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1.  Modulation of Y356 Photooxidation in E. coli Class Ia Ribonucleotide Reductase by Y731 Across the α2:β2 Interface 
Journal of the American Chemical Society  2013;135(36):10.1021/ja405498e.
Substrate turnover in class Ia ribonucleotide reductase (RNR) requires reversible radical transport across two subunits over 35 A, which occurs by a multi-step proton-coupled electron transfer mechanism. Using a photooxidant-labeled β2 subunit of Escherichia coli class Ia RNR, we demonstrate photoinitiated oxidation of a tyrosine in an α2:β2 complex, which results in substrate turnover. Using site-directed mutations of the redox-active tyrosines at the subunit interface—Y356F(β) and Y731F(α)—this oxidation is identified to be localized on Y356. The rate of Y356 oxidation depends on the presence of Y731 across the interface. This observation supports the proposal that unidirectional PCET across the Y356(β)–Y731(α)–Y730(α) triad is crucial to radical transport in RNR.
PMCID: PMC3881532  PMID: 23927429
2.  Electrochemical polymerization of pyrene derivatives on functionalized carbon nanotubes for pseudocapacitive electrodes 
Nature Communications  2015;6:7040.
Electrochemical energy-storage devices have the potential to be clean and efficient, but their current cost and performance limit their use in numerous transportation and stationary applications. Many organic molecules are abundant, economical and electrochemically active; if selected correctly and rationally designed, these organic molecules offer a promising route to expand the applications of these energy-storage devices. In this study, polycyclic aromatic hydrocarbons are introduced within a functionalized few-walled carbon nanotube matrix to develop high-energy, high-power positive electrodes for pseudocapacitor applications. The reduction potential and capacity of various polycyclic aromatic hydrocarbons are correlated with their interaction with the functionalized few-walled carbon nanotube matrix, chemical configuration and electronic structure. These findings provide rational design criteria for nanostructured organic electrodes. When combined with lithium negative electrodes, these nanostructured organic electrodes exhibit energy densities of ∼350 Wh kg−1electrode at power densities of ∼10 kW kg−1electrode for over 10,000 cycles.
Electrochemically active organic molecules are an important class of electrode materials for energy storage. Here, the authors report organic electrodes made of polycyclic aromatic hydrocarbons and functionalized few-walled carbon nanotubes, which show promising electrochemical performance.
PMCID: PMC4432658  PMID: 25943905
3.  Deciphering Radical Transport in the Catalytic Subunit of Class I Ribonucleotide Reductase 
Incorporation of 2,3,6-trifluorotyrosine (F3Y) and a rhenium bipyridine ([Re]) photooxidant into a peptide corresponding to the C-terminus of the β protein (βC19) of Escherichia coli ribonucleotide reductase (RNR) allows for the temporal monitoring of radical transport into the α2 subunit of RNR. Injection of the photogenerated F3Y radical from the [Re]–F3Y–βC19 peptide into the surface accessible Y731 of the α2 subunit is only possible when the second Y730 is present. With the Y–Y established, radical transport occurs with a rate constant of 3 × 105 s−1. Point mutations that disrupt the Y–Y dyad shut down radical transport. The ability to obviate radical transport by disrupting the hydrogen bonding network of the amino acids composing the co-linear proton-coupled electron transfer pathway in α2 suggests a finely tuned evolutionary adaptation of RNR to control the transport of radicals in this enzyme.
PMCID: PMC3268775  PMID: 22121977
Ribonucleotide Reductase; Proton-Coupled Electron Transfer; Radical Transport
4.  Metabolic Tumor Profiling with pH, Oxygen, and Glucose Chemosensors on a Quantum Dot Scaffold 
Inorganic chemistry  2013;53(4):1900-1915.
Acidity, hypoxia and glucose levels characterize the tumor microenvironment rendering pH, pO2 and pGlucose, respectively, important indicators of tumor health. To this end, understanding how these parameters change can be a powerful tool for the development of novel and effective therapeutics. We have designed optical chemosensors that feature a quantum dot and an analyte-responsive dye. These non-invasive chemosensors permit pH, oxygen, and glucose to be monitored dynamically within the tumor microenvironment by using multiphoton imaging.
PMCID: PMC3944830  PMID: 24143874
6.  Two–Photon Oxygen Sensing with Quantum Dot–Porphyrin Conjugates 
Inorganic chemistry  2013;52(18):10.1021/ic4011168.
