium [Cp(2)Fe](+); the formation of carbene radical cations is postulated.     

Formation and structure of 1:1 complexes between aryl hydroxamic acids and vanadate at neutral pH

Although aryl hydroxamic acids are well-known to form coordination complexes with vanadate (V(V)), the nature of these complexes at neutral pH and submillimolar concentrations, the conditions under which such complexes inhibit various serine amidohydrolases, is not well established. A series of qualitative and quantitative experiments, involving UV/vis, (1)H NMR, and (51)V NMR spectroscopies, established that both 1:1 and 1:2 vanadate/hydroxamate complexes form at pH 7.5, with the former dominating at submillimolar concentrations. Formation constants for the complexes of several aryl and alkyl hydroxamic acids were determined; for example, for benzohydroxamic acid, the stepwise formation constants of the 1:1 and 1:2 complexes were 3000 and 400 M(-1), respectively. The (51)V chemical shift of the 1:1 4-nitrobenzohydroxamic acid complex was -497 ppm, and that of its unsubstituted analogue was -498 ppm. A (1)H-(15)N HSQC spectrum of the 4-nitrobenzo-(15)N-hydroxamic acid/vanadate complex indicated the presence of an N-H group with (15)N and (1)H chemical shifts of 115 and 5.83 ppm, respectively. A (13)C NMR spectrum of the complex of 4-nitrobenzo-(13)C-hydroxamic acid with vanadate displayed a resonance at 170.1 ppm and thus a coordination-induced shift (CIS) of +3.8 ppm. In contrast, the CIS value of an established 1:2 complex, thought to contain chelated hydroxamic acid ligands, was +11.9 ppm. These spectral data led to the following structural picture of 1:1 complexes of vanadate and aryl hydroxamic acids. They contain penta- or hexa-coordinated vanadium. The ligand is in the hydroxamate rather than hydroximate form. The ligand is presumably bound to vanadium through the hydroxamic hydroxyl oxygen, but the hydroxamic acid carbonyl oxygen interacts weakly with vanadium. These species are the most likely candidates for the inhibitors of serine amidohydrolases found in vanadate/hydroxamic acid mixtures.     

Simultaneous photoconjugation of methylene blue and cis-Rh(phen)2Cl2+ to DNA via a synergistic effect

Irradiation of the red-light absorbing dye, methylene blue (MB), in the presence of the metal complex, cis-Rh(phen)2Cl2+ (BISPHEN), leads to irreversible photobinding of both reagents to DNA. Evidence from absorption and emission spectroscopy indicates that the dye is strongly complexed to the DNA at the concentrations used in the experiments and that this complex is unaffected by the presence of BISPHEN. The level of covalent binding is proportional to the absorbed light dose, with the quantum efficiency for covalent binding of BISPHEN to the DNA with 633 nm light equal to 3.5 x 10(-4). Electrospray ionization mass spectrum of a mixture of DNA fragments created by enzymatic degradation of DNA isolated following irradiation indicates that purine adducts are formed with both BISPHEN and the dye. In addition, UV-Vis and high-performance liquid chromatography analyses of the irradiated MB/BISPHEN/DNA mixture and isolated adducts show extensive conversion of the dye and metal complex to the corresponding N-demethylated and aquated derivatives, respectively. Triplet quenchers for MB, for example oxygen and benzoquinone, inhibit both the photoconjugation and the photochemistry of BISPHEN. A mechanism for the synergistic interaction is proposed that involves photoconjugation of both partners to the DNA following oxidation and reduction via electron transfer between 1MB*/DNA and 3MB*/BISPHEN.     

Calculation of the Entropy of Lattice Polymer Models from Monte Carlo Trajectories

While lattice models are used extensively for macromolecules (synthetic polymers proteins, etc.), calculation of the absolute entropy, S, and the free energy, F, from a given Monte Carlo (MC) trajectory is not straightforward. Recently, we have developed the hypothetical scanning MC (HSMC) method for calculating S and F of fluids. Here we extend HSMC to self-avoiding walks on a square lattice and discuss its wide applicability to complex polymer lattice models. HSMC is independent of existing techniques and thus constitutes an independent research tool; it provides rigorous upper and lower bounds for F, which can be obtained from a very small sample and even from a single chain conformation.     

