Scientific Publications 2006
2006. "Separation of 47Ti and 49Ti Solid-State NMR Lineshapes by Static QCPMG Experiments at Multiple Fields." Journal of Magnetic Resonance 178(2):228-236. Abstract Experimental procedures are proposed and demonstrated that separate the spectroscopic contribution from both 47Ti and 49Ti in solid-state nuclear magnetic resonance spectra. These take advantage of the different nuclear spin quantum numbers of these nuclei that lead to different ‘effective’ radiofrequency fields for the central transition nutation frequencies when these nuclei occur in sites with a significant electric field gradient. Numerical simulations and solid-state NMR experiments were performed on the TiO2 polymorphs anatase and rutile. For anatase the separation of the two isotopes at high field (21.1 T) facilitated accurate determination of both EFG- and CSA-interactions using the different scaling of the EFG-tensor for the two isotopes. Rutile, having a larger quadrupolar coupling constant (CQ) was examined by 49Ti selective experiments at different magnetic fields to obtain spectra with different scalings of the two anisotropic tensors. A small chemical shielding anisotropy (CSA) of -30 ppm was determined.
2006. "A New Approach to Determining Gas-Particle Reaction Probabilities and Application to the Heterogeneous Reaction of Deliquesced Sodium Chloride Particles with Gas-Phase Hydroxyl Radicals." Journal of Physical Chemistry A 110(36):10619-10627. doi:10.1021/jp063263+ Abstract The reaction kinetics for gaseous hydroxyl radicals (OH) with deliquesced sodium chloride particles (NaClaq) were investigated using a novel experimental approach. The technique utilizes the exposure of substrate-deposited aerosol particles to reactive gases followed by chemical analysis of the particles using computer-controlled scanning electron microscopy with energy-dispersive analysis of X-rays (CCSEM/EDX) capability. Experiments were performed at room temperature and atmospheric pressure with deliquesced NaCl particles in the micron size range at 70-80% RH and with OH concentrations in the range of 1 to 7×109 cm-3. The apparent, pseudo first-order rate constant for the reaction was determined from measurements of changes in the chloride concentration of individual particles upon reaction with OH as a function of the particle loading on the substrate. Quantitative treatment of the data using a model that incorporates both diffusion and reaction kinetics yields a lower-limit to the net reaction probability of γnet > 0.1, with an overall uncertainty of a factor of two.
2006. "Analysis of Individual Environmental Particles Using Modern Methods of Electron Microscopy and X-Ray Microanalysis." Journal of Electron Spectroscopy and Related Phenomena 150(2-3):260-274. Abstract Understanding the composition of particles in the atmosphere is critical because of their health effects and their direct and indirect effects on radiative forcing, and hence on climate. In this manuscript, we demonstrate the utility of single particle off-line analysis to investigate the chemistry of individual atmospheric particles using modern, state-of-the-art electron microscopy and time-of-flight secondary ionization mass spectrometry techniques. We show that these methods provide specific, detailed data on particle composition, chemistry, morphology, phase and internal structure. This information is crucial for evaluating hygroscopic properties of aerosols, understanding aerosol aging and reactivity, and correlating the characteristics of aerosols with their optical properties. The manuscript presents a number of analytical advances in methods of electron probe particle analysis along with a brief review of a number of the research projects carried out in the authors’ laboratory on the chemical characterization of environmental particles. The obtained data offers a rich set of qualitative and quantitative information on the particle chemistry, composition and the mechanisms of gas-particle interactions which are of high importance to atmospheric processes involving particulate matter and air pollution.
2006. "Energetics and Dynamics of Fragmentation of Protonated Leucine Enkephalin from Time-and Energy-Resolved Surface-Induced Dissociation Studies." Journal of Physical Chemistry A 110(27):8554-8562. Abstract Dissociation of singly protonated leucine enkephalin (YGGFL) was studied using surface-induced dissociation (SID) in a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS) specially configured for studying ion activation by collisions with surfaces. The energetics and dynamics of seven primary dissociation channels were deduced from modeling the time- and energy-resolved fragmentation efficiency curves for different fragment ions using an RRKM based approach developed in our laboratory. The following threshold energies and activation entropies were determined in this study: E0=1.20 eV and ∆S‡=-20 e.u.1 (MH+→b5); E0=1.14 eV and ∆S‡=-14.7 e.u. (MH+→b4); E0=1.42 eV and ∆S‡=-2.5 e.u. (MH+→b3); E0=1.30 eV and ∆S‡=-4.1 e.u. (MH+→a4); E0=1.37 eV and ∆S‡=-5.2 e.u. (MH+→y ions); E0=1.50 eV and ∆S‡=1.6 e.u. (MH+→internal fragments); E0=1.62 eV and ∆S‡=5.2 e.u. (MH+→F). Comparison with Arrhenius activation energies reported in the literature demonstrated for the first time the reversal of the order of activation energies as compared to threshold energies for dissociation.
