Supramolecular Porphyrin Cages Assembled at Molecular–Materials Interfaces for Electrocatalytic CO Reduction

DOE PAGES

Gong, Ming; Cao, Zhi; Liu, Wei; ...

2017-09-13

Conversion of carbon monoxide (CO), a major one-carbon product of carbon dioxide (CO 2) reduction, into value-added multicarbon species is a challenge to addressing global energy demands and climate change. Here in this paper, we report a modular synthetic approach for aqueous electrochemical CO reduction to carbon-carbon coupled products via self-assembly of supramolecular cages at molecular-materials interfaces. Heterobimetallic cavities formed by face-to-face coordination of thiol-terminated metalloporphyrins to copper electrodes through varying organic struts convert CO to C2 products with high faradaic efficiency (FE = 83% total with 57% to ethanol) and current density (1.34 mA/cm 2) at a potential ofmore » -0.40 V vs RHE. The cage-functionalized electrodes offer an order of magnitude improvement in both selectivity and activity for electrocatalytic carbon fixation compared to parent copper surfaces or copper functionalized with porphyrins in an edge-on orientation.« less

A switchable self-assembling and disassembling chiral system based on a porphyrin-substituted phenylalanine-phenylalanine motif

NASA Astrophysics Data System (ADS)

Charalambidis, Georgios; Georgilis, Evangelos; Panda, Manas K.; Anson, Christopher E.; Powell, Annie K.; Doyle, Stephen; Moss, David; Jochum, Tobias; Horton, Peter N.; Coles, Simon J.; Linares, Mathieu; Beljonne, David; Naubron, Jean-Valère; Conradt, Jonas; Kalt, Heinz; Mitraki, Anna; Coutsolelos, Athanassios G.; Balaban, Teodor Silviu

2016-09-01

Artificial light-harvesting systems have until now not been able to self-assemble into structures with a large photon capture cross-section that upon a stimulus reversibly can switch into an inactive state. Here we describe a simple and robust FLFL-dipeptide construct to which a meso-tetraphenylporphyrin has been appended and which self-assembles to fibrils, platelets or nanospheres depending on the solvent composition. The fibrils, functioning as quenched antennas, give intense excitonic couplets in the electronic circular dichroism spectra which are mirror imaged if the unnatural FDFD-analogue is used. By slightly increasing the solvent polarity, these light-harvesting fibres disassemble to spherical structures with silent electronic circular dichroism spectra but which fluoresce. Upon further dilution with the nonpolar solvent, the intense Cotton effects are recovered, thus proving a reversible switching. A single crystal X-ray structure shows a head-to-head arrangement of porphyrins that explains both their excitonic coupling and quenched fluorescence.

Conjugated Porphyrin Dimers: Cooperative Effects and Electronic Communication in Supramolecular Ensembles with C60.

PubMed

Moreira, Luis; Calbo, Joaquín; Aragó, Juan; Illescas, Beatriz M; Nierengarten, Iwona; Delavaux-Nicot, Béatrice; Ortí, Enrique; Martín, Nazario; Nierengarten, Jean-François

2016-11-30

Two new conjugated porphyrin-based systems (dimers 3 and 4) endowed with suitable crown ethers have been synthesized as receptors for a fullerene-ammonium salt derivative (1). Association constants in solution have been determined by UV-vis titration experiments in CH 2 Cl 2 at room temperature. The designed hosts are able to associate up to two fullerene-based guest molecules and present association constants as high as ∼5 × 10 8 M -1 . Calculation of the allosteric cooperative factor α for supramolecular complexes [3·1 2 ] and [4·1 2 ] showed a negative cooperative effect in both cases. The interactions accounting for the formation of the associates are based, first, on the complementary ammonium-crown ether interaction and, second, on the π-π interactions between the porphyrin rings and the C 60 moieties. Theoretical calculations have evidenced a significant decrease of the electron density in the porphyrin dimers 3 and 4 upon complexation of the first C 60 molecule, in good agreement with the negative cooperativity found in these systems. This negative effect is partially compensated by the stabilizing C 60 -C 60 interactions that take place in the more stable syn-disposition of [4·1 2 ].

Push-pull quinoidal porphyrins.

PubMed

Smith, Martin J; Blake, Iain M; Clegg, William; Anderson, Harry L

2018-05-01

A family of push-pull quinoidal porphyrin monomers has been prepared from a meso-formyl porphyrin by bromination, thioacetal formation, palladium-catalyzed coupling with malononitrile and oxidation with DDQ. Attempts at extending this synthesis to a push-pull quinoidal/cumulenic porphyrin dimer were not successful. The crystal structures of the quinoidal porphyrins indicate that there is no significant contribution from singlet biradical or zwitterionic resonance forms. The crystal structure of an ethyne-linked porphyrin dimer shows that the torsion angle between the porphyrin units is only about 3°, in keeping with crystallographic results on related compounds, but contrasting with the torsion angle of about 35° predicted by computational studies. The free-base quinoidal porphyrin monomers form tightly π-stacked layer structures, despite their curved geometries and bulky aryl substituents.

Anti-cooperative supramolecular polymerization: a new K2-K model applied to the self-assembly of perylene bisimide dye proceeding via well-defined hydrogen-bonded dimers.

PubMed

Gershberg, Jana; Fennel, Franziska; Rehm, Thomas H; Lochbrunner, Stefan; Würthner, Frank

2016-03-01

A perylene bisimide dye bearing amide functionalities at the imide positions derived from amino acid l-alanine and a dialkoxy-substituted benzyl amine self-assembles into tightly bound dimers by π-π-stacking and hydrogen bonding in chloroform. In less polar or unpolar solvents like toluene and methylcyclohexane, and in their mixtures, these dimers further self-assemble into extended oligomeric aggregates in an anti-cooperative process in which even numbered aggregates are highly favoured. The stepwise transition from dimers into oligomers can not be properly described by conventional K 2 - K model, and thus a new K 2 - K aggregation model has been developed, which interpretes the present anti-cooperative supramolecular polymerization more appropriately. The newly developed K 2 - K model will be useful to describe self-assembly processes of a plethora of other π-conjugated molecules that are characterized by a favored dimer species.

Solvent-Tuned Self-Assembled Nanostructures of Chiral l/d-Phenylalanine Derivatives of Protoporphyrin IX

PubMed Central

Bobe, Mr Sharad R; Al Kobaisi, Mohammad; Bhosale, Sheshanath V; Bhosale, Sidhanath V

2015-01-01

Protoporphyrin IX is a naturally occurring amphiphilic porphyrin with a rigid hydrophobic nonpolar core and two polar propionic acid substitutions on the porphyrin ring. This molecule can be modified on the hydrophilic group, which can lead to strengthened π–π-stacking and spontaneous self-assembly into novel nanostructures. Herein, we use l- phenylalanine and d-phenylalanine to modify protoporphyrin IX, and use the two derivatives for solvophobic-controlled self-assembly. Both derivatives possess two important features: 1) the aromatic core of the porphyrin for dispersive interactions and 2) a chiral amino acid to maximize the influence of chirality on selfassembly. These derivatives lead to the formation of a variety of nanostructure morphologies, such as spheres, nanofibers, lamellar structures, and thread-like and spherical shells. Solution-based self-assembly was determined by UV/Vis, fluorescence, and circular dichroism spectroscopy, and the formed nanostructures were characterized by scanning electron microscopy (SEM). Such engineered porphyrin derivatives could have potential applications in energy transport and storage, supramolecular chemistry, materials science, and medicine. PMID:26478848

Solvent-Tuned Self-Assembled Nanostructures of Chiral l/d-Phenylalanine Derivatives of Protoporphyrin IX.

PubMed

Bobe, Mr Sharad R; Al Kobaisi, Mohammad; Bhosale, Sheshanath V; Bhosale, Sidhanath V

2015-08-01

Protoporphyrin IX is a naturally occurring amphiphilic porphyrin with a rigid hydrophobic nonpolar core and two polar propionic acid substitutions on the porphyrin ring. This molecule can be modified on the hydrophilic group, which can lead to strengthened π-π-stacking and spontaneous self-assembly into novel nanostructures. Herein, we use l- phenylalanine and d-phenylalanine to modify protoporphyrin IX, and use the two derivatives for solvophobic-controlled self-assembly. Both derivatives possess two important features: 1) the aromatic core of the porphyrin for dispersive interactions and 2) a chiral amino acid to maximize the influence of chirality on selfassembly. These derivatives lead to the formation of a variety of nanostructure morphologies, such as spheres, nanofibers, lamellar structures, and thread-like and spherical shells. Solution-based self-assembly was determined by UV/Vis, fluorescence, and circular dichroism spectroscopy, and the formed nanostructures were characterized by scanning electron microscopy (SEM). Such engineered porphyrin derivatives could have potential applications in energy transport and storage, supramolecular chemistry, materials science, and medicine.

Assembly of Multi-Phthalocyanines on a Porphyrin Template by Fourfold Rotaxane Formation.

PubMed

Yamada, Yasuyuki; Kato, Tatsuhisa; Tanaka, Kentaro

2016-08-22

A stacked assembly composed of a porphyrin and two phthalocyanines was prepared through fourfold rotaxane formation. Two phthalocyanine molecules, bearing four 24-crown-8 units, were assembled onto a porphyrin template incorporating four sidechains with two dialkylammonium ions each through pseudorotaxane formation between crown ether units and ammonium ions. The Staudinger phosphite reaction, as the stoppering reaction, resulted in the formation of the stacked heterotrimer composed of a porphyrin and two phthalocyanines connected through a fourfold rotaxane structure. UV/Vis spectroscopic and electrochemical studies of the heterotrimer indicated that there is a significant electronic interaction between the two phthalocyanine units due to the close stacking. The electrochemical oxidation process of the stacked heterotrimer was studied by cyclic voltammetry and spectroelectrochemistry. Electron paramagnetic resonance (EPR) spectroscopy of a dinuclear Cu(II) complex, in which two Cu(II) phthalocyanines were assembled on a metal-free porphyrin template, revealed that two Cu(II) phthalocyanines were located within the stacking distance, which resulted in an antiferromagnetic interaction between the two S=1/2 spins in the ground state of the Cu(2+) ions in the heterotrimer. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Synthesis of porphyrin nanostructures

DOEpatents

Fan, Hongyou; Bai, Feng

2014-10-28

The present disclosure generally relates to self-assembly methods for generating porphyrin nanostructures. For example, in one embodiment a method is provided that includes preparing a porphyrin solution and a surfactant solution. The porphyrin solution is then mixed with the surfactant solution at a concentration sufficient for confinement of the porphyrin molecules by the surfactant molecules. In some embodiments, the concentration of the surfactant is at or above its critical micelle concentration (CMC), which allows the surfactant to template the growth of the nanostructure over time. The size and morphology of the nanostructures may be affected by the type of porphyrin molecules used, the type of surfactant used, the concentration of the porphyrin and surfactant the pH of the mixture of the solutions, and the order of adding the reagents to the mixture, to name a few variables.

Improving Photocatalytic Activity through Electrostatic Self-Assembly: Polyelectrolytes as Tool for Solar Energy Conversion?

NASA Astrophysics Data System (ADS)

Groehn, Franziska

2015-03-01

With regard to the world's decreasing energy resources, developing strategies to exploit solar energy become more and more important. One approach is to take advantage of photocatalysis. Inspired by natural systems such as assemblies performing photosynthesis, it is highly promising to self-assemble synthetic functional species to form more effective or tailored supramolecular units. In this contribution, a new type of photocatalytically active self-assembled nanostructures in aqueous solution will be presented: supramolecular nano-objects obtained through self-assembly of macroions and multivalent organic or inorganic counterions. Polyelectrolyte-porphyrin nanoscale assemblies exhibit up to 10-fold higher photocatalytic activity than the corresponding porphyrins without polymeric template. Other self-assembled catalysts based on polyelectrolytes can exhibit expressed selectivity in a photocatalytic model reaction or even allow catalytic reactions in solution that are not possible with the building blocks only. Further, current results on combining different functional units at the polyelectrolyte template represent a next step towards more complex supramolecular structures for solar energy conversion.

Sparse-coding denoising applied to reversible conformational switching of a porphyrin self-assembled monolayer induced by scanning tunnelling microscopy.

PubMed

Oliveira, J; Bragança, A M; Alcácer, L; Morgado, J; Figueiredo, M; Bioucas-Dias, J; Ferreira, Q

2018-04-14

Scanning tunnelling microscopy (STM) was used to induce conformational molecular switching on a self-assembled monolayer of zinc-octaethylporphyrin on a graphite/tetradecane interface at room temperature. A reversible conformational change controlled by applying a tip voltage was observed. Consecutive STM images acquired at alternating tip voltages showed that at 0.4 V the porphyrin monolayer presents a molecular arrangement formed by alternate rows with two different types of structural conformations and when the potential is increased to 0.7 V the monolayer presents only one type of conformation. In this paper, we characterize these porphyrin conformational dynamics by analyzing the STM images, which were improved for better quality and interpretation by means of a denoising algorithm, adapted to process STM images from state of the art image processing and analysis methods. STM remains the best technique to 'see' and to manipulate the matter at atomic scale. A very sharp tip a few angstroms of the surface can provide images of molecules and atoms with a powerful resolution. However, these images are strongly affected by noise which is necessary to correct and eliminate. This paper is about new computational tools specifically developed to denoise the images acquired with STM. The new algorithms were tested in STM images, obtained at room temperature, of porphyrin monolayer which presents reversible conformational change in function of the tip bias voltage. Images with high resolution, acquired in real time, show that the porphyrins have different molecular arrangements whether the tip voltage is 0.4 V or 0.7 V. © 2018 The Authors Journal of Microscopy © 2018 Royal Microscopical Society.

Two dimensional self-assembly zinc porphyrins and zinc phthalocyanines heterojunctions with record high power conversion efficiencies.

PubMed

Yu, Junting; Jiang, Zhou; Hao, Yifan; Zhu, Qianhong; Zhao, Mingliang; Jiang, Xue; Zhao, Jijun

2018-05-15

Compared to inorganic solar cells, the power conversion efficiencies (PCEs) of organic solar cells are much lower, but they are compensated by many merits such as lower cost, less weight, and tunable structures, making them prospective for further applications. Porphyrin and phthalocyanine are the two most significant materials for organic solar cells due to their strong light-absorbing properties and semiconductor characteristics. However, there is little research on the 2D heterojunction solar cells based on these two materials, meanwhile the PCEs of them are still low. Here we have self-assembled several 2D Zinc-porphyrins (ZnPors) and performed first-principles simulation to demonstrate their good stability, suitable light harvesting, and high charge carrier mobility. By perfectly matching lattice constants and band levels between those 2D ZnPors and our previous proposed ZnPcs, eleven type-II organic heterojunctions are constructed to further improve their charge separation capability. Those advantages endow 2D ZnPors and ZnPcs appreciable PCEs for solar cell. Among them, the theoretical PCE of 2D ZnPors/ZnPcs heterojunctions achieves as high as 19.84%, which prevails all reported organic solar cells, and even approaches the PCEs of inorganic solar cells. These results indicate that our 2D ZnPors and 2D ZnPcs are good candidate materials for future organic solar cells. © 2018 IOP Publishing Ltd.

Two dimensional self-assembly zinc porphyrin and zinc phthalocyanine heterojunctions with record high power conversion efficiencies

NASA Astrophysics Data System (ADS)

Yu, Junting; Jiang, Zhou; Hao, Yifan; Zhu, Qianhong; Zhao, Mingliang; Jiang, Xue; Zhao, Jijun

2018-06-01

Compared to inorganic solar cells, the power conversion efficiencies (PCEs) of organic solar cells are much lower, but they are compensated by many merits such as lower cost, less weight, and tunable structures, making them prospective for further applications. Porphyrin and phthalocyanine are the two most significant materials for organic solar cells due to their strong light-absorbing properties and semiconductor characteristics. However, there is little research on the 2D heterojunction solar cells based on these two materials, meanwhile the PCEs of them are still low. Here we have self-assembled several 2D zinc porphyrins (ZnPors) and performed first-principles simulation to demonstrate their good stability, suitable light harvesting, and high charge carrier mobility. By perfectly matching lattice constants and molecular energy levels between those 2D ZnPors and our previous proposed zinc phthalocyanines (ZnPcs), 11 type-II organic heterojunctions are constructed to further improve their charge separation capability. Those advantages endow 2D ZnPors and ZnPcs appreciable PCEs for solar cells. Among them, the theoretical PCE of 2D ZnPors/ZnPcs heterojunctions achieves as high as 19.84%, which exceeds all reported organic solar cells, and even approaches the PCEs of inorganic solar cells. These results indicate that our 2D ZnPors and 2D ZnPcs are good candidate materials for future organic solar cells.

Self-assembled photosynthesis-inspired light harvesting material and solar cells containing the same

DOEpatents

Lindsey, Jonathan S [Raleigh, NC; Chinnasamy, Muthiah [Raleigh, NC; Fan, Dazhong [Raleigh, NC

2009-12-15

A solar cell is described that comprises: (a) a semiconductor charge separation material; (b) at least one electrode connected to the charge separation material; and (c) a light-harvesting film on the charge separation material, the light-harvesting film comprising non-covalently coupled, self-assembled units of porphyrinic macrocycles. The porphyrinic macrocycles preferably comprise: (i) an intramolecularly coordinated metal; (ii) a first coordinating substituent; and (iii) a second coordinating substituent opposite the first coordinating substituent. The porphyrinic macrocycles can be assembled by repeating intermolecular coordination complexes of the metal, the first coordinating substituent and the second coordinating substituent.

Unique self-assembly properties of a bridge-shaped protein dimer with quantum dots

NASA Astrophysics Data System (ADS)

Wang, Jianhao; Jiang, Pengju; Gao, Liqian; Yu, Yongsheng; Lu, Yao; Qiu, Lin; Wang, Cheli; Xia, Jiang

2013-09-01

How protein-protein interaction affects protein-nanoparticle self-assembly is the key to the understanding of biomolecular coating of nanoparticle in biological fluids. However, the relationship between protein shape and its interaction with nanoparticles is still under-exploited because of lack of a well-conceived binding system and a method to detect the subtle change in the protein-nanoparticle assemblies. Noticing this unresolved need, we cloned and expressed a His-tagged SpeA protein that adopts a bridge-shaped dimer structure, and utilized a high-resolution capillary electrophoresis method to monitor assembly formation between the protein and quantum dots (QDs, 5 nm in diameter). We observed that the bridge-shaped structure rendered a low SpeA:QD stoichiometry at saturation. Also, close monitoring of imidazole (Im) displacement of surface-bound protein revealed a unique two-step process. High-concentration Im could displace surface-bound SpeA protein and form a transient QD-protein intermediate, through a kinetically controlled displacement process. An affinity-driven equilibrium step then followed, resulting in re-assembling of the QD-protein complex in about 1 h. Through a temporarily formed intermediate, Im causes a rearrangement of His-tagged proteins on the surface. Thus, our work showcases that the synergistic interplay between QD-His-tag interaction and protein-protein interaction can result in unique properties of protein-nanoparticle assembly for the first time.

Photocontrolled reversible self-assembly of dodecamer nitrilase.

PubMed

Yu, Qiao; Wang, Yong; Zhao, Shengyun; Ren, Yuhong

2017-01-01

Naturally photoswitchable proteins act as a powerful tool for the spatial and temporal control of biological processes by inducing the formation of a photodimerizer. In this study, a method for the precise and reversible inducible self-assembly of dodecamer nitrilase in vivo (in Escherichia coli ) and in vitro (in a cell-free solution) was developed by means of the photoswitch-improved light-inducible dimer (iLID) system which could induce protein-protein dimerization. Nitrilase was fused with the photoswitch protein AsLOV2-SsrA to achieve the photocontrolled self-assembly of dodecamer nitrilase. The fusion protein self-assembled into a supramolecular assembly when illuminated at 470 nm. Scanning electron microscopy showed that the assembly formed a circular sheet structure. Self-assembly was also induced by light in E. coli . Dynamic light scattering and turbidity assay experiments showed that the assemblies formed within a few seconds under 470-nm light and completely disassembled within 5 min in the dark. Assembly and disassembly could be maintained for at least five cycles. Both in vitro and in vivo, the assemblies retained 90% of the initial activity of nitrilase and could be reused at least four times in vitro with 90% activity. An efficient method was developed for the photocontrolled assembly and disassembly of dodecamer nitrilase and for scaffold-free reversible self-assembly of multiple oligomeric enzymes in vivo and in vitro, providing new ideas and methods for immobilization of enzyme without carrier.

Binary ionic porphyrin nanosheets: electronic and light-harvesting properties regulated by crystal structure

NASA Astrophysics Data System (ADS)

Tian, Yongming; M. Beavers, Christine; Busani, Tito; Martin, Kathleen E.; Jacobsen, John L.; Mercado, Brandon Q.; Swartzentruber, Brian S.; van Swol, Frank; Medforth, Craig J.; Shelnutt, John A.

2012-02-01

Crystalline solids self-assembled from anionic and cationic porphyrins provide a new class of multifunctional optoelectronic micro- and nanomaterials. A 1 : 1 combination of zinc(ii) tetra(4-sulfonatophenyl)porphyrin (ZnTPPS) and tin(iv) tetra(N-methyl-4-pyridiniumyl)porphyrin (SnTNMePyP) gives porphyrin nanosheets with high aspect ratios and varying thickness. The room temperature preparation of the nanosheets has provided the first X-ray crystal structure of a cooperative binary ionic (CBI) solid. The unit cell contains one and one-half molecules of aquo-ZnTPPS4- (an electron donor) and three half molecules of dihydroxy-SnTNMePyP4+ (an electron acceptor). Charge balance in the solid is reached without any non-porphyrinic ions, as previously determined for other CBI nanomaterials by non-crystallographic means. The crystal structure reveals a complicated molecular arrangement with slipped π-π stacking only occurring in isolated dimers of one of the symmetrically unique zinc porphyrins. Consistent with the crystal structure, UV-visible J-aggregate bands indicative of exciton delocalization and extended π-π stacking are not observed. XRD measurements show that the structure of the Zn/Sn nanosheets is distinct from that of Zn/Sn four-leaf clover-like CBI solids reported previously. In contrast with the Zn/Sn clovers that do exhibit J-aggregate bands and are photoconductive, the nanosheets are not photoconductive. Even so, the nanosheets act as light-harvesting structures in an artificial photosynthesis system capable of reducing water to hydrogen but not as efficiently as the Zn/Sn clovers.Crystalline solids self-assembled from anionic and cationic porphyrins provide a new class of multifunctional optoelectronic micro- and nanomaterials. A 1 : 1 combination of zinc(ii) tetra(4-sulfonatophenyl)porphyrin (ZnTPPS) and tin(iv) tetra(N-methyl-4-pyridiniumyl)porphyrin (SnTNMePyP) gives porphyrin nanosheets with high aspect ratios and varying thickness. The room

Self-assembly of Zn(salphen) complexes: steric regulation, stability studies and crystallographic analysis revealing an unexpected dimeric 3,3'-t-Bu-substituted Zn(salphen) complex.

PubMed

Martínez Belmonte, Marta; Wezenberg, Sander J; Haak, Robert M; Anselmo, Daniele; Escudero-Adán, Eduardo C; Benet-Buchholz, Jordi; Kleij, Arjan W

2010-05-21

The self-assembly features of a series of (non)symmetrical Zn(salphen) complexes have been studied in detail by X-ray crystallography, NMR and UV-vis techniques. The combined data demonstrate that the stability of these dimeric assemblies and the relative position of each monomeric unit within the dinuclear structure depend on the location and combination of the aromatic ring substituents.

A spectroscopic and thermodynamic study of porphyrin/DNA supramolecular assemblies.

PubMed Central

Pasternack, R F; Goldsmith, J I; Szép, S; Gibbs, E J

1998-01-01

Assemblies of trans-bis(N-methylpyridinium-4-yl)diphenylporphine ions on the surface of calf thymus DNA have been studied using several spectroscopic techniques: absorbance, circular dichroism, and resonance light scattering. The aggregation equilibrium can be treated as a two-state system-monomer and assembly-each bound to the nucleic acid template. The aggregate absorption spectrum in the Soret region is resolved into two bands of Lorentzian line shape, while the DNA-bound monomer spectrum in this region is composed of two Gaussian bands. The Beer-Lambert law is obeyed by both porphyrin forms. The assembly is also characterized by an extremely large, bisignate induced circular dichroism (CD) profile and by enhanced resonance light scattering (RLS). Both the CD and RLS intensities depend linearly on aggregate concentration. The RLS result is consistent with a model for the aggregates as being either of a characteristic size or of a fixed distribution of sizes, independent of total porphyrin concentration or ionic strength. Above threshold values of concentration and ionic strength, the mass action expression for the equilibrium has a particularly simple form: K' = cac-1; where cac is defined as the "critical assembly concentration."offe dependence of the cac upon temperature and ionic strength (NaCl) has been investigated at a fixed DNA concentration. The value of the cac scales as the inverse square of the sodium chloride concentration and, from temperature dependence studies, the aggregation process is shown to be exothermic. PMID:9675203

Porphyrin-based Nanostructure-Dependent Photodynamic and Photothermal Therapies

NASA Astrophysics Data System (ADS)

Jin, Cheng S.

This thesis presents the investigation of nanostructure-dependent phototherapy. We reviewed the liposomal structures for delivery of photosensitizers, and introduced a novel class of phototransducing liposomes called "porphysomes". Porphysomes are self-assembled from high packing density of pyropheophorbide alpha-conjugated phospholipids, resulting in extreme self-quenching of porphyrin fluorescence and comparable optical absorption to gold nanoparticles for high photothermal efficiency. We demonstrated this self-assembly of porphyrin-lipid conjugates converts a singlet oxygen generating mechanism (photodynamic therapy PDT activity) of porphyrin to photothermal mechanism (photothermal therapy PTT activity). The efficacy of porphysome-enhanced PTT was then evaluated on two pre-clinical animal models. We validated porphysome-enabled focal PTT to treat orthotopic prostate cancer using MRI-guided focal laser placement to closely mimic the current clinic procedure. Furthermore, porphysome-enabled fluorescence-guided transbronchial PTT of lung cancer was demonstrated in rabbit orthotopic lung cancer models, which led to the development of an ultra-minimally invasive therapy for early-stage peripheral lung cancer. On the other hand, the nanostructure-mediated conversion of PDT to PTT can be switched back by nanoparticle dissociation. By incorporating folate-conjugated phospholipids into the formulation, porphysomes were internalized into cells rapidly via folate receptor-mediated endocytosis and resulted in efficient disruption of nanostructures, which turned back on the photodynamic activity of densely packed porphyrins, making a closed loop of conversion between PDT and PTT. The multimodal imaging and therapeutic features of porphysome make it ideal for future personalized cancer treatments.

Investigation of Supramolecular Coordination Self-Assembly and Polymerization Confined on Metal Surfaces Using Scanning Tunneling Microscopy

NASA Astrophysics Data System (ADS)

Lin, Tao

Organic molecules are envisioned as the building blocks for design and fabrication of functional devices in future, owing to their versatility, low cost and flexibility. Although some devices such as organic light-emitting diode (OLED) have been already applied in our daily lives, the field is still in its infancy and numerous challenges still remain. In particular, fundamental understanding of the process of organic material fabrication at a molecular level is highly desirable. This thesis focuses on the design and fabrication of supramolecular and macromolecular nanostructures on a Au(111) surface through self-assembly, polymerization and a combination of two. We used scanning tunneling microscopy (STM) as an experimental tool and Monte Carlo (MC) and kinetic Monte Carlo (KMC) simulations as theoretical tools to characterize the structures of these systems and to investigate the mechanisms of the self-assembly and polymerization processes at a single-molecular level. The results of this thesis consist of four parts as below: Part I addresses the mechanisms of two-dimensional multicomponent supramolecular self-assembly via pyridyl-Fe-terpyridyl coordination. Firstly, we studied four types of self-assembled metal-organic systems exhibiting different dimensionalities using specifically-designed molecular building blocks. We found that the two-dimensional system is under thermodynamic controls while the systems of lower dimension are under kinetic controls. Secondly, we studied the self-assembly of a series of cyclic supramolecular polygons. Our results indicate that the yield of on-surface cyclic polygon structures is very low independent of temperature and concentration and this phenomenon can be attributed to a subtle competition between kinetic and thermodynamic controls. These results shed light on thermodynamic and kinetic controls in on-surface coordination self-assembly. Part II addresses the two-dimensional supramolecular self-assembly of porphyrin

Electron Transport through Porphyrin Molecular Junctions

NASA Astrophysics Data System (ADS)

Zhou, Qi

The goal of this work is to study the properties that would affect the electron transport through a porphyrin molecular junction. This work contributes to the field of electron transport in molecular junctions in the following 3 aspects. First of all, by carrying out experiments comparing the conductance of the iron (III) porphyrin (protected) and the free base porphyrin (protected), it is confirmed that the molecular energy level broadening and shifting occurs for porphyrin molecules when coupled with the metal electrodes, and this level broadening and shifting plays an important role in the electron transport through molecular junctions. Secondly, by carrying out an in-situ deprotection of the acetyl-protected free base porphyrin molecules, it is found out that the presence of acetyl groups reduces the conductance. Thirdly, by incorporating the Matrix-assisted laser desorption/ionization (MALDI) spectrum and the in-situ deprotection prior to formation of molecular junctions, it allows a more precise understanding of the molecules involved in the formation of molecular junctions, and therefore allows an accurate analysis of the conductance histogram. The molecules are prepared by self-assembly and the junctions are formed using a Scanning Tunneling Microscopy (STM) molecular break junction technique. The porphyrin molecules are characterized by MALDI in solution before self-assembly to a gold/mica substrate. The self-assembled monolayers (SAMs) of porphyrins on gold are characterized by Ultraviolet-visible (UV-Vis) reflection spectroscopy to confirm that the molecules are attached to the substrate. The SAMs are then characterized by Angle-Resolved X-ray photoelectron spectroscopy (ARXPS) to determine the thickness and the average molecular orientation of the molecular layer. The electron transport is measured by conductance-displacement (G-S) experiments under a given bias (-0.4V). The conductance value of a single molecule is identified by a statistical analysis

Morphology-Controlled Synthesis and Metalation of Porphyrin Nanoparticles with Enhanced Photocatalytic Performance

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Jiefei; Zhong, Yong; Wang, Liang

The design and engineering of the size, shape, and chemistry of photoactive building blocks enables the fabrication of functional nanoparticles for applications in light harvesting, photocatalytic synthesis, water splitting, phototherapy, and photodegradation. Here, we report the synthesis of such nanoparticles through a surfactant-assisted interfacial self-assembly process using optically active porphyrin as a functional building block. The self-assembly process relies on specific interactions such as π–π stacking and metalation (metal atoms and ligand coordination) between individual porphyrin building blocks. Depending on the kinetic conditions and type of surfactants, resulting structures exhibit well-defined one- to three-dimensional morphologies such as nanowires, nanooctahedra, andmore » hierarchically ordered internal architectures. Specifically, electron microscopy and X-ray diffraction results indicate that these nanoparticles exhibit stable single-crystalline and nanoporous frameworks. In conclusion, due to the hierarchical ordering of the porphyrins, the nanoparticles exhibit collective optical properties resulted from coupling of molecular porphyrins and photocatalytic activities such as photodegradation of methyl orange (MO) pollutants and hydrogen production.« less

Morphology-Controlled Synthesis and Metalation of Porphyrin Nanoparticles with Enhanced Photocatalytic Performance

DOE PAGES

Wang, Jiefei; Zhong, Yong; Wang, Liang; ...

2016-09-12

The design and engineering of the size, shape, and chemistry of photoactive building blocks enables the fabrication of functional nanoparticles for applications in light harvesting, photocatalytic synthesis, water splitting, phototherapy, and photodegradation. Here, we report the synthesis of such nanoparticles through a surfactant-assisted interfacial self-assembly process using optically active porphyrin as a functional building block. The self-assembly process relies on specific interactions such as π–π stacking and metalation (metal atoms and ligand coordination) between individual porphyrin building blocks. Depending on the kinetic conditions and type of surfactants, resulting structures exhibit well-defined one- to three-dimensional morphologies such as nanowires, nanooctahedra, andmore » hierarchically ordered internal architectures. Specifically, electron microscopy and X-ray diffraction results indicate that these nanoparticles exhibit stable single-crystalline and nanoporous frameworks. In conclusion, due to the hierarchical ordering of the porphyrins, the nanoparticles exhibit collective optical properties resulted from coupling of molecular porphyrins and photocatalytic activities such as photodegradation of methyl orange (MO) pollutants and hydrogen production.« less

Induced-Dipole-Directed, Cooperative Self-Assembly of a Benzotrithiophene.

PubMed

Ikeda, Toshiaki; Adachi, Hiroaki; Fueno, Hiroyuki; Tanaka, Kazuyoshi; Haino, Takeharu

2017-10-06

A benzotrithiophene derivative possessing phenylisoxazoles self-assembled to form stacks. The molecule isodesmically self-assembled in chloroform, whereas it self-assembled in a cooperative fashion in decalin and in methylcyclohexane. Thermodynamic studies based on isodesmic, van der Schoot, and Goldstein-Stryer mathematical models revealed that the self-assembly processes are enthalpically driven and entropically opposed. An enthalpy-entropy compensation plot indicates that the assembly processes in chloroform, decalin, and methylcyclohexane are closely related. The enthalpic gains in less-polar solvents are greater than those in more-polar solvents, resulting in the formation of large assemblies in decalin and in methylcyclohexane. The formation of large assemblies leads to cooperative assemblies. The elongation process is enthalpically more favored than the nucleation process, which drives the cooperativity of the self-assembly. DFT calculations suggested that a hexameric assembly is more stable than tetrameric or dimeric assemblies. Cooperative self-assemblies based on intermolecular interactions other than hydrogen bonding have rarely been reported. It is demonstrated herein that van der Waals interactions, including induced dipole-dipole interactions, can drive the cooperative assembly of planar π-conjugated molecules.

Effects of Immersion Solvent on Photovoltaic and Photophysical Properties of Porphyrin-Sensitized Solar Cells.

PubMed

Hayashi, Hironobu; Higashino, Tomohiro; Kinjo, Yuriko; Fujimori, Yamato; Kurotobi, Kei; Chabera, Pavel; Sundström, Villy; Isoda, Seiji; Imahori, Hiroshi

2015-08-26

Memory effects in self-assembled monolayers (SAMs) of zinc porphyrin carboxylic acid on TiO2 electrodes have been demonstrated for the first time by evaluating the photovoltaic and electron transfer properties of porphyrin-sensitized solar cells prepared by using different immersion solvents sequentially. The structure of the SAM of the porphyrin on the TiO2 was maintained even after treating the porphyrin monolayer with different neat immersion solvents (memory effect), whereas it was altered by treatment with solutions containing different porphyrins (inverse memory effect). Infrared spectroscopy shows that the porphyrins in the SAM on the TiO2 could be exchanged with the same or analogous porphyrin, leading to a change in the structure of the porphyrin SAM. The memory and inverse memory effects are well correlated with a change in porphyrin geometry, mainly the tilt angle of the porphyrin along the long molecular axis from the surface normal on the TiO2, as well as with kinetics of electron transfer between the porphyrin and TiO2. Such a new structure-function relationship for DSSCs will be very useful for the rational design and optimization of photoelectrochemical and photovoltaic properties of molecular assemblies on semiconductor surfaces.

J-aggregation in porphyrin nanoparticles induced by diphenylalanine

NASA Astrophysics Data System (ADS)

Li, Fengqing; Liu, Dongzhi; Wang, Tianyang; Hu, Jianxin; Meng, Fancui; Sun, Haiya; Shang, Zhi; Li, Pingan; Feng, Wenhui; Li, Wei; Zhou, Xueqin

2017-08-01

In this report, L-diphenylalanine-decorated tetraphenylporphyrin (TPPtFFC) was synthesized and self-assembled into regular nano-architechtures. The morphology of the assemblies varied with the concentration of TPPtFFC. The absorption spectra of the nanoparticles show the Soret band merges with the Q bands and redistributes with great red-shift, indicative of the formation of J-aggregates of the porphyrin molecules. The fluorescence emission of the nanoparticles is merged and red-shifted to near-infrared region. Studies of absorption and fluorescence spectra reveal an indispensible role of diphenylalanine group in the formation of J-aggregates. The Raman spectra disclose that diprotonation of the porphyrin core contributes to delocalized coherent excited states in the nanoparticles. The positive cotton effect in circular dichroism spectra corresponding to the Soret band of TPPtFFC in solution confirms the formation of J-aggregates with right-handed chirality of the dipole moment. This report will shed light on the rational design of porphyrin-peptide conjugates to mimic naturally light-harvesting complexes.

Synthesis and Self-Assembly of the "Tennis Ball" Dimer and Subsequent Encapsulation of Methane. An Advanced Organic Chemistry Laboratory Experiment

NASA Astrophysics Data System (ADS)

Hof, Fraser; Palmer, Liam C.; Rebek, Julius, Jr.

2001-11-01

While important to the biological and materials sciences, noncovalent interactions, self-folding, and self-assembly often receive little discussion in the undergraduate chemistry curriculum. The synthesis and NMR characterization of a molecular "tennis ball" in an advanced undergraduate organic chemistry laboratory is a simple and effective way to introduce the relevance of these concepts. In appropriate solvents, the monomer dimerizes through a seam of eight hydrogen bonds with encapsulation of a guest molecule and symmetry reminiscent of a tennis ball. The entire experiment can be completed in three lab periods, however large-scale synthetic preparation of the starting monomer by a teaching assistant would reduce the laboratory to a single lab period for NMR studies.

His-Tag-Mediated Dimerization of Chemoreceptors Leads to Assembly of Functional Nanoarrays.

PubMed

Haglin, Elizabeth R; Yang, Wen; Briegel, Ariane; Thompson, Lynmarie K

2017-11-07

Transmembrane chemotaxis receptors are found in bacteria in extended hexagonal arrays stabilized by the membrane and by cytosolic binding partners, the kinase CheA and coupling protein CheW. Models of array architecture and assembly propose receptors cluster into trimers of dimers that associate with one CheA dimer and two CheW monomers to form the minimal "core unit" necessary for signal transduction. Reconstructing in vitro chemoreceptor ternary complexes that are homogeneous and functional and exhibit native architecture remains a challenge. Here we report that His-tag-mediated receptor dimerization with divalent metals is sufficient to drive assembly of nativelike functional arrays of a receptor cytoplasmic fragment. Our results indicate receptor dimerization initiates assembly and precedes formation of ternary complexes with partial kinase activity. Restoration of maximal kinase activity coincides with a shift to larger complexes, suggesting that kinase activity depends on interactions beyond the core unit. We hypothesize that achieving maximal activity requires building core units into hexagons and/or coalescing hexagons into the extended lattice. Overall, the minimally perturbing His-tag-mediated dimerization leads to assembly of chemoreceptor arrays with native architecture and thus serves as a powerful tool for studying the assembly and mechanism of this complex and other multiprotein complexes.

Light-triggered self-assembly of triarylamine-based nanospheres

NASA Astrophysics Data System (ADS)

Moulin, Emilie; Niess, Frédéric; Fuks, Gad; Jouault, Nicolas; Buhler, Eric; Giuseppone, Nicolas

2012-10-01

Tailored triarylamine units modified with terpyridine ligands were coordinated to Zn2+ ions and characterized as discrete dimeric entities. Interestingly, when these complexes were subsequently irradiated with simple visible light in chloroform, they readily self-assembled into monodisperse spheres with a mean diameter of 160 nm.Tailored triarylamine units modified with terpyridine ligands were coordinated to Zn2+ ions and characterized as discrete dimeric entities. Interestingly, when these complexes were subsequently irradiated with simple visible light in chloroform, they readily self-assembled into monodisperse spheres with a mean diameter of 160 nm. Electronic supplementary information (ESI) available: Synthetic procedures and products' characterization (2-4 and 6-9). 1H NMR titration of compound 6 by Zn(OTf)2 to form complex 7. Kinetic measurements by UV-Vis-NIR spectroscopy. Transmission electron microscopy imaging for complexes 8 and 9. UV-Vis-NIR for an Fe2+ analogue of complex 7. Dynamic light scattering and time autocorrelation function for self-assembly of complexes 7-9. Copies of 1H and 13C NMR spectra for compounds 2-4 and 6. See DOI: 10.1039/c2nr32168h

Synthesis and self-organization of zinc β-(dialkoxyphosphoryl)porphyrins in the solid state and in solution.

PubMed

Vinogradova, Ekaterina V; Enakieva, Yulia Y; Nefedov, Sergey E; Birin, Kirill P; Tsivadze, Aslan Y; Gorbunova, Yulia G; Bessmertnykh Lemeune, Alla G; Stern, Christine; Guilard, Roger

2012-11-19

The first synthesis and self-organization of zinc β-phosphorylporphyrins in the solid state and in solution are reported. β-Dialkoxyphosphoryl-5,10,15,20-tetraphenylporphyrins and their Zn(II) complexes have been synthesized in good yields by using Pd- and Cu-mediated carbon-phosphorous bond-forming reactions. The Cu-mediated reaction allowed to prepare the mono-β-(dialkoxyphosphoryl)porphyrins 1 Zn-3 Zn starting from the β-bromo-substituted zinc porphyrinate ZnTPPBr (TPP = tetraphenylporphyrin) and dialkyl phosphites HP(O)(OR)(2) (R = Et, iPr, nBu). The derivatives 1 Zn-3 Zn were obtained in good yields by using one to three equivalents of CuI. When the reaction was carried out in the presence of catalytic amounts of palladium complexes in toluene, the desired zinc derivative 1 Zn was obtained in up to 72% yield. The use of a Pd-catalyzed C-P bond-forming reaction was further extended to the synthesis of β-poly(dialkoxyphosphoryl)porphyrins. An unprecedented one-pot sequence involving consecutive reduction and phosphorylation of H(2)TPPBr(4) led to the formation of a mixture of the 2,12- and 2,13-bis(dialkoxy)phosphorylporphyrins 5 H(2) and 6 H(2) in 81% total yield. According to the X-ray diffraction studies, 1 Zn and 3 Zn are partially overlapped cofacial dimers formed through the coordination of two Zn centers by two phosphoryl groups belonging to the adjacent molecules. The equilibrium between the monomeric and the dimeric species exists in solutions of 1 Zn and 3 Zn in weakly polar solvents according to spectroscopic data (UV/Vis absorption and NMR spectroscopy). The ratio of each form is dependent on the concentration, temperature, and traces of water or methanol. These features demonstrated that zinc β-phosphorylporphyrins can be regarded as new model compounds for the weakly coupled chlorophyll pair in the photosynthesis process. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Porphyrin-induced photogeneration of hydrogen peroxide determined using the luminol chemiluminescence method in aqueous solution: A structure-activity relationship study related to the aggregation of porphyrin.

PubMed

Komagoe, Keiko; Katsu, Takashi

2006-02-01

A luminol chemiluminescence method was used to evaluate the porphyrin-induced photogeneration of hydrogen peroxide (H2O2). This method enabled us to detect H202 in the presence of a high concentration of porphyrin, which was not possible using conventional colorimetry. The limit of detection was about 1 microM. We compared the ability to generate H2O2, using uroporphyrin (UP), hexacarboxylporphyrin (HCP), coproporphyrin (CP), hematoporphyrin (HP), mesoporphyrin (MP), and protoporphyrin (PP). The amount of H2O2 photoproduced was strongly related to the state of the porphyrin in the aqueous solution. UP and HCP, which existed predominantly in a monomeric form, had a good ability to produce H2O2. HP and MP, existing as dimers, showed weak activity. CP, forming a mixture of monomer and dimer, had a moderate ability to produce H2O2. PP, which was highly aggregated, had a good ability. These results demonstrated that the efficiency of porphyrins to produce H2O2 was strongly dependent on their aggregated form, and the dimer suppressed the production of H2O2.

Hierarchical and Helical Self-assembly of ADP-ribosyl Cyclase into Large-scale Protein Microtubes

PubMed Central

Liu, Qun; Kriksunov, Irina A.; Wang, Zhongwu; Graeff, Richard; Lee, Hon Cheung; Hao, Quan

2013-01-01

Proteins are macromolecules with characteristic structures and biological functions. It is extremely challenging to obtain protein microtube structures through self-assembly as proteins are very complex and flexible. Here we present a strategy showing how a specific protein, ADP-ribosyl cyclase, helically self-assembles from monomers into hexagonal nanochains and further to highly ordered crystalline microtubes. The structures of protein nanochains and consequently self-assembled superlattice were determined by X-ray crystallography at 4.5 Å resolution and imaged by Scanning Electron Microscopy. The protein initially forms into dimers that have a fixed size of 5.6 nm, and then, helically self-assembles into 35.6 nm long hexagonal nanochains. One such nanochain consists of six dimers (12 monomers) that stack in order by a pseudo P61 screw axis. Seven nanochains produce a series of largescale assemblies, nanorods, forming the building blocks for microrods. A proposed aging process of microrods results in the formation of hollow microstructures. Synthesis and characterization of large scale self-assembled protein microtubes may pave a new pathway, capable of not only understanding the self-assembly dynamics of biological materials, but also directing design and fabrication of multifunctional nanobuilding blocks with particular applications in biomedical engineering. PMID:18956900

Optoelectronics of organic nanofibers formed by co-assembly of porphyrin and perylenediimide.

PubMed

Li, Yuangang; Wang, Weina; Leow, Wan Ru; Zhu, Bowen; Meng, Fanben; Zheng, Liyan; Zhu, Jia; Chen, Xiaodong

2014-07-23

Organic nanofibers are formed by simple ionic co-assembly of positively charged porphyrin (electron donor) and negatively charged perylenediimide (electron acceptor) derivatives in aqueous solution. Two kinds of electron transfer routes between electron donor and electron acceptor under light excitation in nanofibers are confirmed by DFT calculations and experimental data. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Sequence-selective encapsulation and protection of long peptides by a self-assembled FeII8L6 cubic cage

NASA Astrophysics Data System (ADS)

Mosquera, Jesús; Szyszko, Bartosz; Ho, Sarah K. Y.; Nitschke, Jonathan R.

2017-03-01

Self-assembly offers a general strategy for the preparation of large, hollow high-symmetry structures. Although biological capsules, such as virus capsids, are capable of selectively recognizing complex cargoes, synthetic encapsulants have lacked the capability to specifically bind large and complex biomolecules. Here we describe a cubic host obtained from the self-assembly of FeII and a zinc-porphyrin-containing ligand. This cubic cage is flexible and compatible with aqueous media. Its selectivity of encapsulation is driven by the coordination of guest functional groups to the zinc porphyrins. This new host thus specifically encapsulates guests incorporating imidazole and thiazole moieties, including drugs and peptides. Once encapsulated, the reactivity of a peptide is dramatically altered: encapsulated peptides are protected from trypsin hydrolysis, whereas physicochemically similar peptides that do not bind are cleaved.

Supramolecular complex of a fused zinc phthalocyanine-zinc porphyrin dyad assembled by two imidazole-C60 units: ultrafast photoevents.

PubMed

Follana-Berná, Jorge; Seetharaman, Sairaman; Martín-Gomis, Luis; Charalambidis, Georgios; Trapali, Adelais; Karr, Paul A; Coutsolelos, Athanassios G; Fernández-Lázaro, Fernando; D'Souza, Francis; Sastre-Santos, Ángela

2018-03-14

A new zinc phthalocyanine-zinc porphyrin dyad (ZnPc-ZnP) fused through a pyrazine ring has been synthesized as a receptor for imidazole-substituted C 60 (C 60 Im) electron acceptor. Self-assembly via metal-ligand axial coordination and the pertinent association constants in solution were determined by 1 H-NMR, UV-Vis and fluorescence titration experiments at room temperature. The designed host was able to bind up to two C 60 Im electron acceptor guest molecules to yield C 60 Im:ZnPc-ZnP:ImC 60 donor-acceptor supramolecular complex. The spectral data showed that the two binding sites behave independently with binding constants similar in magnitude. Steady-state fluorescence studies were indicative of an efficient singlet-singlet energy transfer from zinc porphyrin to zinc phthalocyanine within the fused dyad. Accordingly, the transient absorption studies covering a wide timescale of femto-to-milli seconds revealed ultrafast energy transfer from 1 ZnP* to ZnPc (k EnT ∼ 10 12 s -1 ) in the fused dyad. Further, a photo induced electron transfer was observed in the supramolecularly assembled C 60 Im:ZnPc-ZnP:ImC 60 donor-acceptor complex leading to charge separated states, which persisted for about 200 ns.

A competent catalytic active site is necessary for substrate induced dimer assembly in triosephosphate isomerase.

PubMed

Jimenez-Sandoval, Pedro; Vique-Sanchez, Jose Luis; Hidalgo, Marisol López; Velazquez-Juarez, Gilberto; Diaz-Quezada, Corina; Arroyo-Navarro, Luis Fernando; Moran, Gabriela Montero; Fattori, Juliana; Jessica Diaz-Salazar, A; Rudiño-Pinera, Enrique; Sotelo-Mundo, Rogerio; Figueira, Ana Carolina Migliorini; Lara-Gonzalez, Samuel; Benítez-Cardoza, Claudia G; Brieba, Luis G

2017-11-01

The protozoan parasite Trichomonas vaginalis contains two nearly identical triosephosphate isomerases (TvTIMs) that dissociate into stable monomers and dimerize upon substrate binding. Herein, we compare the role of the "ball and socket" and loop 3 interactions in substrate assisted dimer assembly in both TvTIMs. We found that point mutants at the "ball" are only 39 and 29-fold less catalytically active than their corresponding wild-type counterparts, whereas Δloop 3 deletions are 1502 and 9400-fold less active. Point and deletion mutants dissociate into stable monomers. However, point mutants assemble as catalytic competent dimers upon binding of the transition state substrate analog PGH, whereas loop 3 deletions remain monomeric. A comparison between crystal structures of point and loop 3 deletion monomeric mutants illustrates that the catalytic residues in point mutants and wild-type TvTIMs are maintained in the same orientation, whereas the catalytic residues in deletion mutants show an increase in thermal mobility and present structural disorder that may hamper their catalytic role. The high enzymatic activity present in monomeric point mutants correlates with the formation of dimeric TvTIMs upon substrate binding. In contrast, the low activity and lack of dimer assembly in deletion mutants suggests a role of loop 3 in promoting the formation of the active site as well as dimer assembly. Our results suggest that in TvTIMs the active site is assembled during dimerization and that the integrity of loop 3 and ball and socket residues is crucial to stabilize the dimer. Copyright © 2017 Elsevier B.V. All rights reserved.

Cysteine-rich Domain 1 of CD40 Mediates Receptor Self-assembly*

PubMed Central

Smulski, Cristian R.; Beyrath, Julien; Decossas, Marion; Chekkat, Neila; Wolff, Philippe; Estieu-Gionnet, Karine; Guichard, Gilles; Speiser, Daniel; Schneider, Pascal; Fournel, Sylvie

2013-01-01

The activation of CD40 on B cells, macrophages, and dendritic cells by its ligand CD154 (CD40L) is essential for the development of humoral and cellular immune responses. CD40L and other TNF superfamily ligands are noncovalent homotrimers, but the form under which CD40 exists in the absence of ligand remains to be elucidated. Here, we show that both cell surface-expressed and soluble CD40 self-assemble, most probably as noncovalent dimers. The cysteine-rich domain 1 (CRD1) of CD40 participated to dimerization and was also required for efficient receptor expression. Modelization of a CD40 dimer allowed the identification of lysine 29 in CRD1, whose mutation decreased CD40 self-interaction without affecting expression or response to ligand. When expressed alone, recombinant CD40-CRD1 bound CD40 with a KD of 0.6 μm. This molecule triggered expression of maturation markers on human dendritic cells and potentiated CD40L activity. These results suggest that CD40 self-assembly modulates signaling, possibly by maintaining the receptor in a quiescent state. PMID:23463508

Clay induced aggregation of a tetra-cationic metalloporphyrin in Layer by Layer self assembled film

NASA Astrophysics Data System (ADS)

Banik, Soma; Bhattacharjee, J.; Hussain, S. A.; Bhattacharjee, D.

2015-12-01

Porphyrins have a general tendency to form aggregates in ultrathin films. Also electrostatic adsorption of cationic porphyrins onto anionic nano clay platelets results in the flattening of porphyrin moieties. The flattening is evidenced by the red-shifting of Soret band with respect to the aqueous solution. In the present communication, we have studied the clay induced aggregation behaviour of a tetra-cationic metalloporphyrin Manganese (III) 5, 10, 15, 20-tetra (4 pyridyl)-21 H, 23 H-porphine chloride tetrakis (methochloride) (MnTMPyP) in Layer-by-Layer (LbL) self assembled film. The adsorption of dye molecules onto nano clay platelets resulted in the flattening of the meso substituent groups of the dye chromophore. In Layer-by-Layer ultrathin film, the flattened porphyrin molecules tagged nano clay platelets were further associated to form porphyrin aggregates. This has been clearly demonstrated from the UV-vis absorption spectroscopic studies. Atomic Force Microscopic (AFM) studies gave visual evidence of the association of organo-clay hybrid molecules in the LbL film.

Tailorable Exciton Transport in Doped Peptide-Amphiphile Assemblies.

PubMed

Solomon, Lee A; Sykes, Matthew E; Wu, Yimin A; Schaller, Richard D; Wiederrecht, Gary P; Fry, H Christopher

2017-09-26

Light-harvesting biomaterials are an attractive target in photovoltaics, photocatalysis, and artificial photosynthesis. Through peptide self-assembly, complex nanostructures can be engineered to study the role of chromophore organization during light absorption and energy transport. To this end, we demonstrate the one-dimensional transport of excitons along naturally occurring, light-harvesting, Zn-protoporphyrin IX chromophores within self-assembled peptide-amphiphile nanofibers. The internal structure of the nanofibers induces packing of the porphyrins into linear chains. We find that this peptide assembly can enable long-range exciton diffusion, yet it also induces the formation of excimers between adjacent molecules, which serve as exciton traps. Electronic coupling between neighboring porphyrin molecules is confirmed by various spectroscopic methods. The exciton diffusion process is then probed through transient photoluminescence and absorption measurements and fit to a model for one-dimensional hopping. Because excimer formation impedes exciton hopping, increasing the interchromophore spacing allows for improved diffusivity, which we control through porphyrin doping levels. We show that diffusion lengths of over 60 nm are possible at low porphyrin doping, representing an order of magnitude improvement over the highest doping fractions.

Stabilization of higher-valent states of iron porphyrin by hydroxide and methoxide ligands: electrochemical generation of iron(IV)-oxo porphyrins.

PubMed Central

Lee, W A; Calderwood, T S; Bruice, T C

1985-01-01

An electrochemical study of hydroxide- and methoxide-ligated iron(III) tetraphenylporphyrins possessing ortho-phenyl substituents that block mu-oxo dimer formation has been carried out. Ligation by these strongly basic oxyanions promotes the formation of iron(IV)-oxo porphyrins upon one-electron oxidation. Further one-electron oxidation of the latter provides the iron(IV)-oxo porphyrin pi-cation radical. These results are discussed in terms of chemical model studies and the enzymatic intermediate compounds I and II of the peroxidases. PMID:3859865

Electrochemical, spectral, and computational studies of metalloporphyrin dimers formed by cation complexation of crown ether cavities.

PubMed

Chitta, Raghu; Rogers, Lisa M; Wanklyn, Amber; Karr, Paul A; Kahol, Pawan K; Zandler, Melvin E; D'Souza, Francis

2004-11-01

The effect on the electrochemical oxidation and reduction potentials of 5,10,15,20-tetrakis(benzo-15-crown-5)porphyrin (TCP) and its metal derivatives (MTCP; M = Mg(II), VO(IV), Co(II), Ni(II), Cu(II), Zn(II), Pd(II), Ag(II)) upon potassium ion induced dimerization of the porphyrins was systematically performed in benzonitrile containing 0.1 M (TBA)ClO(4) by differential pulse voltammetry technique. The HOMO--LUMO energy level diagram constructed from the electrochemical data revealed destabilization of the HOMO level and stabilization of the LUMO level upon dimer formation while such a perturbation was larger for the HOMO level than the LUMO level. The geometry and electronic structure of a representative ZnTCP and its dimer, K(4)(ZnTCP)(2), were evaluated by the ab initio B3LYP method utilizing a mixed basis set of 3-21G(*) for Zn, K, O, and N and STO-3G for C and H. The inter-porphyrin ring distance of the dimer calculated from the optimized geometry agreed with the spectroscopically determined one, and the calculated HOMO and LUMO frontier orbitals revealed delocalization on both of the porphyrins rings. The metal-metal distances calculated from the triplet ESR spectra of the K(+) induced porphyrin dimers bearing paramagnetic metal ions in the cavity followed the trend Cu--Cu < VO--VO < Ag--Ag. However, the spectral shifts resulting from the exciton coupling of the interacting porphyrin pi-systems revealed no specific trend with respect to the metal ion in the porphyrin cavity. Additionally, linear trends in the electrochemically measured HOMO--LUMO gap and the energy corresponding to the most intense visible band of both MTCP and K(4)(MTCP)(2) were observed. A reduced HOMO--LUMO gap predicted for the dimer by B3LYP/(3-21G(), STO-3G) calculations was confirmed by the results of optical absorption and electrochemical studies.

Competitive Energy and Electron Transfer in β-Functionalized Free-Base Porphyrin-Zinc Porphyrin Dimer Axially Coordinated to C60 : Synthesis, Supramolecular Formation and Excited-State Processes.

PubMed

Hu, Yi; Thomas, Michael B; Jinadasa, R G Waruna; Wang, Hong; D'Souza, Francis

2017-09-18

Simultaneous occurrence of energy and electron transfer events involving different acceptor sites in a newly assembled supramolecular triad comprised of covalently linked free-base porphyrin-zinc porphyrin dyad, H 2 P-ZnP axially coordinated to electron acceptor fullerene, has been successfully demonstrated. The dyad was connected through the β-pyrrole positions of the porphyrin macrocycle instead of the traditionally used meso-positions for better electronic communication. Interestingly, the β-pyrrole functionalization modulated the optical properties to such an extent that it was possible to almost exclusively excite the zinc porphyrin entity in the supramolecular triad. The measured binding constant for the complex with 1:1 molecular stoichiometry was in the order of 10 4  m -1 revealing moderately stable complex formation. An energy level diagram constructed using optical, electrochemical and computational results suggested that both the anticipated energy and electron events are thermodynamically feasible in the triad. Consequently, it was possible to demonstrate occurrence of excited state energy transfer to the covalently linked H 2 P, and electron transfer to the coordinated ImC 60 from studies involving steady-state and time-resolved emission, and femto- and nanosecond transient absorption studies. The estimated energy transfer was around 67 % in the dyad with a rate constant of 1.1×10 9  s -1 . In the supramolecular triad, the charge separated state was rather long-lived although it was difficult to arrive the exact lifetime of charge separated state from nanosecond transient spectral studies due to overlap of strong triplet excited signals of porphyrin in the monitoring wavelength window. Nevertheless, simultaneous occurrence of energy and electron transfer in the appropriately positioned energy and electron acceptor entities in a supramolecular triad was possible to demonstrate in the present study, a step forward to unraveling the complex

Self-organization of porphyrin units induced by magnetic field during sol-gel polymerization.

PubMed

Lerouge, Frédéric; Cerveau, Geneviève; Corriu, Robert J P; Stern, Christine; Guilard, Roger

2007-04-21

The use of a magnetic field as a controlling factor during the hydrolysis-polycondensation of porphyrin precursors substituted by Si(OR)(3) groups, induces a self-organization of porphyrin moieties due to the stacking of these units in the hybrid material and this study also confirms the effect of the magnetic field in the nano- and micrometric organization during the kinetically controlled polycondensation process.

Self-assembled chromophores within mesoporous nanocrystalline TiO2: towards biomimetic solar cells.

PubMed

Marek, Peter L; Sieger, Hermann; Scherer, Torsten; Hahn, Horst; Balaban, Teodor Silviu

2009-06-01

Artificial light-harvesting antennas consisting of self-assembled chromophores that mimic the natural pigments of photosynthetic bacteria have been inserted into voids induced in porous titania (TiO2, anatase) in order to investigate their suitability for hybrid solar cells. Mesoporous nanocrystalline TiO2 with additional uniform macropores was treated with precursor solutions of the pigment which was then induced to self-assemble within the voids. The chromophores were tailored to combine the self-assembly characteristics of the natural bacteriochlorophylls with the robustness of artificial Zn-porphyrins being stable for prolonged periods even upon heating to over 200 degrees C. They assemble on the TiO2 surface to form nano- to micro-crystalline structures with lengths from tens of nm up to several microm and show a photosensitization effect which is supposed to be dependent on the assembly size. The natural examples of these antennas are found in green sulfur bacteria which are able to use photosynthesis in deep water regions with minute light intensities. The implementation of biomimetic antennas for light harvesting and a better photon management may lead to a rise in efficiency of dye-sensitized solar cells also under low light illumination conditions.

Highly fluorescent peptide nanoribbon impregnated with Sn-porphyrin as a potent DNA sensor.

PubMed

Parayil, Sreenivasan Koliyat; Lee, Jooran; Yoon, Minjoong

2013-05-01

Highly fluorescent and thermo-stable peptide nanoribbons (PNRs) were fabricated by solvothermal self-assembly of a single peptide (D,D-diphenyl alanine peptides) with Sn-porphyrin (trans-dihydroxo[5,10,15,20-tetrakis(p-tolyl)porphyrinato] Sn(IV) (SnTTP(OH)2)). The structural characterization of the as-prepared nanoribbons was performed by transmitting electron microscopy (TEM), scanning electron microscopy (SEM) and atomic force microscopy (AFM), FT-IR and Raman spectroscopy, indicating that the lipophilic Sn-porphyrins are impregnated into the porous surface formed in the process of nanoribbon formation through intermolecular hydrogen bonding of the peptide main chains. Consequently the Sn-porphyrin-impregnated peptide nanoribbons (Sn-porphyrin-PNRs) exhibited typical UV-visible absorption spectrum of the monomer porphyrin with a red shifted Q-band, and their fluorescence quantum yield was observed to be enhanced compared to that of free Sn-porphyrin. Interestingly the fluorescence intensity and lifetimes of Sn-porphyrin-PNRs were selectively affected upon interaction with nucleotide base sequences of DNA while those of free Sn-porphyrins were not affected by binding with any of the DNA studied, indicating that DNA-induced changes in the fluorescence properties of Sn-porphyrin-PNRs are due to interaction between DNA and the PNR scaffold. These results imply that Sn-porphyrin-PNR will be useful as a potent fluorescent protein analogue and as a biocompatible DNA sensor.

