Barcoding Biological Reactions with DNA‐Functionalized Vesicles

Targeted vesicle fusion is a promising approach to selectively control interactions between vesicle compartments and would enable the initiation of biological reactions in complex aqueous environments. Here, we explore how two features of vesicle membranes, DNA tethers and phase‐segregated membranes, promote fusion between specific vesicle populations. Membrane phase‐segregation provides an energetic driver for membrane fusion that increases the efficiency of DNA‐mediated fusion events. The orthogonality provided by DNA tethers allows us to direct fusion and delivery of DNA cargo to specific vesicle populations. Vesicle fusion between DNA‐tethered vesicles can be used to initiate in vitro protein expression to produce model soluble and membrane proteins. Engineering orthogonal fusion events between DNA‐tethered vesicles provides a new strategy to control the spatiotemporal dynamics of cell‐free reactions, expanding opportunities to engineer artificial cellular systems.     

Facilitated phosphatidylserine flip-flop across vesicle and cell membranes using urea-derived synthetic translocases

Tris(2-aminoethyl)amine derivatives with appended urea and sulfonamide groups are shown to facilitate the translocation of fluorescent phospholipid probes and endogenous phosphatidylserine across vesicle and erythrocyte cell membranes. The synthetic translocases appear to operate by binding to the phospholipid head groups and forming lipophilic supramolecular complexes which diffuse through the non-polar interior of the bilayer membrane.     

A DFT Study on the Reaction Pathways for Carbon?Carbon Bond‐Forming Reactions between Propargylic Alcohols and Alkenes or Ketones Catalyzed by Thiolate‐Bridged Diruthenium Complexes

The reaction pathways of two types of the carbon? carbon bond‐forming reactions catalyzed by thiolate‐bridged diruthenium complexes have been investigated by density‐functional‐theory calculations. It is clarified that both carbon? carbon bond‐forming reactions proceed through a ruthenium–allenylidene complex as a common reactive intermediate. The attack of π electrons on propene or the vinyl alcohol on the ruthenium–allenylidene complex is the first step of the reaction pathways. The reaction pathways are different after the attack of nucleophiles on the ruthenium–alkynyl complex. In the reaction with propene, the carbon? carbon bond‐forming reaction proceeds through a stepwise process, whereas in the reaction with vinyl alcohol, it proceeds through a concerted process. The interactions between the ruthenium–allenylidene complex and propene or vinyl alcohol have been investigated by applying a simple way of looking at orbital interactions.     

Selective complexation and transport of europium ions at the interface of vesicles

The aim of the present work was to design functionalized lipidic membranes that can selectively interact with lanthanide ions at the interface and to exploit the interaction between membranes induced by this molecular-recognition process with a view to building up self-assembled vesicles or controlling the permeability of the membrane to lanthanide ions. Amphiphilic molecules bearing a beta-diketone unit as head group were synthesized and incorporated into phospholipidic vesicles. Binding of Eu(III) ions to the amphiphilic ligand can lead to formation of a complex involving ligands of the same vesicle membrane (intravesicular complex) or of two different vesicles (intervesicular complex). The effect of Eu(III) ions on vesicle behavior was studied by complementary techniques such as fluorimetry, light scattering, and electron microscopy. The formation of an intravesicular luminescent Eu/beta-diketone ligand (1/2) complex was demonstrated. The linear increase in the binding constant with increasing concentration of ligands in the membrane revealed a cooperative effect of the ligands distributed in the vesicle membrane. The luminescence of this complex can be exploited to monitor the kinetics of complexation at the interface of the vesicles, as well as ion transport across the membrane. By encapsulation of 2,6-dipicolinic acid (DPA) as a competing ligand which forms a luminescent Eu/DPA complex, the kinetics of ion transport across the membrane could be followed. These functional vesicles were shown to be an efficient system for the selective transport of Eu(III) ions across a membrane with assistance by beta-diketone ligands.     

Solid-supported biomimetic membranes with tailored lipopolymer tethers

Stable lipid membranes with controlled substrate-membrane spacing can be prepared using well-defined lipopolymers as a tether. Based on the living cationic ring-opening polymerization of 2-methyl- or 2-ethyl-2-oxazoline, lipopolymers can be synthesized bearing a lipid head group as well as a silanol reactive coupling end group. Using a “grafting onto” procedure these polymers can form dense, brush like monolayers, whose layered structures can be obtained by x-ray reflectivity measurements. By transfer of a pre-organized monolayer that is followed by vesicle fusion, stable polymer supported lipid membranes can be prepared. The substrate-membrane spacing can be controlled via the degree of polymerization, while the lateral diffusion of lipids within the membrane depends on the density of polymer tethers. Preliminary experiments implied that the membrane with long (N = 40) polymer tethers could reside trans-membrane receptors homogeneously, suggesting a large potential of this strategy.     