2006. "Mechanisms of Peptide Fragmentation from Time-and Energy-Resolved Surface-Induced Dissociation Studies: Dissociation of Angiotensin Analogs." International Journal of Mass Spectrometry 249-250:462-472. Abstract Energetics and mechanism of dissociation of singly protonated angiotensin III (RVYIHPF) and its analogs RVYIFPF, RVYIYPF, RVYIHAF, and RVYIHDF was studied using surface-induced dissociation (SID) in a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS) specially configured for studying ion activation by collisions with surfaces. The energetics and dynamics of peptide fragmentation were deduced by modeling the time- and energy-resolved survival curves for each precursor ion using an RRKM based approach developed in our laboratory. Fragmentation mechanisms were inferred from comparison of time- and energy-resolved fragmentation efficiency curves (TFECs) of different fragment ions followed by RRKM modeling of dissociation of angiotensin III into six major families of fragment ions. Detailed modeling demonstrated that dissociation of these peptides is dominated by loss of ammonia from the precursor ion and characterized by a high energy barrier of 1.6 eV. Loss of NH3 and subsequent rearrangement of the MH-NH3 ion results in proton mobilization and release of ca. 30 kcal/mol into internal excitation of the MH-NH3 ion. The resulting highly excited ion accesses a variety of non-specific dissociation pathways with very high rate constants. Fast fragmentation of excited MH-NH3 ion forms a variety of abundant bn-NH3 and an-NH3 fragment ions. Abundant XH and HX internal fragments are also formed, reflecting the stability of histidine-containing diketopiperazine structures.
2006. "Cycloaddition Functionalizations to Preserve or Control the Conductance of Carbon Nanotubes." Physical Review Letters 97(116801):1-4. doi:10.1103/PhysRevLett.97.116801 Abstract The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. We identify a class of covalent functionalizations that preserve or control the conductance of singlewalled metallic carbon nanotubes. [2+1] cycloadditions can induce bond cleaving between adjacent sidewall carbons, recovering in the process the sp(super 2) hybridization and the ideal conductance of the pristine tubes. This is radically at variance with the damage permanently induced by other common ligands, where a single covalent bond is formed with a sidewall carbon. Chirality, curvature, and chemistry determine bond cleaving, and in turn the electrical transport properties of a functionalized tube. Awell-defined range of diameters can be found for which certain addends exhibit a bistable state, where the opening or closing of the sidewall bond, accompanied by a switch in the conductance, could be directed with chemical, optical, or thermal means.
2006. "Characterization of Functionalized Nanoporous Supports for Protein Confinement ." Nanotechnology 17(22):5531-5538. doi:10.1088/0957-4484/17/22/001 Abstract Here we characterize a highly efficient approach for protein confinement and enzyme immobilization in NH2- or HOOC- functionalized mesoporous silica (FMS) with pore sizes as large as tens of nanometers. We observed a dramatic increase of enzyme loading in both enzyme activity and protein amount when using appropriate FMS in comparison with unfunctionalized mesoporous silica and normal porous silica. In principle, the general approach described here should be applicable to many enzymes, proteins, and protein complexes since both pore sizes and functional groups of FMS are controllable.
2006. "Nitrocellulose Templated Hierarchical Pore Structure in Mesoporous Thin Films." Inorganic Chemistry Communications 9(1):7-9. Abstract Over the last decade, a great deal of effort has been expended on the templated synthesis of nanoporous materials. Many different templates have been used to create this nanostructure (surfactants, polymers, latex spheres, etc.), but by far the most widely used has been micelles composed of surfactants. This is a versatile, and highly useful, synthetic method, capable of producing a wide variety of materials and structures. More recently, the synthesis of hierarchical pore structures (i.e. small pores leading to large pores) has been of great interest as a means of enhancing mass transport within these materials. Such hierarchical pore structures have been made by combining surfactant templating methods with latex beads , by assembling as-synthesized MCM-41 particles around block co-polymer micelles, followed by crosslinking and calcination., by spray drying MCM-41 and MCM-48 agglomerates , and by using “evaporation induced self-assembly” [5-9].
2006. "Templated synthesis of mesoporous titanium phosphates for the sequestration of radionuclides ." Inorganic Chemistry Communications 9(3):293-295. Abstract Several mesoporous titanium phosphate phases, with varying pore sizes, were prepared using non-ionic surfactants and easily handled titanium precursors under mild reaction conditions. Preliminary testing reveals that these materials have high affinity for certain radionuclides of environmental concern. Significant amounts of radioactive waste have built up over the last half century as the result of nuclear weapons production and the accumulation of spent nuclear fuel. Ultimately, after processing, this waste is targeted to be buried in a deep geological repository. One plan is to include “getter materials” in with this waste in order to sequester any radionuclides that might leak from the wasteforms. Of particular interest in this regard are the long-lived actinide species (e.g. Pu, Am, Np, etc.) and the anions (e.g. pertechnetate, iodide, etc.). These getter materials must be able to survive long-term exposure to elevated temperatures (>150°C) and moderately high radiation fluxes. Due to their frailty towards radiolytic degradation, organic components cannot be used for either structure or function in the final getter material.
