De novo design of symmetric ferredoxins that shuttle electrons in vivo.

A symmetric origin for bacterial ferredoxins was first proposed over 50 y ago, yet, to date, no functional symmetric molecule has been constructed. It is hypothesized that extant proteins have drifted from their symmetric roots via gene duplication followed by mutations. Phylogenetic analyses of extant ferredoxins support the independent evolution of N- and C-terminal sequences, thereby allowing consensus-based design of symmetric 4Fe-4S molecules. All designs bind two [4Fe-4S] clusters and exhibit strongly reducing midpoint potentials ranging from -405 to -515 mV. One of these constructs efficiently shuttles electrons through a designed metabolic pathway in Escherichia coli These finding establish that ferredoxins consisting of a symmetric core can be used as a platform to design novel electron transfer carriers for in vivo applications. Outer-shell asymmetry increases sequence space without compromising electron transfer functionality.

Design of a Fe4 S4 cluster into the core of a de novo four-helix bundle.

We explore the capacity of the de novo protein, S824, to incorporate a multinuclear iron-sulfur cluster within the core of a single-chain four-helix bundle. This topology has a high intrinsic designability because sequences are constrained largely by the pattern of hydrophobic and hydrophilic amino acids, thereby allowing for the extensive substitution of individual side chains. Libraries of novel proteins based on these constraints have surprising functional potential and have been shown to complement the deletion of essential genes in E. coli. Our structure-based design of four first-shell cysteine ligands, one per helix, in S824 resulted in successful incorporation of a cubane Fe4 S4 cluster into the protein core. A number of challenges were encountered during the design and characterization process, including nonspecific metal-induced aggregation and the presence of competing metal-cluster stoichiometries. The introduction of buried iron-sulfur clusters into the helical bundle is an initial step toward converting libraries of designed structures into functional de novo proteins with catalytic or electron-transfer functionalities.

A Blinking Mesoporous TiO2-x Composed of Nanosized Anatase with Unusually Long-Lived Trapped Charge Carriers.

A mesoporous TiO2-x material comprised of small, crystalline, vacancy-rich anatase nanoparticles (NPs) shows unique optical, thermal, and electronic properties. It is synthesized using polymer-derived mesoporous carbon (PDMC) as a template. The PDMC pores serve as physical barriers during the condensation and pyrolysis of a titania precursor, preventing the titania NPs from growing beyond 10 nm in size. Unlike most titania nanomaterials, during pyrolysis the NPs undergo no transition from the anatase to rutile phase and they become catalytically active reduced TiO2-x . When exposed to a slow electron beam, the NPs exhibit a charge/discharge behavior, lighting up and fading away for an average period of 15 s for an extended period of time. The NPs also show a 50 nm red-shift in their UV/Vis absorption and long-lived charge carriers (electrons and holes) at room temperature in the dark, even long after UV irradiation. The NPs as photocatalysts show a good activity for CO2 reduction.

Minimal Heterochiral de Novo Designed 4Fe-4S Binding Peptide Capable of Robust Electron Transfer.

Ambidoxin is a designed, minimal dodecapeptide consisting of alternating L and D amino acids that binds a 4Fe-4S cluster through ligand-metal interactions and an extensive network of second-shell hydrogen bonds. The peptide can withstand hundreds of oxidation-reduction cycles at room temperature. Ambidoxin suggests how simple, prebiotic peptides may have achieved robust redox catalysis on the early Earth.

A Bis(imidazole)-based cysteine labeling tool for metalloprotein assembly.

Precise metal-protein coordination by design remains a considerable challenge. Polydentate, high-metal-affinity protein modifications, both chemical and recombinant, can enable metal localization. However, these constructs are often bulky, conformationally and stereochemically ill-defined, or coordinately saturated. Here, we expand the biomolecular metal-coordination toolbox with the irreversible attachment to cysteine of bis(1-methylimidazol-2-yl)ethene ("BMIE"), which generates a compact imidazole-based metal-coordinating ligand. Conjugate additions of small-molecule thiols (thiocresol and N-Boc-Cys) with BMIE confirm general thiol reactivity. The BMIE adducts are shown to complex the divalent metal ions Cu++ and Zn++ in bidentate (N2) and tridentate (N2S*) coordination geometries. Cysteine-targeted BMIE modification (>90% yield at pH 8.0) of a model protein, the S203C variant of carboxypeptidase G2 (CPG2), measured with ESI-MS, confirms its utility as a site-selective bioconjugation method. ICP-MS analysis confirms mono-metallation of the BMIE-modified CPG2 protein with Zn++, Cu++, and Co++. EPR characterization of the BMIE-modified CPG2 protein reveals the structural details of the site selective 1:1 BMIE-Cu++ coordination and symmetric tetragonal geometry under physiological conditions and in the presence of various competing and exchangeable ligands (H2O/HO-, tris, and phenanthroline). An X-ray protein crystal structure of BMIE-modified CPG2-S203C demonstrates that the BMIE modification is minimally disruptive to the overall protein structure, including the carboxypeptidase active sites, although Zn++ metalation could not be conclusively discerned at the resolution obtained. The carboxypeptidase catalytic activity of BMIE-modified CPG2-S203C was also assayed and found to be minimally affected. These features, combined with ease of attachment, define the new BMIE-based ligation as a versatile metalloprotein design tool, and enable future catalytic and structural applications.

