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Communications
Improved Precursor Chemistry for the Synthesis of III–V Quantum Dots
Daniel K. Harris - and
Moungi G. Bawendi *
The synthesis of III–V quantum dots has been long known to be more challenging than the synthesis of other types of inorganic quantum dots. This is attributed to highly reactive group-V precursors. We synthesized molecules that are suitable for use as group-V precursors and characterized their reactivity using multiple complementary techniques. We show that the size distribution of indium arsenide quantum dots indeed improves with decreased precursor reactivity.
Selective Targeting of Distinct Active Site Nucleophiles by Irreversible Src-Family Kinase Inhibitors
Nathan N. Gushwa - ,
Sumin Kang - ,
Jing Chen - , and
Jack Taunton *
Src-family tyrosine kinases play pivotal roles in human physiology and disease, and several drugs that target members of this family are in clinical use. None of these drugs appear to discriminate among closely related kinases. However, assessing their selectivity toward endogenous kinases in living cells remains a significant challenge. Here, we report the design of two Src-directed chemical probes, each consisting of a nucleoside scaffold with a 5′-electrophile. A 5′-fluorosulfonylbenzoate (1) reacts with the conserved catalytic lysine (Lys295) and shows little discrimination among related kinases. By contrast, a 5′-vinylsulfonate (2) reacts with a poorly conserved, proximal cysteine (Cys277) found in three Src-family and six unrelated kinases. Both 1 and 2 bear an alkyne tag and efficiently label their respective endogenous kinase targets in intact cells. Using 1 as a competitive probe, we determined the extent to which ponatinib, a clinical Bcr-Abl inhibitor, targets Src-family kinases. Remarkably, while ponatinib had little effect on endogenous Fyn or Src, it potently blocked the critical T-cell kinase, Lck. Probes 1 and 2 thus enable competitive profiling versus distinct kinase subsets in living cells.
Current–Voltage Characteristics and Transition Voltage Spectroscopy of Individual Redox Proteins
Juan M. Artés - ,
Montserrat López-Martínez - ,
Arnaud Giraudet - ,
Ismael Díez-Pérez - ,
Fausto Sanz - , and
Pau Gorostiza *
Understanding how molecular conductance depends on voltage is essential for characterizing molecular electronics devices. We reproducibly measured current–voltage characteristics of individual redox-active proteins by scanning tunneling microscopy under potentiostatic control in both tunneling and wired configurations. From these results, transition voltage spectroscopy (TVS) data for individual redox molecules can be calculated and analyzed statistically, adding a new dimension to conductance measurements. The transition voltage (TV) is discussed in terms of the two-step electron transfer (ET) mechanism. Azurin displays the lowest TV measured to date (0.4 V), consistent with the previously reported distance decay factor. This low TV may be advantageous for fabricating and operating molecular electronic devices for different applications. Our measurements show that TVS is a helpful tool for single-molecule ET measurements and suggest a mechanism for gating of ET between partner redox proteins.
Evidence for an Alternative to the Oxygen Rebound Mechanism in C–H Bond Activation by Non-Heme FeIVO Complexes
Kyung-Bin Cho - ,
Xiujuan Wu - ,
Yong-Min Lee - ,
Yoon Hye Kwon - ,
Sason Shaik *- , and
Wonwoo Nam *
The hydroxylation of alkanes by heme FeIVO species occurs via the hydrogen abstraction/oxygen rebound mechanism. It has been assumed that non-heme FeIVO species follow the heme FeIVO paradigm in C–H bond activation reactions. Herein we report theoretical and experimental evidence that C–H bond activation of alkanes by synthetic non-heme FeIVO complexes follows an alternative mechanism. Theoretical calculations predicted that dissociation of the substrate radical formed via hydrogen abstraction from the alkane is more favorable than the oxygen rebound and desaturation processes. This theoretical prediction was verified by experimental results obtained by analyzing iron and organic products formed in the C–H bond activation of substrates by non-heme FeIVO complexes. The difference in the behaviors of heme and non-heme FeIVO species is ascribed to differences in structural preference and exchange-enhanced reactivity. Thus, the general consensus that C–H bond activation by high-valent metal–oxo species, including non-heme FeIVO, occurs via the conventional hydrogen abstraction/oxygen rebound mechanism should be viewed with caution.
A Heterogeneous Nickel Catalyst for the Hydrogenolysis of Aryl Ethers without Arene Hydrogenation
Alexey G. Sergeev - ,
Jonathan D. Webb - , and
John F. Hartwig *
A heterogeneous nickel catalyst for the selective hydrogenolysis of aryl ethers to arenes and alcohols generated without an added dative ligand is described. The catalyst is formed in situ from the well-defined soluble nickel precursor Ni(COD)2 or Ni(CH2TMS)2(TMEDA) in the presence of a base additive, such as tBuONa. The catalyst selectively cleaves CAr–O bonds in aryl ether models of lignin without hydrogenation of aromatic rings, and it operates at loadings down to 0.25 mol % at 1 bar of H2 pressure. The selectivity of this catalyst for electronically varied aryl ethers differs from that of the homogeneous catalyst reported previously, implying that the two catalysts are distinct from each other.
Cyclopentadiene–Phosphine/Palladium-Catalyzed Cleavage of C–N Bonds in Secondary Amines: Synthesis of Pyrrole and Indole Derivatives from Secondary Amines and Alkenyl or Aryl Dibromides
Weizhi Geng - ,
Wen-Xiong Zhang - ,
Wei Hao - , and
Zhenfeng Xi *
An efficient Pd-catalyzed cleavage of C(sp3)–N bonds in secondary amines and a consequent C(sp2)–N and C(sp3)–N coupling process was developed. Various secondary amines could be used to react with alkenyl or aryl dibromides, affording pyrroles and indoles in high yields. Cyclopentadiene–phosphine ligands, a new type of P–olefin ligand, were found to be able to promote the efficiency of this Pd-catalyzed process remarkably. A reactive Pd complex coordinated with a cyclopentadiene–phosphine ligand was successfully isolated and structurally characterized.
Facile Synthesis of Gold Wavy Nanowires and Investigation of Their Growth Mechanism
Cun Zhu - ,
Hsin-Chieh Peng - ,
Jie Zeng - ,
Jingyue Liu - ,
Zhongze Gu - , and
Younan Xia *
We describe a synthesis of Au wavy nanowires in an aqueous solution in the presence of cetyltrimethylammonium bromide (CTAB). The resultant Au nanowires automatically separated from the solution and floated at the air/water interface. We investigated the formation mechanism by characterizing the samples obtained at different stages of the synthesis. Both particle attachment and cold welding were found to be involved in the formation of such nanowires. Based on X-ray photoelectron spectroscopy and thermogravimetric analysis, the CTAB molecules adsorbed on the surface of a Au nanostructure went through a change in structure from a bilayer to a monolayer, converting the Au surface from hydrophilic to hydrophobic. As a result, the Au wavy nanowires were driven to the air/water interface during the synthesis. This growth mechanism is potentially extendable to many other systems involving small surfactant molecules.
A Facile Approach for Controlling the Orientation of One-Dimensional Mesochannels in Mesoporous Titania Films
Feng Shan - ,
Xuemin Lu *- ,
Qian Zhang - ,
Jun Wu - ,
Yuzhu Wang - ,
Fenggang Bian - ,
Qinghua Lu *- ,
Zhaofu Fei - , and
Paul J. Dyson
Controlling of the orientation of mesochannels in mesostructured thin films is important for the development of novel molecular devices and, in particular, generating vertically aligned mesochannels with respect to the substrate plane is extremely challenging for nonsiliceous materials. We describe a facile and highly effective air flow method, which is able to control the unidirectional alignment of titania mesochannels in a desired direction (e.g., parallel, perpendicular, or oblique) on a large scale, via manipulation of the air flow rate and incident angle. The titania mesochannels were characterized by TEM, SEM, SAXRD, and GISAXS. The unidirectional, vertically aligned mesostructured titania films were found to exhibit excellent ion conductivity.