2006. "Radiation-Induced Effects in Pyrochlore and Nanoscale Materials Engineering." Nuclear Instruments and Methods in Physics Research. Section B, Beam Interactions with Materials and Atoms 250(1-2):128-136. doi:10.1016/j.nimb.2006.04.157 Abstract Pyrochlore materials, A2B2O7, encompass a wide range of compositions and are technological important for energy and environment issues, for example, used as ionic conductor in solid oxide fuel cells and nuclear waste forms for the storage of actinides, particularly Pu. Here, the recent progresses in understanding ion beam irradiation-induced phenomena in pyrochlore compounds are briefly reviewed with the focus of ion beam-induced crystalline-to-amorphous and pyrochlore to fluorite structural transitions. Systematic ion irradiation studies of lanthanide pyrochlores in which B = Ti, Zr, and Sn have suggested that the radiation response of pyrochlore compounds is highly dependent on compositional changes. Both ionic size and the cation electronic configurations (e.g., bond-types) affect the structural distortion from the ideal fluorite structure and the response behavior of pyrochlore-structure types to ion beam irradiation. Ion beam-induced pyrochlore-to-fluorite structural transition occurs in all irradiated pyrochlore compositions, and the independent kinetics of cation and anion disordering processes were discussed. Numerous novel nanostructures have been created by utilizing the ion beam-induced amorphization, order-disorder transition and phase decomposition, such as amorphous and disordered nano-domains, perfectly latticed matched two-dimensional nanolayer, self-organized ripple structure, metallic nanoparticles and nanowires. The potential application of energetic particle irradiation for nano-engineering pyrochlore structured compounds is highlighted.
2006. "Automated Purification of Recombinant Proteins: Combining High-throughput with High Yield." Protein expression and purification 47(1):16-24. Abstract Protein crystallography, mapping protein interactions and other approaches of current functional genomics require not only purifying large numbers of proteins but also obtaining sufficient yield and homogeneity for downstream high-throughput applications. There is a need for the development of robust automated high-throughput protein expression and purification processes to meet these requirements. We developed and compared two alternative workflows for automated purification of recombinant proteins based on expression of bacterial genes in Escherichia coli: First - a filtration separation protocol based on expression of 800 ml E. coli cultures followed by filtration purification using Ni2+-NTATM Agarose (Qiagen). Second - a smaller scale magnetic separation method based on expression in 25 ml cultures of E.coli followed by 96-well purification on MagneHisTM Ni2+ Agarose (Promega). Both workflows provided comparable average yields of proteins about 8 ug of purified protein per unit of OD at 600 nm of bacterial culture. We discuss advantages and limitations of the automated workflows that can provide proteins more than 90 % pure in the range of 100 ug – 45 mg per purification run as well as strategies for optimization of these protocols.
2006. "Electrically Controlled Anion Exchange Based on Polypyrrole and Carbon Nanotubes Nanocomposite for Perchlorate Removal ." Environmental Science and Technology 40(12):4004-4009. Abstract A novel and stable carbon nanotube/polypyrrole nanocomposite film has been electrosynthesized and the feasibility for removing perchlorate ion through an electrically controlled anion exchange has been evaluated.
2006. "Electrosynthesis, Characterization, and Application of Novel Hybrid Materials Based on Carbon Nanotube-Polyaniline-Nickel Hexacyanoferrate Nanocomposites." Journal of Materials Chemistry 16(6):585-592. Abstract Incorporating nanoclusters of nickel hexacyanoferrates (NiHCF) onto a porous polyaniline (PANI)–carbon nanotube (CNT) matrix provides a novel class of hybrid materials with a good ion exchange capacity, high stability, and a selectivity for caesium ions. The CNT-PANI-NiHCF nanocomposite films have been synthesized by electrodeposition step-by-step on glassy carbon electrodes and characterized with cyclic voltammetry (CV), scanning electron microscopy (SEM), transmission electron microscopy (TEM), and X-ray photoelectron spectroscopy (XPS) techniques. CV and XPS investigations confirmed the formation of PANI and NiHCF on the surface of CNTs. The microscopy of NiHCF hybrid materials was characterized by SEM and TEM; the size of NiHCF particles is approximately 20 to 50 nm. The porous high surface area CNT matrix provides the high loading capacity for the deposition of NiHCF nanoparticles, while the PANI thin-film further stabilizes the nanoparticles. The selectivity for caesium ion adsorption of the hybrid materials was investigated. The high selectivity for caesium provides the base to develop a novel electrochemical ion exchange process for the treatment of nuclear wastes and radioactive-caesium contaminated waters.
2006. "Experimental and Computational Studies of Alkali-Metal Coinage-Metal Clusters." Journal of Physical Chemistry A 110(12):4244-4250. doi:10.1021/jp056789n Abstract Coinage and alkali metal mixed clusters, M4Na- (M ) Cu, Au) have been investigated experimentally using photoelectron spectroscopy and computationally at correlated ab initio levels. The related Cu4Li-, Ag4 Li-, Ag4Na-, and Au4Li- clusters as well as the neutral Cu4Li2 and Cu4Na2 clusters have also been studied computationally. The calculations show that the two lowest isomers of the negatively charged clusters include a pyramidal C4V structure and a planar C2V species. For Cu4Li- and Cu4Na-, the C4V structure is calculated at correlated ab initio level to be 30.9 and 16.9 kJ/mol below the planar C2V isomer, whereas the planar isomers of Au4Li- and Au4Na- are found to be 29.7 and 49.4 kJ/mol below the pyramidal ones. For Ag4Li- and Ag4Na-, the pyramidal isomers are the lowest ones. Comparison of the calculated and measured photoelectron spectra of Cu4Na- and Au4Na- shows that the pyramidal Cu4Na- cluster of C4V symmetry and the planar Au4Na- of C2V symmetry are detected experimentally. Calculations of the magnetically induced current density in Cu4Li- and Cu4Li2 using the Gauge-Including Magnetically Induced Current (GIMIC) method show that strong ring currents are sustained mainly by the highest-occupied molecular orbital primarily derived from the Cu 4s. The GIMIC calculations thus show that the Cu4 2- ring is ó-aromatic and that the d orbitals do not play any significant role for the electron delocalization effects. The present study does not support the notion that the square-planar Cu4 2- is the first example of d-orbital aromatic molecules.