One-Dimensional Multichromophor Arrays Based on DNA: From Self-Assembly to Light-Harvesting.

PubMed

Ensslen, Philipp; Wagenknecht, Hans-Achim

2015-10-20

Light-harvesting complexes collect light energy and deliver it by a cascade of energy and electron transfer processes to the reaction center where charge separation leads to storage as chemical energy. The design of artificial light-harvesting assemblies faces enormous challenges because several antenna chromophores need to be kept in close proximity but self-quenching needs to be avoided. Double stranded DNA as a supramolecular scaffold plays a promising role due to its characteristic structural properties. Automated DNA synthesis allows incorporation of artificial chromophore-modified building blocks, and sequence design allows precise control of the distances and orientations between the chromophores. The helical twist between the chromophores, which is induced by the DNA framework, controls energy and electron transfer and thereby reduces the self-quenching that is typically observed in chromophore aggregates. This Account summarizes covalently multichromophore-modified DNA and describes how such multichromophore arrays were achieved by Watson-Crick-specific and DNA-templated self-assembly. The covalent DNA systems were prepared by incorporation of chromophores as DNA base substitutions (either as C-nucleosides or with acyclic linkers as substitutes for the 2'-deoxyribofuranoside) and as DNA base modifications. Studies with DNA base substitutions revealed that distances but more importantly relative orientations of the chromophores govern the energy transfer efficiencies and thereby the light-harvesting properties. With DNA base substitutions, duplex stabilization was faced and could be overcome, for instance, by zipper-like placement of the chromophores in both strands. For both principal structural approaches, DNA-based light-harvesting antenna could be realized. The major disadvantages, however, for covalent multichromophore DNA conjugates are the poor yields of synthesis and the solubility issues for oligonucleotides with more than 5-10 chromophore

Discrete and polymeric self-assembled dendrimers: Hydrogen bond-mediated assembly with high stability and high fidelity

PubMed Central

Corbin, Perry S.; Lawless, Laurence J.; Li, Zhanting; Ma, Yuguo; Witmer, Melissa J.; Zimmerman, Steven C.

2002-01-01

Hydrogen bond-mediated self-assembly is a powerful strategy for creating nanoscale structures. However, little is known about the fidelity of assembly processes that must occur when similar and potentially competing hydrogen-bonding motifs are present. Furthermore, there is a continuing need for new modules and strategies that can amplify the relatively weak strength of a hydrogen bond to give more stable assemblies. Herein we report quantitative complexation studies on a ureidodeazapterin-based module revealing an unprecedented stability for dimers of its self-complementary acceptoracceptor-donor-donor (AADD) array. Linking two such units together with a semirigid spacer that carries a first-, second-, or third-generation Fréchet-type dendron affords a ditopic structure programmed to self assemble. The specific structure that is formed depends both on the size of the dendron and the solvent, but all of the assemblies have exceptionally high stability. The largest discrete nanoscale assembly is a hexamer with a molecular mass of about 17.8 kDa. It is stabilized by 30 hydrogen bonds, including six AADD⋅DDAA contacts. The hexamer forms and is indefinitely stable in the presence of a hexamer containing six ADD⋅DAA hydrogen-bonding arrays. PMID:11917113

Structure and dynamics of optically directed self-assembly of nanoparticles

PubMed Central

Roy, Debjit; Mondal, Dipankar; Goswami, Debabrata

2016-01-01

Self-assembly of nanoparticles leading to the formation of colloidal clusters often serves as the representative analogue for understanding molecular assembly. Unravelling the in situ structure and dynamics of such clusters in liquid suspensions is highly challenging. Presently colloidal clusters are first isolated from their generating environment and then their structures are probed by light scattering methods. In order to measure the in situ structure and dynamics of colloidal clusters, we have generated them using the high-repetition-rate femtosecond laser pulse optical tweezer. Since the constituent of our dimer, trimer or tetramer clusters are 250 nm radius two-photon resonant fluorophore coated nanospheres under the optical trap, they inherently produce Two-Photon Fluorescence, which undergo intra-nanosphere Fluorescence Energy Transfer. This unique energy transfer signature, in turn, enables us to visualize structures and orientations of these colloidal clusters during the process of their formation and subsequent dynamics in a liquid suspension. We also show that due to shape-birefringence, orientation and structural control of these colloidal clusters are possible as the polarization of the trapping laser is changed from linear to circular. We thus report important progress in sampling the smallest possible aggregates of nanoparticles, dimers, trimers or tetramers, formed early in the self-assembly process. PMID:27006305

Construction of energy transfer pathways self-assembled from DNA-templated stacks of anthracene.

PubMed

Iwaura, Rika; Yui, Hiroharu; Someya, Yuu; Ohnishi-Kameyama, Mayumi

2014-01-05

We describe optical properties of anthracene stacks formed from single-component self-assembly of thymidylic acid-appended anthracene 2,6-bis[5-(3'-thymidylic acid)pentyloxy] anthracene (TACT) and the binary self-assembly of TACT and complementary 20-meric oligoadenylic acid (TACT/dA20) in an aqueous buffer. UV-Vis and emission spectra for the single-component self-assembly of TACT and the binary self-assembly of TACT/dA20 were very consistent with stacked acene moieties in both self-assemblies. Interestingly, time-resolved fluorescence spectra from anthracene stacks exhibited very different features of the single-component and binary self-assemblies. In the single-component self-assembly of TACT, a dynamic Stokes shift (DSS) and relatively short fluorescence lifetime (τ=0.35ns) observed at around 450nm suggested that the anthracene moieties were flexible. Moreover, a broad emission at 530nm suggested the formation of an excited dimer (excimer). In the binary self-assembly of TACT/dA20, we detected a broad, red-shifted emission component at 534nm with a lifetime (τ=0.4ns) shorter than that observed in the TACT single-component self-assembly. Combining these results with the emission spectrum of the binary self-assembly of TACT/5'-HEX dA20, we concluded that the energy transfer pathway was constructed by columnar anthracene stacks formed from the DNA-templated self-assembly of TACT. Copyright © 2013 Elsevier B.V. All rights reserved.

Structural Polymorphism in a Self-Assembled Tri-Aromatic Peptide System.

PubMed

Brown, Noam; Lei, Jiangtao; Zhan, Chendi; Shimon, Linda J W; Adler-Abramovich, Lihi; Wei, Guanghong; Gazit, Ehud

2018-04-24

Self-assembly is a process of key importance in natural systems and in nanotechnology. Peptides are attractive building blocks due to their relative facile synthesis, biocompatibility, and other unique properties. Diphenylalanine (FF) and its derivatives are known to form nanostructures of various architectures and interesting and varied characteristics. The larger triphenylalanine peptide (FFF) was found to self-assemble as efficiently as FF, forming related but distinct architectures of plate-like and spherical nanostructures. Here, to understand the effect of triaromatic systems on the self-assembly process, we examined carboxybenzyl-protected diphenylalanine (z-FF) as a minimal model for such an arrangement. We explored different self-assembly conditions by changing solvent compositions and peptide concentrations, generating a phase diagram for the assemblies. We discovered that z-FF can form a variety of structures, including nanowires, fibers, nanospheres, and nanotoroids, the latter were previously observed only in considerably larger or co-assembly systems. Secondary structure analysis revealed that all assemblies possessed a β-sheet conformation. Additionally, in solvent combinations with high water ratios, z-FF formed rigid and self-healing hydrogels. X-ray crystallography revealed a "wishbone" structure, in which z-FF dimers are linked by hydrogen bonds mediated by methanol molecules, with a 2-fold screw symmetry along the c-axis. All-atom molecular dynamics (MD) simulations revealed conformations similar to the crystal structure. Coarse-grained MD simulated the assembly of the peptide into either fibers or spheres in different solvent systems, consistent with the experimental results. This work thus expands the building block library for the fabrication of nanostructures by peptide self-assembly.

Cobalt(IV) corroles as catalysts for the electroreduction of O2: reactions of heterobimetallic dyads containing a face-to-face linked Fe(III) or Mn(III) porphyrin.

PubMed

Kadish, Karl M; Frémond, Laurent; Burdet, Fabien; Barbe, Jean-Michel; Gros, Claude P; Guilard, Roger

2006-04-01

A series of heterobinuclear cofacial porphyrin-corrole dyads containing a Co(IV) corrole linked by one of four different spacers in a face-to-face arrangement with an Fe(III) or Mn(III) porphyrin have been examined as catalysts for the electroreduction of O(2) to H(2)O and/or H(2)O(2) when adsorbed on the surface of a graphite electrode in air-saturated aqueous solutions containing 1M HClO(4). The examined compounds are represented as (PCY)M(III)ClCo(IV)Cl where P is a porphyrin dianion, C is a corrole trianion and Y is a biphenylene (B), 9,9-dimethylxanthene (X), dibenzofuran (O) or anthracene (A) spacer. The catalytic behavior of the seven investigated dyads in the two heterobimetallic (PCY)MClCoCl series of catalysts is compared on one hand to what was previously reported for related dyads with a single Co(III) corrole macrocycle linked to a free-base porphyrin with the same set of linking bridges, (PCY)H(2)Co, and on the other hand to dicobalt porphyrin-corrole dyads of the form (PCY)Co(2) which were shown to efficiently electrocatalyze the four electron reduction of O(2) at a graphite electrode in acid media. Comparisons between the four series of porphyrin-corrole dyads, (PCY)Co(2), (PCY)H(2)Co, (PCY)FeClCoCl and (PCY)MnClCoCl, show that in all cases the biscobalt dyads catalyze O(2) electroreduction at potentials more positive by an average 110mV as compared to the related series of compounds containing a Co(III) or Co(IV) corrole macrocycle linked to a free-base metalloporphyrin or a metalloporphyrin with an Fe(III) or Mn(III) central metal ion. The data indicates that the E(1/2) values where electrocatalysis is initiated is related to the initial site of electron transfer, which is the Co(III)/Co(II) porphyrin reduction process in the case of (PCY)Co(2) and the Co(IV)/Co(III) corrole reduction in the case of (PCY)MnClCoCl, (PCY)FeClCoCl and (PCY)H(2)Co. The overall data also suggests that the catalytically active form of the biscobalt dyad in (PCY)Co(2

Identification of Factors Promoting HBV Capsid Self-Assembly by Assembly-Promoting Antivirals.

PubMed

Rath, Soumya Lipsa; Liu, Huihui; Okazaki, Susumu; Shinoda, Wataru

2018-02-26

Around 270 million individuals currently live with hepatitis B virus (HBV) infection. Heteroaryldihydropyrimidines (HAPs) are a family of antivirals that target the HBV capsid protein and induce aberrant self-assembly. The capsids formed resemble the native capsid structure but are unable to propagate the virus progeny because of a lack of RNA/DNA. Under normal conditions, self-assembly is initiated by the viral genome. The mode of action of HAPs, however, remains largely unknown. In this work, using molecular dynamics simulations, we attempted to understand the action of HAP by comparing the dynamics of capsid proteins with and without HAPs. We found that the inhibitor is more stable in higher oligomers. It retains its stability in the hexamer throughout 1 μs of simulation. Our results also show that the inhibitor might help in stabilizing the C-terminus, the HBc 149-183 arginine-rich domain of the capsid protein. The C-termini of dimers interact with each other, assisted by the HAP inhibitor. During capsid assembly, the termini are supposed to directly interact with the viral genome, thereby suggesting that the viral genome might work in a similar way to stabilize the capsid protein. Our results may help in understanding the underlying molecular mechanism of HBV capsid self-assembly, which should be crucial for exploring new drug targets and structure-based drug design.

Resolving the Magnetic Asymmetry of the Inner Space in Self-assembled Dimeric Capsules Based on Tetraurea-calix[4]pyrrole Components.

PubMed

Espelt, Mónica; Aragay, Gemma; Ballester, Pablo

2015-01-01

The encapsulation of N,N, N',N'-tetramethyl-1,5-pentanediamine-N,N'-dioxide 2 in a non-chiral capsular assembly formed by dimerization of tetraurea-calix[4]pyrrole 1a produced the observation of the N-methyl groups of the encapsulated guest as two separated singlets resonating highly upfield in the (1)H NMR spectrum. In order to clarify the origin of the observed signal splitting we assembled and studied a series of structurally related dimeric capsules. We used the tetraurea-calix[4]pyrrole 1a , the enantiomerically pure tetraurea-calix[4] pyrrole R-1b and the tetraurea-bisloop calix[4]pyrrole 1c as components of the produced assemblies. The (1)H NMR spectra of the assembled encapsulation complexes with bis-N-oxide 2 evidenced diverse splitting patterns of the N-methyl groups. In addition, 2D EXSY/ROESY NMR experiments revealed the existence of chemical exchange processes involving the separated methyl signals of the encapsulated guest. The capsular assemblies were mainly stabilized by a belt of eight head-to-tail hydrogen-bonded urea groups. The interconversion between the two senses of rotation of the unidirectionally oriented urea groups was slow on the (1)H NMR timescale. These characteristics determined the appearance of a new asymmetry element (supramolecular conformational chirality) in the assemblies that accounted for some of the magnetic asymmetries featured by the capsule's inner space. The racemization of the supramolecular chirality element was fast on the EXSY timescale and produced the chemical exchange processes detected for the encapsulation complexes.

Highly planar diarylamine-fused porphyrins and their remarkably stable radical cations† †Electronic supplementary information (ESI) available. CCDC 1469154–1469160. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c6sc02721k Click here for additional data file. Click here for additional data file.

PubMed Central

Fukui, Norihito; Cha, Wonhee; Shimizu, Daiki; Oh, Juwon

2017-01-01

Oxidative fusion reactions of meso-phenoxazino Ni(ii) porphyrin were found to be temperature dependent, giving rise to either a doubly phenylene-fused product at room temperature or a singly phenoxazine-fused product at 70 °C. The latter was further oxidized to a doubly phenoxazine-fused Ni(ii) porphyrin, which was subsequently converted to the corresponding free base porphyrin and Zn(ii) porphyrin. Compared to previously reported diphenylamine-fused porphyrins that displayed a molecular twist, doubly phenoxazine-fused porphyrins exhibited distinctly different properties owing to their highly planar structures, such as larger fluorescence quantum yields, formation of an offset face-to-face dimer both in solution and the solid state, and the generation of a mixed-valence π-radical cation dimer upon electrochemical oxidation. One-electron oxidation of the phenoxazine-fused Ni(ii) porphyrin with Magic Blue gave the corresponding radical cation, which was certainly stable and could be isolated by separation over a silica gel column but slowly chlorinated at the reactive β-positions in the solid state. This finding led to us to examine β,β′-dichlorinated phenoxazine-fused and diphenylamine-fused Ni(ii) porphyrins, which, upon treatment with Magic Blue, provided remarkably stable radical cations to an unprecedented level. It is actually possible to purify these radical cations by silica gel chromatography, and they can be stored for over 6 months without any sign of deterioration. Moreover, they exhibited no degradation even after the CH2Cl2 solution was washed with water. However, subtle structural differences (planar versus partly twisted) led to different crystal packing structures and solid-state magnetic properties. PMID:28451165

Self-assembly micro optical filter

NASA Astrophysics Data System (ADS)

Zhang, Ping (Cerina); Le, Kevin; Malalur-Nagaraja-Rao, Smitha; Hsu, Lun-Chen; Chiao, J.-C.

2006-01-01

Optical communication and sensor industry face critical challenges in manufacturing for system integration. Due to the assembly complexity and integration platform variety, micro optical components require costly alignment and assembly procedures, in which many required manual efforts. Consequently, self-assembly device architectures have become a great interest and could provide major advantages over the conventional optical devices. In this paper, we discussed a self-assembly integration platform for micro optical components. To demonstrate the adaptability and flexibility of the proposed optical device architectures, we chose a commercially available MEMS fabrication foundry service - MUMPs (Multi-User MEMS Process). In this work, polysilicon layers of MUMPS are used as the 3-D structural material for construction of micro component framework and actuators. However, because the polysilicon has high absorption in the visible and near infrared wavelength ranges, it is not suitable for optical interaction. To demonstrate the required optical performance, hybrid integration of materials was proposed and implemented. Organic compound materials were applied on the silicon-based framework to form the required optical interfaces. Organic compounds provide good optical transparency, flexibility to form filters or lens and inexpensive manufacturing procedures. In this paper, we have demonstrated a micro optical filter integrated with self-assembly structures. We will discuss the self-assembly mechanism, optical filter designs, fabrication issues and results.

Dimerization of the SP1 Region of HIV-1 Gag Induces a Helical Conformation and Association into Helical Bundles: Implications for Particle Assembly.

PubMed

Datta, Siddhartha A K; Clark, Patrick K; Fan, Lixin; Ma, Buyong; Harvin, Demetria P; Sowder, Raymond C; Nussinov, Ruth; Wang, Yun-Xing; Rein, Alan

2016-02-15

HIV-1 immature particle (virus-like particle [VLP]) assembly is mediated largely by interactions between the capsid (CA) domains of Gag molecules but is facilitated by binding of the nucleocapsid (NC) domain to nucleic acid. We previously investigated the role of SP1, a "spacer" between CA and NC, in VLP assembly. We found that small changes in SP1 drastically disrupt assembly and that a peptide representing the sequence around the CA-SP1 junction is helical at high but not low concentrations. We suggested that by virtue of such a concentration-dependent change, this region could act as a molecular switch to activate HIV-1 Gag for VLP assembly. A leucine zipper domain can replace NC in Gag and still lead to the efficient assembly of VLPs. We find that SP1 mutants also disrupt assembly by these Gag-Zip proteins and have now studied a small fragment of this Gag-Zip protein, i.e., the CA-SP1 junction region fused to a leucine zipper. Dimerization of the zipper places SP1 at a high local concentration, even at low total concentrations. In this context, the CA-SP1 junction region spontaneously adopts a helical conformation, and the proteins associate into tetramers. Tetramerization requires residues from both CA and SP1. The data suggest that once this region becomes helical, its propensity to self-associate could contribute to Gag-Gag interactions and thus to particle assembly. There is complete congruence between CA/SP1 sequences that promote tetramerization when fused to zippers and those that permit the proper assembly of full-length Gag; thus, equivalent interactions apparently participate in VLP assembly and in SP1-Zip tetramerization. Assembly of HIV-1 Gag into virus-like particles (VLPs) appears to require an interaction with nucleic acid, but replacement of its principal nucleic acid-binding domain with a dimerizing leucine zipper domain leads to the assembly of RNA-free VLPs. It has not been clear how dimerization triggers assembly. Results here show that the

Dimerization of the SP1 Region of HIV-1 Gag Induces a Helical Conformation and Association into Helical Bundles: Implications for Particle Assembly

PubMed Central

Clark, Patrick K.; Fan, Lixin; Ma, Buyong; Harvin, Demetria P.; Sowder, Raymond C.; Nussinov, Ruth; Wang, Yun-Xing

2015-01-01

ABSTRACT HIV-1 immature particle (virus-like particle [VLP]) assembly is mediated largely by interactions between the capsid (CA) domains of Gag molecules but is facilitated by binding of the nucleocapsid (NC) domain to nucleic acid. We previously investigated the role of SP1, a “spacer” between CA and NC, in VLP assembly. We found that small changes in SP1 drastically disrupt assembly and that a peptide representing the sequence around the CA-SP1 junction is helical at high but not low concentrations. We suggested that by virtue of such a concentration-dependent change, this region could act as a molecular switch to activate HIV-1 Gag for VLP assembly. A leucine zipper domain can replace NC in Gag and still lead to the efficient assembly of VLPs. We find that SP1 mutants also disrupt assembly by these Gag-Zip proteins and have now studied a small fragment of this Gag-Zip protein, i.e., the CA-SP1 junction region fused to a leucine zipper. Dimerization of the zipper places SP1 at a high local concentration, even at low total concentrations. In this context, the CA-SP1 junction region spontaneously adopts a helical conformation, and the proteins associate into tetramers. Tetramerization requires residues from both CA and SP1. The data suggest that once this region becomes helical, its propensity to self-associate could contribute to Gag-Gag interactions and thus to particle assembly. There is complete congruence between CA/SP1 sequences that promote tetramerization when fused to zippers and those that permit the proper assembly of full-length Gag; thus, equivalent interactions apparently participate in VLP assembly and in SP1-Zip tetramerization. IMPORTANCE Assembly of HIV-1 Gag into virus-like particles (VLPs) appears to require an interaction with nucleic acid, but replacement of its principal nucleic acid-binding domain with a dimerizing leucine zipper domain leads to the assembly of RNA-free VLPs. It has not been clear how dimerization triggers assembly

A Single Crystalline Porphyrinic Titanium MetalOrganic Framework

DTIC Science & Technology

2015-04-28

22, which was synthesized from preformed titanium -oxo carboxylate clusters and porphyrinic ligands. PCN-22 possesses high porosity and photocatalytic...DOI: 10.1039/c5sc00916b www.rsc.org/chemicalscience 3926 | Chem. Sci., 2015, 6, 3926–3930e porphyrinic titanium metal– organic framework† Shuai Yuan...Scott J. Dalgarnoc and Hong-Cai Zhou*a We successfully assembled the photocatalytic titanium -oxo cluster and photosensitizing porphyrinic linker into a

Tailorable Exciton Transport in Doped Peptide–Amphiphile Assemblies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Solomon, Lee A.; Sykes, Matthew E.; Wu, Yimin A.

Light-harvesting biomaterials are an attractive target in photovoltaics, photocatalysis, and artificial photosynthesis. Through peptide self-assembly, complex nanostructures can be engineered to study the role of chromophore organization during light absorption and energy transport. To this end, we demonstrate the one-dimensional transport of excitons along naturally occurring, light-harvesting, Zn-protoporphyrin IX chromophores within self-assembled peptide-amphiphile nanofibers. The internal structure of the nanofibers induces packing of the porphyrins into linear chains. We find that this peptide assembly can enable long-range exciton diffusion, yet it also induces the formation of excimers between adjacent molecules, which serve as exciton traps. Electronic coupling between neighboring porphyrinmore » molecules is confirmed by various spectroscopic methods. The exciton diffusion process is then probed through transient photoluminescence and absorption measurements and fit to a model for one-dimensional hopping. Because excimer formation impedes exciton hopping, increasing the interchromophore spacing allows for improved diffusivity, which we control through porphyrin doping levels. We show that diffusion lengths of over 60 nm are possible at low porphyrin doping, representing an order of magnitude improvement over the highest doping fractions.« less

DNA assisted self-assembly of PAMAM dendrimers.

PubMed

Mandal, Taraknath; Kumar, Mattaparthi Venkata Satish; Maiti, Prabal K

2014-10-09

We report DNA assisted self-assembly of polyamidoamine (PAMAM) dendrimers using all atom Molecular Dynamics (MD) simulations and present a molecular level picture of a DNA-linked PAMAM dendrimer nanocluster, which was first experimentally reported by Choi et al. (Nano Lett., 2004, 4, 391-397). We have used single stranded DNA (ssDNA) to direct the self-assembly process. To explore the effect of pH on this mechanism, we have used both the protonated (low pH) and nonprotonated (high pH) dendrimers. In all cases studied here, we observe that the DNA strand on one dendrimer unit drives self-assembly as it binds to the complementary DNA strand present on the other dendrimer unit, leading to the formation of a DNA-linked dendrimer dimeric complex. However, this binding process strongly depends on the charge of the dendrimer and length of the ssDNA. We observe that the complex with a nonprotonated dendrimer can maintain a DNA length dependent inter-dendrimer distance. In contrast, for complexes with a protonated dendrimer, the inter-dendrimer distance is independent of the DNA length. We attribute this observation to the electrostatic complexation of a negatively charged DNA strand with the positively charged protonated dendrimer.

Self-assembly of ordered nanostructures

NASA Astrophysics Data System (ADS)

Yin, Jinsong

2000-10-01

Several different kinds of nanostructure materials were studied in this thesis: self-assembled monodispersive nanocrystals, photonic crystals, ordered mesoporous silica and hierarchically ordered nanostructured materials. Tetrahedral nanocrystals of CoO, with edge-lengths of 4.4 +/- 0.2 nm, were synthesized at high purity and monodispersity. The size, shape and phase selections of the nanocrystals were performed using a novel magnetic field separation technique. These nanocrystals behave like molecules, forming a face-centered cubic self-assembly of nanocrystal superlattices. In-situ behavior of self-assembled CoO nanocrystal arrays was also analyzed using transmission electron microscopy and associated techniques. The surface passivation layer started to evaporate/decompose at temperatures as low as ˜200°C, but the exposed cores of nanocrystals preserved the geometrical configuration of the assembly due to the strong adhesion of the carbon substrate. As the temperature is further increased from 300 to 600°C, the intrinsic crystal structure of the CoO nanoparticles experiences a replacement reaction, resulting in the formation of cobalt carbides. Two-dimensional self-assembling of cobalt nanocrystals with an average particle size of 9.2 nm and polydispersity of 9% is processed. Phtonic crystals were processed by a template-assisted method. Ordered self-assembly of pores of titania nanocrystals formed a face-centered cubic packing structure. The walls of the pores were made of anatase nanocrystals of ˜8 nm in diameter. Cobalt can be doped into the walls of the pores by solution infiltration of cobalt carbonyl. Cobalt titanium oxide may be formed on the internal surface of the ordered pore structure. This type of structure is likely to be an excellent supporting material for catalysis. The experimental results suggest that transition metal elements can be incorporated into porous titania without blocking the interconnected pores. Hierarchically ordered

Integrated Nanosystems Templated by Self-assembled Virus Capsids

NASA Astrophysics Data System (ADS)

Stephanopoulos, Nicholas

This dissertation presents the synthesis and modeling of multicomponent nanosystems templated by self-assembled virus capsids. The design principles, synthesis, analysis, and future directions for these capsid-based materials are presented. Chapter 1 gives an overview of the literature on the application of virus capsids in constructing nanomaterials. The uses of capsids in three main areas are considered: (1) as templates for inorganic materials or nanoparticles; (2) as vehicles for biological applications like medical imaging and treatment; and (3) as scaffolds for catalytic materials. In light of this introduction, an overview of the material in this dissertation is described. Chapters 2-4 all describe integrated nanosystems templated by bacteriophage MS2, a spherical icosahedral virus capsid. MS2 possesses an interior and exterior surface that can be modified orthogonally using bioconjugation chemistry to create multivalent, multicomponent constructs with precise localization of components attached to the capsid proteins. Chapter 2 describes the use of MS2 to synthesize a photocatalytic construct by modifying the internal surface with sensitizing chromophores and the external surface with a photocatalytic porphyrin. The chromophores absorbed energy that the porphyrin could not, and transferred it to the porphyrin via FRET through the protein shell. The porphyrin was then able to utilize the energy to carry out photocatalysis at new wavelengths. In Chapter 3, porphyrins were installed on the interior surface of MS2 and DNA aptamers specific for Jurkat leukemia T cells on the exterior surface. The dual-modified capsids were able to bind to Jurkat cells, and upon illumination the porphyrins generated singlet oxygen to kill them selectively over non-targeted cells. Chapter 4 explores integrating MS2 with DNA origami in order to arrange the capsids at larger length scales. Capsids modified with fluorescent dyes inside and single-stranded DNA outside were able to

Intramolecular Oxidative O-Demethylation of an Oxoferryl Porphyrin Complexed with a Per-O-methylated β-Cyclodextrin Dimer.

PubMed

Kitagishi, Hiroaki; Kurosawa, Shun; Kano, Koji

2016-11-22

The intramolecular oxidation of ROCH 3 to ROCH 2 OH, where the latter compound spontaneously decomposed to ROH and HCHO, was observed during the reaction of the supramolecular complex (met-hemoCD3) with cumene hydroperoxide in aqueous solution. Met-hemoCD3 is composed of meso-tetrakis(4-sulfonatophenyl)porphinatoiron(III) (Fe III TPPS) and a per-O-methylated β-cyclodextrin dimer having an -OCH 2 PyCH 2 O- linker (Py=pyridine-3,5-diyl). The O=Fe IV TPPS complex was formed by the reaction of met-hemoCD3 with cumene hydroperoxide, and isolated by gel-filtration chromatography. Although the isolated O=Fe IV TPPS complex in the cyclodextrin cage was stable in aqueous solution at 25 °C, it was gradually converted to Fe II TPPS (t 1/2 =7.6 h). This conversion was accompanied by oxidative O-demethylation of an OCH 3 group in the cyclodextrin dimer. The results indicated that hydrogen abstraction by O=Fe IV TPPS from ROCH 3 yields HO-Fe III TPPS and ROCH 2 . . This was followed by radical coupling to afford Fe II TPPS and ROCH 2 OH. The hemiacetal (ROCH 2 OH) immediately decomposed to ROH and HCHO. This study revealed the ability of oxoferryl porphyrin to induce two-electron oxidation. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Kinetics of DNA Tile Dimerization

PubMed Central

2015-01-01

Investigating how individual molecular components interact with one another within DNA nanoarchitectures, both in terms of their spatial and temporal interactions, is fundamentally important for a better understanding of their physical behaviors. This will provide researchers with valuable insight for designing more complex higher-order structures that can be assembled more efficiently. In this report, we examined several spatial factors that affect the kinetics of bivalent, double-helical (DH) tile dimerization, including the orientation and number of sticky ends (SEs), the flexibility of the double helical domains, and the size of the tiles. The rate constants we obtained confirm our hypothesis that increased nucleation opportunities and well-aligned SEs accelerate tile–tile dimerization. Increased flexibility in the tiles causes slower dimerization rates, an effect that can be reversed by introducing restrictions to the tile flexibility. The higher dimerization rates of more rigid tiles results from the opposing effects of higher activation energies and higher pre-exponential factors from the Arrhenius equation, where the pre-exponential factor dominates. We believe that the results presented here will assist in improved implementation of DNA tile based algorithmic self-assembly, DNA based molecular robotics, and other specific nucleic acid systems, and will provide guidance to design and assembly processes to improve overall yield and efficiency. PMID:24794259

Kinetics of DNA tile dimerization.

PubMed

Jiang, Shuoxing; Yan, Hao; Liu, Yan

2014-06-24

Investigating how individual molecular components interact with one another within DNA nanoarchitectures, both in terms of their spatial and temporal interactions, is fundamentally important for a better understanding of their physical behaviors. This will provide researchers with valuable insight for designing more complex higher-order structures that can be assembled more efficiently. In this report, we examined several spatial factors that affect the kinetics of bivalent, double-helical (DH) tile dimerization, including the orientation and number of sticky ends (SEs), the flexibility of the double helical domains, and the size of the tiles. The rate constants we obtained confirm our hypothesis that increased nucleation opportunities and well-aligned SEs accelerate tile-tile dimerization. Increased flexibility in the tiles causes slower dimerization rates, an effect that can be reversed by introducing restrictions to the tile flexibility. The higher dimerization rates of more rigid tiles results from the opposing effects of higher activation energies and higher pre-exponential factors from the Arrhenius equation, where the pre-exponential factor dominates. We believe that the results presented here will assist in improved implementation of DNA tile based algorithmic self-assembly, DNA based molecular robotics, and other specific nucleic acid systems, and will provide guidance to design and assembly processes to improve overall yield and efficiency.

Extremely strong self-assembly of a bimetallic salen complex visualized at the single-molecule level.

PubMed

Salassa, Giovanni; Coenen, Michiel J J; Wezenberg, Sander J; Hendriksen, Bas L M; Speller, Sylvia; Elemans, Johannes A A W; Kleij, Arjan W

2012-04-25

A bis-Zn(salphen) structure shows extremely strong self-assembly both in solution as well as at the solid-liquid interface as evidenced by scanning tunneling microscopy, competitive UV-vis and fluorescence titrations, dynamic light scattering, and transmission electron microscopy. Density functional theory analysis on the Zn(2) complex rationalizes the very high stability of the self-assembled structures provoked by unusual oligomeric (Zn-O)(n) coordination motifs within the assembly. This coordination mode is strikingly different when compared with mononuclear Zn(salphen) analogues that form dimeric structures having a typical Zn(2)O(2) central unit. The high stability of the multinuclear structure therefore holds great promise for the development of stable self-assembled monolayers with potential for new opto-electronic materials.

Dimerization and actin-bundling properties of villin and its role in the assembly of epithelial cell brush borders.

PubMed

George, Sudeep P; Wang, Yaohong; Mathew, Sijo; Srinivasan, Kamalakkannan; Khurana, Seema

2007-09-07

Villin is a major actin-bundling protein in the brush border of epithelial cells. In this study we demonstrate for the first time that villin can bundle actin filaments using a single F-actin binding site, because it has the ability to self-associate. Using fluorescence resonance energy transfer, we demonstrate villin self-association in living cells in microvilli and in growth factor-stimulated cells in membrane ruffles and lamellipodia. Using sucrose density gradient, size-exclusion chromatography, and matrix-assisted laser desorption ionization time-of-flight, the majority of villin was identified as a monomer or dimer. Villin dimers were also identified in Caco-2 cells, which endogenously express villin and Madin-Darby canine kidney cells that ectopically express villin. Using truncation mutants of villin, site-directed mutagenesis, and fluorescence resonance energy transfer, an amino-terminal dimerization site was identified that regulated villin self-association in parallel conformation as well as actin bundling by villin. This detailed analysis describes for the first time microvillus assembly by villin, redefines the actin-bundling function of villin, and provides a molecular mechanism for actin bundling by villin, which could have wider implications for other actin cross-linking proteins that share a villin-like headpiece domain. Our study also provides a molecular basis to separate the morphologically distinct actin-severing and actin-bundling properties of villin.

Self-assembly of dimeric tetraurea calix[4]pyrrole capsules

PubMed Central

Ballester, Pablo; Gil-Ramírez, Guzmán

2009-01-01

Calix[4]pyrroles having extended aromatic cavities have been functionalized with 4 ureas in the para position of their meso phenyl substituents. This elaboration of the upper rim was completed in 2 synthetic steps starting from the α,α,α,α-tetranitro isomer of the calix[4]pyrrole obtained in the acid catalyzed condensation of p-nitrophenyl methyl ketone and pyrrole. In dichloromethane solution and in the presence of 4,4′-bipyridine N-N′-dioxide the tetraurea calix[4]pyrrole dimerizes reversibly forming a cyclic array of 16 hydrogen bonds and encapsulating 1 molecule of bis-N-oxide. The encapsulated guest is bound in the cavity by hydrogen bonding to the 2 endohedral calix[4]pyrrole centers. Further evidence for dimerization of the tetraurea calix[4]pyrroles is provided by 1H-NMR experiments and by the formation of mixed capsules. PMID:19261848

Molecular Dynamics Studies of Self-Assembling Biomolecules and DNA-functionalized Gold Nanoparticles

NASA Astrophysics Data System (ADS)

Cho, Vince Y.

This thesis is organized as following. In Chapter 2, we use fully atomistic MD simulations to study the conformation of DNA molecules that link gold nanoparticles to form nanoparticle superlattice crystals. In Chapter 3, we study the self-assembly of peptide amphiphiles (PAs) into a cylindrical micelle fiber by using CGMD simulations. Compared to fully atomistic MD simulations, CGMD simulations prove to be computationally cost-efficient and reasonably accurate for exploring self-assembly, and are used in all subsequent chapters. In Chapter 4, we apply CGMD methods to study the self-assembly of small molecule-DNA hybrid (SMDH) building blocks into well-defined cage-like dimers, and reveal the role of kinetics and thermodynamics in this process. In Chapter 5, we extend the CGMD model for this system and find that the assembly of SMDHs can be fine-tuned by changing parameters. In Chapter 6, we explore superlattice crystal structures of DNA-functionalized gold nanoparticles (DNA-AuNP) with the CGMD model and compare the hybridization.

Direct observation of ultrafast coherent exciton dynamics in helical π-stacks of self-assembled perylene bisimides

PubMed Central

Sung, Jooyoung; Kim, Pyosang; Fimmel, Benjamin; Würthner, Frank; Kim, Dongho

2015-01-01

Ever since the discovery of dye self-assemblies in nature, there have been tremendous efforts to exploit biomimetic supramolecular assemblies for tailored artificial photon processing materials. This feature necessarily has resulted in an increasing demand for understanding exciton dynamics in the dye self-assemblies. In a sharp contrast with J-type aggregates, however, the detailed observation of exciton dynamics in H-type aggregates has remained challenging. In this study, as we succeed in measuring transient fluorescence from Frenkel state of π-stacked perylene tetracarboxylic acid bisimide dimer and oligomer aggregates, we present an experimental demonstration on Frenkel exciton dynamics of archetypal columnar π–π stacks of dyes. The analysis of the vibronic peak ratio of the transient fluorescence spectra reveals that unlike the simple π-stacked dimer, the photoexcitation energy in the columnar π-stacked oligomer aggregates is initially delocalized over at least three molecular units and moves coherently along the chain in tens of femtoseconds, preceding excimer formation process. PMID:26492820

Modification of β-Sheet Forming Peptide Hydrophobic Face: Effect on Self-Assembly and Gelation

PubMed Central

2016-01-01

β-Sheet forming peptides have attracted significant interest for the design of hydrogels for biomedical applications. One of the main challenges is the control and understanding of the correlations between peptide molecular structure, the morphology, and topology of the fiber and network formed as well as the macroscopic properties of the hydrogel obtained. In this work, we have investigated the effect that functionalizing these peptides through their hydrophobic face has on their self-assembly and gelation. Our results show that the modification of the hydrophobic face results in a partial loss of the extended β-sheet conformation of the peptide and a significant change in fiber morphology from straight to kinked. As a consequence, the ability of these fibers to associate along their length and form large bundles is reduced. These structural changes (fiber structure and network topology) significantly affect the mechanical properties of the hydrogels (shear modulus and elasticity). PMID:27089379

Mechanisms, pathways, and dynamics of excited-state energy flow in self-assembled wheel-and-spoke light-harvesting architectures.

PubMed

Song, Hee-eun; Kirmaier, Christine; Schwartz, Jennifer K; Hindin, Eve; Yu, Lianhe; Bocian, David F; Lindsey, Jonathan S; Holten, Dewey

2006-10-05

Static and time-resolved optical measurements are reported for two cyclic hexameric porphyrin arrays and their self-assembled complexes with guest chromophores. The hexameric hosts contain zinc porphyrins and 0 or 3 free base (Fb) porphyrins (denoted Zn(6) or Zn(3)Fb(3), respectively). The guests are a tripyridyl arene (TP) and a dipyridyl-substituted free base porphyrin (DPFb), each of which coordinates to zinc porphyrins of a host via pyridyl-zinc dative bonding. Each architecture is designed to have an overall gradient of excited-state energies that affords excitation funneling within the host and ultimately to the guest. Collectively, the studies delineate the various pathways, mechanisms, and rate constants of energy flow among the weakly coupled constituents of the host-guest complexes. The pathways include downhill unidirectional energy transfer between adjacent chromophores, bidirectional energy migration between identical chromophores, and energy transfer between nonadjacent chromophores. The energy transfer to the lowest-energy chromophore(s) within the backbone of a hexameric host (Fb porphyrins in Zn(3)Fb(3) or pyridyl-coordinated zinc porphyrins in Zn(6)*TP and Zn(6)*DPFb) proceeds primarily via a through-bond mechanism; the transfer is rapid (approximately 40 ps depending on the array) and essentially quantitative (>or=98%). The energy transfer from a pyridyl-coordinated zinc porphyrin of the host to the Fb porphyrin guest in the Zn(6)*DPFb complex is almost exclusively Förster through-space in nature; this process is much slower ( approximately 1 ns) and has a lower yield (65%). These studies highlight the utility of cyclic architectures for efficient light harvesting and energy transfer to a designated trapping site.

Porphyrin framework solids. Synthesis and structure of hybrid coordination polymers of tetra(carboxyphenyl)porphyrins and lanthanide-bridging ions.

PubMed

Muniappan, Sankar; Lipstman, Sophia; George, Sumod; Goldberg, Israel

2007-07-09

New types of porphyrin-based framework solids were constructed by reacting meso-tetra(3-carboxyphenyl)porphyrin and meso-tetra(4-carboxyphenyl)metalloporphyrins with common salts of lanthanide metal ions. The large size, high coordination numbers and strong affinity for oxo ligands of the latter, combined with favorable hydrothermal reaction conditions, allowed the formation of open three-dimensional single-framework architectures by coordination polymerization, in which the tetradentate porphyrin units are intercoordinated by multinuclear assemblies of the bridging metal ions. The latter serve as construction pillars of the supramolecular arrays, affording stable structures. Several modes of coordination polymerization were revealed by single-crystal X-ray diffraction. They differ by the spatial functionality of the porphyrin building blocks, the coordination patterns of the lanthanide-carboxylate assemblies, and the topology of the resulting frameworks. The seven new reported structures exhibit periodically spaced 0.4-0.6 nm wide channel voids that perforate the respective crystalline polymeric architectures and are accessible to solvent components. Materials based on the m-carboxyphenyl derivative reveal smaller channels than those based on the p-carboxyphenyl analogues. An additional complex of the former with a smaller third-row transition metal (Co) is characterized by coordination connectivity in two dimensions only. Thermal and powder-diffraction analyses confirm the stability of the lanthanide-TmCPP (TmCPP=tetra(m-carboxyphenyl)porphyrin) frameworks.

Self-assembly of keratin peptides: Its implication on the performance of electrospun PVA nanofibers

PubMed Central

Kadirvelu, Kavitha; Fathima, Nishter Nishad

2016-01-01

Drawing inspiration from the field of designer self-assembling materials, this work is aimed to focus on the self-assembling nature of extracted peptides. Hair keratin, a proteinacious reject in tanning industry has been chosen since they have been extracted and used for wide range of applications. Keratin source was subjected to five hydrolysis treatments (viz., sulphitolysis, β-mercaptoethanol, ionic liquid, thioglycolic acid and alkali) and assayed for functional groups. This was followed by the prediction of secondary structure using circular dichroism, determining the microstructural level to which the extracted peptide has self-assembled. Sulphitolysis and thioglycolic acid based hydrolysates exist in monomeric conformation, whereas β-mercaptoethanol based hydrolysate exhibited dimeric conformation. The subsequent part of the study is to incorporate these peptides into the nanofibers to study the structural implication of keratin peptides on its characteristics. Accordingly, the peptides were electrospun with PVA and subjected to morphological, mechanical, thermal and biological characterizations. Monomeric nanofiber mat has high tensile strength of around 5.5 MPa and offered lower mass transport resistance, whereas dimeric mat has high Tm of around 290 °C and was more biocompatible. These results help in understanding the extraction-structure-function aspect of the hydrolysates stressing the role of extraction methods on the choice of application. PMID:27812004

Molecular dynamics simulations of low-ordered alzheimer β-amyloid oligomers from dimer to hexamer on self-assembled monolayers.

PubMed

Zhao, Jun; Wang, Qiuming; Liang, Guizhao; Zheng, Jie

2011-12-20

Accumulation of small soluble oligomers of amyloid-β (Aβ) in the human brain is thought to play an important pathological role in Alzheimer's disease. The interaction of these Aβ oligomers with cell membrane and other artificial surfaces is important for the understanding of Aβ aggregation and toxicity mechanisms. Here, we present a series of exploratory molecular dynamics (MD) simulations to study the early adsorption and conformational change of Aβ oligomers from dimer to hexamer on three different self-assembled monolayers (SAMs) terminated with CH(3), OH, and COOH groups. Within the time scale of MD simulations, the conformation, orientation, and adsorption of Aβ oligomers on the SAMs is determined by complex interplay among the size of Aβ oligomers, the surface chemistry of the SAMs, and the structure and dynamics of interfacial waters. Energetic analysis of Aβ adsorption on the SAMs reveals that Aβ adsorption on the SAMs is a net outcome of different competitions between dominant hydrophobic Aβ-CH(3)-SAM interactions and weak CH(3)-SAM-water interactions, between dominant electrostatic Aβ-COOH-SAM interactions and strong COOH-SAM-water interactions, and between comparable hydrophobic and electrostatic Aβ-OH-SAM interactions and strong OH-SAM-water interactions. Atomic force microscopy images also confirm that all of three SAMs can induce the adsorption and polymerization of Aβ oligomers. Structural analysis of Aβ oligomers on the SAMs shows a dramatic increase in structural stability and β-sheet content from dimer to trimer, suggesting that Aβ trimer could act as seeds for Aβ polymerization on the SAMs. This work provides atomic-level understanding of Aβ peptides at interface. © 2011 American Chemical Society

Self-assembled thin films of Fe3O4-Ag composite nanoparticles for spintronic applications

NASA Astrophysics Data System (ADS)

Jiang, Chengpeng; Leung, Chi Wah; Pong, Philip W. T.

2017-10-01

Controlled self-assembly of multi-component magnetic nanoparticles could lead to nanomaterial-based magnetic devices with novel structures and intriguing properties. Herein, self-assembled thin films of Fe3O4-Ag composite nanoparticles (CNPs) with hetero-dimeric shapes were fabricated using interfacial assembly method. The CNP-assembled thin films were further transferred to patterned silicon substrates followed by vacuum annealing, producing CNP-based magnetoresistive (MR) devices. Due to the presence of intra-particle interfaces and inter-particle barriers, an enhanced MR ratio and a non-linear current-voltage relation were observed in the device. The results of this work can potentially pave the way to the future exploration and development of spintronic devices built from composite nanomaterials.

Ion Mobility Measurements of Multianionic Metalloporphyrin Dimers: Structural Changes Induced by Countercation Exchange

NASA Astrophysics Data System (ADS)

Schneider, Erik; Brendle, Katrina; Jäger, Patrick; Weis, Patrick; Kappes, Manfred M.

2018-04-01

We present gas-phase structures of dimers of MnIII and FeIII meso-tetra(4-sulfonatophenyl)porphyrin multianions with various amounts of sodium and hydrogen counterions. The structural assignments are achieved by combining mass spectrometry, ion mobility measurements, quantum chemical calculations, and trajectory method collision cross section calculations. For a common charge state, we observe significant topological variations in the dimer structures of [(MTPPS)2+nX](6-n)- (M=MnIII, FeIII; X=H, Na; n = 1-3) induced by replacing hydrogen counterions by sodium. For sodium, the dimer structures are much more compact, a finding that can be rationalized by the stronger interactions of the sodium cations with the anionic sulfonic acid groups of the porphyrins as compared to hydrogen. [Figure not available: see fulltext.

Cofacial porphyrin-ferrocene dyads and a new class of conjugated porphyrin.

PubMed

Cammidge, Andrew N; Scaife, Peter J; Berber, Gûlen; Hughes, David L

2005-08-04

A porphyrin-ferrocene dyad has been synthesized in which there is close face-to-face contact between the two aromatic systems, providing a model for heterobimetallic polymers based on the same repeating unit. Attempts to synthesize the 2:1 adduct instead led to a remarkable intramolecular Heck-type cyclization which planarizes the system and extends the conjugation. [structure: see text

Synthesis and in vitro phototoxicity of multifunctional Zn(II)meso-tetrakis(4-carboxyphenyl)porphyrin-coated gold nanoparticles assembled via axial coordination with imidazole ligands.

PubMed

Alea-Reyes, María E; Penon, Oriol; García Calavia, Paula; Marín, María J; Russell, David A; Pérez-García, Lluïsa

2018-07-01

Metalloporphyrins are extensively investigated for their ability to form reactive oxygen species and as potent photosensitisers for use in photodynamic therapy. However, their hydrophobicity generally causes solubility issues concerning in vivo delivery due to lack of distribution and low clearance from the body. Immobilising porphyrins on carriers, such as gold nanoparticles (GNP), can overcome some of these drawbacks. The mode of assembling the porphyrins to the carrier influences the properties of the resulting drug delivery systems. We describe the synthesis and characterisation of new porphyrin decorated water soluble GNP and we explore Zn-imidazole axial coordination as the mode of linking the porphyrin to the metallic core of the nanoparticles. Quantification of singlet oxygen production, toxicity in dark, cellular uptake by SK-BR-3 cells and phototoxicity have been assessed. Axial coordination limits the number of porphyrins on the gold surface, reduces the formation of aggregates, and diminishes metal exchange in the porphyrin, all of which contribute to enhance the efficiency of singlet oxygen generation from the immobilised porphyrin. In vitro experiments on SK-BR-3 cells reveal a fast uptake followed by more than 80% cell death after irradiation with low doses of light. Copyright © 2018 Elsevier Inc. All rights reserved.

Meshing complex macro-scale objects into self-assembling bricks

PubMed Central

Hacohen, Adar; Hanniel, Iddo; Nikulshin, Yasha; Wolfus, Shuki; Abu-Horowitz, Almogit; Bachelet, Ido

2015-01-01

Self-assembly provides an information-economical route to the fabrication of objects at virtually all scales. However, there is no known algorithm to program self-assembly in macro-scale, solid, complex 3D objects. Here such an algorithm is described, which is inspired by the molecular assembly of DNA, and based on bricks designed by tetrahedral meshing of arbitrary objects. Assembly rules are encoded by topographic cues imprinted on brick faces while attraction between bricks is provided by embedded magnets. The bricks can then be mixed in a container and agitated, leading to properly assembled objects at high yields and zero errors. The system and its assembly dynamics were characterized by video and audio analysis, enabling the precise time- and space-resolved characterization of its performance and accuracy. Improved designs inspired by our system could lead to successful implementation of self-assembly at the macro-scale, allowing rapid, on-demand fabrication of objects without the need for assembly lines. PMID:26226488

Effects of multiple pathways on excited-state energy flow in self-assembled wheel-and-spoke light-harvesting architectures.

PubMed

Song, Hee-eun; Kirmaier, Christine; Schwartz, Jennifer K; Hindin, Eve; Yu, Lianhe; Bocian, David F; Lindsey, Jonathan S; Holten, Dewey

2006-10-05

Static and time-resolved optical measurements are reported for three cyclic hexameric porphyrin arrays and their self-assembled complexes with guest chromophores. The hexameric hosts contain zinc porphyrins and 0, 1, or 2 free base (Fb) porphyrins (denoted Zn(6), Zn(5)Fb, or Zn(4)Fb(2), respectively). The guest is a core-modified (O replacing one of the four N atoms) dipyridyl-substituted Fb porphyrin (DPFbO) that coordinates to zinc porphyrins of a host via pyridyl-zinc dative bonding. Each architecture is designed to have a gradient of excited-state energies for excitation funneling among the weakly coupled constituents of the host to the guest. Energy transfer to the lowest-energy chromophore(s) (coordinated zinc porphyrins or Fb porphyrins) within a hexameric host occurs primarily via a through-bond (TB) mechanism, is rapid ( approximately 40 ps), and is essentially quantitative (>or=98%). Energy transfer from a pyridyl-coordinated zinc porphyrin of the host to the guest in the Zn(6)*DPFbO complex has a yield of approximately 75%, a rate constant of approximately (0.7 ns)(-1), and significant Förster through-space (TS) character. In the case of Zn(5)Fb*DPFbO, which has an additional TS route via the Fb porphyrin with a rate constant of approximately (20 ns)(-1), the yield of energy transfer to the guest is somewhat lower ( approximately 50%) than that for Zn(6)*DPFbO. Complex Zn(4)Fb(2)*DPFbO has an identical TS pathway via the Fb porphyrin plus an additional TS pathway involving the second Fb porphyrin (closer to the guest) with a rate constant of approximately (0.5 ns)(-1). This complex exhibits an energy-transfer yield to the guest that is significantly enhanced over that for Zn(5)Fb*DPFbO and comparable to that for Zn(6)*DPFbO. Collectively, the results for the various arrays suggest designs for similar host-guest complexes that are expected to exhibit much more efficient light harvesting and excitation trapping at the central guest chromophore.

Dynamic Diglyme-Mediated Self-Assembly of Gold Nanoclusters.

PubMed

Compel, W Scott; Wong, O Andrea; Chen, Xi; Yi, Chongyue; Geiss, Roy; Häkkinen, Hannu; Knappenberger, Kenneth L; Ackerson, Christopher J

2015-12-22

We report the assembly of gold nanoclusters by the nonthiolate ligand diglyme into discrete and dynamic assemblies. To understand this surprising phenomenon, the assembly of Au20(SC2H4Ph)15-diglyme into Au20(SC2H4Ph)15-diglyme-Au20(SC2H4Ph)15 is explored in detail. The assembly is examined by high-angle annular dark field scanning transmission electron microscopy, size exclusion chromatography, mass spectrometry, IR spectroscopy, and calorimetry. We establish a dissociation constant for dimer to monomer conversion of 20.4 μM. Theoretical models validated by transient absorption spectroscopy predict a low-spin monomer and a high-spin dimer, with assembly enabled through weak diglyme oxygen-gold interactions. Close spatial coupling allows electron delocalization between the nanoparticle cores. The resulting assemblies thus possess optical and electronic properties that emerge as a result of assembly.

Study of DNA Origami Dimerization and Dimer Dissociation Dynamics and of the Factors that Limit Dimerization.

PubMed

Liber, Miran; Tomov, Toma E; Tsukanov, Roman; Berger, Yaron; Popov, Mary; Khara, Dinesh C; Nir, Eyal

2018-06-01

Organizing DNA origami building blocks into higher order structures is essential for fabrication of large structurally and functionally diverse devices and molecular machines. Unfortunately, the yields of origami building block attachment reactions are typically not sufficient to allow programed assembly of DNA devices made from more than a few origami building blocks. To investigate possible reasons for these low yields, a detailed single-molecule fluorescence study of the dynamics of rectangular origami dimerization and origami dimer dissociation reactions is conducted. Reactions kinetics and yields are investigated at different origami and ion concentrations, for different ion types, for different lengths of bridging strands, and for the "sticky end" and "weaving welding" attachment techniques. Dimerization yields are never higher than 86%, which is typical for such systems. Analysis of the dynamic data shows that the low yield cannot be explained by thermodynamic instability or structural imperfections of the origami constructs. Atomic force microscopy and gel electrophoresis evidence reveal self-dimerization of the origami monomers, likely via blunt-end interactions made possible by the presence of bridging strands. It is suggested that this mechanism is the major factor that inhibits correct dimerization and means to overcome it are discussed. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Chiral signs of TPPS co-assemblies with chiral gelators: role of molecular and supramolecular chirality.

PubMed

Wang, Qiuling; Zhang, Li; Yang, Dong; Li, Tiesheng; Liu, Minghua

2016-10-13

A dianionic tetrakis(4-sulfonatophenyl)porphyrin (TPPS) self-assembled into J-aggregates when it co-assembled with a chiral cationic amphiphile via supramolecular gelation. The chiral signs of TPPS J aggregates followed the supramolecular chirality of amphiphilic assemblies rather than the molecular chirality of the amphiphile.

High-performance thermoelectricity in edge-over-edge zinc-porphyrin molecular wires.

PubMed

Noori, Mohammed; Sadeghi, Hatef; Lambert, Colin J

2017-04-20

If high efficiency organic thermoelectric materials could be identified, then these would open the way to a range of energy harvesting technologies and Peltier coolers using flexible and transparent thin-film materials. We have compared the thermoelectric properties of three zinc porphyrin (ZnP) dimers and a ZnP monomer and found that the "edge-over-edge" dimer formed from stacked ZnP rings possesses a high electrical conductance, negligible phonon thermal conductance and a high Seebeck coefficient of the order of 300 μV K -1 . These combine to yield a predicted room-temperature figure of merit of ZT ≈ 4, which is the highest room-temperature ZT ever reported for a single organic molecule. This high value of ZT is a consequence of the low phonon thermal conductance arising from the stacked nature of the porphyrin rings, which hinders phonon transport through the edge-over-edge molecule and enhances the Seebeck coefficient.

Aggregation and metal-complexation behaviour of THPP porphyrin in ethanol/water solutions as function of pH

NASA Astrophysics Data System (ADS)

Zannotti, Marco; Giovannetti, Rita; Minofar, Babak; Řeha, David; Plačková, Lydie; D'Amato, Chiara A.; Rommozzi, Elena; Dudko, Hanna V.; Kari, Nuerguli; Minicucci, Marco

2018-03-01

The effect of pH change on 5,10,15,20-Tetrakis(4-hydroxyphenyl)-21H,23H-porphine (THPP) with its aggregation as function of water-ethanol mixture was studied with UV-vis, fluorescence, Raman and computational analysis. In neutral pH, THPP was present as free-base and, increasing the water amount, aggregation occurred with the formation of H- and J-aggregates. The aggregation constant and the concentration of dimers were calculated, other information about the dimer aggregation were evaluated by computational study. In acidic pH, by the insertions of two hydrogens in the porphyrin rings, the porphyrin changed its geometry with a ring deformation confirmed by red-shifted spectrum and quenching in fluorescence; at this low pH, increasing the water amount, the acidic form (THPPH2)2 + resulted more stable due to a polar environment with stronger interaction by hydrogen bonding. In basic pH, reached by NH4OH, THPP porphyrin was able to react with alkali metals in order to form sitting-atop complex (M2THPP) confirmed by the typical absorption spectrum of metallo-porphyrin, Raman spectroscopy and by computational analysis.

An ethane-bridged porphyrin dimer as a model of di-heme proteins: inorganic and bioinorganic perspectives and consequences of heme-heme interactions.

PubMed

Sil, Debangsu; Rath, Sankar Prasad

2015-10-07

Interaction between heme centers has been cleverly implemented by Nature in order to regulate different properties of multiheme cytochromes, thereby allowing them to perform a wide variety of functions. Our broad interest lies in unmasking the roles played by heme-heme interactions in modulating different properties viz., metal spin state, redox potential etc., of the individual heme centers using an ethane-bridged porphyrin dimer as a synthetic model of dihemes. The large differences in the structure and properties of the diheme complexes, as compared to the monoheme analogs, provide unequivocal evidence of the role played by heme-heme interactions in the dihemes. This Perspective provides a brief account of our recent efforts to explore these interesting aspects and the subsequent outcomes.

Self-assembly behavior of tail-to-tail superstructure formed by mono-6-O-(4-carbamoylmethoxy-benzoyl)-β-cyclodextrin in solution and the solid state.

PubMed

Xu, Zhe; Chen, Xin; Liu, Jing; Yan, Dong-Qing; Diao, Chun-Hua; Guo, Min-Jie; Fan, Zhi

2014-07-01

A novel mono-modified β-cyclodextrin (β-CD) consisting of 4-carbamoylmethoxy-benzoyl unit at the primary side was synthesized and its self-assembly behavior was determined by X-ray crystallography and NMR spectroscopy. The crystal structure shows a 'Yin-Yang'-like packing mode, in which the modified β-CD exhibits a channel superstructure formed by a tail-to-tail dimer as the repeating motif with the substituted group embedded within the hydrophobic cavity of the facing β-CD. The geometry of the substituted group is determined by the inclusion of the cavity and is further stabilized by two intermolecular hydrogen bonds between the carbonyl O atom and phenyl group. Furthermore, NMR ROESY investigation indicates that the self-assembly behavior of the substituted group within the β-CD cavity is retained in aqueous solution, and the effective binding constant Ka was calculated to be 1330 M(-1) by means of (1)H NMR titration according to iterative determination. Copyright © 2014 Elsevier Ltd. All rights reserved.

Self-assembly behaviours of peptide-drug conjugates: influence of multiple factors on aggregate morphology and potential self-assembly mechanism

NASA Astrophysics Data System (ADS)

Fan, Qin; Ji, Yujie; Wang, Jingjing; Wu, Li; Li, Weidong; Chen, Rui; Chen, Zhipeng

2018-04-01

Peptide-drug conjugates (PDCs) as self-assembly prodrugs have the unique and specific features to build one-component nanomedicines. Supramolecular structure based on PDCs could form various morphologies ranging from nanotube, nanofibre, nanobelt to hydrogel. However, the assembly process of PDCs is too complex to predict or control. Herein, we investigated the effects of extrinsic factors on assembly morphology and the possible formation of nanostructures based on PDCs. To this end, we designed a PDC consisting of hydrophobic drug (S)-ketoprofen (Ket) and valine-glutamic acid dimeric repeats peptide (L-VEVE) to study their assembly behaviour. Our results showed that the critical assembly concentration of Ket-L-VEVE was 0.32 mM in water to form various nanostructures which experienced from micelle, nanorod, nanofibre to nanoribbon. The morphology was influenced by multiple factors including molecular design, assembly time, pH and hydrogen bond inhibitor. On the basis of experimental results, we speculated the possible assembly mechanism of Ket-L-VEVE. The π-π stacking interaction between Ket molecules could serve as an anchor, and hydrogen bonded-induced β-sheets and hydrophilic/hydrophobic balance between L-VEVE peptide play structure-directing role in forming filament-like or nanoribbon morphology. This work provides a new sight to rationally design and precisely control the nanostructure of PDCs based on aromatic fragment.

Self-assembly behaviours of peptide-drug conjugates: influence of multiple factors on aggregate morphology and potential self-assembly mechanism.

PubMed

Fan, Qin; Ji, Yujie; Wang, Jingjing; Wu, Li; Li, Weidong; Chen, Rui; Chen, Zhipeng

2018-04-01

Peptide-drug conjugates (PDCs) as self-assembly prodrugs have the unique and specific features to build one-component nanomedicines. Supramolecular structure based on PDCs could form various morphologies ranging from nanotube, nanofibre, nanobelt to hydrogel. However, the assembly process of PDCs is too complex to predict or control. Herein, we investigated the effects of extrinsic factors on assembly morphology and the possible formation of nanostructures based on PDCs. To this end, we designed a PDC consisting of hydrophobic drug ( S )-ketoprofen (Ket) and valine-glutamic acid dimeric repeats peptide (L-VEVE) to study their assembly behaviour. Our results showed that the critical assembly concentration of Ket-L-VEVE was 0.32 mM in water to form various nanostructures which experienced from micelle, nanorod, nanofibre to nanoribbon. The morphology was influenced by multiple factors including molecular design, assembly time, pH and hydrogen bond inhibitor. On the basis of experimental results, we speculated the possible assembly mechanism of Ket-L-VEVE. The π-π stacking interaction between Ket molecules could serve as an anchor, and hydrogen bonded-induced β-sheets and hydrophilic/hydrophobic balance between L-VEVE peptide play structure-directing role in forming filament-like or nanoribbon morphology. This work provides a new sight to rationally design and precisely control the nanostructure of PDCs based on aromatic fragment.