Design of a minimal di-nickel hydrogenase peptide.

Ancestral metabolic processes involve the reversible oxidation of molecular hydrogen by hydrogenase. Extant hydrogenase enzymes are complex, comprising hundreds of amino acids and multiple cofactors. We designed a 13-amino acid nickel-binding peptide capable of robustly producing molecular hydrogen from protons under a wide variety of conditions. The peptide forms a di-nickel cluster structurally analogous to a Ni-Fe cluster in [NiFe] hydrogenase and the Ni-Ni cluster in acetyl-CoA synthase, two ancient, extant proteins central to metabolism. These experimental results demonstrate that modern enzymes, despite their enormous complexity, likely evolved from simple peptide precursors on early Earth.

Electron spin coherence exceeding seconds in high-purity silicon.

Silicon is one of the most promising semiconductor materials for spin-based information processing devices. Its advanced fabrication technology facilitates the transition from individual devices to large-scale processors, and the availability of a (28)Si form with no magnetic nuclei overcomes a primary source of spin decoherence in many other materials. Nevertheless, the coherence lifetimes of electron spins in the solid state have typically remained several orders of magnitude lower than that achieved in isolated high-vacuum systems such as trapped ions. Here we examine electron spin coherence of donors in pure (28)Si material (residual (29)Si concentration <50 ppm) with donor densities of 10(14)-10(15) cm(-3). We elucidate three mechanisms for spin decoherence, active at different temperatures, and extract a coherence lifetime T(2) up to 2 s. In this regime, we find the electron spin is sensitive to interactions with other donor electron spins separated by ~200 nm. A magnetic field gradient suppresses such interactions, producing an extrapolated electron spin T(2) of 10 s at 1.8 K. These coherence lifetimes are without peer in the solid state and comparable to high-vacuum qubits, making electron spins of donors in silicon ideal components of quantum computers, or quantum memories for systems such as superconducting qubits.

A redox-active Mn(0) dicarbene metalloradical.

We report a rare redox-active Mn0 metalloradical [Mn(CO)3(Ph2B(tBuNHC)2)]- (NHC = N-heterocyclic carbene) with countercations [K(2.2.2)crypt]+, [Na(2.2.2)crypt]+, or [Li(DME)(12-crown-4)]+ (DME = 1,2-dimethoxyethane), all characterized via single crystal X-ray diffraction. Cyclic voltammograms reveal solvation-dependent MnI/0 redox potentials that are modeled using the Born equation.

Coherent state transfer between an electron and nuclear spin in (15)N@C(60).

Electron spin qubits in molecular systems offer high reproducibility and the ability to self-assemble into larger architectures. However, interactions between neighboring qubits are "always on," and although the electron spin coherence times can be several hundred microseconds, these are still much shorter than typical times for nuclear spins. Here we implement an electron-nuclear hybrid scheme which uses coherent transfer between electron and nuclear spin degrees of freedom in order to both effectively turn on or off interqubit coupling mediated by dipolar interactions and benefit from the long nuclear spin decoherence times (T(2n)). We transfer qubit states between the electron and (15)N nuclear spin in (15)N@C(60) with a two-way process fidelity of 88%, using a series of tuned microwave and radio frequency pulses and measure a nuclear spin coherence lifetime of over 100 ms.

Accessing three oxidation states of cobalt in M6L3 nanoprisms with cobalt-porphyrin walls.

Nanocages with porphyrin walls are common, but studies of such structures hosting redox-active metals are rare. Pt2+-linked M6L3 nanoprisms with cobalt-porphyrin walls were prepared and their redox properties were evaluated electrochemically and chemically, leading to the first time that cobalt-porphyrin nanocages have been characterized in CoI, CoII, and CoIII states.

Biophysical Characterization of Iron-Sulfur Proteins.

Iron-sulfur proteins are primordial catalysts and biological electron carriers that today drive major metabolic pathways across all forms of life. They can access a diversity of oxidation states and can mediate electron transfer over an extended range of reduction potentials spanning more than 1 V. Depending on the protein micro-environment and geometry of ligand, co-ordination the iron-sulfur clusters can occur in different forms [2Fe-2S], [3Fe-4S], HiPIP [4Fe-4S], and [4Fe-4S]. There are several spectroscopic methods available to characterize the composition and electronic configuration of the iron-sulfur clusters, such as optical methods and electron paramagnetic resonance. This paper presents the protocols used to characterize the metal center of Coiled-Coil Iron-Sulfur (CCIS), an artificial metalloprotein containing one [4Fe-4S] cluster. It is expected that these protocols will be of general utility for other iron-sulfur proteins.

