Sep 29, 2014

Carbon monoxide reveals new possibilities for substrate binding in nitrogenase [Also see Report by Spatzal et al.]

The structure of an inhibitor bound to nitrogenase reveals rearrangements in the active-site metallocluster. [Also see Perspective by Hognom]


The mechanism of nitrogenase remains enigmatic, with a major unresolved issue concerning how inhibitors and substrates bind to the active site. We report a crystal structure of carbon monoxide (CO)–inhibited nitrogenase molybdenum-iron (MoFe)–protein at 1.50 angstrom resolution, which reveals a CO molecule bridging Fe2 and Fe6 of the FeMo-cofactor. The μ2 binding geometry is achieved by replacing a belt-sulfur atom (S2B) and highlights the generation of a reactive iron species uncovered by the displacement of sulfur. The CO inhibition is fully reversible as established by regain of enzyme activity and reappearance of S2B in the 1.43 angstrom resolution structure of the reactivated enzyme. The substantial and reversible reorganization of the FeMo-cofactor accompanying CO binding was unanticipated and provides insights into a catalytically competent state of nitrogenase.

Water's place in Au catalysis

  • Gregory M. Mullen and
  • C. Buddie Mullins
Science 26 September 2014: 1564-1565.
Water plays a key role in gold-catalyzed CO oxidation [Also see Report by Saavedra et al.]
Adsorbed water enables proton-transfer steps that lower the activation barrier for carbon monoxide oxidation. [Also see Perspective by Mullen and Mullins]
We provide direct evidence of a water-mediated reaction mechanism for room-temperature CO oxidation over Au/TiO2 catalysts. A hydrogen/deuterium kinetic isotope effect of nearly 2 implicates O-H(D) bond breaking in the rate-determining step. Kinetics and in situ infrared spectroscopy experiments showed that the coverage of weakly adsorbed water on TiO2 largely determines catalyst activity by changing the number of active sites. Density functional theory calculations indicated that proton transfer at the metal-support interface facilitates O2 binding and activation; the resulting Au-OOH species readily reacts with adsorbed Au-CO, yielding Au-COOH. Au-COOH decomposition involves proton transfer to water and was suggested to be rate determining. These results provide a unified explanation to disparate literature results, clearly defining the mechanistic roles of water, support OH groups, and the metal-support interface.

Spectroscopy in the laboratory elucidates key steps in ozone’s atmospheric reaction with unsaturated hydrocarbons.
Ozonolysis of alkenes, an important nonphotolytic source of hydroxyl (OH) radicals in the troposphere, proceeds through energized Criegee intermediates that undergo unimolecular decay to produce OH radicals. Here, we used infrared (IR) activation of cold CH3CHOO Criegee intermediates to drive hydrogen transfer from the methyl group to the terminal oxygen, followed by dissociation to OH radicals. State-selective excitation of CH3CHOO in the CH stretch overtone region combined with sensitive OH detection revealed the IR spectrum of CH3CHOO, effective barrier height for the critical hydrogen transfer step, and rapid decay dynamics to OH products. Complementary theory provides insights on the IR overtone spectrum, as well as vibrational excitations, structural changes, and energy required to move from the minimum-energy configuration of CH3CHOO to the transition state for the hydrogen transfer reaction.

Synthesis and detection of a seaborgium carbonyl complex

The radioactive superheavy element seaborgium can form a carbonyl compound during its short lifetime [Also see Report by Even et al.]
A special apparatus enables synthesis of a compound with carbon bonds to a short-lived element produced via nuclear reaction. [Also see Perspective by Loveland]
Experimental investigations of transactinoide elements provide benchmark results for chemical theory and probe the predictive power of trends in the periodic table. So far, in gas-phase chemical reactions, simple inorganic compounds with the transactinoide in its highest oxidation state have been synthesized. Single-atom production rates, short half-lives, and harsh experimental conditions limited the number of experimentally accessible compounds. We applied a gas-phase carbonylation technique previously tested on short-lived molybdenum (Mo) and tungsten (W) isotopes to the preparation of a carbonyl complex of seaborgium, the 106th element. The volatile seaborgium complex showed the same volatility and reactivity with a silicon dioxide surface as those of the hexacarbonyl complexes of the lighter homologs Mo and W. Comparison of the product’s adsorption enthalpy with theoretical predictions and data for the lighter congeners supported a Sg(CO)6 formulation.

