Jan 23, 2015

Facet-Dependent Photoelectrochemical Performance of TiO2 Nanostructures: An Experimental and Computational Study

Publication Date (Web): January 6, 2015 (Article)
DOI: 10.1021/ja5111078
 
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The behavior of crystalline nanoparticles depends strongly on which facets are exposed. Some facets are more active than others, but it is difficult to selectively isolate particular facets. This study provides fundamental insights into photocatalytic and photoelectrochemical performance of three types of TiO2 nanoparticles with predominantly exposed {101}, {010}, or {001} facets, where 86–99% of the surface area is the desired facet. Photodegradation of methyl orange reveals that {001}-TiO2 has 1.79 and 3.22 times higher photocatalytic activity than {010} and {101}-TiO2, respectively. This suggests that the photochemical performance is highly correlated with the surface energy and the number of under-coordinated surface atoms. In contrast, the photoelectrochemical performance of the faceted TiO2 nanoparticles sensitized with the commercially available MK-2 dye was highest with {010}-TiO2 which yielded an overall cell efficiency of 6.1%, compared to 3.2% for {101}-TiO2 and 2.6% for {001}-TiO2 prepared under analogous conditions. Measurement of desorption kinetics and accompanying computational modeling suggests a stronger covalent interaction of the dye with the {010} and {101} facets compared with the {001} facet. Time-resolved THz spectroscopy and transient absorption spectroscopy measure faster electron injection dynamics when MK-2 is bound to {010} compared to other facets, consistent with extensive computational simulations which indicate that the {010} facet provides the most efficient and direct pathway for interfacial electron transfer. Our experimental and computational results establish for the first time that photoelectrochemical performance is dependent upon the binding energy of the dye as well as the crystalline structure of the facet, as opposed to surface energy alone.
 
 
 

Jan 20, 2015

Publication Date (Web): January 2, 2015 (Article)
DOI: 10.1021/ja512302c


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A recently developed instrument for time-resolved infrared detection following pulse radiolysis has been used to measure the ν(C≡N) IR band of the radical anion of a CN-substituted fluorene in tetrahydrofuran. Specific vibrational frequencies can exhibit distinct frequency shifts due to ion pairing, which can be explained in the framework of the vibrational Stark effect. Measurements of the ratio of free ions and ion pairs in different electrolyte concentrations allowed us to obtain an association constant and free energy change for ion pairing. This new method has the potential to probe the geometry of ion pairing and allows the reduction potentials of molecules to be determined in the absence of electrolyte in an environment of low dielectric constant.
Publication Date (Web): January 9, 2015 (Article)
DOI: 10.1021/ja511420n
 
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The low selectivity of currently available photosensitizers, which causes the treatment-related toxicity and side effects on adjacent normal tissues, is a major limitation for clinical photodynamic therapy (PDT) against cancer. Moreover, since PDT process is strongly oxygen dependent, its therapeutic effect is seriously hindered in hypoxic tumor cells. To overcome these problems, a cell-specific, H2O2-activatable, and O2-evolving PDT nanoparticle (HAOP NP) is developed for highly selective and efficient cancer treatment. The nanoparticle is composed of photosensitizer and catalase in the aqueous core, black hole quencher in the polymeric shell, and functionalized with a tumor targeting ligand c(RGDfK). Once HAOP NP is selectively taken up by αvβ3 integrin-rich tumor cells, the intracellular H2O2 penetrates the shell into the core and is catalyzed by catalase to generate O2, leading to the shell rupture and release of photosensitizer. Under irradiation, the released photosensitizer induces the formation of cytotoxic singlet oxygen (1O2) in the presence of O2 to kill cancer cells. The cell-specific and H2O2-activatable generation of 1O2 selectively destroys cancer cells and prevents the damage to normal cells. More significantly, HAOP NP continuously generates O2 in PDT process, which greatly improves the PDT efficacy in hypoxic tumor. Therefore, this work presents a new paradigm for H2O2-triggered PDT against cancer cells and provides a new avenue for overcoming hypoxia to achieve effective treatment of solid tumors.
 
 

Molecular Origin of Enhanced Proton Conductivity in Anhydrous Ionic Systems

Publication Date (Web): December 31, 2014 (Article)
DOI: 10.1021/ja5103458


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Ionic systems with enhanced proton conductivity are widely viewed as promising electrolytes in fuel cells and batteries. Nevertheless, a major challenge toward their commercial applications is determination of the factors controlling the fast proton hopping in anhydrous conditions. To address this issue, we have studied novel proton-conducting materials formed via a chemical reaction of lidocaine base with a series of acids characterized by a various number of proton-active sites. From ambient and high pressure experimental data, we have found that there are fundamental differences in the conducting properties of the examined salts. On the other hand, DFT calculations revealed that the internal proton hopping within the cation structure strongly affects the pathways of mobility of the charge carrier. These findings offer a fresh look on the Grotthuss-type mechanism in protic ionic glasses as well as provide new ideas for the design of anhydrous materials with exceptionally high proton conductivity.