Prato Reaction of M3N@Ih-C80 (M = Sc, Lu, Y, Gd) with Reversible Isomerization
Safwan Aroua - and
Yoko Yamakoshi *
The 1,3-dipolar cycloaddition of an azomethine ylide (Prato reaction) with M3N@Ih-C80 (denoted as M3N@C80; M = Sc, Lu, Y, Gd) was carried out to obtain fulleropyrrolidinebis(carboxylic acid) derivatives as scaffolds for the preparation of various functionalized M3N@C80 materials. The formation of two monoadduct isomers (the [6,6]- and [5,6]-adducts) were detected by HPLC and identified by NMR and vis/NIR spectroscopies. In each Prato reaction with M3N@C80, the initial addition gave a [6,6]-adduct of the Ih-C80 cage, and subsequently, a [5,6]-adduct was obtained by complete or partial thermal isomerization via a rearrangement reaction. The reaction rate of the latter thermal conversion of the adducts was dependent on the size of the metal cluster inside C80, and interestingly, in the reactions of Y3N@C80 and Gd3N@C80, this conversion was found to be reversible for the first time. Detailed kinetic studies provided the enthalpy and entropy barriers for the reactions of the adducts of Lu3N@C80, Y3N@C80, and Gd3N@C80. The utility of the obtained Prato adducts was confirmed by preparation of a highly water-soluble Gd3N@C80 derivative.
Nanoscale Electrochemical Patterning Reveals the Active Sites for Catechol Oxidation at Graphite Surfaces
Anisha N. Patel - ,
Kim McKelvey - , and
Patrick R. Unwin *
Graphite-based electrodes (graphite, graphene, and nanotubes) are used widely in electrochemistry, and there is a long-standing view that graphite step edges are needed to catalyze many reactions, with the basal surface considered to be inert. In the present work, this model was tested directly for the first time using scanning electrochemical cell microscopy reactive patterning and shown to be incorrect. For the electro-oxidation of dopamine as a model process, the reaction rate was measured at high spatial resolution across a surface of highly oriented pyrolytic graphite. Oxidation products left behind in a pattern defined by the scanned electrochemical cell served as surface-site markers, allowing the electrochemical activity to be correlated directly with the graphite structure on the nanoscale. This process produced tens of thousands of electrochemical measurements at different locations across the basal surface, unambiguously revealing it to be highly electrochemically active, with step edges providing no enhanced activity. This new model of graphite electrodes has significant implications for the design of carbon-based biosensors, and the results are additionally important for understanding electrochemical processes on related sp2-hybridized materials such as pristine graphene and nanotubes.
Low-Temperature Carbon–Chlorine Bond Activation by Bimetallic Gold/Palladium Alloy Nanoclusters: An Application to Ullmann Coupling
Raghu Nath Dhital - ,
Choavarit Kamonsatikul - ,
Ekasith Somsook - ,
Karan Bobuatong - ,
Masahiro Ehara *- ,
Sangita Karanjit - , and
Hidehiro Sakurai *
This paper describes the unique catalytic activity of bimetallic Au/Pd alloy nanoclusters (NCs) for Ullmann coupling of chloroarenes in aqueous media at low temperature. The corresponding reaction cannot be achieved by monometallic Au and Pd NCs as well as their physical mixtures. On the basis of quantum chemical calculation, it was found that the crucial step to govern the unusual catalytic activity of Au/Pd is the dissociative chemisorption of ArCl, which is unlikely in the monometallic Au and Pd NCs.
Single-Molecular Enzymatic Elongation of Hyaluronan Polymers Visualized by High-Speed Atomic Force Microscopy
Toshiaki Mori *- ,
Atsushi Hirose - ,
Tatsuya Hagiwara - ,
Masanori Ohtsuka - ,
Yoshimitsu Kakuta - ,
Koji Kimata - , and
Yoshio Okahata *
Using high-speed scanning atomic force microscopy, we directly observed single-molecular enzymatic elongation of hyaluronan polymer chains at intervals of 10 s on a mica or lipid bilayer surface, on which Pasteurella multocida hyaluronic acid synthase (pmHAS) was immobilized. The reaction was started by the addition of both UDP-glucuronic acid and UDP-N-acetylglucosamine monomers. The average catalytic elongation rate constant (kcat) was found to be 1.8 mer s–1 from one active enzyme physically adsorbed on a mica surface. When pmHAS was immobilized by inserting its hydrophobic tail part into lipid bilayers, most of the enzymes retained their activity, and the kcat values were found to be in the range 1–10 mer s–1 for 29 enzymes (average was kcat = 2–4 mer s–1). These kcat values were lowest level of kcat = 1–100 s–1 obtained in bulk solution by radioisotope methods.
Colloidal InSb Nanocrystals
Wenyong Liu - ,
Angela Y. Chang - ,
Richard D. Schaller - , and
Dmitri V. Talapin *
We report the colloidal synthesis of monodisperse nanocrystals (NCs) of InSb, which is an important member of III–V semiconductor family. Colloidal InSb NC quantum dots showed well-resolved excitonic transitions in the near-infrared spectral range, with the optical band gaps tunable from ∼1.03 eV (1200 nm) to ∼0.71 eV (1750 nm) corresponding to 3.3 and 6.5 nm InSb NCs, respectively. We observed size-tunable band edge photoluminescence that could be significantly enhanced by growing InSb/CdSe or InSb/CdS core–shell nanostructures. Films of InSb NCs capped with S2– ions showed ambipolar charge transport.
Iron-Catalyzed Aromatic Amination for Nonsymmetrical Triarylamine Synthesis
Takuji Hatakeyama - ,
Ryuji Imayoshi - ,
Yuya Yoshimoto - ,
Sujit K. Ghorai - ,
Masayoshi Jin - ,
Hikaru Takaya - ,
Kazuhiro Norisuye - ,
Yoshiki Sohrin - , and
Masaharu Nakamura *
Novel iron-catalyzed amination reactions of various aryl bromides have been developed for the synthesis of diaryl- and triarylamines. The key to the success of this protocol is the use of in situ generated magnesium amides in the presence of a lithium halide, which dramatically increases the product yield. The present method is simple and free of precious and expensive metals and ligands, thus providing a facile route to triarylamines, a recurrent core unit in organic electronic materials as well as pharmaceuticals.
Role of Four-Fold Coordinated Titanium and Quantum Confinement in CO2 Reduction at Titania Surface
Donghwa Lee - and
Yosuke Kanai *
Photocatalytic reduction of carbon dioxide (CO2) into hydrocarbons is an attractive approach for mitigating CO2 emission and generating useful fuels at the same time. Titania (TiO2) is one of the most promising photocatalysts for this purpose, and nanostructured TiO2 materials often lead to an increased efficiency for the photocatalytic reactions. However, what aspects of and how such nanomaterials play the important role in the improved efficiency are yet to be understood. Using first-principles calculations, reaction mechanisms on the surface of bulk anatase TiO2(101) and of a small TiO2 nanocluster were investigated to elucidate the role of four-fold coordinated titanium atoms and quantum confinement (QC) in the CO2 reduction. Significant barrier reduction observed on the nanocluster surface is discussed in terms of how the under-coordinated titanium atoms and QC influence CO2 reduction kinetics at surface. It is shown that the reduction to CO can be greatly facilitated by the under-coordinated titanium atoms, and they also make CO2 anion formation favorable at surfaces.
Directional Assembly of α-Helical Peptides Induced by Cyclization
Seunghyun Sim - ,
Yongju Kim - ,
Taehoon Kim - ,
Sunhee Lim - , and
Myongsoo Lee *
Effective stabilization of short peptide chains into a helical structure has been a challenge in the fields of chemistry and biology. Here we report a novel method for α-helix stabilization of short peptides through their confinement in a cyclic architecture. We synthesized block peptides based on a short peptide and a flexible linker as linear precursors. Subsequent cyclization of the peptide precursors resulted in a conformational change of the peptide unit from a random coil to an α-helix. The incorporation of hydrophobic residues into the peptide unit led to a facially amphiphilic conformation of the molecular cycle. The resulting amphiphilic peptide self-assembled into undulated nanofibers through the directional assembly of small oblate micelles.
Artificial, Parallel, Left-Handed DNA Helices
Cheng Tian - ,
Chuan Zhang - ,
Xiang Li - ,
Yingmei Li - ,
Guansong Wang *- , and
Chengde Mao *
This communication reports an engineered DNA architecture. It contains multiple domains of half-turn-long, standard B-DNA duplexes. While each helical domain is right-handed and its two component strands are antiparallel, the global architecture is left-handed and the two component DNA strands are oriented parallel to each other.
Iridium-Catalyzed Enantioselective Polyene Cyclization
Michael A. Schafroth - ,
David Sarlah - ,
Simon Krautwald - , and
Erick M. Carreira *
A highly enantioselective polycyclization method has been developed using the combination of Lewis acid activation with iridium-catalyzed allylic substitution. This strategy relies on direct use of branched, racemic allylic alcohols and furnishes a diverse and unique set of carbo- and heteropolycyclic ring systems in good yields and ≥99% ee.