2006. "Gaseous Arginine Conformers and Their Unique Intramolecular Interactions." Journal of Physical Chemistry A 110(44):12282-12291. doi:10.1021/jp0645115 Abstract Extensive ab initio calculations were employed to characterize stable conformers of gaseous arginine, both the canonical and zwitterionic tautomers. Step-by-step geometry optimizations of possible single-bond rotamers at the B3LYP/6-31G(d), B3LYP/6-31++G(d,p), and MP2/6-31++G(d,p) levels yield numerous structures that are more stable than any known ones. The final electronic energies of the conformers were determined at the CCSD/6-31++G(d,p) level. The lowest energies of the canonical and zwitterionic structures are lower than the existing values by 2.0 and 2.3 kcal/mol, respectively. The relative energies, rotational constants, dipole moments, and harmonic frequencies of the stable conformers remain for future experimental verification. The conformational distributions at various temperatures, estimated according to thermodynamic principles, consist almost exclusively of the newly found structures. One striking feature is the occurrence of blueshifting hydrogen bonds in all six of the most stable conformers. A unique feature of important conformations is the coexistence of dihydrogen and blue- and red-shifting hydrogen bonds. In addition to the hydrogen bonds, the stereoelectronic effects were also found to be important stabilization factors. The calculated and measured proton affinities agree within the theoretical and experimental uncertainties, affirming the high quality of our conformational search. The theoretical gas-phase basicity of 245.9 kcal/mol is also in good agreement with the experimental value of 240.6 kcal/mol. The extensive searches establish firmly that gaseous arginine exists primarily in the canonical and not the zwitterionic form.
2006. "Kinetics of Microbial Reduction of Solid Phase U(VI)." Environmental Science and Technology 40(20):6290-6296. Abstract Sodium boltwoodite (NaUO2SiO3OH ∙1.5H2O) was used to assess the kinetics of microbial reduction of solid phase U(VI) by a dissimilatory metal-reducing bacterium (DMRB), Shewanella oneidensis strain MR-1. The bioreduction kinetics was studied with Na-boltwoodite in suspension or within alginate beads. Concentrations of U(VI)tot and cell number were varied to evaluate the coupling of U(VI) dissolution, diffusion, and microbial activity. Batch experiments were performed in a non-growth medium with lactate as electron donor at pH 6.8 buffered with PIPES. Microscopic and spectroscopic analyses with transmission electron microscopy (TEM), energy dispersive spectroscopy (EDS), and laser-induced fluorescence spectroscopy (LIFS) collectively indicated that solid phase U(VI) was first dissolved and diffused out of grain interiors before it was reduced on bacterial surfaces and/or within the periplasm. The kinetics of solid phase U(VI) bioreduction was well described by a coupled model of bicarbonate-promoted dissolution of Na-boltwoodite, intraparticle uranyl diffusion, and Monod type bioreduction kinetics with respect to dissolved U(VI) concentration. The results demonstrated the intimate coupling of biological, chemical, and physical processes in microbial reduction of solid phase U(VI).
2006. "Microscopic Reactive Diffusion of Uranium in the Contaminated Sediments at Hanford, United States." Water Resources Research 42(W12420):1-15. doi:10.1029/2006WR005031 Abstract Microscopic and spectroscopic analysis of uranium-contaminated sediment cores beneath the BX waste tank farm at the US Department of Energy (DOE) Hanford site revealed that uranium (U) existed as uranyl precipitates primarily associated with the intragrain fractures of granitic clasts in the sediment (McKinley et al. 2005). The dissolution of the precipitates appeared to be controlled by intragrain ion diffusion coupled with the dissolution kinetics of the uranyl precipitates most likely as Na-boltwoodite. Here we presented a coupled microscopic reactive diffusion model by independently characterizing the intragrain diffusion and dissolution kinetics of Na-boltwoodite. Diffusion characterization with a nuclear magnetic resonance (NMR) pulse gradient spin-echo (PGSE) technique showed that the intragrain fractures of the granitic clasts in the Hanford sediment contain two domans with distinct diffusivities. The fast diffusion domain has an apparent tortuosity of about 1.5, while the slow region has a tortuosity of two orders of magnitude larger. A two-domain diffusion model was assembled and used to infer the geochemical conditions that led to intragrain uranyl precipitation when the sediment was contaminated by U-containing wastes at the site. Rapid precipitation of Na-boltwoodite was simulated when a U-containing, alkaline caustic, and high carbonate tank waste solution diffused into intragrain fractures originally containing Si-rich solutions. The model was also used to simulate uranyl dissolution and release from the contaminant sediment to aqueous solutions. With independently characterized parameters for Na-boltwoodite dissolution, the model simulations demonstrated that diffusion could significantly decrease the rates of intragrain uranyl mineral dissolution due to diffusion-induced local solubility limitation, and the intragrain uranyl precipitates could serve as a long-term uranyl source for the vadose porewater and underlying groundwater at this site.
