Synthesis and characterization of monodispersed core-shell spherical colloids with movable cores

Gold nanoparticles have been conformally coated with amorphous silica (using a sol-gel method) and then an organic polymer (via surface-grafted, atom transfer radical polymerization) to form spherical colloids with a core-double-shell structure. The thickness of silica and polymer shells could be conveniently controlled in the range of tens to several hundred nanometers by changing the concentration of the reagent and/or the reaction time. Selective removal of the silica layer (through etching in aqueous HF) led to the formation of hollow polymer beads containing movable gold cores. This new form of core-shell particles provides a unique system for measuring the feature size and transport property associated with hollow particles. In one demonstration, we showed that the thickness of a closed polymer shell could be obtained by mapping the electrons backscattered from the core and shell. In another demonstration, the plasmon resonance band of the gold cores was used as an optical probe to follow the diffusion kinetics of chemical reagents across the polymer shells.     

The phase-dependent photochemical reaction dynamics of halooxides and nitrosyl halides

Recent progress in understanding the phase-dependent reactivity of halooxides and nitrosyl halides is outlined. Halooxide reactivity is represented by the photochemistry of chlorine dioxide (OClO) and dichlorine monoxide (ClOCl). The gas phase photochemical dynamics of OClO are contrasted with the dynamics in condensed environments. The role of excited-state symmetry in defining the reaction dynamics and the observation of photoisomerization resulting in the production of ClOO are discussed. The current understanding of the excited-state reaction dynamics of ClOCl and evidence for photoisomerization of this species resulting in the production of ClClO are outlined. Finally, the photochemical reaction dynamics of the nitrosyl halide ClNO are presented. The main difference between the gas and condensed phase reaction dynamics of this species is that whereas photodissociation to form Cl and NO dominates the gas phase reaction dynamics, photoisomerization resulting in ClON production occurs to an appreciable extent in condensed environments. The observation of photoisomerization for OClO, ClOCl and ClNO suggests that this process is a general feature of the condensed phase reaction dynamics for smaller halooxides and nitrosyl halides. Finally, future areas for study in both halooxide and nitrosyl halide photoreactivity are outlined.     

Beta-diiminate platinum complexes for alkane dehydrogenation

New five-coordinate Pt(IV) complexes [{(o-R2-p-R'-C6H2)NC(R' ')}2CH]PtMe3 (R, R', R' ' = alkyl or H) are reported. The complex with R = Me, R' = tBu, R' ' = Me generates unsaturated Pt(II) species capable of alkane C-H bond activation and stoichiometric dehydrogenation.     

Engineering cytochrome P-450s

Cytochrome P-450 isozymes represent a critical component of nature’s spectrum of detoxification catalysts that could be exploited for bioremediation. The ethanol-inducible human cytochrome P-450 2E1 serves as a model eukaryotic P-450 that complements the bacterial P-450 cam in dehalogenation and detoxification of environmental pollutants. We explored the construction of novel chimeric P-450s using cytochrome P-450 camC and 2E1 genes. For construction of chimera 1 (478 amino acids, 55.14 kDa), 145 amino acids from the N-terminus of P-450 2E1 protein (493 amino acids, 56.84 kDa) were replaced with 130 amino acids from the N-terminus of P-450 camC protein (415 amino acids, 46.66 kDa). In chimera 2 (525 amino acids, 60.24 kDa) the strategy involves replacement of 28 amino acids in the C-terminus of chimera 1 with 75 amino acids from the C-terminus of P-450 camC gene. Homology models of both the chimeric proteins were developed using SWISS-MODEL based on the known crystal structure of cytochrome P-450 camC, BM-3, 1DT6A, and 2C17A. The models indicated that the proposed heme-binding site was intact, which is inevitable for catalytic activity of cytochrome P-450s. The expression of chimera 1 and 2 genes in Escherichia coli DH5α was evident from light-pink cell pellets, protein band in sodium dodecyl sulfate polyacrylamide gel electrophoresis, and diagnostic carbon monoxide-difference spectra. Our studies show that strategies can be developed to exploit the natural diversity of the P-450 superfamily to generate chimeric biocatalysts that would provide new templates amenable to directed evolution.     