Self Assembled Particles

NASA Technical Reports Server (NTRS)

Palacci, Jeremie (Inventor); Pine, David J. (Inventor); Chaikin, Paul Michael (Inventor); Sacanna, Stefano (Inventor)

2017-01-01

A self-assembling structure using non-equilibrium driving forces leading to 'living crystals' and other maniputable particles with a complex dynamics. The dynamic self-assembly assembly results from a competition between self-propulsion of particles and an attractive interaction between the particles. As a result of non-equilibrium driving forces, the crystals form, grow, collide, anneal, repair themselves and spontaneously self-destruct, thereby enabling reconfiguration and assembly to achieve a desired property.

Toward three-dimensional microelectronic systems: directed self-assembly of silicon microcubes via DNA surface functionalization.

PubMed

Lämmerhardt, Nico; Merzsch, Stephan; Ledig, Johannes; Bora, Achyut; Waag, Andreas; Tornow, Marc; Mischnick, Petra

2013-07-02

The huge and intelligent processing power of three-dimensional (3D) biological "processors" like the human brain with clock speeds of only 0.1 kHz is an extremely fascinating property, which is based on a massively parallel interconnect strategy. Artificial silicon microprocessors are 7 orders of magnitude faster. Nevertheless, they do not show any indication of intelligent processing power, mostly due to their very limited interconnectivity. Massively parallel interconnectivity can only be realized in three dimensions. Three-dimensional artificial processors would therefore be at the root of fabricating artificially intelligent systems. A first step in this direction would be the self-assembly of silicon based building blocks into 3D structures. We report on the self-assembly of such building blocks by molecular recognition, and on the electrical characterization of the formed assemblies. First, planar silicon substrates were functionalized with self-assembling monolayers of 3-aminopropyltrimethoxysilane for coupling of oligonucleotides (single stranded DNA) with glutaric aldehyde. The oligonucleotide immobilization was confirmed and quantified by hybridization with fluorescence-labeled complementary oligonucleotides. After the individual processing steps, the samples were analyzed by contact angle measurements, ellipsometry, atomic force microscopy, and fluorescence microscopy. Patterned DNA-functionalized layers were fabricated by microcontact printing (μCP) and photolithography. Silicon microcubes of 3 μm edge length as model objects for first 3D self-assembly experiments were fabricated out of silicon-on-insulator (SOI) wafers by a combination of reactive ion etching (RIE) and selective wet etching. The microcubes were then surface-functionalized using the same protocol as on planar substrates, and their self-assembly was demonstrated both on patterned silicon surfaces (88% correctly placed cubes), and to cube aggregates by complementary DNA

Self-interaction corrections applied to Mg-porphyrin, C60, and pentacene molecules

NASA Astrophysics Data System (ADS)

Pederson, Mark R.; Baruah, Tunna; Kao, Der-you; Basurto, Luis

2016-04-01

We have applied a recently developed method to incorporate the self-interaction correction through Fermi orbitals to Mg-porphyrin, C60, and pentacene molecules. The Fermi-Löwdin orbitals are localized and unitarily invariant to the Kohn-Sham orbitals from which they are constructed. The self-interaction-corrected energy is obtained variationally leading to an optimum set of Fermi-Löwdin orbitals (orthonormalized Fermi orbitals) that gives the minimum energy. A Fermi orbital, by definition, is dependent on a certain point which is referred to as the descriptor position. The degree to which the initial choice of descriptor positions influences the variational approach to the minimum and the complexity of the energy landscape as a function of Fermi-orbital descriptors is examined in detail for Mg-porphyrin. The applications presented here also demonstrate that the method can be applied to larger molecular systems containing a few hundred electrons. The atomization energy of the C60 molecule within the Fermi-Löwdin-orbital self-interaction-correction approach is significantly improved compared to local density approximation in the Perdew-Wang 92 functional and generalized gradient approximation of Perdew-Burke-Ernzerhof functionals. The eigenvalues of the highest occupied molecular orbitals show qualitative improvement.

Optical Gas Sensing of Ammonia and Amines Based on Protonated Porphyrin/TiO2 Composite Thin Films

PubMed Central

Castillero, Pedro; Roales, Javier; Lopes-Costa, Tânia; Sánchez-Valencia, Juan R.; Barranco, Angel; González-Elipe, Agustín R.; Pedrosa, José M.

2016-01-01

Open porous and transparent microcolumnar structures of TiO2 prepared by physical vapour deposition in glancing angle configuration (GLAD-PVD) have been used as host matrices for two different fluorescent cationic porphyrins, 5-(N-methyl 4-pyridyl)-10,15,20-triphenyl porphine chloride (MMPyP) and meso-tetra (N-methyl 4-pyridyl) porphine tetrachloride (TMPyP). The porphyrins have been anchored by electrostatic interactions to the microcolumns by self-assembly through the dip-coating method. These porphyrin/TiO2 composites have been used as gas sensors for ammonia and amines through previous protonation of the porphyrin with HCl followed by subsequent exposure to the basic analyte. UV–vis absorption, emission, and time-resolved spectroscopies have been used to confirm the protonation–deprotonation of the two porphyrins and to follow their spectral changes in the presence of the analytes. The monocationic porphyrin has been found to be more sensible (up to 10 times) than its tetracationic counterpart. This result has been attributed to the different anchoring arrangements of the two porphyrins to the TiO2 surface and their different states of aggregation within the film. Finally, there was an observed decrease of the emission fluorescence intensity in consecutive cycles of exposure and recovery due to the formation of ammonium chloride inside the film. PMID:28025570

Three-Dimensional Self-Assembled Photonic Crystal Waveguide

NASA Astrophysics Data System (ADS)

Baek, Kang-Hyun

Photonic crystals (PCs), two- or three-dimensionally periodic, artificial, and dielectric structures, have a specific forbidden band for electromagnetic waves, referred to as photonic bandgap (PBG). The PBG is analogous to the electronic bandgap in natural crystal structures with periodic atomic arrangement. A well-defined and embedded planar, line, or point defect within the PCs causes a break in its structural periodicity, and introduces a state in the PBG for light localization. It offers various applications in integrated optics and photonics including optical filters, sharp bending light guides and very low threshold lasers. Using nanofabrication processes, PCs of the 2-D slab-type and 3-D layer-by-layer structures have been investigated widely. Alternatively, simple and low-cost self-assembled PCs with full 3-D PBG, inverse opals, have been suggested. A template with face centered cubic closed packed structure, opal, may initially be built by self-assembly of colloidal spheres, and is selectively removed after infiltrating high refractive index materials into the interstitials of spheres. In this dissertation, the optical waveguides utilizing the 3-D self-assembled PCs are discussed. The waveguides were fabricated by microfabrication technology. For high-quality colloidal silica spheres and PCs, reliable synthesis, self-assembly, and characterization techniques were developed. Its theoretical and experimental demonstrations are provided and correlated. They suggest that the self-assembled PCs with PBG are feasible for the applications in integrated optics and photonics.

Complete Structure of an Epithelial Keratin Dimer: Implications for Intermediate Filament Assembly.

PubMed

Bray, David J; Walsh, Tiffany R; Noro, Massimo G; Notman, Rebecca

2015-01-01

Keratins are cytoskeletal proteins that hierarchically arrange into filaments, starting with the dimer sub-unit. They are integral to the structural support of cells, in skin, hair and nails. In skin, keratin is thought to play a critical role in conferring the barrier properties and elasticity of skin. In general, the keratin dimer is broadly described by a tri-domain structure: a head, a central rod and a tail. As yet, no atomistic-scale picture of the entire dimer structure exists; this information is pivotal for establishing molecular-level connections between structure and function in intermediate filament proteins. The roles of the head and tail domains in facilitating keratin filament assembly and function remain as open questions. To address these, we report results of molecular dynamics simulations of the entire epithelial human K1/K10 keratin dimer. Our findings comprise: (1) the first three-dimensional structural models of the complete dimer unit, comprising of the head, rod and tail domains; (2) new insights into the chirality of the rod-domain twist gained from analysis of the full domain structure; (3) evidence for tri-subdomain partitioning in the head and tail domains; and, (4) identification of the residue characteristics that mediate non-covalent contact between the chains in the dimer. Our findings are immediately applicable to other epithelial keratins, such as K8/K18 and K5/K14, and to intermediate filament proteins in general.

Structural and optical properties of self-assembled chains of plasmonic nanocubes

DOE PAGES

Klinkova, Anna; Gang, Oleg; Therien-Aubin, Heloise; ...

2014-10-10

Solution-based linear self-assembly of metal nanoparticles offers a powerful strategy for creating plasmonic polymers, which, so far, have been formed from spherical nanoparticles and nanorods. Here, we report linear solution-based self-assembly of metal nanocubes (NCs), examine the structural characteristics of the NC chains and demonstrate their advanced optical characteristics. Predominant face-to-face assembly of large NCs coated with short polymer ligands led to a larger volume of hot spots in the chains, a nearly uniform E-field enhancement in the gaps between co-linear NCs and a new coupling mode for NC chains, in comparison with chains of nanospheres with similar dimensions, compositionmore » and surface chemistry. The NC chains exhibited a stronger surface enhanced Raman scattering (SERS) signal, in comparison with linear assemblies of nanospheres. The experimental results were in agreement with finite difference time domain (FDTD) simulations.« less

Assemblies of Boron Dipyrromethene/Porphyrin, Phthalocyanine, and C60 Moieties as Artificial Models of Photosynthesis: Synthesis, Supramolecular Interactions, and Photophysical Studies.

PubMed

Chen, Xiao-Fei; El-Khouly, Mohamed E; Ohkubo, Kei; Fukuzumi, Shunichi; Ng, Dennis K P

2018-03-12

A series of light-harvesting conjugates based on a zinc(II) phthalocyanine core with either two or four boron dipyrromethene (BODIPY) or porphyrin units have been synthesized and characterized. The conjugation of BODIPY/porphyrin units can extend the absorptions of the phthalocyanine core to cover most of the visible region. Upon addition of an imidazole-substituted C 60 (C 60 Im), it can axially bind to the zinc(II) center of the phthalocyanine core through metal-ligand interactions. The resulting complexes form photosynthetic antenna-reaction center mimics in which the BODIPY/porphyrin units serve as the antennas to capture the light and transfer the energy to the phthalocyanine core by efficient excitation energy transfer. The excited phthalocyanine is then quenched by the axially bound C 60 Im moiety by electron transfer, which has been supported by computational studies. The photoinduced processes of the assemblies have been studied in detail by various steady-state and time-resolved spectroscopic methods. By femtosecond transient absorption spectroscopic studies, the lifetimes of the charge-separated state of the bis(BODIPY) and bis(porphyrin) systems have been determined to be 3.2 and 4.0 ns, respectively. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Formation of a Fluorous/Organic Biphasic Supramolecular Octopus Assembly for Enhanced Porphyrin Phosphorescence in Air

DOE PAGES

Yang, Chi; Arvapally, Ravi K.; Tekarli, Sammer M.; ...

2015-03-03

The trinuclear triangle-shaped system [tris{3,5-bis(heptafluoropropyl)-1,2,4-triazolatosilver(I)}] (1) and the multi-armed square-shaped metalloporphyrin PtOEP or the free porphyrin base H2OEP serve as excellent octopus hosts (OEP=2,3,7,8,12,13,17,18-octaethyl-21H,23H-porphine). Coupling of the fluorous/organic molecular octopi 1 and H2OEP or PtOEP by strong quadrupole-quadrupole and metal- interactions affords the supramolecular assemblies [1PtOEP] or [1H(2)OEP] (2a), which feature nanoscopic cavities surrounding the upper triangular and lower square cores. The fluorous/organic biphasic configuration of [1PtOEP] leads to an increase in the phosphorescence of PtOEP under ambient conditions. Guest molecules can be included in the biphasic double-octopus assembly in three different site-selective modes.

Chemistry of anthracene-acetylene oligomers XXV: on-surface chirality of a self-assembled molecular network of a fan-blade-shaped anthracene-acetylene macrocycle with a long alkyl chain.

PubMed

Tsuya, Takuya; Iritani, Kohei; Tahara, Kazukuni; Tobe, Yoshito; Iwanaga, Tetsuo; Toyota, Shinji

2015-03-27

An anthracene cyclic dimer with two different linkers and a dodecyl group was synthesized by means of coupling reactions. The calculated structure had a planar macrocyclic π core and a linear alkyl chain. Scanning tunneling microscopy observations at the 1-phenyloctane/graphite interface revealed that the molecules formed a self-assembled monolayer that consisted of linear striped bright and dark bands. In each domain, the molecular network consisted of either Re or Si molecules that differed in the two-dimensional chirality about the macrocyclic faces, which led to a unique conglomerate-type self-assembly. The molecular packing mode and the conformation of the alkyl chains are discussed in terms of the intermolecular interactions and the interactions between the molecules and the graphite surface with the aid of MM3 simulations of a model system. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The Self-Assembly of Nanogold for Optical Metamaterials

NASA Astrophysics Data System (ADS)

Nidetz, Robert A.

2011-12-01

nanoparticles and larger poly(styrene) ligands resulted in larger and smaller assemblies, respectively. Stirring the solution resulted in a wider size distribution of microbead assemblies due to the stirring's shear forces. Two undeveloped methods to self-assemble nanogold were investigated. One method used block-copolymer thin films as chemical templates to direct the electrostatic self-assembly of nanogold. Another method used gold nanorods that are passivated with different ligands on different faces. The stability of an alkanethiol ligand in different acids and bases was investigated to determine which materials could be used to produce Janus nanorods.

Photoelectrocatalytic Synthesis of Hydrogen Peroxide by Molecular Copper-Porphyrin Supported on Titanium Dioxide Nanotubes.

PubMed

Apaydin, Dogukan H; Seelajaroen, Hathaichanok; Pengsakul, Orathip; Thamyongkit, Patchanita; Sariciftci, Niyazi Serdar; Kunze-Liebhäuser, Julia; Portenkirchner, Engelbert

2018-04-24

We report on a self-assembled system comprising a molecular copper-porphyrin photoelectrocatalyst, 5-(4-carboxy-phenyl)-10,15,20-triphenylporphyrinatocopper(II) (CuTPP-COOH), covalently bound to self-organized, anodic titania nanotube arrays (TiO 2 NTs) for photoelectrochemical reduction of oxygen. Visible light irradiation of the porphyrin-covered TiO 2 NTs under cathodic polarization up to -0.3 V vs. Normal hydrogen electrode (NHE) photocatalytically produces H 2 O 2 in pH neutral electrolyte, at room temperature and without need of sacrificial electron donors. The formation of H 2 O 2 upon irradiation is proven and quantified by direct colorimetric detection using 4-nitrophenyl boronic acid ( p -NPBA) as a reactant. This simple approach for the attachment of a small molecular catalyst to TiO 2 NTs may ultimately allow for the preparation of a low-cost H 2 O 2 evolving cathode for efficient photoelectrochemical energy storage under ambient conditions.

Self-Assembly of Flux-Closure Polygons from Magnetite Nanocubes.

PubMed

Szyndler, Megan W; Corn, Robert M

2012-09-06

Well-defined nanoscale flux-closure polygons (nanogons) have been fabricated on hydrophilic surfaces from the face-to-face self-assembly of magnetite nanocubes. Uniform ferrimagnetic magnetite nanocubes (∼86 nm) were synthesized and characterized with a combination of electron microscopy, diffraction, and magnetization measurements. The nanocubes were subsequently cast onto hydrophilic substrates, wherein the cubes lined up face-to-face and formed a variety of polygons due to magnetostatic and hydrophobic interactions. The generated surfaces consist primarily of three- and four-sided nanogons; polygons ranging from two to six sides were also observed. Further examination of the nanogons showed that the constraints of the face-to-face assembly of nanocubes often led to bowed sides, strained cube geometries, and mismatches at the acute angle vertices. Additionally, extra nanocubes were often present at the vertices, suggesting the presence of external magnetostatic fields at the polygon corners. These nanogons are inimitable nanoscale magnetic structures with potential applications in the areas of magnetic memory storage and high-frequency magnetics.

Charge Transfer Modulated Self-Assembly in Poly(aryl ether) Dendron Derivatives with Improved Stability and Transport Characteristics.

PubMed

Satapathy, Sitakanta; Prasad, Edamana

2016-10-05

Alteration of native gelation properties of anthracene and pyrene cored first generation poly(aryl ether) dendrons, G1-An and G1-Py, by introducing a common acceptor, 2,4,7-trinitro-9H-fluoren-9-one (TNF), results in forming charge transfer gels in long chain alcoholic solvents. This strategy leads to significant perturbation of optical and electronic properties within the gel matrix. Consequently, a noticeable increase of their electrical conductivities is observed, making these poly(aryl ether) dendron based gels potential candidates for organic electronics. While the dc-conductivity (σ) value for the native gel from G1-An is 2.8 × 10 -4 S m -1 , the value increased 3 times (σ = 8.7 × 10 -4 S m -1 ) for its corresponding charge transfer gel. Further, the dc-conductivity for the native gel self-assembled from G1-Py dramatically enhanced by approximately an order of magnitude from 4.9 × 10 -4 to 1.3 × 10 -3 S m -1 , under the influence of an acceptor. Apart from H-bonding and π···π interactions, charge transfer results in the formation of a robust 3D network of fibers, with improved aspect ratio, providing high thermo-mechanical stability to the gels compared to the native ones. The charge transfer gels self-assembled from G1-An/TNF (1:1) and G1-Py/TNF exhibit a 7.3- and 2.5-fold increase in their yield stress, respectively, compared to their native assemblies. A similar trend follows in the case of their thermal stabilities. This is attributed to the typical bilayer self-assembly of the former which is not present in the case of G1-Py/TNF charge transfer gel. Density functional calculations provide deeper insights accounting for the role of charge transfer interactions in the mode of self-assembly. The 1D potential energy surface for the G1-An/TNF dimer and G1-Py/TNF dimer is found to be 11.8 and 1.9 kcal mol -1 more stable than their corresponding native gel dimers, G1-An/G1-An and G1-Py/G1-Py, respectively.

Self-assembling of dihydroxypropyl 5,6-dihydrothymine derivatives

NASA Astrophysics Data System (ADS)

Cetina, Mario; Makarević, Janja; Nura-Lama, Afërdita

2010-09-01

( R, S)-1-(2',3'-Dibenzoyloxypropyl)-5,6-dihydrothymine ( 2) was synthesized from ( R, S)-1-(2',3'-dihydroxypropyl)-5,6-dihydrothymine and its structure has been analyzed by X-ray diffraction, NMR and FTIR spectroscopic methods. The molecular structure and supramolecular assembling of 2 is compared with the structure of its dimesyloxypropyl analogue ( 1). Compound 1 crystallizes as cocrystal of two diastereoisomers, while 2 crystallizes as a racemic mixture. Main hydrogen-bonded motif in both compounds is dimer formed by pair of N sbnd H···O( dbnd C) hydrogen bonds, which are further linked by C sbnd H···O hydrogen bonds. Phenyl rings of dibenzoyl-dihydropyrimidine moieties of 2 participate also in supramolecular aggregation via three C sbnd H···π interactions. Hydrogen bonding as driving force of 2 self-assembly was proving by the NMR and FTIR spectroscopy.

Efficient solar-assisted O2 reduction by a cofacial iron porphyrin dimer integrated to a p-CuBi2O4 photocathode prepared by a simple novel method.

PubMed

Zahran, Zaki N; Mohamed, Eman A; Naruta, Yoshinori; Haleem, Ashraf

2017-10-04

A cofacial iron porphyrin hetero-dimer, Fe2TPFPP-TMP showed high electro-catalytic activity, selectivity, and stability for the O2 reduction to H2O both in homogeneous non-aqueous and heterogeneous neutral aqueous solutions. Moreover, when it is integrated to FTO/p-CuBi2O4 (FTO = fluorine doped tin oxide) photocathode prepared by a simple novel method, a remarkable efficient solar-assisted O2 reduction is achieved in neutral potassium phosphate (KPi) or basic NaOH solutions saturated with O2. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Role of local assembly in the hierarchical crystallization of associating colloidal hard hemispheres

NASA Astrophysics Data System (ADS)

Lei, Qun-li; Hadinoto, Kunn; Ni, Ran

2017-10-01

Hierarchical self-assembly consisting of local associations of simple building blocks for the formation of complex structures widely exists in nature, while the essential role of local assembly remains unknown. In this work, by using computer simulations, we study a simple model system consisting of associating colloidal hemispheres crystallizing into face-centered-cubic crystals comprised of spherical dimers of hemispheres, focusing on the effect of dimer formation on the hierarchical crystallization. We found that besides assisting the crystal nucleation because of increasing the symmetry of building blocks, the association between hemispheres can also induce both reentrant melting and reentrant crystallization depending on the range of interaction. Especially when the interaction is highly sticky, we observe a novel reentrant crystallization of identical crystals, which melt only in a certain temperature range. This offers another axis in fabricating responsive crystalline materials by tuning the fluctuation of local association.

Electrically conducting porphyrin and porphyrin-fullerene electropolymers

DOEpatents

Gust, Jr., John Devens; Liddell, Paul Anthony; Gervaldo, Miguel Andres; Bridgewater, James Ward; Brennan, Bradley James; Moore, Thomas Andrew; Moore, Ana Lorenzelli

2014-03-11

Compounds with aryl ring(s) at porphyrin meso position(s) bearing an amino group in position 4 relative to the porphyrin macrocycle, and at least one unsubstituted 5 (hydrogen-bearing) meso position with the 10-, 15-, and/or 20-relationship to the aryl ring bearing the amino group, and metal complexes thereof, feature broad spectral absorption throughout the visible region. These compounds are electropolymerized to form electrically conducting porphyrin and porphyrin-fullerene polymers that are useful in photovoltaic applications. The structure of one such electrically conducting porphyrin polymer is shown below. ##STR00001##

A coarse-grained model of microtubule self-assembly

NASA Astrophysics Data System (ADS)

Regmi, Chola; Cheng, Shengfeng

Microtubules play critical roles in cell structures and functions. They also serve as a model system to stimulate the next-generation smart, dynamic materials. A deep understanding of their self-assembly process and biomechanical properties will not only help elucidate how microtubules perform biological functions, but also lead to exciting insight on how microtubule dynamics can be altered or even controlled for specific purposes such as suppressing the division of cancer cells. Combining all-atom molecular dynamics (MD) simulations and the essential dynamics coarse-graining method, we construct a coarse-grained (CG) model of the tubulin protein, which is the building block of microtubules. In the CG model a tubulin dimer is represented as an elastic network of CG sites, the locations of which are determined by examining the protein dynamics of the tubulin and identifying the essential dynamic domains. Atomistic MD modeling is employed to directly compute the tubulin bond energies in the surface lattice of a microtubule, which are used to parameterize the interactions between CG building blocks. The CG model is then used to study the self-assembly pathways, kinetics, dynamics, and nanomechanics of microtubules.

Subcomponent self-assembly and guest-binding properties of face-capped Fe4L4(8+) capsules.

PubMed

Bilbeisi, Rana A; Clegg, Jack K; Elgrishi, Noémie; de Hatten, Xavier; Devillard, Marc; Breiner, Boris; Mal, Prasenjit; Nitschke, Jonathan R

2012-03-21

A general method for preparing Fe(4)L(4) face-capped tetrahedral cages through subcomponent self-assembly was developed and has been demonstrated using four different C(3)-symmetric triamines, 2-formylpyridine, and iron(II). Three of the triamines were shown also to form Fe(2)L(3) helicates when the appropriate stoichiometry of subcomponents was used. Two of the cages were observed to have nearly identical Fe-Fe distances in the solid state, which enabled their ligands to be coincorporated into a collection of mixed cages. Only one of the cages combined a sufficiently large cavity with the sufficiently small pores required for guest binding, taking up a wide variety of guest species in size- and shape-selective fashion.

Self-assembled squares and triangles by simultaneous hydrogen bonding and metal coordination.

PubMed

Marshall, Laura J; de Mendoza, Javier

2013-04-05

Through the combination of hydrogen bonding and metal-templated self-assembly, molecular squares and molecular triangles are observed in chloroform solution upon the complexation of hydrogen-bonded dimers of para-pyridyl-substituted 2-ureido-4-[1H]-pyrimidinone (UPy) and an appropriate cis-substituted palladium complex. Molecular modeling studies and NMR analysis confirmed the presence of two distinct structures in solution: the tubular structure of the molecular square and propeller-bowl structure of the molecular triangle.

A systematic theoretical study of the electronic structures of porphyrin dimers: DFT and TD-DFT calculations on diporphyrins linked by ethane, ethene, ethyne, imine, and azo bridges.

PubMed

Rintoul, Llew; Harper, Shannon R; Arnold, Dennis P

2013-11-21

Theoretical calculations of the geometries, electronic structures and electronic absorption spectra of a series of covalently-linked porphyrin dimers are reported. The diporphyrins comprise 5,10,15-triphenylporphyrinatozinc(II) (ZnTriPP) units linked through the meso carbons by two-atom bridges, namely 1,2-ethanediyl (1), trans-1,2-ethenediyl (2), ethynediyl (3), 1,2-iminomethenediyl (4), and transdiazenediyl (5). The structures were optimised in toluene solvent by Density Functional Theory (DFT), using the integral equation formalism variant of the polarizable continuum model. The calculations were performed using the B3LYP functional and the 6-31G(d,p) basis set. The complete molecules were modelled, with no substitution of smaller groups on the periphery. In parallel, the compounds 2–5 were prepared by known or novel synthetic routes, to enable comparisons of experimental electronic absorption spectra with those calculated using time dependent-DFT at the same level of theory. As the ethane dimer 1 is not yet synthetically accessible, the model monomer meso-2-phenylethylZnTriPP was used for comparisons with the theoretical predictions. The results form a self-consistent set, enabling for the first time legitimate comparisons of the electronic structures of the series, especially regarding the degree to which the porphyrin p-systems interact by conjugation across the bridges. The theoretical calculations of the electronic transitions match the observed spectra in toluene to a remarkable degree, especially with respect to the peak maximum of the Q band, which represents to a large degree the energy of the HOMO–LUMO transition. The imine 4 is intrinsically polar due to the asymmetric bridge, and the HOMO is located almost exclusively on the ZnTriPP unit attached to the nitrogen of the imine, and the LUMO on the C-attached ring. Thus the Q-band transition is mapped as a comprehensive charge-transfer from the former ring to the latter. This may have consequences

Supramolecular self-assemblies of beta-cyclodextrins with aromatic tethers: factors governing the helical columnar versus linear channel superstructures.

PubMed

Liu, Yu; Fan, Zhi; Zhang, Heng-Yi; Yang, Ying-Wei; Ding, Fei; Liu, Shuang-Xi; Wu, Xue; Wada, Takehiko; Inoue, Yoshihisa

2003-10-31

A series of 6-O-(p-substituted phenyl)-modified beta-cyclodextrin derivatives, i.e., 6-O-(4-bromophenyl)-beta-CD (1), 6-O-(4-nitrophenyl)-beta-CD (2), 6-O-(4-formylphenyl)-beta-CD (3), 6-phenylselenyl-6-deoxy-beta-CD (4), and 6-O-(4-hydroxybenzoyl)-beta-CD (5), were synthesized, and their inclusion complexation behavior in aqueous solution and self-assembling behavior in the solid state were comparatively studied by NMR spectroscopy, microcalorimetry, crystallography, and scanning tunneling microscopy. Interestingly, (seleno)ethers 1-4 and ester 5 displayed distinctly different self-assembling behavior in the solid state, affording a successively threading head-to-tail polymeric helical structure for the (seleno)ethers or a mutually penetrating tail-to-tail dimeric columnar channel structure for the ester. Combining the present and previous structures reported for the relevant beta-CD derivatives, we further deduce that the pivot heteroatom, through which the aromatic substituent is tethered to beta-CD, plays a critical role in determining the helix structure, endowing the 2-fold and 4-fold axes to the N/O- and S/Se-pivoted beta-CD aggregates, respectively. This means that one can control the self-assembling orientation, alignment, and helicity in the solid state by finely tuning the pivot atom and the tether length. Further NMR and calorimetric studies on the self-assembling behavior in aqueous solution revealed that the dimerization step is the key to the formation of linear polymeric supramolecular architecture, which is driven by favorable entropic contributions.

Supramolecular Ferric Porphyrins as Cyanide Receptors in Aqueous Solution

PubMed Central

2011-01-01

All fundamental data about binding of the cyanide to a supramolecular complex composed of a per-O-methylated β-cyclodextrin dimer having an imidazole linker (Im3CD) and an anionic ferric porphyrin (Fe(III)TPPS) indicate that the Fe(III)TPPS/Im3CD complex is much better as an cyanide receptor in vivo than hydroxocobalamin, whose cyanide binding ability is lowered by its strong binding to serum proteins in the blood. PMID:24900285

Self-Assembled Pyridine-Dipyrrolate Cages.

PubMed

Zhang, Huacheng; Lee, Juhoon; Lammer, Aaron D; Chi, Xiaodong; Brewster, James T; Lynch, Vincent M; Li, Hao; Zhang, Zhan; Sessler, Jonathan L

2016-04-06

An inherently nonlinear pyridine dipyrrolate ligand, namely 2,6-bis(3,4-diethyl-5-carboxy-1H-pyrrol-2yl)pyridine (compound 1), is able to distinguish between different zinc(II) cation sources, namely Zn(acac)2 and Zn(OAc)2, respectively. This differentiation is manifest both in terms of the observed fluorescent behavior in mixed organic media and the reaction chemistry. Treatment of 1 with Zn(acac)2 gives rise to a cage dimer, cage-1, wherein two molecules of compound 1 act as double bridging units to connect two individual cage subunits. As inferred from X-ray crystallographic studies, this cage system consists of discrete zinc dimers with hydroxide bridges that, with the assistance of bound DMF solvent molecules, serve to fix the geometry and orientation of the pyridine dipyrrolate building blocks. When a different zinc source, Zn(OAc)2, is used to carry out an ostensibly similar complexation reaction with compound 1, an acetate-bridged 1D abacus-like cage polymer is obtained as inferred from X-ray diffraction analysis. This extended solid state structure, cage-2, contains individual zinc dimer cage submits and appears stabilized by solvent molecules (DMF) and the counteranion (acetate). Rod-like assemblies are also observed by DLS and SEM. This construct, in contrast to cage-1, proved fluorescent in mixed organic media. The structure of the ligand itself (i.e., in the absence of Zn(II)) was confirmed by X-ray crystallographic analysis and was found to assemble into a supramolecular polymer. Conversion to a dimer form was seen upon the addition of TBAOAc. On the basis of the metric parameters, the structures seen in the solid state are stabilized via hydrogen bonding interactions involving solvent molecules.

The impact of viral RNA on the association free energies of capsid protein assembly: bacteriophage MS2 as a case study.

PubMed

ElSawy, Karim M

2017-02-01

A large number of single-stranded RNA viruses assemble their capsid and their genomic material simultaneously. The RNA viral genome plays multiple roles in this process that are currently only partly understood. In this work, we investigated the thermodynamic basis of the role of viral RNA on the assembly of capsid proteins. The viral capsid of bacteriophage MS2 was considered as a case study. The MS2 virus capsid is composed of 60 AB and 30 CC protein dimers. We investigated the effect of RNA stem loop (the translational repressor TR) binding to the capsid dimers on the dimer-dimer relative association free energies. We found that TR binding results in destabilization of AB self-association compared with AB and CC association. This indicates that the association of the AB and CC dimers is the most likely assembly pathway for the MS2 virus, which explains the experimental observation of alternating patterns of AB and CC dimers in dominant assembly intermediates of the MS2 virus. The presence of viral RNA, therefore, dramatically channels virus assembly to a limited number of pathways, thereby enhancing the efficiency of virus self-assembly process. Interestingly, Thr59Ser and Thr45Ala mutations of the dimers, in the absence of RNA stem loops, lead to stabilization of AB self-association compared with the AB and CC associations, thereby channelling virus assembly towards a fivefold (AB) 5 pentamer intermediate, providing a testable hypothesis of our thermodynamic arguments.

STM imaging ortho- and para-fluorothiophenol self-assembled monolayers on Au(111).

PubMed

Jiang, Peng; Deng, Ke; Fichou, Denis; Xie, Si-Shen; Nion, Aymeric; Wang, Chen

2009-05-05

Self-assembled monolayers (SAMs) of para- and ortho-fluorothiophenol (p- and o-FTP) spontaneously formed on Au(111) substrate have been contrasted through investigation by a scanning tunneling microscope (STM) at room temperature. High-resolution STM imaging reveals that p-FTP adopts a 6 x radical3R30 degrees molecule arrangement containing six molecules. Two different kinds of p-FTP molecule dimer line structures have been formed on Au(111) by intermolecular pi-pi stacking along 112 substrate directions, besides a single p-FTP molecule line. In contrast, o-FTP molecules self-assemble into a much looser wave-like SAM, which can be described as a 5 x 3 radical3R30 degrees structure containing two molecules. Periodic density functional theory (DFT) calculations for the two systems suggest that these kinds of FTP molecules preferentially take the asymmetrical positions between 3-fold face-centered cubic (fcc) hollow and bridge sites on Au(111), tilting from the substrate surface. Theoretical simulation gives apparent average tilted angles of 58 degrees and 68 degrees for p-FTP and o-FTP with respect to the surface normal, respectively. This simulation shows that o-FTP is more inclined to lie down toward the Au(111) surface compared to p-FTP. The difference between p-FTP and o-FTP SAM structures can be qualitatively understood in terms of the variation of intermolecular dipole-dipole orientation. This suggests that, besides well-known Au-S and pi-pi interactions, electrostatic interactions including dipole-dipole, quadrupole-quadrupole, and dipole-quadrupole interactions might also play an important role in influencing the SAM structures formed by aromatic thiols with a permanent dipole moment.

Self-organized porphyrin nanomaterials for solar energy harvesting

NASA Astrophysics Data System (ADS)

Radivojevic, Ivana

New concepts in the design and function of organic dyes as sensitizers for solar energy harvesting are needed. Commercial viability constrains these designs: (a) cost effective synthesis, (b) long-term stability, and (c) an important goal is to reduce the environmental impact of the product at the end of its life cycle. Simple porphyrinoid dyes meet these constraints, but new modes of incorporation into devices are needed to increase the efficiency of charge separation that drives any photonic device designed to harvest light. In this thesis, we will show how complex material architectures on surfaces need not to be the result of complex molecular structures or strong intermolecular forces that form in solution and deposit intact onto surfaces. Varying environmental conditions we can dictate morphology of self-organized structures on surfaces. These studies provide further insights into the design principles, processing, and extent of electron and energy transfer in supramolecular porphyrin materials. We are also developing a new strategy to couple porphyrinoid dyes to oxide surfaces using hafnium and zirconium metalloporphyrins and metallophthalocyanines.The mode of dye attachment to oxide surfaces is a key parameter for the construction of efficient dye sensitized solar cells. Porphyrinoid dyes containing oxophylic group (IV) metal ions that protrude from on face of the macrocycle allow connections directly to oxide surfaces, wherein the metal ion serves as the conduit. Since the charge transport efficiency is mediated by appropriate matching of molecular HOMO-LUMO gaps to semiconductor band gaps, we will show characterized solution phase ground and excited redox potentials of these dyes, and also photophysical properties of dye excited state using transient absorbance spectroscopy.

Nucleoplasmin Binds Histone H2A-H2B Dimers through Its Distal Face*

PubMed Central

Ramos, Isbaal; Martín-Benito, Jaime; Finn, Ron; Bretaña, Laura; Aloria, Kerman; Arizmendi, Jesús M.; Ausió, Juan; Muga, Arturo; Valpuesta, José M.; Prado, Adelina

2010-01-01

Nucleoplasmin (NP) is a pentameric chaperone that regulates the condensation state of chromatin extracting specific basic proteins from sperm chromatin and depositing H2A-H2B histone dimers. It has been proposed that histones could bind to either the lateral or distal face of the pentameric structure. Here, we combine different biochemical and biophysical techniques to show that natural, hyperphosphorylated NP can bind five H2A-H2B dimers and that the amount of bound ligand depends on the overall charge (phosphorylation level) of the chaperone. Three-dimensional reconstruction of NP/H2A-H2B complex carried out by electron microscopy reveals that histones interact with the chaperone distal face. Limited proteolysis and mass spectrometry indicate that the interaction results in protection of the histone fold and most of the H2A and H2B C-terminal tails. This structural information can help to understand the function of NP as a histone chaperone. PMID:20696766

Self-organization of a self-assembled supramolecular rectangle, square, and three-dimensional cage on Au111 surfaces.

PubMed

Yuan, Qun-Hui; Wan, Li-Jun; Jude, Hershel; Stang, Peter J

2005-11-23

The structure and conformation of three self-assembled supramolecular species, a rectangle, a square, and a three-dimensional cage, on Au111 surfaces were investigated by scanning tunneling microscopy. These supramolecular assemblies adsorb on Au111 surfaces and self-organize to form highly ordered adlayers with distinct conformations that are consistent with their chemical structures. The faces of the supramolecular rectangle and square lie flat on the surface, preserving their rectangle and square conformations, respectively. The three-dimensional cage also forms well-ordered adlayers on the gold surface, forming regular molecular rows of assemblies. When the rectangle and cage were mixed together, the assemblies separated into individual domains, and no mixed adlayers were observed. These results provide direct evidence of the noncrystalline solid-state structures of these assemblies and information about how they self-organize on Au111 surfaces, which is of importance in the potential manufacturing of functional nanostructures and devices.

A highly directional fourfold hydrogen-bonding motif for supramolecular structures through self-assembly of fullerodendrimers.

PubMed

Hahn, Uwe; González, Juan J; Huerta, Elisa; Segura, Margarita; Eckert, Jean-François; Cardinali, François; de Mendoza, Javier; Nierengarten, Jean-François

2005-11-04

Supramolecular dendrimers resulting from the dimerization of fullerene-functionalized dendrons through a quadruple hydrogen-bonding motif were prepared. The synthetic strategy is based on the esterification of a tert-butoxycarbonyl (Boc)-protected 2-ureido-4-[1H]pyrimidinone precursor possessing an alcohol function with fullerodendrons bearing a carboxylic acid unit at the focal point. Subsequent acidic treatment to cleave the protecting group and reaction of the resulting amine with octylisocyanate affords the targeted compounds. As demonstrated by the results of MALDI-TOF mass spectrometry and 1H NMR spectroscopy, both of the 2-ureido-4-[1H]pyrimidinone derivatives form self-assembled dimers spontaneously through hydrogen-bonding interactions, thus leading to supramolecular structures containing two or ten fullerene moieties.

Self-Assembled Molecular Gear: A 4:1 Complex of Rh(III)Cl Tetraarylporphyrin and Tetra(p-pyridyl)cavitand.

PubMed

Nakamura, Munechika; Kishimoto, Kazuki; Kobori, Yasuhiro; Abe, Tomoka; Yoza, Kenji; Kobayashi, Kenji

2016-09-28

The components of a 4:1 mixture of Rh(III)Cl tetrakis(4-methylphenyl)porphyrin 1 and a bowl-shaped tetra(4-pyridyl)cavitand 4 self-assemble into a 4:1 complex 14•4 via Rh-pyridyl axial coordination bonds. The single-crystal X-ray diffraction analysis and variable-temperature (VT) (1)H NMR study of 14•4 indicated that 14•4 behaves as a quadruple interlocking gear with an inner space, wherein (i) four subunits-1 are gear wheels and four p-pyridyl groups in subunit-4 are axes of gear wheels, (ii) one subunit-1 and two adjacent subunits-1 interlock with one another cooperatively, and (iii) four subunits-1 in 14•4 rotate quickly at 298 K on the NMR time scale. Together, the extremely strong porphyrin-Rh-pyridyl axial coordination bond, the rigidity of the methylene-bridge cavitand as a scaffold of the pyridyl axes, and the cruciform arrangement of the interdigitating p-tolyl groups as the teeth moiety of the gear wheels in the assembling 14-unit make 14•4 function as a quadruple interlocking gear in solution. The gear function of 14•4 was also supported by the rotation behaviors of other 4:1 complexes: 24•4 and 34•4 obtained from Rh(III)Cl tetrakis[4-(4-methylphenyl)phenyl]porphyrin 2 or Rh(III)Cl tetrakis(3,5-dialkoxyphenyl)porphyrin 3 and 4 also served as quadruple interlocking gears, whereas 14•5 obtained from 1 and tetrakis[4-(4-pyridyl)phenyl]cavitand 5 did not behave as a gear. The results of activation parameters (ΔH(⧧), ΔS(⧧), and ΔG(⧧)) obtained from Eyring plots based on line-shape analysis of the VT (1)H NMR spectra of 14•4, 24•4, and 34•4 also support the interlocking rotation (geared coupled rotation) mechanism.

The marriage of peripherally metallated and directly linked porphyrins: bromidobis(phosphine)platinum(II) as a cation-stabilizing substituent on directly linked and fused triply linked diporphyrins.

PubMed

Hartnell, Regan D; Yoneda, Tomoki; Mori, Hirotaka; Osuka, Atsuhiro; Arnold, Dennis P

2013-11-01

A meso-bromidoplatiniobis(triphenylphosphine) η(1)-organometallic porphyrin monomer was prepared by the oxidative addition of meso-bromoZnDPP (DPP=dianion of 5,15-diphenylporphyrin) to a platinum(0) species. The meso-meso directly linked dimeric porphyrin (5) was prepared from this monomer by silver(I)-promoted oxidative coupling and planarized to give a triply linked dizinc(II) porphyrin dimer (8). Acidic demetallation of 8 afforded the bis(free base) 9. Dimer 5 was demetallated then remetallated with nickel(II) to give the dinickel(II) analogue 10, the X-ray crystal structure of which showed a twisted molecule with ruffled, orthogonal NiDPP rings, terminated by square-planar trans-[Pt(PPh3)2Br] units. New compounds were fully characterized spectroscopically, and the fused diporphyrin exhibited a broad, low-energy, near-IR electronic absorption band near 1100 nm. Electrochemical measurements of this series indicate that the organometallic fragment is a strong electron donor towards the porphyrin ring. The triply linked organometallic diporphyrin has a substantially lowered first one-electron oxidation potential (-0.35 V versus the ferrocene/ferrocenium couple (Fc/Fc(+))) and a narrow HOMO-LUMO gap of 0.96 V. Solutions prepared for NMR spectroscopy slowly decompose with degradation of the signals, which is attributed to partial oxidation to the cation radical. This paramagnetic species can be reduced in situ by hydrazine to restore the NMR spectrum to its former appearance. The combined influence of the two [Pt(PPh3)2Br] electron-donating substituents is sufficient to make dimer too aerobically unstable to allow further elaboration. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Grooved nanowires from self-assembling hairpin molecules for solar cells.

PubMed

Tevis, Ian D; Tsai, Wei-Wen; Palmer, Liam C; Aytun, Taner; Stupp, Samuel I

2012-03-27

One of the challenges facing bulk heterojunction organic solar cells is obtaining organized films during the phase separation of intimately mixed donor and acceptor components. We report here on the use of hairpin-shaped sexithiophene molecules to generate by self-assembly grooved nanowires as the donor component in bulk heterojunction solar cells. Photovoltaic devices were fabricated via spin-casting to produce by solvent evaporation a percolating network of self-assembled nanowires and fullerene acceptors. Thermal annealing was found to increase power conversion efficiencies by promoting domain growth while still maintaining this percolating network of nanostructures. The benefits of self-assembly and grooved nanowires were examined by building devices from a soluble sexithiophene derivative that does not form one-dimensional structures. In these systems, excessive phase separation caused by thermal annealing leads to the formation of defects and lower device efficiencies. We propose that the unique hairpin shape of the self-assembling molecules allows the nanowires as they form to interact well with the fullerenes in receptor-ligand type configurations at the heterojunction of the two domains, thus enhancing device efficiencies by 23%. © 2012 American Chemical Society

Synthesis and Characterization of Fatty Acid/Amino Acid Self-Assemblies

PubMed Central

Gajowy, Joanna; Bolikal, Durgadas; Kohn, Joachim; El Fray, Miroslawa

2014-01-01

In this paper, we discuss the synthesis and self-assembling behavior of new copolymers derived from fatty acid/amino acid components, namely dimers of linoleic acid (DLA) and tyrosine derived diphenols containing alkyl ester pendent chains, designated as “R” (DTR). Specific pendent chains were ethyl (E) and hexyl (H). These poly(aliphatic/aromatic-ester-amide)s were further reacted with poly(ethylene glycol) (PEG) and poly(ethylene glycol methyl ether) of different molecular masses, thus resulting in ABA type (hydrophilic-hydrophobic-hydrophilic) triblock copolymers. We used Fourier transform infrared (FTIR) and nuclear magnetic resonance (NMR) spectroscopies to evaluate the chemical structure of the final materials. The molecular masses were estimated by gel permeation chromatography (GPC) measurements. The self-organization of these new polymeric systems into micellar/nanospheric structures in aqueous environment was evaluated using ultraviolet/visible (UV-VIS) spectroscopy, dynamic light scattering (DLS) and transmission electron microscopy (TEM). The polymers were found to spontaneously self-assemble into nanoparticles with sizes in the range 196–239 nm and critical micelle concentration (CMC) of 0.125–0.250 mg/mL. The results are quite promising and these materials are capable of self-organizing into well-defined micelles/nanospheres encapsulating bioactive molecules, e.g., vitamins or antibacterial peptides for antibacterial coatings on medical devices. PMID:25347356

Core-shell nanosized assemblies mediated by the alpha-beta cyclodextrin dimer with a tumor-triggered targeting property.

PubMed

Quan, Chang-Yun; Chen, Jing-Xiao; Wang, Hui-Yuan; Li, Cao; Chang, Cong; Zhang, Xian-Zheng; Zhuo, Ren-Xi

2010-07-27

In this paper, the alpha-beta cyclodextrin dimer is designed via "click" chemistry to connect the hydrophilic and hydrophobic segments to form self-assembled noncovalently connected micelles (NCCMs) through host-guest interactions. A peptide containing the Arg-Gly-Asp (RGD) sequence was introduced to NCCMs as a target ligand to improve the cell uptake efficacy, while PEGylated technology was employed via benzoic-imine bonds to protect the ligands in normal tissues and body fluid. In addition, two fluorescent dyes were conjugated to different segments to track the formation of the micelles as well as the assemblies. It was found that the targeting property of NCCMs was switched off before reaching the tumor sites and switched on after removing the poly(ethylene glycol) (PEG) segment in the tumor sites, which was called "tumor-triggered targeting". With deshielding of the PEG segment, the drugs loaded in NCCMs could be released rapidly due to the thermoinduced phase transition. The new concept of "tumor-triggered targeting" proposed here has great potential for cancer treatment.

Self-Organization in Coordination-Driven Self-Assembly

PubMed Central

Northrop, Brian H.; Zheng, Yao-Rong; Chi, Ki-Whan; Stang, Peter J.

2009-01-01

Conspectus Self-assembly allows for the preparation of highly complex molecular and supramolecular systems from relatively simple starting materials. Typically, self-assembled supramolecules are constructed by combining complementary pairs of two highly symmetric molecular components, thus limiting the chances of forming unwanted side products. Combining asymmetric molecular components or multiple complementary sets of molecules in one complex mixture can produce myriad different ordered and disordered supramolecular assemblies. Alternatively, spontaneous self-organization phenomena can promote the formation of specific product(s) out of a collection of multiple possibilities. Self-organization processes are common throughout much of nature and are especially common in biological systems. Recently, researchers have studied self-organized self-assembly in purely synthetic systems. This Account describes our investigations of self-organization in the coordination-driven self-assembly of platinum(II)-based metallosupramolecules. The modularity of the coordination-driven approach to self-assembly has allowed us to systematically study a wide variety of different factors that can control the extent of supramolecular self-organization. In particular, we have evaluated the effects of the symmetry and polarity of ambidentate donor subunits, differences in geometrical parameters (e.g. the size, angularity, and dimensionality) of Pt(II)-based acceptors and organic donors, the influence of temperature and solvent, and the effects of intermolecular steric interactions and hydrophobic interactions on self-organization. Our studies have shown that the extent of self-organization in the coordination-driven self-assembly of both 2D polygons and 3D polyhedra ranges from no organization (a statistical mixture of multiple products), to amplified organization (wherein a particular product or products are favored over others), and all the way to the absolute self-organization of

From self-organization to self-assembly: a new materialism?

PubMed

Vincent, Bernadette Bensaude

2016-09-01

While self-organization has been an integral part of academic discussions about the distinctive features of living organisms, at least since Immanuel Kant's Critique of Judgement, the term 'self-assembly' has only been used for a few decades as it became a hot research topic with the emergence of nanotechnology. Could it be considered as an attempt at reducing vital organization to a sort of assembly line of molecules? Considering the context of research on self-assembly I argue that the shift of attention from self-organization to self-assembly does not really challenge the boundary between chemistry and biology. Self-assembly was first and foremost investigated in an engineering context as a strategy for manufacturing without human intervention and did not raise new perspectives on the emergence of vital organization itself. However self-assembly implies metaphysical assumptions that this paper tries to disentangle. It first describes the emergence of self-assembly as a research field in the context of materials science and nanotechnology. The second section outlines the metaphysical implications and will emphasize a sharp contrast between the ontology underlying two practices of self-assembly developed under the umbrella of synthetic biology. And unexpectedly, we shall see that chemists are less on the reductionist side than most synthetic biologists. Finally, the third section ventures some reflections on the kind of design involved in self-assembly practices.

Conformational Changes in the Hepatitis B Virus Core Protein Are Consistent with a Role for Allostery in Virus Assembly

DOE Office of Scientific and Technical Information (OSTI.GOV)

Packianathan, Charles; Katen, Sarah P.; Dann, III, Charles E.

2010-01-12

In infected cells, virus components must be organized at the right place and time to ensure assembly of infectious virions. From a different perspective, assembly must be prevented until all components are available. Hypothetically, this can be achieved by allosterically controlling assembly. Consistent with this hypothesis, here we show that the structure of the hepatitis B virus (HBV) core protein dimer, which can spontaneously self-assemble, is incompatible with capsid assembly. Systematic differences between core protein dimer and capsid conformations demonstrate linkage between the intradimer interface and interdimer contact surface. These structures also provide explanations for the capsid-dimer selectivity of somemore » antibodies and the activities of assembly effectors. Solution studies suggest that the assembly-inactive state is more accurately an ensemble of conformations. Simulations show that allostery supports controlled assembly and results in capsids that are resistant to dissociation. We propose that allostery, as demonstrated in HBV, is common to most self-assembling viruses.« less

Self-assembled via axial coordination magnesium porphyrin-imidazole appended fullerene dyad: spectroscopic, electrochemical, computational, and photochemical studies.

PubMed

D'Souza, Francis; El-Khouly, Mohamed E; Gadde, Suresh; McCarty, Amy L; Karr, Paul A; Zandler, Melvin E; Araki, Yasuyaki; Ito, Osamu

2005-05-26

Spectroscopic, redox, and electron transfer reactions of a self-assembled donor-acceptor dyad formed by axial coordination of magnesium meso-tetraphenylporphyrin (MgTPP) and fulleropyrrolidine appended with an imidazole coordinating ligand (C(60)Im) were investigated. Spectroscopic studies revealed the formation of a 1:1 C(60)Im:MgTPP supramolecular complex, and the anticipated 1:2 complex could not be observed because of the needed large amounts of the axial coordinating ligand. The formation constant, K(1), for the 1:1 complex was found to be (1.5 +/- 0.3) x 10(4) M(-1), suggesting fairly stable complex formation. The geometric and electronic structures of the dyads were probed by ab initio B3LYP/3-21G() methods. The majority of the highest occupied frontier molecular orbital (HOMO) was found to be located on the MgTPP entity, while the lowest unoccupied molecular orbital (LUMO) was on the fullerene entity, suggesting that the charge-separated state of the supramolecular complex is C(60)Im(*-):MgTPP(*+). Redox titrations involving MgTPP and C(60)Im allowed accurate determination of the oxidation and reduction potentials of the donor and acceptor entities in the supramolecular complex. These studies revealed more difficult oxidation, by about 100 mV, for MgTPP in the pentacoordinated C(60)Im:MgTPP compared to pristine MgTPP in o-dichlorobenzene. A total of six one-electron redox processes corresponding to the oxidation and reduction of the zinc porphyrin ring and the reduction of fullerene entities was observed within the accessible potential window of the solvent. The excited state events were monitored by both steady state and time-resolved emission as well as transient absorption techniques. In o-dichlorobenzene, upon coordination of C(60)Im to MgTPP, the main quenching pathway involved electron transfer from the singlet excited MgTPP to the C(60)Im moiety. The rate of forward electron transfer, k(CS), calculated from the picosecond time-resolved emission

The unique self-assembly/disassembly property of Archaeoglobus fulgidus ferritin and its implications on molecular release from the protein cage.

PubMed

Sana, Barindra; Johnson, Eric; Lim, Sierin

2015-12-01

In conventional in vitro encapsulation of molecular cargo, the multi-subunit ferritin protein cages are disassembled in extremely acidic pH and re-assembled in the presence of highly concentrated cargo materials, which results in poor yields due to the low-pH treatment. In contrast, Archaeoglobus fulgidus open-pore ferritin (AfFtn) and its closed-pore mutant (AfFtn-AA) are present as dimeric species in neutral buffers that self-assemble into cage-like structure upon addition of metal ions. To understand the iron-mediated self-assembly and ascorbate-mediated disassembly properties, we studied the iron binding and release profile of the AfFtn and AfFtn-AA, and the corresponding oligomerization of their subunits. Fe(2+) binding and conversion to Fe(3+) triggered the self-assembly of cage-like structures from dimeric species of AfFtn and AfFtn-AA subunits, while disassembly was induced by dissolving the iron core with reducing agents. The closed-pore AfFtn-AA has identical iron binding kinetics but lower iron release rates when compared to AfFtn. While the iron binding rate is proportional to Fe(2+) concentration, the iron release rate can be controlled by varying ascorbate concentrations. The AfFtn and AfFtn-AA cages formed by iron mineralization could be disassembled by dissolving the iron core. The open-pores of AfFtn contribute to enhanced reductive iron release while the small channels located at the 3-fold symmetry axis (3-fold channels) are used for iron uptake. The iron-mediated self-assembly/disassembly property of AfFtn offers a new set of molecular trigger for formation and dissociation of the protein cage, which can potentially regulate uptake and release of molecular cargo from protein cages. Copyright © 2015 Elsevier B.V. All rights reserved.

Withholding response to self-face is faster than to other-face.

PubMed

Zhu, Min; Hu, Yinying; Tang, Xiaochen; Luo, Junlong; Gao, Xiangping

2015-01-01

Self-face advantage refers to adults' response to self-face is faster than that to other-face. A stop-signal task was used to explore how self-face advantage interacted with response inhibition. The results showed that reaction times of self-face were faster than that of other-face not in the go task but in the stop response trials. The novelty of the finding was that self-face has shorter stop-signal reaction time compared to other-face in the successful inhibition trials. These results indicated the processing mechanism of self-face may be characterized by a strong response tendency and a corresponding strong inhibition control.

Self-assembling of 2,3-phenyl/thienyl-substituted acrylic acids over polycrystalline gold

NASA Astrophysics Data System (ADS)

Csankó, K.; Kozma, G.; Valkai, L.; Kukovecz, Á.; Kónya, Z.; Sipos, P.; Pálinkó, I.

2013-07-01

Self-assembling layers were formed from sulfur-containing cinnamic acid analogues over polycrystalline Au surface. The horizontal organising forces were strong O-H⋯O and weaker C-H⋯S hydrogen bonds (the former interaction kept together the acid dimers serving as the fundamental unit, while the latter was crucial in the construction of the 2D layers), while the vertical organisation forces were provided by Au-S covalent bonds. Measurements by atomic force, scanning electron, infrared and Raman microscopies attested that the dimers were situated in a nearly perpendicular fashion to the Au surface providing a ˜30-40 nm thick organic "carpet" and out of this layer occasionally, peaks with height of ˜100-120 nm grew out. The outgrowth of these surface structures were most probably governed by the defects of the polycrystalline metal surface.

Stereochemistry in subcomponent self-assembly.

PubMed

Castilla, Ana M; Ramsay, William J; Nitschke, Jonathan R

2014-07-15

incorporated in self-assembly reactions to control the stereochemistry of increasingly complex architectures. This strategy has also allowed exploration of the degree to which stereochemical information is propagated through tetrahedral frameworks cooperatively, leading to the observation of stereochemical coupling across more than 2 nm between metal stereocenters and the enantioselective synthesis of a face-capped tetrahedron containing no carbon stereocenters via a stereochemical memory effect. Several studies on the communication of stereochemistry between the configurationally flexible metal centers in tetrahedral metal-organic cages have shed light on the factors governing this process, allowing the synthesis of an asymmetric cage, obtained in racemic form, in which all symmetry elements have been broken. Finally, we discuss how stereochemical diversity leads to structural complexity in the structures prepared through subcomponent self-assembly. Initial use of octahedral metal templates with facial stereochemistry in subcomponent self-assembly, which predictably gave rise to structures of tetrahedral symmetry, was extended to meridional metal centers. These lower-symmetry linkages have allowed the assembly of a series of increasingly intricate 3D architectures of varying functionality. The knowledge gained from investigating different aspects of the stereochemistry of metal-templated assemblies thus not only leads to new means of structural control but also opens pathways toward functions such as stereoselective guest binding and transformation.

Reduced graphene oxide and porphyrin. An interactive affair in 2-D.

PubMed

Wojcik, Aleksandra; Kamat, Prashant V

2010-11-23

Photoexcited cationic 5,10,15,20-tetrakis(1-methyl-4-pyridinio)porphyrin tetra(p-toluenesulfonate) (TMPyP) undergoes charge-transfer interaction with chemically reduced graphene oxide (RGO). Formation of the ground-state TMPyP-RGO complex in solution is marked by the red-shift of the porphyrin absorption band. This complexation was analyzed by Benesi-Hildebrand plot. Porphyrin fluorescence lifetime reduced from 5 to 1 ns upon complexation with RGO, indicating excited-state interaction between singlet excited porphyrin and RGO. Femtosecond transient absorption measurements carried out with TMPyP adsorbed on RGO film revealed fast decay of the singlet excited state, followed by the formation of a longer-living product with an absorption maximum around 515 nm indicating the formation of a porphyrin radical cation. The ability of TMPyP-RGO to undergo photoinduced charge separation was further confirmed from the photoelectrochemical measurements. TMPyP-RGO coated conducting glass electrodes are capable of generating photocurrent under visible excitation. These results are indicative of the electron transfer between photoexcited porphyrin and RGO. The role of graphene in accepting and shuttling electrons in light-harvesting assemblies is discussed.

Self-face recognition in social context.

PubMed

Sugiura, Motoaki; Sassa, Yuko; Jeong, Hyeonjeong; Wakusawa, Keisuke; Horie, Kaoru; Sato, Shigeru; Kawashima, Ryuta

2012-06-01

The concept of "social self" is often described as a representation of the self-reflected in the eyes or minds of others. Although the appearance of one's own face has substantial social significance for humans, neuroimaging studies have failed to link self-face recognition and the likely neural substrate of the social self, the medial prefrontal cortex (MPFC). We assumed that the social self is recruited during self-face recognition under a rich social context where multiple other faces are available for comparison of social values. Using functional magnetic resonance imaging (fMRI), we examined the modulation of neural responses to the faces of the self and of a close friend in a social context. We identified an enhanced response in the ventral MPFC and right occipitoparietal sulcus in the social context specifically for the self-face. Neural response in the right lateral parietal and inferior temporal cortices, previously claimed as self-face-specific, was unaffected for the self-face but unexpectedly enhanced for the friend's face in the social context. Self-face-specific activation in the pars triangularis of the inferior frontal gyrus, and self-face-specific reduction of activation in the left middle temporal gyrus and the right supramarginal gyrus, replicating a previous finding, were not subject to such modulation. Our results thus demonstrated the recruitment of a social self during self-face recognition in the social context. At least three brain networks for self-face-specific activation may be dissociated by different patterns of response-modulation in the social context, suggesting multiple dynamic self-other representations in the human brain. Copyright © 2011 Wiley-Liss, Inc.

Chemical reactions directed Peptide self-assembly.

PubMed

Rasale, Dnyaneshwar B; Das, Apurba K

2015-05-13

Fabrication of self-assembled nanostructures is one of the important aspects in nanoscience and nanotechnology. The study of self-assembled soft materials remains an area of interest due to their potential applications in biomedicine. The versatile properties of soft materials can be tuned using a bottom up approach of small molecules. Peptide based self-assembly has significant impact in biology because of its unique features such as biocompatibility, straight peptide chain and the presence of different side chain functionality. These unique features explore peptides in various self-assembly process. In this review, we briefly introduce chemical reaction-mediated peptide self-assembly. Herein, we have emphasised enzymes, native chemical ligation and photochemical reactions in the exploration of peptide self-assembly.

Multiplexed mRNA Sensing and Combinatorial-Targeted Drug Delivery Using DNA-Gold Nanoparticle Dimers.

PubMed

Kyriazi, Maria-Eleni; Giust, Davide; El-Sagheer, Afaf H; Lackie, Peter M; Muskens, Otto L; Brown, Tom; Kanaras, Antonios G

2018-04-24

The design of nanoparticulate systems which can perform multiple synergistic functions in cells with high specificity and selectivity is of great importance in applications. Here we combine recent advances in DNA-gold nanoparticle self-assembly and sensing to develop gold nanoparticle dimers that are able to perform multiplexed synergistic functions within a cellular environment. These dimers can sense two mRNA targets and simultaneously or independently deliver one or two DNA-intercalating anticancer drugs (doxorubicin and mitoxantrone) in live cells. Our study focuses on the design of sophisticated nanoparticle assemblies with multiple and synergistic functions that have the potential to advance sensing and drug delivery in cells.