Supramolecular assemblies of a quantum dot (QD) associated to palladium(II) porphyrins have been developed to detect oxygen (pO2) in organic solvents. Palladium porphyrins are sensitive in the 0–160 torr range, making them ideal phosphors for in vivo biological oxygen quantification. Porphyrins with meso pyridyl substituents bind to the surface of the QD to produce self–assembled nanosensors. Appreciable overlap between QD emission and porphyrin absorption features results in efficient Förster resonance energy transfer (FRET) for signal transduction in these sensors. The QD serves as a photon antenna, enhancing porphyrin emission under both one– and two–photon excitation, demonstrating that QD–palladium porphyrin conjugates may be used for oxygen sensing over physiological oxygen ranges.
PMCID: PMC3881537  PMID: 23978247
7.  Alternating layer addition approach to CdSe/CdS core/shell quantum dots with near-unity quantum yield and high on-time fractions 
We report single-particle photoluminescence (PL) intermittency (blinking) with high on-time fractions in colloidal CdSe quantum dots (QD) with conformal CdS shells of 1.4 nm thickness, equivalent to approximately 4 CdS monolayers. All QDs observed displayed on-time fractions > 60% with the majority > 80%. The high-on-time-fraction blinking is accompanied by fluorescence quantum yields (QY) close to unity (up to 98% in an absolute QY measurement) when dispersed in organic solvents and a monoexponential ensemble photoluminescence (PL) decay lifetime. The CdS shell is formed in high synthetic yield using a modified selective ion layer adsorption and reaction (SILAR) technique that employs a silylated sulfur precursor. The CdS shell provides sufficient chemical and electronic passivation of the QD excited state to permit water solubilization with greater than 60% QY via ligand exchange with an imidazole-bearing hydrophilic polymer.
PMCID: PMC4052982  PMID: 24932403
8.  Energy Transfer of CdSe/ZnS Nanocrystals Encapsulated with Rhodamine-Dye Functionalized Poly(acrylic acid) 
Energy transfer between a CdSe/ZnS nanocrystal (NC) donor and a rhodamine isothiocyanate (RITC) acceptor has been achieved via a functionalized poly(acrylic acid) (PAA) encapsulating layer over the surface of the NC. The modification of PAA with both N-octylamine (OA) and 5-amino-1-pentanol (AP), [PAA-OA-AP], allows for the simultaneous water-solubilization and functionalization of the NCs, underscoring the ease of synthesizing NC-acceptor conjugates with this strategy. Photophysical studies of the NC-RITC constructs showed that energy transfer is efficient, with kFRET approaching 108 s−1. The ease of the covalent conjugation of molecules to NCs with PAA-OA-AP coating, together with efficient energy transfer, makes the NCs encapsulated with PAA-OA-AP attractive candidates for sensing applications.
PMCID: PMC4050743  PMID: 24926175
9.  Conformational control of energy transfer: a new mechanism for biocompatible nanocrystal-based sensors** 
Fold-up fluorophore: A new paradigm for designing self-referencing fluorescent nanosensors is demonstrated by interfacing a pH-triggered molecular conformational switch with quantum dots. Analytedependent, large-amplitude conformational motion controls the distance between the nanocrystal energy donor and an organic FRET acceptor. The result is a fluorescence signal capable of reporting pH values from individual endosomes in living cells.
PMCID: PMC3793206  PMID: 23225635
biosensors; fluorescent probes; quantum dots; molecular devices; molecular machines
10.  Energy transfer mediated by asymmetric hydrogen-bonded interfaces† 
Amidine-appended ferrocene derivatives form a supramolecular assembly with Ru(ii)(bpy-COOH) (L)22+ complexes (bpy-COOH is 4-CO2H-4′-CH3-bpy and L = bpy, 2,2′-bipyridine or btfmbpy, 4,4′-bis (trifluoromethyl)-2,2′-bipyridine). Steady-state, time-resolved spectroscopy and kinetic isotope effects establish that the metal-to-ligand charge transfer excited states of the Ru(ii) complexes are quenched by proton-coupled energy transfer (PCEnT). These results show that proton motion can be effective in mediating not only electron transfer (ET) but energy transfer (EnT) as well.
PMCID: PMC3868475  PMID: 24363889
11.  Halogen Photoelimination from Dirhodium Phosphazane Complexes via Chloride-Bridged Intermediates 
Halogen photoelimination is a critical step in HX-splitting photocatalysis. Herein, we report the photoreduction of a pair of valence-isomeric dirhodium phosphazane complexes, and suggest that a common intermediate is accessed in the photochemistry of both mixed-valent and valence-symmetric complexes. The results of these investigations suggest that halogen photoelimination proceeds by two sequential photochemical reactions: ligand dissociation followed by subsequent halogen elimination.