Surprising Intrinsic Photostability of the Disulfide Bridge Common in Proteins
Anne B. Stephansen - ,
Rasmus Y. Brogaard - ,
Thomas S. Kuhlman - ,
Liv B. Klein - ,
Jørn B. Christensen - , and
Theis I. Sølling *
For a molecule to survive evolution and to become a key building block in nature, photochemical stability is essential. The photolytically weak S–S bond does not immediately seem to possess that ability. We mapped the real-time motion of the two sulfur radicals that result from disulfide photolysis on the femtosecond time scale and found the reason for the existence of the S–S bridge as a natural building block in folded structures. The sulfur atoms will indeed move apart on the excited state but only to oscillate around the S–S center of mass. At long S–S distances, there is a strong coupling to the ground state, and the oscillatory motion enables the molecules to continuously revisit that particular region of the potential energy surface. When a structural feature such as a ring prevents the sulfur radicals from flying apart and thus assures a sufficient residence time in the active region of the potential energy surface, the electronic energy is converted into less harmful vibrational energy, thereby restoring the S–S bond in the ground state.
Simultaneous Determination of Both the Enantiomeric Composition and Concentration of a Chiral Substrate with One Fluorescent Sensor
Shanshan Yu - ,
Winston Plunkett - ,
Michael Kim - , and
Lin Pu *
A fluorescent sensor is discovered to exhibit high sensitivity at one emission wavelength and high enantioselectivity at another when treated with a chiral diamine. By using this fluorescent sensor, it is demonstrated for the first time that both the concentration and enantiomeric composition of a chiral substrate can be determined simultaneously with one fluorescence measurement.
Total Structure and Optical Properties of a Phosphine/Thiolate-Protected Au24 Nanocluster
Anindita Das - ,
Tao Li - ,
Katsuyuki Nobusada - ,
Qiong Zeng - ,
Nathaniel L. Rosi - , and
Rongchao Jin *
We report the synthesis and total structure determination of a Au24 nanocluster protected by mixed ligands of phosphine and thiolate. Single crystal X-ray crystallography and electrospray ionization mass spectrometry (ESI-MS) unequivocally determined the cluster formula to be [Au24(PPh3)10(SC2H4Ph)5X2]+, where X = Cl and/or Br. The structure consists of two incomplete (i.e., one vertex missing) icosahedral Au12 units joined by five thiolate linkages. This structure shows interesting differences from the previously reported vertex-sharing biicosahedral [Au25(PPh3)10(SC2H4Ph)5X2]2+ nanocluster protected by the same type and number of phosphine and thiolate ligands. The optical absorption spectrum of Au24 nanocluster was theoretically reproduced and interpreted.
White Electroluminescence from All-Phosphorescent Single Polymers on a Fluorinated Poly(arylene ether phosphine oxide) Backbone Simultaneously Grafted with Blue and Yellow Phosphors
Shiyang Shao - ,
Junqiao Ding *- ,
Lixiang Wang *- ,
Xiabin Jing - , and
Fosong Wang
On the basis of a fluorinated poly(arylene ether phosphine oxide) backbone with both high triplet energy and appropriate HOMO/LUMO levels, highly efficient all-phosphorescent single white-emitting polymers were designed and successfully synthesized via a “two-step addition” strategy. Simultaneous blue and yellow triplet emissions were achieved to generate white electroluminescence with a promising luminous efficiency as high as 18.4 cd/A (8.5 lm/W, 7.1%) and CIE coordinates of (0.31, 0.43).
Atomically Thick Bismuth Selenide Freestanding Single Layers Achieving Enhanced Thermoelectric Energy Harvesting
Yongfu Sun - ,
Hao Cheng - ,
Shan Gao - ,
Qinghua Liu - ,
Zhihu Sun - ,
Chong Xiao - ,
Changzheng Wu - ,
Shiqiang Wei - , and
Yi Xie *
Thermoelectric materials can realize significant energy savings by generating electricity from untapped waste heat. However, the coupling of the thermoelectric parameters unfortunately limits their efficiency and practical applications. Here, a single-layer-based (SLB) composite fabricated from atomically thick single layers was proposed to optimize the thermoelectric parameters fully. Freestanding five-atom-thick Bi2Se3 single layers were first synthesized via a scalable interaction/exfoliation strategy. As revealed by X-ray absorption fine structure spectroscopy and first-principles calculations, surface distortion gives them excellent structural stability and a much increased density of states, resulting in a 2-fold higher electrical conductivity relative to the bulk material. Also, the surface disorder and numerous interfaces in the Bi2Se3 SLB composite allow for effective phonon scattering and decreased thermal conductivity, while the 2D electron gas and energy filtering effect increase the Seebeck coefficient, resulting in an 8-fold higher figure of merit (ZT) relative to the bulk material. This work develops a facile strategy for synthesizing atomically thick single layers and demonstrates their superior ability to optimize the thermoelectric energy harvesting.
Synthesis and Physical Properties of Four Hexazapentacene Derivatives
Gang Li - ,
Yuechao Wu - ,
Junkuo Gao - ,
Chengyuan Wang - ,
Junbo Li - ,
Huacheng Zhang - ,
Yang Zhao - ,
Yanli Zhao - , and
Qichun Zhang *
In two steps from commercially available starting materials, four novel hexazapentacene derivatives have been synthesized through cyclocondensation reaction between tetraamines and 1,2-diketones. The observed optical bandgaps for 2,3,9,10-tetramethyl-1,4,6,8,11,13-hexaza-pentacene (TMHAP, 1), tetraethyl-1,4,6,8,11,13-hexaza-pentacene (TEHAP, 2), 1,2,3,4,10,11,12,13-octahydro-5,7, 9,14,16,18-hexazaheptacene (OHHAH, 3), and tetra(2-thioyl)-1,4,6,8,11,13-hexazapentacene (TTHAP, 4) are 2.55, 2.55, 2.45, and 2.25 eV, respectively. The cyclic voltammetry measurements show that all compounds exhibit one revisable reduction waves. The calculated bandgaps through DFT calculations for TMHAP (1), TEHAP (2), OHAH (3), and TTHAP (4) are 2.41, 2.41, 2.34, and 2.15 eV, respectivly, which are close to the experimental results. Our success in synthesizing hexazapentacene derivatives might offer a promising strategy to challenge larger azaacenes with more N atoms.
In Situ Reaction Monitoring Reveals a Diastereoselective Ligand Exchange Reaction between the Intrinsically Chiral Au38(SR)24 and Chiral Thiols
Stefan Knoppe - ,
Raymond Azoulay - ,
Amala Dass - , and
Thomas Bürgi *
The ligand exchange reaction between racemic Au38(2-PET)24 (2-PET = 2-phenylethylthiolate) clusters and enantiopure 1,1′-binaphthyl-2,2′-dithiol (BINAS) was monitored in situ using a chiral high-performance liquid chromatography approach. In the first exchange step, a clear preference of R-BINAS for the left-handed enantiomer of Au38(2-PET)24 is observed (about 4 times faster than reaction with the right-handed enantiomer). The second exchange step is much slower than the first step. BINAS substitution deactivates the cluster for further exchange, which is attributed to (stereo)electronic effects. The results constitute the first example of a ligand exchange reaction in a thiolate-protected gold cluster with directed enrichment of a defined species in the product mixture. This may open new possibilities for the design of nanomaterials with tailored properties.
Thermolides, Potent Nematocidal PKS-NRPS Hybrid Metabolites from Thermophilic Fungus Talaromyces thermophilus
Ji-Peng Guo - ,
Chun-Yan Zhu - ,
Chuan-Ping Zhang - ,
Yan-Sheng Chu - ,
Yan-Li Wang - ,
Jun-Xian Zhang - ,
De-Kai Wu - ,
Ke-Qin Zhang *- , and
Xue-Mei Niu *
Macrocyclic PKS-NRPS hybrid metabolites represent a unique family of natural products mainly from bacteria with broad and outstanding biological activities. However, their distribution in fungi has rarely been reported, and little has been reported regarding their nematocidal activity. Here we describe an unprecedented class of PKS-NRPS hybrid metabolites possessing a 13-membered lactam-bearing macrolactone, thermolides A–F (1–6) from a thermophilic fungus Talaromyces thermophilus. We showed that 1 and 2 displayed potent inhibitory activity against three notorious nematodes with LC50 values of 0.5–1 μg/mL, as active as commercial avermectins. This work provided a new class of promising lead compounds for nematocide discovery.