Optical fluoride sensor based on monomer-dimer equilibrium of scandium(III)-octaethylporphyrin in a plasticized polymeric film.

PubMed

Kang, Youngjea; Kampf, Jeff W; Meyerhoff, Mark E

2007-08-29

A fluoride-selective optical sensor based on scandium(III)-octaethylporphyrin (Sc(III)OEP) as an ionophore within a plasticized PVC film is described. The presence of fluoride ion in the aqueous sample phase increases the formation of a difluoro-bridged Sc(III)OEP dimer species in the polymer film. The ability of the Sc(III) porphyrin to form the dimeric structure in the presence of fluoride is confirmed by UV-vis spectroscopy and X-ray crystallography. For more practical sensing applications, a pH chromoionophore (ETH 7075) is added to the plasticized PVC film along with Sc(III)OEP and the observed optical response is based on coextraction of protons with sample phase fluoride to create the dimeric porphyrin and a protonated chromoionophore species. The selectivity pattern observed is F- > ClO4(-), SCN-, NO3(-) > Br-, Cl-. Only organic salicylate is a significant interferent. Fast and reversible fluoride response is observed over the range of 10(-4) to 10(-2) M fluoride, allowing use of the sensing film in a waveguide configuration for flow-injection measurements.

Optical Fluoride Sensor Based on Monomer-Dimer Equilibrium of Scandium(III)-Octaethylporphyrin in a Plasticized Polymeric Film

PubMed Central

Kang, Youngjea; Kampf, Jeff W.; Meyerhoff, Mark E.

2007-01-01

A fluoride-selective optical sensor based on scandium(III) octaethylporphyrin (Sc(III)OEP) as an ionophore within a plasticized PVC film is described. The presence of fluoride ion in the aqueous sample phase increases the formation of a difluoro-bridged Sc(III)OEP dimer species in the polymer film. The ability of the Sc(III) porphyrin to form the dimeric structure in the presence of fluoride is confirmed by UV-Vis spectroscopy and X-ray crystallography. For more practical sensing applications, a pH chromoionophore (ETH 7075) is added to the plasticized PVC film along with Sc(III)OEP and the observed optical response is based on co-extraction of protons with sample phase fluoride to create the dimeric porphyrin and a protonated chromoionophore species. The selectivity pattern observed is F-≫ClO4-, SCN-, NO3->Br-, Cl-. Only organic salicylate is a significant interferent. Fast and reversible fluoride response is observed over the range of 10-4 ~10-2 M fluoride, allowing use of the sensing film in a waveguide configuration for flow-injection measurements. PMID:17719905

Conformational adaptation and manipulation of manganese tetra(4-pyridyl)porphyrin molecules on Cu(111)

NASA Astrophysics Data System (ADS)

Chen, Xianwen; Lei, Shulai; Lotze, Christian; Czekelius, Constantin; Paulus, Beate; Franke, Katharina J.

2017-03-01

Porphyrins are highly flexible molecules and well known to adapt to their local environment via conformational changes. We studied the self-assembly of manganese meso-tetra(4-pyridyl)porphyrin (Mn-TPyP) molecules on a Cu(111) surface by low temperature scanning tunneling microscopy (STM) and atomic force microscopy (ATM). We observe molecular chains along the ⟨1 1 ¯ 0 ⟩ direction of the substrate. Within these chains, we identify two molecular conformations, which differ by the orientation of the upward bending of the macrocycle. Using density functional theory, we show that this saddle shape is a consequence of the rotation and inclination of the pyridyl groups towards Cu adatoms, which stabilize the metal-organic chains. The molecular conformations obey a strict alternation, reflecting the mutual enforcement of conformational adaptation in densely packed structures. Tunneling electrons from the STM tip can induce changes in the orientation of the pyridyl endgroups. The switching behaviour varies with the different adsorption configurations.

Chemical Reactions Directed Peptide Self-Assembly

PubMed Central

Rasale, Dnyaneshwar B.; Das, Apurba K.

2015-01-01

Fabrication of self-assembled nanostructures is one of the important aspects in nanoscience and nanotechnology. The study of self-assembled soft materials remains an area of interest due to their potential applications in biomedicine. The versatile properties of soft materials can be tuned using a bottom up approach of small molecules. Peptide based self-assembly has significant impact in biology because of its unique features such as biocompatibility, straight peptide chain and the presence of different side chain functionality. These unique features explore peptides in various self-assembly process. In this review, we briefly introduce chemical reaction-mediated peptide self-assembly. Herein, we have emphasised enzymes, native chemical ligation and photochemical reactions in the exploration of peptide self-assembly. PMID:25984603

Atomic force microscope characterization of self-assembly behaviors of cyclo[8] pyrrole on solid substrates

NASA Astrophysics Data System (ADS)

Xu, Hai; Zhao, Siqi; Xiong, Xiang; Jiang, Jinzhi; Xu, Wei; Zhu, Daoben; Zhang, Yi; Liang, Wenjie; Cai, Jianfeng

2017-04-01

Cyclo [8] pyrrole (CP) is a porphyrin analogue containing eight α-conjugated pyrrole units which are arranged in a nearly coplanar conformation. The π-π interactions between CP molecules lead to regular aggregations through a solution casting process. Using tapping mode atomic force microscope (AFM), we investigated the morphology of self-assembled aggregates formed by deposition of different CP solutions on different substrates. We found that in the n-butanol solution, nanofibrous structures could be formed on the silicon or mica surface. Interestingly, on the highly oriented pyrolytic graphite (HOPG) surface, or silicon and mica surface with a toluene solution, only irregular spherical structures were identified. The difference in the nanomorphology may be attributed to distinct interactions between molecule-molecule, molecule-solvent and molecule-substrate.

Bulk assembly of organic metal halide nanotubes

DOE PAGES

Lin, Haoran; Zhou, Chenkun; Tian, Yu; ...

2017-10-16

The organic metal halide hybrids welcome a new member with a one-dimensional (1D) tubular structure. Herein we report the synthesis and characterization of a single crystalline bulk assembly of organic metal halide nanotubes, (C 6H 13N 4) 3Pb 2Br 7. In a metal halide nanotube, six face-sharing metal halide dimers (Pb 2Br 9 5–) connect at the corners to form rings that extend in one dimension, of which the inside and outside surfaces are coated with protonated hexamethylenetetramine (HMTA) cations (C 6H 13N 4 +). This unique 1D tubular structure possesses highly localized electronic states with strong quantum confinement, resultingmore » in the formation of self-trapped excitons that give strongly Stokes shifted broadband yellowish-white emission with a photoluminescence quantum efficiency (PLQE) of ~7%. Finally, having realized single crystalline bulk assemblies of two-dimensional (2D) wells, 1D wires, and now 1D tubes using organic metal halide hybrids, our work significantly advances the research on bulk assemblies of quantum-confined materials.« less

Self-assembled nanomaterials for photoacoustic imaging

NASA Astrophysics Data System (ADS)

Wang, Lei; Yang, Pei-Pei; Zhao, Xiao-Xiao; Wang, Hao

2016-01-01

In recent years, extensive endeavors have been paid to construct functional self-assembled nanomaterials for various applications such as catalysis, separation, energy and biomedicines. To date, different strategies have been developed for preparing nanomaterials with diversified structures and functionalities via fine tuning of self-assembled building blocks. In terms of biomedical applications, bioimaging technologies are urgently calling for high-efficient probes/contrast agents for high-performance bioimaging. Photoacoustic (PA) imaging is an emerging whole-body imaging modality offering high spatial resolution, deep penetration and high contrast in vivo. The self-assembled nanomaterials show high stability in vivo, specific tolerance to sterilization and prolonged half-life stability and desirable targeting properties, which is a kind of promising PA contrast agents for biomedical imaging. Herein, we focus on summarizing recent advances in smart self-assembled nanomaterials with NIR absorption as PA contrast agents for biomedical imaging. According to the preparation strategy of the contrast agents, the self-assembled nanomaterials are categorized into two groups, i.e., the ex situ and in situ self-assembled nanomaterials. The driving forces, assembly modes and regulation of PA properties of self-assembled nanomaterials and their applications for long-term imaging, enzyme activity detection and aggregation-induced retention (AIR) effect for diagnosis and therapy are emphasized. Finally, we conclude with an outlook towards future developments of self-assembled nanomaterials for PA imaging.

Self-assembled nanomaterials for photoacoustic imaging.

PubMed

Wang, Lei; Yang, Pei-Pei; Zhao, Xiao-Xiao; Wang, Hao

2016-02-07

In recent years, extensive endeavors have been paid to construct functional self-assembled nanomaterials for various applications such as catalysis, separation, energy and biomedicines. To date, different strategies have been developed for preparing nanomaterials with diversified structures and functionalities via fine tuning of self-assembled building blocks. In terms of biomedical applications, bioimaging technologies are urgently calling for high-efficient probes/contrast agents for high-performance bioimaging. Photoacoustic (PA) imaging is an emerging whole-body imaging modality offering high spatial resolution, deep penetration and high contrast in vivo. The self-assembled nanomaterials show high stability in vivo, specific tolerance to sterilization and prolonged half-life stability and desirable targeting properties, which is a kind of promising PA contrast agents for biomedical imaging. Herein, we focus on summarizing recent advances in smart self-assembled nanomaterials with NIR absorption as PA contrast agents for biomedical imaging. According to the preparation strategy of the contrast agents, the self-assembled nanomaterials are categorized into two groups, i.e., the ex situ and in situ self-assembled nanomaterials. The driving forces, assembly modes and regulation of PA properties of self-assembled nanomaterials and their applications for long-term imaging, enzyme activity detection and aggregation-induced retention (AIR) effect for diagnosis and therapy are emphasized. Finally, we conclude with an outlook towards future developments of self-assembled nanomaterials for PA imaging.

Effect of amino acid mutations on intra-dimer tubulin-tubulin binding strength of microtubules.

PubMed

Liu, Ning; Pidaparti, Ramana; Wang, Xianqiao

2017-12-11

Energetic interactions inside αβ-tubulin dimers of a microtubule (MT) with atomic resolutions are of importance in determining the mechanical properties and structural stability of the MT as well as designing self-assembled functional structures from it. Here, we carry out several comprehensive atomistic simulations to investigate the interaction properties within αβ-tubulin dimers and effect of residue mutations on the intra-dimer tubulin-tubulin (IDTT) binding strength. Results indicate that the force-displacement responses of the dimer could be roughly divided into three stages involving increasing, decreasing, and fluctuating forces. Energetic analysis shows that electrostatic interactions dominate the IDTT binding strength. Further per-residue energetic analysis shows that the major part of the interface interaction energy (approximately 72% for α-tubulin and 62% for β-tubulin) comes from amino acid residues with net charges, namely arginine (ARG), lysine (LYS), glutamic acid (GLU), aspartic acid (ASP). Residue mutations are completed for ARG105 on α-tubulin and ASP251 on β-tubulin to study the effect of mutations on the IDTT binding strength. Results indicate that stiffness, rupture force, and interface interaction energy of αβ-tubulin dimer can be improved by up to 28%, 13% and 28%, respectively. Overall, our results provide a thorough atomistic understanding of the IDTT binding strength within αβ-tubulin heterodimers and help pave the way for eventually designing and controlling the self-assembled functional structures from MTs.

Slab photonic crystals with dimer colloid bases

DOE Office of Scientific and Technical Information (OSTI.GOV)

Riley, Erin K.; Liddell Watson, Chekesha M., E-mail: cliddell@ccmr.cornell.edu

2014-06-14

The photonic band gap properties for centered rectangular monolayers of asymmetric dimers are reported. Colloids in suspension have been organized into the phase under confinement. The theoretical model is inspired by the range of asymmetric dimers synthesized via seeded emulsion polymerization and explores, in particular, the band structures as a function of degree of lobe symmetry and degree of lobe fusion. These parameters are varied incrementally from spheres to lobe-tangent dimers over morphologies yielding physically realizable particles. The work addresses the relative scarcity of theoretical studies on photonic crystal slabs with vertical variation that is consistent with colloidal self-assembly. Odd,more » even and polarization independent gaps in the guided modes are determined for direct slab structures. A wide range of lobe symmetry and degree of lobe fusion combinations having Brillouin zones with moderate to high isotropy support gaps between odd mode band indices 3-4 and even mode band indices 1-2 and 2-3.« less

Real-space mapping of the strongly coupled plasmons of nanoparticle dimers.

PubMed

Kim, Deok-Soo; Heo, Jinhwa; Ahn, Sung-Hyun; Han, Sang Woo; Yun, Wan Soo; Kim, Zee Hwan

2009-10-01

We carried out the near-field optical imaging of isolated and dimerized gold nanocubes to directly investigate the strong coupling between two adjacent nanoparticles. The high-resolution (approximately 10 nm) local field maps (intensities and phases) of self-assembled nanocube dimers reveal antisymmetric plasmon modes that are starkly different from a simple superposition of two monomeric dipole plasmons, which is fully reproduced by the electrodynamics simulations. The result decisively proves that, for the closely spaced pair of nanoparticles (interparticle distance/particle size approximately 0.04), the strong Coulombic attraction between the charges at the interparticle gap dominates over the intraparticle charge oscillations, resulting in a hybridized dimer plasmon mode that is qualitatively different from those expected from a simple dipole-dipole coupling model.

Self-Assembly: How Nature Builds

ERIC Educational Resources Information Center

Jones, M. Gail; Falvo, Michael R.; Broadwell, Bethany; Dotger, Sharon

2006-01-01

Self-assembly or spontaneous assembly is a process in which materials build themselves without assistance. This process plays a central role in the construction of biological structures and materials such as cells, viruses, and bone, and also in abiotic processes like phase transitions and crystal formation. The principles of self-assembly help…

Studies on the Dissociation and Urea-Induced Unfolding of FtsZ Support the Dimer Nucleus Polymerization Mechanism

PubMed Central

Montecinos-Franjola, Felipe; Ross, Justin A.; Sánchez, Susana A.; Brunet, Juan E.; Lagos, Rosalba; Jameson, David M.; Monasterio, Octavio

2012-01-01

FtsZ is a major protein in bacterial cytokinesis that polymerizes into single filaments. A dimer has been proposed to be the nucleating species in FtsZ polymerization. To investigate the influence of the self-assembly of FtsZ on its unfolding pathway, we characterized its oligomerization and unfolding thermodynamics. We studied the assembly using size-exclusion chromatography and fluorescence spectroscopy, and the unfolding using circular dichroism and two-photon fluorescence correlation spectroscopy. The chromatographic analysis demonstrated the presence of monomers, dimers, and tetramers with populations dependent on protein concentration. Dilution experiments using fluorescent conjugates revealed dimer-to-monomer and tetramer-to-dimer dissociation constants in the micromolar range. Measurements of fluorescence lifetimes and rotational correlation times of the conjugates supported the presence of tetramers at high protein concentrations and monomers at low protein concentrations. The unfolding study demonstrated that the three-state unfolding of FtsZ was due to the mainly dimeric state of the protein, and that the monomer unfolds through a two-state mechanism. The monomer-to-dimer equilibrium characterized here (Kd = 9 μM) indicates a significant fraction (∼10%) of stable dimers at the critical concentration for polymerization, supporting a role of the dimeric species in the first steps of FtsZ polymerization. PMID:22824282

Inverse Problem in Self-assembly

NASA Astrophysics Data System (ADS)

Tkachenko, Alexei

2012-02-01

By decorating colloids and nanoparticles with DNA, one can introduce highly selective key-lock interactions between them. This leads to a new class of systems and problems in soft condensed matter physics. In particular, this opens a possibility to solve inverse problem in self-assembly: how to build an arbitrary desired structure with the bottom-up approach? I will present a theoretical and computational analysis of the hierarchical strategy in attacking this problem. It involves self-assembly of particular building blocks (``octopus particles''), that in turn would assemble into the target structure. On a conceptual level, our approach combines elements of three different brands of programmable self assembly: DNA nanotechnology, nanoparticle-DNA assemblies and patchy colloids. I will discuss the general design principles, theoretical and practical limitations of this approach, and illustrate them with our simulation results. Our crucial result is that not only it is possible to design a system that has a given nanostructure as a ground state, but one can also program and optimize the kinetic pathway for its self-assembly.

Self-esteem Modulates the P3 Component in Response to the Self-face Processing after Priming with Emotional Faces

PubMed Central

Guan, Lili; Zhao, Yufang; Wang, Yige; Chen, Yujie; Yang, Juan

2017-01-01

The self-face processing advantage (SPA) refers to the research finding that individuals generally recognize their own face faster than another’s face; self-face also elicits an enhanced P3 amplitude compared to another’s face. It has been suggested that social evaluation threats could weaken the SPA and that self-esteem could be regarded as a threat buffer. However, little research has directly investigated the neural evidence of how self-esteem modulates the social evaluation threat to the SPA. In the current event-related potential study, 27 healthy Chinese undergraduate students were primed with emotional faces (angry, happy, or neutral) and were asked to judge whether the target face (self, friend, and stranger) was familiar or unfamiliar. Electrophysiological results showed that after priming with emotional faces (angry and happy), self-face elicited similar P3 amplitudes to friend-face in individuals with low self-esteem, but not in individuals with high self-esteem. The results suggest that as low self-esteem raises fears of social rejection and exclusion, priming with emotional faces (angry and happy) can weaken the SPA in low self-esteem individuals but not in high self-esteem individuals. PMID:28868041

Self-esteem Modulates the P3 Component in Response to the Self-face Processing after Priming with Emotional Faces.

PubMed

Guan, Lili; Zhao, Yufang; Wang, Yige; Chen, Yujie; Yang, Juan

2017-01-01

The self-face processing advantage (SPA) refers to the research finding that individuals generally recognize their own face faster than another's face; self-face also elicits an enhanced P3 amplitude compared to another's face. It has been suggested that social evaluation threats could weaken the SPA and that self-esteem could be regarded as a threat buffer. However, little research has directly investigated the neural evidence of how self-esteem modulates the social evaluation threat to the SPA. In the current event-related potential study, 27 healthy Chinese undergraduate students were primed with emotional faces (angry, happy, or neutral) and were asked to judge whether the target face (self, friend, and stranger) was familiar or unfamiliar. Electrophysiological results showed that after priming with emotional faces (angry and happy), self-face elicited similar P3 amplitudes to friend-face in individuals with low self-esteem, but not in individuals with high self-esteem. The results suggest that as low self-esteem raises fears of social rejection and exclusion, priming with emotional faces (angry and happy) can weaken the SPA in low self-esteem individuals but not in high self-esteem individuals.

Active Glutaminase C Self-assembles into a Supratetrameric Oligomer That Can Be Disrupted by an Allosteric Inhibitor*

PubMed Central

Ferreira, Amanda Petrina Scotá; Cassago, Alexandre; Gonçalves, Kaliandra de Almeida; Dias, Marília Meira; Adamoski, Douglas; Ascenção, Carolline Fernanda Rodrigues; Honorato, Rodrigo Vargas; de Oliveira, Juliana Ferreira; Ferreira, Igor Monteze; Fornezari, Camila; Bettini, Jefferson; Oliveira, Paulo Sérgio Lopes; Paes Leme, Adriana Franco; Portugal, Rodrigo Villares; Ambrosio, Andre Luis Berteli; Dias, Sandra Martha Gomes

2013-01-01

The phosphate-dependent transition between enzymatically inert dimers into catalytically capable tetramers has long been the accepted mechanism for the glutaminase activation. Here, we demonstrate that activated glutaminase C (GAC) self-assembles into a helical, fiber-like double-stranded oligomer and propose a molecular model consisting of seven tetramer copies per turn per strand interacting via the N-terminal domains. The loop 321LRFNKL326 is projected as the major regulating element for self-assembly and enzyme activation. Furthermore, the previously identified in vivo lysine acetylation (Lys311 in humans, Lys316 in mouse) is here proposed as an important down-regulator of superoligomer assembly and protein activation. Bis-2-(5-phenylacetamido-1,3,4-thiadiazol-2-yl)ethyl sulfide, a known glutaminase inhibitor, completely disrupted the higher order oligomer, explaining its allosteric mechanism of inhibition via tetramer stabilization. A direct correlation between the tendency to self-assemble and the activity levels of the three mammalian glutaminase isozymes was established, with GAC being the most active enzyme while forming the longest structures. Lastly, the ectopic expression of a fiber-prone superactive GAC mutant in MDA-MB 231 cancer cells provided considerable proliferative advantages to transformed cells. These findings yield unique implications for the development of GAC-oriented therapeutics targeting tumor metabolism. PMID:23935106

Self-assembled biomimetic nanoreactors I: Polymeric template

NASA Astrophysics Data System (ADS)

McTaggart, Matt; Malardier-Jugroot, Cecile; Jugroot, Manish

2015-09-01

The variety of nanoarchitectures made feasible by the self-assembly of alternating copolymers opens new avenues for biomimicry. Indeed, self-assembled structures allow the development of nanoreactors which combine the efficiency of high surface area metal active centres to the effect of confinement due to the very small cavities generated by the self-assembly process. A novel self-assembly of high molecular weight alternating copolymers is characterized in the present study. The self-assembly is shown to organize into nanosheets, providing a 2 nm hydrophobic cavity with a 1D confinement.

Biocatalytic Self-Assembly on Magnetic Nanoparticles.

PubMed

Conte, Maria P; Sahoo, Jugal Kishore; Abul-Haija, Yousef M; Lau, K H Aaron; Ulijn, Rein V

2018-01-24

Combining (bio)catalysis and molecular self-assembly provides an effective approach for the production and processing of self-assembled materials by exploiting catalysis to direct the assembly kinetics and hence controlling the formation of ordered nanostructures. Applications of (bio)catalytic self-assembly in biologically interfacing systems and in nanofabrication have recently been reported. Inspired by self-assembly in biological cells, efforts to confine catalysts on flat or patterned surfaces to exert spatial control over molecular gelator generation and nanostructure self-assembly have also emerged. Building on our previous work in the area, we demonstrate in this report the use of enzymes immobilized onto magnetic nanoparticles (NPs) to spatially localize the initiation of peptide self-assembly into nanofibers around NPs. The concept is generalized for both an equilibrium biocatalytic system that forms stable hydrogels and a nonequilibrium system that normally has a preset lifetime. Characterization of the hydrogels shows that self-assembly occurs at the site of enzyme immobilization on the NPs to give rise to gels with a "hub-and-spoke" morphology, where the nanofibers are linked through the enzyme-NP conjugates. This NP-controlled arrangement of self-assembled nanofibers enables both remarkable enhancements in the shear strength of hydrogel systems and a dramatic extension of the hydrogel stability in the nonequilibrium system. We are also able to show that the use of magnetic NPs enables the external control of both the formation of the hydrogel and its overall structure by application of an external magnetic field. We anticipate that the enhanced properties and stimuli-responsiveness of our NP-enzyme system will have applications ranging from nanomaterial fabrication to biomaterials and biosensing.

Self-assembled ultrathin nanotubes on diamond (100) surface

NASA Astrophysics Data System (ADS)

Lu, Shaohua; Wang, Yanchao; Liu, Hanyu; Miao, Mao-Sheng; Ma, Yanming

2014-04-01

Surfaces of semiconductors are crucially important for electronics, especially when the devices are reduced to the nanoscale. However, surface structures are often elusive, impeding greatly the engineering of devices. Here we develop an efficient method that can automatically explore the surface structures using structure swarm intelligence. Its application to a simple diamond (100) surface reveals an unexpected surface reconstruction featuring self-assembled carbon nanotubes arrays. Such a surface is energetically competitive with the known dimer structure under normal conditions, but it becomes more favourable under a small compressive strain or at high temperatures. The intriguing covalent bonding between neighbouring tubes creates a unique feature of carrier kinetics (that is, one dimensionality of hole states, while two dimensionality of electron states) that could lead to novel design of superior electronics. Our findings highlight that the surface plays vital roles in the fabrication of nanodevices by being a functional part of them.

Self-Assembly at the Colloidal Scale

NASA Astrophysics Data System (ADS)

Zhong, Xiao

The existence of self-assembly, the phenomenon of spontaneous structural formation from building blocks, transcends many orders of magnitude, ranging from molecular to cosmic. It is arguably the most common, important, and complex question in science. This thesis aims for understanding a spectrum of self-assembly-self assembly at the colloidal scale. Of the whole spectrum of self-assembly, the colloidal scale is of particular interest and importance to researchers, for not only comprehensive tools for colloidal scale studies have been well established, but also the various promising applications colloidal self-assembly can facilitate. In this thesis, a high throughput technique-Polymer Pen Lithography (PPL) is modified and its potential for creating corrals for colloidal assembly is evaluated. Then two different approaches of assembling colloids are explored in depth. One of them is by using a phenomenon called dielectrophoresis (DEP) as driving force to manipulate colloidal nucleation and crystal growth. And the other takes advantage of the Pt-catalyzed H2O 2 redox reaction to drive micrometer-scaled, rod-shaped colloids to swim and assemble. Lastly, an optical method called Holographic Video Microscopy (HVM) is used to monitor and characterize "bad" self-assembly of proteins, that is their aggregations. The four studies discussed in this thesis represent advancements in the colloidal scale from different aspects. The PPL technique enriched the toolbox for colloidal self-assembly. The DEP driven colloidal nucleation and crystal growth shed light on deeper understanding the mechanism of crystallization. And the swimming and assembly of micro-scale rods leads to kinetics reminiscent of bacterial run-and-tumble motion. Finally, the HVM technique for monitoring and understanding protein aggregation could potentially lead to better quality assurance for therapeutic proteins and could be a powerful tool for assessing their shelf lives.

Modular Self-Assembly of Protein Cage Lattices for Multistep Catalysis

PubMed Central

Uchida, Masaki; McCoy, Kimberly; Fukuto, Masafumi; Yang, Lin; Yoshimura, Hideyuki; Miettinen, Heini M.; LaFrance, Ben; Patterson, Dustin P.; Schwarz, Benjamin; Karty, Jonathan A.; Prevelige, Peter E.; Lee, Byeongdu; Douglas, Trevor

2018-01-01

The assembly of individual molecules into hierarchical structures is a promising strategy for developing three-dimensional materials with properties arising from interaction between the individual building blocks. Virus capsids are elegant examples of biomolecular nanostructures, which are themselves hierarchically assembled from a limited number of protein subunits. Here we demonstrate the bio-inspired modular construction of materials with two levels of hierarchy; the formation of catalytically active individual virus-like particles (VLPs) through directed self-assembly of capsid subunits with enzyme encapsulation, and the assembly of these VLP building blocks into three-dimensional arrays. The structure of the assembled arrays was successfully altered from an amorphous aggregate to an ordered structure, with a face-centered cubic lattice, by modifying the exterior surface of the VLP without changing its overall morphology, to modulate interparticle interactions. The assembly behavior and resultant lattice structure was a consequence of interparticle interaction between exterior surfaces of individual particles, and thus independent of the enzyme cargos encapsulated within the VLPs. These superlattice materials, composed of two populations of enzyme packaged VLP modules, retained the coupled catalytic activity in a two-step reaction for isobutanol synthesis. This study demonstrates a significant step toward the bottom-up fabrication of functional superlattice materials using a self-assembly process across multiple length scales, and exhibits properties and function that arise from the interaction between individual building blocks. PMID:29131580

A designed point mutant in Fis1 disrupts dimerization and mitochondrial fission

PubMed Central

Lees, Jonathan P. B.; Manlandro, Cara Marie; Picton, Lora K.; Ebie Tan, Alexandra Z.; Casares, Salvador; Flanagan, John M.; Fleming, Karen G.; Hill, R. Blake

2012-01-01

Mitochondrial and peroxisomal fission are essential processes with defects resulting in cardiomyopathy and neonatal lethality. Central to organelle fission is Fis1, a monomeric tetratricopeptide-like repeat (TPR) protein whose role in assembly of the fission machinery remains obscure. Two non-functional, Saccharomyces cerevisiae Fis1 mutants (L80P or E78D/I85T/Y88H) were previously identified in genetic screens. Here, we find that these two variants in the cytosolic domain of Fis1 (Fis1ΔTM) are unexpectedly dimeric. A truncation variant of Fis1ΔTM that lacks an N-terminal regulatory domain is also found to be dimeric. The ability to dimerize is a property innate to the native Fis1ΔTM amino acid sequence as we find this domain is dimeric after transient exposure to elevated temperature or chemical denaturants and is kinetically trapped at room temperature. This is the first demonstration of a specific self-association in solution for the Fis1 cytoplasmic domain. We propose a three-dimensional domain-swapped model for dimerization that is validated by a designed mutation, A72P, which potently disrupts dimerization of wild type Fis1. A72P also disrupts dimerization of non-functional variants indicating a common structural basis for dimerization. The obligate monomer variant A72P, like the dimer-promoting variants, is non-functional in fission consistent with a model in which Fis1 activity depends on its ability to interconvert between monomer and dimer species. These studies suggest a new functionally important manner in which TPR containing proteins may reversibly self-associate. PMID:22789569

Nanoarchitectonics with Porphyrin Functionalized DNA

PubMed Central

2017-01-01

Conspectus DNA is well-known as bearer of the genetic code. Since its structure elucidation nearly seven decades ago by Watson, Crick, Wilkins, and Franklin, much has been learned about its detailed structure, function, and genetic coding. The development of automated solid-phase synthesis, and with it the availability of synthetic DNA with any desired sequence in lengths of up to hundreds of bases in the best case, has contributed much to the advancement of the field of DNA research. In addition, classic organic synthesis has allowed introduction of a very large number of modifications in the DNA in a sequence specific manner, which have initially been targeted at altering the biological function of DNA. However, in recent years DNA has become a very attractive scaffold in supramolecular chemistry, where DNA is taken out of its biological role and serves as both stick and glue molecule to assemble novel functional structures with nanometer precision. The attachment of functionalities to DNA has led to the creation of supramolecular systems with applications in light harvesting, energy and electron transfer, sensing, and catalysis. Functional DNA is clearly having a significant impact in the field of bioinspired nanosystems. Of particular interest is the use of porphyrins in supramolecular chemistry and bionanotechnology, because they are excellent functional groups due to their electronic properties that can be tailored through chemical modifications of the aromatic core or through insertion of almost any metal of the periodic table into the central cavity. The porphyrins can be attached either to the nucleobase, to the phosphate group, or to the ribose moiety. Additionally, noncovalent templating through Watson–Crick base pairing forms an alternative and attractive approach. With this, the combination of two seemingly simple molecules gives rise to a highly complex system with unprecedented possibilities for modulation of function, and with it applications

LDRD final report on imaging self-organization of proteins in membranes by photocatalytic nano-tagging.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zavadil, Kevin Robert; Shelnutt, John Allen; Sasaki, Darryl Yoshio

We have developed a new nanotagging technology for detecting and imaging the self-organization of proteins and other components of membranes at nanometer resolution for the purpose of investigating cell signaling and other membrane-mediated biological processes. We used protein-, lipid-, or drug-bound porphyrin photocatalysts to grow in-situ nanometer-sized metal particles, which reveal the location of the porphyrin-labeled molecules by electron microscopy. We initially used photocatalytic nanotagging to image assembled multi-component proteins and to monitor the distribution of lipids and porphyrin labels in liposomes. For example, by exchanging the heme molecules in hemoproteins with a photocatalytic tin porphyrin, a nanoparticle was grownmore » at each heme site of the protein. The result obtained from electron microscopy for a tagged multi-subunit protein such as hemoglobin is a symmetric constellation of a specific number of nanoparticle tags, four in the case of the hemoglobin tetramer. Methods for covalently linking photocatalytic porphyrin labels to lipids and proteins were also developed to detect and image the self-organization of lipids, protein-protein supercomplexes, and membrane-protein complexes. Procedures for making photocatalytic porphyrin-drug, porphyrin-lipid, and porphyrin-protein hybrids for non-porphyrin-binding proteins and membrane components were pursued and the first porphyrin-labeled lipids was investigated in liposomal membrane models. Our photocatalytic nanotagging technique may ultimately allow membrane self-organization and cell signaling processes to be imaged in living cells. Fluorescence and plasmonic spectra of the tagged proteins might also provide additional information about protein association and membrane organization. In addition, a porphyrin-aspirin or other NSAID hybrid may be used to grow metal nanotags for the pharmacologically important COX enzymes in membranes so that the distribution of the protein can be imaged at

Design of a single-chain polypeptide tetrahedron assembled from coiled-coil segments.

PubMed

Gradišar, Helena; Božič, Sabina; Doles, Tibor; Vengust, Damjan; Hafner-Bratkovič, Iva; Mertelj, Alenka; Webb, Ben; Šali, Andrej; Klavžar, Sandi; Jerala, Roman

2013-06-01

Protein structures evolved through a complex interplay of cooperative interactions, and it is still very challenging to design new protein folds de novo. Here we present a strategy to design self-assembling polypeptide nanostructured polyhedra based on modularization using orthogonal dimerizing segments. We designed and experimentally demonstrated the formation of the tetrahedron that self-assembles from a single polypeptide chain comprising 12 concatenated coiled coil-forming segments separated by flexible peptide hinges. The path of the polypeptide chain is guided by a defined order of segments that traverse each of the six edges of the tetrahedron exactly twice, forming coiled-coil dimers with their corresponding partners. The coincidence of the polypeptide termini in the same vertex is demonstrated by reconstituting a split fluorescent protein in the polypeptide with the correct tetrahedral topology. Polypeptides with a deleted or scrambled segment order fail to self-assemble correctly. This design platform provides a foundation for constructing new topological polypeptide folds based on the set of orthogonal interacting polypeptide segments.

Novel one-pot synthesis of 5-alkenyl-15-alkynylporphyrins and their derivatisation to a butadiyne-linked benzoporphyrin dimer.

PubMed

Yamada, Hiroko; Kushibe, Kayo; Okujuma, Tetsuo; Uno, Hidemitsu; Ono, Noboru

2006-01-28

5-Alkenyl-15-alkynylporphyrins have been obtained unexpectedly by [2 + 2] acid-catalyzed condensation of dipyrrylmethane and TMS propynal in addition to 5,15-dialkynylporphyrin, and the unsymmetrical porphyrin can be converted to a butadiyne-linked dimer by selective desilylation of the alkynyl TMS.

Monomer–dimer dynamics and distribution of GPI-anchored uPAR are determined by cell surface protein assemblies

PubMed Central

Caiolfa, Valeria R.; Zamai, Moreno; Malengo, Gabriele; Andolfo, Annapaola; Madsen, Chris D.; Sutin, Jason; Digman, Michelle A.; Gratton, Enrico; Blasi, Francesco; Sidenius, Nicolai

2007-01-01

To search for functional links between glycosylphosphatidylinositol (GPI) protein monomer–oligomer exchange and membrane dynamics and confinement, we studied urokinase plasminogen activator (uPA) receptor (uPAR), a GPI receptor involved in the regulation of cell adhesion, migration, and proliferation. Using a functionally active fluorescent protein–uPAR in live cells, we analyzed the effect that extracellular matrix proteins and uPAR ligands have on uPAR dynamics and dimerization at the cell membrane. Vitronectin directs the recruitment of dimers and slows down the diffusion of the receptors at the basal membrane. The commitment to uPA–plasminogen activator inhibitor type 1–mediated endocytosis and recycling modifies uPAR diffusion and induces an exchange between uPAR monomers and dimers. This exchange is fully reversible. The data demonstrate that cell surface protein assemblies are important in regulating the dynamics and localization of uPAR at the cell membrane and the exchange of monomers and dimers. These results also provide a strong rationale for dynamic studies of GPI-anchored molecules in live cells at steady state and in the absence of cross-linker/clustering agents. PMID:18056417

Hierarchical self-assembly: Self-organized nanostructures in a nematically ordered matrix of self-assembled polymeric chains

NASA Astrophysics Data System (ADS)

Mubeena, Shaikh; Chatterji, Apratim

2015-03-01

We report many different nanostructures which are formed when model nanoparticles of different sizes (diameter σn) are allowed to aggregate in a background matrix of semiflexible self-assembled polymeric wormlike micellar chains. The different nanostructures are formed by the dynamical arrest of phase-separating mixtures of micellar monomers and nanoparticles. The different morphologies obtained are the result of an interplay of the available free volume, the elastic energy of deformation of polymers, the density (chemical potential) of the nanoparticles in the polymer matrix, and, of course, the ratio of the size of self-assembling nanoparticles and self-avoidance diameter of polymeric chains. We have used a hybrid semi-grand-canonical Monte Carlo simulation scheme to obtain the (nonequilibrium) phase diagram of the self-assembled nanostructures. We observe rodlike structures of nanoparticles which get self-assembled in the gaps between the nematically ordered chains, as well as percolating gel-like network of conjoined nanotubes. We also find a totally unexpected interlocked crystalline phase of nanoparticles and monomers, in which each crystal plane of nanoparticles is separated by planes of perfectly organized polymer chains. We identified the condition which leads to such interlocked crystal structure. We suggest experimental possibilities of how the results presented in this paper could be used to obtain different nanostructures in the laboratory.

Equilibrium polymerization models of re-entrant self-assembly

NASA Astrophysics Data System (ADS)

Dudowicz, Jacek; Douglas, Jack F.; Freed, Karl F.

2009-04-01

As is well known, liquid-liquid phase separation can occur either upon heating or cooling, corresponding to lower and upper critical solution phase boundaries, respectively. Likewise, self-assembly transitions from a monomeric state to an organized polymeric state can proceed either upon increasing or decreasing temperature, and the concentration dependent ordering temperature is correspondingly called the "floor" or "ceiling" temperature. Motivated by the fact that some phase separating systems exhibit closed loop phase boundaries with two critical points, the present paper analyzes self-assembly analogs of re-entrant phase separation, i.e., re-entrant self-assembly. In particular, re-entrant self-assembly transitions are demonstrated to arise in thermally activated equilibrium self-assembling systems, when thermal activation is more favorable than chain propagation, and in equilibrium self-assembly near an adsorbing boundary where strong competition exists between adsorption and self-assembly. Apparently, the competition between interactions or equilibria generally underlies re-entrant behavior in both liquid-liquid phase separation and self-assembly transitions.

On the origin of the cation templated self-assembly of uranyl-peroxide nanoclusters.

PubMed

Miró, Pere; Pierrefixe, Simon; Gicquel, Mickaël; Gil, Adrià; Bo, Carles

2010-12-22

Uranyl-peroxide nanoclusters display different topologies based on square, pentagonal and hexagonal building blocks. Computed complexation energies of different cations (Li(+), Na(+), K(+), Rb(+), and Cs(+)) with [UO(2)(O(2))(H(2)O)](n) (n = 4, 5, and 6) macrocycles suggest a strong cation templating effect. The inherent bent structure of a U-O(2)-U model dimer is demonstrated and justified through the analysis of its electronic structure, as well as of the inherent curvature of the four-, five-, and six-uranyl macrocyles. The curvature is enhaced by cation coordination, which is suggested to be the driving force for the self-assembly of the nanocapsules.

Self assembling proteins

DOEpatents

Yeates, Todd O.; Padilla, Jennifer; Colovos, Chris

2004-06-29

Novel fusion proteins capable of self-assembling into regular structures, as well as nucleic acids encoding the same, are provided. The subject fusion proteins comprise at least two oligomerization domains rigidly linked together, e.g. through an alpha helical linking group. Also provided are regular structures comprising a plurality of self-assembled fusion proteins of the subject invention, and methods for producing the same. The subject fusion proteins find use in the preparation of a variety of nanostructures, where such structures include: cages, shells, double-layer rings, two-dimensional layers, three-dimensional crystals, filaments, and tubes.

Self-assembled nanolaminate coatings (SV)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fan, H.

2012-03-01

Sandia National Laboratories (Sandia) and Lockheed Martin Aeronautics (LM Aero) are collaborating to develop affordable, self-assembled, nanocomposite coatings and associated fabrication processes that will be tailored to Lockheed Martin product requirements. The purpose of this project is to develop a family of self-assembled coatings with properties tailored to specific performance requirements, such as antireflective (AR) optics, using Sandia-developed self-assembled techniques. The project met its objectives by development of a simple and economic self-assembly processes to fabricate multifunctional coatings. Specifically, materials, functionalization methods, and associated coating processes for single layer and multiple layers coatings have been developed to accomplish high reflectivemore » coatings, hydrophobic coatings, and anti-reflective coatings. Associated modeling and simulations have been developed to guide the coating designs for optimum optical performance. The accomplishments result in significant advantages of reduced costs, increased manufacturing freedom/producibility, improved logistics, and the incorporation of new technology solutions not possible with conventional technologies. These self-assembled coatings with tailored properties will significantly address LMC's needs and give LMC a significant competitive lead in new engineered materials. This work complements SNL's LDRD and BES programs aimed at developing multifunctional nanomaterials for microelectronics and optics as well as structure/property investigations of self-assembled nanomaterials. In addition, this project will provide SNL with new opportunities to develop and apply self-assembled nanocomposite optical coatings for use in the wavelength ranges of 3-5 and 8-12 micrometers, ranges of vital importance to military-based sensors and weapons. The SANC technologies will be applied to multiple programs within the LM Company including the F-35, F-22, ADP (Future Strike Bomber, UAV

Modular Self-Assembly of Protein Cage Lattices for Multistep Catalysis

DOE PAGES

Uchida, Masaki; McCoy, Kimberly; Fukuto, Masafumi; ...

2017-11-13

The assembly of individual molecules into hierarchical structures is a promising strategy for developing three-dimensional materials with properties arising from interaction between the individual building blocks. Virus capsids are elegant examples of biomolecular nanostructures, which are themselves hierarchically assembled from a limited number of protein subunits. Here, we demonstrate the bio-inspired modular construction of materials with two levels of hierarchy: the formation of catalytically active individual virus-like particles (VLPs) through directed self-assembly of capsid subunits with enzyme encapsulation, and the assembly of these VLP building blocks into three-dimensional arrays. The structure of the assembled arrays was successfully altered from anmore » amorphous aggregate to an ordered structure, with a face-centered cubic lattice, by modifying the exterior surface of the VLP without changing its overall morphology, to modulate interparticle interactions. The assembly behavior and resultant lattice structure was a consequence of interparticle interaction between exterior surfaces of individual particles and thus independent of the enzyme cargos encapsulated within the VLPs. These superlattice materials, composed of two populations of enzyme-packaged VLP modules, retained the coupled catalytic activity in a two-step reaction for isobutanol synthesis. As a result, this study demonstrates a significant step toward the bottom-up fabrication of functional superlattice materials using a self-assembly process across multiple length scales and exhibits properties and function that arise from the interaction between individual building blocks.« less

Modular Self-Assembly of Protein Cage Lattices for Multistep Catalysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Uchida, Masaki; McCoy, Kimberly; Fukuto, Masafumi

The assembly of individual molecules into hierarchical structures is a promising strategy for developing three-dimensional materials with properties arising from interaction between the individual building blocks. Virus capsids are elegant examples of biomolecular nanostructures, which are themselves hierarchically assembled from a limited number of protein subunits. Here, we demonstrate the bio-inspired modular construction of materials with two levels of hierarchy: the formation of catalytically active individual virus-like particles (VLPs) through directed self-assembly of capsid subunits with enzyme encapsulation, and the assembly of these VLP building blocks into three-dimensional arrays. The structure of the assembled arrays was successfully altered from anmore » amorphous aggregate to an ordered structure, with a face-centered cubic lattice, by modifying the exterior surface of the VLP without changing its overall morphology, to modulate interparticle interactions. The assembly behavior and resultant lattice structure was a consequence of interparticle interaction between exterior surfaces of individual particles and thus independent of the enzyme cargos encapsulated within the VLPs. These superlattice materials, composed of two populations of enzyme-packaged VLP modules, retained the coupled catalytic activity in a two-step reaction for isobutanol synthesis. As a result, this study demonstrates a significant step toward the bottom-up fabrication of functional superlattice materials using a self-assembly process across multiple length scales and exhibits properties and function that arise from the interaction between individual building blocks.« less

Self-assembly Controls Self-cleavage of HHR from ASBVd (-): a Combined SANS and Modeling Study

NASA Astrophysics Data System (ADS)

Leclerc, Fabrice; Zaccai, Giuseppe; Vergne, Jacques; Řìhovà, Martina; Martel, Anne; Maurel, Marie-Christine

2016-07-01

In the Avocado Sunblotch Viroid (ASBVd: 249-nt) from the Avsunviroidae family, a symmetric rolling-circle replication operates through an autocatalytic mechanism mediated by hammerhead ribozymes (HHR) embedded in both polarity strands. The concatenated multimeric ASBVd (+) and ASBVd (-) RNAs thus generated are processed by cleavage to unit-length where ASBVd (-) self-cleaves with more efficiency. Absolute scale small angle neutron scattering (SANS) revealed a temperature-dependent dimer association in both ASBVd (-) and its derived 79-nt HHR (-). A joint thermodynamic analysis of SANS and catalytic data indicates the rate-determining step corresponds to the dimer/monomer transition. 2D and 3D models of monomeric and dimeric HHR (-) suggest that the inter-molecular contacts stabilizing the dimer (between HI and HII domains) compete with the intra-molecular ones stabilizing the active conformation of the full-length HHR required for an efficient self-cleavage. Similar competing intra- and inter-molecular contacts are proposed in ASBVd (-) though with a remoter region from an extension of the HI domain.

Self-assembled DNA Structures for Nanoconstruction

NASA Astrophysics Data System (ADS)

Yan, Hao; Yin, Peng; Park, Sung Ha; Li, Hanying; Feng, Liping; Guan, Xiaoju; Liu, Dage; Reif, John H.; LaBean, Thomas H.

2004-09-01

In recent years, a number of research groups have begun developing nanofabrication methods based on DNA self-assembly. Here we review our recent experimental progress to utilize novel DNA nanostructures for self-assembly as well as for templates in the fabrication of functional nano-patterned materials. We have prototyped a new DNA nanostructure known as a cross structure. This nanostructure has a 4-fold symmetry which promotes its self-assembly into tetragonal 2D lattices. We have utilized the tetragonal 2D lattices as templates for highly conductive metallic nanowires and periodic 2D protein nano-arrays. We have constructed and characterized a DNA nanotube, a new self-assembling superstructure composed of DNA tiles. We have also demonstrated an aperiodic DNA lattice composed of DNA tiles assembled around a long scaffold strand; the system translates information encoded in the scaffold strand into a specific and reprogrammable barcode pattern. We have achieved metallic nanoparticle linear arrays templated on self-assembled 1D DNA arrays. We have designed and demonstrated a 2-state DNA lattice, which displays expand/contract motion switched by DNA nanoactuators. We have also achieved an autonomous DNA motor executing unidirectional motion along a linear DNA track.

Self assembly of rectangular shapes on concentration programming and probabilistic tile assembly models

PubMed Central

Rajasekaran, Sanguthevar

2013-01-01

Efficient tile sets for self assembling rectilinear shapes is of critical importance in algorithmic self assembly. A lower bound on the tile complexity of any deterministic self assembly system for an n × n square is Ω(log(n)log(log(n))) (inferred from the Kolmogrov complexity). Deterministic self assembly systems with an optimal tile complexity have been designed for squares and related shapes in the past. However designing Θ(log(n)log(log(n))) unique tiles specific to a shape is still an intensive task in the laboratory. On the other hand copies of a tile can be made rapidly using PCR (polymerase chain reaction) experiments. This led to the study of self assembly on tile concentration programming models. We present two major results in this paper on the concentration programming model. First we show how to self assemble rectangles with a fixed aspect ratio (α:β), with high probability, using Θ(α + β) tiles. This result is much stronger than the existing results by Kao et al. (Randomized self-assembly for approximate shapes, LNCS, vol 5125. Springer, Heidelberg, 2008) and Doty (Randomized self-assembly for exact shapes. In: proceedings of the 50th annual IEEE symposium on foundations of computer science (FOCS), IEEE, Atlanta. pp 85–94, 2009)—which can only self assembly squares and rely on tiles which perform binary arithmetic. On the other hand, our result is based on a technique called staircase sampling. This technique eliminates the need for sub-tiles which perform binary arithmetic, reduces the constant in the asymptotic bound, and eliminates the need for approximate frames (Kao et al. Randomized self-assembly for approximate shapes, LNCS, vol 5125. Springer, Heidelberg, 2008). Our second result applies staircase sampling on the equimolar concentration programming model (The tile complexity of linear assemblies. In: proceedings of the 36th international colloquium automata, languages and programming: Part I on ICALP ’09, Springer-Verlag, pp 235�

Self assembly of rectangular shapes on concentration programming and probabilistic tile assembly models.

PubMed

Kundeti, Vamsi; Rajasekaran, Sanguthevar

2012-06-01

Efficient tile sets for self assembling rectilinear shapes is of critical importance in algorithmic self assembly. A lower bound on the tile complexity of any deterministic self assembly system for an n × n square is [Formula: see text] (inferred from the Kolmogrov complexity). Deterministic self assembly systems with an optimal tile complexity have been designed for squares and related shapes in the past. However designing [Formula: see text] unique tiles specific to a shape is still an intensive task in the laboratory. On the other hand copies of a tile can be made rapidly using PCR (polymerase chain reaction) experiments. This led to the study of self assembly on tile concentration programming models. We present two major results in this paper on the concentration programming model. First we show how to self assemble rectangles with a fixed aspect ratio ( α:β ), with high probability, using Θ( α + β ) tiles. This result is much stronger than the existing results by Kao et al. (Randomized self-assembly for approximate shapes, LNCS, vol 5125. Springer, Heidelberg, 2008) and Doty (Randomized self-assembly for exact shapes. In: proceedings of the 50th annual IEEE symposium on foundations of computer science (FOCS), IEEE, Atlanta. pp 85-94, 2009)-which can only self assembly squares and rely on tiles which perform binary arithmetic. On the other hand, our result is based on a technique called staircase sampling . This technique eliminates the need for sub-tiles which perform binary arithmetic, reduces the constant in the asymptotic bound, and eliminates the need for approximate frames (Kao et al. Randomized self-assembly for approximate shapes, LNCS, vol 5125. Springer, Heidelberg, 2008). Our second result applies staircase sampling on the equimolar concentration programming model (The tile complexity of linear assemblies. In: proceedings of the 36th international colloquium automata, languages and programming: Part I on ICALP '09, Springer-Verlag, pp 235

Small Angle X-Ray Scattering Study of Meso-Tetrakis (4-Sulfonatophenyl) Porphyrin in Aqueous Solution: A Self-Aggregation Model

PubMed Central

Gandini, S.C.M.; Gelamo, E.L.; Itri, R.; Tabak, M.

2003-01-01

The aggregate morphology of meso-tetrakis(4-sulfonatophenyl) porphyrin (TPPS4) in aqueous solution is investigated by using small angle x-ray scattering (SAXS) technique. Measurements were performed at pH 4.0 and 9.0 to monitor the pH influence on the structural parameters of the aggregates. Radii of gyration were obtained from distance distribution functions p(r) analysis. The experimental data of TPPS4 at pH 4.0 showed well-defined oscillations characteristic of large aggregates in contrast to the SAXS curve of 5 mM TPPS4 at pH 9.0, where both a significant decrease in the intensity and the disappearance of the oscillation peaks suggest the dissociation of the aggregate. A 340-Å long “hollow” cylinder with shell thickness of 20 Å, compatible to the porphyrin molecule dimension, represents well the scattering curve of the aggregates at pH 4.0. According to the fitting parameters, 26 porphyrin molecules self-associate into a ringlike configuration in the plane of the cylinder cross-section. The total number of porphyrin molecules in the whole aggregate was also estimated as ∼3000. The model compatible to SAXS data of a hollow cylinder with J-aggregation in the cross-section and H-aggregation (columnar stacking) between the cylinder layers is consistent with optical absorption spectroscopic data both in the literature and obtained in this work. PMID:12885669

Self-assembling membranes and related methods thereof

DOEpatents

Capito, Ramille M; Azevedo, Helena S; Stupp, Samuel L

2013-08-20

The present invention relates to self-assembling membranes. In particular, the present invention provides self-assembling membranes configured for securing and/or delivering bioactive agents. In some embodiments, the self-assembling membranes are used in the treatment of diseases, and related methods (e.g., diagnostic methods, research methods, drug screening).

Porphyrin amino acids-amide coupling, redox and photophysical properties of bis(porphyrin) amides.

PubMed

Melomedov, Jascha; Wünsche von Leupoldt, Anica; Meister, Michael; Laquai, Frédéric; Heinze, Katja

2013-07-14

New trans-AB2C meso-substituted porphyrin amino acid esters with meso-substituents of tunable electron withdrawing power (B = mesityl, 4-C6H4F, 4-C6H4CF3, C6F5) were prepared as free amines 3a-3d, as N-acetylated derivatives Ac-3a-Ac-3d and corresponding zinc(II) complexes Zn-Ac-3a-Zn-Ac-3d. Several amide-linked bis(porphyrins) with a tunable electron density at each porphyrin site were obtained from the amino porphyrin precursors by condensation reactions (4a-4d) and mono- and bis(zinc(II)) complexes Zn(2)-4d and Zn(1)Zn(2)-4d were prepared. The electronic interaction between individual porphyrin units in bis(porphyrins) 4 is probed by electrochemical experiments (CV, EPR), electronic absorption spectroscopy, steady-state and time-resolved fluorescence spectroscopy in combination with DFT/PCM calculations on diamagnetic neutral bis(porphyrins) 4 and on respective charged mixed-valent radicals 4(+/-). The interaction via the -C6H4-NHCO-C6H4- bridge, the site of oxidation and reduction and the lowest excited singlet state S1, is tuned by the substituents on the individual porphyrins and the metalation state.

Self-assembled single-crystal silicon circuits on plastic

PubMed Central

Stauth, Sean A.; Parviz, Babak A.

2006-01-01

We demonstrate the use of self-assembly for the integration of freestanding micrometer-scale components, including single-crystal, silicon field-effect transistors (FETs) and diffusion resistors, onto flexible plastic substrates. Preferential self-assembly of multiple microcomponent types onto a common platform is achieved through complementary shape recognition and aided by capillary, fluidic, and gravitational forces. We outline a microfabrication process that yields single-crystal, silicon FETs in a freestanding, powder-like collection for use with self-assembly. Demonstrations of self-assembled FETs on plastic include logic inverters and measured electron mobility of 592 cm2/V-s. Finally, we extend the self-assembly process to substrates each containing 10,000 binding sites and realize 97% self-assembly yield within 25 min for 100-μm-sized elements. High-yield self-assembly of micrometer-scale functional devices as outlined here provides a powerful approach for production of macroelectronic systems. PMID:16968780

Lag periods during the self-assembly of {Mo(72)Fe(30)} macroions: connection to the virus capsid formation process.

PubMed

Zhang, Jie; Li, Dong; Liu, Guang; Glover, Kerney Jebrell; Liu, Tianbo

2009-10-28

The kinetic properties of the self-assembly of hydrophilic Keplerate-type polyoxometalate (POM) {Mo(72)Fe(30)} macroanions into single-layer, vesicle-like blackberry structures in solutions were monitored by the static and dynamic laser light scattering techniques. In the presence of additional electrolytes, an obvious lag period at the initial stage of self-assembly was observed, followed by a fast increase of the scattered intensity. The whole kinetic curve is sigmoidal with a lag phase. A two-step nucleation-growth mechanism is proposed to explain this lag phase: the {Mo(72)Fe(30)} macroanions slowly associate into oligomers (mostly dimers), which are the thermodynamically unfavorable intermediates, at the initial stage; once the oligomers reach a critical concentration, the blackberry formation process is accelerated. Analytical ultracentrifugation (AUC) was used to confirm the oligomeric state in {Mo(72)Fe(30)} solution during the lag period. The length of the lag period is dependent on temperature, ionic strength, and the valent states of the additional salts, as well as the solvent content. The kinetics (including the lag period) of the blackberry formation of the {Mo(72)Fe(30)} macroanions show similarities to the self-assembly of virus capsid proteins (which are also soluble macroions) into spherical capsid shells, suggesting possible connections between the self-assembly behaviors of inorganic species and biological macromolecules.

Self-Organization and the Self-Assembling Process in Tissue Engineering

PubMed Central

Eswaramoorthy, Rajalakshmanan; Hadidi, Pasha; Hu, Jerry C.

2015-01-01

In recent years, the tissue engineering paradigm has shifted to include a new and growing subfield of scaffoldless techniques which generate self-organizing and self-assembling tissues. This review aims to provide a cogent description of this relatively new research area, with special emphasis on applications toward clinical use and research models. Particular emphasis is placed on providing clear definitions of self-organization and the self-assembling process, as delineated from other scaffoldless techniques in tissue engineering and regenerative medicine. Significantly, during formation, self-organizing and self-assembling tissues display biological processes similar to those that occur in vivo. These help lead to the recapitulation of native tissue morphological structure and organization. Notably, functional properties of these tissues also approach native tissue values; some of these engineered tissues are already in clinical trials. This review aims to provide a cohesive summary of work in this field, and to highlight the potential of self-organization and the self-assembling process to provide cogent solutions to current intractable problems in tissue engineering. PMID:23701238

Electrostatic self-assembly of exfoliated niobate nanosheets (Nb3O8-) and cobalt porphyrins (CoIIITMPyP) utilized for rapid construction of intercalated nanocomposite and exploration of electrocatalysis towards oxygen reduction

NASA Astrophysics Data System (ADS)

Xu, Jiasheng; Wang, Mengjun; Pan, Binbin; Li, Jinpeng; Xia, Bin; Zhang, Xiaobo; Tong, Zhiwei

To prepare the novel plate-like nanocomposite CoIIITMPyP/Nb3O8, the cationic cobalt (III) tetrakis-5, 10, 15, 20-(N-methyl-4-pyridyl) porphyrin (CoIIITMPyP) was intercalated into the interlayer of the perovskite structural material KNb3O8 via the electrostatic self-assembly of the positively charged CoIIITMPyP molecules and the electronegative Nb3O8- nanosheets. The Nb3O8- nanosheets was obtained by exfoliating the protonated product of niobate KNb3O8 in the tetrabutyl ammonium hydroxide (TBA+OH-) aqueous solution. The zeta potential was measured to indicate the stability and uniformity of the Nb3O8- nanosheet colloidal dispersion, and the structure and component of the parent material KNb3O8, the acidified product HNb3O8, and the interlayered nanocomposite CoIIITMPyP/Nb3O8 were characterized using XRD, FT-IR, SEM and AFM. Furthermore, the electrocatalytic activity toward the oxygen reduction reaction (ORR) of CoIIITMPyP/Nb3O8 hybrids modified GCE was investigated by the cyclic voltammetry (CV) measurements. The modified GCE exhibited good electrocatalytic activity toward ORR in consideration of the peak shift from -0.723V to -0.300V. The linear correlation of the reduction peak current and the square root of the scan rate suggested a diffusion controlled process.

Alternative dimerization interfaces in the glucocorticoid receptor-α ligand binding domain.

PubMed

Bianchetti, Laurent; Wassmer, Bianca; Defosset, Audrey; Smertina, Anna; Tiberti, Marion L; Stote, Roland H; Dejaegere, Annick

2018-04-30

Nuclear hormone receptors (NRs) constitute a large family of multi-domain ligand-activated transcription factors. Dimerization is essential for their regulation, and both DNA binding domain (DBD) and ligand binding domain (LBD) are implicated in dimerization. Intriguingly, the glucocorticoid receptor-α (GRα) presents a DBD dimeric architecture similar to that of the homologous estrogen receptor-α (ERα), but an atypical dimeric architecture for the LBD. The physiological relevance of the proposed GRα LBD dimer is a subject of debate. We analyzed all GRα LBD homodimers observed in crystals using an energetic analysis based on the PISA and on the MM/PBSA methods and a sequence conservation analysis, using the ERα LBD dimer as a reference point. Several dimeric assemblies were observed for GRα LBD. The assembly generally taken to be physiologically relevant showed weak binding free energy and no significant residue conservation at the contact interface, while an alternative homodimer mediated by both helix 9 and C-terminal residues showed significant binding free energy and residue conservation. However, none of the GRα LBD assemblies found in crystals are as stable or conserved as the canonical ERα LBD dimer. GRα C-terminal sequence (F-domain) forms a steric obstacle to the canonical dimer assembly in all available structures. Our analysis calls for a re-examination of the currently accepted GRα homodimer structure and experimental investigations of the alternative architectures. This work questions the validity of the currently accepted architecture. This has implications for interpreting physiological data and for therapeutic design pertaining to glucocorticoid research. Copyright © 2018. Published by Elsevier B.V.

Physical principles for DNA tile self-assembly.

PubMed

Evans, Constantine G; Winfree, Erik

2017-06-19

DNA tiles provide a promising technique for assembling structures with nanoscale resolution through self-assembly by basic interactions rather than top-down assembly of individual structures. Tile systems can be programmed to grow based on logical rules, allowing for a small number of tile types to assemble large, complex assemblies that can retain nanoscale resolution. Such algorithmic systems can even assemble different structures using the same tiles, based on inputs that seed the growth. While programming and theoretical analysis of tile self-assembly often makes use of abstract logical models of growth, experimentally implemented systems are governed by nanoscale physical processes that can lead to very different behavior, more accurately modeled by taking into account the thermodynamics and kinetics of tile attachment and detachment in solution. This review discusses the relationships between more abstract and more physically realistic tile assembly models. A central concern is how consideration of model differences enables the design of tile systems that robustly exhibit the desired abstract behavior in realistic physical models and in experimental implementations. Conversely, we identify situations where self-assembly in abstract models can not be well-approximated by physically realistic models, putting constraints on physical relevance of the abstract models. To facilitate the discussion, we introduce a unified model of tile self-assembly that clarifies the relationships between several well-studied models in the literature. Throughout, we highlight open questions regarding the physical principles for DNA tile self-assembly.

Structure and Self-Assembly of the Calcium Binding Matrix Protein of Human Metapneumovirus

PubMed Central

Leyrat, Cedric; Renner, Max; Harlos, Karl; Huiskonen, Juha T.; Grimes, Jonathan M.