Mechanisms of Hydride Abstractions by Quinones

Publication Date (Web): September 8, 2014 (Article)
DOI: 10.1021/ja507598y
 
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The kinetics of the hydride abstractions by 2,3-dichloro-5,6-dicyano-p-benzoquinone (DDQ) from 13 C–H hydride donors (acyclic 1,4-dienes, cyclohexa-1,4-dienes, dihydropyridines), tributylstannane, triphenylstannane, and five borane complexes (amine–boranes, carbene–boranes) have been studied photometrically in dichloromethane solution at 20 °C. Analysis of the resulting second-order rate constants by the correlation log k2(20 °C) = sN(E + N) ( J. Am. Chem. Soc. 2001, 123, 9500) showed that the hydride abstractions from the C–H donors on one side and the Sn–H and B–H hydride donors on the other follow separate correlations, indicating different mechanisms for the two reaction series. The interpretation that the C–H donors transfer hydrogen to the carbonyl oxygen of DDQ while Sn–H and B–H hydride donors transfer hydride to a cyano-substituted carbon of DDQ is supported by quantum-chemical intrinsic reaction coordinate calculations and isotope labeling experiments of the reactions of D8-cyclohexa-1,4-diene, Bu3SnD, and pyridine·BD3 with 2,5-dichloro-p-benzoquinone. The second-order rate constants of the reactions of tributylstannane with different quinones correlate linearly with the electrophilicity parameters E of the quinones, which have previously been derived from the reactions of quinones with π-nucleophiles. The fact that the reactions of Bu3SnH with quinones and benzhydrylium ions are on the same log k2 vs E (electrophilicity) correlation shows that both reaction series proceed by the same mechanism and illustrates the general significance of the reactivity parameters E, N, and sN for predicting rates of polar organic reactions.
 

Molecular Catalysis of H2 Evolution: Diagnosing Heterolytic versus Homolytic Pathways

Publication Date (Web): September 4, 2014 (Article)
DOI: 10.1021/ja505845t
 
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Molecular catalysis of H2 production from the electrochemical reduction of acids by transition-metal complexes is one of the key issues of modern energy challenges. The question of whether it proceeds heterolytically (through reaction of an initially formed metal hydride with the acid) or homolytically (through symmetrical coupling of two molecules of hydride) has to date received inconclusive answers for a quite simple reason: the theoretical bases for criteria allowing the distinction between homolytic and heterolytic pathways in nondestructive methods such as cyclic voltammetry have been lacking heretofore. They are provided here, allowing the distinction between the two pathways. The theoretical predictions and the diagnosing strategy are illustrated by catalysis of the reduction of phenol, acetic acid, and protonated triethylamine by electrogenerated iron(0) tetraphenylporphyrin. Rather than being an intrinsic property of the catalytic system, the occurrence of either a heterolytic or a homolytic pathway results from their competition as a function of the concentrations of acid and catalyst and the rate constants for hydride formation and H2 evolution by hydride protonation or dimerization.
 

Oxygen Insertion into Metal Carbon Bonds: Formation of Methylperoxo Pd(II) and Pt(II) Complexes via Photogenerated Dinuclear Intermediates

Publication Date (Web): September 8, 2014 (Article)
DOI: 10.1021/ja5055143
 
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Platinum(II) and palladium(II) complexes [M(CH3)(L)]SbF6 with substituted terpyridine ligands L undergo light-driven oxygen insertion reactions into metal methyl bonds resulting in methylperoxo complexes [M(OOCH3)(L)]SbF6. The oxygen insertion reactions occur readily for complexes with methyl ligands that are activated due to steric interaction with substituents (NH2, NHMe or CH3) at the 6,6″-positions on the terpyridine ligand. All complexes exhibit attractive intermolecular π···π or M···M interactions in the solid state and in solution, which lead to excited triplet dinuclear M–M complexes upon irradiation. A mechanism is proposed whereby a dinuclear intermediate is generated upon irradiation that has a weakened M–C bond in the excited state, resulting in the observed oxygen insertion reactions.
 

Sep 17, 2014

Mechanism of the Reactions of Alcohols with o-Benzynes

Publication Date (Web): September 4, 2014 (Article)
DOI: 10.1021/ja502595m
 
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We have studied reactions of secondary and primary alcohols with benzynes generated by the hexadehydro-Diels–Alder (HDDA) reaction. These alcohols undergo competitive addition vs dihydrogen transfer to produce aryl ethers vs reduced benzenoid products, respectively. During the latter process, an equivalent amount of oxidized ketone (or aldehyde) is formed. Using deuterium labeling studies, we determined that (i) it is the carbinol C–H and adjacent O–H hydrogen atoms that are transferred during this process and (ii) the mechanism is consistent with a hydride-like transfer of the C–H. Substrates bearing an internal trap attached to the reactive, HDDA-derived benzyne intermediate were used to probe the kinetic order of the alcohol trapping agent in the H2-transfer as well as in the alcohol addition process. The H2-transfer reaction is first order in alcohol. Our results are suggestive of a concerted H2-transfer process, which is further supported by density functional theory (DFT) computational studies and results of a kinetic isotope effect experiment. In contrast, alcohol addition to the benzyne is second order in alcohol, a previously unrecognized phenomenon. Additional DFT studies were used to further probe the mechanistic aspects of the alcohol addition process.
 

