Sensitizing DNA Towards Low‐Energy Electrons with 2‐Fluoroadenine

2‐Fluoroadenine (^2FA) is a therapeutic agent, which is suggested for application in cancer radiotherapy. The molecular mechanism of DNA radiation damage can be ascribed to a significant extent to the action of low‐energy (<20 eV) electrons (LEEs), which damage DNA by dissociative electron attachment. LEE induced reactions in ^2FA are characterized both isolated in the gas phase and in the condensed phase when it is incorporated into DNA. Information about negative ion resonances and anion‐mediated fragmentation reactions is combined with an absolute quantification of DNA strand breaks in ^2FA‐containing oligonucleotides upon irradiation with LEEs. The incorporation of ^2FA into DNA results in an enhanced strand breakage. The strand‐break cross sections are clearly energy dependent, whereas the strand‐break enhancements by ^2FA at 5.5, 10, and 15 eV are very similar. Thus, ^2FA can be considered an effective radiosensitizer operative at a wide range of electron energies.     

Glycine Peptide Bond Formation Catalyzed by Faujasite

The catalysis of peptide bond formation between two glycine molecules on H‐FAU zeolite was computationally studied by the M08‐HX density functional. Two reaction pathways, the concerted and the stepwise mechanism, starting from three differently adsorbed reactants, amino‐bound, carboxyl‐bound, and hydroxyl‐bound, are studied. Adsorption energies, activation energies, and reaction energies, as well as the corresponding intrinsic rate constants were calculated. A comparison of the computed energetics of the various reaction paths for glycine indicates that the catalyzed reaction proceeds preferentially via the concerted reaction mechanism of the hydroxyl‐bound configuration. This involves an eight‐membered ring of the transition structure instead of the four‐membered ring of the others. The step from the amino‐bound configuration to glycylglycine is the rate‐determining step of the concerted mechanism. It has an estimated activation energy of 51.2 kcal mol^?1. Although the catalytic reaction can also occur via the stepwise reaction mechanism, this path is not favored.     

A Tightly Stretched Ultralong Supramolecular Multiporphyrin Array Propagated by Double‐Strand Formation

A shape‐programmed linearity through supramolecular polymerization is demonstrated by a step‐growth double‐strand formation of a telechelic oligomeric porphyrin array in which two alternating pyridyl‐porphyrin sequenced units are held together by self‐complementary ligand‐to‐metal coordination. The stiff rod‐like structure and sufficiently large binding constant of the double‐strand unit considerably extended a supramolecular array in the one dimension, which produced a tightly stretched string with a length that exceeded several micrometers.     

A Designed Three‐Stranded β‐Sheet in an α/β Hybrid Peptide

The incorporation of β‐amino acid residues into the antiparallel β‐strand segments of a multi‐stranded β‐sheet peptide is demonstrated for a 19‐residue peptide, Boc‐LV^βFV^DPGL^βFVVL^DPGLVL^βFVV‐OMe (BBH19). Two centrally positioned ^DPro–Gly segments facilitate formation of a stable three‐stranded β‐sheet, in which β‐phenylalanine (^βPhe) residues occur at facing positions 3, 8 and 17. Structure determination in methanol solution is accomplished by using NMR‐derived restraints obtained from NOEs, temperature dependence of amide NH chemical shifts, rates of H/D exchange of amide protons and vicinal coupling constants. The data are consistent with a conformationally well‐defined three‐stranded β‐sheet structure in solution. Cross‐strand interactions between ^βPhe3/^βPhe17 and ^βPhe3/Val15 residues define orientations of these side‐chains. The observation of close contact distances between the side‐chains on the N‐ and C‐terminal strands of the three‐stranded β‐sheet provides strong support for the designed structure. Evidence is presented for multiple side‐chain conformations from an analysis of NOE data. An unusual observation of the disappearance of the Gly NH resonances upon prolonged storage in methanol is rationalised on the basis of a slow aggregation step, resulting in stacking of three‐stranded β‐sheet structures, which in turn influences the conformational interconversion between type I′ and type II′ β‐turns at the two ^DPro–Gly segments. Experimental evidence for these processes is presented. The decapeptide fragment Boc‐LV^βFV^DPGL^βFVV‐OMe (BBH10), which has been previously characterized as a type I′ β‐turn nucleated hairpin, is shown to favour a type II′ β‐turn conformation in solution, supporting the occurrence of conformational interconversion at the turn segments in these hairpin and sheet structures.     