Excited Fluorophores Enhance the Opening of Vesicles at Electrode Surfaces in Vesicle Electrochemical Cytometry

Electrochemical cytometry is a method developed recently to determine the content of an individual cell vesicle. The mechanism of vesicle rupture at the electrode surface involves the formation of a pore at the interface between a vesicle and the electrode through electroporation, which leads to the release and oxidation of the vesicle's chemical cargo. We have manipulated the membrane properties using excited fluorophores conjugated to lipids, which appears to make the membrane more susceptible to electroporation. We propose that by having excited fluorophores in close contact with the membrane, membrane lipids (and perhaps proteins) are oxidized upon production of reactive oxygen species, which then leads to changes in membrane properties and the formation of water defects. This is supported by experiments in which the fluorophores were placed on the lipid tail instead of the headgroup, which leads to a more rapid onset of vesicle opening. Additionally, application of DMSO to the vesicles, which increases the membrane area per lipid, and decreasing the membrane thickness result in the same enhancement in vesicle opening, which confirms the mechanism of vesicle opening with excited fluorophores in the membrane. Light‐induced manipulation of membrane vesicle pore opening might be an attractive means of controlling cell activity and exocytosis. Additionally, our data confirm that in experiments in which cells or vesicle membranes are labeled for fluorescence monitoring, the properties of the excited membrane change substantially.     

Polymeric vesicle permeability: a facile chemical assay

We present a simple method to characterize vesicles and determine, at the same time, the membrane permeability to specific molecules. The method is based on encapsulating highly hydrophilic 3,3',3' '-phosphinidynetris-benzenesulfonic acid (PH) into vesicles and subsequently monitoring its reaction with 5,5'-dithiobis-2-nitrobenzoic acid (DTNB). We tested the method by measuring the membrane permeability of vesicles formed from a series of poly(ethylene oxide)-co-polybutylene oxide (EB) copolymers and egg yolk phosphatidylcholine. We found that the experimental data are in good agreement with calculations based on Fick's first law. We therefore quantified the DTNB permeability across vesicle membranes, finding that polymeric EB membranes have a more selective permeability toward polar molecules compared to phospholipids membranes.     

Inter-Vesicle Signal Transduction Using a Photo-Responsive Zinc Ionophore

Transmission of chemical information between cells and across lipid bilayer membranes is of profound significance in many biological processes. The design of synthetic signalling systems is a critical step towards preparing artificial cells with collective behaviour. Here, we report the first example of a synthetic inter-vesicle signalling system, in which diffusible chemical signals trigger transmembrane ion transport in a manner reminiscent of signalling pathways in biology. The system is derived from novel ortho-nitrobenzyl and BODIPY photo-caged Zn^II transporters, in which cation transport is triggered by photo-decaging with UV or red light, respectively. This decaging reaction can be used to trigger the release of the cationophores from a small population of sender vesicles. This in turn triggers the transport of ions across the membrane of a larger population of receiver vesicles, but not across the sender vesicle membrane, leading to overall inter-vesicle signal transduction and amplification.     

SOLUBILIZATION OF PHOTOSYNTHETIC PIGMENT-PROTEIN COMPLEXES

Studies utilizing fractionation of photosynthetic pigment-protein complexes from the chloroplast thylakoid membrane often employ dodecylsulfate at a concentration of 10 mg mL^?1 to disrupt membrane structure prior to electrophoretic fractionation of the complexes. We investigated the effect of varying dodecylsulfate concentration on the solution/air interfacial surface tension in the absence and presence of the same concentrations of thylakoid membranes used by four different fractionation systems that have been commonly employed to fractionate photosynthetic pigment-protein complexes. Concentrations of dodecylsulfate in the range5–10 mg mL^?1, normally utilized to treat thylakoids prior to fractionation, were effective in reducing the interfacial surface tension to levels equivalent to control solutions without added thylakoid membranes. However, thylakoid membranes treated with these concentrations of dodecylsulfate are not resolved into discrete pigment-protein complexes when subjected to electrophoresis on an agarose gel, and do not produce significant amounts of pigment-containing complexes with a molecular size < 100 000 as measured by filtration with size-exclusion membranes. We conclude that many surfactant systems empirically developed to fractionate photosynthetic pigment-protein complexes may not fully solubilize the complexes prior to the electrophoretic step.     