Jan 16, 2015

Layers of enhanced solvent order are found up to 2 nanometers away from the surfaces of different types of nanoparticles.
Colloidal nanoparticles, used for applications from catalysis and energy applications to cosmetics, are typically embedded in matrixes or dispersed in solutions. The entire particle surface, which is where reactions are expected to occur, is thus exposed. Here, we show with x-ray pair distribution function analysis that polar and nonpolar solvents universally restructure around nanoparticles. Layers of enhanced order exist with a thickness influenced by the molecule size and up to 2 nanometers beyond the nanoparticle surface. These results show that the enhanced reactivity of solvated nanoparticles includes a contribution from a solvation shell of the size of the particle itself.
Publication Date (Web): November 25, 2014 (Article)
DOI: 10.1021/ja508741u


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Ionized nucleobases participate in pairing interactions outside of Watson and Crick’s rules. Base pairing and ionization can be coupled via global conformational changes to raise the apparent pKa of protonated nucleobases to values above physiological pH. To provide the first specific reporter of proton-coupled DNA folding, we developed a “push–pull” fluorescent nucleoside analog composed of dimethylaniline (DMA) fused to deoxycytidine. “DMAC” exhibits the same pKa and base pairing characteristics as native cytosine residues in the human telomeric repeat sequence, where it causes little or no perturbation of DNA structure or stability. Upon protonation of DMAC, enhanced charge transfer results in large red shifting (+40 nm) of its excitation/emission maxima. DMAC’s fluorescence intensity, anisotropy, and energy transfer properties can be used to track conformational changes in real time. Strand displacement assays were conducted by mixing DMAC-labeled duplexes containing a 5′ single-stranded overhang with an excess of unlabeled DNA to initiate thermodynamically favorable unfolding–refolding reactions that release the DMAC-labeled strand from its complement. Rate constants for strand displacement upon addition of i-motif DNA (k = 1.0 M–1 s–1, t1/2 ≈ 12 h) were 320-fold lower than those measured upon addition of unfolded DNA (k = 3.2 × 102 M–1 s–1, t1/2 ≈ 2 min). These results reveal that i-motif structures having only marginal thermodynamic stabilities (Tm < 40 °C) can still pose large kinetic barriers to duplex formation under near-physiological conditions of pH (5.75), temperature (25 °C), and salt (100 mM NaCl).

Publication Date (Web): December 24, 2014 (Article)
DOI: 10.1021/ja5094056


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Controlling the crystal structure of transparent metal oxides is essential for tailoring the properties of these polymorphic materials to specific applications. The structural control is usually done via solid state phase transformation at high temperature or pressure. Here, we report the kinetic study of in situ phase transformation of In2O3 nanocrystals from metastable rhombohedral phase to stable cubic phase during their colloidal synthesis. By examining the phase content as a function of time using the model fitting approach, we identified two distinct coexisting mechanisms, surface and interface nucleation. It is shown that the mechanism of phase transformation can be controlled systematically through modulation of temperature and precursor to solvent ratio. The increase in both of these parameters leads to gradual change from surface to interface nucleation, which is associated with the increased probability of nanocrystal contact formation in the solution phase. The activation energy for surface nucleation is found to be 144 ± 30 kJ/mol, very similar to that for interface nucleation. Despite the comparable activation energy, interface nucleation dominates at higher temperatures due to increased nanocrystal interactions. The results of this work demonstrate enhanced control over polymorphic nanocrystal systems and contribute to further understanding of the kinetic processes at the nanoscale, including nucleation, crystallization, and biomineralization.

A Critical Size for Emergence of Nonbulk Electronic and Geometric Structures in Dodecanethiolate-Protected Au Clusters

Publication Date (Web): December 30, 2014 (Article)
DOI: 10.1021/ja5109968
 
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We report on how the transition from the bulk structure to the cluster-specific structure occurs in n-dodecanethiolate-protected gold clusters, Aun(SC12)m. To elucidate this transition, we isolated a series of Aun(SC12)m in the n range from 38 to ∼520, containing five newly identified or newly isolated clusters, Au104(SC12)45, Au∼226(SC12)∼76, Au∼253(SC12)∼90, Au∼356(SC12)∼112, and Au∼520(SC12)∼130, using reverse-phase high-performance liquid chromatography. Low-temperature optical absorption spectroscopy, powder X-ray diffractometry, and density functional theory (DFT) calculations revealed that the Au cores of Au144(SC12)60 and smaller clusters have molecular-like electronic structures and non-fcc geometric structures, whereas the structures of the Au cores of larger clusters resemble those of the bulk gold. A new structure model is proposed for Au104(SC12)45 based on combined approach between experiments and DFT calculations.