Enhanced fluorescence from arrays of nanoholes in a gold film

Arrays of sub-wavelength holes (nanoholes) in gold films were used as a substrate for enhanced fluorescence spectroscopy. Seven arrays of nanoholes with distinct periodicities (distances between the holes) were fabricated. The arrays were then spin-coated with polystyrene films containing different concentrations of the fluorescent dye oxazine 720. The dye was excited via resonant extraordinary transmission of the laser source through the nanoholes. Enhanced fluorescence was observed when the geometric characteristics of the arrays allowed for an enhancement in the transmitted excitation. This enhancement occurred via surface plasmon excitation by the laser and a consequential increase in the local electromagnetic field in a sub-wavelength region at the metal-film interface. It was demonstrated that the sensitivity of the fluorescence measurement (change in signal vs change in dye concentration in the polymer film) is significantly larger at the surface plasmon resonance conditions than that obtained from equivalent films on glass substrates. Enhancement factors for the fluorescence emission were calculated for each array, with a maximum enhancement of close to 2 orders of magnitude as compared to the emission of films on glass. The results presented here indicate that arrays of nanoholes are interesting substrates for the development of fluorescence sensors based on surface plasmon resonance, as they provide a platform that allows both spatial confinement and enhancement of excitation light. Moreover, the collinear characteristics of the present optical setup, due to the resonant extraordinary transmission through the nanohole arrays, are more conducive to miniaturization and chip integration than more traditional experimental geometries.     

Alkanethiolate self-assembled monolayers as functional spacers to resist protein adsorption upon Au-coated nerve microelectrode

Alkanethiolate self-assembled monolayers (SAMs) of varied chain lengths were adsorbed upon Au-coated nerve microelectrodes and employed as protein-resistant spacers. The microelectrode spiraled as a cuff type can be used for restoring motor function via electrical stimulation on the peripheral nerve system; however, an increase of electrode impedance might occur during implantation. In this work, a thin-film SAMs treatment upon Au/polyimide (PI) surface of the microelectrode provided a hydrophobic characteristic, which retarded protein adsorption at the initial stage and subsequent pileup (or thickening) process. The protein-resistant effect exhibited comparable SAMs of different chain lengths adsorbed upon Au/PI surfaces. The increase of electrode impedance as a function of protein deposition time was mainly correlated with the addition of reactance that was associated with the pileup thickness of the deposited protein. Particularly, the SAMs-modified surface was capable to detach a significant portion of the accumulated protein from the protein-deposited SAMs/Au/PI, whereas the protein-deposited layers exhibited firm adhesion upon Au/PI surface. It is therefore very promising to apply thin-film SAMs adsorbed upon Au-coated surface for bioinvasive devices that have the need of functional electrical stimulations or sensing nerve signals during chronic implantation.     

Measurement of cell migration on surface-bound fibronectin gradients

A novel technique for the quantitative observation of cell migration along linear gradient substrates functionalized with adhesive proteins is presented. Gradients of the cell adhesion molecule fibronectin are generated by the cross diffusion of functionalizable alkanethiols on gold and characterized by X-ray photoelectron spectroscopy and surface plasmon resonance. Two distinct migration assays are described that characterize the movement of either sparsely populated noncontacting cells or a confluent monolayer of cells into free space. The drift speed of bovine aortic endothelial cells is measured and shown to increase along a fibronectin gradient when compared to a uniform control substrate using both assays. The results of these experiments establish reproducible conditions for studies of cell migration on gradients of surface-bound ligands.     