Diversity in structure and function of tethering complexes: evidence for different mechanisms in vesicular transport regulation

The term 'tethering factor' has been coined for a heterogeneous group of proteins that all are required for protein trafficking prior to vesicle docking and SNARE-mediated membrane fusion. Two groups of tethering factors can be distinguished, long coiled-coil proteins and multi-subunit complexes. To date, eight such protein complexes have been identified in yeast, and they are required for different trafficking steps. Homologous complexes are found in all eukaryotic organisms, but conservation seems to be less strict than for other components of the trafficking machinery. In fact, for most proposed multi-subunit tethers their ability to actually bridge two membranes remains to be shown. Here we discuss recent progress in the structural and functional characterization of tethering complexes and present the emerging view that the different complexes are quite diverse in their structure and the molecular mechanisms underlying their function. TRAPP and the exocyst are the structurally best characterized tethering complexes. Their comparison fails to reveal any similarity on a struc nottural level. Furthermore, the interactions with regulatory Rab GTPases vary, with TRAPP acting as a nucleotide exchange factor and the exocyst being an effector. Considering these differences among the tethering complexes as well as between their yeast and mammalian orthologs which is apparent from recent studies, we suggest that tethering complexes do not mediate a strictly conserved process in vesicular transport but are diverse regulators acting after vesicle budding and prior to membrane fusion.     

Substitution reactions at tetracoordinate boron: synthesis of N-heterocyclic carbene boranes with boron-heteroatom bonds

Boryl halide, carboxylate and sulfonate complexes of 1,3-bis(2,6-diisopropylphenyl)imidazol-2-ylidene (dipp-Imd-BH(2)X, X = halide or sulfonate) have been prepared from the parent borane dipp-Imd-BH(3) by (1) substitution reactions with R-X (X = halide or sulfonate), (2) reactions with electrophiles (like I(2) or NIS), or (3) acid/base reactions with HX (provided that HX has a pK(a) of about 2 or less). Dipp-Imd-BH(2)I is most conveniently prepared by reaction with diiodine while dipp-Imd-BH(2)OTf is best prepared by reaction with triflic acid. These and other less reactive complexes behave as electrophiles and can be substituted by a wide range of heteroatom nucleophiles including halides, thiolates and other sulfur-based nucleophiles, isocyanate, azide, nitrite, and cyanide. The resulting products are remarkably stable, and many have been characterized by X-ray crystallography. Several are members of very rare classes of functionalized boron compounds (boron azide, nitro compound, nitrous ester, etc.).     

Electrostatic Localization of RNA to Protocell Membranes by Cationic Hydrophobic Peptides

Cooperative interactions between RNA and vesicle membranes on the prebiotic earth may have led to the emergence of primitive cells. The membrane surface offers a potential platform for the catalysis of reactions involving RNA, but this scenario relies upon the existence of a simple mechanism by which RNA could become associated with protocell membranes. Here, we show that electrostatic interactions provided by short, basic, amphipathic peptides can be harnessed to drive RNA binding to both zwitterionic phospholipid and anionic fatty acid membranes. We show that the association of cationic molecules with phospholipid vesicles can enhance the local positive charge on a membrane and attract RNA polynucleotides. This phenomenon can be reproduced with amphipathic peptides as short as three amino acids. Finally, we show that peptides can cross bilayer membranes to localize encapsulated RNA. This mechanism of polynucleotide confinement could have been important for primitive cellular evolution.     

Theories of reactive scattering

This paper is an overview of the theory of reactive scattering, with emphasis on fully quantum mechanical theories that have been developed to describe simple chemical reactions, especially atom-diatom reactions. We also describe related quasiclassical trajectory applications, and in all of this review the emphasis is on methods and applications concerned with state-resolved reaction dynamics. The review first provides an overview of the development of the theory, including a discussion of computational methods based on coupled channel calculations, variational methods, and wave packet methods. Choices of coordinates, including the use of hyperspherical coordinates are discussed, as are basis set and discrete variational representations. The review also summarizes a number of applications that have been performed, especially the two most comprehensively studied systems, H+H2 and F+H2, along with brief discussions of a large number of other systems, including other hydrogen atom transfer reactions, insertion reactions, electronically nonadiabatic reactions, and reactions involving four or more atoms. For each reaction we describe the method used and important new physical insight extracted from the results.     