Direct Generation of Oxygen-Stabilized Radicals by H• Transfer from Transition Metal Hydrides

Publication Date (Web): January 8, 2015 (Communication)
DOI: 10.1021/ja511883b
 
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Transition-metal hydrides generate α-alkoxy radicals by H• transfer to enol ethers. We have measured the rate constant for transfer from CpCr(CO)3H to n-butyl vinyl ether and have examined the chemistry of radicals generated by such transfers. Radicals from appropriate substrates undergo 5-exo cyclization, with higher diastereoselectivity than the analogous all-carbon radicals. From such radicals it is straightforward to make substituted tetrahydrofurans.
Publication Date (Web): December 23, 2014 (Article)
DOI: 10.1021/ja510550g
 
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The photoreceptor protein cryptochrome is thought to host, upon light absorption, a radical pair that is sensitive to very weak magnetic fields, endowing migratory birds with a magnetic compass sense. The molecular mechanism that leads to formation of a stabilized, magnetic field sensitive radical pair has despite various theoretical and experimental efforts not been unambiguously identified yet. We challenge this unambiguity through a unique quantum mechanical molecular dynamics approach where we perform electron transfer dynamics simulations taking into account the motion of the protein upon the electron transfer. This approach allows us to follow the time evolution of the electron transfer in an unbiased fashion and to reveal the molecular driving force that ensures fast electron transfer in cryptochrome guaranteeing formation of a persistent radical pair suitable for magnetoreception. We argue that this unraveled molecular mechanism is a general principle inherent to all proteins of the cryptochrome/photolyase family and that cryptochromes are, therefore, tailored to potentially function as efficient chemical magnetoreceptors.
 

Identification of Highly Active Fe Sites in (Ni,Fe)OOH for Electrocatalytic Water Splitting

Publication Date (Web): January 5, 2015 (Article)
DOI: 10.1021/ja511559d

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Highly active catalysts for the oxygen evolution reaction (OER) are required for the development of photoelectrochemical devices that generate hydrogen efficiently from water using solar energy. Here, we identify the origin of a 500-fold OER activity enhancement that can be achieved with mixed (Ni,Fe)oxyhydroxides (Ni1–xFexOOH) over their pure Ni and Fe parent compounds, resulting in one of the most active currently known OER catalysts in alkaline electrolyte. Operando X-ray absorption spectroscopy (XAS) using high energy resolution fluorescence detection (HERFD) reveals that Fe3+ in Ni1–xFexOOH occupies octahedral sites with unusually short Fe–O bond distances, induced by edge-sharing with surrounding [NiO6] octahedra. Using computational methods, we establish that this structural motif results in near optimal adsorption energies of OER intermediates and low overpotentials at Fe sites. By contrast, Ni sites in Ni1–xFexOOH are not active sites for the oxidation of water.

Jan 13, 2015

One monomer in a transmembrane dimer transports protons and the other transfers hydride. [Also see Perspective by Krengel and Törnroth-Horsefield]
NADPH/NADP+ (the reduced form of NADP+/nicotinamide adenine dinucleotide phosphate) homeostasis is critical for countering oxidative stress in cells. Nicotinamide nucleotide transhydrogenase (TH), a membrane enzyme present in both bacteria and mitochondria, couples the proton motive force to the generation of NADPH. We present the 2.8 Å crystal structure of the transmembrane proton channel domain of TH from Thermus thermophilus and the 6.9 Å crystal structure of the entire enzyme (holo-TH). The membrane domain crystallized as a symmetric dimer, with each protomer containing a putative proton channel. The holo-TH is a highly asymmetric dimer with the NADP(H)–binding domain (dIII) in two different orientations. This unusual arrangement suggests a catalytic mechanism in which the two copies of dIII alternatively function in proton translocation and hydride transfer.
Publication Date (Web): December 31, 2014 (Communication)
DOI: 10.1021/ja511615s

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Z-schematic water splitting was successfully demonstrated using metal sulfide photocatalysts that were usually unsuitable for water splitting as single particulate photocatalysts due to photocorrosion. When metal sulfide photocatalysts with a p-type semiconductor character as a H2-evolving photocatalyst were combined with reduced graphene oxide-TiO2 composite as an O2-evolving photocatalyst, water splitting into H2 and O2 in a stoichiometric amount proceeded. In this system, photogenerated electrons in the TiO2 with an n-type semiconductor character transferred to the metal sulfide through a reduced graphene oxide to achieve water splitting. Moreover, this system was active for solar water splitting.

