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Sample records for oriented molecular assemblies

  1. Molecular Orientation in Quantasomes

    PubMed Central

    Sauer, Kenneth

    1965-01-01

    A new apparatus is described for measuring dichroism spectra with very high sensitivity for macromolecular structures oriented in a hydrodynamic gradient. The method has been used to explore the dichroism spectrum of quantasome aggregates isolated from spinach chloroplasts. The quantasome flow dichroism resembles qualitatively that observed previously using electric field orientation, in that a pigment absorbing at wavelengths longer than 680 mμ exhibits appreciably greater dichroism than those absorbing at shorter wavelengths. It is shown that the absorption oscillator for this long wavelength absorption lies parallel to the streamlines of the sheer gradient, which is assumed to be the direction in which the planes of the chloroplast lamellae are oriented. PMID:19431337

  2. Visualization Software for Molecular Assemblies

    PubMed Central

    Goddard, Thomas D; Ferrin, Thomas E

    2007-01-01

    Summary Software for viewing three-dimensional models and maps of viruses, ribosomes, filaments and other molecular assemblies is advancing on many fronts. New developments include molecular representations that offer better control over level of detail, lighting that improves the perception of depth, and two-dimensional projections that simplify data interpretation. Programmable graphics processors offer quality, speed and visual effects not previously possible, while 3D printers, haptic interaction devices, and auto-stereo displays show promise in more naturally engaging our senses. Visualization methods are developed by diverse groups of researchers with differing goals: experimental biologists, database developers, computer scientists, and package developers. We survey recent developments and problems faced by the developer community in bringing innovative visualization methods into widespread use. PMID:17728125

  3. Orientation dynamics of azobenzene-based self-assembled monolayers

    NASA Astrophysics Data System (ADS)

    Fang, Guanjiu

    2007-12-01

    Self-assembled monolayers (SAMs) synthesized on glass and incorporating azobenzene are illuminated with actinic light to study the effect of photo-isomerization on in-plane molecular orientation. Measurements of the monolayer birefringence show that the SAM orientation dynamics are non-first-order kinetics, characterized by an exponential relaxation with a distribution of relaxation times. The orientational birefringence decays as a power law with an exponent that decreases with increasing initial writing intensity, indicative of orientational trapping wells with a distribution of depths. The distribution of trapping well depths, resulting from the distribution of free volumes among the SAM molecules, is modified by exposure to light. This depth modification indicates that photoisomerization is a collective process depending on neighboring molecules. Increasing the light intensity enhances the collective effect so that the orientation dynamics are changed from fractal to normal diffusion. With a further increase in light intensity, the collective effect does not change any more so that the mean width of the trapping well depth distribution, characterized by the power law exponent, becomes constant. The liquid crystal alignment in a photo-buffed SAM/rubbed nylon twisted nematic cell is very stable at room temperature, but it is lost upon cooling if the liquid crystal is heated into the isotropic phase, which is attributed to the thermal orientational relaxation of the SAM molecules. The liquid crystal response to reorienting the SAM with polarized light depends on the initial SAM writing time: the harder the initial writing, the slower subsequent reorientation, which is similar to the behavior of bare SAMs. The reorientation of the liquid crystals shows hysteresis compared with that of bare SAMs, with a larger dose required at higher intensity.

  4. Efficient molecular mechanics simulations of the folding, orientation, and assembly of peptides in lipid bilayers using an implicit atomic solvation model

    NASA Astrophysics Data System (ADS)

    Bordner, Andrew J.; Zorman, Barry; Abagyan, Ruben

    2011-10-01

    Membrane proteins comprise a significant fraction of the proteomes of sequenced organisms and are the targets of approximately half of marketed drugs. However, in spite of their prevalence and biomedical importance, relatively few experimental structures are available due to technical challenges. Computational simulations can potentially address this deficit by providing structural models of membrane proteins. Solvation within the spatially heterogeneous membrane/solvent environment provides a major component of the energetics driving protein folding and association within the membrane. We have developed an implicit solvation model for membranes that is both computationally efficient and accurate enough to enable molecular mechanics predictions for the folding and association of peptides within the membrane. We derived the new atomic solvation model parameters using an unbiased fitting procedure to experimental data and have applied it to diverse problems in order to test its accuracy and to gain insight into membrane protein folding. First, we predicted the positions and orientations of peptides and complexes within the lipid bilayer and compared the simulation results with solid-state NMR structures. Additionally, we performed folding simulations for a series of host-guest peptides with varying propensities to form alpha helices in a hydrophobic environment and compared the structures with experimental measurements. We were also able to successfully predict the structures of amphipathic peptides as well as the structures for dimeric complexes of short hexapeptides that have experimentally characterized propensities to form beta sheets within the membrane. Finally, we compared calculated relative transfer energies with data from experiments measuring the effects of mutations on the free energies of translocon-mediated insertion of proteins into lipid bilayers and of combined folding and membrane insertion of a beta barrel protein.

  5. Oriented assembly of polyhedral plasmonic nanoparticle clusters

    PubMed Central

    Henzie, Joel; Andrews, Sean C.; Ling, Xing Yi; Li, Zhiyong; Yang, Peidong

    2013-01-01

    Shaped colloids can be used as nanoscale building blocks for the construction of composite, functional materials that are completely assembled from the bottom up. Assemblies of noble metal nanostructures have unique optical properties that depend on key structural features requiring precise control of both position and connectivity spanning nanometer to micrometer length scales. Identifying and optimizing structures that strongly couple to light is important for understanding the behavior of surface plasmons in small nanoparticle clusters, and can result in highly sensitive chemical and biochemical sensors using surface-enhanced Raman spectroscopy (SERS). We use experiment and simulation to examine the local surface plasmon resonances of different arrangements of Ag polyhedral clusters. High-resolution transmission electron microscopy shows that monodisperse, atomically smooth Ag polyhedra can self-assemble into uniform interparticle gaps that result in reproducible SERS enhancement factors from assembly to assembly. We introduce a large-scale, gravity-driven assembly method that can generate arbitrary nanoparticle clusters based on the size and shape of a patterned template. These templates enable the systematic examination of different cluster arrangements and provide a means of constructing scalable and reliable SERS sensors. PMID:23569275

  6. Origin of collision-induced molecular orientation.

    PubMed

    Brouard, M; Hornung, B; Aoiz, F J

    2013-11-01

    Collision-induced rotational angular momentum orientation is a fundamental property of molecular scattering, which is sensitive to the balance between attractive and repulsive forces at play during collision. Here, we quantify a new mechanism leading to orientation, which is purely quantum mechanical in origin. Although the new mechanism is quite general, and will operate more widely in atomic and molecular scattering, it is observed here for impulsive hard shell collisions, for which the orientation vanishes classically. The quantum mechanism can thus be studied in isolation from other processes. The orientation is proposed to originate from the nonlocal nature of the quantum mechanical collision encounter.

  7. Molecular rectification in oriented polymers

    NASA Astrophysics Data System (ADS)

    Sentein, C.; Fiorini, C.; Lorin, A.; Nunzi, J.-M.; Sicot, L.

    1998-06-01

    We underline the intrinsic rectifying nature of an oriented polymeric material. Orientation of the initially symmetric structure is performed through DC-field ordering of the polar molecules contained in the polymer. The internal field induced in the polymeric material is evidenced by the induction of a rectifying current-voltage characteristic. Our preparation technique opens a new route for the improvement of organic-semiconductor devices efficiency. Nous soulignons la nature intrinsèquement rectifiante d'un polymère orienté. L'orientation moléculaire est induite par polarisation sous champ permanent. Le champ interne piégé dans le matériau induit une rectification de la caractéristique courant tension. Notre technique de préparation ouvre une voie nouvelle pour l'amélioration des performances des dispositifs semiconducteurs organiques.

  8. Rigorous theory of molecular orientational nonlinear optics

    SciTech Connect

    Kwak, Chong Hoon Kim, Gun Yeup

    2015-01-15

    Classical statistical mechanics of the molecular optics theory proposed by Buckingham [A. D. Buckingham and J. A. Pople, Proc. Phys. Soc. A 68, 905 (1955)] has been extended to describe the field induced molecular orientational polarization effects on nonlinear optics. In this paper, we present the generalized molecular orientational nonlinear optical processes (MONLO) through the calculation of the classical orientational averaging using the Boltzmann type time-averaged orientational interaction energy in the randomly oriented molecular system under the influence of applied electric fields. The focal points of the calculation are (1) the derivation of rigorous tensorial components of the effective molecular hyperpolarizabilities, (2) the molecular orientational polarizations and the electronic polarizations including the well-known third-order dc polarization, dc electric field induced Kerr effect (dc Kerr effect), optical Kerr effect (OKE), dc electric field induced second harmonic generation (EFISH), degenerate four wave mixing (DFWM) and third harmonic generation (THG). We also present some of the new predictive MONLO processes. For second-order MONLO, second-order optical rectification (SOR), Pockels effect and difference frequency generation (DFG) are described in terms of the anisotropic coefficients of first hyperpolarizability. And, for third-order MONLO, third-order optical rectification (TOR), dc electric field induced difference frequency generation (EFIDFG) and pump-probe transmission are presented.

  9. Rigorous theory of molecular orientational nonlinear optics

    NASA Astrophysics Data System (ADS)

    Kwak, Chong Hoon; Kim, Gun Yeup

    2015-01-01

    Classical statistical mechanics of the molecular optics theory proposed by Buckingham [A. D. Buckingham and J. A. Pople, Proc. Phys. Soc. A 68, 905 (1955)] has been extended to describe the field induced molecular orientational polarization effects on nonlinear optics. In this paper, we present the generalized molecular orientational nonlinear optical processes (MONLO) through the calculation of the classical orientational averaging using the Boltzmann type time-averaged orientational interaction energy in the randomly oriented molecular system under the influence of applied electric fields. The focal points of the calculation are (1) the derivation of rigorous tensorial components of the effective molecular hyperpolarizabilities, (2) the molecular orientational polarizations and the electronic polarizations including the well-known third-order dc polarization, dc electric field induced Kerr effect (dc Kerr effect), optical Kerr effect (OKE), dc electric field induced second harmonic generation (EFISH), degenerate four wave mixing (DFWM) and third harmonic generation (THG). We also present some of the new predictive MONLO processes. For second-order MONLO, second-order optical rectification (SOR), Pockels effect and difference frequency generation (DFG) are described in terms of the anisotropic coefficients of first hyperpolarizability. And, for third-order MONLO, third-order optical rectification (TOR), dc electric field induced difference frequency generation (EFIDFG) and pump-probe transmission are presented.

  10. Finding Stable Orientations of Assemblies with Linear Programming

    DTIC Science & Technology

    1993-06-01

    AD-A266 990 Finding Stable Orientations of Assemblies with Linear Programming David Baraff Raju Mattikalli Bruno Repetto Pradeep Khosla CMU-RI-TR-93...Mattikalli, Bruno Repetto and Pradeep Khosla 7. PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES) 8. PERFORMING ORGANIZATION REPORT NUMBER The Robotics... Repetto , and D. Baraff. Stability of assemblies. In Interna- tional Conference on Intelligent Robots and Systems, page (to appear). IEEE/RSJ, July 1993

  11. Field-assisted assembly and orientational order of colloidal ellipsoids

    NASA Astrophysics Data System (ADS)

    Solomon, Michael

    2013-03-01

    Colloidal particles with anisotropy in shape and interactions can potentially be assembled into colloidal crystals with unusual structure and symmetry. Field-assisted assembly is likewise a means to produce structures that are otherwise difficult to achieve by equilibrium self-assembly. Here we show, by means of confocal microscopy direct visualization, how controlled application of electric fields can improve general prospects for assembly of any anisotropic colloid. By studying the model case of ellipsoidal colloidal rods, we find that applied fields can be designed which produce liquid crystal phases of colloids in a simple, versatile manner. By directly visualizing the assembled particles in three dimensions we learn that the quality of orientational order achieved is comparable to that of materials such as liquid crystalline polymers. We understand the results in terms of the underlying electrokinetics of the system as well as connect the observed field-induced orientational order to the equilibrium isotropic-nematic transition predicted for rods with prolate spheroidal shape. Specifically, the applied field generates a force that is balanced by a gradient in osmotic pressure generated by the density dependence of the rod suspension. If the field strength is sufficiently large, the resultant osmotic pressure produces a phase transition. We discuss how the required field conditions for assembly can be tailored based on the shape and size of the anisotropic building block.

  12. Computing by molecular self-assembly.

    PubMed

    Jonoska, Nataša; Seeman, Nadrian C

    2012-08-06

    The paper reviews two computing models by DNA self-assembly whose proof of principal have recently been experimentally confirmed. The first model incorporates DNA nano-devices and triple crossover DNA molecules to algorithmically arrange non-DNA species. This is achieved by simulating a finite-state automaton with output where golden nanoparticles are assembled to read-out the result. In the second model, a complex DNA molecule representing a graph emerges as a solution of a computational problem. This supports the idea that in molecular self-assembly computing, it may be necessary to develop the notion of shape processing besides the classical approach through symbol processing.

  13. Molecular self-assembly at solid surfaces.

    PubMed

    Otero, Roberto; Gallego, José María; de Parga, Amadeo L Vázquez; Martín, Nazario; Miranda, Rodolfo

    2011-11-23

    Self-assembly, the process by which objects initially distributed at random arrange into well-defined patterns exclusively due to their local mutual interactions without external intervention, is generally accepted to be the most promising method for large-scale fabrication of functional nanostructures. In particular, the ordering of molecular building-blocks deposited at solid surfaces is relevant for the performance of many organic electronic and optoelectronic devices, such as organic field-effect transistors (OFETs), organic light-emitting diodes (OLEDs) or photovoltaic solar cells. However, the fundamental knowledge on the nature and strength of the intermolecular and molecule-substrate interactions that govern the ordering of molecular adsorbates is, in many cases, rather scarce. In most cases, the structure and morphology of the organic-metal interface is not known and it is just assumed to be the same as in the bulk, thereby implicitly neglecting the role of the surface on the assembly. However, this approximation is usually not correct, and the evidence gathered over the last decades points towards an active role of the surface in the assembly, leading to self-assembled structures that only in a few occasions can be understood by considering just intermolecular interactions in solid or gas phases. In this work we review several examples from our recent research demonstrating the apparently endless variety of ways in which the surface might affect the assembly of organic adsorbates.

  14. Molecular assembly on two-dimensional materials.

    PubMed

    Kumar, Avijit; Banerjee, Kaustuv; Liljeroth, Peter

    2017-02-24

    Molecular self-assembly is a well-known technique to create highly functional nanostructures on surfaces. Self-assembly on two-dimensional (2D) materials is a developing field driven by the interest in functionalization of 2D materials in order to tune their electronic properties. This has resulted in the discovery of several rich and interesting phenomena. Here, we review this progress with an emphasis on the electronic properties of the adsorbates and the substrate in well-defined systems, as unveiled by scanning tunneling microscopy. The review covers three aspects of the self-assembly. The first one focuses on non-covalent self-assembly dealing with site-selectivity due to inherent moiré pattern present on 2D materials grown on substrates. We also see that modification of intermolecular interactions and molecule-substrate interactions influences the assembly drastically and that 2D materials can also be used as a platform to carry out covalent and metal-coordinated assembly. The second part deals with the electronic properties of molecules adsorbed on 2D materials. By virtue of being inert and possessing low density of states near the Fermi level, 2D materials decouple molecules electronically from the underlying metal substrate and allow high-resolution spectroscopy and imaging of molecular orbitals. The moiré pattern on the 2D materials causes site-selective gating and charging of molecules in some cases. The last section covers the effects of self-assembled, acceptor and donor type, organic molecules on the electronic properties of graphene as revealed by spectroscopy and electrical transport measurements. Non-covalent functionalization of 2D materials has already been applied for their application as catalysts and sensors. With the current surge of activity on building van der Waals heterostructures from atomically thin crystals, molecular self-assembly has the potential to add an extra level of flexibility and functionality for applications ranging from

  15. Molecular assembly on two-dimensional materials

    NASA Astrophysics Data System (ADS)

    Kumar, Avijit; Banerjee, Kaustuv; Liljeroth, Peter

    2017-02-01

    Molecular self-assembly is a well-known technique to create highly functional nanostructures on surfaces. Self-assembly on two-dimensional (2D) materials is a developing field driven by the interest in functionalization of 2D materials in order to tune their electronic properties. This has resulted in the discovery of several rich and interesting phenomena. Here, we review this progress with an emphasis on the electronic properties of the adsorbates and the substrate in well-defined systems, as unveiled by scanning tunneling microscopy. The review covers three aspects of the self-assembly. The first one focuses on non-covalent self-assembly dealing with site-selectivity due to inherent moiré pattern present on 2D materials grown on substrates. We also see that modification of intermolecular interactions and molecule–substrate interactions influences the assembly drastically and that 2D materials can also be used as a platform to carry out covalent and metal-coordinated assembly. The second part deals with the electronic properties of molecules adsorbed on 2D materials. By virtue of being inert and possessing low density of states near the Fermi level, 2D materials decouple molecules electronically from the underlying metal substrate and allow high-resolution spectroscopy and imaging of molecular orbitals. The moiré pattern on the 2D materials causes site-selective gating and charging of molecules in some cases. The last section covers the effects of self-assembled, acceptor and donor type, organic molecules on the electronic properties of graphene as revealed by spectroscopy and electrical transport measurements. Non-covalent functionalization of 2D materials has already been applied for their application as catalysts and sensors. With the current surge of activity on building van der Waals heterostructures from atomically thin crystals, molecular self-assembly has the potential to add an extra level of flexibility and functionality for applications ranging

  16. Self assembled monolayers on silicon for molecular electronics.

    PubMed

    Aswal, D K; Lenfant, S; Guerin, D; Yakhmi, J V; Vuillaume, D

    2006-05-24

    We present an overview of various aspects of the self-assembly of organic monolayers on silicon substrates for molecular electronics applications. Different chemical strategies employed for grafting the self-assembled monolayers (SAMs) of alkanes having different chain lengths on native oxide of Si or on bare Si have been reviewed. The utility of different characterization techniques in determination of the thickness, molecular ordering and orientation, surface coverage, growth kinetics and chemical composition of the SAMs has been discussed by choosing appropriate examples. The metal counterelectrodes are an integral part of SAMs for measuring their electrical properties as well as using them for molecular electronic devices. A brief discussion on the variety of options available for the deposition of metal counterelectrodes, that is, soft metal contacts, vapor deposition and soft lithography, has been presented. Various theoretical models, namely, tunneling (direct and Fowler-Nordheim), thermionic emission, Poole-Frenkel emission and hopping conduction, used for explaining the electronic transport in dielectric SAMs have been outlined and, some experimental data on alkane SAMs have been analyzed using these models. It has been found that short alkyl chains show excellent agreement with tunneling models; while more experimental data on long alkyl chains are required to understand their transport mechanism(s). Finally, the concepts and realization of various molecular electronic components, that is, diodes, resonant tunnel diodes, memories and transistors, based on appropriate architecture of SAMs comprising of alkyl chains (sigma- molecule) and conjugated molecules (pi-molecule) have been presented.

  17. Self-Assembly and Orientation of Hydrogen-Bonded Oligothiophene Polymorphs at Liquid-Membrane-Liquid Interfaces

    SciTech Connect

    Tevis, Ian D; Palmer, Liam C; Herman, David J; Murray, Ian P; Stone, David A; Stupp, Samuel I

    2012-03-15

    One of the challenges in organic systems with semiconducting function is the achievement of molecular orientation over large scales. We report here on the use of self-assembly kinetics to control long-range orientation of a quarterthiophene derivative designed to combine intermolecular π-π stacking and hydrogen bonding among amide groups. Assembly of these molecules in the solution phase is prevented by the hydrogen-bond-accepting solvent tetrahydrofuran, whereas formation of H-aggregates is facilitated in toluene. Rapid evaporation of solvent in a solution of the quarterthiophene in a 2:1:1 mixture of 1,4-dioxane/tetrahydrofuran/toluene leads to self-assembly of kinetically trapped mats of bundled fibers. In great contrast, slow drying in a toluene atmosphere leads to the homogeneous nucleation and growth of ordered structures shaped as rhombohedra or hexagonal prisms depending on concentration. Furthermore, exceedingly slow delivery of toluene from a high molecular weight polymer solution into the system through a porous aluminum oxide membrane results in the growth of highly oriented hexagonal prisms perpendicular to the interface. The amide groups of the compound likely adsorb onto the polar aluminum oxide surface and direct the self-assembly pathway toward heterogeneous nucleation and growth to form hexagonal prisms. We propose that the oriented prismatic polymorph results from the synergy of surface interactions rooted in hydrogen bonding on the solid membrane and the slow kinetics of self-assembly. These observations demonstrate how self-assembly conditions can be used to guide the supramolecular energy landscape to generate vastly different structures. These fundamental principles allowed us to grow oriented prismatic assemblies on transparent indium-doped tin oxide electrodes, which are of interest in organic electronics.

  18. Self-assembly and orientation of hydrogen-bonded oligothiophene polymorphs at liquid-membrane-liquid interfaces.

    PubMed

    Tevis, Ian D; Palmer, Liam C; Herman, David J; Murray, Ian P; Stone, David A; Stupp, Samuel I

    2011-10-19

    One of the challenges in organic systems with semiconducting function is the achievement of molecular orientation over large scales. We report here on the use of self-assembly kinetics to control long-range orientation of a quarterthiophene derivative designed to combine intermolecular π-π stacking and hydrogen bonding among amide groups. Assembly of these molecules in the solution phase is prevented by the hydrogen-bond-accepting solvent tetrahydrofuran, whereas formation of H-aggregates is facilitated in toluene. Rapid evaporation of solvent in a solution of the quarterthiophene in a 2:1:1 mixture of 1,4-dioxane/tetrahydrofuran/toluene leads to self-assembly of kinetically trapped mats of bundled fibers. In great contrast, slow drying in a toluene atmosphere leads to the homogeneous nucleation and growth of ordered structures shaped as rhombohedra or hexagonal prisms depending on concentration. Furthermore, exceedingly slow delivery of toluene from a high molecular weight polymer solution into the system through a porous aluminum oxide membrane results in the growth of highly oriented hexagonal prisms perpendicular to the interface. The amide groups of the compound likely adsorb onto the polar aluminum oxide surface and direct the self-assembly pathway toward heterogeneous nucleation and growth to form hexagonal prisms. We propose that the oriented prismatic polymorph results from the synergy of surface interactions rooted in hydrogen bonding on the solid membrane and the slow kinetics of self-assembly. These observations demonstrate how self-assembly conditions can be used to guide the supramolecular energy landscape to generate vastly different structures. These fundamental principles allowed us to grow oriented prismatic assemblies on transparent indium-doped tin oxide electrodes, which are of interest in organic electronics.

  19. Depth analysis of molecular orientation induced by nanoimprint graphoepitaxy

    NASA Astrophysics Data System (ADS)

    Okada, Makoto; Fujii, Ryosuke; Haruyama, Yuichi; Ono, Hiroshi; Kawatsuki, Nobuhiro; Matsui, Shinji

    2017-04-01

    The nanoimprint process is a useful technique for the fabrication of various nanostructures on functional materials without the use of any etching processes. We previously confirmed that the molecular orientation of a photo-crosslinkable liquid crystalline polymer (PLCP) was induced by nanoimprinting using a process called nanoimprint graphoepitaxy. In this work, we repeat the previous O2 reactive ion etching processing and molecular orientation evaluation to examine the depth profile of the unidirectional molecular orientation that is induced by nanoimprint graphoepitaxy. The results obtained indicate that the initial PLCP film thickness affects the resulting unidirectional molecular orientation depth.

  20. Orientational order and translational dynamics of magnetic particle assemblies in liquid crystals.

    PubMed

    Peroukidis, Stavros D; Klapp, Sabine H L

    2016-08-10

    Implementing extensive molecular dynamics simulations we explore the organization of magnetic particle assemblies (clusters) in a uniaxial liquid crystalline matrix comprised of rodlike particles. The magnetic particles are modelled as soft dipolar spheres with diameter significantly smaller than the width of the rods. Depending on the dipolar strength coupling the magnetic particles arrange into head-to-tail configurations forming various types of clusters including rings (closed loops) and chains. In turn, the liquid crystalline matrix induces long range orientational ordering to these structures and promotes their diffusion along the director of the phase. Different translational dynamics are exhibited as the liquid crystalline matrix transforms either from isotropic to nematic or from nematic to smectic state. This is caused due to different collective motion of the magnetic particles into various clusters in the anisotropic environments. Our results offer a physical insight for understanding both the structure and dynamics of magnetic particle assemblies in liquid crystalline matrices.

  1. Controlling Orientational Order in 1-D Assemblies of Multivalent Triangular Prisms.

    PubMed

    Kohlstedt, Kevin L; Olvera de la Cruz, Monica; Schatz, George C

    2013-01-03

    Multivalent nanostructures are becoming an increasingly important player in the self-assembly of supramolecular lattices. Understanding the role that shape plays in the coordination of the assemblies is crucial for the functional response of the material. We develop a simple design rule for the assembly of multivalent Au triangular nanoprisms into 1-D ordered arrays based on both the length of the valent DNA and the aspect ratio of the prism. Using MD simulations, we describe an order parameter that captures the short-range order of the assembly controlled by the design parameters. The order parameter shows that even short chains (N = 4) of prisms have a high degree of orientational order that transitions to no orientational order when the DNA length is similar to the prism length. Unlike isotropic polyvalent assemblies, we find that the highly oriented chains of prisms lose orientational order in discrete steps during melting as the prisms in the arrays dissociate.

  2. Molecular engineering and characterization of self-assembled biorecognition surfaces

    NASA Astrophysics Data System (ADS)

    Pan, Sheng

    The development of molecular engineering techniques for the fabrication of biomaterial surfaces is of importance in the field of biomaterials. It offers opportunities for better understanding of biological processes on material surfaces and rational design of contemporary biomaterials. Our work in this area aims to develop novel engineering strategies to design biorecognition surfaces via self-assembly and surface derivatization. Fundamental issues regarding self-assembled monolayer (SAM) structure, formation kinetics, and chemical derivatization were investigated systematically using electron spectroscopy for chemical analysis (ESCA), time-of-flight secondary ion mass spectrometry (TOF-SIMS), infrared reflection absorption spectroscopy (IRAS), atomic force microscopy (AFM), and contact angle measurements. Novel engineering concepts based on multifunctionality and statistical pattern matching were introduced and applied to develop biomimetic surfaces. Our study illustrated that molecules underwent structural transition and orientation development during self-assembly formation, from a disordered, low-density, more liquid-like structure to a highly ordered, closed-packed crystalline-like structure. Surface properties, such as wettability and the reactivity of outermost functional groups can be related to film structure, packing density, as well as molecular orientation. Given the order and organization of SAMs, the accessibility and reactivity of the outermost functional groups, reaction kinetics, stoichiometry, and SAMs stability were studied systematically by surface derivatization of trifluoroacetic anhydride (TFAA). The TFAA derivatization reactions exhibited rapid kinetics on the hydroxyl-terminated SAMs. The data from complementary surface analytical techniques consistently indicated a nearly complete surface reaction. Biomimetic surfaces were made by random immobilization of amino acid of arginine (R), glycine (G), and aspartic acid (D) on well-defined SAMs

  3. Supramolecular Scaffold for Tailoring the Two-Dimensional Assembly of Functional Molecular Units into Organic Thin Films.

    PubMed

    Leung, Franco King-Chi; Ishiwari, Fumitaka; Kajitani, Takashi; Shoji, Yoshiaki; Hikima, Takaaki; Takata, Masaki; Saeki, Akinori; Seki, Shu; Yamada, Yoichi M A; Fukushima, Takanori

    2016-09-14

    Tailoring structurally anisotropic molecular assemblies while controlling their orientation on solid substrates is an important subject for advanced technologies that use organic thin films. Here we report a supramolecular scaffold based on tripodal triptycene assemblies, which enables functional molecular units to assemble into a highly oriented, multilayered two-dimensional (2D) structure on solid substrates. The triptycene building block carries an ethynyl group and three flexible side chains at the 10- and 1,8,13-positions, respectively. These bridgehead-substituted tripodal triptycenes self-assembled on solid substrates to form a well-defined "2D hexagonal + 1D lamellar" structure, which developed parallel to the surface of the substrates. Remarkably, the assembling properties of the triptycene building blocks, particularly for a derivative with tri(oxyethylene)-containing side chains, were not impaired when the alkyne terminal was functionalized with a large molecular unit such as C60, which is comparable in diameter to the triptycene framework. Consequently, thin films with a multilayered 2D assembly of the C60 unit were obtained. Flash-photolysis time-resolved microwave conductivity (FP-TRMC) measurements revealed that the C60 film exhibits highly anisotropic charge-transport properties. Bridgehead-substituted tripodal triptycenes may provide a versatile supramolecular scaffold for tailoring the 2D assembly of molecular units into a highly oriented thin film, and in turn for exploiting the full potential of anisotropic molecular functions.

  4. An autonomous molecular assembler for programmable chemical synthesis

    NASA Astrophysics Data System (ADS)

    Meng, Wenjing; Muscat, Richard A.; McKee, Mireya L.; Milnes, Phillip J.; El-Sagheer, Afaf H.; Bath, Jonathan; Davis, Benjamin G.; Brown, Tom; O'Reilly, Rachel K.; Turberfield, Andrew J.

    2016-06-01

    Molecular machines that assemble polymers in a programmed sequence are fundamental to life. They are also an achievable goal of nanotechnology. Here, we report synthetic molecular machinery made from DNA that controls and records the formation of covalent bonds. We show that an autonomous cascade of DNA hybridization reactions can create oligomers, from building blocks linked by olefin or peptide bonds, with a sequence defined by a reconfigurable molecular program. The system can also be programmed to achieve combinatorial assembly. The sequence of assembly reactions and thus the structure of each oligomer synthesized is recorded in a DNA molecule, which enables this information to be recovered by PCR amplification followed by DNA sequencing.

  5. Control of colloidal placement by modulated molecular orientation in nematic cells

    PubMed Central

    Peng, Chenhui; Turiv, Taras; Guo, Yubing; Shiyanovskii, Sergij V.; Wei, Qi-Huo; Lavrentovich, Oleg D.

    2016-01-01

    Colloids self-assemble into various organized superstructures determined by particle interactions. There is tremendous progress in both the scientific understanding and the applications of self-assemblies of single-type identical particles. Forming superstructures in which the colloidal particles occupy predesigned sites and remain in these sites despite thermal fluctuations represents a major challenge of the current state of the art. We propose a versatile approach to directing placement of colloids using nematic liquid crystals with spatially varying molecular orientation preimposed by substrate photoalignment. Colloidal particles in a nematic environment are subject to the long-range elastic forces originating in the orientational order of the nematic. Gradients of the orientational order create an elastic energy landscape that drives the colloids into locations with preferred type of deformations. As an example, we demonstrate that colloidal spheres with perpendicular surface anchoring are driven into the regions of maximum splay, whereas spheres with tangential surface anchoring settle into the regions of bend. Elastic forces responsible for preferential placement are measured by exploring overdamped dynamics of the colloids. Control of colloidal self-assembly through patterned molecular orientation opens new opportunities for designing materials and devices in which particles should be placed in predesigned locations. PMID:27652343

  6. Converting molecular information of redox coenzymes via self-assembly.

    PubMed

    Morikawa, Masa-aki; Kimizuka, Nobuo

    2012-11-21

    β-Nicotinamide adenine dinucleotide (NAD(+)) and its reduced form NADH specifically interact with a cyanine dye in aqueous media, giving distinct spectral and nanostructural characteristics to which molecular information of constituent coenzymes are converted via self-assembly.

  7. Magnetotactic molecular architectures from self-assembly of β-peptide foldamers

    PubMed Central

    Kwon, Sunbum; Kim, Beom Jin; Lim, Hyung-Kyu; Kang, Kyungtae; Yoo, Sung Hyun; Gong, Jintaek; Yoon, Eunyoung; Lee, Juno; Choi, Insung S.; Kim, Hyungjun; Lee, Hee-Seung

    2015-01-01

    The design of stimuli-responsive self-assembled molecular systems capable of undergoing mechanical work is one of the most important challenges in synthetic chemistry and materials science. Here we report that foldectures, that is, self-assembled molecular architectures of β-peptide foldamers, uniformly align with respect to an applied static magnetic field, and also show instantaneous orientational motion in a dynamic magnetic field. This response is explained by the amplified anisotropy of the diamagnetic susceptibilities as a result of the well-ordered molecular packing of the foldectures. In addition, the motions of foldectures at the microscale can be translated into magnetotactic behaviour at the macroscopic scale in a way reminiscent to that of magnetosomes in magnetotactic bacteria. This study will provide significant inspiration for designing the next generation of biocompatible peptide-based molecular machines with applications in biological systems. PMID:26510658

  8. Magnetotactic molecular architectures from self-assembly of β-peptide foldamers

    NASA Astrophysics Data System (ADS)

    Kwon, Sunbum; Kim, Beom Jin; Lim, Hyung-Kyu; Kang, Kyungtae; Yoo, Sung Hyun; Gong, Jintaek; Yoon, Eunyoung; Lee, Juno; Choi, Insung S.; Kim, Hyungjun; Lee, Hee-Seung

    2015-10-01

    The design of stimuli-responsive self-assembled molecular systems capable of undergoing mechanical work is one of the most important challenges in synthetic chemistry and materials science. Here we report that foldectures, that is, self-assembled molecular architectures of β-peptide foldamers, uniformly align with respect to an applied static magnetic field, and also show instantaneous orientational motion in a dynamic magnetic field. This response is explained by the amplified anisotropy of the diamagnetic susceptibilities as a result of the well-ordered molecular packing of the foldectures. In addition, the motions of foldectures at the microscale can be translated into magnetotactic behaviour at the macroscopic scale in a way reminiscent to that of magnetosomes in magnetotactic bacteria. This study will provide significant inspiration for designing the next generation of biocompatible peptide-based molecular machines with applications in biological systems.

  9. Thomas double scattering in electron capture from oriented molecular hydrogen

    SciTech Connect

    Alston, S.; Brennan, T.; Bannon, F.

    1995-11-01

    Electron capture from hydrogen molecules by protons is treated using the second-order Born approximation. Differential cross sections in an adiabatic-nuclei approximation for specific molecular orientations and for an equally weighted averaging over all orientations are presented for incident energies of 2.5 and 10 MeV. A Hartree-Fock molecular wave function and linearized-propagator approximation are employed to evaluate the amplitude. An approximate factoring of the amplitude into double scattering and diffraction (arising from the two target nuclei) components is shown to give a poor description of high-velocity molecular capture.

  10. Structural investigations of oriented membrane assemblies by FTIR-ATR spectroscopy

    NASA Astrophysics Data System (ADS)

    Fringeli, Urs Peter; Goette, Jeannette; Reiter, Gerald; Siam, Monira; Baurecht, Dieter

    1998-06-01

    In situ attenuated total reflection (ATR) Fourier transform (FT) spectroscopy is presented as an adequate tool for studying molecular structure and function of biomembranes. In this article emphasis was directed to the production of suitable model bilayer membranes for optimum mimicking of natural biomembranes, and to special FTIR ATR techniques to achieve enhanced selectivity as well as time resolved information on complex membrane assemblies. In this context, the preparation of supported bilayers according to the LB/vesicle method is presented and the use of such model membranes to build more complex assemblies, e.g. with creatine kinase, a surface bound enzyme, and alkaline phosphatase, a membrane anchored enzyme. A comprehensive summary of equations used for quantitative ATR spectroscopy is given and applied to determine the surface concentration and orientation of membrane bound molecules. The use of supported bilayers for drug membrane interaction studies is demonstrated by the local anesthetic dibucaine. Besides of structural information's, such studies result also thermodynamic date, such as adsorption isotherm and partition coefficient. A special ATR set-up for more precise background compensation is presented enabling the conversion of a single beam spectrometer into a pseudo double beam spectrometer. This optical component may be placed in the sample compartment of the spectrometer, and is referred to as single-beam-sample-reference (SBSR) attachment. Finally, a short theoretical introduction into time resolved modulation spectroscopy is given. Temperature modulated excitation of reversible conformational changes in the polypeptide poly-L-lysine and the enzyme RNase are shown as examples.

  11. Orientational anisotropy in simulated vapor-deposited molecular glasses

    SciTech Connect

    Lyubimov, Ivan; Antony, Lucas; Walters, Diane M.; Ediger, M. D.; Rodney, David; Pablo, Juan J. de

    2015-09-07

    Enhanced kinetic stability of vapor-deposited glasses has been established for a variety of glass organic formers. Several recent reports indicate that vapor-deposited glasses can be orientationally anisotropic. In this work, we present results of extensive molecular simulations that mimic a number of features of the experimental vapor deposition process. The simulations are performed on a generic coarse-grained model and an all-atom representation of N,N′-bis(3-methylphenyl)-N,N′-diphenylbenzidine (TPD), a small organic molecule whose vapor-deposited glasses exhibit considerable orientational anisotropy. The coarse-grained model adopted here is found to reproduce several key aspects reported in experiments. In particular, the molecular orientation of vapor-deposited glasses is observed to depend on substrate temperature during deposition. For a fixed deposition rate, the molecular orientation in the glasses changes from isotropic, at the glass transition temperature, T{sub g}, to slightly normal to the substrate at temperatures just below T{sub g}. Well below T{sub g}, molecular orientation becomes predominantly parallel to the substrate. The all-atom model is used to confirm some of the equilibrium structural features of TPD interfaces that arise above the glass transition temperature. We discuss a mechanism based on distinct orientations observed at equilibrium near the surface of the film, which get trapped within the film during the non-equilibrium process of vapor deposition.

  12. Molecular Engineering of Self-assembled Nanoreactors

    DTIC Science & Technology

    2014-08-15

    with the ability to control enzyme encapsulation/release through conformational shifts in the nanostructure in response to environmental changes; (2...Assembly of enzyme and cofactor on a DNA nanostructure to evaluate the essential parameters for modulating catalysis; (3) Switchable enzyme ...structural DNA nanotechnology with the functionality of biological enzymes to produce 1. REPORT DATE (DD-MM-YYYY) 4. TITLE AND SUBTITLE 13

  13. Photon Upconversion and Molecular Solar Energy Storage by Maximizing the Potential of Molecular Self-Assembly.

    PubMed

    Kimizuka, Nobuo; Yanai, Nobuhiro; Morikawa, Masa-Aki

    2016-11-29

    The self-assembly of functional molecules into ordered molecular assemblies and the fulfillment of potentials unique to their nanotomesoscopic structures have been one of the central challenges in chemistry. This Feature Article provides an overview of recent progress in the field of molecular self-assembly with the focus on the triplet-triplet annihilation-based photon upconversion (TTA-UC) and supramolecular storage of photon energy. On the basis of the integration of molecular self-assembly and photon energy harvesting, triplet energy migration-based TTA-UC has been achieved in varied molecular systems. Interestingly, some molecular self-assemblies dispersed in solution or organogels revealed oxygen barrier properties, which allowed TTA-UC even under aerated conditions. The elements of molecular self-assembly were also introduced to the field of molecular solar thermal fuel, where reversible photoliquefaction of ionic crystals to ionic liquids was found to double the molecular storage capacity with the simultaneous pursuit of switching ionic conductivity. A future prospect in terms of innovating molecular self-assembly toward molecular systems chemistry is also discussed.

  14. Harnessing Surface Dislocation Networks for Molecular Self-Assembly

    NASA Astrophysics Data System (ADS)

    Pohl, Karsten

    2009-03-01

    The controlled fabrication of functional wafer-based nano-arrays is one of the ultimate quests in current nanotechnologies. Well-ordered misfit dislocation networks of ultrathin metal films are viable candidates for the growth of two- dimensional ordered cluster arrays in the nanometer regime. Such bottom-up processes can be very complex, involving collective effects from a large number of atoms. Unraveling the fundamental forces that drive these self-assembly processes requires detailed experimental information at the atomic level of large ensembles of hundreds to thousands of atoms. The combination of variable temperature measurements from our home-built STM correlated with 2D Frenkel-Kontorova models based on first-principle interaction parameters is used to explain how uniform arrays can form with the strain in the thin film as the driving force responsible for the surface self-assembly process. This process is generally applicable to assemble many molecular species thus opening avenues towards complex self-assembled structures based on a lock-and-key type approach. Moreover, when increasing the molecular coverage and/or decreasing the strain in the thin film the intermolecular interactions will eventually dominate the elastic effects and dictate the self-assembly process via molecular structure and functionality. We will show that controlling this delicate balance leads to a richness of structures, ranging from disperse ordered arrays of molecular clusters to patterned self-assembled monolayers (SAMs) of functionalized fullerenes and methanethiol.

  15. Molecular Fraction Behavior in Oriented Polymers.

    DTIC Science & Technology

    1980-06-01

    remarkably well the experimental behavior and the reduced shift factors obtained correspond to WI. equation for superposition of low strain linear viscoelastic...the rupture ofa significant number of load-bearing tie chains during loading to fracture. Also, Zhurkov found departure fnn eqlation (I) for low ...than Mn"l Some error il tile determninatioii of Nin may also ha:Ie resulted from the presence of a low molecular weight component 59 (sonic kind of

  16. Molecular mechanism of arenavirus assembly and budding.

    PubMed

    Urata, Shuzo; Yasuda, Jiro

    2012-10-10

    Arenaviruses have a bisegmented negative-strand RNA genome, which encodes four viral proteins: GP and NP by the S segment and L and Z by the L segment. These four viral proteins possess multiple functions in infection, replication and release of progeny viruses from infected cells. The small RING finger protein, Z protein is a matrix protein that plays a central role in viral assembly and budding. Although all arenaviruses encode Z protein, amino acid sequence alignment showed a huge variety among the species, especially at the C-terminus where the L-domain is located. Recent publications have demonstrated the interactions between viral protein and viral protein, and viral protein and host cellular protein, which facilitate transportation and assembly of viral components to sites of virus egress. This review presents a summary of current knowledge regarding arenavirus assembly and budding, in comparison with other enveloped viruses. We also refer to the restriction of arenavirus production by the antiviral cellular factor, Tetherin/BST-2.

  17. Molecular Mechanism of Arenavirus Assembly and Budding

    PubMed Central

    Urata, Shuzo; Yasuda, Jiro

    2012-01-01

    Arenaviruses have a bisegmented negative-strand RNA genome, which encodes four viral proteins: GP and NP by the S segment and L and Z by the L segment. These four viral proteins possess multiple functions in infection, replication and release of progeny viruses from infected cells. The small RING finger protein, Z protein is a matrix protein that plays a central role in viral assembly and budding. Although all arenaviruses encode Z protein, amino acid sequence alignment showed a huge variety among the species, especially at the C-terminus where the L-domain is located. Recent publications have demonstrated the interactions between viral protein and viral protein, and viral protein and host cellular protein, which facilitate transportation and assembly of viral components to sites of virus egress. This review presents a summary of current knowledge regarding arenavirus assembly and budding, in comparison with other enveloped viruses. We also refer to the restriction of arenavirus production by the antiviral cellular factor, Tetherin/BST-2. PMID:23202453

  18. Numerical optimization of laser fields to control molecular orientation

    SciTech Connect

    Ben Haj-Yedder, A.; Auger, A.; Dion, C.M.; Cances, E.; Le Bris, C.; Keller, A.; Atabek, O.

    2002-12-01

    A thorough numerical illustration of an optimal control scenario dealing with the laser-induced orientation of a diatomic molecule (LiF) is presented. Special emphasis is laid on the definition of the various targets dealing with different orientation characteristics, identified in terms of maximum efficiency (i.e., molecular axis direction closest to the direction of the laser polarization vector), maximum duration (i.e., the time interval during which this orientation is maintained), or of a compromise between efficiency and duration. Excellent postpulse orientation is achieved by sudden, intense pulses. Thermal effects are also studied with an extension of the control scenarios to Boltzmann averaged orientation dynamics at T=5 K.

  19. Phase-dependent field-free molecular alignment and orientation

    NASA Astrophysics Data System (ADS)

    Qin, Chaochao; Liu, Yuzhu; Zhang, Xianzhou; Gerber, Thomas

    2014-11-01

    We investigated the temporal behavior of alignment and orientation of LiH following a femtosecond laser pulse excitation comprising two fields at center frequencies ω and 2 ω (e.g., E (t )=E [cos(ω t )+cos(2 ω t +Φ ) ] ) shifted by a phase Φ . The effects of repopulations and rephasing of rotational states on the resulting alignment and orientation were evaluated. The population distribution of rotational states is only changed during the exciting pulse. Afterwards the established rotational state distribution is maintained in the absence of collisions. The phases of rotational states play the most crucial role in determining the time evolution of molecular alignment and orientation. Equal alignment and rotational populations are obtained when the phases are chosen Φ =0 and Φ =π . However, orientation is different due to the fact that in the case Φ =π the mutual phases of even rotation states are not changed but the phases of odd rotational states are shifted by π , comparing with that of Φ =0 . The effect of temperature on molecular orientation was also addressed. It was shown that an efficient field-free molecular orientation can be observed even at room temperature.

  20. Molecular alignment and orientation with a hybrid Raman scattering technique

    NASA Astrophysics Data System (ADS)

    Bustard, Philip J.; Lausten, R.; Sussman, Benjamin J.

    2012-11-01

    We demonstrate a scheme for the preparation of molecular alignment and angular momentum orientation using a hybrid combination of two limits of Raman scattering. First a weak, impulsive pump pulse initializes the system via the nonresonant dynamic Stark effect. Then, having overcome the influence of the vacuum fluctuations, an amplification pulse selectively enhances the initial coherences by transient stimulated Raman scattering, generating alignment and angular momentum orientation of molecular hydrogen. The amplitude and phase of the resulting coherent dynamics are experimentally probed, indicating an amplification factor of 4.5. An analytic theory is developed to model the dynamics.

  1. Easy creation of polymeric systems for molecular dynamics with Assemble!

    NASA Astrophysics Data System (ADS)

    Degiacomi, Matteo T.; Erastova, Valentina; Wilson, Mark R.

    2016-05-01

    We present Assemble!, a program greatly simplifying the preparation of molecular dynamics simulations of polymeric systems. The program is controlled either via command line or an intuitive Graphical User Interface, and runs on all major operating systems. Assemble! allows the creation of a desired system of polymer chains from constituent monomers, packs the chains into a box according to the required concentration and returns all the files needed for simulation with Gromacs. We illustrate the capabilities of Assemble! by demonstrating the easy preparation of a 300 monomers-long polyisoprene in hexane, and a heterogeneous mixture of polybutadiene.

  2. The art and science of self-assembling molecular machines

    NASA Astrophysics Data System (ADS)

    Gómez-López, Marcos; Preece, Jon A.; Fraser Stoddart, J.

    1996-09-01

    In this review, we show how noncovalent bonding interactions between 0957-4484/7/3/004/img1-electron rich aromatic ring systems (e.g. hydroquinone) and the 0957-4484/7/3/004/img1-electron deficient tetracationic cyclophane, cyclobis(paraquat-p-phenylene) can be used to self-assemble novel molecular architectures which are not only interesting to us, because of their fascinating topologies, but also because they have the potential to be developed into molecular structures with switchable properties on the nanometre scale. The high efficiency observed in the self-assembly of a [2]catenane, and its dynamic properties in solution, represent the first step in the design and self-assembly of other molecular assemblies better suited for the study of molecular switching processes. Therefore, a series of [2]rotaxanes, mechanically-interlocked molecular compounds, consisting of a linear 0957-4484/7/3/004/img1-electron rich dumbbell-shaped component and the 0957-4484/7/3/004/img1-electron deficient tetracationic cyclophane as the cyclic component, have been self-assembled and evaluated. All of the so-called molecular shuttles show translational isomerism and one of them, comprising benzidine and biphenol recognition sites as the non-degenerate 0957-4484/7/3/004/img1-electron rich sites, shows molecular switching properties when it is perturbed by external stimuli, such as electrons and protons. The versatility of our approach to nanoscale molecular switches is proven by the description of a series of molecular assemblies and supramolecular arrays, consisting of 0957-4484/7/3/004/img1-electron rich and 0957-4484/7/3/004/img1-electron deficient components, which display molecular switching properties when they are influenced by external stimuli that are photochemical, electrochemical and/or chemical in nature. However, the molecular switching phenomena take place in the solution state. Therefore, finally we describe how simple molecular structures can be ordered on to a solid

  3. Task oriented nonlinear control laws for telerobotic assembly operations

    NASA Technical Reports Server (NTRS)

    Walker, R. A.; Ward, L. S.; Elia, C. F.

    1987-01-01

    The goal of this research is to achieve very intelligent telerobotic controllers which are capable of receiving high-level commands from the human operator and implementing them in an adaptive manner in the object/task/manipulator workspace. Initiatives by the authors at Integrated Systems, Inc. to identify and develop the key technologies necessary to create such a flexible, highly programmable, telerobotic controller are presented. The focus of the discussion is on the modeling of insertion tasks in three dimensions and nonlinear implicit force feedback control laws which incorporate tool/workspace constraints. Preliminary experiments with dual arm beam assembly in 2-D are presented.

  4. High photocatalytic capability of self-assembled nanoporous WO3 with preferential orientation of (002) planes.

    PubMed

    Guo, Yafeng; Quan, Xie; Lu, Na; Zhao, Huimin; Chen, Shuo

    2007-06-15

    Self-assembled nanoporous tungsten oxide (WO3) with preferential orientation (002) planes was successfully synthesized on the tungsten sheet by anodization in a 0.2 wt % NaF and 0.3% (V/V) HF mixture solution in a 1:1 ratio. The pores, of a highly ordered self-assembled structure, had an average size of approximately 70 nm. X-ray diffraction identified a monoclinic WO3 structure and fine preferential orientation of (002) planes. A maximum photoconversion efficiency of 17.2% was obtained for the self-assembled nanoporous WO3 under high-pressure mercury lamp illumination. The photocatalytic (PC) degradation of pentachlorophenol (PCP) in aqueous solution using the self-assembled nanoporous WO3 photocatalyst, performed under both high-pressure mercury lamp and Xe lamp illumination, showed more excellent PC capability than WO3 film and TiO2 nanotube arrays.

  5. Molecular Recognition Directed Self-Assembly of Supramolecular Polymers

    DTIC Science & Technology

    1994-06-30

    SUPRAMOLECULAR POLYMERS by V. Percec, J. Heck, G. Johansson, D. Tomazos, M. Kawasumi and G. Ungar Published in the J. Macromol. SOi: Part A: Pure...W.asetaqIom OC JOS0l 4 TITE AN SUBITLES. FUNDING NUMBERS Molecular Recognition Directed Self-Assembly of Suprainolecular Polymers N00014-89--J-1828 6. AUTHOR(S...comparison between various supramolecular (generated via H-bonding, iions) and molecular " polymer backbones" will be made. The present limitations

  6. Cluster assembly in hierarchically collapsing molecular clouds

    NASA Astrophysics Data System (ADS)

    Vazquez-Semadeni, Enrique

    2015-08-01

    I will discuss the mechanism of cluster formation in hierarchically collapsing molecular clouds. Recent evidence, both observational and numerical, suggests that molecular clouds (MCs) may be undergoing global, hierarchical gravitational collapse. The "hierarchical" regime consists of small-scale collapses within larger-scale ones. The former occur in a more scattered fashion and at slightly earlier times, and are themselves falling into the larger potential well of the still-ongoing large-scale collapse. Instead, the large-scale collapse culminates a few Myr later, in a highly focused region, of higher density, mass, and velocity dispersion. The stars formed in the early, small-scale collapses share the infall velocity of their parent clumps towards the larger potential trough, while those formed later, in the aforementioned trough, form from gas that has already dissipated some of its kinetic energy, and thus have a lower velocity dispersion. This leads to a radial age gradient in the stellar population, in agreement with recent observations.

  7. Molecular assemblies as protective barriers and adhesion promotion interlayer

    DOEpatents

    King, D.E.; Czanderna, A.W.; Kennedy, C.E.

    1996-01-30

    A protective diffusion barrier having adhesive qualities for metalized surfaces is provided by a passivating agent having the formula HS--(CH{sub 2}){sub 11}--COOH which forms a very dense, transparent organized molecular assembly or layer that is impervious to water, alkali, and other impurities and corrosive substances that typically attack metal surfaces. 8 figs.

  8. Molecular assemblies as protective barriers and adhesion promotion interlayer

    DOEpatents

    King, David E.; Czanderna, Alvin W.; Kennedy, Cheryl E.

    1996-01-01

    A protective diffusion barrier having adhesive qualifies for metalized surfaces is provided by a passivating agent having the formula HS--(CH.sub.2).sub.11 --COOH Which forms a very dense, transparent organized molecular assembly or layer that is impervious to water, alkali, and other impurities and corrosive substances that typically attack metal surfaces.

  9. Molecular Recognition Directed Self-Assembly of Supramolecular Architectures

    DTIC Science & Technology

    1994-06-30

    chemistry. The ability of these supramolecular architectures to form liquid crystalline phases is determined by the shape of the self-assembled...be discussed. In the case of TMV-like supramolecular architectures a comparison between various supramolecdr (generated via H-bonding, ionic and...molecular, macromolecular and supramolecular chemistry. The ability of these supramolecular architectures to form liquid crystalline phases is determined

  10. Dipole-Oriented Molecular Solids Can Undergo a Phase Change and Still Maintain Electrical Polarization

    SciTech Connect

    Cassidy, Andrew; Jørgensen, Mads R. V.; Rosu-Finsen, Alexander; Lasne, Jérôme; Jørgensen, Jakob H.; Glavic, Artur; Lauter, Valeria; Iversen, Bo B.; McCoustra, Martin R. S.; Field, David

    2016-10-02

    It has recently been demonstrated that nanoscale molecular films can spontaneously assemble to self-generate intrinsic electric fields that can exceed 108 V/m. These electric fields originate from polarization charges in the material that arise because the films self-assemble to orient molecular dipole moments. This has been called the spontelectric effect. Such growth of spontaneously polarized layers of molecular solids has implications for our understanding of how intermolecular interactions dictate the structure of molecular materials used in a range of applications, for example, molecular semiconductors, sensors, and catalysts. In this paper, we present the first in situ structural characterization of a representative spontelectric solid, nitrous oxide. Infrared spectroscopy, temperature-programmed desorption, and neutron reflectivity measurements demonstrate that polarized films of nitrous oxide undergo a structural phase transformation upon heating above 48 K. A mean-field model can be used to describe quantitatively the magnitude of the spontaneously generated field as a function of film-growth temperature, and this model also recreates the phase change. Finally, this reinforces the spontelectric model as a means of describing long-range dipole–dipole interactions and points to a new type of ordering in molecular thin films.

  11. Dipole-Oriented Molecular Solids Can Undergo a Phase Change and Still Maintain Electrical Polarization

    DOE PAGES

    Cassidy, Andrew; Jørgensen, Mads R. V.; Rosu-Finsen, Alexander; ...

    2016-10-02

    It has recently been demonstrated that nanoscale molecular films can spontaneously assemble to self-generate intrinsic electric fields that can exceed 108 V/m. These electric fields originate from polarization charges in the material that arise because the films self-assemble to orient molecular dipole moments. This has been called the spontelectric effect. Such growth of spontaneously polarized layers of molecular solids has implications for our understanding of how intermolecular interactions dictate the structure of molecular materials used in a range of applications, for example, molecular semiconductors, sensors, and catalysts. In this paper, we present the first in situ structural characterization of amore » representative spontelectric solid, nitrous oxide. Infrared spectroscopy, temperature-programmed desorption, and neutron reflectivity measurements demonstrate that polarized films of nitrous oxide undergo a structural phase transformation upon heating above 48 K. A mean-field model can be used to describe quantitatively the magnitude of the spontaneously generated field as a function of film-growth temperature, and this model also recreates the phase change. Finally, this reinforces the spontelectric model as a means of describing long-range dipole–dipole interactions and points to a new type of ordering in molecular thin films.« less

  12. Effect of cross-linking ultrahigh molecular weight polyethylene: Surface molecular orientation and wear characteristics

    SciTech Connect

    Sambasivan, Sharadha; Fischer, Daniel A.; Hsu, Stephen M.

    2007-07-15

    Molecular orientation at the surface layer of cross-linked ultrahigh molecular weight polyethylene (UHMWPE) has been examined. Molecular orientation has been shown to affect the wear resistance and surface mechanical properties of UHMWPE under biomechanical loading conditions. This study utilizes a nondestructive synchrotron based soft x-ray technique; near edge x-ray absorption fine structure at the carbon K-edge to examine the degree of surface molecular orientation of UHMWPE subjected to various cross-linking/sterilization techniques as a function of stress and wear. UHMWPE samples prepared under gamma irradiation, ethylene-oxide (EtO) treatment, and electron beam irradiation were worn in a wear tester systematically. Results suggest that the cross-linking resists surface orientation when the samples were under tensile and biomechanical stresses. The molecular orientation in the C-C chains in the polymer showed a monotonic decrease with an increase in gamma irradiation dosage levels. EtO sterilized samples showed more C-C chain orientation than the electron beam irradiated samples, but lower than the 30 kGy gamma irradiated samples. Ordered C-C chains in UHMWPE samples have been associated with more crystallinity or large strain plastic deformation of the polymer. Higher levels of gamma irradiation appear to induce cross-linking of C-C chains and render a polymer with more amorphous phase which resists orientation after wear and imparts wear resistance to the polymer.

  13. Effect of contact angle on the orientation, stability, and assembly of dense floating cubes.

    PubMed

    Daniello, Robert; Khan, Kashan; Donnell, Michael; Rothstein, Jonathan P

    2014-02-01

    In this paper, the effect of contact angle, density, and size on the orientation, stability, and assembly of floating cubes was investigated. All the cubes tested were more dense than water. Floatation occurred as a result of capillary stresses induced by deformation of the air-water interface. The advancing contact angle of the bare acrylic cubes was measured to be 85°. The contact angle of the cubes was increased by painting the cubes with a commercially available superhydrophobic paint to reach an advancing contact angle of 150°. Depending on their size, density, and contact angle, the cubes were observed to float in one of three primary orientations: edge up, vertex up, and face up. An experimental apparatus was built such that the sum of the gravitational force, buoyancy force, and capillary forces could be measured using a force transducer as a function of cube position as it was lowered through the air-water interface. Measurements showed that the maximum capillary forces were always experienced for the face up orientation. However, when floatation was possible in the vertex up orientation, it was found to be the most stable cube orientation because it had the lowest center of gravity. A series of theoretical predictions were performed for the cubes floating in each of the three primary orientations to calculate the net force on the cube. The theoretical predictions were found to match the experimental measurements well. A cube stability diagram of cube orientation as a function of cube contact angle and size was prepared from the predictions of theory and found to match the experimental observations quite well. The assembly of cubes floating face up and vertex up were also studied for assemblies of two, three, and many cubes. Cubes floating face up were found to assemble face-to-face and form regular square lattice patterns with no free interface between cubes. Cubes floating vertex up were found to assemble in a variety of different arrangements

  14. Overview of DNA origami for molecular self-assembly.

    PubMed

    Saaem, Ishtiaq; LaBean, Thomas H

    2013-01-01

    Judging by the number of atoms and the precision with which they are organized in three-dimensional space, DNA origami assemblies represent the current acme of human molecular engineering accomplishments. A subset of structural DNA nanotechnology, DNA origami makes use of the programmable molecular recognition of complementary DNA cohesions to assemble designed structures. This review will discuss the development of concepts and methods involved in DNA origami with an eye toward future increases in origami size and sequence complexity, as well as exploring different methods for the production of the DNA molecular components (long biologically synthesized scaffold strands and the complex set of chemically synthesized staple strands). In future applications, the incorporation and organization of other materials (metals and other inorganics, protein enzymes, and other nanomaterials) upon or within DNA origami should result in tools for "bottom-up" nanofabrication of biomedical, electronic, and photonic devices and materials.

  15. Molecular Origins of Thermal Transitions in Polyelectrolyte Assemblies

    NASA Astrophysics Data System (ADS)

    Yildirim, Erol; Zhang, Yanpu; Antila, Hanne S.; Lutkenhaus, Jodie L.; Sammalkorpi, Maria; Aalto Team; Texas A&M Team

    2015-03-01

    Polyelectrolyte (PE) multilayers and complexes formed from oppositely charged polymers can exhibit extraordinary superhydrophobicity, mechanical strength and responsiveness resulting in applications ranging functional membranes, optics, sensors and drug delivery. Depending on the assembly conditions, PE assemblies may undergo a thermal transition from glassy to soft behavior under heating. Our earlier work using thermal analysis measurements shows a distinct thermal transition for PE layer-by-layer (LbL) systems assembled with added salt but no analogous transition in films assembled without added salt or dry systems. These findings raise interesting questions on the nature of the thermal transition; here, we explore its molecular origins through characterization of the PE aggregates by temperature-controlled all-atom molecular dynamics simulations. We show via molecular simulations the thermal transition results from the existence of an LCST (lower critical solution temperature) in the PE systems: the diffusion behavior, hydrogen bond formation, and bridging capacity of water molecules plasticizing the complex changes at the transition temperature. We quantify the behavior, map its chemistry specificity through comparison of strongly and weakly charged PE complexes, and connect the findings to our interrelated QCM-D experiments.

  16. Theoretical Modelling of Self-Assembly of Molecular Networks

    NASA Astrophysics Data System (ADS)

    Mura, Manuela; Martsinovich, Natalia; Kantorovich, Lev

    2008-03-01

    The phenomenon of self-assembly of atomic and molecular superstructures on crystal surfaces has attracted an increasing interest in nanotechnology. Self-organised nano-templates where the self-assembled monolayer traps other molecules with selected functional properties, can be used as building blocks for larger nanoscale structures. These superstructures can form chiral domains ranging from 1D chains to 2D monolayers. In particular, there have been many scanning tunneling microscopy (STM)studies of self-assembly of melamine, perylene tetra-carboxylic di-imide(PTCDI) or perylene tetra-carboxylic di-anhydride (PTCDA) molecules on the Au(111). STM images of these networks do not reveal the exact details of the intermolecular bonding and process of network growth. It is therefore the task of theory to determine the exact atomic structure of these networks. We present a theoretical study of self-assembly of molecular networks based on different molecules by using a systematic approach to build molecular superstructures. The energies of these structures are calculated using the density-functional theory SIESTA code. The theoretically predicted monolayer structures are in very good agreement with the results of STM measurements.

  17. Structure and dynamics of layered molecular assemblies

    NASA Astrophysics Data System (ADS)

    Horne, Jennifer Conrad

    This dissertation focuses on the goal of understanding and controlling layered material properties from a molecular perspective. With this understanding, materials can be synthetically tailored to exhibit predetermined bulk properties. This investigation describes the optical response of a family of metal-phosphonate (MP) monolayers and multilayers, materials that are potentially useful because the films are easy to synthesize and are chemically and thermally stable. MP films have shown potential in a variety of chemical sensing and optical applications, and in this dissertation, the suitability of MP films for optical information storage is explored For this application, the extent of photonic energy transport within and between optically active layers is an important factor in determining the stability and specificity of optical modifications made to a material. Intralayer and interlayer energy transport processes can be studied selectively in MP films because the composition, and thus the properties, of each layer are controlled synthetically. It was determined by fluorescence relaxation dynamics in conjunction with atomic force microscopy (AFM) that the substrate and layer morphologies are key factors in determining the layer optical and physical properties. The initial MP layers in a multilayer are structurally heterogeneous, characterized by randomly distributed islands that are ~50 A in diameter. The population dynamics measured for these layers are non-exponential, chromophore concentration-independent, and identical for two different chromophores. The data is explained in the context of an excitation hopping model in a system where the surface is characterized by islands of aggregated chromophores as well as non-aggregated monomers. Within a MP monolayer, the dynamics are dominated by intra-island excitation hopping. Forster (dipolar) energy transfer between the energetically overlapped chromophores does not play a significant role in determining the

  18. On-surface molecular nanoarchitectonics: From self-assembly to directed assembly

    NASA Astrophysics Data System (ADS)

    Wakayama, Yutaka

    2016-11-01

    The rogress of on-surface molecular nanoarchitectonics over the last two decades has been reviewed. Over the early period in the 1990s-2000s, molecular self-assemblies were intensively studied, where van der Waals (vdW) interaction was predominant. After that, in the 2000s, selective intermolecular interactions based on hydrogen bonds and metal-molecule coordination enabled one to direct the assembling behaviors. Here, the concept of this directed assembly is opposite to that of the vdW-based self-assembly because the resulting architectures are purposefully tailored by programing intermolecular interaction. These efforts brought forth fruit in the on-surface syntheses of covalent bond networks. Particularly in the 2010s, on-surface covalent coupling was applied to graphene nanoribbons, where widths and edge structures can be precisely defined on the atomic scale. These works have the potential to bridge fundamental material nanoarchitectonics and functional device fabrication. In this paper, such a historical development of on-surface molecular nanoarchitectonics is reviewed, with the specific emphasis on the superiority of scanning tunneling microscopy.

  19. Ligand Pose and Orientational Sampling in Molecular Docking

    PubMed Central

    Coleman, Ryan G.; Carchia, Michael; Sterling, Teague; Irwin, John J.; Shoichet, Brian K.

    2013-01-01

    Molecular docking remains an important tool for structure-based screening to find new ligands and chemical probes. As docking ambitions grow to include new scoring function terms, and to address ever more targets, the reliability and extendability of the orientation sampling, and the throughput of the method, become pressing. Here we explore sampling techniques that eliminate stochastic behavior in DOCK3.6, allowing us to optimize the method for regularly variable sampling of orientations. This also enabled a focused effort to optimize the code for efficiency, with a three-fold increase in the speed of the program. This, in turn, facilitated extensive testing of the method on the 102 targets, 22,805 ligands and 1,411,214 decoys of the Directory of Useful Decoys - Enhanced (DUD-E) benchmarking set, at multiple levels of sampling. Encouragingly, we observe that as sampling increases from 50 to 500 to 2000 to 5000 to 20000 molecular orientations in the binding site (and so from about 1×1010 to 4×1010 to 1×1011 to 2×1011 to 5×1011 mean atoms scored per target, since multiple conformations are sampled per orientation), the enrichment of ligands over decoys monotonically increases for most DUD-E targets. Meanwhile, including internal electrostatics in the evaluation ligand conformational energies, and restricting aromatic hydroxyls to low energy rotamers, further improved enrichment values. Several of the strategies used here to improve the efficiency of the code are broadly applicable in the field. PMID:24098414

  20. Functional self-assembled DNA nanostructures for molecular recognition

    NASA Astrophysics Data System (ADS)

    Zhang, Xiaojuan; Yadavalli, Vamsi K.

    2012-03-01

    Nucleic acids present a wonderful toolkit of structural motifs for nanoconstruction. Functional DNA nanostructures can enable protein recognition by the use of aptamers attached to a basic core shape formed by DNA self-assembly. Here, we present a facile, programmable strategy for the assembly of discrete aptamer-tagged DNA shapes and nanostructures that can function for molecular recognition and binding in an aqueous environment. These nanostructures, presented here to bind two different protein targets, are easily synthesized in large numbers, and are portable and stable over long periods of time. This construction modality can facilitate on-demand production of libraries of diverse shapes to recognize and bind proteins or catalyze reactions via functional nucleic acid tags.Nucleic acids present a wonderful toolkit of structural motifs for nanoconstruction. Functional DNA nanostructures can enable protein recognition by the use of aptamers attached to a basic core shape formed by DNA self-assembly. Here, we present a facile, programmable strategy for the assembly of discrete aptamer-tagged DNA shapes and nanostructures that can function for molecular recognition and binding in an aqueous environment. These nanostructures, presented here to bind two different protein targets, are easily synthesized in large numbers, and are portable and stable over long periods of time. This construction modality can facilitate on-demand production of libraries of diverse shapes to recognize and bind proteins or catalyze reactions via functional nucleic acid tags. Electronic supplementary information (ESI) available. See DOI: 10.1039/c2nr11711h

  1. Photon-regulated DNA-enzymatic nanostructures by molecular assembly.

    PubMed

    You, Mingxu; Wang, Ruo-Wen; Zhang, Xiaobing; Chen, Yan; Wang, Kelong; Peng, Lu; Tan, Weihong

    2011-12-27

    Future smart nanostructures will have to rely on molecular assembly for unique or advanced desired functions. For example, the evolved ribosome in nature is one example of functional self-assembly of nucleic acids and proteins employed in nature to perform specific tasks. Artificial self-assembled nanodevices have also been developed to mimic key biofunctions, and various nucleic acid- and protein-based functional nanoassemblies have been reported. However, functionally regulating these nanostructures is still a major challenge. Here we report a general approach to fine-tune the catalytic function of DNA-enzymatic nanosized assemblies by taking advantage of the trans-cis isomerization of azobenzene molecules. To the best of our knowledge, this is the first study to precisely modulate the structures and functions of an enzymatic assembly based on light-induced DNA scaffold switching. Via photocontrolled DNA conformational switching, the proximity of multiple enzyme catalytic centers can be adjusted, as well as the catalytic efficiency of cofactor-mediated DNAzymes. We expect that this approach will lead to the advancement of DNA-enzymatic functional nanostructures in future biomedical and analytical applications.

  2. Molecular Motions in Functional Self-Assembled Nanostructures

    PubMed Central

    Dhotel, Alexandre; Chen, Ziguang; Delbreilh, Laurent; Youssef, Boulos; Saiter, Jean-Marc; Tan, Li

    2013-01-01

    The construction of “smart” materials able to perform specific functions at the molecular scale through the application of various stimuli is highly attractive but still challenging. The most recent applications indicate that the outstanding flexibility of self-assembled architectures can be employed as a powerful tool for the development of innovative molecular devices, functional surfaces and smart nanomaterials. Structural flexibility of these materials is known to be conferred by weak intermolecular forces involved in self-assembly strategies. However, some fundamental mechanisms responsible for conformational lability remain unexplored. Furthermore, the role played by stronger bonds, such as coordination, ionic and covalent bonding, is sometimes neglected while they can be employed readily to produce mechanically robust but also chemically reversible structures. In this review, recent applications of structural flexibility and molecular motions in self-assembled nanostructures are discussed. Special focus is given to advanced materials exhibiting significant performance changes after an external stimulus is applied, such as light exposure, pH variation, heat treatment or electromagnetic field. The crucial role played by strong intra- and weak intermolecular interactions on structural lability and responsiveness is highlighted. PMID:23348927

  3. Mechanical Characterization of Molecular Assemblies at Oil/Water Interfaces

    NASA Astrophysics Data System (ADS)

    Yuan, Wa

    The self-assembly of charged molecules in liquid phases and their ability to form functional layers at immiscible interfaces are areas of great interest. However, the implementation of these assemblies is often limited by a lack of understanding of the detailed assembly mechanisms. In order to enhance the performance of interfacial assemblies it is essential to be able to characterize the physical and mechanical properties of assembled layers, as well as develop model systems that will allow us to examine the factors that govern their interaction with the surrounding environment. The key purpose of this thesis is to develop an understanding of some of the important factors influencing interfacial assemblies at immiscible liquid interfaces. The first portion of the work involves mechanical characterization of interfacial layers formed by large amphiphilic molecules. The study of block and gradient copolymers, reveals the effect of copolymer sequence distribution on the ability of these molecules to form interfacial assemblies. Specifically, the unique network structure formed by gradient copolymers at oil/water interfaces enables us to create a robust membrane at the interface by ionic crosslinking. The second part of this thesis explores smaller molecule assemblies at liquid interfaces, including commonly used commercial surfactant (span 80) and nano particles (graphene oxide). Both studies demonstrate an interesting correlation between molecular structure and overall properties of the assembled layers. Factors such as interfacial density, particle sizes and pH can greatly influence the structure of the assembled layers, resulting in interesting phenomena such as spontaneous emulsification, wrinkling and layer collapse. The bulk of the oil/water interface study was performed using axisymmetric drop shape analysis (DSA), which successfully quantifies the mechanical tension in the interfacial layer. This analysis was further extended by a development of a double

  4. Faunus: An object oriented framework for molecular simulation

    PubMed Central

    Lund, Mikael; Trulsson, Martin; Persson, Björn

    2008-01-01

    Background We present a C++ class library for Monte Carlo simulation of molecular systems, including proteins in solution. The design is generic and highly modular, enabling multiple developers to easily implement additional features. The statistical mechanical methods are documented by extensive use of code comments that – subsequently – are collected to automatically build a web-based manual. Results We show how an object oriented design can be used to create an intuitively appealing coding framework for molecular simulation. This is exemplified in a minimalistic C++ program that can calculate protein protonation states. We further discuss performance issues related to high level coding abstraction. Conclusion C++ and the Standard Template Library (STL) provide a high-performance platform for generic molecular modeling. Automatic generation of code documentation from inline comments has proven particularly useful in that no separate manual needs to be maintained. PMID:18241331

  5. Molecular Microbial Analyses of the Mars Exploration Rovers Assembly Facility

    NASA Technical Reports Server (NTRS)

    Venkateswaran, Kasthuri; LaDuc, Myron T.; Newcombe, David; Kempf, Michael J.; Koke, John. A.; Smoot, James C.; Smoot, Laura M.; Stahl, David A.

    2004-01-01

    During space exploration, the control of terrestrial microbes associated with robotic space vehicles intended to land on extraterrestrial solar system bodies is necessary to prevent forward contamination and maintain scientific integrity during the search for life. Microorganisms associated with the spacecraft assembly environment can be a source of contamination for the spacecraft. In this study, we have monitored the microbial burden of air samples of the Mars Exploration Rovers' assembly facility at the Kennedy Space Center utilizing complementary diagnostic tools. To estimate the microbial burden and identify potential contaminants in the assembly facility, several microbiological techniques were used including culturing, cloning and sequencing of 16S rRNA genes, DNA microarray analysis, and ATP assays to assess viable microorganisms. Culturing severely underestimated types and amounts of contamination since many of the microbes implicated by molecular analyses were not cultivable. In addition to the cultivation of Agrobacterium, Burkholderia and Bacillus species, the cloning approach retrieved 16s rDNA sequences of oligotrophs, symbionts, and y-proteobacteria members. DNA microarray analysis based on rational probe design and dissociation curves complemented existing molecular techniques and produced a highly parallel, high resolution analysis of contaminating microbial populations. For instance, strong hybridization signals to probes targeting the Bacillus species indicated that members of this species were present in the assembly area samples; however, differences in dissociation curves between perfect-match and air sample sequences showed that these samples harbored nucleotide polymorphisms. Vegetative cells of several isolates were resistant when subjected to treatments of UVC (254 nm) and vapor H202 (4 mg/L). This study further validates the significance of non-cultivable microbes in association with spacecraft assembly facilities, as our analyses have

  6. Complex molecular assemblies at hand via interactive simulations.

    PubMed

    Delalande, Olivier; Férey, Nicolas; Grasseau, Gilles; Baaden, Marc

    2009-11-30

    Studying complex molecular assemblies interactively is becoming an increasingly appealing approach to molecular modeling. Here we focus on interactive molecular dynamics (IMD) as a textbook example for interactive simulation methods. Such simulations can be useful in exploring and generating hypotheses about the structural and mechanical aspects of biomolecular interactions. For the first time, we carry out low-resolution coarse-grain IMD simulations. Such simplified modeling methods currently appear to be more suitable for interactive experiments and represent a well-balanced compromise between an important gain in computational speed versus a moderate loss in modeling accuracy compared to higher resolution all-atom simulations. This is particularly useful for initial exploration and hypothesis development for rare molecular interaction events. We evaluate which applications are currently feasible using molecular assemblies from 1900 to over 300,000 particles. Three biochemical systems are discussed: the guanylate kinase (GK) enzyme, the outer membrane protease T and the soluble N-ethylmaleimide-sensitive factor attachment protein receptors complex involved in membrane fusion. We induce large conformational changes, carry out interactive docking experiments, probe lipid-protein interactions and are able to sense the mechanical properties of a molecular model. Furthermore, such interactive simulations facilitate exploration of modeling parameters for method improvement. For the purpose of these simulations, we have developed a freely available software library called MDDriver. It uses the IMD protocol from NAMD and facilitates the implementation and application of interactive simulations. With MDDriver it becomes very easy to render any particle-based molecular simulation engine interactive. Here we use its implementation in the Gromacs software as an example.

