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Biomedical subjects

Daniel G Nocera

Publications and source records attributed to Daniel G Nocera.

At least 19 recordsLinked to original sources
PubMed2006

Hangman salen platforms containing two xanthene scaffolds.

A synthetic strategy for the construction of chiral salen ligands bearing two rigid xanthene spacers functionalized with carboxylic acid and ester groups is presented. Suzuki cross-coupling methodology is used to furnish the appropriately functionalized xanthene spacers to a salicylaldehyde, which is subsequently condensed with (1R,2R)-(-)-1,2-diaminocyclohexane to produce salen ligands featuring an expandable molecular cleft capable of multiple hydrogen-bonding interactions in addition to metallosalen oxidation chemistry. The ability of these "Hangman" platforms to support multielectron chemistry mediated by proton-coupled electron transfer (PCET) is established by their proclivity to promote the catalytic disproportionation of hydrogen peroxide to oxygen and water via a high-valent metal oxo. Within this functionalized Hangman framework, the stereochemistry of the cyclohexyl backbone of the salen platform is revealed in the epoxidation of 1,2-dihydronaphthalene by the metal oxo.

Journal Article↗
PubMed2006

Electron transfer reactions of fluorotyrosyl radicals.

The complex Re(bpy)(CO)3CN is an excited state oxidant of tyrosine upon deprotonation of the tyrosyl phenol. A series of Re(bpy-FnY)(CO)3CN complexes ([Re]-FnY: [Re]-Y, [Re]-3-FY, [Re]-3,5-F2Y, [Re]-2,3-F2Y, [Re]-2,3,5-F3Y, [Re]-2,3,6-F3Y, and [Re]-F4Y) have been prepared so as to vary the FnY*/FnY- reduction potential and thus the driving force for electron transfer in this system. Time-resolved emission and nanosecond absorption spectroscopies have been used to measure the rates for charge separation, CS, and charge recombination, CR, for each complex. A driving force analysis reveals that CS is well described by Marcus' theory for ET, is strongly driving force dependent (activated), and occurs in the normal region for ET. CR, on the other hand, is weakly driving force dependent (near activationless) and occurs in the inverted region for ET. These data demonstrate that fluorotyrosines will be powerful probes for unraveling charge transport mechanisms in enzymes that utilize tyrosyl radicals.

2,2'-Dipyridyl↗
PubMed2006

A ratiometric CdSe/ZnS nanocrystal pH sensor.

The development of a reversible chemical sensor based on a CdSe/ZnS nanocrystal (NC) is described. Signal transduction is accomplished by fluorescence resonance energy transfer (FRET) between the NC and a fluorescent pH-sensitive squaraine dye attached to the surface of the NC. The efficiency of FRET, and consequently the relative intensity of NC and dye emissions, is modulated with the pH-dependent absorption cross section of the squaraine dye. The design of a NC sensor based on FRET results in a ratiometric sensor since the emission intensities of dye and NC may be referenced to the isosbestic point between NC and dye emissions. The ratiometric approach allows sensing to be performed, regardless of issues surrounding collection efficiency (scattering environment, light fluctuations, etc.) and dye:NC loadings.

Biosensing Techniques↗
PubMed2006

Powering the planet: chemical challenges in solar energy utilization.

Global energy consumption is projected to increase, even in the face of substantial declines in energy intensity, at least 2-fold by midcentury relative to the present because of population and economic growth. This demand could be met, in principle, from fossil energy resources, particularly coal. However, the cumulative nature of CO(2) emissions in the atmosphere demands that holding atmospheric CO(2) levels to even twice their preanthropogenic values by midcentury will require invention, development, and deployment of schemes for carbon-neutral energy production on a scale commensurate with, or larger than, the entire present-day energy supply from all sources combined. Among renewable energy resources, solar energy is by far the largest exploitable resource, providing more energy in 1 hour to the earth than all of the energy consumed by humans in an entire year. In view of the intermittency of insolation, if solar energy is to be a major primary energy source, it must be stored and dispatched on demand to the end user. An especially attractive approach is to store solar-converted energy in the form of chemical bonds, i.e., in a photosynthetic process at a year-round average efficiency significantly higher than current plants or algae, to reduce land-area requirements. Scientific challenges involved with this process include schemes to capture and convert solar energy and then store the energy in the form of chemical bonds, producing oxygen from water and a reduced fuel such as hydrogen, methane, methanol, or other hydrocarbon species.

