Science.gov

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. 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.

  4. 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

  5. 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.

  6. 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.

  7. Photoswitchable gel assembly based on molecular recognition

    PubMed Central

    Yamaguchi, Hiroyasu; Kobayashi, Yuichiro; Kobayashi, Ryosuke; Takashima, Yoshinori; Hashidzume, Akihito; Harada, Akira

    2012-01-01

    The formation of effective and precise linkages in bottom-up or top-down processes is important for the development of self-assembled materials. Self-assembly through molecular recognition events is a powerful tool for producing functionalized materials. Photoresponsive molecular recognition systems can permit the creation of photoregulated self-assembled macroscopic objects. Here we demonstrate that macroscopic gel assembly can be highly regulated through photoisomerization of an azobenzene moiety that interacts differently with two host molecules. A photoregulated gel assembly system is developed using polyacrylamide-based hydrogels functionalized with azobenzene (guest) or cyclodextrin (host) moieties. Reversible adhesion and dissociation of the host gel from the guest gel may be controlled by photoirradiation. The differential affinities of α-cyclodextrin or β-cyclodextrin for the trans-azobenzene and cis-azobenzene are employed in the construction of a photoswitchable gel assembly system. PMID:22215078

  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. Self-assembling DNA nanotubes to connect molecular landmarks

    NASA Astrophysics Data System (ADS)

    Mohammed, Abdul M.; Šulc, Petr; Zenk, John; Schulman, Rebecca

    2017-05-01

    Within cells, nanostructures are often organized using local assembly rules that produce long-range order. Because these rules can take into account the cell's current structure and state, they can enable complexes, organelles or cytoskeletal structures to assemble around existing cellular components to form architectures. Although many methods for self-assembling biomolecular nanostructures have been developed, few can be programmed to assemble structures whose form depends on the identity and organization of structures already present in the environment. Here, we demonstrate that DNA nanotubes can grow to connect pairs of molecular landmarks with different separation distances and relative orientations. DNA tile nanotubes nucleate at these landmarks and grow while their free ends diffuse. The nanotubes can then join end to end to form stable connections, with unconnected nanotubes selectively melted away. Connections form between landmark pairs separated by 1-10 µm in more than 75% of cases and can span a surface or three dimensions. This point-to-point assembly process illustrates how self-assembly kinetics can be designed to produce structures with a desired physical property rather than a specific shape.

  14. 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.

  15. 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

  16. 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

  17. Coulombic dragging of molecular assemblies on nanotubes

    NASA Astrophysics Data System (ADS)

    Kral, Petr; Sint, Kyaw; Wang, Boyang

    2009-03-01

    We show by molecular dynamics simulations that polar molecules, ions and their assemblies could be Coulombically dragged on the surfaces of single-wall carbon and boron-nitride nanotubes by ionic solutions or individual ions moving inside the nanotubes [1,2]. We also briefly discuss highly selective ionic sieves based on graphene monolayers with nanopores [3]. These phenomena could be applied in molecular delivery, separation and desalination.[3pt] [1] Boyang Wang and Petr Kral, JACS 128, 15984 (2006). [0pt] [2] Boyang Wang and Petr Kral, Phys. Rev. Lett. 101, 046103 (2008). [0pt] [3] Kyaw Sint, Boyang Wang and Petr Kral, JACS, ASAP (2008).

  18. Dynamic assembly of molecularly imprinted polymer nanoparticles.

    PubMed

    Gong, Haiyue; Hajizadeh, Solmaz; Jiang, Lingdong; Ma, Huiting; Ye, Lei

    2017-09-11

    Manipulation of specific binding and recycling of materials are two important aspects for practical applications of molecularly imprinted polymers. In this work, we developed a new approach to control the dynamic assembly of molecularly imprinted nanoparticles by surface functionalization. Molecularly imprinted polymer nanoparticles with a well-controlled core-shell structure were synthesized using precipitation polymerization. The specific binding sites were created in the core during the first step imprinting reaction. In the second polymerization step, epoxide groups were introduced into the particle shell to act asan intermediate linker to immobilize phenylboronic acids, as well as to introduce cis-diol structures on surface. The imprinted polymer nanoparticles modified with boronic acid and cis-diol structures maintained high molecular binding specificity, and the nanoparticles could be induced to form dynamic particle aggregation that responded to pH variation and chemical stimuli. The possibility of modulating molecular binding and nanoparticle assembly in a mutually independent fashion can be exploited in a number of applications where repeated use of precious nanoparticles is needed. Copyright © 2017 Elsevier Inc. All rights reserved.

  19. 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.

  20. Orientational phase transitions and the assembly of viral capsids

    NASA Astrophysics Data System (ADS)

    Dharmavaram, Sanjay; Xie, Fangming; Klug, William; Rudnick, Joseph; Bruinsma, Robijn

    2017-06-01

    We present a Landau theory for large-l orientational phase transitions and apply it to the assembly of icosahedral viral capsids. The theory predicts two distinct types of ordering transitions. Transitions dominated by the l =6 ,10 ,12 , and 18 icosahedral spherical harmonics resemble robust first-order phase transitions that are not significantly affected by chirality. The remaining transitions depend essentially on including mixed l states denoted as l =15 +16 corresponding to a mixture of l =15 and l =16 spherical harmonics. The l =15 +16 transition is either continuous or weakly first-order and it is strongly influenced by chirality, which suppresses spontaneous chiral symmetry breaking. The icosahedral state is in close competition with states that have tetrahedral, D5, and octahedral symmetries. We present a group-theoretic method to analyze the competition between the different symmetries. The theory is applied to a variety of viral shells.

  1. Cellulose microfibril assembly and orientation in higher plant cells

    SciTech Connect

    Mueller, S.C.; Maclachlan, G.A.; Brown, R.M. Jr.

    1983-01-01

    Freeze-fractured plasma membranes of seedlings of Zea mays L., Burpee's Snowcross, and Pisum sativum L., variety Alsaka, contain terminal complex structures and the impressions of microfibrils from the newest cell wall layer.Terminal complex subunits are on the exoplasmic fracture (EF) face, and rosette subunits are on the protoplasmic fracture (PF) face of the membrane. The association of terminal complexes and rosettes with microfibril tips and their association with newly deposited groups of microfibrils is indirect evidence for their role in microfibril assembly. Microtubules may be responsible for certain orientations of microfibrils, particularly the formation of bands of microfibrils in newly deposited wall layers. However, microfibril orienting mechanisms are more complex, involving factors still present during colchicine treatment. Since UDP-glucose is thought to be a precursor of cellulose microfibrils in higher plant cells, EM radioautography was used to determine the site of incorporation of glucose. However, under the conditions used, glucose was only incorporated from UDP-glucose at the surface of cut or damaged pea stem cells, i.e., in vitro. Thus, incorporation of glucose from UDP-glucose was not useful for probing the patterns of cellulose microfibril synthesis in vivo. 18 references, 8 figures.

  2. 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.

  3. 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.

  4. Effect of head group orientation on phospholipid assembly

    NASA Astrophysics Data System (ADS)

    Paul, Tanay; Saha, Jayashree

    2017-06-01

    The relationship between bilayer stability and lipid head group orientation is reported. In this work, molecular-dynamics simulations are performed to analyze the structure-property relationship of lipid biomembranes, taking into account coarse-grained model lipid interactions. The work explains the molecular scale mechanism of the phase behavior of lipid systems due to ion-lipid or anesthetic-lipid interactions, where reorientations of dipoles play a key role in modifying lipid phases and thereby alter biomembrane function. Our study demonstrates that simple dipolar reorientation is indeed sufficient in tuning a bilayer to a randomly flipped nonbilayer lamellar phase. This study may be used to assess the impact of changes in lipid phase characteristics on biomembrane structure due to the presence of anesthetics and ions.

  5. Relative intermolecular orientation probed via molecular heat transport.

    PubMed

    Chen, Hailong; Bian, Hongtao; Li, Jiebo; Wen, Xiewen; Zheng, Junrong

    2013-07-25

    In this work, through investigating a series of liquid, glassy, and crystalline samples with ultrafast multiple-mode 2D IR and IR transient absorption methods, we demonstrated that the signal anisotropy of vibrational relaxation-induced heat effects is determined by both relative molecular orientations and molecular rotations. If the relative molecular orientations are randomized or molecular rotations are fast compared to heat transfer, the signal anisotropy of heat effects is zero. If the relative molecular orientations are anisotropic and the molecular rotations are slow, the signal anisotropy of heat effects can be nonzero, which is determined by the relative orientations of the energy source mode and the heat sensor mode within the same molecule and in different molecules. We also demonstrated that the correlation between the anisotropy value of heat signal and the relative molecular orientations can be quantitatively calculated.

  6. 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.

  7. 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.

  8. Functional Molecular Junctions Derived from Double Self-Assembled Monolayers.

    PubMed

    Seo, Sohyeon; Hwang, Eunhee; Cho, Yunhee; Lee, Junghyun; Lee, Hyoyoung

    2017-09-25

    Information processing using molecular junctions is becoming more important as devices are miniaturized to the nanoscale. Herein, we report functional molecular junctions derived from double self-assembled monolayers (SAMs) intercalated between soft graphene electrodes. Newly assembled molecular junctions are fabricated by placing a molecular SAM/(top) electrode on another molecular SAM/(bottom) electrode by using a contact-assembly technique. Double SAMs can provide tunneling conjugation across the van der Waals gap between the terminals of each monolayer and exhibit new electrical functions. Robust contact-assembled molecular junctions can act as platforms for the development of equivalent contact molecular junctions between top and bottom electrodes, which can be applied independently to different kinds of molecules to enhance either the structural complexity or the assembly properties of molecules. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. Self-Assembled Monolayers with Molecular Gradients

    NASA Astrophysics Data System (ADS)

    Schäferling, Michael; Riepl, Michael; Liedberg, Bo

    In recent years, biosensors and sensor arrays have developed into very important analytical tools, which found applications in many fields such as pharmaceutical (high-throughput) screening, medical diagnosis, or industrial process control. One of the major challenges for material research is the preparation of appropriate sensor surfaces, providing an interface with a high sensitivity and selectivity toward a given analyte. This chapter discusses some straightforward and flexible approaches to study structure and/or composition-function relationships and response characteristics of polymeric and molecular sensor materials. The controlled continuous deposition of self-assembled monolayers (SAMs), e.g. of substituted thiols or silanes, paves the way for the generation of molecular gradients on solid surfaces. These are useful for the preparation of interfaces with spatially controlled chemical composition and/ or physical properties. These tools can help to improve the selectivity and specificity of surfaces for biosensors and biochips. They can also be utilized for the study of fundamental protein adsorption and exchange phenomena.

  10. Molecular Engineering of Self-assembled Nanoreactors

    DTIC Science & Technology

    2014-08-15

    substrate diffusion. We demonstrated spatial control of the GOx/HRP cascade organized by DNA origami structures. As shown in Figure 13, the...quantify the level of protein assembly on the DNA origami tiles - assembled enzymes exhibited higher surface landscapes than the underlying origami ... origami tiles with assembled Gox/HRP pairs with inter-enzyme distances ranging from 10 nm to 65 nm. GOx/HRP co-assembly yields were determined from AFM

  11. An assembly process model based on object-oriented hierarchical time Petri Nets

    NASA Astrophysics Data System (ADS)

    Wang, Jiapeng; Liu, Shaoli; Liu, Jianhua; Du, Zenghui

    2017-04-01

    In order to improve the versatility, accuracy and integrity of the assembly process model of complex products, an assembly process model based on object-oriented hierarchical time Petri Nets is presented. A complete assembly process information model including assembly resources, assembly inspection, time, structure and flexible parts is established, and this model describes the static and dynamic data involved in the assembly process. Through the analysis of three-dimensional assembly process information, the assembly information is hierarchically divided from the whole, the local to the details and the subnet model of different levels of object-oriented Petri Nets is established. The communication problem between Petri subnets is solved by using message database, and it reduces the complexity of system modeling effectively. Finally, the modeling process is presented, and a five layer Petri Nets model is established based on the hoisting process of the engine compartment of a wheeled armored vehicle.

  12. 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

  13. 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.

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

    PubMed Central

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

    2005-01-01

    A self-assembled supramolecular metallacyclic rectangle was investigated with scanning tunneling microscopy on highly oriented pyrolytic graphite and Au(111) surfaces. The rectangles spontaneously adsorb on both surfaces and self-organize into well ordered adlayers. On highly oriented pyrolytic graphite, the long edge of the rectangle stands on the surface, forming a 2D molecular network. In contrast, the face of the rectangle lays flat on the Au(111) surface, forming linear chains. The structures and intramolecular features obtained through high-resolution scanning tunneling microscopy imaging are discussed. PMID:15657148

  15. 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.

  16. 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.

  17. 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.

  18. 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

  19. A physical operation of hydrodynamic orientation of an azobenzene supramolecular assembly with light and sound.

    PubMed

    Hotta, Yasuhisa; Suiko, Shunsuke; Motoyanagi, Jin; Onishi, Hiroshi; Ihozaki, Taisuke; Arakawa, Ryuichi; Tsuda, Akihiko

    2014-05-30

    Photoisomerizations of a newly designed azobenzene derivative reversibly change its self-assembly in a solution to form twisted supramolecular nanofibers and amorphous aggregates, respectively. When irradiating the sample solution with audible sound, the former assembly exhibits a LD response due to its hydrodynamic orientation, but the latter one is LD silent, in the sound-induced fluid flows.

  20. 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.

  1. 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

  2. Control of liquid crystal molecular orientation using ultrasound vibration

    SciTech Connect

    Taniguchi, Satoki; Koyama, Daisuke; Matsukawa, Mami; Shimizu, Yuki; Emoto, Akira; Nakamura, Kentaro

    2016-03-07

    We propose a technique to control the orientation of nematic liquid crystals using ultrasound and investigate the optical characteristics of the oriented samples. An ultrasonic liquid crystal cell with a thickness of 5–25 μm and two ultrasonic lead zirconate titanate transducers was fabricated. By exciting the ultrasonic transducers, the flexural vibration modes were generated on the cell. An acoustic radiation force to the liquid crystal layer was generated, changing the molecular orientation and thus the light transmission. By modulating the ultrasonic driving frequency and voltage, the spatial distribution of the molecular orientation of the liquid crystals could be controlled. The distribution of the transmitted light intensity depends on the thickness of the liquid crystal layer because the acoustic field in the liquid crystal layer is changed by the orientational film.

  3. Self-assembled FePt nanodot arrays with mono-dispersion and -orientation

    SciTech Connect

    Gai, Prof. Zheng; Howe, Jane Y; Guo, Jiandong; Blom, Douglas Allen; Plummer, E Ward; Shen, Jian

    2005-01-01

    For self-assembled nanodots, the ultimate dream is to simultaneously achieve tunable uniformity in size, spatial distribution, chemical composition, and crystallographic orientation. By utilizing the Volmer-Weber growth mode in thin film epitaxy, we have grown self-assembled two-dimensional arrays of FePt alloy nanodots that are uniform in size, chemical composition, and are all crystallgraphically aligned. These dot assemblies are ferromagnetic at room temperature and can be easily transferred onto other templates without destroying the size and orientation uniformity.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. Molecular dynamics simulations on PGLa using NMR orientational constraints.

    PubMed

    Sternberg, Ulrich; Witter, Raiker

    2015-11-01

    NMR data obtained by solid state NMR from anisotropic samples are used as orientational constraints in molecular dynamics simulations for determining the structure and dynamics of the PGLa peptide within a membrane environment. For the simulation the recently developed molecular dynamics with orientational constraints technique (MDOC) is used. This method introduces orientation dependent pseudo-forces into the COSMOS-NMR force field. Acting during a molecular dynamics simulation these forces drive molecular rotations, re-orientations and folding in such a way that the motional time-averages of the tensorial NMR properties are consistent with the experimentally measured NMR parameters. This MDOC strategy does not depend on the initial choice of atomic coordinates, and is in principle suitable for any flexible and mobile kind of molecule; and it is of course possible to account for flexible parts of peptides or their side-chains. MDOC has been applied to the antimicrobial peptide PGLa and a related dimer model. With these simulations it was possible to reproduce most NMR parameters within the experimental error bounds. The alignment, conformation and order parameters of the membrane-bound molecule and its dimer were directly derived with MDOC from the NMR data. Furthermore, this new approach yielded for the first time the distribution of segmental orientations with respect to the membrane and the order parameter tensors of the dimer systems. It was demonstrated the deuterium splittings measured at the peptide to lipid ratio of 1/50 are consistent with a membrane spanning orientation of the peptide.

  9. 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.

  10. 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

  11. 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.

  12. 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

  13. Associative Pattern Recognition Through Macro-molecular Self-Assembly

    NASA Astrophysics Data System (ADS)

    Zhong, Weishun; Schwab, David J.; Murugan, Arvind

    2017-05-01

    We show that macro-molecular self-assembly can recognize and classify high-dimensional patterns in the concentrations of N distinct molecular species. Similar to associative neural networks, the recognition here leverages dynamical attractors to recognize and reconstruct partially corrupted patterns. Traditional parameters of pattern recognition theory, such as sparsity, fidelity, and capacity are related to physical parameters, such as nucleation barriers, interaction range, and non-equilibrium assembly forces. Notably, we find that self-assembly bears greater similarity to continuous attractor neural networks, such as place cell networks that store spatial memories, rather than discrete memory networks. This relationship suggests that features and trade-offs seen here are not tied to details of self-assembly or neural network models but are instead intrinsic to associative pattern recognition carried out through short-ranged interactions.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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

  19. 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.

  20. 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.

  1. Tailored Surfaces/Assemblies for Molecular Plasmonics and Plasmonic Molecular Electronics.

    PubMed

    Lacroix, Jean-Christophe; Martin, Pascal; Lacaze, Pierre-Camille

    2017-06-12

    Molecular plasmonics uses and explores molecule-plasmon interactions on metal nanostructures for spectroscopic, nanophotonic, and nanoelectronic devices. This review focuses on tailored surfaces/assemblies for molecular plasmonics and describes active molecular plasmonic devices in which functional molecules and polymers change their structural, electrical, and/or optical properties in response to external stimuli and that can dynamically tune the plasmonic properties. We also explore an emerging research field combining molecular plasmonics and molecular electronics.

  2. 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

  3. Molecular pathways regulating mitotic spindle orientation in animal cells

    PubMed Central

    Lu, Michelle S.; Johnston, Christopher A.

    2013-01-01

    Orientation of the cell division axis is essential for the correct development and maintenance of tissue morphology, both for symmetric cell divisions and for the asymmetric distribution of fate determinants during, for example, stem cell divisions. Oriented cell division depends on the positioning of the mitotic spindle relative to an axis of polarity. Recent studies have illuminated an expanding list of spindle orientation regulators, and a molecular model for how cells couple cortical polarity with spindle positioning has begun to emerge. Here, we review both the well-established spindle orientation pathways and recently identified regulators, focusing on how communication between the cell cortex and the spindle is achieved, to provide a contemporary view of how positioning of the mitotic spindle occurs. PMID:23571210

  4. 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.

  5. 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

  6. 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.

  7. 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.

  8. 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

  9. 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.

  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. 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.

  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. 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.

  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. 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

  17. Surface chemical reactions induced by well-controlled molecular beams: translational energy and molecular orientation control.

    PubMed

    Okada, Michio

    2010-07-07

    I review our recent studies of chemical reactions on single-crystalline Cu and Si surfaces induced by hyperthermal oxygen molecular beams and by oriented molecular beams, respectively. Studies of oxide formation on Cu induced by hyperthermal molecular beams suggest that the translational energy of the incident molecules plays a significant role. The use of hyperthermal molecular beams enables us to open up new chemical reaction paths, and to develop new methods for the fabrication of thin films. Oriented molecular beams also demonstrate the possibility for controlling surface chemical reactions by varying the orientation of the incident molecules. The steric effects found on Si surfaces hint at new ways of achieving material fabrication on Si surfaces. Controlling the initial conditions of incoming molecules is a powerful tool for creating new materials on surfaces with well-controlled chemical reactions. © 2010 IOP Publishing Ltd

  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. Long-Range Orientational Self-Assembly, Spatially Controlled Deprotonation, and Off-Centered Metalation of an Expanded Porphyrin.

    PubMed

    Cirera, Borja; Trukhina, Olga; Björk, Jonas; Bottari, Giovanni; Rodríguez-Fernández, Jonathan; Martin-Jimenez, Alberto; Islyaikin, Mikhail K; Otero, Roberto; Gallego, José M; Miranda, Rodolfo; Torres, Tomás; Ecija, David

    2017-09-27

    Expanded porphyrins are large-cavity macrocycles with enormous potential in coordination chemistry, anion sensing, photodynamic therapy, and optoelectronics. In the last two decades, the surface science community has assessed the physicochemical properties of tetrapyrrolic-like macrocycles. However, to date, the sublimation, self-assembly and atomistic insights of expanded porphyrins on surfaces have remained elusive. Here, we show the self-assembly on Au(111) of an expanded aza-porphyrin, namely, an "expanded hemiporphyrazine", through a unique growth mechanism based on long-range orientational self-assembly. Furthermore, a spatially controlled "writing" protocol on such self-assembled architecture is presented based on the STM tip-induced deprotonation of the inner protons of individual macrocycles. Finally, the capability of these surface-confined macrocycles to host lanthanide elements is assessed, introducing a novel off-centered coordination motif. The presented findings represent a milestone in the fields of porphyrinoid chemistry and surface science, revealing a great potential for novel surface patterning, opening new avenues for molecular level information storage, and boosting the emerging field of surface-confined coordination chemistry involving f-block elements.

  20. Edge-to-Edge Oriented Self-Assembly of ReS2 Nanoflakes.

    PubMed

    Zhang, Qin; Wang, Wenjie; Kong, Xin; Mendes, Rafael G; Fang, Liwen; Xue, Yinghui; Xiao, Yao; Rümmeli, Mark H; Chen, Shengli; Fu, Lei

    2016-09-07

    The self-assembly of two-dimensional (2D) nanomaterials, an emerging research area, still remains largely unexplored. The strong interlayer attraction between 2D nanosheets leads to face-to-face stacking rather than edge-to-edge coupling. We demonstrate, for the first time, how one can induce and control an edge-to-edge self-assembly process for 2D nanomaterials. The extremely weak van der Waals coupling and strong anisotropy of ReS2 allow us to realize an oriented self-assembly (OSA) process. The aspect ratio of the resulting ReS2 nanoscrolls can be well controlled. In addition, we perform simulations to further explain and confirm the OSA process, demonstrating its great potential to be expanded as a general edge-to-edge self-assembly process suitable for other 2D nanomaterials.

  1. Synthesis of FePt nanocubes and their oriented self-assembly.

    PubMed

    Chen, Min; Kim, Jaemin; Liu, J P; Fan, Hongyou; Sun, Shouheng

    2006-06-07

    Monodisperse FePt nanocubes are synthesized at 205 degrees C by controlling decomposition of Fe(CO)5 and reduction of Pt(acac)2 and addition sequence of oleic acid and oleylamine. Different from the assembly of the sphere-like FePt nanoparticles, which shows 3D random structure orientation, self-assembly of the FePt nanocubes leads to a superlattice array with each FePt cube exhibiting (100) texture. Thermal annealing converts the chemically disordered fcc FePt to chemically ordered fct FePt, and the annealed assembly shows a strong (001) texture in the directions both parallel and perpendicular to the substrate. This shape-controlled synthesis and self-assembly offers a promising approach to fabrication of magnetically aligned FePt nanocrystal arrays for high density information storage and high performance permanent magnet applications.