  7. Assembling molecular Sierpiński triangle fractals.

    PubMed

    Shang, Jian; Wang, Yongfeng; Chen, Min; Dai, Jingxin; Zhou, Xiong; Kuttner, Julian; Hilt, Gerhard; Shao, Xiang; Gottfried, J Michael; Wu, Kai

    2015-05-01

    Fractals, being "exactly the same at every scale or nearly the same at different scales" as defined by Benoit B. Mandelbrot, are complicated yet fascinating patterns that are important in aesthetics, mathematics, science and engineering. Extended molecular fractals formed by the self-assembly of small-molecule components have long been pursued but, to the best of our knowledge, not achieved. To tackle this challenge we designed and made two aromatic bromo compounds (4,4″-dibromo-1,1':3',1″-terphenyl and 4,4‴-dibromo-1,1':3',1″:4″,1‴-quaterphenyl) to serve as building blocks. The formation of synergistic halogen and hydrogen bonds between these molecules is the driving force to assemble successfully a whole series of defect-free molecular fractals, specifically Sierpiński triangles, on a Ag(111) surface below 80 K. Several critical points that govern the preparation of the molecular Sierpiński triangles were scrutinized experimentally and revealed explicitly. This new strategy may be applied to prepare and explore various planar molecular fractals at surfaces.

  8. Molecular and electronic structure of electroactive self-assembled monolayers

    NASA Astrophysics Data System (ADS)

    Méndez De Leo, Lucila P.; de la Llave, Ezequiel; Scherlis, Damián; Williams, Federico J.

    2013-03-01

    Self-assembled monolayers (SAMs) containing electroactive functional groups are excellent model systems for the formation of electronic devices by self-assembly. In particular ferrocene-terminated alkanethiol SAMs have been extensively studied in the past. However, there are still open questions related with their electronic structure including the influence of the ferrocene group in the SAM-induced work function changes of the underlying metal. We have thus carried out a thorough experimental and theoretical investigation in order to determine the molecular and electronic structure of ferrocene-terminated alkanethiol SAMs on Au surfaces. In agreement with previous studies we found that the Fc-containing alkanethiol molecules adsorb forming a thiolate bond with the Au surface with a molecular geometry 30° tilted with respect to the surface normal. Measured surface coverages indicate the formation of a compact monolayer. We found for the first time that the ferrocene group has little influence on the observed work function decrease which is largely determined by the alkanethiol. Furthermore, the ferrocene moiety lies 14 Å above the metal surface covalently bonded to the alkanethiol SAM and its HOMO is located at -1.6 eV below the Fermi level. Our results provide new valuable insight into the molecular and electronic structure of electroactive SAMs which are of fundamental importance in the field of molecular electronics.

  9. Molecular and electronic structure of electroactive self-assembled monolayers.

    PubMed

    Méndez De Leo, Lucila P; de la Llave, Ezequiel; Scherlis, Damián; Williams, Federico J

    2013-03-21

    Self-assembled monolayers (SAMs) containing electroactive functional groups are excellent model systems for the formation of electronic devices by self-assembly. In particular ferrocene-terminated alkanethiol SAMs have been extensively studied in the past. However, there are still open questions related with their electronic structure including the influence of the ferrocene group in the SAM-induced work function changes of the underlying metal. We have thus carried out a thorough experimental and theoretical investigation in order to determine the molecular and electronic structure of ferrocene-terminated alkanethiol SAMs on Au surfaces. In agreement with previous studies we found that the Fc-containing alkanethiol molecules adsorb forming a thiolate bond with the Au surface with a molecular geometry 30° tilted with respect to the surface normal. Measured surface coverages indicate the formation of a compact monolayer. We found for the first time that the ferrocene group has little influence on the observed work function decrease which is largely determined by the alkanethiol. Furthermore, the ferrocene moiety lies 14 Å above the metal surface covalently bonded to the alkanethiol SAM and its HOMO is located at -1.6 eV below the Fermi level. Our results provide new valuable insight into the molecular and electronic structure of electroactive SAMs which are of fundamental importance in the field of molecular electronics.

  10. Molecular pathways for defect annihilation in directed self-assembly.

    DOE PAGES

    Hur, Su-Mi; Thapar, Vikram; Ramirez-Hernandez, Abelardo; ...

    2015-11-17

    Over the last few years, the directed self-assembly of block copolymers by surface patterns has transitioned from academic curiosity to viable contender for commercial fabrication of next-generation nanocircuits by lithography. Recently, it has become apparent that kinetics, and not only thermodynamics, plays a key role for the ability of a polymeric material to self-assemble into a perfect, defect-free ordered state. Perfection, in this context, implies not more than one defect, with characteristic dimensions on the order of 5 nm, over a sample area as large as 100 cm2. In this work, we identify the key pathways and the corresponding free-energymore » barriers for eliminating defects, and we demonstrate that an extraordinarily large thermodynamic driving force is not necessarily sufficient for their removal. By adopting a concerted computational and experimental approach, we explain the molecular origins of these barriers, how they depend on material characteristics, and we propose strategies designed to over-come them. The validity of our conclusions for industrially-relevant patterning processes is established by relying on instruments and assembly lines that are only available at state-of-the-art fabrication facilities and, through this confluence of fundamental and applied research, we are able to discern the evolution of morphology at the smallest relevant length scales - a handful of nanometers -, and present a view of defect annihilation in directed self-assembly at an unprecedented level of detail.« less

  11. Molecular pathways for defect annihilation in directed self-assembly.

    SciTech Connect

    Hur, Su-Mi; Thapar, Vikram; Ramirez-Hernandez, Abelardo; Khaira, Gurdaman S.; Segal-Peretz, Tamar; Rincon-Delgadillo, Paulina A.; Li, Weihua; Muller, Marcus; Nealey, Paul F.; de Pablo, Juan J.

    2015-11-17

    Over the last few years, the directed self-assembly of block copolymers by surface patterns has transitioned from academic curiosity to viable contender for commercial fabrication of next-generation nanocircuits by lithography. Recently, it has become apparent that kinetics, and not only thermodynamics, plays a key role for the ability of a polymeric material to self-assemble into a perfect, defect-free ordered state. Perfection, in this context, implies not more than one defect, with characteristic dimensions on the order of 5 nm, over a sample area as large as 100 cm2. In this work, we identify the key pathways and the corresponding free-energy barriers for eliminating defects, and we demonstrate that an extraordinarily large thermodynamic driving force is not necessarily sufficient for their removal. By adopting a concerted computational and experimental approach, we explain the molecular origins of these barriers, how they depend on material characteristics, and we propose strategies designed to over-come them. The validity of our conclusions for industrially-relevant patterning processes is established by relying on instruments and assembly lines that are only available at state-of-the-art fabrication facilities and, through this confluence of fundamental and applied research, we are able to discern the evolution of morphology at the smallest relevant length scales - a handful of nanometers -, and present a view of defect annihilation in directed self-assembly at an unprecedented level of detail.

  12. Molecular dynamics simulations of evaporation-induced nanoparticle assembly

    NASA Astrophysics Data System (ADS)

    Cheng, Shengfeng; Grest, Gary S.

    2013-02-01

    While evaporating solvent is a widely used technique to assemble nano-sized objects into desired superstructures, there has been limited work on how the assembled structures are affected by the physical aspects of the process. We present large scale molecular dynamics simulations of the evaporation-induced assembly of nanoparticles suspended in a liquid that evaporates in a controlled fashion. The quality of the nanoparticle crystal formed just below the liquid/vapor interface is found to be better at relatively slower evaporation rates, as less defects and grain boundaries appear. This trend is understood as the result of the competition between the accumulation and diffusion times of nanoparticles at the liquid/vapor interface. When the former is smaller, nanoparticles are deposited so fast at the interface that they do not have sufficient time to arrange through diffusion, which leads to the prevalence of defects and grain boundaries. Our results have important implications in understanding assembly of nanoparticles and colloids in non-equilibrium liquid environments.

  13. Molecular pathways for defect annihilation in directed self-assembly.

    PubMed

    Hur, Su-Mi; Thapar, Vikram; Ramírez-Hernández, Abelardo; Khaira, Gurdaman; Segal-Peretz, Tamar; Rincon-Delgadillo, Paulina A; Li, Weihua; Müller, Marcus; Nealey, Paul F; de Pablo, Juan J

    2015-11-17

    Over the last few years, the directed self-assembly of block copolymers by surface patterns has transitioned from academic curiosity to viable contender for commercial fabrication of next-generation nanocircuits by lithography. Recently, it has become apparent that kinetics, and not only thermodynamics, plays a key role for the ability of a polymeric material to self-assemble into a perfect, defect-free ordered state. Perfection, in this context, implies not more than one defect, with characteristic dimensions on the order of 5 nm, over a sample area as large as 100 cm(2). In this work, we identify the key pathways and the corresponding free energy barriers for eliminating defects, and we demonstrate that an extraordinarily large thermodynamic driving force is not necessarily sufficient for their removal. By adopting a concerted computational and experimental approach, we explain the molecular origins of these barriers and how they depend on material characteristics, and we propose strategies designed to overcome them. The validity of our conclusions for industrially relevant patterning processes is established by relying on instruments and assembly lines that are only available at state-of-the-art fabrication facilities, and, through this confluence of fundamental and applied research, we are able to discern the evolution of morphology at the smallest relevant length scales-a handful of nanometers-and present a view of defect annihilation in directed self-assembly at an unprecedented level of detail.

  14. Role of redox centre in charge transport investigated by novel self-assembled conjugated polymer molecular junctions

    PubMed Central

    Wang, Zongrui; Dong, Huanli; Li, Tao; Hviid, Rune; Zou, Ye; Wei, Zhongming; Fu, Xiaolong; Wang, Erjing; Zhen, Yonggang; Nørgaard, Kasper; Laursen, Bo W.; Hu, Wenping

    2015-01-01

    Molecular electronics describes a field that seeks to implement electronic components made of molecular building blocks. To date, few studies have used conjugated polymers in molecular junctions despite the fact that they potentially transport charge more efficiently than the extensively investigated small-molecular systems. Here we report a novel type of molecular tunnelling junction exploring the use of conjugated polymers, which are self-assembled into ultrathin films in a distinguishable ‘planar' manner from the traditional vertically oriented small-molecule monolayers. Electrical measurements on the junctions reveal molecular-specific characteristics of the polymeric molecules in comparison with less conjugated small molecules. More significantly, we decorate redox-active functionality into polymeric backbones, demonstrating a key role of redox centre in the modulation of charge transport behaviour via energy level engineering and external stimuli, and implying the potential of employing tailor-made polymeric components as alternatives to small molecules for future molecular-scale electronics. PMID:26085081

  15. Stable doping of carbon nanotubes via molecular self assembly

    SciTech Connect

    Lee, B.; Chen, Y.; Podzorov, V.; Cook, A.; Zakhidov, A.

    2014-10-14

    We report a novel method for stable doping of carbon nanotubes (CNT) based on methods of molecular self assembly. A conformal growth of a self-assembled monolayer of fluoroalkyl trichloro-silane (FTS) at CNT surfaces results in a strong increase of the sheet conductivity of CNT electrodes by 60–300%, depending on the CNT chirality and composition. The charge carrier mobility of undoped partially aligned CNT films was independently estimated in a field-effect transistor geometry (~100 cm²V⁻¹s⁻¹). The hole density induced by the FTS monolayer in CNT sheets is estimated to be ~1.8 ×10¹⁴cm⁻². We also show that FTS doping of CNT anodes greatly improves the performance of organic solar cells. This large and stable doping effect, easily achieved in large-area samples, makes this approach very attractive for applications of CNTs in transparent and flexible electronics.

  16. Light-controlled nitric oxide delivering molecular assemblies.

    PubMed

    Sortino, Salvatore

    2010-08-01

    The multiple roles nitric oxide (NO) plays as a bioregulatory, anticancer, antimicrobial and antioxidant agent has triggered an explosive interest in recent years in compounds able to deliver this diatomic radical for therapeutic purposes. A major issue associated with NO donors is the precise control of the NO release, which effect is highly concentration and flux dependent. Light represents a convenient non-invasive on/off trigger to deliver NO on demand since it allows the accurate control of site, timing and dosage. The assembling of NO photodonors through different approaches may lead to intriguing light-responsive molecular constructs including nanostructured films, polymers, gels, nanoparticles and molecular conjugates which exhibit promising potential in view of practical applications. This tutorial review illustrates the recent research from our and other laboratories towards the fabrication of these molecular assemblies, highlighting the logical design and the relevance in the biomedical field. Therefore, this review is aimed to be a source of inspiration for a wide range of scientists belonging to the chemical, materials science and biochemical communities, facing the common challenge of fabricating controllable NO dispensers.

  17. Enhanced Rates of Photoinduced Molecular Orientation in a Series of Molecular Glassy Thin Films.

    PubMed

    Snell, Kristen E; Hou, Renjie; Ishow, Eléna; Lagugné-Labarthet, François

    2015-07-07

    Photoinduced orientation in a series of molecular glasses made of small push-pull azo derivatives is dynamically investigated for the first time. Birefringence measurements at 632.8 nm are conducted with a temporal resolution of 100 ms to probe the fast rate of the azo orientation induced under polarized light and its temporal stability over several consecutive cycles. To better evaluate the influence of the azo chemical substituents and their electronic properties on the orientation of the whole molecule, a series of push-pull azo derivatives involving a triphenylaminoazo core substituted with distinct electron-withdrawing moieties is studied. All resulting thin films are probed using polarization modulation infrared spectroscopy that yields dynamical linear dichroism measurements during a cycle of orientation followed by relaxation. We show here in particular that the orientation rates of small molecule-based azo materials are systematically increased up to 7-fold compared to those of a reference polymer counterpart. For specific compounds, the percentage of remnant orientation is also higher, which makes these materials of great interest and promising alternatives to azobenzene-containing polymers for a variety of applications requiring a fast response and absolute control over the molecular weight.

  18. Nanostructure and molecular mechanics of spider dragline silk protein assemblies.

    PubMed

    Keten, Sinan; Buehler, Markus J

    2010-12-06

    Spider silk is a self-assembling biopolymer that outperforms most known materials in terms of its mechanical performance, despite its underlying weak chemical bonding based on H-bonds. While experimental studies have shown that the molecular structure of silk proteins has a direct influence on the stiffness, toughness and failure strength of silk, no molecular-level analysis of the nanostructure and associated mechanical properties of silk assemblies have been reported. Here, we report atomic-level structures of MaSp1 and MaSp2 proteins from the Nephila clavipes spider dragline silk sequence, obtained using replica exchange molecular dynamics, and subject these structures to mechanical loading for a detailed nanomechanical analysis. The structural analysis reveals that poly-alanine regions in silk predominantly form distinct and orderly beta-sheet crystal domains, while disorderly regions are formed by glycine-rich repeats that consist of 3₁-helix type structures and beta-turns. Our structural predictions are validated against experimental data based on dihedral angle pair calculations presented in Ramachandran plots, alpha-carbon atomic distances, as well as secondary structure content. Mechanical shearing simulations on selected structures illustrate that the nanoscale behaviour of silk protein assemblies is controlled by the distinctly different secondary structure content and hydrogen bonding in the crystalline and semi-amorphous regions. Both structural and mechanical characterization results show excellent agreement with available experimental evidence. Our findings set the stage for extensive atomistic investigations of silk, which may contribute towards an improved understanding of the source of the strength and toughness of this biological superfibre.

  19. Nitrogen Substituted Phenothiazine Derivatives: Modelling of Molecular Self-Assembling

    PubMed Central

    Bende, Attila; Turcu, Ioan

    2011-01-01

    The study aims to present a detailed theoretical investigation of noncovalent intermolecular interactions between different π–π stacking nitrogen substituted phenothiazine derivatives by applying second-order Møller-Plesset perturbation (MP2), density functional (DFT) and semiempirical theories. The conformational stability of these molecular systems is mainly given by the dispersion-type electron correlation effects. The density functional tight-binding (DFTB) method applied for dimer structures are compared with the results obtained by the higher level theoretical methods. Additionally, the optimal configuration of the investigated supramolecular systems and their self-assembling properties are discussed. PMID:21686172

  20. Molecular wires self-assembled on a graphite surface.

    PubMed

    Riemann, Andreas; Nelson, Brittany

    2009-04-21

    We report a scanning tunneling microscopy study of the amino acid l-methionine on highly ordered pyrolytic graphite deposited under ambient conditions. Our experiments demonstrate the ability of l-methionine to form highly regular structures on the surface of the graphite template. By means of self-assembly, the amino acid arranges itself into an array of molecular wires, i.e., well-ordered stripes of uniform width and separation. The spacing of these wires can be controlled with the deposition amount of the amino acid, whereas the width stays constant. The width of the wires is determined by two methionine molecules arranged with their carboxyl group facing each other. The regular separation of individual wires suggest a long-range interaction among them. Molecular mechanics calculations are used to compare the experimental results with a basic model for the methionine configuration on the surface. A model for the adsorption geometry of methionine on graphite is presented.

  1. Surface confined assemblies and polymers for sensing and molecular logic

    NASA Astrophysics Data System (ADS)

    de Ruiter, Graham; Altman, Marc; Motiei, Leila; Lahav, Michal; van der Boom, Milko E.

    2013-05-01

    Since the development of molecule-based sensors and the introduction of molecules mimicking the behavior of the AND gate in solution by de Silva in 1993, molecular (Boolean) Logic and Computing (MBLC) has become increasingly popular. The molecular approach toward Boolean logic resulted in intriguing proofs of concepts in solution including logic gates, half-adders, multiplexers, and flip-flop logic circuits. Molecular assemblies can perform diverse logic tasks by reconfiguring their inputs. Our recent research activities focus on MBLC with electrochromic polymers and immobilized polypyridyl complexes on solid support. We have designed a series of coordination-based thin films that are formed linearly by stepwise wet-chemical deposition or by self-propagating molecular assembly. The electrochromic properties of these films can be used for (i) detecting various analytes in solution and in the air, (ii) MBLC, (iii) electron-transfer studies, and (iv) interlayers for efficient inverted bulk-heterojunction solar cells. Our concept toward MBLC with functionalized surfaces is applicable to electrochemical and chemical inputs coupled with optical readout. Using this approach, we demonstrated various logic architectures with redox-active functionalized surfaces. Electrochemically operated sequential logic systems (e.g., flip-flops), multi-valued logic, and multi-state memory have been designed, which can improve computational power without increasing spatial requirements. Applying multi-valued digits in data storage and information processing could exponentially increase memory capacity. Our approach is applicable to highly diverse electrochromic thin films that operate at practical voltages (< 1.5 V).

  2. Molecular mechanics methods for individual carbon nanotubes and nanotube assemblies

    NASA Astrophysics Data System (ADS)

    Eberhardt, Oliver; Wallmersperger, Thomas

    2015-04-01

    Since many years, carbon nanotubes (CNTs) have been considered for a wide range of applications due to their outstanding mechanical properties. CNTs are tubular structures, showing a graphene like hexagonal lattice. Our interest in the calculation of the mechanical properties is motivated by several applications which demand the knowledge of the material behavior. One application in which the knowledge of the material behavior is vital is the CNT based fiber. Due to the excellent stiffness and strength of the individual CNTs, these fibers are expected to be a promising successor for state of the art carbon fibers. However, the mechanical properties of the fibers fall back behind the properties of individual CNTs. It is assumed that this gap in the properties is a result of the van-der-Waals interactions of the individual CNTs within the fiber. In order to understand the mechanical behavior of the fibers we apply a molecular mechanics approach. The mechanical properties of the individual CNTs are investigated by using a modified structural molecular mechanics approach. This is done by calculating the properties of a truss-beam element framework representing the CNT with the help of a chemical force field. Furthermore, we also investigate the interactions of CNTs arranged in basic CNT assemblies, mimicking the ones in a simple CNT fiber. We consider the van-der-Waals interactions in the structure and calculate the potential surface of the CNT assemblies.

  3. Relaxation Phenomena of a Magnetic Nanoparticle Assembly with Randomly Oriented Anisotropy

    NASA Astrophysics Data System (ADS)

    Fang; WenXiao; He; ZhenHui; Chen; DiHu; En; YunFei; Kong; XueDong

    2011-03-01

    The effects of a randomly oriented anisotropy on relaxation phenomena including the memory effect of a noninteracting magnetic nanoparticle assembly, are numerically studied with a localized partition function and a master equation, leading to the following results. During the zero-field-cooled (ZFC) process, the energy barrier histogram changes with temperature, while during the field-cooled (FC) process it remains stable. In the relaxation process after ZFC initialization, the effective energy barrier distribution, which is derived from the Tln (t/τ0) (T temperature, t time, and τ0 characteristic time constant) scaling curve, only reflects the low-energy region of the energy barrier histogram. The memory effect with temporary cooling during time evolution occurs in the studied assembly even without volume distribution and particle interaction involved.

  4. Highly Luminescent Colloidal Nanoplates of Perovskite Cesium Lead Halide and Their Oriented Assemblies.

    PubMed

    Bekenstein, Yehonadav; Koscher, Brent A; Eaton, Samuel W; Yang, Peidong; Alivisatos, A Paul

    2015-12-30

    Anisotropic colloidal quasi-two-dimensional nanoplates (NPLs) hold great promise as functional materials due to their combination of low dimensional optoelectronic properties and versatility through colloidal synthesis. Recently, lead-halide perovskites have emerged as important optoelectronic materials with excellent efficiencies in photovoltaic and light-emitting applications. Here we report the synthesis of quantum confined all inorganic cesium lead halide nanoplates in the perovskite crystal structure that are also highly luminescent (PLQY 84%). The controllable self-assembly of nanoplates either into stacked columnar phases or crystallographic-oriented thin-sheet structures is demonstrated. The broad accessible emission range, high native quantum yields, and ease of self-assembly make perovskite NPLs an ideal platform for fundamental optoelectronic studies and the investigation of future devices.

  5. Self-assembly of thiophene derivatives on highly oriented pyrolytic graphite: hydrogen bond effect.

    PubMed

    Xu, Li-Ping; Liu, Yibiao; Zhao, Jing; Wang, Shuqi; Lin, Chen-Sheng; Zhang, Rui-Qin; Wen, Yongqiang; Du, Hongwu; Zhang, Xueji

    2013-02-01

    In this paper, to elucidate the hydrogen bond effect on the assembly behavior, we studied the assembly structures of two carboxylic substituted thiophene derivatives on highly oriented pyrolytic graphite (HOPG) by scanning tunneling microscopy. Here thiophene-2-carboxylic acid (TCA) and thiophene-2,5-dicarboxylic acid (TDA) were employed. TDA molecules spontaneously adsorb on the HOPG surface and self-organize into a two-dimensional (2D) assembly with well-defined structure. Two types of domain could be observed. Each TDA molecule appears as a round circle with two small faint dots and forms hydrogen bonds with neighbours. Besides monolayer structure, a bilayer structure of TDA adlayer on HOPG was also observed in this research. Remnant TDA molecules adsorb on the monolayer of TDA and bilayer structure is formed. In contrast to TDA, no ordered structure of TCA on HOPG can be observed. TCA molecules have high propensity to form dimers through H-bond between carboxylic groups. But TCA dimer is not stable enough for either adsorption or imaging. Our result provides a new example for understanding hydrogen effect on stabilizing and controlling two-dimensional assembly structure and is helpful for surface nanofabrication and development of electric nanodevices.

  6. Molecularly Oriented Polymeric Thin Films for Space Applications

    NASA Technical Reports Server (NTRS)

    Fay, Catharine C.; Stoakley, Diane M.; St.Clair, Anne K.

    1997-01-01

    The increased commitment from NASA and private industry to the exploration of outer space and the use of orbital instrumentation to monitor the earth has focused attention on organic polymeric materials for a variety of applications in space. Some polymeric materials have exhibited short-term (3-5 yr) space environmental durability; however, future spacecraft are being designed with lifetimes projected to be 10-30 years. This gives rise to concern that material property change brought about during operation may result in unpredicted spacecraft performance. Because of their inherent toughness and flexibility, low density, thermal stability, radiation resistance and mechanical strength, aromatic polyimides have excellent potential use as advanced materials on large space structures. Also, there exists a need for high temperature (200-300 C) stable, flexible polymeric films that have high optical transparency in the 300-600nm range of the electromagnetic spectrum. Polymers suitable for these space applications were fabricated and characterized. Additionally, these polymers were molecularly oriented to further enhance their dimensional stability, stiffness, elongation and strength. Both unoriented and oriented polymeric thin films were also cryogenically treated to temperatures below -184 C to show their stability in cold environments and determine any changes in material properties.

  7. Functionality in Electrospun Nanofibrous Membranes Based on Fiber's Size, Surface Area, and Molecular Orientation

    PubMed Central

    Matsumoto, Hidetoshi; Tanioka, Akihiko

    2011-01-01

    Electrospinning is a versatile method for forming continuous thin fibers based on an electrohydrodynamic process. This method has the following advantages: (i) the ability to produce thin fibers with diameters in the micrometer and nanometer ranges; (ii) one-step forming of the two- or three-dimensional nanofiber network assemblies (nanofibrous membranes); and (iii) applicability for a broad spectrum of molecules, such as synthetic and biological polymers and polymerless sol-gel systems. Electrospun nanofibrous membranes have received significant attention in terms of their practical applications. The major advantages of nanofibers or nanofibrous membranes are the functionalities based on their nanoscaled-size, highly specific surface area, and highly molecular orientation. These functionalities of the nanofibrous membranes can be controlled by their fiber diameter, surface chemistry and topology, and internal structure of the nanofibers. This report focuses on our studies and describes fundamental aspects and applications of electrospun nanofibrous membranes. PMID:24957735

  8. Pyridine coordination chemistry for molecular assemblies on surfaces.

    PubMed

    de Ruiter, Graham; Lahav, Michal; van der Boom, Milko E

    2014-12-16

    CONSPECTUS: Since the first description of coordination complexes, many types of metal-ligand interactions have creatively been used in the chemical sciences. The rich coordination chemistry of pyridine-type ligands has contributed significantly to the incorporation of diverse metal ions into functional materials. Here we discuss molecular assemblies (MAs) formed with a variety of pyridine-type compounds and a metal containing cross-linker (e.g., PdCl2(PhCN2)). These MAs are formed using Layer-by-Layer (LbL) deposition from solution that allows for precise fitting of the assembly properties through molecular programming. The position of each component can be controlled by altering the assembly sequence, while the degree of intermolecular interactions can be varied by the level of π-conjugation and the availability of metal coordination sites. By setting the structural parameters (e.g., bond angles, number of coordination sites, geometry) of the ligand, control over MA structure was achieved, resulting in surface-confined metal-organic networks and oligomers. Unlike MAs that are constructed with organic ligands, MAs with polypyridyl complexes of ruthenium, osmium, and cobalt are active participants in their own formation and amplify the growth of the incoming molecular layer. Such a self-propagating behavior for molecular systems is rare, and the mechanism of their formation will be discussed. These exponentially growing MAs are capable of storing metal salts that can be used during the buildup of additional molecular layers. Various parameters influencing the film growth mechanism will be presented, including (i) the number of binding sites and geometry of the organic ligands, (ii) the metal and the structure of the polypyridyl complexes, (iii) the influence of the metal cross-linker (e.g., second or third row transition metals), and (iv) the deposition conditions. By systematic variation of these parameters, switching between linear and exponential growth could

  9. Molecular Self-Assembly and Nanochemistry: A Chemical Strategy for the Synthesis of Nanostructures

    DTIC Science & Technology

    1991-12-01

    AD-A243 530iV1111I I II 11111 I I(/• MOLECULAR SELF-ASSEMBLY AND NANOCHEMISTRY : A CHEMICAL STRATEGY FOR THE SYNTHESIS OF NANOSTRUCTURES George M...Classfication) "Molecular Self-Assembly and Nanochemistry : A Chemistry Strategy for the Synthesis of Nanostructures." 12, PERSONAL AUTHOR(S) G.M...8217. .. .... ......... Molecular Self-Assembly and Nanochemistry : A Chemical Strategy for the Synthesis of Nanostructures George M. Whitesides, John P. Mathias

  10. Self-Assembled Monolayers: a Molecular Resolution STM Study

    NASA Astrophysics Data System (ADS)

    Dhirani, Al-Amin

    Building on studies of self-assembled monolayers (SAMs) based on the (CH_3(CH _2)_{rm n{-}1}SH) + Au(111) prototype, we have designed and constructed a high impedance STM to consider the formation and properties of new SAM systems with molecular resolution. On Au-, Ag-, and Pt-(111), the monolayer structures of n-decanethiol were found to be (1) ordered on gold and silver but not platinum (2) strongly correlated with the structures formed by simpler sulfur components. In addition the potential formation and properties of new molecular classes of ordered SAMs were considered by studying monolayers of H(C _6H_4Cequiv C)_{rm n}C _6H_4SH (n = 0 - 2) (1a - c) on Au(111). An increase in order with chain length as well as the formation of an ordered SAM by 1c were observed. Finally, current-voltage (I-V) measurements of 1 monolayers displayed an increasing nonlinearity with chain length and an asymmetry for 1c. The electrical behavior is consistent with a model based on a semi-classical tunneling formalism using the barrier height and molecular polarizability of 1.

  11. De Novo Transcriptome Assembly of Pummelo and Molecular Marker Development

    PubMed Central

    Liang, Mei; Yang, Xiaoming; Li, Hang; Su, Shiying; Yi, Hualin; Chai, Lijun; Deng, Xiuxin

    2015-01-01

    Pummelo (Citrus grandis) is an important fruit crop worldwide because of its nutritional value. To accelerate the pummelo breeding program, it is essential to obtain extensive genetic information and develop relative molecular markers. Here, we obtained a 12-Gb transcriptome dataset of pummelo through a mixture of RNA from seven tissues using Illumina pair-end sequencing, assembled into 57,212 unigenes with an average length of 1010 bp. The annotation and classification results showed that a total of 39,584 unigenes had similar hits to the known proteins of four public databases, and 31,501 were classified into 55 Gene Ontology (GO) functional sub-categories. The search for putative molecular markers among 57,212 unigenes identified 10,276 simple sequence repeats (SSRs) and 64,720 single nucleotide polymorphisms (SNPs). High-quality primers of 1174 SSR loci were designed, of which 88.16% were localized to nine chromosomes of sweet orange. Of 100 SSR primers that were randomly selected for testing, 87 successfully amplified clear banding patterns. Of these primers, 29 with a mean PIC (polymorphic information content) value of 0.52 were effectively applied for phylogenetic analysis. Of the 20 SNP primers, 14 primers, including 54 potential SNPs, yielded target amplifications, and 46 loci were verified via Sanger sequencing. This new dataset will be a valuable resource for molecular biology studies of pummelo and provides reliable information regarding SNP and SSR marker development, thus expediting the breeding program of pummelo. PMID:25799271

  12. NMR Studies of Molecular Orientation and Dynamics in Spider silk

    NASA Astrophysics Data System (ADS)

    Michal, Carl; Eles, Philip

    2004-05-01

    Spider dragline silk has a unique combination of strength and extensibility that has been difficult to achieve in synthetic polymer fibres and has inspired industrial efforts to produce genetically engineered analogues. In light of these efforts elsewhere, we describe solid-state NMR experiments that elucidate the molecular structure and dynamics of this remarkable material. These experiments include the use of a 2-D exchange NMR experiment known as DECODER in which the sample is reoriented through a discrete angle during the mixing time. This experiment allows a reconstruction of the orientation distribution of the protein backbone. Our data is well described by a two-component distribution where the protein backbones of both components are preferentially aligned along the silk fibre. This experiment is also sensitive to molecular motion on a wide range of time-scales, and is employed to study changes in the silk as a function of fibre extension and hydration. Hydrated silk undergoes a remarkable phenomena known as supercontraction where fibres shrink by up to 50% in length while swelling in diameter. DECODER NMR of fully and partially supercontracted silk reveals that supercontraction occurs through a process of local phase transitions where water disrupts inter- and intra-chain hydrogen bonds.

  13. Orientation and self-assembly of cylindrical particles by anisotropic capillary interactions.

    PubMed

    Lewandowski, Eric P; Cavallaro, Marcello; Botto, Lorenzo; Bernate, Jorge C; Garbin, Valeria; Stebe, Kathleen J

    2010-10-05

    In this research, we study cylindrical microparticles at fluid interfaces. Cylinders orient and assemble with high reliability to form end-to-end chains in dilute surfaces or dense rectangular lattices in crowded surfaces owing to capillary interactions. In isolation, a cylinder assumes one of two possible equilibrium states, the end-on state, in which the cylinder axis is perpendicular to the interface, or the side-on state, in which the cylinder axis is parallel to the interface. A phase diagram relating aspect ratio and contact angle is constructed to predict the preferred state and verified in experiment. Cylinders in the side-on state create distortions that result in capillary interactions. Overlapping deformations by neighboring particles drive oriented capillary assembly. Interferometry, electron microscopy, and numerical simulations are used to characterize the interface shape around isolated particles. Experiments and numerics show that "side-on" cylinders have concentrated excess area near the end faces, and that the interface distortion resembles an elliptical quadrupole a few radii away from the particle surface. To model the cylinder interactions for separations greater than a few radii, an anisotropic potential is derived based on elliptical quadrupoles. This potential predicts an attractive force and a torque, both of which depend strongly on aspect ratio, in keeping with experiment. Particle trajectories and angular orientations recorded by video microscopy agree with the predicted potential. In particular, the analysis predicts the rate of rotation, a feature lacking in prior analyses. To understand interactions near contact, the concentrated excess area near the cylinder ends is quantified and its role in creating stable end-to-end assemblies is discussed. When a pair of cylinders is near contact, these high excess area regions overlap to form a capillary bridge between the particles. This capillary bridge may stabilize the end-to-end chains

  14. A self-assembling lanthanide molecular nanoparticle for optical imaging†

    PubMed Central

    Brown, Katherine A.; Yang, Xiaoping; Schipper, Desmond; Hall, Justin W.; DePue, Lauren J.; Gnanam, Annie J.; Arambula, Jonathan F.; Jones, Jessica N.; Swaminathan, Jagannath; Dieye, Yakhya; Vadivelu, Jamuna; Chandler, Don J.; Marcotte, Edward M.; Sessler, Jonathan L.; Ehrlich, Lauren I. R.; Jones, Richard A.

    2015-01-01

    Chromophores that incorporate f-block elements have considerable potential for use in bioimaging applications because of their advantageous photophysical properties compared to organic dye, which are currently widely used. We are developing new classes of lanthanide-based self-assembling molecular nanoparticles as reporters for imaging and as multi-functional nanoprobes or nanosensors for use with biological samples. One class of these materials, which we call lanthanide “nano-drums”, are homogeneous 4d–4f clusters approximately 25 to 30 Å in diameter. These are capable of emitting from the visible to near-infrared wavelengths. Here, we present the synthesis, crystal structure, photophysical properties and comparative cytotoxicity data for a 32 metal Eu-Cd nano-drum [Eu8Cd24L12(OAc)48] (1). We also explored the imaging capabilities of this nano-drum using epifluorescence, TIRF, and two-photon microscopy platforms. PMID:25512085

  15. Molecular Self-Assembly at Metal-Electrolyte Interfaces

    PubMed Central

    Phan, Thanh Hai; Wandelt, Klaus

    2013-01-01

    The self-assembly of molecular layers has become an important strategy in modern design of functional materials. However, in particular, large organic molecules may no longer be sufficiently volatile to be deposited by vapor deposition. In this case, deposition from solution may be a promising route; in ionic form, these molecules may even be soluble in water. In this contribution, we present and discuss results on the electrochemical deposition of viologen- and porphyrin molecules as well as their co-adsorption on chloride modified Cu(100) and Cu(111) single crystal electrode surfaces from aqueous acidic solutions. Using in situ techniques like cyclic voltametry and high resolution scanning tunneling microscopy, as well as ex-situ photoelectron spectroscopy data the highly ordered self-assembled organic layers are characterized with respect to their electrochemical behavior, lateral order and inner conformation as well as phase transitions thereof as a function of their redox-state and the symmetry of the substrate. As a result, detailed structure models are derived and are discussed in terms of the prevailing interactions. PMID:23439555

  16. Topological defects in liquid crystals as templates for molecular self-assembly

    NASA Astrophysics Data System (ADS)

    Wang, Xiaoguang; Miller, Daniel S.; Bukusoglu, Emre; de Pablo, Juan J.; Abbott, Nicholas L.

    2016-01-01

    Topological defects in liquid crystals (LCs) have been widely used to organize colloidal dispersions and template polymerization, leading to a range of assemblies, elastomers and gels. However, little is understood about molecular-level assembly processes within defects. Here, we report that nanoscopic environments defined by LC topological defects can selectively trigger processes of molecular self-assembly. By using fluorescence microscopy, cryogenic transmission electron microscopy and super-resolution optical microscopy, we observed signatures of molecular self-assembly of amphiphilic molecules in topological defects, including cooperativity, reversibility and controlled growth. We also show that nanoscopic o-rings synthesized from Saturn-ring disclinations and other molecular assemblies templated by defects can be preserved by using photocrosslinkable amphiphiles. Our results reveal that, in analogy to other classes of macromolecular templates such as polymer-surfactant complexes, topological defects in LCs are a versatile class of three-dimensional, dynamic and reconfigurable templates that can direct processes of molecular self-assembly.

  17. Structural Investigations of Surfaces and Orientation-SpecificPhenomena in Nanocrystals and Their Assemblies

    SciTech Connect

    Aruguete, Deborah Michiko

    2006-01-01

    Studies of colloidal nanocrystals and their assemblies are presented. Two of these studies concern the atomic-level structural characterization of the surfaces, interfaces, and interiors present in II-VI semiconductor nanorods. The third study investigates the crystallographic arrangement of cobalt nanocrystals in self-assembled aggregates. Crystallographically-aligned assemblies of colloidal CdSe nanorods are examined with linearly-polarized Se-EXAFS spectroscopy, which probes bonding along different directions in the nanorod. This orientation-specific probe is used, because it is expected that the presence of specific surfaces in a nanorod might cause bond relaxations specific to different crystallographic directions. Se-Se distances are found to be contracted along the long axis of the nanorod, while Cd-Se distances display no angular dependence, which is different from the bulk. Ab-initio density functional theory calculations upon CdSe nanowires indicate that relaxations on the rod surfaces cause these changes. ZnS/CdS-CdSe core-shell nanorods are studied with Se, Zn, Cd, and S X-ray absorption spectroscopy (XAS). It is hypothesized that there are two major factors influencing the core and shell structures of the nanorods: the large surface area-to-volume ratio, and epitaxial strain. The presence of the surface may induce bond rearrangements or relaxations to minimize surface energy; epitaxial strain might cause the core and shell lattices to contract or expand to minimize strain energy. A marked contraction of Zn-S bonds is observed in the core-shell nanorods, indicating that surface relaxations may dominate the structure of the nanorod (strain might otherwise drive the Zn-S lattice to accommodate the larger CdS or CdSe lattices via bond expansion). EXAFS and X-ray diffraction (XRD) indicate that Cd-Se bond relaxations might be anisotropic, an expected phenomenon for a rod-shaped nanocrystal. Ordered self-assembled aggregates of cobalt nanocrystals are

  18. Applications of molecular self-assembly in tissue engineering

    NASA Astrophysics Data System (ADS)

    Harrington, Daniel Anton

    This thesis studied the application of three self-assembling molecular systems, as potential biomaterials for tissue engineering applications. Cholesteryl-(L-lactic acid)n molecules form thermotropic liquid crystals, which could be coated onto the inner and outer pores of biodegradable PLLA scaffolds, while retaining the lamellar order of the neat material. Primary bovine chondrocytes were cultured on these structures, demonstrating improved attachment and extended retention of phenotype on the C-LA-coated scaffolds. No difference in fibronectin adsorption to C-LA and PLLA surfaces was observed, suggesting a strong role for cholesterol in influencing cell phenotype. A family of peptide-amphiphiles, bearing the "RGD" adhesion sequence from fibronectin, was also assessed in the contexts of cartilage and bladder repair. These molecules self-assemble into one-dimensional fibers, with diameters of 6--8 nm, and lengths of 500 nm or greater. Chondrocytes were seeded and cultured on covalently-crosslinked PA gels and embedded within calcium-triggered PA gels. Cells became dormant over time, but remained viable, suggesting an inappropriate display of the adhesion sequence to cells. A family of "branched" PA molecules with lysine dendron headgroups was designed, in an effort to increase the spatial separation between molecules in the assembled state, and to theoretically improve epitope accessibility. These molecules coated reliably onto PGA fiber scaffolds, and dramatically increased the attachment of human bladder smooth muscle cells, possibly through better epitope display or electrostatic attraction. They also formed strong gels with several negatively-charged biologically-relevant macromolecules. In a third system, amphiphilic segmented dendrimers based on phenylene vinylene and L-lysine entered cells through an endocytic pathway with no discernible toxic effect on cell proliferation or morphology. These amphiphiles formed complex aggregates in aqueous solution, likely

  19. Molecularly oriented surface relief formation in polymethacrylates comprising N-benzylideneaniline derivative side groups

    NASA Astrophysics Data System (ADS)

    Kawatsuki, Nobuhiro; Hosoda, Risa; Kondo, Mizuho; Sasaki, Tomoyuki; Ono, Hiroshi

    2014-12-01

    Molecularly oriented surface relief (SR) formation in polymethacrylates with N-benzylideneaniline (NBA) derivative side groups is investigated by holographic exposure using a 325 nm He-Cd laser. Because the NBA moieties show a photoinduced orientation perpendicular to the polarization of light, polarization holography successfully forms a molecularly oriented SR structure in accordance with the polarization distribution that includes p-polarized components. Although intensity holography induces molecular orientation, it does not generate a satisfactory SR structure. In all the holographic modes, the SR depth depends on the direction of the C=N bonds in the NBA moieties and the photoproducts affect the SR formation ability.

  20. Self-assembly of multilevel branched rutile-type TiO2 structures via oriented lateral and twin attachment

    PubMed Central

    Jordan, Vanja; Javornik, Uroš; Plavec, Janez; Podgornik, Aleš; Rečnik, Aleksander

    2016-01-01

    Recent breakthrough of novel hierarchic materials, orchestrated through oriented attachment of crystal subunits, opened questions on what is the mechanism of their self-assembly. Using rutile-type TiO2, synthesized by hydrothermal reaction of Ti(IV)-butoxide in highly acidic aqueous medium, we uncovered the key processes controlling this nonclassical crystallization process. Formation of complex branched mesocrystals of rutile is accomplished by oriented assembly of precipitated fibers along the two low-energy planes, i.e. {110} and {101}, resulting in lateral attachment and twinning. Phase analysis of amorphous material enclosed in pockets between imperfectly assembled rutile fibers clearly shows harmonic ordering resembling that of the adjacent rutile structure. To our understanding this may be the first experimental evidence indicating the presence of electromagnetic force-fields that convey critical structural information through which oriented attachment of nanocrystals is made possible. PMID:27063110

  1. Surface-confined assemblies and polymers for molecular logic.

    PubMed

    de Ruiter, Graham; van der Boom, Milko E

    2011-08-16

    Stimuli responsive materials are capable of mimicking the operation characteristics of logic gates such as AND, OR, NOR, and even flip-flops. Since the development of molecular sensors and the introduction of the first AND gate in solution by de Silva in 1993, Molecular (Boolean) Logic and Computing (MBLC) has become increasingly popular. In this Account, we present recent research activities that focus on MBLC with electrochromic polymers and metal polypyridyl complexes on a solid support. Metal polypyridyl complexes act as useful sensors to a variety of analytes in solution (i.e., H(2)O, Fe(2+/3+), Cr(6+), NO(+)) and in the gas phase (NO(x) in air). This information transfer, whether the analyte is present, is based on the reversible redox chemistry of the metal complexes, which are stable up to 200 °C in air. The concurrent changes in the optical properties are nondestructive and fast. In such a setup, the input is directly related to the output and, therefore, can be represented by one-input logic gates. These input-output relationships are extendable for mimicking the diverse functions of essential molecular logic gates and circuits within a set of Boolean algebraic operations. Such a molecular approach towards Boolean logic has yielded a series of proof-of-concept devices: logic gates, multiplexers, half-adders, and flip-flop logic circuits. MBLC is a versatile and, potentially, a parallel approach to silicon circuits: assemblies of these molecular gates can perform a wide variety of logic tasks through reconfiguration of their inputs. Although these developments do not require a semiconductor blueprint, similar guidelines such as signal propagation, gate-to-gate communication, propagation delay, and combinatorial and sequential logic will play a critical role in allowing this field to mature. For instance, gate-to-gate communication by chemical wiring of the gates with metal ions as electron carriers results in the integration of stand-alone systems: the

  2. Nanoparticle decoration with surfactants: Molecular interactions, assembly, and applications

    NASA Astrophysics Data System (ADS)

    Heinz, Hendrik; Pramanik, Chandrani; Heinz, Ozge; Ding, Yifu; Mishra, Ratan K.; Marchon, Delphine; Flatt, Robert J.; Estrela-Lopis, Irina; Llop, Jordi; Moya, Sergio; Ziolo, Ronald F.

    2017-02-01

    Nanostructures of diverse chemical nature are used as biomarkers, therapeutics, catalysts, and structural reinforcements. The decoration with surfactants has a long history and is essential to introduce specific functions. The definition of surfactants in this review is very broad, following its lexical meaning ;surface active agents;, and therefore includes traditional alkyl modifiers, biological ligands, polymers, and other surface active molecules. The review systematically covers covalent and non-covalent interactions of such surfactants with various types of nanomaterials, including metals, oxides, layered materials, and polymers as well as their applications. The major themes are (i) molecular recognition and noncovalent assembly mechanisms of surfactants on the nanoparticle and nanocrystal surfaces, (ii) covalent grafting techniques and multi-step surface modification, (iii) dispersion properties and surface reactions, (iv) the use of surfactants to influence crystal growth, as well as (v) the incorporation of biorecognition and other material-targeting functionality. For the diverse materials classes, similarities and differences in surfactant assembly, function, as well as materials performance in specific applications are described in a comparative way. Major factors that lead to differentiation are the surface energy, surface chemistry and pH sensitivity, as well as the degree of surface regularity and defects in the nanoparticle cores and in the surfactant shell. The review covers a broad range of surface modifications and applications in biological recognition and therapeutics, sensors, nanomaterials for catalysis, energy conversion and storage, the dispersion properties of nanoparticles in structural composites and cement, as well as purification systems and classical detergents. Design principles for surfactants to optimize the performance of specific nanostructures are discussed. The review concludes with challenges and opportunities.

  3. Highly oriented, self-assembled alkanephosphate monolayers on tantalum(V) oxide surfaces

    SciTech Connect

    Brovelli, D.; Haehner, G.; Ruiz, L.

    1999-06-22

    Octadecyl phosphoric acid ester has been found to produce oriented, well-ordered monolayers on a flat tantalum(V) oxide surface, via self-assembly from a heptane/propan-2-ol solution. By means of contact angle, optical waveguide lightmode spectroscopy (OWLS), near-edge X-ray absorption fine structure spectroscopy (NEXASFS), and X-ray photoelectron spectroscopy (XPS) measurements, it has been shown that these layers closely resemble those formed by the corresponding thiol-gold system, with respect to packing density, inclination, and order. The system shows promise as an approach to functionalizing oxide surfaces with well-ordered organic monolayers, with potential applications in the fields of biochemical analysis and sensors.

  4. Coordinated Spindle Assembly and Orientation Requires Clb5p-Dependent Kinase in Budding Yeast

    PubMed Central

    Segal, Marisa; Clarke, Duncan J.; Maddox, Paul; Salmon, E.D.; Bloom, Kerry; Reed, Steven I.

    2000-01-01

    The orientation of the mitotic spindle along a polarity axis is critical in asymmetric cell divisions. In the budding yeast, Saccharomyces cerevisiae, loss of the S-phase B-type cyclin Clb5p under conditions of limited cyclin-dependent kinase activity (cdc28-4 clb5Δ cells) causes a spindle positioning defect that results in an undivided nucleus entering the bud. Based on time-lapse digital imaging microscopy of microtubules labeled with green fluorescent protein fusions to either tubulin or dynein, we observed that the asymmetric behavior of the spindle pole bodies during spindle assembly was lost in the cdc28-4 clb5Δ cells. As soon as a spindle formed, both poles were equally likely to interact with the bud cell cortex. Persistent dynamic interactions with the bud ultimately led to spindle translocation across the bud neck. Thus, the mutant failed to assign one spindle pole body the task of organizing astral microtubules towards the mother cell. Our data suggest that Clb5p-associated kinase is required to confer mother-bound behavior to one pole in order to establish correct spindle polarity. In contrast, B-type cyclins, Clb3p and Clb4p, though partially redundant with Clb5p for an early role in spindle morphogenesis, preferentially promote spindle assembly. PMID:10662771

  5. Nanoscale Electric Characteristics and Oriented Assembly of Halobacterium salinarum Membrane Revealed by Electric Force Microscopy

    PubMed Central

    Li, Denghua; Wang, Yibing; Du, Huiwen; Xu, Shiwei; Li, Zhemin; Yang, Yanlian; Wang, Chen

    2016-01-01

    Purple membranes (PM) of the bacteria Halobacterium salinarum are a unique natural membrane where bacteriorhodopsin (BR) can convert photon energy and pump protons. Elucidating the electronic properties of biomembranes is critical for revealing biological mechanisms and developing new devices. We report here the electric properties of PMs studied by using multi-functional electric force microscopy (EFM) at the nanoscale. The topography, surface potential, and dielectric capacity of PMs were imaged and quantitatively measured in parallel. Two orientations of PMs were identified by EFM because of its high resolution in differentiating electrical characteristics. The extracellular (EC) sides were more negative than the cytoplasmic (CP) side by 8 mV. The direction of potential difference may facilitate movement of protons across the membrane and thus play important roles in proton pumping. Unlike the side-dependent surface potentials observed in PM, the EFM capacitive response was independent of the side and was measured to be at a dC/dz value of ~5.25 nF/m. Furthermore, by modification of PM with de novo peptides based on peptide-protein interaction, directional oriented PM assembly on silicon substrate was obtained for technical devices. This work develops a new method for studying membrane nanoelectronics and exploring the bioelectric application at the nanoscale. PMID:28335325

  6. Molecular self-assembly for biological investigations and nanoscale lithography

    NASA Astrophysics Data System (ADS)

    Cheunkar, Sarawut

    Small, diffusible molecules when recognized by their binding partners, such as proteins and antibodies, trigger enzymatic activity, cell communication, and immune response. Progress in analytical methods enabling detection, characterization, and visualization of biological dynamics at the molecular level will advance our exploration of complex biological systems. In this dissertation, analytical platforms were fabricated to capture membrane-associated receptors, which are essential proteins in cell signaling pathways. The neurotransmitter serotonin and its biological precursor were immobilized on gold substrates coated with self-assembled monolayers (SAMs) of oligo(ethylene glycol)alkanethiols and their reactive derivatives. The SAM-coated substrates present the biologically selective affinity of immobilized molecules to target native membrane-associated receptors. These substrates were also tested for biospecificity using antibodies. In addition, small-molecule-functionalized platforms, expressing neurotransmitter pharmacophores, were employed to examine kinetic interactions between G-protein-coupled receptors and their associated neurotransmitters. The binding interactions were monitored using a quartz crystal microbalance equipped with liquid-flow injection. The interaction kinetics of G-protein-coupled serotonin 1A receptor and 5-hydroxytyptophan-functionalized surfaces were studied in a real-time, label-free environment. Key binding parameters, such as equilibrium dissociation constants, binding rate constants, and dissociative half-life, were extracted. These parameters are critical for understanding and comparing biomolecular interactions in modern biomedical research. By integrating self-assembly, surface functionalization, and nanofabrication, small-molecule microarrays were created for high-throughput screening. A hybrid soft-lithography, called microcontact insertion printing, was used to pattern small molecules at the dilute scales necessary for highly

  7. A Molecular View of Kinetochore Assembly and Function

    PubMed Central

    Musacchio, Andrea; Desai, Arshad

    2017-01-01

    Kinetochores are large protein assemblies that connect chromosomes to microtubules of the mitotic and meiotic spindles in order to distribute the replicated genome from a mother cell to its daughters. Kinetochores also control feedback mechanisms responsible for the correction of incorrect microtubule attachments, and for the coordination of chromosome attachment with cell cycle progression. Finally, kinetochores contribute to their own preservation, across generations, at the specific chromosomal loci devoted to host them, the centromeres. They achieve this in most species by exploiting an epigenetic, DNA-sequence-independent mechanism; notable exceptions are budding yeasts where a specific sequence is associated with centromere function. In the last 15 years, extensive progress in the elucidation of the composition of the kinetochore and the identification of various physical and functional modules within its substructure has led to a much deeper molecular understanding of kinetochore organization and the origins of its functional output. Here, we provide a broad summary of this progress, focusing primarily on kinetochores of humans and budding yeast, while highlighting work from other models, and present important unresolved questions for future studies. PMID:28125021

  8. Molecular Architecture of  Yeast Chromatin Assembly Factor 1

    PubMed Central

    Kim, Daegeun; Setiaputra, Dheva; Jung, Taeyang; Chung, Jaehee; Leitner, Alexander; Yoon, Jungmin; Aebersold, Ruedi; Hebert, Hans; Yip, Calvin K.; Song, Ji-Joon

    2016-01-01

    Chromatin Assembly Complex 1 (CAF-1) is a major histone chaperone involved in deposition of histone H3 and H4 into nucleosome. CAF-1 is composed of three subunits; p150, p60 and p48 for human and Cac1, Cac2 and Cac3 for yeast. Despite of its central role in chromatin formation, structural features of the full CAF-1 in complex with histones and other chaperones have not been well characterized. Here, we dissect molecular architecture of yeast CAF-1 (yCAF-1) by cross-linking mass spectrometry (XL-MS) and negative stain single-particle electron microscopy (EM). Our work revealed that Cac1, the largest subunit of yCAF-1, might serve as a major histone binding platform linking Cac2 and Cac3. In addition, EM analysis showed that yCAF-1 adopts a bilobal shape and Cac1 connecting Cac2 and Cac3 to generate a platform for binding histones. This study provides the first structural glimpse of the full CAF-1 complex and a structural framework to understand histone chaperoning processes. PMID:27221973

  9. High molecular weight DNA assembly in vivo for synthetic biology applications.

    PubMed

    Juhas, Mario; Ajioka, James W

    2017-05-01

    DNA assembly is the key technology of the emerging interdisciplinary field of synthetic biology. While the assembly of smaller DNA fragments is usually performed in vitro, high molecular weight DNA molecules are assembled in vivo via homologous recombination in the host cell. Escherichia coli, Bacillus subtilis and Saccharomyces cerevisiae are the main hosts used for DNA assembly in vivo. Progress in DNA assembly over the last few years has paved the way for the construction of whole genomes. This review provides an update on recent synthetic biology advances with particular emphasis on high molecular weight DNA assembly in vivo in E. coli, B. subtilis and S. cerevisiae. Special attention is paid to the assembly of whole genomes, such as those of the first synthetic cell, synthetic yeast and minimal genomes.

  10. Self assembled films of porphyrins with amine groups at different positions: influence of their orientation on the corrosion inhibition and the electrocatalytic activity.

    PubMed

    Lokesh, Koodlur Sannegowda; De Keersmaecker, Michel; Adriaens, Annemie

    2012-06-26

    Self-assembled molecular films of two cobalt porphyrins with amine groups at different positions-(5,10,15,20-tetrakis-(2-aminophenyl) porphyrin-cobalt(II), [Co(II) (T(o-NH(2))PP)] and (5,10,15,20-tetrakis-(4-aminophenyl) porphyrin-cobalt(II), [Co(II)(T(p-NH(2))PP)]-were formed on a gold substrate. The functionalized surfaces were characterized using Raman spectroscopy, atomic force microscopy and electrochemical methods. Both modified gold surfaces completely mask the charge transfer of a [Fe(CN)(6)](3-/4-) redox couple in solution, indicating the layer is highly resistive in behavior. Electrochemical impedance spectroscopy analyses revealed that the porphyrin film with amine groups at ortho positions shows a higher charge-transfer resistance with a better protective behavior compared to the para position modified surface. Raman, AFM and EIS data suggests that an ortho amine positioned molecule forms a more compact layer compared to the para-positioned molecule. This can be explained in terms of their orientation on the gold surface. [Co(II)(T(o-NH(2))PP)] adopted a saddle shape orientation whereas [Co(II)(T(p-NH(2))PP)] adopted a flat orientation on the gold surface. The porphyrin modified gold electrode catalyzes the oxygen reduction at lower potentials compared to the bare gold electrode. The shift in the overvoltage was higher in case of molecules with flat orientation compared to the saddle shaped oriented porphyrin molecules on the surface.

  11. Controlling Molecular Motion, Assembly and Coupling as a Step towards Molecular Actuators

    NASA Astrophysics Data System (ADS)

    Murphy, Colin James

    changes in the supramolecular self-assembly of thioethers. Chapter 9 details how the ordering and length of surface-bound hydrogen-bonded chains of methanol are dictated by the underlying surface and examines an unreported chiral meta-stable methanol hexamer. Single-molecule measurements can answer many of the current questions in the field of molecular machines and lead to control of molecular motion. Development of mechanisms to direct molecular motion and to couple this motion to external systems is crucial for the rational design of new molecular machinery with functionalities such as mass transport, propulsion, separations, sensing, signaling and chemical reactions.

  12. Synthesis and sonication-induced assembly of Si-DDR particles for close-packed oriented layers.

    PubMed

    Kim, Eunjoo; Cai, Wanxi; Baik, Hionsuck; Nam, Jaewook; Choi, Jungkyu

    2013-08-28

    Here, we report a seeded growth protocol for synthesizing monodisperse Si-DDR particles of ~1.3-10 μm by varying the seed amount. These Si-DDR particles were deposited onto porous α-Al2O3 discs via sonication-induced assembly, constituting close-packed h0h-oriented layers.

  13. Effect of Crystal Orientation on Self-Assembly Nanocones Formed on Tungsten Surface Induced by Helium Ion Irradiation and Annealing

    PubMed Central

    Huang, Shilin; Ran, Guang; Lei, Penghui; Wu, Shenghua; Chen, Nanjun; Li, Ning

    2016-01-01

    The self-assembly nanocone structures on the surface of polycrystalline tungsten were created by He+ ion irradiation and then annealing, and the resulting topography and morphology were characterized using atomic force microscopy and scanning electron microscopy. The cross-sectional samples of the self-assembly nanocones were prepared using an in situ–focused ion beam and then observed using transmission electron microscopy. The self-assembly nanocones were induced by the combined effect of He+ ion irradiation, the annealing process and the chromium impurity. The distribution characteristics, density and morphology of the nanocones exhibited a distinct difference relating to the crystal orientations. The highest density of the nanocones was observed on the grain surface with a (1 1 1) orientation, with the opposite for that with a (0 0 1) orientation and a medium value on the (1 0 1)-oriented grain. The size of the self-assembly nanocones increased with increasing the annealing time which met a power-law relationship. Irradiation-induced defects acted as the nucleation locations of the protrusions which attracted the migration of the tiny amount of chromium atoms. Under the action of temperature, the protrusions finally evolved into the nanocones. PMID:28335337

  14. Molecular microbial diversity of a spacecraft assembly facility

    NASA Technical Reports Server (NTRS)

    Venkateswaran, K.; Satomi, M.; Chung, S.; Kern, R.; Koukol, R.; Basic, C.; White, D.

    2001-01-01

    In ongoing investigations to map and archive the microbial footprints in various components of the spacecraft and its accessories, we have examined the microbial populations of the Jet Propulsion Laboratory's Spacecraft Assembly Facility (JPL-SAF). Witness plates made up of spacecraft materials, some painted with spacecraft qualified paints, were exposed for approximately 7 to 9 months at JPL-SAF and examined the particulate materials collected for the incidence of total cultivable aerobic heterotrophs and heat-tolerant (80 degrees C for 15-min.) spore-formers. The results showed that the witness plates coated with spacecraft qualified paints attracted more dust particles than the non-coated stainless steel witness plates. Among the four paints tested, witness plates coated with NS43G accumulated the highest number of particles, and hence attracted more cultivable microbes. The conventional microbiological examination revealed that the JPL-SAF harbors mainly Gram-positive microbes and mostly spore-forming Bacillus species. Most of the isolated microbes were heat resistant to 80 degrees C and proliferate at 60 degrees C. The phylogenetic relationships among 23 cultivable heat-tolerant microbes were examined using a battery of morphological, physiological, molecular and chemotaxonomic characterizations. By 16S rDNA sequence analysis, the isolates fell into seven clades: Bacillus licheniformis, B. pumilus, B. cereus, B. circulans, Staphylococcus capitis, Planococcus sp. and Micrococcus lylae. In contrast to the cultivable approach, direct DNA isolation, cloning and 16S rDNA sequencing analysis revealed equal representation of both Gram-positive and Gram-negative microorganisms.

  15. Molecular microbial diversity of a spacecraft assembly facility.

    PubMed

    Venkateswaran, K; Satomi, M; Chung, S; Kern, R; Koukol, R; Basic, C; White, D

    2001-07-01

    In ongoing investigations to map and archive the microbial footprints in various components of the spacecraft and its accessories, we have examined the microbial populations of the Jet Propulsion Laboratory's Spacecraft Assembly Facility (JPL-SAF). Witness plates made up of spacecraft materials, some painted with spacecraft qualified paints, were exposed for approximately 7 to 9 months at JPL-SAF and examined the particulate materials collected for the incidence of total cultivable aerobic heterotrophs and heat-tolerant (80 degrees C for 15-min.) spore-formers. The results showed that the witness plates coated with spacecraft qualified paints attracted more dust particles than the non-coated stainless steel witness plates. Among the four paints tested, witness plates coated with NS43G accumulated the highest number of particles, and hence attracted more cultivable microbes. The conventional microbiological examination revealed that the JPL-SAF harbors mainly Gram-positive microbes and mostly spore-forming Bacillus species. Most of the isolated microbes were heat resistant to 80 degrees C and proliferate at 60 degrees C. The phylogenetic relationships among 23 cultivable heat-tolerant microbes were examined using a battery of morphological, physiological, molecular and chemotaxonomic characterizations. By 16S rDNA sequence analysis, the isolates fell into seven clades: Bacillus licheniformis, B. pumilus, B. cereus, B. circulans, Staphylococcus capitis, Planococcus sp. and Micrococcus lylae. In contrast to the cultivable approach, direct DNA isolation, cloning and 16S rDNA sequencing analysis revealed equal representation of both Gram-positive and Gram-negative microorganisms.

  16. Etomica: an object-oriented framework for molecular simulation.

    PubMed

    Schultz, Andrew J; Kofke, David A

    2015-03-30

    We describe the design of an object-oriented library of software components that are suitable for constructing simulations of systems of interacting particles. The emphasis of the discussion is on the general design of the components and how they interact, and less on details of the programming interface or its implementation. Example code is provided as an aid to understanding object-oriented programming structures and to demonstrate how the framework is applied.

  17. Enhancing molecular orientation by combining electrostatic and four-color laser fields

    NASA Astrophysics Data System (ADS)

    Xu, Shuwu; Yao, Yunhua; Lu, Chenhui; Jia, Tianqing; Ding, Jingxin; Zhang, Shian; Sun, Zhenrong

    2014-09-01

    We propose a scheme to enhance molecular orientation by combing an intense electrostatic field and a four-color laser field. We show that molecular orientation by the combined field can be obtained under a laser-field-free condition, and the maximal orientation degree can be enhanced by comparing with the sum of that individually created by the electrostatic field and the four-color laser field. Our results show that the orientation enhancement results from the larger asymmetry of the four-color laser field because of the existence of the electrostatic field. Furthermore, we also discuss the dependence of the orientation enhancement on the carrier-envelope phase, laser intensity, and pulse duration of the four-color laser field and the molecular rotational temperature.

  18. Molecular Processes Underlying the Structure and Assembly of Thin Films and Nanoparticles at Complex interfaces

    SciTech Connect

    Richmond, Geraldine

    2016-06-03

    differences in how water behaves at hydrophobic self-assembled monolayer (SAMS)/water interfaces relative to the organic liquid/water interfaces. Several monolayer films have been examined in these studies using a combination of vibrational sum frequency spectroscopy (VSFS), contact angle measurements and AFM. At the hydrocarbon monolayer/water interface we find that water has a weak bonding interaction with the monolayer film that results in an orientation of water at the terminus of these hydrocarbon chains. The water-film interaction is still present for fluorinated films but it is found to be considerably weaker. Hydration and Surfactant Adsorption at Salt/Water Interfaces This set of studies has examined the molecular characteristics of the CaF2/water interface using VSFS. Our first studies detailed the structure and orientation of water molecules adsorbed at this mineral surfaces including studies of the surface in the presence of aqueous solutions of salts. These studies have been followed by a series of static and time-resolved studies of the adsorption of carboxylic acid containing organics at this surface, specifically carboxylic acid surfactants and acetic acid. In the latter we have developed a new method for time resolved studies that involve sequential wavelength tuning and automated control of spatial beam overlap at the target can probe amplitude changes of sum-frequency resonances in widely spaced infrared regions. This offers great advantages for the study of the synchronism of molecular processes at interfaces. This approach is particularly suitable to investigate the synchronization of interfacial processes such as surfactant adsorption at charged mineral surfaces. Macromolecular Assembly at Liquid/Liquid Interfaces Macromolecular assembly at the interface between water and a hydrophobic surface underlies some of the most important biological and environmental processes on the planet. Our work has examined polymer adsorption and assembly of

  19. Mechanisms of two-color laser-induced field-free molecular orientation.

    PubMed

    Spanner, Michael; Patchkovskii, Serguei; Frumker, Eugene; Corkum, Paul

    2012-09-14

    Two mechanisms of two-color (ω+2ω) laser-induced field-free molecular orientation, based on the hyperpolarizability and ionization depletion, are explored and compared. The CO molecule is used as a computational example. While the hyperpolarizability mechanism generates small amounts of orientation at intensities below the ionization threshold, ionization depletion quickly becomes the dominant mechanism as soon as ionizing intensities are reached. Only the ionization mechanism leads to substantial orientation (e.g., on the order of ≳0.1). For intensities typical of laser-induced molecular alignment and orientation experiments, the two mechanisms lead to robust, characteristic timings of the field-free orientation wave-packet revivals relative to the alignment revivals and the revival time. The revival timings can be used to detect the active orientation mechanism experimentally.

  20. Supramolecular star polymers. Increased molecular weight with decreased polydispersity through self-assembly.

    PubMed

    Todd, Eric M; Zimmerman, Steven C

    2007-11-28

    A ditopic structure containing two heterocyclic DeAP units and programmed to self-assemble is used as an initiation unit for the synthesis of polylactide and polystyrene. The resultant polymers self-assemble into higher molecular weight structures with a lower molecular weight distribution. The largest discrete nanoscale polymeric assembly is proposed to be a hexameric star with a molecular weight of ca. 92.7 kDa. All polymeric assemblies generally exhibit PDI values of 1.3 to 1.5, which are lower than the PDI value of the corresponding polymeric arms. A hexameric assembly is stabilized by 30 hydrogen bonds, including six AADD.DDAA contacts. The hexameric star is formed under conditions that are at least partially controlled by kinetics.

  1. Anisotropic demineralization and oriented assembly of hydroxyapatite crystals in enamel: smart structures of biominerals.

    PubMed

    Pan, Haihua; Tao, Jinhui; Yu, Xinwei; Fu, Lei; Zhang, Jiali; Zeng, Xiangxuan; Xu, Guohua; Tang, Ruikang

    2008-06-19

    It is interesting to note that the demineralization of natural enamel does not happen as readily as that of the synthesized hydroxyapatite (HAP), although they share a similar chemical composition. We suggest that the hierarchical structure of enamel is an important factor in the preservation of the natural material against dissolution. The anisotropic demineralization of HAP is revealed experimentally, and this phenomenon is understood by the different interfacial structures of HAP-water at the atomic level. It is found that HAP {001} facets can be more resistant against dissolution than {100} under acidic conditions. Although {100} is the largest surface of the typical HAP crystal, it is {001}, the smallest habit face, that is chosen by the living organisms to build the outer surface of enamel by an oriented assembly of the rodlike crystals. We reveal that such a biological construction can confer on enamel protections against erosion, since {001} is relatively dissolution-insensitive. Thus, the spontaneous dissolution of enamel surface can be retarded in biological milieu by such a smart construction. The current study demonstrates the importance of hierarchical structures in the functional biomaterials.

  2. Influence of solute-solvent coordination on the orientational relaxation of ion assemblies in polar solvents.

    PubMed

    Ji, Minbiao; Hartsock, Robert W; Sung, Zheng; Gaffney, Kelly J

    2012-01-07

    We have investigated the rotational dynamics of lithium thiocyanate (LiNCS) dissolved in various polar solvents with time and polarization resolved vibrational spectroscopy. LiNCS forms multiple distinct ionic structures in solution that can be distinguished with the CN stretch vibrational frequency of the different ionic assemblies. By varying the solvent and the LiNCS concentration, the number and type of ionic structures present in solution can be controlled. Control of the ionic structure provides control over the volume, shape, and dipole moment of the solute, critical parameters for hydrodynamic and dielectric continuum models of friction. The use of solutes with sizes comparable to or smaller than the solvent molecules also helps amplify the sensitivity of the measurement to the short-ranged solute-solvent interaction. The measured orientational relaxation dynamics show many clear and distinct deviations from simple hydrodynamic behavior. All ionic structures in all solvents exhibit multi-exponential relaxation dynamics that do not scale with the solute volume. For Lewis base solvents such as benzonitrile, dimethyl carbonate, and ethyl acetate, the observed dynamics strongly show the effect of solute-solvent complex formation. For the weak Lewis base solvent nitromethane, we see no evidence for solute-solvent complex formation, but still see strong deviation from the predictions of simple hydrodynamic theory.

  3. Donor/Acceptor Molecular Orientation-Dependent Photovoltaic Performance in All-Polymer Solar Cells.

    PubMed

    Zhou, Ke; Zhang, Rui; Liu, Jiangang; Li, Mingguang; Yu, Xinhong; Xing, Rubo; Han, Yanchun

    2015-11-18

    The correlated donor/acceptor (D/A) molecular orientation plays a crucial role in solution-processed all-polymer solar cells in term of photovoltaic performance. For the conjugated polymers PTB7-th and P(NDI2OD-T2), the preferential molecular orientation of neat PTB7-th films kept face-on regardless of the properties of processing solvents. However, an increasing content of face-on molecular orientation in the neat P(NDI2OD-T2) films could be found by changing processing solvents from chloronaphthalene (CN) and o-dichlorobenzene (oDCB) to chlorobenzene (CB). Besides, the neat P(NDI2OD-T2) films also exhibited a transformation of preferential molecular orientation from face-on to edge-on when extending film drying time by casting in the same solution. Consequently, a distribution diagram of molecular orientation for P(NDI2OD-T2) films was depicted and the same trend could be observed for the PTB7-th/P(NDI2OD-T2) blend films. By manufacture of photovoltaic devices with blend films, the relationship between the correlated D/A molecular orientation and device performance was established. The short-circuit current (Jsc) of devices processed by CN, oDCB, and CB enhanced gradually from 1.24 to 8.86 mA/cm(2) with the correlated D/A molecular orientation changing from face-on/edge-on to face-on/face-on, which could be attributed to facile exciton dissociation at D/A interface with the same molecular orientation. Therefore, the power conversion efficiency (PCE) of devices processed by CN, oDCB, and CB improved from 0.53% to 3.52% ultimately.

  4. Molecular Self-Assembly and Nanochemistry: A Chemical Strategy for the Synthesis of Nanostructures

    NASA Astrophysics Data System (ADS)

    Whitesides, George M.; Mathias, John P.; Seto, Christopher T.

    1991-11-01

    Molecular self-assembly is the spontaneous association of molecules under equilibrium conditions into stable, structurally well-defined aggregates joined by noncovalent bonds. Molecular self-assembly is ubiquitous in biological systems and underlies the formation of a wide variety of complex biological structures. Understanding self-assembly and the associated noncovalent interactions that connect complementary interacting molecular surfaces in biological aggregates is a central concern in structural biochemistry. Self-assembly is also emerging as a new strategy in chemical synthesis, with the potential of generating nonbiological structures with dimensions of 1 to 10^2 nanometers (with molecular weights of 10^4 to 1010 daltons). Structures in the upper part of this range of sizes are presently inaccessible through chemical synthesis, and the ability to prepare them would open a route to structures comparable in size (and perhaps complementary in function) to those that can be prepared by microlithography and other techniques of microfabrication.

  5. Molecular self-assembly and nanochemistry: a chemical strategy for the synthesis of nanostructures.

    PubMed

    Whitesides, G M; Mathias, J P; Seto, C T

    1991-11-29

    Molecular self-assembly is the spontaneous association of molecules under equilibrium conditions into stable, structurally well-defined aggregates joined by noncovalent bonds. Molecular self-assembly is ubiquitous in biological systems and underlies the formation of a wide variety of complex biological structures. Understanding self-assembly and the associated noncovalent interactions that connect complementary interacting molecular surfaces in biological aggregates is a central concern in structural biochemistry. Self-assembly is also emerging as a new strategy in chemical synthesis, with the potential of generating nonbiological structures with dimensions of 1 to 10(2) nanometers (with molecular weights of 10(4) to 10(10) daltons). Structures in the upper part of this range of sizes are presently inaccessible through chemical synthesis, and the ability to prepare them would open a route to structures comparable in size (and perhaps complementary in function) to those that can be prepared by microlithography and other techniques of microfabrication.