Carbon↗
PubMed2006

Electron transfer driven by proton fluctuations in a hydrogen-bonded donor-acceptor assembly.

The temperature-isotope dependence of proton-coupled electron transfer (PCET) for a noncovalent molecular dyad is reported. The system consists of an excited-state Zn(II) porphyrin that transfers an electron to a naphthalene diimide acceptor through an amidinium-carboxylate interface. Two different isotope effects are observed for variant temperature regimes. A reverse isotope effect (i.e., kH/kD < 1) is observed as T approaches 120 K (kH/kD = 0.9, 120 K), whereas a normal isotope effect (i.e., kH/kD > 1) is recovered as the temperature is increased (kH/kD = 1.2, 300 K). The transition between these limits is smooth, with a crossover temperature of T approximately 160 K. These observations are in accordance with charge-transfer dynamics that are susceptible to bath-induced fluctuations in the proton coordinate.

Electron Transport↗
PubMed2006

Mechanistic studies of Hangman salophen-mediated activation of O-O bonds.

Stopped-flow kinetic studies of a HSX-Mn-SalophOMe (1) catalyst provide spectroscopic evidence for the direct generation of a manganese(V) oxo salophen from a manganese(III) perbenzoate. The O-O bond heterolysis reaction that produces the oxo is not facilitated by intramolecular proton transfer from the acid hanging group of the HSX platform. Instead, the hanging group stabilizes the catalyst against oxidative degradation and, consistent with recent predictions of theory, is geometrically matched to promote the end-on coordination of a H2O2 substrate prior to its oxidation at the manganese(V) oxo center.

Catalysis↗
PubMed2006

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 35A away via an amino acid radical-hopping pathway spanning two protein subunits.

Amino Acids↗
PubMed2006

Spectroscopic determination of proton position in the proton-coupled electron transfer pathways of donor-acceptor supramolecule assemblies.

A homologous set of porphyrin derivatives possessing an isocyclic five-membered ring appended with an amidinium functionality has been used to examine proton-coupled electron transfer (PCET) through well-characterized amidine-carboxylic acid interfaces. Conjugation between the porphyrin chromophore and the amidinium interface can be altered by selective reduction of the isocyclic ring of an amidinium-purpurin to produce an amidinium-chlorin. The highly conjugated amidinium-purpurin displays large spectral shifts in the visible region upon alteration of the amidinium/amidine protonation state; no such change is observed for the chlorin homologue. Analysis of the UV-vis absorption and emission profiles of the amidinium-purpurin upon deprotonation allows for the measurement of the porphyrinic-amidinium acidity constant for the ground state (pKa = 9.55 +/- 0.1 in CH3CN) and excited state (pKa)= 10.40 +/- 0.1 in CH3CN). The absorption spectrum of the purpurin also provides a convenient handle for determining the protonation state of assembled interfaces. In this way, the purpurin macrocycle provides a general tool for PCET studies because it can be used to determine the location of a proton within PCET interfaces formed from carboxylic acid electron acceptors including dinitrobenzenes (DNBs) and naphthalenediimide (NI), which have been used extensively in previous PCET studies. An amidine-carboxylic acid interface is observed for electron-rich acceptors, whereas the ionized amidinium-carboxylate interface is observed for electron-poor acceptors. The PCET kinetics for purpurin/chlorin associated to NI are consistent with an amidine-carboxylic acid interface, which is also verified spectrally.

Algorithms↗
PubMed2006

A solvent-stable nanocrystal-silica composite laser.

We have developed a photostable nanocrystal-silica (NC-silica) laser that is robust under different chemical environments, making it suitable for integration with a microfluidic network. We demonstrate that the optical properties of this microscale laser can be a dynamic function of its local environment, thus providing a platform for potential applications such as nonlinear optical chemosensing on a miniaturized scale.

Journal Article↗
PubMed2006

Mono-, di-, tri-, and tetra-substituted fluorotyrosines: new probes for enzymes that use tyrosyl radicals in catalysis.