CO2 Conversion into Esters by Fluoride‐Mediated Carboxylation of Organosilanes and Halide Derivatives

A one‐step conversion of CO₂ into heteroaromatic esters is presented under metal‐free conditions. Using fluoride anions as promoters for the C?Si bond activation, pyridyl, furanyl, and thienyl organosilanes are successfully carboxylated with CO₂ in the presence of an electrophile. The mechanism of this unprecedented reaction has been elucidated based on experimental and computational results, which show a unique catalytic influence of CO₂ in the C?Si bond activation of pyridylsilanes. The methodology is applied to 18 different esters, and it has enabled the incorporation of CO₂ into a polyester material for the first time.     

Analysis of an Active Deformylation Mechanism of 5‐Formyl‐deoxycytidine (fdC) in Stem Cells

The removal of 5‐methyl‐deoxycytidine (mdC) from promoter elements is associated with reactivation of the silenced corresponding genes. It takes place through an active demethylation process involving the oxidation of mdC to 5‐hydroxymethyl‐deoxycytidine (hmdC) and further on to 5‐formyl‐deoxycytidine (fdC) and 5‐carboxy‐deoxycytidine (cadC) with the help of α‐ketoglutarate‐dependent Tet oxygenases. The next step can occur through the action of a glycosylase (TDG), which cleaves fdC out of the genome for replacement by dC. A second pathway is proposed to involve C?C bond cleavage that converts fdC directly into dC. A 6‐aza‐5‐formyl‐deoxycytidine (a‐fdC) probe molecule was synthesized and fed to various somatic cell lines and induced mouse embryonic stem cells, together with a 2′‐fluorinated fdC analogue (F‐fdC). While deformylation of F‐fdC was clearly observed in vivo, it did not occur with a‐fdC, thus suggesting that the C?C bond‐cleaving deformylation is initiated by nucleophilic activation.     

Initial Subsurface Incorporation of Oxygen into Ru(0001): A Density Functional Theory Study

The adsorption and diffusion of oxygen on Ru(0001) surfaces as a function of coverage are systematically investigated by using density functional theory. A high incorporation barrier of low‐coverage adsorbed oxygen into the subsurface is discovered. Calculations show that the adsorption of additional on‐surface oxygen can lower the penetration barrier dramatically. The minimum penetration barrier obtained is 1.81 eV for a path starting with oxygen in mixed on‐surface hcp and fcc sites at an oxygen coverage of 0.75 ML, which should be regarded as close to 1 ML. Energy diagrams show that oxygen‐diffusion barriers on the surface and in the subsurface are much lower than the penetration barrier. Oxygen diffusion on the surface is an indispensable step for its initial incorporation into the subsurface.     

Application of Si‐doped graphene as a metal‐free catalyst for decomposition of formic acid: A theoretical study

Using density functional theory calculations, the adsorption and catalytic decomposition of formic acid (HCOOH) over Si‐doped graphene are investigated. For the stable adsorption geometries of HCOOH over Si‐doped graphene, the electronic structure properties are analyzed by adsorption energy, density of states, and charge density difference. A comparison of the reaction pathways reveals that both dehydration and dehydrogenation of HCOOH can occur over Si‐doped graphene. The estimated reaction energies and the activation barriers suggest that for the dehydration of HCOOH on the Si‐doped graphene, the rate‐controlling step is H + OH → H₂O reaction. For the dehydrogenation of HCOOH, the rate‐determining step is the breaking of the C? H bond of the HCOO group to form the CO₂ molecule and the atomic H. Our results reveal that the low cost Si‐doped graphene can be used as an efficient nonmetal catalyst for O? H bond cleavage of HCOOH. © 2015 Wiley Periodicals, Inc.     