  6. Pincer-plus-one ligands in self-assembly with palladium(ii): a molecular square and a molecular tetrahedron.

    PubMed

    Behnia, Ava; Boyle, Paul D; Fard, Mahmood A; Blacquiere, Johanna M; Puddephatt, Richard J

    2016-12-06

    The combination of a palladium(ii) precursor with a diimine-phenol ligand and an oxidant (H2O2 or O2) under different conditions has, serendipitously, given both a molecular square and a molecular tetrahedron by self-assembly of building blocks comprising palladium(ii) centres coordinated to the oxidised forms of the ligand.

  7. Molecular orientation and lattice ordering of C60 molecules on the polar FeO/Pt(111) surface.

    PubMed

    Qin, Zhihui; Liu, Cunding; Chen, Jian; Guo, Qinmin; Yu, Yinghui; Cao, Gengyu

    2012-01-14

    C(60) molecules assemble into close packing layer under the domination of the intermolecular interaction when deposited onto Pt(111)-supported FeO layer kept at 400 K. From corresponding high resolution scanning tunneling microscopy (STM) image, a kind of C(60) molecular orientational ordering stabilized by the intermolecular interaction is revealed as C(60)/FeO(111)-(√133 × √133) R17.5° structure and determined from the commensurability between the C(60) nearest-neighbor distance and the lattice of the underlying oxygen layer. Moreover, due to the inhomogeneously distributed work function of the underlying FeO layer, the C(60) molecular electronic state is periodically modulated resulting in a bright-dim STM contrast. In addition, one coincidence lattice ordering is determined as 8 × 8 superstructure with respect to the C(60) primitive cell, which overlays a 3 × 3 moiré cell of the underlying FeO layer.

  8. Molecular orientation and lattice ordering of C60 molecules on the polar FeO/Pt(111) surface

    NASA Astrophysics Data System (ADS)

    Qin, Zhihui; Liu, Cunding; Chen, Jian; Guo, Qinmin; Yu, Yinghui; Cao, Gengyu

    2012-01-01

    C60 molecules assemble into close packing layer under the domination of the intermolecular interaction when deposited onto Pt(111)-supported FeO layer kept at 400 K. From corresponding high resolution scanning tunneling microscopy (STM) image, a kind of C60 molecular orientational ordering stabilized by the intermolecular interaction is revealed as C60/FeO(111)-(√133 × √133) R17.5° structure and determined from the commensurability between the C60 nearest-neighbor distance and the lattice of the underlying oxygen layer. Moreover, due to the inhomogeneously distributed work function of the underlying FeO layer, the C60 molecular electronic state is periodically modulated resulting in a bright-dim STM contrast. In addition, one coincidence lattice ordering is determined as 8 × 8 superstructure with respect to the C60 primitive cell, which overlays a 3 × 3 moiré cell of the underlying FeO layer.

  9. The mechanism for molecular assembly of the proteasome.

    PubMed

    Sahara, Kazutaka; Kogleck, Larissa; Yashiroda, Hideki; Murata, Shigeo

    2014-01-01

    In eukaryotic cells, the ubiquitin proteasome system plays important roles in diverse cellular processes. The 26S proteasome is a large enzyme complex that degrades ubiquitinated proteins. It consists of 33 different subunits that form two subcomplexes, the 20S core particle and the 19S regulatory particle. Recently, several chaperones dedicated to the accurate assembly of this protease complex have been identified, but the complete mechanism of the 26S proteasome assembly is still unclear. In this review, we summarize what is known about the assembly of proteasome to date and present our group's recent findings on the role of the GET pathway in the assembly of the 26S proteasome, in addition to its role in mediating the insertion of tail-anchored (TA) proteins into the ER membrane.

  10. Self-assembled monolayers from biphenyldithiol derivatives: optimization of the deprotection procedure and effect of the molecular conformation.

    PubMed

    Shaporenko, Andrey; Elbing, Mark; Błaszczyk, Alfred; von Hänisch, Carsten; Mayor, Marcel; Zharnikov, Michael

    2006-03-09

    A series of biphenyl-derived dithiol (BDDT) compounds with terminal acetyl-protected sulfur groups and different structural arrangements of both phenyl rings have been synthesized and fully characterized. The different arrangements were achieved by introducing hydrocarbon substituents in the 2 and 2' positions of the biphenyl backbone. The presented model compounds enable the investigation of the correlation between the intramolecular conformation and other physical properties of interest, like, e.g., molecular assembly or electronic transport properties. Here, the ability of these model compounds to form self-assembled monolayers (SAMs) on Au(111) and Ag(111) is investigated in details. The deprotection of the target molecules was performed in situ using either NH4OH or triethylamine (TEA) deprotection agent. The fabricated films were characterized by synchrotron-based high-resolution photoelectron spectroscopy and near-edge absorption fine structure spectroscopy. Whereas the deprotection by NH4OH was found to result in the formation of multilayer films, the deprotection by TEA allowed the preparation of densely packed BDDT SAMs with a noticeably higher orientational order and smaller molecular inclination on Ag than on Au. Introduction of the alkyl bridge between the individual rings of the biphenyl backbone did not lead to a noticeable change in the structure and packing density of the BDDT SAMs as long as the molecule had a planar conformation in the respective SAM. The deviation from this conformation resulted in the deterioration of the film quality and a decrease of the orientational order.

  11. Topological defects in liquid crystals as templates for molecular self-assembly

    NASA Astrophysics Data System (ADS)

    Wang, Xiaoguang; Miller, Daniel; Bukusoglu, Emre; de Pablo, Juan; Abbott, Nicholas

    Topological defects in liquid crystals (LCs) have been widely used to organize colloidal dispersions and template polymerizations, leading to a range of elastomers and gels with complex mechanical and optical properties. However, little is understood about molecular-level assembly processes within defects. This presentation will describe an experimental study that reveals that nanoscopic environments defined by LC defects can selectively trigger processes of molecular self-assembly. By using fluorescence microscopy, cryogenic transmission electron microscopy and super-resolution optical microscopy, key signatures of molecular self-assembly of amphiphilic molecules in topological defects are observed - including cooperativity, reversibility, and controlled growth of the molecular assemblies. By using polymerizable amphiphiles, we also demonstrate preservation of molecular assemblies templated by defects, including nanoscopic o-rings synthesized from Saturn-ring disclinations. Our results reveal that topological defects in LCs are a versatile class of three-dimensional, dynamic and reconfigurable templates can direct processes of molecular self-assembly in a manner that is strongly analogous to other classes of macromolecular templates.

  12. Molecular tectonics: tubular crystals with controllable channel size and orientation.

    PubMed

    Lin, Mei-Jin; Jouaiti, Abdelaziz; Pocic, David; Kyritsakas, Nathalie; Planeix, Jean-Marc; Hosseini, Mir Wais

    2010-01-07

    The combination of flexible neutral organic tectons based on two pyridines interconnected by a thioether or thioester type spacer with an inorganic ZnSiF(6) pillar leads to the formation of 2-D coordination networks and the packing of the latter generates crystals offering controllable tubular channels with imposed orientation along the pillar axis.

  13. Molecular simulation studies of the structure of phosphorylcholine self-assembled monolayers

    NASA Astrophysics Data System (ADS)

    Zheng, Jie; He, Yi; Chen, Shengfu; Li, Lingyan; Bernards, Matthew T.; Jiang, Shaoyi

    2006-11-01

    We report a study of the structure of phosphorylcholine self-assembled monolayers (PC-SAMs) on Au(111) surfaces using both molecular mechanics (MM) and molecular dynamics (MD) simulation techniques. The lattice structure (i.e., packing densities and patterns) of the PC chains was determined first, by examining the packing energies of different structures by MM simulations in an implicit solvent. The chain orientation (i.e., antiparallel and parallel arrangements of the PC head groups) was then evaluated. The initial azimuthal angles of the PC chains were also adjusted to ensure that the optimal lattice structure was found. Finally, the two most probable lattice structures were solvated with explicit water molecules and their energies were compared after 1.5ns of MD simulations to verify the optimal structures obtained from MM. We found that the optimal lattice structure of the PC-SAM corresponds to a √7×√7 R19° lattice structure (i.e., surface coverage of 50.4Å2/molecule) with a parallel arrangement of the head groups. The corresponding thickness of the optimal PC-SAM is 13.4Å which is in agreement with that from experiments. The head groups of the PC chains are aligned on the surface in such a way that their dipole components are minimized. The P →N vector of the head groups forms an angle of 82° with respect to the surface normal. The tilt direction of molecular chains was observed to be towards their next nearest neighbor.

  14. Propargyl Vinyl Ethers and Tertiary Skipped Diynes: Two Pluripotent Molecular Platforms for Diversity-Oriented Synthesis.

    PubMed

    Tejedor, David; López-Tosco, Sara; Méndez-Abt, Gabriela; Cotos, Leandro; García-Tellado, Fernando

    2016-04-19

    During the last years, we have been involved in the development of a diversity-oriented synthetic strategy aimed at transforming simple, linear, and densely functionalized molecular platforms into collections of topologically diverse scaffolds incorporating biologically relevant structural motifs such as N- and O- heterocycles, multifunctionalized aromatic rings, fused macrocycles, etc. The strategy merges the concepts of pluripotency (the property of an array of chemical functionalities to express different chemical outcomes under different chemical environments) and domino chemistry (chemistry based on processes involving two or more bond-forming transformations that take place while the initial reaction conditions are maintained, with the subsequent reaction resulting as a consequence of the functionality installed in the previous one) to transform common multifunctional substrates into complex and diverse molecular frameworks. This design concept constitutes the ethos of the so-called branching cascade strategy, a branch of diversity-oriented synthesis focused on scaffold diversity generation. Two pluripotent molecular platforms have been extensively studied under this merging (branching) paradigm: C4-O-C3 propargyl vinyl ethers (PVEs) and C7 tertiary skipped diynes (TSDs). These are conveniently constructed from simple and commercially available raw materials (alkyl propiolates, ketones, aldehydes, acid chlorides) through multicomponent manifolds (ABB' three-component reaction for PVEs; A2BB' four-component reaction for TSDs) or a simple two-step procedure (for PVEs). Their modular origin facilitates their structural/functional diversification without increasing the number of synthetic steps for their assembly. These two pluripotent molecular platforms accommodate a well-defined and dense array of through-bond/through-space interrelated functionalities on their structures, which defines their primary reactivity principles and establishes the reactivity profile

  15. Molecular Water Lilies: Orienting Single Molecules in a Polymer Film by Solvent Vapor Annealing.

    PubMed

    Würsch, Dominik; Hofmann, Felix J; Eder, Theresa; Aggarwal, A Vikas; Idelson, Alissa; Höger, Sigurd; Lupton, John M; Vogelsang, Jan

    2016-11-17

    The microscopic orientation and position of photoactive molecules is crucial to the operation of optoelectronic devices such as OLEDs and solar cells. Here, we introduce a shape-persistent macrocyclic molecule as an excellent fluorescent probe to simply measure (i) its orientation by rotating the excitation polarization and recording the strength of modulation in photoluminescence (PL) and (ii) its position in a film by analyzing the overall PL brightness at the molecular level. The unique shape, the absorption and the fluorescence properties of this probe yield information on molecular orientation and position. We control orientation and positioning of the probe in a polymer film by solvent vapor annealing (SVA). During the SVA process the molecules accumulate at the polymer/air interface, where they adopt a flat orientation, much like water lilies on the surface of a pond. The results are potentially significant for OLED fabrication and single-molecule spectroscopy (SMS) in general.

  16. Atomic Diffusion and Molecular Self-Assembly on Metal Surfaces

    NASA Astrophysics Data System (ADS)

    Jewell, April D.

    The research described herein focuses on understanding and exploiting nanometer-scale surface phenomena with respect to surface reactivity and self-assembled systems. Using scanning tunneling miscroscopy, atoms and small molecules ( i.e., fewer than 30 atoms) adsorbed on metal surfaces were studied with the objective being to capture, understand, and manipulate the events occurring at the interface between gases and solid surfaces. The specific approach was to examine a variety of different but related chemical species in order to understand how chemical functionality affects the assembly behavior of technologically important species on metal surfaces. Using this systematic approach, in which, for example, only a single atom (or group of atoms) in the adsorbed species was varied, it was possible to uncover subtle differences in assembly behavior and overlayer stability. These differences are explained in terms of the chemical properties of the differing atom(s), which are based on well-established periodic trends and governed by electrostatics. Similar studies focusing on varying ligand functionality are also presented. Findings from this research add to our understanding of fundamental chemical interactions that govern assembly at the gas/solid interface. Importantly, the work here contributes to the establishment of heuristic rules that, in the future, could help predict assembly behavior. The impact of this research has the potential to transform our approach to sensor technology, heterogeneous catalysis, and other related fields.

  17. Molecular self-assembly using peptide nucleic acids.

    PubMed

    Berger, Or; Gazit, Ehud

    2017-01-01

    Peptide nucleic acids (PNAs) are extensively studied for the control of genetic expression since their design in the 1990s. However, the application of PNAs in nanotechnology is much more recent. PNAs share the specific base-pair recognition characteristic of DNA together with material-like properties of polyamides, both proteins and synthetic polymers, such as Kevlar and Nylon. The first application of PNA was in the form of PNA-amphiphiles, resulting in the formation of either lipid integrated structures, hydrogels or fibrillary assemblies. Heteroduplex DNA-PNA assemblies allow the formation of hybrid structures with higher stability as compared with pure DNA. A systematic screen for minimal PNA building blocks resulted in the identification of guanine-containing di-PNA assemblies and protected guanine-PNA monomer spheres showing unique optical properties. Finally, the co-assembly of PNA with thymine-like three-faced cyanuric acid allowed the assembly of poly-adenine PNA into fibers. In summary, we believe that PNAs represent a new and important family of building blocks which converges the advantages of both DNA- and peptide-nanotechnologies.

  18. Ultrafast electron transfer at organic semiconductor interfaces: Importance of molecular orientation

    DOE PAGES

    Ayzner, Alexander L.; Nordlund, Dennis; Kim, Do -Hwan; ...

    2014-12-04

    Much is known about the rate of photoexcited charge generation in at organic donor/acceptor (D/A) heterojunctions overaged over all relative arrangements. However, there has been very little experimental work investigating how the photoexcited electron transfer (ET) rate depends on the precise relative molecular orientation between D and A in thin solid films. This is the question that we address in this work. We find that the ET rate depends strongly on the relative molecular arrangement: The interface where the model donor compound copper phthalocyanine is oriented face-on with respect to the fullerene C60 acceptor yields a rate that is approximatelymore » 4 times faster than that of the edge-on oriented interface. Our results suggest that the D/A electronic coupling is significantly enhanced in the face-on case, which agrees well with theoretical predictions, underscoring the importance of controlling the relative interfacial molecular orientation.« less

  19. Ultrafast electron transfer at organic semiconductor interfaces: Importance of molecular orientation

    SciTech Connect

    Ayzner, Alexander L.; Nordlund, Dennis; Kim, Do -Hwan; Bao, Zhenan; Toney, Michael F.

    2014-12-04

    Much is known about the rate of photoexcited charge generation in at organic donor/acceptor (D/A) heterojunctions overaged over all relative arrangements. However, there has been very little experimental work investigating how the photoexcited electron transfer (ET) rate depends on the precise relative molecular orientation between D and A in thin solid films. This is the question that we address in this work. We find that the ET rate depends strongly on the relative molecular arrangement: The interface where the model donor compound copper phthalocyanine is oriented face-on with respect to the fullerene C60 acceptor yields a rate that is approximately 4 times faster than that of the edge-on oriented interface. Our results suggest that the D/A electronic coupling is significantly enhanced in the face-on case, which agrees well with theoretical predictions, underscoring the importance of controlling the relative interfacial molecular orientation.

  20. A molecular assembly system that renders antigens of choice highly repetitive for induction of protective B cell responses.

    PubMed

    Jegerlehner, Andrea; Tissot, Alain; Lechner, Franziska; Sebbel, Peter; Erdmann, Iris; Kündig, Thomas; Bächi, Thomas; Storni, Tazio; Jennings, Gary; Pumpens, Paul; Renner, Wolfgang A; Bachmann, Martin F

    2002-08-19

    Virus like particles (VLPs) are known to induce potent B cell responses in the absence of adjuvants. Moreover, epitope-specific antibody responses may be induced by VLPs that contain peptides inserted in their immunodominant regions. However, due to steric problems, the size of the peptides capable of being incorporated into VLPs while still permitting capsid assembly, is rather limited. While peptides genetically fused to either the N- or C-terminus of VLPs present fewer assembly problems, the immune responses obtained against such epitopes are often limited, most likely because the epitopes are not optimally exposed. In addition, such particles may be less stable in vivo. Here, we show that peptides and proteins engineered to contain a free cys can be chemically coupled to VLPs formed from the hepatitis B core antigen (HBcAg) containing a lys in the immuno-dominant region. By using this approach steric hindrance of capsid assembly is abrogated. Peptides or protein coupled to VLPs in an oriented fashion are shown to induce strong and protective B cell responses even against self-epitopes in the absence of adjuvants. This molecular assembly system may be used to induce strong B cell responses against most antigens.

  1. Orientational order parameter estimated from molecular polarizabilities - an optical study

    NASA Astrophysics Data System (ADS)

    Lalitha Kumari, J.; Datta Prasad, P. V.; Madhavi Latha, D.; Pisipati, V. G. K. M.

    2012-01-01

    An optical study of N-(p-n-alkyloxybenzylidene)-p-n-butyloxyanilines, nO.O4 compounds with the alkoxy chain number n = 1, 3, 6, 7, and 10 has been carried out by measuring the refractive indices using modified spectrometer and direct measurement of birefringence employing the Newton's rings method. Further, the molecular polarizability anisotropies are evaluated using Lippincott δ-function model, the molecular vibration method, Haller's extrapolation method, and scaling factor method. The molecular polarizabilities α e and α 0 are calculated using Vuk's isotropic and Neugebauer anisotropic local field models. The order parameter S is estimated by employing the molecular polarizability values determined from experimental refractive indices and density data and the polarizability anisotropy values. Further, the order parameter S is also obtained directly from the birefringence data. A comparison has been carried out among the order parameter obtained from different ways and the results are compared with the body of the data available in the literature.

  2. Molecular self-assembly and nanochemistry: A chemical strategy for the synthesis of nanostructures

    NASA Astrophysics Data System (ADS)

    Whitesides, George M.; Mathias, John P.; Seto, Christopher T.

    1991-12-01

    Molecular self assembly is the spontaneous association of molecules under equilibrium conditions into stable, structurally well-defined aggregates joined by non-covalent bonds. Molecular self-assembly is ubiquitous in biological systems, and underlies the formation of a wide variety of complex biological structures. Understanding self-assembly and the associated non-covalent interactions that connect complementary interacting molecular surfaces in biological aggregates is a central concern in structural biochemistry. Self-assembly is also emerging as a new strategy in chemical synthesis, with the potential of generating non-biological structures having dimensions of 1-10(exp 2) nanometers. Structures in the upper part of this range of sizes are presently inaccessible through chemical synthesis, and the ability to prepare them would open a route to structures comparable in size (and perhaps complementary in function) to those that can be prepared by microlithography and other techniques of microfabrication.

  3. Quantitative Sum-Frequency Generation Vibrational Spectroscopy of Molecular Surfaces and Interfaces: Lineshape, Polarization and Orientation

    SciTech Connect

    Wang, Hongfei; Velarde, Luis; Gan, Wei; Fu, Li

    2015-04-01

    Sum-frequency generation vibrational spectroscopy (SFG) can provide detailed information and understanding of molecular vibrational spectroscopy, orientational and conformational structure, and interactions of molecular surfaces and interfaces, through quantitative measurement and analysis. In this review, we present the current status and discuss the main developments on the measurement of intrinsic SFG spectral lineshape, formulations for polarization measurement and orientation analysis of the SFG-VS spectra. The main focus is to present a coherent formulation and discuss the main concepts or issues that can help to make SFG-VS a quantitative analytical and research tool in revealing the chemistry and physics of complex molecular surface and interface.

  4. Molecular simulations of mixed self-assembled monolayer coated gold nanoparticles in water.

    PubMed

    J, Meena Devi

    2015-06-01

    Molecular dynamics simulations have been employed to study the hydration of a series of nanoparticles, each of which was coated with a mixed self-assembled monolayer (SAM) comprising methyl- and hydroxy-terminated alkane thiol chains. The mixing ratio of those chains are different for each nanoparticle. The simulations focused on the wetting behavior of the SAM-coated gold nanoparticles and the distribution and structure of their interfacial water molecules. The interactions of the mixed SAM-coated gold nanoparticles with water were analyzed by evaluating the radial distribution function, hydrogen bonds, the dipole orientations of the water molecules, and the water residence time in the interfacial region. The wettability of the mixed SAM-coated gold nanoparticles improved as the concentration of terminal hydroxy moieties was increased. The distribution and dynamics of the interfacial water molecules were found to be influenced by the mixing ratio of the terminal moieties of the SAM chains. The results of our simulations suggest that the surface interactions of the mixed SAM-coated gold nanoparticles with the aqueous medium can be modulated by systematically altering the mixing ratio of the terminal methyl and hydroxy moieties. This work may lead to new biological and technological applications and inspire the development of novel biomimetic materials. Graphical Abstract Mixed SAM-coated gold nanoparticles.

  5. Self-assembly of gold nanorods coated with phospholipids: a coarse-grained molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Wan, Mingwei; Li, Xiaoxu; Gao, Lianghui; Fang, Weihai

    2016-11-01

    The self-assembly of phospholipid-coated gold nanorods (GNRs) was investigated by coarse-grained molecular dynamics simulations. We predict that in addition to the formation of deformed vesicles encapsulating GNRs with diverse orientations, the lipid-coated GNRs can form a semi-ring attached to an excess vesicle phase, a branch with excess vesicle phase, a ring phase, a branch phase, a stack phase, and a vortex phase. The morphologies of the lipid-GNR complexes depend on the lipid/GNR molar ratio and the interaction strength between the nanorod surface and the lipid head groups. At given lipid-nanorod interactions, removing the lipid induces a phase transition from an isolated ring or branch phase to an aggregated vortex or stack phase and vice versa. As the lipid-coated GNRs transit from an isolated phase to an aggregated phase, the structure of the lipid at the nanorod surface converts from a bilayer state to a non-bilayer state.

  6. Molecular Arrangement in Self-Assembled Azobenzene-Containing Thiol Monolayers at the Individual Domain Level Studied through Polarized Near-Field Raman Spectroscopy

    PubMed Central

    Chaigneau, Marc; Picardi, Gennaro; Ossikovski, Razvigor

    2011-01-01

    6-[4-(phenylazo)phenoxy]hexane-1-thiol self-assembled monolayers deposited on a gold surface form domain-like structures possessing a high degree of order with virtually all the molecules being identically oriented with respect to the surface plane. We show that, by using polarized near-field Raman spectroscopy, it is possible to derive the Raman scattering tensor of the ordered layer and consequently, the in-plane molecular orientation at the individual domain level. More generally, this study extends the application domain of the near-field Raman scattering selection rules from crystals to ordered organic structures. PMID:21541056

  7. Molecular self-assembly strategy for generating catalytic hybrid polypeptides

    DOE PAGES

    Maeda, Yoshiaki; Fang, Justin; Ikezoe, Yasuhiro; ...

    2016-04-26

    Recently, catalytic peptides were introduced that mimicked protease activities and showed promising selectivity of products even in organic solvents where protease cannot perform well. However, their catalytic efficiency was extremely low compared to natural enzyme counterparts presumably due to the lack of stable tertiary fold. We hypothesized that assembling these peptides along with simple hydrophobic pockets, mimicking enzyme active sites, could enhance the catalytic activity. Here we fused the sequence of catalytic peptide CP4, capable of protease and esterase-like activities, into a short amyloidogenic peptide fragment of Aβ. When the fused CP4-Aβ construct assembled into antiparallel β- sheets and amyloidmore » fibrils, a 4.0-fold increase in the hydrolysis rate of p-nitrophenyl acetate (p-NPA) compared to neat CP4 peptide was observed. Furthermore, the enhanced catalytic activity of CP4-Aβ assembly could be explained both by pre-organization of a catalytically competent Ser-His-acid triad and hydrophobic stabilization of a bound substrate between the triad and p-NPA, indicating that a design strategy for self-assembled peptides is important to accomplish the desired functionality.« less

  8. Molecular self-assembly strategy for generating catalytic hybrid polypeptides

    SciTech Connect

    Maeda, Yoshiaki; Fang, Justin; Ikezoe, Yasuhiro; Pike, Douglas H.; Nanda, Vikas; Matsui, Hiroshi

    2016-04-26

    Recently, catalytic peptides were introduced that mimicked protease activities and showed promising selectivity of products even in organic solvents where protease cannot perform well. However, their catalytic efficiency was extremely low compared to natural enzyme counterparts presumably due to the lack of stable tertiary fold. We hypothesized that assembling these peptides along with simple hydrophobic pockets, mimicking enzyme active sites, could enhance the catalytic activity. Here we fused the sequence of catalytic peptide CP4, capable of protease and esterase-like activities, into a short amyloidogenic peptide fragment of Aβ. When the fused CP4-Aβ construct assembled into antiparallel β- sheets and amyloid fibrils, a 4.0-fold increase in the hydrolysis rate of p-nitrophenyl acetate (p-NPA) compared to neat CP4 peptide was observed. Furthermore, the enhanced catalytic activity of CP4-Aβ assembly could be explained both by pre-organization of a catalytically competent Ser-His-acid triad and hydrophobic stabilization of a bound substrate between the triad and p-NPA, indicating that a design strategy for self-assembled peptides is important to accomplish the desired functionality.

  9. Molecular Assemblies, Genes and Genomics Integrated Efficiently (MAGGIE)

    SciTech Connect

    Baliga, Nitin S

    2011-05-26

    Final report on MAGGIE. We set ambitious goals to model the functions of individual organisms and their community from molecular to systems scale. These scientific goals are driving the development of sophisticated algorithms to analyze large amounts of experimental measurements made using high throughput technologies to explain and predict how the environment influences biological function at multiple scales and how the microbial systems in turn modify the environment. By experimentally evaluating predictions made using these models we will test the degree to which our quantitative multiscale understanding wilt help to rationally steer individual microbes and their communities towards specific tasks. Towards this end we have made substantial progress towards understanding evolution of gene families, transcriptional structures, detailed structures of keystone molecular assemblies (proteins and complexes), protein interactions, biological networks, microbial interactions, and community structure. Using comparative analysis we have tracked the evolutionary history of gene functions to understand how novel functions evolve. One level up, we have used proteomics data, high-resolution genome tiling microarrays, and 5' RNA sequencing to revise genome annotations, discover new genes including ncRNAs, and map dynamically changing operon structures of five model organisms: For Desulfovibrio vulgaris Hildenborough, Pyrococcus furiosis, Sulfolobus solfataricus, Methanococcus maripaludis and Haiobacterium salinarum NROL We have developed machine learning algorithms to accurately identify protein interactions at a near-zero false positive rate from noisy data generated using tagfess complex purification, TAP purification, and analysis of membrane complexes. Combining other genome-scale datasets produced by ENIGMA (in particular, microarray data) and available from literature we have been able to achieve a true positive rate as high as 65% at almost zero false positives when

  10. Bulk and Surface Molecular Orientation Distribution in Injection-molded Liquid Crystalline Polymers: Experiment and Simulation

    SciTech Connect

    Fang, J.; Burghardt, W; Bubeck, R; Burgard, S; Fischer, D

    2010-01-01

    Bulk and surface distributions of molecular orientation in injection-molded plaques of thermotropic liquid crystalline polymers (TLCPs) have been studied using a combination of techniques, coordinated with process simulations using the Larson-Doi 'polydomain' model. Wide-angle X-ray scattering was used to map out the bulk orientation distribution. Fourier Transform Infrared Attenuated Total Reflectance (FTIR-ATR) and Near-Edge X-ray Absorption Fine Structure (NEXAFS) were utilized to probe the molecular orientation states to within about {approx}5 {micro}m and {approx}2 nm, respectively, of the sample surface. These noninvasive, surface-sensitive techniques yield reasonable self-consistency, providing complementary validation of the robustness of these methods. An analogy between Larson-Doi and fiber orientation models has allowed the first simulations of TLCP injection molding. The simulations capture many fine details in the bulk orientation distribution across the sample plaque. Direct simulation of surface orientation at the level probed by FTIR-ATR and NEXAFS was not possible due to the limited spatial resolution of the simulations. However, simulation results extracted from the shear-dominant skin region are found to provide a qualitatively accurate indicator of surface orientation. Finally, simulations capture the relation between bulk and surface orientation states across the different regions of the sample plaque.

  11. Computational Study of Orientation-dependent Molecular High Harmonic Spectra

    NASA Astrophysics Data System (ADS)

    Dutoi, Anthony; Seideman, Tamar

    2007-03-01

    Recently, there has been much interest in high harmonic generation (HHG) by aligned molecules [Phys. Rev. A 67 023819, Nature 432 867, Nature 435 470]. During HHG, an electron is ionized and driven back to the cation by a strong, low-frequency field, and radiation is emitted at harmonics of this driving pulse. Because this process is sensitive to the orientation of a molecule, rotational dynamics can be probed on very short time scales. We are working to predict the time-dependent HHG spectra for aligned rotational wavepackets. In conjunction with experiment, these simulations should be valuable for studying the loss of rotational coherence in media such as dense gases. Within the presented formalism, Born-Oppenheimer rotational dynamics are handled exactly, while HHG at any given orientation is estimated by numerical time integration of a one-electron Schr"odinger equation. Propagation outside of the integration grid can be handled using an analytical Volkov propagator at the expense of ignoring the cation field at this distance.

  12. Orientation and morphology of self-assembled oligothiophene semiconductors and development of hybrid nanostructures for photovoltaic devices

    NASA Astrophysics Data System (ADS)

    Tevis, Ian David

    This dissertation examines the self-assembly of electronically active small molecules for heterojunction photovoltaic devices and the synthesis of nanoscale hybrid materials with a focus on orientation and morphology. A hairpin-shaped self-assembling molecule featuring two semiconducting sexithiophene arms connected through a diamidocyclohexane linker was found to form p-type semiconducting nanowires through H-aggregation as well as J-aggregated bundles. This molecule was incorporated into heterojunction photovoltaics with phenyl-(C61/C71)-butyric acid methyl ester through spin-coating. The sexithiophene assembled during drying to form a percolating network of nanowires and fullerenes. Thermal annealing enhanced efficiencies by increasing domain sizes and organizing the fullerenes into the groves of the nanofibers to produce 0.48% efficient devices. A p-type quarterthiophene derivative was designed and synthesized to assemble through pi-pi stacking and hydrogen bonding and its assembly was explored. Solutions of the quarterthiophene drop-cast on poly(tetrafluoroethylene) dried quickly to form bundled fibers parallel to the substrate. Slower drying and higher concentrations led to the formation of rhombohedra and randomly oriented hexagonal prisms, respectively. Liquid-liquid interfacial precipitation was used with a porous aluminum oxide membrane between a solution of quarterthiophene and toluene to orient the hexagonal prisms perpendicular to the membrane. Depositing the molecule from solution onto a UV/Ozone treated transparent conducting oxide subtrated affored prisms and sheets with perpendicular pi-pi stacking was anisotropy observed by 2D-GISAXS. This perpendicular pi-pi stacking orientation and sheet formation on a planar electrode shortens charge transport distances and minimizes film defects, which could lead to improved photovoltaic devices. Interpenetrating donor and acceptor hybrid materials with perpendicular orientation for enhanced morphological

  13. Chemical and entropic control on the molecular self-assembly process

    NASA Astrophysics Data System (ADS)

    Packwood, Daniel M.; Han, Patrick; Hitosugi, Taro

    2017-02-01

    Molecular self-assembly refers to the spontaneous assembly of molecules into larger structures. In order to exploit molecular self-assembly for the bottom-up synthesis of nanomaterials, the effects of chemical control (strength of the directionality in the intermolecular interaction) and entropic control (temperature) on the self-assembly process should be clarified. Here we present a theoretical methodology that unambiguously distinguishes the effects of chemical and entropic control on the self-assembly of molecules adsorbed to metal surfaces. While chemical control simply increases the formation probability of ordered structures, entropic control induces a variety of effects. These effects range from fine structure modulation of ordered structures, through to degrading large, amorphous structures into short, chain-shaped structures. Counterintuitively, the latter effect shows that entropic control can improve molecular ordering. By identifying appropriate levels of chemical and entropic control, our methodology can, therefore, identify strategies for optimizing the yield of desired nanostructures from the molecular self-assembly process.

  14. Chemical and entropic control on the molecular self-assembly process

    PubMed Central

    Packwood, Daniel M.; Han, Patrick; Hitosugi, Taro

    2017-01-01

    Molecular self-assembly refers to the spontaneous assembly of molecules into larger structures. In order to exploit molecular self-assembly for the bottom-up synthesis of nanomaterials, the effects of chemical control (strength of the directionality in the intermolecular interaction) and entropic control (temperature) on the self-assembly process should be clarified. Here we present a theoretical methodology that unambiguously distinguishes the effects of chemical and entropic control on the self-assembly of molecules adsorbed to metal surfaces. While chemical control simply increases the formation probability of ordered structures, entropic control induces a variety of effects. These effects range from fine structure modulation of ordered structures, through to degrading large, amorphous structures into short, chain-shaped structures. Counterintuitively, the latter effect shows that entropic control can improve molecular ordering. By identifying appropriate levels of chemical and entropic control, our methodology can, therefore, identify strategies for optimizing the yield of desired nanostructures from the molecular self-assembly process. PMID:28195175

  15. Light-Induced Conversion of Chemical Permeability to Enhance Electron and Molecular Transfer in Nanoscale Assemblies

    SciTech Connect

    Balgley, Renata; de Ruiter, Graham; Evmenenko, Guennadi; Bendikov, Tatyana; Lahav, Michal; van der Boom, Milko E.

    2016-12-21

    In this paper, we demonstrate how photochemically enhancing the permeability of metal–organic assemblies results in a significant enhancement of the electrochemical activity of metal complexes located within the assembly. The molecular assemblies consist of different layers of redox-active metal complexes ([M(mbpy-py)3][PF6]2; M = Ru or Os) that are separated by redox-inactive spacers consisting of 1,4-bis[2-(4-pyridyl)ethenyl]benzene (BPEB) and PdCl2 of variable thicknesses (0–13.4 nm). UV-irradiation (λ = 254 nm) of our assemblies induces a photochemical reaction in the redox-inactive spacer increasing the permeability of the assembly. The observed increase was evident by trapping organic (nBu4NBF4) and inorganic (NiCl2) salts inside the assemblies, and by evaluating the electrochemical response of quinones absorbed inside the molecular assemblies before and after UV irradiation. The increase in permeability is reflected by higher currents and a change in the directionality of electron transfer, i.e., from mono- to bidirectional, between the redox-active metal complexes and the electrode surface. The supramolecular structure of the assemblies dominates the overall electron transfer properties and overrules possible electron transfer mediated by the extensive π-conjugation of its individual organic components.

  16. Fabrication and Characterization of Oriented Carbon Atom Wires Assembled on Gold

    SciTech Connect

    Xue,K.H.; Wu,L.; Chen, S.-P.; Wanga, L.X.; Wei, R.-B.; Xu, S.-M.; Cui, L.; Mao, B.-W.; Tian, Z.-Q.; Zen, C.-H.; Sun, S.-G.; Zhu, Y.-M.

    2009-02-17

    Carbon atom wires (CAWs) are of the sp-hybridized allotrope of carbon. To augment the extraordinary features based on sp-hybridization, we developed an approach to make CAWs be self-assembled and orderly organized on Au substrate. The self-assembling process was investigated in situ by using scanning tunneling microscopy (STM) and electrochemical quartz crystal microbalance (EQCM). The properties of the assembled film were characterized by voltammetry, Raman spectroscopy, electron energy loss spectroscopy (EELS), and the contact angle measurements. Experimental results indicated that the assembled CAW film was of the good structural integrity and well organized, with the sp-hybridized features enhanced.

  17. Magnetic Orientation in Biology:. Virus Structure - Blood Clot Assembly - Cell Guidance

    NASA Astrophysics Data System (ADS)

    Torbet, J.

    2005-07-01

    Our childhood games with permanent magnets leave us with the impression that matter, in general, does not respond to a magnetic field. In reality, virtually everything is subjected to minute forces of attraction, repulsion or orientation. Strong fields combined with better understanding allow us to exploit these effects to tackle biological problems. In particular, the very weak diamagnetic anisotropy associated with individual molecules can give rise to high orientation of well organized structures such as crystals, liquid-crystals, semi-rigid polymers and individual cells. High orientation is often accompanied by better data and superior properties. In some circumstances, such as in crystallization, the orientating torque might induce effects over and above simple orientation. Magnetic field orientation has a number of advantages over other orienting techniques. Drawing or spinning produce fibers and can alter structure or cause damage while template methods invariable work only over a short range. The application of an electric field can cause heating and electrophoresis. In contrast, a magnetic field acts at a distance allowing uniform orientation in bulk and the creation of composites with components having different orientations. The contribution that magnetic orientation has made to a range of biological topics is illustrated by briefly describing a number of examples. For example, it has been a boon to x-ray studies of some non-crystalline filamentous complexes (e.g. fibrin, actin, microtubules, bacterial flagella and filamentous viruses) and is being vigorously exploited in NMR. The blood-clot polymer, fibrin, forms highly oriented gels when polymerized in a strong field and a number of its properties have been elucidated as a result. Magnetically oriented scaffolds of collagen, the major connective tissue protein, and fibrin are being used to study cell contact guidance. Oriented biomaterials might eventually be incorporated into specialized wound

  18. Molecular Recognition Directed Self-Assembly of Supramolecular Liquid Crystals

    DTIC Science & Technology

    1994-06-30

    supramolecular (generated via H-bonding, ionic and electrostatic interactions) and molecular " polymer backbones" will be made. The formation of columnar hexagonal...electrostatic interactions) and molecular " polymer backbones" will be made. The formation of columnar hexagonal (0h), nematic and re-entrant isotropic phases by...trihydroxybenzoate with either bromoalkanes or with alkoxybenzyloxybenzyl chloride. Variants of these taper shaped side groups were attached to polymer

  19. Crystal orientation mechanism of ZnTe epilayers formed on different orientations of sapphire substrates by molecular beam epitaxy

    SciTech Connect

    Nakasu, T. Yamashita, S.; Aiba, T.; Hattori, S.; Sun, W.; Taguri, K.; Kazami, F.; Kobayashi, M.

    2014-10-28

    The electrooptic effect in ZnTe has recently attracted research attention, and various device structures using ZnTe have been explored. For application to practical terahertz wave detector devices based on ZnTe thin films, sapphire substrates are preferred because they enable the optical path alignment to be simplified. ZnTe/sapphire heterostructures were focused upon, and ZnTe epilayers were prepared on highly mismatched sapphire substrates by molecular beam epitaxy. Epitaxial relationships between the ZnTe thin films and the sapphire substrates with their various orientations were investigated using an X-ray diffraction pole figure method. (0001) c-plane, (1-102) r-plane, (1-100) m-plane, and (11-20) a-plane oriented sapphire substrates were used in this study. The epitaxial relationship between ZnTe and c-plane sapphire was found to be (111) ZnTe//(0001) sapphire with an in-plane orientation relationship of [−211] ZnTe//[1-100] sapphire. It was found that the (211)-plane ZnTe layer was grown on the m-plane of the sapphire substrates, and the (100)-plane ZnTe layer was grown on the r-plane sapphire. When the sapphire substrates were inclined from the c-plane towards the m-axis direction, the orientation of the ZnTe thin films was then tilted from the (111)-plane to the (211)-plane. The c-plane of the sapphire substrates governs the formation of the (111) ZnTe domain and the ZnTe epilayer orientation. These crystallographic features were also related to the atom arrangements of ZnTe and sapphire.

  20. Recent emergence of photon upconversion based on triplet energy migration in molecular assemblies.

    PubMed

    Yanai, Nobuhiro; Kimizuka, Nobuo

    2016-04-07

    An emerging field of triplet energy migration-based photon upconversion (TEM-UC) is reviewed. Highly efficient photon upconversion has been realized in a wide range of chromophore assemblies, such as non-solvent liquids, ionic liquids, amorphous solids, gels, supramolecular assemblies, molecular crystals, and metal-organic frameworks (MOFs). The control over their assembly structures allows for unexpected air-stability and maximum upconversion quantum yield at weak solar irradiance that has never been achieved by the conventional molecular diffusion-based mechanism. The introduction of the "self-assembly" concept offers a new perspective in photon upconversion research and triplet exciton science, which show promise for numerous applications ranging from solar energy conversion to chemical biology.

  1. Macrocyclic peptides self-assemble into robust vesicles with molecular recognition capabilities.

    PubMed

    Jeong, Woo-jin; Lim, Yong-beom

    2014-11-19

    In this study, we developed macrocyclic peptide building blocks that formed self-assembled peptide vesicles with molecular recognition capabilities. Macrocyclic peptides were significantly different from conventional amphiphiles, in that they could self-assemble into vesicles at very high hydrophilic-to-total mass ratios. The flexibility of the hydrophobic self-assembly segment was critical for vesicle formation. The unique features of this peptide vesicle system include a homogeneous size distribution, unusually small size, and robust structural and thermal stability. The peptide vesicles successfully entrapped a hydrophilic model drug, released the payload very slowly, and were internalized by cells in a highly efficient manner. Moreover, the peptide vesicles exhibited molecular recognition capabilities, in that they selectively bound to target RNA through surface-displayed peptides. This study demonstrates that self-assembled peptide vesicles can be used as strong intracellular delivery vehicles that recognize specific biomacromolecular targets.

  2. The use of photolithography on molecular orientation of the liquid crystals

    NASA Astrophysics Data System (ADS)

    Yilmaz, Suleyman

    2017-02-01

    The photolithography was used on molecular orientation of liquid crystals as an alternative to other conventional methods. Either planar or homeotropic orientation were provided with surface anchoring energy for the molecular alignment. The photolithography were applied to provide micro-grooving on the film surface, which is including polyimide coatings, UV exposure, chemical etching and thermal curing process, respectively. Three type liquid crystal cells were made by provided rubbing and photolithography for planar alignment and also homeotropic alignment. Electro-optical properties of the liquid crystals were examined under the electric field at phase transition region for three type liquid crystal cells. It was observed that the photolithographic method was the more effective and acceptable results than the other conventional methods on the molecular orientations.

  3. Effects of substrate orientation on the growth of InSb nanostructures by molecular beam epitaxy

    NASA Astrophysics Data System (ADS)

    Chou, C. Y.; Torfi, A.; Pei, C.; Wang, W. I.

    2016-05-01

    In this work, the effects of substrate orientation on InSb quantum structure growth by molecular beam epitaxy (MBE) are presented. Motivated by the observation that (411) evolves naturally as a stable facet during MBE crystal growth, comparison studies have been carried out to investigate the effects of the crystal orientation of the underlying GaSb substrate on the growth of InSb by MBE. By depositing InSb on a number of different substrate orientations, namely: (100), (311), (411), and (511), a higher nanostructure density was observed on the (411) surface compared with the other orientations. This result suggests that the (411) orientation presents a superior surface in MBE growth to develop a super-flat GaSb buffer surface, naturally favorable for nanostructure growth.

  4. Tuning Open-Circuit Voltage in Organic Solar Cells with Molecular Orientation.

    PubMed

    Kitchen, Brent; Awartani, Omar; Kline, R Joseph; McAfee, Terry; Ade, Harald; O'Connor, Brendan T

    2015-06-24

    The role of molecular orientation of a polar conjugated polymer in polymer-fullerene organic photovoltaic (OPV) cells is investigated. A planar heterojunction (PHJ) OPV cell composed of poly(3-hexylthiophene) (P3HT) and [6,6]-phenyl C61-butyric acid methyl ester (PCBM) is used as a model system to isolate the effect of the interfacial orientation on the photovoltaic properties. The molecular orientation of the aggregate P3HT relative to the PCBM layer is varied from highly edge-on (conjugated ring plane perpendicular to the interface plane) to appreciably face-on (ring plane parallel to the interface). It is found that as the P3HT stacking becomes more face-on there is a positive correlation to the OPV open-circuit voltage (V(OC)), attributed to a shift in the highest occupied molecular orbital (HOMO) energy level of P3HT. In addition, the PHJ OPV cell with a broad P3HT stacking orientation distribution has a V(OC) comparable to an archetypal bulk heterojunction (BHJ) device. These results suggest that, in the BHJ OPV cell, the hole energy level in the charge transfer state is defined in part by the orientation distribution of the P3HT at the interface with PCBM. Finally, the photoresponses of the devices are also shown to have a dependence on P3HT stacking orientation.

  5. Rigid Biopolymer Nanocrystal Systems for Controlling Multicomponent Nanoparticle Assembly and Orientation in Thin Film Solar Cells

    SciTech Connect

    Cha, Jennifer

    2016-10-31

    We have discovered techniques to synthesize well-defined DN conjugated nanostructures that are stable in a wide variety of conditions needed for DNA mediated assembly. Starting from this, we have shown that DNA can be used to control the assembly and integration of semiconductor nanocrystals into thin film devices that show photovoltaic effects.

  6. Hierarchical protein patterning by meso to molecular scale self-assembly

    NASA Astrophysics Data System (ADS)

    Andersen, Andreas S.; Sutherland, Duncan S.; Ogaki, Ryosuke

    2015-10-01

    Numerous protein patterning methodologies are used extensively for biomedical research and development. We have developed a novel bottom-up protein patterning method using a combination of self-assembly processes in the meso to molecular scale range to allow hierarchical protein patterns to be straightforwardly fabricated with low cost over large areas. As a proof of principle, we patterned vitronectin in various dimensional hierarchies using meso to nanoscale colloids and self-assembled monolayers.

  7. Effect of horizontal molecular orientation on triplet-exciton diffusion in amorphous organic films

    NASA Astrophysics Data System (ADS)

    Sawabe, T.; Takasu, I.; Yonehara, T.; Ono, T.; Yoshida, J.; Enomoto, S.; Amemiya, I.; Adachi, C.

    2012-09-01

    Triplet harvesting is a candidate technology for highly efficient and long-life white OLEDs, where green or red phosphorescent emitters are activated by the triplet-excitons diffused from blue fluorescent emitters. We examined two oxadiazole-based electron transport materials with different horizontal molecular orientation as a triplet-exciton diffusion layer (TDL) in triplet-harvesting OLEDs. The device characteristics and the transient electroluminescent analyses of the red phosphorescent emitter showed that the triplet-exciton diffusion was more effective in the highly oriented TDL. The results are ascribed to the strong orbital overlap between the oriented molecules, which provides rapid electron exchange (Dexter energy transfer) in the TDL.

  8. Gamma Peptide Nucleic Acids: As Orthogonal Nucleic Acid Recognition Codes for Organizing Molecular Self-Assembly.

    PubMed

    Sacui, Iulia; Hsieh, Wei-Che; Manna, Arunava; Sahu, Bichismita; Ly, Danith H

    2015-07-08

    Nucleic acids are an attractive platform for organizing molecular self-assembly because of their specific nucleobase interactions and defined length scale. Routinely employed in the organization and assembly of materials in vitro, however, they have rarely been exploited in vivo, due to the concerns for enzymatic degradation and cross-hybridization with the host's genetic materials. Herein we report the development of a tight-binding, orthogonal, synthetically versatile, and informationally interfaced nucleic acid platform for programming molecular interactions, with implications for in vivo molecular assembly and computing. The system consists of three molecular entities: the right-handed and left-handed conformers and a nonhelical domain. The first two are orthogonal to each other in recognition, while the third is capable of binding to both, providing a means for interfacing the two conformers as well as the natural nucleic acid biopolymers (i.e., DNA and RNA). The three molecular entities are prepared from the same monomeric chemical scaffold, with the exception of the stereochemistry or lack thereof at the γ-backbone that determines if the corresponding oligo adopts a right-handed or left-handed helix, or a nonhelical motif. These conformers hybridize to each other with exquisite affinity, sequence selectivity, and level of orthogonality. Recognition modules as short as five nucleotides in length are capable of organizing molecular assembly.

  9. Detection of Alzheimer's amyloid beta aggregation by capturing molecular trails of individual assemblies

    SciTech Connect

    Vestergaard, Mun'delanji Hamada, Tsutomu; Saito, Masato; Yajima, Yoshifumi; Kudou, Monotori; Tamiya, Eiichi; Takagi, Masahiro

    2008-12-12

    Assembly of Amyloid beta (A{beta}) peptides, in particular A{beta}-42 is central to the formation of the amyloid plaques associated with neuro-pathologies such as Alzheimer's disease (AD). Molecular assembly of individual A{beta}-42 species was observed using a simple fluorescence microscope. From the molecular movements (aka Brownian motion) of the individual peptide assemblies, we calculated a temporal evolution of the hydrodynamic radius (R{sub H}) of the peptide at physiological temperature and pH. The results clearly show a direct relationship between R{sub H} of A{beta}-42 and incubation period, corresponding to the previously reported peptide's aggregation kinetics. The data correlates highly with in solution-based label-free electrochemical detection of the peptide's aggregation, and A{beta}-42 deposited on a solid surface and analysed using atomic force microscopy (AFM). To the best of our knowledge, this is the first analysis and characterisation of A{beta} aggregation based on capturing molecular trails of individual assemblies. The technique enables both real-time observation and a semi-quantitative distribution profile of the various stages of A{beta} assembly, at microM peptide concentration. Our method is a promising candidate for real-time observation and analysis of the effect of other pathologically-relevant molecules such as metal ions on pathways to A{beta} oligomerisation and aggregation. The method is also a promising screening tool for AD therapeutics that target A{beta} assembly.

  10. Cellular automata with object-oriented features for parallel molecular network modeling.

    PubMed

    Zhu, Hao; Wu, Yinghui; Huang, Sui; Sun, Yan; Dhar, Pawan

    2005-06-01

    Cellular automata are an important modeling paradigm for studying the dynamics of large, parallel systems composed of multiple, interacting components. However, to model biological systems, cellular automata need to be extended beyond the large-scale parallelism and intensive communication in order to capture two fundamental properties characteristic of complex biological systems: hierarchy and heterogeneity. This paper proposes extensions to a cellular automata language, Cellang, to meet this purpose. The extended language, with object-oriented features, can be used to describe the structure and activity of parallel molecular networks within cells. Capabilities of this new programming language include object structure to define molecular programs within a cell, floating-point data type and mathematical functions to perform quantitative computation, message passing capability to describe molecular interactions, as well as new operators, statements, and built-in functions. We discuss relevant programming issues of these features, including the object-oriented description of molecular interactions with molecule encapsulation, message passing, and the description of heterogeneity and anisotropy at the cell and molecule levels. By enabling the integration of modeling at the molecular level with system behavior at cell, tissue, organ, or even organism levels, the program will help improve our understanding of how complex and dynamic biological activities are generated and controlled by parallel functioning of molecular networks. Index Terms-Cellular automata, modeling, molecular network, object-oriented.

  11. Molecular Coplanarity and Self-Assembly Promoted by Intramolecular Hydrogen Bonds.

    PubMed

    Zhu, Congzhi; Mu, Anthony U; Lin, Yen-Hao; Guo, Zi-Hao; Yuan, Tianyu; Wheeler, Steven E; Fang, Lei

    2016-12-16

    Active conformational control is realized in a conjugated system using intramolecular hydrogen bonds to achieve tailored molecular, supramolecular, and solid-state properties. The hydrogen bonding functionalities are fused to the backbone and precisely preorganized to enforce a fully coplanar conformation of the π-system, leading to short π-π stacking distances, controllable molecular self-assembly, and solid-state growth of one-dimensional nano-/microfibers. This investigation demonstrates the efficiency and significance of an intramolecular noncovalent approach in promoting conformational control and self-assembly of organic molecules.

  12. Method of assembly of molecular-sized nets and scaffolding

    DOEpatents

    Michl, Josef; Magnera, Thomas F.; David, Donald E.; Harrison, Robin M.

    1999-01-01

    The present invention relates to methods and starting materials for forming molecular-sized grids or nets, or other structures based on such grids and nets, by creating molecular links between elementary molecular modules constrained to move in only two directions on an interface or surface by adhesion or bonding to that interface or surface. In the methods of this invention, monomers are employed as the building blocks of grids and more complex structures. Monomers are introduced onto and allowed to adhere or bond to an interface. The connector groups of adjacent adhered monomers are then polymerized with each other to form a regular grid in two dimensions above the interface. Modules that are not bound or adhered to the interface are removed prior to reaction of the connector groups to avoid undesired three-dimensional cross-linking and the formation of non-grid structures. Grids formed by the methods of this invention are useful in a variety of applications, including among others, for separations technology, as masks for forming regular surface structures (i.e., metal deposition) and as templates for three-dimensional molecular-sized structures.

  13. Method of assembly of molecular-sized nets and scaffolding

    DOEpatents

    Michl, J.; Magnera, T.F.; David, D.E.; Harrison, R.M.

    1999-03-02

    The present invention relates to methods and starting materials for forming molecular-sized grids or nets, or other structures based on such grids and nets, by creating molecular links between elementary molecular modules constrained to move in only two directions on an interface or surface by adhesion or bonding to that interface or surface. In the methods of this invention, monomers are employed as the building blocks of grids and more complex structures. Monomers are introduced onto and allowed to adhere or bond to an interface. The connector groups of adjacent adhered monomers are then polymerized with each other to form a regular grid in two dimensions above the interface. Modules that are not bound or adhered to the interface are removed prior to reaction of the connector groups to avoid undesired three-dimensional cross-linking and the formation of non-grid structures. Grids formed by the methods of this invention are useful in a variety of applications, including among others, for separations technology, as masks for forming regular surface structures (i.e., metal deposition) and as templates for three-dimensional molecular-sized structures. 9 figs.

  14. Genetic and Molecular Characterization of Flagellar Assembly in Shewanella oneidensis

    PubMed Central

    Wu, Lin; Wang, Jixuan; Tang, Peng; Chen, Haijiang; Gao, Haichun

    2011-01-01

    Shewanella oneidensis is a highly motile organism by virtue of a polar flagellum. Unlike most flagellated bacteria, it contains only one major chromosome segment encoding the components of the flagellum with the exception of the motor proteins. In this region, three genes encode flagellinsaccording to the original genome annotation. However, we find that only flaA and flaB encode functional filament subunits. Although these two genesare under the control of different promoters, they are actively transcribed and subsequently translated, producing a considerable number of flagellin proteins. Additionally, both flagellins are able to interact with their chaperon FliS and are subjected to feedback regulation. Furthermore, FlaA and FlaB are glycosylated by a pathwayinvolving a major glycosylating enzyme,PseB, in spite of the lack of the majority of theconsensus glycosylation sites. In conclusion, flagellar assembly in S. oneidensis has novel features despite the conservation of homologous genes across taxa. PMID:21731763

  15. A 16-bit parallel processing in a molecular assembly

    PubMed Central

    Bandyopadhyay, Anirban; Acharya, Somobrata

    2008-01-01

    A machine assembly consisting of 17 identical molecules of 2,3,5,6-tetramethyl-1–4-benzoquinone (DRQ) executes 16 instructions at a time. A single DRQ is positioned at the center of a circular ring formed by 16 other DRQs, controlling their operation in parallel through hydrogen-bond channels. Each molecule is a logic machine and generates four instructions by rotating its alkyl groups. A single instruction executed by a scanning tunneling microscope tip on the central molecule can change decisions of 16 machines simultaneously, in four billion (416) ways. This parallel communication represents a significant conceptual advance relative to today's fastest processors, which execute only one instruction at a time. PMID:18332437

  16. Self-Assembly and Dynamics of Organic 2D Molecular Sieves: Ab Initio and Molecular Dynamics Studies

    NASA Astrophysics Data System (ADS)

    St. John, Alexander; Wexler, Carlos

    2015-03-01

    Spontaneous molecular self-assembly is a promising route for bottom-up manufacturing of two-dimensional (2D) nanostructures with specific topologies on atomically flat surfaces. Of particular interest is the possibility of selective lock-and-key interaction of guest molecules inside cavities formed by complex self-assembled host structures. Our host structure is a monolayer consisting of interdigitated 1,3,5-tristyrylbenzene substituted by alkoxy peripheral chains containing n = 6, 8, 10, 12, or 14 carbon atoms (TSB3,5-C n) deposited on a highly ordered pyrolytic graphite (HOPG) surface. Using ab initio methods from quantum chemistry and molecular dynamics simulations, we construct and analyze the structure and functionality of the TSB3,5-C n monolayer as a molecular sieve. Supported by ACS-PRF 52696-ND5.

  17. Rational design of oriented assembly of gold nanospheres with nanorods by biotin-streptavidin connectors.

    PubMed

    Zhou, Xi; Wang, Yan; Zhong, Lubin; Bao, Shixiong; Han, Yu; Ren, Lei; Zhang, Qiqing

    2012-10-21

    Through the different functionalities on Au nanosphere (AuNSs) and Au nanorod (AuNRs) surfaces, we successfully control AuNSs attachment onto either the end or side surface of anisotropic AuNRs via bio-recognition, and then consciously construct side-by-side or end-to-end assembly nanostructures. This study provides a feasible approach to organize nanoparticles with different morphologies into controllable assembly geometries, which can potentially benefit the construction of future nanodevices.

  18. Self-assembled molecular films incorporating a ligand

    DOEpatents

    Bednarski, M.D.; Wilson, T.E.; Mastandra, M.S.

    1996-04-23

    Functionalized monomers are presented which can be used in the fabrication of molecular films for controlling adhesion, detection of receptor-ligand binding and enzymatic reactions; new coatings for lithography; and for semiconductor materials. The monomers are a combination of a ligand, a linker, optionally including a polymerizable group, and a surface attachment group. The processes and an apparatus for making films from these monomers, as well as methods of using the films are also provided. 7 figs.

  19. Self-assembled molecular films incorporating a ligand

    DOEpatents

    Bednarski, Mark D.; Wilson, Troy E.; Mastandra, Mark S.

    1996-01-01

    Functionalized monomers are presented which can be used in the fabrication of molecular films for controlling adhesion, detection of receptor-ligand binding and enzymatic reactions; new coatings for lithography; and for semiconductor materials. The monomers are a combination of a ligand, a linker, optionally including a polymerizable group, and a surface attachment group. The processes and an apparatus for making films from these monomers, as well as methods of using the films are also provided.

  20. Molecular self-assembly of nylon-12 nanorods cylindrically confined to nanoporous alumina

    PubMed Central

    Cao, Yan; Wu, Hui; Higaki, Yuji; Jinnai, Hiroshi; Takahara, Atsushi

    2014-01-01

    Molecular self-assembly of nylon-12 rods in self-organized nanoporous alumina cylinders with two different diameters (65 and 300 nm) is studied with transmission electron microscopy (TEM) and wide-angle X-ray diffraction (WAXD) in symmetrical reflection mode. In a rod with a 300 nm diameter, the tendency of the hydrogen-bonding direction of a γ-form crystal parallel to the long axis of the rod is not clear because of weak two-dimensional confinement. In a rod with a diameter of 65 nm, the tendency of the hydrogen-bonding direction of a γ-form crystal parallel to the long axis of the rod is more distinct because of strong two-dimensional confinement. For the first time, selected-area electron diffraction (SAED) is applied in a transmission electron microscope to a polymer nanorod in order to determine the hydrogen-bond sheet and lamellar orientations. Results of TEM–SAED and WAXD showed that the crystals within the rod possess the γ-form of nylon-12 and that the b axis (stem axis) of the γ-form crystals is perpendicular to the long axis of the rod. These results revealed that only lamellae with 〈h0l〉 directions are able to grow inside the nanopores and the growth of lamellae with 〈hkl〉 (k ≠ 0) directions is stopped owing to impingements against the cylinder walls. The dominant crystal growth direction of the 65 nm rod in stronger two-dimensional confinement is in between the [−201] and [001] directions due to the development of a hydrogen-bonded sheet restricted along the long axis of the rod. PMID:25485124

  1. Phylogeny of Oriental voles (Rodentia: Muridae: Arvicolinae): molecular and morphological evidence.

    PubMed

    Liu, Shaoying; Liu, Yang; Guo, Peng; Sun, Zhiyu; Murphy, Robert W; Fan, Zhenxin; Fu, Jianrong; Zhang, Yaping

    2012-09-01

    The systematics of Oriental voles remains controversial despite numerous previous studies. In this study, we explore the systematics of all species of Oriental voles, except Eothenomys wardi, using a combination of DNA sequences and morphological data. Our molecular phylogeny, based on two mitochondrial genes (COI and cyt b), resolves the Oriental voles as a monophyletic group with strong support. Four distinct lineages are resolved: Eothenomys, Anteliomys, Caryomys, and the new subgenus Ermites. Based on morphology, we consider Caryomys and Eothenomys to be valid genera. Eothenomys, Anteliomys, and Ermites are subgenera of Eothenomys. The molecular phylogeny resolves subgenera Anteliomys and Ermites as sister taxa. Subgenus Eothenomys is sister to the clade Anteliomys + Ermites. Caryomys is the sister group to genus Eothenomys. Further, the subspecies E. custos hintoni and E. chinensis tarquinius do not cluster with E. custos custos and E. chinensis chinensis, respectively, and the former two taxa are elevated to species level and assigned to the new subgenus Ermites.

  2. Molecular orientation in soft matter thin films studied by resonant soft X-ray reflectivity

    SciTech Connect

    Mezger, Markus; Jerome, Blandine; Kortright, Jeffrey B.; Valvidares, Manuel; Gullikson, Eric; Giglia, Angelo; Mahne, Nicola; Nannarone, Stefano

    2011-01-12

    We present a technique to study depth profiles of molecular orientation in soft matter thin films with nanometer resolution. The method is based on dichroism in resonant soft X-ray reflectivity using linear s- and p-polarization. It combines the chemical sensitivity of Near-Edge X-ray Absorption Fine Structure spectroscopy to specific molecular bonds and their orientation relative to the polarization of the incident beam with the precise depth profiling capability of X-ray reflectivity. We demonstrate these capabilities on side chain liquid crystalline polymer thin films with soft X-ray reflectivity data at the carbon K edge. Optical constants of the anisotropic refractive index ellipsoid were obtained from a quantitative analysis using the Berreman formalism. For films up to 50 nm thickness we find that the degree of orientation of the long axis exhibits no depth variation and isindependent of the film thickness.

  3. High degree of molecular orientation by a combination of THz and femtosecond laser pulses

    SciTech Connect

    Kitano, Kenta; Ishii, Nobuhisa; Itatani, Jiro

    2011-11-15

    We propose a method for achieving molecular orientation by two-step excitation with intense femtosecond laser and terahertz (THz) pulses. First, the femtosecond laser pulse induces off-resonant impulsive Raman excitation to create rotational wave packets. Next, a delayed intense THz pulse effectively induces resonant dipole transition between neighboring rotational states. By controlling the intensities of both the pulses and the time delay, we can create rotational wave packets consisting of states with different parities in order to achieve a high degree of molecular orientation under a field-free condition. We numerically demonstrate that the highest degree of orientation of >0.8 in HBr molecules is feasible under experimentally available conditions.

  4. Thermal fluctuations in shape, thickness, and molecular orientation in lipid bilayers

    NASA Astrophysics Data System (ADS)

    Watson, Max C.; Penev, Evgeni S.; Welch, Paul M.; Brown, Frank L. H.

    2011-12-01

    We present a unified continuum-level model for bilayer energetics that includes the effects of bending, compression, lipid orientation (tilting relative to the monolayer surface normal), and microscopic noise (protrusions). Expressions for thermal fluctuation amplitudes of several physical quantities are derived. These predictions are shown to be in good agreement with molecular simulations.

  5. Tunable molecular orientation and elevated thermal stability of vapor-deposited organic semiconductors

    PubMed Central

    Walters, Diane M.; Lyubimov, Ivan; de Pablo, Juan J.; Ediger, M. D.

    2015-01-01

    Physical vapor deposition is commonly used to prepare organic glasses that serve as the active layers in light-emitting diodes, photovoltaics, and other devices. Recent work has shown that orienting the molecules in such organic semiconductors can significantly enhance device performance. We apply a high-throughput characterization scheme to investigate the effect of the substrate temperature (Tsubstrate) on glasses of three organic molecules used as semiconductors. The optical and material properties are evaluated with spectroscopic ellipsometry. We find that molecular orientation in these glasses is continuously tunable and controlled by Tsubstrate/Tg, where Tg is the glass transition temperature. All three molecules can produce highly anisotropic glasses; the dependence of molecular orientation upon substrate temperature is remarkably similar and nearly independent of molecular length. All three compounds form “stable glasses” with high density and thermal stability, and have properties similar to stable glasses prepared from model glass formers. Simulations reproduce the experimental trends and explain molecular orientation in the deposited glasses in terms of the surface properties of the equilibrium liquid. By showing that organic semiconductors form stable glasses, these results provide an avenue for systematic performance optimization of active layers in organic electronics. PMID:25831545

  6. Directed nanoscale self-assembly of molecular wires interconnecting nodal points using Monte Carlo simulations

    SciTech Connect

    Boscoboinik, A. M.; Manzi, S. J.; Tysoe, W. T.; Pereyra, V. D.; Boscoboinik, J. A.

    2015-09-10

    The influence of directing agents in the self-assembly of molecular wires to produce two-dimensional electronic nanoarchitectures is studied here using a Monte Carlo approach to simulate the effect of arbitrarily locating nodal points on a surface, from which the growth of self-assembled molecular wires can be nucleated. This is compared to experimental results reported for the self-assembly of molecular wires when 1,4-phenylenediisocyanide (PDI) is adsorbed on Au(111). The latter results in the formation of (Au-PDI)n organometallic chains, which were shown to be conductive when linked between gold nanoparticles on an insulating substrate. The present study analyzes, by means of stochastic methods, the influence of variables that affect the growth and design of self-assembled conductive nanoarchitectures, such as the distance between nodes, coverage of the monomeric units that leads to the formation of the desired architectures, and the interaction between the monomeric units. As a result, this study proposes an approach and sets the stage for the production of complex 2D nanoarchitectures using a bottom-up strategy but including the use of current state-of-the-art top-down technology as an integral part of the self-assembly strategy.

  7. Directed nanoscale self-assembly of molecular wires interconnecting nodal points using Monte Carlo simulations

    DOE PAGES

    Boscoboinik, A. M.; Manzi, S. J.; Tysoe, W. T.; ...

    2015-09-10

    The influence of directing agents in the self-assembly of molecular wires to produce two-dimensional electronic nanoarchitectures is studied here using a Monte Carlo approach to simulate the effect of arbitrarily locating nodal points on a surface, from which the growth of self-assembled molecular wires can be nucleated. This is compared to experimental results reported for the self-assembly of molecular wires when 1,4-phenylenediisocyanide (PDI) is adsorbed on Au(111). The latter results in the formation of (Au-PDI)n organometallic chains, which were shown to be conductive when linked between gold nanoparticles on an insulating substrate. The present study analyzes, by means of stochasticmore » methods, the influence of variables that affect the growth and design of self-assembled conductive nanoarchitectures, such as the distance between nodes, coverage of the monomeric units that leads to the formation of the desired architectures, and the interaction between the monomeric units. As a result, this study proposes an approach and sets the stage for the production of complex 2D nanoarchitectures using a bottom-up strategy but including the use of current state-of-the-art top-down technology as an integral part of the self-assembly strategy.« less

  8. Organization of inorganic nanomaterials via programmable DNA self-assembly and peptide molecular recognition.

    PubMed

    Carter, Joshua D; LaBean, Thomas H

    2011-03-22

    An interesting alternative to top-down nanofabrication is to imitate biology, where nanoscale materials frequently integrate organic molecules for self-assembly and molecular recognition with ordered, inorganic minerals to achieve mechanical, sensory, or other advantageous functions. Using biological systems as inspiration, researchers have sought to mimic the nanoscale composite materials produced in nature. Here, we describe a combination of self-assembly, molecular recognition, and templating, relying on an oligonucleotide covalently conjugated to a high-affinity gold-binding peptide. After integration of the peptide-coupled DNA into a self-assembling superstructure, the templated peptides recognize and bind gold nanoparticles. In addition to providing new ways of building functional multinanoparticle systems, this work provides experimental proof that a single peptide molecule is sufficient for immobilization of a nanoparticle. This molecular construction strategy, combining DNA assembly and peptide recognition, can be thought of as programmable, granular, artificial biomineralization. We also describe the important observation that the addition of 1-2% Tween 20 surfactant to the solution during gold particle binding allows the gold nanoparticles to remain soluble within the magnesium-containing DNA assembly buffer under conditions that usually lead to the aggregation and precipitation of the nanoparticles.

  9. High-fidelity self-assembly pathways for hydrogen-bonding molecular semiconductors

    PubMed Central

    Lin, Xu; Suzuki, Mika; Gushiken, Marina; Yamauchi, Mitsuaki; Karatsu, Takashi; Kizaki, Takahiro; Tani, Yuki; Nakayama, Ken-ichi; Suzuki, Mitsuharu; Yamada, Hiroko; Kajitani, Takashi; Fukushima, Takanori; Kikkawa, Yoshihiro; Yagai, Shiki

    2017-01-01

    The design of molecular systems with high-fidelity self-assembly pathways that include several levels of hierarchy is of primary importance for the understanding of structure-function relationships, as well as for controlling the functionality of organic materials. Reported herein is a high-fidelity self-assembly system that comprises two hydrogen-bonding molecular semiconductors with regioisomerically attached short alkyl chains. Despite the availability of both discrete cyclic and polymeric linear hydrogen-bonding motifs, the two regioisomers select one of the two motifs in homogeneous solution as well as at the 2D-confined liquid-solid interface. This selectivity arises from the high directionality of the involved hydrogen-bonding interactions, which renders rerouting to other self-assembly pathways difficult. In thin films and in the bulk, the resulting hydrogen-bonded assemblies further organize into the expected columnar and lamellar higher-order architectures via solution processing. The contrasting organized structures of these regioisomers are reflected in their notably different miscibility with soluble fullerene derivatives in the solid state. Thus, electron donor-acceptor blend films deliver a distinctly different photovoltaic performance, despite their virtually identical intrinsic optoelectronic properties. Currently, we attribute this high-fidelity control via self-assembly pathways to the molecular design of these supramolecular semiconductors, which lacks structure-determining long aliphatic chains. PMID:28225029

  10. High-fidelity self-assembly pathways for hydrogen-bonding molecular semiconductors.

    PubMed

    Lin, Xu; Suzuki, Mika; Gushiken, Marina; Yamauchi, Mitsuaki; Karatsu, Takashi; Kizaki, Takahiro; Tani, Yuki; Nakayama, Ken-Ichi; Suzuki, Mitsuharu; Yamada, Hiroko; Kajitani, Takashi; Fukushima, Takanori; Kikkawa, Yoshihiro; Yagai, Shiki

    2017-02-22

    The design of molecular systems with high-fidelity self-assembly pathways that include several levels of hierarchy is of primary importance for the understanding of structure-function relationships, as well as for controlling the functionality of organic materials. Reported herein is a high-fidelity self-assembly system that comprises two hydrogen-bonding molecular semiconductors with regioisomerically attached short alkyl chains. Despite the availability of both discrete cyclic and polymeric linear hydrogen-bonding motifs, the two regioisomers select one of the two motifs in homogeneous solution as well as at the 2D-confined liquid-solid interface. This selectivity arises from the high directionality of the involved hydrogen-bonding interactions, which renders rerouting to other self-assembly pathways difficult. In thin films and in the bulk, the resulting hydrogen-bonded assemblies further organize into the expected columnar and lamellar higher-order architectures via solution processing. The contrasting organized structures of these regioisomers are reflected in their notably different miscibility with soluble fullerene derivatives in the solid state. Thus, electron donor-acceptor blend films deliver a distinctly different photovoltaic performance, despite their virtually identical intrinsic optoelectronic properties. Currently, we attribute this high-fidelity control via self-assembly pathways to the molecular design of these supramolecular semiconductors, which lacks structure-determining long aliphatic chains.

  11. Sample handling for kinetics and molecular assembly in flow cytometry

    SciTech Connect

    Sklar, L.A. |; Seamer, L.C.; Kuckuck, F.; Prossnitz, E.; Edwards, B.; Posner, G.

    1998-07-01

    Flow cytometry discriminates particle associated fluorescence from the fluorescence of the surrounding medium. It permits assemblies of macromolecular complexes on beads or cells to be detected in real-time with precision and specificity. The authors have investigated two types of robust sample handling systems which provide sub-second resolution and high throughput: (1) mixers which use stepper-motor driven syringes to initiate chemical reactions in msec time frames; and (2) flow injection controllers with valves and automated syringes used in chemical process control. In the former system, the authors used fast valves to overcome the disparity between mixing 100 {micro}ls of sample in 100 msecs and delivering sample to a flow cytometer at 1 {micro}l/sec. Particles were detected within 100 msec after mixing, but turbulence was created which lasted for 1 sec after injection of the sample into the flow cytometer. They used optical criteria to discriminate particles which were out of alignment due to the turbulent flow. Complex sample handling protocols involving multiple mixing steps and sample dilution have also been achieved. With the latter system they were able to automate sample handling and delivery with intervals of a few seconds. The authors used a fluidic approach to defeat turbulence caused by sample introduction. By controlling both sheath and sample with individual syringes, the period of turbulence was reduced to {approximately} 200 msecs. Automated sample handling and sub-second resolution should permit broad analytical and diagnostic applications of flow cytometry.

  12. Chiral hierarchical molecular nanostructures on two-dimensional surface by controllable trinary self-assembly.

    PubMed

    Liu, Jia; Chen, Ting; Deng, Xin; Wang, Dong; Pei, Jian; Wan, Li-Jun

    2011-12-28

    The bottom-up fabrication of surface hierarchical nanostructures is of great importance for the development of molecular nanostructures for chiral molecular recognition and enantioselective catalysis. Herein, we report the construction of a series of 2D chiral hierarchical structures by trinary molecular self-assembly with copper phthalocyanine (CuPc), 2,3,7,8,12,13-hexahexyloxy-truxenone (TrO23), and 1,3,5-tris(10-carboxydecyloxy) benzene (TCDB). A series of flower-like chiral hierarchical molecular architectures with increased generations are formed, and the details of these structures are investigated by high resolution scanning tunneling microscopy (STM). The flower-like hierarchical molecular architectures could be described by a unified configuration in which the lobe of each architecture is composed of a different number of triangular shape building units (TBUs). The off-axis edge-to-edge packing of TBUs confers the organizational chirality of the hierarchical assemblies. On the other hand, the TBUs can tile the surface in a vertex-sharing configuration, resulting in the expansion of chiral unit cells, which thereby further modulate the periodicity of chiral voids in the multilevel hierarchical assemblies. The formation of desired hierarchical structures could be controlled through tuning the molar ratio of each component in liquid phase. The results are significant for the design and fabrication of multicomponent chiral hierarchical molecular nanostructures.