Metal–Organic Transmembrane Nanopores
Mariangela Boccalon - ,
Elisabetta Iengo *- , and
Paolo Tecilla *
A stable tetraporphyrin metallacycle with Re(I) corners (1) is capable of forming nanopores in a liposomial membrane, provided that the porphyrin units are properly functionalized with peripheral carboxylic acid residues that, by establishing an hydrogen bond network, allow the formation of dimers that span the depth of the membrane.
Interactions of the Antitumor Macrolide Aplyronine A with Actin and Actin-Related Proteins Established by Its Versatile Photoaffinity Derivatives
Masaki Kita *- ,
Yuichiro Hirayama - ,
Kota Yamagishi - ,
Kozo Yoneda - ,
Ryosuke Fujisawa - , and
Hideo Kigoshi *
The antitumor and apoptogenic macrolide aplyronine A (ApA) is a potent actin-depolymerizing agent. We developed an ApA acetylene analog that bears the aryldiazirine group at the C34 terminus, which formed a covalent bond with actin. With the use of the photoaffinity biotin derivatives of aplyronines A and C, Arp2 and Arp3 (actin-related proteins) were specifically purified as binding proteins along with actin from tumor cell lysate. However, Arp2 and Arp3 did not covalently bind to aplyronine photoaffinity derivatives. Thus, actin-related proteins might indirectly bind to ApA as the ternary adducts of the actin/ApA complex or through the oligomeric actin.
Nanomole-Scale Assignment of Configuration for Primary Amines Using a Kinetic Resolution Strategy
Shawn M. Miller - ,
Renzo A. Samame - , and
Scott D. Rychnovsky *
The absolute configurations of primary amines were assigned using a kinetic resolution strategy with Mioskowski’s enantioselective 1-(R,R) and 2-(S,S) acylating agents. A simple mnemonic was developed to determine the configuration. A pseudoenantiomeric pair of reagents, 1-(R,R) and 2-(S,S)-d3, was prepared and used to assay primary amines on a micromolar scale. The ESI-MS readout of the resulting acetamide products reproduced the selectivity factors from kinetic experiments. The method can be used on mixtures of amines and was validated with amine samples as small as 50 nmol.
Cyclic Host Liquids for Facile and High-Yield Synthesis of [2]Rotaxanes
Tomoki Ogoshi *- ,
Takamichi Aoki - ,
Ryohei Shiga - ,
Ryo Iizuka - ,
Seita Ueda - ,
Kazuki Demachi - ,
Daiki Yamafuji - ,
Hitoshi Kayama - , and
Tada-aki Yamagishi
We developed “cyclic host liquids (CHLs)” as a new type of solvent. The CHLs are a nonvolatile liquid over a wide temperature range, are biocompatible and recyclable, have high thermal stability, and are miscible with many organic solvents. Compared with typical complexation systems, the CHL system is extremely efficient for maintaining host–guest complexation because an additional solvent is not required. Based on the efficient host–guest complexation in the CHL system, we demonstrated synthesis of [2]rotaxanes in pillar[5]arene-based CHL. High yields were obtained for [2]rotaxanes capped by cationization (yield 91%) and Huisgen reaction (yield 88%) between the axle and the stopper components in the CHL system, while the association constants between the axles and wheels were quite low (10–15 M–1) in CDCl3. The CHL system provides a new powerful approach for synthesis of mechanically interlocked molecules (MIMs) even with unfavorable statistical combinations of host–guest complexes.
Re-Mediated C–C Coupling of Pyridines and Imidazoles
Maialen Espinal Viguri - ,
Miguel A. Huertos - ,
Julio Pérez *- ,
Lucía Riera *- , and
Irene Ara
Rhenium tricarbonyl complexes with three N-heterocyclic ligands (N-alkylimidazoles or pyridines) undergo deprotonation with KN(SiMe3)2 and then oxidation with AgOTf to afford complexes with pyridylimidazole or bipyridine bidentate ligands resulting from deprotonation, C–C coupling and rearomatization.
Articles
Groove Binding Mechanism of Ionic Liquids: A Key Factor in Long-Term Stability of DNA in Hydrated Ionic Liquids?
Aneesh Chandran - ,
Debostuti Ghoshdastidar - , and
Sanjib Senapati *
Nucleic acid sample storage is of paramount importance in biotechnology and forensic sciences. Very recently, hydrated ionic liquids (ILs) have been identified as ideal media for long-term DNA storage. Hence, understanding the binding characteristics and molecular mechanism of interactions of ILs with DNA is of both practical and fundamental interest. Here, we employ molecular dynamics simulations and spectroscopic experiments to unravel the key factors that stabilize DNA in hydrated ILs. Both simulation and experimental results show that DNA maintains the native B-conformation in ILs. Simulation results further suggest that, apart from the electrostatic association of IL cations with the DNA backbone, groove binding of IL cations through hydrophobic and polar interactions contributes significantly to DNA stability. Circular dichroism spectral measurements and fluorescent dye displacement assay confirm the intrusion of IL molecules into the DNA minor groove. Very interestingly, the IL ions were seen to disrupt the water cage around DNA, including the spine of hydration in the minor groove. This partial dehydration by ILs likely prevents the hydrolytic reactions that denature DNA and helps stabilize DNA for the long term. The detailed understanding of IL–DNA interactions provided here could guide the future development of novel ILs, specific for nucleic acid solutes.
Unraveling the Mechanisms of Nonradiative Deactivation in Model Peptides Following Photoexcitation of a Phenylalanine Residue
Momir Mališ - ,
Yohan Loquais - ,
Eric Gloaguen - ,
Himansu S. Biswal - ,
François Piuzzi - ,
Benjamin Tardivel - ,
Valérie Brenner - ,
Michel Broquier - ,
Christophe Jouvet - ,
Michel Mons *- ,
Nađa Došlić - , and
Ivan Ljubić *
The mechanisms of nonradiative deactivation of a phenylalanine residue after near-UV photoexcitation have been investigated in an isolated peptide chain model (N-acetylphenylalaninylamide, NAPA) both experimentally and theoretically. Lifetime measurements at the origin of the first ππ* state of jet-cooled NAPA molecules have shown that (i) among the three most stable conformers of the molecule, the folded conformer NAPA B is ∼50-times shorter lived than the extended major conformer NAPA A and (ii) this lifetime is virtually insensitive to deuteration at the NH2 and NH sites. Concurrent time-dependent density functional theory (TDDFT) based nonadiabatic dynamics simulations in the full dimensionality, carried out for the NAPA B conformer, provided direct insights on novel classes of ultrafast deactivation mechanisms, proceeding through several conical intersections and leading in fine to the ground state. These mechanisms are found to be triggered either (i) by a stretch of the NPheH bond, which leads to an H-transfer to the ring, or (ii) by specific backbone amide distortions. The potential energy surfaces of the NAPA conformers along these critical pathways have been characterized more accurately using the coupled cluster doubles (CC2) method and shown to exhibit barriers that can be overcome with moderate excess energies. These results analyzed in the light of the experimental findings enabled us to assign the short lifetime of NAPA B conformer to a number of easily accessible exit channels from the initial ππ* surface, most importantly the one involving a transfer of electronic excitation to an nπ* surface, induced by distortions of the backbone peptide bond.
Reversible C–C Bond Formation between Redox-Active Pyridine Ligands in Iron Complexes
Thomas R. Dugan - ,
Eckhard Bill - ,
K. Cory MacLeod - ,
Gemma J. Christian - ,
Ryan E. Cowley - ,
William W. Brennessel - ,
Shengfa Ye - ,
Frank Neese *- , and
Patrick L. Holland *
This manuscript describes the formally iron(I) complexes LMeFe(Py-R)2 (LMe = bulky β-diketiminate; R = H, 4-tBu), in which the basal pyridine ligands preferentially accept significant unpaired spin density. Structural, spectroscopic, and computational studies on the complex with 4-tert-butylpyridine (tBupy) indicate that the S = 3/2 species is a resonance hybrid between descriptions as (a) high-spin iron(II) with antiferromagnetic coupling to a pyridine anion radical and (b) high-spin iron(I). When the pyridine lacks the protection of the tert-butyl group, it rapidly and reversibly undergoes radical coupling reactions that form new C–C bonds. In one reaction, the coordinated pyridine couples to triphenylmethyl radical, and in another, it dimerizes to give a pyridine-derived dianion that bridges two iron(II) ions. The rapid, reversible C–C bond formation in the dimer stores electrons from the formally reduced metal as a C–C bond in the ligands, as demonstrated by using the coupled diiron(II) complex to generate products that are known to come from iron(I) precursors.