2014-01-01

Summary The matrix protein (M) of paramyxoviruses plays a key role in determining virion morphology by directing viral assembly and budding. Here, we report the crystal structure of the human metapneumovirus M at 2.8 Å resolution in its native dimeric state. The structure reveals the presence of a high-affinity Ca2+ binding site. Molecular dynamics simulations (MDS) predict a secondary lower-affinity site that correlates well with data from fluorescence-based thermal shift assays. By combining small-angle X-ray scattering with MDS and ensemble analysis, we captured the structure and dynamics of M in solution. Our analysis reveals a large positively charged patch on the protein surface that is involved in membrane interaction. Structural analysis of DOPC-induced polymerization of M into helical filaments using electron microscopy leads to a model of M self-assembly. The conservation of the Ca2+ binding sites suggests a role for calcium in the replication and morphogenesis of pneumoviruses. PMID:24316400

Peptide-directed self-assembly of hydrogels

PubMed Central

Kopeček, Jindřich; Yang, Jiyuan

2009-01-01

This review focuses on the self-assembly of macromolecules mediated by the biorecognition of peptide/protein domains. Structures forming α-helices and β-sheets have been used to mediate self-assembly into hydrogels of peptides, reactive copolymers and peptide motifs, block copolymers, and graft copolymers. Structural factors governing the self-assembly of these molecules into precisely defined three-dimensional structures (hydrogels) are reviewed. The incorporation of peptide motifs into hybrid systems, composed of synthetic and natural macromolecules, enhances design opportunities for new biomaterials when compared to individual components. PMID:18952513

Dissociations of subliminal and supraliminal self-face from other-face processing: behavioral and ERP evidence.

PubMed

Geng, Haiyan; Zhang, Shen; Li, Qi; Tao, Ran; Xu, Shan

2012-10-01

Self-related information has been found to be processed more quickly and accurately in studies with supraliminal self-stimuli and traditional paradigms such as masked priming. We conducted two experiments to investigate whether subliminal self-face processing enjoys this advantage and the neural correlates of processing self-faces at both subliminal and supraliminal levels. We found that self-faces were quicker than famous-other faces to gain dominance against dynamic noise patterns during prolonged interocular suppression to enter awareness (Experiment 1). Meanwhile, subliminal contrast of self- and famous-other face processing was reflected in a reduced early vertex positive potential (VPP) component, whereas supraliminal self-other face differentiation was reflected in an enhanced N170, as well as a more positive late component (300-580ms, Experiment 2) to the self-face. The clear dissociations of self- and other-face processing found across our two experiments validate the self advantage. Our findings also contribute to understandings of the mechanisms underlying self-face processing at different levels of awareness. Copyright © 2012 Elsevier Ltd. All rights reserved.

High-Definition Self-Assemblies driven by the Hydrophobic Effect: Synthesis and Properties of a Supramolecular Nano-Capsule

PubMed Central

Liu, Simin

2008-01-01

High definition self-assemblies, those that possess order at the molecular level, are most commonly made from subunits possessing metals and metal coordination sites, or groups capable of partaking in hydrogen bonding. In other words, enthalpy is the driving force behind the free energy of assembly. The hydrophobic effect engenders the possibility of (nominally) relying not on enthalpy but entropy to drive assembly. Towards this idea, we describe how template molecules can trigger the dimerization of a cavitand in aqueous solution, and in doing so are encapsulated within the resulting capsule. Although not held together by (enthalpically) strong and directional non-covalent forces, these capsules possess considerable thermodynamic and kinetic stability. As a result, they display unusual and even unique properties. We discuss some of these, including the use of the capsule as a nano-scale reaction chamber and how they can bring about the separation of hydrocarbon gases. PMID:18685753

Encapsulation of [F4(H2O)10](4-) in a dimeric assembly of an unidirectional arene based hexapodal amide receptor.

PubMed

Arunachalam, M; Ghosh, Pradyut

2011-06-14

An unidirectional orientation of all six arms of an arene based hexapodal amide receptor shows dimeric capsular assembly templated by a [F(4)(H(2)O)(10)](4-) cluster. This journal is © The Royal Society of Chemistry 2011

Self-assembled nanogaps for molecular electronics.

PubMed

Tang, Qingxin; Tong, Yanhong; Jain, Titoo; Hassenkam, Tue; Wan, Qing; Moth-Poulsen, Kasper; Bjørnholm, Thomas

2009-06-17

A nanogap for molecular devices was realized using solution-based self-assembly. Gold nanorods were assembled to gold nanoparticle-coated conducting SnO2:Sb nanowires via thiol end-capped oligo(phenylenevinylene)s (OPVs). The molecular gap was easily created by the rigid molecule itself during self-assembly and the gap length was determined by the molecule length. The gold nanorods and gold nanoparticles, respectively covalently bonded at the two ends of the molecule, had very small dimensions, e.g. a width of approximately 20 nm, and hence were expected to minimize the screening effect. The ultra-long conducting SnO2:Sb nanowires provided the bridge to connect one of the electrodes of the molecular device (gold nanoparticle) to the external circuit. The tip of the atomic force microscope (AFM) was contacted onto the other electrode (gold nanorod) for the electrical measurement of the OPV device. The conductance measurement confirmed that the self-assembly of the molecules and the subsequent self-assembly of the gold nanorods was a feasible method for the fabrication of the nanogap of the molecular devices.

Colloidosome like structures: self-assembly of silica microrods

DOE PAGES

Datskos, P.; Polizos, G.; Bhandari, M.; ...

2016-03-07

Self-assembly of one-dimensional structures is attracting a great deal of interest because assembled structures can provide better properties compared to individual building blocks. We demonstrate silica microrod self-assembly by exploiting Pickering emulsion based strategy. Micron-sized silica rods were synthesized employing previously reported methods based on polyvinylpyrrolidone/ pentanol emulsion droplets. Moreover, rods self-assembled to make structures in the range of z10 40 mm. Smooth rods assembled better than segmented rods. Finally, the assembled structures were bonded by weak van der Waals forces.

Self-Assembly of Optical Molecules with Supramolecular Concepts

PubMed Central

Okamoto, Ken; Chithra, Parayalil; Richards, Gary J.; Hill, Jonathan P.; Ariga, Katsuhiko

2009-01-01

Fabrication of nano-sized objects is one of the most important issues in nanoscience and nanotechnology. Soft nanomaterials with flexible properties have been given much attention and can be obtained through bottom-up processing from functional molecules, where self-assembly based on supramolecular chemistry and designed assembly have become crucial processes and techniques. Among the various functional molecules, dyes have become important materials in certain areas of nanotechnology and their self-assembling behaviors have been actively researched. In this short review, we briefly introduce recent progress in self-assembly of optical molecules and dyes, based mainly on supramolecular concepts. The introduced examples are classified into four categories: self-assembly of (i) low-molecular-weight dyes and (ii) polymeric dyes and dye self-assembly (iii) in nanoscale architectures and (iv) at surfaces. PMID:19564931

Tuning peptide self-assembly by an in-tether chiral center

PubMed Central

Hu, Kuan; Xiong, Wei; Li, Hu; Zhang, Pei-Yu; Yin, Feng; Zhang, Qianling; Jiang, Fan; Li, Zigang

2018-01-01

The self-assembly of peptides into ordered nanostructures is important for understanding both peptide molecular interactions and nanotechnological applications. However, because of the complexity and various self-assembling pathways of peptide molecules, design of self-assembling helical peptides with high controllability and tunability is challenging. We report a new self-assembling mode that uses in-tether chiral center-induced helical peptides as a platform for tunable peptide self-assembly with good controllability. It was found that self-assembling behavior was governed by in-tether substitutional groups, where chirality determined the formation of helical structures and aromaticity provided the driving force for self-assembly. Both factors were essential for peptide self-assembly to occur. Experiments and theoretical calculations indicate long-range crystal-like packing in the self-assembly, which was stabilized by a synergy of interpeptide π-π and π-sulfur interactions and hydrogen bond networks. In addition, the self-assembled peptide nanomaterials were demonstrated to be promising candidate materials for applications in biocompatible electrochemical supercapacitors.

Self-assembled lipid bilayer materials

DOEpatents

Sasaki, Darryl Y.; Waggoner, Tina A.; Last, Julie A.

2005-11-08

The present invention is a self-assembling material comprised of stacks of lipid bilayers formed in a columnar structure, where the assembly process is mediated and regulated by chemical recognition events. The material, through the chemical recognition interactions, has a self-regulating system that corrects the radial size of the assembly creating a uniform diameter throughout most of the structure. The materials form and are stable in aqueous solution. These materials are useful as structural elements for the architecture of materials and components in nanotechnology, efficient light harvesting systems for optical sensing, chemical processing centers, and drug delivery vehicles.

Self-assembly of nanocomposite materials

DOEpatents

Brinker, C. Jeffrey; Sellinger, Alan; Lu, Yunfeng

2001-01-01

A method of making a nanocomposite self-assembly is provided where at least one hydrophilic compound, at least one hydrophobic compound, and at least one amphiphilic surfactant are mixed in an aqueous solvent with the solvent subsequently evaporated to form a self-assembled liquid crystalline mesophase material. Upon polymerization of the hydrophilic and hydrophobic compounds, a robust nanocomposite self-assembled material is formed. Importantly, in the reaction mixture, the amphiphilic surfactant has an initial concentration below the critical micelle concentration to allow formation of the liquid-phase micellar mesophase material. A variety of nanocomposite structures can be formed, depending upon the solvent evaporazation process, including layered mesophases, tubular mesophases, and a hierarchical composite coating composed of an isotropic worm-like micellar overlayer bonded to an oriented, nanolaminated underlayer.

Self-assembly concepts for multicompartment nanostructures

NASA Astrophysics Data System (ADS)

Gröschel, André H.; Müller, Axel H. E.

2015-07-01

Compartmentalization is ubiquitous to many biological and artificial systems, be it for the separate storage of incompatible matter or to isolate transport processes. Advancements in the synthesis of sequential block copolymers offer a variety of tools to replicate natural design principles with tailor-made soft matter for the precise spatial separation of functionalities on multiple length scales. Here, we review recent trends in the self-assembly of amphiphilic block copolymers to multicompartment nanostructures (MCNs) under (semi-)dilute conditions, with special emphasis on ABC triblock terpolymers. The intrinsic immiscibility of connected blocks induces short-range repulsion into discrete nano-domains stabilized by a third, soluble block or molecular additive. Polymer blocks can be synthesized from an arsenal of functional monomers directing self-assembly through packing frustration or response to various fields. The mobility in solution further allows the manipulation of self-assembly processes into specific directions by clever choice of environmental conditions. This review focuses on practical concepts that direct self-assembly into predictable nanostructures, while narrowing particle dispersity with respect to size, shape and internal morphology. The growing understanding of underlying self-assembly mechanisms expands the number of experimental concepts providing the means to target and manipulate progressively complex superstructures.

[Neural basis of self-face recognition: social aspects].

PubMed

Sugiura, Motoaki

2012-07-01

Considering the importance of the face in social survival and evidence from evolutionary psychology of visual self-recognition, it is reasonable that we expect neural mechanisms for higher social-cognitive processes to underlie self-face recognition. A decade of neuroimaging studies so far has, however, not provided an encouraging finding in this respect. Self-face specific activation has typically been reported in the areas for sensory-motor integration in the right lateral cortices. This observation appears to reflect the physical nature of the self-face which representation is developed via the detection of contingency between one's own action and sensory feedback. We have recently revealed that the medial prefrontal cortex, implicated in socially nuanced self-referential process, is activated during self-face recognition under a rich social context where multiple other faces are available for reference. The posterior cingulate cortex has also exhibited this activation modulation, and in the separate experiment showed a response to attractively manipulated self-face suggesting its relevance to positive self-value. Furthermore, the regions in the right lateral cortices typically showing self-face-specific activation have responded also to the face of one's close friend under the rich social context. This observation is potentially explained by the fact that the contingency detection for physical self-recognition also plays a role in physical social interaction, which characterizes the representation of personally familiar people. These findings demonstrate that neuroscientific exploration reveals multiple facets of the relationship between self-face recognition and social-cognitive process, and that technically the manipulation of social context is key to its success.

Functionalized expanded porphyrins

DOEpatents

Sessler, Jonathan L; Pantos, Patricia J

2013-11-12

Disclosed are functionalized expanded porphyrins that can be used as spectrometric sensors for high-valent actinide cations. The disclosed functionalized expanded porphyrins have the advantage over unfunctionalized systems in that they can be immobilized via covalent attachment to a solid support comprising an inorganic or organic polymer or other common substrates. Substrates comprising the disclosed functionalized expanded porphyrins are also disclosed. Further, disclosed are methods of making the disclosed compounds (immobilized and free), methods of using them as sensors to detect high valent actinides, devices that comprise the disclosed compounds, and kits.

Nano-imaging enabled via self-assembly

PubMed Central

McLeod, Euan; Ozcan, Aydogan

2014-01-01

SUMMARY Imaging object details with length scales below approximately 200 nm has been historically difficult for conventional microscope objective lenses because of their inability to resolve features smaller than one-half the optical wavelength. Here we review some of the recent approaches to surpass this limit by harnessing self-assembly as a fabrication mechanism. Self-assembly can be used to form individual nano- and micro-lenses, as well as to form extended arrays of such lenses. These lenses have been shown to enable imaging with resolutions as small as 50 nm half-pitch using visible light, which is well below the Abbe diffraction limit. Furthermore, self-assembled nano-lenses can be used to boost contrast and signal levels from small nano-particles, enabling them to be detected relative to background noise. Finally, alternative nano-imaging applications of self-assembly are discussed, including three-dimensional imaging, enhanced coupling from light-emitting diodes, and the fabrication of contrast agents such as quantum dots and nanoparticles. PMID:25506387

Thermophilic Ferritin 24mer Assembly and Nanoparticle Encapsulation Modulated by Interdimer Electrostatic Repulsion.

PubMed

Pulsipher, Katherine W; Villegas, Jose A; Roose, Benjamin W; Hicks, Tacey L; Yoon, Jennifer; Saven, Jeffery G; Dmochowski, Ivan J

2017-07-18

Protein cage self-assembly enables encapsulation and sequestration of small molecules, macromolecules, and nanomaterials for many applications in bionanotechnology. Notably, wild-type thermophilic ferritin from Archaeoglobus fulgidus (AfFtn) exists as a stable dimer of four-helix bundle proteins at a low ionic strength, and the protein forms a hollow assembly of 24 protomers at a high ionic strength (∼800 mM NaCl). This assembly process can also be initiated by highly charged gold nanoparticles (AuNPs) in solution, leading to encapsulation. These data suggest that salt solutions or charged AuNPs can shield unfavorable electrostatic interactions at AfFtn dimer-dimer interfaces, but specific "hot-spot" residues controlling assembly have not been identified. To investigate this further, we computationally designed three AfFtn mutants (E65R, D138K, and A127R) that introduce a single positive charge at sites along the dimer-dimer interface. These proteins exhibited different assembly kinetics and thermodynamics, which were ranked in order of increasing 24mer propensity: A127R < wild type < D138K ≪ E65R. E65R assembled into the 24mer across a wide range of ionic strengths (0-800 mM NaCl), and the dissociation temperature for the 24mer was 98 °C. X-ray crystal structure analysis of the E65R mutant identified a more compact, closed-pore cage geometry. A127R and D138K mutants exhibited wild-type ability to encapsulate and stabilize 5 nm AuNPs, whereas E65R did not encapsulate AuNPs at the same high yields. This work illustrates designed protein cages with distinct assembly and encapsulation properties.

From Solvolysis to Self-Assembly*

PubMed Central

Stang, Peter J.

2009-01-01

My sojourn from classical physical-organic chemistry and solvolysis to self-assembly and supramolecular chemistry, over the last forty years, is described. My contributions to unsaturated reactive intermediates, namely vinyl cations and unsaturated carbenes, along with my decade long involvement with polyvalent iodine chemistry, especially alkynyliodonium salts, as well as my more recent research with metal-ligand, coordination driven and directed self-assembly of finite supramolecular ensembles are discussed. PMID:19111062

Porphyrin Induced Laser Deactivation of Trypsinogen-Trypsin Conversion

NASA Astrophysics Data System (ADS)

Perido, Joanna; Brancaleon, Lorenzo

2015-03-01

Pancreatitis is caused by the inflammation of the pancreas, where the digestive enzyme trypsin is activated from the precursor enzyme trypsinogen while still in the pancreas. The presence of trypsin in the pancreas causes auto-activation of trypsinogen, resulting in greater inflammation and auto-digestion of the pancreas. In severe cases, this cascade effect can lead to organ failure, diabetes, and pancreatic cancer. Our hypothesis is that if trypsinogen is prevented from auto-activating into trypsin, then this cascade can be stopped. We propose to do this by inducing conformational changes in trypsinogen when bound to a photoactive porphyrin dye. Porphyrins are comprised of four linked heterocyclic groups forming a flat ring, and bind well with proteins such as trypsinogen. In this study we used spectroscopic techniques to probe the binding of meso-tetrakis (4-sulfonatephenyl) porphyrin (TSPP) to trypsinogen in vitro, as a preliminary step to then prompt and characterize conformational changes of trypsinogen through irradiation. If conformational changes are detected the trypsinogen will be tested for trypsin inactivation. This investigation may provide promising initial results to the possible use of porphyrins as an inhibitor of the self-activation of trypsinogen into trypsin, and a potential inhibitor of pancreatitis. MARC*U-STAR.

Building polyhedra by self-assembly: theory and experiment.

PubMed

Kaplan, Ryan; Klobušický, Joseph; Pandey, Shivendra; Gracias, David H; Menon, Govind

2014-01-01

We investigate the utility of a mathematical framework based on discrete geometry to model biological and synthetic self-assembly. Our primary biological example is the self-assembly of icosahedral viruses; our synthetic example is surface-tension-driven self-folding polyhedra. In both instances, the process of self-assembly is modeled by decomposing the polyhedron into a set of partially formed intermediate states. The set of all intermediates is called the configuration space, pathways of assembly are modeled as paths in the configuration space, and the kinetics and yield of assembly are modeled by rate equations, Markov chains, or cost functions on the configuration space. We review an interesting interplay between biological function and mathematical structure in viruses in light of this framework. We discuss in particular: (i) tiling theory as a coarse-grained description of all-atom models; (ii) the building game-a growth model for the formation of polyhedra; and (iii) the application of these models to the self-assembly of the bacteriophage MS2. We then use a similar framework to model self-folding polyhedra. We use a discrete folding algorithm to compute a configuration space that idealizes surface-tension-driven self-folding and analyze pathways of assembly and dominant intermediates. These computations are then compared with experimental observations of a self-folding dodecahedron with side 300 μm. In both models, despite a combinatorial explosion in the size of the configuration space, a few pathways and intermediates dominate self-assembly. For self-folding polyhedra, the dominant intermediates have fewer degrees of freedom than comparable intermediates, and are thus more rigid. The concentration of assembly pathways on a few intermediates with distinguished geometric properties is biologically and physically important, and suggests deeper mathematical structure.

Interplay between spherical confinement and particle shape on the self-assembly of rounded cubes.

PubMed

Wang, Da; Hermes, Michiel; Kotni, Ramakrishna; Wu, Yaoting; Tasios, Nikos; Liu, Yang; de Nijs, Bart; van der Wee, Ernest B; Murray, Christopher B; Dijkstra, Marjolein; van Blaaderen, Alfons

2018-06-08

Self-assembly of nanoparticles (NPs) inside drying emulsion droplets provides a general strategy for hierarchical structuring of matter at different length scales. The local orientation of neighboring crystalline NPs can be crucial to optimize for instance the optical and electronic properties of the self-assembled superstructures. By integrating experiments and computer simulations, we demonstrate that the orientational correlations of cubic NPs inside drying emulsion droplets are significantly determined by their flat faces. We analyze the rich interplay of positional and orientational order as the particle shape changes from a sharp cube to a rounded cube. Sharp cubes strongly align to form simple-cubic superstructures whereas rounded cubes assemble into icosahedral clusters with additionally strong local orientational correlations. This demonstrates that the interplay between packing, confinement and shape can be utilized to develop new materials with novel properties.

Light Irradiation as Key to Shape and Function of Nano-Assemblies in Solution

NASA Astrophysics Data System (ADS)

Groehn, Franziska

Developing strategies to exploit solar energy become more and more important. Inspired by natural systems it is highly promising to self-assemble functional species into effective tailored supramolecular units. Here we report self-assembled polymer structures in solution, taking advantage of optical properties of hybrid structures and light responsiveness. A new type of photocatalytically active self-assembled polymer structure in aqueous solution consists of supramolecular nano-objects obtained from macroions and multivalent inorganic ``counterions'' such as nanoparticles or clusters. These can exhibit expressed selectivity or even allow catalytic reactions in solution that are not possible with the building blocks only. Further, polyelectrolyte-porphyrin nanoscale assemblies exhibit tunable optical properties including strong fluorescence and an up to 20-fold higher photocatalytic activity than without polymeric template. A different approach is to transfer light energy into mechanical energy. Here, light energy is converted into nanoscale shape changes. This route for the conversion of light is highly promising for applications in drug delivery, nanosensors and solar energy conversion. Membership of DPG, Germany ID 153159-.

Self-Assembly Behavior of Pullulan Abietate

NASA Astrophysics Data System (ADS)

Gradwell, Sheila; Esker, Alan; Glasser, Wolgang; Heinze, Thomas

2003-03-01

Wood is one of nature's most fascinating biological composites due to its toughness and resistance to fracture properties. These properties stem from the self-assembly of cellulose microfibrils in an amorphous matrix of hemicellulose and lignin. In recent years, science has looked to nature for guidance in preparing synthetic materials with desirable physical properties. In order to study the self-assembly process in wood, a model system composed of a polysaccharide, pullulan abietate, and a biomimetic cellulose substrate prepared by the Langmuir-Blodgett technique has been developed. Interfacial tension and surface plasmon resonance measurements used to study the self-assembly process will be discussed for different pullulan derivatives.

Mesoscopic self-organization of a self-assembled supramolecular rectangle on highly oriented pyrolytic graphite and Au(111) surfaces.

PubMed

Gong, Jian-Ru; Wan, Li-Jun; Yuan, Qun-Hui; Bai, Chun-Li; Jude, Hershel; Stang, Peter J

2005-01-25

A self-assembled supramolecular metallacyclic rectangle was investigated with scanning tunneling microscopy on highly oriented pyrolytic graphite and Au(111) surfaces. The rectangles spontaneously adsorb on both surfaces and self-organize into well ordered adlayers. On highly oriented pyrolytic graphite, the long edge of the rectangle stands on the surface, forming a 2D molecular network. In contrast, the face of the rectangle lays flat on the Au(111) surface, forming linear chains. The structures and intramolecular features obtained through high-resolution scanning tunneling microscopy imaging are discussed.

Active control of complex, multicomponent self-assembly processes

NASA Astrophysics Data System (ADS)

Schulman, Rebecca

The kinetics of many complex biological self-assembly processes such as cytoskeletal assembly are precisely controlled by cells. Spatiotemporal control over rates of filament nucleation, growth and disassembly determine how self-assembly occurs and how the assembled form changes over time. These reaction rates can be manipulated by changing the concentrations of the components needed for assembly by activating or deactivating them. I will describe how we can use these principles to design driven self-assembly processes in which we assemble and disassemble multiple types of components to create micron-scale networks of semiflexible filaments assembled from DNA. The same set of primitive components can be assembled into many different, structures depending on the concentrations of different components and how designed, DNA-based chemical reaction networks manipulate these concentrations over time. These chemical reaction networks can in turn interpret environmental stimuli to direct complex, multistage response. Such a system is a laboratory for understanding complex active material behaviors, such as metamorphosis, self-healing or adaptation to the environment that are ubiquitous in biological systems but difficult to quantitatively characterize or engineer.

Hyper-Assembly of Self-Assembled Glycoclusters Mediated by Specific Carbohydrate-Carbohydrate Interactions.

PubMed

Yan, Gengwei; Yamaguchi, Takumi; Suzuki, Tatsuya; Yanaka, Saeko; Sato, Sota; Fujita, Makoto; Kato, Koichi

2017-05-04

Hybridization of a self-assembled, spherical complex with oligosaccharides containing Lewis X, a functional trisaccharide displayed on various cell surfaces, yielded well-defined glycoclusters. The self-assembled glycoclusters exhibited homophilic hyper-assembly in aqueous solution in a Ca 2+ -dependent manner through specific carbohydrate-carbohydrate interactions, offering a structural scaffold for functional biomimetic systems. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

1-[(Anthracen-9-yl)carbon­yl]-2,7-di­meth­oxy­naphthalene: a chain-like structure composed of face-to-face type dimeric mol­ecular aggregates

PubMed Central

Siqingaowa; Tsumuki, Takehiro; Ogata, Kazuki; Yonezawa, Noriyuki; Okamoto, Akiko

2016-01-01

The asymmetric unit of the title compound, C27H20O3, contains two independent mol­ecules (A and B). The anthracene ring system is connected to the 2,7-di­meth­oxy­naphthalene core in a twisted manner, with dihedral angles of 86.38 (5) and 79.36 (8)°, respectively, for conformers A and B. In the crystal, face-to-face type dimeric mol­ecular aggregates of each conformer are observed. The dimer of conformer A is formed by two pairs of C—H⋯π inter­actions, and that of conformer B by a pair of (sp 2)C—H⋯O hydrogen bonds. The dimers of conformer A are linked to each other via a π–π stacking inter­action between the anthracene rings to form a chain along the b axis and the chains are aligned along the c axis, forming a sheet structure. The dimers of conformer B are connected to each other via a couple of C—H⋯π inter­actions to form a chain along the b axis. The chains are aligned along the c axis through (sp 2)C—H⋯O=C hydrogen bonds, forming a sheet parallel to the bc plane. The sheets of conformers A and B are alternately stacked along the a axis via two kinds of inter­molecular (sp 2)C—H⋯O=C hydrogen bonds. PMID:27980839

Self-assembling biomolecular catalysts for hydrogen production

NASA Astrophysics Data System (ADS)

Jordan, Paul C.; Patterson, Dustin P.; Saboda, Kendall N.; Edwards, Ethan J.; Miettinen, Heini M.; Basu, Gautam; Thielges, Megan C.; Douglas, Trevor

2016-02-01

The chemistry of highly evolved protein-based compartments has inspired the design of new catalytically active materials that self-assemble from biological components. A frontier of this biodesign is the potential to contribute new catalytic systems for the production of sustainable fuels, such as hydrogen. Here, we show the encapsulation and protection of an active hydrogen-producing and oxygen-tolerant [NiFe]-hydrogenase, sequestered within the capsid of the bacteriophage P22 through directed self-assembly. We co-opted Escherichia coli for biomolecular synthesis and assembly of this nanomaterial by expressing and maturing the EcHyd-1 hydrogenase prior to expression of the P22 coat protein, which subsequently self assembles. By probing the infrared spectroscopic signatures and catalytic activity of the engineered material, we demonstrate that the capsid provides stability and protection to the hydrogenase cargo. These results illustrate how combining biological function with directed supramolecular self-assembly can be used to create new materials for sustainable catalysis.

Self-assembled peptide nanostructures for functional materials

NASA Astrophysics Data System (ADS)

Sardan Ekiz, Melis; Cinar, Goksu; Aref Khalily, Mohammad; Guler, Mustafa O.

2016-10-01

Nature is an important inspirational source for scientists, and presents complex and elegant examples of adaptive and intelligent systems created by self-assembly. Significant effort has been devoted to understanding these sophisticated systems. The self-assembly process enables us to create supramolecular nanostructures with high order and complexity, and peptide-based self-assembling building blocks can serve as suitable platforms to construct nanostructures showing diverse features and applications. In this review, peptide-based supramolecular assemblies will be discussed in terms of their synthesis, design, characterization and application. Peptide nanostructures are categorized based on their chemical and physical properties and will be examined by rationalizing the influence of peptide design on the resulting morphology and the methods employed to characterize these high order complex systems. Moreover, the application of self-assembled peptide nanomaterials as functional materials in information technologies and environmental sciences will be reviewed by providing examples from recently published high-impact studies.

An exactly solvable model of hierarchical self-assembly

NASA Astrophysics Data System (ADS)

Dudowicz, Jacek; Douglas, Jack F.; Freed, Karl F.

2009-06-01

Many living and nonliving structures in the natural world form by hierarchical organization, but physical theories that describe this type of organization are scarce. To address this problem, a model of equilibrium self-assembly is formulated in which dynamically associating species organize into hierarchical structures that preserve their shape at each stage of assembly. In particular, we consider symmetric m-gons that associate at their vertices into Sierpinski gasket structures involving the hierarchical association of triangles, squares, hexagons, etc., at their corner vertices, thereby leading to fractal structures after many generations of assembly. This rather idealized model of hierarchical assembly yields an infinite sequence of self-assembly transitions as the morphology progressively organizes to higher levels of the hierarchy, and these structures coexists at dynamic equilibrium, as found in real hierarchically self-assembling systems such as amyloid fiber forming proteins. Moreover, the transition sharpness progressively grows with increasing m, corresponding to larger and larger loops in the assembled structures. Calculations are provided for several basic thermodynamic properties (including the order parameters for assembly for each stage of the hierarchy, average mass of clusters, specific heat, transition sharpness, etc.) that are required for characterizing the interaction parameters governing this type of self-assembly and for elucidating other basic qualitative aspects of these systems. Our idealized model of hierarchical assembly gives many insights into this ubiquitous type of self-organization process.

Subatomic electronic feature from dynamic motion of Si dimer defects in Bi nanolines on Si(001)

NASA Astrophysics Data System (ADS)

Kirkham, C. J.; Longobardi, M.; Köster, S. A.; Renner, Ch.; Bowler, D. R.

2017-08-01

Scanning tunneling microscopy (STM) reveals unusual sharp features in otherwise defect-free Bi nanolines self-assembled on Si(001). They appear as subatomic thin lines perpendicular to the Bi nanoline at positive biases and as atomic size beads at negative biases. Density functional theory (DFT) simulations show that these features can be attributed to buckled Si dimers substituting for Bi dimers in the nanoline, where the sharp feature is the counterintuitive signature of these dimers flipping during scanning. The perfect correspondence between the STM data and the DFT simulation demonstrated in this paper highlights the detailed understanding we have of the complex Bi-Si(001) Haiku system. This discovery has applications in the patterning of Si dangling bonds for nanoscale electronics.

S-Layer Protein Self-Assembly

PubMed Central

Pum, Dietmar; Toca-Herrera, Jose Luis; Sleytr, Uwe B.

2013-01-01

Crystalline S(urface)-layers are the most commonly observed cell surface structures in prokaryotic organisms (bacteria and archaea). S-layers are highly porous protein meshworks with unit cell sizes in the range of 3 to 30 nm, and thicknesses of ~10 nm. One of the key features of S-layer proteins is their intrinsic capability to form self-assembled mono- or double layers in solution, and at interfaces. Basic research on S-layer proteins laid foundation to make use of the unique self-assembly properties of native and, in particular, genetically functionalized S-layer protein lattices, in a broad range of applications in the life and non-life sciences. This contribution briefly summarizes the knowledge about structure, genetics, chemistry, morphogenesis, and function of S-layer proteins and pays particular attention to the self-assembly in solution, and at differently functionalized solid supports. PMID:23354479

Vancomycin: ligand recognition, dimerization and super-complex formation.

PubMed

Jia, ZhiGuang; O'Mara, Megan L; Zuegg, Johannes; Cooper, Matthew A; Mark, Alan E

2013-03-01

The antibiotic vancomycin targets lipid II, blocking cell wall synthesis in Gram-positive bacteria. Despite extensive study, questions remain regarding how it recognizes its primary ligand and what is the most biologically relevant form of vancomycin. In this study, molecular dynamics simulation techniques have been used to examine the process of ligand binding and dimerization of vancomycin. Starting from one or more vancomycin monomers in solution, together with different peptide ligands derived from lipid II, the simulations predict the structures of the ligated monomeric and dimeric complexes to within 0.1 nm rmsd of the structures determined experimentally. The simulations reproduce the conformation transitions observed by NMR and suggest that proposed differences between the crystal structure and the solution structure are an artifact of the way the NMR data has been interpreted in terms of a structural model. The spontaneous formation of both back-to-back and face-to-face dimers was observed in the simulations. This has allowed a detailed analysis of the origin of the cooperatively between ligand binding and dimerization and suggests that the formation of face-to-face dimers could be functionally significant. The work also highlights the possible role of structural water in stabilizing the vancomycin ligand complex and its role in the manifestation of vancomycin resistance. © 2013 The Authors Journal compilation © 2013 FEBS.

Toward a molecular programming language for algorithmic self-assembly

NASA Astrophysics Data System (ADS)

Patitz, Matthew John

Self-assembly is the process whereby relatively simple components autonomously combine to form more complex objects. Nature exhibits self-assembly to form everything from microscopic crystals to living cells to galaxies. With a desire to both form increasingly sophisticated products and to understand the basic components of living systems, scientists have developed and studied artificial self-assembling systems. One such framework is the Tile Assembly Model introduced by Erik Winfree in 1998. In this model, simple two-dimensional square 'tiles' are designed so that they self-assemble into desired shapes. The work in this thesis consists of a series of results which build toward the future goal of designing an abstracted, high-level programming language for designing the molecular components of self-assembling systems which can perform powerful computations and form into intricate structures. The first two sets of results demonstrate self-assembling systems which perform infinite series of computations that characterize computably enumerable and decidable languages, and exhibit tools for algorithmically generating the necessary sets of tiles. In the next chapter, methods for generating tile sets which self-assemble into complicated shapes, namely a class of discrete self-similar fractal structures, are presented. Next, a software package for graphically designing tile sets, simulating their self-assembly, and debugging designed systems is discussed. Finally, a high-level programming language which abstracts much of the complexity and tedium of designing such systems, while preventing many of the common errors, is presented. The summation of this body of work presents a broad coverage of the spectrum of desired outputs from artificial self-assembling systems and a progression in the sophistication of tools used to design them. By creating a broader and deeper set of modular tools for designing self-assembling systems, we hope to increase the complexity which is

A single crystalline porphyrinic titanium metal–organic framework

DOE PAGES

Yuan, Shuai; Liu, Tian -Fu; Feng, Dawei; ...

2015-04-28

We successfully assembled the photocatalytic titanium-oxo cluster and photosensitizing porphyrinic linker into a metal–organic framework (MOF), namely PCN-22. A preformed titanium-oxo carboxylate cluster is adopted as the starting material to judiciously control the MOF growth process to afford single crystals. This synthetic method is useful to obtain highly crystalline titanium MOFs, which has been a daunting challenge in this field. Moreover, PCN-22 demonstrated permanent porosity and photocatalytic activities toward alcohol oxidation.

Safety Evaluation of Self-assembling Peptide Gel after Intracranial Administration to Rats Using the Open Field Test.

PubMed

Tsunoda, Masashi; Sugaya, Chiemi; Sugiura, Yumiko; Nagai, Yusuke; Sakanishi, Kotaro

2016-01-01

Self-assembling peptides have been developed as clinical materials, which could scaffold to regenerate nerve cells and hemostatic materials in vivo. However, there has not been enough information for their in vivo application. The safety of self-assembling peptides for the application on the brain was examined using behavioral tests for each rat in this study. Self-assembling peptide gel was administered to the surface of the brain at a volume of 20 µL at 1.5%. After 2 months, the open field test and the prepulse inhibition (PPI) test were performed. There were no significant differences between the peptide gel and the control groups in locomotor distances and in %PPIs in the PPI test. The mean values of the percentage of time the rats stayed in the central area of the open field during the first 5 min and instances of center rearing or face washing in the peptide gel group were significantly higher than those in the control. There were amorphous substance in the subarachnoid region, and infiltrations of mononuclear cells were also observed in the self-assembling peptide gel group. Although the meaning of the effects observed in this study was not fully elucidated, the self-assembling gel produced marginal but significant behavioral and histological effects.

Understanding of assembly phenomena by aromatic-aromatic interactions: benzene dimer and the substituted systems.

PubMed

Lee, Eun Cheol; Kim, Dongwook; Jurecka, Petr; Tarakeshwar, P; Hobza, Pavel; Kim, Kwang S

2007-05-10

Interactions involving aromatic rings are important in molecular/biomolecular assembly and engineering. As a consequence, there have been a number of investigations on dimers involving benzene or other substituted pi systems. In this Feature Article, we examine the relevance of the magnitudes of their attractive and repulsive interaction energy components in governing the geometries of several pi-pi systems. The geometries and the associated binding energies were evaluated at the complete basis set (CBS) limit of coupled cluster theory with singles, doubles, and perturbative triples excitations [CCSD(T)] using a least biased scheme for the given data set. The results for the benzene dimer indicate that the floppy T-shaped structure (center-to-center distance: 4.96 A, with an axial benzene off-centered above the facial benzene) is isoenergetic in zero-point-energy (ZPE) corrected binding energy (D0) to the displaced-stacked structure (vertical interplanar distance: 3.54 A). However, the T-shaped structure is likely to be slightly more stable (D0 approximately equal to 2.4-2.5 kcal/mol) if quadruple excitations are included in the coupled cluster calculations. The presence of substituents on the aromatic ring, irrespective of their electron withdrawing or donating nature, leads to an increase in the binding energy, and the displaced-stacked conformations are more stabilized than the T-shaped conformers. This explains the wide prevalence of displaced stacked structures in organic crystals. Despite that the dispersion energy is dominating, the substituent as well as the conformational effects are correlated to the electrostatic interaction. This electrostatic origin implies that the substituent effect would be reduced in polar solution, but important in apolar media, in particular, for assembling processes.

Self-assembling amphiphilic peptides†

PubMed Central

Dehsorkhi, Ashkan; Castelletto, Valeria; Hamley, Ian W

2014-01-01

The self-assembly of several classes of amphiphilic peptides is reviewed, and selected applications are discussed. We discuss recent work on the self-assembly of lipopeptides, surfactant-like peptides and amyloid peptides derived from the amyloid-β peptide. The influence of environmental variables such as pH and temperature on aggregate nanostructure is discussed. Enzyme-induced remodelling due to peptide cleavage and nanostructure control through photocleavage or photo-cross-linking are also considered. Lastly, selected applications of amphiphilic peptides in biomedicine and materials science are outlined. © 2014 The Authors. Journal of Peptide Science published by European Peptide Society and John Wiley & Sons, Ltd. PMID:24729276

Self-assembly of self-limiting monodisperse supraparticles from polydisperse nanoparticles

NASA Astrophysics Data System (ADS)

Xia, Yunsheng; Nguyen, Trung Dac; Yang, Ming; Lee, Byeongdu; Santos, Aaron; Podsiadlo, Paul; Tang, Zhiyong; Glotzer, Sharon C.; Kotov, Nicholas A.

2011-09-01

Nanoparticles are known to self-assemble into larger structures through growth processes that typically occur continuously and depend on the uniformity of the individual nanoparticles. Here, we show that inorganic nanoparticles with non-uniform size distributions can spontaneously assemble into uniformly sized supraparticles with core-shell morphologies. This self-limiting growth process is governed by a balance between electrostatic repulsion and van der Waals attraction, which is aided by the broad polydispersity of the nanoparticles. The generic nature of the interactions creates flexibility in the composition, size and shape of the constituent nanoparticles, and leads to a large family of self-assembled structures, including hierarchically organized colloidal crystals.

Challenges and breakthroughs in recent research on self-assembly

PubMed Central

Ariga, Katsuhiko; Hill, Jonathan P; Lee, Michael V; Vinu, Ajayan; Charvet, Richard; Acharya, Somobrata

2008-01-01

The controlled fabrication of nanometer-scale objects is without doubt one of the central issues in current science and technology. However, existing fabrication techniques suffer from several disadvantages including size-restrictions and a general paucity of applicable materials. Because of this, the development of alternative approaches based on supramolecular self-assembly processes is anticipated as a breakthrough methodology. This review article aims to comprehensively summarize the salient aspects of self-assembly through the introduction of the recent challenges and breakthroughs in three categories: (i) types of self-assembly in bulk media; (ii) types of components for self-assembly in bulk media; and (iii) self-assembly at interfaces. PMID:27877935

Soluble porphyrin polymers

DOEpatents

Gust, Jr., John Devens; Liddell, Paul Anthony

2015-07-07

Porphyrin polymers of Structure 1, where n is an integer (e.g., 1, 2, 3, 4, 5, or greater) ##STR00001## are synthesized by the method shown in FIGS. 2A and 2B. The porphyrin polymers of Structure 1 are soluble in organic solvents such as 2-MeTHF and the like, and can be synthesized in bulk (i.e., in processes other than electropolymerization). These porphyrin polymers have long excited state lifetimes, making the material suitable as an organic semiconductor for organic electronic devices including transistors and memories, as well as solar cells, sensors, light-emitting devices, and other opto-electronic devices.

Structure and self-assembly of the calcium binding matrix protein of human metapneumovirus.

PubMed

Leyrat, Cedric; Renner, Max; Harlos, Karl; Huiskonen, Juha T; Grimes, Jonathan M

2014-01-07

The matrix protein (M) of paramyxoviruses plays a key role in determining virion morphology by directing viral assembly and budding. Here, we report the crystal structure of the human metapneumovirus M at 2.8 Å resolution in its native dimeric state. The structure reveals the presence of a high-affinity Ca²⁺ binding site. Molecular dynamics simulations (MDS) predict a secondary lower-affinity site that correlates well with data from fluorescence-based thermal shift assays. By combining small-angle X-ray scattering with MDS and ensemble analysis, we captured the structure and dynamics of M in solution. Our analysis reveals a large positively charged patch on the protein surface that is involved in membrane interaction. Structural analysis of DOPC-induced polymerization of M into helical filaments using electron microscopy leads to a model of M self-assembly. The conservation of the Ca²⁺ binding sites suggests a role for calcium in the replication and morphogenesis of pneumoviruses. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

Hierarchical self-assembly of a bow-shaped molecule bearing self-complementary hydrogen bonding sites into extended supramolecular assemblies.

PubMed

Ikeda, Masato; Nobori, Tadahito; Schmutz, Marc; Lehn, Jean-Marie

2005-01-07

The bow-shaped molecule 1 bearing a self-complementary DAAD-ADDA (D=donor A=acceptor) hydrogen-bonding array generates, in hydrocarbon solvents, highly ordered supramolecular sheet aggregates that subsequently give rise to gels by formation of an entangled network. The process of hierarchical self-assembly of compound 1 was investigated by the concentration and temperature dependence of UV-visible and (1)H NMR spectra, fluorescence spectra, and electron microscopy data. The temperature dependence of the UV-visible spectra indicates a highly cooperative process for the self-assembly of compound 1 in decaline. The electron micrograph of the decaline solution of compound 1 (1.0 mM) revealed supramolecular sheet aggregates forming an entangled network. The selected area electronic diffraction patterns of the supramolecular sheet aggregates were typical for single crystals, indicative of a highly ordered assembly. The results exemplify the generation, by hierarchical self-assembly, of highly organized supramolecular materials presenting novel collective properties at each level of organization.

Collagen peptide-based biomaterials for protein delivery and peptide-promoted self-assembly of gold nanoparticles

NASA Astrophysics Data System (ADS)

Ernenwein, Dawn M.

2011-12-01

ordered hydrophobic face had no effect on GNP assembly. The self-assembly system herein is advantageous due to its reversible nature upon addition of high salt concentrations which masks the surface charge. There is great potential for using this uniquely designed self-assembled peptide-gold nanoparticle system for exploring the interplay between peptide ligation and GNP self-assembly.

A Geometric Principle May Guide Self-Assembly of Fullerene Cages from Clathrin Triskelia and from Carbon Atoms☆

PubMed Central

Schein, Stan; Sands-Kidner, Michelle

2008-01-01

Abstract Clathrin triskelia and carbon atoms alike self-assemble into a limited selection of fullerene cages (with n three connected vertices, 3n/2 edges, 12 pentagonal faces, and (n−20)/2 hexagonal faces). We show that a geometric constraint—exclusion of head-to-tail dihedral angle discrepancies (DADs)—explains this limited selection as well as successful assembly into such closed cages in the first place. An edge running from a pentagon to a hexagon has a DAD, since the dihedral angles about the edge broaden from its pentagon (tail) end to its hexagon (head) end. Of the 21 configurations of a central face and surrounding faces, six have such DAD vectors arranged head-to-tail. Of the 5770 mathematically possible fullerene cages for n ≤ 60, excluding those with any of the six configurations leaves just 15 cages plus buckminsterfullerene (n = 60), among them the known clathrin cages. Of the 216,739 mathematically possible cages for 60 < n ≤ 84, just the 50 that obey the isolated-pentagon rule, among them known carbon cages, pass. The absence of likely fullerenes for some n (30,34,46,48,52–58,62–68) explains the abundance of certain cages, including buckminsterfullerene. These principles also suggest a “probable roads” path to self-assembly in place of pentagon-road and fullerene-road hypotheses. PMID:17921209

Programmable Assembly of Hybrid Nanoclusters.

PubMed

Ni, Songbo; Wolf, Heiko; Isa, Lucio

2018-02-20

Hybrid nanoparticle clusters (often metallic) are interesting plasmonic materials with tunable resonances and a near-field electromagnetic enhancement at interparticle junctions. Therefore, in recent years, we have witnessed a surge in both the interest in these materials and the efforts to obtain them. However, a versatile fabrication of hybrid nanoclusters, that is, combining more than one material, still remains an open challenge. Current lithographical or self-assembly methods are limited to the preparation of hybrid clusters with up to two different materials and typically to the fabrication of hybrid dimers. Here, we provide a novel strategy to deposit and align not only hybrid dimers but also hybrid nanoclusters possessing more complex shapes and compositions. Our strategy is based on the downscaling of sequential capillarity-assisted particle assembly over topographical templates. As a proof of concept, we demonstrate dimers, linear trimers, and 2D nanoclusters with programmable compositions from a range of metallic nanoparticles. Our process does not rely on any specific chemistry and can be extended to a large variety of particles and shapes. The template also simultaneously aligns the hybrid (often anisotropic) nanoclusters, which could facilitate device integration, for example, for optical readout after transfer to other substrates by a printing step. We envisage that this new fabrication route will enable the assembly and positioning of complex hybrid nanoclusters of different functional nanoparticles to study coupling effects not only locally but also at larger scales for new nanoscale optical devices.

The neural basis of self-face recognition after self-concept threat and comparison with important others.

PubMed

Guan, Lili; Qi, Mingming; Zhang, Qinglin; Yang, Juan

2014-01-01

The implicit positive association (IPA) theory attributed self-face advantage to the IPA with self-concept. Previous behavioral study has found that self-concept threat (SCT) could eliminate the self-advantage in face recognition over familiar-face, without taking levels of facial familiarity into account. The current event-related potential study aimed to investigate whether SCT could eliminate the self-face advantage over stranger-face. Fifteen participants completed a "self-friend" comparison task in which participants identified the face orientation of self-face and friend-face after SCT and non-self-concept threat (NSCT) priming, and a "self-stranger" comparison task was also completed in which participants identified the face orientation of self-face and stranger-face after SCT and NSCT priming. The results showed that the N2 amplitudes were more negative for processing friend-face than self-face after NSCT priming, but there was no significant difference between them after SCT priming. Moreover, the N2 amplitudes were more negative for processing stranger-face than self-face both after SCT priming and after NSCT priming. Furthermore, SCT manipulated the N2 amplitudes of friend-face rather than self-face. Overall, the present study made a supplementary to the current IPA theory and further indicated that SCT would only eliminate this self-face recognition advantage when comparing with important others.

The Self-Assembly of Particles with Multipolar Interactions

DTIC Science & Technology

2004-01-01

the LATEX template in which this thesis has been written. I also thank Kevin Van Workum and Jack Douglas for contributing simulation work and some...of the computational expense of simulating such complex self-assembly systems at the molecular level and a desire to understand the self-assembly at...Dissertation directed by: Professor Wolfgang Losert Department of Physics In this thesis , we describe results from investigations of the self-assembly of

Fabrication of a TiO2@porphyrin nanofiber hybrid material: a highly efficient photocatalyst under simulated sunlight irradiation

NASA Astrophysics Data System (ADS)

La, Duong Duc; Rananaware, Anushri; Phuong Nguyen Thi, Hoai; Jones, Lathe; Bhosale, Sheshanath V.

2017-03-01

The solar spectrum consists of 8% UV radiation, while 45% of solar energy is from visible light. It is therefore desirable to fabricate a hybrid material which is able to harvest energy from a wide range of photons from the sun for applications such as solar cells, photovoltaics, and photocatalysis. In this study we report on the fabrication of a TiO2@porphyrin hybrid material by surfactant-assisted co-assembly of monomeric porphyrin molecules with TiO2 nanoparticles. The obtained TiO2@porphyrin composite shows excellent integration of TiO2 particles with diameters of 15-30 nm into aggregated porphyrin nanofibers, which have a width of 70-90 nm and are several µm long. SEM, XPS, XRD, FTIR, UV-Vis and fluorescence spectroscopy were employed to characterize the TiO2@TCPP hybrid material. This material exhibits efficient photocatalytic performance under simulated sunlight, due to synergistic photocatalytic activities of the porphyrin aggregates in visible light and TiO2 particles in the UV region. A plausible mechanism for photocatalytic degradation is also proposed and discussed.

Quantifying quality in DNA self-assembly

PubMed Central

Wagenbauer, Klaus F.; Wachauf, Christian H.; Dietz, Hendrik

2014-01-01

Molecular self-assembly with DNA is an attractive route for building nanoscale devices. The development of sophisticated and precise objects with this technique requires detailed experimental feedback on the structure and composition of assembled objects. Here we report a sensitive assay for the quality of assembly. The method relies on measuring the content of unpaired DNA bases in self-assembled DNA objects using a fluorescent de-Bruijn probe for three-base ‘codons’, which enables a comparison with the designed content of unpaired DNA. We use the assay to measure the quality of assembly of several multilayer DNA origami objects and illustrate the use of the assay for the rational refinement of assembly protocols. Our data suggests that large and complex objects like multilayer DNA origami can be made with high strand integration quality up to 99%. Beyond DNA nanotechnology, we speculate that the ability to discriminate unpaired from paired nucleic acids in the same macromolecule may also be useful for analysing cellular nucleic acids. PMID:24751596

Differentially photo-crosslinked polymers enable self-assembling microfluidics

PubMed Central

Jamal, Mustapha; Zarafshar, Aasiyeh M.; Gracias, David H.

2012-01-01

An important feature of naturally self-assembled systems such as leaves and tissues is that they are curved and have embedded fluidic channels that enable the transport of nutrients to, or removal of waste from, specific three-dimensional (3D) regions. Here, we report the self-assembly of photopatterned polymers, and consequently microfluidic devices, into curved geometries. We discovered that differentially photo-crosslinked SU-8 films spontaneously and reversibly curved upon film de-solvation and re-solvation. Photolithographic patterning of the SU-8 films enabled the self-assembly of cylinders, cubes, and bidirectionally folded sheets. We integrated polydimethylsiloxane (PDMS) microfluidic channels with these SU-8 films to self-assemble curved microfluidic networks. PMID:22068594

Self assembly of organic nanostructures and dielectrophoretic assembly of inorganic nanowires.

NASA Astrophysics Data System (ADS)

Dholakia, Geetha; Kuo, Steven; Allen, E. L.

2007-03-01

Self assembly techniques enable the organization of organic molecules into nanostructures. Currently engineering strategies for efficient assembly and routine integration of inorganic nanoscale objects into functional devices is very limited. AC Dielectrophoresis is an efficient technique to manipulate inorganic nanomaterials into higher dimensional structures. We used an alumina template based sol-gel synthesis method for the growth of various metal oxide nanowires with typical diameters of 100-150 nm, ranging in length from 3-10 μm. Here we report the dielectrophoretic assembly of TiO2 nanowires, an important material for photocatalysis and photovoltaics, onto interdigitated devices. Self assembly in organic nanostructures and its dependence on structure and stereochemistry of the molecule and dielectrophoretic field dependence in the assembly of inorganic nanowires will be compared and contrasted. Tunneling spectroscopy and DOS of these nanoscale systems will also be discussed.

Programmable self-assembly of three-dimensional nanostructures from 104 unique components

PubMed Central

Ong, Luvena L.; Hanikel, Nikita; Yaghi, Omar K.; Grun, Casey; Strauss, Maximilian T.; Bron, Patrick; Lai-Kee-Him, Josephine; Schueder, Florian; Wang, Bei; Wang, Pengfei; Kishi, Jocelyn Y.; Myhrvold, Cameron A.; Zhu, Allen; Jungmann, Ralf

2017-01-01

Nucleic acids (DNA and RNA) are widely used to construct nanoscale structures with ever increasing complexity1–14 for possible applications in fields as diverse as structural biology, biophysics, synthetic biology and photonics. The nanostructures are formed through one-pot self-assembly, with early examples typically containing on the order of 10 unique DNA strands. The introduction of DNA origami4, which uses many staple strands to fold one long scaffold strand into a desired structure, gave access to kilo- to mega-dalton nanostructures containing about 102 unique DNA strands6,7,10,13 . Aiming for even larger DNA origami structures is in principle possible15,16, but faces the challenge of having to manufacture and route an increasingly long scaffold strand. An alternative and in principle more readily scalable approach uses DNA brick assembly8,9, which doesn’t need a scaffold and instead uses hundreds of short DNA brick strands that self-assemble according to specific inter-brick interactions. First-generation bricks used to create 3D structures are 32-nt long with four 8-nt binding domains that directed 102 distinct bricks into well-formed assemblies, but attempts to create larger structures encountered practical challenges and had limited success.9 Here we show that a new generation of DNA bricks with longer binding domains makes it possible to self-assemble 0.1 – 1 giga-dalton three-dimensional nanostructures from 104 unique components, including a 0.5 giga-dalton cuboid containing 30,000 unique bricks and a 1 giga-dalton rotationally symmetric tetramer. We also assemble a cuboid containing 10,000 bricks and 20,000 uniquely addressable ‘nano-voxels’ that serves as a molecular canvas for three-dimensional sculpting, with introduction of sophisticated user-prescribed 3D cavities yielding structures such as letters, a complex helicoid and a teddy bear. We anticipate that, with further optimization, even larger assemblies might be accessible and prove

Metal-coupled folding as the driving force for the extreme stability of Rad50 zinc hook dimer assembly

NASA Astrophysics Data System (ADS)

Kochańczyk, Tomasz; Nowakowski, Michał; Wojewska, Dominika; Kocyła, Anna; Ejchart, Andrzej; Koźmiński, Wiktor; Krężel, Artur

2016-11-01

The binding of metal ions at the interface of protein complexes presents a unique and poorly understood mechanism of molecular assembly. A remarkable example is the Rad50 zinc hook domain, which is highly conserved and facilitates the Zn2+-mediated homodimerization of Rad50 proteins. Here, we present a detailed analysis of the structural and thermodynamic effects governing the formation and stability (logK12 = 20.74) of this evolutionarily conserved protein assembly. We have dissected the determinants of the stability contributed by the small β-hairpin of the domain surrounding the zinc binding motif and the coiled-coiled regions using peptides of various lengths from 4 to 45 amino acid residues, alanine substitutions and peptide bond-to-ester perturbations. In the studied series of peptides, an >650 000-fold increase of the formation constant of the dimeric complex arises from favorable enthalpy because of the increased acidity of the cysteine thiols in metal-free form and the structural properties of the dimer. The dependence of the enthalpy on the domain fragment length is partially compensated by the entropic penalty of domain folding, indicating enthalpy-entropy compensation. This study facilitates understanding of the metal-mediated protein-protein interactions in which the metal ion is critical for the tight association of protein subunits.

Self-assembly of active amphiphilic Janus particles

NASA Astrophysics Data System (ADS)

Mallory, S. A.; Alarcon, F.; Cacciuto, A.; Valeriani, C.

2017-12-01

In this article, we study the phenomenology of a two dimensional dilute suspension of active amphiphilic Janus particles. We analyze how the morphology of the aggregates emerging from their self-assembly depends on the strength and the direction of the active forces. We systematically explore and contrast the phenomenologies resulting from particles with a range of attractive patch coverages. Finally, we illustrate how the geometry of the colloids and the directionality of their interactions can be used to control the physical properties of the assembled active aggregates and suggest possible strategies to exploit self-propulsion as a tunable driving force for self-assembly.

Spintronic characteristics of self-assembled neurotransmitter acetylcholine molecular complexes enable quantum information processing in neural networks and brain

NASA Astrophysics Data System (ADS)

Tamulis, Arvydas; Majauskaite, Kristina; Kairys, Visvaldas; Zborowski, Krzysztof; Adhikari, Kapil; Krisciukaitis, Sarunas

2016-09-01

Implementation of liquid state quantum information processing based on spatially localized electronic spin in the neurotransmitter stable acetylcholine (ACh) neutral molecular radical is discussed. Using DFT quantum calculations we proved that this molecule possesses stable localized electron spin, which may represent a qubit in quantum information processing. The necessary operating conditions for ACh molecule are formulated in self-assembled dimer and more complex systems. The main quantum mechanical research result of this paper is that the neurotransmitter ACh systems, which were proposed, include the use of quantum molecular spintronics arrays to control the neurotransmission in neural networks.

Synthesis of borylated porphyrin and bromo- porphyrin as building blocks for light harvesting antenna molecule

NASA Astrophysics Data System (ADS)

Radzuan, Nuur Haziqah Mohd; Hassan, Nurul Izzaty; Bakar, Muntaz Abu

2018-04-01

The building blocks for synthesis of light harvesting antenna which are 5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolane)-10,20-diphenylporphyrin, 5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolane)-10,20-dihexylporphyrin and 5,10,15,20-tetra-(bromophenyl)porphyrin were synthesized. Borylated porphyrin was synthesized by Suzuki coupling reaction between A2BC bromo-porphyrin and pinacolborane. Whereas 5,10,15,20-tetra-(bromophenyl) porphyrin was synthesized by Lindsey condensation reaction between pyrrole and 4-bromobenzaldehyde. 1H-NMR, 13C-NMR spectroscopy and UV-visible spectroscopy confirmed the successful formation of all compounds.

Halogen-Adatom Mediated Phase Transition of Two-Dimensional Molecular Self-Assembly on a Metal Surface.

PubMed

Niu, Tianchao; Wu, Jinge; Ling, Faling; Jin, Shuo; Lu, Guanghong; Zhou, Miao

2018-01-09

Construction of tunable and robust two-dimensional (2D) molecular arrays with desirable lattices and functionalities over a macroscopic scale relies on spontaneous and reversible noncovalent interactions between suitable molecules as building blocks. Halogen bonding, with active tunability of direction, strength, and length, is ideal for tailoring supramolecular structures. Herein, by combining low-temperature scanning tunneling microscopy and systematic first-principles calculations, we demonstrate novel halogen bonding involving single halogen atoms and phase engineering in 2D molecular self-assembly. On the Au(111) surface, we observed catalyzed dehalogenation of hexabromobenzene (HBB) molecules, during which negatively charged bromine adatoms (Br δ- ) were generated and participated in assembly via unique C-Br δ+ ···Br δ- interaction, drastically different from HBB assembly on a chemically inert graphene substrate. We successfully mapped out different phases of the assembled superstructure, including densely packed hexagonal, tetragonal, dimer chain, and expanded hexagonal lattices at room temperature, 60 °C, 90 °C, and 110 °C, respectively, and the critical role of Br δ- in regulating lattice characteristics was highlighted. Our results show promise for manipulating the interplay between noncovalent interactions and catalytic reactions for future development of molecular nanoelectronics and 2D crystal engineering.

Understanding the effects of packing and chemical terminations on the optical excitations of azobenzene-functionalized self-assembled monolayers

NASA Astrophysics Data System (ADS)

Cocchi, Caterina; Draxl, Claudia

2017-10-01

In a first-principles study based on many-body perturbation theory, we analyze the optical excitations of azobenzene-functionalized self-assembled monolayers (SAMs) with increasing packing density and different terminations, considering for comparison the corresponding gas-phase molecules and dimers. Intermolecular coupling increases with the density of the chromophores independently of the functional groups. The intense π → π* resonance that triggers photo-isomerization is present in the spectra of isolated dimers and diluted SAMs, but it is almost completely washed out in tightly packed architectures. Intermolecular coupling is partially inhibited by mixing differently functionalized azobenzene derivatives, in particular when large groups are involved. In this way, the excitation band inducing the photo-isomerization process is partially preserved and the effects of dense packing partly counterbalanced. Our results suggest that a tailored design of azobenzene-functionalized SAMs which optimizes the interplay between the packing density of the chromophores and their termination can lead to significant improvements in the photo-switching efficiency of these systems.

Quantitative computational models of molecular self-assembly in systems biology

PubMed Central

Thomas, Marcus; Schwartz, Russell

2017-01-01

Molecular self-assembly is the dominant form of chemical reaction in living systems, yet efforts at systems biology modeling are only beginning to appreciate the need for and challenges to accurate quantitative modeling of self-assembly. Self-assembly reactions are essential to nearly every important process in cell and molecular biology and handling them is thus a necessary step in building comprehensive models of complex cellular systems. They present exceptional challenges, however, to standard methods for simulating complex systems. While the general systems biology world is just beginning to deal with these challenges, there is an extensive literature dealing with them for more specialized self-assembly modeling. This review will examine the challenges of self-assembly modeling, nascent efforts to deal with these challenges in the systems modeling community, and some of the solutions offered in prior work on self-assembly specifically. The review concludes with some consideration of the likely role of self-assembly in the future of complex biological system models more generally. PMID:28535149

Quantitative computational models of molecular self-assembly in systems biology.

PubMed

Thomas, Marcus; Schwartz, Russell

2017-05-23

Molecular self-assembly is the dominant form of chemical reaction in living systems, yet efforts at systems biology modeling are only beginning to appreciate the need for and challenges to accurate quantitative modeling of self-assembly. Self-assembly reactions are essential to nearly every important process in cell and molecular biology and handling them is thus a necessary step in building comprehensive models of complex cellular systems. They present exceptional challenges, however, to standard methods for simulating complex systems. While the general systems biology world is just beginning to deal with these challenges, there is an extensive literature dealing with them for more specialized self-assembly modeling. This review will examine the challenges of self-assembly modeling, nascent efforts to deal with these challenges in the systems modeling community, and some of the solutions offered in prior work on self-assembly specifically. The review concludes with some consideration of the likely role of self-assembly in the future of complex biological system models more generally.