  13. Molecular basis of outer kinetochore assembly on CENP-T

    PubMed Central

    Huis in 't Veld, Pim J; Jeganathan, Sadasivam; Petrovic, Arsen; Singh, Priyanka; John, Juliane; Krenn, Veronica; Weissmann, Florian; Bange, Tanja; Musacchio, Andrea

    2016-01-01

    Stable kinetochore-microtubule attachment is essential for cell division. It requires recruitment of outer kinetochore microtubule binders by centromere proteins C and T (CENP-C and CENP-T). To study the molecular requirements of kinetochore formation, we reconstituted the binding of the MIS12 and NDC80 outer kinetochore subcomplexes to CENP-C and CENP-T. Whereas CENP-C recruits a single MIS12:NDC80 complex, we show here that CENP-T binds one MIS12:NDC80 and two NDC80 complexes upon phosphorylation by the mitotic CDK1:Cyclin B complex at three distinct CENP-T sites. Visualization of reconstituted complexes by electron microscopy supports this model. Binding of CENP-C and CENP-T to MIS12 is competitive, and therefore CENP-C and CENP-T act in parallel to recruit two MIS12 and up to four NDC80 complexes. Our observations provide a molecular explanation for the stoichiometry of kinetochore components and its cell cycle regulation, and highlight how outer kinetochore modules bridge distances of well over 100 nm. DOI: http://dx.doi.org/10.7554/eLife.21007.001 PMID:28012276

  14. Facile assembly of light-driven molecular motors onto a solid surface.

    PubMed

    Chen, Jiawen; Chen, Kuang-Yen; Carroll, Gregory T; Feringa, Ben L

    2014-10-28

    In order to improve the rotary motion of surface assembled light-driven molecular motors, tetra-acid-functionalized motors were bound to an amine-coated quartz surface without prior activation of the acid groups. In contrast to earlier bipodal motors, the tetravalent motor showed no significant reduction in the rotation speed when attached to a surface.

  15. Characterization of the mixed self-assembled monolayer at the molecular scale.

    PubMed

    Ta, Van-Thao; Nimse, Satish Balasaheb; Song, Keum-Soo; Kim, Junghoon; Sayyed, Danishmalik Rafiq; Nguyen, Van-Thuan; Kim, Taisun

    2011-10-28

    The mixed SAM obtained by the self-assembly of the monothiolated calix[4]crown-5 receptor 1 and the subsequent addition of the thiolated alkylferrocene guest 3 was characterized at the molecular scale by the favorable receptor-guest interactions by using cyclic voltammetry (CV).

  16. Effect of Interfacial Molecular Orientation on Power Conversion Efficiency of Perovskite Solar Cells.

    PubMed

    Xiao, Minyu; Joglekar, Suneel; Zhang, Xiaoxian; Jasensky, Joshua; Ma, Jialiu; Cui, Qingyu; Guo, L Jay; Chen, Zhan

    2017-03-08

    A wide variety of charge carrier dynamics, such as transport, separation, and extraction, occur at the interfaces of planar heterojunction solar cells. Such factors can affect the overall device performance. Therefore, understanding the buried interfacial molecular structure in various devices and the correlation between interfacial structure and function has become increasingly important. Current characterization techniques for thin films such as X-ray diffraction, cross section scanning electronmicroscopy, and UV-visible absorption spectroscopy are unable to provide the needed molecular structural information at buried interfaces. In this study, by controlling the structure of the hole transport layer (HTL) in a perovskite solar cell and applying a surface/interface-sensitive nonlinear vibrational spectroscopic technique (sum frequency generation vibrational spectroscopy (SFG)), we successfully probed the molecular structure at the buried interface and correlated its structural characteristics to solar cell performance. Here, an edge-on (normal to the interface) polythiophene (PT) interfacial molecular orientation at the buried perovskite (photoactive layer)/PT (HTL) interface showed more than two times the power conversion efficiency (PCE) of a lying down (tangential) PT interfacial orientation. The difference in interfacial molecular structure was achieved by altering the alkyl side chain length of the PT derivatives, where PT with a shorter alkyl side chain showed an edge-on interfacial orientation with a higher PCE than that of PT with a longer alkyl side chain. With similar band gap alignment and bulk structure within the PT layer, it is believed that the interfacial molecular structural variation (i.e., the orientation difference) of the various PT derivatives is the underlying cause of the difference in perovskite solar cell PCE.

  17. Following the nanostructural molecular orientation guidelines for sulfur versus thiophene units in small molecule photovoltaic cells.

    PubMed

    Kim, Yu Jin; Park, Chan Eon

    2016-04-14

    In bulk heterojunction (BHJ) organic photovoltaics, particularly those using small molecules, electron donor and/or electron acceptor materials form a distributed network in the photoactive layer where critical photo-physical processes occur. Extensive research has recently focused on the importance of sulfur atoms in the small molecules. Little is known about the three-dimensional orientation of these sulfur atom-containing molecules. Herein, we report on our research concerning the heterojunction textures of the crystalline molecular orientation of small compounds having sulfur-containing units in the side chains, specifically, compounds known as DR3TSBDT that contain the alkylthio group and DR3TBDTT that does not. The improved performance of the DR3TBDTT-based devices, particularly in the photocurrent and the fill factor, was attributed to the large population of donor compound crystallites with a favorable face-on orientation along the perpendicular direction. This orientation resulted in efficient charge transport and a reduction in charge recombination. These findings underscore the great potential of small-molecule solar cells and suggest that even higher efficiencies can be achieved through materials development and molecular orientation control.

  18. Rational design of oriented assembly of gold nanospheres with nanorods by biotin-streptavidin connectors

    NASA Astrophysics Data System (ADS)

    Zhou, Xi; Wang, Yan; Zhong, Lubin; Bao, Shixiong; Han, Yu; Ren, Lei; Zhang, Qiqing

    2012-09-01

    Through the different functionalities on Au nanosphere (AuNSs) and Au nanorod (AuNRs) surfaces, we successfully control AuNSs attachment onto either the end or side surface of anisotropic AuNRs via bio-recognition, and then consciously construct side-by-side or end-to-end assembly nanostructures. This study provides a feasible approach to organize nanoparticles with different morphologies into controllable assembly geometries, which can potentially benefit the construction of future nanodevices.Through the different functionalities on Au nanosphere (AuNSs) and Au nanorod (AuNRs) surfaces, we successfully control AuNSs attachment onto either the end or side surface of anisotropic AuNRs via bio-recognition, and then consciously construct side-by-side or end-to-end assembly nanostructures. This study provides a feasible approach to organize nanoparticles with different morphologies into controllable assembly geometries, which can potentially benefit the construction of future nanodevices. Electronic supplementary information (ESI) available: Experimental details. See DOI: 10.1039/c2nr32022c

  19. Rational peptide design for functional materials via molecular self-assembly

    NASA Astrophysics Data System (ADS)

    Rajagopal, Karthikan

    Supra-molecular self-assembly of rationally designed peptides is a promising approach to construct functional materials. This thesis specifically focuses on hydrogels, an important class of materials with potential for applications in tissue engineering, drug delivery and micro-fluidic systems. The objective is to design short peptides that would specifically adopt a stimulus dependent conformation that is strongly amenable to self-assembly resulting in material formation. With this concept the rational design of a 20 amino acid peptide (MAX1) that folds into an amphiphilic beta-hairpin structure and then self-assembles to form a rigid hydrogel under alkaline conditions is presented. The molecular level conformation of MAX1 was characterized using circular dichroism and FTIR spectroscopies. The mesoscale structure of the hydrogel assessed using confocal and transmission electron micron microscopies and neutron scattering techniques shows that peptide self-assembly results in the formation of fibrils that are homogeneously 3 nm in diameter. The mechanical properties of the hydrogel probed using oscillatory rheology shows that MAX1 forms a stiff hydrogel. Since the self-assembly process is coupled to the intra-molecularly folded state of the peptide, stimulus responsiveness can be specifically engineered into the sequence by rational design. This was demonstrated in the design of peptides that form hydrogels in response to a specific stimulus such as temperature, pH or ionic strength. The significance of peptide design in the context of self-assembly and its relationship to the nanostructure was studied by designing a series of peptides derived from MAX1. Evolving from these studies is an understanding of the relationship between molecular level peptide structure and the nanoscale supra-molecular morphology. Based on this, it has been shown that alternate morphologies distinct from those observed with the gel forming peptides, such as non-twisting laminates or tube

  20. Molecular assemblies and membrane domains in multivesicular endosome dynamics

    SciTech Connect

    Falguieres, Thomas; Luyet, Pierre-Philippe; Gruenberg, Jean

    2009-05-15

    Along the degradation pathway, endosomes exhibit a characteristic multivesicular organization, resulting from the budding of vesicles into the endosomal lumen. After endocytosis and transport to early endosomes, activated signaling receptors are incorporated into these intralumenal vesicles through the action of the ESCRT machinery, a process that contributes to terminate signaling. Then, the vesicles and their protein cargo are further transported towards lysosomes for degradation. Evidence also shows that intralumenal vesicles can undergo 'back-fusion' with the late endosome limiting membrane, a route exploited by some pathogens and presumably followed by proteins and lipids that need to be recycled from within the endosomal lumen. This process depends on the late endosomal lipid lysobisphosphatidic acid and its putative effector Alix/AIP1, and is presumably coupled to the invagination of the endosomal limiting membrane at the molecular level via ESCRT proteins. In this review, we discuss the intra-endosomal transport routes in mammalian cells, and in particular the different mechanisms involved in membrane invagination, vesicle formation and fusion in a space inaccessible to proteins known to control intracellular membrane traffic.

  1. Kinetically forbidden transformations of water molecular assemblies in hydrophobic micropores.

    PubMed

    Ohba, Tomonori; Kaneko, Katsumi

    2011-06-21

    Water adsorption hysteresis is one of the most important phenomena observed during the interaction of water with hydrophobic surfaces. Adsorption hysteresis in micropores has strong relevance to the structure of adsorbed water. We used three typical models (cluster, monolayer, and uniform distribution structure models) to determine the structure of the water molecules adsorbed in hydrophobic slit-shaped carbon micropores. In each model, stabilization energy profiles were calculated for various fractional fillings by using the interaction potential theory. Simultaneously, molecular dynamics (MD) simulations of water adsorbed in the micropore of 1.1 nm pore width, which shows significant adsorption hysteresis, were performed to determine the kinetics of the observed structural transformations. The transformations between monolayer and cluster were slow, that is, kinetically forbidden at the fractional filling of 0.2 and 0.6, whereas the cluster-uniform distribution structure and uniform distribution structure-monolayer transformations were kinetically allowed. The kinetically forbidden transformation resulted in the occurrence of metastable structure of adsorbed water and was responsible for the observed adsorption hysteresis.

  2. Molecular Orientation and Photocurrent of Alkyl-Aromatic Polyimide Films Prepared by Vapor Deposition Polymerization

    NASA Astrophysics Data System (ADS)

    Iida, Kazuo; Nohara, Tsukasa; Totani, Kazuyuki; Nakamura, Shuhei; Sawa, Goro

    1989-12-01

    Vapor deposition polymerization by a coevaporation of pyromellitic dianhydride and decamethylenediamine monomers has been employed for the preparation of polyamic acid as a precursor for polyimide films. By curing at temperatures of 200-250°C the polyamic acid became the polyimide with directional arrangement of the molecular chain in the normal to the substrate observed by wide-angle X-ray diffraction. The sample containing a large amount of oriented crystals showed a small photocurrent. It was concluded that the oriented chain containing a decamethylene moiety hinders the carrier transfer between pyromellitimide moieties, resulting in a decrease of current.

  3. OOPSE: an object-oriented parallel simulation engine for molecular dynamics.

    PubMed

    Meineke, Matthew A; Vardeman, Charles F; Lin, Teng; Fennell, Christopher J; Gezelter, J Daniel

    2005-02-01

    OOPSE is a new molecular dynamics simulation program that is capable of efficiently integrating equations of motion for atom types with orientational degrees of freedom (e.g. "sticky" atoms and point dipoles). Transition metals can also be simulated using the embedded atom method (EAM) potential included in the code. Parallel simulations are carried out using the force-based decomposition method. Simulations are specified using a very simple C-based meta-data language. A number of advanced integrators are included, and the basic integrator for orientational dynamics provides substantial improvements over older quaternion-based schemes.

  4. Precise Characterisation of Molecular Orientation in a Single Crystal Field-Effect Transistor Using Polarised Raman Spectroscopy

    PubMed Central

    Wood, Sebastian; Rigas, Grigorios-Panagiotis; Zoladek-Lemanczyk, Alina; Blakesley, James C.; Georgakopoulos, Stamatis; Mas-Torrent, Marta; Shkunov, Maxim; Castro, Fernando A.

    2016-01-01

    Charge transport in organic semiconductors is strongly dependent on the molecular orientation and packing, such that manipulation of this molecular packing is a proven technique for enhancing the charge mobility in organic transistors. However, quantitative measurements of molecular orientation in micrometre-scale structures are experimentally challenging. Several research groups have suggested polarised Raman spectroscopy as a suitable technique for these measurements and have been able to partially characterise molecular orientations using one or two orientation parameters. Here we demonstrate a new approach that allows quantitative measurements of molecular orientations in terms of three parameters, offering the complete characterisation of a three-dimensional orientation. We apply this new method to organic semiconductor molecules in a single crystal field-effect transistor in order to correlate the measured orientation with charge carrier mobility measurements. This approach offers the opportunity for micrometre resolution (diffraction limited) spatial mapping of molecular orientation using bench-top apparatus, enabling a rational approach towards controlling this orientation to achieve optimum device performance. PMID:27619423

  5. Molecular Recognition: Use of Metal-Containing Molecular Clefts for Supramolecular Self-Assembly and Host-Guest Formation

    SciTech Connect

    Crowley, James D.; Bosnich, Brice

    2008-10-03

    Molecular clefts consisting of a rigid spacer linked to two parallel cofacially disposed terpy-M-X (M = Pd{sup 2+}, Pt{sup 2+}) units, which can vary in separation from 6.6 to 7.2 {angstrom}, have been used as molecular receptors and for self-assembly with linear and triangular linkers to produce rectangles and trigonal prisms, respectively. Aromatic molecules form multiple host-guest adducts with the molecular cleft receptors and with the rectangles and trigonal prisms. Planar complexes of Pt{sup 2+} also form host-guest adducts. The forces that control this molecular recognition, namely, {pi}-{pi} interactions, charge-induced dipole interactions, charge-charge forces, weak metal-metal interactions and solvation effects, are discussed and assigned to the various adducts.

  6. Subtle balance of tropoelastin molecular shape and flexibility regulates dynamics and hierarchical assembly

    PubMed Central

    Yeo, Giselle C.; Tarakanova, Anna; Baldock, Clair; Wise, Steven G.; Buehler, Markus J.; Weiss, Anthony S.

    2016-01-01

    The assembly of the tropoelastin monomer into elastin is vital for conferring elasticity on blood vessels, skin, and lungs. Tropoelastin has dual needs for flexibility and structure in self-assembly. We explore the structure-dynamics-function interplay, consider the duality of molecular order and disorder, and identify equally significant functional contributions by local and global structures. To study these organizational stratifications, we perturb a key hinge region by expressing an exon that is universally spliced out in human tropoelastins. We find a herniated nanostructure with a displaced C terminus and explain by molecular modeling that flexible helices are replaced with substantial β sheets. We see atypical higher-order cross-linking and inefficient assembly into discontinuous, thick elastic fibers. We explain this dysfunction by correlating local and global structural effects with changes in the molecule’s assembly dynamics. This work has general implications for our understanding of elastomeric proteins, which balance disordered regions with defined structural modules at multiple scales for functional assembly. PMID:26998516

  7. Understanding Molecular Interactions within Chemically Selective Layered Polymer Assemblies

    SciTech Connect

    Gary J. Blanchard

    2009-06-30

    This work focuses on two broad issues. These are (1) the molecular origin of the chemical selectivity achieved with ultrathin polymer multilayers, and (2) how the viscoelastic properties of the polymer layers are affected by exposure to solvent and analytes. These issues are inter-related, and to understand them we need to design experiments that probe both the energetic and kinetic aspects of interfacial adsorption processes. This project focuses on controling the chemical structure, thickness, morphology and sequential ordering of polymer layers bound to interfaces using maleimide-vinyl ether and closely related alternating copolymerization chemistry and efficient covalent cross-linking reactions that allow for layer-by-layer polymer deposition. This chemistry has been developed during the funding cycle of this Grant. We have measure the equilibrium constants for interactions between specific layers within the polymer interfaces and size-controlled, surface-functionalized gold nanoparticles. The ability to control both size and functionality of gold nanoparticle model analytes allows us to evaluate the average “pore size” that characterizes our polymer films. We have measured the “bulk” viscosity and shear modulus of the ultrathin polymer films as a function of solvent overlayer identity using quartz crystal microbalance complex impedance measurements. We have measured microscopic viscosity at specific locations within the layered polymer interfaces with time-resolved fluorescence lifetime and depolarization techniques. We combine polymer, cross-linking and nanoparticle synthetic expertise with a host of characterization techniques, including QCM gravimetry and complex impedance analysis, steady state and time-resolved spectroscopies.

  8. The centrosome orientation checkpoint is germline stem cell specific and operates prior to the spindle assembly checkpoint in Drosophila testis.

    PubMed

    Venkei, Zsolt G; Yamashita, Yukiko M

    2015-01-01

    Asymmetric cell division is utilized by a broad range of cell types to generate two daughter cells with distinct cell fates. In stem cell populations asymmetric cell division is believed to be crucial for maintaining tissue homeostasis, failure of which can lead to tissue degeneration or hyperplasia/tumorigenesis. Asymmetric cell divisions also underlie cell fate diversification during development. Accordingly, the mechanisms by which asymmetric cell division is achieved have been extensively studied, although the check points that are in place to protect against potential perturbation of the process are poorly understood. Drosophila melanogaster male germline stem cells (GSCs) possess a checkpoint, termed the centrosome orientation checkpoint (COC), that monitors correct centrosome orientation with respect to the component cells of the niche to ensure asymmetric stem cell division. To our knowledge, the COC is the only checkpoint mechanism identified to date that specializes in monitoring the orientation of cell division in multicellular organisms. Here, by establishing colcemid-induced microtubule depolymerization as a sensitive assay, we examined the characteristics of COC activity and find that it functions uniquely in GSCs but not in their differentiating progeny. We show that the COC operates in the G2 phase of the cell cycle, independently of the spindle assembly checkpoint. This study may provide a framework for identifying and understanding similar mechanisms that might be in place in other asymmetrically dividing cell types.

  9. Molecular-Orientation-Induced Rapid Roughening and Morphology Transition in Organic Semiconductor Thin-Film Growth

    PubMed Central

    Yang, Junliang; Yim, Sanggyu; Jones, Tim S.

    2015-01-01

    We study the roughening process and morphology transition of organic semiconductor thin film induced by molecular orientation in the model of molecular semiconductor copper hexadecafluorophthalocyanine (F16CuPc) using both experiment and simulation. The growth behaviour of F16CuPc thin film with the thickness, D, on SiO2 substrate takes on two processes divided by a critical thickness: (1) D ≤ 40 nm, F16CuPc thin films are composed of uniform caterpillar-like crystals. The kinetic roughening is confirmed during this growth, which is successfully analyzed by Kardar-Parisi-Zhang (KPZ) model with scaling exponents α = 0.71 ± 0.12, β = 0.36 ± 0.03, and 1/z = 0.39 ± 0.12; (2) D > 40 nm, nanobelt crystals are formed gradually on the caterpillar-like crystal surface and the film growth shows anomalous growth behaviour. These new growth behaviours with two processes result from the gradual change of molecular orientation and the formation of grain boundaries, which conversely induce new molecular orientation, rapid roughening process, and the formation of nanobelt crystals. PMID:25801646

  10. Molecular-orientation-induced rapid roughening and morphology transition in organic semiconductor thin-film growth.

    PubMed

    Yang, Junliang; Yim, Sanggyu; Jones, Tim S

    2015-03-24

    We study the roughening process and morphology transition of organic semiconductor thin film induced by molecular orientation in the model of molecular semiconductor copper hexadecafluorophthalocyanine (F16CuPc) using both experiment and simulation. The growth behaviour of F16CuPc thin film with the thickness, D, on SiO2 substrate takes on two processes divided by a critical thickness: (1) D ≤ 40 nm, F16CuPc thin films are composed of uniform caterpillar-like crystals. The kinetic roughening is confirmed during this growth, which is successfully analyzed by Kardar-Parisi-Zhang (KPZ) model with scaling exponents α = 0.71 ± 0.12, β = 0.36 ± 0.03, and 1/z = 0.39 ± 0.12; (2) D > 40 nm, nanobelt crystals are formed gradually on the caterpillar-like crystal surface and the film growth shows anomalous growth behaviour. These new growth behaviours with two processes result from the gradual change of molecular orientation and the formation of grain boundaries, which conversely induce new molecular orientation, rapid roughening process, and the formation of nanobelt crystals.

  11. Programmable concatenation of conductively linked gold nanorods using molecular assembly and femtosecond irradiation

    NASA Astrophysics Data System (ADS)

    Fontana, Jake; Flom, Steve; Naciri, Jawad; Ratna, Banahalli

    The ability to tune the resonant frequency in plasmonic nanostructures is fundamental to developing novel optical properties and ensuing materials. Recent theoretical insights show that the plasmon resonance can be exquisitely controlled through the conductive concatenation of plasmonic nanoparticles. Furthermore these charge transfer systems may mimic complex and hard to build nanostructures. Here we experimentally demonstrate a directed molecular assembly approach to controllably concatenate gold nanorods end to end into discrete linear structures, bridged with gold nanojunctions, using femtosecond laser light. By utilizing high throughput and nanometer resolution this approach offers a pragmatic assembly strategy for charge transfer plasmonic systems.

  12. Critical CuI buffer layer surface density for organic molecular crystal orientation change

    SciTech Connect

    Ahn, Kwangseok; Kim, Jong Beom; Lee, Dong Ryeol; Kim, Hyo Jung; Lee, Hyun Hwi

    2015-01-21

    We have determined the critical surface density of the CuI buffer layer inserted to change the preferred orientation of copper phthalocyanine (CuPc) crystals grown on the buffer layer. X-ray reflectivity measurements were performed to obtain the density profiles of the buffer layers and out-of-plane and 2D grazing-incidence X-ray diffraction measurements were performed to determine the preferred orientations of the molecular crystals. Remarkably, it was found that the preferred orientation of the CuPc film is completely changed from edge-on (1 0 0) to face-on (1 1 −2) by a CuI buffer layer with a very low surface density, so low that a large proportion of the substrate surface is bare.

  13. Preferred Molecular Orientation of Coumarin 343 on TiO2 Surfaces: Application to Dye-Sensitized Solar Cells.

    PubMed

    McCree-Grey, Jonathan; Cole, Jacqueline M; Evans, Peter J

    2015-08-05

    The dye···TiO2 interfacial structure in working electrodes of dye-sensitized solar cells (DSCs) is known to influence its photovoltaic device performance. Despite this, direct and quantitative reports of such structure remain sparse. This case study presents the application of X-ray reflectometry to determine the preferred structural orientation and molecular packing of the organic dye, Coumarin 343, adsorbed onto amorphous TiO2. Results show that the dye molecules are, on average, tilted by 61.1° relative to the TiO2 surface, and are separated from each other by 8.2 Å. These findings emulate the molecular packing arrangement of a monolayer of Coumarin 343 within its crystal structure. This suggests that the dye adsorbs onto TiO2 in one of its lowest energy configurations; that is, dye···TiO2 self-assembly is driven more by thermodynamic rather than kinetic means. Complementary DSC device tests illustrate that this interfacial structure compromises photovoltaic performance, unless a suitably sized coadsorbant is interdispersed between the Coumarin 343 chromophores on the TiO2 surface.

  14. Exploration of molecular orientation in polymers using novel vibrational spectroscopy methods

    NASA Astrophysics Data System (ADS)

    Frisk, Simon

    The knowledge of the structure-processing-property relationships is critical to any application in materials science. This project proposes a multidimensional approach to study the structure of polymer fibers as a function of different processing parameters. The tremendous potential of polarized Raman spectroscopy for the study of oriented polymers was demonstrated using quantitative and spectral analyses. A comparison of three methods to determine the first two coefficients of the orientation distribution function is presented. Based on these results, a graphical representation of the distribution of molecular orientations and its evolution in a series of poly(propylene terephthalate) fibers melt-spun under different processing conditions was attempted. A new method to determine an orientation independent Raman scattered intensity based on various polarized Raman measurements was developed and is introduced. The equivalent term in infrared spectroscopy is the structural absorbance. As with the structural absorbance, the calculated Raman intensity allows one to observe spectral changes that are due uniquely to morphological changes in a set of different samples in the presence of orientation differences. The correlation of the quantitative and spectral analyses yielded valuable information regarding the evolution of the molecular orientation and the structure as a function of spinning speed in the series of melt-spun PPT fibers. A monotonic increase in molecular orientation was observed through the entire spin speed range. Initially, this increase was accompanied by a large increase in density. Due to the absence of a significant increase in crystallinity, it was concluded that an oriented non-crystalline phase was formed. The onset of significant crystallinity was observed for the higher spin speeds. A second objective of this work was to gain a better understanding of the deformation mechanisms in the fibers when subjected to both permanent and reversible

  15. Molecular recognition and self-assembly special feature: Self-assembled biomimetic [2Fe2S]-hydrogenase-based photocatalyst for molecular hydrogen evolution.

    PubMed

    Kluwer, A M; Kapre, R; Hartl, F; Lutz, M; Spek, A L; Brouwer, A M; van Leeuwen, P W N M; Reek, J N H

    2009-06-30

    The large-scale production of clean energy is one of the major challenges society is currently facing. Molecular hydrogen is envisaged as a key green fuel for the future, but it becomes a sustainable alternative for classical fuels only if it is also produced in a clean fashion. Here, we report a supramolecular biomimetic approach to form a catalyst that produces molecular hydrogen using light as the energy source. It is composed of an assembly of chromophores to a bis(thiolate)-bridged diiron ([2Fe2S]) based hydrogenase catalyst. The supramolecular building block approach introduced in this article enabled the easy formation of a series of complexes, which are all thoroughly characterized, revealing that the photoactivity of the catalyst assembly strongly depends on its nature. The active species, formed from different complexes, appears to be the [Fe(2)(micro-pdt)(CO)(4){PPh(2)(4-py)}(2)] (3) with 2 different types of porphyrins (5a and 5b) coordinated to it. The modular supramolecular approach was important in this study as with a limited number of building blocks several different complexes were generated.

  16. Photodissociation of laboratory oriented molecules: Revealing molecular frame properties of nonaxial recoil

    SciTech Connect

    Brom, Alrik J. van den; Rakitzis, T. Peter; Janssen, Maurice H.M.

    2004-12-15

    We report the photodissociation of laboratory oriented OCS molecules. A molecular beam of OCS molecules is hexapole state-selected and spatially oriented in the electric field of a velocity map imaging lens. The oriented OCS molecules are dissociated at 230 nm with the linear polarization set at 45 deg. to the orientation direction of the OCS molecules. The CO({nu}=0,J) photofragments are quantum state-selectively ionized by the same 230 nm pulse and the angular distribution is measured using the velocity map imaging technique. The observed CO({nu}=0,J) images are strongly asymmetric and the degree of asymmetry varies with the CO rotational state J. From the observed asymmetry in the laboratory frame we can directly extract the molecular frame angles between the final photofragment recoil velocity and the permanent dipole moment and the transition dipole moment. The data for CO fragments with high rotational excitation reveal that the dissociation dynamics is highly nonaxial, even though conventional wisdom suggests that the nearly limiting {beta} parameter results from fast axial recoil dynamics. From our data we can extract the relative contribution of parallel and perpendicular transitions at 230 nm excitation.

  17. Mapping molecular orientational distributions for biological sample in 3D (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    HE, Wei; Ferrand, Patrick; Richter, Benjamin; Bastmeyer, Martin; Brasselet, Sophie

    2016-04-01

    Measuring molecular orientation properties is very appealing for scientists in molecular and cell biology, as well as biomedical research. Orientational organization at the molecular scale is indeed an important brick to cells and tissues morphology, mechanics, functions and pathologies. Recent work has shown that polarized fluorescence imaging, based on excitation polarization tuning in the sample plane, is able to probe molecular orientational order in biological samples; however this applies only to information in 2D, projected in the sample plane. To surpass this limitation, we extended this approach to excitation polarization tuning in 3D. The principle is based on the decomposition of any arbitrary 3D linear excitation in a polarization along the longitudinal z-axis, and a polarization in the transverse xy-sample plane. We designed an interferometer with one arm generating radial polarization light (thus producing longitudinal polarization under high numerical aperture focusing), the other arm controlling a linear polarization in the transverse plane. The amplitude ratio between the two arms can vary so as to get any linear polarized excitation in 3D at the focus of a high NA objective. This technique has been characterized by polarimetry imaging at the back focal plane of the focusing objective, and modeled theoretically. 3D polarized fluorescence microscopy is demonstrated on actin stress fibers in non-flat cells suspended on synthetic polymer structures forming supporting pillars, for which heterogeneous actin orientational order could be identified. This technique shows a great potential in structural investigations in 3D biological systems, such as cell spheroids and tissues.

  18. Self-assembly of mixed lipids into bicelles and vesicles: molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Sharma, Hari; Wang, Zilu; Dormidontova, Elena

    Formation of complex supramolecular nanostructures, such as micelles, bicelles, vesicles (liposomes) etc. via self-assembly of simple molecules has provided a new pathway for the design and development of effective drug carriers. Solid nanoparticles or functional biopolymers, such as RNA, DNA, peptides can be encapsulated into these carriers for controlled delivery or selective targeting. We performed coarse grained molecular dynamics simulation using the MARTINI force field to study the self-assembly of a binary surfactant mixture composed of long and short phospholipids, DPPC and DHPC, in the ratio 3:1. We found that at low temperature lipids self-assemble into a bicelle (nanodisc) with the longer lipid mainly forming the interior and short lipid the rim of the bicelle. At higher temperature the nanodisc transforms into a vesicle with homogeneously distributed lipids. The structural changes of these nanodiscs and vesicles imposed by gold nanoparticle encapsulation and pegylation will be addressed.

  19. Rings of single-walled carbon nanotubes: molecular-template directed assembly and Monte Carlo modeling.

    PubMed

    Zou, Shengli; Maspoch, Daniel; Wang, Yuhuang; Mirkin, Chad A; Schatz, George C

    2007-02-01

    Rings of single-walled carbon nanotubes (SWNTs) were assembled by dip-pen nanolithography (DPN) generated molecular templates consisting of COOH-terminated monolayers in circular patterns surrounded by passivating CH3-terminated SAMs. Experimental data and atomic-level Monte Carlo simulations show that SWNTs assemble into rings with radii as small as 100 nm at the edge of the COOH templates. This directed assembly is strongly length-dependent; only when the length of a SWNT is longer than half of the circumference of the circle does the SWNT bend to precisely follow the interface of the COOH-terminated monolayer. The theoretical modeling shows that the strain energy of each SWNT is balanced by the energy difference between the van der Waals interactions of the tube with COOH and CH3 templates to produce the resulting ring structure.

  20. Oriented-assembly of hollow FePt nanochains with tunable catalytic and magnetic properties

    NASA Astrophysics Data System (ADS)

    Liu, Jialong; Xia, Tianyu; Wang, Shouguo; Yang, Guang; Dong, Bowen; Wang, Chao; Ma, Qidi; Sun, Young; Wang, Rongming

    2016-06-01

    Hollow nanoparticles with large surface areas exhibit a lot of advantages for applications such as catalysis and energy storage. Furthermore, their performance can be manipulated by their deliberate assemblies. Dispersive hollow FePt nanospheres have been assembled into one-dimensional hollow FePt nanochains under the magnetic fields at room temperature. Based on the activation of galvanic replacement at different reaction stages, the size of hollow FePt nanochains can be deliberately manipulated varying from 20 nm to 300 nm, together with the length changing from 200 nm to 10 μm. The competition between movement of paramagnetic Fe3+ ions and shape recovering due to thermal fluctuations plays a critical effect on the structure of contact area between hollow nanospheres, leading to perforative structures. Compared with commercial Pt/C, well aligned hollow FePt nanochains show greatly enhanced catalytic activities in the methanol oxidation reaction (MOR) due to more favorable mass flow. Magnetic measurements indicate that the magnetic properties including Curie temperature and saturation magnetization can be tuned by the control of the size and shape of hollow nanochains.Hollow nanoparticles with large surface areas exhibit a lot of advantages for applications such as catalysis and energy storage. Furthermore, their performance can be manipulated by their deliberate assemblies. Dispersive hollow FePt nanospheres have been assembled into one-dimensional hollow FePt nanochains under the magnetic fields at room temperature. Based on the activation of galvanic replacement at different reaction stages, the size of hollow FePt nanochains can be deliberately manipulated varying from 20 nm to 300 nm, together with the length changing from 200 nm to 10 μm. The competition between movement of paramagnetic Fe3+ ions and shape recovering due to thermal fluctuations plays a critical effect on the structure of contact area between hollow nanospheres, leading to perforative

  1. Molecular and electronic structure of osmium complexes confined to Au(111) surfaces using a self-assembled molecular bridge

    SciTech Connect

    Llave, Ezequiel de la; Herrera, Santiago E.; Adam, Catherine; Méndez De Leo, Lucila P.; Calvo, Ernesto J.; Williams, Federico J.

    2015-11-14

    The molecular and electronic structure of Os(II) complexes covalently bonded to self-assembled monolayers (SAMs) on Au(111) surfaces was studied by means of polarization modulation infrared reflection absorption spectroscopy, photoelectron spectroscopies, scanning tunneling microscopy, scanning tunneling spectroscopy, and density functional theory calculations. Attachment of the Os complex to the SAM proceeds via an amide covalent bond with the SAM alkyl chain 40° tilted with respect to the surface normal and a total thickness of 26 Å. The highest occupied molecular orbital of the Os complex is mainly based on the Os(II) center located 2.2 eV below the Fermi edge and the LUMO molecular orbital is mainly based on the bipyridine ligands located 1.5 eV above the Fermi edge.

  2. In situ real-time spectroscopic ellipsometry measurement for the investigation of molecular orientation in organic amorphous multilayer structures

    NASA Astrophysics Data System (ADS)

    Yokoyama, Daisuke; Adachi, Chihaya

    2010-06-01

    To investigate molecular orientation in organic amorphous films, in situ real-time spectroscopic ellipsometry measurements were performed during vacuum deposition. Three materials with different molecular shapes were adopted to confirm the generality of the molecular orientation. In all three cases, more than 200 000 values for the ellipsometric parameters measured during deposition were well simulated simultaneously over the entire spectral range and measurement period using a simple model where the films possessed homogeneous optical anisotropy. This demonstrated the homogeneity of the molecular orientation in the direction of film thickness. The molecular orientation can be controlled by the substrate temperature even in multilayer structures. It is also demonstrated that a "multilayer structure" can be fabricated using only one material, where each layer has different optical and electrical properties.

  3. Telechelic star polymers as self-assembling units from the molecular to the macroscopic scale.

    PubMed

    Capone, Barbara; Coluzza, Ivan; LoVerso, Federica; Likos, Christos N; Blaak, Ronald

    2012-12-07

    By means of multiscale molecular simulations, we show that telechelic-star polymers are a simple, robust, and tunable system, which hierarchically self-assembles into soft-patchy particles and mechanically stabilizes selected, open crystalline structures. The self-aggregating patchy behavior can be fully controlled by the number of arms per star and by the fraction of attractive monomeric units at the free ends of the arms. Such self-assembled soft-patchy particles while forming, upon augmenting density, gel-like percolating networks, preserve properties as particle size, number, and arrangement of patches per particle. In particular, we demonstrate that the flexibility inherent in the soft-patchy particles brings forward a novel mechanism that leads to the mechanical stability of diamond and simple cubic crystals over a wide range of densities, and for molecular sizes ranging from about 10 nm up to the micrometer scale.

  4. Molecular bacterial community analysis of clean rooms where spacecraft are assembled.

    PubMed

    Moissl, Christine; Osman, Shariff; La Duc, Myron T; Dekas, Anne; Brodie, Eoin; DeSantis, Todd; Desantis, Tadd; Venkateswaran, Kasthuri

    2007-09-01

    Molecular bacterial community composition was characterized from three geographically distinct spacecraft-associated clean rooms to determine whether such populations are influenced by the surrounding environment or the maintenance of the clean rooms. Samples were collected from facilities at the Jet Propulsion Laboratory (JPL), Kennedy Space Flight Center (KSC), and Johnson Space Center (JSC). Nine clone libraries representing different surfaces within the spacecraft facilities and three libraries from the surrounding air were created. Despite the highly desiccated, nutrient-bare conditions within these clean rooms, a broad diversity of bacteria was detected, covering all the main bacterial phyla. Furthermore, the bacterial communities were significantly different from each other, revealing only a small subset of microorganisms common to all locations (e.g. Sphingomonas, Staphylococcus). Samples from JSC assembly room surfaces showed the greatest diversity of bacteria, particularly within the Alpha- and Gammaproteobacteria and Actinobacteria. The bacterial community structure of KSC assembly surfaces revealed a high presence of proteobacterial groups, whereas the surface samples collected from the JPL assembly facility showed a predominance of Firmicutes. Our study presents the first extended molecular survey and comparison of NASA spacecraft assembly facilities, and provides new insights into the bacterial diversity of clean room environments .

  5. Role of Bassoon and Piccolo in Assembly and Molecular Organization of the Active Zone

    PubMed Central

    Gundelfinger, Eckart D.; Reissner, Carsten; Garner, Craig C.

    2016-01-01

    Bassoon and Piccolo are two very large scaffolding proteins of the cytomatrix assembled at the active zone (CAZ) where neurotransmitter is released. They share regions of high sequence similarity distributed along their entire length and seem to share both overlapping and distinct functions in organizing the CAZ. Here, we survey our present knowledge on protein-protein interactions and recent progress in understanding of molecular functions of these two giant proteins. These include roles in the assembly of active zones (AZ), the localization of voltage-gated Ca2+ channels (VGCCs) in the vicinity of release sites, synaptic vesicle (SV) priming and in the case of Piccolo, a role in the dynamic assembly of the actin cytoskeleton. Piccolo and Bassoon are also important for the maintenance of presynaptic structure and function, as well as for the assembly of CAZ specializations such as synaptic ribbons. Recent findings suggest that they are also involved in the regulation activity-dependent communication between presynaptic boutons and the neuronal nucleus. Together these observations suggest that Bassoon and Piccolo use their modular structure to organize super-molecular complexes essential for various aspects of presynaptic function. PMID:26793095

  6. New orientations in the stereographic triangle for self-assembled faceting

    NASA Astrophysics Data System (ADS)

    Méndez-Camacho, R.; Méndez-García, V. H.; López-López, M.; Cruz-Hernández, E.

    2016-06-01

    Energetically unstable crystalline surfaces, among their uses, can be templates for the growth of periodic arrays of one-dimensional (1D) nanoscale structures. However, few studies have explored self-assembled faceting on high-index (HI) planes inside the stereographic triangle, and extant studies have not produced any criteria for encouraging the formation of one-dimensional periodic arrays. In this Letter, by analyzing the MBE growth of homoepitaxial facets on (631)A GaAs, a HI plane inside the triangle, we present a criteria to produce highly uniform 1D periodic arrays on unexplored surfaces. These families of planes are those belonging to the lines connecting the energetically stable HI GaAs (11 5 2) plane with any of the (100), (110), and (111) planes at the corners of the stereographic triangle. This novel strategy can lead to new possibilities in self-assembling 1D structures and manipulating physical properties, which in turn may result in new HI- and 1D-based experiments and devices.

  7. Molecular design driving tetraporphyrin self-assembly on graphite: a joint STM, electrochemical and computational study

    NASA Astrophysics Data System (ADS)

    El Garah, M.; Santana Bonilla, A.; Ciesielski, A.; Gualandi, A.; Mengozzi, L.; Fiorani, A.; Iurlo, M.; Marcaccio, M.; Gutierrez, R.; Rapino, S.; Calvaresi, M.; Zerbetto, F.; Cuniberti, G.; Cozzi, P. G.; Paolucci, F.; Samorì, P.

    2016-07-01

    Tuning the intermolecular interactions among suitably designed molecules forming highly ordered self-assembled monolayers is a viable approach to control their organization at the supramolecular level. Such a tuning is particularly important when applied to sophisticated molecules combining functional units which possess specific electronic properties, such as electron/energy transfer, in order to develop multifunctional systems. Here we have synthesized two tetraferrocene-porphyrin derivatives that by design can selectively self-assemble at the graphite/liquid interface into either face-on or edge-on monolayer-thick architectures. The former supramolecular arrangement consists of two-dimensional planar networks based on hydrogen bonding among adjacent molecules whereas the latter relies on columnar assembly generated through intermolecular van der Waals interactions. Scanning Tunneling Microscopy (STM) at the solid-liquid interface has been corroborated by cyclic voltammetry measurements and assessed by theoretical calculations to gain multiscale insight into the arrangement of the molecule with respect to the basal plane of the surface. The STM analysis allowed the visualization of these assemblies with a sub-nanometer resolution, and cyclic voltammetry measurements provided direct evidence of the interactions of porphyrin and ferrocene with the graphite surface and offered also insight into the dynamics within the face-on and edge-on assemblies. The experimental findings were supported by theoretical calculations to shed light on the electronic and other physical properties of both assemblies. The capability to engineer the functional nanopatterns through self-assembly of porphyrins containing ferrocene units is a key step toward the bottom-up construction of multifunctional molecular nanostructures and nanodevices.Tuning the intermolecular interactions among suitably designed molecules forming highly ordered self-assembled monolayers is a viable approach to

  8. Conformational Change in Molecular Assembly of Nickel(II) Tetra(n-propyl)porphycene Triggered by Potential Manipulation.

    PubMed

    Yoshimoto, Soichiro; Kawamoto, Teppei; Okawara, Toru; Hisaeda, Yoshio; Abe, Masaaki

    2016-12-27

    Metal-coordinated porphyrin and related compounds are important for developing molecular architectures that mimic enzymes. Porphycene, a structural isomer of porphyrin, has shown unique properties in semiartificial myoglobin. To explore its potential as a molecular building block, we studied the molecular assembly of nickel(II) tetra(n-propyl)porphycene (NiTPrPc), a metalloporphycene with introduced tetra n-propyl moieties, on the Au(111) electrode surface using in situ scanning tunneling microscopy. Because of the low molecular symmetry of NiTPrPc, the molecular assembly undergoes unique phase transitions due to conformational change of the n-propyl moieties. The phase transitions can be precisely controlled by the electrode potential, demonstrating that the latter can play an important role in the porphycene molecular assembly on Au surface. This new discovery indicates possible uses of this porphycene framework in molecular engineering.

  9. A 1-D Model of the 4 Bed Molecular Sieve of the Carbon Dioxide Removal Assembly

    NASA Technical Reports Server (NTRS)

    Coker, Robert; Knox, Jim

    2015-01-01

    Developments to improve system efficiency and reliability for water and carbon dioxide separation systems on crewed vehicles combine sub-scale systems testing and multi-physics simulations. This paper describes the development of COMSOL simulations in support of the Life Support Systems (LSS) project within NASA's Advanced Exploration Systems (AES) program. Specifically, we model the 4 Bed Molecular Sieve (4BMS) of the Carbon Dioxide Removal Assembly (CDRA) operating on the International Space Station (ISS).

  10. The Design of a Molecular Assembly Line Based on Biological Molecules

    DTIC Science & Technology

    2003-06-01

    and will demonstrate how one can construct a purely synthetic analogue of a polyketide synthase . 15. SUBJECT TERMS 16. SECURITY CLASSIFICATION OF...scaffold in programmed assembly and molecular electronics. It is based on the principles of the biological molecules polyketide synthase and kinesin, and in...stereoselective centers) with any reasonable yield, not including the R&D and process development time. Figure 1.6 shows how a polyketide synthase

  11. Some aspects of radical chemistry in the assembly of complex molecular architectures

    PubMed Central

    Quiclet-Sire, Béatrice

    2013-01-01

    Summary This review article describes briefly some of the radical processes developed in the authors’ laboratory as they pertain to the concise assembly of complex molecular scaffolds. The emphasis is placed on the use of nitrogen-centred radicals, on the degenerate addition–transfer of xanthates, especially on its potential for intermolecular carbon–carbon bond formation, and on the generation and capture of radicals through electron transfer processes. PMID:23616797

  12. Unveiling self-assembled monolayers' potential for molecular spintronics: spin transport at high voltage.

    PubMed

    Galbiati, Marta; Barraud, Clément; Tatay, Sergio; Bouzehouane, Karim; Deranlot, Cyrile; Jacquet, Eric; Fert, Albert; Seneor, Pierre; Mattana, Richard; Petroff, Frédéric

    2012-12-18

    Molecular magnetic tunnel junctions using self-assembled monolayers (SAMs) as tunnel barriers show stable and efficient spin transport properties. Large tunnel magnetoresistance with a flat bias voltage dependence of the magnetoresistance is observed in La(2/3) Sr(1/3) MnO(3) /dodecylphosphonic acid SAM/Co nanocontacts. This opens the door to spintronic tailoring though SAM engineering and could also lead to new venues for spin injection in organic devices.

  13. Molecular codes for neuronal individuality and cell assembly in the brain.

    PubMed

    Yagi, Takeshi

    2012-01-01

    The brain contains an enormous, but finite, number of neurons. The ability of this limited number of neurons to produce nearly limitless neural information over a lifetime is typically explained by combinatorial explosion; that is, by the exponential amplification of each neuron's contribution through its incorporation into "cell assemblies" and neural networks. In development, each neuron expresses diverse cellular recognition molecules that permit the formation of the appropriate neural cell assemblies to elicit various brain functions. The mechanism for generating neuronal assemblies and networks must involve molecular codes that give neurons individuality and allow them to recognize one another and join appropriate networks. The extensive molecular diversity of cell-surface proteins on neurons is likely to contribute to their individual identities. The clustered protocadherins (Pcdh) is a large subfamily within the diverse cadherin superfamily. The clustered Pcdh genes are encoded in tandem by three gene clusters, and are present in all known vertebrate genomes. The set of clustered Pcdh genes is expressed in a random and combinatorial manner in each neuron. In addition, cis-tetramers composed of heteromultimeric clustered Pcdh isoforms represent selective binding units for cell-cell interactions. Here I present the mathematical probabilities for neuronal individuality based on the random and combinatorial expression of clustered Pcdh isoforms and their formation of cis-tetramers in each neuron. Notably, clustered Pcdh gene products are known to play crucial roles in correct axonal projections, synaptic formation, and neuronal survival. Their molecular and biological features induce a hypothesis that the diverse clustered Pcdh molecules provide the molecular code by which neuronal individuality and cell assembly permit the combinatorial explosion of networks that supports enormous processing capability and plasticity of the brain.

  14. Effect of Zn(2+) ions on the assembly of amylin oligomers: insight into the molecular mechanisms.

    PubMed

    Wineman-Fisher, Vered; Miller, Yifat

    2016-08-03

    Amylin is an endocrine hormone and is a member of the family of amyloid peptides and proteins that emerge as potential scaffolds by self-assembly processes. Zn(2+) ions can bind to amylin peptides to form self-assembled Zn(2+)-amylin oligomers. In the current work the binding sites of Zn(2+) ions in the self-assembled amylin oligomers at various concentrations of zinc have been investigated. Our results yield two conclusions. First, in the absence of Zn(2+) ions polymorphic states (i.e. various classes of amylin oligomers) are obtained, but when Zn(2+) ions bind to amylin peptides to form Zn(2+)-amylin oligomers, the polymorphism is decreased, i.e. Zn(2+) ions bind only to specific classes of amylin. At low concentrations of Zn(2+) ions the polymorphism is smaller than at high concentrations. Second, the structural features of the self-assembled amylin oligomers are not affected by the presence of Zn(2+) ions. This study proposes new molecular mechanisms of the self-assembly of Zn(2+)-amylin oligomers.

  15. Molecular design driving tetraporphyrin self-assembly on graphite: a joint STM, electrochemical and computational study.

    PubMed

    El Garah, M; Santana Bonilla, A; Ciesielski, A; Gualandi, A; Mengozzi, L; Fiorani, A; Iurlo, M; Marcaccio, M; Gutierrez, R; Rapino, S; Calvaresi, M; Zerbetto, F; Cuniberti, G; Cozzi, P G; Paolucci, F; Samorì, P

    2016-07-14

    Tuning the intermolecular interactions among suitably designed molecules forming highly ordered self-assembled monolayers is a viable approach to control their organization at the supramolecular level. Such a tuning is particularly important when applied to sophisticated molecules combining functional units which possess specific electronic properties, such as electron/energy transfer, in order to develop multifunctional systems. Here we have synthesized two tetraferrocene-porphyrin derivatives that by design can selectively self-assemble at the graphite/liquid interface into either face-on or edge-on monolayer-thick architectures. The former supramolecular arrangement consists of two-dimensional planar networks based on hydrogen bonding among adjacent molecules whereas the latter relies on columnar assembly generated through intermolecular van der Waals interactions. Scanning Tunneling Microscopy (STM) at the solid-liquid interface has been corroborated by cyclic voltammetry measurements and assessed by theoretical calculations to gain multiscale insight into the arrangement of the molecule with respect to the basal plane of the surface. The STM analysis allowed the visualization of these assemblies with a sub-nanometer resolution, and cyclic voltammetry measurements provided direct evidence of the interactions of porphyrin and ferrocene with the graphite surface and offered also insight into the dynamics within the face-on and edge-on assemblies. The experimental findings were supported by theoretical calculations to shed light on the electronic and other physical properties of both assemblies. The capability to engineer the functional nanopatterns through self-assembly of porphyrins containing ferrocene units is a key step toward the bottom-up construction of multifunctional molecular nanostructures and nanodevices.

  16. Structure Prediction of Self-Assembled Dye Aggregates from Cryogenic Transmission Electron Microscopy, Molecular Mechanics, and Theory of Optical Spectra

    PubMed Central

    2016-01-01

    Cryogenic transmission electron microscopy (cryo-TEM) studies suggest that TTBC molecules self-assemble in aqueous solution to form single-walled tubes with a diameter of about 35 Å. In order to reveal the arrangement and mutual orientations of the individual molecules in the tube, we combine information from crystal structure data of this dye with a calculation of linear absorbance and linear dichroism spectra and molecular dynamics simulations. We start with wrapping crystal planes in different directions to obtain tubes of suitable diameter. This set of tube models is evaluated by comparing the resulting optical spectra with experimental data. The tubes that can explain the spectra are investigated further by molecular dynamics simulations, including explicit solvent molecules. From the trajectories of the most stable tube models, the short-range ordering of the dye molecules is extracted and the optimization of the structure is iteratively completed. The final structural model is a tube of rings with 6-fold rotational symmetry, where neighboring rings are rotated by 30° and the transition dipole moments of the chromophores form an angle of 74° with respect to the symmetry axis of the tube. This model is in agreement with cryo-TEM images and can explain the optical spectra, consisting of a sharp red-shifted J-band that is polarized parallel to to the symmetry axis of the tube and a broad blue-shifted H-band polarized perpendicular to this axis. The general structure of the homogeneous spectrum of this hybrid HJ-aggregate is described by an analytical model that explains the difference in redistribution of oscillator strength inside the vibrational manifolds of the J- and H-bands and the relative intensities and excitation energies of those bands. In addition to the particular system investigated here, the present methodology can be expected to aid the structure prediction for a wide range of self-assembled dye aggregates. PMID:27642380

  17. Molecular dynamics simulations and electronic excited state properties of a self-assembled peptide amphiphile nanofiber with metalloporphyrin arrays.

    PubMed

    Yu, Tao; Lee, One-Sun; Schatz, George C

    2014-09-18

    We have employed molecular dynamics simulations and quantum chemistry methods to study the structures and electronic absorption properties of a novel type of photonic nanowire gel constructed by the self-assembly of peptide amphiphiles (PAs) and the chromophore-(PPIX)Zn molecules. Using molecular dynamics simulations, structures of the self-assembled fiber were determined with atomistic detail, including the distribution of chromophores along the nanofiber and the relative distances and orientations of pairs of chromophores. In addition, quantum chemistry calculations were used to determine the electronic structure and absorption properties of the chromophores in the fiber, so as to assess the capabilities of the nanofiber for photonics applications. The calculations show that the PA nanofiber provides an effective scaffold for the chromophores in which the chromophores form several clusters in which nearest neighbor chromophores are separated by less than 20 Å. The calculations also indicate that the chromophores can be in both the hydrophilic shell and hydrophobic core portions of the fiber. There are only small spectral shifts to the B-band of the porphyrins arising from the inhomogeneous microelectronic environment provided by the fiber. However, there are much stronger electronic interactions between nearby pairs of chromophores, leading to a more significant red shift of the B-band that is similar to what is found in the experiments and to significant excitonic coupling that is seen in circular dichroism spectra. This electronic interaction between chromophores associated with the PA nanofiber structure is crucial to future applications of these fibers for light-harvesting applications.

  18. Structure Prediction of Self-Assembled Dye Aggregates from Cryogenic Transmission Electron Microscopy, Molecular Mechanics, and Theory of Optical Spectra.

    PubMed

    Friedl, Christian; Renger, Thomas; Berlepsch, Hans V; Ludwig, Kai; Schmidt Am Busch, Marcel; Megow, Jörg

    2016-09-01

    Cryogenic transmission electron microscopy (cryo-TEM) studies suggest that TTBC molecules self-assemble in aqueous solution to form single-walled tubes with a diameter of about 35 Å. In order to reveal the arrangement and mutual orientations of the individual molecules in the tube, we combine information from crystal structure data of this dye with a calculation of linear absorbance and linear dichroism spectra and molecular dynamics simulations. We start with wrapping crystal planes in different directions to obtain tubes of suitable diameter. This set of tube models is evaluated by comparing the resulting optical spectra with experimental data. The tubes that can explain the spectra are investigated further by molecular dynamics simulations, including explicit solvent molecules. From the trajectories of the most stable tube models, the short-range ordering of the dye molecules is extracted and the optimization of the structure is iteratively completed. The final structural model is a tube of rings with 6-fold rotational symmetry, where neighboring rings are rotated by 30° and the transition dipole moments of the chromophores form an angle of 74° with respect to the symmetry axis of the tube. This model is in agreement with cryo-TEM images and can explain the optical spectra, consisting of a sharp red-shifted J-band that is polarized parallel to to the symmetry axis of the tube and a broad blue-shifted H-band polarized perpendicular to this axis. The general structure of the homogeneous spectrum of this hybrid HJ-aggregate is described by an analytical model that explains the difference in redistribution of oscillator strength inside the vibrational manifolds of the J- and H-bands and the relative intensities and excitation energies of those bands. In addition to the particular system investigated here, the present methodology can be expected to aid the structure prediction for a wide range of self-assembled dye aggregates.

  19. A slippery molecular assembly allows water as a self-erasable security marker

    PubMed Central

    Thirumalai, Rajasekaran; Mukhopadhyay, Rahul Dev; Praveen, Vakayil K.; Ajayaghosh, Ayyappanpillai

    2015-01-01

    Protection of currency and valuable documents from counterfeit continues to be a challenge. While there are many embedded security features available for document safety, they are not immune to forgery. Fluorescence is a sensitive property, which responds to external stimuli such as solvent polarity, temperature or mechanical stress, however practical use in security applications is hampered due to several reasons. Therefore, a simple and specific stimuli responsive security feature that is difficult to duplicate is of great demand. Herein we report the design of a fluorescent molecular assembly on which water behaves as a self-erasable security marker for checking the authenticity of documents at point of care. The underlying principle involves the disciplined self-assembly of a tailor-made fluorescent molecule, which initially form a weak blue fluorescence (λem = 425 nm, Φf = 0.13) and changes to cyan emission (λem = 488 nm,Φf = 0.18) in contact with water due to a reversible molecular slipping motion. This simple chemical tool, based on the principles of molecular self-assembly and fluorescence modulation, allows creation of security labels and optically masked barcodes for multiple documents authentication. PMID:25940779

  20. Self-assembly of Spherical Macroions in Solution: A Coarse-grained Molecular Dynamics Study

    NASA Astrophysics Data System (ADS)

    Liu, Zhuonan; Liu, Tianbo; Tsige, Mesfin

    2015-03-01

    Macroions (such as polyoxometalates) in solution can form a stable hollow spherical super-molecular structure called blackberry when they have moderate surface charge density and size (1-10 nm). Depending on the surface charge density of macroions, the size of the blackberry can be from 20 to more than 100 nm. Other macroions such as dendrimers can also self-assemble into similar super-molecular structure in solution. Existing theories such as Debye-Hückel and DLVO theories cannot explain this phenomenon and we are not aware of any other theory that can explain this. Previous studies using all-atom Molecular Dynamics simulations have shown identical macroions forming oligomers mediated by counterions. Due to the limitations in all-atom simulation and available computational capabilities, these studies handled only small systems with simple macroions, leading to less conclusive but still relevant results on the self-assembly behavior. To overcome these limitations, in this work large-scale coarse-grained modeling of macroions in solution is used. In order to understand the origin of the attractive force that is responsible for the self-assembly of macroions, different types of macroions in different solution conditions are studied. This work was supported by NSF Grant DMR0847580.

  1. A slippery molecular assembly allows water as a self-erasable security marker.

    PubMed

    Thirumalai, Rajasekaran; Mukhopadhyay, Rahul Dev; Praveen, Vakayil K; Ajayaghosh, Ayyappanpillai

    2015-05-05

    Protection of currency and valuable documents from counterfeit continues to be a challenge. While there are many embedded security features available for document safety, they are not immune to forgery. Fluorescence is a sensitive property, which responds to external stimuli such as solvent polarity, temperature or mechanical stress, however practical use in security applications is hampered due to several reasons. Therefore, a simple and specific stimuli responsive security feature that is difficult to duplicate is of great demand. Herein we report the design of a fluorescent molecular assembly on which water behaves as a self-erasable security marker for checking the authenticity of documents at point of care. The underlying principle involves the disciplined self-assembly of a tailor-made fluorescent molecule, which initially form a weak blue fluorescence (λem = 425 nm, Φf = 0.13) and changes to cyan emission (λem = 488 nm,Φf = 0.18) in contact with water due to a reversible molecular slipping motion. This simple chemical tool, based on the principles of molecular self-assembly and fluorescence modulation, allows creation of security labels and optically masked barcodes for multiple documents authentication.

  2. Self-Assembly and Horizontal Orientation Growth of VO2 Nanowires

    PubMed Central

    Cheng, Chun; Guo, Hua; Amini, Abbas; Liu, Kai; Fu, Deyi; Zou, Jian; Song, Haisheng

    2014-01-01

    Single-crystalline vanadium dioxide (VO2) nanostructures have attracted an intense research interest recently because of their unique single-domain metal-insulator phase transition property. Synthesis of these nanostructures in the past was limited in density, alignment, or single-crystallinity. The assembly of VO2 nanowires (NWs) is desirable for a “bottom-up” approach to the engineering of intricate structures using nanoscale building blocks. Here, we report the successful synthesis of horizontally aligned VO2 NWs with a dense growth mode in the [1-100]quartz direction of a polished x-cut quartz surface using a simple vapor transport method. Our strategy of controlled growth of VO2 NWs promisingly paves the way for designing novel metal-insulator transition devices based on VO2 NWs. PMID:24965899

  3. Performance oriented packaging testing of safety and arming assemblies for the BLU 91/B and BLU 92/B mines packed 90 per wood box. Final report

    SciTech Connect

    Dzury, C.

    1992-11-30

    This report contains the test results and test procedures for Performance Oriented Packaging Tests performed on the pack for both the Safety and Arming Assembly for the BLU 91/B Mine and the BLU 92/B Mine. This pack consists of 90 Safety and Arming Assemblies in a fiberboard box inner pack with a wooden box outer pack. Both Safety and Arming Assemblies are packed in the same way and have the same Proper Shipping Name and Identification Number which is Fuzes, Detonating UN 0257.

  4. Performance oriented packaging testing of safety and arming assemblies for the BLU 91/B and BLU 92/B mines, packed 144 per wood box. Final report

    SciTech Connect

    Dzury, C.

    1992-12-07

    This report contains the test results and test procedures for Performance Oriented Packaging Tests performed on the pack for both the Safety and Arming Assembly for the BLU 91/B Mine and the BLU 92/B Mine. This pack consists of - 144 Safety and Arming Assemblies in a fiberboard box inner pack with a wooden box outer pack. Both Safety and Arming Assemblies are packed in the same way and have the same Proper Shipping Name and Identification Number which in Fuzes, Detonating UN 0257.

  5. Assembly of Oriented Virus Arrays by Chemo-Selective Ligation Methods and Nanolithography Techniques

    SciTech Connect

    Camarero, J A; Cheung, C L; Lin, T; Johnson, J E; Weeks, B L; Noy, A; De Yoreo, J J

    2002-12-02

    The present work describes our ongoing efforts towards the creation of nano-scaled ordered arrays of protein/virus covalently attached to site-specific chemical linkers patterned by different nanolithograpy techniques. We will present a new and efficient solid-phase approach for the synthesis of chemically modified long alkyl-thiols. These compounds can be used to introduce chemoselective reacting groups onto gold and silicon-based surfaces. Furthermore, these modified thiols have been used to create nanometric patterns by using different nanolithography techniques. We will show that these patterns can react chemoselectively with proteins and/or virus which have been chemically or recombinantly modified to contain complementary chemical groups at specific positions thus resulting in the oriented attachment of the protein or virus to the surface.

  6. Paramagnetic particle assemblies as colloidal models for atomic and molecular systems

    NASA Astrophysics Data System (ADS)

    Li, Dichuan

    2011-12-01

    Colloidal particles are ideal models for studying the behavior of atomic and molecular systems. They resemble their atomic and molecular analogues in that their dynamics are driven by thermal energy and their equilibrium properties are controlled by inter-particle interactions. Based on this analogy, it is reasonable to construct colloidal chains, where each particle represents a repeat unit, as models for polymers. The advantages of this system over molecular systems are its controllable rigidity, contour length and diameter, as well as the convenience to capture its instantaneous shape and position via video microscopy, which are not trivial to realize in molecular systems. By utilizing the dipolar properties of magnetic colloids, a number of groups have assembled semiflexible and rigid colloidal chains by cross-linking magnetic beads under a magnetic field using polymer linkers. Recently, efforts in constructing colloidal chains led even to anisotropic magnetic colloidal chains that mimic the detailed atomic arrangements of polymers. These properties make colloidal chains possible candidates for the classic bead-spring or bead-rod model systems for semiflexible and rigid polymers. In my thesis, I present a method for generating linear colloidal chain structures by linking surface functionalized paramagnetic particles using DNA. First, I investigate the force interactions between individual magnetic particles under different conditions to optimize the resulting chain stability. A systematic study the bending and rotational diffusion dynamics of the chains and their relationship with the DNA linking chemistry is presented. I then demonstrate their use as a ideal model system to study polymer dynamics In addition, a technique to measure short-range repulsive surface forces between these colloids with high precision was developed. Building on these repulsive force studies, a colloidal system to study 2-D phase transitions was created. This thesis provides insights

  7. Parity-selective enhancement of field-free molecular orientation in an intense two-color laser field

    SciTech Connect

    Yun, Hyeok; Nam, Chang Hee; Kim, Hyung Taek; Kim, Chul Min; Lee, Jongmin

    2011-12-15

    We investigated the characteristics of molecular orientation induced by a nonresonant two-color femtosecond laser field. By analyzing the rotational dynamics of asymmetric linear molecules, we revealed that the critical parameter in characterizing the molecular orientation was the hyperpolarizability of molecules that selected the excitation paths of rotational states between parity-changing and parity-conserving transitions. Especially, in the case of molecules with small hyperpolarizability, a significant enhancement of orientation was achieved at the half-rotational period, instead of the full-rotational period. This deeper understanding of the hyperpolarizability-dependent characteristics of molecular orientation in a two-color scheme can provide an effective method to achieve significantly enhanced field-free orientation for various polar molecules.

  8. The influence of molecular pre-orientation on the resonance-enhanced multi-photon ionization dynamics

    NASA Astrophysics Data System (ADS)

    Zhang, Xiao-Miao; Li, Jing-Lun; Yu, Jie; Cong, Shu-Lin

    2017-03-01

    We investigate theoretically the influence of molecular pre-orientation on the resonance-enhanced multi-photon ionization (REMPI) dynamics, taking the LiH molecule for example. The LiH molecule is first pre-oriented by a single-cycle pulse (SCP) in terahertz (THz) region, and then excited by the femtosecond pump pulse, and finally ionized by the femtosecond probe pulse. We focus on the impact of the pre-orientation on the ionization probability, energy- and angle-resolved photoelectron spectra and photoelectron angular distribution (PAD). It is found that the ionization probability and peak intensity of energy-resolved photoelectron spectra are significantly affected by molecular orientation. The angle-resolved photoelectron spectra are related to the molecular orientation. The PAD can be changed by varying the delay time between the THz SCP and pump pulse. We also investigate the effect of temperature on excitation and ionization dynamics.

  9. Polarization-Dependent Measurements of Molecular Super Rotors with Oriented Angular Momenta

    NASA Astrophysics Data System (ADS)

    Murray, Matthew J.; Toro, Carlos; Liu, Qingnan; Mullin, Amy S.

    2014-05-01

    Controlling molecular motion would enable manipulation of energy flow between molecules. Here we have used an optical centrifuge to investigate energy transfer between molecular super rotors with oriented angular momenta. The polarizable electron cloud of the molecules interacts with the electric field of linearly polarized light that angularly accelerates over the time of the optical pulse. This process drives molecules into high angular momentum states that are oriented with the optical field and have energies far from equilibrium. High resolution transient IR spectroscopy reveals the dynamics of collisional energy transfer for these super excited rotors. The results of this study leads to a more fundamental understanding of energy balance in non-equilibrium environments and the physical and chemical properties of gases in a new regime of energy states. Results will be presented for several super rotor species including carbon monoxide, carbon dioxide, and acetylene. Polarization-dependent measurements reveal the extent to which the super rotors maintain spatial orientation of high angular momentum states.

  10. Molecularly self-assembled nucleic acid nanoparticles for targeted in vivo siRNA delivery

    NASA Astrophysics Data System (ADS)

    Lee, Hyukjin; Lytton-Jean, Abigail K. R.; Chen, Yi; Love, Kevin T.; Park, Angela I.; Karagiannis, Emmanouil D.; Sehgal, Alfica; Querbes, William; Zurenko, Christopher S.; Jayaraman, Muthusamy; Peng, Chang G.; Charisse, Klaus; Borodovsky, Anna; Manoharan, Muthiah; Donahoe, Jessica S.; Truelove, Jessica; Nahrendorf, Matthias; Langer, Robert; Anderson, Daniel G.

    2012-06-01

    Nanoparticles are used for delivering therapeutics into cells. However, size, shape, surface chemistry and the presentation of targeting ligands on the surface of nanoparticles can affect circulation half-life and biodistribution, cell-specific internalization, excretion, toxicity and efficacy. A variety of materials have been explored for delivering small interfering RNAs (siRNAs)--a therapeutic agent that suppresses the expression of targeted genes. However, conventional delivery nanoparticles such as liposomes and polymeric systems are heterogeneous in size, composition and surface chemistry, and this can lead to suboptimal performance, a lack of tissue specificity and potential toxicity. Here, we show that self-assembled DNA tetrahedral nanoparticles with a well-defined size can deliver siRNAs into cells and silence target genes in tumours. Monodisperse nanoparticles are prepared through the self-assembly of complementary DNA strands. Because the DNA strands are easily programmable, the size of the nanoparticles and the spatial orientation and density of cancer-targeting ligands (such as peptides and folate) on the nanoparticle surface can be controlled precisely. We show that at least three folate molecules per nanoparticle are required for optimal delivery of the siRNAs into cells and, gene silencing occurs only when the ligands are in the appropriate spatial orientation. In vivo, these nanoparticles showed a longer blood circulation time (t1/2 ~ 24.2 min) than the parent siRNA (t1/2 ~ 6 min).

  11. Molecularly self-assembled nucleic acid nanoparticles for targeted in vivo siRNA delivery.

    PubMed

    Lee, Hyukjin; Lytton-Jean, Abigail K R; Chen, Yi; Love, Kevin T; Park, Angela I; Karagiannis, Emmanouil D; Sehgal, Alfica; Querbes, William; Zurenko, Christopher S; Jayaraman, Muthusamy; Peng, Chang G; Charisse, Klaus; Borodovsky, Anna; Manoharan, Muthiah; Donahoe, Jessica S; Truelove, Jessica; Nahrendorf, Matthias; Langer, Robert; Anderson, Daniel G

    2012-06-03

    Nanoparticles are used for delivering therapeutics into cells. However, size, shape, surface chemistry and the presentation of targeting ligands on the surface of nanoparticles can affect circulation half-life and biodistribution, cell-specific internalization, excretion, toxicity and efficacy. A variety of materials have been explored for delivering small interfering RNAs (siRNAs)--a therapeutic agent that suppresses the expression of targeted genes. However, conventional delivery nanoparticles such as liposomes and polymeric systems are heterogeneous in size, composition and surface chemistry, and this can lead to suboptimal performance, a lack of tissue specificity and potential toxicity. Here, we show that self-assembled DNA tetrahedral nanoparticles with a well-defined size can deliver siRNAs into cells and silence target genes in tumours. Monodisperse nanoparticles are prepared through the self-assembly of complementary DNA strands. Because the DNA strands are easily programmable, the size of the nanoparticles and the spatial orientation and density of cancer-targeting ligands (such as peptides and folate) on the nanoparticle surface can be controlled precisely. We show that at least three folate molecules per nanoparticle are required for optimal delivery of the siRNAs into cells and, gene silencing occurs only when the ligands are in the appropriate spatial orientation. In vivo, these nanoparticles showed a longer blood circulation time (t(1/2) ≈ 24.2 min) than the parent siRNA (t(1/2) ≈ 6 min).

  12. Exploiting orientation-selective DEER: determining molecular structure in systems containing Cu(ii) centres.

    PubMed

    Bowen, Alice M; Jones, Michael W; Lovett, Janet E; Gaule, Thembanikosi G; McPherson, Michael J; Dilworth, Jonathan R; Timmel, Christiane R; Harmer, Jeffrey R

    2016-02-17

    Orientation-selective DEER (Double Electron-Electron Resonance) measurements were conducted on a series of rigid and flexible molecules containing Cu(ii) ions. A system with two rigidly held Cu(ii) ions was afforded by the protein homo-dimer of copper amine oxidase from Arthrobacter globiformis. This system provided experimental DEER data between two Cu(ii) ions with a well-defined distance and relative orientation to assess the accuracy of the methodology. Evaluation of orientation-selective DEER (os DEER) on systems with limited flexibility was probed using a series of porphyrin-based Cu(ii)-nitroxide and Cu(ii)-Cu(ii) model systems of well-defined lengths synthesized for this project. Density functional theory was employed to generate molecular models of the conformers for each porphyrin-based Cu(ii) dimer studied. Excellent agreement was found between DEER traces simulated using these computed conformers and the experimental data. The performance of different parameterised structural models in simulating the experimental DEER data was also investigated. The results of this analysis demonstrate the degree to which the DEER data define the relative orientation of the two Cu(ii) ions and highlight the need to choose a parameterised model that captures the essential features of the flexibility (rotational freedom) of the system being studied.

  13. Formation of hierarchical molecular assemblies from poly(oxypropylene)-segmented amido acids under AFM tapping.

    PubMed

    Lin, Jiang-Jen; Tsai, Wei-Cheng; Wang, Chi-He

    2007-04-10

    Molecular self-aligning of amphiphilic molecules into bundles with a constant width of 7-13 nm was observed under tapping-mode atomic force microscopy (TM-AFM). The requisite amphiphile, a poly(oxypropylene)-trimellitic amido acid sodium salt, is constituted of a symmetric amido acid structure with potential noncovalent forces of ionic charges, hydrogen bonds, pi-pi aromatic stacking, and hydrophobic interactions for intermolecular interaction. The amphiphiles are able to self-align into orderly hierarchical assemblies after simply being dissolved in water and dried under spin-coated evaporation. Under the TM-AFM tapping process, the bundles increased their length from an initial 20 to 600 nm. A sequential TM-AFM scanning and interval heating process was designed to probe the morphological transformations from the molecular bundles to lengthy strips (nearly micrometer scale) and to columns (with 5-7 nm spacing between the parallel strips). The formation of hierarchical arrays via molecular stretching, aligning, and connecting to each other was simultaneously observed and accelerated under the TM-AFM vibration energy. The molecular self-alignment caused by vibrations is envisioned to be a potential methodology for manipulating molecules into assembled templates, sensors, and optoelectronic devices.

  14. Self-assembled molecular wires of discotic liquid crystal formed with the crucial contribution of solvents

    NASA Astrophysics Data System (ADS)

    Park, Ji Hyun; Kim, Kyung Ho; Sosa Vargas, Lydia; Takanishi, Yoichi; Kim, Youn Sang; Yamamoto, Jun; Shimizu, Yo; Park, Yung Woo; Lagerwall, Jan Pf; Scalia, Giusy

    The self-organization of discotic liquid crystal molecules allows the spontaneous formation of well-aligned and tens of micrometer long molecular wires. In this work, we present a study based on hexapentyloxytriphenylene (HAT5) to investigate the molecular wire formation mechanism induced by solvents with selected characteristics, including chemical structure, boiling point, vapor pressure, and surface tension. The aromaticity in solvents such as toluene and benzene promotes the assembly into very long and thin wires entering into the structures, while chain-like solvents promotes more disordered structures. This finding allows a guided formation of different nanostructures from the same type of molecules just by choosing the type of solvent according to the need. Raman spectroscopy supports the idea of an active role of aromatic solvents entering into the molecular structure between discotic molecules with good quality intermolecular order. Highly aligned molecular wires bridging electrodes on SiO2 substrate show a clearly higher electrical conductivity compared to disorganized aggregates and bare HAT5. DLS and X-ray scattering were also used to investigate films and solutions. We finally discuss possible mechanisms behind the hierarchical assembly of the nanowires. NRF.

  15. Self-assembled molecular magnets on patterned silicon substrates: bridging bio-molecules with nanoelectronics.

    PubMed

    Chang, Chia-Ching; Sun, Kien Wen; Lee, Shang-Fan; Kan, Lou-Sing

    2007-04-01

    The paper reports the methods of preparing molecular magnets and patterning of the molecules on a semiconductor surface. A highly magnetically aligned metallothionein containing Mn and Cd (Mn,Cd-MT-2) is first synthesized, and the molecules are then placed into nanopores prepared on silicon (001) surfaces using electron beam lithography and reactive ion-etching techniques. We have observed the self-assemble growth of the MT molecules on the patterned Si surface such that the MT molecules have grown into rod or ring type three-dimensional nanostructures, depending on the patterned nanostructures on the surface. We also provide scanning electron microscopy, atomic force microscopy, and magnetic force microscope studies of the molecular nanostructures. This engineered molecule shows molecular magnetization and is biocompatible with conventional semiconductors. These features make Mn,Cd-MT-2 a good candidate for biological applications and sensing sources of new nanodevices. Using molecular self-assembly and topographical patterning of the semiconductor substrate, we can close the gap between bio-molecules and nanoelectronics built into the semiconductor chip.