Sep 16, 2014

Decoupled catalytic hydrogen evolution from a molecular metal oxide redox mediator in water splitting

  • Benjamin Rausch,
  • Mark D. Symes,
  • Greig Chisholm,
  • and Leroy Cronin
Science 12 September 2014: 1326-1330.
A silicotungstic acid cluster can store protons and electrons during water electrolysis and later rapidly release hydrogen.

 

Abstract

The electrolysis of water using renewable energy inputs is being actively pursued as a route to sustainable hydrogen production. Here we introduce a recyclable redox mediator (silicotungstic acid) that enables the coupling of low-pressure production of oxygen via water oxidation to a separate, catalytic hydrogen production step outside the electrolyzer that requires no post-electrolysis energy input. This approach sidesteps the production of high-pressure gases inside the electrolytic cell (a major cause of membrane degradation) and essentially eliminates the hazardous issue of product gas crossover at the low current densities that characterize renewables-driven water-splitting devices. We demonstrated that a platinum-catalyzed system can produce pure hydrogen over 30 times faster than state-of-the-art proton exchange membrane electrolyzers at equivalent platinum loading.

Isotope Effects, Dynamic Matching, and Solvent Dynamics in a Wittig Reaction. Betaines as Bypassed Intermediates

Publication Date (Web): September 11, 2014 (Communication)
DOI: 10.1021/ja506497b


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The mechanism of the Wittig reaction of anisaldehyde with a stabilized ylide was studied by a combination of 13C kinetic isotope effects, conventional calculations, and molecular dynamics calculations in a cluster of 53 THF molecules. The isotope effects support a cycloaddition mechanism involving two sequential transition states associated with separate C–C and P–O bond formations. However, the betaine structure in between the two transition states is bypassed as an equilibrated intermediate in most trajectories. The role of the dynamics of solvent equilibration in the nature of mechanistic intermediates is discussed.

Sep 10, 2014

Significant Expansion of Fluorescent Protein Sensing Ability through the Genetic Incorporation of Superior Photo-Induced Electron-Transfer Quenchers

Publication Date (Web): September 8, 2014 (Communication)
DOI: 10.1021/ja505219r
 
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Photo-induced electron transfer (PET) is ubiquitous for photosynthesis and fluorescent sensor design. However, genetically coded PET sensors are underdeveloped, due to the lack of methods to site-specifically install PET probes on proteins. Here we describe a family of acid and Mn(III) turn-on fluorescent protein (FP) sensors, named iLovU, based on PET and the genetic incorporation of superior PET quenchers in the fluorescent flavoprotein iLov. Using the iLovU PET sensors, we monitored the cytoplasmic acidification process, and achieved Mn(III) fluorescence sensing for the first time. The iLovU sensors should be applicable for studying pH changes in living cells, monitoring biogentic Mn(III) in the environment, and screening for efficient manganese peroxidase, which is highly desirable for lignin degradation and biomass conversion. Our work establishes a platform for many more protein PET sensors, facilitates the de novo design of metalloenzymes harboring redox active residues, and expands our ability to probe protein conformational dynamics.
 

Reversible H Atom Abstraction Catalyzed by the Radical S-Adenosylmethionine Enzyme HydG

Publication Date (Web): August 6, 2014 (Communication)
DOI: 10.1021/ja504618y
 
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The organometallic H-cluster at the active site of [FeFe]-hydrogenases is synthesized by three accessory proteins, two of which are radical S-adenosylmethionine enzymes (HydE, HydG) and one of which is a GTPase (HydF). In this work we probed the specific role of H atom abstraction in HydG-catalyzed carbon monoxide and cyanide production from tyrosine. The isotope distributions of 5′-deoxyadenosine and p-cresol were evaluated using deuterium-labeled tyrosine substrates in H2O and D2O. The observation of multiply deuterated 5′-deoxyadenosine and deuterated S-adenosylmethionine when the reaction is carried out in D2O provides evidence for a 5′-deoxyadenosyl radical-mediated abstraction of a hydrogen atom from a solvent-exchangeable position as a reversible event.
 