Design of an Intercalating Linker Leading to the First Efficiently 5′,5′‐Linked Alternate‐Strand Hoogsteen Triplex with High Stability and Specificity

This is the first report describing the design, synthesis, and incorporation of an intercalating linker leading to an efficiently 5′,5′‐linked alternate strand Hoogsteen triplex. Using molecular modeling, the 5′,5′ problem was solved in a rather simple way. The two relatively distant 5′‐ends have been connected with a molecule that provides rigidity to the structure, while being flexible enough to allow stacking upon all four strands. The synthesis of the core of the designed molecule was conducted by Sonogashira coupling of an appropriately substituted iodobenzene with 1,3‐diethynylbenzene to give a conjugated system with three benzene rings interconnected with triple bonds. For the alternate‐strand triplex obtained with the intercalating linker, the stability obtained is higher than that of the corresponding homotriplex of equivalent total length and with the same nucleotides. This is deduced from a 5° higher melting temperature of the alternating triplex. The sensitivity towards mismatches in the alternate‐strand triplex is in the same range (ΔT_m=?13° to ?19°) as those observed for homotriplexes.     

Mechanism of Gold(I)‐Catalyzed Conia‐ene Reaction of β‐Ketoesters with Alkynes: A DFT Study

Density functional calculations have been performed to comparatively investigate two possible pathways of Au(I)‐catalyzed Conia‐ene reaction of β‐ketoesters with alkynes. Our studies find that, under the assistance of trifluoromethanesulfonate (TfO), the β‐ketoester is the most likely to undergo Model II to isomerize into its enol form, in which TfO plays a proton transfer role through a 6‐membered ring transition state. The coordination of the Au(I) catalyst to the alkynes triple bond can enhance the eletrophilic capability and reaction activity of the alkynes moiety, which triggers the nucleophilic addition of the enol moiety on the alkynes moiety to give a vinyl‐Au intermediate. This cycloisomerizaion step is exothermal by 21.3 kJ/mol with an energy barrier of 56.0 kJ/mol. In the whole catalytic process, the protonation of vinyl‐Au is almost spontaneous, and the formation of enol is a rate‐limiting step. The generation of enol and the activation of Au(I) catalyst on the alkynes are the key reasons why the Conia‐ene reaction can occur in mild condition. These calculations support that Au(I)‐catalyzed Conia‐ene reactions of β‐ketoesters with alkynes go through the pathway 2 proposed by Toste.     

Kinetics of Helix‐Handedness Inversion: Folding and Unfolding in Aromatic Amide Oligomers

A series of helically folded oligoamides of 8‐amino‐2‐quinoline carboxylic acid possessing 6, 7, 8, 9, 10 or 16 units are prepared following convergent synthetic schemes. The right‐handed (P) and the left‐handed (M) helical conformers of these oligomers undergo an exchange slow enough to allow their chromatographic separation on a chiral stationary phase. Thus, the M conformer is isolated for each of these oligomers and its slow racemization in hexane/CHCl₃ solutions is monitored at various temperatures using chiral HPLC. The kinetics of racemization at different temperatures in hexane/CHCl₃ (75:25 vol/vol) are fitted to a first order kinetic model to yield the kinetic constant and the Gibbs energy of activation for oligomers having 6, 7, 8, 9, 10 or 16 quinoline units. This energy gives the first quantitative measure of the exceptional stability of the helical conformers of an aromatic amide foldamer with respect to its partly unfolded conformations that occur between an M helix and a P helix. The trend of the Gibbs energy as a function of oligomer length suggests that helix‐handedness inversion does not require a complete unfolding of a helical strand and may instead occur through the propagation of a local unfolding separating two segments of opposite handedness.     