Guided molecular self-assembly: a review of recent efforts

NASA Astrophysics Data System (ADS)

Huie, Jiyun C.

2003-04-01

This paper serves as an introductory review of significant and novel successes achieved in the fields of nanotechnology, particularly in the formation of nanostructures using guided molecular self-assembly methods. Self-assembly is a spontaneous process by which molecules and nanophase entities may materialize into organized aggregates or networks. Through various interactive mechanisms of self-assembly, such as electrostatics, chemistry, surface properties, and via other mediating agents, the technique proves indispensable to recent functional materials and device realizations. The discussion will extend to spontaneous and Langmuir-Blodgett formation of self-assembled monolayers on various substrates, and a number of different categories of self-assembly techniques based on the type of interaction exploited. Combinatorial techniques, known as soft lithography, of micro-contact printing and dip-pen nanolithography, which can be effectively used to up-size nanostructured molecular assemblies to submicrometer and micrometer scale patterns, will also be mentioned.

Is the Self Always Better than a Friend? Self-Face Recognition in Christians and Atheists

PubMed Central

Ma, Yina; Han, Shihui

2012-01-01

Early behavioral studies found that human adults responded faster to their own faces than faces of familiar others or strangers, a finding referred to as self-face advantage. Recent research suggests that the self-face advantage is mediated by implicit positive association with the self and is influenced by sociocultural experience. The current study investigated whether and how Christian belief and practice affect the processing of self-face in a Chinese population. Christian and Atheist participants were recruited for an implicit association test (IAT) in Experiment 1 and a face-owner identification task in Experiment 2. Experiment 1 found that atheists responded faster to self-face when it shared the same response key with positive compared to negative trait adjectives. This IAT effect, however, was significantly reduced in Christians. Experiment 2 found that atheists responded faster to self-face compared to a friend’s face, but this self-face advantage was significantly reduced in Christians. Hierarchical regression analyses further showed that the IAT effect positively predicted self-face advantage in atheists but not in Christians. Our findings suggest that Christian belief and practice may weaken implicit positive association with the self and thus decrease the advantage of the self over a friend during face recognition in the believers. PMID:22662231

Is the self always better than a friend? Self-face recognition in Christians and atheists.

PubMed

Ma, Yina; Han, Shihui

2012-01-01

Early behavioral studies found that human adults responded faster to their own faces than faces of familiar others or strangers, a finding referred to as self-face advantage. Recent research suggests that the self-face advantage is mediated by implicit positive association with the self and is influenced by sociocultural experience. The current study investigated whether and how Christian belief and practice affect the processing of self-face in a Chinese population. Christian and Atheist participants were recruited for an implicit association test (IAT) in Experiment 1 and a face-owner identification task in Experiment 2. Experiment 1 found that atheists responded faster to self-face when it shared the same response key with positive compared to negative trait adjectives. This IAT effect, however, was significantly reduced in Christians. Experiment 2 found that atheists responded faster to self-face compared to a friend's face, but this self-face advantage was significantly reduced in Christians. Hierarchical regression analyses further showed that the IAT effect positively predicted self-face advantage in atheists but not in Christians. Our findings suggest that Christian belief and practice may weaken implicit positive association with the self and thus decrease the advantage of the self over a friend during face recognition in the believers.

CHEMO/mechanical energy conversiona via supramolecular self-assembly

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lynn, David G.; Conticello, Vincent

With the assembly codes for protein/peptide self-assembly sufficiently developed to control these phases, we are positioned to address critical requirements for generating unique self-propagating functional assemblies such as chemical batteries and engines that can be used to extend the capability of living cells. These integrative functional assemblies can then be used within cells to create new functions that will address the world’s energy challenges.

Fluidic self-actuating control assembly

DOEpatents

Grantz, Alan L.

1979-01-01

A fluidic self-actuating control assembly for use in a reactor wherein no external control inputs are required to actuate (scram) the system. The assembly is constructed to scram upon sensing either a sudden depressurization of reactor inlet flow or a sudden increase in core neutron flux. A fluidic control system senses abnormal flow or neutron flux transients and actuates the system, whereupon assembly coolant flow reverses, forcing absorber balls into the reactor core region.

Centrioles: some self-assembly required.

PubMed

Song, Mi Hye; Miliaras, Nicholas B; Peel, Nina; O'Connell, Kevin F

2008-12-01

Centrioles play an important role in organizing microtubules and are precisely duplicated once per cell cycle. New (daughter) centrioles typically arise in association with existing (mother) centrioles (canonical assembly), suggesting that mother centrioles direct the formation of daughter centrioles. However, under certain circumstances, centrioles can also selfassemble free of an existing centriole (de novo assembly). Recent work indicates that the canonical and de novo pathways utilize a common mechanism and that a mother centriole spatially constrains the self-assembly process to occur within its immediate vicinity. Other recently identified mechanisms further regulate canonical assembly so that during each cell cycle, one and only one daughter centriole is assembled per mother centriole.

Reward Promotes Self-Face Processing: An Event-Related Potential Study

PubMed Central

Zhan, Youlong; Chen, Jie; Xiao, Xiao; Li, Jin; Yang, Zilu; Fan, Wei; Zhong, Yiping

2016-01-01

The present study adopted a reward-priming paradigm to investigate whether and how monetary reward cues affected self-face processing. Event-related potentials were recorded during judgments of head orientation of target faces (self, friend, and stranger), with performance associated with a monetary reward. The results showed self-faces elicited larger N2 mean amplitudes than other-faces, and mean N2 amplitudes increased after monetary reward as compared with no reward cue. Moreover, an interaction effect between cue type and face type was observed for the P3 component, suggesting that both self-faces and friend-faces elicited larger P3 mean amplitudes than stranger-faces after no reward cue, with no significant difference between self-faces and friend-faces under this condition. However, self-faces elicited larger P3 mean amplitudes than friend-faces when monetary reward cues were provided. Interestingly, the enhancement of reward on friend-faces processing was observed at late positive potentials (LPP; 450–600 ms), suggesting that the LPP difference between friend-faces and stranger-faces was enhanced with monetary reward cues. Thus, we found that the enhancement effect of reward on self-relevant processing occurred at the later stages, but not at the early stage. These findings suggest that the activation of the reward expectations can enhance self-face processing, yielding a robust and sustained modulation over their overlapped brain areas where reward and self-relevant processing mechanisms may operate together. PMID:27242637

DNAzyme-Based Logic Gate-Mediated DNA Self-Assembly.

PubMed

Zhang, Cheng; Yang, Jing; Jiang, Shuoxing; Liu, Yan; Yan, Hao

2016-01-13

Controlling DNA self-assembly processes using rationally designed logic gates is a major goal of DNA-based nanotechnology and programming. Such controls could facilitate the hierarchical engineering of complex nanopatterns responding to various molecular triggers or inputs. Here, we demonstrate the use of a series of DNAzyme-based logic gates to control DNA tile self-assembly onto a prescribed DNA origami frame. Logic systems such as "YES," "OR," "AND," and "logic switch" are implemented based on DNAzyme-mediated tile recognition with the DNA origami frame. DNAzyme is designed to play two roles: (1) as an intermediate messenger to motivate downstream reactions and (2) as a final trigger to report fluorescent signals, enabling information relay between the DNA origami-framed tile assembly and fluorescent signaling. The results of this study demonstrate the plausibility of DNAzyme-mediated hierarchical self-assembly and provide new tools for generating dynamic and responsive self-assembly systems.

Self-Face and Self-Body Recognition in Autism

ERIC Educational Resources Information Center

Gessaroli, Erica; Andreini, Veronica; Pellegri, Elena; Frassinetti, Francesca

2013-01-01

The advantage in responding to self vs. others' body and face-parts (the so called self-advantage) is considered to reflect the implicit access to the bodily self representation and has been studied in healthy and brain-damaged adults in previous studies. If the distinction of the self from others is a key aspect of social behaviour and is a…

Freezing-induced self-assembly of amphiphilic molecules

NASA Astrophysics Data System (ADS)

Albouy, P. A.; Deville, S.; Fulkar, A.; Hakouk, K.; Impéror-Clerc, M.; Klotz, M.; Liu, Q.; Marcellini, M.; Perez, J.

The self-assembly of amphiphilic molecules usually takes place in a liquid phase, near room temperature. Here, using small angle X-ray scattering (SAXS) experiments performed in real time, we show that freezing of aqueous solutions of copolymer amphiphilic molecules can induce self-assembly below 0{\\deg}C.

Freezing-induced self-assembly of amphiphilic molecules.

PubMed

Albouy, P A; Deville, S; Fulkar, A; Hakouk, K; Impéror-Clerc, M; Klotz, M; Liu, Q; Marcellini, M; Perez, J

2017-03-01

The self-assembly of amphiphilic molecules usually takes place in a liquid phase, near room temperature. Here, using small angle X-ray scattering (SAXS) experiments performed in real time, we show that freezing of aqueous solutions of copolymer amphiphilic molecules can induce self-assembly below 0 °C.

Mutual friends' social support and self-disclosure in face-to-face and instant messenger communication.

PubMed

Trepte, Sabine; Masur, Philipp K; Scharkow, Michael

2018-01-01

In the present study, we investigated long-term effects of self-disclosure on social support in face-to-face and instant messenger (IM) communication between mutual friends. Using a representative sample of 583 German IM users, we explored whether self-disclosure and positive experiences with regard to social support would dynamically interact in the form of a reinforcing spiral across three measurement occasions. If mutual friends self-disclose today, will they receive more social support 6 months later? In turn, will this affect their willingness to self-disclose another 6 months later? We further analyzed spill-over effects from face-to-face to IM communication and vice versa. We found that self-disclosure predicted social support and vice versa in IM communication, but not in face-to-face communication. In light of these results, the impact of IM communication on how individuals maneuver friendships through the interplay between self-disclosure and social support are discussed.

Three Short Stories about Hexaarylbenzene-Porphyrin Scaffolds.

PubMed

Lungerich, Dominik; Hitzenberger, Jakob F; Donaubauer, Wolfgang; Drewello, Thomas; Jux, Norbert

2016-11-14

A feasible two-step synthesis and characterization of a full series of hexaarylbenzene (HAB) substituted porphyrins and tetrabenzoporphyrins is presented. Key steps represent the microwave-assisted porphyrin condensation and the statistical Diels-Alder reaction to the desired HAB-porphyrins. Regarding their applications, they proved to be easily accessible and effective high molecular mass calibrants for (MA)LDI mass spectrometry. The free-base and zinc(II) porphyrin systems, as well as the respective tetrabenzoporphyrins, demonstrate in solid state experiments strong red- and near-infrared-light emission and are potentially interesting for the application in "truly organic" light-emitting devices. Lastly, they represent facile precursors to large polycyclic aromatic hydrocarbon (PAH) substituted porphyrins. We prepared the first tetra-hexa-peri-hexabenzocoronene substituted porphyrin, which represents the largest prepared PAH-porphyrin conjugate to date. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Oxide nanostructures through self-assembly

NASA Astrophysics Data System (ADS)

Aggarwal, S.; Ogale, S. B.; Ganpule, C. S.; Shinde, S. R.; Novikov, V. A.; Monga, A. P.; Burr, M. R.; Ramesh, R.; Ballarotto, V.; Williams, E. D.

2001-03-01

A prominent theme in inorganic materials research is the creation of uniformly flat thin films and heterostructures over large wafers, which can subsequently be lithographically processed into functional devices. This letter proposes an approach that will lead to thin film topographies that are directly counter to the above-mentioned philosophy. Recent years have witnessed considerable research activity in the area of self-assembly of materials, stimulated by observations of self-organized behavior in biological systems. We have fabricated uniform arrays of nonplanar surface features by a spontaneous assembly process involving the oxidation of simple metals, especially under constrained conditions on a variety of substrates, including glass and Si. In this letter we demonstrate the pervasiveness of this process through examples involving the oxidation of Pd, Cu, Fe, and In. The feature sizes can be controlled through the grain size and thickness of the starting metal thin film. Finally, we demonstrate how such submicron scale arrays can serve as templates for the design and development of self-assembled, nanoelectronic devices.

Dynamics of self-assembled cytosine nucleobases on graphene

NASA Astrophysics Data System (ADS)

Saikia, Nabanita; Johnson, Floyd; Waters, Kevin; Pandey, Ravindra

2018-05-01

Molecular self-assembly of cytosine (C n ) bases on graphene was investigated using molecular dynamics methods. For free-standing C n bases, simulation conditions (gas versus aqueous) determine the nature of self-assembly; the bases prefer to aggregate in the gas phase and are stabilized by intermolecular H-bonds, while in the aqueous phase, the water molecules disrupt base-base interactions, which facilitate the formation of π-stacked domains. The substrate-induced effects, on the other hand, find the polarity and donor-acceptor sites of the bases to govern the assembly process. For example, in the gas phase, the assembly of C n bases on graphene displays short-range ordered linear arrays stabilized by the intermolecular H-bonds. In the aqueous phase, however, there are two distinct configurations for the C n bases assembly on graphene. For the first case corresponding to low surface coverage, the bases are dispersed on graphene and are isolated. The second configuration archetype is disordered linear arrays assembled with medium and high surface coverage. The simulation results establish the role of H-bonding, vdW π-stacking, and the influence of graphene surface towards the self-assembly. The ability to regulate the assembly into well-defined patterns can aid in the design of self-assembled nanostructures for the next-generation DNA based biosensors and nanoelectronic devices.

Self-assembly in the ferritin nano-cage protein superfamily.

PubMed

Zhang, Yu; Orner, Brendan P

2011-01-01

Protein self-assembly, through specific, high affinity, and geometrically constraining protein-protein interactions, can control and lead to complex cellular nano-structures. Establishing an understanding of the underlying principles that govern protein self-assembly is not only essential to appreciate the fundamental biological functions of these structures, but could also provide a basis for their enhancement for nano-material applications. The ferritins are a superfamily of well studied proteins that self-assemble into hollow cage-like structures which are ubiquitously found in both prokaryotes and eukaryotes. Structural studies have revealed that many members of the ferritin family can self-assemble into nano-cages of two types. Maxi-ferritins form hollow spheres with octahedral symmetry composed of twenty-four monomers. Mini-ferritins, on the other hand, are tetrahedrally symmetric, hollow assemblies composed of twelve monomers. This review will focus on the structure of members of the ferritin superfamily, the mechanism of ferritin self-assembly and the structure-function relations of these proteins.

Self-assembly of nanorod motors into geometrically regular multimers and their propulsion by ultrasound.

PubMed

Ahmed, Suzanne; Gentekos, Dillon T; Fink, Craig A; Mallouk, Thomas E

2014-11-25

Segmented gold-ruthenium nanorods (300 ± 30 nm in diameter and 2.0 ± 0.2 μm in length) with thin Ni segments at one end assemble into few-particle, geometrically regular dimers, trimers, and higher multimers while levitated in water by ∼4 MHz ultrasound at the midpoint of a cylindrical acoustic cell. The assembly of the nanorods into multimers is controlled by interactions between the ferromagnetic Ni segments. These assemblies are propelled autonomously in fluids by excitation with ∼4 MHz ultrasound and exhibit several distinct modes of motion. Multimer assembly and disassembly are dynamic in the ultrasonic field. The relative numbers of monomers, dimers, trimers, and higher multimers are dependent upon the number density of particles in the fluid and their speed, which is in turn determined by the ultrasonic power applied. The magnetic binding energy of the multimers estimated from their speed-dependent equilibria is in agreement with the calculated strength of the magnetic dipole interactions. These autonomously propelled multimers can also be steered with an external magnetic field and remain intact after removal from the acoustic chamber for SEM imaging.

Host-Guest Chemistry in Integrated Porous Space Formed by Molecular Self-Assembly at Liquid-Solid Interfaces.

PubMed

Iritani, Kohei; Tahara, Kazukuni; De Feyter, Steven; Tobe, Yoshito

2017-05-16

Host-guest chemistry in two-dimensional (2D) space, that is, physisorbed monolayers of a single atom or a single molecular thickness on surfaces, has become a subject of intense current interest because of perspectives for various applications in molecular-scale electronics, selective sensors, and tailored catalysis. Scanning tunneling microscopy has been used as a powerful tool for the visualization of molecules in real space on a conducting substrate surface. For more than a decade, we have been investigating the self-assembly of a series of triangle-shaped phenylene-ethynylene macrocycles called dehydrobenzo[12]annulenes (DBAs). These molecules are substituted with six alkyl chains and are capable of forming hexagonal porous 2D molecular networks via van der Waals interactions between interdigitated alkyl chains at the interface of organic solvents and graphite. The dimension of the nanoporous space or nanowell formed by the self-assembly of DBAs can be controlled from 1.6 to 4.7 nm by simply changing the alkyl chain length from C 6 to C 20 . Single molecules as well as homoclusters and heteroclusters are capable of coadsorbing within the host matrix using shape- and size-complementarity principles. Moreover, on the basis of the versatility of the DBA molecules that allows chemical modification of the alkyl chain terminals, we were able to decorate the interior space of the nanoporous networks with functional groups such as azobenzenedicarboxylic acid for photoresponsive guest adsorption/desorption or fluoroalkanes and tetraethylene glycol groups for selective guest binding by electrostatic interactions and zinc-porphyrin units for complexation with a guest by charge-transfer interactions. In this Feature Article, we describe the general aspects of molecular self-assembly at liquid/solid interfaces, followed by the formation of programmed porous molecular networks using rationally designed molecular building blocks. We focus on our own work involving host

Regulating DNA Self-assembly by DNA-Surface Interactions.

PubMed

Liu, Longfei; Li, Yulin; Wang, Yong; Zheng, Jianwei; Mao, Chengde

2017-12-14

DNA self-assembly provides a powerful approach for preparation of nanostructures. It is often studied in bulk solution and involves only DNA-DNA interactions. When confined to surfaces, DNA-surface interactions become an additional, important factor to DNA self-assembly. However, the way in which DNA-surface interactions influence DNA self-assembly is not well studied. In this study, we showed that weak DNA-DNA interactions could be stabilized by DNA-surface interactions to allow large DNA nanostructures to form. In addition, the assembly can be conducted isothermally at room temperature in as little as 5 seconds. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Probabilistic Analysis of Pattern Formation in Monotonic Self-Assembly

PubMed Central

Moore, Tyler G.; Garzon, Max H.; Deaton, Russell J.

2015-01-01

Inspired by biological systems, self-assembly aims to construct complex structures. It functions through piece-wise, local interactions among component parts and has the potential to produce novel materials and devices at the nanoscale. Algorithmic self-assembly models the product of self-assembly as the output of some computational process, and attempts to control the process of assembly algorithmically. Though providing fundamental insights, these computational models have yet to fully account for the randomness that is inherent in experimental realizations, which tend to be based on trial and error methods. In order to develop a method of analysis that addresses experimental parameters, such as error and yield, this work focuses on the capability of assembly systems to produce a pre-determined set of target patterns, either accurately or perhaps only approximately. Self-assembly systems that assemble patterns that are similar to the targets in a significant percentage are “strong” assemblers. In addition, assemblers should predominantly produce target patterns, with a small percentage of errors or junk. These definitions approximate notions of yield and purity in chemistry and manufacturing. By combining these definitions, a criterion for efficient assembly is developed that can be used to compare the ability of different assembly systems to produce a given target set. Efficiency is a composite measure of the accuracy and purity of an assembler. Typical examples in algorithmic assembly are assessed in the context of these metrics. In addition to validating the method, they also provide some insight that might be used to guide experimentation. Finally, some general results are established that, for efficient assembly, imply that every target pattern is guaranteed to be assembled with a minimum common positive probability, regardless of its size, and that a trichotomy exists to characterize the global behavior of typical efficient, monotonic self-assembly

Self-assembly of coiled coil peptides into nanoparticles vs 2-d plates: effects of assembly pathway

NASA Astrophysics Data System (ADS)

Kim, Kyunghee; Pochan, Darrin

Molecular solution assembly, or self-assembly, is a process by which ordered nanostructures or patterns are formed by non-covalent interactions during assembly. Biomimicry, the use of bioinspired molecules or biologically relevant materials, is an important area of self-assembly research with peptides serving a critical role as molecular tools. The morphology of peptide assemblies can be controlled by adjusting solution conditions such as the concentration of peptides, the temperature, and pH. Herein, spherical nanostructures, which have potential for creating an encapsulation system, are formed by self-assembly when coiled coil peptides are combined in solution. These peptides are homotrimeric and heterodimeric coiled-coil bundles and the homotrimer is connected with each of heterodimer through their external surfaces via disulfide bonds. The resultant covalent constructs could co-assemble into complementary trimeric hubs, respectively. The two peptide constructs are directly mixed and assembled in solution in order to produce either spherical particles or 2-d plates depending on the solution conditions and kinetic pathway of assembly. In particular, structural changes of the self-assembled peptides are explored by control of the thermal history of the assembly solution.

Self-assembling segmented coiled tubing

DOEpatents

Raymond, David W.

2016-09-27

Self-assembling segmented coiled tubing is a concept that allows the strength of thick-wall rigid pipe, and the flexibility of thin-wall tubing, to be realized in a single design. The primary use is for a drillstring tubular, but it has potential for other applications requiring transmission of mechanical loads (forces and torques) through an initially coiled tubular. The concept uses a spring-loaded spherical `ball-and-socket` type joint to interconnect two or more short, rigid segments of pipe. Use of an optional snap ring allows the joint to be permanently made, in a `self-assembling` manner.

LPT. Low power assembly and test building (TAN640). Camera facing ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

LPT. Low power assembly and test building (TAN-640). Camera facing west. Rollup doors to each test cell face east. Concrete walls poured in place. Apparatus at right of view was part of a post-ANP program. INEEL negative no. HD-40-1-1 - Idaho National Engineering Laboratory, Test Area North, Scoville, Butte County, ID

Porphyrin coordination polymer nanospheres and nanorods

DOEpatents

Wang, Zhongchun; Shelnutt, John A.; Medforth, Craig J.

2012-12-04

A porphyrin coordination polymer nanostructure comprising a network of pyridyl porphyrin molecules and coordinating metal ions coordinatively bound through the pyridyl groups. In some embodiments, the porphyrins are metalloporphyrins. A variety of nanostructures are formed by the network polymer, including nanospheres, polygonal nanostructures, nanorods, and nanofibers, depending on a variety of factors including coordination metal ion, porphyrin type, metal of the metalloporphyrin, and degree of agitation during nanostructure formation. Reduction of coordinating metal ions may be used to form metal nanoparticles on the coordination polymer nanostructure.

Porphyrin coordination polymer nanospheres and nanorods

DOEpatents

Wang, Zhongchun; Shelnutt, John A.; Medforth, Craig J.

2013-09-10

A porphyrin coordination polymer nanostructure comprising a network of pyridyl porphyrin molecules and coordinating metal ions coordinatively bound through the pyridyl groups. In some embodiments, the porphyrins are metalloporphyrins. A variety of nanostructures are formed by the network polymer, including nanospheres, polygonal nanostructures, nanorods, and nanofibers, depending on a variety of factors including coordination metal ion, porphyrin type, metal of the metalloporphyrin, and degree of agitation during nanostructure formation. Reduction of coordinating metal ions may be used to form metal nanoparticles on the coordination polymer nanostructure.

Efficacy of face-to-face versus self-guided treatments for disordered gambling: A meta-analysis.

PubMed

Goslar, Martina; Leibetseder, Max; Muench, Hannah M; Hofmann, Stefan G; Laireiter, Anton-Rupert

2017-06-01

Background and aims In the light of growing traditional and novel forms of gambling, the treatment of disordered gambling is gaining increasing importance and practical relevance. Most studies have examined face-to-face treatments. Although trials implementing self-guided treatments have recently been conducted, these options have not yet been systematically examined. The primary objective of this meta-analysis, therefore, was to analyze the efficacy of all types of psychological face-to-face and self-guided treatments. Methods A multilevel literature search yielded 27 randomized controlled studies totaling 3,879 participants to provide a comprehensive comparative evaluation of the short- and long-term efficacies of face-to-face and self-guided treatments for disordered gambling. Results As expected, the results revealed significantly higher effect sizes for face-to-face treatments (16 studies with Hedges's g ranging from 0.67 to 1.15) as compared with self-guided treatments (11 studies with Hedges's g ranging from 0.12 to 0.30) regarding the reduction of problematic gambling behavior. The intensity of treatment moderated the therapy effect, particularly for self-guided treatments. Discussion and Conclusions The results of this meta-analysis favor face-to-face treatments over self-guided treatments for the reduction of disordered gambling. Although the findings broaden the scope of knowledge about psychological treatment modalities for disordered gambling, further research is needed to identify the reasons for these differences with the goal to optimize the treatment for this disabling condition.

Self-Assembly of Large Amyloid Fibers

NASA Astrophysics Data System (ADS)

Ridgley, Devin M.

Functional amyloids found throughout nature have demonstrated that amyloid fibers are potential industrial biomaterials. This work introduces a new "template plus adder" cooperative mechanism for the spontaneous self-assembly of micrometer sized amyloid fibers. A short hydrophobic template peptide induces a conformation change within a highly alpha-helical adder protein to form beta-sheets that continue to assemble into micrometer sized amyloid fibers. This study utilizes a variety of proteins that have template or adder characteristics which suggests that this mechanism may be employed throughout nature. Depending on the amino acid composition of the proteins used the mixtures form amyloid fibers of a cylindrical ( 10 mum diameter, 2 GPa Young's modulus) or tape (5- 10 mum height, 10-20 mum width and 100-200 MPa Young's modulus) morphology. Processing conditions are altered to manipulate the morphology and structural characteristics of the fibers. Spectroscopy is utilized to identify certain amino acid groups that contribute to the self-assembly process. Aliphatic amino acids (A, I, V and L) are responsible for initiating conformation change of the adder proteins to assemble into amyloid tapes. Additional polyglutamine segments (Q-blocks) within the protein mixtures will form Q hydrogen bonds to reinforce the amyloid structure and form a cylindrical fiber of higher modulus. Atomic force microscopy is utilized to delineate the self-assembly of amyloid tapes and cylindrical fibers from protofibrils (15-30 nm width) to fibers (10-20 mum width) spanning three orders of magnitude. The aliphatic amino acid content of the adder proteins' alpha-helices is a good predictor of high density beta-sheet formation within the protein mixture. Thus, it is possible to predict the propensity of a protein to undergo conformation change into amyloid structures. Finally, Escherichia coli is genetically engineered to express a template protein which self-assembles into large amyloid

Albumin binds self-assembling dyes as specific polymolecular ligands.

PubMed

Stopa, Barbara; Rybarska, Janina; Drozd, Anna; Konieczny, Leszek; Król, Marcin; Lisowski, Marek; Piekarska, Barbara; Roterman, Irena; Spólnik, Paweł; Zemanek, Grzegorz

2006-12-15

Self-assembling dyes with a structure related to Congo red (e.g. Evans blue) form polymolecular complexes with albumin. The dyes, which are lacking a self-assembling property (Trypan blue, ANS) bind as single molecules. The supramolecular character of dye ligands bound to albumin was demonstrated by indicating the complexation of dye molecules outnumbering the binding sites in albumin and by measuring the hydrodynamic radius of albumin which is growing upon complexation of self-assembling dye in contrast to dyes lacking this property. The self-assembled character of Congo red was also proved using it as a carrier introducing to albumin the intercalated nonbonding foreign compounds. Supramolecular, ordered character of the dye in the complex with albumin was also revealed by finding that self-assembling dyes become chiral upon complexation. Congo red complexation makes albumin less resistant to low pH as concluded from the facilitated N-F transition, observed in studies based on the measurement of hydrodynamic radius. This particular interference with protein stability and the specific changes in digestion resulted from binding of Congo red suggest that the self-assembled dye penetrates the central crevice of albumin.

Bioinspired Photonic Pigments from Colloidal Self-Assembly.

PubMed

Goerlitzer, Eric S A; Klupp Taylor, Robin N; Vogel, Nicolas

2018-05-07

The natural world is a colorful environment. Stunning displays of coloration have evolved throughout nature to optimize camouflage, warning, and communication. The resulting flamboyant visual effects and remarkable dynamic properties, often caused by an intricate structural design at the nano- and microscale, continue to inspire scientists to unravel the underlying physics and to recreate the observed effects. Here, the methodologies to create bioinspired photonic pigments using colloidal self-assembly approaches are considered. The physics governing the interaction of light with structural features and natural examples of structural coloration are briefly introduced. It is then outlined how the self-assembly of colloidal particles, acting as wavelength-scale building blocks, can be particularly useful to replicate coloration from nature. Different coloration effects that result from the defined structure of the self-assembled colloids are introduced and it is highlighted how these optical properties can be translated into photonic pigments by modifications of the assembly processes. The importance of absorbing elements, as well as the role of surface chemistry and wettability to control structural coloration is discussed. Finally, approaches to integrate dynamic control of coloration into such self-assembled photonic pigments are outlined. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Stepwise syntheses of bisporphyrins, bischlorins, and biscorroles and of porphyrin-chlorin and porphyrin-corrole heterodimers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Paolesse, R.; Pandey, R.K.; Forsyth, T.P.

The stepwise syntheses and characterization of a series of symmetrical and unsymmetrical bisporphyrins, bischlorins, and biscorroles, and of porphyrin-chlorin and porphyrin-corrole dyads possessing ethylene, phenyl, and stilbene linking units are described. The methodology for synthesis of 10-substituted corroles 2 and their cobalt complexes 9 via a,c-biladiene salts 1 was first developed, and then extended to provide biscorroles (e.g., 4 and 5) linked through the 10-positions with phenyl linker units. Using a similar methodology, phenyl-linked corrole-porphyrin dyads 28 and 30 were also prepared. By way of intermediate phenyl-linked unsymmetrical bisdipyrromethanes, a completely unsymmetrical heterobimetallic bisporphyrin system, 45, was synthesized. Low-valent titaniummore » coupling (McMurry) reactions were used to prepare stilbene-linked bisdipyrromethanes (e.g., 46) which were subsequently transformed into stilbene-linked bisporphyrins (e.g., 48). McMurry cross-coupling reactions of porphyrins bearing p-formylphenyl substituents also afforded an unsymmetrically substituted bisporphyrinylstilbene, 60, as well as the corresponding homodimers 56 and 59. Likewise, McMurry cross-coupling of a p-formylphenyl-substituted porphyrin, 62, with a formylchlorin, 63, afforded a stilbene-linked bisporphyrin, 64, a bischlorin, 66, and a novel porphyrin-chlorin heterodimer, 65. 54 refs., 1 fig., 1 tab.« less

Self-assembled software and method of overriding software execution

DOEpatents

Bouchard, Ann M.; Osbourn, Gordon C.

2013-01-08

A computer-implemented software self-assembled system and method for providing an external override and monitoring capability to dynamically self-assembling software containing machines that self-assemble execution sequences and data structures. The method provides an external override machine that can be introduced into a system of self-assembling machines while the machines are executing such that the functionality of the executing software can be changed or paused without stopping the code execution and modifying the existing code. Additionally, a monitoring machine can be introduced without stopping code execution that can monitor specified code execution functions by designated machines and communicate the status to an output device.

Self-Assembly of Human Serum Albumin: A Simplex Phenomenon

PubMed Central

Thakur, Garima; Prashanthi, Kovur; Jiang, Keren; Thundat, Thomas

2017-01-01

Spontaneous self-assemblies of biomolecules can generate geometrical patterns. Our findings provide an insight into the mechanism of self-assembled ring pattern generation by human serum albumin (HSA). The self-assembly is a process guided by kinetic and thermodynamic parameters. The generated protein ring patterns display a behavior which is geometrically related to a n-simplex model and is explained through thermodynamics and chemical kinetics. PMID:28930179

Elucidating dominant pathways of the nano-particle self-assembly process.

PubMed

Zeng, Xiangze; Li, Bin; Qiao, Qin; Zhu, Lizhe; Lu, Zhong-Yuan; Huang, Xuhui

2016-09-14

Self-assembly processes play a key role in the fabrication of functional nano-structures with widespread application in drug delivery and micro-reactors. In addition to the thermodynamics, the kinetics of the self-assembled nano-structures also play an important role in determining the formed structures. However, as the self-assembly process is often highly heterogeneous, systematic elucidation of the dominant kinetic pathways of self-assembly is challenging. Here, based on mass flow, we developed a new method for the construction of kinetic network models and applied it to identify the dominant kinetic pathways for the self-assembly of star-like block copolymers. We found that the dominant pathways are controlled by two competing kinetic parameters: the encounter time Te, characterizing the frequency of collision and the transition time Tt for the aggregate morphology change from rod to sphere. Interestingly, two distinct self-assembly mechanisms, diffusion of an individual copolymer into the aggregate core and membrane closure, both appear at different stages (with different values of Tt) of a single self-assembly process. In particular, the diffusion mechanism dominates the middle-sized semi-vesicle formation stage (with large Tt), while the membrane closure mechanism dominates the large-sized vesicle formation stage (with small Tt). Through the rational design of the hydrophibicity of the copolymer, we successfully tuned the transition time Tt and altered the dominant self-assembly pathways.

Cytoskeletal motor-driven active self-assembly in in vitro systems

DOE PAGES

Lam, A. T.; VanDelinder, V.; Kabir, A. M. R.; ...

2015-11-11

Molecular motor-driven self-assembly has been an active area of soft matter research for the past decade. Because molecular motors transform chemical energy into mechanical work, systems which employ molecular motors to drive self-assembly processes are able to overcome kinetic and thermodynamic limits on assembly time, size, complexity, and structure. Here, we review the progress in elucidating and demonstrating the rules and capabilities of motor-driven active self-assembly. Lastly, we focus on the types of structures created and the degree of control realized over these structures, and discuss the next steps necessary to achieve the full potential of this assembly mode whichmore » complements robotic manipulation and passive self-assembly.« less

Metal-coupled folding as the driving force for the extreme stability of Rad50 zinc hook dimer assembly

PubMed Central

Kochańczyk, Tomasz; Nowakowski, Michał; Wojewska, Dominika; Kocyła, Anna; Ejchart, Andrzej; Koźmiński, Wiktor; Krężel, Artur

2016-01-01

The binding of metal ions at the interface of protein complexes presents a unique and poorly understood mechanism of molecular assembly. A remarkable example is the Rad50 zinc hook domain, which is highly conserved and facilitates the Zn2+-mediated homodimerization of Rad50 proteins. Here, we present a detailed analysis of the structural and thermodynamic effects governing the formation and stability (logK12 = 20.74) of this evolutionarily conserved protein assembly. We have dissected the determinants of the stability contributed by the small β-hairpin of the domain surrounding the zinc binding motif and the coiled-coiled regions using peptides of various lengths from 4 to 45 amino acid residues, alanine substitutions and peptide bond-to-ester perturbations. In the studied series of peptides, an >650 000-fold increase of the formation constant of the dimeric complex arises from favorable enthalpy because of the increased acidity of the cysteine thiols in metal-free form and the structural properties of the dimer. The dependence of the enthalpy on the domain fragment length is partially compensated by the entropic penalty of domain folding, indicating enthalpy-entropy compensation. This study facilitates understanding of the metal-mediated protein-protein interactions in which the metal ion is critical for the tight association of protein subunits. PMID:27808280

Nonequilibrium Self-Assembly of π-Conjugated Oligopeptides in Solution.

PubMed

Li, Bo; Li, Songsong; Zhou, Yuecheng; Ardoña, Herdeline Ann M; Valverde, Lawrence R; Wilson, William L; Tovar, John D; Schroeder, Charles M

2017-02-01

Supramolecular assembly is a powerful method that can be used to generate materials with well-defined structures across multiple length scales. Supramolecular assemblies consisting of biopolymer-synthetic polymer subunits are specifically known to exhibit exceptional structural and functional diversity as well as programmable control of noncovalent interactions through hydrogen bonding in biopolymer subunits. Despite recent progress, there is a need to control and quantitatively understand assembly under nonequilibrium conditions. In this work, we study the nonequilibrium self-assembly of π-conjugated synthetic oligopeptides using a combination of experiments and analytical modeling. By isolating an aqueous peptide solution droplet within an immiscible organic layer, the rate of peptide assembly in the aqueous solution can be controlled by tuning the transport rate of acid that is used to trigger assembly. Using this approach, peptides are guided to assemble under reaction-dominated and diffusion-dominated conditions, with results showing a transition from a diffusion-limited reaction front to spatially homogeneous assembly as the transport rate of acid decreases. Interestingly, our results show that the morphology of self-assembled peptide fibers is controlled by the assembly kinetics such that increasingly homogeneous structures of self-assembled synthetic oligopeptides were generally obtained using slower rates of assembly. We further developed an analytical reaction-diffusion model to describe oligopeptide assembly, and experimental results are compared to the reaction-diffusion model across a range of parameters. Overall, this work highlights the importance of molecular self-assembly under nonequilibrium conditions, specifically showing that oligopeptide assembly is governed by a delicate balance between reaction kinetics and transport processes.

Generic concept to program the time domain of self-assemblies with a self-regulation mechanism.

PubMed

Heuser, Thomas; Steppert, Ann-Kathrin; Lopez, Catalina Molano; Zhu, Baolei; Walther, Andreas

2015-04-08

Nature regulates complex structures in space and time via feedback loops, kinetically controlled transformations, and under energy dissipation to allow non-equilibrium processes. Although man-made static self-assemblies realize excellent control over hierarchical structures via molecular programming, managing their temporal destiny by self-regulation is a largely unsolved challenge. Herein, we introduce a generic concept to control the time domain by programming the lifetimes of switchable self-assemblies in closed systems. We conceive dormant deactivators that, in combination with fast promoters, enable a unique kinetic balance to establish an autonomously self-regulating, transient pH-state, whose duration can be programmed over orders of magnitude-from minutes to days. Coupling this non-equilibrium state to pH-switchable self-assemblies allows predicting their assembly/disassembly fate in time, similar to a precise self-destruction mechanism. We demonstrate a platform approach by programming self-assembly lifetimes of block copolymers, nanoparticles, and peptides, enabling dynamic materials with a self-regulation functionality.

Three Dimensional Assembly in Directed Self-assembly of Block Copolymers

DOE PAGES

Segal-Peretz, Tamar; Zhou, Chun; Ren, Jiaxing; ...

2016-09-02

The three-dimensional assembly of poly (styrene-b-methyl methacrylate) (PS-b-PMMA) in chemoepitaxy and graphoepitaxy directed self-assembly (DSA) was investigated using scanning transmission electron microscopy (STEM) tomography. The tomographic characterization revealed hidden morphologies and defects at the BCP- chemical pattern interface in lamellar DSA, and probed the formation of cylinders at the bottom of cylindrical DSA for contact hole shrink. Lastly, future work will include control over 3D assembly in sub-10 nm processes.

Self-Assembled Structures of Benzoic Acid on Au(111) Surface

NASA Astrophysics Data System (ADS)

Vu, Thu-Hien; Wandlowski, Thomas

2017-06-01

Electrochemical scanning tunneling microscopy combined with cyclic voltammetry were employed to explore the self-assembly of benzoic acid (BA) on a Au(111) substrate surface in a 0.1-M HClO4 solution. At the negatively charged surface, BA molecules form two highly ordered physisorbed adlayers with their phenyl rings parallel to the substrate surface. High-resolution scanning tunneling microscopy images reveal the packing arrangement and internal molecular structures. The striped pattern and zigzag structure of the BA adlayers are composed of parallel rows of dimers, in which two BA molecules are bound through a pair of O-H···O hydrogen bonds. Increasing the electrode potential further to positive charge densities of Au(111) leads to the desorption of the physisorbed hydrogen-bonded networks and the formation of a chemisorbed adlayer. BA molecules change their orientation from planar to upright fashion, which is accompanied by the deprotonation of the carboxyl group. Furthermore, potential-induced formation and dissolution of BA adlayers were also investigated. Structural transitions between the various types of ordered adlayers occur according to a nucleation and growth mechanism.

Energy landscapes of the monomer and dimer of the Alzheimer's peptide A β (1 -28 )

NASA Astrophysics Data System (ADS)

Dong, Xiao; Chen, Wei; Mousseau, Normand; Derreumaux, Philippe

2008-03-01

The cytoxicity of Alzheimer's disease has been linked to the self-assembly of the 40 /42 amino acid of the amyloid-β (A β ) peptide into oligomers. To understand the assembly process, it is important to characterize the very first steps of aggregation at an atomic level of detail. Here, we focus on the N-terminal fragment 1-28, known to form fibrils in vitro. Circular dichroism and NMR experiments indicate that the monomer of A β (1 -28 ) is α -helical in a membranelike environment and random coil in aqueous solution. Using the activation-relaxation technique coupled with the OPEP coarse grained force field, we determine the structures of the monomer and of the dimer of A β (1 -28 ) . In agreement with experiments, we find that the monomer is predominantly random coil in character, but displays a non-negligible β -strand probability in the N-terminal region. Dimerization impacts the structure of each chain and leads to an ensemble of intertwined conformations with little β -strand content in the region Leu17-Ala21. All these structural characteristics are inconsistent with the amyloid fibril structure and indicate that the dimer has to undergo significant rearrangement en route to fibril formation.

Evaluation of strategies to control Fab light chain dimer during mammalian expression and purification: A universal one-step process for purification of correctly assembled Fab.

PubMed

Spooner, Jennifer; Keen, Jenny; Nayyar, Kalpana; Birkett, Neil; Bond, Nicholas; Bannister, David; Tigue, Natalie; Higazi, Daniel; Kemp, Benjamin; Vaughan, Tristan; Kippen, Alistair; Buchanan, Andrew

2015-07-01

Fabs are an important class of antibody fragment as both research reagents and therapeutic agents. There are a plethora of methods described for their recombinant expression and purification. However, these do not address the issue of excessive light chain production that forms light chain dimers nor do they describe a universal purification strategy. Light chain dimer impurities and the absence of a universal Fab purification strategy present persistent challenges for biotechnology applications using Fabs, particularly around the need for bespoke purification strategies. This study describes methods to address light chain dimer formation during Fab expression and identifies a novel CH 1 affinity resin as a simple and efficient one-step purification for correctly assembled Fab. © 2015 Wiley Periodicals, Inc.

The influence of fatty acids on the GpA dimer interface by coarse-grained molecular dynamics simulation.

PubMed

Flinner, Nadine; Mirus, Oliver; Schleiff, Enrico

2014-08-15

The hydrophobic thickness of membranes, which is manly defined by fatty acids, influences the packing of transmembrane domains of proteins and thus can modulate the activity of these proteins. We analyzed the dynamics of the dimerization of Glycophorin A (GpA) by molecular dynamics simulations to describe the fatty acid dependence of the transmembrane region assembly. GpA represents a well-established model for dimerization of single transmembrane helices containing a GxxxG motif in vitro and in silico. We performed simulations of the dynamics of the NMR-derived dimer as well as self-assembly simulations of monomers in membranes composed of different fatty acid chains and monitored the formed interfaces and their transitions. The observed dimeric interfaces, which also include the one known from NMR, are highly dynamic and converted into each other. The frequency of interface formation and the preferred transitions between interfaces similar to the interface observed by NMR analysis strongly depend on the fatty acid used to build the membrane. Molecular dynamic simulations after adaptation of the helix topology parameters to better represent NMR derived structures of single transmembrane helices yielded an enhanced occurrence of the interface determined by NMR in molecular dynamics simulations. Taken together we give insights into the influence of fatty acids and helix conformation on the dynamics of the transmembrane domain of GpA.

The Influence of Fatty Acids on the GpA Dimer Interface by Coarse-Grained Molecular Dynamics Simulation

PubMed Central

Flinner, Nadine; Mirus, Oliver; Schleiff, Enrico

2014-01-01

The hydrophobic thickness of membranes, which is manly defined by fatty acids, influences the packing of transmembrane domains of proteins and thus can modulate the activity of these proteins. We analyzed the dynamics of the dimerization of Glycophorin A (GpA) by molecular dynamics simulations to describe the fatty acid dependence of the transmembrane region assembly. GpA represents a well-established model for dimerization of single transmembrane helices containing a GxxxG motif in vitro and in silico. We performed simulations of the dynamics of the NMR-derived dimer as well as self-assembly simulations of monomers in membranes composed of different fatty acid chains and monitored the formed interfaces and their transitions. The observed dimeric interfaces, which also include the one known from NMR, are highly dynamic and converted into each other. The frequency of interface formation and the preferred transitions between interfaces similar to the interface observed by NMR analysis strongly depend on the fatty acid used to build the membrane. Molecular dynamic simulations after adaptation of the helix topology parameters to better represent NMR derived structures of single transmembrane helices yielded an enhanced occurrence of the interface determined by NMR in molecular dynamics simulations. Taken together we give insights into the influence of fatty acids and helix conformation on the dynamics of the transmembrane domain of GpA. PMID:25196522

Impaired processing of self-face recognition in anorexia nervosa.

PubMed

Hirot, France; Lesage, Marine; Pedron, Lya; Meyer, Isabelle; Thomas, Pierre; Cottencin, Olivier; Guardia, Dewi

2016-03-01

Body image disturbances and massive weight loss are major clinical symptoms of anorexia nervosa (AN). The aim of the present study was to examine the influence of body changes and eating attitudes on self-face recognition ability in AN. Twenty-seven subjects suffering from AN and 27 control participants performed a self-face recognition task (SFRT). During the task, digital morphs between their own face and a gender-matched unfamiliar face were presented in a random sequence. Participants' self-face recognition failures, cognitive flexibility, body concern and eating habits were assessed with the Self-Face Recognition Questionnaire (SFRQ), Trail Making Test (TMT), Body Shape Questionnaire (BSQ) and Eating Disorder Inventory-2 (EDI-2), respectively. Subjects suffering from AN exhibited significantly greater difficulties than control participants in identifying their own face (p = 0.028). No significant difference was observed between the two groups for TMT (all p > 0.1, non-significant). Regarding predictors of self-face recognition skills, there was a negative correlation between SFRT and body mass index (p = 0.01) and a positive correlation between SFRQ and EDI-2 (p < 0.001) or BSQ (p < 0.001). Among factors involved, nutritional status and intensity of eating disorders could play a part in impaired self-face recognition.

Temperature-Dependent Conformations of a Membrane Supported ‘Zinc Porphyrin Tweezer’ by 2D Fluorescence Spectroscopy

PubMed Central

Widom, Julia R.; Lee, Wonbae; Perdomo-Ortiz, Alejandro; Rappoport, Dmitrij; Molinski, Tadeusz F.; Aspuru-Guzik, Alán; Marcus, Andrew H.

2013-01-01

We studied the equilibrium conformations of a ‘zinc porphyrin tweezer’ composed of two carboxylphenyl-functionalized zinc tetraphenyl porphyrin subunits connected by a 1,4 butyndiol spacer, which was suspended inside the amphiphilic regions of 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC) liposomes. By combining phase-modulation two-dimensional fluorescence spectroscopy (2D FS) with linear absorbance and fluorimetry, we determined that the zinc porphyrin tweezer adopts a mixture of ‘folded’ and ‘extended’ conformations in the membrane. By fitting an exciton-coupling model to a series of data sets recorded over a range of temperatures (17 – 85 °C) and at different laser center wavelengths, we determined that the folded form of the tweezer is stabilized by a favorable change in the entropy of the local membrane environment. Our results provide insights toward understanding the balance of thermodynamic factors that govern molecular assembly in membranes. PMID:23480874

The Effect of Self-Referential Expectation on Emotional Face Processing

PubMed Central

McKendrick, Mel; Butler, Stephen H.; Grealy, Madeleine A.

2016-01-01

The role of self-relevance has been somewhat neglected in static face processing paradigms but may be important in understanding how emotional faces impact on attention, cognition and affect. The aim of the current study was to investigate the effect of self-relevant primes on processing emotional composite faces. Sentence primes created an expectation of the emotion of the face before sad, happy, neutral or composite face photos were viewed. Eye movements were recorded and subsequent responses measured the cognitive and affective impact of the emotion expressed. Results indicated that primes did not guide attention, but impacted on judgments of valence intensity and self-esteem ratings. Negative self-relevant primes led to the most negative self-esteem ratings, although the effect of the prime was qualified by salient facial features. Self-relevant expectations about the emotion of a face and subsequent attention to a face that is congruent with these expectations strengthened the affective impact of viewing the face. PMID:27175487

The Effect of Self-Referential Expectation on Emotional Face Processing.

PubMed

McKendrick, Mel; Butler, Stephen H; Grealy, Madeleine A

2016-01-01

The role of self-relevance has been somewhat neglected in static face processing paradigms but may be important in understanding how emotional faces impact on attention, cognition and affect. The aim of the current study was to investigate the effect of self-relevant primes on processing emotional composite faces. Sentence primes created an expectation of the emotion of the face before sad, happy, neutral or composite face photos were viewed. Eye movements were recorded and subsequent responses measured the cognitive and affective impact of the emotion expressed. Results indicated that primes did not guide attention, but impacted on judgments of valence intensity and self-esteem ratings. Negative self-relevant primes led to the most negative self-esteem ratings, although the effect of the prime was qualified by salient facial features. Self-relevant expectations about the emotion of a face and subsequent attention to a face that is congruent with these expectations strengthened the affective impact of viewing the face.

Expression of human inducible nitric oxide synthase in a tetrahydrobiopterin (H4B)-deficient cell line: H4B promotes assembly of enzyme subunits into an active dimer.

PubMed Central

Tzeng, E; Billiar, T R; Robbins, P D; Loftus, M; Stuehr, D J

1995-01-01

Murine inducible nitric oxide (NO) synthase (iNOS) is catalytically active only in dimeric form. Assembly of its purified subunits into a dimer requires H4B. To understand the structure-activity relationships of human iNOS, we constitutively expressed recombinant human iNOS in NIH 3T3 cells by using a retroviral vector. These cells are deficient in de novo H4B biosynthesis and the role of H4B in the expression and assembly of active iNOS in an intact cell system could be studied. In the absence of added H4B, NO synthesis by the cells was minimal, whereas cells grown with supplemental H4B or the H4B precursor sepiapterin generated NO (74.1 and 63.3 nmol of nitrite per 10(6) cells per 24 h, respectively). NO synthesis correlated with an increase in intracellular H4B but no increase in iNOS protein. Instead, an increased percentage of dimeric iNOS was observed, rising from 20% in cytosols from unsupplemented cells to 66% in H4B-supplemented cell cytosols. In all cases, only dimeric iNOS displayed catalytic activity. Cytosols prepared from H4B-deficient cells exhibited little iNOS activity but acquired activity during a 60- to 120-min incubation with H4B, reaching final activities of 60-72 pmol of citrulline per mg of protein per min. Reconstitution of cytosolic NO synthesis activity was associated with conversion of monomers into dimeric iNOS during the incubation. Thus, human iNOS subunits dimerize to form an active enzyme, and H4B plays a critical role in promoting dimerization in intact cells. This reveals a post-translational mechanism by which intracellular H4B can regulate iNOS expression. Images Fig. 1 Fig. 3 Fig. 4 Fig. 5 PMID:8524846

The self-assembled behavior of DNA bases on the interface.

PubMed

Liu, Lei; Xia, Dan; Klausen, Lasse H; Dong, Mingdong

2014-01-27

A successful example of self-assembly in a biological system is that DNA can be an excellent agent to self-assemble into desirable two and three-dimensional nanostructures in a well-ordered manner by specific hydrogen bonding interactions between the DNA bases. The self-assembly of DNA bases have played a significant role in constructing the hierarchical nanostructures. In this review article we will introduce the study of nucleic acid base self-assembly by scanning tunneling microscopy (STM) at vacuum and ambient condition (the liquid/solid interface), respectively. From the ideal condition to a more realistic environment, the self-assembled behaviors of DNA bases are introduced. In a vacuum system, the energetic advantages will dominate the assembly formation of DNA bases, while at ambient condition, more factors such as conformational freedom and the biochemical environment will be considered. Therefore, the assemblies of DNA bases at ambient condition are different from the ones obtained under vacuum. We present the ordered nanostructures formed by DNA bases at both vacuum and ambient condition. To construct and tailor the nanostructure through the interaction between DNA bases, it is important to understand the assembly behavior and features of DNA bases and their derivatives at ambient condition. The utilization of STM offers the advantage of investigating DNA base self-assembly with sub-molecular level resolution at the surface.

The Self-Assembled Behavior of DNA Bases on the Interface

PubMed Central

Liu, Lei; Xia, Dan; Klausen, Lasse H.; Dong, Mingdong

2014-01-01

A successful example of self-assembly in a biological system is that DNA can be an excellent agent to self-assemble into desirable two and three-dimensional nanostructures in a well-ordered manner by specific hydrogen bonding interactions between the DNA bases. The self-assembly of DNA bases have played a significant role in constructing the hierarchical nanostructures. In this review article we will introduce the study of nucleic acid base self-assembly by scanning tunneling microscopy (STM) at vacuum and ambient condition (the liquid/solid interface), respectively. From the ideal condition to a more realistic environment, the self-assembled behaviors of DNA bases are introduced. In a vacuum system, the energetic advantages will dominate the assembly formation of DNA bases, while at ambient condition, more factors such as conformational freedom and the biochemical environment will be considered. Therefore, the assemblies of DNA bases at ambient condition are different from the ones obtained under vacuum. We present the ordered nanostructures formed by DNA bases at both vacuum and ambient condition. To construct and tailor the nanostructure through the interaction between DNA bases, it is important to understand the assembly behavior and features of DNA bases and their derivatives at ambient condition. The utilization of STM offers the advantage of investigating DNA base self-assembly with sub-molecular level resolution at the surface. PMID:24473140

Bulky melamine-based Zn-porphyrin tweezer as a CD probe of molecular chirality.

PubMed

Petrovic, Ana G; Vantomme, Ghislaine; Negrón-Abril, Yashira L; Lubian, Elisa; Saielli, Giacomo; Menegazzo, Ileana; Cordero, Roselynn; Proni, Gloria; Nakanishi, Koji; Carofiglio, Tommaso; Berova, Nina

2011-10-01

The transfer of chirality from a guest molecule to an achiral host is the subject of significant interest especially when, upon chiral induction, the chiroptical response of the host/guest complex can effectively report the absolute configuration (AC) of the guest. For more than a decade, dimeric metalloporphyrin hosts (tweezers) have been successfully applied as chirality probes for determination of the AC for a wide variety of chiral synthetic compounds and natural products. The objective of this study is to investigate the utility of a new class of melamine-bridged Zn-porphyrin tweezers as sensitive AC reporters. A combined approach based on an experimental CD analysis and a theoretical prediction of the prevailing interporphyrin helicity demonstrates that these tweezers display favorable properties for chiral recognition. Herein, we discuss the application of the melamine-bridged tweezer to the chiral recognition of a diverse set of chiral guests, such as 1,2-diamines, α-amino-esters and amides, secondary alcohols, and 1,2-amino-alcohols. The bulky periphery and the presence of a rigid porphyrin linkage lead, in some cases, to a more enhanced CD sensitivity than that reported earlier with other tweezers. Copyright © 2011 Wiley-Liss, Inc.

Layer-by-Layer Fabrication of Porphyrin Multilayer Films via Copper(I)-Catalyzed Azide-Alkyne Cycloaddition: Film Properties and Applications in Dye-Sensitized Solar Cells

NASA Astrophysics Data System (ADS)

Palomaki, Peter Karl Bunk

Solar energy may be the only renewable source of energy available to the human race that could provide the energy we require while at the same time minimizing negative impacts on the planet and population. These characteristics may be instrumental in diminishing the potential for societal conflict. In order for photovoltaic devices to succeed on a global scale, research and development must lead to reduced costs and/or increased efficiency. Dye-Sensitized Solar Cells (DSSCs) are one class of nextgeneration photovoltaic technologies with the potential to realize these goals. Herein, I describe efforts towards developing a new light harvesting array of chromophores assembled on oxide substrates using copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC or ‘click’ chemistry) that could prove useful in improving DSCC performance while maintaining low cost and simple fabrication. Specifically, molecular multilayers of porphyrin-based chromophores have been fabricated via sequential selflimiting CuAAC reactions to generate multilayered light harvesting films. Films of synthetic porphyrins, perylenes, and mixtures of the two are constructed in order to highlight the versatility of this molecular layer-by-layer (LbL) technique. Characterization in the form of electrochemical techniques, UV-Visible spectroscopy, infrared spectroscopy (IR), and water contact angle all indicate that the films are reacting as expected. Film thickness and morphology are investigated using X-ray reflectivity showing that film growth displays a high degree of linearity, while the roughness increases with thickness. Growth angles based on the porphyrin plane are estimated via a comparison of molecular models and experimentally determined thickness measurements. A more finite measurement of growth angle (and as a result the primary bonding mode) is determined by grazing angle IR spectroscopy. Blocking layer studies suggest that the films could be useful as a self-passivating layer in DSSCs to

Prodrugs as self-assembled hydrogels: a new paradigm for biomaterials.

PubMed

Vemula, Praveen Kumar; Wiradharma, Nikken; Ankrum, James A; Miranda, Oscar R; John, George; Karp, Jeffrey M

2013-12-01

Prodrug-based self-assembled hydrogels represent a new class of active biomaterials that can be harnessed for medical applications, in particular the design of stimuli responsive drug delivery devices. In this approach, a promoiety is chemically conjugated to a known-drug to generate an amphiphilic prodrug that is capable of forming self-assembled hydrogels. Prodrug-based self-assembled hydrogels are advantageous as they alter the solubility of the drug, enhance drug loading, and eliminate the use of harmful excipients. In addition, self-assembled prodrug hydrogels can be designed to undergo controlled drug release or tailored degradation in response to biological cues. Herein we review the development of prodrug-based self-assembled hydrogels as an emerging class of biomaterials that overcome several common limitations encountered in conventional drug delivery. Published by Elsevier Ltd.

Porphyrins at interfaces

NASA Astrophysics Data System (ADS)

Auwärter, Willi; Écija, David; Klappenberger, Florian; Barth, Johannes V.

2015-02-01

Porphyrins and other tetrapyrrole macrocycles possess an impressive variety of functional properties that have been exploited in natural and artificial systems. Different metal centres incorporated within the tetradentate ligand are key for achieving and regulating vital processes, including reversible axial ligation of adducts, electron transfer, light-harvesting and catalytic transformations. Tailored substituents optimize their performance, dictating their arrangement in specific environments and mediating the assembly of molecular nanoarchitectures. Here we review the current understanding of these species at well-defined interfaces, disclosing exquisite insights into their structural and chemical properties, and also discussing methods by which to manipulate their intramolecular and organizational features. The distinct characteristics arising from the interfacial confinement offer intriguing prospects for molecular science and advanced materials. We assess the role of surface interactions with respect to electronic and physicochemical characteristics, and describe in situ metallation pathways, molecular magnetism, rotation and switching. The engineering of nanostructures, organized layers, interfacial hybrid and bio-inspired systems is also addressed.

Self-assembly of silica microparticles in magnetic multiphase flows: Experiment and simulation

NASA Astrophysics Data System (ADS)

Li, Xiang; Niu, Xiao-Dong; Li, You; Chen, Mu-Feng

2018-04-01

Dynamic self-assembly, especially self-assembly under magnetic field, is vital not only for its marvelous phenomenon but also for its mechanisms. Revealing the underlying mechanisms is crucial for a deeper understanding of self-assembly. In this paper, several magnetic induced self-assembly experiments by using the mixed magnetic multiphase fluids comprised of silica microspheres were carried out. The relations of the strength of external magnetic field, the inverse magnetorheological effect, and the structures of self-assembled particles were investigated. In addition, a momentum-exchanged immersed boundary-based lattice Boltzmann method (MEIB-LBM) for modeling multi-physical coupling multiphase flows was employed to numerically study the magnetic induced self-assembly process in detail. The present work showed that the external magnetic field can be used to control the form of self-assembly of nonmagnetic microparticles in a chain-like structure, and the self-assembly process can be classified into four stages with magnetic hysteresis, magnetization of nonmagnetic microparticles, self-assembly in chain-like structures, and the stable chain state. The combination of experimental and numerical results could offer a method to control the self-assembled nonmagnetic microparticles, which can provide the technical and theoretical support for the design and fabrication of micro/nanomaterials.

Directed self-assembly of proteins into discrete radial patterns

PubMed Central

Thakur, Garima; Prashanthi, Kovur; Thundat, Thomas

2013-01-01

Unlike physical patterning of materials at nanometer scale, manipulating soft matter such as biomolecules into patterns is still in its infancy. Self-assembled monolayer (SAM) with surface density gradient has the capability to drive biomolecules in specific directions to create hierarchical and discrete structures. Here, we report on a two-step process of self-assembly of the human serum albumin (HSA) protein into discrete ring structures based on density gradient of SAM. The methodology involves first creating a 2-dimensional (2D) polyethylene glycol (PEG) islands with responsive carboxyl functionalities. Incubation of proteins on such pre-patterned surfaces results in direct self-assembly of protein molecules around PEG islands. Immobilization and adsorption of protein on such structures over time evolve into the self-assembled patterns. PMID:23719678

Neural basis of distorted self-face recognition in social anxiety disorder.

PubMed

Kim, Min-Kyeong; Yoon, Hyung-Jun; Shin, Yu-Bin; Lee, Seung-Koo; Kim, Jae-Jin

2016-01-01

The observer perspective causes patients with social anxiety disorder (SAD) to excessively inspect their performance and appearance. This study aimed to investigate the neural basis of distorted self-face recognition in non-social situations in patients with SAD. Twenty patients with SAD and 20 age- and gender-matched healthy controls participated in this fMRI study. Data were acquired while participants performed a Composite Face Evaluation Task, during which they had to press a button indicating how much they liked a series of self-faces, attractively transformed self-faces, and attractive others' faces. Patients had a tendency to show more favorable responses to the self-face and unfavorable responses to the others' faces compared with controls, but the two groups' responses to the attractively transformed self-faces did not differ. Significant group differences in regional activity were observed in the middle frontal and supramarginal gyri in the self-face condition (patients < controls); the inferior frontal gyrus in the attractively transformed self-face condition (patients > controls); and the middle frontal, supramarginal, and angular gyri in the attractive others' face condition (patients > controls). Most fronto-parietal activities during observation of the self-face were negatively correlated with preference scores in patients but not in controls. Patients with SAD have a positive point of view of their own face and experience self-relevance for the attractively transformed self-faces. This distorted cognition may be based on dysfunctions in the frontal and inferior parietal regions. The abnormal engagement of the fronto-parietal attentional network during processing face stimuli in non-social situations may be linked to distorted self-recognition in SAD.