Parallel and Competitive Pathways for Substrate Desaturation, Hydroxylation, and Radical Rearrangement by the Non-heme Diiron Hydroxylase AlkB
Harriet L. R. Cooper - ,
Girish Mishra - ,
Xiongyi Huang - ,
Marilla Pender-Cudlip - ,
Rachel N. Austin - ,
John Shanklin *- , and
John T. Groves *
A purified and highly active form of the non-heme diiron hydroxylase AlkB was investigated using the diagnostic probe substrate norcarane. The reaction afforded C2 (26%) and C3 (43%) hydroxylation and desaturation products (31%). Initial C–H cleavage at C2 led to 7% C2 hydroxylation and 19% 3-hydroxymethylcyclohexene, a rearrangement product characteristic of a radical rearrangement pathway. A deuterated substrate analogue, 3,3,4,4-norcarane-d4, afforded drastically reduced amounts of C3 alcohol (8%) and desaturation products (5%), while the radical rearranged alcohol was now the major product (65%). This change in product ratios indicates a large kinetic hydrogen isotope effect of ∼20 for both the C–H hydroxylation at C3 and the desaturation pathway, with all of the desaturation originating via hydrogen abstraction at C3 and not C2. The data indicate that AlkB reacts with norcarane via initial C–H hydrogen abstraction from C2 or C3 and that the three pathways, C3 hydroxylation, C3 desaturation, and C2 hydroxylation/radical rearrangement, are parallel and competitive. Thus, the incipient radical at C3 either reacts with the iron-oxo center to form an alcohol or proceeds along the desaturation pathway via a second H-abstraction to afford both 2-norcarene and 3-norcarene. Subsequent reactions of these norcarenes lead to detectable amounts of hydroxylation products and toluene. By contrast, the 2-norcaranyl radical intermediate leads to C2 hydroxylation and the diagnostic radical rearrangement, but this radical apparently does not afford desaturation products. The results indicate that C–H hydroxylation and desaturation follow analogous stepwise reaction channels via carbon radicals that diverge at the product-forming step.
Molecular and Cellular Characterization of the Biological Effects of Ruthenium(II) Complexes Incorporating 2-Pyridyl-2-pyrimidine-4-carboxylic Acid
Vanessa Pierroz - ,
Tanmaya Joshi - ,
Anna Leonidova - ,
Cristina Mari - ,
Julia Schur - ,
Ingo Ott - ,
Leone Spiccia *- ,
Stefano Ferrari *- , and
Gilles Gasser *
A great majority of the Ru complexes currently studied in anticancer research exert their antiproliferative activity, at least partially, through ligand exchange. In recent years, however, coordinatively saturated and substitutionally inert polypyridyl Ru(II) compounds have emerged as potential anticancer drug candidates. In this work, we present the synthesis and detailed characterization of two novel inert Ru(II) complexes, namely, [Ru(bipy)2(Cpp-NH-Hex-COOH)]2+ (2) and [Ru(dppz)2(CppH)]2+ (3) (bipy = 2,2′-bipyridine; CppH = 2-(2′-pyridyl)pyrimidine-4-carboxylic acid; Cpp-NH-Hex-COOH = 6-(2-(pyridin-2-yl)pyrimidine-4-carboxamido)hexanoic acid; dppz = dipyrido[3,2-a:2′,3′-c]phenazine). 3 is of particular interest as it was found to have IC50 values comparable to cisplatin, a benchmark standard in the field, on three cancer cell lines and a better activity on one cisplatin-resistant cell line than cisplatin itself. The mechanism of action of 3 was then investigated in detail and it could be demonstrated that, although 3 binds to calf-thymus DNA by intercalation, the biological effects that it induces did not involve a nuclear DNA related mode of action. On the contrary, confocal microscopy colocalization studies in HeLa cells showed that 3 specifically targeted mitochondria. This was further correlated by ruthenium quantification using High-resolution atomic absorption spectrometry. Furthermore, as determined by two independent assays, 3 induced apoptosis at a relatively late stage of treatment. The generation of reactive oxygen species could be excluded as the cause of the observed cytotoxicity. It was demonstrated that the mitochondrial membrane potential in HeLa was impaired by 3 as early as 2 h after its introduction and even more with increasing time.
Energetics of Adsorbed Methanol and Methoxy on Pt(111) by Microcalorimetry
Eric M. Karp - ,
Trent L. Silbaugh - ,
Matthew C. Crowe - , and
Charles T. Campbell *
The heat of adsorption and sticking probability of methanol were measured on clean Pt(111) at 100, 150, and 210 K and on oxygen-precovered Pt(111) at 150 K by single-crystal adsorption calorimetry (SCAC). On clean Pt(111) at 100 K, the heat of methanol adsorption was found to be 60.5 ± 0.8 kJ/mol in the limit of low coverage, resulting in a standard enthalpy of formation (ΔHf°) of CH3OH(ad) of −263 ± 0.8 kJ/mol. The results at 150 and 210 K on clean Pt(111) were indistinguishable from the energetics measured at 100 K in the same coverage range. Calorimetry of methanol on oxygen-precovered Pt(111) at 150 K yielded the energetics of adsorbed methoxy, giving ΔHf°[CH3O(ad)] = −170 ± 10 kJ/mol and a CH3O–Pt(111) bond enthalpy of 187 ± 11 kJ/mol. By use of these enthalpies, the dissociation of adsorbed methanol on Pt(111) to form methoxy and a hydrogen adatom is found to be uphill by +57 kJ/mol. At coverages below 0.2 monolayer (ML), the sticking probability for methanol on both surfaces at or below 150 K was >0.95. At 210 K, ∼80% of the methanol beam pulse transiently adsorbs to clean Pt(111) with a surface residence time of 238 ms and heat of adsorption of 61.2 ± 2.0 kJ/mol, giving a prefactor for methanol desorption of 4 × 1015±0.5 s–1. These measured energetics for methoxy and methanol were compared to density functional theory (DFT) calculations from previous literature, showing DFT to routinely underestimate the bond energy of both adsorbed methanol and methoxy by 15–52 kJ/mol.
Mechanical Transition from α-Helical Coiled Coils to β-Sheets in Fibrin(ogen)
Artem Zhmurov - ,
Olga Kononova - ,
Rustem I. Litvinov - ,
Ruxandra I. Dima - ,
Valeri Barsegov *- , and
John W. Weisel *
We characterized the α-to-β transition in α-helical coiled-coil connectors of the human fibrin(ogen) molecule using biomolecular simulations of their forced elongation and theoretical modeling. The force (F)–extension (X) profiles show three distinct regimes: (1) the elastic regime, in which the coiled coils act as entropic springs (F < 100–125 pN; X < 7–8 nm); (2) the constant-force plastic regime, characterized by a force-plateau (F ≈ 150 pN; X ≈ 10–35 nm); and (3) the nonlinear regime (F > 175–200 pN; X > 40–50 nm). In the plastic regime, the three-stranded α-helices undergo a noncooperative phase transition to form parallel three-stranded β-sheets. The critical extension of the α-helices is 0.25 nm, and the energy difference between the α-helices and β-sheets is 4.9 kcal/mol per helical pitch. The soft α-to-β phase transition in coiled coils might be a universal mechanism underlying mechanical properties of filamentous α-helical proteins.
Modulating Semiconductor Surface Electronic Properties by Inorganic Peptide–Binders Sequence Design
Maayan Matmor - and
Nurit Ashkenasy *
The use of proteins and peptides as part of biosensors and electronic devices has been the focus of intense research in recent years. However, despite the fact that the interface between the bioorganic molecules and the inorganic matter plays a significant role in determining the properties of such devices, information on the electronic properties of such interfaces is sparse. In this work, we demonstrate that the identity and position of single amino acid in short inorganic binding protein-segments can significantly modulate the electronic properties of semiconductor surfaces on which they are bound. Specifically, we show that the introduction of tyrosine or tryptophan, both possessing an aromatic side chain which higher occupied molecular orbitals are positioned in proximity to the edge of GaAs valence band, to the sequence of a peptide that binds to GaAs (100) results in changes of both the electron affinity and surface potential of the semiconductor. These effects were found to be more pronounced than the effects induced by the same amino acids once bound on the surface in a head–tail configuration. Furthermore, the relative magnitude of each effect was found to depend on the position of the modification in the sequence. This sequence dependent behavior is induced both indirectly by changes in the peptide surface coverage, and directly, probably, due to changes in the orientation and proximity of the tyrosine/tryptophan side group with respect to the surface due to the preferred conformation the peptide adopts on the surface. These studies reveal that despite the use of short protein oligomers and aiming at a non-natural-electronic task, the well-known relations between the proteins’ structure and function is preserved. Combining the ability to tune the electronic properties at the interface with the ability to direct the growth of inorganic materials makes peptides promising building blocks for the construction of novel hybrid electronic devices and biosensors.