  2. 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

  3. Rational molecular design of complementary self-assembling peptide hydrogels.

    PubMed

    Kyle, Stuart; Felton, Susan H; McPherson, Michael J; Aggeli, Amalia; Ingham, Eileen

    2012-09-01

    Rational molecular design of self- assembling peptide-based materials that spontaneously form self-supporting hydrogels shows potential in many healthcare applications. Binary peptides based on complementary charged sequences are developed, and the use of biophysical analysis and cell-based studies highlights that the charged interactions can influence the properties of peptide materials and ultimately affect biomaterial applications. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Spectroscopic studies of the molecular imprinting self-assembly process.

    PubMed

    Svenson, J; Andersson, H S; Piletsky, S A; Nicholls, I A

    1998-01-01

    A method for the rapid estimation of the extent of complex formation in molecular imprinting prepolymerization mixtures is described. By the use of a UV spectroscopy titration procedure, apparent binding constants for such self-assembly processes have been obtained. This method was used for comparison of the interactions between a dipeptide template (N-acetyl-L-phenylalaninyl-L-tryptophanyl methyl ester) and the functional monomer methacrylic acid, and the monomer analogues acetic acid and trifluoroacetic acid. The importance of template-monomer association during the molecular imprinting prepolymerization phase is discussed with respect to the systems studied.

  5. Morphological changes of amphiphilic molecular assemblies induced by chemical reactions.

    PubMed

    Nakagawa, Koh M; Noguchi, Hiroshi

    2015-02-04

    Shape transformations of amphiphilic molecular assemblies induced by chemical reactions are studied using coarse-grained molecular simulations. A binding reaction between hydrophilic and hydrophobic molecules is considered. It is found that the reaction induces transformation of an oil droplet to a tubular vesicle via bicelles and vesicles with discoidal arms. The discoidal arms close into vesicles, which are subsequently fused into the tubular vesicle. Under the chemical reaction, the bicelle-to-vesicle transition occurs at smaller sizes than in the absence of the hydrophobic molecules. It is revealed that the enhancement of this transition is due to embedded hydrophobic particles that reduce the membrane bending rigidity.

  6. 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

  7. Molecular recognition directed self-assembly of supramolecular architectures

    NASA Astrophysics Data System (ADS)

    Percec, C.; Heck, J.; Johansson, G.; Tomazos, D.; Kawasumi, M.

    1994-06-01

    This paper reviews some of our research on three classes of supramolecular architectures which are generated via various combinations of molecular, macromolecular and supramolecular chemistry. The ability of these supramolecular architectures to form liquid crystalline phases is determined by the shape of the self-assembled architecture and will be used to visualize it via various characterization techniques. The molecular design of selected examples of structural units containing taper shaped exo-receptors and crown-ether, oligooxyethylenic, and H-bonding based endo-receptors which self-assemble into cylindrical channel-like architectures via principles resembling those of tobacco mosaic virus (TMV), of macrocyclics which self-assemble into a willow-like architecture will be discussed. In the case of TMV-like supramolecular architectures a comparison between various supramolecular (generated via H-bonding, ionic and electrostatic interactions) and molecular 'polymer backbones' will be made. The present state of the art of the engineering of these supramolecular architectures and some possible novel material functions derived from them will be briefly mentioned.

  8. 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

  9. Birefringent Stable Glass with Predominantly Isotropic Molecular Orientation

    NASA Astrophysics Data System (ADS)

    Liu, Tianyi; Exarhos, Annemarie L.; Alguire, Ethan C.; Gao, Feng; Salami-Ranjbaran, Elmira; Cheng, Kevin; Jia, Tiezheng; Subotnik, Joseph E.; Walsh, Patrick J.; Kikkawa, James M.; Fakhraai, Zahra

    2017-09-01

    Birefringence in stable glasses produced by physical vapor deposition often implies molecular alignment similar to liquid crystals. As such, it remains unclear whether these glasses share the same energy landscape as liquid-quenched glasses that have been aged for millions of years. Here, we produce stable glasses of 9-(3,5-di(naphthalen-1-yl)phenyl)anthracene molecules that retain three-dimensional shapes and do not preferentially align in a specific direction. Using a combination of angle- and polarization-dependent photoluminescence and ellipsometry experiments, we show that these stable glasses possess a predominantly isotropic molecular orientation while being optically birefringent. The intrinsic birefringence strongly correlates with increased density, showing that molecular ordering is not required to produce stable glasses or optical birefringence, and provides important insights into the process of stable glass formation via surface-mediated equilibration. To our knowledge, such novel amorphous packing has never been reported in the past.

  10. 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

  11. 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

  12. 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.

  13. Directed orientation of asymmetric composite dumbbells by electric field induced assembly.

    PubMed

    Nagao, Daisuke; Sugimoto, Maki; Okada, Ayako; Ishii, Haruyuki; Konno, Mikio; Imhof, Arnout; van Blaaderen, Alfons

    2012-04-24

    Assembly and directed orientation of anisotropic particles with an external ac electric field in a range from 1 kHz to 2 MHz were studied for asymmetric composite dumbbells incorporating a silica, titania, or titania/silica (titania:silica = 75:25 vol %) sphere. The asymmetric composite dumbbells, which were composed of a polymethylmethacrylate (PMMA)-coated sphere (core-shell part) and a polystyrene (PSt) lobe, were synthesized with a soap-free emulsion polymerization to prepare PMMA-coated inorganic spheres and another soap-free emulsion polymerization to form a polystyrene (PSt) lobe from the PMMA-coated inorganic spheres. The composite dumbbells dispersed in water were directly observed with optical microscopy. The dumbbells incorporating a silica sphere oriented parallel to an electric field in the whole frequency range and they formed a pearl chain structure at a high frequency of 2 MHz. The titania-incorporated dumbbells formed chain structures, in which they contacted their core-shell parts and oriented perpendicularly to a low-frequency (kHz) field, whereas they oriented parallel to a high-frequency (MHz) field. Since the alignment of dumbbells in the chains depends not only on the interparticle forces but also on the torque that the induced dipoles in the dumbbells experience in the electric field, the orientation of dumbbells perpendicular to the electric field was the case dominated by the interparticle force, whereas the other orientation was the case dominated by the torque. The present experiments show that the incorporation of inorganic dumbbells is an effective way to control the assembled structure and orientation with an electric field.

  14. Molecular self-assembly into one-dimensional nanostructures.

    PubMed

    Palmer, Liam C; Stupp, Samuel I

    2008-12-01

    Self-assembly of small molecules into one-dimensional nanostructures offers many potential applications in electronically and biologically active materials. The recent advances discussed in this Account demonstrate how researchers can use the fundamental principles of supramolecular chemistry to craft the size, shape, and internal structure of nanoscale objects. In each system described here, we used atomic force microscopy (AFM) and transmission electron microscopy (TEM) to study the assembly morphology. Circular dichroism, nuclear magnetic resonance, infrared, and optical spectroscopy provided additional information about the self-assembly behavior in solution at the molecular level. Dendron rod-coil molecules self-assemble into flat or helical ribbons. They can incorporate electronically conductive groups and can be mineralized with inorganic semiconductors. To understand the relative importance of each segment in forming the supramolecular structure, we synthetically modified the dendron, rod, and coil portions. The self-assembly depended on the generation number of the dendron, the number of hydrogen-bonding functions, and the length of the rod and coil segments. We formed chiral helices using a dendron-rod-coil molecule prepared from an enantiomerically enriched coil. Because helical nanostructures are important targets for use in biomaterials, nonlinear optics, and stereoselective catalysis, researchers would like to precisely control their shape and size. Tripeptide-containing peptide lipid molecules assemble into straight or twisted nanofibers in organic solvents. As seen by AFM, the sterics of bulky end groups can tune the helical pitch of these peptide lipid nanofibers in organic solvents. Furthermore, we demonstrated the potential for pitch control using trans-to-cis photoisomerization of a terminal azobenzene group. Other molecules called peptide amphiphiles (PAs) are known to assemble in water into cylindrical nanostructures that appear as nanofiber

  15. 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.

  16. Assembling molecular Sierpiński triangle fractals

    NASA Astrophysics Data System (ADS)

    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.

  17. 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.

  18. 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.

  19. 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

  20. 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.

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

    PubMed Central

    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.

    2015-01-01

    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 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. PMID:26515095

  2. 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.

  3. 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.

  4. Ligand pose and orientational sampling in molecular docking.

    PubMed

    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 20,000 molecular orientations in the binding site (and so from about 1×10(10) to 4×10(10) to 1×10(11) to 2×10(11) to 5×10(11) 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.

  5. Orientational dynamics of fluctuating dipolar particles assembled in a mesoscopic colloidal ribbon

    NASA Astrophysics Data System (ADS)

    Massana-Cid, Helena; Martinez-Pedrero, Fernando; Cebers, Andrejs; Tierno, Pietro

    2017-07-01

    We combine experiments and theory to investigate the dynamics and orientational fluctuations of ferromagnetic microellipsoids that form a ribbonlike structure due to attractive dipolar forces. When assembled in the ribbon, the ellipsoids display orientational thermal fluctuations with an amplitude that can be controlled via application of an in-plane magnetic field. We use video microscopy to investigate the orientational dynamics in real time and space. Theoretical arguments are used to derive an analytical expression that describes how the distribution of the different angular configurations depends on the strength of the applied field. The experimental data are in good agreement with the developed model for all the range of field parameters explored. Understanding the role of fluctuations in chains composed of dipolar particles is important not only from a fundamental point of view, but it may also help understanding the stability of such structures against thermal noise, which is relevant in microfluidics and laboratory-on-a-chip applications.

  6. Micro-/nanostructured multicomponent molecular materials: design, assembly, and functionality.

    PubMed

    Yan, Dongpeng

    2015-03-23

    Molecule-based micro-/nanomaterials have attracted considerable attention because their properties can vary greatly from the corresponding macro-sized bulk systems. Recently, the construction of multicomponent molecular solids based on crystal engineering principles has emerged as a promising alternative way to develop micro-/nanomaterials. Unlike single-component materials, the resulting multicomponent systems offer the advantages of tunable composition, and adjustable molecular arrangement, and intermolecular interactions within their solid states. The study of these materials also supplies insight into how the crystal structure, molecular components, and micro-/nanoscale effects can influence the performance of molecular materials. In this review, we describe recent advances and current directions in the assembly and applications of crystalline multicomponent micro-/nanostructures. Firstly, the design strategies for multicomponent systems based on molecular recognition and crystal engineering principles are introduced. Attention is then focused on the methods of fabrication of low-dimensional multicomponent micro-/nanostructures. Their new applications are also outlined. Finally, we briefly discuss perspectives for the further development of these molecular crystalline micro-/nanomaterials. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. 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.

  8. 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

  9. Cyclization and Catenation Directed by Molecular Self-Assembly

    SciTech Connect

    Wang, Wei; Wang, Li Q; Palmer, Bruce J; Exarhos, Gregory J; Li, Alexander D

    2006-08-30

    We report here that molecular self-assembly can effectively direct and enhance specific reaction pathways. Using perylene π-π stacking weak attractive forces, we succeeded in synthesizing perylene bisimide macrocyclic dimer and a concatenated dimer-dimer ring from dynamic self-assembly of monomeric bis-N, N’-(2-(2-(2-(2-thioacetyl ethoxy) ethoxy) ethoxy) ethyl) perylene tetracarboxylic diimide. The monocyclic ring closure and the dimer-dimer ring concatenation were accomplished through formation of disulfide bonds, which was readily triggered by air oxidization under basic deacetylation conditions. The perylene cyclic dimer and its concatenated tetramer were characterized using both structural methods (NMR, mass spectroscopy) and photophysical measurements (UV-vis spectroscopy). Kinetic analyses offer informative insights about reaction pathways and possible mechanisms, which lead to the formation of fascinating concatenated rings. Molecular dynamic behaviors of both the monocyclic dimer and the concatenated dimer-dimer ring were modeled with the NWChem molecular dynamics software module, which shows distinct stacking activities for the monocyclic dimer and the concatenated tetramer.

  10. Molecular assembly and organic film growth on complex intermetallic surfaces

    NASA Astrophysics Data System (ADS)

    Al-Mahboob, Abdullah; Sharma, Hem Raj; Sadowski, Jerzy T.; Ledieu, Julian; Fournée, Vincent; McGrath, Ronan

    We extensively studied the role of molecular symmetry and symmetry/structures of wide ranges of substrate-surfaces from non-periodic to periodic to quasi-crystalline in nucleation, growth and phase transition in films made of organic molecular materials. Recently, most interest in quasicrystals is due to the generalization of aperiodic ordering to several classes of systems. Compared to periodic materials, these provide a closer approximation to an isotropic first Brillouin zone, which is of great importance to the design of new functional materials. Here, we present results obtained from our ongoing study of interface mediated molecular assembly extended on complex intermetallic surfaces with specific examples of C60 and Zn-phthalocyanine on quasicrystalline and approximant surfaces. We employed in-situ real-time low-energy electron microscopy (LEEM) for investigation of the processes in assembly and film growth and post-growth STM study and DFT calculations to understand structural details and growth mechanism. Research were carried out in part at the Center for Functional Nanomaterials, Brookhaven National Lab, USA; partly at Institut Jean Lamour, Université de Lorraine, France; and partly at the Surface Science Research Centre, University of Liverpool, UK.

  11. 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.

  12. 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.

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

    PubMed Central

    Keten, Sinan; Buehler, Markus J.

    2010-01-01

    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. PMID:20519206

  14. Molecular Understanding of Aβ-hIAPP Cross-Seeding Assemblies on Lipid Membranes.

    PubMed

    Zhang, Mingzhen; Hu, Rundong; Ren, Baiping; Chen, Hong; Jiang, Binbo; Ma, Jie; Zheng, Jie

    2017-03-15

    Amyloid-β (Aβ) and human islet polypeptide (hIAPP) are the causative agents responsible for Alzheimer's disease (AD) and type II diabetes (T2D), respectively. While numerous studies have reported the cross-seeding behavior of Aβ and hIAPP in solution, little effort has been made to examine the cross-seeding of Aβ and hIAPP in the presence of cell membranes, which is more biologically relevant to the pathological link between AD and T2D. In this work, we computationally study the cross-seeding and adsorption behaviors of Aβ and hIAPP on zwitterionic POPC and anionic 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC)/1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylglycerol (POPG) mixed bilayers using all-atom molecular dynamics (MD) simulations, particularly aiming to the effects of the initial orientation of the Aβ-hIAPP assembly and the lipid composition of cell membranes on mutual structural and interaction changes in both Aβ-hIAPP assembly and lipid bilayers at the atomic level. Aβ-hIAPP cross-seeding assembly always preferred to adopt a specific orientation and interface to associate with both lipid bilayers strongly via the N-terminal strands of Aβ. Such membrane-bound orientation explains experimental observation that hybrid Aβ-hIAPP fibrils on cell membranes showed similar morphologies to pure hIAPP fibrils. Moreover, Aβ-hIAPP assembly, regardless of its initial orientations, interacted more strongly with POPC/POPG bilayer than POPC bilayer, indicating that electrostatic interactions are the major forces governing peptide-lipid interactions. Strong electrostatic interactions were also attributed to the formation of Ca(2+) bridges connecting both negatively charged Glu of Aβ and PO4 head groups of lipids, which facilitate the association of Aβ-hIAPP with the POPC/POPG bilayer. It was also found that the strong peptide-lipid binding reduced lipid fluidity. Both facts imply that Aβ-hIAPP assembly may induce cell damage by altering calcium

  15. Molecular structure of self-assembled chiral nanoribbons and nanotubules revealed in the hydrated state.

    PubMed

    Oda, Reiko; Artzner, Franck; Laguerre, Michel; Huc, Ivan

    2008-11-05

    A detailed molecular organization of racemic 16-2-16 tartrate self-assembled multi-bilayer ribbons in the hydrated state is proposed where 16-2-16 amphiphiles, tartrate ions, and water molecules are all accurately positioned by comparing experimental X-ray powder diffraction and diffraction patterns derived from modeling studies. X-ray diffuse scattering studies show that molecular organization is not fundamentally altered when comparing the flat ribbons of the racemate to chirally twisted or helical ribbons of the pure tartrate enantiomer. Essential features of the three-dimensional molecular organizations of these structures include interdigitation of alkyl chains within each bilayer and well-defined networks of ionic and hydrogen bonds between cations, anions, and water molecules between bilayers. The detailed study of diffraction patterns also indicated that the gemini headgroups are oriented parallel to the long edge of the ribbons. The structure thus possesses a high cohesion and good crystallinity, and for the first time, we could relate the packing of the chiral molecules to the expression of the chirality at a mesoscopic scale. The organization of the ribbons at the molecular level sheds light on a number of their macroscopic features. Among these are the reason why enantiomerically pure 16-2-16 tartrate forms ribbons that consist of exactly two bilayers, and a plausible mechanism by which a chirally twisted or helical shape may emerge from the packing of chiral tartrate ions. Importantly, the distinction between commonly observed helical and twisted morphologies could be related to a subtle symmetry breaking. These results demonstrate that accurately solving the molecular structure of self-assembled soft materials--a process rarely achieved--is within reach, that it is a valid approach to correlate molecular parameters to macroscopic properties, and thus that it offers opportunities to modulate properties through molecular design.

  16. 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

  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. Surface Tension, Adsorption, and Molecular Orientations at the Liquid-Vapor Interface of Molecular Mixtures.

    NASA Astrophysics Data System (ADS)

    Thurtell, John Harland

    A generalized van der Waal's Mean Field Theory and Molecular Dynamics computer simulations have been used to study the liquid-vapor interface of simple liquid crystals, atomic mixtures, polar mixtures, and polar solvent-surfactant mixtures. Surface tensions, density profiles, and orientational order parameters have been calculated at the planar liquid -vapor interfaces of liquid crystals, argon-krypton mixtures, and polar mixtures using a mean field theory of molecular liquids. The effect of size, shape and dipole strength on the thickness, concentration and orientational ordering of adsorbed layers have been studied in detail. These parameters yield widely varying interfacial structures and can lead to interfacial and bulk phase transitions. Molecular dynamics simulations of simple surfactant models in a polar solvent have been carried out for varying intermolecular potentials. In particular the effect of the surfactant dipole strength, orientation and position were examined. The dipole has a large influence on the surface tension, molecular orientations and thickness of the interfacial region of these systems. We find a number of competing effects which result in unpredictable behavior in some situations.

  19. 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.

  20. 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).

  1. Molecular Composite Coatings on Nafion Using Layer-by-Layer Self-Assembly.

    PubMed

    Lefaux, Christophe J; Kim, Byoung-Suhk; Venkat, Narayanan; Mather, Patrick T

    2015-05-20

    Controlled growth of nanometer-scale multilayered coatings of negatively charged sulfonated poly(benzobisimidazole) (SPBI), complexed with positively charged poly(2-vinylpyridine) (P2VP) on quartz, and Nafion membrane as substrates has been explored. Both polymers, SPBI and P2VP, possess a net charge in methanol as a result of the dissolution of SPBI by complexation with triethylamine (TEA) and the protonation of P2VP with HCl, respectively, and thereby can form a multilayered molecular composite of alternating anionic SPBI and cationic P2VP via an electrostatic layer-by-layer (LbL) self-assembly. UV-vis absorption spectrophotometry was used to monitor the buildup and growth rate of such SPBI/P2VP multilayer films. Atomic force microscopy (AFM) was used to determine the roughness and thickness of the resulting SPBI/P2VP multilayers. As a result, it was found that a steady-state linear growth regime for the LbL self-assembled SPBI/P2VP multilayer films and coatings onto quartz and Nafion membranes was observed after completion of the first few deposition cycles, indicating the successful formation of the SPBI/P2VP multilayered assembly in methanol solutions. In addition, the SPBI/P2VP multilayer films in the perpendicular direction (flat view) demonstrated isotropic orientation distribution on the Nafion membrane, while the SPBI/P2VP multilayer films examined by X-ray scattering in the parallel direction (edge view) revealed anisotropic orientation, the combined observations indicating confinement of SPBI rods to the plane of the coating. We further found that the SPBI/P2VP multilayer coated Nafion possesses good thermal stability, as indicated by isothermal gravimetric analysis at 310 °C, and it was further observed that SPBI/P2VP multilayer coatings using the LbL self-assembly technique on Nafion membrane significantly increased the membrane stiffness, despite the small coating thickness employed.

  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. Surface modification: how nanoparticles assemble to molecular imaging probes

    NASA Astrophysics Data System (ADS)

    Tan, Huilong; Yu, Lun; Gao, Feng; Liao, Weihua; Wang, Wei; Zeng, Wenbin

    2013-12-01

    Nanomaterials have attracted widespread attention due to their unique chemical and physical properties, such as size-dependent optical, magnetic, or catalytic properties, thus have the great potential application, especially in the fields of new materials and devices. The emergence of nanoparticle-based probe has led to important innovations in molecular imaging field. Several types of nanoparticles have been employed for molecular imaging application, including Au/Ag nanoparticles, upconversion nanoparticles (UCNPs), quantum dots, dye-doped nanoparticles, magnetic nanoparticles (MNPs), etc. The preparation of nanoparticle-based probe for molecular imaging routinely includes three steps: synthesis, surface modification, and bioconjugation, among which surface modification plays an important role for the whole procedure. Surface modification usually possesses the safety, biocompatibility, stability, hydrophilicity, and terminal functional groups for further conjugation. This review aims to outline the surface modification of how nanoparticles assemble to probes, focusing on the developments of two widely used nanoparticles, UCNPs and MNPs. Recent advances of different types of linkers, a core component for surface modification, are summarized. It shows the intimate relationship between chemistry and nanoscience. Finally, perspectives and challenges of nanoparticle-based probe in the field of molecular imaging are expected.

  4. 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.

  5. Highly luminescent colloidal nanoplates of perovskite cesium lead halide and their oriented assemblies

    DOE PAGES

    Bekenstein, Yehonadav; Koscher, Brent A.; Eaton, Samuel W.; ...

    2015-12-15

    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. Furthermore, the broad accessible emission range, high native quantum yields, and ease of self-assembly make perovskitemore » NPLs an ideal platform for fundamental optoelectronic studies and the investigation of future devices.« less

  6. Highly luminescent colloidal nanoplates of perovskite cesium lead halide and their oriented assemblies

    SciTech Connect

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

    2015-12-15

    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. Furthermore, 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.

  7. 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.

  8. 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.

  9. Influence of Molecular Shape on Molecular Orientation and Stability of Vapor-Deposited Organic Semiconductors

    NASA Astrophysics Data System (ADS)

    Walters, Diane M.; Johnson, Noah D.; Ediger, M. D.