Sep 8, 2014

ATP Binding and Aspartate Protonation Enhance Photoinduced Electron Transfer in Plant Cryptochrome

Publication Date (Web): August 26, 2014 (Article)
DOI: 10.1021/ja506084f
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Abstract

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Cryptochromes are flavoproteins encountered in most vegetal and animal species. They play a role of blue-light receptors in plants and in invertebrates. The putative resting state of the FAD cofactor in these proteins is its fully oxidized form, FADox. Upon blue-light excitation, the isoalloxazine ring (ISO) may undergo an ultrafast reduction by a nearby tryptophan residue W400. This primary reduction triggers a cascade of electron and proton transfers, ultimately leading to the formation of the FADH° radical. A recent experimental study has shown that the yield of FADH° formation in Arabidopsis cryptochrome can be strongly modulated by ATP binding and by pH, affecting the protonation state of D396 (proton donor to FAD°). Here we provide a detailed molecular analysis of these effects by means of combined classical molecular dynamics simulations and time-dependent density functional theory calculations. When ATP is present and D396 protonated, FAD remains in close contact with W400, thereby enhancing electron transfer (ET) from W400 to ISO*. In contrast, deprotonation of D396 and absence of ATP introduce flexibility to the photoactive site prior to FAD excitation, with the consequence of increased ISO-W400 distance and diminished tunneling rate by almost two orders of magnitude. We show that under these conditions, ET from the adenine moiety of FAD becomes a competitive relaxation pathway. Overall, our data suggest that the observed effects of ATP and pH on the FAD photoreduction find their roots in the earliest stage of the photoreduction process; i.e., ATP binding and the protonation state of D396 determine the preferred pathway of ISO* relaxation.

Untangling the Condensation Network of Organosiloxanes on Nanoparticles using 2D 29Si–29Si Solid-State NMR Enhanced by Dynamic Nuclear Polarization

Publication Date (Web): August 25, 2014 (Article)
DOI: 10.1021/ja506688m


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Silica (SiO2) nanoparticles (NPs) were functionalized by silanization to produce a surface covered with organosiloxanes. Information about the surface coverage and the nature, if any, of organosiloxane polymerization, whether parallel or perpendicular to the surface, is highly desired. To this extent, two-dimensional homonuclear 29Si solid-state NMR could be employed. However, owing to the sensitivity limitations associated with the low natural abundance (4.7%) of 29Si and the difficulty and expense of isotopic labeling here, this technique would usually be deemed impracticable. Nevertheless, we show that recent developments in the field of dynamic nuclear polarization under magic angle spinning (MAS-DNP) could be used to dramatically increase the sensitivity of the NMR experiments, resulting in a timesaving factor of ∼625 compared to conventional solid-state NMR. This allowed the acquisition of previously infeasible data. Using both through-space and through-bond 2D 29Si–29Si correlation experiments, it is shown that the required reaction conditions favor lateral polymerization and domain growth. Moreover, the natural abundance correlation experiments permitted the estimation of 2JSi–O–Si-couplings (13.8 ± 1.4 Hz for surface silica) and interatomic distances (3.04 ± 0.08 Å for surface silica) since complications associated with many-spin systems and also sensitivity were avoided. The work detailed herein not only demonstrates the possibility of using MAS-DNP to greatly facilitate the acquisition of 2D 29Si–29Si correlation spectra but also shows that this technique can be used in a routine fashion to characterize surface grafting networks and gain structural constraints, which can be related to a system’s chemical and physical properties.

Sep 3, 2014

Electronic Control of the Protonation Rates of Fe–Fe Bonds

Publication Date (Web): August 12, 2014 (Article)
DOI: 10.1021/ja506693m


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Protonation at metal–metal bonds is of fundamental interest in the context of the function of the active sites of hydrogenases and nitrogenases. In diiron dithiolate complexes bearing carbonyl and electron-donating ligands, the metal–metal bond is the highest occupied molecular orbital (HOMO) with a “bent” geometry. Here we show that the experimentally measured rates of protonation (kH) of this bond and the energy of the HOMO as measured by the oxidation potential of the complexes (E1/2ox) correlate in a linear free energy relationship: ln kH = ((F(c – βE1/2ox))/(RT)), where c is a constant and β is the dimensionless Brønsted coefficient. The value of β of 0.68 is indicative of a strong dependence upon energy of the HOMO: measured rates of protonation vary over 6 orders of magnitude for a change in E1/2ox of ca. 0.55 V (ca. 11 orders of magnitude/V). This relationship allows prediction of protonation rates of systems that are either too fast to measure experimentally or that possess additional protonation sites. It is further suggested that the nature of the bridgehead in the dithiolate ligand can exert a stereoelectronic influence: bulky substituents destabilize the HOMO, thereby increasing the rate of protonation.
Publication Date (Web): August 15, 2014 (Perspective)
DOI: 10.1021/ja504441h