A set of N-acylated, carboxyamide fluorotyrosine (F(n)()Y) analogues [Ac-3-FY-NH(2), Ac-3,5-F(2)Y-NH(2), Ac-2,3-F(2)Y-NH(2), Ac-2,3,5-F(3)Y-NH(2), Ac-2,3,6-F(3)Y-NH(2) and Ac-2,3,5,6-F(4)Y-NH(2)] have been synthesized from their corresponding amino acids to interrogate the detailed reaction mechanism(s) accessible to F(n)()Y*s in small molecules and in proteins. These Ac-F(n)()Y-NH(2) derivatives span a pK(a) range from 5.6 to 8.4 and a reduction potential range of 320 mV in the pH region accessible to most proteins (6-9). DFT electronic-structure calculations capture the observed trends for both the reduction potentials and pK(a)s. Dipeptides of the methyl ester of 4-benzoyl-l-phenylalanyl-F(n)()Ys at pH 4 were examined with a nanosecond laser pulse and transient absorption spectroscopy to provide absorption spectra of F(n)()Y*s. The EPR spectrum of each F(n)()Y* has also been determined by UV photolysis of solutions at pH 11 and 77 K. The ability to vary systematically both pK(a) and radical reduction potential, together with the facility to monitor radical formation with distinct absorption and EPR features, establishes that F(n)()Ys will be useful in the study of biological charge-transport mechanisms involving tyrosine. To demonstrate the efficacy of the fluorotyrosine method in unraveling charge transport in complex biological systems, we report the global substitution of tyrosine by 3-fluorotyrosine (3-FY) in the R2 subunit of ribonucleotide reductase (RNR) and present the EPR spectrum along with its simulation of 3-FY122*. In the companion paper, we demonstrate the utility of F(n)()Ys in providing insight into the mechanism of tyrosine oxidation in biological systems by incorporating them site-specifically at position 356 in the R2 subunit of Escherichia coli RNR.

Catalysis↗
PubMed2006

pH Rate profiles of FnY356-R2s (n = 2, 3, 4) in Escherichia coli ribonucleotide reductase: evidence that Y356 is a redox-active amino acid along the radical propagation pathway.

The Escherichia coli ribonucleotide reductase (RNR), composed of two subunits (R1 and R2), catalyzes the conversion of nucleotides to deoxynucleotides. Substrate reduction requires that a tyrosyl radical (Y(122)*) in R2 generate a transient cysteinyl radical (C(439)*) in R1 through a pathway thought to involve amino acid radical intermediates [Y(122)* --> W(48) --> Y(356) within R2 to Y(731) --> Y(730) --> C(439) within R1]. To study this radical propagation process, we have synthesized R2 semisynthetically using intein technology and replaced Y(356) with a variety of fluorinated tyrosine analogues (2,3-F(2)Y, 3,5-F(2)Y, 2,3,5-F(3)Y, 2,3,6-F(3)Y, and F(4)Y) that have been described and characterized in the accompanying paper. These fluorinated tyrosine derivatives have potentials that vary from -50 to +270 mV relative to tyrosine over the accessible pH range for RNR and pK(a)s that range from 5.6 to 7.8. The pH rate profiles of deoxynucleotide production by these F(n)()Y(356)-R2s are reported. The results suggest that the rate-determining step can be changed from a physical step to the radical propagation step by altering the reduction potential of Y(356)* using these analogues. As the difference in potential of the F(n)()Y* relative to Y* becomes >80 mV, the activity of RNR becomes inhibited, and by 200 mV, RNR activity is no longer detectable. These studies support the model that Y(356) is a redox-active amino acid on the radical-propagation pathway. On the basis of our previous studies with 3-NO(2)Y(356)-R2, we assume that 2,3,5-F(3)Y(356), 2,3,6-F(3)Y(356), and F(4)Y(356)-R2s are all deprotonated at pH > 7.5. We show that they all efficiently initiate nucleotide reduction. If this assumption is correct, then a hydrogen-bonding pathway between W(48) and Y(356) of R2 and Y(731) of R1 does not play a central role in triggering radical initiation nor is hydrogen-atom transfer between these residues obligatory for radical propagation.

Escherichia coli↗
PubMed2005

Spin-frustrated organic-inorganic hybrids of lindgrenite.

We report the syntheses and magnetic properties of hybrid organic-inorganic materials that represent layer-expanded versions of the rare mineral lindgrenite (Cu3(OH)2(MoO4)2). The structures of these compounds feature one-dimensional chains of alternating corner- and edge-sharing Cu(II) triangles. By expanding the inorganic layers of lindgrenite with 4,4'-bipyridine, spin-frustrated antiferromagnetism is revealed by a change of the spin frustration parameter f from 1.2 in lindgrenite to 19.4 in (4,4'-bpy)Cu3(OH)2(MoO4)2.