    Physical vapor deposition is commonly used to prepare active layers in organic electronics. Recently, it has been shown that molecular orientation and packing can be tuned by changing the substrate temperature during deposition, while still producing macroscopically homogeneous films. These amorphous materials can be highly anisotropic when prepared with low substrate temperatures, and they can exhibit exceptional kinetic stability; films retain their favorable packing when heated to high temperatures. Here, we study the influence of molecular shape on molecular orientation and stability. We investigate disc-shaped molecules, such as TCTA and m-MTDATA, nearly spherical molecules, such as Alq3, and linear molecules covering a broad range of aspect ratios, such as p-TTP and BSB-Cz. Disc-shaped molecules have preferential horizontal orientation when deposited at low substrate temperatures, and their orientation can be tuned by changing the substrate temperature. Alq3 forms stable, amorphous films that are optically isotropic when vapor deposited over a broad range of substrate temperatures. This work may guide the choice of material and deposition conditions for vapor-deposited films used in organic electronics and allow for more efficient devices to be fabricated.

  10. Smart dust: Self-assembling, self-orienting photonic crystals of porous Si

    PubMed Central

    Link, Jamie R.; Sailor, Michael J.

    2003-01-01

    Micrometer-sized one-dimensional photonic crystals of porous Si that spontaneously assemble, orient, and sense their local environment are prepared. The photonic crystals are generated by electrochemically etching two discrete porous multilayered dielectric mirrors into Si, one on top of the other. The first mirror is chemically modified by hydrosilylation with dodecene before the etching of the second mirror, which is prepared with an optical reflectivity spectrum that is distinct from the first. The entire film is removed from the substrate, and the second mirror is then selectively modified by mild thermal oxidation. The films are subsequently fractured into small particles by sonication. The chemically asymmetric particles spontaneously align at an organic liquid–water interface, with the hydrophobic side oriented toward the organic phase and the hydrophilic side toward the water. Sensing is accomplished when liquid at the interface infuses into the porous mirrors, inducing predictable shifts in the optical spectra of both mirrors. PMID:12947036

  11. Smart dust: self-assembling, self-orienting photonic crystals of porous Si.

    PubMed

    Link, Jamie R; Sailor, Michael J

    2003-09-16

    Micrometer-sized one-dimensional photonic crystals of porous Si that spontaneously assemble, orient, and sense their local environment are prepared. The photonic crystals are generated by electrochemically etching two discrete porous multilayered dielectric mirrors into Si, one on top of the other. The first mirror is chemically modified by hydrosilylation with dodecene before the etching of the second mirror, which is prepared with an optical reflectivity spectrum that is distinct from the first. The entire film is removed from the substrate, and the second mirror is then selectively modified by mild thermal oxidation. The films are subsequently fractured into small particles by sonication. The chemically asymmetric particles spontaneously align at an organic liquid-water interface, with the hydrophobic side oriented toward the organic phase and the hydrophilic side toward the water. Sensing is accomplished when liquid at the interface infuses into the porous mirrors, inducing predictable shifts in the optical spectra of both mirrors.

  12. Device-oriented graphene nanopatterning by mussel-inspired directed block copolymer self-assembly.

    PubMed

    Park, Seokhan; Yun, Je Moon; Maiti, Uday Narayan; Moon, Hyoung-Seok; Jin, Hyeong Min; Kim, Sang Ouk

    2014-01-10

    Directed self-assembly of a block copolymer is successfully employed to fabricate device-oriented graphene nanostructures from CVD grown graphene. We implemented mussel-inspired polydopamine adhesive in conjunction with the graphoepitaxy principle to tailor graphene nanoribbon arrays and a graphene nanomesh located between metal electrodes. Polydopamine adhesive was utilized for facile and damage-free surface treatment to complement the low surface energy of pristine graphene. Our process minimizes the damage to the ideal graphitic structures and electrical properties of graphene during the nanopatterning process. Multi-channel graphene nanoribbon arrays and a graphene nanomesh were successfully fabricated between metal electrodes.

  13. Device-oriented graphene nanopatterning by mussel-inspired directed block copolymer self-assembly

    NASA Astrophysics Data System (ADS)

    Park, Seokhan; Yun, Je Moon; Narayan Maiti, Uday; Moon, Hyoung-Seok; Jin, Hyeong Min; Ouk Kim, Sang

    2014-01-01

    Directed self-assembly of a block copolymer is successfully employed to fabricate device-oriented graphene nanostructures from CVD grown graphene. We implemented mussel-inspired polydopamine adhesive in conjunction with the graphoepitaxy principle to tailor graphene nanoribbon arrays and a graphene nanomesh located between metal electrodes. Polydopamine adhesive was utilized for facile and damage-free surface treatment to complement the low surface energy of pristine graphene. Our process minimizes the damage to the ideal graphitic structures and electrical properties of graphene during the nanopatterning process. Multi-channel graphene nanoribbon arrays and a graphene nanomesh were successfully fabricated between metal electrodes.

  14. Structures and orientation-dependent interaction forces of titania nanowires using molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Okeke, George; Antony, S. Joseph; Hammond, Robert B.; Ahmed, Kamran

    2017-07-01

    Engineering nanowires to develop new products and processes is highly topical due to their ability to provide highly enhanced physical, chemical, mechanical, thermal and electrical properties. In this work, using molecular dynamics simulations, we report fundamental information, about the structural and thermodynamic properties of individual anatase titania (TiO2) nanowires with cross-sectional diameters between 2 and 6 nm, and aspect ratio (length to diameter) of 6:1 at temperatures ranging from 300 to 3000 K. Estimates of the melting transition temperature of the nanowires are between 2000 and 2500 K. The melting transition temperature predicted from the radial distribution functions (RDFs) shows strong agreement with those predicted from the total energy profiles. Overall, the transition temperature is in reasonable agreement with melting points predicted from experiments and simulations reported in the literature for spherical nanoparticles of similar sizes. Hence, the melting transition temperature of TiO2 nanowires modelled here can be considered as shape independent. Furthermore, for the first time based on MD simulations, interaction forces between two nanowires are reported at ambient temperature (300 K) for different orientations: parallel, perpendicular and end-to-end. It is observed that end-to-end orientations manifested the strongest attraction forces, while the parallel and perpendicular orientations displayed weaker attractions. The results reported here could form a foundation in future multiscale modelling studies of the structured titania nanowire assemblies, depending on the inter-wire interaction forces.

  15. 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.

  16. 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

  17. 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

  18. 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

  19. 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.

  20. 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

  1. Effect of surface roughness, chemical composition, and native oxide crystallinity on the orientation of self-assembled GaN nanowires on Ti foils.

    PubMed

    Calabrese, G; Pettersen, S V; Pfüller, C; Ramsteiner, M; Grepstad, J K; Brandt, O; Geelhaar, L; Fernández-Garrido, S

    2017-10-20

    We report on plasma-assisted molecular beam epitaxial growth of almost randomly oriented, uniformly tilted, and vertically aligned self-assembled GaN nanowires (NWs), respectively, on different types of polycrystalline Ti foils. The NW orientation with respect to the substrate normal, which is affected by an in situ treatment of the foil surface before NW growth, depends on the crystallinity of the native oxide. Direct growth on the as-received foils results in the formation of ensembles of nearly randomly oriented NWs due to the strong roughening of the surface induced by chemical reactions between the impinging elements and Ti. Surface nitridation preceding the NW growth is found to reduce this roughening by transformation of the uppermost layers into TiN and TiO x N y species. These compounds are more stable against chemical reactions and facilitate the growth of uniformly oriented GaN NW ensembles on the surface of the individual grains of the polycrystalline Ti foils. If an amorphous oxide layer is present at the foil surface, vertically oriented NWs are obtained all across the substrate because this layer blocks the transfering of the epitaxial information from the underlying grains. The control of NW orientation and the understanding behind the achievement of vertically oriented NWs obtained in this study represent an important step towards the realization of GaN NW-based bendable devices on polycrystalline metal foils.

  2. Effect of surface roughness, chemical composition, and native oxide crystallinity on the orientation of self-assembled GaN nanowires on Ti foils

    NASA Astrophysics Data System (ADS)

    Calabrese, G.; Pettersen, S. V.; Pfüller, C.; Ramsteiner, M.; Grepstad, J. K.; Brandt, O.; Geelhaar, L.; Fernández-Garrido, S.

    2017-10-01

    We report on plasma-assisted molecular beam epitaxial growth of almost randomly oriented, uniformly tilted, and vertically aligned self-assembled GaN nanowires (NWs), respectively, on different types of polycrystalline Ti foils. The NW orientation with respect to the substrate normal, which is affected by an in situ treatment of the foil surface before NW growth, depends on the crystallinity of the native oxide. Direct growth on the as-received foils results in the formation of ensembles of nearly randomly oriented NWs due to the strong roughening of the surface induced by chemical reactions between the impinging elements and Ti. Surface nitridation preceding the NW growth is found to reduce this roughening by transformation of the uppermost layers into TiN and TiO x N y species. These compounds are more stable against chemical reactions and facilitate the growth of uniformly oriented GaN NW ensembles on the surface of the individual grains of the polycrystalline Ti foils. If an amorphous oxide layer is present at the foil surface, vertically oriented NWs are obtained all across the substrate because this layer blocks the transfering of the epitaxial information from the underlying grains. The control of NW orientation and the understanding behind the achievement of vertically oriented NWs obtained in this study represent an important step towards the realization of GaN NW-based bendable devices on polycrystalline metal foils.

  3. 3D Orientational Control in Self-Assembled Thin Films with Sub-5 nm Features by Light.

    PubMed

    Nickmans, Koen; Bögels, Gerardus M; Sánchez-Somolinos, Carlos; Murphy, Jeffrey N; Leclère, Philippe; Voets, Ilja K; Schenning, Albertus P H J

    2017-09-01

    While self-assembled molecular building blocks could lead to many next-generation functional organic nanomaterials, control over the thin-film morphologies to yield monolithic sub-5 nm patterns with 3D orientational control at macroscopic length scales remains a grand challenge. A series of photoresponsive hybrid oligo(dimethylsiloxane) liquid crystals that form periodic cylindrical nanostructures with periodicities between 3.8 and 5.1 nm is studied. The liquid crystals can be aligned in-plane by exposure to actinic linearly polarized light and out-of-plane by exposure to actinic unpolarized light. The photoalignment is most efficient when performed just under the clearing point of the liquid crystal, at which the cylindrical nanostructures are reoriented within minutes. These results allow the generation of highly ordered sub-5 nm patterns in thin films at macroscopic length scales, with control over the orientation in a noncontact fashion. © 2017 The Authors. Published by WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Assembly of the Escherichia coli RuvABC resolvasome directs the orientation of Holliday junction resolution

    PubMed Central

    van Gool, Alain J.; Hajibagheri, Nasser M.A.; Stasiak, Andrzej; West, Stephen C.

    1999-01-01

    Genetic recombination can lead to the formation of intermediates in which DNA molecules are linked by Holliday junctions. Movement of a junction along DNA, by a process known as branch migration, leads to heteroduplex formation, whereas resolution of a junction completes the recombination process. Holliday junctions can be resolved in either of two ways, yielding products in which there has, or has not, been an exchange of flanking markers. The ratio of these products is thought to be determined by the frequency with which the two isomeric forms (conformers) of the Holliday junction are cleaved. Recent studies with enzymes that process Holliday junctions in Escherichia coli, the RuvABC proteins, however, indicate that protein binding causes the junction to adopt an open square-planar configuration. Within such a structure, DNA isomerization can have little role in determining the orientation of resolution. To determine the role that junction-specific protein assembly has in determining resolution bias, a defined in vitro system was developed in which we were able to direct the assembly of the RuvABC resolvasome. We found that the bias toward resolution in one orientation or the other was determined simply by the way in which the Ruv proteins were positioned on the junction. Additionally, we provide evidence that supports current models on RuvABC action in which Holliday junction resolution occurs as the resolvasome promotes branch migration. PMID:10421637

  5. 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

  6. 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

  7. Comparative molecular dynamics study of Abeta adsorption on the self-assembled monolayers.

    PubMed

    Wang, Qiuming; Zhao, Chao; Zhao, Jun; Wang, Jingdai; Yang, Jui-Chen; Yu, Xiang; Zheng, Jie

    2010-03-02

    The adsorption and aggregation of the amyloid-beta (Abeta) peptides on the cell membrane plays a causal role in the pathogenesis of Alzheimer's disease. Here, we report all-atom molecular dynamics (MD) simulations to study the interactions of Abeta oligomer with self-assembled monolayers (SAMs) terminated with hydrophobic CH(3) and hydrophilic OH functional groups, with particular interests in how surface chemistry and Abeta orientation affect the adsorption behavior of Abeta. Simulation results show that the CH(3)-SAM has a stronger binding affinity to Abeta than the OH-SAM does, although both surfaces can induce Abeta adsorption. Regardless of the characteristics of the surface, the hydrophobic C-terminal region is more likely to be adsorbed on the SAMs, indicating a preferential orientation and interface for Abeta adsorption. Structural and energetic comparison among six Abeta-SAM systems further reveals that Abeta orientation, SAM surface hydrophobicity, and interfacial waters all determine Abeta adsorption behavior on the surface, highlighting the importance of hydrophobic interactions at the interface. This work may provide parallel insights into the interactions of Abeta with lipid bilayers.

  8. 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

  9. 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.

  10. 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.

  11. 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

  12. 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

  13. Coherent Radiative Decay of Molecular Rotations: A Comparative Study of Terahertz-Oriented versus Optically Aligned Molecular Ensembles

    NASA Astrophysics Data System (ADS)

    Damari, Ran; Rosenberg, Dina; Fleischer, Sharly

    2017-07-01

    The decay of field-free rotational dynamics is experimentally studied by two complementary methods: laser-induced molecular alignment and terahertz-field-induced molecular orientation. A comparison between the decay rates of different molecular species at various gas pressures reveals that oriented molecular ensembles decay faster than aligned ensembles. The discrepancy in decay rates is attributed to the coherent radiation emitted by the transiently oriented ensembles and is absent from aligned molecules. The experimental results reveal the dramatic contribution of coherent radiative emission to the observed decay of rotational dynamics and underline a general phenomenon expected whenever field-free coherent dipole oscillations are induced.

  14. Coherent Radiative Decay of Molecular Rotations: A Comparative Study of Terahertz-Oriented versus Optically Aligned Molecular Ensembles.

    PubMed

    Damari, Ran; Rosenberg, Dina; Fleischer, Sharly

    2017-07-21

    The decay of field-free rotational dynamics is experimentally studied by two complementary methods: laser-induced molecular alignment and terahertz-field-induced molecular orientation. A comparison between the decay rates of different molecular species at various gas pressures reveals that oriented molecular ensembles decay faster than aligned ensembles. The discrepancy in decay rates is attributed to the coherent radiation emitted by the transiently oriented ensembles and is absent from aligned molecules. The experimental results reveal the dramatic contribution of coherent radiative emission to the observed decay of rotational dynamics and underline a general phenomenon expected whenever field-free coherent dipole oscillations are induced.

  15. Development of simulation approach for two-dimensional chiral molecular self-assembly driven by hydrogen bond at the liquid/solid interface

    NASA Astrophysics Data System (ADS)

    Qin, Yuan; Yao, Man; Hao, Ce; Wan, Lijun; Wang, Yunhe; Chen, Ting; Wang, Dong; Wang, Xudong; Chen, Yonggang

    2017-09-01

    Two-dimensional (2D) chiral self-assembly system of 5-(benzyloxy)-isophthalic acid derivative/(S)-(+)-2-octanol/highly oriented pyrolytic graphite was studied. A combined density functional theory/molecular mechanics/molecular dynamics (DFT/MM/MD) approach for system of 2D chiral molecular self-assembly driven by hydrogen bond at the liquid/solid interface was thus proposed. Structural models of the chiral assembly were built on the basis of scanning tunneling microscopy (STM) images and simplified for DFT geometry optimization. Merck Molecular Force Field (MMFF) was singled out as the suitable force field by comparing the optimized configurations of MM and DFT. MM and MD simulations for hexagonal unit model which better represented the 2D assemble network were then preformed with MMFF. The adhesion energy, evolution of self-assembly process and characteristic parameters of hydrogen bond were obtained and analyzed. According to the above simulation, the stabilities of the clockwise and counterclockwise enantiomorphous networks were evaluated. The calculational results were supported by STM observations and the feasibility of the simulation method was confirmed by two other systems in the presence of chiral co-absorbers (R)-(-)-2-octanol and achiral co-absorbers 1-octanol. This theoretical simulation method assesses the stability trend of 2D enantiomorphous assemblies with atomic scale and can be applied to the similar hydrogen bond driven 2D chirality of molecular self-assembly system.

  16. 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

  17. 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

  18. 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.

  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. Molecular dynamics simulations of a hydrated protein vectorially oriented on polar and nonpolar soft surfaces.

    PubMed Central

    Nordgren, C E; Tobias, D J; Klein, M L; Blasie, J K

    2002-01-01

    We present a collection of molecular dynamics computer simulation studies on a model protein-membrane system, namely a cytochrome c monolayer attached to an organic self-assembled monolayer (SAM). Modifications of the system are explored, including the polarity of the SAM endgroups, the amount of water present for hydration, and the coordination number of the heme iron atom. Various structural parameters are measured, e.g., the protein radius of gyration and eccentricity, the deviation of the protein backbone from the x-ray crystal structure, the orientation of the protein relative to the SAM surface, and the profile structures of the SAM, protein, and water. The polar SAM appears to interact more strongly with the protein than does the nonpolar SAM. Increased hydration of the system tends to reduce the effects of other parameters. The choice of iron coordination model has a significant effect on the protein structure and the heme orientation. The overall protein structure is largely conserved, except at each end of the sequence and in one loop region. The SAM structure is only perturbed in the region of its direct contact with the protein. Our calculations are in reasonably good agreement with experimental measurements (polarized optical absorption/emission spectroscopy, x-ray interferometry, and neutron interferometry). PMID:12496067

  1. 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.

  2. 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

  3. 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

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

    PubMed

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

    2016-11-02

    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.

  5. Orienting rigid and flexible biological assemblies in ferrofluids for small-angle neutron scattering studies

    PubMed Central

    Sosnick, T.; Charles, S.; Stubbs, G.; Yau, P.; Bradbury, E. M.; Timmins, P.; Trewhella, J.

    1991-01-01

    Small-angle scattering from macromolecules in solution is widely used to study their structures, but the information content is limited because the molecules are generally randomly oriented and hence the data are spherically averaged. The use of oriented rodlike structures for scattering, as in fiber diffraction, greatly increases the amount of structural detail that can be obtained. A new technique using a ferromagnetic fluid has been developed to align elongated structures independent of their intrinsic magnetic properties. This technique is ideal for small-angle neutron scattering because the scattering from the ferrofluid particles can be reduced significantly by matching the neutron scattering length density of the particles to a D2O solvent (“contrast matching”). The net result is scattering primarily from the ordered biological assembly in a solution environment that can be adjusted to physiological pH and ionic strength. Scattering results from ordered tobacco mosaic virus, tobacco rattle virus, and chromain fibers are presented. ImagesFIGURE 4FIGURE 4 PMID:19431809

  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. Towards a molecular description of intermediate filament structure and assembly

    SciTech Connect

    Parry, David A.D.; Strelkov, Sergei V.; Burkhard, Peter; Aebi, Ueli; Herrmann, Harald . E-mail: h.herrmann@dkfz.de

    2007-06-10

    Intermediate filaments (IFs) represent one of the prominent cytoskeletal elements of metazoan cells. Their constituent proteins are coded by a multigene family, whose members are expressed in complex patterns that are controlled by developmental programs of differentiation. Hence, IF proteins found in epidermis differ significantly from those in muscle or neuronal tissues. Due to their fibrous nature, which stems from a fairly conserved central {alpha}-helical coiled-coil rod domain, IF proteins have long resisted crystallization and thus determination of their atomic structure. Since they represent the primary structural elements that determine the shape of the nucleus and the cell more generally, a major challenge is to arrive at a more rational understanding of how their nanomechanical properties effect the stability and plasticity of cells and tissues. Here, we review recent structural results of the coiled-coil dimer, assembly intermediates and growing filaments that have been obtained by a hybrid methods approach involving a rigorous combination of X-ray crystallography, small angle X-ray scattering, cryo-electron tomography, computational analysis and molecular modeling.

  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. Gold nanoparticles assembled with dithiocarbamate-anchored molecular wires

    PubMed Central

    Reeler, Nini E. A.; Lerstrup, Knud A.; Somerville, Walter; Speder, Jozsef; Petersen, Søren V.; Laursen, Bo W.; Arenz, Matthias; Qiu, Xiaohui; Vosch, Tom; Nørgaard, Kasper

    2015-01-01

    A protocol for the bottom-up self-assembly of nanogaps is developed through molecular linking of gold nanoparticles (AuNPs). Two π-conjugated oligo(phenylene ethynylene) molecules (OPE) with dithiocarbamate anchoring groups are used as ligands for the AuNPs. OPE-4S with a dithiocarbamate in each end of the molecule and a reference molecule OPE-2S with only a single dithiocarbamate end group. The linking mechanism of OPE-4S is investigated by using a combination of TEM, UV-Vis absorption and surface enhanced Raman spectroscopy (SERS) as well as studying the effect of varying the OPE-4S to AuNP concentration ratio. UV-Vis absorption confirms the formation of AuNP aggregates by the appearance of an extended plasmon band (EPB) for which the red shift and intensity depend on the OPE-4S:AuNP ratio. SERS confirms the presence of OPE-4S and shows a gradual increase of the signal intensity with increasing OPE-4S:AuNP ratios up to a ratio of about 4000, after which the SERS intensity does not increase significantly. For OPE-2S, no linking is observed below full coverage of the AuNPs indicating that the observed aggregate formation at high OPE-2S:AuNP ratios, above full AuNP coverage, is most likely of a physical nature (van der Waals forces or π-π interactions). PMID:26471461

  10. 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

  11. 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.

  12. Multiple-step method for making exceptionally well-oriented liquid-crystalline sols of macromolecular assemblies.

    PubMed

    Yamashita, I; Suzuki, H; Namba, K

    1998-05-08

    X-ray fiber diffraction is potentially powerful in solving the atomic structure of filamentous assemblies of macromolecules, as demonstrated for tobacco mosaic virus. However, it requires extremely well-oriented sols to allow for extraction of intensities on closely located layer-lines. A high degree of orientation requires a high filament concentration to restrain the orientational freedom, but orienting concentrated sols is hampered by their high viscosity. Here, we report a systematic method that reproducibly produces extremely good orientation, which involves three steps; liquid crystallization, centrifugation and magnetic orientation. We found that a slow centrifugation can trigger a dynamic self-orientation process to form perfectly homogeneous liquid-crystalline sols, and further centrifugation to concentrate sols followed by magnetic orientation produces exceptionally well-oriented sols. The best-oriented flagellar sol showed a disorientation angle of 0.6 degrees as 1sigma of its Gaussian distribution. The new method has been successfully applied to many other systems, such as tobacco mosaic virus and F-actin. Copyright 1998 Academic Press Limited.