“Donor–Two-Acceptor” Dye Design: A Distinct Gateway to NIR Fluorescence
Naama Karton-Lifshin - ,
Lorenzo Albertazzi - ,
Michael Bendikov - ,
Phil S. Baran - , and
Doron Shabat *
The detection of chemical or biological analytes upon molecular reactions relies increasingly on fluorescence methods, and there is a demand for more sensitive, more specific, and more versatile fluorescent molecules. We have designed long wavelength fluorogenic probes with a turn-ON mechanism based on a donor–two-acceptor π-electron system that can undergo an internal charge transfer to form new fluorochromes with longer π-electron systems. Several latent donors and multiple acceptor molecules were incorporated into the probe modular structure to generate versatile dye compounds. This new library of dyes had fluorescence emission in the near-infrared (NIR) region. Computational studies reproduced the observed experimental trends well and suggest factors responsible for high fluorescence of the donor–two-acceptor active form and the low fluorescence observed from the latent form. Confocal images of HeLa cells indicate a lysosomal penetration pathway of a selected dye. The ability of these dyes to emit NIR fluorescence through a turn-ON activation mechanism makes them promising candidate probes for in vivo imaging applications.
Proton Transfer Reactions of Triazol-3-ylidenes: Kinetic Acidities and Carbon Acid pKa Values for Twenty Triazolium Salts in Aqueous Solution
Richard S. Massey - ,
Christopher J. Collett - ,
Anita G. Lindsay - ,
Andrew D. Smith *- , and
AnnMarie C. O’Donoghue *
Second-order rate constants have been determined for deuteroxide ion-catalyzed exchange of the C(3)-proton for deuterium, kDO (M–1 s–1), of a series of 20 triazolium salts in aqueous solution at 25 °C and ionic strength I = 1.0 (KCl). Evidence is presented that the rate constant for the reverse protonation of the triazol-3-ylidenes by solvent water is close to that for dielectric relaxation of solvent (1011 s–1). These data enabled the calculation of carbon acid pKa values in the range 16.5–18.5 for the 20 triazolium salts. pD rate profiles for deuterium exchange of the triazolium salts reveal that protonation at nitrogen to give dicationic triazolium species occurs under acidic conditions, with estimates of pKaN1 = −0.2 to 0.5.
A New Method To Generate Arene-Terminated Si(111) and Ge(111) Surfaces via a Palladium-Catalyzed Arylation Reaction
Yoshinori Yamanoi *- ,
Junya Sendo - ,
Tetsuhiro Kobayashi - ,
Hiroaki Maeda - ,
Yusuke Yabusaki - ,
Mariko Miyachi - ,
Ryota Sakamoto - , and
Hiroshi Nishihara *
Formation of silicon–aryl and germanium–aryl direct bonds on the semiconductor surface is a key issue to realize molecular electronic devices, but the conventional methods based on radical intermediates have problems to accompany the side reactions. We developed the first example of versatile and efficient methods to form clean organic monolayers with Si–aryl and Ge–aryl bonds on hydrogen-terminated silicon and germanium surfaces by applying our original catalytic arylation reactions of hydrosilanes and hydrogermanes using Pd catalyst and base in homogeneous systems. We could immobilize aromatic groups with redox-active and photoluminescent properties, and further applied in the field of rigid π-conjugated redox molecular wire composites, as confirmed by the successive coordination of terpyridine molecules with transition metal ions. The surfaces were characterized using cyclic voltammetry (CV), water contact angle measurements, X-ray photoelectron spectroscopy (XPS), fluorescence spectroscopy, and atomic force microscopy (AFM). Especially, the AFM analysis of 17 nm-long metal complex molecular wires confirmed their vertical connection to the plane surface.
Importance of Direct Metal−π Coupling in Electronic Transport Through Conjugated Single-Molecule Junctions
Jeffrey S. Meisner - ,
Seokhoon Ahn - ,
Sriharsha V. Aradhya - ,
Markrete Krikorian - ,
Radha Parameswaran - ,
Michael Steigerwald *- ,
Latha Venkataraman *- , and
Colin Nuckolls *
We study the effects of molecular structure on the electronic transport and mechanical stability of single-molecule junctions formed with Au point contacts. Two types of linear conjugated molecular wires are compared: those functionalized with methylsulfide or amine aurophilic groups at (1) both or (2) only one of its phenyl termini. Using scanning tunneling and atomic force microscope break-junction techniques, the conductance of mono- and difunctionalized molecular wires and its dependence on junction elongation and rupture forces were studied. Charge transport through monofunctionalized wires is observed when the molecular bridge is coupled through a S–Au donor–acceptor bond on one end and a relatively weak Au−π interaction on the other end. For monofunctionalized molecular wires, junctions can be mechanically stabilized by installing a second aurophilic group at the meta position that, however, does not in itself contribute to a new conduction pathway. These results reveal the important interplay between electronic coupling through metal−π interactions and quantum mechanical effects introduced by chemical substitution on the conjugated system. This study affords a strategy to deterministically tune the electrical and mechanical properties through molecular wires.
Optimized End-Stacking Provides Specificity of N-Methyl Mesoporphyrin IX for Human Telomeric G-Quadruplex DNA
John M. Nicoludis - ,
Stephen T. Miller - ,
Philip D. Jeffrey - ,
Steven P. Barrett - ,
Paul R. Rablen - ,
Thomas J. Lawton - , and
Liliya A. Yatsunyk *
N-Methyl mesoporphyrin IX (NMM) is exceptionally selective for G-quadruplexes (GQ) relative to duplex DNA and, as such, has found a wide range of applications in biology and chemistry. In addition, NMM is selective for parallel versus antiparallel GQ folds, as was recently demonstrated in our laboratory. Here, we present the X-ray crystal structure of a complex between NMM and human telomeric DNA dAGGG(TTAGGG)3, Tel22, determined in two space groups, P21212 and P6, at 1.65 and 2.15 Å resolution, respectively. The former is the highest resolution structure of the human telomeric GQ DNA reported to date. The biological unit contains a Tel22 dimer of 5′-5′ stacked parallel-stranded quadruplexes capped on both ends with NMM, supporting the spectroscopically determined 1:1 stoichiometry. NMM is capable of adjusting its macrocycle geometry to closely match that of the terminal G-tetrad required for efficient π–π stacking. The out-of-plane N-methyl group of NMM fits perfectly into the center of the parallel GQ core where it aligns with potassium ions. In contrast, the interaction of the N-methyl group with duplex DNA or antiparallel GQ would lead to steric clashes that prevent NMM from binding to these structures, thus explaining its unique selectivity. On the basis of the biochemical data, binding of NMM to Tel22 does not rely on relatively nonspecific electrostatic interactions, which characterize most canonical GQ ligands, but rather it is hydrophobic in nature. The structural features observed in the NMM–Tel22 complex described here will serve as guidelines for developing new quadruplex ligands that have excellent affinity and precisely defined selectivity.
Toward Highly Stable Electrocatalysts via Nanoparticle Pore Confinement
Carolina Galeano - ,
Josef C. Meier - ,
Volker Peinecke - ,
Hans Bongard - ,
Ioannis Katsounaros - ,
Angel A. Topalov - ,
Anhui Lu - ,
Karl J. J. Mayrhofer *- , and
Ferdi Schüth *
The durability of electrode materials is a limiting parameter for many electrochemical energy conversion systems. In particular, electrocatalysts for the essential oxygen reduction reaction (ORR) present some of the most challenging instability issues shortening their practical lifetime. Here, we report a mesostructured graphitic carbon support, Hollow Graphitic Spheres (HGS) with a specific surface area exceeding 1000 m2 g–1 and precisely controlled pore structure, that was specifically developed to overcome the long-term catalyst degradation, while still sustaining high activity. The synthetic pathway leads to platinum nanoparticles of approximately 3 to 4 nm size encapsulated in the HGS pore structure that are stable at 850 °C and, more importantly, during simulated accelerated electrochemical aging. Moreover, the high stability of the cathode electrocatalyst is also retained in a fully assembled polymer electrolyte membrane fuel cell (PEMFC). Identical location scanning and scanning transmission electron microscopy (IL-SEM and IL-STEM) conclusively proved that during electrochemical cycling the encapsulation significantly suppresses detachment and agglomeration of Pt nanoparticles, two of the major degradation mechanisms in fuel cell catalysts of this particle size. Thus, beyond providing an improved electrocatalyst, this study describes the blueprint for targeted improvement of fuel cell catalysts by design of the carbon support.