Folding of Oligoviologens Induced by Radical–Radical Interactions

Publication Date (Web): December 10, 2014 (Article)
DOI: 10.1021/ja5111305
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We report the synthesis of a series of homologous oligoviologens in which different numbers of 4,4′-bipyridinium (BIPY2+) subunits are linked by p-xylylene bridges, as a prelude to investigating how their radical cationic forms self-assemble both in solution and in the solid state. The strong radical–radical interactions between the radical cationic forms of the BIPY2+ units—namely, BIPY•+—in these oligoviologens induce intra- or intermolecular folding of these homologues. UV/Vis/NIR spectroscopic studies and DFT quantum mechanics indicate that the folding of the shorter oligoviologens is dominated by intermolecular radical–radical interactions. In addition to intermolecular interactions, strong intramolecular radical–radical interactions, which give rise to an NIR absorption band at 900 nm, tend to play a crucial role in governing the folding of the longer oligoviologens. The solid-state superstructure of the oligoviologen with three BIPY2+ units reveals that two intertwining chains fold together to form a dimer, stabilized by intermolecular radical–radical interactions. These dimers continue to stack in an infinite column through intermolecular radical–radical interactions between them. This research features an artificial biomimetic system which sustains delicate secondary and tertiary structures, reminiscent of those present in nucleic acids and proteins.
 
Publication Date (Web): January 12, 2015 (Article)
DOI: 10.1021/ja512014z
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With the aim of understanding the basis for the high rate of hydrogen atom abstraction (HAT) from dihydroanthracene (DHA) by the complex LCuOH (1; L = N,N′-bis(2,6-diisopropylphenyl)-2,6-pyridinedicarboxamide), the bond dissociation enthalpy of the reaction product LCu(H2O) (2) was determined through measurement of its pKa and E1/2 in THF solution. In so doing, an equilibrium between 2 and LCu(THF) was characterized by UV–vis and EPR spectroscopy and cyclic voltammetry (CV). A high pKa of 18.8 ± 1.8 and a low E1/2 of −0.074 V vs Fc/Fc+ in THF combined to yield an O–H BDE for 2 of 90 ± 3 kcal mol–1 that is large relative to values for most transition metal oxo/hydroxo complexes. By taking advantage of the increased stability of 1 observed in 1,2-difluorobenzene (DFB) solvent, the kinetics of the reactions of 1 with a range of substrates with varying BDE values for their C–H bonds were measured. The oxidizing power of 1 was revealed through the accelerated decay of 1 in the presence of the substrates, including THF (BDE = 92 kcal mol–1) and cyclohexane (BDE = 99 kcal mol–1). CV experiments in THF solvent showed that 1 reacted with THF via rate-determining attack at the THF C–H(D) bonds with a kinetic isotope effect of 10.2. Analysis of the kinetic and thermodynamic data provides new insights into the basis for the high reactivity of 1 and the possible involvement of species like 1 in oxidation catalysis.
Publication Date (Web): January 12, 2015 (Communication)
DOI: 10.1021/ja511401g
 
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C2′-Nucleotide radicals have been proposed as key intermediates in direct strand break formation in RNA exposed to ionizing radiation. Uridin-2′-yl radical (1) was independently generated in single- and double-stranded RNA via photolysis of a ketone precursor. Direct stand breaks result from heterolytic cleavage of the adjacent C3′-carbon–oxygen bond. Trapping of 1 by O2 or β-mercaptoethanol (1 M) does not compete with strand scission, indicating that phosphate elimination is >106 s–1. Uracil loss also does not compete with strand scission. When considered in conjunction with reports that nucleobase radicals produce 1, this chemistry explains why RNA is significantly more susceptible to strand scission by ionizing radiation (hydroxyl radical) than is DNA.
 