  13. Liquid Crystalline Polymers and Networks -- orientation, molecular shape change, mechanics

    NASA Astrophysics Data System (ADS)

    Warner, Mark

    2008-03-01

    In a prescient paper of 1969, Pierre-Gilles de Gennes envisaged both liquid crystal polymers and elastomers. 10 years later, these systems were realised. After 25 years, monodomain elastomers were prepared and displayed phenomena he had predicted: rods incorporated into polymers induce liquid crystallinity in polymer melts and elastomers; orientational order causes shape changes in the back bones of such polymers; mechanical ramifications follow in networks, e.g. spontaneous elongations and contractions on changing order. The latter are proposed as the basis of micro-actuation and artificial muscles, both heat and light-driven. In 1969, de Gennes already described ideal networks heated through the nematic-isotropic transition losing all their order by mechanical relaxation. It is not obvious, but is true in theory and largely in experiment, even in highly non-ideal networks. He also envisaged that a cholesteric network, where there is a topological memory of chirality imprinted by crosslinking chains in a twisted state. Chirality cannot relax away on entering the isotropic phase, even in systems without molecular chirality (for instance those crosslinked in the presence of chiral solvent that is subsequently exchanged away). His chiral elastomers have found application as mechanically-tuneable, rubber lasers. De Gennes also constructed the first continuum elastic theories of nematic elastomers (1982), though distortions are generally very large. His elasticity has informed non-linear elasticity that works even at large amplitudes. I shall describe de Gennes' many contributions, and the current state of a field that has since yielded still more remarkable phenomena.

  14. Molecular relaxations, molecular orientation, and the friction characteristics of polyimide films. [wear characteristics of polymeric lubricant

    NASA Technical Reports Server (NTRS)

    Fusaro, R. L.

    1975-01-01

    The friction characteristics of polyimide films bonded to metallic substrates were studied from 25 to 500 C. These results were interpreted in terms of molecular orientation and thermomechanical data obtained by torsional braid analysis (TBA). A large friction transition was found to occur at 40 + or - 10 C in a dry argon atmosphere (10 ppm H2O). It was postulated that the mechanical stresses of sliding transform or reorder the molecules on the surface into a configuration conducive to easy shear, such as an extended chain. The molecular relaxation which occurs in this temperature region appears to give the molecules the necessary freedom for this reordering process to occur. The effects of velocity, reversibility, and thermal prehistory on the friction properties of polyimide were also studied.

  15. 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.

  16. 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.

  17. 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

  18. 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.

  19. 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.

  20. 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.

  1. Hierarchical star cluster assembly in globally collapsing molecular clouds

    NASA Astrophysics Data System (ADS)

    Vázquez-Semadeni, Enrique; González-Samaniego, Alejandro; Colín, Pedro

    2017-05-01

    We discuss the mechanism of cluster formation in a numerical simulation of a molecular cloud (MC) undergoing global hierarchical collapse, focusing on how the gas motions in the parent cloud control the assembly of the cluster. The global collapse implies that the star formation rate (SFR) increases over time. The collapse is hierarchical because it consists of small-scale collapses within larger scale ones. The latter culminate a few Myr later than the first small-scale ones and consist of filamentary flows that accrete on to massive central clumps. The small-scale collapses consist of clumps that are embedded in the filaments and falling on to the large-scale collapse centres. The stars formed in the early, small-scale collapses share the infall motion of their parent clumps, so that the filaments feed both gas and stars to the massive central clump. This process leads to the presence of a few older stars in a region where new protostars are forming, and also to a self-similar structure, in which each unit is composed of smaller scale subunits that approach each other and may merge. Because the older stars formed in the filaments share the infall motion of the gas on to the central clump, they tend to have larger velocities and to be distributed over larger areas than the younger stars formed in the central clump. Finally, interpreting the initial mass function (IMF) simply as a probability distribution implies that massive stars only form once the local SFR is large enough to sample the IMF up to high masses. In combination with the increase of the SFR, this implies that massive stars tend to appear late in the evolution of the MC, and only in the central massive clumps. We discuss the correspondence of these features with observed properties of young stellar clusters, finding very good qualitative agreement.

  2. 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.

  3. Influence of Molecular Shape on the Thermal Stability and Molecular Orientation of Vapor-Deposited Organic Semiconductors

    DOE Data Explorer

    Walters, Diane M [University of Wisconsin-Madison] (ORCID:0000000253706563); Antony, Lucas [University of Chicago] (ORCID:0000000319336500); de Pablo, Juan [University of Chicago] (ORCID:000000023526516X); Ediger, Mark [University of Wisconsin-Madison] (ORCID:0000000347158473)

    2017-07-25

    High thermal stability and anisotropic molecular orientation enhance the performance of vapor-deposited organic semiconductors, but controlling these properties is a challenge in amorphous materials. To understand the influence of molecular shape on these properties, vapor-deposited glasses of three disk-shaped molecules were prepared. For all three systems, enhanced thermal stability is observed for glasses prepared over a wide range of substrate temperatures and anisotropic molecular orientation is observed at lower substrate temperatures. For two of the disk-shaped molecules, atomistic simulations of thin films were also performed and anisotropic molecular orientation was observed at the equilibrium liquid surface. We find that the structure and thermal stability of these vapor-deposited glasses results from high surface mobility and partial equilibration toward the structure of the equilibrium liquid surface during the deposition process. For the three molecules studied, molecular shape is a dominant factor in determining the anisotropy of vapor-deposited glasses.

  4. 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

  5. Layer-by-Layer Molecular Assemblies for Dye-Sensitized Photoelectrosynthesis Cells Prepared by Atomic Layer Deposition.

    PubMed

    Wang, Degao; Sheridan, Matthew V; Shan, Bing; Farnum, Byron H; Marquard, Seth L; Sherman, Benjamin D; Eberhart, Michael S; Nayak, Animesh; Dares, Christopher J; Das, Atanu K; Bullock, R Morris; Meyer, Thomas J

    2017-08-30

    In a dye sensitized photoelectrosynthesis cell (DSPEC), the relative orientation of the catalyst and chromophore plays an important role in determining the device efficiency. Here we introduce a new, robust atomic layer deposition (ALD) procedure for the preparation of molecular chromophore-catalyst assemblies on wide bandgap semiconductors. In this procedure, solution deposited, phosphonate derivatized metal complexes on metal oxide surfaces are treated with reactive metal reagents in the gas phase by ALD to form an outer metal ion bridging group, which can bind a second phosphonate containing species from solution to establish a R1-PO2-O-M-O-PO2-R2 type surface assembly. With the ALD procedure, assemblies bridged by Al(III), Sn(IV), Ti(IV), or Zr(IV) metal oxide units have been prepared. To evaluate the performance of this new type of surface assembly, intra-assembly electron transfer was investigated by transient absorption spectroscopy, and light-driven water splitting experiments under steady-state illumination were conducted. A SnO2 bridged assembly on SnO2/TiO2 core/shell electrodes undergoes light-driven water oxidation with an incident photon to current efficiency (IPCE) of 17.1% at 440 nm. Light-driven water reduction with a ruthenium trisbipyridine chromophore and molecular Ni(II) catalyst on NiO films was also used to produce H2. Compared to conventional solution-based procedures, the ALD approach offers significant advantages in scope and flexibility for the preparation of stable surface structures.

  6. 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.

  7. 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.

  8. Lamellar orientation of block copolymer using polarity switch of nitrophenyl self-assembled monolayer induced by electron beam

    NASA Astrophysics Data System (ADS)

    Yamamoto, Hiroki; Dawson, Guy; Kozawa, Takahiro; Robinson, Alex P. G.

    2017-03-01

    Directed self-assembly (DSA) was investigated on self-assembled monolayers (SAMs) of 6-(4-nitrophenoxy) hexane-1-thiol (NPHT), which were chemically modified by electron beam (EB) irradiation. By irradiating a responsive interfacial surface, the orientation and selective patterning of block copolymer domains could be achieved. We demonstrated that spatially-selective lamellar orientation of polystyrene-block-poly(methyl methacrylate) (PS-b-PMMA) could be induced via modification of an underlying SAM; for instance the conversion of an NO2 group to an NH2 group, induced by EB. The lamellar orientation of PS-b-PMMA was controlled by the change in the polarity of different regions of the SAM using EB lithography. The reductive treatment of SAM substrates plays a crucial role in the orientation of block copolymer. This method might greatly simplify block copolymer DSA processes as compared to the conventional multi-step chemo-epitaxy DSA process. By examining the lamellae orientation by EB, we found that the vertical orientation persists only for appropriate an irradiation dose and annealing temperature.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2012-01-01

    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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. Antibody-Mediated Bacteriorhodopsin Orientation for Molecular Device Architectures

    NASA Astrophysics Data System (ADS)

    Koyama, Koichi; Yamaguchi, Naoto; Miyasaka, Tsutomu

    1994-08-01

    A rational method for constructing highly oriented films of purple membrane (PM) has been established by using two kinds of bispecific antibodies with different antigen-binding sites, one binding to a specific side of bacteriorhodopsin and the other to a phospholipid hapten. A hapten monolayer deposited on a metal electrode was treated with a bispecific antibody solution and incubated with a PM suspension to produce a highly oriented PM film, as confirmed by electron microscopy in which an immunogold labeling technique was used. This antibody-mediated PM monolayer was then used in the construction of a light-sensing photoelectric device. A comparison of the two incorporated PM monolayers showed that highly efficient photocurrents were produced by the PM monolayer whose unidirectionally oriented cytoplasmic surface faces the electrode.

  2. 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.

  3. 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.

  4. Topological defects in liquid crystals and molecular self-assembly (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Abbott, Nicholas L.

    2017-02-01

    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 topological 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 that can direct processes of molecular self-assembly in a manner that is strongly analogous to other classes of macromolecular templates (e.g., polymer—surfactant complexes). Opportunities for the design of exquisitely responsive soft materials will be discussed using bacterial endotoxin as an example.

  5. 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.

  6. 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.

  7. Planar-orientation polycrystalline thin film of liquid-crystalline organic semiconductor by template-directed self-assembly

    NASA Astrophysics Data System (ADS)

    Wang, Yi-Fei; Iino, Hiroaki; Hanna, Jun-ichi

    2017-10-01

    We fabricated planar-orientation crystalline thin films of organic semiconductors, in which molecules sit parallel, i.e., “face-on”, on the substrate and favor vertical charge transport. Thanks to molecular orientation that is sensitive to surface properties and the self-organization of liquid crystals, planar-orientation crystalline thin films can be prepared by simply cooling a smectic liquid-crystalline organic semiconductor from isotropic temperature with the aid of a poly(vinyl alcohol) (PVA) microtemplate. The molecular orientation of crystalline thin films was investigated by polarized optical microscopy (POM) and X-ray diffraction (XRD) analysis, and the current–voltage characteristics of the films were studied in a diode configuration. The results showed high potential for device applications.

  8. 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.

  9. 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.

  10. Variable-angle ellipsometry and molecular orientation in monoclinic organic semiconductors

    NASA Astrophysics Data System (ADS)

    Tavazzi, S.; Campione, M.

    2006-02-01

    Variable-angle ellipsometry has been used to characterize oligothiophene crystals with principal axes inclined at an angle to the surface normal. The results allow deducing with high sensitivity the orientation of the molecules in these anisotropic and absorbing organic solids, thus allowing one to follow the evolution of the molecular orientation after inducing the transition of the crystallographic structure between the two polymorphs of quaterthiophene. This material is representative of a large class of solids with technological applications in either crystal or thin-film form, where different structural properties and molecular orientation may arise from different preparation conditions.

  11. 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.

  12. 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

  13. Intercalators as molecular chaperones in DNA self-assembly.

    PubMed

    Greschner, Andrea A; Bujold, Katherine E; Sleiman, Hanadi F

    2013-07-31

    DNA intercalation has found many diagnostic and therapeutic applications. Here, we propose the use of simple DNA intercalators, such as ethidium bromide, as tools to facilitate the error-free self-assembly of DNA nanostructures. We show that ethidium bromide can influence DNA self-assembly, decrease the formation of oligomeric side products, and cause libraries of multiple equilibrating structures to converge into a single product. Using a variety of 2D- and 3D-DNA systems, we demonstrate that intercalators present a powerful alternative for the adjustment of strand-end alignment, favor the formation of fully duplexed "closed" structures, and create an environment where the smallest, most stable structure is formed. A new 3D-DNA motif, the ninja star, was self-assembled in quantitative yield with this method. Moreover, ethidium bromide can be readily removed using isoamyl alcohol extractions combined with intercalator-specific spin columns, thereby yielding the desired ready-to-use DNA structure.

  14. 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.

  15. 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.

  16. 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

  17. 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.

  18. Molecular architecture of the human Mediator-RNA polymerase II-TFIIF assembly.

    PubMed

    Bernecky, Carrie; Grob, Patricia; Ebmeier, Christopher C; Nogales, Eva; Taatjes, Dylan J

    2011-03-01

    The macromolecular assembly required to initiate transcription of protein-coding genes, known as the Pre-Initiation Complex (PIC), consists of multiple protein complexes and is approximately 3.5 MDa in size. At the heart of this assembly is the Mediator complex, which helps regulate PIC activity and interacts with the RNA polymerase II (pol II) enzyme. The structure of the human Mediator-pol II interface is not well-characterized, whereas attempts to structurally define the Mediator-pol II interaction in yeast have relied on incomplete assemblies of Mediator and/or pol II and have yielded inconsistent interpretations. We have assembled the complete, 1.9 MDa human Mediator-pol II-TFIIF complex from purified components and have characterized its structural organization using cryo-electron microscopy and single-particle reconstruction techniques. The orientation of pol II within this assembly was determined by crystal structure docking and further validated with projection matching experiments, allowing the structural organization of the entire human PIC to be envisioned. Significantly, pol II orientation within the Mediator-pol II-TFIIF assembly can be reconciled with past studies that determined the location of other PIC components relative to pol II itself. Pol II surfaces required for interacting with TFIIB, TFIIE, and promoter DNA (i.e., the pol II cleft) are exposed within the Mediator-pol II-TFIIF structure; RNA exit is unhindered along the RPB4/7 subunits; upstream and downstream DNA is accessible for binding additional factors; and no major structural re-organization is necessary to accommodate the large, multi-subunit TFIIH or TFIID complexes. The data also reveal how pol II binding excludes Mediator-CDK8 subcomplex interactions and provide a structural basis for Mediator-dependent control of PIC assembly and function. Finally, parallel structural analysis of Mediator-pol II complexes lacking TFIIF reveal that TFIIF plays a key role in stabilizing pol II

  19. 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.

  20. Brownian molecular dynamics simulation on self-assembly behavior of diblock copolymers: influence of chain conformation.

    PubMed

    Lin, Shaoliang; He, Xiaohua; Li, Yongliang; Lin, Jiaping; Nose, Takuhei

    2009-10-22

    Brownian molecular dynamic simulations are applied on the self-assembly behavior of AB-type diblock copolymers. The influence of chain conformation of core-forming A-block changing from rigid to flexible on the aggregation structure formed by AB copolymers is investigated. It is found that at a high rigid fraction f(R) of A-block, a disk structure can be formed at a high aggregation interaction epsilon(AA) of A-bead pairs because of the tendency of orientational packing of rigid portion within the aggregate core. Transitions of aggregation structure from disk to string, further to small aggregates, and to unimers are observed with decreasing epsilon(AA). The packing of A-blocks becomes more random at relatively lower values of f(R), resulting in the formation of spherical structure. The region of string becomes narrower while the regions of the small aggregates and sphere become wider as decreasing f(R). Meanwhile, the onsets of string, disk, and sphere formation move to higher epsilon(AA). The phase diagrams for the influences of rigid potion location within the A-block and the chain rigidity of the A-block are mapped. The comparison of simulation results with existing experimental observations is also presented. Our simulation results tend to bridge a gap of different micellization behaviors between rod-coil block copolymers and coil-coil block copolymers and extend to investigate chain conformation influence on phase diagram.

  1. 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.

  2. 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.

  3. 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

  4. 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.

  5. 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

  6. 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.

  7. 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

  8. BALLView: An object-oriented molecular visualization and modeling framework

    NASA Astrophysics Data System (ADS)

    Moll, Andreas; Hildebrandt, Andreas; Lenhof, Hans-Peter; Kohlbacher, Oliver

    2005-11-01

    We present BALLView, an extensible tool for visualizing and modeling bio-molecular structures. It provides a variety of different models for bio-molecular visualization, e.g. ball-and-stick models, molecular surfaces, or ribbon models. In contrast to most existing visualization tools, BALLView also offers rich functionality for molecular modeling and simulation, including molecular mechanics methods (AMBER and CHARMM force fields), continuum electrostatics methods employing a Finite-Difference Poisson Boltzmann solver, and secondary structure calculation. Results of these computations can be exported as publication quality images or as movies. Even unexperienced users have direct access to this functionality through an intuitive graphical user interface, which makes BALLView particularly useful for teaching. For more advanced users, BALLView is extensible in different ways. Owing to its framework design, extension on the level of C‰+‰‰+ code is very convenient. In addition, an interface to the scripting language Python allows the interactive rapid prototyping of new methods. BALLView is portable and runs on all major platforms (Windows, MacOS X, Linux, most Unix flavors). It is available free of charge under the GNU Public License (GPL) from our website http://www.ballview.org.

  9. A new class of purple membrane variants for the construction of highly oriented membrane assemblies on the basis of noncovalent interactions.

    PubMed

    Baumann, Roelf-Peter; Busch, Annegret P; Heidel, Björn; Hampp, Norbert

    2012-04-12

    Purple membranes (PM) from Halobacterium salinarum have been discussed for several technical applications. These ideas started just several years after its discovery. The biological function of bacteriorhodopsin (BR), the only protein in PM, is the light-driven proton translocation across the membrane thereby converting light energy into chemical energy. The astonishing physicochemical robustness of this molecular assembly and the ease of its isolation triggered ideas for technical uses. All basic molecular functions of BR, that is, photochromism, photoelectrism, and proton pumping, are key elements for technical applications like optical data processing and data storage, ultrafast light detection and processing, and direct utilization of sunlight in adenosine 5'-triphospate (ATP) generation or seawater desalination. In spite of the efforts of several research groups worldwide, which confirmed the proof-of-principle for all these potential applications, only the photochromism-based applications have reached a technical level. The physical reason for this is that no fixation or orientation of the PMs is required. The situation is quite different for photoelectrism and proton pumping where the macroscopic orientation of PMs is a prerequisite. For proton pumping, in addition, the formation of artificial membranes which prevent passive proton leakage is necessary. In this manuscript, we describe a new class of PM variants with oppositely charged membrane sides which enable an almost 100% orientation on a surface, which is the key element for photoelectric applications of BR. As an example, the mutated BR, BR-E234R7, was prepared and analyzed. A nearly 100% self-orientation on mica was obtained.

  10. Electrostatic screening mediated by interfacial charge transfer in molecular assemblies on semiconductor substrates

    NASA Astrophysics Data System (ADS)

    Tan, A.; Wagner, S. R.; Zhang, P. P.

    2017-07-01

    Using scanning tunneling microscopy and spectroscopy (STM, STS), we report the electronic structures of self-assembled zinc phthalocyanine (ZnPc) and hexadecafluorinated zinc phthalocyanine (F16ZnPc ) monolayers on the Si(111)-B surface. We show that interfacial charge transfer occurs in the F16ZnPc monolayer, which gives rise to a pronounced spatial variation of the occupied molecular state across the molecular assembly, a feature not observed in the molecular states of the ZnPc overlayer without the presence of interfacial charge transfer. We attribute this observation to the inhomogeneous electrostatic screening of the intraorbital Coulomb interaction in molecular adsorbates arising from the substrate boron distribution. This study highlights the impact of the substrate electrostatic environment on molecular electronic structures, an essential aspect in the applications of organic and molecular electronic devices.

  11. 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

  12. 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.

  13. Universality and specificity in molecular orientation in anisotropic gels prepared by diffusion method.

    PubMed

    Maki, Yasuyuki; Furusawa, Kazuya; Yasuraoka, Sho; Okamura, Hideki; Hosoya, Natsuki; Sunaga, Mari; Dobashi, Toshiaki; Sugimoto, Yasunobu; Wakabayashi, Katsuzo

    2014-08-08

    Molecular orientation in anisotropic gels of chitosan, Curdlan and DNA obtained by dialysis of those aqueous solutions in gelation-inducing solutions was investigated. In this diffusion method (or dialysis method), the gel formation was induced by letting small molecules diffuse in or out of the polymer solutions through the surface. For the gels of DNA and chitosan, the polymer chains aligned perpendicular to the diffusion direction. The same direction of molecular orientation was observed for the Curdlan gel prepared in the dialysis cell. On the other hand, a peculiar nature was observed for the Curdlan gel prepared in the dialysis tube: the molecular orientation was perpendicular to the diffusion direction in the outermost layer of the gel, while the orientation was parallel to the diffusion direction in the inner translucent layer. The orientation parallel to the diffusion direction is attributed to a small deformation of the inner translucent layer caused by a slight shrinkage of the central region after the gel formation. At least near the surface of the gel, the molecular orientation perpendicular to the diffusion direction is a universal characteristic for the gels prepared by the diffusion method. Copyright © 2014 Elsevier Ltd. All rights reserved.

  14. 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.

  15. 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

  16. 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.

  17. The molecular mechanisms of sexual orientation and gender identity.

    PubMed

    Fisher, Alessandra D; Ristori, Jiska; Morelli, Girolamo; Maggi, Mario

    2017-08-25

    Differences between males and females are widely represented in nature. There are gender differences in phenotypes, personality traits, behaviors and interests, cognitive performance, and proneness to specific diseases. The most marked difference in humans is represented by sexual orientation and core gender identity, the origins of which are still controversial and far from being understood. Debates continue on whether sexual behavior and gender identity are a result of biological (nature) or cultural (nurture) factors, with biology possibly playing a major role. The main goal of this review is to summarize the studies available to date on the biological factors involved in the development of both sexual orientation and gender identity. A systematic search of published evidence was performed using Medline (from January 1948 to June 2017). Review of the relevant literature was based on authors' expertise. Indeed, different studies have documented the possible role and interaction of neuroanatomic, hormonal and genetic factors. The sexual dimorphic brain is considered the anatomical substrate of psychosexual development, on which genes and gonadal hormones may have a shaping effect. In particular, growing evidence shows that prenatal and pubertal sex hormones permanently affect human behavior. In addition, heritability studies have demonstrated a role of genetic components. However, a convincing candidate gene has not been identified. Future studies (e.i. genome wide studies) are needed to better clarify the complex interaction between genes, anatomy and hormonal influences on psychosexual development. Copyright © 2017. Published by Elsevier B.V.

  18. 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.

  19. 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.

  20. 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

  1. 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

  2. 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.

  3. 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.

  4. 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.

  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. 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.

  7. 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.

  8. 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.