  16. Oriented cube-on-cube nanocrystal assembly of SrTiO3 tubules.

    PubMed

    Zagar, Kristina; Recnik, Aleksander; Ajayan, Pulickel M; Ceh, Miran

    2010-09-17

    We report on an unusual crystallization phenomenon that results in the self-assembly of sub-micron tubules of crystalline SrTiO(3). The deposition of the tubular structures was done in the pores of anodized aluminum oxide templates by the electrophoretic deposition of SrTiO(3) sols and subsequent annealing. Homogeneous nucleation inside the pores produces a critical number of crystallites leading to their self-organization when the nanocrystals reach sizes that equal the mean free distances between the nuclei. Due to steric constraints the crystals start to organize in order to most efficiently fill the available surface of the pore walls. This process leads to the formation of domains containing a large number of idiomorphic SrTiO(3) nano-cubes that are self-aligned into almost perfect cube-on-cube and cube-to-wall registry, which makes up the walls of the tubules. The described mechanism shows the ability of nanocrystals with well defined morphologies to adapt spatial constraints and self-organize into desired geometries.

  17. Composite film polarizer based on the oriented assembly of electrospun nanofibers

    NASA Astrophysics Data System (ADS)

    Hu, Zhongliang; Ma, Zhijun; Peng, Mingying; He, Xin; Zhang, Hang; Li, Yang; Qiu, Jianrong

    2016-04-01

    Polarizers are widely applied in antiglare glasses, planner displays, photography filters and optical communications, etc. In this investigation, we propose a new strategy for the preparation of a flexible film polarizer based on the electrospinning technique. An aligned assembly of polyvinyl acetate (PVA) nanofibers was electrospun and collected by a fast-rotating drum, then soaked in polymethyl methacrylate (PMMA) solution and dried thoroughly to obtain a transparent PVA-PMMA composite film polarizer. The morphology, structure and optical performance of the PVA nanofibers and the film polarizers were characterized with a scanning electron microscope, UV-vis-IR spectrometer and polarized Raman spectra, etc. The PVA-PMMA film polarizer demonstrated efficient polarizing activity toward visible and near-infrared light, while keeping fair transparency in the range of 400-1400 nm. Due to the protection from the hydrophobic PMMA matrix, the PVA-PMMA film polarizers show high moisture resistance, making it applicable in a humid environment. Considering the scalability and versatility of the strategy employed here, the PVA-PMMA film polarizer prepared could replace the conventional film polarizers in a wide range of applications.

  18. Composite film polarizer based on the oriented assembly of electrospun nanofibers.

    PubMed

    Hu, Zhongliang; Ma, Zhijun; Peng, Mingying; He, Xin; Zhang, Hang; Li, Yang; Qiu, Jianrong

    2016-04-01

    Polarizers are widely applied in antiglare glasses, planner displays, photography filters and optical communications, etc. In this investigation, we propose a new strategy for the preparation of a flexible film polarizer based on the electrospinning technique. An aligned assembly of polyvinyl acetate (PVA) nanofibers was electrospun and collected by a fast-rotating drum, then soaked in polymethyl methacrylate (PMMA) solution and dried thoroughly to obtain a transparent PVA-PMMA composite film polarizer. The morphology, structure and optical performance of the PVA nanofibers and the film polarizers were characterized with a scanning electron microscope, UV-vis-IR spectrometer and polarized Raman spectra, etc. The PVA-PMMA film polarizer demonstrated efficient polarizing activity toward visible and near-infrared light, while keeping fair transparency in the range of 400-1400 nm. Due to the protection from the hydrophobic PMMA matrix, the PVA-PMMA film polarizers show high moisture resistance, making it applicable in a humid environment. Considering the scalability and versatility of the strategy employed here, the PVA-PMMA film polarizer prepared could replace the conventional film polarizers in a wide range of applications.

  19. Orientated binding of photosynthetic reaction centers on gold using Ni-NTA self-assembled monolayers.

    PubMed

    Trammell, Scott A; Wang, Leyu; Zullo, Joseph M; Shashidhar, Ranganathan; Lebedev, Nikolai

    2004-07-15

    Coupling of photosynthetic reaction centers (RCs) with inorganic surfaces is attractive for the identification of the mechanisms of interprotein electron transfer (ET) and for possible applications in construction of photo- and chemosensors. Here we show that RCs from Rhodobacter sphaeroides can be immobilized on gold surfaces with the RC primary donor looking towards the substrate by using a genetically engineered poly-histidine tag (His(7)) at the C-terminal end of the M-subunit and a Ni-NTA terminated self-assembled monolayer (SAM). In the presence of an electron acceptor, ubiquinone-10, illumination of this RC electrode generates a cathodic photocurrent. The action spectrum of the photocurrent coincides with the absorption spectrum of RC and the photocurrent decreases in response to the herbicide, atrazine, confirming that the RC is the primary source of the photoresponse. Disruption of the Ni-NTA-RC bond by imidazole leads to about 80% reduction of the photocurrent indicating that most of the photoactive protein is specifically bound to the electrode through the linker.

  20. Mesoporous carbons with self-assembled surfaces of defined crystal orientation.

    PubMed

    Jian, Kengqing; Truong, Trung C; Hoffman, Wesley P; Hurt, Robert H

    2008-02-01

    The design of carbon sorbents traditionally focuses on the control of pore structure and the number and type of surface functional groups. The present paper explores the potential of also controlling the carbon crystal structure, or graphene layer orientation, in the immediate vicinity of the internal surfaces. We hypothesize that this crystal structure influences the properties of the carbon surfaces and affects the number and type of active sites for functionalization. Here a series of mesoporous carbons are fabricated by capillary infiltration of mesophase pitch (naphthalene homopolymer) into a series of controlled pore glass templates of different characteristic pore size followed by carbonization and template etching. The liquid crystalline mesogens are known to adopt perpendicular alignment (anchoring) at liquid/silica interfaces, which after carbonization lead to a high concentration of graphene edge sites at the inner surfaces. These surfaces are shown to have elevated chemical reactivity, and the pore structures are shown to be consistent with predictions of a quantitative model based on the negative replica concept. Overall, the use of mesophase pitch for templated mesoporous carbons allows systematic and simultaneous control of both pore structure and interfacial crystal structure through the well-defined rules of liquid crystal surface anchoring.

  1. Mesoporous carbons with self-assembled surfaces of defined crystal orientation

    PubMed Central

    Jian, Kengqing; Truong, Trung C.; Hoffman, Wesley P.; Hurt, Robert H.

    2008-01-01

    The design of carbon sorbents traditionally focuses on the control of pore structure and the number and type of surface functional groups. The present paper explores the potential of also controlling the carbon crystal structure, or graphene layer orientation, in the immediate vicinity of the internal surfaces. We hypothesize that this crystal structure influences the properties of the carbon surfaces and affects the number and type of active sites for functionalization. Here a series of mesoporous carbons are fabricated by capillary infiltration of mesophase pitch (naphthalene homopolymer) into a series of controlled pore glass templates of different characteristic pore size followed by carbonization and template etching. The liquid crystalline mesogens are known to adopt perpendicular alignment (anchoring) at liquid/silica interfaces, which after carbonization lead to a high concentration of graphene edge sites at the inner surfaces. These surfaces are shown to have elevated chemical reactivity, and the pore structures are shown to be consistent with predictions of a quantitative model based on the negative replica concept. Overall, the use of mesophase pitch for templated mesoporous carbons allows systematic and simultaneous control of both pore structure and interfacial crystal structure through the well-defined rules of liquid crystal surface anchoring. PMID:19190761

  2. CCM3/PDCD10 stabilizes GCKIII proteins to promote Golgi assembly and cell orientation.

    PubMed

    Fidalgo, Miguel; Fraile, María; Pires, Ana; Force, Thomas; Pombo, Celia; Zalvide, Juan

    2010-04-15

    Mutations in CCM3/PDCD10 result in cerebral cavernous malformations (CCMs), a major cause of cerebral hemorrhage. Despite intense interest in CCMs, very little is known about the function of CCM3. Here, we report that CCM3 is located on the Golgi apparatus, forming a complex with proteins of the germinal center kinase III (GCKIII) family and GM130, a Golgi-resident protein. Cells depleted of CCM3 show a disassembled Golgi apparatus. Furthermore, in wound-healing assays, CCM3-depleted cells cannot reorient the Golgi and centrosome properly, and demonstrate impaired migration. Golgi disassembly after either depletion of CCM3 or dissociation of CCM3 from the GM130-GCKIII complex is the result of destabilization of GCKIII proteins and dephosphorylation of their substrate, 14-3-3zeta. Significantly, the phenotype induced by CCM3 depletion can be reverted by expression of wild-type CCM3, but not by disease-associated mutants. Our findings suggest that Golgi dysfunction and the ensuing abnormalities of cell orientation and migration resulting from CCM3 mutations contribute to CCM pathogenesis.

  3. Coarse-Grained Molecular Simulation of the Hierarchical Self-Assembly of π-Conjugated Optoelectronic Peptides

    DOE PAGES

    Mansbach, Rachael A.; Ferguson, Andrew L.

    2017-02-10

    Self-assembled aggregates of peptides containing aromatic groups possess optoelectronic properties that make them attractive targets for the fabrication of biocompatible electronics. Molecular-level understanding of how the microscopic peptide chemistry influences the properties of the aggregates is vital for rational peptide design. We construct a coarse-grained model of Asp-Phe-Ala-Gly-OPV3-Gly-Ala-Phe-Asp (DFAG-OPV3-GAFD) peptides containing OPV3 (distyrylbenzene) π-conjugated cores explicitly parameterized against all-atom calculations and perform molecular dynamics simulations of the self-assembly of hundreds of molecules over hundreds of nanoseconds. We observe a hierarchical assembly mechanism wherein ~2-8 peptides assemble into stacks with aligned aromatic cores that subsequently form elliptical aggregates and ultimately amore » branched network with a fractal dimensionality of ~1.5. The assembly dynamics are well described by a Smoluchowski coagulation process for which we extract rate constants from the molecular simulations to both furnish insight into the microscopic assembly kinetics and extrapolate our aggregation predictions to time and length scales beyond the reach of molecular simulation. Lastly, this study presents new molecular-level understanding of the morphology and dynamics of the spontaneous self-assembly of DFAG-OPV3-GAFD peptides and establishes a systematic protocol to develop coarse-grained models of optoelectronic peptides for the exploration and design of π-conjugated peptides with tunable optoelectronic properties.« less

  4. Quantitative analysis of molecular orientation in chlorophyll a Langmuir monolayer: a polarized visible reflection spectroscopic study.

    PubMed Central

    Okamura, E; Hasegawa, T; Umemura, J

    1995-01-01

    Polarized visible reflection spectra of a chlorophyll a (Chl.a) Langmuir monolayer have been measured in situ at various surface pressures. By applying Hansen's optics to the three-phase plane-bounded system (air/Chl.a monolayer/water), the negative reflection absorbances observed were reproduced satisfactorily by the theoretical calculation. Molecular orientation of Chl.a in the monolayer was evaluated quantitatively as a function of surface pressure, from the reflection absorbance of p- and s-polarized spectra of the red (Qy) band. It has been proven that Chl.a molecules in the monolayer form aggregates (islands) even in the low surface pressure region and that during the monolayer compression the molecules are gradually reorganized from inhomogeneous islands to ordered structures, with the chromophores oriented on the average vertically to the water surface. Images FIGURE 1 PMID:8519968

  5. Mapping molecular conformation and orientation of polyimide surfaces for homeotropicliquid crystal alignment by nonlinear optical spectroscopy

    NASA Astrophysics Data System (ADS)

    Oh-E, Masahito; Yokoyama, Hiroshi; Kim, Doseok

    2004-05-01

    Surface-specific sum-frequency vibrational spectroscopy and second-harmonic generation were used to study the structures of polyimide (PI) surfaces for homeotropic liquid crystal (LC) alignment and the molecular orientation of LC adsobates on these surfaces. The imide ring was perpendicular to the surface with one of CO bonds protruding out of the surface and the other pointing into the bulk rather than flat on the surface. The ester CO bond in the side chain was sticking out of the surface with a tilt angle of about 45° 55° from the surface normal, indicating that the rigid side chain core was, more or less, along the surface normal. The part of alkyl chain on the top of the side chain followed the orientation of the side chain core and protruded out of the surface with some gauche defects. The cyano biphenyl LC molecules were adsorbed on the PI preferentially with the terminal cyano group facing the PI surface.

  6. Mapping molecular orientation in dry and wet Nephila clavipes dragline spider silk

    NASA Astrophysics Data System (ADS)

    Lefèvre, Thierry; Pézolet, Michel; Cooper, Glyn; Hernández Cruz, Daniel; West, Marcia M.; Obst, Martin; Hitchcock, Adam P.; Karunakaran, Chithra; Kaznatcheev, Konstantine

    2009-09-01

    The alignment of β-sheets within spider dragline silk fibers is an important factor in their tensile strength and extensibility. We are using linear dichroism of the C 1s → π*amide transition measured using scanning transmission X-ray microscopy (STXM) to generate quantitative maps of the orientation parameters with 30 nm spatial resolution. Here we have extended these measurements from dry samples to samples with partial or full hydration. A device for monitoring and controlling the humidity of a sample in the STXM is described and used to measure the effect of saturated humidity on a section of N. clavipes dragline spider silk. The microstructure and distributions of molecular orientation change considerably with hydration in ways consistent with the supercontraction observed in free standing dragline spider silk. The STXM results are compared to infrared and Raman microscopy results.

  7. Molecular dynamics simulations of the orientation properties of cytochrome c on the surface of single-walled carbon nanotubes.

    PubMed

    Zhang, Bing; Xu, Jia; Mo, Shu-Fan; Yao, Jian-Xi; Dai, Song-Yuan

    2016-12-01

    Electron transfer between cytochrome c (Cytc) and electrodes can be influenced greatly by the orientation of protein on the surface of the electrodes. In the present study, different initial orientations of Cytc on the surface of five types of single-walled carbon nanotubes (SWNTs), with different diameters and chirality, were constructed. Properties of the orientations of proteins on the surface of these tubes were first investigated through molecular dynamics simulations. It was shown that variations in SWNT diameter do not significantly affect the orientation; however, the chirality of the SWNTs is crucial to the orientation of the heme embedded in Cytc, and the orientation of the protein can consequently be influenced by the heme orientation. A new electron pathway between Cytc and SWNT, which hopefully benefits electron transfer efficiency, has also been proposed. This study promises to provide theoretical guidance for the rational design of bio-sensors or bio-fuel cells by using Cytc-decorated carbon nanotube electrodes.

  8. Electrostatically self-assembled polyoxometalates on molecular-dye-functionalized diamond.

    PubMed

    Zhong, Yu Lin; Ng, Wibowo; Yang, Jia-Xiang; Loh, Kian Ping

    2009-12-30

    We have successfully immobilized phosphotungstic acid (PTA), a polyoxometalate, on the surface of boron-doped diamond (BDD) surface through electrostatic self-assembly of PTA on pyridinium dye-functionalized-BDD. The inorganic/organic bilayer structure on BDD is found to exhibit fast surface-confined reversible electron transfer. The molecular dye-grafted BDD can undergo controllable electrical stripping and regeneration of PTA which can be useful for electronics or sensing applications. Furthermore, we have demonstrated the use of PTA as a molecular switch in which the direction of photocurrent from diamond to methyl viologen is reversed by the surface bound PTA. Robust photocurrent converter based on such molecular system-diamond platform can operate in corrosive medium which is not tolerated by indium tin oxide electrodes.

  9. Enhanced self-assembly for the solubilization of cholesterol in molecular solvent/ionic liquid mixtures.

    PubMed

    Jin, Wenbin; Ke, Yuqi; Liu, Xianxian; Yang, Qiwei; Bao, Zongbi; Su, Baogen; Ren, Qilong; Yang, Yiwen; Xing, Huabin

    2017-04-07

    The development of new solvents combining greatly enhanced solubility for sparingly soluble compounds and good kinetic properties is challenging. In this study, we constructed a family of new molecular solvent/ionic liquid (IL) mixtures with amphiphilic, anionic functional long-chain carboxylate ionic liquids (LCC-ILs) as a key component for the solubilization of sparingly soluble compounds, using cholesterol as a model solute. Polarized optical microscopy (POM), wide angle X-ray diffraction (WAXD), Fourier-transform infrared (FTIR) spectra and (1)H NMR showed that ordered mesoscopic structures, such as liquid crystals (LCs), were formed when cholesterol was dissolved in the mixtures, presenting a self-assembly induced dissolution mechanism driven by H-bond interaction and van der Waals forces in the mixtures. A synergistic effect between the molecular solvents and LCC-ILs was revealed, which contributed to enhanced solute-solvent self-assembly in dissolution over pure LCC-ILs and thus elevated solubility. Additionally, the effect of IL concentration, solvent type and anionic alkyl-chain length on self-assembly and solubility was investigated. These mixtures showed unparalleled solubilities for cholesterol, while maintaining a low viscosity. The quantitative solubilities (g g(-1)) of cholesterol were as high as 0.70, 0.84 and 0.82, respectively, at 25 °C in ethyl acetate/[P4444][C15H31COO] (50 wt%), n-heptane/[P4444][C15H31COO] (40 wt%) and ethyl acetate/[P4444][C17H35COO] (50 wt%) mixtures, which were the highest solubilities of cholesterol ever reported, six- to 980-fold higher than traditional molecular solvents and even one- to seven-fold higher compared to pure LCC-ILs. These results demonstrated the considerable potential of molecular solvent/LCC-ILs mixtures as promising solvents for solubilization and advanced separation processes.

  10. Molecular self-assembly on graphene on SiO2 and h-BN substrates.

    PubMed

    Järvinen, Päivi; Hämäläinen, Sampsa K; Banerjee, Kaustuv; Häkkinen, Pasi; Ijäs, Mari; Harju, Ari; Liljeroth, Peter

    2013-07-10

    One of the suggested ways of controlling the electronic properties of graphene is to establish a periodic potential modulation on it, which could be achieved by self-assembly of ordered molecular lattices. We have studied the self-assembly of cobalt phthalocyanines (CoPc) on chemical vapor deposition (CVD) grown graphene transferred onto silicon dioxide (SiO2) and hexagonal boron nitride (h-BN) substrates. Our scanning tunneling microscopy (STM) experiments show that, on both substrates, CoPc forms a square lattice. However, on SiO2, the domain size is limited by the corrugation of graphene, whereas on h-BN, single domain extends over entire terraces of the underlying h-BN. Additionally, scanning tunneling spectroscopy (STS) measurements suggest that CoPc molecules are doped by the substrate and that the level of doping varies from molecule to molecule. This variation is larger on graphene on SiO2 than on h-BN. These results suggest that graphene on h-BN is an ideal substrate for the study of molecular self-assembly toward controlling the electronic properties of graphene by engineered potential landscapes.

  11. Solvent-free, molecular-level modeling of self-assembling amphiphiles in water

    NASA Astrophysics Data System (ADS)

    Dey, Somajit; Saha, Jayashree

    2017-02-01

    Aggregation mesophases of self-assembling amphiphiles in water are highly important in the context of biology (biomembranes), therapy (liposomes), industry (polymer surfactants), and condensed-matter physics (lyotropic liquid crystals). Besides helping to increase fundamental understanding of collective molecular behavior, simulations of these lyotropic phases are pivotal to technological and medical developments such as smart drug carriers for gene therapy. Implicit-solvent, coarse-grained, low resolution modeling with a simple pair potential is the key to realizing the larger length and time scales associated with such mesoscopic phenomena during a computer simulation. Modeling amphiphiles by directed, soft, ellipsoidal cores interacting via a computationally simple yet tunable anisotropic pair potential, we have come to such a single-site model amphiphile that can rapidly self-assemble to give diverse lyotropic phases (such as fluid bilayers, micelles, etc.) without requiring the explicit incorporation of solvent particles. The model directly represents a tunable packing parameter that manifests in the spontaneous curvature of the amphiphile aggregates. Besides the all-important hydrophobic interaction, the hydration force is also treated implicitly. Thanks to the efficient solvent-free molecular-level coarse graining, this model is suitable for generic mesoscale studies of phenomena such as self-assembly, amphiphile mixing, domain formation, fusion, elasticity, etc., in amphiphile aggregates.

  12. Electrolyte-induced reorganization of SDS self-assembly on graphene: a molecular simulation study.

    PubMed

    Liu, Shuyan; Wu, Bin; Yang, Xiaoning

    2014-04-23

    A molecular dynamics simulation was conducted to study the structure and morphology of sodium dodecyl sulfate (SDS) surfactants adsorbed on a nanoscale graphene nanostructure in the presence of an electrolyte. The self-assembly structure can be reorganized by the electrolyte-induced effect. An increase in the ionic strength of the added electrolyte can enhance the stretching of adsorbed surfactants toward the bulk aqueous phase and make headgroups assemble densely, leading to a more compact structure of the SDS/graphene composite. The change in the self-assembly structure is attributed to the accumulation/condensation of electrolyte cations near the surfactant aggregate, consequently screening the electrostatic repulsion between charged headgroups. The role of the electrolyte revealed here provides direct microscopic evidence or an explanation of the reported experiments in the electrolyte tuning of the interfacial structure of a surfactant aggregate on the surface of carbon nanoparticles. Additionally, the buoyant density of the SDS/graphene assembly has been computed. With an increase in the ionic strength of the electrolyte, the buoyant density of the SDS/graphene composite rises. The interfacial accumulation of electrolytes provides an important contribution to the density enhancement. The study will be valuable for the dispersion and application of graphene nanomaterials.

  13. Folding coupled with assembly in split green fluorescent proteins studied by structure-based molecular simulations.

    PubMed

    Ito, Mashiho; Ozawa, Takeaki; Takada, Shoji

    2013-10-24

    Split green fluorescent protein (GFP) is a powerful tool for imaging of protein-protein interactions in living cells, but molecular mechanisms of the folding and the assembly of split GFPs are poorly understood. Here, using a simple Go model that is based on the energy landscape theory, we performed comprehensive folding simulations of six split GFPs with different split points. Of the six, the fluorescence recovery was reported in four but not in the other two. In the simulations, we found that when the complete folding and assembly were observed, the N-terminal fragment always folded earlier than the C-terminal fragment. The in silico folding rates of the split GFPs were larger for the four split GFPs that the fluorescence recovery was reported in literature. The stability of standalone N-terminal fragments were well-correlated with the folding rates of split GFPs. These suggest that the efficient folding and assembly of split GFPs are realized when the N-terminal fragment folds spontaneously with the central α-helix as a nucleation core and that the C-terminal fragment folding is coupled to the assembly to the preformed N-terminal fragment.

  14. Synthetic Molecular Machines for Active Self-Assembly: Prototype Algorithms, Designs, and Experimental Study

    NASA Astrophysics Data System (ADS)

    Dabby, Nadine L.

    Computer science and electrical engineering have been the great success story of the twentieth century. The neat modularity and mapping of a language onto circuits has led to robots on Mars, desktop computers and smartphones. But these devices are not yet able to do some of the things that life takes for granted: repair a scratch, reproduce, regenerate, or grow exponentially fast--all while remaining functional. This thesis explores and develops algorithms, molecular implementations, and theoretical proofs in the context of "active self-assembly" of molecular systems. The long-term vision of active self-assembly is the theoretical and physical implementation of materials that are composed of reconfigurable units with the programmability and adaptability of biology's numerous molecular machines. En route to this goal, we must first find a way to overcome the memory limitations of molecular systems, and to discover the limits of complexity that can be achieved with individual molecules. One of the main thrusts in molecular programming is to use computer science as a tool for figuring out what can be achieved. While molecular systems that are Turing-complete have been demonstrated [Winfree, 1996], these systems still cannot achieve some of the feats biology has achieved. One might think that because a system is Turing-complete, capable of computing "anything," that it can do any arbitrary task. But while it can simulate any digital computational problem, there are many behaviors that are not "computations" in a classical sense, and cannot be directly implemented. Examples include exponential growth and molecular motion relative to a surface. Passive self-assembly systems cannot implement these behaviors because (a) molecular motion relative to a surface requires a source of fuel that is external to the system, and (b) passive systems are too slow to assemble exponentially-fast-growing structures. We call these behaviors "energetically incomplete" programmable

  15. Molecular self-assembly of amphiphilic cyclic phosphoryl gemcitabine with different N-fatty acyl tails and enhanced anticancer effects of the self-assembled nanostructures.

    PubMed

    Jin, Yiguang; Wang, Shan; Yao, Weishang; Du, Lina

    2015-09-01

    Molecular self-assembly of nucleosides is important, and the self-assembled nanostructures may be used for drug delivery and targeting. Gemcitabine (GEM) is an important anticancer nucleoside analog though deactivation and multi-drug resistance frequently happen. Four N-fatty acyl derivatives of cyclic phosphoryl GEM were prepared based on the theory of self-assembled drug delivery systems and the HepDirect prodrug technique wherein the prodrug could be degraded by the cytochrome P450 isozymes in hepatocytes to release active drugs. They are cyclic phosphoryl N-octyl gemcitabine (CPOG), cyclic phosphoryl N-dodecanoyl gemcitabine (CPDG), cyclic phosphoryl N-hexadecanoyl gemcitabine (CPHG), and cyclic phosphoryl N-octadecanoyl gemcitabine (CPODG). Their amphiphilicity and self-assembling property were explored. The self-assembled nanostructures of them were prepared and simulated. The in vitro anticancer activities of the nanostructures were investigated. The derivatives formed the Langmuir monolayers at the air/water interface, though their surface pressure-molecular area isotherms were different with dependency of the length of lipid chains. The derivatives self-assembled into the vesicular or rice-like nanostructures based on the hydrophobic interaction between lipid chains when injected into water, in accordance with the results of computer simulation. The nanostructures showed higher anticancer effects on HepG2 cells than GEM. The nanostructures are promising anticancer nanomedicines.

  16. DNA self-assembly-driven positioning of molecular components on nanopatterned surfaces

    NASA Astrophysics Data System (ADS)

    Szymonik, M.; Davies, A. G.; Wälti, C.

    2016-09-01

    We present a method for the specific, spatially targeted attachment of DNA molecules to lithographically patterned gold surfaces—demonstrated by bridging DNA strands across nanogap electrode structures. An alkanethiol self-assembled monolayer was employed as a molecular resist, which could be selectively removed via electrochemical desorption, allowing the binding of thiolated DNA anchoring oligonucleotides to each electrode. After introducing a bridging DNA molecule with single-stranded ends complementary to the electrode-tethered anchoring oligonucleotides, the positioning of the DNA molecule across the electrode gap, driven by self-assembly, occurred autonomously. This demonstrates control of molecule positioning with resolution limited only by the underlying patterned structure, does not require any alignment, is carried out entirely under biologically compatible conditions, and is scalable.

  17. From Fullerene-Polymer to All-Polymer Solar Cells: The Importance of Molecular Packing, Orientation, and Morphology Control.

    PubMed

    Kang, Hyunbum; Lee, Wonho; Oh, Jiho; Kim, Taesu; Lee, Changyeon; Kim, Bumjoon J

    2016-11-15

    All-polymer solar cells (all-PSCs), consisting of conjugated polymers as both electron donor (PD) and acceptor (PA), have recently attracted great attention. Remarkable progress has been achieved during the past few years, with power conversion efficiencies (PCEs) now approaching 8%. In this Account, we first discuss the major advantages of all-PSCs over fullerene-polymer solar cells (fullerene-PSCs): (i) high light absorption and chemical tunability of PA, which affords simultaneous enhancement of both the short-circuit current density (JSC) and the open-circuit voltage (VOC), and (ii) superior long-term stability (in particular, thermal and mechanical stability) of all-PSCs due to entangled long PA chains. In the second part of this Account, we discuss the device operation mechanism of all-PSCs and recognize the major challenges that need to be addressed in optimizing the performance of all-PSCs. The major difference between all-PSCs and fullerene-PSCs originates from the molecular structures and interactions, i.e., the electron transport ability in all-PSCs is significantly affected by the packing geometry of two-dimensional PA chains relative to the electrodes (e.g., face-on or edge-on orientation), whereas spherically shaped fullerene acceptors can facilitate isotropic electron transport properties in fullerene-PSCs. Moreover, the crystalline packing structures of PD and PA at the PD-PA interface greatly affect their free charge carrier generation efficiencies. The design of PA polymers (e.g., main backbone, side chain, and molecular weight) should therefore take account of optimizing three major aspects in all-PSCs: (1) the electron transport ability of PA, (2) the molecular packing structure and orientation of PA, and (3) the blend morphology. First, control of the backbone and side-chain structures, as well as the molecular weight, is critical for generating strong intermolecular assembly of PA and its network, thus enabling high electron transport ability

  18. Molecular transport through nanoporous silicon nitride membranes produced from self-assembling block copolymers.

    PubMed

    Montagne, Franck; Blondiaux, Nicolas; Bojko, Alexandre; Pugin, Raphaël

    2012-09-28

    To achieve fast and selective molecular filtration, membrane materials must ideally exhibit a thin porous skin and a high density of pores with a narrow size distribution. Here, we report the fabrication of nanoporous silicon nitride membranes (NSiMs) at the full wafer scale using a versatile process combining block copolymer (BCP) self-assembly and conventional photolithography/etching techniques. In our method, self-assembled BCP micelles are used as templates for creating sub-100 nm nanopores in a thin low-stress silicon nitride layer, which is then released from the underlying silicon wafer by etching. The process yields 100 nm thick free-standing NSiMs of various lateral dimensions (up to a few mm(2)). We show that the membranes exhibit a high pore density, while still retaining excellent mechanical strength. Permeation experiments reveal that the molecular transport rate across NSiMs is up to 16-fold faster than that of commercial polymeric membranes. Moreover, using dextran molecules of various molecular weights, we also demonstrate that size-based separation can be achieved with a very good selectivity. These new silicon nanosieves offer a relevant technological alternative to commercially available ultra- and microfiltration membranes for conducting high resolution biomolecular separations at small scales.

  19. Synthesis and Self-Assembly Behaviors of Polyhedral Oligomeric Silsesquioxane Based Giant Molecular Shape Amphiphiles

    NASA Astrophysics Data System (ADS)

    Yue, Kan; Yu, Xinfei; Liu, Chang; Zhang, Wen-Bin; Cheng, Stephen

    2013-03-01

    Recently, our group has focus on the synthesis and characterization of novel giant molecular shape amphiphiles (GMSAs) based on functionalized molecular nanoparticles (MNPs), such as polyhedral oligomeric silsesquioxane (POSS), tethered with polymeric tails. A general synthetic method via the combination of sequential ?click? reactions has been developed and several model GMSAs with various tail lengths and distinct molecular topologies, which can be referred as the ?giant surfactants?, ?giant lipids?, ?giant gemini surfactants?, and ?giant bolaform surfactants? etc., have been demonstrated. Studies on their self-assembly behaviors in the bulk have revealed the formation of different ordered mesophase structures with feature sizes around 10 nanometers, which have been investigated in detail by small angle X-ray scattering (SAXS) technique and transmission electron microscopy (TEM). These findings have general implications on understanding the underlying principles of self-assembly behaviors of GMSAs, and might have potential applications in nano-patterning technology. This work is supported by NSF (DMR-0906898) and the Joint-Hope Foundation.

  20. Molecular basis of cooperativity in pH-triggered supramolecular self-assembly

    NASA Astrophysics Data System (ADS)

    Li, Yang; Zhao, Tian; Wang, Chensu; Lin, Zhiqiang; Huang, Gang; Sumer, Baran D.; Gao, Jinming

    2016-10-01

    Supramolecular self-assembly offers a powerful strategy to produce high-performance, stimuli-responsive nanomaterials. However, lack of molecular understanding of stimulated responses frequently hampers our ability to rationally design nanomaterials with sharp responses. Here we elucidated the molecular pathway of pH-triggered supramolecular self-assembly of a series of ultra-pH sensitive (UPS) block copolymers. Hydrophobic micellization drove divergent proton distribution in either highly protonated unimer or neutral micelle states along the majority of the titration coordinate unlike conventional small molecular or polymeric bases. This all-or-nothing two-state solution is a hallmark of positive cooperativity. Integrated modelling and experimental validation yielded a Hill coefficient of 51 in pH cooperativity for a representative UPS block copolymer, by far the largest reported in the literature. These data suggest hydrophobic micellization and resulting positive cooperativity offer a versatile strategy to convert responsive nanomaterials into binary on/off switchable systems for chemical and biological sensing, as demonstrated in an additional anion sensing model.

  1. Molecular basis of cooperativity in pH-triggered supramolecular self-assembly

    PubMed Central

    Li, Yang; Zhao, Tian; Wang, Chensu; Lin, Zhiqiang; Huang, Gang; Sumer, Baran D.; Gao, Jinming

    2016-01-01

    Supramolecular self-assembly offers a powerful strategy to produce high-performance, stimuli-responsive nanomaterials. However, lack of molecular understanding of stimulated responses frequently hampers our ability to rationally design nanomaterials with sharp responses. Here we elucidated the molecular pathway of pH-triggered supramolecular self-assembly of a series of ultra-pH sensitive (UPS) block copolymers. Hydrophobic micellization drove divergent proton distribution in either highly protonated unimer or neutral micelle states along the majority of the titration coordinate unlike conventional small molecular or polymeric bases. This all-or-nothing two-state solution is a hallmark of positive cooperativity. Integrated modelling and experimental validation yielded a Hill coefficient of 51 in pH cooperativity for a representative UPS block copolymer, by far the largest reported in the literature. These data suggest hydrophobic micellization and resulting positive cooperativity offer a versatile strategy to convert responsive nanomaterials into binary on/off switchable systems for chemical and biological sensing, as demonstrated in an additional anion sensing model. PMID:27786266

  2. Capturing the embryonic stages of self-assembly - design rules for molecular computation.

    PubMed

    Nirmalraj, Peter N; Thompson, Damien; Riel, Heike E

    2015-05-11

    The drive towards organic computing is gaining momentum. Interestingly, the building blocks for such architectures is based on molecular ensembles extending from nucleic acids to synthetic molecules. Advancement in this direction requires devising precise nanoscopic experiments and model calculations to decipher the mechanisms governing the integration of a large number of molecules over time at room-temperature. Here, we report on ultrahigh-resolution scanning tunnelling microscopic measurements to register the motion of molecules in the absence of external stimulus in liquid medium. We observe the collective behavior of individual molecules within a swarm which constantly iterate their position to attain an energetically favourable site. Our approach provides a consistent pathway to register molecular self-assembly in sequential steps from visualising thermodynamically driven repair of defects up until the formation of a stable two-dimensional configuration. These elemental findings on molecular surface dynamics, self-repair and intermolecular kinetic pathways rationalised by atom-scale simulations can be explored for developing new models in algorithmic self-assembly to realisation of evolvable hardware.

  3. Capturing the embryonic stages of self-assembly - design rules for molecular computation

    PubMed Central

    Nirmalraj, Peter N.; Thompson, Damien; Riel, Heike E.

    2015-01-01

    The drive towards organic computing is gaining momentum. Interestingly, the building blocks for such architectures is based on molecular ensembles extending from nucleic acids to synthetic molecules. Advancement in this direction requires devising precise nanoscopic experiments and model calculations to decipher the mechanisms governing the integration of a large number of molecules over time at room-temperature. Here, we report on ultrahigh-resolution scanning tunnelling microscopic measurements to register the motion of molecules in the absence of external stimulus in liquid medium. We observe the collective behavior of individual molecules within a swarm which constantly iterate their position to attain an energetically favourable site. Our approach provides a consistent pathway to register molecular self-assembly in sequential steps from visualising thermodynamically driven repair of defects up until the formation of a stable two-dimensional configuration. These elemental findings on molecular surface dynamics, self-repair and intermolecular kinetic pathways rationalised by atom-scale simulations can be explored for developing new models in algorithmic self-assembly to realisation of evolvable hardware. PMID:25960364

  4. Molecular self-assembly in substituted alanine derivatives: XRD, Hirshfeld surfaces and DFT studies

    NASA Astrophysics Data System (ADS)

    Rajalakshmi, Periasamy; Srinivasan, Navaneethakrishnan; Sivaraman, Gandhi; Razak, Ibrahim Abdul; Rosli, Mohd Mustaqim; Krishnakumar, Rajaputi Venkatraman

    2014-06-01

    The molecular assemblage in the crystal structures of three modified chiral amino acids, two of which are isomeric D- and L-pairs boc-L-benzothienylalanine (BLA), boc-D-benzothienylalanine (BDA) and the other boc-D-naphthylalanine (NDA) differing from this pair very slightly in the chemical modification introduced, is accurately described. The aggregation of amino acid molecules is similar in all the crystals and may be described as a twisted double helical ladder in which two complementary long helical chains formed through O-H⋯O hydrogen bonds are interconnected through the characteristic head-to-tail N-H⋯O hydrogen bonds. Thus the molecular aggregation enabled through classical hydrogen bonds may be regarded as a mimic of the characteristic double helical structure of DNA. Also, precise structural information involving these amino acid molecules with lower symmetry exhibiting higher trigonal symmetry in their self-assembly is expected to throw light on the nature and strength of intermolecular interactions and their role in self-assembly of molecular aggregates, which are crucial in developing new or at least supplement existing crystal engineering strategies. Single crystal X-ray analysis and their electronic structures were calculated at the DFT level with a detailed analysis of Hirshfeld surfaces and fingerprint plots facilitating a comparison of intermolecular interactions in building different supramolecular architectures.

  5. Lipoate-based imprinted self-assembled molecular thin films for biosensor applications.

    PubMed

    Tappura, Kirsi; Vikholm-Lundin, Inger; Albers, Willem M

    2007-01-15

    Lipoate derivatives were used for the formation of imprinted self-assembled molecular thin films for the recognition of morphine. A large collection of lipoate derivatives was screened by molecular dynamics simulations in various solvents. A set of ligands showing favourable interactions with morphine in aqueous environment was selected for synthesis. Morphine-imprinted layers were then produced on gold substrates in mixed monolayers with morphine added as the template. The binding of ligands and morphine to gold, as well as the association/dissociation of morphine to the formed layers were studied with Surface Plasmon Resonance. Imprinted factors were highly variable and were dependent on ligand/morphine mixing ratio, lipoate derivative and monolayer preparation method. The imprinted factors were as high as 100 and 600 for one of the ligands. The results show that the simulations are able to provide correct information of the relative strengths of the molecular interactions between the ligand and morphine molecules in different solutions. The liquid phase simulations are, however, not able to predict the imprinted factors (i.e. distinguish between specific and non-specific binding), because the specificity is not formed before self-assembly on the surface.

  6. NH3 molecular doping of silicon nanowires grown along the [112], [110], [001], and [111] orientations

    PubMed Central

    2012-01-01

    The possibility that an adsorbed molecule could provide shallow electronic states that could be thermally excited has received less attention than substitutional impurities and could potentially have a high impact in the doping of silicon nanowires (SiNWs). We show that molecular-based ex-situ doping, where NH3 is adsorbed at the sidewall of the SiNW, can be an alternative path to n-type doping. By means of first-principle electronic structure calculations, we show that NH3 is a shallow donor regardless of the growth orientation of the SiNWs. Also, we discuss quantum confinement and its relation with the depth of the NH3 doping state, showing that the widening of the bandgap makes the molecular donor level deeper, thus more difficult to activate. PMID:22709657

  7. EFFECTS OF MAGNETIC FIELD STRENGTH AND ORIENTATION ON MOLECULAR CLOUD FORMATION

    SciTech Connect

    Heitsch, Fabian; Hartmann, Lee W.; Stone, James M.

    2009-04-10

    We present a set of numerical simulations addressing the effects of magnetic field strength and orientation on the flow-driven formation of molecular clouds. Fields perpendicular to the flows sweeping up the cloud can efficiently prevent the formation of massive clouds but permit the buildup of cold, diffuse filaments. Fields aligned with the flows lead to substantial clouds, whose degree of fragmentation and turbulence strongly depends on the background field strength. Adding a random field component leads to a 'selection effect' for molecular cloud formation: high column densities are only reached at locations where the field component perpendicular to the flows is vanishing. Searching for signatures of colliding flows should focus on the diffuse, warm gas, since the cold gas phase making up the cloud will have lost the information about the original flow direction because the magnetic fields redistribute the kinetic energy of the inflows.

  8. Self-assembled tetranuclear palladium catalysts that produce high molecular weight linear polyethylene.

    PubMed

    Shen, Zhongliang; Jordan, Richard F

    2010-01-13

    The phosphine-bis-arenesulfonate ligand PPh(2-SO(3)Li-4-Me-Ph)(2) (Li(2)[OPO]) coordinates as a kappa(2)-P,O chelator in Li[(Li-OPO)PdMe(Cl)] (2a) and (Li-OPO)PdMe(L) (L = pyridine (2b); MeOH (2d); 4-(5-nonyl)pyridine) (py', 3)). 2a reacts with AgPF(6) to form {(Li-OPO)PdMe}(n) (2c). Photolysis of 2d yields {(OPO)Pd}(2) (5) in which the [OPO](2-) ligand coordinates as a kappa(3)-O,P,O pincer. 3 self-assembles into a tetramer in which four (Li-OPO)PdMe(py') units are linked by Li-O bonds that form a central Li(4)S(4)O(12) cage. The Pd centers are equivalent but are spatially separated into two identical pairs. The Pd-Pd distance within each pair is 6.04 A. IR data (upsilon(ArSO(3)(-)) region) suggest that the solid state structures of 2a-c are similar to that of 3. 3 reacts with the cryptand Krypt211 to form [Li(Krypt211)][(OPO)PdMe(py')] (4). 3 is in equilibrium with a monomeric (Li-OPO)PdMe(py') species (3') in solution. 2a-c and 3 produce polyethylene (PE) with high molecular weight and a broad molecular weight distribution, characteristic of multisite catalysis. Under conditions where the tetrameric structure remains substantially intact, the PE contains a substantial high molecular weight fraction, while, under conditions where fragmentation is more extensive, the PE contains a large low molecular weight fraction. These results suggest that the tetrameric assembly gives rise to the high molecular weight polymer. In contrast, the monomeric complex 4, which contains a free pendant sulfonate group that can bind to Pd, oligomerizes ethylene to a Schultz-Flory distribution of C(4)-C(18) oligomers.

  9. Foldectures: 3D Molecular Architectures from Self-Assembly of Peptide Foldamers.

    PubMed

    Yoo, Sung Hyun; Lee, Hee-Seung

    2017-02-13

    The wide range of fascinating supramolecular architectures found in nature, from DNA double helices to giant protein shells, inspires researchers to mimic the diverse shapes and functions of natural systems. Thus, a variety of artificial molecular platforms have been developed by assembling DNA-, peptide-, and protein-based building blocks for medicinal and biological applications. There has also been a significant interest in the research of non-natural oligomers (i.e., foldamers) that fold into well-defined secondary structures analogous to those found in proteins, because the assemblies of foldamers are expected not only to form biomimetic supramolecular architectures that resemble those of nature but also to display unique functions and unprecedented topologies at the same time due to their different folding propensities from those of natural building blocks. Foldamer-based supramolecular architectures have been reported in the form of nanofibers, nanochannels, nanosheets, and finite three-dimensional (3D) shapes. We have developed a new class of crystalline peptidic materials termed "foldectures" (a compound of foldamer and architecture) with unprecedented topological complexity derived from the rapid and nonequilibrium aqueous phase self-assembly of foldamers. In this Account, we discuss the morphological features, molecular packing structures, physical properties, and potential applications of foldectures. Foldectures exhibit well-defined, microscale, homogeneous, and finite structures with unique morphologies such as windmill, tooth, and trigonal bipyramid shapes. The symmetry elements of the morphologies vary with the foldamer building blocks and are retained upon surfactant-assisted shape evolution. Structural characterization by powder X-ray diffraction (PXRD) revealed the molecular packing structures, suggesting how the foldamer building blocks assembled in the 3D structure. The analysis by PXRD showed that intermolecular hydrogen bonding connects

  10. Bistable molecular orientation of a fluorene derivative with an intramolecular charge transfer in a poly(methyl methacrylate) host

    NASA Astrophysics Data System (ADS)

    Apostoluk, Aleksandra; Nunzi, Jean-Michel; Perepichka, Igor F.

    2006-04-01

    The orientation of bistable molecules incorporated in a polymer host is addressed and studied by means of all-optical poling. Molecular reorientation between two stable molecular forms is assigned as the origin of the optically induced second-order nonlinear optical susceptibility. We found a new non-photochromic photo-induced reaction scheme by which efficient all-optical poling is achieved.

  11. Light-dependent magnetic compass orientation in amphibians and insects: candidate receptors and candidate molecular mechanisms.

    PubMed

    Phillips, John B; Jorge, Paulo E; Muheim, Rachel

    2010-04-06

    Magnetic compass orientation by amphibians, and some insects, is mediated by a light-dependent magnetoreception mechanism. Cryptochrome photopigments, best known for their role in circadian rhythms, are proposed to mediate such responses. In this paper, we explore light-dependent properties of magnetic sensing at three levels: (i) behavioural (wavelength-dependent effects of light on magnetic compass orientation), (ii) physiological (photoreceptors/photopigment systems with properties suggesting a role in magnetoreception), and (iii) molecular (cryptochrome-based and non-cryptochrome-based signalling pathways that are compatible with behavioural responses). Our goal is to identify photoreceptors and signalling pathways that are likely to play a specialized role in magnetoreception in order to definitively answer the question of whether the effects of light on magnetic compass orientation are mediated by a light-dependent magnetoreception mechanism, or instead are due to input from a non-light-dependent (e.g. magnetite-based) magnetoreception mechanism that secondarily interacts with other light-dependent processes.

  12. Light-dependent magnetic compass orientation in amphibians and insects: candidate receptors and candidate molecular mechanisms

    PubMed Central

    Phillips, John B.; Jorge, Paulo E.; Muheim, Rachel

    2010-01-01

    Magnetic compass orientation by amphibians, and some insects, is mediated by a light-dependent magnetoreception mechanism. Cryptochrome photopigments, best known for their role in circadian rhythms, are proposed to mediate such responses. In this paper, we explore light-dependent properties of magnetic sensing at three levels: (i) behavioural (wavelength-dependent effects of light on magnetic compass orientation), (ii) physiological (photoreceptors/photopigment systems with properties suggesting a role in magnetoreception), and (iii) molecular (cryptochrome-based and non-cryptochrome-based signalling pathways that are compatible with behavioural responses). Our goal is to identify photoreceptors and signalling pathways that are likely to play a specialized role in magnetoreception in order to definitively answer the question of whether the effects of light on magnetic compass orientation are mediated by a light-dependent magnetoreception mechanism, or instead are due to input from a non-light-dependent (e.g. magnetite-based) magnetoreception mechanism that secondarily interacts with other light-dependent processes. PMID:20124357

  13. Molecular self-assemblies might discriminate the diffusion of chiral molecules.

    PubMed

    Galstian, Tigran; Allahverdyan, Karen

    2015-06-07

    Biological tissue has many self-aligned anisotropic molecular organizations, which are able to undergo reversible orientational deformations and spatially transfer them. At the same time, the majority of drugs and many biologically important molecules contain chiral centers. It is therefore important to understand the factors affecting the diffusion of chiral molecules in such elastic environments. We experimentally study the diffusion of chiral molecules in a nematic liquid crystal host representing the model of biological tissue. The analogy of Cano's quantization effect is observed (due to the gradient of the chiral dopant) and used to estimate the corresponding diffusion coefficients. It is shown that thanks to the collective orientational correlation of host molecules the diffusion of chiral dopants is noticeably reduced (by a factor of ≈1.6) for the case of rigid alignment of host molecules compared to the case when the same matrix is free to adjust that alignment.

  14. Model of self assembled monolayer based molecular diodes made of ferrocenyl-alkanethiols

    NASA Astrophysics Data System (ADS)

    Duche, David; Planchoke, Ujwol; Dang, Florian-Xuan; Le Rouzo, Judikael; Bescond, Marc; Simon, Jean-Jacques; Balaban, Teodor Silviu; Escoubas, Ludovic

    2017-03-01

    There has been significant work investigating the use of self assembled monolayers (SAMs) made of ferrocenyl terminated alkanethiols for realizing molecular diodes, leading to remarkably large forward-to-reverse current rectification ratios. In this study, we use a multiband barrier tunneling model to examine the electrical properties of SAM-based molecular diodes made of HSC9Fc, HSC11Fc, and HSCiFcC13-i (0 ≤ i ≤ 13). Using our simple physical model, we reproduce the experimental data of charge transport across various ferrocenyl substituted alkanethiols performed by Nijhuis, Reus, and Whitesides [J. Am. Chem. Soc. 132, 18386-184016 (2010)] and Yuan et al. [Nat. Commun. 6, 6324 (2015)]. Especially, the model allows predicting the rectification direction in HSCiFcC13-i (0 ≤ i ≤ 13) based molecular diodes depending on the position of the ferrocenyl (Fc) moiety within the molecules. We show that the asymmetry of the barrier length at both sides of the Highest Occupied Molecular Orbital of the ferrocenyl moiety strongly contributes to the rectifying properties of ferrocenyl-alkanethiol based molecular junctions. Furthermore, our results reveal that bound and quasi-bound states play an important role in the charge transport.

  15. Positional isomers of cyanostilbene: two-component molecular assembly and multiple-stimuli responsive luminescence

    PubMed Central

    Fan, Guoling; Yan, Dongpeng

    2014-01-01

    An understanding of the aggregates and properties of positional isomers can not only uncover how a slight difference in molecular structure alter crystal packing and bulk solid-state properties, but also plays an important role in developing new types of molecule-based functional materials. Herein, we report a study of the molecular packing and static/dynamic luminescence properties of three cyanostilbene (CS)-based isomers (CS1, CS2, CS3) within their single- and two-component molecular solids. Changing the positions of the cyano substitutents in the CS isomers has a marked influence on their packing modes and luminescent properties. Moreover, two-component CS-based materials have been constructed, which exhibit tunable conformations and packing fashions, as well as fluorescence properties, which differ from the pristine CS solids. The CS-based two-component molecular materials show solvent-responsive luminescence due to the dynamic disassembly of the samples. Moreover, it was found that the system based on CS2 and octafluoronaphthalene shows reversible photochromic fluorescence upon alternating light illumination and grinding. Such co-assembly procedures provide a facile way to fabricate patterned luminescent film materials. Therefore, this work not only affords new insight into the relationship between isomers and luminescence from molecular and supramolecular perspectives, but provides an effective strategy to develop multiple-stimuli-responsive luminescent materials. PMID:24816686

  16. Positional isomers of cyanostilbene: two-component molecular assembly and multiple-stimuli responsive luminescence

    NASA Astrophysics Data System (ADS)

    Fan, Guoling; Yan, Dongpeng

    2014-05-01

    An understanding of the aggregates and properties of positional isomers can not only uncover how a slight difference in molecular structure alter crystal packing and bulk solid-state properties, but also plays an important role in developing new types of molecule-based functional materials. Herein, we report a study of the molecular packing and static/dynamic luminescence properties of three cyanostilbene (CS)-based isomers (CS1, CS2, CS3) within their single- and two-component molecular solids. Changing the positions of the cyano substitutents in the CS isomers has a marked influence on their packing modes and luminescent properties. Moreover, two-component CS-based materials have been constructed, which exhibit tunable conformations and packing fashions, as well as fluorescence properties, which differ from the pristine CS solids. The CS-based two-component molecular materials show solvent-responsive luminescence due to the dynamic disassembly of the samples. Moreover, it was found that the system based on CS2 and octafluoronaphthalene shows reversible photochromic fluorescence upon alternating light illumination and grinding. Such co-assembly procedures provide a facile way to fabricate patterned luminescent film materials. Therefore, this work not only affords new insight into the relationship between isomers and luminescence from molecular and supramolecular perspectives, but provides an effective strategy to develop multiple-stimuli-responsive luminescent materials.

  17. Molecular dynamics simulations of ferrocene-terminated self-assembled monolayers.

    PubMed

    Goujon, F; Bonal, C; Limoges, B; Malfreyt, P

    2010-05-20

    The present work describes our studies of the Fc(CH(2))(12)S-/C(10)S-Au monolayers to provide a more detailed molecular description. Molecular dynamics simulations of these mixed monolayers are carried out in conditions close to the electrochemical ones. For this purpose, a supporting electrolyte is added (NaClO(4) 1 M) and the electron transfer process is modeled through molecular simulations of ferrocene both in its neutral (initial state) and oxidized form (final state). The heterogeneity of the surface, that is, "clustered " or "isolated" ferrocene moieties, has been considered for the ferrocenylalkylthiolates using the same grafting densities. The structural properties (density profiles and angular distributions) are described in terms of redox induced orientation changes by comparison between the initial and final states. It is established that this orientation change due to the oxidation of the ferrocene to the ferrocenium is mainly observed in the random system, and it is less pronounced in the cluster system. Finally, the energy contributions underline the role played by the supporting electrolyte.

  18. Self assembled molecular monolayers on high surface area materials as molecular getters

    DOEpatents

    King, D.E.; Herdt, G.C.; Czanderna, A.W.

    1997-01-07

    The present invention relates to a gettering material that may be used as a filtration medium to remove pollutants from the environment. The gettering material comprises a high surface area material having a metal surface that chemically bonds n-alkanethiols in an organized manner thereby forming a molecular monolayer over the metal surface. The n-alkanethiols have a free functional group that interacts with the environment thereby binding specific pollutants that may be present. The gettering material may be exposed to streams of air in heating, ventilation, and air conditioning systems or streams of water to remove specific pollutants from either medium. 9 figs.

  19. Self assembled molecular monolayers on high surface area materials as molecular getters

    DOEpatents

    King, David E.; Herdt, Gregory C.; Czanderna, Alvin W.

    1997-01-01

    The present invention relates to a gettering material that may be used as a filtration medium to remove pollutants from the environment. The gettering material comprises a high surface area material having a metal surface that chemically bonds n-alkanethiols in an organized manner thereby forming a molecular monolayer over the metal surface. The n-alkanethiols have a free functional group that interacts with the environment thereby binding specific pollutants that may be present. The gettering material may be exposed to streams of air in heating, ventilation, and air conditioning systems or streams of water to remove specific pollutants from either medium.

  20. Studies of molecular monolayers at air-liquid interfaces by second harmonic generation: question of orientational phase transition

    SciTech Connect

    Rasing, T.; Shen, Y.R.; Kim, M.W.; Grubb, S.; Bock, J.

    1985-06-01

    Insoluble molecular monolayers at gas-liquid interfaces provide an insight to the understanding of surfactants, wetting, microemulsions and membrane structures and offer a possibility to study the rich world of 2-dimensional phase transitions. In the interpretation of the observed properties of these systems various assumptions about the molecular orientation are often made, but so far few clear experimental data exist. In this paper we will show how optical second harmonic generation (SHG) can be used to measure the molecular orientation of monolayers of surfactant molecules at water-air interfaces. By simultaneously measuring the surface pressure versus surface molecular area we can show for the first time that the observed liquid condensed-liquid expanded transition is an orientational phase transition. 7 refs., 4 figs.

  1. The role of molecular dipole orientation in single-molecule fluorescence microscopy and implications for super-resolution imaging.

    PubMed

    Backlund, Mikael P; Lew, Matthew D; Backer, Adam S; Sahl, Steffen J; Moerner, W E

    2014-03-17

    Numerous methods for determining the orientation of single-molecule transition dipole moments from microscopic images of the molecular fluorescence have been developed in recent years. At the same time, techniques that rely on nanometer-level accuracy in the determination of molecular position, such as single-molecule super-resolution imaging, have proven immensely successful in their ability to access unprecedented levels of detail and resolution previously hidden by the optical diffraction limit. However, the level of accuracy in the determination of position is threatened by insufficient treatment of molecular orientation. Here we review a number of methods for measuring molecular orientation using fluorescence microscopy, focusing on approaches that are most compatible with position estimation and single-molecule super-resolution imaging. We highlight recent methods based on quadrated pupil imaging and on double-helix point spread function microscopy and apply them to the study of fluorophore mobility on immunolabeled microtubules.

  2. Cooperative light-induced molecular movements of highly ordered azobenzene self-assembled monolayers.

    PubMed

    Pace, Giuseppina; Ferri, Violetta; Grave, Christian; Elbing, Mark; von Hänisch, Carsten; Zharnikov, Michael; Mayor, Marcel; Rampi, Maria Anita; Samorì, Paolo

    2007-06-12

    Photochromic systems can convert light energy into mechanical energy, thus they can be used as building blocks for the fabrication of prototypes of molecular devices that are based on the photomechanical effect. Hitherto a controlled photochromic switch on surfaces has been achieved either on isolated chromophores or within assemblies of randomly arranged molecules. Here we show by scanning tunneling microscopy imaging the photochemical switching of a new terminally thiolated azobiphenyl rigid rod molecule. Interestingly, the switching of entire molecular 2D crystalline domains is observed, which is ruled by the interactions between nearest neighbors. This observation of azobenzene-based systems displaying collective switching might be of interest for applications in high-density data storage.

  3. Cooperative light-induced molecular movements of highly ordered azobenzene self-assembled monolayers

    PubMed Central

    Pace, Giuseppina; Ferri, Violetta; Grave, Christian; Elbing, Mark; von Hänisch, Carsten; Zharnikov, Michael; Mayor, Marcel; Rampi, Maria Anita; Samorì, Paolo

    2007-01-01

    Photochromic systems can convert light energy into mechanical energy, thus they can be used as building blocks for the fabrication of prototypes of molecular devices that are based on the photomechanical effect. Hitherto a controlled photochromic switch on surfaces has been achieved either on isolated chromophores or within assemblies of randomly arranged molecules. Here we show by scanning tunneling microscopy imaging the photochemical switching of a new terminally thiolated azobiphenyl rigid rod molecule. Interestingly, the switching of entire molecular 2D crystalline domains is observed, which is ruled by the interactions between nearest neighbors. This observation of azobenzene-based systems displaying collective switching might be of interest for applications in high-density data storage. PMID:17535889

  4. Molecular Self-Assembly in a Poorly Screened Environment: F4TCNQ on Graphene/BN

    PubMed Central

    2015-01-01

    We report a scanning tunneling microscopy and noncontact atomic force microscopy study of close-packed 2D islands of tetrafluorotetracyanoquinodimethane (F4TCNQ) molecules at the surface of a graphene layer supported by boron nitride. While F4TCNQ molecules are known to form cohesive 3D solids, the intermolecular interactions that are attractive for F4TCNQ in 3D are repulsive in 2D. Our experimental observation of cohesive molecular behavior for F4TCNQ on graphene is thus unexpected. This self-assembly behavior can be explained by a novel solid formation mechanism that occurs when charged molecules are placed in a poorly screened environment. As negatively charged molecules coalesce, the local work function increases, causing electrons to flow into the coalescing molecular island and increase its cohesive binding energy. PMID:26482218

  5. Molecular dynamics simulations of shock waves in oriented nitromethane single crystals

    NASA Astrophysics Data System (ADS)

    He, Lan; Sewell, Thomas D.; Thompson, Donald L.

    2011-03-01

    The structural relaxation of crystalline nitromethane initially at T = 200 K subjected to moderate (˜15 GPa) supported shocks on the (100), (010), and (001) crystal planes has been studied using microcanonical molecular dynamics with the nonreactive Sorescu-Rice-Thompson force field [D. C. Sorescu, B. M. Rice, and D. L. Thompson, J. Phys. Chem. B 104, 8406 (2000)]. The responses to the shocks were determined by monitoring the mass density, the intermolecular, intramolecular, and total temperatures (average kinetic energies), the partitioning of total kinetic energy among Cartesian directions, the radial distribution functions for directions perpendicular to those of shock propagation, the mean-square displacements in directions perpendicular to those of shock propagation, and the time dependence of molecular rotational relaxation as a function of time. The results show that the mechanical response of crystalline nitromethane strongly depends on the orientation of the shock wave. Shocks propagating along [100] and [001] result in translational disordering in some crystal planes but not in others, a phenomenon that we refer to as plane-specific disordering; whereas for [010] the shock-induced stresses are relieved by a complicated structural rearrangement that leads to a paracrystalline structure. The plane-specific translational disordering is more complete by the end of the simulations (˜6 ps) for shock propagation along [001] than along [100]. Transient excitation of the intermolecular degrees of freedom occurs in the immediate vicinity of the shock front for all three orientations; the effect is most pronounced for the [010] shock. In all three cases excitation of molecular vibrations occurs more slowly than the intermolecular excitation. The intermolecular and intramolecular temperatures are nearly equal by the end of the simulations, with 400-500 K of net shock heating. Results for two-dimensional mean-square molecular center-of-mass displacements, calculated

  6. Molecular Behavior of DNA Origami in Higher-Order Self-Assembly

    PubMed Central

    Li, Zhe; Liu, Minghui; Wang, Lei; Nangreave, Jeanette; Yan, Hao; Liu, Yan

    2011-01-01

    DNA-based self-assembly is a unique method for achieving higher-order molecular architectures made possible by the fact that DNA is a programmable information-coding polymer. In the past decade, two main types of DNA nanostructures have been developed: branch-shaped DNA tiles with small dimensions (commonly up to ~20 nm) and DNA origami tiles with larger dimensions (up to ~100 nm). Here we aimed to determine the important factors involved in the assembly of DNA origami superstructures. We constructed a new series of rectangular-shaped DNA origami tiles in which parallel DNA helices are arranged in a zigzag pattern when viewed along the DNA helical axis, a design conceived in order to relax an intrinsic global twist found in the original planar, rectangular origami tiles. Self-associating zigzag tiles were found to form linear arrays in both diagonal directions, while planar tiles showed significant growth in only one direction. Although the series of zigzag tiles were designed to promote two-dimensional array formation, one-dimensional linear arrays and tubular structures were observed instead. We discovered that the dimensional aspect ratio of the origami unit tiles and intertile connection design play important roles in determining the final products, as revealed by atomic force microscopy imaging. This study provides insight into the formation of higher-order structures from self-assembling DNA origami tiles, revealing their unique behavior in comparison with conventional DNA tiles having smaller dimensions. PMID:20825190

  7. Molecular Behavior of DNA Origami in Higher-Order Self-Assembly

    SciTech Connect

    Li, Zhe; Liu, Minghui; Lei, Wang; Nangreave, Jeanette; Yan, Hao; Liu, Yan

    2010-09-08

    DNA-based self-assembly is a unique method for achieving higher-order molecular architectures made possible by the fact that DNA is a programmable information-coding polymer. In the past decade, two main types of DNA nanostructures have been developed: branch-shaped DNA tiles with small dimensions (commonly up to ~20 nm) and DNA origami tiles with larger dimensions (up to ~100 nm). Here we aimed to determine the important factors involved in the assembly of DNA origami superstructures. We constructed a new series of rectangular-shaped DNA origami tiles in which parallel DNA helices are arranged in a zigzag pattern when viewed along the DNA helical axis, a design conceived in order to relax an intrinsic global twist found in the original planar, rectangular origami tiles. Self-associating zigzag tiles were found to form linear arrays in both diagonal directions, while planar tiles showed significant growth in only one direction. Although the series of zigzag tiles were designed to promote two-dimensional array formation, one-dimensional linear arrays and tubular structures were observed instead. We discovered that the dimensional aspect ratio of the origami unit tiles and intertile connection design play important roles in determining the final products, as revealed by atomic force microscopy imaging. This study provides insight into the formation of higher-order structures from self-assembling DNA origami tiles, revealing their unique behavior in comparison with conventional DNA tiles having smaller dimensions.

  8. Folding and self-assembly of polypeptides: Dynamics and thermodynamics from molecular simulation

    NASA Astrophysics Data System (ADS)

    Fluitt, Aaron Michael

    Empowered by their exquisite three-dimensional structures, or "folds," proteins carry out biological tasks with high specificity, efficiency, and fidelity. The fold that optimizes biological function represents a stable configuration of the constituent polypeptide molecule(s) under physiological conditions. Proteins and polypeptides are not static, however: battered by thermal motion, they explore a distribution of folds that is determined by the sequence of amino acids, the presence and identity of other molecules, and the thermodynamic conditions. In this dissertation, we apply molecular simulation techniques to the study of two polypeptides that have unusually diffuse distributions of folds under physiological conditions: polyglutamine (polyQ) and islet amyloid polypeptide (IAPP). Neither polyQ nor IAPP adopts a predominant fold in dilute aqueous solution, but at sufficient concentrations, both are prone to self-assemble into stable, periodic, and highly regular aggregate structures known as amyloid. The appearance of amyloid deposits of polyQ in the brain, and of IAPP in the pancreas, are associated with Huntington's disease and type 2 diabetes, respectively. A molecular view of the mechanism(s) by which polyQ and IAPP fold and self-assemble will enhance our understanding of disease pathogenesis, and it has the potential to accelerate the development of therapeutics that target early-stage aggregates. Using molecular simulations with spatial and temporal resolution on the atomic scale, we present analyses of the structural distributions of polyQ and IAPP under various conditions, both in and out of equilibrium. In particular, we examine amyloid fibers of polyQ, the IAPP dimer in solution, and single IAPP fragments at a lipid bilayer. We also benchmark the molecular models, or "force fields," available for such studies, and we introduce a novel simulation algorithm.

  9. Energy level alignment at planar organic heterojunctions: influence of contact doping and molecular orientation.

    PubMed

    Opitz, Andreas

    2017-04-05

    Planar organic heterojunctions are widely used in photovoltaic cells, light-emitting diodes, and bilayer field-effect transistors. The energy level alignment in the devices plays an important role in obtaining the aspired gap arrangement. Additionally, the π-orbital overlap between the involved molecules defines e.g. the charge-separation efficiency in solar cells due to charge-transfer effects. To account for both aspects, direct/inverse photoemission spectroscopy and near edge x-ray absorption fine structure spectroscopy were used to determine the energy level landscape and the molecular orientation at prototypical planar organic heterojunctions. The combined experimental approach results in a comprehensive model for the electronic and morphological characteristics of the interface between the two investigated molecular semiconductors. Following an introduction on heterojunctions used in devices and on energy levels of organic materials, the energy level alignment of planar organic heterojunctions will be discussed. The observed energy landscape is always determined by the individual arrangement between the energy levels of the molecules and the work function of the electrode. This might result in contact doping due to Fermi level pinning at the electrode for donor/acceptor heterojunctions, which also improves the solar cell efficiency. This pinning behaviour can be observed across an unpinned interlayer and results in charge accumulation at the donor/acceptor interface, depending on the transport levels of the respective organic semiconductors. Moreover, molecular orientation will affect the energy levels because of the anisotropy in ionisation energy and electron affinity and is influenced by the structural compatibility of the involved molecules at the heterojunction. High structural compatibility leads to π-orbital stacking between different molecules at a heterojunction, which is of additional interest for photovoltaic active interfaces and for ground

  10. Energy level alignment at planar organic heterojunctions: influence of contact doping and molecular orientation

    NASA Astrophysics Data System (ADS)

    Opitz, Andreas

    2017-04-01

    Planar organic heterojunctions are widely used in photovoltaic cells, light-emitting diodes, and bilayer field-effect transistors. The energy level alignment in the devices plays an important role in obtaining the aspired gap arrangement. Additionally, the π-orbital overlap between the involved molecules defines e.g. the charge-separation efficiency in solar cells due to charge-transfer effects. To account for both aspects, direct/inverse photoemission spectroscopy and near edge x-ray absorption fine structure spectroscopy were used to determine the energy level landscape and the molecular orientation at prototypical planar organic heterojunctions. The combined experimental approach results in a comprehensive model for the electronic and morphological characteristics of the interface between the two investigated molecular semiconductors. Following an introduction on heterojunctions used in devices and on energy levels of organic materials, the energy level alignment of planar organic heterojunctions will be discussed. The observed energy landscape is always determined by the individual arrangement between the energy levels of the molecules and the work function of the electrode. This might result in contact doping due to Fermi level pinning at the electrode for donor/acceptor heterojunctions, which also improves the solar cell efficiency. This pinning behaviour can be observed across an unpinned interlayer and results in charge accumulation at the donor/acceptor interface, depending on the transport levels of the respective organic semiconductors. Moreover, molecular orientation will affect the energy levels because of the anisotropy in ionisation energy and electron affinity and is influenced by the structural compatibility of the involved molecules at the heterojunction. High structural compatibility leads to π-orbital stacking between different molecules at a heterojunction, which is of additional interest for photovoltaic active interfaces and for ground

  11. ESR study of molecular orientation and dynamics of TEMPO derivatives in CLPOT 1D nanochannels.

    PubMed

    Kobayashi, Hirokazu; Furuhashi, Yuta; Nakagawa, Haruka; Asaji, Tetsuo

    2016-08-01

    The molecular orientations and dynamics of 2,2,6,6-tetramethyl-1-piperidinyloxyl (TEMPO) radical derivatives with large substituent groups at the 4-position (4-X-TEMPO) in the organic one-dimensional nanochannels within the nanosized molecular template 2,4,6-tris(4-chlorophenoxy)-1,3,5-triazine (CLPOT) were examined using ESR. The concentrations of guest radicals, including 4-methoxy-TEMPO (MeO-TEMPO) or 4-oxo-TEMPO (TEMPONE), in the CLPOT nanochannels in each inclusion compound (IC) were reduced by co-including 4-substituted-2,2,6,6-tetramethylpiperidine (4-R-TEMP) compounds at a ratio of 1 : 30-1 : 600. At higher temperatures, the guest radicals in each IC underwent anisotropic rotational diffusion in the CLPOT nanochannels. The rotational diffusion activation energy, Ea , associated with MeO-TEMPO or TEMPONE in the CLPOT nanochannels (6-7 kJ mol(-1) ), was independent of the size and type of substituent group and was similar to the Ea values obtained for TEMPO and 4- hydroxy-TEMPO (TEMPOL) in our previous study. However, in the case in which TEMP was used as a guest compound for dilution (spacer), the tilt of the rotational axis to the principal axis system of the g-tensor, and the rotational diffusion correlation time, τR , of each guest radical in the CLPOT nanochannels were different from the case with other 4-R-TEMP. These results indicate the possibility of controlling molecular orientation and dynamics of guest radicals in CLPOT ICs through the appropriate choice of spacer. Copyright © 2016 John Wiley & Sons, Ltd.

  12. Molecular Structure of a Helical ribbon in a Peptide Self-Assembly

    NASA Astrophysics Data System (ADS)

    Hwang, Wonmuk; Marini, Davide; Kamm, Roger D.; Zhang, Shuguang

    2002-03-01

    We have studied the molecular structure of nanometer scale helical ribbons observed during self-assembly of the peptide KFE8 (amino acid sequence: FKFEFKFE) (NanoLetters (2002, in press)). By analyzing the hydrogen bonding patterns between neighboring peptide backbones, we constructed a number of possible β-sheets. Using all possible combinations of these, we built helical ribbons with dimensions close to those found experimentally and performed molecular dynamics simulations to identify the most stable structure. Solvation effects were implemented by the analytic continuum electrostatics (ACE) model developed by Schaefer and Karplus (J. Phys. Chem. 100, 1578 (1996)). By applying electrostatic double layer theory, we incorporated the effect of pH by scaling the amount of charge on the sidechains. Our results suggest that the helical ribbon is comprised of a double β-sheet where the inner and the outer helices have distinct hydrogen bonding patterns. Our approach has general applicability to the study of helices formed by the self-assembly of β-sheet forming peptides with various amino acid sequences.

  13. Assembly and Characterization ofWell-DefinedHigh-Molecular-Weight Poly(p-phenylene) Polymer Brushes

    SciTech Connect

    Chen, Jihua; Dadmun, Mark D; Mays, Jimmy; Messman, Jamie M; Hong, Kunlun; Britt, Phillip F; Sumpter, Bobby G; Alonzo Calderon, Jose E; Kilbey, II, S Michael; Ankner, John Francis; Bredas, Jean-Luc E; Malagoli, Massimo; Deng, Suxiang; Swader, Onome A; Yu, Xiang

    2011-01-01

    The assembly and characterization of well-de ned, end-tethered poly- (p-phenylene) (PPP) brushes having high molecular weight, low polydispersity and high 1,4-stereoregularity are presented. The PPP brushes are formed using a precursor route that relies on either self-assembly or spin coating of high molecular weight (degrees of poly- merizations 54, 146, and 238) end-functionalized poly(1,3-cyclohexadiene) (PCHD) chains from benzene solutions onto silicon or quartz substrates, followed by aromatization of the end-attached PCHD chains on the surface. The approach allows the thickness (grafting density) of the brushes to be easily varied. The dry brushes before and after aromatization are characterized by ellipsometry, atomic force microscopy, grazing angle attenuated total re ectance Fourier transform infrared spectroscopy, and UV-Vis spectros- copy. The properties of the PPP brushes are compared with those of lms made using oligo- paraphenylenes and with ab initio density functional theory simulations of optical proper- ties. Our results suggest conversion to fully aromatized, end-tetheredPPPpolymerbrusheshaving eective conjugation lengths of 5 phenyl units.

  14. Assembly and Characterization of Well Defined High Molecular Weight Poly(p-phenylene) Polymer Brushes

    SciTech Connect

    Alonzo Calderon, Jose E; Kilbey, II, S Michael; Ankner, John Francis; Britt, Phillip F; Chen, Jihua; Dadmun, Mark D; Deng, Suxiang; Hong, Kunlun; Mays, Jimmy; Messman, Jamie M; Sumpter, Bobby; Swader, Onome A; Yu, Xiang; Bredas, Jean-Luc E; Malagoli, Massimo

    2011-01-01

    The assembly and characterization of well-defined, end-tethered poly(p-phenylene) (PPP) brushes having high molecular weight, low polydispersity and high 1,4-stereoregularity are presented. The PPP brushes are formed using a precursor route that relies on either self-assembly or spin coating of high molecular weight (degrees of polymerizations 54, 146, and 238) end-functionalized poly(1,3-cyclohexadiene) (PCHD) chains from benzene solutions onto silicon or quartz substrates, followed by aromatization of the end-attached PCHD chains on the surface. The approach allows the thickness (grafting density) of the brushes to be easily varied. The dry brushes before and after aromatization are characterized by ellipsometry, atomic force microscopy, grazing angle attenuated total reflectance Fourier transform infrared spectroscopy, and UV-Vis spectroscopy. The properties of the PPP brushes are compared with those of films made using oligo-paraphenylenes and with ab initio density functional theory simulations of optical properties. Our results suggest conversion to fully aromatized, end-tethered PPP polymer brushes having effective conjugation lengths of 5 phenyl units.