Nonequilibrium synthesis and assembly of hybrid inorganic-protein nanostructures using an engineered DNA binding protein

We show that a protein with no intrinsic inorganic synthesis activity can be endowed with the ability to control the formation of inorganic nanostructures under thermodynamically unfavorable (nonequilibrium) conditions, reproducing a key feature of biological hard-tissue growth and assembly. The nonequilibrium synthesis of Cu(2)O nanoparticles is accomplished using an engineered derivative of the DNA-binding protein TraI in a room-temperature precursor electrolyte. The functional TraI derivative (TraIi1753::CN225) is engineered to possess a cysteine-constrained 12-residue Cu(2)O binding sequence, designated CN225, that is inserted into a permissive site in TraI. When TraIi1753::CN225 is included in the precursor electrolyte, stable Cu(2)O nanoparticles form, even though the concentrations of [Cu(+)] and [OH(-)] are at 5% of the solubility product (K(sp,Cu2O)). Negative control experiments verify that Cu(2)O formation is controlled by inclusion of the CN225 binding sequence. Transmission electron microscopy and electron diffraction reveal a core-shell structure for the nonequilibrium nanoparticles: a 2 nm Cu(2)O core is surrounded by an adsorbed protein shell. Quantitative protein adsorption studies show that the unexpected stability of Cu(2)O is imparted by the nanomolar surface binding affinity of TraIi1753::CN225 for Cu(2)O (K(d) = 1.2 x 10(-)(8) M), which provides favorable interfacial energetics (-45 kJ/mol) for the core-shell configuration. The protein shell retains the DNA-binding traits of TraI, as evidenced by the spontaneous organization of nanoparticles onto circular double-stranded DNA.     

Pyrene.pyrene complexes at the active site of cytochrome P450 3A4: evidence for a multiple substrate binding site

Cytochrome P450 monooxygenases (CYPs) metabolize nearly all drugs and toxins. Recently, it has become clear that CYPs exhibit both homotropic and heterotropic allosteric kinetics for many substrates. However, the mechanism of cooperative kinetics has not been established for any specific human CYP/substrate combination. Suggested mechanisms include binding of multiple substrates within distinct, static, subsites of a single large active site or binding of multiple substrates within a single fluid active site. CYP3A4 hydroxylates pyrene with positive cooperativity. Therefore, experiments were designed to exploit the fluorescence properties of pyrene, which diagnostically distinguish between pyrene.pyrene complexes versus spatially separated pyrene substrates. Pyrene complexes (excimers) yield an emission spectrum clearly distinct from pyrene monomers. In lipid-free aqueous/glycerol solutions of CYP3A4, addition of pyrene affords a concentration-dependent low-spin to high-spin conversion of the CYP3A4 heme prosthetic group, indicating occupancy of the active site by pyrene. Under the same conditions, in the presence of CYP3A4 but not other heme proteins, the excimer/monomer ratio (E/M) of pyrene was decreased in emission spectra, compared to pyrene alone. However, excitation spectra indicate a CYP3A4-dependent increase in the wavelength shift for the excimer excitation spectrum versus the monomer excitation spectrum, as well as changes in the excimer excitation peak shape and vibronic structure. These changes are reversed by the CYP3A4 substrate testosterone. Together, the results demonstrate that pyrene.pyrene ground-state complexes occupy the CYP3A4 active site, and they provide the first spectroscopic evidence for substrate complexes within a single fluid active site. Functional implications include the possibility that turnover rate, regioselectivity, and stereoselectivity of the reaction are determined by the substrate.substrate complex rather than individual substrates.     