  9. Reprogrammable Assembly of Molecular Motor on Solid Surfaces via Dynamic Bonds.

    PubMed

    Yu, Li; Sun, Jian; Wang, Qian; Guan, Yan; Zhou, Le; Zhang, Jingxuan; Zhang, Lanying; Yang, Huai

    2017-06-01

    Controllable assembly of molecular motors on solid surfaces is a fundamental issue for providing them to perform physical tasks. However, it can hardly be achieved by most previous methods due to their inherent limitations. Here, a general strategy is designed for the reprogrammable assembly of molecular motors on solid surfaces based on dynamic bonds. In this method, molecular motors with disulfide bonds can be remotely, reversibly, and precisely attached to solid surfaces with disulfide bonds, regardless of their chemical composition and microstructure. More importantly, it not only allows encoding geometric information referring to a pattern of molecular motors, but also enables erasing and re-encoding of geometric information via hemolytic photocleavage and recombination of disulfide bonds. Thus, solid surfaces can be regarded as "computer hardware", where molecular motors can be reformatted and reprogramed as geometric information. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Theoretical modeling of the formation of chiral molecular patterns in self-assembled overlayers

    NASA Astrophysics Data System (ADS)

    Kasperski, A.; Szabelski, P.

    2014-11-01

    Formation of complex ordered patterns by simple molecular building blocks adsorbed on solid substrates is an intriguing phenomenon in which small changes in the geometry and chemistry of the molecular brick can lead to entirely different 2D architectures. In this contribution we demonstrate how theoretical modeling can be effectively used to predict the morphology of adsorbed overlayers comprising cross-shaped functional molecules equipped with active interaction centers. In particular, we use the Monte Carlo lattice model to explore the effect of distribution of the centers within the probe molecule on the structure of the corresponding molecular assemblies. The simulated results show that, depending on the number and position of the active centers, the outcome of the self-assembly can be extended homochiral porous networks, molecular strings and dispersed molecular clusters. Our theoretical investigations can be helpful in custom designing methods for imparting chirality to solid surfaces via the adsorption of functional molecules.

  11. 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.

  12. 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.

  13. 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.

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

    NASA Astrophysics Data System (ADS)

    Thomas, Marcus; Schwartz, Russell

    2017-06-01

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

  15. 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.

  16. Constructing a molecular theory of self-assembly: Interplay of ideas from surfactants and block copolymers.

    PubMed

    Nagarajan, Ramanathan

    2017-06-01

    Low molecular weight surfactants and high molecular weight block copolymers display analogous self-assembly behavior in solutions and at interfaces, generating nanoscale structures of different shapes. Understanding the link between the molecular structure of these amphiphiles and their self-assembly behavior has been the goal of theoretical studies. Despite the analogies between surfactants and block copolymers, models predicting their self-assembly behavior have evolved independent of one another, each overlooking the molecular feature considered critical to the other. In this review, we focus on the interplay of ideas pertaining to surfactants and block copolymers in three areas of self-assembly. First, we show how improved free energy models have evolved by applying ideas from surfactants to block copolymers and vice versa, giving rise to a unitary theoretical framework and better predictive capabilities for both classes of amphiphiles. Second we show that even though molecular packing arguments are often used to explain aggregate shape transitions resulting from self-assembly, the molecular packing considerations are more relevant in the case of surfactants whereas free energy criteria are relevant for block copolymers. Third, we show that even though the surfactant and block copolymer aggregates are small nanostructures, the size differences between them is significant enough to make the interfacial effects control the solubilization of molecules in surfactant micelles while the bulk interactions control the solubilization in block copolymer micelles. Finally, we conclude by identifying recent theoretical progress in adapting the micelle model to a wide variety of self-assembly phenomena and the challenges to modeling posed by emerging novel classes of amphiphiles with complex biological, inorganic or nanoparticle moieties. Published by Elsevier B.V.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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

  2. 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

  3. 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.

  4. Self-Assembly of Escin Molecules at the Air-Water Interface as Studied by Molecular Dynamics.

    PubMed

    Tsibranska, Sonya; Ivanova, Anela; Tcholakova, Slavka; Denkov, Nikolai

    2017-08-22

    Escin belongs to a large class of natural biosurfactants, called saponins, that are present in more than 500 plant species. Saponins are applied in the pharmaceutical, cosmetics, and food and beverage industries due to their variously expressed bioactivity and surface activity. In particular, escin adsorption layers at the air-water interface exhibit an unusually high surface elastic modulus (>1100 mN/m) and a high surface viscosity (ca. 130 N·s/m). The molecular origin of these unusual surface rheological properties is still unclear. We performed classical atomistic dynamics simulations of adsorbed neutral and ionized escin molecules to clarify their orientation and interactions on the water surface. The orientation and position of the escin molecules with respect to the interface, the intermolecular interactions, and the kinetics of molecular aggregation into surface clusters are characterized in detail. Significant differences in the behavior of the neutral and the charged escin molecules are observed. The neutral escin rapidly assembles in a compact and stable surface cluster. This process is explained by the action of long-range attraction between the hydrophobic aglycones, combined with intermediate dipole-dipole attraction and short-range hydrogen bonds between the sugar residues in escin molecules. The same interactions are expected to control the viscoelastic properties of escin adsorption layers.

  5. 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.

  6. 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.

  7. Correlated rotational switching in two-dimensional self-assembled molecular rotor arrays

    NASA Astrophysics Data System (ADS)

    Wasio, Natalie A.; Slough, Diana P.; Smith, Zachary C.; Ivimey, Christopher J.; Thomas, Samuel W., III; Lin, Yu-Shan; Sykes, E. Charles H.

    2017-07-01

    Molecular devices are capable of performing a number of functions from mechanical motion to simple computation. Their utility is somewhat limited, however, by difficulties associated with coupling them with either each other or with interfaces such as electrodes. Self-assembly of coupled molecular devices provides an option for the construction of larger entities that can more easily integrate with existing technologies. Here we demonstrate that ordered organometallic arrays can be formed spontaneously by reaction of precursor molecular rotor molecules with a metal surface. Scanning tunnelling microscopy enables individual rotors in the arrays to be switched and the resultant switches in neighbouring rotors imaged. The structure and dimensions of the ordered molecular rotor arrays dictate the correlated switching properties of the internal submolecular rotor units. Our results indicate that self-assembly of two-dimensional rotor crystals produces systems with correlated dynamics that would not have been predicted a priori.

  8. 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

  9. Substrate temperature controls molecular orientation in two-component vapor-deposited glasses

    DOE PAGES

    Jiang, J.; Walters, D. M.; Zhou, D.; ...

    2016-02-22

    Vapor-deposited glasses can be anisotropic and molecular orientation is important for organic electronics applications. In organic light emitting diodes (OLEDs), for example, the orientation of dye molecules in two-component emitting layers significantly influences emission efficiency. Here we investigate how substrate temperature during vapor deposition influences the orientation of dye molecules in a model two-component system. We determine the average orientation of a linear blue light emitter 1,4-di-[4-(N,N-diphenyl)amino]styrylbenzene (DSA-Ph) in mixtures with aluminum-tris(8-hydroxyquinoline) (Alq3) by spectroscopic ellipsometry and IR dichroism. We find that molecular orientation is controlled by the ratio of the substrate temperature during deposition and the glass transition temperaturemore » of the mixture. Furthermore, these findings extend recent results for single component vapor-deposited glasses and suggest that, during vapor deposition, surface mobility allows partial equilibration towards orientations preferred at the free surface of the equilibrium liquid.« less

  10. Substrate temperature controls molecular orientation in two-component vapor-deposited glasses

    SciTech Connect

    Jiang, J.; Walters, D. M.; Zhou, D.; Ediger, M. D.

    2016-02-22

    Vapor-deposited glasses can be anisotropic and molecular orientation is important for organic electronics applications. In organic light emitting diodes (OLEDs), for example, the orientation of dye molecules in two-component emitting layers significantly influences emission efficiency. Here we investigate how substrate temperature during vapor deposition influences the orientation of dye molecules in a model two-component system. We determine the average orientation of a linear blue light emitter 1,4-di-[4-(N,N-diphenyl)amino]styrylbenzene (DSA-Ph) in mixtures with aluminum-tris(8-hydroxyquinoline) (Alq3) by spectroscopic ellipsometry and IR dichroism. We find that molecular orientation is controlled by the ratio of the substrate temperature during deposition and the glass transition temperature of the mixture. Furthermore, these findings extend recent results for single component vapor-deposited glasses and suggest that, during vapor deposition, surface mobility allows partial equilibration towards orientations preferred at the free surface of the equilibrium liquid.

  11. Enhancing Organic Semiconductor-Surface Plasmon Polariton Coupling with Molecular Orientation.

    PubMed

    Brown, Steven J; DeCrescent, Ryan A; Nakazono, David M; Willenson, Samuel H; Ran, Niva A; Liu, Xiaofeng; Bazan, Guillermo C; Nguyen, Thuc-Quyen; Schuller, Jon A

    2017-10-11

    Due to strong electric field enhancements, surface plasmon polaritons (SPPs) are capable of drastically increasing light-molecule coupling in organic optoelectronic devices. The electric field enhancement, however, is anisotropic, offering maximal functional benefits if molecules are oriented perpendicular to the interface. To provide a clear demonstration of this orientation dependence, we study SPP dispersion and SPP-mediated photoluminescence at a model Au/small-molecule interface where identical molecules can be deposited with two very different molecular backbone orientations depending on processing conditions. First, we demonstrate that thin films of p-SIDT(FBTTh2)2 can be deposited with either all "in-plane" (parallel to substrate) or a 50/50 mix of in-plane/"out-of-plane" (perpendicular to substrate) optical transition dipoles by the absence or presence, respectively, of diiodooctane during spin-coating. In contrast to typical orientation control observed in organic thin films, for this particular molecule, this corresponds to films with conjugated backbones purely in-plane, or with a 50/50 mix of in-plane/out-of-plane backbones. Then, using momentum-resolved reflectometry and momentum-resolved photoluminescence, we study and quantify changes in SPP dispersion and photoluminescence intensity arising solely from changes in molecular orientation. We demonstrate increased SPP momentum and a 2-fold enhancement in photoluminescence for systems with out-of-plane oriented transition dipoles. These results agree well with theory and have direct implications for the design and analysis of organic optoelectronic devices.

  12. 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.

  13. 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

  14. 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.

  15. 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.

  16. 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

  17. Examining the Scope and Thermodynamics of Assembly in Nesting Complexes Comprising Molecular Baskets and TPA Ligands.

    PubMed

    Zhiquan, Lei; Polen, Shane M; Hadad, Christopher M; RajanBabu, T V; Badjić, Jovica D

    2017-09-15

    Molecular baskets capture various tris(2-pyridylmethyl)amine ligands, with and without zinc(II) cation, to form nesting complexes. The results of our computational (MD) and experimental ((1)H NMR/ITC) studies suggest that the assembly is driven by the hydrophobic effect with the charge of complementary molecular components playing an important role in the formation of nesting complexes. In brief, the complexation only takes place when the basket and the ligand carry either oppositely charged or noncharged groups.

  18. 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.

  19. Molecular Architecture and Assembly of the Eukaryotic Proteasome

    PubMed Central

    Tomko, Robert J.; Hochstrasser, Mark

    2013-01-01

    The eukaryotic ubiquitin-proteasome system is responsible for most cellular quality-control and regulatory protein degradation. Its substrates, which are usually modified by polymers of ubiquitin, are ultimately degraded by the 26S proteasome. This 2.6 MDa protein complex is separated into a barrel-shaped proteolytic 20S core particle (CP) of 28 subunits capped on one or both ends by a 19S regulatory particle (RP) comprising at least 19 subunits. The RP coordinates substrate recognition, removal of substrate polyubiquitin chains, and substrate unfolding and translocation into the CP for degradation. While many atomic structures of the CP have been determined, the RP has resisted high-resolution analysis. Recently, however, a combination of cryo-electron microscopy (cryo-EM), biochemical analysis, and crystal structure determination of several RP subunits has yielded a near-atomic resolution view of much of the complex. Major new insights into chaperone-assisted proteasome assembly have also recently been made. Here we review these novel findings. PMID:23495936

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

    NASA Astrophysics Data System (ADS)

    Kim, Yu Jin; Park, Chan Eon

    2016-03-01

    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.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

  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. 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

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

    DOE PAGES

    Dalal, Shakeel S.; Walters, Diane M.; Lyubimov, Ivan; ...

    2015-03-23

    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. In this paper, 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. Allmore » 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. Finally, by showing that organic semiconductors form stable glasses, these results provide an avenue for systematic performance optimization of active layers in organic electronics.« less

  6. 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.

  7. Chemical synthesis of oriented ferromagnetic LaSr-2 × 4 manganese oxide molecular sieve nanowires.

    PubMed

    Carretero-Genevrier, Adrián; Gazquez, Jaume; Magén, César; Varela, María; Ferain, Etienne; Puig, Teresa; Mestres, Narcís; Obradors, Xavier

    2012-06-25

    We report a chemical solution based method using nanoporous track-etched polymer templates for producing long and oriented LaSr-2 × 4 manganese oxide molecular sieve nanowires. Scanning transmission electron microscopy and electron energy loss spectroscopy analyses show that the nanowires are ferromagnetic at room temperature, single crystalline, epitaxially grown and self-aligned.

  8. Chemical synthesis of oriented ferromagnetic LaSr-2 × 4 manganese oxide molecular sieve nanowires

    SciTech Connect

    Carretero-Genevrier, Adrián; Gazquez, Jaume; Magen, Cesar; Varela, Maria; Ferain, Etienne; Puig, Teresa; Mestres, Narcis; Obradors, Xavier

    2012-04-25

    Here we report a chemical solution based method using nanoporous track-etched polymer templates for producing long and oriented LaSr-2 × 4 manganese oxide molecular sieve nanowires. Scanning transmission electron microscopy and electron energy loss spectroscopy analyses show that the nanowires are ferromagnetic at room temperature, single crystalline, epitaxially grown and self-aligned.

  9. 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.

  10. 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

  11. Precise Macroscopic Supramolecular Assembly by Combining Spontaneous Locomotion Driven by the Marangoni Effect and Molecular Recognition.

    PubMed

    Xiao, Meng; Xian, Yiming; Shi, Feng

    2015-07-27

    Macroscopic supramolecular assembly bridges fundamental research on molecular recognition and the potential applications as bulk supramolecular materials. However, challenges remain to realize stable precise assembly, which is significant for further functions. To handle this issue, the Marangoni effect is applied to achieve spontaneous locomotion of macroscopic building blocks to reach interactive distance, thus contributing to formation of ordered structures. By increasing the density of the building blocks, the driving force for assembly transforms from a hydrophobic-hydrophobic interaction to hydrophilic-hydrophilic interaction, which is favorable for introducing hydrophilic coatings with supramolecular interactive groups on matched surfaces, consequently realizing the fabrication of stable precise macroscopic supramolecular assemblies. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. J-selective Stark orientation of molecular rotation in a beam

    NASA Astrophysics Data System (ADS)

    Auzinsh, Marcis P.; Ferber, Ruvin S.

    1992-12-01

    We propose a facile method to transform alignment of molecular rotation in a beam into transverse orientation with high efficiency via the second-order Stark effect in a homogeneous electric field scrE. The calculated J-orientation magnitude for a specific rotational level J exhibits a regular structure of equidistant dispersion-form signals in scrE2 coordinates. Estimates performed for the NaK molecule show the possibility to produce rotational and isotopic selective J orientation for a fixed beam velocity v. The orientation appears in the direction perpendicular to the (v,scrE) plane, and the optimal angle between v and scrE is 45°.

  13. 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.

  14. 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).

  15. Molecular linker-mediated self-assembly of gold nanoparticles: understanding and controlling the dynamics.

    PubMed

    Abbas, Abdennour; Kattumenu, Ramesh; Tian, Limei; Singamaneni, Srikanth

    2013-01-08

    This study sheds light on the mechanism and dynamics of self-assembly of gold nanoparticles (AuNPs) using molecular linkers such as aminothiols. An experimental model is established that enables a fine control and prediction of both assembly rate and degree. Furthermore, we have found that under certain conditions, the increase in the molar ratio of linker/AuNPs beyond a certain threshold unexpectedly and dramatically slows down the assembly rate by charge reversal of the surface of nanoparticles. As a result, the assembly rate can be easily tuned to reach a maximum growth within seconds to several days. The decrease of the same molar ratio (linker/AuNPs) below a certain value leads to self-termination of the reaction at different phases of the assembly process, thus providing nanoparticles chains of different length. This work introduces new handles for a rational design of novel self-assembled architectures in a very time-effective manner and contributes to the understanding of the effect of the assembly morphology on the optical properties of gold nanoparticles.

  16. Self-assembling, reactivity and molecular dynamics of fullerenol nanoparticles.

    PubMed

    Vraneš, Milan; Borišev, Ivana; Tot, Aleksandar; Armaković, Stevan; Armaković, Sanja; Jović, Danica; Gadžurić, Slobodan; Djordjevic, Aleksandar

    2016-12-21

    In this work structuring of water and insight into intermolecular interactions between water and fullerenol are studied throughout the process of forming nanoagglomerates at different temperatures applying both experimental and computational approaches. The obtained fullerenol nanoparticles (FNPs) are firstly characterized using dynamic light scattering, atomic force microscopy and transmission electron microscopy. The density, electrical conductivity and dynamic viscosity of aqueous fullerenol solutions are measured in the temperature range of 293.15 to 315.15 K. From the experimental density results other important thermodynamic values, such as apparent molar volumes and the partial molar volumes of water and fullerenol, are also calculated. To support the conclusion derived from the experimental density and calculated volumetric parameters, and to better understand the nature of the interactions with water, molecular dynamics simulations and radial distribution functions are also employed.

  17. A computer-oriented system for assembling and displaying land management information

    Treesearch

    Elliot L. Amidon

    1964-01-01

    Maps contain information basic to land management planning. By transforming conventional map symbols into numbers which are punched into cards, the land manager can have a computer assemble and display information required for a specific job. He can let a computer select information from several maps, combine it with such nonmap data as treatment cost or benefit per...

  18. 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.

  19. Molecular Origin of the Self-Assembly of Lanreotide into Nanotubes: A Mutational Approach☆

    PubMed Central

    Valéry, Céline; Pouget, Emilie; Pandit, Anjali; Verbavatz, Jean-Marc; Bordes, Luc; Boisdé, Isabelle; Cherif-Cheikh, Roland; Artzner, Franck; Paternostre, Maité

    2008-01-01

    Lanreotide, a synthetic, therapeutic octapeptide analog of somatostatin, self-assembles in water into perfectly hollow and monodisperse (24-nm wide) nanotubes. Lanreotide is a cyclic octapeptide that contains three aromatic residues. The molecular packing of the peptide in the walls of a nanotube has recently been characterized, indicating four hierarchical levels of organization. This is a fascinating example of spontaneous self-organization, very similar to the formation of the gas vesicle walls of Halobacterium halobium. However, this unique peptide self-assembly raises important questions about its molecular origin. We adopted a directed mutation approach to determine the molecular parameters driving the formation of such a remarkable peptide architecture. We have modified the conformation by opening the cycle and by changing the conformation of a Lys residue, and we have also mutated the aromatic side chains of the peptide. We show that three parameters are essential for the formation of lanreotide nanotubes: i), the specificity of two of the three aromatic side chains, ii), the spatial arrangement of the hydrophilic and hydrophobic residues, and iii), the aromatic side chain in the β-turn of the molecule. When these molecular characteristics are modified, either the peptides lose their self-assembling capability or they form less-ordered architectures, such as amyloid fibers and curved lamellae. Thus we have determined key elements of the molecular origins of lanreotide nanotube formation. PMID:17993497

  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. 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

  3. 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.

  4. 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

  5. Programming molecular self-assembly of intrinsically disordered proteins containing sequences of low complexity

    NASA Astrophysics Data System (ADS)

    Simon, Joseph R.; Carroll, Nick J.; Rubinstein, Michael; Chilkoti, Ashutosh; López, Gabriel P.

    2017-06-01

    Dynamic protein-rich intracellular structures that contain phase-separated intrinsically disordered proteins (IDPs) composed of sequences of low complexity (SLC) have been shown to serve a variety of important cellular functions, which include signalling, compartmentalization and stabilization. However, our understanding of these structures and our ability to synthesize models of them have been limited. We present design rules for IDPs possessing SLCs that phase separate into diverse assemblies within droplet microenvironments. Using theoretical analyses, we interpret the phase behaviour of archetypal IDP sequences and demonstrate the rational design of a vast library of multicomponent protein-rich structures that ranges from uniform nano-, meso- and microscale puncta (distinct protein droplets) to multilayered orthogonally phase-separated granular structures. The ability to predict and program IDP-rich assemblies in this fashion offers new insights into (1) genetic-to-molecular-to-macroscale relationships that encode hierarchical IDP assemblies, (2) design rules of such assemblies in cell biology and (3) molecular-level engineering of self-assembled recombinant IDP-rich materials.

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

    PubMed

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

    2016-02-01

    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.

  7. 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.

  8. 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.

  9. Elucidating energy and electron transfer dynamics within molecular assemblies for solar energy conversion

    NASA Astrophysics Data System (ADS)

    Morseth, Zachary Aaron

    The use of sunlight to make chemical fuels (i.e. solar fuels) is an attractive approach in the quest to develop sustainable energy sources. Using nature as a guide, assemblies for artificial photosynthesis will need to perform multiple functions. They will need to be able to harvest light across a broad region of the solar spectrum, transport excited-state energy to charge-separation sites, and then transport and store redox equivalents for use in the catalytic reactions that produce chemical fuels. This multifunctional behavior will require the assimilation of multiple components into a single macromolecular system. A wide variety of different architectures including porphyrin arrays, peptides, dendrimers, and polymers have been explored, with each design posing unique challenges. Polymer assemblies are attractive due to their relative ease of production and facile synthetic modification. However, their disordered nature gives rise to stochastic dynamics not present in more ordered assemblies. The rational design of assemblies requires a detailed understanding of the energy and electron transfer events that follow light absorption, which can occur on timescales ranging from femtoseconds to hundreds of microseconds, necessitating the use of sophisticated techniques. We have used a combination of time-resolved absorption and emission spectroscopies with observation times that span nine orders of magnitude to follow the excited-state evolution within single-site and polymer-based molecular assemblies. We complement experimental observations with electronic structure calculations, molecular dynamics simulations, and kinetic modeling to develop a microscopic view of these dynamics. This thesis provides an overview of work on single-site molecular assemblies and polymers decorated with pendant chromophores, both in solution and on surfaces. This work was made possible through extensive collaboration with Dr. Kirk Schanze's and Dr. John Reynolds' research groups who

  10. 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. (c) 2004 Wiley Periodicals, Inc.

  11. 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.

  12. 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

  13. 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.

  14. 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.