In Vivo Biogenesis of a De Novo Designed Iron-Sulfur Protein.

In vivo expression of metalloproteins requires specific metal trafficking and incorporation machinery inside the cell. Synthetic designed metalloproteins are typically purified without the target metal, which is subsequently introduced through in vitro reconstitution. The extra step complicates protein optimization by high-throughput library screening or laboratory evolution. We demonstrate that a designed coiled-coil iron-sulfur protein (CCIS) assembles robustly with [4Fe-4S] clusters in vivo. While in vitro reconstitution produces a mixture of oligomers that depends on solution conditions, in vivo production generates a stable homotrimer coordinating a single, diamagnetic [4Fe-4S]2+ cluster. The multinuclear cluster of in vivo assembled CCIS is more resistant to degradation by molecular oxygen. Only one of the two metal coordinating half-sites is required in vivo, indicating specificity of molecular recognition in recruitment of the metal cluster. CCIS, unbiased by evolution, is a unique platform to examine iron-sulfur protein biogenesis and develop synthetic multinuclear oxidoreductases.

Observation of an environmentally insensitive solid-state spin defect in diamond.

Engineering coherent systems is a central goal of quantum science. Color centers in diamond are a promising approach, with the potential to combine the coherence of atoms with the scalability of a solid-state platform. We report a color center that shows insensitivity to environmental decoherence caused by phonons and electric field noise: the neutral charge state of silicon vacancy (SiV0). Through careful materials engineering, we achieved >80% conversion of implanted silicon to SiV0 SiV0 exhibits spin-lattice relaxation times approaching 1 minute and coherence times approaching 1 second. Its optical properties are very favorable, with ~90% of its emission into the zero-phonon line and near-transform-limited optical linewidths. These combined properties make SiV0 a promising defect for quantum network applications.

All-electric control of donor nuclear spin qubits in silicon.

The electronic and nuclear spin degrees of freedom of donor impurities in silicon form ultra-coherent two-level systems that are potentially useful for applications in quantum information and are intrinsically compatible with industrial semiconductor processing. However, because of their smaller gyromagnetic ratios, nuclear spins are more difficult to manipulate than electron spins and are often considered too slow for quantum information processing. Moreover, although alternating current magnetic fields are the most natural choice to drive spin transitions and implement quantum gates, they are difficult to confine spatially to the level of a single donor, thus requiring alternative approaches. In recent years, schemes for all-electrical control of donor spin qubits have been proposed but no experimental demonstrations have been reported yet. Here, we demonstrate a scalable all-electric method for controlling neutral 31P and 75As donor nuclear spins in silicon. Using coplanar photonic bandgap resonators, we drive Rabi oscillations on nuclear spins exclusively using electric fields by employing the donor-bound electron as a quantum transducer, much in the spirit of recent works with single-molecule magnets. The electric field confinement leads to major advantages such as low power requirements, higher qubit densities and faster gate times. Additionally, this approach makes it possible to drive nuclear spin qubits either at their resonance frequency or at its first subharmonic, thus reducing device bandwidth requirements. Double quantum transitions can be driven as well, providing easy access to the full computational manifold of our system and making it convenient to implement nuclear spin-based qudits using 75As donors.

Carbonate complexation of Mn2+ in the aqueous phase: redox behavior and ligand binding modes by electrochemistry and EPR spectroscopy.

The chemical speciation of Mn2+ within cells is critical for its transport, availability, and redox properties. Herein we investigate the redox behavior and complexation equilibria of Mn2+ in aqueous solutions of bicarbonate by voltammetry and electron paramagnetic resonance (EPR) spectroscopy and discuss the implications for the uptake of Mn2+ by mangano-cluster enzymes such as photosystem II (PSII). Both the electrochemical reduction of Mn2+ to Mn0 at an Hg electrode and EPR (in the absence of a polarizing electrode) revealed the formation of 1:1 and 1:2 Mn-(bi)carbonate complexes as a function of Mn2+ and bicarbonate concentrations. Pulsed EPR spectroscopy, including ENDOR, ESEEM, and 2D-HYSCORE, were used to probe the hyperfine couplings to 1H and 13C nuclei of the ligand(s) bound to Mn2+. For the 1:2 complex, the complete 13C hyperfine tensor for one of the (bi)carbonate ligands was determined and it was established that this ligand coordinates to Mn2+ in bidentate mode with a 13C-Mn distance of 2.85 +/- 0.1 angstroms. The second (bi)carbonate ligand in the 1:2 complex coordinates possibly in monodentate mode, which is structurally less defined, and its 13C signal is broad and unobservable. 1H ENDOR reveals that 1-2 water ligands are lost upon binding of one bicarbonate ion in the 1:1 complex while 3-4 water ligands are lost upon forming the 1:2 complex. Thus, we deduce that the dominant species above 0.1 M bicarbonate concentration is the 1:2 complex, [Mn(CO3)(HCO3)(OH2)3]-.