PMCID: PMC3819227  PMID: 24224081
12.  Photochemical Tyrosine Oxidation with a Hydrogen-Bonded Proton Acceptor by Bidirectional Proton-Coupled Electron Transfer 
Amino acid radical generation and transport are fundamentally important to numerous essential biological processes to which small molecule models lend valuable mechanistic insights. Pyridyl-amino acid-methyl esters are appended to a rhenium(I) tricarbonyl 1,10-phenanthroline core to yield rhenium–amino acid complexes with tyrosine ([Re]–Y–OH) and phenylalanine ([Re]–F). The emission from the [Re] center is more significantly quenched for [Re]–Y–OH upon addition of base. Time-resolved studies establish that excited-state quenching occurs by a combination of static and dynamic mechanisms. The degree of quenching depends on the strength of the base, consistent with a proton-coupled electron transfer (PCET) quenching mechanism. Comparative studies of [Re]–Y–OH and [Re]–F enable a detailed mechanistic analysis of a bidirectional PCET process.
PMCID: PMC3594118  PMID: 23495362
13.  Re(bpy)(CO)3CN as a Probe of Conformational Flexibility in a Photochemical Ribonucleotide Reductase† 
Biochemistry  2009;48(25):5832-5838.
Photochemical ribonucleotide reductases (photoRNRs) have been developed to study the proton-coupled electron transfer (PCET) mechanism of radical transport in class I E. coli ribonucleotide reductase (RNR). The transport of the effective radical occurs along several conserved aromatic residues across two subunits: β2(•Y122→W48→Y356)→ α2(Y731→Y730→C439). The current model for RNR activity suggests that radical transport is strongly controlled by conformational gating. The C-terminal tail peptide (Y- βC19) of β2 is the binding determinant of β2 to α2 and contains the redox active Y356 residue. A photoRNR has been generated synthetically by appending a Re(bpy)(CO)3CN ([Re]) photo-oxidant next to Y356 of the 20-mer peptide. Emission from the [Re] center dramatically increases upon peptide binding, serving as a probe for conformational dynamics and Y356 protonation state. The diffusion coefficient of [Re]-Y-βC19 has been measured (kd1 = 6.1 × 10−7 cm−1 s–1), along with the dissociation rate constant for the [Re]-Y-βC19:α2 complex (7000 s−1 > koff > 400 s−1). Results from detailed time-resolved emission and absorption spectroscopies reveal biexponential kinetics, suggesting a large degree of conformational flexibility in the α2:[Re]-Y-βC19 complex that partitions the N-terminus of the peptide into both bound and solvent-exposed fractions.
PMCID: PMC3340421  PMID: 19402704
14.  Two-Photon Absorbing Nanocrystal Sensors for Ratiometric Detection of Oxygen 
Journal of the American Chemical Society  2009;131(36):12994-13001.
Two nanocrystal-osmium(II) polypyridyl (NC-Os(II)PP) conjugates have been designed to detect oxygen in biological environments. Polypyridines appended with a single free amine were linked with facility to a carboxylic acid functionality of a semiconductor NC overlayer to afford a biologically stable amide bond. The Os(II)PP complexes possess broad absorptions that extend into the red spectral region; this absorption feature makes them desirable acceptors of energy from NC donors. Fluorescence resonance energy transfer (FRET) from the NC to the Os(II)PP causes an enhanced Os(II)PP emission with a concomitant quenching of the NC emission. Owing to the large two-photon absorption cross-section of the NCs, FRET from NC to the Os(II)PP can be established under two-photon excitation conditions. In this way, two-photon processes of metal polypyridyl complexes can be exploited for sensing. The emission of the NC is insensitive to oxygen, even at 1 atm, whereas excited states of both osmium complexes are quenched in the presence of oxygen. The NC emission may thus be used as an internal reference to correct for fluctuations in the photoluminescence intensity signal. These properties taken together establish NC-Os(II)PP conjugates as competent ratiometric, two-photon oxygen sensors for application in biological microenvironments.
PMCID: PMC3340422  PMID: 19697933
15.  Chemistry of Personalized Solar Energy 
Inorganic Chemistry  2009;48(21):10001-10017.