  15. Self-assembled monolayer-functionalized half-metallic manganite for molecular spintronics.

    PubMed

    Tatay, Sergio; Barraud, Clément; Galbiati, Marta; Seneor, Pierre; Mattana, Richard; Bouzehouane, Karim; Deranlot, Cyrile; Jacquet, Eric; Forment-Aliaga, Alicia; Jegou, Pascale; Fert, Albert; Petroff, Frédéric

    2012-10-23

    (La,Sr)MnO(3) manganite (LSMO) has emerged as the standard ferromagnetic electrode in organic spintronic devices due to its highly spin-polarized character and air stability. Whereas organic semiconductors and polymers have been mainly envisaged to propagate spin information, self-assembled monolayers (SAMs) have been overlooked and should be considered as promising materials for molecular engineering of spintronic devices. Surprisingly, up to now the first key step of SAM grafting protocols over LSMO surface thin films is still missing. We report the grafting of dodecyl (C12P) and octadecyl (C18P) phosphonic acids over the LSMO half-metallic oxide. Alkylphosphonic acids form ordered self-assembled monolayers, with the phosphonic group coordinated to the surface and alkyl chains tilted from the surface vertical by 43° (C12P) and 27° (C18P). We have electrically characterized these SAMs in nanodevices and found that they act as tunnel barriers, opening the door toward the integration of alkylphosphonic acid//LSMO SAMs into future molecular/organic spintronic devices such as spin OLEDs.

  16. Molecular details of the yeast frataxin-Isu1 interaction during mitochondrial Fe-S cluster assembly

    PubMed Central

    Cook, Jeremy D.; Kondapalli, Kalyan C.; Rawat, Swati; Childs, William C.; Murugesan, Yogapriya; Dancis, Andrew; Stemmler, Timothy L.

    2010-01-01

    Frataxin, a conserved nuclear encoded mitochondrial protein, plays a direct role in iron-sulfur cluster biosynthesis within the ISC assembly pathway. Humans with frataxin deficiency have Friedreich’s ataxia, a neurodegenerative disorder characterized by mitochondrial iron overload and disruption in Fe-S cluster synthesis. Biochemical and genetic studies have shown frataxin interacts with the iron-sulfur cluster assembly scaffold protein (in yeast, there are two: Isu1 and Isu2), indicating frataxin plays a direct role in cluster assembly, possibly by serving as an iron chaperone n the assembly pathway. Here we provide molecular details of how yeast frataxin (Yfh1) interacts with Isu1 as a structural module to better understand the multiprotein complex assembly that completes Fe-S cluster assembly; this complex also includes the cysteine desulfurase (Nfs1 in yeast) and the accessory protein (Isd11), together in the mitochondria. Thermodynamic binding parameters for protein partner and iron binding were measured for the yeast orthologs using isothermal titration calorimetry (ITC). Nuclear magnetic resonance spectroscopy was used to provide the molecular details to understand how Yfh1 interacts with Isu1. X-ray absorption studies were used to electronically and structurally characterize how iron is transferred to Isu1 and then incorporated into a Fe-S cluster. These results were combined with previously published data to generate a structural model for how the Fe-S cluster protein assembly complex can come together to accomplish Fe-S cluster assembly. PMID:20815377

  17. Correlating the magic numbers of inorganic nanomolecular assemblies with a {Pd84} molecular-ring Rosetta Stone

    PubMed Central

    Xu, Feng; Miras, Haralampos N.; Scullion, Rachel A.; Long, De-Liang; Thiel, Johannes; Cronin, Leroy

    2012-01-01

    Molecular self-assembly has often been suggested as the ultimate route for the bottom-up construction of building blocks atom-by-atom for functional nanotechnology, yet structural design or prediction of nanomolecular assemblies is still far from reach. Whereas nature uses complex machinery such as the ribosome, chemists use painstakingly engineered step-by-step approaches to build complex molecules but the size and complexity of such molecules, not to mention the accessible yields, can be limited. Herein we present the discovery of a palladium oxometalate {Pd84}-ring cluster 3.3 nm in diameter; [Pd84O42(OAc)28(PO4)42]70- ({Pd84} ≡ {Pd12}7) that is formed in water just by mixing two reagents at room temperature, giving crystals of the compound in just a few days. The structure of the {Pd84}-ring has sevenfold symmetry, comprises 196 building blocks, and we also show, using mass spectrometry, that a large library of other related nanostructures is present in solution. Finally, by analysis of the symmetry and the building block library that construct the {Pd84} we show that the correlation of the symmetry, subunit number, and overall cluster nuclearity can be used as a “Rosetta Stone” to rationalize the “magic numbers” defining a number of other systems. This is because the discovery of {Pd84} allows the relationship between seemingly unrelated families of molecular inorganic nanosystems to be decoded from the overall cluster magic-number nuclearity, to the symmetry and building blocks that define such structures allowing the prediction of other members of these nanocluster families. PMID:22753516

  18. Correlating the magic numbers of inorganic nanomolecular assemblies with a {Pd84} molecular-ring Rosetta Stone.

    PubMed

    Xu, Feng; Miras, Haralampos N; Scullion, Rachel A; Long, De-Liang; Thiel, Johannes; Cronin, Leroy

    2012-07-17

    Molecular self-assembly has often been suggested as the ultimate route for the bottom-up construction of building blocks atom-by-atom for functional nanotechnology, yet structural design or prediction of nanomolecular assemblies is still far from reach. Whereas nature uses complex machinery such as the ribosome, chemists use painstakingly engineered step-by-step approaches to build complex molecules but the size and complexity of such molecules, not to mention the accessible yields, can be limited. Herein we present the discovery of a palladium oxometalate {Pd(84)}-ring cluster 3.3 nm in diameter; [Pd(84)O(42)(OAc)(28)(PO(4))(42)](70-) ({Pd(84)} ≡ {Pd(12)}(7)) that is formed in water just by mixing two reagents at room temperature, giving crystals of the compound in just a few days. The structure of the {Pd(84)}-ring has sevenfold symmetry, comprises 196 building blocks, and we also show, using mass spectrometry, that a large library of other related nanostructures is present in solution. Finally, by analysis of the symmetry and the building block library that construct the {Pd(84)} we show that the correlation of the symmetry, subunit number, and overall cluster nuclearity can be used as a "Rosetta Stone" to rationalize the "magic numbers" defining a number of other systems. This is because the discovery of {Pd(84)} allows the relationship between seemingly unrelated families of molecular inorganic nanosystems to be decoded from the overall cluster magic-number nuclearity, to the symmetry and building blocks that define such structures allowing the prediction of other members of these nanocluster families.

  19. Molecular organization, localization and orientation of antifungal antibiotic amphotericin B in a single lipid bilayer

    PubMed Central

    Grudzinski, Wojciech; Sagan, Joanna; Welc, Renata; Luchowski, Rafal; Gruszecki, Wieslaw I.

    2016-01-01

    Amphotericin B is a popular antifungal antibiotic, a gold standard in treatment of systemic mycotic infections, due to its high effectiveness. On the other hand, applicability of the drug is limited by its considerable toxicity to patients. Biomembranes are a primary target of physiological activity of amphotericin B and both the pharmacologically desired and toxic side effects of the drug relay on its molecular organization in the lipid phase. In the present work, molecular organization, localization and orientation of amphotericin B, in a single lipid bilayer system, was analysed simultaneously, thanks to application of a confocal fluorescence lifetime imaging microscopy of giant unilamellar vesicles. The results show that the presence of sterols, in the lipid phase, promotes formation of supramolecular structures of amphotericin B and their penetration into the membrane hydrophobic core. The fact that such an effect is substantially less pronounced in the case of cholesterol than ergosterol, the sterol of fungal membranes, provides molecular insight into the selectivity of the drug. PMID:27620838

  20. Molecular orientation of copper phthalocyanine thin films on different monolayers of fullerene on SiO{sub 2} or highly oriented pyrolytic graphite

    SciTech Connect

    Wang, Chenggong; Wang, Congcong; Liu, Xiaoliang; Xu, Xumei; Li, Youzhen; Xie, Fangyan; Gao, Yongli

    2015-03-23

    The interface electronic structures of copper phthalocyanine (CuPc) have been studied using ultraviolet photoemission spectroscopy as different monolayers of C{sub 60} were inserted between CuPc and a SiO{sub 2} or highly ordered pyrolytic graphite (HOPG) substrate. The results show that CuPc has standing up configuration with one monolayer of C{sub 60} insertion on SiO{sub 2} while lying down on HOPG, indicating that the insertion layer propagates the CuPc-substrate interaction. Meanwhile, CuPc on more than one monolayers of C{sub 60} on different substrates show that the substrate orientation effect quickly vanished. Our study elucidates intriguing molecular interactions that manipulate molecular orientation and donor-acceptor energy level alignment.

  1. Reduction-Triggered Self-Assembly of Nanoscale Molybdenum Oxide Molecular Clusters

    DOE PAGES

    Yin, Panchao; Wu, Bin; Li, Tao; ...

    2016-07-26

    A 2.9 nm molybdenum oxide cluster {Mo132} (Formula: [MoVI72MoV60O372(CH3COO)30(H2O)72]42-) can be obtained by reducing ammonium molybdate with hydrazine sulfate in weakly acidic CH3COOH/CH3COO- buffers. This reaction has been monitored by time-resolved UV-Vis, 1H-NMR, small angle X-ray/neutron scattering, and X-ray absorption near edge structure spectroscopy. The growth of {Mo132} cluster shows a typical sigmoid curve, suggesting a multi-step assembly mechanism for this reaction. The reaction starts with a lag phase period when partial MoVI centers of molybdate precursors are reduced to form {MoV2(acetate)} structures under the coordination effect of the acetate groups. Once the concentration of {MoV2(acetate)} reaches a critical value,more » it triggers the assembly of MoV and MoVI species into {Mo132} clusters. Parameters such as the type and amount of reducing agent, the pH, the type of cation, and the type of organic ligand in the reaction buffer, have been studied for the roles they play in the formation of the target clusters.Understanding the formation mechanism of giant molecular clusters is essential for rational design and synthesis of cluster-based nanomaterials with required morphologies and functionalities. Here, typical synthetic reactions of a 2.9 nm spherical molybdenum oxide cluster, {Mo132} (formula: [MoVI72MoV60O372(CH3COO)30(H2O)72]42), with systematically varied reaction parameters have been fully explored to determine the morphologies and concentration of products, reduction of metal centers, and chemical environments of the organic ligands. The growth of these clusters shows a typical sigmoid curve, suggesting a general multistep self-assembly mechanism for the formation of giant molecular clusters. The reaction starts with a lag phase period when partial MoVI centers of molybdate precursors are reduced to form {MoV2(acetate)} structures under the coordination effect of the acetate groups. Once the concentration of {MoV2(acetate)} reaches a

  2. HackaMol: An Object-Oriented Modern Perl Library for Molecular Hacking on Multiple Scales

    DOE PAGES

    Riccardi, Demian M.; Parks, Jerry M.; Johs, Alexander; ...

    2015-03-20

    HackaMol is an open source, object-oriented toolkit written in Modern Perl that organizes atoms within molecules and provides chemically intuitive attributes and methods. The library consists of two components: HackaMol, the core that contains classes for storing and manipulating molecular information, and HackaMol::X, the extensions that use the core. We tested the core; it is well-documented and easy to install across computational platforms. Our goal for the extensions is to provide a more flexible space for researchers to develop and share new methods. In this application note, we provide a description of the core classes and two extensions: HackaMol::X::Calculator, anmore » abstract calculator that uses code references to generalize interfaces with external programs, and HackaMol::X::Vina, a structured class that provides an interface with the AutoDock Vina docking program.« less

  3. HackaMol: An Object-Oriented Modern Perl Library for Molecular Hacking on Multiple Scales

    SciTech Connect

    Riccardi, Demian M.; Parks, Jerry M.; Johs, Alexander; Smith, Jeremy C.

    2015-03-20

    HackaMol is an open source, object-oriented toolkit written in Modern Perl that organizes atoms within molecules and provides chemically intuitive attributes and methods. The library consists of two components: HackaMol, the core that contains classes for storing and manipulating molecular information, and HackaMol::X, the extensions that use the core. We tested the core; it is well-documented and easy to install across computational platforms. Our goal for the extensions is to provide a more flexible space for researchers to develop and share new methods. In this application note, we provide a description of the core classes and two extensions: HackaMol::X::Calculator, an abstract calculator that uses code references to generalize interfaces with external programs, and HackaMol::X::Vina, a structured class that provides an interface with the AutoDock Vina docking program.

  4. Enhanced Raman scattering at dielectric surfaces. 2. Molecular orientations from polarized surface Raman scattering

    SciTech Connect

    Walls, D.J.; Bohn, P.W. )

    1990-03-08

    The ability to obtain polarized Raman scattering for monolayer adsorbates deposited on oxide covered noble-metal island film structures has been closely examined. The relationship of the relative intensities of the in-plane enhanced electric field components to the depolarization ratios of the totally symmetric Raman vibrational modes of p-nitrobenzoic acid and phthalazine was found to indicate a constant depolarization of the in-plane electric field components induced by the island film particles themselves. With this information and with polarized Raman scattering information from nontotally symmetric phthalazine vibrations, we report a quantitative determination of the average surface molecular orientation of phthalazine monolayers at sputtered SiO{sub 2} surfaces.

  5. Molecular parameters and olfaction in the oriental fruit fly Dacus dorsalis

    PubMed Central

    Metcalf, Robert L.; Metcalf, Esther R.; Mitchell, W. C.

    1981-01-01

    The methyl eugenol receptor of the male oriental fruit fly (Dacus dorsalis) has been further characterized by evaluating the role of the linear free energy parameters ∏ and σ in the depolarization of the receptor by 37 substituted 3,4-dimethoxybenzenes. There was a strong positive correlation between the hydrophobic character of the primary substituent and intense odor and a positive correlation between the electron donating property of the primary substituent and intense odor. Maximum odor intensity was also associated with substituents of 3 atomic diameters and was improved by a center of unsaturation. Preference tests suggest that this simple and versatile odor receptor can serve as a model for investigation of molecular interactions between receptors and odorant molecules. PMID:16593048

  6. HackaMol: An Object-Oriented Modern Perl Library for Molecular Hacking on Multiple Scales.

    PubMed

    Riccardi, Demian; Parks, Jerry M; Johs, Alexander; Smith, Jeremy C

    2015-04-27

    HackaMol is an open source, object-oriented toolkit written in Modern Perl that organizes atoms within molecules and provides chemically intuitive attributes and methods. The library consists of two components: HackaMol, the core that contains classes for storing and manipulating molecular information, and HackaMol::X, the extensions that use the core. The core is well-tested, well-documented, and easy to install across computational platforms. The goal of the extensions is to provide a more flexible space for researchers to develop and share new methods. In this application note, we provide a description of the core classes and two extensions: HackaMol::X::Calculator, an abstract calculator that uses code references to generalize interfaces with external programs, and HackaMol::X::Vina, a structured class that provides an interface with the AutoDock Vina docking program.

  7. Lightweight object oriented structure analysis: tools for building tools to analyze molecular dynamics simulations.

    PubMed

    Romo, Tod D; Leioatts, Nicholas; Grossfield, Alan

    2014-12-15

    LOOS (Lightweight Object Oriented Structure-analysis) is a C++ library designed to facilitate making novel tools for analyzing molecular dynamics simulations by abstracting out the repetitive tasks, allowing developers to focus on the scientifically relevant part of the problem. LOOS supports input using the native file formats of most common biomolecular simulation packages, including CHARMM, NAMD, Amber, Tinker, and Gromacs. A dynamic atom selection language based on the C expression syntax is included and is easily accessible to the tool-writer. In addition, LOOS is bundled with over 140 prebuilt tools, including suites of tools for analyzing simulation convergence, three-dimensional histograms, and elastic network models. Through modern C++ design, LOOS is both simple to develop with (requiring knowledge of only four core classes and a few utility functions) and is easily extensible. A python interface to the core classes is also provided, further facilitating tool development.

  8. Single orientation graphene synthesized on iridium thin films grown by molecular beam epitaxy

    NASA Astrophysics Data System (ADS)

    Dangwal Pandey, A.; Krausert, K.; Franz, D.; Grânäs, E.; Shayduk, R.; Müller, P.; Keller, T. F.; Noei, H.; Vonk, V.; Stierle, A.

    2016-08-01

    Heteroepitaxial iridium thin films were deposited on (0001) sapphire substrates by means of molecular beam epitaxy, and subsequently, one monolayer of graphene was synthesized by chemical vapor deposition. The influence of the growth parameters on the quality of the Ir films, as well as of graphene, was investigated systematically by means of low energy electron diffraction, x-ray reflectivity, x-ray diffraction, Auger electron spectroscopy, scanning electron microscopy, and atomic force microscopy. Our study reveals (111) oriented iridium films with high crystalline quality and extremely low surface roughness, on which the formation of large-area epitaxial graphene is achieved. The presence of defects, like dislocations, twins, and 30° rotated domains in the iridium films is also discussed. The coverage of graphene was found to be influenced by the presence of 30° rotated domains in the Ir films. Low iridium deposition rates suppress these rotated domains and an almost complete coverage of graphene was obtained. This synthesis route yields inexpensive, air-stable, and large-area graphene with a well-defined orientation, making it accessible to a wider community of researchers for numerous experiments or applications, including those which use destructive analysis techniques or irreversible processes. Moreover, this approach can be used to tune the structural quality of graphene, allowing a systematic study of the influence of defects in various processes like intercalation below graphene.

  9. Deformation Localization in Molecular Layers Constrained between Self-Assembled Au Nanoparticles.

    PubMed

    Copie, G; Biaye, M; Diesinger, H; Melin, T; Krzeminski, C; Cleri, F

    2017-03-14

    The localized deformation of molecular monolayers constrained between the spherical surfaces of Au nanoparticles is studied by means of molecular dynamics simulations. Alkyl or polyethylene glycol long-chain molecules were homogeneously distributed over the curved Au surface, pushed against each other by repeated cycles of force relaxation and constant-volume equilibration at temperatures increasing from 50 to 300 K before being slowly quenched to near-zero temperature. Plots of minimum configurational energy can be obtained as a function of the nanoparticle distance, according to different directions of approach; therefore, such simulations describe a range of deformations, from perfectly uniaxial compression to a combination of compression and shear. Despite the relative rigidity of molecular backbones, the deformation is always found to be localized at the interface between the opposing molecular monolayers. We find that shorter ligands can be more densely packed on the surface but do no interdigitate upon compression; they respond to the applied force by bending and twisting, thus changing their conformation while remaining disjointed. On the contrary, longer ligands attain lower surface densities and can interprenetrate when the nanoparticles are compressed against each other; such molecules remain rather straight and benefit from the increased overlap to maximize the adhesion by dispersion forces. The apparent Young's and shear moduli of a dense nanostructure, composed of a triangular arrangement of identical MUDA-decorated Au nanoparticles, are found to be smaller than estimates indirectly deduced by atomic-force experiments but quite close to previous computer simulations of molecular monolayers on flat surfaces and of bulk nanoparticle assemblies.

  10. Molecular orientation distributions during injection molding of liquid crystalline polymers: Ex situ investigation of partially filled moldings

    SciTech Connect

    Fang, Jun; Burghardt, Wesley R.; Bubeck, Robert A.

    2013-01-10

    The development of molecular orientation in thermotropic liquid crystalline polymers (TLCPs) during injection molding has been investigated using two-dimensional wide-angle X-ray scattering coordinated with numerical computations employing the Larson-Doi polydomain model. Orientation distributions were measured in 'short shot' moldings to characterize structural evolution prior to completion of mold filling, in both thin and thick rectangular plaques. Distinct orientation patterns are observed near the filling front. In particular, strong extension at the melt front results in nearly transverse molecular alignment. Far away from the flow front shear competes with extension to produce complex spatial distributions of orientation. The relative influence of shear is stronger in the thin plaque, producing orientation along the filling direction. Exploiting an analogy between the Larson-Doi model and a fiber orientation model, we test the ability of process simulation tools to predict TLCP orientation distributions during molding. Substantial discrepancies between model predictions and experimental measurements are found near the flow front in partially filled short shots, attributed to the limits of the Hele-Shaw approximation used in the computations. Much of the flow front effect is however 'washed out' by subsequent shear flow as mold filling progresses, leading to improved agreement between experiment and corresponding numerical predictions.

  11. Self-assembly of single-walled carbon nanotubes into multiwalled carbon nanotubes in water: molecular dynamics simulations.

    PubMed

    Zou, Jian; Ji, Baohua; Feng, Xi-Qiao; Gao, Huajian

    2006-03-01

    We report discoveries from a series of molecular dynamics simulations that single-walled carbon nanotubes, with different diameters, lengths, and chiralities, can coaxially self-assemble into multiwalled carbon nanotubes in water via spontaneous insertion of smaller tubes into larger ones. The assembly process is tube-size-dependent, and the driving force is primarily the intertube van der Waals interactions. The simulations also suggest that a multiwalled carbon nanotube may be separated into single-walled carbon nanotubes under appropriate solvent conditions. This study suggests possible bottom-up self-assembly routes for the fabrication of novel nanodevices and systems.

  12. Assembly of bipolar microtubule structures by passive cross-linkers and molecular motors.

    PubMed

    Johann, D; Goswami, D; Kruse, K

    2016-06-01

    During cell division, sister chromatids are segregated by the mitotic spindle, a bipolar assembly of interdigitating antiparallel polar filaments called microtubules. The spindle contains the midzone, a stable region of overlapping antiparallel microtubules, that is essential for maintaining bipolarity. Although a lot is known about the molecular players involved, the mechanism underlying midzone formation and maintenance is still poorly understood. We study the interaction of polar filaments that are cross-linked by molecular motors moving directionally and by passive cross-linkers diffusing along microtubules. Using a particle-based stochastic model, we find that the interplay of motors and passive cross-linkers can generate a stable finite overlap between a pair of antiparallel polar filaments. We develop a mean-field theory to study this mechanism in detail and investigate the influence of steric interactions between motors and passive cross-linkers on the overlap dynamics. In the presence of interspecies steric interactions, passive cross-linkers mimic the behavior of molecular motors and stable finite overlaps are generated even for non-cross-linking motors. Finally, we develop a mean-field theory for a bundle of aligned polar filaments and show that they can self-organize into a spindlelike pattern. Our work suggests possible ways as to how cells can generate spindle midzones and control their extensions.

  13. Assembly of bipolar microtubule structures by passive cross-linkers and molecular motors

    NASA Astrophysics Data System (ADS)

    Johann, D.; Goswami, D.; Kruse, K.

    2016-06-01

    During cell division, sister chromatids are segregated by the mitotic spindle, a bipolar assembly of interdigitating antiparallel polar filaments called microtubules. The spindle contains the midzone, a stable region of overlapping antiparallel microtubules, that is essential for maintaining bipolarity. Although a lot is known about the molecular players involved, the mechanism underlying midzone formation and maintenance is still poorly understood. We study the interaction of polar filaments that are cross-linked by molecular motors moving directionally and by passive cross-linkers diffusing along microtubules. Using a particle-based stochastic model, we find that the interplay of motors and passive cross-linkers can generate a stable finite overlap between a pair of antiparallel polar filaments. We develop a mean-field theory to study this mechanism in detail and investigate the influence of steric interactions between motors and passive cross-linkers on the overlap dynamics. In the presence of interspecies steric interactions, passive cross-linkers mimic the behavior of molecular motors and stable finite overlaps are generated even for non-cross-linking motors. Finally, we develop a mean-field theory for a bundle of aligned polar filaments and show that they can self-organize into a spindlelike pattern. Our work suggests possible ways as to how cells can generate spindle midzones and control their extensions.

  14. ATTRACT-EM: A New Method for the Computational Assembly of Large Molecular Machines Using Cryo-EM Maps

    PubMed Central

    de Vries, Sjoerd J.; Zacharias, Martin

    2012-01-01

    Many of the most important functions in the cell are carried out by proteins organized in large molecular machines. Cryo-electron microscopy (cryo-EM) is increasingly being used to obtain low resolution density maps of these large assemblies. A new method, ATTRACT-EM, for the computational assembly of molecular assemblies from their components has been developed. Based on concepts from the protein-protein docking field, it utilizes cryo-EM density maps to assemble molecular subunits at near atomic detail, starting from millions of initial subunit configurations. The search efficiency was further enhanced by recombining partial solutions, the inclusion of symmetry information, and refinement using a molecular force field. The approach was tested on the GroES-GroEL system, using an experimental cryo-EM map at 23.5 Å resolution, and on several smaller complexes. Inclusion of experimental information on the symmetry of the systems and the application of a new gradient vector matching algorithm allowed the efficient identification of docked assemblies in close agreement with experiment. Application to the GroES-GroEL complex resulted in a top ranked model with a deviation of 4.6 Å (and a 2.8 Å model within the top 10) from the GroES-GroEL crystal structure, a significant improvement over existing methods. PMID:23251350

  15. Molecular photovoltaic system based on fullerenes and carotenoids co-assembled in lipid/alkanethiol hybrid bilayers.

    PubMed

    Liu, Lixia; Zhan, Wei

    2012-03-13

    A hybrid molecular photovoltaic system, based on fullerene C(60) and lutein (a natural photosynthetic carotenoid pigment) that are assembled in a phospholipid/alkanethiol bilayer matrix, is described here. The assembly and photoconversion behaviors of such a system were studied by UV-vis spectroscopy, cyclic voltammetry, impedance spectroscopy, photoelectrochemical action spectroscopy, and photocurrent generation. While lutein itself is inefficient in generating photocurrent, it can strongly modulate photocurrents produced by fullerenes when coassembled in the lipid bilayer matrix presumably via photoinduced electron transfer. Our results thus provide a successful example of combining both synthetic and natural photoactive components in building molecular photovoltaic systems.

  16. Inorganic molecular-scale MoSI nanowire-gold nanoparticle networks exhibit self-organized critical self-assembly.

    PubMed

    Strle, Jure; Vengust, Damjan; Mihailovic, Dragan

    2009-03-01

    We investigate for the first time the topological characteristics of large molecular-scale inorganic networks self-assembled in solution using the unique sulfur-bonding chemistry of conducting MoSI molecular wires and gold nanoparticles (GNPs). The network self-assembly is shown to display power-law distribution of graph edges, indicating an intrinsic tendency to self-organize into scale-invariant critical state, without any external control parameter. We discuss the electronic transport properties of such networks particularly with regard to the possibility of data processing.

  17. Molecular Origin and Self-Assembly of Fluorescent Carbon Nanodots in Polar Solvents.

    PubMed

    Sharma, Arjun; Gadly, Trilochan; Neogy, Suman; Ghosh, Sunil Kumar; Kumbhakar, Manoj

    2017-02-17

    Despite numerous efforts, there are several fundamental ambiguities regarding the photoluminescence of carbon dots (CDs). Spectral shift measurements display characteristic of both π-π* and n-π* transitions for the main absorption or excitation band at ∼350 nm, contrary to common assignment of exclusive n-π* transition. Additionally, the generally perceived core-state transition at ∼250 nm, involving sp(2)-networked carbogenic domains shielded from external environments, needs to be reassessed because it fails to explain the observed fluorescence quenching and spectral shift. These results have been explained based on the molecular origin of PL in CDs invoking the similarity between CD and citrazinic acid. Fluorescent derivatives of the latter are recognized to be produced during citric-acid-based CD synthesis. Concentration-dependent spectral splitting of the main excitation band in combination with the temperature-dependent PL results has been envisioned assuming self-assembly of CDs into various H-aggregates.

  18. Solution-growth kinetics and thermodynamics of nanoporous self-assembled molecular monolayers

    NASA Astrophysics Data System (ADS)

    Bellec, Amandine; Arrigoni, Claire; Schull, Guillaume; Douillard, Ludovic; Fiorini-Debuisschert, Céline; Mathevet, Fabrice; Kreher, David; Attias, André-Jean; Charra, Fabrice

    2011-03-01

    The temperature and concentration dependences of the self-assembly onto graphite from solution of a series of molecular building blocks able to form nanoporous structures are analyzed experimentally by in situ scanning tunneling microscopy. It is shown that the commonly observed coexistence of dense and nanoporous domains results from kinetic blockades rather than a thermodynamic equilibrium. The ripening can be favored by high densities of domain boundaries, which can be obtained by cooling the substrate before the nucleation and growth. Then ripening at higher-temperature yields large defect-free domains of a single structure. This thermodynamically stable structure can be either the dense or the nanoporous one, depending on the tecton concentration in the supernatant solution. A sharp phase transition from dense to honeycomb structures is observed at a critical concentration. This collective phenomenon is explained by introducing interactions between adsorbed molecules in the thermodynamic description of the whole system.

  19. A Virtual Laboratory for the 4 Bed Molecular Sieve of the Carbon Dioxide Removal Assembly

    NASA Technical Reports Server (NTRS)

    Coker, Robert; Knox, James; O'Connor, Brian

    2016-01-01

    Ongoing work to improve water and carbon dioxide separation systems to be used on crewed space vehicles combines sub-scale systems testing and multi-physics simulations. Thus, as part of NASA's Advanced Exploration Systems (AES) program and the Life Support Systems Project (LSSP), fully predictive COMSOL Multiphysics models of the Four Bed Molecular Sieve (4BMS) of the Carbon Dioxide Removal Assembly (CDRA) on the International Space Station (ISS) have been developed. This Virtual Laboratory is being used to help reduce mass, power, and volume requirements for exploration missions. In this paper we describe current and planned modeling developments in the area of carbon dioxide removal to support future missions as well as the resolution of anomalies observed in the ISS CDRA.

  20. Self-assembly and molecular "recognition" phenomena in solutions of (bio)polyelectrolyte complexes

    NASA Astrophysics Data System (ADS)

    Izumrudov, V. A.

    2008-04-01

    Recently published data on polyelectrolyte complexes formed by both oppositely charged synthetic polyions and natural polyelectrolytes (proteins, enzymes, nucleic acids) are summarised. The properties of these complexes and the phase behaviour of their solutions is shown to obey the general trends found in the studies of cooperative interpolyelectrolyte interactions. The principles of functioning of polyelectrolyte complexes that underlie the self-assembly of complexes in solution and determine the ability of complexes to retain stability over a specified broad range of external conditions and then to quickly and reversibly respond with high sensitivity to a change in the environment by changing their molecular characteristics and phase state are considered. The successful use of the results of fundamental research of (bio)polyelectrolyte complexes for the solution of topical problems of biotechnology, materials science and medicine are demonstrated.

  1. Molecular Design of Bioinspired Nanostructures for Biomedical Applications: Synthesis, Self-Assembly and Functional Properties

    NASA Astrophysics Data System (ADS)

    Xu, Hesheng Victor; Zheng, Xin Ting; Mok, Beverly Yin Leng; Ibrahim, Salwa Ali; Yu, Yong; Tan, Yen Nee

    2016-08-01

    Biomolecules are the nanoscale building blocks of cells, which play multifaceted roles in the critical biological processes such as biomineralization in a living organism. In these processes, the biological molecules such as protein and nucleic acids use their exclusive biorecognition properties enabled from their unique chemical composition, shape and function to initiate a cascade of cellular events. The exceptional features of these biomolecules, coupled with the recent advancement in nanotechnology, have led to the emergence of a new research field that focuses on the molecular design of bioinspired nanostructures that inherit the extraordinary function of natural biomaterials. These “bioinspired” nanostructures could be formulated by biomimetic approaches through either self-assembling of biomolecules or acting as a biomolecular template/precursor to direct the synthesis of nanocomposite. In either situation, the resulting nanomaterials exhibit phenomenal biocompatibility, superb aqueous solubility and excellent colloidal stability, branding them exceptionally desirable for both in vitro and in vivo biomedical applications. In this review, we will present the recent developments in the preparation of “bioinspired” nanostructures through biomimetic self-assembly and biotemplating synthesis, as well as highlight their functional properties and potential applications in biomedical diagnostics and therapeutic delivery. Lastly, we will conclude this topic with some personal perspective on the challenges and future outlooks of the “bioinspired” nanostructures for nanomedicine.

  2. Molecular dynamics simulation of reversibly self-assembling shells in solution using trapezoidal particles

    NASA Astrophysics Data System (ADS)

    Rapaport, D. C.

    2012-11-01

    The self-assembly of polyhedral shells, each constructed from 60 trapezoidal particles, is simulated using molecular dynamics. The spatial organization of the component particles in this shell is similar to the capsomer proteins forming the capsid of a T=1 virus. Growth occurs in the presence of an atomistic solvent and, under suitable conditions, achieves a high yield of complete shells. The simulations provide details of the structure and lifetime of the particle clusters that appear as intermediate states along the growth pathway, and the nature of the transitions between them. In certain respects the growth of size-60 shells from trapezoidal particles resembles the growth of icosahedral shells from triangular particles studied previously, with reversible bonding playing a major role in avoiding incorrect assembly, although the details differ due to particle shape and bond organization. The strong preference for maximal bonding exhibited by the triangular particle clusters is also apparent for trapezoidal particles, but this is now confined to early growth and is less pronounced as shells approach completion along a variety of pathways.

  3. Molecular Insights into Aqueous NaCl Electrolytes Confined within Vertically-oriented Graphenes

    PubMed Central

    Bo, Zheng; Yang, Huachao; Zhang, Shuo; Yang, Jinyuan; Yan, Jianhua; Cen, Kefa

    2015-01-01

    Vertically-oriented graphenes (VGs) are promising active materials for electric double layer capacitors (EDLCs) due to their unique morphological and structural features. This study, for the first time, reports the molecular dynamics (MD) simulations on aqueous NaCl electrolytes confined within VG channels with different surface charge densities and channel widths. Simulation results show that the accessibility of ions and the structure of EDLCs are determined by the ion type/size, surface charging, and VG channel width. For relatively narrow VG channels with the same width, the threshold charge density (to compensate the energy penalty for shedding hydration shell) and the dehydration rate of Cl− ions are larger than those of Na+ ions. To achieve the highest ion concentration coefficient, the effective VG channel width should be between the crystal and hydration diameters of the ions. The results are further quantified and elucidated by calculating the electrolyte density profiles. The molecular insights obtained in the current work are useful in guiding the design and fabrication of VGs for advancing their EDLC applications. PMID:26424365

  4. Molecular Chaperones and the Assembly of the Prion Ure2p in Vitro*

    PubMed Central

    Savistchenko, Jimmy; Krzewska, Joanna; Fay, Nicolas; Melki, Ronald

    2008-01-01

    The protein Ure2 from Saccharomyces cerevisiae possesses prion properties at the origin of the [URE3] trait. In vivo, a high molecular weight form of inactive Ure2p is associated to [URE3]. The faithful and continued propagation of [URE3]is dependent on the expression levels of molecular chaperones from the Hsp100, -70, and -40 families; however, so far, their role is not fully documented. Here we investigate the effects of molecular chaperones from the Hsp40, Hsp70, Hsp90, and Hsp100 families and the chaperonin CCT/Tric on the assembly of full-length Ure2p. We show that Hsp104p greatly stimulates Ure2p aggregation, whereas Ssa1p, Ydj1p, Sis1p, and Hsp82p inhibit aggregation to different extents. The nature of the high molecular weight Ure2p species that forms in the presence of the different molecular chaperones and their nucleotide dependence is described. We show that Hsp104p favors the aggregation of Ure2p into non-fibrillar high molecular weight particles, whereas Ssa1p, Ydj1p, Sis1p, and Hsp82p sequester Ure2p in spherical oligomers. Using fluorescently labeled full-length Ure2p and Ure2p-(94–354) and fluorescence polarization, we show that Ssa1p binding to Ure2p is ATP-dependent, whereas that of Hsp104p is not. We also show that Ssa1p preferentially interacts with the N-terminal domain of Ure2p that is critical for prion propagation, whereas Ydj1p preferentially interacts with the C-terminal domain of the protein, and we discuss the significance of this observation. Finally, the affinities of Ssa1p, Ydj1p, and Hsp104p for Ure2p are determined. Our in vitro observations bring new insight into the mechanism by which molecular chaperones influence the propagation of [URE3]. PMID:18400756

  5. A Flexible Nanoarray Approach for the Assembly and Probing of Molecular Complexes

    PubMed Central

    Krasnoslobodtsev, Alexey V.; Zhang, Yuliang; Viazovkina, Ekaterina; Gall, Alexander; Bertagni, Chad; Lyubchenko, Yuri L.

    2015-01-01

    Immobilization is a key step involved in probing molecular interactions using single-molecule force spectroscopy methods, including atomic force microscopy (AFM). To our knowledge, we describe a novel approach termed flexible nanoarray (FNA) in which the interaction between the two internally immobilized amyloid β peptides is measured by pulling of the tether. The FNA tether was synthesized with nonnucleotide phosphoramidite monomers using the DNA synthesis chemistry. The two anchoring points for immobilization of the peptides inside the tether were incorporated at defined distances between them and from the ends of the polymer. Decamers of amyloid β peptide capable of dimer formation were selected as a test system. The formation of the peptide dimers was verified by AFM force spectroscopy by pulling the tether at the ends. In these experiments, the thiolated end of the FNA tether was covalently immobilized on the AFM substrate functionalized with maleimide. The other end of the FNA tether was functionalized with biotin to form a noncovalent link with the streptavidin functionalized AFM tip during the approach stage. The dimers’ rupture fingerprint was unambiguously identified on the force curves by its position and the force value. The FNA design allowed reversible experiments in which the monomers were allowed to associate after the rupture of the dimers by performing the approach stage before the rupture of the biotin-streptavidin link. This suggests that the FNA technique is capable of analyzing multiple intermolecular interactions in the same molecular complex. The computational analysis showed that the tethered peptides assemble into the same dimer structure as that formed by nontethered peptides, suggesting that the FNA tether has the necessary flexibility to enable assembly of the dimer even during the course of the force spectroscopy experiment. PMID:25954890

  6. Bifunctional star-burst amorphous molecular materials for OLEDs: achieving highly efficient solid-state luminescence and carrier transport induced by spontaneous molecular orientation.

    PubMed

    Kim, Jun Yun; Yasuda, Takuma; Yang, Yu Seok; Adachi, Chihaya

    2013-05-21

    Bifunctional star-burst amorphous molecular materials displaying both efficient solid-state luminescence and high hole-transport properties are developed in this study. A high external electroluminescence quantum efficiency up to 5.9% is attained in OLEDs employing the developed amorphous materials. It is revealed that the spontaneous horizontal orientation of these light-emitting molecules in their molecular-condensed states leads to a remarkable enhancement of the electroluminescence efficiencies and carrier-transport properties.

  7. Molecular and ultrastructural analysis of forisome subunits reveals the principles of forisome assembly

    PubMed Central

    Müller, Boje; Groscurth, Sira; Menzel, Matthias; Rüping, Boris A.; Twyman, Richard M.; Prüfer, Dirk; Noll, Gundula A.

    2014-01-01

    Background and Aims Forisomes are specialized structural phloem proteins that mediate sieve element occlusion after wounding exclusively in papilionoid legumes, but most studies of forisome structure and function have focused on the Old World clade rather than the early lineages. A comprehensive phylogenetic, molecular, structural and functional analysis of forisomes from species covering a broad spectrum of the papilionoid legumes was therefore carried out, including the first analysis of Dipteryx panamensis forisomes, representing the earliest branch of the Papilionoideae lineage. The aim was to study the molecular, structural and functional conservation among forisomes from different tribes and to establish the roles of individual forisome subunits. Methods Sequence analysis and bioinformatics were combined with structural and functional analysis of native forisomes and artificial forisome-like protein bodies, the latter produced by expressing forisome genes from different legumes in a heterologous background. The structure of these bodies was analysed using a combination of confocal laser scanning microscopy (CLSM), scanning electron microscopy (SEM) and transmission electron microscopy (TEM), and the function of individual subunits was examined by combinatorial expression, micromanipulation and light microscopy. Key Results Dipteryx panamensis native forisomes and homomeric protein bodies assembled from the single sieve element occlusion by forisome (SEO-F) subunit identified in this species were structurally and functionally similar to forisomes from the Old World clade. In contrast, homomeric protein bodies assembled from individual SEO-F subunits from Old World species yielded artificial forisomes differing in proportion to their native counterparts, suggesting that multiple SEO-F proteins are required for forisome assembly in these plants. Structural differences between Medicago truncatula native forisomes, homomeric protein bodies and heteromeric bodies

  8. Thermodynamic insights into the self-assembly of capped nanoparticles using molecular dynamic simulations.

    PubMed

    de Moura, André F; Bernardino, Kalil; Dalmaschio, Cleocir J; Leite, Edson R; Kotov, Nicholas A

    2015-02-07

    Although the molecular modeling of self-assembling processes stands as a challenging research issue, there have been a number of breakthroughs in recent years. This report describes the use of large-scale molecular dynamics simulations with coarse grained models to study the spontaneous self-assembling of capped nanoparticles in chloroform suspension. A model system comprising 125 nanoparticles in chloroform evolved spontaneously from a regular array of independent nanoparticles to a single thread-like, ramified superstructure spanning the whole simulation box. The aggregation process proceeded by means of two complementary mechanisms, the first characterized by reactive collisions between monomers and oligomers, which were permanently trapped into the growing superstructure, and the second a slow structural reorganization of the nanoparticle packing. Altogether, these aggregation processes were over after ca. 0.6 μs and the system remained structurally and energetically stable until 1 μs. The thread-like structure closely resembles the TEM images of capped ZrO2, but a better comparison with experimental results was obtained by the deposition of the suspension over a graphene solid substrate, followed by the complete solvent evaporation. The agreement between the main structural features from this simulation and those from the TEM experiment was excellent and validated the model system. In order to shed further light on the origins of the stable aggregation of the nanoparticles, the Gibbs energy of aggregation was computed, along with its enthalpy and entropy contributions, both in chloroform and in a vacuum. The thermodynamic parameters arising from the modeling are consistent with larger nanoparticles in chloroform due to the solvent-swelled organic layer and the overall effect of the solvent was the partial destabilization of the aggregated state as compared to the vacuum system. The modeling strategy has been proved effective and reliable to describe the self-assembling

  9. Assembly of supramolecular nanotubes from molecular triangles and 1,2-dihalohydrocarbons.

    PubMed

    Liu, Zhichang; Liu, Guoliang; Wu, Yilei; Cao, Dennis; Sun, Junling; Schneebeli, Severin T; Nassar, Majed S; Mirkin, Chad A; Stoddart, J Fraser

    2014-11-26

    Precise control of molecular assembly is a challenging goal facing supramolecular chemists. Herein, we report the highly specific assembly of a range of supramolecular nanotubes from the enantiomeric triangular naphthalenediimide-based macrocycles (RRRRRR)- and (SSSSSS)-NDI-Δ and a class of similar solvents, namely, the 1,2-dihalo-ethanes and -ethenes (DXEs). Three kinds of supramolecular nanotubes are formed from the columnar stacking of NDI-Δ units with a 60° mutual rotation angle as a result of cooperative [C-H···O] interactions, directing interactions of the [X···X]-bonded DXE chains inside the nanotubes and lateral [X···π] or [π···π] interactions. They include (i) semiflexible infinite nanotubes formed in the gel state from NDI-Δ and (E)-1,2-dichloroethene, (ii) rigid infinite nonhelical nanotubes produced in the solid state from NDI-Δ and BrCH2CH2Br, ClCH2CH2Br, and ClCH2CH2I, and (iii) a pair of rigid tetrameric, enantiomeric single-handed (P)- and (M)-helical nanotubes formed in the solid state from the corresponding (RRRRRR)- and (SSSSSS)-NDI-Δ with ClCH2CH2Cl. In case (i), only the electron-rich C═C double bond of (E)-1,2-dichloroethene facilitates the gelation of NDI-Δ. In cases (ii) and (iii), the lengths of anti-DXEs determine the translation of the chirality of NDI-Δ into the helicity of nanotubes. Only ClCH2CH2Cl induces single-handed helicity into the nanotubes. The subtle interplay of noncovalent bonding interactions, resulting from the tiny structural variations involving the DXE guests, is responsible for the diverse and highly specific assembly of NDI-Δ. This research highlights the critical role that guests play in constructing assembled superstructures of hosts and offers a novel approach to creating supramolecular nanotubes.

  10. Determination of 3D molecular orientation by concurrent polarization analysis of multiple Raman modes in broadband CARS spectroscopy

    PubMed Central

    2016-01-01

    A theoretical description is presented about a new analysis method to determine three-dimensional (3D) molecular orientation by concurrently analyzing multiple Raman polarization profiles. Conventional approaches to polarization Raman spectroscopy are based on single peaks, and their 2D-projected polarization profiles are limited in providing 3D orientational information. Our new method analyzes multiple Raman profiles acquired by a single polarization scanning measurement of broadband coherent anti-Stokes Raman scattering (BCARS). Because the analysis uses only dimensionless quantities, such as intensity ratios and phase difference between multiple profiles, the results are not affected by sample concentration and the system response function. We describe how to determine the 3D molecular orientation with the dimensionless observables by using two simplified model cases. In addition, we discuss the effect of orientational broadening on the polarization profiles in the two model cases. We find that in the presence of broadening we can still determine the mean 3D orientation angles and, furthermore, the degree of orientational broadening. PMID:26561197

  11. Coarse-grained molecular dynamics study on the self-assembly of Gemini surfactants: the effect of spacer length.

    PubMed

    Wang, Pan; Pei, Shuai; Wang, Muhan; Yan, Youguo; Sun, Xiaoli; Zhang, Jun

    2017-02-08

    Gemini surfactants cause a lot of concerns owing to their unusual aggregation morphologies and superior physicochemical properties over the conventional surfactants. Research shows that the unique structure of Gemini surfactants, especially the spacer group, has a great impact on the self-assembly behaviors. To understand the determinants of this behavior on the molecular level, we carried out coarse-grained molecular dynamics (CGMD) simulations on aqueous solutions of alkanediyl-a,w-bis (dimethylcetylammonium bromide)-based surfactants with different spacer group lengths. Our simulation results demonstrated that the self-assembled morphologies of Gemini changed from spherical micelles, wormlike micelles to vesicles with the decrease in the spacer length, which were qualitatively consistent with the experimental observations. Both the microscopic dynamics processes and the self-assembly mechanisms for the formation of spherical micelles, wormlike micelles and vesicles were systematically studied through the CGMD simulations. In addition, based on the microscopic analysis, a strategy was proposed to predict the self-assembled morphology of surfactant-based systems based on simulation. This work shed light on new views in the understanding of the self-assembly of Gemini surfactants at a molecular-level and the proposed predicting strategy showed promise for practical applications.

  12. Hydroxyl and water molecule orientations in trypsin: Comparison to molecular dynamics structures

    SciTech Connect

    McDowell, R.S.; Kossiakoff, A.A.

    1994-12-31

    A comparison is presented of experimentally observed hydroxyl and water hydrogens in trypsin determined from neutron density maps with the results of a 140ps molecular dynamics (MD) simulation. Experimental determination of hydrogen and deuterium atom positions in molecules as large as proteins is a unique capability of neutron diffraction. The comparison addresses the degree to which a standard force-field approach can adequately describe the local electrostatic and van der Waals forces that determine the orientations of these hydrogens. Neutron densities, derived from 2.1{Angstrom} D{sub 2}O-H{sub 2}O difference Fourier maps, provide a database of 27 well-ordered hydroxyl hydrogens. Most of the simulated hydroxyl orientations are within a standard deviation of the experimentally-observed positions, including several examples in which both the simulation and the neutron density indicate that a hydroxyl group is shifted from a {open_quote}standard{close_quote} rotamer. For the most highly ordered water molecules, the hydrogen distributions calculated from the trajectory were in good agreement with neutron density; simulated water molecules that displayed multiple hydrogen bonding networks had correspondingly broadened neutron density profiles. This comparison was facilitated by development of a method to construct a pseudo 2{Angstrom} density map based on the hydrogen atom distributions from the simulation. The degree of disorder of internal water molecules is shown to result primarily from the electrostatic environment surrounding that water molecule as opposed to the cavity size available to the molecule. A method is presented for comparing the discrete observations sampled in a dynamics trajectory with the time- averaged data obtained from X-ray or neutron diffraction studies. This method is particularly useful for statically-disordered water molecules, in which the average location assigned from a trajectory may represent a site of relatively low occupancy.

  13. On the optimal design of molecular sensing interfaces with lipid bilayer assemblies - A knowledge based approach

    NASA Astrophysics Data System (ADS)

    Siontorou, Christina G.

    2012-12-01

    Biosensors are analytic devices that incorporate a biochemical recognition system (biological, biologicalderived or biomimic: enzyme, antibody, DNA, receptor, etc.) in close contact with a physicochemical transducer (electrochemical, optical, piezoelectric, conductimetric, etc.) that converts the biochemical information, produced by the specific biological recognition reaction (analyte-biomolecule binding), into a chemical or physical output signal, related to the concentration of the analyte in the measuring sample. The biosensing concept is based on natural chemoreception mechanisms, which are feasible over/within/by means of a biological membrane, i.e., a structured lipid bilayer, incorporating or attached to proteinaceous moieties that regulate molecular recognition events which trigger ion flux changes (facilitated or passive) through the bilayer. The creation of functional structures that are similar to natural signal transduction systems, correlating and interrelating compatibly and successfully the physicochemical transducer with the lipid film that is self-assembled on its surface while embedding the reconstituted biological recognition system, and at the same time manage to satisfy the basic conditions for measuring device development (simplicity, easy handling, ease of fabrication) is far from trivial. The aim of the present work is to present a methodological framework for designing such molecular sensing interfaces, functioning within a knowledge-based system built on an ontological platform for supplying sub-systems options, compatibilities, and optimization parameters.

  14. Structural changes in a Schiff base molecular assembly initiated by scanning tunneling microscopy tip.

    PubMed

    Tomak, A; Bacaksiz, C; Mendirek, G; Sahin, H; Hur, D; Görgün, K; Senger, R T; Birer, Ö; Peeters, F M; Zareie, H M

    2016-08-19

    We report the controlled self-organization and switching of newly designed Schiff base (E)-4-((4-(phenylethynyl) benzylidene) amino) benzenethiol (EPBB) molecules on a Au (111) surface at room temperature. Scanning tunneling microscopy and spectroscopy (STM/STS) were used to image and analyze the conformational changes of the EPBB molecules. The conformational change of the molecules was induced by using the STM tip while increasing the tunneling current. The switching of a domain or island of molecules was shown to be induced by the STM tip during scanning. Unambiguous fingerprints of the switching mechanism were observed via STM/STS measurements. Surface-enhanced Raman scattering was employed, to control and identify quantitatively the switching mechanism of molecules in a monolayer. Density functional theory calculations were also performed in order to understand the microscopic details of the switching mechanism. These calculations revealed that the molecular switching behavior stemmed from the strong interaction of the EPBB molecules with the STM tip. Our approach to controlling intermolecular mechanics provides a path towards the bottom-up assembly of more sophisticated molecular machines.

  15. Animal Hairs as Water-stimulated Shape Memory Materials: Mechanism and Structural Networks in Molecular Assemblies

    NASA Astrophysics Data System (ADS)

    Xiao, Xueliang; Hu, Jinlian

    2016-05-01

    Animal hairs consisting of α-keratin biopolymers existing broadly in nature may be responsive to water for recovery to the innate shape from their fixed deformation, thus possess smart behavior, namely shape memory effect (SME). In this article, three typical animal hair fibers were first time investigated for their water-stimulated SME, and therefrom to identify the corresponding net-points and switches in their molecular and morphological structures. Experimentally, the SME manifested a good stability of high shape fixation ratio and reasonable recovery rate after many cycles of deformation programming under water stimulation. The effects of hydration on hair lateral size, recovery kinetics, dynamic mechanical behaviors and structural components (crystal, disulfide and hydrogen bonds) were then systematically studied. SME mechanisms were explored based on the variations of structural components in molecular assemblies of such smart fibers. A hybrid structural network model with single-switch and twin-net-points was thereafter proposed to interpret the water-stimulated shape memory mechanism of animal hairs. This original work is expected to provide inspiration for exploring other natural materials to reveal their smart functions and natural laws in animals including human as well as making more remarkable synthetic smart materials.

  16. Self-assembled diacetylene molecular wire polymerization on an insulating hexagonal boron nitride (0001) surface

    NASA Astrophysics Data System (ADS)

    Makarova, Marina V.; Okawa, Yuji; Verveniotis, Elisseos; Watanabe, Kenji; Taniguchi, Takashi; Joachim, Christian; Aono, Masakazu

    2016-09-01

    The electrical characterization of single-polymer chains on a surface is an important step towards novel molecular device development. The main challenge is the lack of appropriate atomically flat insulating substrates for fabricating single-polymer chains. Here, using atomic force microscopy, we demonstrate that the (0001) surface of an insulating hexagonal boron nitride (h-BN) substrate leads to a flat-lying self-assembled monolayer of diacetylene compounds. The subsequent heating or ultraviolet irradiation can initiate an on-surface polymerization process leading to the formation of long polydiacetylene chains. The frequency of photo-polymerization occurrence on h-BN(0001) is two orders of magnitude higher than that on graphite(0001). This is explained by the enhanced lifetime of the molecular excited state, because relaxation via the h-BN is suppressed due to a large band gap. We also demonstrate that on-surface polymerization on h-BN(0001) is possible even after the lithography process, which opens up the possibility of further electrical investigations.

  17. Molecular dynamics simulations of discoidal bilayers assembled from truncated human lipoproteins.

    PubMed

    Shih, Amy Y; Denisov, Ilia G; Phillips, James C; Sligar, Stephen G; Schulten, Klaus

    2005-01-01

    Human apolipoprotein A-1 (apo A-1) is the major protein component of high-density lipoproteins. The apo A-1 lipid-binding domain was used as a template for the synthesis of amphipathic helical proteins termed membrane scaffold proteins, employed to self-assemble soluble monodisperse discoidal particles called Nanodiscs. In these particles, membrane scaffold proteins surround a lipid bilayer in a belt-like fashion forming bilayer disks of discrete size and composition. Here we investigate the structure of Nanodiscs through molecular dynamics simulations in which Nanodiscs were built from scaffold proteins of various lengths. The simulations showed planar or deformed Nanodiscs depending on optimal length and alignment of the scaffold proteins. Based on mean surface area per lipid calculations, comparison of small-angle x-ray scattering curves, and the relatively planar shape of Nanodiscs made from truncated scaffold proteins, one can conclude that the first 17 to 18 residues of the 200-residue apo A-1 lipid-binding domain are not involved in formation of the protein "belts" surrounding the lipid bilayer. To determine whether the addition of an integral membrane protein has an effect on the overall structure of a Nanodisc, bacteriorhodopsin was embedded into a Nanodisc and simulated using molecular dynamics, revealing a planar disk with a slightly rectangular shape.

  18. Amyloid β-Protein Assembly: The Effect of Molecular Tweezers CLR01 and CLR03

    PubMed Central

    2015-01-01

    The early oligomerization of amyloid β-protein (Aβ) has been shown to be an important event in the pathology of Alzheimer’s disease (AD). Designing small molecule inhibitors targeting Aβ oligomerization is one attractive and promising strategy for AD treatment. Here we used ion mobility spectrometry coupled to mass spectrometry (IMS-MS) to study the different effects of the molecular tweezers CLR01 and CLR03 on Aβ self-assembly. CLR01 was found to bind to Aβ directly and disrupt its early oligomerization. Moreover, CLR01 remodeled the early oligomerization of Aβ42 by compacting the structures of dimers and tetramers and as a consequence eliminated higher-order oligomers. Unexpectedly, the negative-control derivative, CLR03, which lacks the hydrophobic arms of the tweezer structure, was found to facilitate early Aβ oligomerization. Our study provides an example of IMS as a powerful tool to study and better understand the interaction between small molecule modulators and Aβ oligomerization, which is not attainable by other methods, and provides important insights into therapeutic development of molecular tweezers for AD treatment. PMID:25751170

  19. Animal Hairs as Water-stimulated Shape Memory Materials: Mechanism and Structural Networks in Molecular Assemblies

    PubMed Central

    Xiao, Xueliang; Hu, Jinlian

    2016-01-01

    Animal hairs consisting of α-keratin biopolymers existing broadly in nature may be responsive to water for recovery to the innate shape from their fixed deformation, thus possess smart behavior, namely shape memory effect (SME). In this article, three typical animal hair fibers were first time investigated for their water-stimulated SME, and therefrom to identify the corresponding net-points and switches in their molecular and morphological structures. Experimentally, the SME manifested a good stability of high shape fixation ratio and reasonable recovery rate after many cycles of deformation programming under water stimulation. The effects of hydration on hair lateral size, recovery kinetics, dynamic mechanical behaviors and structural components (crystal, disulfide and hydrogen bonds) were then systematically studied. SME mechanisms were explored based on the variations of structural components in molecular assemblies of such smart fibers. A hybrid structural network model with single-switch and twin-net-points was thereafter proposed to interpret the water-stimulated shape memory mechanism of animal hairs. This original work is expected to provide inspiration for exploring other natural materials to reveal their smart functions and natural laws in animals including human as well as making more remarkable synthetic smart materials. PMID:27230823

  20. Self-assembly formation of palm-based esters nano-emulsion: A molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Abdul Rahman, Mohd. Basyaruddin; Huan, Qiu-Yi; Tejo, Bimo A.; Basri, Mahiran; Salleh, Abu Bakar; Rahman, Raja Noor Zaliha Abdul

    2009-10-01

    Palm-oil esters (POEs) are unsaturated and non-ionic esters that can be prepared by enzymatic synthesis from palm oil. Their nano-emulsion properties possess great potential to act as drug carrier for transdermal drug delivery system. A ratio of 75:5:20 (water/POEs/Span20) was chosen from homogenous region in the phase diagram of our previous experimental work to undergo molecular dynamics simulation. A 15 ns molecular dynamics simulation of nano-emulsion system (water/POEs/Span20) was carried out using OPLS-AA force field. The aggregations of the oil and surfactant molecules are observed throughout the simulation. After 8 ns of simulation, the molecules start to aggregate to form one spherical micelle where the POEs molecules are surrounded by the non-ionic surfactant (Span20) molecules with an average size of 4.2 ± 0.05 nm. The size of the micelle and the ability of palm-based nano-emulsion to self-assemble suggest that this nano-emulsion can potentially use in transdermal drug delivery system.

  1. Metamaterial Absorbers for Infrared Detection of Molecular Self-Assembled Monolayers.

    PubMed

    Ishikawa, Atsushi; Tanaka, Takuo

    2015-07-31

    The emerging field of plasmonic metamaterials has introduced new degree of freedom to manipulate optical field from nano to macroscopic scale, offering an attractive platform for sensing applications. So far, metamaterial sensor concepts, however, have focused on hot-spot engineering to improve the near-field enhancement, rather than fully exploiting tailored material properties. Here, we present a novel spectroscopic technique based on the metamaterial infrared (IR) absorber allowing for a low-background detection scheme as well as significant plasmonic enhancement. Specifically, we experimentally demonstrate the resonant coupling of plasmonic modes of a metamaterial absorber and IR vibrational modes of a molecular self-assembled monolayer. The metamaterial consisting of an array of Au/MgF2/Au structures exhibits an anomalous absorption at ~ 3000 cm(-1), which spectrally overlaps with C-H stretching vibrational modes. Symmetric/asymmetric C-H stretching modes of a 16-Mercaptohexadecanoic acid monolayer are clearly observed as Fano-like anti-resonance peaks within a broad plasmonic absorption of the metamaterial. Spectral analysis using Fano line-shape fitting reveals the underlying resonant interference in plasmon-molecular coupled systems. Our metamaterial approach achieves the attomole sensitivity with a large signal-to-noise ratio in the far-field measurement, thus may open up new avenues for realizing ultrasensitive IR inspection technologies.

  2. Molecular Dynamics Study of Surfactant Self-Assembly on Single-Walled Carbon Nanotubes (SWCNTs)

    NASA Astrophysics Data System (ADS)

    Phelan, Frederick, Jr.

    2015-03-01

    Single-walled carbon nanotubes (SWNCTs) are materials with structural, electronic and optical properties that make them attractive for a myriad of advanced technology applications. Increased adaptation of these materials requires advancement in separation techniques which enables them to be sorted with increased reliability into monodisperse fractions with respect to length and chirality. Most separation techniques currently in use rely on dispersion of tubes in aqueous solution using surfactants. This results in a colloidal mixture in which tubes are packed and individually dispersed in a surfactant shell. Understanding the structure and properties of the SWCNT-surfactant complex at the molecular level, and how this is affected by chirality, will help to improve separations processes. In this work, we study the structure and properties of SWCNT-surfactant colloidal complexes using all-atom molecular dynamics. Self-assembled structures are computed for a number of combinations SWCNT/surfactant, and also, co-surfactant mixtures for the bile salt surfactant sodium deoxycholate (DOC) and the anionic surfactant sodium dodecyl sulfate (SDS). From the radial distribution function we estimate the size of the SWCNT hydration layer, and use that information to compute the buoyant densities of unfilled tubes for a number of concentrations. Estimates of the change in hydrodynamic radius with increased surfactant packing and the binding energies of the individual surfactants are also obtained.

  3. Molecular Modeling of Triton X Micelles: Force Field Parameters, Self-Assembly, and Partition Equilibria.

    PubMed

    Yordanova, D; Smirnova, I; Jakobtorweihen, S

    2015-05-12

    Nonionic surfactants of the Triton X-series find various applications in extraction processes and as solubilizing agents for the purification of membrane proteins. However, so far no optimized parameters are available to perform molecular simulations with a biomolecular force field. Therefore, we have determined the first optimized set of CHARMM parameters for the Triton X-series, enabling all-atom molecular dynamics (MD) simulations. In order to validate the new parameters, micellar sizes (aggregation numbers) of Triton X-114 and Triton X-100 have been investigated as a function of temperature and surfactant concentration. These results are comparable with experimental results. Furthermore, we have introduced a new algorithm to obtain micelle structures from self-assembly MD simulations for the COSMOmic method. This model allows efficient partition behavior predictions once a representative micelle structure is available. The predicted partition coefficients for the systems Triton X-114/water and Triton X-100/water are in excellent agreement with experimental results. Therefore, this method can be applied as a screening tool to find optimal solute-surfactant combinations or suitable surfactant systems for a specific application.

  4. Innovative interactive flexible docking method for multi-scale reconstruction elucidates dystrophin molecular assembly.

    PubMed

    Molza, A-E; Férey, N; Czjzek, M; Le Rumeur, E; Hubert, J-F; Tek, A; Laurent, B; Baaden, M; Delalande, O

    2014-01-01

    At present, our molecular knowledge of dystrophin, the protein encoded by the DMD gene and mutated in myopathy patients, remains limited. To get around the absence of its atomic structure, we have developed an innovative interactive docking method based on the BioSpring software in combination with Small-angle X-ray Scattering (SAXS) data. BioSpring allows interactive handling of biological macromolecules thanks to an augmented Elastic Network Model (aENM) that combines the spring network with non-bonded terms between atoms or pseudo-atoms. This approach can be used for building molecular assemblies even on a desktop or a laptop computer thanks to code optimizations including parallel computing and GPU programming. By combining atomistic and coarse-grained models, the approach significantly simplifies the set-up of multi-scale scenarios. BioSpring is remarkably efficient for the preparation of numeric simulations or for the design of biomolecular models integrating qualitative experimental data restraints. The combination of this program and SAXS allowed us to propose the first high-resolution models of the filamentous central domain of dystrophin, covering repeats 11 to 17. Low-resolution interactive docking experiments driven by a potential grid enabled us to propose how dystrophin may associate with F-actin and nNOS. This information provides an insight into medically relevant discoveries to come.

  5. Molecular assembly of Clostridium botulinum progenitor M complex of type E

    DOE PAGES

    Eswaramoorthy, Subramaniam; Sun, Jingchuan; Li, Huilin; ...

    2015-12-07

    Clostridium botulinum neurotoxin (BoNT) is released as a progenitor complex, in association with a non-toxic-non-hemagglutinin protein (NTNH) and other associated proteins. We have determined the crystal structure of M type Progenitor complex of botulinum neurotoxin E [PTC-E(M)], a heterodimer of BoNT and NTNH. The crystal structure reveals that the complex exists as a tight, interlocked heterodimer of BoNT and NTNH. The crystal structure explains the mechanism of molecular assembly of the complex and reveals several acidic clusters at the interface responsible for association at low acidic pH and disassociation at basic/neutral pH. Furthermore, the similarity of the general architecture betweenmore » the PTC-E(M) and the previously determined PTC-A(M) strongly suggests that the progenitor M complexes of all botulinum serotypes may have similar molecular arrangement, although the neurotoxins apparently can take very different conformation when they are released from the M complex.« less

  6. Molecular Assembly of Clostridium botulinum progenitor M complex of type E.

    PubMed

    Eswaramoorthy, Subramaniam; Sun, Jingchuan; Li, Huilin; Singh, Bal Ram; Swaminathan, Subramanyam

    2015-12-07

    Clostridium botulinum neurotoxin (BoNT) is released as a progenitor complex, in association with a non-toxic-non-hemagglutinin protein (NTNH) and other associated proteins. We have determined the crystal structure of M type Progenitor complex of botulinum neurotoxin E [PTC-E(M)], a heterodimer of BoNT and NTNH. The crystal structure reveals that the complex exists as a tight, interlocked heterodimer of BoNT and NTNH. The crystal structure explains the mechanism of molecular assembly of the complex and reveals several acidic clusters at the interface responsible for association at low acidic pH and disassociation at basic/neutral pH. The similarity of the general architecture between the PTC-E(M) and the previously determined PTC-A(M) strongly suggests that the progenitor M complexes of all botulinum serotypes may have similar molecular arrangement, although the neurotoxins apparently can take very different conformation when they are released from the M complex.

  7. Molecular assembly of Clostridium botulinum progenitor M complex of type E

    SciTech Connect

    Eswaramoorthy, Subramaniam; Sun, Jingchuan; Li, Huilin; Singh, Bal Ram; Swaminathan, Subramanyam

    2015-12-07

    Clostridium botulinum neurotoxin (BoNT) is released as a progenitor complex, in association with a non-toxic-non-hemagglutinin protein (NTNH) and other associated proteins. We have determined the crystal structure of M type Progenitor complex of botulinum neurotoxin E [PTC-E(M)], a heterodimer of BoNT and NTNH. The crystal structure reveals that the complex exists as a tight, interlocked heterodimer of BoNT and NTNH. The crystal structure explains the mechanism of molecular assembly of the complex and reveals several acidic clusters at the interface responsible for association at low acidic pH and disassociation at basic/neutral pH. Furthermore, the similarity of the general architecture between the PTC-E(M) and the previously determined PTC-A(M) strongly suggests that the progenitor M complexes of all botulinum serotypes may have similar molecular arrangement, although the neurotoxins apparently can take very different conformation when they are released from the M complex.

  8. One-Step Assembly of Molecular Separation Membranes by Direct Atomizing Oligomers.

    PubMed

    Fan, Hongwei; Wang, Ren; Shan, Linglong; Yan, Hao; Li, Jie; Ji, Shulan; Lin, Haiqing; Zhang, Guojun

    2017-02-01

    Polymeric membranes are important materials for efficient sieving of targeted components at the molecular level and have made significant advancement in many industrial applications such as biofuel production, water purification, fuel combustion, and carbon dioxide capture. Although their separation efficiencies have been widely investigated, lack of more efficient, greener, and lower-cost membrane fabrication mechanisms is still a major hurdle for mass production, because the conventional membrane-making process is always time-consuming, highly inefficient, and consumes a large amount of organic solvents. Herein we report a one-step assembly concept capable of directly processing low-viscosity oligomers into polymer-based molecular separation membranes in an ultrafast and green manner. This process was implemented by alternate atomizing-depositing of low-viscosity oligomers and reaction auxiliary agents onto a rotating support and followed by an ultrafast interfacial reaction under solvent-free conditions. Without the need for dissolution processing of polymer, solvent evaporation, and any post-treatments, the whole technological process could be accomplished within a few seconds/minutes, which is 2-3 orders of magnitude faster than conventional solution-coating technologies. The universality of this facile approach has also been demonstrated by successfully producing various defect-free polymeric membranes and homodispersed nanohybrid membranes with excellent and stable performance for bioalcohol production and recovery of different trace organics from dilute solutions.

  9. Final Report: Photo-Directed Molecular Assembly of Multifunctional Inorganic Materials

    SciTech Connect

    B.G. Potter, Jr.

    2010-10-15

    This final report details results, conclusions, and opportunities for future effort derived from the study. The work involved combining the molecular engineering of photoactive Ti-alkoxide systems and the optical excitation of hydrolysis and condensation reactions to influence the development of the metal-oxygen-metal network at the onset of material formation. Selective excitation of the heteroleptic alkoxides, coupled with control of alkoxide local chemical environment, enabled network connectivity to be influenced and formed the basis for direct deposition and patterning of Ti-oxide-based materials. The research provided new insights into the intrinsic photoresponse and assembly of these complex, alkoxide molecules. Using a suite of electronic, vibrational, and nuclear spectroscopic probes, coupled with quantum chemical computation, the excitation wavelength and fluence dependence of molecular photoresponse and the nature of subsequent hydrolysis and condensation processes were probed in pyridine-carbinol-based Ti-alkoxides with varied counter ligand groups. Several methods for the patterning of oxide material formation were demonstrated, including the integration of this photoprocessing approach with conventional, dip-coating methodologies.

  10. Metamaterial Absorbers for Infrared Detection of Molecular Self-Assembled Monolayers

    PubMed Central

    Ishikawa, Atsushi; Tanaka, Takuo

    2015-01-01

    The emerging field of plasmonic metamaterials has introduced new degree of freedom to manipulate optical field from nano to macroscopic scale, offering an attractive platform for sensing applications. So far, metamaterial sensor concepts, however, have focused on hot-spot engineering to improve the near-field enhancement, rather than fully exploiting tailored material properties. Here, we present a novel spectroscopic technique based on the metamaterial infrared (IR) absorber allowing for a low-background detection scheme as well as significant plasmonic enhancement. Specifically, we experimentally demonstrate the resonant coupling of plasmonic modes of a metamaterial absorber and IR vibrational modes of a molecular self-assembled monolayer. The metamaterial consisting of an array of Au/MgF2/Au structures exhibits an anomalous absorption at ~3000 cm−1, which spectrally overlaps with C-H stretching vibrational modes. Symmetric/asymmetric C-H stretching modes of a 16-Mercaptohexadecanoic acid monolayer are clearly observed as Fano-like anti-resonance peaks within a broad plasmonic absorption of the metamaterial. Spectral analysis using Fano line-shape fitting reveals the underlying resonant interference in plasmon-molecular coupled systems. Our metamaterial approach achieves the attomole sensitivity with a large signal-to-noise ratio in the far-field measurement, thus may open up new avenues for realizing ultrasensitive IR inspection technologies. PMID:26229011

  11. Molecular orientation of asphaltenes and PAH model compounds in Langmuir-Blodgett films using sum frequency generation spectroscopy.

    PubMed

    Andrews, A Ballard; McClelland, Arthur; Korkeila, Oona; Demidov, Alexander; Krummel, Amber; Mullins, Oliver C; Chen, Zhan

    2011-05-17

    Asphaltenes are an important class of compounds in crude oil whose surface activity is important for establishing reservoir rock wettability which impacts reservoir drainage. While many phenomenological interfacial studies with crude oils and asphaltenes have been reported, there is very little known about the molecular level interactions between asphaltenes and mineral surfaces. In this study, we analyze Langmuir-Blodgett films of asphaltenes and related model compounds with sum frequency generation (SFG) vibrational spectroscopy. In SFG, the polarization of the input (vis, IR) and output (SFG) beams can be varied, which allows the orientation of different functional groups at the interface to be determined. SFG clearly indicates that asphaltene polycyclic aromatic hydrocarbons (PAHs) are highly oriented in the plane of the interface and that the peripheral alkanes are transverse to the interface. In contrast, model compounds with oxygen functionality have PAHs oriented transverse to the interface. Computational quantum chemistry is used to support corresponding band assignments, enabling robust determination of functional group orientations.

  12. [Forming the nanosized molecular assemblies (nanoassociates) is a key to understand the properties of highly diluted aqueous solutions].

    PubMed

    Konovalov, A I; Ryzhkina, I S; Murtazina, L I; Kiseleva, Iu V

    2014-01-01

    In the present study it was shown that biological effects of highly diluted aqueous solutions were due to the formation of nano-sized (up to 400 nm) molecular assemblies, called nanoassociates mainly consisting of aqueous molecules (up to 500 million) under the influence of two effectors: solute and external electromagnetic fields.

  13. Diffusion-coupled molecular assembly: structuring of coordination polymers across multiple length scales.

    PubMed

    Hirai, Kenji; Reboul, Julien; Morone, Nobuhiro; Heuser, John E; Furukawa, Shuhei; Kitagawa, Susumu

    2014-10-22

    Porous coordination polymers (PCPs) are an intriguing class of molecular-based materials because of the designability of framework scaffolds, pore sizes and pore surface functionalities. Besides the structural designability at the molecular scale, the structuring of PCPs into mesoscopic/macroscopic morphologies has attracted much attention due to the significance for the practical applications. The structuring of PCPs at the mesoscopic/macroscopic scale has been so far demonstrated by the spatial localization of coordination reactions on the surface of templates or at the phase boundaries. However, these methodologies have never been applied to the fabrication of solid-solution or multivariate metal-organic frameworks (MOFs), in which multiple components are homogeneously mixed. Herein, we demonstrate the structuring of a box-type superstructure comprising of a solid-solution PCP by integrating a bidirectional diffusion of multiple organic ligands into molecular assembly. The parent crystals of [Zn2(ndc)2(bpy)]n were placed in the DMF solution of additional organic component of H2bdc, and the temperature was rapidly elevated up to 80 °C (ndc = 1,4-naphthalenedicarboxylate, bpy = 4,4'-bipyridyl, bdc = 1,4-benzenedicarboxylate). The dissolution of the parent crystals induced the outward diffusion of components; contrariwise, the accumulation of the other organic ligand of H2bdc induced the inward diffusion toward the surface of the parent crystals. This bidirectional diffusion of multiple components spatially localized the recrystallization at the surface of cuboid parent crystals; therefore, the nanocrystals of a solid-solution PCP ([Zn2(bdc)1.5(ndc)0.5(bpy)]n) were organized into a mesoscopic box superstructure. Furthermore, we demonstrated that the box superstructures enhanced the mass transfer kinetics for the separation of hydrocarbons.