A Versatile Approach for the Site‐Specific Modification of Recombinant Antibodies Using a Combination of Enzyme‐Mediated Bioconjugation and Click Chemistry

A unique two‐step modular system for site‐specific antibody modification and conjugation is reported. The first step of this approach uses enzymatic bioconjugation with the transpeptidase Sortase A for incorporation of strained cyclooctyne functional groups. The second step of this modular approach involves the azide–alkyne cycloaddition click reaction. The versatility of the two‐step approach has been exemplified by the selective incorporation of fluorescent dyes and a positron‐emitting copper‐64 radiotracer for fluorescence and positron‐emission tomography imaging of activated platelets, platelet aggregates, and thrombi, respectively. This flexible and versatile approach could be readily adapted to incorporate a large array of tailor‐made functional groups using reliable click chemistry whilst preserving the activity of the antibody or other sensitive biological macromolecules.     

Benzannulation of Triynes to Generate Functionalized Arenes by Spontaneous Incorporation of Nucleophiles

The thermal reaction of ester‐tethered 1,3,8‐triynes provides novel benzannulation products with concomitant incorporation of a nucleophile. Evidence suggests that this reaction proceeds via an allene‐enyne intermediate generated by an Alder‐ene reaction in the first step. Depending on the substituent of the alkyne moiety on the allene‐enyne intermediate, the subsequent transformation can take one of two different paths, each leading to discrete aromatization products. The benzannulation of a silane‐substituted 1,3,8‐triynes provides arene products with a nucleophile incorporated onto the newly formed benzene core, whereas an aryl substituent leads to nucleophile trapping at the benzylic carbon atom connected to the aryl substituent. The formation of these two different products results from the involvement of two regioisomeric allene‐enyne intermediates.     

Synthesis of Morphology Processable α‐AlPO4 Nanoparticles,Nanowires, and Multi‐strand Nano‐ropes

In this paper we present aluminum phosphate nanocrystals, prepared by a hydrothermal reaction, using amphiphilic triblock copolymer F127 [(EO)₁₀₆(PO)₇₀(EO)₁₀₆] as a morphology‐directing template. By verifying the pH from 10 to 12, the morphology progression of AlPO₄ nanocrystals from nanoparticles to nanoparticle‐aggregated nanowires, and finally to multi‐strand nano‐ropes, was successfully demonstrated. The most influential factors in the morphology process were the initial pH level, the participation of surfactant‐template F127, and the change in pH during the reaction. We proposed a pH‐dependent model to illustrate both the growth of AlPO₄ nanocrystals inside F127 amphiphilic domains and the chemical driving force that aggregated the nanoparticles into chain‐shaped nanowires. The incorporation of water molecules as H‐bonding linkers, to combine single nanowires into multi‐strand nano‐ropes, is also discussed in this model. Powder X‐ray diffraction (XRD) patterns of the nanoparticle‐aggregated nanowires and multi‐strand nano‐ropes were consistent with a mixed phase of berlinite and cristobalite structures, corresponding to the low‐temperature form (a‐form), while the AlPO₄ nanoparticles showed a pure berlinite phase only.     

Fuzzy DNA Strand Displacement: A Strategy to Decrease the Complexity of DNA Network Design

Toehold‐mediated DNA strand displacement endows DNA nanostructures with dynamic response capability. However, the complexity of sequence design dramatically increases as the size of the DNA network increases. We attribute this problem to the mechanism of toehold‐mediated strand displacement, termed exact strand displacement (ESD), in which one input strand corresponds to one specific substrate. In this work, we propose an alternative to toehold‐mediated DNA strand displacement, termed fuzzy strand displacement (FSD), in which one‐to‐many and many‐to‐one relationships are established between the input strand and the substrate, to reduce the complexity. We have constructed four modules, termed converter, reporter, fuzzy detector, and fuzzy trigger, and demonstrated that a sequence pattern recognition network composed of these modules requires less complex sequence design than an equivalent network based on toehold‐mediated DNA strand displacement.     