Personalized energy (PE) is a transformative idea that provides a new modality for the planet’s energy future. By providing solar energy to the individual, an energy supply becomes secure and available to people of both legacy and non-legacy worlds, and minimally contributes to increasing the anthropogenic level of carbon dioxide. Because PE will be possible only if solar energy is available 24 hours a day, 7 day a week, the key enabler for solar PE is an inexpensive storage mechanism. HX (X = halide or OH−) splitting is a fuel-forming reaction of sufficient energy density for large scale solar storage but the reaction relies on chemical transformations that are not understood at the most basic science level. Critical among these are multielectron transfers that are proton-coupled and involve the activation of bonds in energy poor substrates. The chemistry of these three italicized areas is developed, and from this platform, discovery paths leading to new HX and H2O splitting catalysts are delineated. For the case of the water splitting catalyst, it captures many of the functional elements of photosynthesis. In doing so, a highly manufacturable and inexpensive method has been discovered for solar PE storage.
PMCID: PMC3332084  PMID: 19775081
16.  A Comparative PCET Study of a Donor-Acceptor Pair Linked by Ionized and Non-ionized Asymmetric Hydrogen-Bonded Interfaces 
A Zn(II) porphyrin-amidinium is the excited state electron donor (D) to a naphthalene diimide acceptor (A) appended with either a carboxylate or sulfonate functionality. The two-point hydrogen bond (---[H+]---) formed between the amidinium and carboxylate or sulfonate establishes a proton-coupled electron transfer (PCET) pathway for charge transfer. The two D---[H+]---A assemblies differ only by the proton configuration within the hydrogen bonding interface. Specifically, the amidinium transfers a proton to the carboxylate to form a non-ionized amidine-carboxylic acid two-point hydrogen network whereas the amidinium maintains both protons when bound to the sulfonate functionality forming an ionized amidinium-sulfonate two-point hydrogen network. These two interface configurations within the dyads thus allow for a direct comparison of PCET kinetics for the same donor and acceptor juxtaposed by an ionized and non-ionized hydrogen-bonded interface. Analysis of PCET kinetics ascertained from transient absorption and transient emission spectroscopy reveal that the ionized interface is more strongly impacted by the local solvent environment, thus establishing that the initial static configuration of the proton interface is a critical determinant to the kinetics of PCET.
PMCID: PMC3278395  PMID: 19489645
19.  Ru-Porphyrin Protein Scaffolds for Sensing O2 
Hemoprotein-based scaffolds containing phosphorescent ruthenium(II) CO mesoporphyrin IX (RuMP) are reported here for oxygen (O2) sensing in biological contexts. RuMP was incorporated into the protein scaffolds during protein expression utilizing a novel method that we have described previously. A high-resolution (2.00 Å) crystal structure revealed that the unnatural porphyrin binds to the proteins in a manner similar to the native heme and does not perturb the protein fold. The protein scaffolds were found to provide unique coordination environments for RuMP and modulate the porphyrin emission properties. Emission lifetime measurements demonstrate a linear O2 response within the physiological range and precision comparable to commercial O2 sensors. The RuMP proteins are robust, readily-modifiable platforms and display promising O2 sensing properties for future in vivo applications.
PMCID: PMC2859244  PMID: 20373741
20.  Compact biocompatible quantum dots via RAFT-mediated synthesis of imidazole-based random copolymer ligand 
We present a new class of polymeric ligands for quantum dot (QD) water solubilization to yield biocompatible and derivatizable QDs with compact size (~10-12 nm diameter), high quantum yields (>50%), excellent stability across a large pH range (pH 5-10.5), and low nonspecific binding. To address the fundamental problem of thiol instability in traditional ligand exchange systems, the polymers here employ a stable multidentate imidazole binding motif to the QD surface. The polymers are synthesized via reversible addition-fragmentation chain transfer (RAFT)-mediated polymerization to produce molecular weight controlled monodisperse random copolymers from three types of monomers that feature imidazole groups for QD binding, polyethylene glycol (PEG) groups for water solubilization, and either primary amines or biotin groups for derivatization. The polymer architecture can be tuned by the monomer ratios to yield aqueous QDs with targeted surface functionalities. By incorporating amino-PEG monomers, we demonstrate covalent conjugation of a dye to form a highly efficient QD-dye energy transfer pair as well as covalent conjugation to streptavidin for high-affinity single molecule imaging of biotinylated receptors on live cells with minimal non-specific binding. The small size and low serum binding of these polymer-coated QDs also allow us to demonstrate their utility for in-vivo imaging of the tumor microenvironment in live mice.