  15. Manipulation of Self-Assembled Nanostructure Dimensions in Molecular Janus Particles.

    PubMed

    Liu, Hao; Luo, Jiancheng; Shan, Wenpeng; Guo, Dong; Wang, Jing; Hsu, Chih-Hao; Huang, Mingjun; Zhang, Wei; Lotz, Bernard; Zhang, Wen-Bin; Liu, Tianbo; Yue, Kan; Cheng, Stephen Z D

    2016-07-26

    The ability to manipulate self-assembly of molecular building blocks is the key to achieving precise "bottom-up" fabrications of desired nanostructures. Herein, we report a rational design, facile synthesis, and self-assembly of a series of molecular Janus particles (MJPs) constructed by chemically linking α-Keggin-type polyoxometalate (POM) nanoclusters with functionalized polyhedral oligomeric silsesquioxane (POSS) cages. Diverse nanostructures were obtained by tuning secondary interactions among the building blocks and solvents via three factors: solvent polarity, surface functionality of POSS derivatives, and molecular topology. Self-assembled morphologies of KPOM-BPOSS (B denotes isobutyl groups) were found dependent on solvent polarity. In acetonitrile/water mixtures with a high dielectric constant, colloidal nanoparticles with nanophase-separated internal lamellar structures quickly formed, which gradually turned into one-dimensional nanobelt crystals upon aging, while stacked crystalline lamellae were dominantly observed in less polar methanol/chloroform solutions. When the crystallizable BPOSS was replaced with noncrystallizable cyclohexyl-functionalized CPOSS, the resulting KPOM-CPOSS also formed colloidal spheres; however, it failed to further evolve into crystalline nanobelt structures. In less polar solvents, KPOM-CPOSS crystallized into isolated two-dimensional nanosheets, which were composed of two inner crystalline layers of Keggin POM covered by two monolayers of amorphous CPOSS. In contrast, self-assembly of KPOM-2BPOSS was dominated by crystallization of the BPOSS cages, which was hardly sensitive to solvent polarity. The BPOSS cages formed the crystalline inner bilayer, sandwiched by two outer layers of Keggin POM clusters. These results illustrate a rational strategy to purposely fabricate self-assembled nanostructures with diverse dimensionality from MJPs with controlled molecular composition and topology.

  16. 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.

  17. 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

  18. Multi-component coordination-driven self-assembly: construction of alkyl-based structures and molecular modelling.

    PubMed

    Pollock, J Bryant; Cook, Timothy R; Schneider, Gregory L; Stang, Peter J

    2013-10-01

    The design of supramolecular coordination complexes (SCCs) is typically predicated on the use of rigid molecular building blocks through which the structural outcome is determined based on the number and orientation of labile coordination sites on metal acceptors, and the angularity of the ligand donors that are to bridge these nodes. Three-component systems extend the complexity of self-assembly by utilizing two different Lewis base donors in concert with a metal that favors a heteroligated coordination environment. The thermodynamic preference for heteroligation provides a new design principle to the formation of SCCs, wherein multicomponent architectures need not employ only rigid donors. Herein, we exploit the self-selection processes of bis(phosphine) Pt(II) metal centers which favor mixed Pt(pyridyl)(carboxylate) coordination spheres over their homoligated counterparts, specifically using alkyl-based dicarboxylate ligands instead of traditionally rigid phenyl, alkenyl, or ethynyl variants. Using this mode of assembly, flexible-based 2D and 3D SCCs containing long alkyl chains were synthesized and characterized. Density functional theory (DFT) and natural population analysis (NPA) calculations were performed on model systems to probe the thermodynamic preference for heteroligated coordination spheres in the experimental systems. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Probing Gelation and Rheological Behavior of a Self-Assembled Molecular Gel.

    PubMed

    Hashemnejad, Seyed Meysam; Kundu, Santanu

    2017-08-08

    Molecular gels have been investigated over the last few decades; however, mechanical behavior of these self-assembled gels is not well understood, particularly how these materials fail at large strain. Here, we report the gelation and rheological behavior of a molecular gel formed by self-assembly of a low molecular weight gelator (LMWG), di-Fmoc-l-lysine, in 1-propanol/water mixture. Gels were prepared by solvent-triggered technique, and gelation was tracked using Fourier transform infrared (FTIR) spectroscopy and shear rheology. FTIR spectroscopy captures the formation of hydrogen bonding between the gelator molecules, and the change in IR spectra during the gelation process correlates with the gelation kinetics results captured by rheology. Self-assembly of gelator molecules leads to a fiber-like structure, and these long fibers topologically interact to form a gel-like material. Stretched-exponential function can capture the stress-relaxation data. Stress-relaxation time for these gels have been found to be long owing to long fiber dimensions, and the stretching exponent value of 1/3 indicates polydispersity in fiber dimensions. Cavitation rheology captures fracture-like behavior of these gels, and critical energy release rate has been estimated to be of the order 0.1 J/m(2). Our results provide new understanding of the rheological behavior of molecular gels and their structural origin.

  20. 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.

  1. 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.

  2. 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.

  3. 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

  4. 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.

  5. 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.

  6. Layer-by-layer assembly of charged nanoparticles on porous substrates: molecular dynamics simulations.

    PubMed

    Carrillo, Jan-Michael Y; Dobrynin, Andrey V

    2011-04-26

    We performed molecular dynamics simulations of a multilayer assembly of oppositely charged nanoparticles on porous substrates with cylindrical pores. The film was constructed by sequential adsorption of oppositely charged nanoparticles in layer-by-layer fashion from dilute solutions. The multilayer assembly proceeds through surface overcharging after completion of each deposition step. There is almost linear growth in the surface coverage and film thickness during the deposition process. The multilayer assembly also occurs inside cylindrical pores. The adsorption of nanoparticles inside pores is hindered by the electrostatic interactions of newly adsorbing nanoparticles with the multilayer film forming inside the pores and on the substrate. This is manifested in the saturation of the average thickness of the nanoparticle layers formed on the pore walls with an increasing number of deposition steps. The distribution of nanoparticles inside the cylindrical pore was nonuniform with a significant excess of nanoparticles at the pore entrance.

  7. Molecular Self-Assembly of Short Aromatic Peptides: From Biology to Nanotechnology and Material Science

    NASA Astrophysics Data System (ADS)

    Gazit, Ehud

    2013-03-01

    The formation of ordered amyloid fibrils is the hallmark of several diseases of unrelated origin. In spite of grave clinical consequence, the mechanism of amyloid formation is not fully understood. We have suggested, based on experimental and bioinformatic analysis, that aromatic interactions may provide energetic contribution as well as order and directionality in the molecular-recognition and self-association processes that lead to the formation of these assemblies. This is in line with the well-known central role of aromatic-stacking interactions in self-assembly processes. Our works on the mechanism of aromatic peptide self-assembly, lead to the discovery that the diphenylalanine recognition motif self-assembles into peptide nanotubes with a remarkable persistence length. Other aromatic homodipeptides could self-assemble in nano-spheres, nano-plates, nano-fibrils and hydrogels with nano-scale order. We demonstrated that the peptide nanostructures have unique chemical, physical and mechanical properties including ultra-rigidity as aramides, semi-conductive, piezoelectric and non-linear optic properties. We also demonstrated the ability to use these peptide nanostructures as casting mold for the fabrication of metallic nano-wires and coaxial nano-cables. The application of the nanostructures was demonstrated in various fields including electrochemical biosensors, tissue engineering, and molecular imaging. Finally, we had developed ways for depositing of the peptide nanostructures and their organization. We had use inkjet technology as well as vapour deposition methods to coat surface and from the peptide ``nano-forests''. We recently demonstrated that even a single phenylalanine amino-acid can form well-ordered fibrilar assemblies.

  8. Orientation and conformation of a lipase at an interface studied by molecular dynamics simulations.

    PubMed Central

    Jensen, Morten Ø; Jensen, Torben R; Kjaer, Kristian; Bjørnholm, Thomas; Mouritsen, Ole G; Peters, Günther H

    2002-01-01

    Electron density profiles calculated from molecular dynamics trajectories are used to deduce the orientation and conformation of Thermomyces lanuginosa lipase and a mutant adsorbed at an air-water interface. It is demonstrated that the profiles display distinct fine structures, which uniquely characterize enzyme orientation and conformation. The density profiles are, on the nanosecond timescale, determined by the average enzyme conformation. We outline a computational scheme that from a single molecular dynamics trajectory allows for extraction of electron density profiles referring to different orientations of the lipase relative to an implicit interface. Profiles calculated for the inactive and active conformations of the lipase are compared with experimental electron density profiles measured by x-ray reflectivity for the lipase adsorbed at an air-water interface. The experimental profiles contain less fine structural information than the calculated profiles because the resolution of the experiment is limited by the intrinsic surface roughness of water. Least squares fits of the calculated profiles to the experimental profiles provide areas per adsorbed enzyme and suggest that Thermomyces lanuginosa lipase adsorbs to the air-water interface in a semiopen conformation with the lid oriented away from the interface. PMID:12080103

  9. 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.

  10. 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

  11. Molecular architecture of a dynamin adaptor: implications for assembly of mitochondrial fission complexes

    PubMed Central

    Koirala, Sajjan; Bui, Huyen T.; Schubert, Heidi L.; Eckert, Debra M.; Hill, Christopher P.

    2010-01-01

    Recruitment and assembly of some dynamin-related guanosine triphosphatases depends on adaptor proteins restricted to distinct cellular membranes. The yeast Mdv1 adaptor localizes to mitochondria by binding to the membrane protein Fis1. Subsequent Mdv1 binding to the mitochondrial dynamin Dnm1 stimulates Dnm1 assembly into spirals, which encircle and divide the mitochondrial compartment. In this study, we report that dimeric Mdv1 is joined at its center by a 92-Å antiparallel coiled coil (CC). Modeling of the Fis1–Mdv1 complex using available crystal structures suggests that the Mdv1 CC lies parallel to the bilayer with N termini at opposite ends bound to Fis1 and C-terminal β-propeller domains (Dnm1-binding sites) extending into the cytoplasm. A CC length of appropriate length and sequence is necessary for optimal Mdv1 interaction with Fis1 and Dnm1 and is important for proper Dnm1 assembly before membrane scission. Our results provide a framework for understanding how adaptors act as scaffolds to orient and stabilize the assembly of dynamins on membranes. PMID:21149566

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

    PubMed

    de la Llave, Ezequiel; 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.

  13. 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.

  14. 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.

  15. Molecular Beam Epitaxial Growth of GaAs on (631) Oriented Substrates

    SciTech Connect

    Cruz Hernandez, Esteban; Rojas Ramirez, Juan-Salvador; Contreras Hernandez, Rocio; Lopez Lopez, Maximo; Pulzara Mora, Alvaro; Mendez Garcia, Victor H.

    2007-02-09

    In this work, we report the study of the homoepitaxial growth of GaAs on (631) oriented substrates by molecular beam epitaxy (MBE). We observed the spontaneous formation of a high density of large scale features on the surface. The hilly like features are elongated towards the [-5, 9, 3] direction. We show the dependence of these structures with the growth conditions and we present the possibility of to create quantum wires structures on this surface.

  16. 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 .

  17. 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

  18. Synchronized assembly of gold nanoparticles driven by a dynamic DNA-fueled molecular machine.

    PubMed

    Song, Tingjie; Liang, Haojun

    2012-07-04

    A strategy for gold nanoparticle (AuNP) assembly driven by a dynamic DNA-fueled molecular machine is revealed here. In this machine, the aggregation of DNA-functionalized AuNPs is regulated by a series of toehold-mediated strand displacement reactions of DNA. The aggregation rate of the AuNPs can be regulated by controlling the amount of oligonucleotide catalyst. The versatility of the dynamic DNA-fueled molecular machine in the construction of two-component "OR" and "AND" logic gates has been demonstrated. This newly established strategy may find broad potential applications in terms of building up an "interface" that allows the combination of the strand displacement-based characteristic of DNA with the distinct assembly properties of inorganic nanoparticles, ultimately leading to the fabrication of a wide range of complex multicomponent devices and architectures.

  19. State-space reduction and equivalence class sampling for a molecular self-assembly model.

    PubMed

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

    2016-07-01

    Direct simulation of a model with a large state space will generate enormous volumes of data, much of which is not relevant to the questions under study. In this paper, we consider a molecular self-assembly model as a typical example of a large state-space model, and present a method for selectively retrieving 'target information' from this model. This method partitions the state space into equivalence classes, as identified by an appropriate equivalence relation. The set of equivalence classes H, which serves as a reduced state space, contains none of the superfluous information of the original model. After construction and characterization of a Markov chain with state space H, the target information is efficiently retrieved via Markov chain Monte Carlo sampling. This approach represents a new breed of simulation techniques which are highly optimized for studying molecular self-assembly and, moreover, serves as a valuable guideline for analysis of other large state-space models.

  20. 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.

  1. Guided self-assembly of molecular dipoles on a substrate surface

    NASA Astrophysics Data System (ADS)

    Gao, Y. F.; Suo, Z.

    2003-04-01

    Molecules adsorbed on a substrate surface can self-assemble into a monolayer. This article models the process of self-assembly guided by an external object. The molecules are electric dipoles, diffusing on the surface at an elevated temperature. Pre-pattern a flat mask with a submonolayer of immobile atoms, which gives rise to a patterned contact potential field. Bring the mask to a small distance above the substrate. The electrostatic interaction transfers the pattern on the mask to a molecular pattern on the substrate. Similarly, one can place above the molecules a charged conducting tip, or a mask that is pre-patterned with a topographic surface. Our model includes the mobile molecular dipoles on the substrate surface, the guiding object, and the electrostatic field in the intervening space. A nonlinear diffusion equation simulates the pattern transfer process. Numerical results are presented when the guiding object is a flat metal, patterned with a submonolayer of immobile atoms.

  2. 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

  3. 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.

  4. 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).

  5. 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.

  6. 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.

  7. Molecular layer-by-layer assembled thin-film composite membranes for water desalination.

    PubMed

    Gu, Joung-Eun; Lee, Seunghye; Stafford, Christopher M; Lee, Jong Suk; Choi, Wansuk; Kim, Bo-Young; Baek, Kyung-Youl; Chan, Edwin P; Chung, Jun Young; Bang, Joona; Lee, Jung-Hyun

    2013-09-14

    Molecular layer-by-layer (mLbL) assembled thin-film composite membranes fabricated by alternating deposition of reactive monomers on porous supports exhibit both improved salt rejection and enhanced water flux compared to traditional reverse osmosis membranes prepared by interfacial polymerization. Additionally, the well-controlled structures achieved by mLbL deposition further lead to improved antifouling performance. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. 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

  9. 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.

  10. 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.

  11. 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.

  12. 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

  13. 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.

  14. 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.

  15. 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

  16. Self-assembly of high molecular weight polypeptide copolymers studied via diffusion limited aggregation.

    PubMed

    Meier, Christoph; Wu, Yuzhou; Pramanik, Goutam; Weil, Tanja

    2014-01-13

    The assembly of high molecular weight polypeptides into complex architectures exhibiting structural complexity ranging from the nano- to the mesoscale is of fundamental importance for various protein-related diseases but also hold great promise for various nano- and biotechnological applications. Here, the aggregation of partially unfolded high molecular weight polypeptides into multiscale fractal structures is investigated by means of diffusion limited aggregation and atomic force microscopy. The zeta potential, the hydrodynamic radius, and the obtained fractal morphologies were correlated with the conformation of the polypeptide backbones as obtained from circular dichroism measurements. The polypeptides are modified with polyethylene oxide side chains to stabilize the polypeptides and to normalize intermolecular interactions. The modification with the hydrophobic thioctic acid alters the folding of the polypeptide backbone, resulting in a change in solution aggregation and fractal morphology. We found that a more compact folding results in dense and highly branched structures, whereas a less compact folded polypeptide chain yields a more directional assembly. Our results provide first evidence for the role of compactness of polypeptide folding on aggregation. Furthermore, the mesoscale-structured biofilms were used to achieve a hierarchical protein assembly, which is demonstrated by deposition of Rhodamine-labeled HSA with the preassembled fractal structures. These results contribute important insights to the fundamental understanding of the aggregation of high molecular weight polypeptides in general and provide opportunities to study nanostructure-related effects on biological systems such as adhesion, proliferation, and the development of, for example, neuronal cells.

  17. 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.

  18. 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.

  19. Effect of the molecular structure on the hierarchical self-assembly of semifluorinated alkanes at the air/water interface.

    PubMed

    de Viguerie, Laurence; Keller, Rabea; Jonas, Ulrich; Berger, Rüdiger; Clark, Christopher G; Klein, Christopher O; Geue, Thomas; Müllen, Klaus; Butt, Hans-Jürgen; Vlassopoulos, Dimitris

    2011-07-19

    Semifluorinated alkanes (C(n)F(2n+1)C(m)H(2m+1)), short FnHm display local phase separation of mutually incompatible hydrocarbon and fluorocarbon chain moieties, which has been utilized as a structure-forming motif in supramolecular architectures. The packing of semifluorinated alkanes, nominally based on dodecyl subunits, such as perfluoro(dodecyl)dodecane (F12H12) and perfluoro(dodecyl)eicosane (F12H20), as well as a core extended analogue, 1,4-dibromo-2-((perfluoroundecyl)methoxy)-5-(dodecyloxy)benzene) (F11H1-core-H12), was studied at the air/water interface. Langmuir monolayers were investigated by means of neutron reflectivity directly at the air/water interface and scanning force microscopy after transfer to silicon wafers. Narrowly disperse surface micelles formed in all three cases; however, they were found to bear different morphologies with respect to molecular orientation and assembly dimensionality, which gives rise to different hierarchical aggregate topologies. For F12H12, micelles of ca. 30 nm in diameter, composed of several circular or "spherical cap" substructures, were observed and a monolayer model with the fluorocarbon block oriented toward air is proposed. F12H20 molecules formed larger (ca. 50 nm diameter) hexagonally shaped surface micelles that were hexagonally, densely packed, besides more elongated but tightly interlocked wormlike structures. Conversely, F11H1-core-H12 films organized into linear rows of elongated surface micelles with comparable width, but an average length of ca. 400 nm, apparently formed by antiparallel molecular packing.

  20. 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

  1. Aqueous Self-Assembly of Non-Ionic Bottlebrush Block Copolymer Surfactants with Tunable Molecular Shapes

    NASA Astrophysics Data System (ADS)

    Rzayev, Javid

    2015-03-01

    Polymer amphiphiles provide a robust and versatile platform for the fabrication of nanostructured soft matter. In this research, we explore a new class of polymer surfactants based on comb-like bottlebrush architecture as highly tunable molecular building blocks for aqueous self-assembly. Excluded volume interactions between densely grafted polymer side chains in the bottlebrush architecture are alleviated by backbone stretching, which leads to the formation of shape-persistent cylindrical macromolecules whose molecular dimensions can be precisely tailored during chemical synthesis. Amphiphilic bottlebrush block copolymers containing hydrophobic polylactide (PLA) and hydrophilic poly(oligoethylene oxide methacrylate) (PEO) side chains of various lengths were synthesized by a combination of controlled radical and ring-opening polymerizations. In dilute aqueous solutions, bottlebrush surfactants rapidly assembled into spherical, cylindrical and bilayer aggregates, as visualized by cryogenic transmission electron microscopy (cryo-TEM). Depending on the compositional side chain asymmetry, the formation of spherical micelles with different sizes and dispersities was observed. The molecular shape-dependent assembly was analyzed with help of a packing parameter (p) computed from the molecular composition data akin to small molecule surfactants, with most uniform spherical aggregates observed for bottlebrush amphiphiles with p close to 0.3. The formation of highly uniform micelles and the presence of a rich morphological diagram with relatively narrow compositional windows were attributed to the lack of conformational freedom in bottlebrush surfactants. Similarly, the unusual formation of cylindrical micelles with long aspect ratios for such high molecular weight amphiphiles was attributed to their inability to stabilize morphological defects, such as Y-junctions, with large deviations from mean curvature. Financial support for this work was provided by the National

  2. 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

  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. 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).

  7. Molecularly Self-Assembled Nucleic Acid Nanoparticles for Targeted In Vivo siRNA Delivery

    PubMed Central

    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.

    2013-01-01

    Nanoparticles are employed for delivering therapeutics into cells1,2. 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 efficacy3-7. A variety of materials have been explored for delivering small interfering RNAs (siRNAs) - a therapeutic agent that suppresses the expression of targeted genes8,9. 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, lack of tissue specificity and potential toxicity10-12. 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 precisely controlled. We show that at least three folate molecules per nanoparticle is 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). PMID:22659608

  8. 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).

  9. Molecular simulations of self-assembly processes in metal-organic frameworks: Model dependence

    NASA Astrophysics Data System (ADS)

    Biswal, Debasmita; Kusalik, Peter G.

    2017-07-01

    Molecular simulation is a powerful tool for investigating microscopic behavior in various chemical systems, where the use of suitable models is critical to successfully reproduce the structural and dynamic properties of the real systems of interest. In this context, molecular dynamics simulation studies of self-assembly processes in metal-organic frameworks (MOFs), a well-known class of porous materials with interesting chemical and physical properties, are relatively challenging, where a reasonably accurate representation of metal-ligand interactions is anticipated to play an important role. In the current study, we both investigate the performance of some existing models and introduce and test new models to help explore the self-assembly in an archetypal Zn-carboxylate MOF system. To this end, the behavior of six different Zn-ion models, three solvent models, and two ligand models was examined and validated against key experimental structural parameters. To explore longer time scale ordering events during MOF self-assembly via explicit solvent simulations, it is necessary to identify a suitable combination of simplified model components representing metal ions, organic ligands, and solvent molecules. It was observed that an extended cationic dummy atom (ECDA) Zn-ion model combined with an all-atom carboxylate ligand model and a simple dipolar solvent model can reproduce characteristic experimental structures for the archetypal MOF system. The successful use of these models in extensive sets of molecular simulations, which provide key insights into the self-assembly mechanism of this archetypal MOF system occurring during the early stages of this process, has been very recently reported.

  10. 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.

  11. 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.

  12. 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.

  13. Tunable Affinity and Molecular Architecture Lead to Diverse Self-Assembled Supramolecular Structures in Thin Films

    SciTech Connect

    Hsu, Chin-Hao; Dong, Xuehui; Lin, Zhiwei; Ni, Bo; Lu, Pengatao; Jiang, Zhang; Tian, Ding; Cheng, Stephen Z.D.

    2016-01-01

    The self-assembly behaviors of specifically designed giant surfactants are systematically studied in thin films using grazing incident X-ray and transmission electron microscopy (TEM), focusing on the effects of head surface functionalities and molecular architectures on nanostructure formation. Two molecular nanoparticles (MNPs) with different affinities, i.e., hydrophilic carboxylic acid functionalized [60]fullerene (AC60) and omniphobic fluorinated polyhedral oligomeric silsesquioxane (FPOSS), are utilized as heads of the giant surfactants. By covalently tethering these functional MNPs onto the chain end or the junction point of polystyrene-block-poly(ethylene oxide) (PS-b-PEO) diblock copolymer, linear and star-like giant surfactants possess distinct molecular architectures are constructed. With fixed length of the PEO block, the molecular weight change of the PS block originates the phase formation and transition. Due to the distinct affinity, the AC60-based giant surfactants form two-component morphologies, while three-component morphologies are found in the FPOSS-based ones. A PS block stretching parameter is introduced to characterize the PS chain conformation in different morphologies. The highly diverse self-assembly behaviors and the tunable dimensions in thin films suggest the giant surfactants could be a promising and robust platform for nanolithography applications.