Well‐Arranged and Confined Incorporation of PdCo Nanoparticles within a Hollow and Porous Metal–Organic Framework for Superior Catalytic Activity

A convenient method for the confined incorporation of highly active bimetallic PdCo nanocatalysts within a hollow and porous metal–organic framework (MOF) support is presented. Several chemical conversions occur simultaneously during the one‐step low temperature pyrolysis of well‐designed polystyrene@ZIF‐67/Pd²⁺ core–shell microspheres, where ZIF (zeolitic imidazolate framework) is a subclass of MOF: the polystyrene core is removed, resulting in a beneficial hollow and porous ZIF support; the ZIF‐67 shell acts as a well‐defined porous support and as a felicitous Co²⁺ supplier for metal nanoparticle formation; and Pd²⁺ and Co²⁺ are reduced to form catalytically active bimetallic PdCo nanoparticles in the well‐defined micropores, inducing the confined growth of PdCo nanoparticles with excellent dispersity.     

Visible‐Light‐Induced Passerini Multicomponent Polymerization

Herein, we introduce an additive‐free visible‐light‐induced Passerini multicomponent polymerization (MCP) for the generation of high molar mass chains. In place of classical aldehydes (or ketones), highly reactive, in situ photogenerated thioaldehydes are exploited along with isocyanides and carboxylic acids. Prone to side reactions, the thioaldehyde moieties create a complex reaction environment which can be tamed by optimizing the synthetic conditions utilizing stochastic reaction path analysis, highlighting the potential of semi‐batch procedures. Once the complex MCP environment is understood, step‐growth polymers can be synthesized under mild reaction conditions which—after a Mumm rearrangement—result in the incorporation of thioester moieties directly into the polymer backbone, leading to soft matter materials that can be degraded by straightforward aminolysis or chain expanded by thiirane insertion.     

Conformational changes in Akt1 activation probed by amide hydrogen/deuterium exchange and nano‐electrospray ionization mass spectrometry

Amide hydrogen exchange coupled to nano‐electrospray ionization mass spectrometry (nano‐ESI‐MS) has been used to identify and characterize localized conformational changes of Akt upon activation. Active or inactive Akt was incubated in D₂O buffer, digested with pepsin, and analyzed by nano‐ESI‐MS to determine the deuterium incorporation. The hydrogen/deuterium (H/D) exchange profiles revealed that Akt undergoes considerable conformational changes in the core structures of all three individual domains after activation. In the PH domain, four β‐strand (β1, β2 β5 and β6) regions containing membrane‐binding residues displayed higher solvent accessibility in the inactive state, suggesting that the PH domain is readily available for the binding to the plasma membrane for activation. In contrast, these β‐strands became less exposed or more folded in the active form, which is favored for the dissociation of Akt from the membrane. The beginning α‐helix J region and the C‐terminal locus (T450‐470P) of the regulatory domain showed less folded structures that probably enable substrate entry. Our data also revealed detailed conformational changes of Akt in the kinase domain due to activation, some of which may be attributed to the interaction of the basic residues with phosphorylation sites. Our H/D exchange results indicating the conformational status of Akt at different activation states provided new insight for the regulation of this critical protein involved in cell survival. Published in 2009 by John Wiley & Sons, Ltd.     

Superhelices Self‐Assembled from Polypeptide‐Based Polymer Mixtures: Multistranded Features

Poly(γ‐benzyl‐l ‐glutamate)‐block‐poly(ethylene glycol) (PBLG‐b ‐PEG) rod–coil block copolymers and poly(γ‐benzyl‐l ‐glutamate) (PBLG) homopolymers can cooperatively self‐assemble into superhelical structures in aqueous solution. Herein, we discovered that the helices can have multiple strands with tunable characteristics. The strand number was dependent on the initial polymer concentration of the self‐assembly, the self‐assembly temperature, and the weight fraction of the block copolymers in the mixture. Higher initial polymer concentrations or lower weight fractions of the block copolymers induced the formation of helices with larger diameters and higher strand numbers, and helices prepared at higher temperatures had higher strand numbers. Based on an analysis of the correlation between the geometric parameters of the helices and the strand number, a possible mechanism for the formation of multistranded superhelices is suggested.