PMCID: PMC2871316  PMID: 20025223
21.  Compact Biocompatible Quantum Dots Functionalized for Cellular Imaging 
We present a family of water-soluble quantum dots (QDs) that exhibit low nonspecific binding to cells, small hydrodynamic diameter, tunable surface charge, high quantum yield, and good solution stability across a wide pH range. These QDs are amenable to covalent modification via simple carbodiimide coupling chemistry, which is achieved by functionalizing the surface of QDs with a new class of heterobifunctional ligands incorporating dihydrolipoic acid, a short poly(ethylene glycol) (PEG) spacer, and an amine or carboxylate terminus. The covalent attachment of molecules is demonstrated by appending a rhodamine dye to form a QD-dye conjugate exhibiting fluorescence resonance energy transfer (FRET). High-affinity labeling is demonstrated by covalent attachment of streptavidin, thus enabling the tracking of biotinylated epidermal growth factor (EGF) bound to EGF receptor on live cells. In addition, QDs solubilized with the heterobifunctional ligands retain their metal-affinity driven conjugation chemistry with polyhistidine-tagged proteins. This dual functionality is demonstrated by simultaneous covalent attachment of a rhodamine FRET acceptor and binding of polyhistidine-tagged streptavidin on the same nanocrystal to create a targeted QD, which exhibits dual-wavelength emission. Such emission properties could serve as the basis for ratiometric sensing of the cellular receptor’s local chemical environment.
PMCID: PMC2665712  PMID: 18177042
22.  A ligand field chemistry of oxygen generation by the oxygen-evolving complex and synthetic active sites 
Oxygen–oxygen bond formation and O2 generation occur from the S4 state of the oxygen-evolving complex (OEC). Several mechanistic possibilities have been proposed for water oxidation, depending on the formal oxidation state of the Mn atoms. All fall under two general classifications: the AB mechanism in which nucleophilic oxygen (base, B) attacks electrophilic oxygen (acid, A) of the Mn4Ca cluster or the RC mechanism in which radical-like oxygen species couple within OEC. The critical intermediate in either mechanism involves a metal oxo, though the nature of this oxo for AB and RC mechanisms is disparate. In the case of the AB mechanism, assembly of an even-electron count, high-valent metal-oxo proximate to a hydroxide is needed whereas, in an RC mechanism, two odd-electron count, high-valent metal oxos are required. Thus the two mechanisms give rise to very different design criteria for functional models of the OEC active site. This discussion presents the electron counts and ligand geometries that support metal oxos for AB and RC O–O bond-forming reactions. The construction of architectures that bring two oxygen functionalities together under the purview of the AB and RC scenarios are described.
PMCID: PMC2614088  PMID: 17971328
photosynthesis; water oxidation; oxygen-evolving complex; catalysis; solar energy
23.  Proton-coupled electron transfer: the mechanistic underpinning for radical transport and catalysis in biology 
Charge transport and catalysis in enzymes often rely on amino acid radicals as intermediates. The generation and transport of these radicals are synonymous with proton-coupled electron transfer (PCET), which intrinsically is a quantum mechanical effect as both the electron and proton tunnel. The caveat to PCET is that proton transfer (PT) is fundamentally limited to short distances relative to electron transfer (ET). This predicament is resolved in biology by the evolution of enzymes to control PT and ET coordinates on highly different length scales. In doing so, the enzyme imparts exquisite thermodynamic and kinetic controls over radical transport and radical-based catalysis at cofactor active sites. This discussion will present model systems containing orthogonal ET and PT pathways, thereby allowing the proton and electron tunnelling events to be disentangled. Against this mechanistic backdrop, PCET catalysis of oxygen–oxygen bond activation by mono-oxygenases is captured at biomimetic porphyrin redox platforms. The discussion concludes with the case study of radical-based quantum catalysis in a natural biological enzyme, class I Escherichia coli ribonucleotide reductase. Studies are presented that show the enzyme utilizes both collinear and orthogonal PCET to transport charge from an assembled diiron-tyrosyl radical cofactor to the active site over 35 Å away via an amino acid radical-hopping pathway spanning two protein subunits.
PMCID: PMC1647304  PMID: 16873123
proton-coupled electron transfer; amino acid radicals; tunnelling; tyrosine; catalysis; ribonucleotide reductase

Results 1-23 (23)