  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 DNA Structures for Molecular Force Measurement: A Magnetically Actuated Approach

    NASA Astrophysics Data System (ADS)

    Armstrong, M.; Lauback, S.; Miller, C.; Peace, C.; Castro, C.; Sooryakumar, R.

    2015-03-01

    Understanding molecular forces is important to comprehend many of the underlying properties of molecular machines and biological processes. The relevant forces in these cases often lie in the picoNewton range, and thus experiments on individual biomolecules must integrate techniques capable of measuring such forces. A mechanical system to measure molecular forces associated with interacting DNA strands is being developed by using self-assembled DNA nanostructures and super-paramagnetic beads. The DNA nanostructure consists of single-stranded DNA molecules which can be folded into a precise compact geometry using hundreds of short oligonucleotides, i.e., staples, via programmed molecular self-assembly. These nanostructures can be polymerized into micron-scale filaments. By functionalizing the filament ends with bispecific conjugate staples, the structure can be attached to a surface as well as labeled with magnetic beads in order to apply a force on the system. External magnetic fields provide the means to maneuver and manipulate the magnetically labeled DNA structures. Preliminary findings associated with the DNA constructs and their manipulation lay the groundwork to establish real-time control of DNA nanodevices with micromanipulation.

  16. Monitoring molecular orientational order in NLO push-pull based polymeric films via photoacoustic measurements

    NASA Astrophysics Data System (ADS)

    Torres-Zúñiga, V.; Castañeda-Guzmán, R.; Morales-Saavedra, O. G.; Pérez-Martínez, A. L.; Ogawa, T.

    2011-12-01

    The pulsed-laser photoacoustic-technique (PLPA) was implemented to characterize molecular orientational order and anisotropy in push-pull poled polymeric films as function of temperature and laser polarization. Traditionally, photoacoustic signals are considered to be directly proportional to the linear optical absorption in amorphous media. In this work, however, it is shown that photoacoustic signals can also be highly sensitive to the material anisotropy when convenient polarization dependent photoacoustic analyses are performed. Thus, variation of the molecular orientation in organic films, comprising rod-like polar chromophores, can be unambiguously monitored via rms-analyses performed on the amplitude of the generated opto-acoustical PLPA-signals as function of the incident laser polarization. This result can be useful for the characterization of organic-based nonlinear optical (NLO) poled films and, in general, in studies of anisotropic materials. In fact, in this work we were able to accurately determine the molecular order parameter ( ϕ) of a NLO-active spin-coated polymeric film containing optically active push-pull chromophores. These molecules, previously oriented via an electrical-poling procedure, are capable to exhibit strong second harmonic generation (SHG) effects. The PLPA-measurements were systematically compared to the linear UV-vis optical absorbance spectra while heating the poled film sample in order to monitor the thermally induced molecular disorder, so that the order parameter may be photo-acoustically evaluated via the PLPA-signals generated from the poled to the unpoled film phase. These PLPA-experiments were performed taking into account the UV-vis reference spectra for calibration and comparison purposes in the evaluation of the order parameter. A significant advantage of the PLPA-technique over commonly used optical spectral methodologies is its convenient applicability in samples exhibiting poor or null optical transmission.

  17. Bottom-up assembly of high density molecular nanowire cross junctions at a solid/liquid interface.

    PubMed

    Lei, Shengbin; Puigmartí-Luis, Josep; Minoia, Andrea; Van der Auweraer, Mark; Rovira, Concepció; Lazzaroni, Roberto; Amabilino, David B; De Feyter, Steven

    2008-02-14

    A monoalkylated tetrathiafulvalene derivative forms multilayer structures at the solid-liquid interface, with high density of cross junctions, which are interesting for molecular electronic circuit self-assembly.

  18. 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.

  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. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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

  5. Manipulating spins using spin-valves of self-assembled molecular wires

    NASA Astrophysics Data System (ADS)

    Burtman, Vladimir; Vardeny, Valy Z.

    2007-03-01

    We studied spin transport using spin-valves of self-assembled monolayer (SAM) devices sandwiched between two ferromagnetic electrodes, namely La0.33Sr0.66MnO3 (LSMO) and Co having different coercive fields. The SAM film contained isolated molecular wires that bond with both electrodes, in an otherwise insulating molecular matrix that bond only with one electrode. The relative resistance change, or magnetoresistance (MR), DR/R between the device resistance with the electrodes magnetizations parallel and anti-parallel to each other serves as a figure of merit and show spin injection through the isolated molecular wires. We found a giant MR of up to 80% at 10K. The MR response was measured at various temperatures and biasing voltages to obtain the complete magneto-transport characteristic properties of the organic spin-valve devices.

  6. 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.

  7. 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.

  8. 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

  9. 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.

  10. 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.

  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. 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.

  13. 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.

  14. Chemiresistive properties regulated by nanoscale curvature in molecularly-linked nanoparticle composite assembly.

    PubMed

    Cheng, Han-Wen; Yan, Shan; Han, Li; Chen, Yong; Kang, Ning; Skeete, Zakiya; Luo, Jin; Zhong, Chuan-Jian

    2017-03-17

    Interparticle spatial properties influence the electrical and functional properties of nanoparticle-structured assemblies. This report describes the nanoscale curvature-induced change in chemiresistive properties of molecularly-linked assemblies of gold nanoparticles on multiwalled carbon nanotubes, which are exploited for sensitive detection of volatile organic compounds. In addition to using linking/capping molecules to define interparticle spatial distances, the nanoscale curvature radius of the carbon nanotubes provides intriguing tunability of the interparticle spatial properties to influence electrical properties, which contrast with those observed for nanoparticle thin films assembled directly on chemiresistor devices. The electrical characteristics of the nanoparticle-nanotube composite give positive response profiles for the vapor molecules that are distinctively different to those observed for conventional nanoparticle thin-film assemblies. The dominant effect of electron coupling on overall chemiresistive properties is shown in relation to that of nanoscale curvature radius on the nanoparticle thin-film sensing properties. Sensing data are also further assessed in correlation with the solubility parameters of the vapor molecule. These findings have significant implications for the design of sensitive interfaces with nanocomposite-structured sensing materials and microfabricated chemiresistor devices.

  15. 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.

  16. General strategy for self-assembly of highly oriented nanocrystalline semiconducting polymers with high mobility.

    PubMed

    Luo, Chan; Kyaw, Aung Ko Ko; Perez, Louis A; Patel, Shrayesh; Wang, Ming; Grimm, Bruno; Bazan, Guillermo C; Kramer, Edward J; Heeger, Alan J

    2014-05-14

    Solution processable semiconducting polymers with excellent film forming capacity and mechanical flexibility are considered among the most progressive alternatives to conventional inorganic semiconductors. However, the random packing of polymer chains and the disorder of the polymer matrix typically result in low charge transport mobilities (10(-5)-10(-2) cm(2) V(-1) s(-1)). These low mobilities compromise their performance and development. Here, we present a strategy, by utilizing capillary action, to mediate polymer chain self-assembly and unidirectional alignment on nanogrooved substrates. We designed a sandwich tunnel system separated by functionalized glass spacers to induce capillary action for controlling the polymer nanostructure, crystallinity, and charge transport. Using capillary action, we demonstrate saturation mobilities with average values of 21.3 and 18.5 cm(2) V(-1 )s(-1) on two different semiconducting polymers at a transistor channel length of 80 μm. These values are limited by the source-drain contact resistance, Rc. Using a longer channel length of 140 μm where the contact resistance is less important, we measured μh = 36.3 cm(2) v(-1) s(-1). Extrapolating to infinite channel length where Rc is unimportant, the intrinsic mobility for poly[4-(4,4-dihexadecyl-4H-cyclopenta[1,2-b:5,4-b']dithiophen-2-yl)-alt-[1,2,5]thiadiazolo[3,4-c]pyridine] (Mn = 140 kDa) at this degree of chain alignment and structural order is μh ≈ 47 cm(2 )v(-1) s(-1). Our results create a promising pathway toward high performance, solution processable, and low-cost organic electronics.

  17. 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

  18. 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.

  19. 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

  20. 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.

  1. Molecular orientation and anisotropic carrier mobility in poorly soluble polythiophene thin films

    NASA Astrophysics Data System (ADS)

    Hosokawa, Yuki; Misaki, Masahiro; Yamamoto, Satoshi; Torii, Masafumi; Ishida, Kenji; Ueda, Yasukiyo

    2012-05-01

    Oriented thin films of a poorly soluble polythiophene, poly[benzo[1,2-d:4,5-d']bisthiazole-2,6-diyl(3',4,4″,4″'-tetradodecyl[2,2':5',2″:5″,2″'-quaterthiophene]-5,5″'-diyl)], were fabricated using the friction-transfer technique. The detail of the film structure was investigated using polarized UV-vis spectroscopy, transmission electron microscopy, and grazing-incidence x-ray diffraction observations. The friction-transfer technique enables control of the anisotropic carrier transport according to the face-on and/or edge-on molecular orientations in films with one-directionally aligned polymer backbones.

  2. 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.

  3. 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.

  4. Oriented assembly of bacteriorhodopsin on ZnO nanostructured electrode for enhanced photocurrent generation.

    PubMed

    Molaeirad, Ahmad; Rezaeian, Niloofar

    2015-01-01

    Bacteriorhodopsin (bR) is a photoactive protein that has great potential to be used in bioelectronics applications. For the first time, a monolayer of bR created by the Langmuir-Blodgett method is immobilized on a ZnO nanoporous film. Scanning electron microscopy and atomic force microscopy analyses are used to study the morphological properties of the electrodes. In addition, an efficient biosolar cell is designed and fabricated, and the performance of produced nano-biohybrid electrode is investigated by the measurement of power conversion efficiency of biosolar cell. Under AM1.5 irradiation, a short-circuit current of 0.39 mA cm(-2) , open-circuit voltages of 0.5 V, fill factor of 0.52, and an overall energy conversion efficiency of 0.1% are achieved. © 2014 International Union of Biochemistry and Molecular Biology, Inc.

  5. Charge-directed fiber surface modification by molecular assemblies of functional polysaccharides.

    PubMed

    Vega, Beatriz; Wondraczek, Holger; Zarth, Cíntia Salomão Pinto; Heikkilä, Elina; Fardim, Pedro; Heinze, Thomas

    2013-11-05

    Molecular assemblies, namely, polyelectrolyte complexes (PECs) composed of negatively charged xylan-based derivatives and a novel positively charged cellulose derivative (CN(+)), were used for interfacial modification of wood fibers by charge directed self-assembly. The adsorption process was studied using polyelectrolyte titration and elemental analysis. X-ray spectroscopy (XPS) and time-of-flight secondary ion mass spectrometry (ToF-SIMS) were used as advanced techniques for the characterization of the modified fiber surfaces. The measurements revealed an intense interaction between the pulp fibers and PECs, and provided essential information for a better understanding of the adsorption process. The information gathered on this paper might contribute to the basis for the development of new value added products by the use of underutilized biomass.

  6. 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.

  7. Re-orientation transition in molecular thin films: Potts model with dipolar interaction.

    PubMed

    Hoang, Danh-Tai; Kasperski, Maciej; Puszkarski, Henryk; Diep, H T

    2013-02-06

    We study the low-temperature behavior and the phase transition of a thin film by Monte Carlo simulation. The thin film has a simple cubic lattice structure where each site is occupied by a Potts parameter which indicates the molecular orientation of the site. We take only three molecular orientations in this paper, which correspond to the three-state Potts model. The Hamiltonian of the system includes (i) the exchange interaction J(ij) between nearest-neighbor sites i and j, (ii) the long-range dipolar interaction of amplitude D truncated at a cutoff distance r(c), and (iii) a single-ion perpendicular anisotropy of amplitude A. We allow J(ij) = J(s) between surface spins, and J(ij) = J otherwise. We show that the ground state depends on the ratio D/A and r(c). For a single layer, for a given A, there is a critical value D(c) below (above) which the ground-state (GS) configuration of molecular axes is perpendicular (parallel) to the film surface. When the temperature T is increased, a re-orientation transition occurs near D(c): the low-T in-plane ordering undergoes a transition to the perpendicular ordering at a finite T, below the transition to the paramagnetic phase. The same phenomenon is observed in the case of a film with a thickness. Comparison with the Fe/Gd experiment is given. We show that the surface phase transition can occur below or above the bulk transition depending on the ratio J(s)/J. Surface and bulk order parameters as well as other physical quantities are shown and discussed.

  8. Infectious bursal disease virus capsid assembly and maturation by structural rearrangements of a transient molecular switch.

    PubMed

    Luque, Daniel; Saugar, Irene; Rodríguez, José F; Verdaguer, Nuria; Garriga, Damiá; Martín, Carmen San; Velázquez-Muriel, Javier A; Trus, Benes L; Carrascosa, José L; Castón, José R

    2007-07-01

    Infectious bursal disease virus (IBDV), a double-stranded RNA (dsRNA) virus belonging to the Birnaviridae family, is an economically important avian pathogen. The IBDV capsid is based on a single-shelled T=13 lattice, and the only structural subunits are VP2 trimers. During capsid assembly, VP2 is synthesized as a protein precursor, called pVP2, whose 71-residue C-terminal end is proteolytically processed. The conformational flexibility of pVP2 is due to an amphipathic alpha-helix located at its C-terminal end. VP3, the other IBDV major structural protein that accomplishes numerous roles during the viral cycle, acts as a scaffolding protein required for assembly control. Here we address the molecular mechanism that defines the multimeric state of the capsid protein as hexamers or pentamers. We used a combination of three-dimensional cryo-electron microscopy maps at or close to subnanometer resolution with atomic models. Our studies suggest that the key polypeptide element, the C-terminal amphipathic alpha-helix, which acts as a transient conformational switch, is bound to the flexible VP2 C-terminal end. In addition, capsid protein oligomerization is also controlled by the progressive trimming of its C-terminal domain. The coordination of these molecular events correlates viral capsid assembly with different conformations of the amphipathic alpha-helix in the precursor capsid, as a five-alpha-helix bundle at the pentamers or an open star-like conformation at the hexamers. These results, reminiscent of the assembly pathway of positive single-stranded RNA viruses, such as nodavirus and tetravirus, add new insights into the evolutionary relationships of dsRNA viruses.

  9. 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.

  10. 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

  11. 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.

  12. 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

  13. 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.

  14. Selective self-assembly of molecular clusters with designed sizes on metal surfaces

    NASA Astrophysics Data System (ADS)

    Wang, Jun; Li, Qing; Fuentes-Cabrera, Miguel; Sumpter, Bobby G.; Baddorf, Arthur P.; Pan, Minghu

    2014-03-01

    The self-assembly of ``magic'' molecular clusters on various substrates provides a new arena for studies of surface nanocatalysis and molecular electronics. Here we present the self-assembly of phenylacetylene molecules on Cu(100) by a combined low-temperature STM and in-depth density functional theory investigation. We observe the molecules form distinct tetramer clusters on Cu(100) at 40 K. Each cluster has a four-fold symmetry and consists of four molecules. A delicate balance of intramolecular and dipole-dipole interactions between clusters maintains this magic tetramer configuration on Cu(100). The strong interaction between the molecules and the copper surface creates an anchor at each adsorption site. Through comparison with our previous observed hexamer (six-molecule) clusters on Au(111), we conclude that the epitaxial relationship between the molecules and metal surfaces is crucial in defining magic numbers of surface-supported molecular clusters under weak intermolecular interaction. This research was conducted at the Center for Nanophase Materials Sciences, which is sponsored at Oak Ridge National Laboratory by the Scientific User Facilities Division, Office of Basic Energy Sciences, U.S. Department of Energy.

  15. 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.

  16. Self-assembly and molecular packing in cholesteryl esters at interfaces

    NASA Astrophysics Data System (ADS)

    Sarkar, Arup; Suresh, K. A.

    2017-06-01

    To understand the self-assembly and molecular packing in cholesteryl esters relevant to biological processes, we have studied them at the air-water and air-solid interfaces. Our phase and thickness studies employing imaging ellipsometry and atomic force microscopy along with surface manometry show that the molecular packing of cholesteryl esters at interfaces can be related to Craven's model of packing, given for bulk. At the air-water interface, following Craven's model, cholesteryl nonanoate and cholesteryl laurate exhibit a fluidic bilayer phase. Interestingly, we find the fluidic bilayer phase of cholesteryl laurate to be unstable and it switches to a crystalline bilayer phase. However, according to Craven, only cholesteryl esters with longer chain lengths starting from cholesteryl tridecanoate should show the crystalline bilayer phase. The thickness behavior of different phases was also studied by transferring the films onto a silicon substrate by using the Langmuir-Blodgett technique. Texture studies show that cholesterol, cholesteryl acetate, cholesteryl nonanoate, cholesteryl laurate, and cholesteryl myristate exhibit homogeneous films with large size domains, whereas cholesteryl palmitate and cholesteryl stearate exhibit less homogeneous films with smaller size domains. We suggest that such an assembly of molecules can be related to their molecular structures. Simulation studies may confirm such a relation.

  17. 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.

  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. 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

  20. 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.

  1. 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

  2. Scattering properties of gas molecules on self-assembled monolayers using molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Takeuchi, Hideki

    2016-11-01

    The scattering properties of argon gas molecules on the SAM (self-assembled monolayer) surface which consists of 1-propanethiol molecules chemically adsorbed on a gold surface have been investigated by using the molecular dynamics method. The trapping probability, the angular distribution and the angular scattering distribution for the gas molecule have been obtained for various incident energies and angles. It is shown that the trapping probability decreases with increasing the incident energy. The angular distribution for small incident angle is almost close to the cosine distribution. In addition, the partial accommodation coefficients of tangential momentum and energy for gas molecules are discussed.

  3. 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

  4. 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.

  5. 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.

  6. Analysis of Molecular Orientation in Organic Semiconducting Thin Films Using Static Dynamic Nuclear Polarization Enhanced Solid-State NMR.

    PubMed

    Suzuki, Katsuaki; Kubo, Shosei; Aussenac, Fabien; Engelke, Frank; Fukushima, Tatsuya; Kaji, Hironori

    2017-10-09

    Molecular orientation in amorphous organic semiconducting thin film devices is an important issue affecting device performances. However, to date it has not been possible to analyze the "distribution" of the orientations. Although solid-state NMR (ssNMR) can provide information on the distribution of molecular orientations, the technique is limited because of the small amounts of sample in the devices and the low sensitivity of ssNMR. Here, we report the first application of dynamic nuclear polarization enhanced ssNMR (DNP-ssNMR) to orientational analysis of amorphous phenyldi(pyren-1-yl)phosphine oxide (POPy2). The 31P DNP-ssNMR spectra exhibited a sufficient signal-to-noise ratio to quantify the distribution of molecular orientations in amorphous films: the P=O axis of the vacuum-deposited and drop-cast POPy2 shows anisotropic and isotropic distribution, respectively. The different molecular orientations reflect the molecular origin of the different charge transport behaviors. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. 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

  8. 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.

  9. 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.

  10. Chain Flexibility in Self-Assembled Monolayers Affects Protein Adsorption and Surface Hydration: A Molecular Dynamics Study.

    PubMed

    Beckner, Wesley; He, Yi; Pfaendtner, Jim

    2016-10-04

    Recent developments in the antifouling properties of Self-Assembled Monolayers (SAMs) have largely focused on increasing the enthalpic association of a hydration layer along the interface of those surfaces with water. However, an entropic penalty due to chain restriction also disfavors biomolecule-surface adsorption. To isolate the effect of this entropic penalty amid changing packing densities, molecular dynamics simulations of explicitly solvated systems of lysozyme and seven monomer length oligo (ethylene glycol) (OEG) SAMs were performed. SAM surfaces were constructed at 100%, 74%, and 53% of a maximum packing (MP) density of 4.97 Å interchain spacing and the effect of chain flexibility was isolated by selectively freezing chain monomers. The rate of protein adsorption as well as the conformation and orientation of the protein upon adsorption were examined. It was found that chain spacing was a strong determinant in adsorption properties while chain flexibility played a secondary role. Of the three packing densities, 74% of MP was the most antifouling with increased antifouling behavior at moderate chain flexibility, i.e. two to four free monomer groups.

  11. Molecular organization of histidine-tagged biomolecules at self-assembled lipid interfaces using a novel class of chelator lipids.

    PubMed

    Dietrich, C; Schmitt, L; Tampé, R

    1995-09-26

    In molecular biology, the expression of fusion proteins is a very useful and well-established technique for the identification and one-step purification of gene products. Even a short fused sequence of five or six histidines enables proteins to bind to an immobilized metal ion chelate complex. By synthesis of a class of chelator lipids, we have transferred this approach to the concept of self-assembly. The specific interaction and lateral organization of a fluorescent fusion molecule containing a C-terminal oligohistidine sequence was studied by film balance techniques in combination with epifluorescence microscopy. Due to the phase behavior of the various lipid mixtures used, the chelator lipids can be laterally structured, generating two-dimensional arrays of histidine-tagged biomolecules. Because of the large variety of fusion proteins already available, this concept represents a powerful technique for orientation and organization of proteins at lipid interfaces with applications in biosensing, biofunctionalization of nanostructured interfaces, two-dimensional crystallization, and studies of lipid-anchored proteins.

  12. Molecular Organization of Histidine-Tagged Biomolecules at Self-Assembled Lipid Interfaces Using a Novel Class of Chelator Lipids

    NASA Astrophysics Data System (ADS)

    Dietrich, Christian; Schmitt, Lutz; Tampe, Robert

    1995-09-01

    In molecular biology, the expression of fusion proteins is a very useful and well-established technique for the identification and one-step purification of gene products. Even a short fused sequence of five or six histidines enables proteins to bind to an immobilized metal ion chelate complex. By synthesis of a class of chelator lipids, we have transferred this approach to the concept of self-assembly. The specific interaction and lateral organization of a fluorescent fusion molecule containing a C-terminal oligohistidine sequence was studied by film balance techniques in combination with epifluorescence microscopy. Due to the phase behavior of the various lipid mixtures used, the chelator lipids can be laterally structured, generating two-dimensional arrays of histidine-tagged biomolecules. Because of the large variety of fusion proteins already available, this concept represents a powerful technique for orientation and organization of proteins at lipid interfaces with applications in biosensing, biofunctionalization of nanostructured interfaces, two-dimensional crystallization, and studies of lipid-anchored proteins.

  13. 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.

  14. 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.

  15. 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.

  16. 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

  17. 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.

  18. Localization and orientation of heavy-atom cluster compounds in protein crystals using molecular replacement.

    PubMed

    Dahms, Sven O; Kuester, Miriam; Streb, Carsten; Roth, Christian; Sträter, Norbert; Than, Manuel E

    2013-02-01

    Heavy-atom clusters (HA clusters) containing a large number of specifically arranged electron-dense scatterers are especially useful for experimental phase determination of large complex structures, weakly diffracting crystals or structures with large unit cells. Often, the determination of the exact orientation of the HA cluster and hence of the individual heavy-atom positions proves to be the critical step in successful phasing and subsequent structure solution. Here, it is demonstrated that molecular replacement (MR) with either anomalous or isomorphous differences is a useful strategy for the correct placement of HA cluster compounds. The polyoxometallate cluster hexasodium α-metatungstate (HMT) was applied in phasing the structure of death receptor 6. Even though the HA cluster is bound in alternate partially occupied orientations and is located at a special position, its correct localization and orientation could be determined at resolutions as low as 4.9 Å. The broad applicability of this approach was demonstrated for five different derivative crystals that included the compounds tantalum tetradecabromide and trisodium phosphotungstate in addition to HMT. The correct placement of the HA cluster depends on the length of the intramolecular vectors chosen for MR, such that both a larger cluster size and the optimal choice of the wavelength used for anomalous data collection strongly affect the outcome.