High Anhydrous Proton Conductivity of Imidazole-Loaded Mesoporous Polyimides over a Wide Range from Subzero to Moderate Temperature
Publication Date (Web): December 30, 2014 (Article)
DOI: 10.1021/ja511389q

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On-board fuel cell technology requires proton conducting materials with high conductivity not only at intermediate temperatures for work but also at room temperature and even at subzero temperature for startup when exposed to the colder climate. To develop such materials is still challenging because many promising candidates for the proton transport on the basis of extended microstructures of water molecules suffer from significant damage by heat at temperatures above 80 °C or by freeze below −5 °C. Here we show imidazole loaded tetrahedral polyimides with mesopores and good stability (Im@Td-PNDI 1 and Im@Td-PPI 2) exhibiting a high anhydrous proton conductivity over a wide temperature range from −40 to 90 °C. Among all anhydrous proton conductors, the conductivity of 2 is the highest at temperatures below 40 °C and comparable with the best materials, His@[Al(OH)(1,4-ndc)]n and [Zn3(H2PO4)6(H2O)3](Hbim), above 40 °C.

Jan 12, 2015

How Does Tunneling Contribute to Counterintuitive H-Abstraction Reactivity of Nonheme Fe(IV)O Oxidants with Alkanes?

Publication Date (Web): December 16, 2014 (Article)
DOI: 10.1021/ja509465w
 
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This article addresses the intriguing hydrogen-abstraction (H-abstraction) and oxygen-transfer (O-transfer) reactivity of a series of nonheme [FeIV(O)(TMC)(Lax)]z+ complexes, with a tetramethyl cyclam ligand and a variable axial ligand (Lax), toward three substrates: 1,4-cyclohexadiene, 9,10-dihydroanthracene, and triphenyl phosphine. Experimentally, O-transfer-reactivity follows the relative electrophilicity of the complexes, whereas the corresponding H-abstraction-reactivity generally increases as the axial ligand becomes a better electron donor, hence exhibiting an antielectrophilic trend. Our theoretical results show that the antielectrophilic trend in H-abstraction is affected by tunneling contributions. Room-temperature tunneling increases with increase of the electron donation power of the axial-ligand, and this reverses the natural electrophilic trend, as revealed through calculations without tunneling, and leads to the observed antielectrophilic trend. By contrast, O-transfer-reactivity, not being subject to tunneling, retains an electrophilic-dependent reactivity trend, as revealed experimentally and computationally. Tunneling-corrected kinetic-isotope effect (KIE) calculations matched the experimental KIE values only if all of the H-abstraction reactions proceeded on the quintet state (S = 2) surface. As such, the present results corroborate the initially predicted two-state reactivity (TSR) scenario for these reactions. The increase of tunneling with the electron-releasing power of the axial ligand, and the reversal of the “natural” reactivity pattern, support the “tunneling control” hypothesis (Schreiner et al., ref 19). Should these predictions be corroborated, the entire field of C–H bond activation in bioinorganic chemistry would lay open to reinvestigation.
 

Nanoparticle-Assisted NMR Detection of Organic Anions: From Chemosensing to Chromatography

Publication Date (Web): December 22, 2014 (Article)
DOI: 10.1021/ja511205e
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Monolayer-protected nanoparticles provide a straightforward access to self-organized receptors that selectively bind different substrates in water. Molecules featuring different kinds of noncovalent interactions (namely, hydrophobic, ion pairing, and metal–ligand coordination) can be grafted on the nanoparticle surface to provide tailored binding sites for virtually any class of substrate. Not only the selectivity but also the strength of these interactions can be modulated. Such recognition ability can be exploited with new sensing protocols, based on NMR magnetization transfer and diffusion-ordered spectroscopy (DOSY), to detect and identify organic molecules in complex mixtures.
 

Role of the Active Site Guanine in the glmS Ribozyme Self-Cleavage Mechanism: Quantum Mechanical/Molecular Mechanical Free Energy Simulations

Publication Date (Web): December 19, 2014 (Article)
DOI: 10.1021/ja510387y
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The glmS ribozyme catalyzes a self-cleavage reaction at the phosphodiester bond between residues A-1 and G1. This reaction is thought to occur by an acid–base mechanism involving the glucosamine-6-phosphate cofactor and G40 residue. Herein quantum mechanical/molecular mechanical free energy simulations and pKa calculations, as well as experimental measurements of the rate constant for self-cleavage, are utilized to elucidate the mechanism, particularly the role of G40. Our calculations suggest that an external base deprotonates either G40(N1) or possibly A-1(O2′), which would be followed by proton transfer from G40(N1) to A-1(O2′). After this initial deprotonation, A-1(O2′) starts attacking the phosphate as a hydroxyl group, which is hydrogen-bonded to deprotonated G40, concurrent with G40(N1) moving closer to the hydroxyl group and directing the in-line attack. Proton transfer from A-1(O2′) to G40 is concomitant with attack of the scissile phosphate, followed by the remainder of the cleavage reaction. A mechanism in which an external base does not participate, but rather the proton transfers from A-1(O2′) to a nonbridging oxygen during nucleophilic attack, was also considered but deemed to be less likely due to its higher effective free energy barrier. The calculated rate constant for the favored mechanism is in agreement with the experimental rate constant measured at biological Mg2+ ion concentration. According to these calculations, catalysis is optimal when G40 has an elevated pKa rather than a pKa shifted toward neutrality, although a balance among the pKa’s of A-1, G40, and the nonbridging oxygen is essential. These results have general implications, as the hammerhead, hairpin, and twister ribozymes have guanines at a similar position as G40.
 