  14. Reduction-Triggered Self-Assembly of Nanoscale Molybdenum Oxide Molecular Clusters

    SciTech Connect

    Yin, Panchao; Wu, Bin; Li, Tao; Bonnesen, Peter V.; Hong, Kunlun; Seifert, Soenke; Porcar, Lionel; Do, Changwoo; Keum, Jong Kahk

    2016-07-26

    A 2.9 nm molybdenum oxide cluster {Mo132} (Formula: [MoVI72MoV60O372(CH3COO)30(H2O)72]42-) can be obtained by reducing ammonium molybdate with hydrazine sulfate in weakly acidic CH3COOH/CH3COO- buffers. This reaction has been monitored by time-resolved UV-Vis, 1H-NMR, small angle X-ray/neutron scattering, and X-ray absorption near edge structure spectroscopy. The growth of {Mo132} cluster shows a typical sigmoid curve, suggesting a multi-step assembly mechanism for this reaction. The reaction starts with a lag phase period when partial MoVI centers of molybdate precursors are reduced to form {MoV2(acetate)} structures under the coordination effect of the acetate groups. Once the concentration of {MoV2(acetate)} reaches a critical value, it triggers the assembly of MoV and MoVI species into {Mo132} clusters. Parameters such as the type and amount of reducing agent, the pH, the type of cation, and the type of organic ligand in the reaction buffer, have been studied for the roles they play in the formation of the target clusters.Understanding the formation mechanism of giant molecular clusters is essential for rational design and synthesis of cluster-based nanomaterials with required morphologies and functionalities. Here, typical synthetic reactions of a 2.9 nm spherical molybdenum oxide cluster, {Mo132} (formula: [MoVI72MoV60O372(CH3COO)30(H2O)72]42), with systematically varied reaction parameters have been fully explored to determine the morphologies and concentration of products, reduction of metal centers, and chemical environments of the organic ligands. The growth of these clusters shows a typical sigmoid curve, suggesting a general

  15. In Situ Electrochemical Synthesis of Oriented and Defect-Free AEL Molecular-Sieve Films Using Ionic Liquids.

    PubMed

    Yu, Tongwen; Chu, Wenling; Cai, Rui; Liu, Yanchun; Yang, Weishen

    2015-10-26

    Simply preparing oriented and defect-free molecular-sieve films have been a long-standing challenge both in academia and industry. Most of the early works focus on the careful and multiple controls of the seeds layer or synthesis conditions. Herein, we report a one-step in situ electrochemical ionothermal method that combines a controllable electric field with ionic liquids. We demonstrate that an in-plane oriented and defect-free AEL (one molecular-sieve framework type) molecular-sieve film was obtained using an Al electrode as the Al source. The excellent corrosion-resistant performance of the film makes this technology promising in multiple applications, such as anti-corrosion coatings.

  16. Dipole moments and orientation polarizabilities of diatomic molecular ions for precision atomic mass measurement

    NASA Astrophysics Data System (ADS)

    Cheng, Michelle; Brown, John M.; Rosmus, Pavel; Linguerri, Roberto; Komiha, Najia; Myers, Edmund G.

    2007-01-01

    In high precision Penning trap mass spectrometry the cyclotron frequency of a polarizable ion is perturbed due to the Stark interaction with the motional electric field. For polar diatomic molecular ions, which have adjacent rotational levels of opposite parity, these shifts can be particularly large—especially for the lowest rotational levels, which are those occupied by ions stored for many hours in cryogenic Penning traps. In order to provide corrections to precision atomic mass measurements, we consider the calculation of orientation polarizabilities of CO+ and the positive ions of the first and second row diatomic hydrides, LiH+ to ArH+ . Dipole moments for these ions have been calculated using the restricted coupled cluster method with perturbative triples and large basis sets. Using these dipoles and an effective Hamiltonian, we have obtained rotational-state dependent polarizabilities of the open-shell diatomic ions CO+ , NH+ , OH+ , FH+ , PH+ , SH+ , and ClH+ . Results are given for those rotational levels that are significantly populated at 4.2K , for magnetic fields up to 10T . For the remaining first and second row hydride cations, polarizabilities at the magnetic fields of interest can be obtained from a simple formula valid for closed-shell molecules. Conversely, in cases where the polarizability shifts can be measured, our results enable experimental determination of dipole moments.

  17. Effect of substrate orientation on CdS homoepitaxy by molecular dynamics

    DOE PAGES

    Almeida, S.; Chavez, J. J.; Zhou, X. W.; ...

    2016-02-10

    CdS homoepitaxy growth was performed by molecular dynamics using different substrate orientations and structures in order to analyze the CdS crystallinity. As anticipated from thermodynamics of homoepitaxy, highly crystalline films with only point defects were obtained on substrates with rectangular surface geometries, including View the MathML source[112¯] zinc blende (ZB), [101¯0] wurtzite (WZ), [112¯0] WZ, [110][110] ZB, [010][010] ZB, and View the MathML source[1101110] ZB. In contrast, films grown on substrates with hexagonal surface geometries, corresponding to the [0001][0001] WZ and [111][111] ZB growth directions, showed structures with a large number of defects including; anti-sites, vacancies, stacking faults, twinning, andmore » polytypism. WZ and ZB transitions and grain boundaries are identified using a lattice identification algorithm and represented graphically in a structural map. A dislocation analysis was performed to detect, identify, and quantify linear defects within the atomistic data. Systematic simulations using different temperatures, deposition rates, and substrate polarities were perform to analyze the trends of dislocation densities on [0001][0001] WZ direction and showed persistent polytypism. As a result, the polytypism observed in the films grown on the substrates with hexagonal surface geometry is attributed to the similar formation energies of the WZ and ZB phases.« less

  18. Effect of substrate orientation on CdS homoepitaxy by molecular dynamics

    SciTech Connect

    Almeida, S.; Chavez, J. J.; Zhou, X. W.; Zubia, D.

    2016-02-10

    CdS homoepitaxy growth was performed by molecular dynamics using different substrate orientations and structures in order to analyze the CdS crystallinity. As anticipated from thermodynamics of homoepitaxy, highly crystalline films with only point defects were obtained on substrates with rectangular surface geometries, including View the MathML source[112¯] zinc blende (ZB), [101¯0] wurtzite (WZ), [112¯0] WZ, [110][110] ZB, [010][010] ZB, and View the MathML source[1101110] ZB. In contrast, films grown on substrates with hexagonal surface geometries, corresponding to the [0001][0001] WZ and [111][111] ZB growth directions, showed structures with a large number of defects including; anti-sites, vacancies, stacking faults, twinning, and polytypism. WZ and ZB transitions and grain boundaries are identified using a lattice identification algorithm and represented graphically in a structural map. A dislocation analysis was performed to detect, identify, and quantify linear defects within the atomistic data. Systematic simulations using different temperatures, deposition rates, and substrate polarities were perform to analyze the trends of dislocation densities on [0001][0001] WZ direction and showed persistent polytypism. As a result, the polytypism observed in the films grown on the substrates with hexagonal surface geometry is attributed to the similar formation energies of the WZ and ZB phases.

  19. Influence of molecular ordering on electrical and friction properties of omega-(trans-4-stilbene)alkylthiol self-assembled monolayers on Au (111)

    SciTech Connect

    Qi, Yabing; Liu, Xiaosong; Hendriksen, B.L.M.; Navarro, V.; Park, Jeong Y.; Ratera, Imma; Klopp, J.M.; Edder, C.; Himpsel, Franz J.; Frechet, J.M.J.; Haller, Eugene E.; Salmeron, Miquel

    2010-04-21

    The electrical and friction properties of omega-(trans-4-stilbene)alkylthiol self-assembled monolayers (SAMs) on Au(111) were investigated using atomic force microscopy (AFM) and near edge x-ray absorption fine structure spectroscopy (NEXAFS). The sample surface was uniformly covered with a molecular film consisting of very small grains. Well-ordered and flat monolayer islands were formed after the sample was heated in nitrogen at 120 oC for 1 h. While lattice resolved AFM images revealed a crystalline phase in the islands, the area between islands showed no order. The islands exhibit substantial reduction (50percent) in friction, supporting the existence of good ordering. NEXAFS measurements revealed an average upright molecular orientation in the film, both before and after heating, with a narrower tilt-angle distribution for the heated fim. Conductance-AFM measurements revealed a two orders of magnitude higher conductivity on the ordered islands than on the disordered phase. We propose that the conductance enhancement is a result of a better pi-pi stacking between the trans-stilbene molecular units as a result of improved ordering in islands.

  20. Influence of substrate orientation on the structural quality of GaAs nanowires in molecular beam epitaxy.

    PubMed

    Zhang, Zhi; Shi, Sui-Xing; Chen, Ping-Ping; Lu, Wei; Zou, Jin

    2015-01-26

    In this study, the effect of substrate orientation on the structural quality of Au-catalyzed epitaxial GaAs nanowires grown by a molecular beam epitaxy reactor has been investigated. It was found that the substrate orientations can be used to manipulate the nanowire catalyst composition and the catalyst surface energy and, therefore, to alter the structural quality of GaAs nanowires grown on different substrates. Defect-free wurtzite-structured GaAs nanowires grown on the GaAs (110) substrate have been achieved under our growth conditions.

  1. Spontaneous orientation-tuning driven by the strain variation in self-assembled ZnO-SrRuO{sub 3} heteroepitaxy

    SciTech Connect

    Zhu, Yuanmin; Liu, Ruirui; Zhan, Qian; Chang, Wei Sea; Yu, Rong; Wei, Tzu-Chiao; He, Jr-Hau; Chu, Ying-Hao

    2015-11-09

    Heteroepitaxial ZnO and SrRuO{sub 3} were grown on SrTiO{sub 3} (111) substrates and formed a self-assembled wurtzite-perovskite nanostructure. Spontaneous orientation-tuning of the SrRuO{sub 3} pillars was observed, with the growth direction changing from [111]{sub SRO} to [011]{sub SRO} as the film thickness increased, which is attributed to a misfit strain transition from the biaxial strain imposed by the SrTiO{sub 3} substrate to the vertical strain provided by the ZnO matrix. The [011]-SrRuO{sub 3} and [0001]-ZnO combination presents a favorable matching in the nanocomposite films, resulting in higher charge carrier mobility. This vertically integrated configuration and regulation on the crystallographic orientations are expected to be employed in designing multi-functional nanocomposite systems for applications in electronic devices.

  2. Investigating the Self-Assembly and Nanopatterning Characteristics of Organic Molecular Adlayers on Silicon and Graphene via Scanning Tunneling Microscopy

    NASA Astrophysics Data System (ADS)

    Karmel, Hunter Jason

    The controlled nanostructuring of matter on the atomic and molecular scale requires deep insight into the complex physical and chemical interactions that occur between adsorbates and surfaces. This dissertation examines the self assembly of molecularly thin organic adlayers on technologically significant nanoelectronic substrates using ultra high vacuum (UHV) scanning tunneling microscopy (STM). The three material systems considered in this work are cyclopentene monolayers on silicon, perylenetetracarboxylic diimide (PTCDI) adlayers on epitaxial graphene, and PTCDI melamine nanoporous molecular arrays on epitaxial graphene. The nanolithographic properties of each of these organic inorganic hybrid interfaces are extensively characterized at the molecular level. First, the molecularly precise desorption of individual cyclopentene molecules from a saturated organic passivation layer is demonstrated using feedback controlled lithography (FCL), thus achieving sub nanometer patterning resolution and the possibility of generating molecularly abrupt nanostructures on the silicon (100) surface. Second, the exceptional structural and thermal stability of PTCDI adlayers on epitaxial graphene is established using a combination of STM and X ray reflectivity (XRR) measurements. The enhanced stability of the PTCDI adlayer allows it to accommodate sub 5 nanometer voids with molecularly defined boundaries in addition to isolated molecular vacancies at room temperature. Third, a hydrogen bonded molecularly thin organic heteromolecular nanoporous network is generated on epitaxial graphene, formed by the intermixing of PTCDI and melamine. This molecular array exhibits a sub 5 nanometer two dimensional periodicity with hexagonal symmetry and is in atomic registry with the underlying graphene lattice. Overall this thesis explores the richly diverse physical and chemical interactions that promote molecularly precise lithography on nanoelectronic surfaces. In conclusion, the key insights

  3. Urea-Functionalized Self-Assembled Molecular Prism for Heterogeneous Catalysis in Water.

    PubMed

    Howlader, Prodip; Das, Paramita; Zangrando, Ennio; Mukherjee, Partha Sarathi

    2016-02-10

    Reaction of a ditopic urea "strut" (L1) with cis-(tmen)Pd(NO3)2 yielded a [3+3] self-assembled molecular triangle (T) [L1 = 1,4-di(4-pyridylureido)benzene; tmen = N,N,N',N'-tetramethylethane-1,2-diamine]. Replacing cis-(tmen)Pd(NO3)2 in the above reaction with an equimolar mixture of Pd(NO3)2 and a clip-type donor (L2) yielded a template-free multicomponent 3D trigonal prism (P) decorated with multiple urea moieties [L2 = 3,3'-(1H-1,2,4-triazole-3,5-diyl)dipyridine]. This prism (P) was characterized by NMR spectroscopy, and the structure was confirmed by X-ray crystallography. The P was employed as an effective hydrogen-bond-donor catalyst for Michael reactions of a series of water-insoluble nitro-olefins in an aqueous medium. The P showed better catalytic activity compared to the urea-based ligand L1 and the triangle T. Moreover, the confined nanospace of P in addition to large product outlet windows makes this 3D architecture a perfect molecular vessel to catalyze Diels-Alder reactions of 9-hydroxymethylanthracene with N-substituted maleimide in the aqueous medium. The present results demonstrate new observations on catalytic aqueous Diels-Alder and Michael reactions in heterogeneous fashion employing a discrete 3D architecture of Pd(II). The prism was recycled by simple filtration and reused several times without significant loss of activity.

  4. Self-assembly of amyloid-forming peptides by molecular dynamics simulations.

    PubMed

    Wei, Guanghong; Song, Wei; Derreumaux, Philippe; Mousseau, Normand

    2008-05-01

    Protein aggregation is associated with many neurodegenerative diseases. Understanding the aggregation mechanisms is a fundamental step in order to design rational drugs interfering with the toxic intermediates. This self-assembly process is however difficult to observe experimentally, which gives simulations an important role in resolving this problem. This study shows how we can proceed to gain knowledge about the first steps of aggregation. We first start by characterizing the free energy surface of the Abeta (16-22) dimer, a well-studied system numerically, using molecular dynamics simulations with OPEP coarse-grained force field. We then turn to the study of the NHVTLSQ peptide in 4-mers and 16-mers, extracting information on the onset of aggregation. In particular, the simulations indicate that the peptides are mostly random coil at room temperature, but can visit diverse amyloid-competent topologies, albeit with a low probability. The fact that the 16-mers constantly move from one structure to another is consistent with the long lag phase measured experimentally, but the rare critical steps leading to the rapid formation of amyloid fibrils still remain to be determined.

  5. Molecular assembly, interfacial rheology and foaming properties of oligofructose fatty acid esters.

    PubMed

    van Kempen, Silvia E H J; Schols, Henk A; van der Linden, Erik; Sagis, Leonard M C

    2014-01-01

    Two major types of food-grade surfactants used to stabilize foams are proteins and low molecular weight (LMW) surfactants. Proteins lower the surface tension of interfaces and tend to unfold and stabilize the interface by the formation of a visco-elastic network, which leads to high surface moduli. In contrast, LMW surfactants lower the surface tension more than proteins, but do not form interfaces with a high modulus. Instead, they stabilize the interface through the Gibbs-Marangoni mechanism that relies on rapid diffusion of surfactants, when surface tension gradients develop as a result of deformations of the interface. A molecule than can lower the surface tension considerably, like a LMW surfactant, but also provide the interface with a high modulus, like a protein, would be an excellent foam stabilizer. In this article we will discuss molecules with those properties: oligofructose fatty acid esters, both in pure and mixed systems. First, we will address the synthesis and structural characterization of the esters. Next, we will address self-assembly and rheological properties of air/water interfaces stabilized by the esters. Subsequently, this paper will deal with mixed systems of mono-esters with either di-esters and lauric acid, or proteins. Then, the foaming functionality of the esters is discussed.

  6. Probing self assembly in biological mixed colloids by SANS, deuteration and molecular manipulation

    SciTech Connect

    Hjelm, R.P.; Thiyagarajan, P.; Hoffman, A.; Alkan-Onyuksel, H.

    1994-12-31

    Small-angle neutron scattering was used to obtain information on the form and molecular arrangement of particles in mixed colloids of bile salts with phosphatidylcholine, and bile salts with monoolein. Both types of systems showed the same general characteristics. The particle form was highly dependent on total lipid concentration. At the highest concentrations the particles were globular mixed micelles with an overall size of 50{Angstrom}. As the concentration was reduced the mixed micelles elongated, becoming rodlike with diameter about 50{Angstrom}. The rods had a radial core-shell structure in which the phosphatidylcholine or monoolein fatty tails were arranged radially to form the core with the headgroups pointing outward to form the shell. The bile salts were at the interface between the shell and core with the hydrophilic parts facing outward as part of the shell. The lengths of the rods increased and became more polydispersed with dilution. At sufficiently low concentrations the mixed micelles transformed into single bilayer vesicles. These results give insight on the physiological function of bile and on the rules governing the self assembly of bile particles in the hepatic duct and the small intestine.

  7. Molecular Understanding on the Underwater Oleophobicity of Self-Assembled Monolayers: Zwitterionic versus Nonionic.

    PubMed

    Cheng, Gang; Liao, Mingrui; Zhao, Daohui; Zhou, Jian

    2017-02-21

    Molecular dynamics simulations are conducted to investigate the underwater oleophobicity of self-assembled monolayers (SAMs) with different head groups. Simulation results show that the order of underwater oleophobicity of SAMs is methyl < amide < oligo(ethylene glycol) (OEG) < ethanolamine (ETA) < hydroxyl < mixed-charged zwitterionic. The underwater-oil contact angles (OCAs) are <133° for all nonionic hydrophilic SAMs, while the mixed-charged zwitterionic SAMs are underwater superoleophobic (OCA can reach 180°). It appears that surfaces with stronger underwater oleophobicity have better antifouling performance. Further study on the effect of different alkyl ammonium ions on mixed-charged SAMs reveals that the underwater OCAs are >143.6° for all SAMs; mixed-charged SAMs containing primary alkyl ammonium ion are likely to possess the best underwater oleophobicity for its strong hydration capacity. It seems that alkyl sulfonate anion (SO3(-)) is more hydrophilic than alkyl trimethylammonium ion (NC3(+)) for the hydrophobic methyl groups on nitrogen atoms and that the hydration of SO3(-) in mixed-charged SAMs can be seriously blocked by NC3(+). The monomer of SO3(-) should be slightly longer than that of NC3(+) to obtain better underwater oleophobicity in NC3(+)-/SO3(-)-SAMs. In addition, the underwater oleophobicity of SAMs might become worse at low grafting densities. This work systematically proves that a zwitterionic surface is more underwater oleophobic than a nonionic surface. These results will help for the design and development of superoleophobic surfaces.

  8. A molecular model for self-assembly of amyloid fibrils: Immunoglobulin light chains

    SciTech Connect

    Stevens, F.J.; Myatt, E.A.; Westholm, F.A.

    1995-08-29

    The formation and pathological deposition of amyloid fibrils are defining features of many acquired and inherited disorders, including primary or light-chain-associated amyloidosis, Alzheimer`s disease, and adult-onset diabetes. No pharmacological methods exist to block this process or to effect the removal of fibrils from tissue, and thus, little can be done to prevent organ failure and ultimate death that result from deposition of amyloid. Knowledge of the pathogenesis, treatment, or prevention of these presently incurable diseases is limited due to the relative paucity of information regarding the biophysical basis of amyloid formation. Antibody light chains of different amino acid sequence show differential amyloid-forming tendencies and, as such, can provide insight into the structural organization of amyloid fibrils as well as into basic mechanisms of protein self-assembly. We have compared primary structures of 180 human monoclonal light chains and have identified particular residues and positions within the variable domain that differentiate amyloid-from nonamyloid-associated proteins. We propose a molecular model that accounts for amyloid formation by antibody light chains and might also have implications for other forms of amyloidosis. 24 refs., 2 figs., 1 tab.

  9. Probing the Orientation and Conformation of alpha-Helix and beta-Strand Model Peptides on Self-Assembled Monolayers Using Sum Frequency Generation and NEXAFS Spectroscopy

    SciTech Connect

    Weidner, T.; Apte, J; Gamble, L; Castner, D

    2010-01-01

    The structure and orientation of amphiphilic {alpha}-helix and {beta}-strand model peptide films on self-assembled monolayers (SAMs) have been studied with sum frequency generation (SFG) vibrational spectroscopy and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy. The {alpha}-helix peptide is a 14-mer, and the {beta}-strand is a 15-mer of hydrophilic lysine and hydrophobic leucine residues with hydrophobic periodicities of 3.5 and 2, respectively. These periodicities result in the leucine side chains located on one side of the peptides and the lysine side chains on the other side. The SAMs were prepared from the assembly of either carboxylic acid- or methyl-terminated alkyl thiols onto gold surfaces. For SFG studies, the deuterated analog of the methyl SAM was used. SFG vibrational spectra in the C-H region of air-dried peptides films on both SAMs exhibit strong peaks near 2965, 2940, and 2875 cm{sup -1} related to ordered leucine side chains. The orientation of the leucine side chains was determined from the phase of these features relative to the nonresonant gold background. The relative phase for both the {alpha}-helix and {beta}-strand peptides showed that the leucine side chains were oriented away from the carboxylic acid SAM surface and oriented toward the methyl SAM surface. Amide I peaks observed near 1656 cm{sup -1} for the {alpha}-helix peptide confirm that the secondary structure is preserved on both SAMs. Strong linear dichroism related to the amide {pi}* orbital at 400.8 eV was observed in the nitrogen K-edge NEXAFS spectra for the adsorbed {beta}-strand peptides, suggesting that the peptide backbones are oriented parallel to the SAM surface with the side chains pointing toward or away from the interface. For the {alpha}-helix the dichroism of the amide {pi}* is significantly weaker, probably because of the broad distribution of amide bond orientations in the {alpha}-helix secondary structure.

  10. Control over Structure and Function of Peptide Amphiphile Supramolecular Assemblies through Molecular Design and Energy Landscapes

    NASA Astrophysics Data System (ADS)

    Tantakitti, Faifan

    Supramolecular chemistry is a powerful tool to create a material of a defined structure with tunable properties. This strategy has led to catalytically active, bioactive, and environment-responsive materials, among others, that are valuable in applications ranging from sensor technology to energy and medicine. Supramolecular polymers formed by peptide amphiphiles (PAs) have been especially relevant in tissue regeneration due to their ability to form biocompatible structures and mimic many important signaling molecules in biology. These supramolecular polymers can form nanofibers that create networks which mimic natural extracellular matrices. PA materials have been shown to induce growth of blood vessels, bone, cartilage, and nervous tissue, among others. The work described in this thesis not only studied the relationship between molecular structure and functions of PA assemblies, but also uncovered a powerful link between the energy landscape of their supramolecular self-assembly and the ability of PA materials to interact with cells. In chapter 2, it is argued that fabricating fibrous nanostructures with defined mechanical properties and decoration with bioactive molecules is not sufficient to create a material that can effectively communicate with cells. By systemically placing the fibronectin-derived RGDS epitope at increasing distances from the surface of PA nanofibers through a linker of one to five glycine residues, integrin-mediated RGDS signaling was enhanced. The results suggested that the spatial presentation of an epitope on PA nanofibers strongly influences the bioactivity of the PA substrates. In further improving functionality of a PA-based scaffold to effectively direct cell growth and differentiation, chapter 3 explored the use of a cell microcarrier to compartmentalize and simultaneously tune insoluble and soluble signals in a single matrix. PA nanofibers were incorporated at the surface of the microcarrier in order to promote cell adhesion, while

  11. Assembly of the transmembrane domain of E. coli PhoQ histidine kinase: implications for signal transduction from molecular simulations.

    PubMed

    Lemmin, Thomas; Soto, Cinque S; Clinthorne, Graham; DeGrado, William F; Dal Peraro, Matteo

    2013-01-01

    The PhoQP two-component system is a signaling complex essential for bacterial virulence and cationic antimicrobial peptide resistance. PhoQ is the histidine kinase chemoreceptor of this tandem machine and assembles in a homodimer conformation spanning the bacterial inner membrane. Currently, a full understanding of the PhoQ signal transduction is hindered by the lack of a complete atomistic structure. In this study, an atomistic model of the key transmembrane (TM) domain is assembled by using molecular simulations, guided by experimental cross-linking data. The formation of a polar pocket involving Asn202 in the lumen of the tetrameric TM bundle is crucial for the assembly and solvation of the domain. Moreover, a concerted displacement of the TM helices at the periplasmic side is found to modulate a rotation at the cytoplasmic end, supporting the transduction of the chemical signal through a combination of scissoring and rotational movement of the TM helices.

  12. An automated spin-assisted approach for molecular layer-by-layer assembly of crosslinked polymer thin films

    SciTech Connect

    Chan, Edwin P.; Chung, Jun Young; Stafford, Christopher M.; Lee, Jung-Hyun

    2012-11-15

    We present the design of an automated spin-coater that facilitates fabrication of polymer films based on molecular layer-by-layer (mLbL) assembly. Specifically, we demonstrate the synthesis of ultrathin crosslinked fully-aromatic polyamide (PA) films that are chemically identical to polymer membranes used in water desalination applications as measured by X-ray photoelectron spectroscopy. X-ray reflectivity measurements indicate that the automated mLbL assembly creates films with a constant film growth rate and minimal roughness compared with the traditional interfacial polymerization of PA. This automated spin-coater improves the scalability and sample-to-sample consistency by reducing human involvement in the mLbL assembly.

  13. Self-assembly, redox activity, and charge transport of functional surface nano-architectures by molecular design

    NASA Astrophysics Data System (ADS)

    Skomski, Daniel

    Surface-assisted molecular self-assembly is a promising strategy to program the structure and chemical state of atoms and molecules in nano-architectures to achieve a specific function. The experiments described in this thesis demonstrate that the design and programming of basic organic components leads to desired characteristics by self-assembly. The fabrication of uniform single-site metal centers at surfaces, important for high selectivity in next-generation catalysts, was accomplished by coordination to redox non-innocent phenanthroline and tetrazine-based ligands. These examples were the first demonstrating tuning of the metal oxidation state in surface coordination architectures through rational ligand design. The molecular-scale coordination architectures were the first formed from chromium and vanadium, and the first from platinum in a non-porphyrin system. The first mixed valence metal-ligand surface structure was fabricated that attained the same ligand coordination number for all metal sites. A new surface reaction method was demonstrated between an inexpensive sodium chloride reagent and carboxylate ligands. High-temperature, molecular-resolution microscopy and spectroscopy of the ordered metal-organic structures demonstrated thermal stability up to 300 °C, the highest molecular-level thermal stability in organic surface nanostructures yet achieved, making such systems potential candidates for moderate-temperature catalytic reactions. Molecular self-assembly was expanded into organic semiconductor thin films. In a two-component, bi-layered system, hydrogen bonding between carboxylates and carboxylic acid-substituted thiophenes was utilized, yielding the first real-space images of phenyl-thiophene stacking. In a one-component system, multiple donor-acceptor pi-pi contacts between phenyltriazole building blocks accomplished assembly of flat-lying molecules from a surface with molecular-scale precision through more than twenty molecular layers. Sufficient

  14. Electronic polymers and DNA self-assembled in nanowire transistors.

    PubMed

    Hamedi, Mahiar; Elfwing, Anders; Gabrielsson, Roger; Inganäs, Olle

    2013-02-11

    Aqueous self-assembly of DNA and molecular electronic materials can lead to the creation of innumerable copies of identical devices, and inherently programmed complex nanocircuits. Here self-assembly of a water soluble and highly conducting polymer PEDOT-S with DNA in aqueous conditions is shown. Orientation and assembly of the conducting DNA/PEDOT-S complex into electrochemical DNA nanowire transistors is demonstrated.

  15. Oncogenic K-Ras Binds to an Anionic Membrane in Two Distinct Orientations: A Molecular Dynamics Analysis.

    PubMed

    Prakash, Priyanka; Zhou, Yong; Liang, Hong; Hancock, John F; Gorfe, Alemayehu A

    2016-03-08

    K-Ras is a membrane-associated GTPase that cycles between active and inactive conformational states to regulate a variety of cell signaling pathways. Somatic mutations in K-Ras are linked to 15-20% of all human tumors. K-Ras attaches to the inner leaflet of the plasma membrane via a farnesylated polybasic domain; however, the structural details of the complex remain poorly understood. Based on extensive (7.5 μs total) atomistic molecular dynamics simulations here we show that oncogenic mutant K-Ras interacts with a negatively charged lipid bilayer membrane in multiple orientations. Of these, two highly populated orientations account for ∼54% of the conformers whose catalytic domain directly interacts with the bilayer. In one of these orientation states, membrane binding involves helices 3 and 4 of the catalytic domain in addition to the farnesyl and polybasic motifs. In the other orientation, β-strands 1-3 and helix 2 on the opposite face of the catalytic domain contribute to membrane binding. Flexibility of the linker region was found to be important for the reorientation. The biological significance of these observations was evaluated by initial experiments in cells overexpressing mutant K-Ras as well as by an analysis of Ras-effector complex structures. The results suggest that only one of the two major orientation states is capable of effector binding. We propose that the different modes of membrane binding may be exploited in structure-based drug design efforts for cancer therapy.

  16. Chiral separation of sertraline with microemulsion electrokinetic chromatography on a polymer/β-cyclodextrin assembling molecular film modified capillary.

    PubMed

    Cheng, Hongying; He, Baoku; Zhang, Qianli; Tu, Yifeng

    2010-01-01

    A capillary modified by assembling a molecular film was presented for the chiral separation of sertraline by microemulsion electrokinetic chromatography. The assembling molecular film was constructed with poly(diallyldimethylammonium-chloride) and β-cyclodextrin via inclusion complexation. The separation efficiency of cis-trans isomers and enantiomers of sertraline was improved with a running microemulsion that contained the acetonitrile, sodium dodecyl sulfate, n-butanol and n-hexane buffered with sodium tetraborate. The baseline separation of four sertraline cis-trans isomers and enantiomers was achieved under the optimum conditions. The detection limit for isomers and enantiomers of sertraline (1S,4S, 1R,4R, 1S,4R, 1R,4S) was 0.15, 0.15, 0.30, 0.30 mg/L, respectively. The mechanism of chiral separation was studied and it could be applied for the determination of commercial Zoloft tablet samples satisfactorily.

  17. Supra-molecular assembly of a lumican-derived peptide amphiphile enhances its collagen-stimulating activity.

    PubMed

    Walter, Merlin N M; Dehsorkhi, Ashkan; Hamley, Ian W; Connon, Che J

    2016-02-01

    C16-YEALRVANEVTLN, a peptide amphiphile (PA) incorporating a biologically active amino acid sequence found in lumican, has been examined for its influence upon collagen synthesis by human corneal fibroblasts in vitro, and the roles of supra-molecular assembly and activin receptor-like kinase ALK receptor signaling in this effect were assessed. Cell viability was monitored using the Alamar blue assay, and collagen synthesis was assessed using Sirius red. The role of ALK signaling was studied by receptor inhibition. Cultured human corneal fibroblasts synthesized significantly greater amounts of collagen in the presence of the PA over both 7-day and 21-day periods. The aggregation of the PA to form nanotapes resulted in a notable enhancement in this activity, with an approximately two-fold increase in collagen production per cell. This increase was reduced by the addition of an ALK inhibitor. The data presented reveal a stimulatory effect upon collagen synthesis by the primary cells of the corneal stroma, and demonstrate a direct influence of supra-molecular assembly of the PA upon the cellular response observed. The effects of PA upon fibroblasts were dependent upon ALK receptor function. These findings elucidate the role of self-assembled nanostructures in the biological activity of peptide amphiphiles, and support the potential use of a self-assembling lumican derived PA as a novel biomaterial, intended to promote collagen deposition for wound repair and tissue engineering purposes.

  18. 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

    2017-02-23

    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 C6 to C20. 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

  19. 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.

  20. Molecular protein adaptor with genetically encoded interaction sites guiding the hierarchical assembly of plasmonically active nanoparticle architectures

    NASA Astrophysics Data System (ADS)

    Schreiber, Andreas; Huber, Matthias C.; Cölfen, Helmut; Schiller, Stefan M.

    2015-03-01

    The control over the defined assembly of nano-objects with nm-precision is important to create systems and materials with enhanced properties, for example, metamaterials. In nature, the precise assembly of inorganic nano-objects with unique features, for example, magnetosomes, is accomplished by efficient and reliable recognition schemes involving protein effectors. Here we present a molecular approach using protein-based ‘adaptors/connectors’ with genetically encoded interaction sites to guide the assembly and functionality of different plasmonically active gold nanoparticle architectures (AuNP). The interaction of the defined geometricaly shaped protein adaptors with the AuNP induces the self-assembly of nanoarchitectures ranging from AuNP encapsulation to one-dimensional chain-like structures, complex networks and stars. Synthetic biology and bionanotechnology are applied to co-translationally encode unnatural amino acids as additional site-specific modification sites to generate functionalized biohybrid nanoarchitectures. This protein adaptor-based nano-object assembly approach might be expanded to other inorganic nano-objects creating biohybrid materials with unique electronic, photonic, plasmonic and magnetic properties.

  1. Self-assembled molecular p/n junctions for applications in dye-sensitized solar energy conversion.

    PubMed

    Farnum, Byron H; Wee, Kyung-Ryang; Meyer, Thomas J

    2016-09-01

    The achievement of long-lived photoinduced redox separation lifetimes has long been a central goal of molecular-based solar energy conversion strategies. The longer the redox-separation lifetime, the more time available for useful work to be extracted from the absorbed photon energy. Here we describe a novel strategy for dye-sensitized solar energy applications in which redox-separated lifetimes on the order of milliseconds to seconds can be achieved based on a simple toolkit of molecular components. Specifically, molecular chromophores (C), electron acceptors (A) and electron donors (D) were self-assembled on the surfaces of mesoporous, transparent conducting indium tin oxide nanoparticle (nanoITO) electrodes to prepare both photoanode (nanoITO|-A-C-D) and photocathode (nanoITO|-D-C-A) assemblies. Nanosecond transient-absorption and steady-state photolysis measurements show that the electrodes function microscopically as molecular analogues of semiconductor p/n junctions. These results point to a new chemical strategy for dye-sensitized solar energy conversion based on molecular excited states and electron acceptors/donors on the surfaces of transparent conducting oxide nanoparticle electrodes.

  2. Self-assembled molecular p/n junctions for applications in dye-sensitized solar energy conversion

    NASA Astrophysics Data System (ADS)

    Farnum, Byron H.; Wee, Kyung-Ryang; Meyer, Thomas J.

    2016-09-01

    The achievement of long-lived photoinduced redox separation lifetimes has long been a central goal of molecular-based solar energy conversion strategies. The longer the redox-separation lifetime, the more time available for useful work to be extracted from the absorbed photon energy. Here we describe a novel strategy for dye-sensitized solar energy applications in which redox-separated lifetimes on the order of milliseconds to seconds can be achieved based on a simple toolkit of molecular components. Specifically, molecular chromophores (C), electron acceptors (A) and electron donors (D) were self-assembled on the surfaces of mesoporous, transparent conducting indium tin oxide nanoparticle (nanoITO) electrodes to prepare both photoanode (nanoITO|-A-C-D) and photocathode (nanoITO|-D-C-A) assemblies. Nanosecond transient-absorption and steady-state photolysis measurements show that the electrodes function microscopically as molecular analogues of semiconductor p/n junctions. These results point to a new chemical strategy for dye-sensitized solar energy conversion based on molecular excited states and electron acceptors/donors on the surfaces of transparent conducting oxide nanoparticle electrodes.

  3. Pulse-fluence-specified optimal control simulation with applications to molecular orientation and spin-isomer-selective molecular alignment

    SciTech Connect

    Yoshida, Masataka; Nakashima, Kaoru; Ohtsuki, Yukiyoshi

    2015-12-31

    We propose an optimal control simulation with specified pulse fluence and amplitude. The simulation is applied to the orientation control of CO molecules to examine the optimal combination of THz and laser pulses, and to discriminate nuclear-spin isomers of {sup 14}N{sub 2} as spatially anisotropic distributions.

  4. Self-assembled shape- and orientation-controlled synthesis of nanoscale Cu3Si triangles, squares, and wires.

    PubMed

    Zhang, Zhou; Wong, Lai Mun; Ong, Hock Guan; Wang, Xin Jiao; Wang, Jun Ling; Wang, Shi Jie; Chen, Hongyu; Wu, Tom

    2008-10-01

    Controlling shape and orientation is important for the synthesis of functional nanomaterials. In this work, nanoscale Cu3Si triangles, squares, and wires have been grown on Si(111), (100), and (110) substrates, respectively, through a template-free Au-nanoparticle-assisted vapor transport method. The sides of nanotriangles and nanosquares and the growth direction of the nanowires are all along Si <110>, giving rise to long-range ordering of the nanostructures. Au nanoparticles absorb Cu vapor and facilitate the rate-limited diffusion of Si, which is critical for the shape-controlled growth of Cu3Si. This bottom-up approach to synthesize shape- and orientation-controlled Cu3Si nanostructures might be applicable to the tailored growth of other materials.

  5. An Experiment-Oriented Approach to Teaching the Kinetic Molecular Theory.

    ERIC Educational Resources Information Center

    Wiseman, Frank L., Jr.

    1979-01-01

    This paper reports an experiment in the teaching of the kinetic molecular theory to nonscience majors by the inquiry method. It allows the student to develop an essentially correct view of gases, liquids, and solids on the atomic or molecular level, and illustrates how one can draw conclusions about the molecular level by simple visual…

  6. Bacteriophage assembly.

    PubMed

    Aksyuk, Anastasia A; Rossmann, Michael G

    2011-03-01

    Bacteriophages have been a model system to study assembly processes for over half a century. Formation of infectious phage particles involves specific protein-protein and protein-nucleic acid interactions, as well as large conformational changes of assembly precursors. The sequence and molecular mechanisms of phage assembly have been elucidated by a variety of methods. Differences and similarities of assembly processes in several different groups of bacteriophages are discussed in this review. The general principles of phage assembly are applicable to many macromolecular complexes.

  7. Molecular orientation, thermal behavior and density of electron and hole transport layers and the implication on device performance for OLEDs

    NASA Astrophysics Data System (ADS)

    Kearns, Kenneth L.; Na, Hong-Yeop; Froese, Robert D.; Mukhopadhyay, Sukrit; Woodward, Hunter; Welsh, Dean; De Vries, Timothy; Devore, David; Trefonas, Peter; Hong, Liang

    2014-10-01

    Recent progress has shown that molecular orientation in vapor-deposited glasses can affect device performance. The deposition process can result in films where the molecular axis of the glass material is preferentially ordered to lie parallel to the plane of the substrate. Here, materials made within Dow's Electronic Materials business showed enhanced performance when the orientation of the molecules, as measured by variable angle spectroscopic ellipsometry, was oriented in a more parallel fashion as compared to other materials. For one material, the anisotropic packing was observed in the as-deposited glass and was isotropic for solution-cast and annealed films. In addition, the density of an as-deposited N,N'-bis(naphthalene-1-yl)-N,N'-bis(phenyl)-2,2'-dimethylbenzidine (NPD) film was 0.8% greater than what was realized from slowly cooling the supercooled liquid. This enhanced density indicated that vapor-deposited molecules were packing more closely in addition to being anisotropic. Finally, upon heating the NPD film into the supercooled liquid state, both the density and anisotropic packing of the as-deposited glass was lost.

  8. Boundary conditions for fluids with internal orientational degrees of freedom: apparent velocity slip associated with the molecular alignment.

    PubMed

    Heidenreich, Sebastian; Ilg, Patrick; Hess, Siegfried

    2007-06-01

    Boundary effects are investigated for fluids with internal orientational degrees of freedom such as molecular liquids, thermotropic and lyotropic liquid crystals, and polymeric fluids. The orientational degrees of freedom are described by the second rank alignment tensor which is related to the birefringence. We use a standard model to describe the orientational dynamics in the presence of flow, the momentum balance equations, and a constitutive law for the pressure tensor to describe our system. In the spirit of irreversible thermodynamics, boundary conditions are formulated for the mechanical slip velocity and the flux of the alignment. They are set up such that the entropy production at the wall inferred from the entropy flux is positive definite. Even in the absence of a true mechanical slip, the coupling between orientation and flow leads to flow profiles with an apparent slip. This has consequences for the macroscopically measurable effective velocity. In analytical investigations, we consider the simplified case of an isotropic fluid in the Newtonian and stationary flow regime. For special geometries such as plane and cylindrical Couette flow, plane Poiseuille flow, and a flow down an inclined plane, we demonstrate explicitly how the boundary conditions lead to an apparent slip. Furthermore, we discuss the dependence of the effective viscosity and of the effective slip length on the model parameters.

  9. Boundary conditions for fluids with internal orientational degrees of freedom: Apparent velocity slip associated with the molecular alignment

    SciTech Connect

    Heidenreich, Sebastian; Hess, Siegfried; Ilg, Patrick

    2007-06-15

    Boundary effects are investigated for fluids with internal orientational degrees of freedom such as molecular liquids, thermotropic and lyotropic liquid crystals, and polymeric fluids. The orientational degrees of freedom are described by the second rank alignment tensor which is related to the birefringence. We use a standard model to describe the orientational dynamics in the presence of flow, the momentum balance equations, and a constitutive law for the pressure tensor to describe our system. In the spirit of irreversible thermodynamics, boundary conditions are formulated for the mechanical slip velocity and the flux of the alignment. They are set up such that the entropy production at the wall inferred from the entropy flux is positive definite. Even in the absence of a true mechanical slip, the coupling between orientation and flow leads to flow profiles with an apparent slip. This has consequences for the macroscopically measurable effective velocity. In analytical investigations, we consider the simplified case of an isotropic fluid in the Newtonian and stationary flow regime. For special geometries such as plane and cylindrical Couette flow, plane Poiseuille flow, and a flow down an inclined plane, we demonstrate explicitly how the boundary conditions lead to an apparent slip. Furthermore, we discuss the dependence of the effective viscosity and of the effective slip length on the model parameters.

  10. Avoiding polar catastrophe in the growth of polarly orientated nickel perovskite thin films by reactive oxide molecular beam epitaxy

    NASA Astrophysics Data System (ADS)

    Yang, H. F.; Liu, Z. T.; Fan, C. C.; Yao, Q.; Xiang, P.; Zhang, K. L.; Li, M. Y.; Liu, J. S.; Shen, D. W.

    2016-08-01

    By means of the state-of-the-art reactive oxide molecular beam epitaxy, we synthesized (001)- and (111)-orientated polar LaNiO3 thin films. In order to avoid the interfacial reconstructions induced by polar catastrophe, screening metallic Nb-doped SrTiO3 and iso-polarity LaAlO3 substrates were chosen to achieve high-quality (001)-orientated films in a layer-by-layer growth mode. For largely polar (111)-orientated films, we showed that iso-polarity LaAlO3 (111) substrate was more suitable than Nb-doped SrTiO3. In situ reflection high-energy electron diffraction, ex situ high-resolution X-ray diffraction, and atomic force microscopy were used to characterize these films. Our results show that special attentions need to be paid to grow high-quality oxide films with polar orientations, which can prompt the explorations of all-oxide electronics and artificial interfacial engineering to pursue intriguing emergent physics like proposed interfacial superconductivity and topological phases in LaNiO3 based superlattices.

  11. Anisotropic orientational motion of molecular adsorbates at the air-water interface

    SciTech Connect

    Zimdars, D.; Dadap, J.I.; Eisenthal, K.B.; Heinz, T.F.

    1999-04-29

    The ultrafast orientational motions of coumarin 314 (C314) adsorbed at the air/water interface were investigated by time-resolved surface second harmonic generation (TRSHG). The theory and method of using TRSHG to detect both out-of-plane and in-plane orientational motions are discussed. The interfacial solute motions were found to be anisotropic, with differing out-of-plane and in-plane reorientation time constants. This report presents the first direct observation of in-plane orientational motion of a molecule (C314) at the air/water interface using TRSHG. The in-plane reorientation time constant is 600 {+-} 40 ps. The out-of-plane reorientation time constant is 350 {+-} 20 ps. The out-of-plane orientational motion of C314 is similar to the previous results on rhodamine 6G at the air/water interface which indicated increased interfacial friction compared with bulk aqueous solution. The surface reorientation times are 2--3 times slower than the bulk isotropic orientational diffusion time.

  12. Mechanical and charge transport properties of alkanethiol self-assembled monolayers on Au (111) surface: The Role of Molecular Tilt

    SciTech Connect

    Mulleregan, Alice; Qi, Yabing; Ratera, Imma; Park, Jeong Y.; Ashby, Paul D.; Quek, Su Ying; Neaton, J. B.; Salmeron, Miquel

    2007-11-12

    The relationship between charge transport and mechanical properties of alkanethiol self-assembled monolayers (SAM) on Au(111) films has been investigated using an atomic force microscope with a conductive tip. Molecular tilts induced by the pressure applied by the tip cause stepwise increases in film conductivity. A decay constant {beta} = 0.57 {+-} 0.03 {angstrom}{sup -1} was found for the current passing through the film as a function of tip-substrate separation due to this molecular tilt. This is significantly smaller than the value of {approx} 1 {angstrom}{sup -1} found when the separation is changed by changing the length of the alkanethiol molecules. Calculations indicate that for isolated dithiol molecules S-bonded to hollow sites, the junction conductance does not vary significantly as a function of molecular tilt. The impact of S-Au bonding on SAM conductance is discussed.

  13. Molecular dynamics simulations of peptide adsorption on self-assembled monolayers

    NASA Astrophysics Data System (ADS)

    Xie, Yun; Liu, Meifeng; Zhou, Jian

    2012-08-01

    All-atom molecular dynamics simulations are performed to investigate the neuromedin-B peptide adsorption on the self-assembled monolayers (SAMs) of SH(CH2)10N+(CH3)2CH2CH(OH)CH2SO3- (SBT), SH(CH2)10OH and SH(CH2)10CH3. The force-distance profiles show that the surface resistance to peptide adsorption is mainly generated by the water molecules tightly bound to surfaces via hydrogen bonds (hydration water molecules); but surfaces themselves may also set an energy barrier for the approaching peptide. For the SBT-SAM, the surface first exerts a relatively high repulsive force and then a rather week attractive force on the approaching peptide; meanwhile the hydration water molecules exert a strong repulsive force on the peptide. Therefore, SBT-SAM has an excellent performance on resisting protein adsorption. For the OH-SAM and CH3-SAM, surfaces show low or little energy barrier but strong affinity to the peptide; and the hydration water molecules apply merely a repulsive force within a much narrower range and with lower intensity compared with the case for the SBT-SAM. The analysis of structural and dynamical properties of the peptide, surface and water indicates that possible factors contributing to surface resistance include the hydrogen-bond formation capability of surfaces, mobility of water molecules near surfaces, surface packing density and chain flexibility of SAMs. There are a large number of hydrogen bonds formed between the hydration water molecules and the functional groups of the SBT-SAM, which greatly lowers the mobility of water molecules near the surface. This tightly-bound water layer effectively reduces the direct contact between the surface and the peptide. Furthermore, the SBT-SAM also has a high flexibility and a low surface packing density, which allows water molecules to penetrate into the surface to form tightly-bound networks and therefore reduces the affinity between the peptide and the surface. The results show that the protein

  14. Post-Self-Assembly Cross-Linking to Integrate Molecular Nanofibers with Copolymers in Oscillatory Hydrogels

    DTIC Science & Technology

    2013-05-09

    polymerizable sites for copolymerizing with N-isopropylacrylamide and for attaching a catalytic ruthenium bipyridine complex on the copolymer. The... ruthenium complex containing a vinyl group. This post- self-assembly cross-linking approach not only demonstrated the stability of the peptide bond under...attaching a catalytic ruthenium bipyridine complex on the copolymer. The combination of supramolecular self-assembly with copolymerization offers a

  15. Surface Patterning of Benzene Carboxylic Acids on Graphite: Influence of structure, solvent, and concentration on molecular self-assembly

    NASA Astrophysics Data System (ADS)

    Florio, Gina; Stiso, Kimberly; Campanelli, Joseph; Dessources, Kimberly; Folkes, Trudi

    2012-02-01

    Scanning tunneling microscopy (STM) was used to investigate the molecular self-assembly of four different benzene carboxylic acid derivatives at the liquid/graphite interface: pyromellitic acid (1,2,4,5-benzenetetracarboxylic acid), trimellitic acid (1,2,4-benzenetricarboxylic acid), trimesic acid (1,3,5-benzenetricarboxylic acid), and 1,3,5-benzenetriacetic acid. A range of two dimensional networks are observed that depend sensitively on the number of carboxylic acids present, the nature of the solvent, and the solution concentration. We will describe our recent efforts to determine (a) the preferential two-dimensional structure(s) for each benzene carboxylic acid at the liquid/graphite interface, (b) the thermodynamic and kinetic factors influencing self-assembly (or lack thereof), (c) the role solvent plays in the assembly, (e) the effect of in situ versus ex situ dilution on surface packing density, and (f) the temporal evolution of the self-assembled monolayer. Results of computational analysis of analog molecules and model monolayer films will also be presented to aid assignment of network structures and to provide a qualitative picture of surface adsorption and network formation.

  16. Graphene as a spacer to layer-by-layer assemble electrochemically functionalized nanostructures for molecular bioelectronic devices.

    PubMed

    Wang, Xiang; Wang, Jingfang; Cheng, Hanjun; Yu, Ping; Ye, Jianshan; Mao, Lanqun

    2011-09-06

    This study demonstrates the capability of graphene as a spacer to form electrochemically functionalized multilayered nanostructures onto electrodes in a controllable manner through layer-by-layer (LBL) chemistry. Methylene green (MG) and positively charged methylimidazolium-functionalized multiwalled carbon nanotubes (MWNTs) were used as examples of electroactive species and electrochemically useful components for the assembly, respectively. By using graphene as the spacer, the multilayered nanostructures of graphene/MG and graphene/MWNT could be readily formed onto electrodes with the LBL method on the basis of the electrostatic and/or π-π interaction(s) between graphene and the electrochemically useful components. Scanning electron microscopy (SEM), ultraviolet-visible spectroscopy (UV-vis), and cyclic voltammetry (CV) were used to characterize the assembly processes, and the results revealed that nanostructure assembly was uniform and effective with graphene as the spacer. Electrochemical studies demonstrate that the assembled nanostructures possess excellent electrochemical properties and electrocatalytic activity toward the oxidation of NADH and could thus be used as electronic transducers for bioelectronic devices. This potential was further demonstrated by using an alcohol dehydrogenase-based electrochemical biosensor and glucose dehydrogenase-based glucose/O(2) biofuel cell as typical examples. This study offers a simple route to the controllable formation of graphene-based electrochemically functionalized nanostructures that can be used for the development of molecular bioelectronic devices such as biosensors and biofuel cells.

  17. Structure of a bacterial virus DNA-injection protein complex reveals a decameric assembly with a constricted molecular channel

    SciTech Connect

    Zhao, Haiyan; Speir, Jeffrey A.; Matsui, Tsutomu; Lin, Zihan; Liang, Lingfei; Lynn, Anna Y.; Varnado, Brittany; Weiss, Thomas M.; Tang, Liang; Schuch, Raymond

    2016-02-16

    The multi-layered cell envelope structure of Gram-negative bacteria represents significant physical and chemical barriers for short-tailed phages to inject phage DNA into the host cytoplasm. Here we show that a DNA-injection protein of bacteriophage Sf6, gp12, forms a 465-kDa, decameric assembly in vitro. The electron microscopic structure of the gp12 assembly shows a ~150-Å, mushroom-like architecture consisting of a crown domain and a tube-like domain, which embraces a 25-Å-wide channel that could precisely accommodate dsDNA. The constricted channel suggests that gp12 mediates rapid, uni-directional injection of phage DNA into host cells by providing a molecular conduit for DNA translocation. The assembly exhibits a 10-fold symmetry, which may be a common feature among DNA-injection proteins of P22-like phages and may suggest a symmetry mismatch with respect to the 6-fold symmetric phage tail. As a result, the gp12 monomer is highly flexible in solution, supporting a mechanism for translocation of the protein through the conduit of the phage tail toward the host cell envelope, where it assembles into a DNA-injection device.

  18. Structure of a bacterial virus DNA-injection protein complex reveals a decameric assembly with a constricted molecular channel

    DOE PAGES

    Zhao, Haiyan; Speir, Jeffrey A.; Matsui, Tsutomu; ...

    2016-02-16

    The multi-layered cell envelope structure of Gram-negative bacteria represents significant physical and chemical barriers for short-tailed phages to inject phage DNA into the host cytoplasm. Here we show that a DNA-injection protein of bacteriophage Sf6, gp12, forms a 465-kDa, decameric assembly in vitro. The electron microscopic structure of the gp12 assembly shows a ~150-Å, mushroom-like architecture consisting of a crown domain and a tube-like domain, which embraces a 25-Å-wide channel that could precisely accommodate dsDNA. The constricted channel suggests that gp12 mediates rapid, uni-directional injection of phage DNA into host cells by providing a molecular conduit for DNA translocation. Themore » assembly exhibits a 10-fold symmetry, which may be a common feature among DNA-injection proteins of P22-like phages and may suggest a symmetry mismatch with respect to the 6-fold symmetric phage tail. As a result, the gp12 monomer is highly flexible in solution, supporting a mechanism for translocation of the protein through the conduit of the phage tail toward the host cell envelope, where it assembles into a DNA-injection device.« less

  19. Self-assembled ultra-nanocrystalline silicon films with preferred <2 2 0> crystallographic orientation for solar cell applications

    NASA Astrophysics Data System (ADS)

    Banerjee, Amit; Das, Debajyoti

    2015-03-01

    Using low-pressure planar inductively coupled plasma CVD at 87% H2-dilution to the SiH4 plasma, nc-Si:H films are prepared that possess preferential growth along <2 2 0> crystallographic orientation with I220/I111 > 1.2, bonded H-content of ∼5.5 at.%, a low microstructure factor of ∼0.56, along with a reasonably high σD ∼ 5.2 × 10-4 S cm-1, ΔE ∼ 143 meV and σPh ∼ 1.4 × 10-3 S cm-1. The growth of the nc-Si:H network has been optimized to a moderately high nanocrystallinity (∼68%), with an average grain size of ∼8 nm. The overall network comprises a significant fraction of ultra-nanocrystalline component, Xunc/Xnc ∼ 0.47, which are dominantly inhabited by the thermodynamically preferred <2 2 0> crystallographic orientation that provides convenient electrical transport perpendicular to the film surface and subsequently could facilitate photovoltaic performance. The cross-sectional view of the fracture surface demonstrates columnar structures, closely correlated to the favored growth of the nanocrystallites along <2 2 0> crystallographic orientation that retains direction perpendicular to the substrate surface. The underlying phenomena could be demonstrated as a consequence of preferential growth induced by high atomic H density present in the planar inductively coupled SiH4 plasma obtained via much lower H2-dilution compared to that realized in conventional capacitively coupled plasma-CVD. The nc-Si:H films with precise material properties as well as the allied low-pressure ICP-CVD growth process could be of significant use in further progress of nc-Si solar cells.

  20. Inner/Outer nuclear membrane fusion in nuclear pore assembly: biochemical demonstration and molecular analysis.

    PubMed

    Fichtman, Boris; Ramos, Corinne; Rasala, Beth; Harel, Amnon; Forbes, Douglass J

    2010-12-01

    Nuclear pore complexes (NPCs) are large proteinaceous channels embedded in double nuclear membranes, which carry out nucleocytoplasmic exchange. The mechanism of nuclear pore assembly involves a unique challenge, as it requires creation of a long-lived membrane-lined channel connecting the inner and outer nuclear membranes. This stabilized membrane channel has little evolutionary precedent. Here we mapped inner/outer nuclear membrane fusion in NPC assembly biochemically by using novel assembly intermediates and membrane fusion inhibitors. Incubation of a Xenopus in vitro nuclear assembly system at 14°C revealed an early pore intermediate where nucleoporin subunits POM121 and the Nup107-160 complex were organized in a punctate pattern on the inner nuclear membrane. With time, this intermediate progressed to diffusion channel formation and finally to complete nuclear pore assembly. Correct channel formation was blocked by the hemifusion inhibitor lysophosphatidylcholine (LPC), but not if a complementary-shaped lipid, oleic acid (OA), was simultaneously added, as determined with a novel fluorescent dextran-quenching assay. Importantly, recruitment of the bulk of FG nucleoporins, characteristic of mature nuclear pores, was not observed before diffusion channel formation and was prevented by LPC or OA, but not by LPC+OA. These results map the crucial inner/outer nuclear membrane fusion event of NPC assembly downstream of POM121/Nup107-160 complex interaction and upstream or at the time of FG nucleoporin recruitment.

  1. Horizontal molecular orientation in solution-processed organic light-emitting diodes

    SciTech Connect

    Zhao, L.; Inoue, M.; Komino, T.; Kim, J.-H.; Ribierre, J. C. E-mail: adachi@cstf.kyushu-u.ac.jp [Center for Organic Photonics and Electronics Research , Kyushu University, 744 Motooka, Nishi, Fukuoka 819-0395; Japan Science and Technology Agency , ERATO, Adachi Molecular Exciton Engineering Project, c and others

    2015-02-09

    Horizontal orientation of the emission transition dipole moments achieved in glassy vapor-deposited organic thin films leads to an enhancement of the light out-coupling efficiency in organic light-emitting diodes (OLEDs). Here, our combined study of variable angle spectroscopic ellipsometry and angle dependent photoluminescence demonstrates that such a horizontal orientation can be achieved in glassy spin-coated organic films based on a composite blend of a heptafluorene derivative as a dopant and a 4,4′-bis(N-carbazolyl)-1,1′-biphenyl as a host. Solution-processed fluorescent OLEDs with horizontally oriented heptafluorene emitters were then fabricated and emitted deep blue electroluminescence with an external quantum efficiency as high as 5.3%.

  2. A multiscale simulation technique for molecular electronics: design of a directed self-assembled molecular n-bit shift register memory device.

    PubMed

    Lambropoulos, Nicholas A; Reimers, Jeffrey R; Crossley, Maxwell J; Hush, Noel S; Silverbrook, Kia

    2013-12-20

    A general method useful in molecular electronics design is developed that integrates modelling on the nano-scale (using quantum-chemical software) and on the micro-scale (using finite-element methods). It is applied to the design of an n-bit shift register memory that could conceivably be built using accessible technologies. To achieve this, the entire complex structure of the device would be built to atomic precision using feedback-controlled lithography to provide atomic-level control of silicon devices, controlled wet-chemical synthesis of molecular insulating pillars above the silicon, and controlled wet-chemical self-assembly of modular molecular devices to these pillars that connect to external metal electrodes (leads). The shift register consists of n connected cells that read data from an input electrode, pass it sequentially between the cells under the control of two external clock electrodes, and deliver it finally to an output device. The proposed cells are trimeric oligoporphyrin units whose internal states are manipulated to provide functionality, covalently connected to other cells via dipeptide linkages. Signals from the clock electrodes are conveyed by oligoporphyrin molecular wires, and μ-oxo porphyrin insulating columns are used as the supporting pillars. The developed multiscale modelling technique is applied to determine the characteristics of this molecular device, with in particular utilization of the inverted region for molecular electron-transfer processes shown to facilitate latching and control using exceptionally low energy costs per logic operation compared to standard CMOS shift register technology.

  3. Molecular orientation in dry and hydrated cellulose fibers: a coherent anti-Stokes Raman scattering microscopy study.

    PubMed

    Zimmerley, Maxwell; Younger, Rebecca; Valenton, Tiffany; Oertel, David C; Ward, Jimmie L; Potma, Eric O

    2010-08-12

    Coherent anti-Stokes Raman scattering (CARS) microscopy is combined with spontaneous Raman scattering microspectroscopy and second harmonic generation (SHG) microscopy to interrogate the molecular alignment in dry and hydrated cellulose fibers. Two types of cellulose were investigated: natural cellulose I in cotton fibers and regenerated cellulose II in rayon fibers. On the basis of the orientation of the methylene symmetric stretching vibration, the molecular alignment of cellulose microfibrils is found to be conserved on the micrometer scale. Whereas the molecular orientation in cotton shows modest variability along the fiber, the alignment of the cellulose units in rayon is highly consistent throughout the fiber. The ordered alignment is retained upon fiber hydration. Upon hydration of the cellulose fibers, an anisotropic electronic contribution is observed, which indicates an ordered incorporation of water molecules into the fiber structure. The third-order and second-order electronic polarizability of cellulose I are directed along the axis of the polyglucan chain. No second-order optical response is observed in cellulose II, supporting the antiparallel arrangement of the polyglucan chains in regenerated cellulose.

  4. Stability, orientation and position preference of the stem region (residues 689-703) in Hepatitis C Virus (HCV) envelope glycoprotein E2: a molecular dynamics study

    PubMed Central

    Jusoh, Siti Azma

    2013-01-01

    Envelope glycoproteins of Hepatitis C Virus (HCV) play an important role in the virus assembly and initial entry into host cells. Conserved charged residues of the E2 transmembrane (TM) domain were shown to be responsible for the heterodimerization with envelope glycoprotein E1. Despite intensive research on both envelope glycoproteins, the structural information is still not fully understood. Recent findings have revealed that the stem (ST) region of E2 also functions in the initial stage of the viral life cycle. We have previously shown the effect of the conserved charged residues on the TM helix monomer of E2. Here, we extended the model of the TM domain by adding the adjacent ST segment. Explicit molecular dynamics simulations were performed for the E2 amphiphilic segment of the ST region connected to the putative TM domain (residues 683-746). Structural conformation and behavior are studied and compared with the nuclear magnetic resonance (NMR)-derived segment of E2 ( 2KQZ.pdb). We observed that the central helix of the ST region (residues 689 - 703) remained stable as a helix in-plane to the lipid bilayer. Furthermore, the TM domain appeared to provide minimal contribution to the structural stability of the amphipathic region. This study also provides insight into the orientation and positional preferences of the ST segment with respect to the membrane lipid-water interface. PMID:24555044

  5. Single-Crystalline Gold Nanowires Synthesized from Light-Driven Oriented Attachment and Plasmon-Mediated Self-Assembly of Gold Nanorods or Nanoparticles.

    PubMed

    Yu, Shang-Yang; Gunawan, Hariyanto; Tsai, Shiao-Wen; Chen, Yun-Ju; Yen, Tzu-Chen; Liaw, Jiunn-Woei

    2017-03-16

    Through the light-driven geometrically oriented attachment (OA) and self-assembly of Au nanorods (NRs) or nanoparticles (NPs), single-crystalline Au nanowires (NWs) were synthesized by the irradiation of a linearly-polarized (LP) laser. The process was conducted in a droplet of Au colloid on a glass irradiated by LP near-infrared (e.g. 1064 nm and 785 nm) laser beam of low power at room temperature and atmospheric pressure, without any additive. The FE-SEM images show that the cross sections of NWs are various: tetragonal, pentagonal or hexagonal. The EDS spectrum verifies the composition is Au, and the pattern of X-ray diffraction identifies the crystallinity of NWs with the facets of {111}, {200}, {220} and {311}. We proposed a hypothesis for the mechanism that the primary building units are aligned and coalesced by the plasmon-mediated optical torque and force to form the secondary building units. Subsequently, the secondary building units undergo the next self-assembly, and so forth the tertiary ones. The LP light guides the translational and rotational motions of these building units to perform geometrically OA in the side-by-side, end-to-end and T-shaped manners. Consequently, micron-sized ordered mesocrystals are produced. Additionally, the concomitant plasmonic heating causes the annealing for recrystallizing the mesocrystals in water.

  6. Single-Crystalline Gold Nanowires Synthesized from Light-Driven Oriented Attachment and Plasmon-Mediated Self-Assembly of Gold Nanorods or Nanoparticles

    PubMed Central

    Yu, Shang-Yang; Gunawan, Hariyanto; Tsai, Shiao-Wen; Chen, Yun-Ju; Yen, Tzu-Chen; Liaw, Jiunn-Woei

    2017-01-01

    Through the light-driven geometrically oriented attachment (OA) and self-assembly of Au nanorods (NRs) or nanoparticles (NPs), single-crystalline Au nanowires (NWs) were synthesized by the irradiation of a linearly-polarized (LP) laser. The process was conducted in a droplet of Au colloid on a glass irradiated by LP near-infrared (e.g. 1064 nm and 785 nm) laser beam of low power at room temperature and atmospheric pressure, without any additive. The FE-SEM images show that the cross sections of NWs are various: tetragonal, pentagonal or hexagonal. The EDS spectrum verifies the composition is Au, and the pattern of X-ray diffraction identifies the crystallinity of NWs with the facets of {111}, {200}, {220} and {311}. We proposed a hypothesis for the mechanism that the primary building units are aligned and coalesced by the plasmon-mediated optical torque and force to form the secondary building units. Subsequently, the secondary building units undergo the next self-assembly, and so forth the tertiary ones. The LP light guides the translational and rotational motions of these building units to perform geometrically OA in the side-by-side, end-to-end and T-shaped manners. Consequently, micron-sized ordered mesocrystals are produced. Additionally, the concomitant plasmonic heating causes the annealing for recrystallizing the mesocrystals in water. PMID:28300218

  7. Single-Crystalline Gold Nanowires Synthesized from Light-Driven Oriented Attachment and Plasmon-Mediated Self-Assembly of Gold Nanorods or Nanoparticles

    NASA Astrophysics Data System (ADS)

    Yu, Shang-Yang; Gunawan, Hariyanto; Tsai, Shiao-Wen; Chen, Yun-Ju; Yen, Tzu-Chen; Liaw, Jiunn-Woei

    2017-03-01

    Through the light-driven geometrically oriented attachment (OA) and self-assembly of Au nanorods (NRs) or nanoparticles (NPs), single-crystalline Au nanowires (NWs) were synthesized by the irradiation of a linearly-polarized (LP) laser. The process was conducted in a droplet of Au colloid on a glass irradiated by LP near-infrared (e.g. 1064 nm and 785 nm) laser beam of low power at room temperature and atmospheric pressure, without any additive. The FE-SEM images show that the cross sections of NWs are various: tetragonal, pentagonal or hexagonal. The EDS spectrum verifies the composition is Au, and the pattern of X-ray diffraction identifies the crystallinity of NWs with the facets of {111}, {200}, {220} and {311}. We proposed a hypothesis for the mechanism that the primary building units are aligned and coalesced by the plasmon-mediated optical torque and force to form the secondary building units. Subsequently, the secondary building units undergo the next self-assembly, and so forth the tertiary ones. The LP light guides the translational and rotational motions of these building units to perform geometrically OA in the side-by-side, end-to-end and T-shaped manners. Consequently, micron-sized ordered mesocrystals are produced. Additionally, the concomitant plasmonic heating causes the annealing for recrystallizing the mesocrystals in water.

  8. Oncogenic K-Ras Binds to an Anionic Membrane in Two Distinct Orientations: A Molecular Dynamics Analysis

    PubMed Central

    Prakash, Priyanka; Zhou, Yong; Liang, Hong; Hancock, John F.; Gorfe, Alemayehu A.

    2016-01-01

    K-Ras is a membrane-associated GTPase that cycles between active and inactive conformational states to regulate a variety of cell signaling pathways. Somatic mutations in K-Ras are linked to 15–20% of all human tumors. K-Ras attaches to the inner leaflet of the plasma membrane via a farnesylated polybasic domain; however, the structural details of the complex remain poorly understood. Based on extensive (7.5 μs total) atomistic molecular dynamics simulations here we show that oncogenic mutant K-Ras interacts with a negatively charged lipid bilayer membrane in multiple orientations. Of these, two highly populated orientations account for ∼54% of the conformers whose catalytic domain directly interacts with the bilayer. In one of these orientation states, membrane binding involves helices 3 and 4 of the catalytic domain in addition to the farnesyl and polybasic motifs. In the other orientation, β-strands 1–3 and helix 2 on the opposite face of the catalytic domain contribute to membrane binding. Flexibility of the linker region was found to be important for the reorientation. The biological significance of these observations was evaluated by initial experiments in cells overexpressing mutant K-Ras as well as by an analysis of Ras-effector complex structures. The results suggest that only one of the two major orientation states is capable of effector binding. We propose that the different modes of membrane binding may be exploited in structure-based drug design efforts for cancer therapy. PMID:26958889

  9. Molecular tectonics: design of enantiomerically pure helical tubular crystals with controlled channel size and orientation.

    PubMed

    Lin, Mei-Jin; Jouaiti, Abdelaziz; Grosshans, Philippe; Kyritsakas, Nathalie; Hosseini, Mir Wais

    2011-07-21

    The combination of four enantiomerically pure organic tectons composed of a rigid chiral backbone bearing two terminal pyridyl coordinating sites with ZnSiF(6) behaving as an infinite pillar leads to the formation of tubular 2-D enantiomerically pure helical channels with controlled size and orientation.

  10. Surface-enhanced raman spectra and molecular orientation of phthalazine adsorbed on a silver electrode

    NASA Astrophysics Data System (ADS)

    Takahashi, Machiko; Fujita, Masato; Ito, Masatoki

    1984-08-01

    SERS from phthalazine adsorbed on an Ag electrode was investigated under several conditions of applied voltage and solution concentration. Spectral assignments of the Raman bands were successfully performed and two differently oriented adsorbates, i.e. flat and end-on species, were identified. The contribution of the image field to the SERS intensity was considerable.

  11. Electro-molecular Assembly: Electrical Writing of Information into an Erasable Polysaccharide Medium.

    PubMed

    Yan, Kun; Xiong, Yuan; Wu, Si; Bentley, William E; Deng, Hongbing; Du, Yumin; Payne, Gregory F; Shi, Xiao-Wen

    2016-08-03

    We report that information can be written into an erasable hydrogel medium by precisely imposing controlled electrical signals that trigger supramolecular self-assembly. We prepare the medium from a blend of two stimuli-responsive self-assembling polysaccharides agarose (thermally responsive) and chitosan (pH-responsive). Upon cooling the blend, agarose forms the hydrogel medium while the embedded chitosan chains can be induced to self-assemble in response to imposed pH cues. Importantly, these triggering pH-cues can be imposed electrically (by inserted electrodes) enabling complex messages (e.g., self-assembled multilayers) to be written within the hydrogel medium. The reversibility of these self-assembly mechanisms allow the written information, and the medium itself, to be erased. These physicochemical properties enable this dual responsive medium to encrypt information, while the responsiveness of this structural information and the biocompatibility of the medium suggest uses for accessing/reporting information in diverse life science applications, such as foods, cosmetics, medicine, and the environment.

  12. Oriented immobilization of antibodies by a self-assembled monolayer of 2-(biotinamido)ethanethiol for immunoarray preparation.

    PubMed

    Jung, Se-Hui; Son, Ha-Young; Yuk, Jong Seol; Jung, Jae-Wan; Kim, Kyung Hwan; Lee, Chang-Hee; Hwang, Hoon; Ha, Kwon-Soo

    2006-01-15

    Orientation of antibodies is very important in the preparation of immunoarrays to keep the activity of antibodies on solid surfaces. Thus, we synthesized a new bifunctional compound, 2-(biotinamido)ethanethiol, and investigated whether the thiol compound is useful to analyze antibody-antigen interactions on immunoarrays with a spectral SPR biosensor. The synthesized organic thiol was characterized by nuclear magnetic resonance spectroscopy and mass spectrometry. 2-(Biotinamido)ethanethiol formed a monolayer on a gold surface and properly immobilized antibodies via streptavidin and biotinylated protein G. Optimal molar ratio of 2-(biotinamido)ethanethiol and mercaptohexanol for antigen-antibody interactions was 1:2. Thus, 2-(biotinamido)ethanethiol is an useful bifunctional linker in the preparation of immunoarrays on gold surfaces.

  13. Mechanisms of the self-assembly of EAK16-family peptides into fibrillar and globular structures: molecular dynamics simulations from nano- to micro-seconds.

    PubMed

    Emamyari, Soheila; Kargar, Faezeh; Sheikh-Hasani, Vahid; Emadi, Saeed; Fazli, Hossein

    2015-05-01

    The self-assembly of EAK16-family peptides in a bulk solution was studied using a combination of all-atom and coarse-grained molecular dynamics simulations. In addition, specified concentrations of EAK16 peptides were induced to form fibrillary or globular assemblies in vitro. The results show that the combination of all-atom molecular dynamics simulations on the single- and double-chain levels and coarse-grained simulations on the many-chain level predicts the experimental observations reasonably well. At neutral pH conditions, EAK16-I and EAK16-II assemble into fibrillary structures, whereas EAK16-IV aggregates into globular assemblies. Mechanisms of the formation of fibrillar and globular assemblies are described using the simulation results.

  14. Highly-oriented molecular arrangements and enhanced magnetic interactions in thin films of CoTTDPz using PTCDA templates.

    PubMed

    Eguchi, Keitaro; Nanjo, Chihiro; Awaga, Kunio; Tseng, Hsiang-Han; Robaschik, Peter; Heutz, Sandrine

    2016-07-14

    In the present work, the templating effect of thin layers of perylene-3,4,9,10-tetracarboxylic dianhydride (PTCDA) on the growth of cobalt tetrakis(thiadiazole)porphyrazine (CoTTDPz) thin films was examined. X-ray diffraction and optical absorption spectra indicate that while CoTTDPz forms amorphous thin films on the bare substrates, it forms crystalline thin films on the PTCDA templates, in which the molecular planes of CoTTDPz are considered to be parallel to the substrates. Magnetic measurements reveal a significantly enhanced antiferromagnetic interaction of CoTTDPz in the templated thin films, with values reaching over 13 K. The ability to generate crystalline films and to control their orientation using molecular templates is an important strategy in the fields of organic electronics and spintronics in order to tailor the physical properties of organic thin films to suit their intended application.

  15. ParFit: A Python-Based Object-Oriented Program for Fitting Molecular Mechanics Parameters to ab Initio Data.

    PubMed

    Zahariev, Federico; De Silva, Nuwan; Gordon, Mark S; Windus, Theresa L; Dick-Perez, Marilu

    2017-03-27

    A newly created object-oriented program for automating the process of fitting molecular-mechanics parameters to ab initio data, termed ParFit, is presented. ParFit uses a hybrid of deterministic and stochastic genetic algorithms. ParFit can simultaneously handle several molecular-mechanics parameters in multiple molecules and can also apply symmetric and antisymmetric constraints on the optimized parameters. The simultaneous handling of several molecules enhances the transferability of the fitted parameters. ParFit is written in Python, uses a rich set of standard and nonstandard Python libraries, and can be run in parallel on multicore computer systems. As an example, a series of phosphine oxides, important for metal extraction chemistry, are parametrized using ParFit. ParFit is in an open source program available for free on GitHub ( https://github.com/fzahari/ParFit ).

  16. ParFit: A Python-Based Object-Oriented Program for Fitting Molecular Mechanics Parameters to ab Initio Data

    DOE PAGES

    Zahariev, Federico; De Silva, Nuwan; Gordon, Mark S.; ...