非钯催化剂催化Heck反应研究进展

非钯催化剂用于催化Heck反应有较多的报道.与钯催化剂相比,一些非钯催化剂(如镍、铜、钴等)显示了更优越的性能.近年来,铂、铑、钌、铁等催化体系也被用于Heck反应.对近年来非钯催化剂用于催化Heck反应的研究进行了归纳总结.     

Light-harvesting and structural organization of Photosystem II: from individual complexes to thylakoid membrane

Photosystem II (PSII) is responsible for the water oxidation in photosynthesis and it consists of many proteins and pigment-protein complexes in a variable composition, depending on environmental conditions. Sunlight-induced charge separation lies at the basis of the photochemical reactions and it occurs in the reaction center (RC). The RC is located in the PSII core which also contains light-harvesting complexes CP43 and CP47. The PSII core of plants is surrounded by external light-harvesting complexes (lhcs) forming supercomplexes, which together with additional external lhcs, are located in the thylakoid membrane where they perform their functions. In this paper we provide an overview of the available information on the structure and organization of pigment-protein complexes in PSII and relate this to experimental and theoretical results on excitation energy transfer (EET) and charge separation (CS). This is done for different subcomplexes, supercomplexes, PSII membranes and thylakoid membranes. Differences in experimental and theoretical results are discussed and the question is addressed how results and models for individual complexes relate to the results on larger systems. It is shown that it is still very difficult to combine all available results into one comprehensive picture.     

Giant phospholipid/block copolymer hybrid vesicles: mixing behavior and domain formation

Lipids and block copolymers can be individually assembled into unsupported, spherical membranes (liposomes or polymersomes), each having their own particular benefits and limitations. Here we demonstrate the preparation of microscale, hybrid "lipopolymersomes" composed of the common lipid POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine) and the commercially available copolymer PBd-b-PEO (polybutadiene-b-poly(ethylene oxide)) with the goal of incorporating the advantageous qualities of the unitary systems into mixed-membrane capsules. We investigate the lipopolymersomes using confocal fluorescence microscopy and demonstrate that these hybrid membranes are well mixed on nanoscopic length scales within the permittable compositional windows for hybrid vesicle formation. We measure the intramembrane dynamics and mechanical properties of these hybrid membranes by fluorescence recovery after photobleaching (FRAP) and micropipet aspiration, respectively. For the first time, we demonstrate the demixing of lipid-rich and polymer-rich membrane domains within the same vesicle membrane. This is achieved by the biotinylation of one of the constituent species and cross linking with the protein NeutrAvidin. The resultant domain patterning is dependent upon which component carries the biotin functionality: cross linking of the copolymer species results in domains that ripen into a single, large, copolymer-rich island, and cross linking of the lipids yields many small, "spot-like", lipid-rich domains within a copolymer-rich matrix. We discuss these morphological differences in terms of the fluidity and mechanical properties of the membrane phases and the possible resultant interdomain interactions within the membrane. These heterogeneous hybrid lipopolymersomes could find applications in fields such as targeted delivery, controlled release, and environmental detection assays where these capsules possess the characteristics of biocompatible lipid membranes combined with enhanced mechanical strength and stability from the copolymer matrix.     

Atom Economy—A Challenge for Organic Synthesis: Homogeneous Catalysis Leads the Way

Enhancing the efficiency of the synthesis of complex organic products constitutes one of the most exciting challenges to the synthetic chemist. Increasing the catalogue of reactions that are simple additions or that minimize waste production is the necessary first step. Transition metal complexes, which can be tunable both electronically and sterically by varying the metal and/or ligands, are a focal point for such invention. Except for catalytic hydrogenation, such methods have been rare in complex synthesis and virtually unknown for C? C bond formation until the advent of cross-coupling reactions. These complexes may orchestrate a variety of C? C bond-forming processes, important for creation of the basic skeleton of the organic structure. Their ability to insert into C? H bonds primes a number of different types of additions to relatively nonpolar π-electron systems. Besides imparting selectivity, they make feasible reactions that uncatalyzed were previously unknown. The ability of these complexes to preorganize π-electron systems serves as the basis both of simple additions usually accompanied by subsequent hydrogen shifts and of cycloadditions. The ability to generate “reactive” intermediates under mild conditions also provides prospects for new types of C? C bond-forming reactions. While the examples reveal a diverse array of successes, the opportunities for new invention are vast and largely untapped.     