2006. "Amperometric Glucose Biosensor Based on Self-Assembling Glucose Oxidase on Carbon Nanotubes." Electrochemistry Communications 8:251-256. Abstract A flow injection amperometric glucose biosensor based on electrostatic self-assembling glucose oxidase (GOx) on a carbon nanotube (CNT)-modified glassy carbon transducer is described. GOx is immobilized on the negatively charged CNT surface by alternatively assembling a cationic polydiallyldimethylammonium chloride (PDDA) layer and a GOx layer. The unique sandwich-like layer structure (PDDA/GOx/PDDA/CNT) formed by self-assembling provides a favorable microenvironment to keep the bioactivity of GOx and to prevent enzyme molecule leakage. The direct electrochemistry behavior of GOx and electrocatalysis of H2O2 on the fabricated PDDA/GOx/PDDA/CNT electrode demonstrated that such a biosensor fabrication method preserves the activity of enzyme molecules and the mechanical and electrocatalytic properties of carbon nanotubes, enabling sensitive determination of glucose. Flow injection amperometric detection of glucose is carried out at -100 mV (vs Ag/AgCl) in 0.05 M phosphate buffer solution (pH 7.4) with wide linear response range of 15 uM- 6 mM and a detection limit of 7 uM. The PDDA/GOx/PDDA/CNT/GC biosensor showed excellent properties for the sensitive determination of glucose with good reproducibility, remarkable stability, and free of interference from other co-existing electroactive species. The present methods can be applied to assemble other enzyme molecules and biological molecules, such as antibody, antigen, and DNA, to the CNT surface for wide biosensor and bioassay applications.
2006. "Apoferritin Templated Synthesis of Metal Phosphate Nanoparticle Labels for Electrochemical Immunoassay." Small 2(10):1139-1143. Abstract W have introduced template-synthesized metal phosphate nanoparticle labels for electrochemical immunoassay. Such use of an apoferritin template offers a simple and convenient route to prepare metallic nanoparticle labels for electrochemical immunoassays and avoid the complicated and time-consuming nanoparticle synthesis process (QD synthesis). Releasing metal ions from metal phosphate in an acetate buffer (pH 4.6) eliminates the harsh condition in the traditional metallic nanoparticle dissolution (e.g., strong acid dissolution of QDs and gold nanoparticles). This method is ultrasensitive and its DL is low to 77fM. The simultaneous detection of multiple protein targets is easily performed by using different metal phosphate nanoparticle labels (cadmium phosphate and lead phosphate). This approach can be extended to prepare multiple metal (such as zinc, lead, cadmium, copper, indium, gold, silver) phosphate nanoparticle labels or hybrid metal (bimetallic or trimetallic with predetermined ratios) phosphate nanoparticle labels for a multiplex electrochemical immunoassay. The new nanoparticle labels could be applicable to other electrochemical bioassays, such as DNA, and is thus expected to lead to wide applications for protein diagnostics and for bioanalysis in general.
2006. "Bioassay Labels Based on Apoferritin Nanovehicles." Chembiochem 7(9):1315-1319. doi:10.1002/cbic.200600225 Abstract Here we report a nanoparticle label based on apoferritin nanovehicle loaded internally with markers for sensitive electrochemical DNA detection. The central cavity structure, the dissociation and reconstitute properties at different pHs of apoferritin provide a facile method to load and release markers. Hexacynoferrate(III) was used as model marker to load into the cavity of apoferritin protein cage. The loaded nanoparticle surface was functionalized with amino-modified DNA probe. Electrochemical DNA hybridization assay based on the hexacynoferrate loaded apoferritin nanovehicle could detect 23 atmol DNA targets in 50 ul sample solution. The concept could be readily extended to load other redox and fluorescence markers for bioassay applications. The new nanoparticle labels hold great promise for multi-target detection (in connection to nanoparticles loaded with different markers) and for enhancing the sensitivity of other bioassays.
2006. "Bioelectrochemical Magnetic Immunosensing of Trichloropyridinol: A Potential Insecticide Biomarker." Electroanalysis 18(16):1605-1613. Abstract A magnetic beads-based bioelectrochemical magnetic immunosensor was developed for the fast and sensitive determination of the trichloropyridinol (TCP) biomarker in environmental samples. After liquid phrase competitive immunoreaction among a limited amount of TCP antibody coated-magnetic beads (Ab-MBs), TCP analyte, and horseradish peroxidase (HRP) labeled TCP (HRP-TCP), a magnet/glassy carbon (MGC) electrode was used to collect a TCP-Abs-MBs and a HRP-TCP-Ab-MBs immunocomplex assembly. The activity of HRP tracers bound to the beads was monitored with highly sensitive square wave voltammetry (SWV) by accumulating an electroactive enzymatic product to the MGC electrode surface under constant potential (0.5 V) during enzymatic reaction in the presence of 3’,3’,5’,5’-tetramethylbenzidine (TMB)-H2O2 substrate solution. The electrochemical characteristics of substrate and product were investigated, and the parameters of the immunoassay were optimized.