    2017-02-23

    Here, a newly created object-oriented program for automating the process of fitting molecular-mechanics parameters to ab initio data, termed ParFit, is presented. ParFit uses a hybrid of deterministic and stochastic genetic algorithms. ParFit can simultaneously handle several molecular-mechanics parameters in multiple molecules and can also apply symmetric and antisymmetric constraints on the optimized parameters. The simultaneous handling of several molecules enhances the transferability of the fitted parameters. ParFit is written in Python, uses a rich set of standard and nonstandard Python libraries, and can be run in parallel on multicore computer systems. As an example, a series of phosphine oxides,more » important for metal extraction chemistry, are parametrized using ParFit.« less

  17. Isomorphism Within the Hexagonal Columnar Mesophase of Molecular and Macromolecular Self- and Co-Assembled Columns Containing Tapered Groups

    DTIC Science & Technology

    1994-06-30

    ttni " O-m ’mm OFFICE OF NAVAL RESEARCH CONTRACT N00014-89-J- 1828 O R &T Code 3132080 Abstract Report #3 ISOMORPHISM WITHIN THE HEXAGONAL COLUMNAR...MESOPHASE OF MOLECULAR AND MACROMOLECULAR SELF- AND CO-ASSEMBLED COLUMNS CONTAINING TAPERED GROUPS by D. Tomazos, R . Out, J. Heck, G. Johansson, V...Containing Tapered Grouls 6. AUTHOR(S) D. Tomazos, R . Out, J. Heckc, G. Johansson, V. Percec, and M. Moeller 7. PERFORMING ORGANIZATION NAME(S) AND

  18. Electrical conductivity of single molecular junctions assembled from Co- and Co3C-encapsulating carbon nanocapsules.

    PubMed

    Matsuura, Daisuke; Kizuka, Tokushi

    2014-03-01

    Single molecular junctions (SMJs) were assembled from cobalt (Co)- and Co carbide (Co3C)-encapsulating carbon nanocapsules (CNCs) and two gold electrodes inside a high-resolution transmission electron microscope equipped with a specimen-piezomanipulation system. The structure and electrical transport properties of the SMJs were investigated in situ. The current density depended on the perimeter of the contact area between CNCs and the electrodes, showing that the current flowed not through the encapsulated region but rather along the graphene layers of CNCs. It was demonstrated that the properties of graphene can be applied to nanodevices using CNCs irrespective of the encapsulating materials.

  19. A molecular simulation study of methylated and hydroxyl sugar-based self-assembled monolayers: Surface hydration and resistance to protein adsorption

    NASA Astrophysics Data System (ADS)

    Hower, Jason C.; He, Yi; Jiang, Shaoyi

    2008-12-01

    In this work molecular simulations are performed to investigate protein interactions with hydroxylated and methylated mannitol and sorbitol terminated self-assembled monolayer (SAM) surfaces in the presence of explicit water molecules. The role of surface hydrogen bond donor versus acceptor groups is evaluated by comparing the hydration layer structure and resulting forces generated by the two classes of sugar SAM surfaces. Both hydroxyl and methyl-terminated sugar SAM surfaces interact with hydrating water molecules. Regardless of hydrogen bond donor or acceptor groups, both classes of sugar SAM surface groups interact strongly with hydrating water molecules to induce significant repulsive forces and resistance to protein adsorption. Our results indicate that the repulsive force generated on the probe protein is related to the ability of the surface to orient the hydration layer water. The repulsive force is also proportional to the number of hydrating water molecules interacting with the protein. The repulsive force and subsequent resistance to protein adsorption are dependent on the surface hydration, not the origin of that hydration.

  20. Nanoimprint-assisted directed self-assembly of low-molecular weight block copolymers: a route for 3D and multilevel nanostructures

    NASA Astrophysics Data System (ADS)

    Simão, C.; Khunsin, W.; Kehagias, N.; Francone, A.; Zelsmann, M.; Morris, M. A.; Sotomayor Torres, C. M.

    2014-06-01

    Multilevel controllable nanoimprint driven molecular orientation has been obtained in thin films of block copolymer polystyrene-b-polyethylene oxide( PS-b-PEO) by means of solvent vapours assisted nanoimprint lithography (SAIL). The NIL setup using solvent vapours was capable of imprinting nanoscale features over a large area and simultaneously annealing PS-b-PEO thin films. A line pattern stamp was replicated in the BCP film in over a large area with a high resolution registry, and was also observed that the PS-b-PEO film exhibited microphase segregation in the residual layer exhibits a nanodot array from showing hexagonally packed PEO dots in the PS matrix, with a diameter of 20 nm with 40 nm pitch. The order of the hexagonally arranged nanodot lattice seen in the nanodots array was quantified from SEM images using by the opposite partner method from SEM images analysis and compared with to conventionally solvent annealed BCP films, demonstrating an improvement of the ordering of up to 50%. Grazing-incidence small-angle X-ray scattering (GISAXS) study demonstrates the excellent fidelity of the pattern transfer and confirms the periodicity of the BCP in the mesas. In addition, applying the SAIL methodology to BCP thin films in nanopatterned silsequioxane substrates, it was possible to obtain multilevel structures decorated with the BCP microphase segregation. The SAIL technique is a versatile and robust platform to obtain complex high density periodic nanostructures, particularly for second generation block copolymers directed self-assembly.

  1. Novel Interphases: Synthesis, Molecular Orientation and Grafting of Liquid Crystal Polymers on Carbon Fibers

    DTIC Science & Technology

    1990-01-01

    rigid molecules into an anisotropic phase have been reported. Lars Onsager (13) showed that steric interactions between rigid rods can lead to...will eventually undergo an Onsager orientational transition. From a properties point of view the occurrence of a high density surface layer with...Plate’, N. A., Adv. in Polym. Sci., 1984, 173. (12) Flory, P. J., Proc. Royal Soc. London, 1956, A234, 73. (13) Onsager , L., Ann. N. Y. Acad. Sci

  2. Fluoropolymer Microstructure and Dynamics: Influence of Molecular Orientation Induced by Uniaxial Drawing

    NASA Astrophysics Data System (ADS)

    Miranda, Daniel; Yin, Chaoqing; Runt, James

    Fluorinated semi-crystalline polymer films are attractive for dielectric film applications due to their chemical inertness, heat resistance, and high thermal stability. In the present investigation we explore the influence of orientation induced by uniaxial drawing on the crystalline microstructure and relaxation processes of poly(ethylene-tetrafluoroethylene) (ETFE), in order to ascertain how morphological control can benefit polymer dielectric design. When drawn below or near the Tg, the crystallinity of the drawn films is unchanged, and oriented amorphous structures and crystalline microfibrils form at high draw ratios. This orientation slows segmental relaxation, reflected by an increase in the dynamic Tg, and also delays the transition to the high temperature crystalline form of ETFE. When drawing above the Tg, the films undergo strain-induced crystallization at high draw ratios. For these films an increase in the dynamic Tg is also observed, in addition to a second segmental relaxation process, appearing as a shoulder on the primary process. We propose that this represents a contribution from a rigid amorphous fraction, having slowed chain dynamics. Supported by Office of Naval Research.

  3. Self-assembly of microtubules and motors

    NASA Astrophysics Data System (ADS)

    Aranson, Igor; Tsimring, Lev

    2005-03-01

    We derive a model describing spatio-temporal assembly of an array of microtubules interacting via molecular motors. Starting from a stochastic model of inelastic polar rods with a generic anisotropic interaction kernel we obtain a set of equations for the local rods concentration and orientation. At large enough mean density of rods and concentration of motors, the model describes orientational instability. We demonstrate that the orientational instability leads to the formation of vortices and (for large density and/or kernel anisotropy) asters seen in recent experiments.

  4. Analysis of Pigment Orientation in Photosystem II at Different Temperatures by Polarization Fluorescence and Molecular Exciton Theory

    NASA Astrophysics Data System (ADS)

    Lu, L.; Wei, L.; Luo, X.; Ni, X.; Lu, J.

    2014-05-01

    The effect of temperature on pigment orientation in photosystem II (PSII) was studied by fl uorescence excitation and polarization fl uorescence spectra of spinach thylakoid solution and molecular exciton theory. Experimental results showed that at 15 to 45 °C, the absorption band of chlorophyll a at 436 nm at room tempe rature red-shifted with increased temperature. The excitation spectra intensity reached the maximum at 35 °C but signifi cantly dropped at 65 and 78 °C. The polarization fl uorescence spectra revealed that the fl uorescence peak of PSII did not change at 15 and 45 °C, and the calculated degree of fl uorescence polarization increased with increased temperature. Spectral and molecular exciton theory analyses indicated that temperature affected pigment orientation in PSII, as well as the coupling strength between pigments or pigment and protein, thereby changing photosynthetic effi ciency. These results can serve as a reference for studies on energy absorption, energy transmission, regulation mechanism, and prospective applications in solar cell materials.

  5. 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.

  6. Selective Synthesis of Molecular Borromean Rings: Engineering of Supramolecular Topology via Coordination-Driven Self-Assembly.

    PubMed

    Kim, Taegeun; Singh, Nem; Oh, Jihun; Kim, Eun-Hee; Jung, Jaehoon; Kim, Hyunuk; Chi, Ki-Whan

    2016-07-13

    Molecular Borromean rings (BRs) is one of the rare topology among interlocked molecules. Template-free synthesis of BRs via coordination-driven self-assembly of tetracene-based Ru(II) acceptor and ditopic pyridyl donors is reported. NMR and single-crystal XRD analysis observed sequential transformation of a fully characterized monomeric rectangle to molecular BRs and vice versa. Crystal structure of BRs revealed that the particular topology was enforced by the appropriate geometry of the metallacycle and multiple parallel-displaced π-π interactions between the donor and tetracene moiety of the acceptor. Computational studies based on density functional theory also supported the formation of BRs through dispersive intermolecular interactions in solution.

  7. Amyloidogenic Processing but not AICD Production Requires a Precisely Oriented APP Dimer Assembled by Transmembrane GXXXG Motifs

    PubMed Central

    Kienlen-Campard, Pascal; Tasiaux, Bernadette; Van Hees, Joanne; Li, Mingli; Huysseune, Sandra; Sato, Takeshi; Fei, Jeffrey Z.; Aimoto, Saburo; Courtoy, Pierre J.; Smith, Steven O.; Constantinescu, Stefan N.; Octave, Jean-Noël

    2009-01-01

    The β-amyloid peptide (Aβ) is the major constituent of the amyloid core of senile plaques found in the brain of patients with Alzheimer's disease (AD). Aβ is produced by the sequential cleavage of the Amyloid Precursor Protein (APP) by β- and γ-secretases. Cleavage of APP by γ-secretase also generates the APP Intracellular C-terminal Domain (AICD) peptide, which might be involved in regulation of gene transcription. APP contains three glycine-xxx-glycine (GxxxG) motifs in its juxtamembrane and transmembrane (TM) regions. Such motifs are known to promote dimerization via close apposition of TM sequences. We demonstrate that pairwise replacement of glycines by leucines or isoleucines, but not alanines, in a GxxxG motif led to a drastic reduction of Aβ40 and Aβ42 secretion. β-Cleavage of mutant APP was not inhibited, and reduction of Aβ secretion resulted from inhibition of γ-cleavage. It was anticipated that decreased γ-cleavage of mutant APP would result from inhibition of its dimerization. Surprisingly, mutations of the GxxxG motif actually enhanced dimerization of the APP C-terminal fragments, possibly via a different TM α-helical interface. Increased dimerization of the TM APP C-terminal domain did not affect AICD production. These results clearly demonstrate that both orientation and dimerization of the APP TM domain differently affect Aβ and AICD production. PMID:18201969

  8. Density dependence of hydrogen bonding and the translational-orientational structural order in supercritical water: a molecular dynamics study.

    PubMed

    Ma, Haibo; Ma, Jing

    2011-08-07

    Molecular dynamics simulation have been performed with a wide range of densities along a near critical isotherm of supercritical water (SCW) in order to study the density dependence of the structure order and hydrogen bonding (HB). It is revealed that the translational structure order is nearly invariant while the orientational tetrahedral structure order is very sensitive to the bulk density under supercritical conditions. Meanwhile, some energetically unfavorable intermediate water dimer structures are found to appear under supercritical conditions due to the reduced energy difference and the enhanced energy fluctuation. As a consequence, a general geometrical criterion or the inclusion of a energy-based criterion instead of currently widely adopted pure r(OH)-based geometric criterion is suggested to be used in the HB statistics under supercritical conditions. It is found that the average HB number per H(2)O molecule (n(HB)) reduces with the decreasing SCW bulk density although a given pair of H(2)O molecules are shown to have a stronger ability to form a hydrogen bond under lower SCW bulk densities. Accordingly, the orientational tetrahedral structure order q decreases with the reducing bulk density under supercritical conditions. However, when the fluid is dilute with ρ ≤ 0.19ρ(c) (ρ(c) = 0.322 g/cm(3)), the energy fluctuation increases sharply and the short-range order is destroyed, signifying the supercritical fluid (SCF)-gas state transition. Accordingly, the orientational tetrahedral structure order q gets reversal around ρ = 0.19ρ(c) and approaches zero under very dilute conditions. The sensitivity of the orientational order to the density implies the microscopic origin of the significant dependence of SCF's physicochemical properties on the pressure.

  9. Understanding self-assembly of charged-neutral block copolymer (BCP) and surfactant complexes using molecular dynamics (MD) simulation

    NASA Astrophysics Data System (ADS)

    Goswami, Monojoy; Sumpter, Bobby; Kilbey, Michael

    Here we report the formation of phase separated BCP-surfactant complexes resulting from the electrostatic self-assembly of charge-neutral block copolymers with oppositely charged surfactants. Complexation behaviors of oppositely charged polyelectrolytes has gained considerable attention in the field of soft condensed matter physics due to their potential application as functional nanomaterials for batteries, wastewater treatment and drug delivery systems. Numerous experiments have examined the self-assembled structures resulting from complexation of charge-neutral BCP and surfactants, however, there is a lack of comprehensive understanding at the fundamental level. To help bridge this gap, we use, MD simulations to study self-assembly and dynamics of the BCP-surfactant complex at the molecular level. Our results show an overcharging effect in BCPs with hydrophobic neutral blocks and a formation of core-shell colloidal structure. Hydrophilic neutral blocks, on the other hand, show stable, hairy colloidal structures with neutral blocks forming a loosely-bound, fuzzy outer layer. Our results qualitatively agree with previous SANS and SAXS experiments. This work was supported by the U.S. Department of Energy (DOE), Office of Basic Energy Sciences, Materials Science and Engineering Division.

  10. Anti-fouling surfaces by combined molecular self-assembly and surface-initiated ATRP for micropatterning active proteins.

    PubMed

    Xiu, K M; Cai, Q; Li, J S; Yang, X P; Yang, W T; Xu, F J

    2012-02-01

    A simple method by combined molecular self assembly and surface-initiated atom transfer radical polymerization (SI-ATRP) was proposed to prepare a biologically inert surface for micropatterning active proteins. The MPEG microdomains having a short terminal poly(ethylene glycol) (PEG) unit were prepared by self assembly of 2-(methyoxy(polyethylenoxy) propyl)trimethoxy silane (MPEG-silane). The remaining local regions or poly(poly(ethylene glycol)methyl ether methacrylate-co-glycidyl methacrylate) (P(PEGMEMA-co-GMA)) microdomains were produced via SI-ATRP of PEGMEMA and GMA comonomers. The epoxy groups of the P(PEGMEMA-co-GMA) microdomains were used directly for covalent coupling of an active protein (human immunoglobulin or IgG) via the ring-opening reaction to produce the IgG-coupled microdomains. The IgG-coupled microdomains interact only and specifically with target anti-IgG, while the other antifouling microregions from self-assembled monolayers with short terminal PEG units effectively prevent specific and non-specific protein fouling. When extended to other active biomolecules, microarrays for specific and non-specific analyte interactions with a high signal-to-noise ratio could be readily tailored.

  11. Synthesis and self-assembly of 1-deoxyglucose derivatives as low molecular weight organogelators

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Low molecular weight gelators are an important class of molecules. The supramolecular gels formed by carbohydrate derived low molecular weight gelators, are interesting soft materials that show great potential for many applications. Previously, we synthesized a series of methyl 4,6-O-benzylidene-a-D...

  12. Orientational properties of poly-gamma-benzyl-L-glutamate: influence of molecular weight and solvent on order parameters of the solute.

    PubMed

    Marx, Andreas; Thiele, Christina

    2009-01-01

    Residual dipolar couplings (RDCs) have recently become increasingly important in organic structure determination due to their unique information content. One main limitation for the use of RDCs in organic compounds, however, is that the compound in question needs to be oriented with respect to the magnetic field in order to measure RDCs. So far, there are very few possibilities for modulating the induced degree of orientation. The situation is even worse when chiral orienting media are considered, which could allow absolute configuration determination in the future. We have conducted a systematic investigation into modulating the orientation induced by one chiral orienting medium, namely organic solutions of PBLG (poly-gamma-benzyl-L-glutamate), as a function of its molecular weight and the organic co-solvent used, and have obtained significant insights into factors that influence the order induced. With increasing molecular weight of the polypeptide the orientation of the solutes decreases, leading to well-resolved spectra with improved line shapes. This can be attributed exclusively to the fact that the critical concentration of the liquid-crystalline phase decreases with increasing molecular weight (pure dilution effect). Any influence of increasing flexibility on the orientation can be ruled out.

  13. Taurine Boosts Cellular Uptake of Small D-Peptides for Enzyme-Instructed Intracellular Molecular Self-Assembly.

    PubMed

    Zhou, Jie; Du, Xuewen; Li, Jie; Yamagata, Natsuko; Xu, Bing

    2015-08-19

    Due to their biostability, D-peptides are emerging as an important molecular platform for biomedical applications. Being proteolytically resistant, D-peptides lack interactions with endogenous transporters and hardly enter cells. Here we show that taurine, a natural amino acid, drastically boosts the cellular uptake of small D-peptides in mammalian cells by >10-fold, from 118 μM (without conjugating taurine) to >1.6 mM (after conjugating taurine). The uptake of a large amount of the ester conjugate of taurine and D-peptide allows intracellular esterase to trigger intracellular self-assembly of the D-peptide derivative, further enhancing their cellular accumulation. The study on the mechanism of the uptake reveals that the conjugates enter cells via both dynamin-dependent endocytosis and macropinocytosis, but likely not relying on taurine transporters. Differing fundamentally from the positively charged cell-penetrating peptides, the biocompatibility, stability, and simplicity of the enzyme-cleavable taurine motif promise new ways to promote the uptake of bioactive molecules for countering the action of efflux pump and contributing to intracellular molecular self-assembly.

  14. Scanning tunneling microscope investigations of organic heterostructures prepared by a combination of self-assembly and molecular beam epitaxy

    NASA Astrophysics Data System (ADS)

    Staub, R.; Toerker, M.; Fritz, T.; Schmitz-Hübsch, T.; Sellam, F.; Leo, K.

    2000-01-01

    We report the realization of organic-organic heteroepitaxy by combining liquid-phase self-assembly with ultrahigh vacuum (UHV) gas-phase molecular beam epitaxy. As a model system, we have used self-assembled monolayers (SAMs) prepared by exposing an Au(111)-mica substrate to a dilute solution of decanethiol in ethanol, with subsequent evaporation of 3,4,9,10-perylene-tetracarboxylic-dianhydride (PTCDA) dye molecules. The well-known (3×3)R30° superstructure of almost upright standing molecules after chemisorption is replaced by the 11.5×3 (33.2 Å) pin-stripe phase with flat lying molecules when the samples are annealed in UHV and coverage decreases. The deposition of PTCDA induces reordering and displacement in the decanethiol SAM. Additional to the 33.2 Å periodicity, the previously reported 22 Å thiol stripe phase can be observed by scanning tunneling microscopy. Several PTCDA structures are observed: single and double rows of PTCDA that grow along decanethiol stripes on top of the flat-lying alkane chain groups, as well as densely packed PTCDA monolayer domains embedded into the thiol layer. These exhibit the well-known herringbone structure or a novel square lattice structure. We have also investigated thicker PTCDA islands and observed molecular resolution for a thickness of several monolayers. The structure of the three-dimensional islands can be identified as the α bulk modification.

  15. Modeling and characterization of molecular structures in self assembled and Langmuir-Blodgett films for controlled fabrication

    SciTech Connect

    Cesarano, J. III

    1997-10-01

    Self Assembled (SA) thin films and Langmuir-Blodgett (LB) thin films are emerging technologies for the development of chemical and bio-chemical sensors, electrooptic films, second harmonic generators (frequency doublers), templates for biomimetic growth etc. One of the goals of this project was to extend Sandia`s characterization techniques and molecular modeling capabilities for these complex two-dimensional geometries with the objective of improving the control of the fabrication of these structures for specific applications. Achieving this requires understanding both the structure throughout the thickness of the films and the in-plane lattice of the amphiphilic molecules. To meet these objectives they used atomic force microscopy (AFM), X-ray reflectivity, and molecular modeling. While developing these capabilities, three different materials systems were fabricated and characterized: (1) Self Assembled Monolayers (SAMs) of octadecyltrichlorosilane (OTS) and LB films of arachidic acid on silicon wafers; (2) SAMs on PZT substrates; and (3) electrochemical deposition of CdS on LB film templates.

  16. Molecular orientation behavior of chiral nematic liquid crystals based on the presence of blue phases using polarized microscopic FT-IR spectroscopy

    NASA Astrophysics Data System (ADS)

    Matsumura, Masanori; Katayama, Norihisa

    2016-07-01

    Study on molecular orientation behavior of highly twisted chiral nematic liquid crystals (N∗LCs) expressing blue phases (BPs) is important for developing new devices. This study examines the change of molecular orientation of N∗LCs due to the presence of BPs. Polarized microscopic FT-IR spectroscopy was used to study the in- and out-of-plane molecular orientations of N∗LCs that undergo a phase transition involving BPs. The band intensity ratio of CN to CH2 stretching modes (CN/CH2) in the IR spectra was used to determine the orientation of N∗LC molecules. The measured spectra indicated that the helical axis of N∗LC molecules was perpendicular to the substrate before heating and inclined on the substrate after cooling the sample which has phase transition from BP I to chiral nematic (N∗). The N∗LC molecule in the cell of rubbed orientation film exhibited the in-plane anisotropy after a heating-cooling ramp only in samples that passed through BP I. These results indicate that the changes of molecular orientation of N∗LC by phase transition are affected by BP I.

  17. Adsorption of organosulfur species at aqueous surfaces: molecular bonding and orientation.

    PubMed

    Tarbuck, Teresa L; Richmond, Geraldine L

    2005-11-10

    Four sulfur-containing compounds important to tropospheric chemistry have been examined at the vapor/H2O and vapor/D2O interfaces. These adsorbates, DMS, DMSO, DMSO2, and DMSO3, were studied by surface tension and vibrational sum-frequency spectroscopy (VSFS). Each adsorbate is surface active and each orients with the hydrophobic methyl groups pointed out of the plane of the interface. Their influence on the interfacial water structure is adsorbate dependent. Strong and weak interactions with surface water are observed as well as reorientation of subsurface water molecules, resulting in an increase in interfacial thickness.

  18. Specific ion effects on the self-assembly of ionic surfactants: a molecular thermodynamic theory of micellization with dispersion forces.

    PubMed

    Lukanov, Boris; Firoozabadi, Abbas

    2014-06-10

    The self-assembly of amphiphilic molecules is a key process in numerous biological and chemical systems. When salts are present, the formation and properties of molecular aggregates can be altered dramatically by the specific types of ions in the electrolyte solution. We present a molecular thermodynamic model for the micellization of ionic surfactants that incorporates quantum dispersion forces to account for specific ion effects explicitly through ionic polarizabilities and sizes. We assume that counterions are distributed in the diffuse region according to a modified Poisson-Boltzmann equation and can reach all the way to the micelle surface of charge. Stern layers of steric exclusion or distances of closest approach are not imposed externally; these are accounted for through the counterion radial distribution profiles due to the incorporation of dispersion potentials, resulting in a simple and straightforward treatment. There are no adjustable or fitted parameters in the model, which allows for a priori quantitative prediction of surfactant aggregation behavior based only on the initial composition of the system and the surfactant molecular structure. The theory is validated by accurately predicting the critical micelle concentration (CMC) for the well-studied sodium dodecyl sulfate (SDS) surfactant and its alkaline-counterion derivatives in mono- and divalent salts, as well as the molecular structure parameters of SDS micelles such as aggregation numbers and micelle surface potential.

  19. pH-responsive self-assembly by molecular recognition on a macroscopic scale.

    PubMed

    Zheng, Yongtai; Hashidzume, Akihito; Harada, Akira

    2013-07-12

    Macroscopic pH-responsive self-assembly is successfully constructed by polyacrylamide(pAAm)-based gels carrying dansyl (Dns) and β-cyclodextrin (βCD) residues, which are represented as Dns-gel and βCD-gel, respectively. Dns-gel and βCD-gel assemble together at pH ≥ 4.0, but disassemble at pH ≤ 3.0. The adhesion strengths for pairs of Dns-gel/βCD-gel increase with increasing pH. The fluorescence study on the model system of pAAm modified with 1 mol% Dns moieties (pAAm/Dns) reveals that Dns residues are protonated at a lower pH, which results in the reduction in binding constant (K) for Dns residues and βCD.

  20. Unfolding a molecular trefoil derived from a zwitterionic metallopeptide to form self-assembled nanostructures.

    PubMed

    Zhang, Ye; Zhou, Ning; Shi, Junfeng; Pochapsky, Susan Sondej; Pochapsky, Thomas C; Zhang, Bei; Zhang, Xixiang; Xu, Bing

    2015-02-19

    While used extensively by nature to control the geometry of protein structures, and dynamics of proteins, such as self-organization, hydration forces and ionic interactions received less attention for controlling the behaviour of small molecules. Here we describe the synthesis and characterization of a novel zwitterionic metallopeptide consisting of a cationic core and three distal anionic groups linked by self-assembling peptide motifs. 2D NMR spectra, total correlated spectroscopy and nuclear Overhauser effect spectroscopy, show that the molecule exhibits a three-fold rotational symmetry and adopts a folded conformation in dimethyl sulfoxide due to Coulombic forces. When hydrated in water, the molecule unfolds to act as a self-assembling building block of supramolecular nanostructures. By combining ionic interactions with the unique geometry from metal complex and hydrophobic interactions from simple peptides, we demonstrate a new and effective way to design molecules for smart materials through mimicking a sophisticated biofunctional system using a conformational switch.

  1. Determination of enantiomeric excess in amine derivatives with molecular self-assemblies.

    PubMed

    Shcherbakova, Elena G; Minami, Tsuyoshi; Brega, Valentina; James, Tony D; Anzenbacher, Pavel

    2015-06-08

    We report the first fluorescence-based assay for the rapid determination of the ee value of amines, amino alcohols, and amino acid esters. The method uses the self-assembly of 2-formylphenylboronic acid with a chiral diol and a chiral amine or derivatives (of unknown chirality) to produce two diastereomeric iminoboronates that differ in their fluorescence intensity and polarization. The approach allows for the accurate determination of the ee value of chiral amines with errors of just 1-2%. We believe that this application of orthogonal dynamic covalent self-assembly in the determination of the enantioselectivity will lead to the development of high-throughput procedures for the determination of chirality.

  2. From molecular to supramolecular: an exploration into the modes of self- assembly in conformationally locked polycyclitols.

    PubMed

    Mehta, Goverdhan; Sen, Saikat

    2012-01-01

    This brief account highlights the notable findings of our investigation into the supramolecular chemistry of conformationally locked polycyclitols in the solid state. The study was aimed at analyzing the crystal packing and unraveling the modalities of non-covalent interactions (particularly, intramolecular vis-à-vis intermolecular O-H˙˙˙O hydrogen bonds) in polyols. The know-how obtained thereof, was successfully utilized to engineer self-assemblies of designer polycyclitols, having hydrogen bond donors and acceptors fettered onto a trans-decalin scaffold. The results seek to draw particular attention to the intrinsic attribute of this rigid carbocyclic framework to lock functional groups into spatially invariant positions and bring potential intramolecular hydrogen bonding partners into favorable interaction geometry to engender predictability in the self-assembly patterns.

  3. [Molecular Dynamics of Self-assembling and Rheology of Superhelical Structure of Protofiber of Spider Web].

    PubMed

    Shaitan, K V; Orshanskiy, I A

    2015-01-01

    In this study we suggested a dynamics simulation for the formation of protofiber of spider web nanofiber. It was shown that a bundle of parallel polyalanine β-strands of sufficient length is arranged through self-assembly into a stable right-handed super helix. By numerical analysis we investigated the rheological properties and provided in nonlinear regime a generalization of the model of Singer for description of the rheological behaviour of super helix.

  4. The mechanism of a nuclear pore assembly: a molecular biophysics view.

    PubMed

    Kuvichkin, Vasily V

    2011-06-01

    The basic problem of nuclear pore assembly is the big perinuclear space that must be overcome for nuclear membrane fusion and pore creation. Our investigations of ternary complexes: DNA-PC liposomes-Mg²⁺, and modern conceptions of nuclear pore structure allowed us to introduce a new mechanism of nuclear pore assembly. DNA-induced fusion of liposomes (membrane vesicles) with a single-lipid bilayer or two closely located nuclear membranes is considered. After such fusion on the lipid bilayer surface, traces of a complex of ssDNA with lipids were revealed. At fusion of two identical small liposomes (membrane vesicles) < 100 nm in diameter, a "big" liposome (vesicle) with ssDNA on the vesicle equator is formed. ssDNA occurrence on liposome surface gives a biphasic character to the fusion kinetics. The "big" membrane vesicle surrounded by ssDNA is the base of nuclear pore assembly. Its contact with the nuclear envelope leads to fast fusion of half of the vesicles with one nuclear membrane; then ensues a fusion delay when ssDNA reaches the membrane. The next step is to turn inside out the second vesicle half and its fusion to other nuclear membrane. A hole is formed between the two membranes, and nucleoporins begin pore complex assembly around the ssDNA. The surface tension of vesicles and nuclear membranes along with the kinetic energy of a liquid inside a vesicle play the main roles in this process. Special cases of nuclear pore formation are considered: pore formation on both nuclear envelope sides, the difference of pores formed in various cell-cycle phases and linear nuclear pore clusters.

  5. Emergent Catalytic Behavior of Self-Assembled Low Molecular Weight Peptide-Based Aggregates and Hydrogels.

    PubMed

    Tena-Solsona, Marta; Nanda, Jayanta; Díaz-Oltra, Santiago; Chotera, Agata; Ashkenasy, Gonen; Escuder, Beatriu

    2016-05-04

    We report a series of short peptides possessing the sequence (FE)n or (EF)n and bearing l-proline at their N-terminus that self-assemble into high aspect ratio aggregates and hydrogels. We show that these aggregates are able to catalyze the aldol reaction, whereas non-aggregated analogues are catalytically inactive. We have undertaken an analysis of the results, considering the accessibility of catalytic sites, pKa value shifts, and the presence of hydrophobic pockets. We conclude that the presence of hydrophobic regions is indeed relevant for substrate solubilization, but that the active site accessibility is the key factor for the observed differences in reaction rates. The results presented here provide an example of the emergence of a new chemical property caused by self-assembly, and support the relevant role played by self-assembled peptides in prebiotic scenarios. In this sense, the reported systems can be seen as primitive aldolase I mimics, and have been successfully tested for the synthesis of simple carbohydrate precursors.

  6. Light-powered autonomous and directional molecular motion of a dissipative self-assembling system

    NASA Astrophysics Data System (ADS)

    Ragazzon, Giulio; Baroncini, Massimo; Silvi, Serena; Venturi, Margherita; Credi, Alberto

    2015-01-01

    Biomolecular motors convert energy into directed motion and operate away from thermal equilibrium. The development of dynamic chemical systems that exploit dissipative (non-equilibrium) processes is a challenge in supramolecular chemistry and a premise for the realization of artificial nanoscale motors. Here, we report the relative unidirectional transit of a non-symmetric molecular axle through a macrocycle powered solely by light. The molecular machine rectifies Brownian fluctuations by energy and information ratchet mechanisms and can repeat its working cycle under photostationary conditions. The system epitomizes the conceptual and practical elements forming the basis of autonomous light-powered directed motion with a minimalist molecular design.

  7. Deriving molecular bonding from a macromolecular self-assembly using kinetic Monte Carlo simulations

    NASA Astrophysics Data System (ADS)

    Silly, Fabien; Weber, Ulrich K.; Shaw, Adam Q.; Burlakov, Victor M.; Castell, Martin R.; Briggs, G. A. D.; Pettifor, David G.

    2008-05-01

    Macromolecules can form regular structures on inert surfaces. We have developed a combined empirical and modeling approach to derive the bonding. From experimental scanning tunneling microscopy images of structures formed on Au(111) by melamine, by 3,4,9,10-perylene-tetracarboxylic-dianhydride, and by a 2:3 mixture of the two, we determine the molecular bonding morphologies. Within these bonding morphologies and by recognizing the distinction between cohesive and adhesive molecular interactions, we simultaneously simulated different molecular structures by using a lattice Monte Carlo method.

  8. Growth of Thin, Anisotropic, π-Conjugated Molecular Films by Step-Wise `Click' Assembly of Molecular Building Blocks: Characterizing Reaction Yield, Surface Coverage, and Film Thickness vs. Addition Step Number

    NASA Astrophysics Data System (ADS)

    Demissie, Abel; Haugstad, Greg; Frisbie, C. Daniel

    2015-03-01

    Molecular electronics is an active field of nanotechnology that has gained much interest due to the advent of modern microscopy techniques, and thin film synthesis using click chemistry - an approach which has enabled scientists to achieve a sub-angstrom control of monolayer length. Among the major challenges to grow oriented, surface-confined wires by click chemistry is development of synthetic routes that yield monodisperse wires, and lack of systematic way to measure the surface coverage of molecules. In this work, we report a comprehensive characterization of π-conjugated oligophenylene imine (OPI) wires synthesized step-wise by imine condensation click chemistry. OPI wire synthesis began with a self-assembled monolayer (SAM) of 4-formylthiophenol or 4-aminothiophenol on Au, followed by alternate addition of terepthaldehyde or phenylenediamine. OPI wires were characterized after each monomer addition via Rutherford backscattering spectrometry, x-ray photoelectron spectroscopy, cyclic voltammetry, reflection-absorption infra-red spectroscopy, and nuclear reaction analysis. We have determined an average extent of reaction greater than 98% completion for each growth step using five different techniques. Overall, these nanoscale scale surface characterization techniques proved to be an extremely sufficient method for monitoring wire growth and surface coverage.

  9. Effects of excluded volume and correlated molecular orientations on Förster resonance energy transfer in liquid water

    SciTech Connect

    Yang, Mino

    2014-04-14

    Förster theory for the survival probability of excited chromophores is generalized to include the effects of excluded volume and orientation correlation in the molecular distribution. An analytical expression for survival probability was derived and written in terms of a few simple elementary functions. Because of the excluded volume, the survival probability exhibits exponential decay at early times and stretched exponential decay at later times. Experimental schemes to determine the size of the molecular excluded volume are suggested. With the present generalization of theory, we analyzed vibrational resonance energy transfer kinetics in neat water. Excluded volume effects prove to be important and slow down the kinetics at early times. The majority of intermolecular resonance energy transfer was found to occur with exponential kinetics, as opposed to the stretched exponential behavior predicted by Förster theory. Quantum yields of intra-molecular vibrational relaxation, intra-, and intermolecular energy transfer were calculated to be 0.413, 0.167, and 0.420, respectively.

  10. Conformation, orientation and interaction in molecular monolayers: A surface second harmonic and sum frequency generation study

    SciTech Connect

    Superfine, R.; Huang, J.Y.; Shen, Y.R.

    1988-12-01

    We have used sum frequency generation (SFG) to study the order in a silane monolayer before and after the deposition of a coadsorbed liquid crystal monolayer. We observe an increase in the order of the chain of the silane molecule induced by the interpenetration of the liquid crystal molecules. By using second harmonic generation (SHG) and SFG, we have studied the orientation and conformation of the liquid crystal molecule on clean and silane coated glass surfaces. On both surfaces, the biphenyl group is tilted by 70{degree} with the alkyl chain end pointing away from the surface. The shift in the C-H stretch frequencies in the coadsorbed system indicates a significant interaction between molecules. 9 refs., 3 figs.

  11. Early stage P22 viral capsid self-assembly mediated by scaffolding protein: atom-resolved model and molecular dynamics simulation.

    PubMed

    Jiang, Jiajian; Yang, Jing; Sereda, Yuriy V; Ortoleva, Peter J

    2015-04-23

    Molecular dynamics simulation of an atom-resolved bacteriophage P22 capsid model is used to delineate the underlying mechanism of early stage P22 self-assembly. A dimer formed by the C-terminal fragment of scaffolding protein with a new conformation is demonstrated to catalyze capsomer (hexamer and pentamer) aggregation efficiently. Effects of scaffolding protein/coat protein binding patterns and scaffolding protein concentration on efficiency, fidelity, and capsid curvature of P22 self-assembly are identified.

  12. Hemolysin coregulated protein 1 as a molecular gluing unit for the assembly of nanoparticle hybrid structures

    PubMed Central

    Pham, Tuan Anh; Schreiber, Andreas; Sturm (née Rosseeva), Elena V

    2016-01-01

    Summary Hybrid nanoparticle (NP) structures containing organic building units such as polymers, peptides, DNA and proteins have great potential in biosensor and electronic applications. The nearly free modification of the polymer chain, the variation of the protein and DNA sequence and the implementation of functional moieties provide a great platform to create inorganic structures of different morphology, resulting in different optical and magnetic properties. Nevertheless, the design and modification of a protein structure with functional groups or sequences for the assembly of biohybrid materials is not trivial. This is mainly due to the sensitivity of its secondary, tertiary and quaternary structure to the changes in the interaction (e.g., hydrophobic, hydrophilic, electrostatic, chemical groups) between the protein subunits and the inorganic material. Here, we use hemolysin coregulated protein 1 (Hcp1) from Pseudomonas aeruginosa as a building and gluing unit for the formation of biohybrid structures by implementing cysteine anchoring points at defined positions on the protein rim (Hcp1_cys3). We successfully apply the Hcp1_cys3 gluing unit for the assembly of often linear, hybrid structures of plasmonic gold (Au NP), magnetite (Fe3O4 NP), and cobalt ferrite nanoparticles (CoFe2O4 NP). Furthermore, the assembly of Au NPs into linear structures using Hcp1_cys3 is investigated by UV–vis spectroscopy, TEM and cryo-TEM. One key parameter for the formation of Au NP assembly is the specific ionic strength in the mixture. The resulting network-like structure of Au NPs is characterized by Raman spectroscopy, showing surface-enhanced Raman scattering (SERS) by a factor of 8·104 and a stable secondary structure of the Hcp1_cys3 unit. In order to prove the catalytic performance of the gold hybrid structures, they are used as a catalyst in the reduction reaction of 4-nitrophenol showing similar catalytic activity as the pure Au NPs. To further extend the functionality

  13. Molecular Dynamics Study of Alkanethiolate Self-Assembled Monolayer Coated Gold Nanoparticle

    DTIC Science & Technology

    2007-06-01

    component of function results for the uncoated gold nanoparticle to the the Irving -Kirkwood (IK) pressure tensor. [321 The normal results for an...pp. 24-34, 1983. Studies." Langmuir , 4, pp. 546-558, 1988. 23. Shevade, A. V., J. Zhou, M. T. Zin, and S. Jiang. Phase 8. Rosenbaum, A.W, M.A. Freedman...Au(l 11): A Configurational-Bias Monte Carlo Assembled Monolayers of Varying Chain Length." Journal of Simulation Study. Langmuir 17, pp. 7566-7572

  14. Self-Assembly of Reconfigurable By-Design Optical Materials with Molecular-Level Control

    DTIC Science & Technology

    2014-09-21

    scans  obtained  by  AFM  for  (a)  monolayer  of  gold   nanoparticles  and  (b)  4  layers   of  gold   nanoparticles ...gold   nanoparticle  layers  for  self-­‐assembly  mediated  by  various  molecules.  _   5   Figure  5.     Optical ...520 nm. When TP was added, the solution immediately turned purple. The optical extinction spectrum revealed the

  15. Polarization dependence of Raman scattering from a thin film involving optical anisotropy theorized for molecular orientation analysis.

    PubMed

    Itoh, Yuki; Hasegawa, Takeshi

    2012-06-14

    Polarized Raman scattering from a thin film involving uniaxial optical anisotropy deposited on a dielectric substrate has analytically been theorized. The analyte film is modeled as a three-phase system (air/film/substrate) to calculate the electromagnetic fields of the incident and scattered light propagating across the system with an aid of the transfer matrix method to exactly take the optical anisotropy of the film into account. On the new theory, a methodology for molecular orientation analysis of an extended polymethylene chain in the film is proposed, which is employed for determination of the tilt angles of the chains in single- and five-monolayer Langmuir-Blodgett (LB) films of cadmium stearate deposited on a glass plate. The results agree well with those obtained by infrared spectroscopy, which confirms reliability of the present method.

  16. Effect of molecular orientation angle of imidazolium ring on frictional properties of imidazolium-based ionic liquid.

    PubMed

    Watanabe, S; Nakano, M; Miyake, K; Tsuboi, R; Sasaki, S

    2014-07-15

    Ionic liquids have significant potential as lubricants, and it is known that ionic liquids exhibit characteristic behavior at solid-liquid interfaces. Although it is believed that the structure of ionic liquids at the interface contributes to the tribological properties in the region of boundary-mixed lubrication, this contribution has not been clarified because such analysis is difficult. In this research, we clarify the lubrication mechanism of an imidazolium-based ionic liquid by comparing the results of friction tests with interfacial molecular orientation analysis using sum frequency generation spectroscopy. Consequently, we clarify that the tilt angle of the imidazolium ring affects the friction coefficient of the ionic liquid; that is, the larger tilt angle, the lower the friction coefficient.

  17. Tuning molecular weights of Bombyx mori (B. mori) silk sericin to modify its assembly structures and materials formation.

    PubMed

    Yang, Mingying; Shuai, Yajun; Zhou, Guanshan; Mandal, Namita; Zhu, Liangjun; Mao, Chuanbin

    2014-08-27

    Bombyx mori (B. mori) silk sericin is a protein with features desirable as a biomaterial, such as increased hydrophilicity and biodegradation, as well as resistance to oxidation, bacteria, and ultraviolet light. In contrast to other widely studied B. mori silk proteins such as fibroin, sericin is still unexplored as a building block for fabricating biomaterial, and thus a facile technique of processing it into a material is needed. Here, electrospinning technology was used to fabricate it into biomaterials from two forms of B. mori silk sericin with different molecular weights, one is a low (12.0 kDa) molecular sericin (LS) form and another is a high (66.0 kDa) molecular weight sericin (HS) form. Circular dichroism (CD) spectra showed that LS in hexafluoroacetone (HFA) solvent adopted a predominantly random coil conformation, whereas HS tended to form a β-sheet structure along with a large content of random coils. In addition, LS and HS in HFA solvent were found to form cylinder-like smaller nanoparticles and larger irregular aggregates before electrospinning, respectively. As a result, biomaterials based on microparticles and nanofibers were successfully fabricated by electrospinning of LS and HS dissolved in HFA, respectively. The cell viability and differentiation assay indicated that nanofibers and microparticles improved cell adhesion, growth, and differentiation, proving that the scaffolds electrospun from sericin are biocompatible regardless of its molecular weight. The microparticles, not common in electrospinning of silk proteins reported previously, were found to promote the osteogenic differentiation of mesenchymal stem cells in comparison to the nanofibers. This study suggested that molecular weight of sericin mediates its secondary structure and assembly structure, which in turn leads to a control of final morphology of the electrospun materials. The microparticles and nanofibers of sericin can be potentially used as building blocks for fabricating

  18. Tuning Molecular Weights of Bombyx mori (B. mori) Silk Sericin to Modify Its Assembly Structures and Materials Formation

    PubMed Central

    2015-01-01

    Bombyx mori (B. mori) silk sericin is a protein with features desirable as a biomaterial, such as increased hydrophilicity and biodegradation, as well as resistance to oxidation, bacteria, and ultraviolet light. In contrast to other widely studied B. mori silk proteins such as fibroin, sericin is still unexplored as a building block for fabricating biomaterial, and thus a facile technique of processing it into a material is needed. Here, electrospinning technology was used to fabricate it into biomaterials from two forms of B. mori silk sericin with different molecular weights, one is a low (12.0 kDa) molecular sericin (LS) form and another is a high (66.0 kDa) molecular weight sericin (HS) form. Circular dichroism (CD) spectra showed that LS in hexafluoroacetone (HFA) solvent adopted a predominantly random coil conformation, whereas HS tended to form a β-sheet structure along with a large content of random coils. In addition, LS and HS in HFA solvent were found to form cylinder-like smaller nanoparticles and larger irregular aggregates before electrospinning, respectively. As a result, biomaterials based on microparticles and nanofibers were successfully fabricated by electrospinning of LS and HS dissolved in HFA, respectively. The cell viability and differentiation assay indicated that nanofibers and microparticles improved cell adhesion, growth, and differentiation, proving that the scaffolds electrospun from sericin are biocompatible regardless of its molecular weight. The microparticles, not common in electrospinning of silk proteins reported previously, were found to promote the osteogenic differentiation of mesenchymal stem cells in comparison to the nanofibers. This study suggested that molecular weight of sericin mediates its secondary structure and assembly structure, which in turn leads to a control of final morphology of the electrospun materials. The microparticles and nanofibers of sericin can be potentially used as building blocks for fabricating

  19. Probing molecular pathways for DNA orientational trapping, unzipping and translocation in nanopores by using a tunable overhang sensor

    NASA Astrophysics Data System (ADS)

    Wang, Yong; Tian, Kai; Hunter, Lehr L.; Ritzo, Brandon; Gu, Li-Qun

    2014-09-01

    Nanopores provide a unique single-molecule platform for genetic and epigenetic detection. The target nucleic acids can be accurately analyzed by characterizing their specific electric fingerprints or signatures in the nanopore. Here we report a series of novel nanopore signatures generated by target nucleic acids that are hybridized with a probe. A length-tunable overhang appended to the probe functions as a sensor to specifically modulate the nanopore current profile. The resulting signatures can reveal multiple mechanisms for the orientational trapping, unzipping, escaping and translocation of nucleic acids in the nanopore. This universal approach can be used to program various molecular movement pathways, elucidate their kinetics, and enhance the sensitivity and specificity of the nanopore sensor for nucleic acid detection.Nanopores provide a unique single-molecule platform for genetic and epigenetic detection. The target nucleic acids can be accurately analyzed by characterizing their specific electric fingerprints or signatures in the nanopore. Here we report a series of novel nanopore signatures generated by target nucleic acids that are hybridized with a probe. A length-tunable overhang appended to the probe functions as a sensor to specifically modulate the nanopore current profile. The resulting signatures can reveal multiple mechanisms for the orientational trapping, unzipping, escaping and translocation of nucleic acids in the nanopore. This universal approach can be used to program various molecular movement pathways, elucidate their kinetics, and enhance the sensitivity and specificity of the nanopore sensor for nucleic acid detection. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr03195d

  20. Helical molecular duplex strands: multiple hydrogen-bond-mediated assembly of self-complementary oligomeric hydrazide derivatives.

    PubMed

    Yang, Yong; Yang, Zhi-Yong; Yi, Yuan-Ping; Xiang, Jun-Feng; Chen, Chuan-Feng; Wan, Li-Jun; Shuai, Zhi-Gang

    2007-06-22

    Careful examination of the X-ray structure of a ditopic hydrazide derivative 7 led to the concept that with malonyl groups as interhydrazide linkers hydrogen-bonding-mediated molecular duplex strands might be obtained. Complexation studies between 7, 8, and 9 confirmed this hypothesis. Two quadruple hydrogen-bonded heterodimers formed, in which spectator repulsive secondary electrostatic interaction was found to play an important role in determining the stability of the complexes. Extensive studies on 1-4 indicated that the hydrogen-bonding mode could persist in longer oligomeric hydrazide derivatives with chain extension from monomer to tetramer. Molecular duplex strands via two to fourteen interstrand hydrogen bonds were obtained. In addition to affecting the stability of the duplex strands, spectator repulsive secondary electrostatic interaction also played an important role in determining dynamic behavior of the duplex strands as exemplified by variable temperature (1)H NMR experiments. IR studies confirmed stronger hydrogen bonding in the longer oligomers. The assemblies of 1-4 on HOPG were also studied by STM technology. Molecular mechanical calculations further revealed double-helical structures for the longer oligomers. The results provide new opportunities for development of polymeric helical duplexes with well-defined structures.

  1. Molecular basis of APC/C regulation by the spindle assembly checkpoint

    PubMed Central

    Zhang, Ziguo; Yang, Jing; Maslen, Sarah; Skehel, Mark; Barford, David

    2016-01-01

    In the dividing eukaryotic cell the spindle assembly checkpoint (SAC) ensures each daughter cell inherits an identical set of chromosomes. The SAC coordinates the correct attachment of sister chromatid kinetochores to the mitotic spindle with activation of the anaphase-promoting complex/cyclosome (APC/C), the E3 ubiquitin ligase that initiates chromosome separation. In response to unattached kinetochores, the SAC generates the mitotic checkpoint complex (MCC), a multimeric assembly that inhibits the APC/C, delaying chromosome segregation. Here, using cryo-electron microscopy we determined the near-atomic resolution structure of an APC/C-MCC complex (APC/CMCC). We reveal how degron-like sequences of the MCC subunit BubR1 block degron recognition sites on Cdc20, the APC/C coactivator subunit (Cdc20APC/C) responsible for substrate interactions. BubR1 also obstructs binding of UbcH10 (APC/C’s initiating E2) to repress APC/C ubiquitination activity. Conformational variability of the complex allows for UbcH10 association, and we show from a structure of APC/CMCC in complex with UbcH10 how the Cdc20 subunit intrinsic to the MCC (Cdc20MCC) is ubiquitinated, a process that results in APC/C reactivation when the SAC is silenced. PMID:27509861

  2. Possible Room-Temperature Ferromagnetism in Self-Assembled Ensembles of Paramagnetic and Diamagnetic Molecular Semiconductors.

    PubMed

    Dhara, Barun; Tarafder, Kartick; Jha, Plawan K; Panja, Soumendra N; Nair, Sunil; Oppeneer, Peter M; Ballav, Nirmalya

    2016-12-15

    Owing to long spin-relaxation time and chemically customizable physical properties, molecule-based semiconductor materials like metal-phthalocyanines offer promising alternatives to conventional dilute magnetic semiconductors/oxides (DMSs/DMOs) to achieve room-temperature (RT) ferromagnetism. However, air-stable molecule-based materials exhibiting both semiconductivity and magnetic-order at RT have so far remained elusive. We present here the concept of supramolecular arrangement to accomplish possibly RT ferromagnetism. Specifically, we observe a clear hysteresis-loop (Hc ≈ 120 Oe) at 300 K in the magnetization versus field (M-H) plot of the self-assembled ensembles of diamagnetic Zn-phthalocyanine having peripheral F atoms (ZnFPc; S = 0) and paramagnetic Fe-phthalocyanine having peripehral H atoms (FePc; S = 1). Tauc plot of the self-assembled FePc···ZnFPc ensembles showed an optical band gap of ∼1.05 eV and temperature-dependent current-voltage (I-V) studies suggest semiconducting characteristics in the material. Using DFT+U quantum-chemical calculations, we reveal the origin of such unusual ferromagnetic exchange-interaction in the supramolecular FePc···ZnFPc system.

  3. Assembly, molecular organization, and membrane-binding properties of development-specific septins

    PubMed Central

    Garcia, Galo; Finnigan, Gregory C.; Heasley, Lydia R.; Sterling, Sarah M.; Aggarwal, Adeeti; Pearson, Chad G.

    2016-01-01

    Septin complexes display remarkable plasticity in subunit composition, yet how a new subunit assembled into higher-order structures confers different functions is not fully understood. Here, this question is addressed in budding yeast, where during meiosis Spr3 and Spr28 replace the mitotic septin subunits Cdc12 and Cdc11 (and Shs1), respectively. In vitro, the sole stable complex that contains both meiosis-specific septins is a linear Spr28–Spr3–Cdc3–Cdc10–Cdc10–Cdc3–Spr3–Spr28 hetero-octamer. Only coexpressed Spr3 and Spr28 colocalize with Cdc3 and Cdc10 in mitotic cells, indicating that incorporation requires a Spr28-Spr3 protomer. Unlike their mitotic counterparts, Spr28-Spr3–capped rods are unable to form higher-order structures in solution but assemble to form long paired filaments on lipid monolayers containing phosphatidylinositol-4,5-bisphosphate, mimicking presence of this phosphoinositide in the prospore membrane. Spr28 and Spr3 fail to rescue the lethality of a cdc11Δ cdc12Δ mutant, and Cdc11 and Cdc12 fail to restore sporulation proficiency to spr3Δ/spr3Δ spr28Δ/spr28Δ diploids. Thus, specific meiotic and mitotic subunits endow septin complexes with functionally distinct properties. PMID:26929450

  4. Structual and Molecular Basis of the Assembly of the TRPP2/PKD1 Complex

    SciTech Connect

    Yu, Y.; Ulbrich, M; Li, M; Buraei, Z; Chen, X; Ong, A; Tong, L; Isacoff, E; Yang, J

    2009-01-01

    Mutations in PKD1 and TRPP2 account for nearly all cases of autosomal dominant polycystic kidney disease (ADPKD). These 2 proteins form a receptor/ion channel complex on the cell surface. Using a combination of biochemistry, crystallography, and a single-molecule method to determine the subunit composition of proteins in the plasma membrane of live cells, we find that this complex contains 3 TRPP2 and 1 PKD1. A newly identified coiled-coil domain in the C terminus of TRPP2 is critical for the formation of this complex. This coiled-coil domain forms a homotrimer, in both solution and crystal structure, and binds to a single coiled-coil domain in the C terminus of PKD1. Mutations that disrupt the TRPP2 coiled-coil domain trimer abolish the assembly of both the full-length TRPP2 trimer and the TRPP2/PKD1 complex and diminish the surface expression of both proteins. These results have significant implications for the assembly, regulation, and function of the TRPP2/PKD1 complex and the pathogenic mechanism of some ADPKD-producing mutations.

  5. Molecular doping of MoS2 transistors by self-assembled oleylamine networks

    NASA Astrophysics Data System (ADS)

    Lockhart de la Rosa, César J.; Phillipson, Roald; Teyssandier, Joan; Adisoejoso, Jinne; Balaji, Yashwanth; Huyghebaert, Cedric; Radu, Iuliana; Heyns, Marc; De Feyter, Steven; De Gendt, Stefan

    2016-12-01

    Thin MoS2 films continue to be of key interest for numerous applications; however, effective doping and high metal to MoS2 contact resistance are challenges for future applications. We report on the self-assembly of oleylamine on top of MoS2 thin-films and the effective doping of MoS2 thin-film field effect transistors by oleylamine. Atomic force microscopy revealed that oleylamine organizes in lamellae domains on MoS2 thin films with similar characteristics of those previously observed on highly ordered pyrolytic graphite. A carrier concentration increase from 7.1 × 1011 cm-2 up to 1.9 × 1013 cm-2 at 0 V gate voltage is achieved together with a reduction of the contact resistance by a factor of 5 when using gold as metal contact. Furthermore, this non-covalent doping proves to be removable and reproducible among different flakes and does not degrade the electron mobility. Thus, this work opens the path for future works on controlling the doping of MoS2 by proper selection of the self-assembled species.

  6. Large cell carcinoma of the lung: clinically oriented classification integrating immunohistochemistry and molecular biology.

    PubMed

    Rossi, G; Mengoli, M C; Cavazza, A; Nicoli, D; Barbareschi, M; Cantaloni, C; Papotti, M; Tironi, A; Graziano, P; Paci, M; Stefani, A; Migaldi, M; Sartori, G; Pelosi, G

    2014-01-01

    This study aimed at challenging pulmonary large cell carcinoma (LLC) as tumor entity and defining different subgroups according to immunohistochemical and molecular features. Expression of markers specific for glandular (TTF-1, napsin A, cytokeratin 7), squamous cell (p40, p63, cytokeratins 5/6, desmocollin-3), and neuroendocrine (chromogranin, synaptophysin, CD56) differentiation was studied in 121 LCC across their entire histological spectrum also using direct sequencing for epidermal growth factor receptor (EGFR) and v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog (KRAS) mutations and FISH analysis for ALK gene translocation. Survival was not investigated. All 47 large cell neuroendocrine carcinomas demonstrated a true neuroendocrine cell lineage, whereas all 24 basaloid and both 2 lymphoepithelioma-like carcinomas showed squamous cell markers. Eighteen out of 22 clear cell carcinomas had glandular differentiation, with KRAS mutations being present in 39 % of cases, whereas squamous cell differentiation was present in four cases. Eighteen out of 20 large cell carcinomas, not otherwise specified, had glandular differentiation upon immunohistochemistry, with an exon 21 L858R EGFR mutation in one (5 %) tumor, an exon 2 KRAS mutation in eight (40 %) tumors, and an ALK translocation in one (5 %) tumor, whereas two tumors positive for CK7 and CK5/6 and negative for all other markers were considered adenocarcinoma. All six LCC of rhabdoid type expressed TTF-1 and/or CK7, three of which also harbored KRAS mutations. When positive and negative immunohistochemical staining for these markers was combined, three subsets of LCC emerged exhibiting glandular, squamous, and neuroendocrine differentiation. Molecular alterations were restricted to tumors classified as adenocarcinoma. Stratifying LCC into specific categories using immunohistochemistry and molecular analysis may significantly impact on the choice of therapy.

  7. Molecular recognition and self-assembly special feature: Encapsulated-guest rotation in a self-assembled heterocapsule directed toward a supramolecular gyroscope.

    PubMed

    Kitagawa, Hitomi; Kobori, Yasuhiro; Yamanaka, Masamichi; Yoza, Kenji; Kobayashi, Kenji

    2009-06-30

    The self-assembled heterocapsule 1.2, which is formed by the hydrogen bonds of tetra(4-pyridyl)-cavitand 1 and tetrakis(4-hydroxyphenyl)-cavitand 2, encapsulates 1 molecule of guests such as 1,4-diacetoxybenzene 3a, 1,4-diacetoxy-2,5-dimethylbenzene 3b, 1,4-diacetoxy-2,5-dialkoxybenzenes (3c, OCH(3); 3d, OC(2)H(5); 3e, OC(3)H(7); 3f, OC(4)H(9); 3g, OC(5)H(11); 3h, OC(6)H(13); 3i, OC(8)H(17)), 1,4-diacetoxy-2,5-difluorobenzene 4a, and 1,4-diacetoxy-2,3-difluorobenzene 4b. The X-ray crystallographic analysis of 3c@(1.2) showed that the acetoxy groups at the 1,4-positions of 3c are oriented toward the 2 aromatic cavity ends of 1.2 and that 3c can rotate along the long axis of 1.2. Thus, the 1.2 (stator) with the encapsulation guest (rotator) behaves as a supramolecular gyroscope. A variable temperature (VT) (1)H NMR study in CDCl(3) showed that 3a, 3b, 4a, and 4b within 1.2 rotate rapidly even at 218 K, whereas guest rotation is almost inhibited for 3h and 3i even at 323 K. In this respect, 4b with a large dipole moment is a good candidate for the rotator of 1.2. For 3c-3g, the enthalpic (DeltaH(double dagger)) and entropic (DeltaS(double dagger)) contributions to the free energy of activation (DeltaG(double dagger)) for the guest-rotational steric barriers within 1.2 were obtained from Eyring plots based on line-shape analysis of the VT (1)H NMR spectra. The value of DeltaG(double dagger) increased in the order 3c < 3d < 3e < 3f < 3g. Thus, the elongation of the alkoxy chains at the 2,5-positions of 3 puts the brakes on guest rotation within 1.2.

  8. Molecular cloning and expression pattern of oriental river prawn (Macrobrachium nipponense) nitric oxide synthase.

    PubMed

    Rahman, N M A; Fu, H T; Sun, S M; Qiao, H; Jin, S; Bai, H K; Zhang, W Y; Liang, G X; Gong, Y S; Xiong, Y W; Wu, Y

    2016-08-29

    Nitric oxide synthase (NOS) produces nitric oxide (NO) by catalyzing the conversion of l-arginine to l-citrulline, with the concomitant oxidation of nicotinamide adenine dinucleotide phosphate. Recently, various studies have verified the importance of NOS invertebrates and invertebrates. However, the NOS gene family in the oriental river prawn Macrobrachium nipponense is poorly understood. In this study, we cloned the full-length NOS complementary DNA from M. nipponense (MnNOS) and characterized its expression pattern in different tissues and at different developmental stages. Real-time quantitative polymerase chain reaction (RT-qPCR) showed the MnNOS gene to be expressed in all investigated tissues, with the highest levels observed in the androgenic gland (P < 0.05). Our results revealed that the MnNOS gene may play a key role in M. nipponense male sexual differentiation. Moreover, RT-qPCR revealed that MnNOS mRNA expression was significantly increased in post-larvae 10 days after metamorphosis (P < 0.05). The expression of this gene in various tissues indicates that it may perform versatile biological functions in M. nipponense.

  9. Molecular-level control of feature separation in one-dimensional nanostructure assemblies formed by biomolecular nanolithography.

    PubMed

    Woehrle, Gerd H; Warner, Marvin G; Hutchison, James E

    2004-07-06

    In this paper, we present a convenient and reliable method to organize small gold nanoparticles (d(CORE) = 1.5 nm) into linear chains with precisely controlled interparticle spacing over a range of 1.5-2.8 nm through biomolecular nanolithography. Controlling the feature separations of 1 to a few nanometers with angstrom-level precision is a key requirement in electronic and optical applications of nanostructures to tune the properties of the nanostructures and manipulate the interactions between neighboring structures. Here, chains are formed in solution by utilizing functional-group-directed self-assembly to organize ligand-stabilized gold nanoparticles onto DNA templates. The spacing between neighboring nanoparticles can be controlled chemically and tuned at the molecular level by utilizing nanoparticles possessing ligand shells of varying thickness to achieve angstrom-level resolution at spacings of 1.5, 2.1, and 2.8 nm. The small standard deviation (< or = 20%) in the values for the interparticle spacing illustrates the reproducibility of the approach. Because the interparticle spacing is enforced by the ligand shell rather than the scaffold, the spacing is uniform even in nonlinear sections of the chain. We further show that the assembly process is robust and produces extended linear nanoparticle chains of up to 1 microm in length and a total coverage of > 90%. All structures and interparticle spacings were analyzed using transmission electron microscopy. Our results demonstrate the potential of scaffold-assisted assembly approaches for patterning features with tunable dimensions on a length scale that is important for future applications of these materials in nanoscale electronics and optics.

  10. Ullmann coupling mediated assembly of an electrically driven altitudinal molecular rotor.

    PubMed

    Murphy, Colin J; Smith, Zachary C; Pronschinski, Alex; Lewis, Emily A; Liriano, Melissa L; Wong, Chloe; Ivimey, Christopher J; Duffy, Mitchell; Musial, Wojciech; Therrien, Andrew J; Thomas, Samuel W; Sykes, E Charles H

    2015-12-21

    Surface-bound molecular rotation can occur with the rotational axis either perpendicular (azimuthal) or parallel (altitudinal) to the surface. The majority of molecular rotor studies involve azimuthal rotors, whereas very few altitudinal rotors have been reported. In this work, altitudinal rotors are formed by means of coupling aryl halides through a surface-mediated Ullmann coupling reaction, producing a reaction state-dependent altitudinal molecular rotor/stator. All steps in the reaction on a Cu(111) surface are visualized by low-temperature scanning tunneling microscopy. The intermediate stage of the coupling reaction is a metal-organic complex consisting of two aryl groups attached to a single copper atom with the aryl rings angled away from the surface. This conformation leads to nearly unhindered rotational motion of ethyl groups at the para positions of the aryl rings. Rotational events of the ethyl group are both induced and quantified by electron tunneling current versus time measurements and are only observed for the intermediate structure of the Ullmann coupling reaction, not the starting material or finished product in which the ethyl groups are static. We perform an extensive set of inelastic electron tunneling driven rotation experiments that reveal that torsional motion around the ethyl group is stimulated by tunneling electrons in a one-electron process with an excitation energy threshold of 45 meV. This chemically tunable system offers an ideal platform for examining many fundamental aspects of the dynamics of chemically tunable molecular rotor and motors.

  11. Dansyl-labeled anionic amphiphile with a hexadecanoic carbon chain: synthesis and detection for shape transitions in organized molecular assemblies.

    PubMed

    Gao, Lining; Xia, Huiyun; Wang, Xiaoman; Li, Li; Chen, Huaxin

    2015-03-15

    The probing properties of a new fluorophore-labeled anionic surfactant, sodium 16-(N-dansyl)aminocetylate (16-DAN-ACA) were investigated systematically in molecular assemblies, especially in the transitions between micelles and vesicles. 16-DAN-ACA can efficiently differentiate the two different aggregate types in mixed cationic and anionic surfactant systems. The fluorescence anisotropy of 16-DAN-ACA was found to be sensitive for directly detecting the micellar growth in micelles containing oppositely charged surfactants; both cationic cetyltrimethylammonium bromide (CTAB) systems and anionic sodium dodecyl sulfate (SDS) systems were studied. The results indicated that the 16-DAN-ACA is a good fluorescent probe for differentiating the different aggregates, and even more can be used to detect the micellar growth.

  12. Comparative electrochemical and impedance studies of self-assembled rigid-rod molecular wires and alkanethiols on gold substrates.

    PubMed

    Aguiar, Francisco A; Campos, Rui; Wang, Changsheng; Jitchati, Rukkiat; Batsanov, Andrei S; Bryce, Martin R; Kataky, Ritu

    2010-11-28

    A study of the charge transfer and self-assembly characteristics of two new rigid-rod molecular wires 1 and 2 assembled on polycrystalline gold electrodes was carried out using electrochemical impedance spectroscopy and cyclic voltammetry. This class of wires have precisely controlled (ca. 1.5-2.5 nm) lengths of π-conjugation, with extended HOMO and LUMO wavefunctions. While rotations can occur around the C-C single bonds, the molecules cannot isomerise or fold due to their rigid backbone structures. The behaviour of these wires was compared with SAMs of heptanethiol (HPT) and dodecanethiol (DDT). It was found that SAMs of 1, which bears flexible hexyloxy sidechains, had randomly distributed pinholes which show microelectrode behaviour even when diluted with DDT. SAMs of 2, which do not have any sidechains, were well-organised at open-circuit potentials enabling evaluation of electron transfer kinetics assuming an average film thickness. However, impedance studies show that deviations from open circuit potentials resulted in an exponential decrease in charge transfer resistance, whereas capacitance remained constant, possibly attributable to conformational changes of the SAM. The syntheses and characterisation of the molecules is described.

  13. Structure and dynamics of a protein-surfactant assembly studied by ion-mobility mass spectrometry and molecular dynamics simulations.

    PubMed

    Borysik, Antoni J

    2015-09-01

    The structure and dynamics of a protein-surfactant assembly studied by ion-mobility mass spectrometry (IMS) and vacuum molecular dynamics (MD) simulations is reported. Direct evidence is provided for the ability of the surfactant dodecyl-β-D-maltoside (DDM) to prevent charge-induced unfolding of the membrane protein (PagP) in the gas-phase. Restraints obtained by IMS are used to map the surfactant positions onto the protein surface. Surfactants occupying more exposed positions at the apexes of the β-barrel structure are most in-line with the experimental observations. MD simulations provide additional evidence for this assembly organization through surfactant inversion and migration on the protein structure in the absence of solvent. Surfactant migration entails a net shift from apolar membrane spanning regions to more polar regions of the protein structure with the DDM molecule remaining attached to the protein via headgroup interactions. These data provide evidence for the role of protein-DDM headgroup interactions in stabilizing membrane protein structure from gas-phase unfolding.

  14. pH-dependent self-assembly of EAK16 peptides in the presence of a hydrophobic surface: coarse-grained molecular dynamics simulation.

    PubMed

    Emamyari, Soheila; Fazli, Hossein

    2014-06-28

    Self-assembly behavior of the three types of ionic peptide, EAK16, is studied in the presence of a hydrophobic surface using coarse-grained molecular dynamics simulations at three pH ranges of the solution. It is found that the peptide chains of all the three types assemble on the hydrophobic surface. EAK16-I and EAK16-II peptides assemble into ribbon-like structures, regardless of the value of pH. EAK16-IV peptide chains, however, assemble into ribbon-like structures at low and high pH ranges and form disc-shaped assemblies on the hydrophobic surface at the isoelectric point, pH = 7. Strong intra-chain electrostatic interactions in the case of EAK16-IV peptide play the main role in dependence of its self-assembly behavior on pH and the different morphology of its assembly relative to those of the two other types. Kinetics of growth of the assemblies on the hydrophobic surface is also studied.

  15. Self-Assembling Molecular Capsules Based on α,γ-Cyclic Peptides.

    PubMed

    Ozores, Haxel Lionel; Amorín, Manuel; Granja, Juan R

    2017-01-18

    A new capsule based on a β-sheet self-assembling cyclic peptide with the ability to recognize and release several guests is described. The host structure is composed of two self-complementary α,γ-cyclic peptides bearing a Zn porphyrin cap that is used for the selective recognition of the guest. The two components are linked through two dynamic covalent bonds. The combination of binding forces, including hydrogen bonding, metal coordination, and dynamic hydrazone bonds, allows the reversible recognition of long bipyridine guests. The affinity for these ligands showed a strong dependence on the guest length. Delivery of the encapsulated ligand can be achieved by hydrolysis of hydrazones to disrupt the sandwich complex structure.

  16. Introduction of heterofunctional groups onto molecular hexagons via coordination-driven self-assembly.

    PubMed

    Ghosh, Koushik; Hu, Jiming; Yang, Hai-Bo; Northrop, Brian H; White, Henry S; Stang, Peter J

    2009-07-03

    The design and synthesis of two new heterofunctional hexagons containing both redox-active ferrocenyl and host-guest crown ether functionalities has been achieved via coordination-driven self-assembly. The size and relative distribution of functional groups on the supramolecular metallacycles can be precisely controlled. The host-guest recognition properties of the crown ether moieties and their ability to complex cationic guests to form tris[2]pseudorotaxane complexes have been investigated. The electronic properties of the ferrocenyl moieties have been obtained through electrochemical studies. The functional moieties are shown to operate orthogonally, resulting in discrete supramolecular hexagons that are capable of carrying out a variety of functions both simultaneously and independently.

  17. Hierarchical Assembly of a Dual-responsive Macroscopic Insulated Molecular Wire Bundle in a Gradient System

    PubMed Central

    Sheng, Yujie; Chen, Qibin; Yao, Junyao; Wang, Ying; Liu, Honglai

    2015-01-01

    Here, we report the hierarchical self-assembly of a cationic gemini amphiphile, Azo 1, in a composition gradient solution generated using solvent evaporation. As the gradient solution is formed, Azo 1 forms nanorods in the lower region of the solution. Depending on solvent composition, these nanorods can further develop into nanofibres, which can then intertwine to form double helices and other types of nanohelices in the upper region of the solution. Finally, a macroscopic wire bundle is formed via the fusion of nanohelices; this ribbon-like bundle exhibits elasticity and linear ohmic resistance properties. More intriguingly, this bundle exhibits photoresponsive properties that affect its deformation and conductivity, as well as a rapid electroresponse that affects its conductivity, indicating that it is feasible to control the charge pathway. PMID:25588881

  18. Molecular self-assembly of two-terminal, voltammetric microsensors with internal references.

    PubMed

    Hickman, J J; Ofer, D; Laibinis, P E; Whitesides, G M; Wrighton, M S

    1991-05-03

    Self-assembly of a ferrocenyl thiol and a quinone thiol onto Au microelectrodes forms the basis for a new microsensor concept: a two-terminal, voltammetric microsensor with reference and sensor functions on the same electrode. The detection is based on measurement of the potential difference of current peaks for oxidation and reduction of the reference (ferrocene) and indicator (quinone) in aqueous electrolyte in a two-terminal, linear sweep voltammogram in which a counterelectrode of relatively large surface area is used. The quinone has a half-wave potential, E((1/2)), that is pH-sensitive and can be used as a pH indicator; the ferrocene center has an E(1/2) that is a pH-insensitive reference. The key advantages are that such sensors require no separate reference electrode and function as long as current peaks can be located for reference and indicator molecules.

  19. Molecular Self-Assembly of Two-Terminal, Voltammetric Microsensors with Internal References

    NASA Astrophysics Data System (ADS)

    Hickman, James J.; Ofer, David; Laibinis, Paul E.; Whitesides, George M.; Wrighton, Mark S.

    1991-05-01

    Self-assembly of a ferrocenyl thiol and a quinone thiol onto Au microelectrodes forms the basis for a new microsensor concept: a two-terminal, voltammetric microsensor with reference and sensor functions on the same electrode. The detection is based on measurement of the potential difference of current peaks for oxidation and reduction of the reference (ferrocene) and indicator (quinone) in aqueous electrolyte in a two-terminal, linear sweep voltammogram in which a counterelectrode of relatively large surface area is used. The quinone has a half-wave potential, E1/2, that is pH-sensitive and can be used as a pH indicator; the ferrocene center has an E1/2 that is a pH-insensitive reference. The key advantages are that such sensors require no separate reference electrode and function as long as current peaks can be located for reference and indicator molecules.

  20. Self-assembly, reorganization, and photophysical properties of silver(I)-Schiff-base molecular rectangle and polymeric array species.

    PubMed

    Wu, Huang-Chun; Thanasekaran, P; Tsai, Chi-Hwe; Wu, Jing-Yun; Huang, Sheng-Ming; Wen, Yuh-Sheng; Lu, Kuang-Lieh

    2006-01-09

    A self-assembly of AgClO(4) with a Schiff-base ligand N,N'-bis(pyridin-2-ylmethylene)benzene-1,4-diamine (1) gave a 1D zigzag polymeric array [[Ag(2)(C(18)H(14)N(4))(2)](ClO(4))(2)(CH(3)CN)](n) (3), while the self-assembly of AgClO(4) with 3,3'-dimethyl-N,N'-bis(pyridin-2-ylmethylene)biphenyl-4,4'-diamine (2) afforded the molecular rectangle [[Ag(2)(C(26)H(22)N(4))(2)](ClO(4))(2)] (4). The structures of 3 and 4 were characterized by single-crystal X-ray diffraction analysis. Structural data for 3 indicate that the Ag(I) ion is coordinated by two ligands of 1 in a distorted tetrahedral fashion thereby leading to a 1D zigzag polymeric array. The zigzag chains are interdigitated with weak pi-pi stacking interactions. The structure of 4 consists of a discrete molecular rectangle where the silver atom has a distorted square-planar coordination with the pyridyl ligands and azomethine nitrogen atoms of 2. An intramolecular pi-pi interaction between the phenyl rings of adjacent Schiff-base 2 functions to stabilize the rectangular architecture. The Ag(I)-Schiff-base coordination polymer 3 is not stable in solution. The degradation and reorganization of 3 to form a [2 x 2] grid architecture [[Ag(4)(C(26)H(22)N(4))(4)](ClO(4))(4)] (3g) was supported in a FAB-MS study. The rectangular structure of 4 remains intact in solution at ambient temperature. The complexes 3g and 4 exhibit unusual luminescence behavior in solution at room temperature with significantly red-shifted emission in the visible region.