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In life science, water is the ubiquitous solvent, sometimes even called the “matrix of life”. There is increasing experimental and theoretical evidence that solvation water is not a passive spectator in biomolecular processes. New experimental techniques can quantify how water interacts with biomolecules and, in doing so, differs from “bulk” water. Terahertz (THz) absorption spectroscopy has turned out to be a powerful tool to study (bio)molecular hydration. The main concepts that have been developed in the recent years to describe the underlying solute-induced sub-picosecond dynamics of the hydration shell are discussed herein. Moreover, we highlight recent findings that show the significance of hydrogen bond dynamics for the function of antifreeze proteins and for molecular recognition. In all of these examples, a gradient of water motion toward functional sites of proteins is observed, the so-called “hydration funnel”. By means of molecular dynamics simulations, we provide new evidence for a specific water–protein coupling as the cause of the observed dynamical heterogeneity. The efficiency of the coupling at THz frequencies is explained in terms of a two-tier (short- and long-range) solute–solvent interaction.

Aug 28, 2014

Nitrite and Hydroxylamine as Nitrogenase Substrates: Mechanistic Implications for the Pathway of N2 Reduction

Publication Date (Web): August 19, 2014 (Article)
DOI: 10.1021/ja507123d


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Investigations of reduction of nitrite (NO2) to ammonia (NH3) by nitrogenase indicate a limiting stoichiometry, NO2 + 6e + 12ATP + 7H+ → NH3 + 2H2O + 12ADP + 12Pi. Two intermediates freeze-trapped during NO2 turnover by nitrogenase variants and investigated by Q-band ENDOR/ESEEM are identical to states, denoted H and I, formed on the pathway of N2 reduction. The proposed NO2 reduction intermediate hydroxylamine (NH2OH) is a nitrogenase substrate for which the H and I reduction intermediates also can be trapped. Viewing N2 and NO2 reductions in light of their common reduction intermediates and of NO2 reduction by multiheme cytochrome c nitrite reductase (ccNIR) leads us to propose that NO2 reduction by nitrogenase begins with the generation of NO2H bound to a state in which the active-site FeMo-co (M) has accumulated two [e/H+] (E2), stored as a (bridging) hydride and proton. Proton transfer to NO2H and H2O loss leaves M–[NO+]; transfer of the E2 hydride to the [NO+] directly to form HNO bound to FeMo-co is one of two alternative means for avoiding formation of a terminal M–[NO] thermodynamic “sink”. The N2 and NO2 reduction pathways converge upon reduction of NH2NH2 and NH2OH bound states to form state H with [−NH2] bound to M. Final reduction converts H to I, with NH3 bound to M. The results presented here, combined with the parallels with ccNIR, support a N2 fixation mechanism in which liberation of the first NH3 occurs upon delivery of five [e/H+] to N2, but a total of seven [e/H+] to FeMo-co when obligate H2 evolution is considered, and not earlier in the reduction process.

Facile Surface Functionalization of Hydrophobic Magnetic Nanoparticles

Publication Date (Web): August 20, 2014 (Communication)
DOI: 10.1021/ja5060324


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Nonpolar phase synthesized hydrophobic nanocrystals show attractive properties and have demonstrated prominent potential in biomedical applications. However, the preparation of biocompatible nanocrystals is made difficult by the presence of hydrophobic surfactant stabilizer on their surfaces. To address this limitation, we have developed a facile, high efficiency, single-phase and low-cost method to convert hydrophobic magnetic nanoparticles (MNPs) to an aqueous phase using tetrahydrofuran, NaOH and 3,4-dihydroxyhydrocinnamic acid without any complicated organic synthesis. The as-transferred hydrophilic MNPs are water-soluble over a wide pH range (pH = 3–12), and the solubility is pH-controllable. Furthermore, the as-transferred MNPs with carboxylate can be readily adapted with further surface functionalization, varying from small molecule dyes to oligonucleotides and enzymes. Finally, the strategy developed here can easily be extended to other types of hydrophobic nanoparticles to facilitate biomedical applications of nanomaterials.

Direct Comparison of Electrochemical and Spectrochemical Kinetics for Catalytic Oxygen Reduction

Publication Date (Web): August 19, 2014 (Communication)
DOI: 10.1021/ja505667t
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