Evolution of Self-Assembled ZnTe Magic-Sized Nanoclusters

Publication Date (Web): December 22, 2014 (Article)
DOI: 10.1021/ja509782n
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Three families of ZnTe magic-sized nanoclusters (MSNCs) were obtained exclusively using polytellurides as a tellurium precursor in a one-pot reaction by simply varying the reaction temperature and time only. Different ZnTe MSNCs exhibit different self-assembling or aggregation behavior, owing to their different structure, cluster size, and dipole–dipole interactions. The smallest family of ZnTe MSNCs (F323) does not reveal a crystalline structure and as a result assembles into lamellar triangle plates. Continuous heating of as synthesized ZnTe F323 assemblies resulted in the formation of ZnTe F398 MSNCs with wurzite structure and concomitant transformation into lamellar rectangle assemblies with the organization of nanoclusters along the ⟨002⟩ direction. Further annealing of ZnTe F398 assembled lamellar rectangles leads to full organization of MSNCs in all directions and formation of larger ZnTe F444 NCs that spontaneously form ultrathin nanowires following an oriented attachment mechanism. The key step in control over the size distribution of ZnTe ultrathin nanowires is, in fact, the growth mechanism of ZnTe F398 MSNCs; namely, the step growth mechanism enables formation of more uniform nanowires compared to those obtained by continuous growth mechanism. High yield of ZnTe nanowires is achieved as a result of the wurzite structure of F398 precursor. Transient absorption (TA) measurements show that all three families possess ultrafast dynamics of photogenerated electrons, despite their different crystalline structures.
 

Jan 7, 2015

Adatoms underneath Single Porphyrin Molecules on Au(111)

Publication Date (Web): December 11, 2014 (Article)
DOI: 10.1021/ja510528x


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The adsorption of porphyrin derivatives on a Au(111) surface was studied by scanning tunneling microscopy and spectroscopy at low temperatures in combination with density functional theory calculations. Different molecular appearances were found and could be assigned to the presence of single gold adatoms bonded by a coordination bond underneath the molecular monolayer, causing a characteristic change of the electronic structure of the molecules. Moreover, this interpretation could be confirmed by manipulation experiments of individual molecules on and off a single gold atom. This study provides a detailed understanding of the role of metal adatoms in surface–molecule bonding and anchoring and of the appearance of single molecules, and it should prove relevant for the imaging of related molecule–metal systems.

Jan 4, 2015

Molecular beam spectroscopy reveals unanticipated transient states along particular pathways of a well-studied reaction.
The Cl + H2 reaction is an important benchmark system in the study of chemical reaction dynamics that has always appeared to proceed via a direct abstraction mechanism, with no clear signature of reaction resonances. Here we report a high-resolution crossed–molecular beam study on the Cl + HD (v = 1, j = 0) → DCl + H reaction (where v is the vibrational quantum number and j is the rotational quantum number). Very few forward scattered products were observed. However, two distinctive peaks at collision energies of 2.4 and 4.3 kilocalories per mole for the DCl (v′ = 1) product were detected in the backward scattering direction. Detailed quantum dynamics calculations on a highly accurate potential energy surface suggested that these features originate from two very short-lived dynamical resonances trapped in the peculiar H-DCl (v′ = 2) vibrational adiabatic potential wells that result from chemical bond softening. We anticipate that dynamical resonances trapped in such wells exist in many reactions involving vibrationally excited molecules.
A soluble rhodium catalyst converts alkenes to aldehydes without the need for toxic or explosive gas-phase reactants [Also see Report by Murphy et al.]
A catalyst to selectively reverse a common chemical reaction offers versatile opportunities in molecular synthesis. [Also see Perspective by Landis]
The dehydroformylation of aldehydes to generate olefins occurs during the biosynthesis of various sterols, including cholesterol in humans. Here, we implement a synthetic version that features the transfer of a formyl group and hydride from an aldehyde substrate to a strained olefin acceptor. A Rhodium (Xantphos)(benzoate) catalyst activates aldehyde carbon-hydrogen (C–H) bonds with high chemoselectivity to trigger carbon-carbon (C–C) bond cleavage and generate olefins at low loadings (0.3 to 2 mole percent) and temperatures (22° to 80°C). This mild protocol can be applied to various natural products and was used to achieve a three-step synthesis of (+)-yohimbenone. A study of the mechanism reveals that the benzoate counterion acts as a proton shuttle to enable transfer hydroformylation.