Classification of gasoline data obtained by gas chromatography using a piecewise alignment algorithm combined with feature selection and principal component analysis

A fast and objective chemometric classification method is developed and applied to the analysis of gas chromatography (GC) data from five commercial gasoline samples. The gasoline samples serve as model mixtures, whereas the focus is on the development and demonstration of the classification method. The method is based on objective retention time alignment (referred to as piecewise alignment) coupled with analysis of variance (ANOVA) feature selection prior to classification by principal component analysis (PCA) using optimal parameters. The degree-of-class-separation is used as a metric to objectively optimize the alignment and feature selection parameters using a suitable training set thereby reducing user subjectivity, as well as to indicate the success of the PCA clustering and classification. The degree-of-class-separation is calculated using Euclidean distances between the PCA scores of a subset of the replicate runs from two of the five fuel types, i.e., the training set. The unaligned training set that was directly submitted to PCA had a low degree-of-class-separation (0.4), and the PCA scores plot for the raw training set combined with the raw test set failed to correctly cluster the five sample types. After submitting the training set to piecewise alignment, the degree-of-class-separation increased (1.2), but when the same alignment parameters were applied to the training set combined with the test set, the scores plot clustering still did not yield five distinct groups. Applying feature selection to the unaligned training set increased the degree-of-class-separation (4.8), but chemical variations were still obscured by retention time variation and when the same feature selection conditions were used for the training set combined with the test set, only one of the five fuels was clustered correctly. However, piecewise alignment coupled with feature selection yielded a reasonably optimal degree-of-class-separation for the training set (9.2), and when the same alignment and ANOVA parameters were applied to the training set combined with the test set, the PCA scores plot correctly classified the gasoline fingerprints into five distinct clusters.     

Quantized Hamilton Dynamics

The paper describes the quantized Hamilton dynamics (QHD) approach that extends classical Hamiltonian dynamics and captures quantum effects, such as zero point energy, tunneling, decoherence, branching, and state-specific dynamics. The approximations are made by closures of the hierarchy of Heisenberg equations for quantum observables with the higher order observables decomposed into products of the lower order ones. The technique is applied to the vibrational energy exchange in a water molecule, the tunneling escape from a metastable state, the double-slit interference, the population transfer, dephasing and vibrational coherence transfer in a two-level system coupled to a phonon, and the scattering of a light particle off a surface phonon, where QHD is coupled to quantum mechanics in the Schrödinger representation. Generation of thermal ensembles in the extended space of QHD variables is discussed. QHD reduces to classical mechanics at the first order, closely resembles classical mechanics at the higher orders, and requires little computational effort, providing an efficient tool for treatment of the quantum effects in large systems.     

MPW1K Performs Much Better than B3LYP in DFT Calculations on Reactions that Proceed by Proton-Coupled Electron Transfer (PCET)

DFT calculations have been performed with the B3LYP and MPW1K functional on the hydrogen atom abstraction reactions of ethenoxyl with ethenol and of phenoxyl with both phenol and alpha-naphthol. Comparison with the results of G3 calculations shows that B3LYP seriously underestimates the barrier heights for the reaction of ethenoxyl with ethenol by both proton-coupled electron transfer (PCET) and hydrogen atom transfer (HAT) mechanisms. The MPW1K functional also underestimates the barrier heights, but by much less than B3LYP. Similarly, comparison with the results of experiments on the reaction of phenoxyl radical with alpha-naphthol indicates that the barrier height for the preferred PCET mechanism is calculated more accurately by MPW1K than by B3LYP. These findings indicate that the MPW1K functional is much better suited than B3LYP for calculations on hydrogen abstraction reactions by both HAT and PCET mechanisms.     

Square-wave adsorptive stripping voltammetry of menadione (vitamin K(3))

Menadione (vitamin K₃) undergoes a reversible two-electron transfer involving the quinone structure in acidic medium. As demonstrated by using cyclic voltammetry, the reduced form is more strongly adsorbed than the oxidized one. Stripping voltammetry of an adsorbed layer has been applied to the determination of this molecule after preconcentration of the reduced compound and scanning the potential towards less negative values. Adsorption, which is highly effective when stirring is used, approaches an equilibrium process in quiescent solution, as evidenced by a loss of part of the adsorbed material when stirring is stopped. A square-wave mode has been selected owing to its high sensitivity (the current is 20 times that for the differential pulse mode), but also to its high scan-rate, which minimizes the slow desorption process occurring during the scan. A concentration range from 2 × 10⁻¹⁰ to 5 × 10⁻⁷ M is easily investigated, the detection limit being 1.3 × 10⁻¹⁰ M. The influence of several operational parameters has also been considered.