Journal Article↗
PubMed2005

A photocycle for hydrogen production from two-electron mixed-valence complexes.

Dihydrides of the formula Rh2(II,II)(tfepma)3H2Cl2 (tfepma = (bis[bis(trifluoroethoxy)phosphino]methylamine, MeN(P[OCH2CF3]2)2), have been prepared by the addition of H2 to the two-electron mixed-valence complex, Rh2(0,II)(tfepma)3Cl2 (1). Three isomeric forms with hydrides in syn (2), anti (3), and cis (4) conformations have been characterized by X-ray diffraction. Photolysis of 2 results in prompt formation of a short-lived blue photoproduct (lambda(max) = 600 nm) and a stoichiometric quantity of H2, as determined by Toepler pump and isotopic labeling experiments. The blue photoproduct was identified as a Rh2(I,I) complex resulting from the reductive elimination of H2, as determined from the examination of bimetallic cores coordinated by tfepm (tfepm = (bis[bis(trifluoroethoxy)phosphino]methane, CH2(P[OCH2CF3]2)2), for which complexes of the formula M2(I,I)(tfepm)3Cl2 (5, M = Rh and 6, M = Ir) have been isolated. The d8...d8 dimer of 5 converts to Rh2(0,II)(tfepm)3Cl2CN(t)Bu (8) upon the addition of 1 equiv of tert-butylisonitrile, a result of halogen migration and disproportionation of the valence symmetric core of 5, which is structurally compared to its two-electron mixed-valence analogue, Rh2(0,II)(dfpma)3Cl2CN(t)Bu (9) (dfpma = bis(difluorophosphino)methylamine, MeN(PF2)2). The halogen migration is captured in Ir2(I,I)(tfepm)3(mu-Cl)Cl (7), which is distinguished by the presence of a chloride that bridges the diiridium centers. Taken together, complexes 1-9 permit the construction of a complete photocycle for the photogeneration of H2 by dirhodium dfpma complexes in homogeneous solutions of hydrohalic acids.

Journal Article↗
PubMed2005

A structurally perfect S = (1/2) kagomé antiferromagnet.

The syntheses and magnetic susceptibilities of a pure series of rare copper minerals from the atacamite family with general formula ZnxCu4-x(OH)6Cl2 (0 </= x </= 1) are reported. The structure of these compounds features a corner-sharing triangular kagomé lattice of antiferromagnetically coupled Cu(II) ions. We correlate the onset of magnetic ordering with the mole fraction of paramagnetic Cu(II) ions located between kagomé layers and demonstrate that the fully Zn-substituted compound shows no magnetic ordering down to 2 K, resulting in a highly spin-frustrated S = 1/2 lattice.

Journal Article↗
PubMed2005

Molecular chemistry of consequence to renewable energy.

Energy conversion cycles are aimed at driving unfavorable, small-molecule activation reactions with a photon harnessed directly by a transition-metal catalyst or indirectly by a transition-metal catalyst at the surface of a photovoltaic cell. The construction of such cycles confronts daunting challenges because they rely on chemical transformations not understood at the most basic levels. These transformations include multielectron transfer, proton-coupled electron transfer, and bond-breaking and -making reactions of energy-poor substrates. We have begun to explore these poorly understood areas of molecular science with transition-metal complexes that promote hydrogen production and oxygen bond-breaking and -making chemistry of consequence to water splitting.

Electric Power Supplies↗
PubMed2005

Structural tuning of ligand-based two-electron intervalence charge transfer.

The lowest-energy optical transition of two-electron-oxidized porphyrinogens [L(Delta)M] is a ligand-based charge transfer. The color of the intermediary, two-electron mixed-valent oxidation state shifts from vermilion (lambdamax = 480 nm) to yellow (lambdamax = 270 nm) upon increasing the ionic radius of the central metal dication from Mg2+ to Zn2+ and Ca2+. Structural, spectroscopic, and computational studies establish that the relative energies of the highest occupied and lowest unoccupied orbitals, between which the intervalence charge-transfer optical transition occurs, are modulated by the molecular dipole moment, which in turn depends on the only structural variable among the [L(Delta)M] compounds, the position of M2+ relative to the dianionic dipyrrole unit.

Journal Article↗