2006. "Biosensor Based on Self-Assembling Acetylcholinesterase on Carbon Nanotubes for Flow injection/Amperometric Detection of Organophosphate Pesticides and Nerve Agents." Analytical Chemistry 78(3):835-843. doi:10.1021/ac051559q Abstract A highly sensitive flow-injection amperometric biosensor for organophosphate pesticides and nerve agents based on self-assembly of acetylcholinesterase (AChE) on carbon nanotube (CNT)-modified glassy carbon (GC) electrode is described. AChE is immobilized on the negatively-charged CNT surface by alternatively assembling a cationic polydiallyldimethylammonium chloride (PDDA) layer and an AChE layer. Transmission electron microscopy images confirm the formation of layer-by-layer nanostructures on carboxyl functionalized CNTs. The unique sandwich-like structure (PDDA/AChE/PDDA) on the CNT surface formed by self-assembly provides a favorable microenvironment to keep the bioactivity of AChE and to prevent enzyme molecule leakage. The electrocatalytic activity of CNT leads to a greatly improved electrochemical detection of the enzymatically generated thiocholine product, including a low oxidation overvoltage (+150 mV), higher sensitivity, and stability. The developed PDDA/AChE/PDDA/CNT/GC biosensor integrated into a flow injection system was used to monitor organophosphate pesticides and nerve agents, such as paraoxon. The sensor performance, including inhibition time and regeneration conditions, was optimized with respect to operating conditions. Under the optimal conditions, the biosensor was used to measure as low as 0.4 pM paraoxon with a 6-min inhibition time. The biosensor had excellent operational lifetime stability with no decrease in the activity of enzymes for more than 20 repeated measurements over a 1-week period. The developed biosensor system is an ideal tool for online monitoring of organophosphate pesticides and nerve agents.
2006. "Carbon Nanotube Templated Asembly of Protein." Journal of Nanoscience and Nanotechnology 6(4):948-953. Abstract This paper describes a novel general strategy for fabricating protein-polyion multilayers by electrostatic layer-by-layer (LBL) self-assembly on a carbon nanotube (CNT) template. Such a noncovalent functionalization method is important for preserving the activity of biomolecules and the mechanical and electrical properties of CNTs. Glucose oxidase and poly (diallydimethylammonium) chloride polymer were used as a model to investigate the LBL process on a CNT template. High-resolution transmission electron microscopy and electrochemical characterization confirm the formation of LBL nanostructures on carboxyl functionalized CNTs. We have also demonstrated the applications of these nanoshell bioreactors to the direct electrochemistry of proteins and biosensing. This strategy can be applied to assemble other biological molecules, such as antibodies, antigens, and DNA, for wide bioassay applications.
2006. "Electrochemical Proteolytic Beacon for Detection of Matrix Metalloproteinase Activities ." Journal of the American Chemical Society 128(38):12382-12383. doi:10.1021/ja0626638 Abstract This communication describes a novel method for detecting of matrix metalloproteinase-7 activity using a peptide substrate labeled with a ferrocene reporter. The substrate serves as a selective ‘electrochemical proteolytic beacon’ (EPB) for this metalloproteinase. The EPB is immobilized on a gold electrode surface to enable ‘on-off’ electrochemical signaling capability for uncleaved and cleaved events. The EPB is efficiently and selectively cleaved by MMP-7 as measured by the rate of decrease in redox current of ferrocene. Direct transduction of a signal corresponding to peptide cleavage events into an electronic signal thus provides a simple, sensitive route for detecting the MMP activity. The new method allows for identification of the activity of MMP-7 in concentrations as low as 3.4 pM. The concept can be extended to design multiple peptide substrate labeled with different electroactive reporters for assaying multiple MMPs activities.
2006. "Versatile Apoferritin Nanoparticle Labels for Assay of Protein ." Analytical Chemistry 78(21):7417-7423. doi:10.1021/ac060653j Abstract A versatile bioassay label based on marker-loaded-apoferritin nanoparticles (MLAN) have been developed for sensitive protein detection. Dissociation and reconstitution characteristics at different pH as well as the special cavity structure of apoferritin provide a facile route to prepare nanoparticle labels, and avoid complicated and tedious synthesis process of conventional nanoparticle labels. The optical and electrochemical characteristics of the prepared nanoparticle labels are easily controlled by loading different optical or electrochemical markers. A fluorescence marker (fluorescein anion) and a redox marker [hexacyanoferrate (III)] were used as model markers to load into the cavity of apoferritin nanoparticle and developed for microscopic fluorescence immunoassay and electrochemical immunoassay, respectively. Detection limits of 0.06 ng mL-1 (0.39 pM) and 0.08 ng mL-1 (0.51 pM) of IgG were obtained with fluorescein MLAP and hexacyanoferrate MLAN, respectively. The new nanoparticle labels hold great promise for multiplex protein detection (in connection to nanoparticles loaded with different markers) and for enhancing the sensitivity of other bioassay.
2006. "Surface and Interface Control on Photochemically Initiated Immobilization ." Journal of the American Chemical Society 128(43):14067 (6 pages). Abstract Surface and interface properties are important in controlling the yield and efficiency of the photochemically initiated immobilization. Using a silane-functionalized perfluorophenylazide (PFPA-silane) as the photoactive crosslinker, the immobilization of polymers was studied by adjusting the density of the surface azido groups. Dilution of the photolinker resulted in a gradual decrease in the density of surface azido groups as well as the thickness of the immobilized film. When a non-photoactive silane was added to PFPA-silane, the film thickness decreased more rapidly, indicating that the additive competed with PFPA-silane and effectively reduced the density of the surface azido groups. The effect of surface topography was studied by adding a non-photoactive silane with either a shorter (n-propyltrimethoxysilane (PTMS)) or a longer spacer (n-octadecyltrimethoxysilane (ODTMS)). In most cases the long chain ODTMS shielded the surface azido groups resulting in more rapid decrease in film thickness as compared to PTMS treated under the same conditions. As the density of the surface azido groups decreased, the immobilized polymer changed from smooth films to patched structures, and eventually single polymer molecules.