Automated technology enables chemical reaction optimization using micrograms of material.
At the forefront of new synthetic endeavors, such as drug discovery or natural product synthesis, large quantities of material are rarely available and timelines are tight. A miniaturized automation platform enabling high-throughput experimentation for synthetic route scouting to identify conditions for preparative reaction scale-up would be a transformative advance. Because automated, miniaturized chemistry is difficult to carry out in the presence of solids or volatile organic solvents, most of the synthetic “toolkit” cannot be readily miniaturized. Using palladium-catalyzed cross-coupling reactions as a test case, we developed automation-friendly reactions to run in dimethyl sulfoxide at room temperature. This advance enabled us to couple the robotics used in biotechnology with emerging mass spectrometry–based high-throughput analysis techniques. More than 1500 chemistry experiments were carried out in less than a day, using as little as 0.02 milligrams of material per reaction.
The x-ray structure of a protein complex shows how this enzyme pumps protons across the mitochondrial membrane.
Proton-pumping complex I of the mitochondrial respiratory chain is among the largest and most complicated membrane protein complexes. The enzyme contributes substantially to oxidative energy conversion in eukaryotic cells. Its malfunctions are implicated in many hereditary and degenerative disorders. We report the x-ray structure of mitochondrial complex I at a resolution of 3.6 to 3.9 angstroms, describing in detail the central subunits that execute the bioenergetic function. A continuous axis of basic and acidic residues running centrally through the membrane arm connects the ubiquinone reduction site in the hydrophilic arm to four putative proton-pumping units. The binding position for a substrate analogous inhibitor and blockage of the predicted ubiquinone binding site provide a model for the “deactive” form of the enzyme. The proposed transition into the active form is based on a concerted structural rearrangement at the ubiquinone reduction site, providing support for a two-state stabilization-change mechanism of proton pumping.
A monomeric redox protein can be engineered into a tetrameric β-lactamase that confers antibiotic resistance in vivo.
The generation of new enzymatic activities has mainly relied on repurposing the interiors of preexisting protein folds because of the challenge in designing functional, three-dimensional protein structures from first principles. Here we report an artificial metallo-β-lactamase, constructed via the self-assembly of a structurally and functionally unrelated, monomeric redox protein into a tetrameric assembly that possesses catalytic zinc sites in its interfaces. The designed metallo-β-lactamase is functional in the Escherichia coli periplasm and enables the bacteria to survive treatment with ampicillin. In vivo screening of libraries has yielded a variant that displays a catalytic proficiency [(kcat/Km)/kuncat] for ampicillin hydrolysis of 2.3 × 106 and features the emergence of a highly mobile loop near the active site, a key component of natural β-lactamases to enable substrate interactions.
A designed protein transports ions across a membrane [Also see Report by Joh et al.]
Computational design yields a transmembrane protein that selectively transports zinc cations. [Also see Perspective by Lupas]
The design of functional membrane proteins from first principles represents a grand challenge in chemistry and structural biology. Here, we report the design of a membrane-spanning, four-helical bundle that transports first-row transition metal ions Zn2+ and Co2+, but not Ca2+, across membranes. The conduction path was designed to contain two di-metal binding sites that bind with negative cooperativity. X-ray crystallography and solid-state and solution nuclear magnetic resonance indicate that the overall helical bundle is formed from two tightly interacting pairs of helices, which form individual domains that interact weakly along a more dynamic interface. Vesicle flux experiments show that as Zn2+ ions diffuse down their concentration gradients, protons are antiported. These experiments illustrate the feasibility of designing membrane proteins with predefined structural and dynamic properties.
Local electric fields accelerate an enzymatic reaction [Also see Report by Fried et al.]
Vibrational spectroscopy pinpoints a surprisingly large local electric field where an enzyme binds its substrate. [Also see Perspective by Hildebrandt]
Enzymes use protein architecture to impose specific electrostatic fields onto their bound substrates, but the magnitude and catalytic effect of these electric fields have proven difficult to quantify with standard experimental approaches. Using vibrational Stark effect spectroscopy, we found that the active site of the enzyme ketosteroid isomerase (KSI) exerts an extremely large electric field onto the C=O chemical bond that undergoes a charge rearrangement in KSI’s rate-determining step. Moreover, we found that the magnitude of the electric field exerted by the active site strongly correlates with the enzyme’s catalytic rate enhancement, enabling us to quantify the fraction of the catalytic effect that is electrostatic in origin. The measurements described here may help explain the role of electrostatics in many other enzymes and biomolecular systems.