Atomic clock transitions in silicon-based spin qubits.

A major challenge in using spins in the solid state for quantum technologies is protecting them from sources of decoherence. This is particularly important in nanodevices where the proximity of material interfaces, and their associated defects, can play a limiting role. Spin decoherence can be addressed to varying degrees by improving material purity or isotopic composition, for example, or active error correction methods such as dynamic decoupling (or even combinations of the two). However, a powerful method applied to trapped ions in the context of atomic clocks is the use of particular spin transitions that are inherently robust to external perturbations. Here, we show that such 'clock transitions' can be observed for electron spins in the solid state, in particular using bismuth donors in silicon. This leads to dramatic enhancements in the electron spin coherence time, exceeding seconds. We find that electron spin qubits based on clock transitions become less sensitive to the local magnetic environment, including the presence of (29)Si nuclear spins as found in natural silicon. We expect the use of such clock transitions will be of additional significance for donor spins in nanodevices, mitigating the effects of magnetic or electric field noise arising from nearby interfaces and gates.

Kinetic model for Ca2+-induced permeability transition in energized liver mitochondria discriminates between inhibitor mechanisms.

Cytotoxicity associated with pathophysiological Ca(2+) overload (e.g. in stroke) appears mediated by an event termed the mitochondrial permeability transition (mPT). We built and solved a kinetic model of the mPT in populations of isolated rat liver mitochondria that quantitatively describes Ca(2+)-induced mPT as a two-step sequence of pre-swelling induction followed by Ca(2+)-driven, positive feedback, autocatalytic propagation. The model was formulated as two differential equations, each directly related to experimental parameters (Ca(2+) flux/mitochondrial swelling). These parameters were simultaneously assessed using a spectroscopic approach to monitor multiple mitochondrial properties. The derived kinetic model correctly identifies a correlation between initial Ca(2+) concentration and delay interval prior to mPT induction. Within the model's framework, Ru-360 (a ruthenium complex) and Mg(2+) were shown to compete with the Ca(2+)-stimulated initiation phase of mPT induction, consistent with known inhibition at the phenomenological level of the Ca(2+) uniporter. The model further reveals that Mg(2+), but not Ru-360, inhibits Ca(2+)-induced effects on a downstream stage of mPT induction at a site distinct from the uniporter. The analytical approach was then applied to promethazine, an FDA-approved drug previously shown to inhibit both mPT and ischemia-reperfusion injury. Kinetic analysis revealed that promethazine delayed mPT induction in a manner qualitatively distinct from that of lower concentrations of Mg(2+). In summary, we have developed a kinetic model to aid in the quantitative characterization of mPT induction. This model is consistent with/informative about the biochemistry of several mPT inhibitors, and its success suggests that this kinetic approach can aid in the classification of agents or targets that modulate mPT induction.

Will spin-relaxation times in molecular magnets permit quantum information processing?

Using X-band pulsed electron-spin resonance, we report the intrinsic spin-lattice (T1) and phase-coherence (T2) relaxation times in molecular nanomagnets for the first time. In Cr7M heterometallic wheels, with M=Ni and Mn, phase-coherence relaxation is dominated by the coupling of the electron spin to protons within the molecule. In deuterated samples T2 reaches 3 micros at low temperatures, which is several orders of magnitude longer than the duration of spin manipulations, satisfying a prerequisite for the deployment of molecular nanomagnets in quantum information applications.

Davies electron-nuclear double resonance revisited: enhanced sensitivity and nuclear spin relaxation.

Over the past 50 years, electron-nuclear double resonance (ENDOR) has become a fairly ubiquitous spectroscopic technique, allowing the study of spin transitions for nuclei which are coupled to electron spins. However, the low spin number sensitivity of the technique continues to pose serious limitations. Here we demonstrate that signal intensity in a pulsed Davies ENDOR experiment depends strongly on the nuclear relaxation time T(1n), and can be severely reduced for long T(1n). We suggest a development of the original Davies ENDOR sequence that overcomes this limitation, thus offering dramatically enhanced signal intensity and spectral resolution. Finally, we observe that the sensitivity of the original Davies method to T(1n) can be exploited to measure nuclear relaxation, as we demonstrate for phosphorous donors in silicon and for endohedral fullerenes N@C(60) in CS(2).