2006. "Revealing Two-State Protein-Protein Interaction of Calmodulin by Single-Molecule Spectroscopy." Journal of the American Chemical Society 128(31):10034-10042. Abstract We report a single-molecule fluorescence resonance energy transfer (FRET) and polarization study of conformational dynamics of calmodulin (CaM) interacting with a target peptide, C28W of 28 amino-acid oligomer. The C28W peptide represents the essential binding sequence domain of the Ca-ATPase protein interacting with CaM, which is important in cellular signaling for the regulation of energy in metabolism. However, the mechanism of the CaM-C28W recognition complex formation is still unclear. The amino-terminal (N-terminal) domain of the CaM was labeled with a fluorescein-based arsenical hairpin binder (F1AsH) that enables our unambiguously probing the CaM N-terminal target-binding domain motions at a millisecond timescale without convolution of the probe-dye random motions. By analyzing the distribution of FRET efficiency between F1AsH labeled CaM and Texas Red labeled C28W and the polarization fluctuation dynamics and distributions of the CaM N-terminal domain, we reveal slow (at sub-second time scale) binding-unbinding motions of the N-terminal domain of the CaM in CaM-C28W complexes, which is a strong evidence of a two-state binding interaction of CaM-mediated cell signaling.
2006. "Evaluation of Multi-Protein Immunoaffinity Subtraction for Plasma Proteomics and Candidate Biomarker Discovery Using Mass Spectrometry." Molecular & Cellular Proteomics. MCP 5(11):2167-2174. Abstract The detection of low-abundance protein disease biomarkers from human blood poses significant challenges due to the high dynamic range of protein concentrations that span more than 10 orders of magnitude, as well as the extreme complexity of the serum/plasma proteome. Therefore, experimental strategies that include the removal of high-abundance proteins have been increasingly utilized in proteomic studies of serum, plasma, and other body fluids to enhance detection of low-abundance proteins and achieve broader proteome coverage. However, both the specificity and reproducibility of the high-abundance protein depletion process represent common concerns. Here, we report a detailed evaluation of the performance of two commercially available immunoaffinity subtraction systems commonly used in human serum/plasma proteome characterization by high resolution LC-MS/MS. One system uses mammalian IgG antibodies to remove six of the most abundant plasma proteins, and the other uses chicken immunoglobulin yolk (IgY) antibodies to remove twelve of the most abundant plasma proteins. Plasma samples were repeatedly processed using these two systems, and the resulting flow-through fractions and bound fractions were individually analyzed for comparison. Removal of target proteins by both immunoaffinity subtraction systems proved reproducible and efficient. Nontarget proteins, including spiked protein standards, were also observed to bind to the columns, but in a fairly reproducible manner. The results suggest that these multi-protein immunoaffinity subtraction systems are both highly effective and reproducible for removing high-abundance proteins and therefore, can be readily integrated into quantitative strategies to enhance detection of low-abundance proteins in biomarker discovery studies.
2006. "High Dynamic Range Characterization of the Trauma Patient Plasma Proteome ." Molecular & Cellular Proteomics. MCP 5(10):1899-1913. doi:10.1074/mcp.M600068-MCP200 Abstract While human plasma represents an attractive sample for disease biomarker discovery, the extreme complexity and large dynamic range in protein concentrations present significant challenges for characterization, candidate biomarker discovery, and validation. Herein, we describe a strategy that combines immunoaffinity subtraction and chemical fractionation based on cysteinyl peptide and N-glycopeptide captures with 2D-LC-MS/MS to increase the dynamic range of analysis for plasma. Application of this “divide-and-conquer” strategy to trauma patient plasma significantly improved the overall dynamic range of detection and resulted in confident identification of 22,267 unique peptides from four different peptide populations (cysteinyl peptides, non-cysteinyl peptides, N-glycopeptides, and non-glycopeptides) that covered 3654 nonredundant proteins. Numerous low-abundance proteins were identified, exemplified by 78 “classic” cytokines and cytokine receptors and by 136 human cell differentiation molecules. Additionally, a total of 2910 different N-glycopeptides that correspond to 662 N-glycoproteins and 1553 N-glycosylation sites were identified. A panel of the proteins identified in this study is known to be involved in inflammation and immune responses. This study established an extensive reference protein database for trauma patients, which provides a foundation for future high-throughput quantitative plasma proteomic studies designed to elucidate the mechanisms that underlie systemic inflammatory responses.
2006. "Analysis of Anions in Ambient Aerosols by Microchip Capillary Electrophoresis." The Analyst 131(11):1226-1231. doi:10.1039/b608945c Abstract We describe a microchip capillary electrophoresis method for the analysis of nitrate and sulfate in ambient aerosols. Investigating the chemical composition of ambient aerosol particles is essential for understanding their sources and effects. Significant progress has been made towards developing mass spectrometry-based instrumentation for rapid qualitative analysis of aerosols. Alternative methods for rapid quantification of selected high abundance compounds are needed to augment the capacity for widespread routine analysis. Such methods could provide much higher temporal and spatial resolution than can be achieved currently. Inorganic anions comprise a large percentage of particulate mass with nitrate and sulfate among the most abundant species. While ion chromatography has proven very useful for analyzing extracts of time-integrated ambient aerosol samples collected on filters and for semi-continuous, on-line particle composition measurements, there is a growing need for development of new compact, inexpensive approaches to routine on-line aerosol ion analysis for deployment in spatially dense, atmospheric measurement networks. Microchip capillary electrophoresis provides the necessary speed and portability to address this need. In this report, on-column contact conductivity detection is used with hydrodynamic injection to create a simple microchip instrument for analysis of nitrate and sulfate. On-column contact conductivity detection was achieved using a Pd decoupler placed upstream from the working electrodes. Microchips containing two Au or Pd working electrodes showed a good linear range (5-500 µM) and low limits-of-detection for sulfate and nitrate with Au providing the lowest detection limits (1 µM) for both ions. The completed microchip system was used to analyze ambient aerosol filter samples. Nitrate and sulfate concentrations measured by the microchip matched the concentrations measured by ion chromatography.