Dimensionality Transformation through Paddlewheel Reconfiguration in a Flexible and Porous Zn-Based Metal–Organic Framework
Kyriakos C. Stylianou - ,
Jeremy Rabone - ,
Samantha Y. Chong - ,
Romain Heck - ,
Jayne Armstrong - ,
Paul V. Wiper - ,
Kim E. Jelfs - ,
Sergey Zlatogorsky - ,
John Bacsa - ,
Alec G. McLennan - ,
Christopher P. Ireland - ,
Yaroslav Z. Khimyak - ,
K. Mark Thomas - ,
Darren Bradshaw *- , and
Matthew J. Rosseinsky *
The reaction between Zn and a pyrene-based ligand decorated with benzoate fragments (H4TBAPy) yields a 2D layered porous network with the metal coordination based on a paddlewheel motif. Upon desolvation, the structure undergoes a significant and reversible structural adjustment with a corresponding reduction in crystallinity. The combination of computationally assisted structure determination and experimental data analysis of the desolvated phase revealed a structural change in the metal coordination geometry from square-pyramidal to tetrahedral. Simulations of desolvation showed that the local distortion of the ligand geometry followed by the rotation and displacement of the pyrene core permits the breakup of the metal-paddlewheel motifs and the formation of 1D Zn–O chains that cross-link adjacent layers, resulting in a dimensionality change from the 2D layered structure to a 3D structure. Constrained Rietveld refinement of the powder X-ray diffraction pattern of the desolvated phase and the use of other analytical techniques such as porosity measurements, 13C CP MAS NMR spectroscopy, and fluorescence spectroscopy strongly supported the observed structural transformation. The 3D network is stable up to 425 °C and is permanently porous to CO2 with an apparent BET surface area of 523(8) m2/g (p/p° = 0.02–0.22). Because of the hydrophobic nature, size, and shape of the pores of the 3D framework, the adsorption behavior of the structure toward p-xylene and m-xylene was studied, and the results indicated that the shape of the isotherm and the kinetics of the adsorption process are determined mainly by the shape of the xylene isomers, with each xylene isomer interacting with the host framework in a different manner.
Ru Nanocrystals with Shape-Dependent Surface-Enhanced Raman Spectra and Catalytic Properties: Controlled Synthesis and DFT Calculations
An-Xiang Yin - ,
Wen-Chi Liu - ,
Jun Ke - ,
Wei Zhu - ,
Jun Gu - ,
Ya-Wen Zhang *- , and
Chun-Hua Yan *
Despite its multidisciplinary interests and technological importance, the shape control of Ru nanocrystals still remains a great challenge. In this article, we demonstrated a facile hydrothermal approach toward the controlled synthesis of Ru nanocrystals with the assistance of first-principles calculations. For the first time, Ru triangular and irregular nanoplates as well as capped columns with tunable sizes were prepared with high shape selectivity. In consistency with the experimental observations and density functional theory (DFT) calculations confirmed that both the intrinsic characteristics of Ru crystals and the adsorption of certain reaction species were responsible for the shape control of Ru nanocrystals. Ultrathin Ru nanoplates exposed a large portion of (0001) facets due to the lower surface energy of Ru(0001). The selective adsorption of oxalate species on Ru(10–10) would retard the growth of the side planes of the Ru nanocrystals, while the gradual thermolysis of the oxalate species would eliminate their adsorption effects, leading to the shape evolution of Ru nanocrystals from prisms to capped columns. The surface-enhanced Raman spectra (SERS) signals of these Ru nanocrystals with 4-mercaptopyridine as molecular probes showed an enhancement sequence of capped columns > triangle nanoplates > nanospheres, probably due to the sharp corners and edges in the capped columns and nanoplates as well as the shrunk interparticle distance in their assemblies. CO-selective methanation tests on these Ru nanocrystals indicated that the nanoplates and nanospheres had comparable activities, but the former has much better CO selectivity than the latter.
Remote Control of Lipophilic Nucleic Acids Domain Partitioning by DNA Hybridization and Enzymatic Cleavage
Matthias Schade - ,
Andrea Knoll - ,
Alexander Vogel - ,
Oliver Seitz - ,
Jürgen Liebscher - ,
Daniel Huster - ,
Andreas Herrmann - , and
Anna Arbuzova *
Lateral partitioning of lipid-modified molecules between liquid-disordered (ld) and liquid-ordered (lo) domains depends on the type of lipid modification, presence of a spacer, membrane composition, and temperature. Here, we show that the lo domain partitioning of the palmitoylated peptide nucleic acid (PNA) can be influenced by formation of a four-component complex with the ld domain partitioning tocopherol-modified DNA: the PNA–DNA complex partitioned into the ld domains. Enzymatic cleavage of the DNA linker led to the disruption of the complex and restored the initial distribution of the lipophilic nucleic acids into the respective domains. This modular system offers strategies for dynamic functionalization of biomimetic surfaces, for example, in nanostructuring and regulation of enzyme catalysis, and it provides a tool to study the molecular basis of controlled reorganization of lipid-modified proteins in membranes, for example, during signal transduction.
Radical-Translocation Intermediates and Hurdling of Pathway Defects in “Super-oxidized” (MnIV/FeIV) Chlamydia trachomatis Ribonucleotide Reductase
Laura M. K. Dassama - ,
Wei Jiang - ,
Paul T. Varano - ,
Maria-Eirini Pandelia - ,
Denise A. Conner - ,
Jiajia Xie - ,
J. Martin Bollinger Jr., *- , and
Carsten Krebs *
A class I ribonucleotide reductase (RNR) uses either a tyrosyl radical (Y•) or a MnIV/FeIII cluster in its β subunit to oxidize a cysteine residue ∼35 Å away in its α subunit, generating a thiyl radical that abstracts hydrogen (H•) from the substrate. With either oxidant, the inter-subunit “hole-transfer” or “radical-translocation” (RT) process is thought to occur by a “hopping” mechanism involving multiple tyrosyl (and perhaps one tryptophanyl) radical intermediates along a specific pathway. The hopping intermediates have never been directly detected in a Mn/Fe-dependent (class Ic) RNR nor in any wild-type (wt) RNR. The MnIV/FeIII cofactor of Chlamydia trachomatis RNR assembles via a MnIV/FeIV intermediate. Here we show that this cofactor-assembly intermediate can propagate a hole into the RT pathway when α is present, accumulating radicals with EPR spectra characteristic of Y•’s. The dependence of Y• accumulation on the presence of substrate suggests that RT within this “super-oxidized” enzyme form is gated by the protein, and the failure of a β variant having the subunit-interfacial pathway Y substituted by phenylalanine to support radical accumulation implies that the Y•(s) in the wt enzyme reside(s) within the RT pathway. Remarkably, two variant β proteins having pathway substitutions rendering them inactive in their MnIV/FeIII states can generate the pathway Y•’s in their MnIV/FeIV states and also effect nucleotide reduction. Thus, the use of the more oxidized cofactor permits the accumulation of hopping intermediates and the “hurdling” of engineered defects in the RT pathway.
Ligand-Induced Active Sites: Reactivity of Iodine-Protected Aluminum Superatoms with Methanol
Marissa Baddick Abreu - ,
Christopher Powell - ,
Arthur C. Reber - , and
Shiv N. Khanna *
The quantum states in metal clusters are bunched into electronic shells as in atoms. Ligands including halogens or thiols modify the electronic structure through bonding, resulting in stable clusters with filled electronic shells that are resistant to oxygen etching. We demonstrate that the stabilization afforded by ligands is partially confounded because the ligands perturb the charge density of the metallic core, inducing Lewis acid–base sites that make the cluster reactive in a protic environment. We demonstrate the importance of induced active sites by studying the reactivity of methanol with two classes of iodine-passivated aluminum cluster anions: Al13Ix–, which has a closed geometric shell, and Al14Iy–, which has an adatom-decorated core. Two adjacent ligands on the closed geometric shell of Al13– activate the cluster, while in Al14I3– the I induces an active site on the adatom, making the cluster reactive, explaining ligand-protected clusters’ preference for closed geometric shells.