Self-assembling electroactive hydrogels for flexible display technology

NASA Astrophysics Data System (ADS)

Jones, Scott L.; Hou Wong, Kok; Thordarson, Pall; Ladouceur, François

2010-12-01

We have assessed the potential of self-assembling hydrogels for use in conformal displays. The self-assembling process can be used to alter the transparency of the material to all visible light due to scattering by fibres. The reversible transition is shown to be of low energy by differential scanning calorimetry. For use in technology it is imperative that this transition is controlled electrically. We have thus synthesized novel self-assembling hydrogelator molecules which contain an electroactive group. The well-known redox couple of anthraquinone/anthrahydroquinone has been used as the hydrophobic component for a series of small molecule gelators. They are further functionalized with peptide combinations of L-phenylalanine and glycine to provide the hydrophilic group to complete 'head-tail' models of self-assembling gels. The gelation and electroactive characteristics of the series were assessed. Cyclic voltammetry shows the reversible redox cycle to be only superficially altered by functionalization. Additionally, spectroelectrochemical measurements show a reversible transparency and colour change induced by the redox process.

DNA-Based Self-Assembly of Fluorescent Nanodiamonds.

PubMed

Zhang, Tao; Neumann, Andre; Lindlau, Jessica; Wu, Yuzhou; Pramanik, Goutam; Naydenov, Boris; Jelezko, Fedor; Schüder, Florian; Huber, Sebastian; Huber, Marinus; Stehr, Florian; Högele, Alexander; Weil, Tanja; Liedl, Tim

2015-08-12

As a step toward deterministic and scalable assembly of ordered spin arrays we here demonstrate a bottom-up approach to position fluorescent nanodiamonds (NDs) with nanometer precision on DNA origami structures. We have realized a reliable and broadly applicable surface modification strategy that results in DNA-functionalized and perfectly dispersed NDs that were then self-assembled in predefined geometries. With optical studies we show that the fluorescence properties of the nitrogen-vacancy color centers in NDs are preserved during surface modification and DNA assembly. As this method allows the nanoscale arrangement of fluorescent NDs together with other optically active components in complex geometries, applications based on self-assembled spin lattices or plasmon-enhanced spin sensors as well as improved fluorescent labeling for bioimaging could be envisioned.

Porphyrin-Based Nanostructures for Photocatalytic Applications

PubMed Central

Chen, Yingzhi; Li, Aoxiang; Huang, Zheng-Hong; Wang, Lu-Ning; Kang, Feiyu

2016-01-01

Well-defined organic nanostructures with controllable size and morphology are increasingly exploited in optoelectronic devices. As promising building blocks, porphyrins have demonstrated great potentials in visible-light photocatalytic applications, because of their electrical, optical and catalytic properties. From this perspective, we have summarized the recent significant advances on the design and photocatalytic applications of porphyrin-based nanostructures. The rational strategies, such as texture or crystal modification and interfacial heterostructuring, are described. The applications of the porphyrin-based nanostructures in photocatalytic pollutant degradation and hydrogen evolution are presented. Finally, the ongoing challenges and opportunities for the future development of porphyrin nanostructures in high-quality nanodevices are also proposed. PMID:28344308

Peptide self-assembly: thermodynamics and kinetics.

PubMed

Wang, Juan; Liu, Kai; Xing, Ruirui; Yan, Xuehai

2016-10-21

Self-assembling systems play a significant role in physiological functions and have therefore attracted tremendous attention due to their great potential for applications in energy, biomedicine and nanotechnology. Peptides, consisting of amino acids, are among the most popular building blocks and programmable molecular motifs. Nanostructures and materials assembled using peptides exhibit important potential for green-life new technology and biomedical applications mostly because of their bio-friendliness and reversibility. The formation of these ordered nanostructures pertains to the synergistic effect of various intermolecular non-covalent interactions, including hydrogen-bonding, π-π stacking, electrostatic, hydrophobic, and van der Waals interactions. Therefore, the self-assembly process is mainly driven by thermodynamics; however, kinetics is also a critical factor in structural modulation and function integration. In this review, we focus on the influence of thermodynamic and kinetic factors on structural assembly and regulation based on different types of peptide building blocks, including aromatic dipeptides, amphiphilic peptides, polypeptides, and amyloid-relevant peptides.

Self-assembly from milli- to nanoscales: methods and applications

PubMed Central

Mastrangeli, M; Abbasi, S; Varel, C; Van Hoof, C; Celis, J-P; Böhringer, K F

2009-01-01

The design and fabrication techniques for microelectromechanical systems (MEMS) and nanodevices are progressing rapidly. However, due to material and process flow incompatibilities in the fabrication of sensors, actuators and electronic circuitry, a final packaging step is often necessary to integrate all components of a heterogeneous microsystem on a common substrate. Robotic pick-and-place, although accurate and reliable at larger scales, is a serial process that downscales unfavorably due to stiction problems, fragility and sheer number of components. Self-assembly, on the other hand, is parallel and can be used for device sizes ranging from millimeters to nanometers. In this review, the state-of-the-art in methods and applications for self-assembly is reviewed. Methods for assembling three-dimensional (3D) MEMS structures out of two-dimensional (2D) ones are described. The use of capillary forces for folding 2D plates into 3D structures, as well as assembling parts onto a common substrate or aggregating parts to each other into 2D or 3D structures, is discussed. Shape matching and guided assembly by magnetic forces and electric fields are also reviewed. Finally, colloidal self-assembly and DNA-based self-assembly, mainly used at the nanoscale, are surveyed, and aspects of theoretical modeling of stochastic assembly processes are discussed. PMID:20209016

Self-recognition in the coordination driven self-assembly of 2-D polygons.

PubMed

Addicott, Chris; Das, Neeladri; Stang, Peter J

2004-08-23

Self-recognition in the transition-metal-mediated self-assembly of some 2-D polygons is presented. Prolonged heating of two or three organoplatinum reagents with 4,4'-dipyridyl in aqueous acetone results in the predominant formation of a rectangle, triangle, and/or square. All mixtures are characterized with NMR and electrospray ionization mass spectrometry (ESIMS). Despite the potential for ill-defined oligomeric products, these mixed ligand systems prefer to self-assemble into discrete species.

Self-assembly of inorganic nanoparticles: Ab ovo

NASA Astrophysics Data System (ADS)

Kotov, Nicholas A.

2017-09-01

There are numerous remarkable studies related to the self-organization of polymers, coordination compounds, microscale particles, biomolecules, macroscale particles, surfactants, and reactive molecules on surfaces. The focus of this paper is on the self-organization of nanoscale inorganic particles or simply nanoparticles (NPs). Although there are fascinating and profound discoveries made with other self-assembling structures, the ones involving NPs deserve particular attention because they (a) are omnipresent in Nature; (b) have relevance to numerous disciplines (physics, chemistry, biology, astronomy, Earth sciences, and others); (c) embrace most of the features, geometries, and intricacies observed for the self-organization of other chemical species; (d) offer new tools for studies of self-organization phenomena; and (e) have a large economic impact, extending from energy and construction industries, to optoelectronics, biomedical technologies, and food safety. Despite the overall success of the field it is necessary to step back from its multiple ongoing research venues and consider two questions: What is self-assembly of nanoparticles? and Why do we need to study it? The reason to bring them up is to achieve greater scientific depth in the understanding of these omnipresent phenomena and, perhaps, deepen their multifaceted impact. Contribution to the Focus Issue Self-assemblies of Inorganic and Organic Nanomaterials edited by Marie-Paule Pileni.

Self-assembly of chlorophenols in water

PubMed Central

Rogalska, Ewa; Rogalski, Marek; Gulik-Krzywicki, Tadeusz; Gulik, Annette; Chipot, Christophe

1999-01-01

In saturated solutions of some di- and trichlorophenols, structures with complex morphologies, consisting of thin, transparent sheets often coiling into helices and ultimately twisting into filaments, were observed under the optical microscope. Freeze-fracture electron microscopy, x-ray diffraction, phase diagrams, and molecular modeling were performed to elucidate the observed phenomena. Here, we present evidence that the chlorophenols studied, when interacting with water, self-assemble into bilayers. The fact that some chlorophenols form the same supramolecular structures as those described previously for structurally nonrelated surfactants sheds light on the mechanisms of self-assembly. PMID:10359753

Self-assembly of knots and links

NASA Astrophysics Data System (ADS)

Orlandini, Enzo; Polles, Guido; Marenduzzo, Davide; Micheletti, Cristian

2017-03-01

Guiding the self-assembly of identical building blocks towards complex three-dimensional structures with a set of desired properties is a major goal in material science, chemistry and physics. A particularly challenging problem, especially explored in synthetic chemistry, is that of self-assembling closed structures with a target topology starting by simple geometrical templates. Here we overview and revisit recent advancements, based on stochastic simulations, where the geometry of rigid helical templates with functionalised sticky ends has been designed for self-assembling efficiently and reproducibly into a wide range of three-dimensional closed structures. Notably, these include non trivial topologies of links and knots, including the 819 knot that we had predicted to be highly encodable and that has only recently been obtained experimentally. By appropriately tuning the parameters that define the template shape, we show that, for fixed concentration of templates, the assembly process can be directed towards the formation of specific knotted and linked structures such as the trefoils, pentafoil knots, Hopf and Solomon links. More exotic and unexpected knots and links are also found. Our results should be relevant to the design of new protocols that can both increase and broaden the population of synthetise molecular knots and catenanes.

Light-induced Self-Assembly and Diffusion of Nanoclusters

NASA Astrophysics Data System (ADS)

Lian, Wenxuan

Novel methods to build multiple types of three-dimensional structures from various nanoscale components are the most exciting and challenging questions in nano-science. The properties of the assembled structures can be potentially and designed, but the development of such approaches is challenging. In order to realize such rational assembly, a tunable interaction medium is often introduced into the system. Soft matter, such as polymers, surfactants and biomolecules are used to modify the surfaces of the nanoscale building blocks. Deoxyribonucleic acid (DNA) strands are known as polynucleotides since they are composed of simpler units called nucleotides. There are unique base pairing rules that are predictable and programmable, which can be used to regulate self-assembly process with high degree of control. Besides controlling static structure, it is important to develop methods for controlling systems in dynamic matter, with chemical stimuli or external fields. For example, here we study the use of azobezene-trimethylammonium bromide (AzoTAB) as a molecular agent that can control self-assembly via light excitation. In this thesis, DNA assisted self-assembly was conducted. The ability of AzoTAB as a light induced surfactant to control DNA assisted self-assembly was confirmed. The mechanism of AzoTAB as a light controlled self-assembly promoter was studied. In the second project, diffusion of nanoclusters was studied. The presence of polymers brings strong entanglement with nanoclusters. This entanglement is more obvious when the nanocluster is a framed structure like the octahedron in the study. The diffusion coefficient of the octahedron becomes larger during traveling. The following up studies are required to elucidate the origin of the observed effect.

Multicomponent Supramolecular Systems: Self-Organization in Coordination-Driven Self-Assembly

PubMed Central

Zheng, Yao-Rong; Yang, Hai-Bo; Ghosh, Koushik; Zhao, Liang; Stang, Peter J.

2009-01-01

The self-organization of multicomponent supramolecular systems involving a variety of two-dimensional (2-D) polygons and three-dimensional (3-D) cages is presented. Nine self-organizing systems, SS1–SS9, have been studied. Each involving the simultaneous mixing of organoplatinum acceptors and pyridyl donors of varying geometry and their selective self-assembly into three to four specific 2-D (rectangular, triangular, and rhomboid) and/or 3-D (triangular prism and distorted and nondistorted trigonal bipyramidal) supramolecules. The formation of these discrete structures is characterized using NMR spectroscopy and electrospray ionization mass spectrometry (ESI-MS). In all cases, the self-organization process is directed by: (1) the geometric information encoded within the molecular subunits and (2) a thermodynamically driven dynamic self-correction process. The result is the selective self-assembly of multiple discrete products from a randomly formed complex. The influence of key experimental variables – temperature and solvent – on the self-correction process and the fidelity of the resulting self-organization systems is also described. PMID:19544512

Sensitive determination of dopamine levels via surface-enhanced Raman scattering of Ag nanoparticle dimers.

PubMed

Yu, Xiantong; He, XiaoXiao; Yang, Taiqun; Zhao, Litao; Chen, Qichen; Zhang, Sanjun; Chen, Jinquan; Xu, Jianhua

2018-01-01

Dopamine (DA) is an important neurotransmitter in the hypothalamus and pituitary gland, which can produce a direct influence on mammals' emotions in midbrain. Additionally, the level of DA is highly related with some important neurologic diseases such as schizophrenia, Parkinson, and Huntington's diseases, etc. In light of the important roles that DA plays in the disease modulation, it is of considerable significance to develop a sensitive and reproducible approach for monitoring DA. The objective of this study was to develop an efficient approach to quantitatively monitor the level of DA using Ag nanoparticle (NP) dimers and enhanced Raman spectroscopy. Ag NP dimers were synthesized for the sensitive detection of DA via surface-enhanced Raman scattering (SERS). Citrate was used as both the capping agent of NPs and sensing agent to DA, which is self-assembled on the surface of Ag NP dimers by reacting with the surface carboxyl group to form a stable amide bond. To improve accuracy and precision, the multiplicative effects model for surface-enhanced Raman spectroscopy was utilized to analyze the SERS assays. A low limits of detection (LOD) of 20 pM and a wide linear response range from 30 pM to 300 nM were obtained for DA quantitative detection. The SERS enhancement factor was theoretically valued at approximately 10 7 by discrete dipole approximation. DA was self-assembled on the citrate capped surface of Ag NPs dimers through the amide bond. The adsorption energy was estimated to be 256 KJ/mol using the Langmuir isotherm model. The density functional theory was used to simulate the spectral characteristics of SERS during the adsorption of DA on the surface of the Ag dimers. Furthermore, to improve the accuracy and precision of quantitative analysis of SERS assays with a multiplicative effects model for surface-enhanced Raman spectroscopy. A LOD of 20 pM DA-level was obtained, and the linear response ranged from 30 pM to 300 nM for quantitative DA detection. The

Sensitive determination of dopamine levels via surface-enhanced Raman scattering of Ag nanoparticle dimers

PubMed Central

Yu, Xiantong; He, XiaoXiao; Yang, Taiqun; Zhao, Litao; Chen, Qichen; Zhang, Sanjun; Chen, Jinquan; Xu, Jianhua

2018-01-01

Background Dopamine (DA) is an important neurotransmitter in the hypothalamus and pituitary gland, which can produce a direct influence on mammals’ emotions in midbrain. Additionally, the level of DA is highly related with some important neurologic diseases such as schizophrenia, Parkinson, and Huntington’s diseases, etc. In light of the important roles that DA plays in the disease modulation, it is of considerable significance to develop a sensitive and reproducible approach for monitoring DA. Purpose The objective of this study was to develop an efficient approach to quantitatively monitor the level of DA using Ag nanoparticle (NP) dimers and enhanced Raman spectroscopy. Methods Ag NP dimers were synthesized for the sensitive detection of DA via surface-enhanced Raman scattering (SERS). Citrate was used as both the capping agent of NPs and sensing agent to DA, which is self-assembled on the surface of Ag NP dimers by reacting with the surface carboxyl group to form a stable amide bond. To improve accuracy and precision, the multiplicative effects model for surface-enhanced Raman spectroscopy was utilized to analyze the SERS assays. Results A low limits of detection (LOD) of 20 pM and a wide linear response range from 30 pM to 300 nM were obtained for DA quantitative detection. The SERS enhancement factor was theoretically valued at approximately 107 by discrete dipole approximation. DA was self-assembled on the citrate capped surface of Ag NPs dimers through the amide bond. The adsorption energy was estimated to be 256 KJ/mol using the Langmuir isotherm model. The density functional theory was used to simulate the spectral characteristics of SERS during the adsorption of DA on the surface of the Ag dimers. Furthermore, to improve the accuracy and precision of quantitative analysis of SERS assays with a multiplicative effects model for surface-enhanced Raman spectroscopy. Conclusion A LOD of 20 pM DA-level was obtained, and the linear response ranged from 30 p

Adhesive Dimerization of Human P-Cadherin Catalyzed by a Chaperone-like Mechanism.

PubMed

Kudo, Shota; Caaveiro, Jose M M; Tsumoto, Kouhei

2016-09-06

Orderly assembly of classical cadherins governs cell adhesion and tissue maintenance. A key event is the strand-swap dimerization of the extracellular ectodomains of two cadherin molecules from apposing cells. Here we have determined crystal structures of P-cadherin in six different conformational states to elaborate a motion picture of its adhesive dimerization at the atomic level. The snapshots revealed that cell-adhesive dimerization is facilitated by several intermediate states collectively termed X-dimer in analogy to other classical cadherins. Based on previous studies and on the combined structural, kinetic, thermodynamic, biochemical, and cellular data reported herein, we propose that the adhesive dimerization of human P-cadherin is achieved by a stepwise mechanism analogous to that of assembly chaperones. This mechanism, applicable to type I classical cadherins, confers high specificity and fast association rates. We expect these findings to guide innovative therapeutic approaches targeting P-cadherin in cancer. Copyright © 2016 Elsevier Ltd. All rights reserved.

Self-assembled nanotubes from single fluorescent amino acid

NASA Astrophysics Data System (ADS)

Babar, Dipak Gorakh; Sarkar, Sabyasachi

2017-04-01

Self-assembly of biomolecules has gained increasing attention as it generates various supramolecular structural assemblies having potential applications principally in biomedical sciences. Here, we show that amino acid like tryptophan or tyrosine readily aggregates as nanotubes via a simple self-assembly process. These were characterized by FTIR, scanning electron microscopy, and by fluorescence microscopy. Nanotubes prepared from tryptophan are having 200 nm inner diameter and those from tyrosine are having the same around 50 nm diameter.

Dimer self-organization of impurity ytterbium ions in synthetic forsterite single crystals

NASA Astrophysics Data System (ADS)

Tarasov, V. F.; Sukhanov, A. A.; Dudnikova, V. B.; Zharikov, E. V.; Lis, D. A.; Subbotin, K. A.

2017-07-01

Paramagnetic centers formed by impurity Yb3+ ions in synthetic forsterite (Mg2SiO4) grown by the Czochralski technique are studied by X-band CW and pulsed EPR spectroscopy. These centers are single ions substituting magnesium in two different crystallographic positions denoted M1 and M2, and dimer associates formed by two Yb3+ ions in nearby positions M1. It is established that there is a pronounced mechanism favoring self-organization of ytterbium ions in dimer associates during the crystal growth, and the mechanism of the spin-spin coupling between ytterbium ions in the associate has predominantly a dipole-dipole character, which makes it possible to control the energy of the spin-spin interaction by changing the orientation of the external magnetic field. The structural computer simulation of cluster ytterbium centers in forsterite crystals is carried out by the method of interatomic potentials using the GULP 4.0.1 code (General Utility Lattice Program). It is established that the formation of dimer associates in the form of a chain parallel to the crystallographic axis consisting of two ytterbium ions with a magnesium vacancy between them is the most energetically favorable for ytterbium ions substituting magnesium in the position M1.

Enabling complex nanoscale pattern customization using directed self-assembly.

PubMed

Doerk, Gregory S; Cheng, Joy Y; Singh, Gurpreet; Rettner, Charles T; Pitera, Jed W; Balakrishnan, Srinivasan; Arellano, Noel; Sanders, Daniel P

2014-12-16

Block copolymer directed self-assembly is an attractive method to fabricate highly uniform nanoscale features for various technological applications, but the dense periodicity of block copolymer features limits the complexity of the resulting patterns and their potential utility. Therefore, customizability of nanoscale patterns has been a long-standing goal for using directed self-assembly in device fabrication. Here we show that a hybrid organic/inorganic chemical pattern serves as a guiding pattern for self-assembly as well as a self-aligned mask for pattern customization through cotransfer of aligned block copolymer features and an inorganic prepattern. As informed by a phenomenological model, deliberate process engineering is implemented to maintain global alignment of block copolymer features over arbitrarily shaped, 'masking' features incorporated into the chemical patterns. These hybrid chemical patterns with embedded customization information enable deterministic, complex two-dimensional nanoscale pattern customization through directed self-assembly.

Bioinspired synthesis and self-assembly of hybrid organic–inorganic nanomaterials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Honghu

Nature is replete with complex organic–inorganic hierarchical materials of diverse yet specific functions. These materials are intricately designed under physiological conditions through biomineralization and biological self-assembly processes. Tremendous efforts have been devoted to investigating mechanisms of such biomineralization and biological self-assembly processes as well as gaining inspiration to develop biomimetic methods for synthesis and self-assembly of functional nanomaterials. In this work, we focus on the bioinspired synthesis and self-assembly of functional inorganic nanomaterials templated by specialized macromolecules including proteins, DNA and polymers. The in vitro biomineralization process of the magnetite biomineralizing protein Mms6 has been investigated using small-angle X-ray scattering.more » Templated by Mms6, complex magnetic nanomaterials can be synthesized on surfaces and in the bulk. DNA and synthetic polymers have been exploited to construct macroscopic two- and three-dimensional (2D and 3D) superlattices of gold nanocrystals. Employing X-ray scattering and spectroscopy techniques, the self-assembled structures and the self-assembly mechanisms have been studied, and theoretical models have been developed. Our results show that specialized macromolecules including proteins, DNA and polymers act as effective templates for synthesis and self-assembly of nanomaterials. These bottom-up approaches provide promising routes to fabricate hybrid organic–inorganic nanomaterials with rationally designed hierarchical structures, targeting specific functions.« less

Self-esteem, interpersonal risk, and preference for e-mail to face-to-face communication.

PubMed

Joinson, Adam N

2004-08-01

The media choices made by high and low self-esteem Internet users were studied using web-based methodology (n = 265). Participants were asked to rank four media (face-to-face, e-mail, letter, and telephone) in order of preference across four different communication scenarios designed to pose an interpersonal risk. The level of interpersonal risk posed by two of the scenarios (asking for a pay rise and asking for a date) were also experimentally manipulated by randomly allocating participants to a 25%, 50%, or 75% chance of rejection. Low self-esteem users (LSE) showed a significant preference toward e-mail communication compared to high self-esteem users (HSE). This pattern was reversed for face-to-face preferences. Similarly, a greater chance of rejection in a scenario led to e-mail being preferred to face-to-face communication. The results are discussed in light of both the strategic use of different media and the motivated Internet user.

Syntheses and Functionalizations of Porphyrin Macrocycles

PubMed Central

Vicente, Maria da G.H.; Smith, Kevin M.

2014-01-01

Porphyrin macrocycles have been the subject of intense study in the last century because they are widely distributed in nature, usually as metal complexes of either iron or magnesium. As such, they serve as the prosthetic groups in a wide variety of primary metabolites, such as hemoglobins, myoglobins, cytochromes, catalases, peroxidases, chlorophylls, and bacteriochlorophylls; these compounds have multiple applications in materials science, biology and medicine. This article describes current methodology for preparation of simple, symmetrical model porphyrins, as well as more complex protocols for preparation of unsymmetrically substituted porphyrin macrocycles similar to those found in nature. The basic chemical reactivity of porphyrins and metalloporphyrin is also described, including electrophilic and nucleophilic reactions, oxidations, reductions, and metal-mediated cross-coupling reactions. Using the synthetic approaches and reactivity profiles presented, eventually almost any substituted porphyrin system can be prepared for applications in a variety of areas, including in catalysis, electron transport, model biological systems and therapeutics. PMID:25484638

Design of fluidic self-assembly bonds for precise component positioning

NASA Astrophysics Data System (ADS)

Ramadoss, Vivek; Crane, Nathan B.

2008-02-01

Self Assembly is a promising alternative to conventional pick and place robotic assembly of micro components. Its benefits include parallel integration of parts with low equipment costs. Various approaches to self assembly have been demonstrated, yet demanding applications like assembly of micro-optical devices require increased positioning accuracy. This paper proposes a new method for design of self assembly bonds that addresses this need. Current methods have zero force at the desired assembly position and low stiffness. This allows small disturbance forces to create significant positioning errors. The proposed method uses a substrate assembly feature to provide a high accuracy alignment guide to the part. The capillary bond region of the part and substrate are then modified to create a non-zero positioning force to maintain the part in the desired assembly position. Capillary force models show that this force aligns the part to the substrate assembly feature and reduces sensitivity of part position to process variation. Thus, the new configuration can substantially improve positioning accuracy of capillary self-assembly. This will result in a dramatic decrease in positioning errors in the micro parts. Various binding site designs are analyzed and guidelines are proposed for the design of an effective assembly bond using this new approach.

Self-assembled Nanomaterials for Chemotherapeutic Applications

NASA Astrophysics Data System (ADS)

Shieh, Aileen

The self-assembly of short designed peptides into functional nanostructures is becoming a growing interest in a wide range of fields from optoelectronic devices to nanobiotechnology. In the medical field, self-assembled peptides have especially attracted attention with several of its attractive features for applications in drug delivery, tissue regeneration, biological engineering as well as cosmetic industry and also the antibiotics field. We here describe the self-assembly of peptide conjugated with organic chromophore to successfully deliver sequence independent micro RNAs into human non-small cell lung cancer cell lines. The nanofiber used as the delivery vehicle is completely non-toxic and biodegradable, and exhibit enhanced permeability effect for targeting malignant tumors. The transfection efficiency with nanofiber as the delivery vehicle is comparable to that of the commercially available RNAiMAX lipofectamine while the toxicity is significantly lower. We also conjugated the peptide sequence with camptothecin (CPT) and observed the self-assembly of nanotubes for chemotherapeutic applications. The peptide scaffold is non-toxic and biodegradable, and drug loading of CPT is high, which minimizes the issue of systemic toxicity caused by extensive burden from the elimination of drug carriers. In addition, the peptide assembly drastically increases the solubility and stability of CPT under physiological conditions in vitro, while active CPT is gradually released from the peptide chain under the slight acidic tumor cell environment. Cytotoxicity results on human colorectal cancer cells and non-small cell lung cancer cell lines display promising anti-cancer properties compared to the parental CPT drug, which cannot be used clinically due to its poor solubility and lack of stability in physiological conditions. Moreover, the peptide sequence conjugated with 5-fluorouracil formed a hydrogel with promising topical chemotherapeutic applications that also display

Controlled intracellular self-assembly of gadolinium nanoparticles as smart molecular MR contrast agents.

PubMed

Cao, Chun-Yan; Shen, Ying-Ying; Wang, Jian-Dong; Li, Li; Liang, Gao-Lin

2013-01-01

Herein we developed a new "smart" Gd-based MR contrast agent (i.e., 1) which is susceptive to furin, a protease overexpressed in tumor. Under the action of furin, 1 condenses to form dimers (1-Ds) and the latter self-assemble into gadolinium nanparticles (Gd-NPs). Relaxivity of 1-D is more than 2 folds of those of 1 and magnevist at 1.5 T, and 1.4 folds of that of 1 at 3 T. Intracellular condensation of 1 in furin-overexpressed MDA-MB-468 cells was proven with direct two-photon laser microscopy (TPLM) fluorescence imaging of the cells incubated with the europium analog of 1 (i.e., 2). Intracellular Gd-NPs of 1 were uncovered and characterized for the first time. MRI of MDA-MB-468 tumors showed that 1 has enhanced MR contrast within the tumors than that of its scrambled control 1-Scr.

Cellular membrane enrichment of self-assembling D-peptides for cell surface engineering.

PubMed

Wang, Huaimin; Wang, Youzhi; Han, Aitian; Cai, Yanbin; Xiao, Nannan; Wang, Ling; Ding, Dan; Yang, Zhimou

2014-06-25

We occasionally found that several self-assembling peptides containing D-amino acids would be preferentially enriched in cellular membranes at self-assembled stages while distributed evenly in the cytoplasma of cells at unassembled stages. Self-assembling peptides containing only Lamino acids distributed evenly in cytoplasma of cells at both self-assembled and unassembled stages. The self-assembling peptides containing D-amino acids could therefore be applied for engineering cell surface with peptides. More importantly, by integrating a protein binding peptide (a PDZ domain binding hexapeptide of WRESAI) with the self-assembling peptide containing D-amino acids, protein could also be introduced to the cell surface. This study not only provided a novel approach to engineer cell surface, but also highlighted the unusual properties and potential applications of self-assembling peptides containing D-amino acids in regenerative medicine, drug delivery, and tissue engineering.

Novel agrochemical conjugates with self-assembling behaviour.

PubMed

Liu, Qingtao; Graham, Bim; Hawley, Adrian; Dong, Yao-Da; Boyd, Ben J

2018-02-15

That conjugation of agrichemicals to pro-assembly hydrophobic moieties will enable enhanced compatibility and loading with host lyotropic liquid crystalline carrier matrix, and potentially self-assemble in their own right in aqueous environments. A series of lipid-like agrochemical-conjugates were synthesized using specific amphiphilic entities conjugated onto the agrochemicals, picloram and 2,4-dichlorophenoxyacetic acid (2,4-D). The self-assembly behaviour and compatibility of the novel entities when incorporated into phytantriol and monoolein-based liquid crystalline systems were examined using small angle X-ray scattering, cryo-TEM and polarized optical microscopy. Compared to agrochemical-conjugates with simple alkyl ester groups, the esterification of the agrochemicals with amphiphilic groups such as phytantriol and monoolein led to greater structural compatibility and consequently a greater loading of the agrochemicals in the liquid crystalline systems without destabilizing phase structure. Picloram-monoolein and picloram-monoelaidin can self-assemble to form lamellar structures in water. However, certain agrochemical-conjugates such as picloram-monoelaidin and picloram-PEGn-oleate showed poor compatibility with liquid crystalline systems, resulting in phase separation. Copyright © 2017 Elsevier Inc. All rights reserved.

Neural Mechanism for Mirrored Self-face Recognition

PubMed Central

Sugiura, Motoaki; Miyauchi, Carlos Makoto; Kotozaki, Yuka; Akimoto, Yoritaka; Nozawa, Takayuki; Yomogida, Yukihito; Hanawa, Sugiko; Yamamoto, Yuki; Sakuma, Atsushi; Nakagawa, Seishu; Kawashima, Ryuta

2015-01-01

Self-face recognition in the mirror is considered to involve multiple processes that integrate 2 perceptual cues: temporal contingency of the visual feedback on one's action (contingency cue) and matching with self-face representation in long-term memory (figurative cue). The aim of this study was to examine the neural bases of these processes by manipulating 2 perceptual cues using a “virtual mirror” system. This system allowed online dynamic presentations of real-time and delayed self- or other facial actions. Perception-level processes were identified as responses to only a single perceptual cue. The effect of the contingency cue was identified in the cuneus. The regions sensitive to the figurative cue were subdivided by the response to a static self-face, which was identified in the right temporal, parietal, and frontal regions, but not in the bilateral occipitoparietal regions. Semantic- or integration-level processes, including amodal self-representation and belief validation, which allow modality-independent self-recognition and the resolution of potential conflicts between perceptual cues, respectively, were identified in distinct regions in the right frontal and insular cortices. The results are supportive of the multicomponent notion of self-recognition and suggest a critical role for contingency detection in the co-emergence of self-recognition and empathy in infants. PMID:24770712

Morphology and Pattern Control of Diphenylalanine Self-Assembly via Evaporative Dewetting.

PubMed

Chen, Jiarui; Qin, Shuyu; Wu, Xinglong; Chu, And Paul K

2016-01-26

Self-assembled peptide nanostructures have unique physical and biological properties and promising applications in electrical devices and functional molecular recognition. Although solution-based peptide molecules can self-assemble into different morphologies, it is challenging to control the self-assembly process. Herein, controllable self-assembly of diphenylalanine (FF) in an evaporative dewetting solution is reported. The fluid mechanical dimensionless numbers, namely Rayleigh, Marangoni, and capillary numbers, are introduced to control the interaction between the solution and FF molecules in the self-assembly process. The difference in the film thickness reflects the effects of Rayleigh and Marangoni convection, and the water vapor flow rate reveals the role of viscous fingering in the emergence of aligned FF flakes. By employing dewetting, various FF self-assembled patterns, like concentric and spokelike, and morphologies, like strips and hexagonal tubes/rods, can be produced, and there are no significant lattice structural changes in the FF nanostructures.

Self-assembled Nanofibrils for Immunomodulation

NASA Astrophysics Data System (ADS)

Zhao, Fan

This thesis has been mainly focused on applying self-assembled nanofibrils as unique depots for controlled release to modulate immune system, with two major chapters on modulation of innate immunity in chapter 2 and adaptive immunity in chapter 3, respectively. There are 5 chapters in the thesis. Chapter 1 gives a detailed review on the discovery, synthesis and application of self-assembled nanofibrils of therapeutic agents (termed as "self-delivery drugs"), including bioactive molecules; Chapter 2 demonstrates the supramolecular hydrogel of chemotactic peptides as a prolonged inflammation model through proper molecular engineering; Chapter 3 reports a suppressive antibody response achieved by encapsulation of antigens by supramolecular hydrogel of glycopeptide; Chapter 4 illustrates an example of supramolecular hydrogel formation of molecules with extremely low solubility, based on the fact that many small organic drugs have poor solubility. Chapter 5 used beta-galatosidase as a model to study glycosidase-instructed supramolecular hydrogel formation, with potential to target cancer cells due to their distinct metabolic profile.

Prioritization of arbitrary faces associated to self: An EEG study.

PubMed

Woźniak, Mateusz; Kourtis, Dimitrios; Knoblich, Günther

2018-01-01

Behavioral and neuroimaging studies have demonstrated that people process preferentially self-related information such as an image of their own face. Furthermore, people rapidly incorporate stimuli into their self-representation even if these stimuli do not have an intrinsic relation to self. In the present study, we investigated the time course of the processes involved in preferential processing of self-related information. In two EEG experiments three unfamiliar faces were identified with verbal labels as either the participant, a friend, or a stranger. Afterwards, participants judged whether two stimuli presented in succession (ISI = 1500ms) matched. In experiment 1, faces were followed by verbal labels and in experiment 2, labels were followed by faces. Both experiments showed the same pattern of behavioral and electrophysiological results. If the first stimulus (face or label) was associated with self, reaction times were faster and the late frontal positivity following the first stimulus was more pronounced. The self-association of the second stimulus (label or face) did not affect response times. However, the central-parietal P3 following presentation of the second stimulus was more pronounced when the second stimulus was preceded by self-related first stimulus. These results indicate that even unfamiliar faces that are associated to self can activate a self-representation. Once the self-representation has been activated the processing of ensuing stimuli is facilitated, irrespective of whether they are associated with the self.

Prioritization of arbitrary faces associated to self: An EEG study

PubMed Central

Kourtis, Dimitrios; Knoblich, Günther

2018-01-01

Behavioral and neuroimaging studies have demonstrated that people process preferentially self-related information such as an image of their own face. Furthermore, people rapidly incorporate stimuli into their self-representation even if these stimuli do not have an intrinsic relation to self. In the present study, we investigated the time course of the processes involved in preferential processing of self-related information. In two EEG experiments three unfamiliar faces were identified with verbal labels as either the participant, a friend, or a stranger. Afterwards, participants judged whether two stimuli presented in succession (ISI = 1500ms) matched. In experiment 1, faces were followed by verbal labels and in experiment 2, labels were followed by faces. Both experiments showed the same pattern of behavioral and electrophysiological results. If the first stimulus (face or label) was associated with self, reaction times were faster and the late frontal positivity following the first stimulus was more pronounced. The self-association of the second stimulus (label or face) did not affect response times. However, the central-parietal P3 following presentation of the second stimulus was more pronounced when the second stimulus was preceded by self-related first stimulus. These results indicate that even unfamiliar faces that are associated to self can activate a self-representation. Once the self-representation has been activated the processing of ensuing stimuli is facilitated, irrespective of whether they are associated with the self. PMID:29293670

Quantitative self-assembly prediction yields targeted nanomedicines

NASA Astrophysics Data System (ADS)

Shamay, Yosi; Shah, Janki; Işık, Mehtap; Mizrachi, Aviram; Leibold, Josef; Tschaharganeh, Darjus F.; Roxbury, Daniel; Budhathoki-Uprety, Januka; Nawaly, Karla; Sugarman, James L.; Baut, Emily; Neiman, Michelle R.; Dacek, Megan; Ganesh, Kripa S.; Johnson, Darren C.; Sridharan, Ramya; Chu, Karen L.; Rajasekhar, Vinagolu K.; Lowe, Scott W.; Chodera, John D.; Heller, Daniel A.

2018-02-01

Development of targeted nanoparticle drug carriers often requires complex synthetic schemes involving both supramolecular self-assembly and chemical modification. These processes are generally difficult to predict, execute, and control. We describe herein a targeted drug delivery system that is accurately and quantitatively predicted to self-assemble into nanoparticles based on the molecular structures of precursor molecules, which are the drugs themselves. The drugs assemble with the aid of sulfated indocyanines into particles with ultrahigh drug loadings of up to 90%. We devised quantitative structure-nanoparticle assembly prediction (QSNAP) models to identify and validate electrotopological molecular descriptors as highly predictive indicators of nano-assembly and nanoparticle size. The resulting nanoparticles selectively targeted kinase inhibitors to caveolin-1-expressing human colon cancer and autochthonous liver cancer models to yield striking therapeutic effects while avoiding pERK inhibition in healthy skin. This finding enables the computational design of nanomedicines based on quantitative models for drug payload selection.

Mechanistic aspects of thioflavin-T self-aggregation and DNA binding: evidence for dimer attack on DNA grooves.

PubMed

Biancardi, A; Biver, T; Burgalassi, A; Mattonai, M; Secco, F; Venturini, M

2014-10-07

Thioflavin-T (TFT) is a fluorescent marker widely employed in biomedical research but the mechanism of its binding to polynucleotides has been poorly understood. This paper presents a study of the mechanisms of TFT self-aggregation and binding to DNA. Relaxation kinetics of TFT solutions show that the cyanine undergoes dimerization followed by dimer isomerisation. The interaction of TFT with DNA has been investigated using static methods, such as spectrophotometric and spectrofluorometric titrations under different conditions (salt content, temperature), fluorescence quenching, viscometric experiments and the T-jump relaxation method. The combined use of these techniques enabled us to show that the TFT monomer undergoes intercalation between the DNA base pairs and external binding according to a branched mechanism. Moreover, it has also been observed that, under dye excess conditions, the TFT dimer binds to the DNA grooves. The molecular structures of intercalated TFT and the groove-bound TFT dimer are obtained by performing QM/MM MD simulations.

Sequential energy and charge transfer processes in mixed host-guest complexes of subphthalocyanine, porphyrin and phthalocyanine chromophores.

PubMed

Menting, Roel; Ng, Dennis K P; Röder, Beate; Ermilov, Eugeny A

2012-11-14

Porphyrins, phthalocyanines and subphthalocyanines are three attractive classes of chromophores with intriguing properties making them suitable for the design of artificial photosynthetic systems. The assembly of these components by a supramolecular approach is of particular interest as it provides a facile means to build multi-chromophoric arrays with various architectures and tuneable photophysical properties. In this paper, we show the formation of mixed host-guest supramolecular complexes that consist of a β-cyclodextrin-conjugated subphthalocyanine, a tetrasulfonated porphyrin and a series of silicon(IV) phthalocyanines substituted axially with two β-cyclodextrins via different spacers. We found that the three components form supramolecular complexes held by host-guest interactions in aqueous solution. Upon excitation of the subphthalocyanine part of the complex, the excitation energy is delivered to the phthalocyanine unit via excitation energy transfer and the porphyrin chromophore acts as an energy transfer bridge enabling this process. It was shown that photo-induced charge transfer also takes place. A sequential electron transfer process from the porphyrin unit to the phthalocyanine moiety and subsequently from the subphthalocyanine moiety to the porphyrin unit takes place, and the probability of this process is controlled by the linker between β-cyclodextrin and phthalocyanine. The lifetime of the charge-separated state was found to be 1.7 ns by transient absorption spectroscopy.

Imaging enzyme-triggered self-assembly of small molecules inside live cells

PubMed Central

Gao, Yuan; Shi, Junfeng; Yuan, Dan; Xu, Bing

2012-01-01

Self-assembly of small molecules in water to form nanofibers, besides generating sophisticated biomaterials, promises a simple system inside cells for regulating cellular processes. But lack of a convenient approach for studying the self-assembly of small molecules inside cells hinders the development of such systems. Here we report a method to image enzyme-triggered self-assembly of small molecules inside live cells. After linking a fluorophore to a self-assembly motif to make a precursor, we confirmed by 31P NMR and rheology that enzyme-triggered conversion of the precursor to a hydrogelator results in the formation of a hydrogel via self-assembly. The imaging contrast conferred by the nanofibers of the hydrogelators allowed the evaluation of intracellular self-assembly; the dynamics, and the localization of the nanofibers of the hydrogelators in live cells. This approach explores supramolecular chemistry inside cells and may lead to new insights, processes, or materials at the interface of chemistry and biology. PMID:22929790

Applying AFM-based nanofabrication for measuring the thickness of nanopatterns: the role of head groups in the vertical self-assembly of omega-functionalized n-alkanethiols.

PubMed

Kelley, Algernon T; Ngunjiri, Johnpeter N; Serem, Wilson K; Lawrence, Steve O; Yu, Jing-Jiang; Crowe, William E; Garno, Jayne C

2010-03-02

Molecules of n-alkanethiols with methyl head groups typically form well-ordered monolayers during solution self-assembly for a wide range of experimental conditions. However, we have consistently observed that, for either carboxylic acid or thiol-terminated n-alkanethiols, under certain conditions nanografted patterns are generated with a thickness corresponding precisely to a double layer. To investigate the role of head groups for solution self-assembly, designed patterns of omega-functionalized n-alkanethiols were nanografted with systematic changes in concentration. Nanografting is an in situ approach for writing patterns of thiolated molecules on gold surfaces by scanning with an AFM tip under high force, accomplished in dilute solutions of desired ink molecules. As the tip is scanned across the surface of a self-assembled monolayer under force, the matrix molecules are displaced from the surface and are immediately replaced with fresh molecules from solution to generate nanopatterns. In this report, side-by-side comparison of nanografted patterns is achieved for different matrix molecules using AFM images. The chain length and head groups (i.e., carboxyl, hydroxyl, methyl, thiol) were varied for the nanopatterns and matrix monolayers. Interactions such as head-to-head dimerization affect the vertical self-assembly of omega-functionalized n-alkanethiol molecules within nanografted patterns. At certain threshold concentrations, double layers were observed to form when nanografting with head groups of carboxylic acid and dithiols, whereas single layers were generated exclusively for nanografted patterns with methyl and hydroxyl groups, regardless of changes in concentration.

Detection of Intermediates And Kinetic Control During Assembly of Bacteriophage P22 Procapsid

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tuma, R.; Tsuruta, H.; French, K.H.

2009-05-26

Bacteriophage P22 serves as a model for the assembly and maturation of other icosahedral double-stranded DNA viruses. P22 coat and scaffolding proteins assemble in vitro into an icosahedral procapsid, which then expands during DNA packaging (maturation). Efficient in vitro assembly makes this system suitable for design and production of monodisperse spherical nanoparticles (diameter {approx} 50 nm). In this work, we explore the possibility of controlling the outcome of assembly by scaffolding protein engineering. The scaffolding protein exists in monomer-dimer-tetramer equilibrium. We address the role of monomers and dimers in assembly by using three different scaffolding proteins with altered monomer-dimer equilibriummore » (weak dimer, covalent dimer, monomer). The progress and outcome of assembly was monitored by time-resolved X-ray scattering, which allowed us to distinguish between closed shells and incomplete assembly intermediates. Binding of scaffolding monomer activates the coat protein for assembly. Excess dimeric scaffolding protein resulted in rapid nucleation and kinetic trapping yielding incomplete shells. Addition of monomeric wild-type scaffold with excess coat protein completed these metastable shells. Thus, the monomeric scaffolding protein plays an essential role in the elongation phase by activating the coat and effectively lowering its critical concentration for assembly.« less

Waveguide electro-optic modulators based on intrinsically polar self-assembled superlattices (SASs)

NASA Astrophysics Data System (ADS)

Liu, Zhifu; Ho, Seng Tiong; Chang, Seongsik; Zhao, Yiguang; Marks, Tobin J.; Kang, Hu; van der Boom, Milko E.; Zhu, Peiwang

2002-12-01

In this paper we describe methods of fabricating and characterizing organic electro-optic modulators based on intrinsically polar self-assembled superlattices. These structures are intrinsically acentric, and exhibit large second harmonic generation and electro-optic responses without the requirement of poling by an external electric field. A novel wet chemical protection-deprotection approach for the growth of self-assembled superlattices have been developed, and the refractive indices of self-assembled organic electro-optic superlattices may be tuned during the self-assembly process. Prototype electro-optic modulators based on chromophoric self-assembled superlattices have been designed and fabricated. The effective electro-optic coefficient of the self-assembled superlattice film in a phase modulator is estimated as about 20 pm/V at a wavelength of 1064 nm.

Tuning the nature and stability of self-assemblies formed by ester benzene 1,3,5-tricarboxamides: the crucial role played by the substituents.

PubMed

Desmarchelier, Alaric; Alvarenga, Bruno Giordano; Caumes, Xavier; Dubreucq, Ludovic; Troufflard, Claire; Tessier, Martine; Vanthuyne, Nicolas; Idé, Julien; Maistriaux, Thomas; Beljonne, David; Brocorens, Patrick; Lazzaroni, Roberto; Raynal, Matthieu; Bouteiller, Laurent

2016-09-20

As the benzene 1,3,5-tricarboxamide (BTA) moiety is commonly used as the central assembling unit for the construction of functionalized supramolecular architectures, strategies to tailor the nature and stability of BTA assemblies are needed. The assembly properties of a library of structurally simple BTAs derived from amino dodecyl esters (ester BTAs, 13 members) have been studied, either in the bulk or in cyclohexane solutions, by means of a series of analytical methods (NMR, DSC, POM, FT-IR, UV-Vis, CD, ITC, high-sensitivity DSC, SANS). Two types of hydrogen-bonded species have been identified and characterized: the expected amide-bonded helical rods (or stacks) that are structurally similar to those formed by BTAs with simple alkyl side chains (alkyl BTAs), and ester-bonded dimers in which the BTAs are connected by means of hydrogen bonds linking the amide N-H and the ester C[double bond, length as m-dash]O. MM/MD calculations coupled with simulations of CD spectra allow for the precise determination of the molecular arrangement and of the hydrogen bond pattern of these dimers. Our study points out the crucial influence of the substituent attached on the amino-ester α-carbon on the relative stability of the rod-like versus dimeric assemblies. By varying this substituent, one can precisely tune the nature of the dominant hydrogen-bonded species (stacks or dimers) in the neat compounds and in cyclohexane over a wide range of temperatures and concentrations. In the neat BTAs, stacks are stable up to 213 °C and dimers above 180 °C whilst in cyclohexane stacks form at c* > 3 × 10 -5 M at 20 °C and dimers are stable up to 80 °C at 7 × 10 -6 M. Ester BTAs that assemble into stacks form a liquid-crystalline phase and yield gels or viscous solutions in cyclohexane, demonstrating the importance of controlling the structure of these assemblies. Our systematic study of these structurally similar ester BTAs also allows for a better understanding of how a single atom

An Active Approach to Colloidal Self-Assembly

NASA Astrophysics Data System (ADS)

Mallory, Stewart A.; Valeriani, Chantal; Cacciuto, Angelo

2018-04-01

In this review, we discuss recent advances in the self-assembly of self-propelled colloidal particles and highlight some of the most exciting results in this field, with a specific focus on dry active matter. We explore this phenomenology through the lens of the complexity of the colloidal building blocks. We begin by considering the behavior of isotropic spherical particles. We then discuss the case of amphiphilic and dipolar Janus particles. Finally, we show how the geometry of the colloids and/or the directionality of their interactions can be used to control the physical properties of the assembled active aggregates, and we suggest possible strategies for how to exploit activity as a tunable driving force for self-assembly. The unique properties of active colloids lend promise to the design of the next generation of functional, environment-sensing microstructures able to perform specific tasks in an autonomous and targeted manner.

Multi-modular, tris(triphenylamine) zinc porphyrin-zinc phthalocyanine-fullerene conjugate as a broadband capturing, charge stabilizing, photosynthetic 'antenna-reaction center' mimic.

PubMed

Kc, Chandra B; Lim, Gary N; D'Souza, Francis

2015-04-21

A broadband capturing, charge stabilizing, photosynthetic antenna-reaction center model compound has been newly synthesized and characterized. The model compound is comprised of a zinc porphyrin covalently linked to three units of triphenylamine entities and a zinc phthalocyanine entity. The absorption and fluorescence spectra of zinc porphyrin complemented that of zinc phthalocyanine offering broadband coverage. Stepwise energy transfer from singlet excited triphenylamine to zinc porphyrin, and singlet excited zinc porphyrin to zinc phthalocyanine (kENT ∼ 10(11) s(-1)) was established from spectroscopic and time-resolved transient absorption techniques. Next, an electron acceptor, fullerene was introduced via metal-ligand axial coordination to both zinc porphyrin and zinc phthalocyanine centers, and they were characterized by spectroscopic and electrochemical techniques. An association constant of 4.9 × 10(4) M(-1) for phenylimidazole functionalized fullerene binding to zinc porphyrin, and 5.1 × 10(4) M(-1) for it binding to zinc phthalocyanine was obtained. An energy level diagram for the occurrence of different photochemical events within the multi-modular donor-acceptor conjugate was established from spectral and electrochemical data. Unlike the previous zinc porphyrin-zinc phthalocyanine-fullerene conjugates, the newly assembled donor-acceptor conjugate has been shown to undergo the much anticipated initial charge separation from singlet excited zinc porphyrin to the coordinated fullerene followed by a hole shift process to zinc phthalocyanine resulting in a long-lived charge separated state as revealed by femto- and nanosecond transient absorption spectroscopic techniques. The lifetime of the final charge separated state was about 100 ns.

Sequential programmable self-assembly: Role of cooperative interactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jonathan D. Halverson; Tkachenko, Alexei V.

Here, we propose a general strategy of “sequential programmable self-assembly” that enables a bottom-up design of arbitrary multi-particle architectures on nano- and microscales. We show that a naive realization of this scheme, based on the pairwise additive interactions between particles, has fundamental limitations that lead to a relatively high error rate. This can be overcome by using cooperative interparticle binding. The cooperativity is a well known feature of many biochemical processes, responsible, e.g., for signaling and regulations in living systems. Here we propose to utilize a similar strategy for high precision self-assembly, and show that DNA-mediated interactions provide a convenientmore » platform for its implementation. In particular, we outline a specific design of a DNA-based complex which we call “DNA spider,” that acts as a smart interparticle linker and provides a built-in cooperativity of binding. We demonstrate versatility of the sequential self-assembly based on spider-functionalized particles by designing several mesostructures of increasing complexity and simulating their assembly process. This includes a number of finite and repeating structures, in particular, the so-called tetrahelix and its several derivatives. Due to its generality, this approach allows one to design and successfully self-assemble virtually any structure made of a “GEOMAG” magnetic construction toy, out of nanoparticles. According to our results, once the binding cooperativity is strong enough, the sequential self-assembly becomes essentially error-free.« less

Sequential programmable self-assembly: Role of cooperative interactions

DOE PAGES

Jonathan D. Halverson; Tkachenko, Alexei V.

2016-03-04

Here, we propose a general strategy of “sequential programmable self-assembly” that enables a bottom-up design of arbitrary multi-particle architectures on nano- and microscales. We show that a naive realization of this scheme, based on the pairwise additive interactions between particles, has fundamental limitations that lead to a relatively high error rate. This can be overcome by using cooperative interparticle binding. The cooperativity is a well known feature of many biochemical processes, responsible, e.g., for signaling and regulations in living systems. Here we propose to utilize a similar strategy for high precision self-assembly, and show that DNA-mediated interactions provide a convenientmore » platform for its implementation. In particular, we outline a specific design of a DNA-based complex which we call “DNA spider,” that acts as a smart interparticle linker and provides a built-in cooperativity of binding. We demonstrate versatility of the sequential self-assembly based on spider-functionalized particles by designing several mesostructures of increasing complexity and simulating their assembly process. This includes a number of finite and repeating structures, in particular, the so-called tetrahelix and its several derivatives. Due to its generality, this approach allows one to design and successfully self-assemble virtually any structure made of a “GEOMAG” magnetic construction toy, out of nanoparticles. According to our results, once the binding cooperativity is strong enough, the sequential self-assembly becomes essentially error-free.« less

Urinary porphyrin excretion in neurotypical and autistic children.

PubMed

Woods, James S; Armel, Sarah E; Fulton, Denise I; Allen, Jason; Wessels, Kristine; Simmonds, P Lynne; Granpeesheh, Doreen; Mumper, Elizabeth; Bradstreet, J Jeffrey; Echeverria, Diana; Heyer, Nicholas J; Rooney, James P K

2010-10-01

Increased urinary concentrations of pentacarboxyl-, precopro- and copro-porphyrins have been associated with prolonged mercury (Hg) exposure in adults, and comparable increases have been attributed to Hg exposure in children with autism (AU). This study was designed to measure and compare urinary porphyrin concentrations in neurotypical (NT) children and same-age children with autism, and to examine the association between porphyrin levels and past or current Hg exposure in children with autism. This exploratory study enrolled 278 children 2-12 years of age. We evaluated three groups: AU, pervasive developmental disorder-not otherwise specified (PDD-NOS), and NT. Mothers/caregivers provided information at enrollment regarding medical, dental, and dietary exposures. Urine samples from all children were acquired for analyses of porphyrin, creatinine, and Hg. Differences between groups for mean porphyrin and Hg levels were evaluated. Logistic regression analysis was conducted to determine whether porphyrin levels were associated with increased risk of autism. Mean urinary porphyrin concentrations are naturally high in young children and decline by as much as 2.5-fold between 2 and 12 years of age. Elevated copro- (p < 0.009), hexacarboxyl- (p < 0.01) and pentacarboxyl- (p < 0.001) porphyrin concentrations were significantly associated with AU but not with PDD-NOS. No differences were found between NT and AU in urinary Hg levels or in past Hg exposure as determined by fish consumption, number of dental amalgam fillings, or vaccines received. These findings identify disordered porphyrin metabolism as a salient characteristic of autism. Hg exposures were comparable between diagnostic groups, and a porphyrin pattern consistent with that seen in Hg-exposed adults was not apparent.

Urinary Porphyrin Excretion in Neurotypical and Autistic Children

PubMed Central

Woods, James S.; Armel, Sarah E.; Fulton, Denise I.; Allen, Jason; Wessels, Kristine; Simmonds, P. Lynne; Granpeesheh, Doreen; Mumper, Elizabeth; Bradstreet, J. Jeffrey; Echeverria, Diana; Heyer, Nicholas J.; Rooney, James P.K.

2010-01-01

Background Increased urinary concentrations of pentacarboxyl-, precopro- and copro-porphyrins have been associated with prolonged mercury (Hg) exposure in adults, and comparable increases have been attributed to Hg exposure in children with autism (AU). Objectives This study was designed to measure and compare urinary porphyrin concentrations in neurotypical (NT) children and same-age children with autism, and to examine the association between porphyrin levels and past or current Hg exposure in children with autism. Methods This exploratory study enrolled 278 children 2–12 years of age. We evaluated three groups: AU, pervasive developmental disorder-not otherwise specified (PDD-NOS), and NT. Mothers/caregivers provided information at enrollment regarding medical, dental, and dietary exposures. Urine samples from all children were acquired for analyses of porphyrin, creatinine, and Hg. Differences between groups for mean porphyrin and Hg levels were evaluated. Logistic regression analysis was conducted to determine whether porphyrin levels were associated with increased risk of autism. Results Mean urinary porphyrin concentrations are naturally high in young children and decline by as much as 2.5-fold between 2 and 12 years of age. Elevated copro- (p < 0.009), hexacarboxyl- (p < 0.01) and pentacarboxyl- (p < 0.001) porphyrin concentrations were significantly associated with AU but not with PDD-NOS. No differences were found between NT and AU in urinary Hg levels or in past Hg exposure as determined by fish consumption, number of dental amalgam fillings, or vaccines received. Conclusions These findings identify disordered porphyrin metabolism as a salient characteristic of autism. Hg exposures were comparable between diagnostic groups, and a porphyrin pattern consistent with that seen in Hg-exposed adults was not apparent. PMID:20576582

The single transmembrane segment drives self-assembly of OutC and the formation of a functional type II secretion system in Erwinia chrysanthemi.

PubMed

Login, Frédéric H; Shevchik, Vladimir E

2006-11-03

Many pathogenic Gram-negative bacteria secrete toxins and lytic enzymes via a multiprotein complex called the type II secretion system. This system, named Out in Erwinia chrysanthemi, consists of 14 proteins integrated or associated with the two bacterial membranes. OutC, a key player in this process, is probably implicated in the recognition of secreted proteins and signal transduction. OutC possesses a short cytoplasmic sequence, a single transmembrane segment (TMS), and a large periplasmic region carrying a putative PDZ domain. A hydrodynamic study revealed that OutC forms stable dimers of an elongated shape, whereas the PDZ domain adopts a globular shape. Bacterial two-hybrid, cross-linking, and pulldown assays revealed that the self-association of OutC is driven by the TMS, whereas the periplasmic region is dispensable for self-association. Site-directed mutagenesis of the TMS revealed that cooperative interactions between three polar residues located at the same helical face provide adequate stability for OutC self-assembly. An interhelical H-bonding mediated by Gln(29) appears to be the main driving force, and two Arg residues located at the TMS boundaries are essential for the stabilization of OutC oligomers. Stepwise mutagenesis of these residues gradually diminished OutC functionality and self-association ability. The triple OutC mutant R15V/Q29L/R36A became monomeric and nonfunctional. Self-association and functionality of the triple mutant were partially restored by the introduction of a polar residue at an alternative position in the interhelical interface. Thus, the OutC TMS is more than just a membrane anchor; it drives the protein self-association that is essential for formation of a functional secretion system.

Neural Mechanism for Mirrored Self-face Recognition.

PubMed

Sugiura, Motoaki; Miyauchi, Carlos Makoto; Kotozaki, Yuka; Akimoto, Yoritaka; Nozawa, Takayuki; Yomogida, Yukihito; Hanawa, Sugiko; Yamamoto, Yuki; Sakuma, Atsushi; Nakagawa, Seishu; Kawashima, Ryuta

2015-09-01

Self-face recognition in the mirror is considered to involve multiple processes that integrate 2 perceptual cues: temporal contingency of the visual feedback on one's action (contingency cue) and matching with self-face representation in long-term memory (figurative cue). The aim of this study was to examine the neural bases of these processes by manipulating 2 perceptual cues using a "virtual mirror" system. This system allowed online dynamic presentations of real-time and delayed self- or other facial actions. Perception-level processes were identified as responses to only a single perceptual cue. The effect of the contingency cue was identified in the cuneus. The regions sensitive to the figurative cue were subdivided by the response to a static self-face, which was identified in the right temporal, parietal, and frontal regions, but not in the bilateral occipitoparietal regions. Semantic- or integration-level processes, including amodal self-representation and belief validation, which allow modality-independent self-recognition and the resolution of potential conflicts between perceptual cues, respectively, were identified in distinct regions in the right frontal and insular cortices. The results are supportive of the multicomponent notion of self-recognition and suggest a critical role for contingency detection in the co-emergence of self-recognition and empathy in infants. © The Author 2014. Published by Oxford University Press.

Monolithically self-assembled organic active materials integrated with thermoelectric for large spectrum solar harvesting system (Presentation Recording)

NASA Astrophysics Data System (ADS)

Busani, Tito L.; Lavrova, Olga; Erdman, Matthew; Martinez, Julio; Dawson, Noel M.

2015-10-01

We designed and studied a radial junction composed by a photovoltaic and thermoelectric array based on ZnO and CdTe nanowires surrounded by an absorbing organic self assembled in order to efficiently convert UV-visible and IR energy into electricity. The hot anode of n-type ZnO nanowires was fabricated using a thermal process on pre-seeded layer and results to be crystalline with a transmittance up to 92 % and a bandgap of ~ 3.32 eV. Conductivity measurements reveal diode-like behavior for the ZnO nanowires. The organic layer was deposited between the anode and cathode at room temperature The organic layer is composed of oppositely charged porphyrin metal (Zn(II) and Sn(IV)(OH)2) derivatives that are separately water soluble, but when combined form a virtually insoluble solid. The electron donor/acceptor properties (energy levels, band gaps) of the solid can be controlled by the choice of metals and the nature of the peripheral substituent groups of the porphyrin ring. A defect free sub nanometer deposition was achieved using a layer-by-layer deposition onto both ZnO and Bi2Te3 nanowires. The highly thermoelectric structure, which acts as a cold cathode, is composed of p-type Bi2Te3 nanowires with a thermoelectric efficiency (ZT) between ~0.7 to 1, values that are twice that expected for bulk Bi2Te3. Optoelectronic and structural properties shows that with 6 nm of organic layer it is possible to form a 3% efficient solar device with an enhanced thermo electric effected with a temperature gradient of 300 C.

Charge Separation Mechanisms in Ordered Films of Self-Assembled Donor–Acceptor Dyad Ribbons

DOE Office of Scientific and Technical Information (OSTI.GOV)

Logsdon, Jenna L.; Hartnett, Patrick E.; Nelson, Jordan N.