Synthesis, structure determination, and spectroscopic/computational characterization of a series of Fe(II)-thiolate model complexes: implications for Fe-S bonding in superoxide reductases

A combined synthetic/spectroscopic/computational approach has been employed to prepare and characterize a series of Fe(II)-thiolate complexes that model the square-pyramidal [Fe(II)(N(His))(4)(S(Cys))] structure of the reduced active site of superoxide reductases (SORs), a class of enzymes that detoxify superoxide in air-sensitive organisms. The high-spin (S = 2) Fe(II) complexes [(Me(4)cyclam)Fe(SC(6)H(4)-p-OMe)]OTf (2) and [FeL]PF(6) (3) (where Me(4)cyclam = 1,4,8,11-tetramethylcyclam and L is the pentadentate monoanion of 1-thioethyl-4,8,11-trimethylcyclam) were synthesized and subjected to structural, magnetic, and electrochemical characterization. X-ray crystallographic studies confirm that 2 and 3 possess an N(4)S donor set similar to that found for the SOR active site and reveal molecular geometries intermediate between square pyramidal and trigonal bipyramidal for both complexes. Electronic absorption, magnetic circular dichroism (MCD), and variable-temperature variable-field MCD (VTVH-MCD) spectroscopies were utilized, in conjunction with density functional theory (DFT) and semiemperical INDO/S-CI calculations, to probe the ground and excited states of complexes 2 and 3, as well as the previously reported Fe(II) SOR model [(L(8)py(2))Fe(SC(6)H(4)-p-Me)]BF(4) (1) (where L(8)py(2) is a tetradentate pyridyl-appended diazacyclooctane macrocycle). These studies allow for a detailed interpretation of the S-->Fe(II) charge transfer transitions observed in the absorption and MCD spectra of complexes 1-3 and provide significant insights into the nature of Fe(II)-S bonding in complexes with axial thiolate ligation. Of the three models investigated, complex 3 exhibits an absorption spectrum that is particularly similar to the one reported for the reduced SOR enzyme (SOR(red)), suggesting that this model accurately mimics key elements of the electronic structure of the enzyme active site; namely, highly covalent Fe-S pi- and sigma-interactions. These spectral similarities are shown to arise from the fact that 3 contains an alkyl thiolate tethered to the equatorial cyclam ring, resulting in a thiolate orientation that is very similar to the one adopted by the Cys residue in the SOR(red) active site. Possible implications of our results with respect to the electronic structure and reactivity of SOR(red) are discussed.     

Nucleophilic Addition of CH, NH, and OH Bonds to the Phosphadiazonium Cation and Interpretation of (31)P Chemical Shifts at Dicoordinate Phosphorus Centers

The phosphadiazonium cation [MesNP](+) reacts quantitatively with the fluorenylide anion, MesNH(2), and MesOH (Mes = 2,4,6-tri-tert-butylphenyl), resulting in formal insertion of the N-P moiety into the H-Y (Y = C, N, O) bonds. Specifically, reaction of MesNPCl with fluorenyllithium gives the aminofluorenylidenephosphine [crystal data: C(31)H(38)NP, monoclinic, P2(1)/c, a = 9.568(8) ?, b = 24.25(2) ?, c = 11.77(1) ?, beta = 101.38(8) degrees, Z = 4]. Similarly, reaction of [MesNP][GaCl(4)] with MesNH(2) gives the diaminophosphenium salt [MesN(H)PN(H)Mes][GaCl(4)] [crystal data: C(36)H(60)Cl(4)GaN(2)P, monoclinic, C2/c, a = 24.921(2) ?, b = 10.198(4) ?, c = 16.445(2) ?, beta = 93.32(1) degrees, Z = 4], and reaction with MesOH gives the first example of an aminooxyphosphenium salt [MesN(H)POMes][GaCl(4)]. It is proposed that the reactions involve nucleophilic attack at phosphorus followed by a 1,3-hydrogen migration from Y to N. Experimental evidence for the formation of sigma-complex intermediates is provided by the isolation of [MesNP-PPh(3)][SO(3)CF(3)] [crystal data: C(37)H(44)F(3)NO(3)P(2)S, triclinic, P&onemacr;, a = 10.663(1) ?, b = 19.439(1) ?, c = 10.502(1) ?, alpha = 103.100(7) degrees, beta = 113.311(7) degrees, gamma = 93.401(7) degrees, Z = 2]. As part of the unequivocal characterization of the aminooxyphosphenium salt, detailed solid-state (31)P NMR studies and GIAO calculations on the phosphenium cations have been performed. Contrary to popular belief, the phosphorus shielding in dicoordinate cations is not caused by the positive charge but results from efficient mixing between the phosphorus lone pair and pi orbitals.