2006. "Comparison of Water-Soluble CdTe Nanoparticles Synthesized In Air and In Nitrogen." Journal of Physical Chemistry B 110(34):16992-17000. Abstract It is commonly believed that high quality CdTe nanoparticles with strong luminescence can only be prepared under the protection of an inert gas such as nitrogen or argon. Here we report the preparation of highly luminescent CdTe nanoparticles in air and compare their luminescence properties with CdTe nanoparticles made in nitrogen. We find that both CdTe nanoparticles made in air and in nitrogen exhibit strong photoluminescence as well as upconversion luminescence at room temperature. However, differences do exist between the particles made in air and in nitrogen. In particular, the particles prepared in air display a faster growth rate, grow to larger sizes, and display stronger electron coupling relative to the particles prepared in nitrogen. X-ray photoelectron spectroscopy analysis indicates that the oxygen content in the nanoparticles synthesized in air is higher that in particles synthesized in N2, likely resulting in a higher availability of excess free cadmium. Cytotoxicology measurements reveal that the particles made in air appear slightly more toxic, possibly due to the excess of free cadmium.
2006. "Peptide Ozonolysis: Product Structures and Relative Reactivities for Oxidation of Tyrosine and Histidine Residues ." Journal of the American Society for Mass Spectrometry 17(9):1289-1298. doi:10.1016/j.jasms.2006.05.009 Abstract Angiotensin II (DRVYIHPF) and two analogs (DRVYIAPA, and DRVAIHPA) were used as model systems to study the ozonolysis of peptides containing tyrosine and histidine residues. The ESI mass spectrum of angiotensin II following exposure to ozone showed the formation of adducts containing one, three and four oxygen atoms. CID and SID spectra of these adducts were consistent with formation of Tyr + O and His + 3O as expected from previous work with amino acids. Additional ions in the CID and SID spectra suggested formation of Tyr + 3O and a small amount of Phe + O. Two analogs were also studied, one in which His and Phe were replaced by Ala (DRVYIAPA) and the other in which Tyr and Phe were replaced by Ala (DRVAIHPA). Exposure of DRVYIAPA to ozone resulted in the addition of one and three oxygen atoms, while DRVAIHPA showed only the addition of three oxygen atoms. Tandem mass spectra of these adducts confirmed the formation of Tyr + 3O in addition to Tyr + O and His + 3O. Other noteworthy minor oxidation products were observed from these analogs including Tyr + 34 u, His + 34 u, and His + 82 u. Modified reaction schemes for peptide ozonolysis are proposed which account for each of these newly observed adducts.
2006. "Photostructural relaxation in As–Se–S glasses: Effect of network fragility." Journal of Non-crystalline Solids 352(21-22):2067-2072. doi:10.1016/j.jnoncrysol.2006.03.004 Abstract The effect of photoinduced structural relaxation in As–S–Se glass is investigated during sub-bandgap irradiation. It is shown that the glass undergoes rapid optically induced structural relaxation upon photoexcitation of bonding electrons. Fragile systems exhibit larger relaxation as expected from their enthalpy profile. This suggests that the process is thermodynamically driven and that the kinetic impediment to relaxation at low temperature is lifted through photoinduced softening of the glass matrix. Activation energy for enthalpy relaxation measurement and an annealing study near Tg show that the photorelaxation effect is not a thermally activated process. The árñ dependence of photostructural changes is addressed and explained using the energy landscape formalism.
2006. "More sensitive and quantitative proteomic measurements using very low flow rate porous silica monolithic LC columns with electrospray ionization-mass spectrometry ." Journal of Proteome Research 5(5):1091-1097. Abstract The sensitivity of proteomics measurements using liquid chromatography (LC) separations interfaced with electrospray ionization-mass spectrometry (ESI-MS) improves approximately inversely with liquid flow rate, making attractive the use of smaller inner diameter LC columns. We report the development and initial application of 10 µm i.d. silica-based monolithic LC columns providing more sensitive proteomics measurements. The implementation provides robust performance and suitability for automated proteome analyses due to integration with a micro solid phase extraction pre-column for ease of sample injection and clean-up prior to the reversed phased LC separation. Greater than 10-fold improvement in sensitivity was obtained compared to analyses using more conventional capillary LC, enabling e.g. the identification of >5000 different peptides by MS/MS from 100-ng of a Shewanella oneidensis tryptic digest using an ion trap MS. The low nL/min LC flow rates provide more uniform signal intensities for different peptides, and provided improved quantitative measurements compared to conventional separation systems without the use of internal standards or isotopic labeling. The improved sensitivity allowed LC-MS measurements of immunopurified protein phosphatase 5 that were in good agreement with quantitative western blot analyses.