Platinum-rich phases that initially form create the edges and corners of octahedral nanoparticle alloys.
Morphological shape in chemistry and biology owes its existence to anisotropic growth and is closely coupled to distinct functionality. Although much is known about the principal growth mechanisms of monometallic shaped nanocrystals, the anisotropic growth of shaped alloy nanocrystals is still poorly understood. Using aberration-corrected scanning transmission electron microscopy, we reveal an element-specific anisotropic growth mechanism of platinum (Pt) bimetallic nano-octahedra where compositional anisotropy couples to geometric anisotropy. A Pt-rich phase evolves into precursor nanohexapods, followed by a slower step-induced deposition of an M-rich (M = Ni, Co, etc.) phase at the concave hexapod surface forming the octahedral facets. Our finding explains earlier reports on unusual compositional segregations and chemical degradation pathways of bimetallic polyhedral catalysts and may aid rational synthesis of shaped alloy catalysts with desired compositional patterns and properties.
Alkali atoms help disperse catalytically active gold on high–surface-area alumina and silica supports.
We report that the addition of alkali ions (sodium or potassium) to gold on KLTL-zeolite and mesoporous MCM-41 silica stabilizes mononuclear gold in Au-O(OH)x-(Na or K) ensembles. This single-site gold species is active for the low-temperature (<200°C) water-gas shift (WGS) reaction. Unexpectedly, gold is thus similar to platinum in creating –O linkages with more than eight alkali ions and establishing an active site on various supports. The intrinsic activity of the single-site gold species is the same on irreducible supports as on reducible ceria, iron oxide, and titania supports, apparently all sharing a common, similarly structured gold active site. This finding paves the way for using earth-abundant supports to disperse and stabilize precious metal atoms with alkali additives for the WGS and potentially other fuel-processing reactions.
A photochemical route to a nylon precursor could prove more environmentally benign than current approaches.
Nitric acid oxidation of cyclohexane accounts for ~95% of the worldwide adipic acid production and is also responsible for ~5 to 8% of the annual worldwide anthropogenic emission of the ozone-depleting greenhouse gas nitrous oxide (N2O). Here we report a N2O-free process for adipic acid synthesis. Treatment of neat cyclohexane, cyclohexanol, or cyclohexanone with ozone at room temperature and 1 atmosphere of pressure affords adipic acid as a solid precipitate. Addition of acidic water or exposure to ultraviolet (UV) light irradiation (or a combination of both) dramatically enhances the oxidative conversion of cyclohexane to adipic acid.
Vibrational excitation can modulate electron transfer probabilities in real time.
Electron transfer (ET) from donor to acceptor is often mediated by nuclear-electronic (vibronic) interactions in molecular bridges. Using an ultrafast electronic-vibrational-vibrational pulse-sequence, we demonstrate how the outcome of light-induced ET can be radically altered by mode-specific infrared (IR) excitation of vibrations that are coupled to the ET pathway. Picosecond narrow-band IR excitation of high-frequency bridge vibrations in an electronically excited covalent trans-acetylide platinum(II) donor-bridge-acceptor system in solution alters both the dynamics and the yields of competing ET pathways, completely switching a charge separation pathway off. These results offer a step toward quantum control of chemical reactivity by IR excitation.
Mutations can alter protein conformations in the same way that allosteric small molecules do.
Evolution and design of protein complexes are almost always viewed through the lens of amino acid mutations at protein interfaces. We showed previously that residues not involved in the physical interaction between proteins make important contributions to oligomerization by acting indirectly or allosterically. In this work, we sought to investigate the mechanism by which allosteric mutations act, using the example of the PyrR family of pyrimidine operon attenuators. In this family, a perfectly sequence-conserved helix that forms a tetrameric interface is exposed as solvent-accessible surface in dimeric orthologs. This means that mutations must be acting from a distance to destabilize the interface. We identified 11 key mutations controlling oligomeric state, all distant from the interfaces and outside ligand-binding pockets. Finally, we show that the key mutations introduce conformational changes equivalent to the conformational shift between the free versus nucleotide-bound conformations of the proteins.