2017-04-21

Orthogonal attachment of polar and nonpolar side-chains to a zinc porphyrin-perylenediimide dyad (ZnP-PDI, 1a) is shown to result in self-assembly of ordered supramolecular ribbons in which the ZnP and PDI molecules form segregated π-stacked columns. Following photoexcitation of the ordered ribbons, ZnP+•-PDI–• radical ion pairs form in <200 fs and subsequently produce a 30 ± 3% yield of free charge carriers that live for about 100 μs. Elongating the side chains on ZnP and PDI in 1b enhances the order of the films, but does not result in an increase in free charge carrier yield. In addition, this yield ismore » independent of temperature, free energy of reaction, and the ZnP-PDI distance in the covalent dyad. These results suggest that the free charge carrier yield in this system is not limited by a bound charge transfer (CT) state or promoted by a vibronically hot CT state. Instead, it is likely that π-stacking of the segregated donors and acceptors within the ribbons results in delocalization of the charges following photoexcitation, allowing them to overcome Coulombic attraction and generate free charge carriers.« less

Peptide-oligonucleotide conjugates as nanoscale building blocks for assembly of an artificial three-helix protein mimic

NASA Astrophysics Data System (ADS)

Lou, Chenguang; Martos-Maldonado, Manuel C.; Madsen, Charlotte S.; Thomsen, Rasmus P.; Midtgaard, Søren Roi; Christensen, Niels Johan; Kjems, Jørgen; Thulstrup, Peter W.; Wengel, Jesper; Jensen, Knud J.

2016-07-01

Peptide-based structures can be designed to yield artificial proteins with specific folding patterns and functions. Template-based assembly of peptide units is one design option, but the use of two orthogonal self-assembly principles, oligonucleotide triple helix and a coiled coil protein domain formation have never been realized for de novo protein design. Here, we show the applicability of peptide-oligonucleotide conjugates for self-assembly of higher-ordered protein-like structures. The resulting nano-assemblies were characterized by ultraviolet-melting, gel electrophoresis, circular dichroism (CD) spectroscopy, small-angle X-ray scattering and transmission electron microscopy. These studies revealed the formation of the desired triple helix and coiled coil domains at low concentrations, while a dimer of trimers was dominating at high concentration. CD spectroscopy showed an extraordinarily high degree of α-helicity for the peptide moieties in the assemblies. The results validate the use of orthogonal self-assembly principles as a paradigm for de novo protein design.

Watching Nanoscale Self-Assembly Kinetics of Gold Prisms in Liquids

NASA Astrophysics Data System (ADS)

Kim, Juyeong; Ou, Zihao; Jones, Matthew R.; Chen, Qian

We use liquid-phase transmission electron microscopy to watch self-assembly of gold triangular prisms into polymer-like structures. The in situ dynamics monitoring enabled by liquid-phase transmission electron microscopy, single nanoparticle tracking, and the marked conceptual similarity between molecular reactions and nanoparticle self-assembly combined elucidate the following mechanistic understanding: a step-growth polymerization based assembly statistics, kinetic pathways sampling particle curvature dependent energy minima and their interconversions, and directed assembly into polymorphs (linear or cyclic chains) through in situ modulation of the prism bonding geometry. Our study bridges the constituent kinetics on the molecular and nanoparticle length scales, which enriches the design rules in directed self-assembly of anisotropic nanoparticles.

Student Learning about Biomolecular Self-Assembly Using Two Different External Representations

PubMed Central

Höst, Gunnar E.; Larsson, Caroline; Olson, Arthur; Tibell, Lena A. E.

2013-01-01

Self-assembly is the fundamental but counterintuitive principle that explains how ordered biomolecular complexes form spontaneously in the cell. This study investigated the impact of using two external representations of virus self-assembly, an interactive tangible three-dimensional model and a static two-dimensional image, on student learning about the process of self-assembly in a group exercise. A conceptual analysis of self-assembly into a set of facets was performed to support study design and analysis. Written responses were collected in a pretest/posttest experimental design with 32 Swedish university students. A quantitative analysis of close-ended items indicated that the students improved their scores between pretest and posttest, with no significant difference between the conditions (tangible model/image). A qualitative analysis of an open-ended item indicated students were unfamiliar with self-assembly prior to the study. Students in the tangible model condition used the facets of self-assembly in their open-ended posttest responses more frequently than students in the image condition. In particular, it appears that the dynamic properties of the tangible model may support student understanding of self-assembly in terms of the random and reversible nature of molecular interactions. A tentative difference was observed in response complexity, with more multifaceted responses in the tangible model condition. PMID:24006395

Student learning about biomolecular self-assembly using two different external representations.

PubMed

Höst, Gunnar E; Larsson, Caroline; Olson, Arthur; Tibell, Lena A E

2013-01-01

Self-assembly is the fundamental but counterintuitive principle that explains how ordered biomolecular complexes form spontaneously in the cell. This study investigated the impact of using two external representations of virus self-assembly, an interactive tangible three-dimensional model and a static two-dimensional image, on student learning about the process of self-assembly in a group exercise. A conceptual analysis of self-assembly into a set of facets was performed to support study design and analysis. Written responses were collected in a pretest/posttest experimental design with 32 Swedish university students. A quantitative analysis of close-ended items indicated that the students improved their scores between pretest and posttest, with no significant difference between the conditions (tangible model/image). A qualitative analysis of an open-ended item indicated students were unfamiliar with self-assembly prior to the study. Students in the tangible model condition used the facets of self-assembly in their open-ended posttest responses more frequently than students in the image condition. In particular, it appears that the dynamic properties of the tangible model may support student understanding of self-assembly in terms of the random and reversible nature of molecular interactions. A tentative difference was observed in response complexity, with more multifaceted responses in the tangible model condition.

Opal-like Multicolor Appearance of Self-Assembled Photonic Array.

PubMed

Arnon, Zohar A; Pinotsi, Dorothea; Schmidt, Matthias; Gilead, Sharon; Guterman, Tom; Sadhanala, Aditya; Ahmad, Shahab; Levin, Aviad; Walther, Paul; Kaminski, Clemens F; Fändrich, Marcus; Kaminski Schierle, Gabriele S; Adler-Abramovich, Lihi; Shimon, Linda J W; Gazit, Ehud

2018-06-20

Molecular self-assembly of short peptide building blocks leads to the formation of various material architectures that may possess unique physical properties. Recent studies had confirmed the key role of biaromaticity in peptide self-assembly, with the diphenylalanine (FF) structural family as an archetypal model. Another significant direction in the molecular engineering of peptide building blocks is the use of fluorenylmethoxycarbonyl (Fmoc) modification, which promotes the assembly process and may result in nanostructures with distinctive features and macroscopic hydrogel with supramolecular features and nanoscale order. Here, we explored the self-assembly of the protected, noncoded fluorenylmethoxycarbonyl-β,β-diphenyl-Ala-OH (Fmoc-Dip) amino acid. This process results in the formation of elongated needle-like crystals with notable aromatic continuity. By altering the assembly conditions, arrays of spherical particles were formed that exhibit strong light scattering. These arrays display vivid coloration, strongly resembling the appearance of opal gemstones. However, unlike the Rayleigh scattering effect produced by the arrangement of opal, the described optical phenomenon is attributed to Mie scattering. Moreover, by controlling the solution evaporation rate, i.e., the assembly kinetics, we were able to manipulate the resulting coloration. This work demonstrates a bottom-up approach, utilizing self-assembly of a protected amino acid minimal building block, to create arrays of organic, light-scattering colorful surfaces.

Effects of Dimers on Cooperation in the Spatial Prisoner's Dilemma Game

NASA Astrophysics Data System (ADS)

Li, Hai-Hong; Cheng, Hong-Yan; Dai, Qiong-Lin; Ju, Ping; Zhang, Mei; Yang, Jun-Zhong

2011-11-01

We investigate the evolutionary prisoner's dilemma game in structured populations by introducing dimers, which are defined as that two players in each dimer always hold a same strategy. We find that influences of dimers on cooperation depend on the type of dimers and the population structure. For those dimers in which players interact with each other, the cooperation level increases with the number of dimers though the cooperation improvement level depends on the type of network structures. On the other hand, the dimers, in which there are not mutual interactions, will not do any good to the cooperation level in a single community, but interestingly, will improve the cooperation level in a population with two communities. We explore the relationship between dimers and self-interactions and find that the effects of dimers are similar to that of self-interactions. Also, we find that the dimers, which are established over two communities in a multi-community network, act as one type of interaction through which information between communities is communicated by the requirement that two players in a dimer hold a same strategy.

Controlling Self-Assembly in Al(110) Homoepitaxy

NASA Astrophysics Data System (ADS)

Tiwary, Yogesh; Fichthorn, Kristen

2010-03-01

Homoepitaxial growth on Al(110) exhibits nanoscale self-assembly into huts with well-defined (100) and (111) facets [1]. Although some of the diffusion mechanisms underlying this kinetic self-assembly were identified and incorporated into a two-dimensional model [2], we used density-functional theory (DFT) to identify many other mechanisms that are needed to describe the three-dimensional assembly seen experimentally [3]. We developed a three-dimensional kinetic Monte Carlo (KMC) model of Al(110) homoepitaxy. The inputs to the model were obtained from DFT [3,4]. Our model is in agreement with experimentally observed trends for this system. We used KMC to predict self-assembly under various growth conditions. To achieve precise placement of Al nanohuts, we simulated thermal-field-directed assembly [5]. Our results indicate that this technique can be used to create uniform arrays of nanostructures. [1] F. Buatier de Mongeot, W. Zhu, A. Molle, R. Buzio, C. Boragno, U. Valbusa, E. Wang, and Z. Zhang, Phys. Rev. Lett. 91, 016102 (2003). [2] W. Zhu, F. Buatier de Mongeot, U. Valbusa, E. G. Wang, and Z. Y. Zhang, Phys. Rev. Lett. 92, 106102 (2004). [3] Y. Tiwary and K. A. Fichthorn, submitted to Phys. Rev. B. [4] Y. Tiwary and K. A. Fichthorn, Phys. Rev. B 78, 205418 (2008). [5] C. Zhang and R. Kalyanaraman, Appl. Phys. Lett. 83, 4827 (2003).

Mechanisms of kinetic trapping in self-assembly and phase transformation

PubMed Central

Hagan, Michael F.; Elrad, Oren M.; Jack, Robert L.

2011-01-01

In self-assembly processes, kinetic trapping effects often hinder the formation of thermodynamically stable ordered states. In a model of viral capsid assembly and in the phase transformation of a lattice gas, we show how simulations in a self-assembling steady state can be used to identify two distinct mechanisms of kinetic trapping. We argue that one of these mechanisms can be adequately captured by kinetic rate equations, while the other involves a breakdown of theories that rely on cluster size as a reaction coordinate. We discuss how these observations might be useful in designing and optimising self-assembly reactions. PMID:21932884

Electrodynamic tailoring of self-assembled three-dimensional electrospun constructs

NASA Astrophysics Data System (ADS)

Reis, Tiago C.; Correia, Ilídio J.; Aguiar-Ricardo, Ana

2013-07-01

The rational design of three-dimensional electrospun constructs (3DECs) can lead to striking topographies and tailored shapes of electrospun materials. This new generation of materials is suppressing some of the current limitations of the usual 2D non-woven electrospun fiber mats, such as small pore sizes or only flat shaped constructs. Herein, we pursued an explanation for the self-assembly of 3DECs based on electrodynamic simulations and experimental validation. We concluded that the self-assembly process is driven by the establishment of attractive electrostatic forces between the positively charged aerial fibers and the already collected ones, which tend to acquire a negatively charged network oriented towards the nozzle. The in situ polarization degree is strengthened by higher amounts of clustered fibers, and therefore the initial high density fibrous regions are the preliminary motifs for the self-assembly mechanism. As such regions increase their in situ polarization electrostatic repulsive forces will appear, favoring a competitive growth of these self-assembled fibrous clusters. Highly polarized regions will evidence higher distances between consecutive micro-assembled fibers (MAFs). Different processing parameters - deposition time, electric field intensity, concentration of polymer solution, environmental temperature and relative humidity - were evaluated in an attempt to control material's design.The rational design of three-dimensional electrospun constructs (3DECs) can lead to striking topographies and tailored shapes of electrospun materials. This new generation of materials is suppressing some of the current limitations of the usual 2D non-woven electrospun fiber mats, such as small pore sizes or only flat shaped constructs. Herein, we pursued an explanation for the self-assembly of 3DECs based on electrodynamic simulations and experimental validation. We concluded that the self-assembly process is driven by the establishment of attractive

Active turbulence in a gas of self-assembled spinners

PubMed Central

Kokot, Gašper; Das, Shibananda; Winkler, Roland G.; Aranson, Igor S.; Snezhko, Alexey

2017-01-01

Colloidal particles subject to an external periodic forcing exhibit complex collective behavior and self-assembled patterns. A dispersion of magnetic microparticles confined at the air–liquid interface and energized by a uniform uniaxial alternating magnetic field exhibits dynamic arrays of self-assembled spinners rotating in either direction. Here, we report on experimental and simulation studies of active turbulence and transport in a gas of self-assembled spinners. We show that the spinners, emerging as a result of spontaneous symmetry breaking of clock/counterclockwise rotation of self-assembled particle chains, generate vigorous vortical flows at the interface. An ensemble of spinners exhibits chaotic dynamics due to self-generated advection flows. The same-chirality spinners (clockwise or counterclockwise) show a tendency to aggregate and form dynamic clusters. Emergent self-induced interface currents promote active diffusion that could be tuned by the parameters of the external excitation field. Furthermore, the erratic motion of spinners at the interface generates chaotic fluid flow reminiscent of 2D turbulence. Our work provides insight into fundamental aspects of collective transport in active spinner materials and yields rules for particle manipulation at the microscale. PMID:29158382

Active turbulence in a gas of self-assembled spinners

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kokot, Gasper; Das, Shibananda; Winkler, Roland G.

Colloidal particles subject to an external periodic forcing exhibit complex collective behavior and self-assembled patterns. A dispersion of magnetic microparticles confined at the air-liquid interface and energized by a uniform uniaxial alternating magnetic field exhibits dynamic arrays of self-assembled spinners rotating in either direction. Here, we report on experimental and simulation studies of active turbulence and transport in a gas of self-assembled spinners. We show that the spinners, emerging as a result of spontaneous symmetry breaking of clock/counterclockwise rotation of self-assembled particle chains, generate vigorous vortical flows at the interface. An ensemble of spinners exhibits chaotic dynamics due to self-generatedmore » advection flows. The same-chirality spinners (clockwise or counterclock-wise) show a tendency to aggregate and form dynamic clusters. Emergent self-induced interface currents promote active diffusion that could be tuned by the parameters of the external excitation field. Furthermore, the erratic motion of spinners at the interface generates chaotic fluid flow reminiscent of 2D turbulence. As a result, our work provides insight into fundamental aspects of collective transport in active spinner materials and yields rules for particle manipulation at the microscale.« less

Active turbulence in a gas of self-assembled spinners

DOE PAGES

Kokot, Gasper; Das, Shibananda; Winkler, Roland G.; ...

2017-11-20

Colloidal particles subject to an external periodic forcing exhibit complex collective behavior and self-assembled patterns. A dispersion of magnetic microparticles confined at the air-liquid interface and energized by a uniform uniaxial alternating magnetic field exhibits dynamic arrays of self-assembled spinners rotating in either direction. Here, we report on experimental and simulation studies of active turbulence and transport in a gas of self-assembled spinners. We show that the spinners, emerging as a result of spontaneous symmetry breaking of clock/counterclockwise rotation of self-assembled particle chains, generate vigorous vortical flows at the interface. An ensemble of spinners exhibits chaotic dynamics due to self-generatedmore » advection flows. The same-chirality spinners (clockwise or counterclock-wise) show a tendency to aggregate and form dynamic clusters. Emergent self-induced interface currents promote active diffusion that could be tuned by the parameters of the external excitation field. Furthermore, the erratic motion of spinners at the interface generates chaotic fluid flow reminiscent of 2D turbulence. As a result, our work provides insight into fundamental aspects of collective transport in active spinner materials and yields rules for particle manipulation at the microscale.« less

A randomised controlled trial of face to face versus pure online self-help cognitive behavioural treatment for perfectionism.

PubMed

Egan, Sarah J; van Noort, Emily; Chee, Abby; Kane, Robert T; Hoiles, Kimberley J; Shafran, Roz; Wade, Tracey D

2014-12-01

Previous research has shown cognitive-behavioural treatment (CBT) to be effective in reducing perfectionism. The present study investigated the efficacy of two formats of CBT for perfectionism (CBT-P), face-to-face and pure online self-help, in reducing perfectionism and associated psychological symptoms. Participants were randomly allocated to face-to-face CBT-P (n = 18), pure online self-help CBT-P (n = 16), or a waitlist control period (n = 18). There was no significant change for the waitlist group on any of the outcome measures at the end of treatment. Both the face-to-face and pure online self-help groups reported significant reductions at the end of treatment for the perfectionism variables which were maintained at the 6-month follow-up. The face-to-face group also reported significant reductions over this time in depression, anxiety, and stress, and a significant pre-post increase in self-esteem, all of which were maintained at the 6-month follow-up. In contrast, the pure online self-help group showed no significant changes on these outcomes. The face-to-face group was statistically superior to the pure online self-help group at follow-up on the perfectionism measures, concern over mistakes and personal standards. The results show promising evidence for CBT for perfectionism, especially when offered face to face, where sustained benefit across a broad range of outcomes can be expected. Crown Copyright © 2014. Published by Elsevier Ltd. All rights reserved.

Rapid self-assembly of DNA on a microfluidic chip

PubMed Central

Zheng, Yao; Footz, Tim; Manage, Dammika P; Backhouse, Christopher James

2005-01-01

Background DNA self-assembly methods have played a major role in enabling methods for acquiring genetic information without having to resort to sequencing, a relatively slow and costly procedure. However, even self-assembly processes tend to be very slow when they rely upon diffusion on a large scale. Miniaturisation and integration therefore hold the promise of greatly increasing this speed of operation. Results We have developed a rapid method for implementing the self-assembly of DNA within a microfluidic system by electrically extracting the DNA from an environment containing an uncharged denaturant. By controlling the parameters of the electrophoretic extraction and subsequent analysis of the DNA we are able to control when the hybridisation occurs as well as the degree of hybridisation. By avoiding off-chip processing or long thermal treatments we are able to perform this hybridisation rapidly and can perform hybridisation, sizing, heteroduplex analysis and single-stranded conformation analysis within a matter of minutes. The rapidity of this analysis allows the sampling of transient effects that may improve the sensitivity of mutation detection. Conclusions We believe that this method will aid the integration of self-assembly methods upon microfluidic chips. The speed of this analysis also appears to provide information upon the dynamics of the self-assembly process. PMID:15717935

Polymeric amphiphile branching leads to rare nanodisc shaped planar self-assemblies.

PubMed

Qu, Xiaozhong; Omar, Leila; Le, Thi Bich Hang; Tetley, Laurence; Bolton, Katherine; Chooi, Kar Wai; Wang, Wei; Uchegbu, Ijeoma F

2008-09-16

Self-assembly is fundamental to the biological function of cells and the fabrication of nanomaterials. However, the origin of the shape of various self-assemblies, such as the shape of cells, is not altogether clear. Polymeric, oligomeric, or low molecular weight amphiphiles are a rich source of nanomaterials, and controlling their self-assembly is the route to tailored nanosystems with specific functionalities. Here, we provide direct evidence that a particular molecular architecture, polymeric branching, leads to a rare form of self-assembly, the planar nanodisc. Cholesterol containing self-assemblies formed from amphiphilic linear or branched cetyl poly(ethylenimine) (Mn approximately 1000 Da) or amphiphilic cetyl poly(propylenimine) dendrimer derivatives (Mn approximately 2000 Da) show that branching, by reducing the hydrophilic headgroup area, alters the shape of the self-assemblies transforming closed 60 nm spherical bilayer vesicles to rare 50 nm x 10 nm planar bilayer discs. Increasing the hydrophilic headgroup area, by the inclusion of methoxy poly(ethylene glycol) moieties into the amphiphilic headgroup, transforms the planar discs to 100 nm spherical bilayer vesicles. This study provides insight into the key role played by molecular shape on molecular self-organization into rare nanodiscs.

Functional dissociation of the left and right fusiform gyrus in self-face recognition.

PubMed

Ma, Yina; Han, Shihui

2012-10-01

It is well known that the fusiform gyrus is engaged in face perception, such as the processes of face familiarity and identity. However, the functional role of the fusiform gyrus in face processing related to high-level social cognition remains unclear. The current study assessed the functional role of individually defined fusiform face area (FFA) in the processing of self-face physical properties and self-face identity. We used functional magnetic resonance imaging to monitor neural responses to rapidly presented face stimuli drawn from morph continua between self-face (Morph 100%) and a gender-matched friend's face (Morph 0%) in a face recognition task. Contrasting Morph 100% versus Morph 60% that differed in self-face physical properties but were both recognized as the self uncovered neural activity sensitive to self-face physical properties in the left FFA. Contrasting Morphs 50% that were recognized as the self versus a friend on different trials revealed neural modulations associated with self-face identity in the right FFA. Moreover, the right FFA activity correlated with the frequency of recognizing Morphs 50% as the self. Our results provide evidence for functional dissociations of the left and right FFAs in the representations of self-face physical properties and self-face identity. Copyright © 2011 Wiley Periodicals, Inc.

Cyclic Bis-porphyrin-Based Flexible Molecular Containers: Controlling Guest Arrangements and Supramolecular Catalysis by Tuning Cavity Size.

PubMed

Mondal, Pritam; Sarkar, Sabyasachi; Rath, Sankar Prasad

2017-05-23

Three cyclic zinc(II) bis-porphyrins (CB) with highly flexible linkers are employed as artificial molecular containers that efficiently encapsulate/coordinate various aromatic aldehydes within their cavities. Interestingly, the arrangements of guests and their reactivity inside the molecular clefts are significantly influenced by the cavity size of the cyclic containers. In the presence of polycyclic aromatic aldehydes, such as 3-formylperylene, as a guest, the cyclic bis-porphyrin host with a smaller cavity (CB1) forms a 1:1 sandwich complex. Upon slightly increasing the spacer length and thereby the cavity size, the cyclic host (CB2) encapsulates two molecules of 3-formylperylene that are also stacked together due to strong π-π interactions between them and CH-π interactions with the porphyrin rings. However, in the cyclic host (CB3) with an even larger cavity, two metal centers of the bis-porphyrin axially coordinate two molecules of 3-formylperylene within its cavity. Different arrangements of guest inside the cyclic bis-porphyrin hosts are investigated by using UV/Vis, ESI-MS, and 1 H NMR spectroscopy, along with X-ray structure determination of the host-guest complexes. Moreover, strong binding of guests within the cyclic bis-porphyrin hosts support the robust nature of the host-guest assemblies in solution. Such preferential binding of the bis-porphyrinic cavity towards aromatic aldehydes through encapsulation/coordination has been employed successfully to catalyze the Knoevenagel condensation of a series of polycyclic aldehydes with active methylene compounds (such as Meldrum's acid and 1, 3-dimethylbarbituric acid) under ambient conditions. Interestingly, the yields of the condensed products significantly increase upon increasing spacer lengths of the cyclic bis-porphyrins because more substrates can then be encapsulated within the cavity. Such controllable cavity size of the cyclic containers has profound implications for constructing highly

Photoinduced oxidation of a water-soluble manganese(III) porphyrin

PubMed Central

Maliyackel, Anthony C.; Otvos, John W.; Spreer, Larry O.; Calvin, Melvin

1986-01-01

The photoinduced oxidation of tetra(N-methyl-4-pyridyl)porphyrinmanganese(III) has been achieved in homogeneous solution. The manganese porphyrin was used as an electron donor in a three-component system with tris-(2,2′-bipyridine)ruthenium(II) as the photosensitizer and chloropentaamminecobalt(III) as the electron acceptor. The photooxidized manganese porphyrin is unstable in aqueous solution, reverting to the starting manganese(III) porphyrin. The oxidation of manganese(III) porphyrin and the subsequent reduction of the oxidized porphyrin can be cycled repeatedly. PMID:16593699

Self-assembled liposomal nanoparticles in photodynamic therapy

PubMed Central

Sadasivam, Magesh; Avci, Pinar; Gupta, Gaurav K.; Lakshmanan, Shanmugamurthy; Chandran, Rakkiyappan; Huang, Ying-Ying; Kumar, Raj; Hamblin, Michael R.

2013-01-01

Photodynamic therapy (PDT) employs the combination of non-toxic photosensitizers (PS) together with harmless visible light of the appropriate wavelength to produce reactive oxygen species that kill unwanted cells. Because many PS are hydrophobic molecules prone to aggregation, numerous drug delivery vehicles have been tested to solubilize these molecules, render them biocompatible and enhance the ease of administration after intravenous injection. The recent rise in nanotechnology has markedly expanded the range of these nanoparticulate delivery vehicles beyond the well-established liposomes and micelles. Self-assembled nanoparticles are formed by judicious choice of monomer building blocks that spontaneously form a well-oriented 3-dimensional structure that incorporates the PS when subjected to the appropriate conditions. This self-assembly process is governed by a subtle interplay of forces on the molecular level. This review will cover the state of the art in the preparation and use of self-assembled liposomal nanoparticles within the context of PDT. PMID:24348377

Integrating DNA strand-displacement circuitry with DNA tile self-assembly

PubMed Central

Zhang, David Yu; Hariadi, Rizal F.; Choi, Harry M.T.; Winfree, Erik

2013-01-01

DNA nanotechnology has emerged as a reliable and programmable way of controlling matter at the nanoscale through the specificity of Watson–Crick base pairing, allowing both complex self-assembled structures with nanometer precision and complex reaction networks implementing digital and analog behaviors. Here we show how two well-developed frameworks, DNA tile self-assembly and DNA strand-displacement circuits, can be systematically integrated to provide programmable kinetic control of self-assembly. We demonstrate the triggered and catalytic isothermal self-assembly of DNA nanotubes over 10 μm long from precursor DNA double-crossover tiles activated by an upstream DNA catalyst network. Integrating more sophisticated control circuits and tile systems could enable precise spatial and temporal organization of dynamic molecular structures. PMID:23756381

Balancing the intermolecular forces in peptide amphiphiles for controlling self-assembly transitions.

PubMed

Buettner, C J; Wallace, A J; Ok, S; Manos, A A; Nicholl, M J; Ghosh, A; Tweedle, M F; Goldberger, J E

2017-06-21

While the influence of alkyl chain length and headgroup size on self-assembly behaviour has been well-established for simple surfactants, the rational control over the pH- and concentration-dependent self-assembly behaviour in stimuli responsive peptides remains an elusive goal. Here, we show that different amphiphilic peptides can have similar self-assembly phase diagrams, providing the relative strengths of the attractive and repulsive forces are balanced. Using palmitoyl-YYAAEEEEK(DO3A:Gd)-NH 2 and palmitoyl-YAAEEEEK(DO3A:Gd)-NH 2 as controls, we show that reducing hydrophobic attractive forces through fewer methylene groups in the alkyl chain will lead to a similar self-assembly phase diagram as increasing the electrostatic repulsive forces via the addition of a glutamic acid residue. These changes allow creation of self-assembled MRI vehicles with slightly different micelle and nanofiber diameters but with minimal changes in the spin-lattice T 1 relaxivity. These findings reveal a powerful strategy to design self-assembled vehicles with different sizes but with similar self-assembly profiles.

Modeling Protein Self Assembly

ERIC Educational Resources Information Center

Baker, William P.; Jones, Carleton Buck; Hull, Elizabeth

2004-01-01

Understanding the structure and function of proteins is an important part of the standards-based science curriculum. Proteins serve vital roles within the cell and malfunctions in protein self assembly are implicated in degenerative diseases. Experience indicates that this topic is a difficult one for many students. We have found that the concept…

Self-Assembly of Supramolecular Composites under Cylindrical Confinement

NASA Astrophysics Data System (ADS)

Bai, Peter; Thorkelsson, Kari; Ercius, Peter; Xu, Ting

2014-03-01

Block copolymer (BCP) or BCP-based supramolecules are useful platforms to direct nanoparticle (NP) assemblies. However, the variety of NP assemblies is rather limited in comparison to those shown by DNA-guided approach. By subjecting supramolecular nanocomposites to 2-D cylindrical confinement afforded by anodic aluminum oxide membranes, a range of new NP assemblies such as stacked rings, and single and double helices can be readily obtained, as confirmed by TEM and TEM tomography. At low NP loadings (3 v%), the nanostructure conforms to the supramolecule morphology. However, at higher NP loadings (6-9 v%), the nanostructure deviates significantly from the morphology of supramolecular nanocomposites in bulk or in thin film, suggesting that frustrated NP packing, in addition to simple supramolecule templating, may play a significant role in the self-assembly process. The present studies demonstrate that 2-D confinement can be an effective means to tailor self-assembled NP structures and may open further opportunities to manipulate the macroscopic properties of NP assemblies.

Intracellular formation of "undisruptable" dimers of inducible nitric oxide synthase.

PubMed

Kolodziejski, Pawel J; Rashid, Mohammad B; Eissa, N Tony

2003-11-25

Overproduction of nitric oxide (NO) by inducible NO synthase (iNOS) has been implicated in the pathogenesis of many diseases. iNOS is active only as a homodimer. Dimerization of iNOS represents a potentially critical target for therapeutic intervention. In this study, we show that intracellular iNOS forms dimers that are "undisruptable" by boiling, denaturants, or reducing agents. Undisruptable (UD) dimers are clearly distinguishable from the easily dissociated dimers formed by iNOS in vitro. UD dimers do not form in Escherichia coli-expressed iNOS and could not be assembled in vitro, which suggests that an in vivo cellular process is required for their formation. iNOS UD dimers are not affected by intracellular depletion of H4B. However, the mutation of Cys-115 (critical for zinc binding) greatly affects the formation of UD dimers. This study reveals insight into the mechanisms of in vivo iNOS dimer formation. UD dimers represent a class of iNOS dimers that had not been suspected. This unanticipated finding revises our understanding of the mechanisms of iNOS dimerization and lays the groundwork for future studies aimed at modulating iNOS activity in vivo.

Nickel porphyrins for memory optical applications

DOEpatents

Shelnutt, John A.; Jia, Songling; Medforth, Craig; Holten, Dewey; Nelson, Nora Y.; Smith, Kevin M.

2000-01-01

The present invention relates to a nickel-porphyrin derivative in a matrix, the nickel-porphyrin derivative comprising at least two conformational isomers, a lower-energy-state conformer and a higher-energy-state conformer, such that when the higher-energy-state conformer is generated from the lower-energy-state conformer following absorption of a photon of suitable energy, the time to return to the lower-energy-state conformer is greater than 40 nanoseconds at approximately room temperature. The nickel-porphyrin derivative is useful in optical memory applications.

Self-assembling peptide-based building blocks in medical applications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Acar, Handan; Srivastava, Samanvaya; Chung, Eun Ji

Peptides and peptide-conjugates, comprising natural and synthetic building blocks, are an increasingly popular class of biomaterials. Self-assembled nanostructures based on peptides and peptide-conjugates offer advantages such as precise selectivity and multifunctionality that can address challenges and limitations in the clinic. In this review article, we discuss recent developments in the design and self-assembly of various nanomaterials based on peptides and peptide-conjugates for medical applications, and categorize them into two themes based on the driving forces of molecular self-assembly. First, we present the self-assembled nanostructures driven by the supramolecular interactions between the peptides, with or without the presence of conjugates. Themore » studies where nanoassembly is driven by the interactions between the conjugates of peptide-conjugates are then presented. Particular emphasis is given to in vivo studies focusing on therapeutics, diagnostics, immune modulation and regenerative medicine. Finally, challenges and future perspectives are presented.« less

In Silico Study, Synthesis, and Cytotoxic Activities of Porphyrin Derivatives

PubMed Central

Kurniawan, Fransiska; Miura, Youhei; Kartasasmita, Rahmana Emran; Mutalib, Abdul

2018-01-01

Five known porphyrins, 5,10,15,20-tetrakis(p-tolyl)porphyrin (TTP), 5,10,15,20-tetrakis(p-bromophenyl)porphyrin (TBrPP), 5,10,15,20-tetrakis(p-aminophenyl)porphyrin (TAPP), 5,10,15-tris(tolyl)-20-mono(p-nitrophenyl)porphyrin (TrTMNP), 5,10,15-tris(tolyl)-20-mono(p-aminophenyl)porphyrin (TrTMAP), and three novel porphyrin derivatives, 5,15-di-[bis(3,4-ethylcarboxymethylenoxy)phenyl]-10,20-di(p-tolyl)porphyrin (DBECPDTP), 5,10-di-[bis(3,4-ethylcarboxymethylenoxy)phenyl]-15,20-di-(methylpyrazole-4-yl)porphyrin (cDBECPDPzP), 5,15-di-[bis(3,4-ethylcarboxymethylenoxy)phenyl]-10,20-di-(methylpyrazole-4-yl)porphyrin (DBECPDPzP), were used to study their interaction with protein targets (in silico study), and were synthesized. Their cytotoxic activities against cancer cell lines were tested using 3-(4,5-dimetiltiazol-2-il)-2,5-difeniltetrazolium bromide (MTT) assay. The interaction of porphyrin derivatives with carbonic anhydrase IX (CAIX) and REV-ERBβ proteins were studied by molecular docking and molecular dynamic simulation. In silico study results reveal that DBECPDPzP and TrTMNP showed the highest binding interaction with REV- ERBβ and CAIX, respectively, and both complexes of DBECPDPzP-REV-ERBβ and TrTMNP-CAIX showed good and comparable stability during molecular dynamic simulation. The studied porphyrins have selective growth inhibition activities against tested cancer cells and are categorized as marginally active compounds based on their IC50. PMID:29361701

Graphene oxide vs. reduced graphene oxide as carbon support in porphyrin peroxidase biomimetic nanomaterials.

PubMed

Socaci, C; Pogacean, F; Biris, A R; Coros, M; Rosu, M C; Magerusan, L; Katona, G; Pruneanu, S

2016-02-01

The paper describes the preparation of supramolecular assemblies of tetrapyridylporphyrin (TPyP) and its metallic complexes with graphene oxide (GO) and thermally reduced graphene oxide (TRGO). The two carbon supports are introducing different characteristics in the absorption spectra of the investigated nanocomposites. Raman spectroscopy shows that the absorption of iron-tetrapyridylporphyrin is more efficient on GO than TRGO, suggesting that oxygen functionalities are involved in the non-covalent interaction between the iron-porphyrin and graphene. The biomimetic peroxidase activity is investigated and the two iron-containing composites exhibit a better catalytic activity than each component of the assembly, and their cobalt and manganese homologues, respectively. The main advantages of this work include the demonstration of graphene oxide as a very good support for graphene-based nanomaterials with peroxidase-like activity (K(M)=0.292 mM), the catalytic activity being observed even with very small amounts of porphyrins (the TPyP:graphene ratio=1:50). Its potential application in the detection of lipophilic antioxidants (vitamin E can be measured in the 10(-5)-10(-4) M range) is also shown. Copyright © 2015 Elsevier B.V. All rights reserved.

Self-Assembled Materials Made from Functional Recombinant Proteins.

PubMed

Jang, Yeongseon; Champion, Julie A

2016-10-18

Proteins are potent molecules that can be used as therapeutics, sensors, and biocatalysts with many advantages over small-molecule counterparts due to the specificity of their activity based on their amino acid sequence and folded three-dimensional structure. However, they also have significant limitations in their stability, localization, and recovery when used in soluble form. These opportunities and challenges have motivated the creation of materials from such functional proteins in order to protect and present them in a way that enhances their function. We have designed functional recombinant fusion proteins capable of self-assembling into materials with unique structures that maintain or improve the functionality of the protein. Fusion of either a functional protein or an assembly domain to a leucine zipper domain makes the materials design strategy modular, based on the high affinity between leucine zippers. The self-assembly domains, including elastin-like polypeptides (ELPs) and defined-sequence random coil polypeptides, can be fused with a leucine zipper motif in order to promote assembly of the fusion proteins into larger structures upon specific stimuli such as temperature and ionic strength. Fusion of other functional domains with the counterpart leucine zipper motif endows the self-assembled materials with protein-specific functions such as fluorescence or catalytic activity. In this Account, we describe several examples of materials assembled from functional fusion proteins as well as the structural characterization, functionality, and understanding of the assembly mechanism. The first example is zipper fusion proteins containing ELPs that assemble into particles when introduced to a model extracellular matrix and subsequently disassemble over time to release the functional protein for drug delivery applications. Under different conditions, the same fusion proteins can self-assemble into hollow vesicles. The vesicles display a functional protein on

From porphyrins to pyrphyrins: adsorption study and metalation of a molecular catalyst on Au(111)

NASA Astrophysics Data System (ADS)

Mette, Gerson; Sutter, Denys; Gurdal, Yeliz; Schnidrig, Stephan; Probst, Benjamin; Iannuzzi, Marcella; Hutter, Jürg; Alberto, Roger; Osterwalder, Jürg

2016-04-01

The molecular ligand pyrphyrin, a tetradentate bipyridine based macrocycle, represents an interesting but widely unexplored class of molecules. It resembles the well-known porphyrin, but consists of pyridyl subunits instead of pyrroles. Metal complexes based on pyrphyrin ligands have recently shown promise as water reduction catalysts in homogeneous photochemical water splitting reactions. In this study, the adsorption and metalation of pyrphyrin on a single crystalline Au(111) surface is investigated in an ultrahigh vacuum by means of scanning tunneling microscopy, low-energy electron diffraction, X-ray photoelectron spectroscopy and density functional theory. Pyrphyrin coverages of approximately one monolayer and less are obtained by sublimation of the molecules on the substrate kept at room temperature. The molecules self-assemble in two distinct phases of long-range molecular ordering depending on the surface coverage. The deposition of cobalt metal and subsequent annealing lead to the formation of Co-ligated pyrphyrin molecules accompanied by a pronounced change of the molecular self-assembly. Electronic structure calculations taking the herringbone reconstruction of Au(111) into account show that the molecules are physisorbed, but preferred adsorption sites are identified where Co and the N atoms of the two terminal cyano groups are optimally coordinated to the surface Au atoms. An intermediate state of the metalation reaction is observed and the reaction steps for the Co metalation of pyrphyrin molecules on Au(111) are established in a joint experimental and computational effort.The molecular ligand pyrphyrin, a tetradentate bipyridine based macrocycle, represents an interesting but widely unexplored class of molecules. It resembles the well-known porphyrin, but consists of pyridyl subunits instead of pyrroles. Metal complexes based on pyrphyrin ligands have recently shown promise as water reduction catalysts in homogeneous photochemical water splitting

Nanosystem self-assembly pathways discovered via all-atom multiscale analysis.

PubMed

Pankavich, Stephen D; Ortoleva, Peter J

2012-07-26

We consider the self-assembly of composite structures from a group of nanocomponents, each consisting of particles within an N-atom system. Self-assembly pathways and rates for nanocomposites are derived via a multiscale analysis of the classical Liouville equation. From a reduced statistical framework, rigorous stochastic equations for population levels of beginning, intermediate, and final aggregates are also derived. It is shown that the definition of an assembly type is a self-consistency criterion that must strike a balance between precision and the need for population levels to be slowly varying relative to the time scale of atomic motion. The deductive multiscale approach is complemented by a qualitative notion of multicomponent association and the ensemble of exact atomic-level configurations consistent with them. In processes such as viral self-assembly from proteins and RNA or DNA, there are many possible intermediates, so that it is usually difficult to predict the most efficient assembly pathway. However, in the current study, rates of assembly of each possible intermediate can be predicted. This avoids the need, as in a phenomenological approach, for recalibration with each new application. The method accounts for the feedback across scales in space and time that is fundamental to nanosystem self-assembly. The theory has applications to bionanostructures, geomaterials, engineered composites, and nanocapsule therapeutic delivery systems.

Self-Assembly of Nanostructured Electronic Devices (454th Brookhaven Lecture)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Black, Charles

2009-12-16

Given suitable atmospheric conditions, water vapor from the air will crystallize into beautiful structures: snowflakes. Nature provides many other examples of spontaneous organization of materials into regular patterns, which is a process known as self-assembly. Since self-assembly works at all levels, it can be a useful tool for organizing materials on the nanometer scale. In particular, self-assembly provides a precise method for designing materials with improved electronic properties, thereby enabling advances in semiconductor electronics and solar devices. On Wednesday, December 16, at 4 p.m. in Berkner Hall, Charles Black of the Center for Functional Nanomaterials (CFN) will explore this topicmore » during the 454th Brookhaven Lecture, entitled “Self-Assembly of Nanostructured Electronic Devices.” Refreshments will be offered before and after the lecture. To attend this open-to-the-public event, visitors to the Lab ages 16 and older must present photo ID at the Main Gate. During this talk, Dr. Black will discuss examples of how self-assembly is being integrated into semiconductor microelectronics, as advances in the ability to define circuit elements at higher resolution have fueled more than 40 years of performance improvements. Self-assembly also promises advances in the performance of solar devices; thus he will describe his group’s recent results with nanostructured photovoltaic devices.« less

Micellar Self-Assembly of Recombinant Resilin-/Elastin-Like Block Copolypeptides.

PubMed

Weitzhandler, Isaac; Dzuricky, Michael; Hoffmann, Ingo; Garcia Quiroz, Felipe; Gradzielski, Michael; Chilkoti, Ashutosh

2017-08-14

Reported here is the synthesis of perfectly sequence defined, monodisperse diblock copolypeptides of hydrophilic elastin-like and hydrophobic resilin-like polypeptide blocks and characterization of their self-assembly as a function of structural parameters by light scattering, cryo-TEM, and small-angle neutron scattering. A subset of these diblock copolypeptides exhibit lower critical solution temperature and upper critical solution temperature phase behavior and self-assemble into spherical or cylindrical micelles. Their morphologies are dictated by their chain length, degree of hydrophilicity, and hydrophilic weight fraction of the ELP block. We find that (1) independent of the length of the corona-forming ELP block there is a minimum threshold in the length of the RLP block below which self-assembly does not occur, but that once that threshold is crossed, (2) the RLP block length is a unique molecular parameter to independently tune self-assembly and (3) increasing the hydrophobicity of the corona-forming ELP drives a transition from spherical to cylindrical morphology. Unlike the self-assembly of purely ELP-based block copolymers, the self-assembly of RLP-ELPs can be understood by simple principles of polymer physics relating hydrophilic weight fraction and polymer-polymer and polymer-solvent interactions to micellar morphology, which is important as it provides a route for the de novo design of desired nanoscale morphologies from first principles.

Self-assembly of tetravalent Goldberg polyhedra from 144 small components

NASA Astrophysics Data System (ADS)

Fujita, Daishi; Ueda, Yoshihiro; Sato, Sota; Mizuno, Nobuhiro; Kumasaka, Takashi; Fujita, Makoto

2016-12-01

Rational control of the self-assembly of large structures is one of the key challenges in chemistry, and is believed to become increasingly difficult and ultimately impossible as the number of components involved increases. So far, it has not been possible to design a self-assembled discrete molecule made up of more than 100 components. Such molecules—for example, spherical virus capsids—are prevalent in nature, which suggests that the difficulty in designing these very large self-assembled molecules is due to a lack of understanding of the underlying design principles. For example, the targeted assembly of a series of large spherical structures containing up to 30 palladium ions coordinated by up to 60 bent organic ligands was achieved by considering their topologies. Here we report the self-assembly of a spherical structure that also contains 30 palladium ions and 60 bent ligands, but belongs to a shape family that has not previously been observed experimentally. The new structure consists of a combination of 8 triangles and 24 squares, and has the symmetry of a tetravalent Goldberg polyhedron. Platonic and Archimedean solids have previously been prepared through self-assembly, as have trivalent Goldberg polyhedra, which occur naturally in the form of virus capsids and fullerenes. But tetravalent Goldberg polyhedra have not previously been reported at the molecular level, although their topologies have been predicted using graph theory. We use graph theory to predict the self-assembly of even larger tetravalent Goldberg polyhedra, which should be more stable, enabling another member of this polyhedron family to be assembled from 144 components: 48 palladium ions and 96 bent ligands.

Photoconductivity in DNA-Porphyrin Complexes

NASA Astrophysics Data System (ADS)

Myint, Peco; Oxford, Emma; Nyazenga, Collence; Smith, Walter; Qi, Zhengqing; Johnson, A. T.

2015-03-01

We have measured the photoconductivity of λ - DNA that is modified by intercalating a porphyrin compound, meso-tetrakis(N-methyl-4-pyridiniumyl)porphyrin (TMPyP), into its base stacks. Intercalation was verified by a red shift and hypochromism of the Soret absorption peak. The DNA/porphyrin strands were then deposited onto oxidized silicon substrates which had been patterned with interdigitated electrodes, and blown dry. Electrical measurements were carried out under nitrogen, using illumination from a 445 nm laser; this wavelength falls within the absorption peak of the DNA/porphyrin complexes. When initially measured under dry nitrogen, the complexes show no photoconductivity or dark conductivity. However, at relative humidities of 30% and above, we do observe dark conductivity, and also photoconductivity that grows with time. Photoconductivity gets larger at higher relative humidity. Remarkably, when the humidity is lowered again, some photoconductivity is now observed, indicating a change that persists for more than 24 hours. It may be that the humidity alters the structure of the DNA, perhaps allowing for better alignment of the bases. This work was supported by NSF Grant BMAT-1306170.

Effectiveness of online and face-to-face fatigue self-management programmes for adults with neurological conditions.

PubMed

Ghahari, Setareh; Packer, Tanya

2012-01-01

To evaluate effectiveness of a face-to-face and an online fatigue self-management programme and to compare these to two control groups (information-only and no-intervention) in a sample of adults (n = 115) with neurological conditions reporting extreme fatigue. Non-equivalent pre-test post-test control group design using the Fatigue Impact Scale, Personal Wellbeing Index and Activity Card Sort as primary outcome measures. Participants in the two intervention groups and the information-only group showed clinically significant improvements in fatigue over time (p < 0.05). When compared to the no-intervention group, face-to-face participants showed significantly greater improvement in overall and cognitive fatigue, while participants in the online group showed significant improvement in self-efficacy and stress. Participation in either the online or face-to-face programme appears to result in improved self-management, however, with different potency depending on outcomes. The improvement in the online information only group further complicates the understanding of the results. With few other comparisons of online and face-to-face self-management protocols available, further research is needed to understand differential impacts which may be related to the delivery format, the rural versus urban split of participants or other unknown factors.

Looking for myself: current multisensory input alters self-face recognition.

PubMed

Tsakiris, Manos

2008-01-01

How do I know the person I see in the mirror is really me? Is it because I know the person simply looks like me, or is it because the mirror reflection moves when I move, and I see it being touched when I feel touch myself? Studies of face-recognition suggest that visual recognition of stored visual features inform self-face recognition. In contrast, body-recognition studies conclude that multisensory integration is the main cue to selfhood. The present study investigates for the first time the specific contribution of current multisensory input for self-face recognition. Participants were stroked on their face while they were looking at a morphed face being touched in synchrony or asynchrony. Before and after the visuo-tactile stimulation participants performed a self-recognition task. The results show that multisensory signals have a significant effect on self-face recognition. Synchronous tactile stimulation while watching another person's face being similarly touched produced a bias in recognizing one's own face, in the direction of the other person included in the representation of one's own face. Multisensory integration can update cognitive representations of one's body, such as the sense of ownership. The present study extends this converging evidence by showing that the correlation of synchronous multisensory signals also updates the representation of one's face. The face is a key feature of our identity, but at the same time is a source of rich multisensory experiences used to maintain or update self-representations.

Differential interaction of porphyrins used in photoradiation therapy with ferrochelatase.

PubMed Central

Dailey, H A; Smith, A

1984-01-01

The mechanism of porphyrin accumulation by tumours is not yet established. If metabolism aids porphyrin elimination, tumours, unlike normal tissues, may not metabolize porphyrins used clinically, such as proto-, haemato-, OO'-diacetyl-haemato- and monohydroxyethyl-monovinyl-deutero-porphyrin. Proto-, haemato- and monohydroxyethyl-monovinyl-deutero-porphyrin are substrates for the mitochondrial enzyme ferrochelatase (EC 4.99.1.1), which can form haem analogues from exogenous porphyrins. The Km values for proto-, haemato- and monohydroxyethyl-monovinyl-deutero-porphyrin are 11, 22 and 23 microM respectively. However, OO'-diacetyl-haematoporphyrin is an effective competitive inhibitor with Ki of 11 microM. Hepatic ferrochelatase specific activity is 5.9 and 5.5 nmol of haem/h per mg of protein respectively in normal Buffalo rat and in those bearing the extrahepatic Morris 7288C hepatoma, and is only 0.13 nmol/h per mg in the hepatomas. Therefore low ferrochelatase activity in cancerous cells may provide one means whereby some porphyrins accumulate in tumours, and the ability of certain porphyrins to act as ferrochelatase inhibitors may provide another. PMID:6497856

A Theoretical and Experimental Study of DNA Self-assembly

NASA Astrophysics Data System (ADS)

Chandran, Harish

The control of matter and phenomena at the nanoscale is fast becoming one of the most important challenges of the 21st century with wide-ranging applications from energy and health care to computing and material science. Conventional top-down approaches to nanotechnology, having served us well for long, are reaching their inherent limitations. Meanwhile, bottom-up methods such as self-assembly are emerging as viable alternatives for nanoscale fabrication and manipulation. A particularly successful bottom up technique is DNA self-assembly where a set of carefully designed DNA strands form a nanoscale object as a consequence of specific, local interactions among the different components, without external direction. The final product of the self-assembly process might be a static nanostructure or a dynamic nanodevice that performs a specific function. Over the past two decades, DNA self-assembly has produced stunning nanoscale objects such as 2D and 3D lattices, polyhedra and addressable arbitrary shaped substrates, and a myriad of nanoscale devices such as molecular tweezers, computational circuits, biosensors and molecular assembly lines. In this dissertation we study multiple problems in the theory, simulations and experiments of DNA self-assembly. We extend the Turing-universal mathematical framework of self-assembly known as the Tile Assembly Model by incorporating randomization during the assembly process. This allows us to reduce the tile complexity of linear assemblies. We develop multiple techniques to build linear assemblies of expected length N using far fewer tile types than previously possible. We abstract the fundamental properties of DNA and develop a biochemical system, which we call meta-DNA, based entirely on strands of DNA as the only component molecule. We further develop various enzyme-free protocols to manipulate meta-DNA systems and provide strand level details along with abstract notations for these mechanisms. We simulate DNA circuits by

Homochiral Evolution in Self-Assembled Chiral Polymers and Block Copolymers.

PubMed

Wen, Tao; Wang, Hsiao-Fang; Li, Ming-Chia; Ho, Rong-Ming

2017-04-18

The significance of chirality transfer is not only involved in biological systems, such as the origin of homochiral structures in life but also in man-made chemicals and materials. How the chiral bias transfers from molecular level (molecular chirality) to helical chain (conformational chirality) and then to helical superstructure or phase (hierarchical chirality) from self-assembly is vital for the chemical and biological processes in nature, such as communication, replication, and enzyme catalysis. In this Account, we summarize the methodologies for the examination of homochiral evolution at different length scales based on our recent studies with respect to the self-assembly of chiral polymers and chiral block copolymers (BCPs*). A helical (H*) phase to distinguish its P622 symmetry from that of normal hexagonally packed cylinder phase was discovered in the self-assembly of BCPs* due to the chirality effect on BCP self-assembly. Enantiomeric polylactide-containing BCPs*, polystyrene-b-poly(l-lactide) (PS-PLLA) and polystyrene-b-poly(d-lactide) (PS-PDLA), were synthesized for the examination of homochiral evolution. The optical activity (molecular chirality) of constituted chiral repeating unit in the chiral polylactide is detected by electronic circular dichroism (ECD) whereas the conformational chirality of helical polylactide chain can be explicitly determined by vibrational circular dichroism (VCD). The H* phases of the self-assembled polylactide-containing BCPs* can be directly visualized by 3D transmission electron microscopy (3D TEM) technique at which the handedness (hierarchical chirality) of the helical nanostructure is thus determined. The results from the ECD, VCD, and 3D TEM for the investigated chirality at different length scales suggest the homochiral evolution in the self-assembly of the BCPs*. For chiral polylactides, twisted lamellae in crystalline banded spherulite can be formed by dense packing scheme and effective interactions upon helical

Self-assembly of convex particles on spherocylindrical surfaces.

PubMed

Lázaro, Guillermo R; Dragnea, Bogdan; Hagan, Michael F

2018-05-25

The precise control of assembly and packing of proteins and colloids on curved surfaces has fundamental implications in nanotechnology. In this paper, we describe dynamical simulations of the self-assembly of conical subunits around a spherocylindrical template, and a continuum theory for the bending energy of a triangular lattice with spontaneous curvature on a surface with arbitrary curvature. We find that assembly depends sensitively on mismatches between subunit spontaneous curvature and the mean curvature of the template, as well as anisotropic curvature of the template (mismatch between the two principal curvatures). Our simulations predict assembly morphologies that closely resemble those observed in experiments in which virus capsid proteins self-assemble around metal nanorods. Below a threshold curvature mismatch, our simulations identify a regime of optimal assembly leading to complete, symmetrical particles. Outside of this regime we observe defective particles, whose morphologies depend on the degree of curvature mismatch. To learn how assembly is affected by the nonuniform curvature of a spherocylinder, we also study the simpler cases of assembly around spherical and cylindrical cores. Our results show that both the intrinsic (Gaussian) and extrinsic (mean) curvatures of a template play significant roles in guiding the assembly of anisotropic subunits, providing a rich design space for the formation of nanoscale materials.

Field-induced self-assembly of iron oxide nanoparticles investigated using small-angle neutron scattering.

PubMed

Fu, Zhendong; Xiao, Yinguo; Feoktystov, Artem; Pipich, Vitaliy; Appavou, Marie-Sousai; Su, Yixi; Feng, Erxi; Jin, Wentao; Brückel, Thomas

2016-11-03

The magnetic-field-induced assembly of magnetic nanoparticles (NPs) provides a unique and flexible strategy in the design and fabrication of functional nanostructures and devices. We have investigated the field-induced self-assembly of core-shell iron oxide NPs dispersed in toluene by means of small-angle neutron scattering (SANS). The form factor of the core-shell NPs was characterized and analyzed using SANS with polarized neutrons. Large-scale aggregates of iron oxide NPs formed above 0.02 T as indicated by very-small-angle neutron scattering measurements. A three-dimensional long-range ordered superlattice of iron oxide NPs was revealed under the application of a moderate magnetic field. The crystal structure of the superlattice has been identified to be face-centred cubic.

Self-assembled three-dimensional chiral colloidal architecture

NASA Astrophysics Data System (ADS)

Ben Zion, Matan Yah; He, Xiaojin; Maass, Corinna C.; Sha, Ruojie; Seeman, Nadrian C.; Chaikin, Paul M.

2017-11-01

Although stereochemistry has been a central focus of the molecular sciences since Pasteur, its province has previously been restricted to the nanometric scale. We have programmed the self-assembly of micron-sized colloidal clusters with structural information stemming from a nanometric arrangement. This was done by combining DNA nanotechnology with colloidal science. Using the functional flexibility of DNA origami in conjunction with the structural rigidity of colloidal particles, we demonstrate the parallel self-assembly of three-dimensional microconstructs, evincing highly specific geometry that includes control over position, dihedral angles, and cluster chirality.

Direct protein photoinduced conformational changes using porphyrins.

NASA Astrophysics Data System (ADS)

Brancaleon, Lorenzo; Silva, Ivan; Fernandez, Nicholas; Johnson, Eric; Sansone, Samuel

2008-03-01

Most proteins functions depend on the interaction with other ligands. These interactions depend on uniquely structured binding sites formed by the folding of the proteins. Ligands can often prompt intended as well as ``accidental'' protein structural changes. One can foresee that the ability to prompt and control post-translational protein folding could be a powerful tool to investigate protein folding mechanisms but also to inhibit certain proteins or induce new properties to proteins. One possible way to produce such structural disruption is the combination of light and photoactive ligands. This option has been investigated in recent years by exploiting photoisomerization and other properties of non-physiological dyes. We used an alternative approach which uses porphyrins as the ``triggers'' of structural changes. The advantage of porphyrins is that they can be found naturally in living cells. The photophysical properties of porphyrins can induce local as well as long range effects on the structure of the bound protein. Porphyrins are known to produce structural changes in porphyrin-specific proteins, however the novelty of our results is that we demonstrated that these dyes can also produce structural changes in non-porphyrin-specific globular proteins. We will present an overview of our research to-date in this field and its potential applications.

Method for forming cooperative binary ionic solids

DOEpatents

Shelnutt, John A.; Martin, Kathleen E.; Wang, Zhongchun; Medforth, Craig J.

2013-03-05

A nanostructured molecular unit and method for forming is described where a cationic porphyrin having an ethanolic substituent species and a metal in the porphyrin cavity is combined with an anionic porphyrin having a sulfonate substituent species and a metal in the porphyrin cavity to form by self-assembly a nanostructured molecular unit with a morphology comprising four dendritic elements connected at a central node.

Method for forming cooperative binary ionic solids

DOEpatents

Shelnutt, John A.; Martin, Kathleen E.; Wang, Zhongchun; Medforth, Craig J.

2014-09-09

A nanostructured molecular unit and method for forming is described where a cationic porphyrin having an ethanolic substituent species and a metal in the porphyrin cavity is combined with an anionic porphyrin having a sulfonate substituent species and a metal in the porphyrin cavity to form by self-assembly a nanostructured molecular unit with a morphology comprising four dendritic elements connected at a central node.

Porphyrin Tests

MedlinePlus

... variability can occur due to differences in testing equipment, chemical reagents, and techniques. This is a reason ... healthcare practitioner's office? No. Porphyrin tests require specialized equipment and technical skills. Some tests may be performed ...

Multilayer block copolymer meshes by orthogonal self-assembly

PubMed Central

Tavakkoli K. G., Amir; Nicaise, Samuel M.; Gadelrab, Karim R.; Alexander-Katz, Alfredo; Ross, Caroline A.; Berggren, Karl K.

2016-01-01

Continued scaling-down of lithographic-pattern feature sizes has brought templated self-assembly of block copolymers (BCPs) into the forefront of nanofabrication research. Technologies now exist that facilitate significant control over otherwise unorganized assembly of BCP microdomains to form both long-range and locally complex monolayer patterns. In contrast, the extension of this control into multilayers or 3D structures of BCP microdomains remains limited, despite the possible technological applications in next-generation devices. Here, we develop and analyse an orthogonal self-assembly method in which multiple layers of distinct-molecular-weight BCPs naturally produce nanomesh structures of cylindrical microdomains without requiring layer-by-layer alignment or high-resolution lithographic templating. The mechanisms for orthogonal self-assembly are investigated with both experiment and simulation, and we determine that the control over height and chemical preference of templates are critical process parameters. The method is employed to produce nanomeshes with the shapes of circles and Y-intersections, and is extended to produce three layers of orthogonally oriented cylinders. PMID:26796218

Self- or familiar-face recognition advantage? New insight using ambient images.

PubMed

Bortolon, Catherine; Lorieux, Siméon; Raffard, Stéphane

2018-06-01

Self-face recognition has been widely explored in the past few years. Nevertheless, the current literature relies on the use of standardized photographs which do not represent daily-life face recognition. Therefore, we aim for the first time to evaluate self-face processing in healthy individuals using natural/ambient images which contain variations in the environment and in the face itself. In total, 40 undergraduate and graduate students performed a forced delayed-matching task, including images of one's own face, friend, famous and unknown individuals. For both reaction time and accuracy, results showed that participants were faster and more accurate when matching different images of their own face compared to both famous and unfamiliar faces. Nevertheless, no significant differences were found between self-face and friend-face and between friend-face and famous-face. They were also faster and more accurate when matching friend and famous faces compared to unfamiliar faces. Our results suggest that faster and more accurate responses to self-face might be better explained by a familiarity effect - that is, (1) the result of frequent exposition to one's own image through mirror and photos, (2) a more robust mental representation of one's own face and (3) strong face recognition units as for other familiar faces.

High-resolution Crystal Structure of Dimeric VP40 From Sudan ebolavirus.

PubMed

Clifton, Matthew C; Bruhn, Jessica F; Atkins, Kateri; Webb, Terry L; Baydo, Ruth O; Raymond, Amy; Lorimer, Donald D; Edwards, Thomas E; Myler, Peter J; Saphire, Erica Ollmann

2015-10-01

Ebolaviruses cause severe hemorrhagic fever. Central to the Ebola life cycle is the matrix protein VP40, which oligomerizes and drives viral budding. Here we present the crystal structure of the Sudan virus (SUDV) matrix protein. This structure is higher resolution (1.6 Å) than previously achievable. Despite differences in the protein purification, we find that it still forms a stable dimer in solution, as was noted for other Ebola VP40s. Although the N-terminal domain interface by which VP40 dimerizes is conserved between Ebola virus and SUDV, the C-terminal domain interface by which VP40 dimers may further assemble is significantly smaller in this SUDV assembly. © The Author 2015. Published by Oxford University Press on behalf of the Infectious Diseases Society of America. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Self-face Captures, Holds, and Biases Attention.

PubMed

Wójcik, Michał J; Nowicka, Maria M; Kotlewska, Ilona; Nowicka, Anna

2017-01-01

The implicit self-recognition process may take place already in the pre-attentive stages of perception. After a silent stimulus has captured attention, it is passed on to the attentive stage where it can affect decision making and responding. Numerous studies show that the presence of self-referential information affects almost every cognitive level. These effects may share a common and fundamental basis in an attentional mechanism, conceptualized as attentional bias: the exaggerated deployment of attentional resources to a salient stimulus. A gold standard in attentional bias research is the dot-probe paradigm. In this task, a prominent stimulus (cue) and a neutral stimulus are presented in different spatial locations, followed by the presentation of a target. In the current study we aimed at investigating whether the self-face captures, holds and biases attention when presented as a task-irrelevant stimulus. In two dot-probe experiments coupled with the event-related potential (ERP) technique we analyzed the following relevant ERPs components: N2pc and SPCN which reflect attentional shifts and the maintenance of attention, respectively. An inter-stimulus interval separating face-cues and probes (800 ms) was introduced only in the first experiment. In line with our predictions, in Experiment 1 the self-face elicited the N2pc and the SPCN component. In Experiment 2 in addition to N2pc, an attentional bias was observed. Our results indicate that unintentional self-face processing disables the top-down control setting to filter out distractors, thus leading to the engagement of attentional resources and visual short-term memory.