Mechanisms of the Cycloaddition Reaction of Methylenecyclopropane-Palladium and Oxa- and Azatrimethylenemethane-Palladium Complexes with Olefins

Mechanisms of palladium-catalyzed cycloaddition reactions of methylenecyclopropane with olefins and those of oxatrimethylenemethane (OTMM) and azatrimethylenemethane (ATMM) complexes with olefins have been studied by applying the ab initio molecular orbital method. Assuming an intramolecular coupling mechanism, we have examined some model complexes, Pd(eta(2)-methylenecyclopropane)(ethylene)(PH(3)) and Pd(eta(3)-OTMM or eta(3)-ATMM)(ethylene)(PH(3)), to determine the transition state structures. The coupling of methylenecyclopropane, OTMM, and ATMM with ethylene on the metal center takes place in two steps. In the reaction of methylenecyclopropane, the first step involves an opening of the cyclopropane ring promoted by an attack of ethylene. The methylenecyclopropane moiety has a pi-allylic form at the first transition state which leads to a metallacyclic intermediate. The first transition state of the reactions of OTMM and ATMM complexes looks very similar to that of the methylenecyclopropane complex, having pi-allylic coordinations. The two paths are separated in the second step. A [3 + 2] addition product is obtained by a reductive elimination from the intermediate metallacycle, whereas a prototropic shift followed by a reductive elimination affords a [2 + 1] addition product. It is the energetics of the second stage starting from the metallacycles that differentiates the reactions of the OTMM and ATMM complexes from the reaction of the methylenecyclopropane complex. The relative stabilities of various isomeric forms of these complexes have also been studied.     

Vesicle shapes from molecular dynamics simulations

Lipid bilayer membranes are known to form various structures such as large sheets or vesicles. When the two leaflets of the bilayer have an equal composition, the membrane preferentially forms a flat sheet or a spherical vesicle. However, a difference in the composition of the two leaflets may result in a curved bilayer or in a wide variety of vesicle shapes. Vesicles with different shapes have already been shown in experiments and diverse vesicle shapes have been predicted theoretically from energy minimization of continuous curves. Here we present a molecular dynamics study of the effect of small changes in the phospholipid headgroups on the spontaneous curvature of the bilayer and on the resulting vesicle shape transformations. Small asymmetries in the bilayers already result in high spontaneous curvature and large vesicle deformations. Vesicle shapes that are formed include ellipsoids, discoids, pear-shaped vesicles, cup-shaped vesicles, as well as budded vesicles. Comparison of these vesicles with theoretically derived vesicle shapes shows both resemblances and differences.     

Cu(I)-amido complexes in the Ullmann reaction: reactions of Cu(I)-amido complexes with iodoarenes with and without autocatalysis by CuI

A series of Cu(I)-amido complexes both lacking ancillary ligands and containing 1,10-phenanthroline (phen) as ancillary ligand have been prepared. These complexes react with iodoarenes to form arylamine products, and this reactivity is consistent with the intermediacy of such complexes in catalytic Ullmann amination reactions. The stoichiometric reactions of the Cu(I)-amido complexes with iodoarenes are autocatalytic, with the free CuI generated during the reaction serving as the catalyst. Such autocatalytic behavior was not observed for reactions of iodoarenes with copper(I) amidates, imidates, or phenoxides. The selectivity of these complexes for two sterically distinct aryl halides under various conditions imply that the autocatalytic reaction proceeds by forming highly reactive [CuNPh(2)](n) lacking phen. Reactions with radical probes imply that the reactions of phen-ligated Cu(I)-amido complexes with iodoarenes occur without the intermediacy of aryl radicals. Density functional theory calculations on the oxidative addition of iodoarenes to Cu(I) species are consistent with faster reactions of iodoarenes with CuNPh(2) species lacking phen in DMSO than reactions of iodoarenes with LCuNPh(2) in which L = phen. The free-energy barrier computed for the reaction of PhI with (DMSO)CuNPh(2) was 21.8 kcal/mol, while that for the reaction of PhI with (phen)CuNPh(2) was 33.4 kcal/mol.