Computational Design of an α-Gliadin Peptidase
Sydney R. Gordon - ,
Elizabeth J. Stanley - ,
Sarah Wolf - ,
Angus Toland - ,
Sean J. Wu - ,
Daniel Hadidi - ,
Jeremy H. Mills - ,
David Baker - ,
Ingrid Swanson Pultz *- , and
Justin B. Siegel *
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The ability to rationally modify enzymes to perform novel chemical transformations is essential for the rapid production of next-generation protein therapeutics. Here we describe the use of chemical principles to identify a naturally occurring acid-active peptidase, and the subsequent use of computational protein design tools to reengineer its specificity toward immunogenic elements found in gluten that are the proposed cause of celiac disease. The engineered enzyme exhibits a kcat/KM of 568 M–1 s–1, representing a 116-fold greater proteolytic activity for a model gluten tetrapeptide than the native template enzyme, as well as an over 800-fold switch in substrate specificity toward immunogenic portions of gluten peptides. The computationally engineered enzyme is resistant to proteolysis by digestive proteases and degrades over 95% of an immunogenic peptide implicated in celiac disease in under an hour. Thus, through identification of a natural enzyme with the pre-existing qualities relevant to an ultimate goal and redefinition of its substrate specificity using computational modeling, we were able to generate an enzyme with potential as a therapeutic for celiac disease.
Suite of Activity-Based Probes for Cellulose-Degrading Enzymes
Lacie M. Chauvigné-Hines - ,
Lindsey N. Anderson - ,
Holly M. Weaver - ,
Joseph N. Brown - ,
Phillip K. Koech - ,
Carrie D. Nicora - ,
Beth A. Hofstad - ,
Richard D. Smith - ,
Michael J. Wilkins - ,
Stephen J. Callister - , and
Aaron T. Wright *
Microbial glycoside hydrolases play a dominant role in the biochemical conversion of cellulosic biomass to high-value biofuels. Anaerobic cellulolytic bacteria are capable of producing multicomplex catalytic subunits containing cell-adherent cellulases, hemicellulases, xylanases, and other glycoside hydrolases to facilitate the degradation of highly recalcitrant cellulose and other related plant cell wall polysaccharides. Clostridium thermocellum is a cellulosome-producing bacterium that couples rapid reproduction rates to highly efficient degradation of crystalline cellulose. Herein, we have developed and applied a suite of difluoromethylphenyl aglycone, N-halogenated glycosylamine, and 2-deoxy-2-fluoroglycoside activity-based protein profiling (ABPP) probes to the direct labeling of the C. thermocellum cellulosomal secretome. These activity-based probes (ABPs) were synthesized with alkynes to harness the utility and multimodal possibilities of click chemistry and to increase enzyme active site inclusion for liquid chromatography–mass spectrometry (LC–MS) analysis. We directly analyzed ABP-labeled and unlabeled global MS data, revealing ABP selectivity for glycoside hydrolase (GH) enzymes, in addition to a large collection of integral cellulosome-containing proteins. By identifying reactivity and selectivity profiles for each ABP, we demonstrate our ability to widely profile the functional cellulose-degrading machinery of the bacterium. Derivatization of the ABPs, including reactive groups, acetylation of the glycoside binding groups, and mono- and disaccharide binding groups, resulted in considerable variability in protein labeling. Our probe suite is applicable to aerobic and anaerobic microbial cellulose-degrading systems and facilitates a greater understanding of the organismal role associated with biofuel development.
Ordered Phosphorylation Events in Two Independent Cascades of the PTEN C-tail Revealed by NMR
Florence Cordier *- ,
Alain Chaffotte - ,
Elouan Terrien - ,
Christophe Préhaud - ,
François-Xavier Theillet - ,
Muriel Delepierre - ,
Monique Lafon - ,
Henri Buc - , and
Nicolas Wolff
PTEN phosphatase is a tumor suppressor controlling notably cell growth, proliferation and survival. The multisite phosphorylation of the PTEN C-terminal tail regulates PTEN activity and intracellular trafficking. The dynamical nature of such regulatory events represents a crucial dimension for timing cellular decisions. Here we show that NMR spectroscopy allows reporting on the order and kinetics of clustered multisite phosphorylation events. We first unambiguously identify in vitro seven bona fide sites modified by CK2 and GSK3β kinases and two new sites on the PTEN C-terminal tail. Then, monitoring the formation of transient intermediate phosphorylated states, we determine the sequence of these reactions and calculate their apparent rate constants. Finally, we assess the dynamic formation of these phosphorylation events induced by endogenous kinases directly in extracts of human neuroblastoma cells. Taken together, our data indicate that two cascades of events controlled by CK2 and GSK3β occur independently on two clusters of sites (S380–S385 and S361–S370) and that in each cluster the reactions follow an ordered model with a distributive kinetic mechanism. Besides emphasizing the ability of NMR to quantitatively and dynamically follow post-translational modifications, these results bring a temporal dimension on the establishment of PTEN phosphorylation cascades.
Theoretical Study of the Mechanism of the Hydride Transfer between Ferredoxin–NADP+ Reductase and NADP+: The Role of Tyr303
Isaias Lans - ,
Milagros Medina *- ,
Edina Rosta - ,
Gerhard Hummer - ,
Mireia Garcia-Viloca *- ,
José M. Lluch - , and
Àngels González-Lafont
During photosynthesis, ferredoxin–NADP+ reductase (FNR) catalyzes the electron transfer from ferredoxin to NADP+ via its FAD cofactor. The final hydride transfer event between FNR and the nucleotide is a reversible process. Two different transient charge-transfer complexes form prior to and upon hydride transfer, FNRrd–NADP+ and FNRox–NADPH, regardless of the hydride transfer direction. Experimental structures of the FNRox:NADP+ interaction have suggested a series of conformational rearrangements that might contribute to attaining the catalytically competent complex, but to date, no direct experimental information about the structure of this complex is available. Recently, a molecular dynamics (MD) theoretical approach was used to provide a putative organization of the active site that might represent a structure close to the transient catalytically competent interaction of Anabaena FNR with its coenzyme, NADP+. Using this structure, we performed fully microscopic simulations of the hydride transfer processes between Anabaena FNRrd/FNRox and NADP+/H, accounting also for the solvation. A dual-level QM/MM hybrid approach was used to describe the potential energy surface of the whole system. MD calculations using the finite-temperature string method combined with the WHAM method provided the potential of mean force for the hydride transfer processes. The results confirmed that the structural model of the reactants evolves to a catalytically competent transition state through very similar free energy barriers for both the forward and reverse reactions, in good agreement with the experimental hydride transfer rate constants reported for this system. This theoretical approach additionally provides subtle structural details of the mechanism in wild-type FNR and provides an explanation why Tyr303 makes possible the photosynthetic reaction, a process that cannot occur when this Tyr is replaced by a Ser.
Photoluminescence Enhancement of CdSe Quantum Dots: A Case of Organogel–Nanoparticle Symbiosis
Prashant D. Wadhavane - ,
Raquel E. Galian - ,
M. Angeles Izquierdo *- ,
Jordi Aguilera-Sigalat - ,
Francisco Galindo - ,
Luciana Schmidt - ,
M. Isabel Burguete - ,
Julia Pérez-Prieto *- , and
Santiago V. Luis *
Highly fluorescent organogels (QD–organogel), prepared by combining a pseudopeptidic macrocycle and different types of CdSe quantum dots (QDs), have been characterized using a battery of optical and microscopic techniques. The results indicate that the presence of the QDs not only does not disrupt the supramolecular organization of the internal fibrillar network of the organogel to a significant extent, but it also decreases the critical concentration of gelator needed to form stable and thermoreversible organogels. Regarding the photophysical properties of the QDs, different trends were observed depending on the presence of a ZnS inorganic shell around the CdSe core. Thus, while the core–shell QDs preserve their photophysical properties in the organogel medium, a high to moderate increase of the fluorescence intensity (up to 528%) and the average lifetime (up to 1.7), respectively, was observed for the core QDs embedded in the organogel. The results are relevant for the development of luminescent organogels based on quantum dots, which have potential applications as advanced hybrid materials in different fields.
Additions and Corrections
Withdrawal of “Rhodium-Catalyzed Arylative and Alkenylative Cyclization of 1,5-Enynes Induced by Geminal Carbometalation of Alkynes”
Yiyun Chen - and
Chulbom Lee
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Correction to “Biochemical Characterization of NotB as an FAD-Dependent Oxidase in the Biosynthesis of Notoamide Indole Alkaloids”
Shengying Li - ,
Jennifer M. Finefield - ,
James D. Sunderhaus - ,
Timothy J. McAfoos - ,
Robert M. Williams - , and
David H. Sherman
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Correction to “Photoinduced Multistep Charge Separation in a Heteroleptic Cu(I) Bis(phenanthroline)-Based Donor–Chromophore–Acceptor Triad
Megan S. Lazorski - ,
Riley H. Gest - , and
C. Michael Elliott
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