  19. 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.

  20. Efficient assembly of threaded molecular machines for sequence-specific synthesis.

    PubMed

    De Bo, Guillaume; Kuschel, Sonja; Leigh, David A; Lewandowski, Bartosz; Papmeyer, Marcus; Ward, John W

    2014-04-16

    We report on an improved strategy for the preparation of artificial molecular machines that can pick up and assemble reactive groups in sequence by traveling along a track. In the new approach a preformed rotaxane synthon is attached to the end of an otherwise fully formed strand of building blocks. This "rotaxane-capping" protocol is significantly more efficient than the "final-step-threading" method employed previously and enables the synthesis of threaded molecular machines that operate on extended oligomer, and potentially polymer, tracks. The methodology is exemplified through the preparation of a machine that adds four amino acid building blocks from a strand in sequence, featuring up to 20-membered ring native chemical ligation transition states.

  1. 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

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

    DOE PAGES

    Tsai, Hsin-Zon; Omrani, Arash A.; Coh, Sinisa; ...

    2015-10-20

    Here we report a scanning tunneling microscopy and noncontact atomic force microscopy study of close-packed 2D islands of tetrafluoro-tetracyanoquinodimethane (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, themore » local work function increases, causing electrons to flow into the coalescing molecular island and increase its cohesive binding energy.« less

  3. 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.

  4. 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

  5. Impact of interfacial molecular orientation on radiative recombination and charge generation efficiency

    DOE PAGES

    Ran, Niva A.; Roland, Steffen; Love, John A.; ...

    2017-07-19

    Here, a long standing question in organic electronics concerns the effects of molecular orientation at donor/acceptor heterojunctions. Given a well-controlled donor/acceptor bilayer system, we uncover the genuine effects of molecular orientation on charge generation and recombination. These effects are studied through the point of view of photovoltaics—however, the results have important implications on the operation of all optoelectronic devices with donor/acceptor interfaces, such as light emitting diodes and photodetectors. Our findings can be summarized by two points. First, devices with donor molecules face-on to the acceptor interface have a higher charge transfer state energy and less non-radiative recombination, resulting inmore » larger open-circuit voltages and higher radiative efficiencies. Second, devices with donor molecules edge-on to the acceptor interface are more efficient at charge generation, attributed to smaller electronic coupling between the charge transfer states and the ground state, and lower activation energy for charge generation.« less

  6. Optical birefringence and molecular orientation of crazed fibres utilizing the phase shifting interferometric technique

    NASA Astrophysics Data System (ADS)

    Sokkar, T. Z. N.; El-Farahaty, K. A.; El-Bakary, M. A.; Omar, E. Z.; Hamza, A. A.

    2017-09-01

    In this article, the features of the phase shifting interferometric technique were utilized to investigate the effect of the presence of crazes in both outer and inner layers on optical birefringence and molecular orientation of polypropylene fibres. The Pluta polarizing interference microscope was used as a phase shifting technique. This method includes adding a stepper motor with a control unit to the micrometer screw of the Pluta microscope. This optical system was calibrated to be used as a phase shifting interferometric technique. The advantage of this technique is that it can detect the crazes in both inner and outer layers of the sample under test. Via this method, the relation between the presence of the crazes (in both inner and outer layers) and the optical molecular orientation of polypropylene (PP) fibres was demonstrated. To clarify the role of this method, the spatial carrier frequency technique was used to show the effect of the presence of the crazes only in the outer layers on the phase distribution values and hence the structural properties of PP fibres.

  7. The Exploitation of Versatile Building Blocks for the Self-Assembly of Novel Molecular Magnets

    NASA Astrophysics Data System (ADS)

    Pilkington, M.; Gross, M.; Franz, P.; Biner, M.; Decurtins, S.; Stoeckli-Evans, H.; Neels, A.

    2001-07-01

    Using molecular building blocks to self-assemble lattices supporting long-range magnetic order is currently an active area of solid-state chemistry. Consequently, it is the realm of supramolecular chemistry that synthetic chemists are turning to in order to develop techniques for the synthesis of structurally well-defined supramolecular materials. In recent years we have investigated the versatility and usefulness of two classes of molecular building blocks, namely, tris-oxalato transition-metal (M. Pilkington and S. Decurtins, in "Magnetoscience-From Molecules to Materials," Wiley-VCH, 2000), and octacyanometalate complexes (Pilkington and Decurtins, Chimia 54, 593 (2001)), for applications in the field of molecule-based magnets. Anionic, tris-chelated oxalato building blocks are able to build up two-dimensional honeycomb-layered structural motifs as well as three-dimensional decagon frameworks. The discrimination between the crystallization of the two- or three-dimensional structures relies on the choice of the templating counterions (Decurtins, Chimia 52, 539 (1998); Decurtins et al. Mol. Cryst. Liq. Cryst. 273, 167 (1995); New J. Chem. 117 (1998)). These structural types display a range of ferro, ferri, and antiferromagnetic properties (Pilkington and Decurtins, in "Magnetoscience-From Molecules to Materials"). Octacyanometalate building blocks self-assemble to afford two new classes of cyano-bridged compounds namely, molecular clusters and extended three dimensional networks (J. Larionova et al., Angew. Chem. Int. Ed. 39, 1605 (2000); Pilkington et al., in preparation). The molecular cluster with a MnII9MoV6 core has the highest ground state spin value, S=51/2, reported to-date (Larionova et al., Angew. Chem. Int. Ed. 39, 1605 (2000)). In the high-temperature regime, the magnetic properties are characterized by ferromagnetic intracluster coupling. In the magnetic range below 44 K, the magnetic cluster signature is lost as possibly a bulk behavior starts to

  8. 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

  9. Vertebrate Presynaptic Active Zone Assembly: a Role Accomplished by Diverse Molecular and Cellular Mechanisms.

    PubMed

    Torres, Viviana I; Inestrosa, Nibaldo C

    2017-07-06

    Among all the biological systems in vertebrates, the central nervous system (CNS) is the most complex, and its function depends on specialized contacts among neurons called synapses. The assembly and organization of synapses must be exquisitely regulated for a normal brain function and network activity. There has been a tremendous effort in recent decades to understand the molecular and cellular mechanisms participating in the formation of new synapses and their organization, maintenance, and regulation. At the vertebrate presynapses, proteins such as Piccolo, Bassoon, RIM, RIM-BPs, CAST/ELKS, liprin-α, and Munc13 are constant residents and participate in multiple and dynamic interactions with other regulatory proteins, which define network activity and normal brain function. Here, we review the function of these active zone (AZ) proteins and diverse factors involved in AZ assembly and maintenance, with an emphasis on axonal trafficking of precursor vesicles, protein homo- and hetero-oligomeric interactions as a mechanism of AZ trapping and stabilization, and the role of F-actin in presynaptic assembly and its modulation by Wnt signaling.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. Molecularly mediated thin film assembly of nanoparticles on flexible devices: electrical conductivity versus device strains in different gas/vapor environment.

    PubMed

    Yin, Jun; Hu, Peipei; Luo, Jin; Wang, Lingyan; Cohen, Melissa F; Zhong, Chuan-Jian

    2011-08-23

    The ability to precisely control nanoparticle-enabled electrical devices for applications involving conformal wrapping/bending adaptability in various complex sensing environments requires an understanding of the electrical correlation with the device strain and exposure to the molecular environment. This report describes novel findings of an investigation of molecularly mediated thin film assembly of gold nanoparticles on flexible chemiresistor devices under different device strains and exposure molecules. Both theoretical and experimental data have revealed that the electrical conductivity of the nanoparticle assembly depends on a combination of the device strain and the exposure molecules. Under no device strain, the electrical conductivity is sensitive to the molecular nature in the exposure environment, revealing a clear increase in electrical conductivity with the dielectric constant of vapor molecules. Under small device strains, the electrical conductivity is shown to respond sensitively to the strain directions (tensile vs compressive strain) and also to the dielectric constant of the vapor molecules in a way resembling the characteristic under no device strain. Under large device strains, the electrical conductivity is shown to respond to the difference in dielectric constant of the vapor molecules but, more significantly, to the device tensile and compressive strains than those under small device strains. This combination of device strain and dielectric characteristic is also dependent on the orientation of the microelectrode patterns with respect to the device strain direction, a finding that has important implications to the design of flexible arrays for a complex sensing environment. © 2011 American Chemical Society

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

    PubMed

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

    2011-03-28

    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

  16. 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

  17. 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.

  18. 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.

  19. Molecular mechanisms of kinesin-14 motors in spindle assembly and chromosome segregation.

    PubMed

    She, Zhen-Yu; Yang, Wan-Xi

    2017-07-01

    During eukaryote cell division, molecular motors are crucial regulators of microtubule organization, spindle assembly, chromosome segregation and intracellular transport. The kinesin-14 motors are evolutionarily conserved minus-end-directed kinesin motors that occur in diverse organisms from simple yeasts to higher eukaryotes. Members of the kinesin-14 motor family can bind to, crosslink or slide microtubules and, thus, regulate microtubule organization and spindle assembly. In this Commentary, we present the common subthemes that have emerged from studies of the molecular kinetics and mechanics of kinesin-14 motors, particularly with regard to their non-processive movement, their ability to crosslink microtubules and interact with the minus- and plus-ends of microtubules, and with microtubule-organizing center proteins. In particular, counteracting forces between minus-end-directed kinesin-14 and plus-end-directed kinesin-5 motors have recently been implicated in the regulation of microtubule nucleation. We also discuss recent progress in our current understanding of the multiple and fundamental functions that kinesin-14 motors family members have in important aspects of cell division, including the spindle pole, spindle organization and chromosome segregation. © 2017. Published by The Company of Biologists Ltd.

  20. Peptides as new smart bionanomaterials: molecular-recognition and self-assembly capabilities.

    PubMed

    Sawada, Toshiki; Mihara, Hisakazu; Serizawa, Takeshi

    2013-04-01

    Biomolecules express exquisite properties that are required for molecular recognition and self-assembly on the nanoscale. These smart capabilities have developed through evolution and such biomolecules operate based on smart functions in natural systems. Recently, these remarkable smart capabilities have been utilized in not only biologically related fields, but also in materials science and engineering. A peptide-screening technology that uses phage-display systems has been developed based on this natural smart evolution for the generation of new functional peptide bionanomaterials. We focused on peptides that specifically bound to synthetic polymers. These polymer-binding peptides were screened by using a phage-display peptide library to recognize nanostructures that were derived from polymeric structural features and were utilized for possible applications as new bionanomaterials. We also focused on self-assembling peptides with β-sheet structures that formed nanoscale, fibrous structures for applications in new bottom-up nanomaterials. Moreover, nanofiber-binding peptides were also screened to introduce the desired functionalities into nanofibers without the need for additional molecular design. Our approach to construct new bionanomaterials that employ peptides will open up excellent opportunities for the next generation of materials science and technology. Copyright © 2013 The Chemical Society of Japan and Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. 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.

  2. 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.

  3. Recruitment, Assembly, and Molecular Architecture of the SpoIIIE DNA Pump Revealed by Superresolution Microscopy

    PubMed Central

    Fiche, Jean-Bernard; Cattoni, Diego I.; Diekmann, Nele; Langerak, Julio Mateos; Clerte, Caroline; Royer, Catherine A.; Margeat, Emmanuel; Doan, Thierry; Nöllmann, Marcelo

    2013-01-01

    ATP-fuelled molecular motors are responsible for rapid and specific transfer of double-stranded DNA during several fundamental processes, such as cell division, sporulation, bacterial conjugation, and viral DNA transport. A dramatic example of intercompartmental DNA transfer occurs during sporulation in Bacillus subtilis, in which two-thirds of a chromosome is transported across a division septum by the SpoIIIE ATPase. Here, we use photo-activated localization microscopy, structured illumination microscopy, and fluorescence fluctuation microscopy to investigate the mechanism of recruitment and assembly of the SpoIIIE pump and the molecular architecture of the DNA translocation complex. We find that SpoIIIE assembles into ∼45 nm complexes that are recruited to nascent sites of septation, and are subsequently escorted by the constriction machinery to the center of sporulation and division septa. SpoIIIE complexes contain 47±20 SpoIIIE molecules, a majority of which are assembled into hexamers. Finally, we show that directional DNA translocation leads to the establishment of a compartment-specific, asymmetric complex that exports DNA. Our data are inconsistent with the notion that SpoIIIE forms paired DNA conducting channels across fused membranes. Rather, our results support a model in which DNA translocation occurs through an aqueous DNA-conducting pore that could be structurally maintained by the divisional machinery, with SpoIIIE acting as a checkpoint preventing membrane fusion until completion of chromosome segregation. Our findings and proposed mechanism, and our unique combination of innovating methodologies, are relevant to the understanding of bacterial cell division, and may illuminate the mechanisms of other complex machineries involved in DNA conjugation and protein transport across membranes. PMID:23667326

  4. Molecular Details of the Yeast Frataxin-Isu1 Interaction during Mitochondrial Fe-S Cluster Assembly

    SciTech Connect

    Cook, J.; Kondapalli, K; Rawat, S; Childs, W; Murugesan, Y; Dancis, A; Stemmler, T

    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 in the assembly pathway. Here we provide molecular details of how yeast frataxin (Yfh1) interacts with Isu1 as a structural module to improve our understanding of 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. 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 an 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.

  5. 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

  6. Transcriptome survey of Patagonian southern beech Nothofagus nervosa (= N. Alpina): assembly, annotation and molecular marker discovery.

    PubMed

    Torales, Susana L; Rivarola, Máximo; Pomponio, María F; Fernández, Paula; Acuña, Cintia V; Marchelli, Paula; Gonzalez, Sergio; Azpilicueta, María M; Hopp, Horacio Esteban; Gallo, Leonardo A; Paniego, Norma B; Poltri, Susana N Marcucci

    2012-07-02

    Nothofagus nervosa is one of the most emblematic native tree species of Patagonian temperate forests. Here, the shotgun RNA-sequencing (RNA-Seq) of the transcriptome of N. nervosa, including de novo assembly, functional annotation, and in silico discovery of potential molecular markers to support population and associations genetic studies, are described. Pyrosequencing of a young leaf cDNA library generated a total of 111,814 high quality reads, with an average length of 447 bp. De novo assembly using Newbler resulted into 3,005 tentative isotigs (including alternative transcripts). The non-assembled sequences (singletons) were clustered with CD-HIT-454 to identify natural and artificial duplicates from pyrosequencing reads, leading to 21,881 unique singletons. 15,497 out of 24,886 non-redundant sequences or unigenes, were successfully annotated against a plant protein database. A substantial number of simple sequence repeat markers (SSRs) were discovered in the assembled and annotated sequences. More than 40% of the SSR sequences were inside ORF sequences. To confirm the validity of these predicted markers, a subset of 73 SSRs selected through functional annotation evidences were successfully amplified from six seedlings DNA samples, being 14 polymorphic. This paper is the first report that shows a highly precise representation of the mRNAs diversity present in young leaves of a native South American tree, N. nervosa, as well as its in silico deduced putative functionality. The reported Nothofagus transcriptome sequences represent a unique resource for genetic studies and provide a tool to discover genes of interest and genetic markers that will greatly aid questions involving evolution, ecology, and conservation using genetic and genomic approaches in the genus.

  7. Transcriptome survey of Patagonian southern beech Nothofagus nervosa (= N. Alpina): assembly, annotation and molecular marker discovery

    PubMed Central

    2012-01-01

    Background Nothofagus nervosa is one of the most emblematic native tree species of Patagonian temperate forests. Here, the shotgun RNA-sequencing (RNA-Seq) of the transcriptome of N. nervosa, including de novo assembly, functional annotation, and in silico discovery of potential molecular markers to support population and associations genetic studies, are described. Results Pyrosequencing of a young leaf cDNA library generated a total of 111,814 high quality reads, with an average length of 447 bp. De novo assembly using Newbler resulted into 3,005 tentative isotigs (including alternative transcripts). The non-assembled sequences (singletons) were clustered with CD-HIT-454 to identify natural and artificial duplicates from pyrosequencing reads, leading to 21,881 unique singletons. 15,497 out of 24,886 non-redundant sequences or unigenes, were successfully annotated against a plant protein database. A substantial number of simple sequence repeat markers (SSRs) were discovered in the assembled and annotated sequences. More than 40% of the SSR sequences were inside ORF sequences. To confirm the validity of these predicted markers, a subset of 73 SSRs selected through functional annotation evidences were successfully amplified from six seedlings DNA samples, being 14 polymorphic. Conclusions This paper is the first report that shows a highly precise representation of the mRNAs diversity present in young leaves of a native South American tree, N. nervosa, as well as its in silico deduced putative functionality. The reported Nothofagus transcriptome sequences represent a unique resource for genetic studies and provide a tool to discover genes of interest and genetic markers that will greatly aid questions involving evolution, ecology, and conservation using genetic and genomic approaches in the genus. PMID:22747958

  8. 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

  9. 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.

  10. Pattern dimensions and feature shapes of ternary blends of block copolymer and low molecular weight homopolymers directed to assemble on chemically nanopatterned surfaces.

    PubMed

    Nagpal, Umang; Kang, Huiman; Craig, Gordon S W; Nealey, Paul F; de Pablo, Juan J

    2011-07-26

    Ternary blends of cylinder-forming polystyrene-block-poly(methyl methacrylate) (PS-b-PMMA) and low molecular weight PS and PMMA were directed to assemble on chemically patterned surfaces with hexagonal symmetry. The chemical patterns consisted of strongly PMMA preferential spots, patterned by electron-beam lithography, in a matrix of PS. The spot-to-spot spacing of the chemical patterns (L(s)) was varied between 0.9L(0) and 1.1L(0), where L(0) is the cylinder-to-cylinder spacing of the pure block copolymer in bulk. The homopolymer volume fraction of the blends (ϕ(H)) was varied between 0 and 0.3. In addition, chemical patterns were formed with selected spots missing from the perfect hexagonal array, such that the interpolation of domains between patterned spots could be examined on patterns where the polymer/pattern feature density ranged from 1:1 to 4:1. The assemblies were analyzed with top-down SEM, from which orientational order parameter (OP(o)) values were determined. The SEM analysis was complemented by Monte Carlo simulations, which offered insights into the shapes of the assembled cylindrical domains. It was found that, in comparison to pure block copolymer, adding homopolymer increased the range of L(s) values over which assemblies with high OP(o) values could be achieved for 1:1 assemblies. However, the corresponding simulations showed that in the 1:1 assemblies the shape of the cylinders was more uniform for pure block copolymer than for blends. In the case of the 4:1 assemblies, the range of L(s) values over which assemblies with high OP(o) values could be achieved was the same for all values of ϕ(H) tested, but the domains of the pure block copolymer had a more uniform shape. Overall, the results provided insights into the blend composition to be used to meet technological requirements for directed assembly with density multiplication.

  11. Dragline silk: a fiber assembled with low-molecular-weight cysteine-rich proteins.

    PubMed

    Pham, Thanh; Chuang, Tyler; Lin, Albert; Joo, Hyun; Tsai, Jerry; Crawford, Taylor; Zhao, Liang; Williams, Caroline; Hsia, Yang; Vierra, Craig

    2014-11-10

    Dragline silk has been proposed to contain two main protein constituents, MaSp1 and MaSp2. However, the mechanical properties of synthetic spider silks spun from recombinant MaSp1 and MaSp2 proteins have yet to approach natural fibers, implying the natural spinning dope is missing critical factors. Here we report the discovery of novel molecular constituents within the spinning dope that are extruded into dragline silk. Protein studies of the liquid spinning dope from the major ampullate gland, coupled with the analysis of dragline silk fibers using mass spectrometry, demonstrate the presence of a new family of low-molecular-weight cysteine-rich proteins (CRPs) that colocalize with the MA fibroins. Expression of the CRP family members is linked to dragline silk production, specifically MaSp1 and MaSp2 mRNA synthesis. Biochemical data support that CRP molecules are secreted into the spinning dope and assembled into macromolecular complexes via disulfide bond linkages. Sequence analysis supports that CRP molecules share similarities to members that belong to the cystine slipknot superfamily, suggesting that these factors may have evolved to increase fiber toughness by serving as molecular hubs that dissipate large amounts of energy under stress. Collectively, our findings provide molecular details about the components of dragline silk, providing new insight that will advance materials development of synthetic spider silk for industrial applications.

  12. 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

  13. 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.

  14. 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

  15. Unoccupied electronic structure and molecular orientation of rubrene; from evaporated films to single crystals

    NASA Astrophysics Data System (ADS)

    Ueba, T.; Park, J.; Terawaki, R.; Watanabe, Y.; Yamada, T.; Munakata, T.

    2016-07-01

    Two-photon photoemission (2PPE) spectroscopy and ultraviolet photoemission spectroscopy (UPS) have been performed for rubrene single crystals and evaporated thin films on highly oriented pyrolytic graphite (HOPG). The changes in the 2PPE intensity from the single crystals by the polarization of the light and by the angle of the light incident plane against the crystalline axes indicate that the molecular arrangement on the surface is similar to that in the bulk crystal. On the other hand, in the case of evaporated films, the polarization dependence of 2PPE indicates that the tetracene backbone becomes standing upright as the thickness increases. In spite of the alignment of molecules, the broadened 2PPE spectral features for thick films suggest that the films are amorphous and molecules are in largely different environments. The film structures are confirmed by scanning tunneling microscopy (STM). The highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) derived levels of the single crystal are shifted by + 0.18 and - 0.20 eV, respectively, from those of the 0.8 ML film. The shifts are attributed to the packing density of molecules. It is shown that the unoccupied electronic structure is more sensitively affected by the film structure than the occupied electronic structure.

  16. 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

  17. 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.

  18. 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

  19. 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.

  20. 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.

  1. Micro-FTIR study of molecular orientation at crack tip in nylon 6/clay nanocomposite: insight into fracture mechanism.

    PubMed

    Xu, Wenfei; Lv, Ruihua; Na, Bing; Tian, Nana; Li, Zhujun; Fu, Qiang

    2009-07-23

    A study on the mechanism for the degraded toughness in nylon 6/clay nanocomposite is explored in this article. Such a nanocomposite exhibits lower specific essential work of fracture we and specific nonessential work of fracture betawp than its pure nylon 6 counterpart, as revealed by essential work of fracture (EWF) measurements. Furthermore, the molecular orientation in a small region (20x20 microm2) ahead of crack tip, obtained from micro-FTIR measurements for the first time, is found to be lower in the nanocomposite during crack initiation and propagation. The decreased molecular orientation, mostly resulted from severe microvoiding at crack tips, is responsible for the reduced specific essential work of fracture we. Meanwhile, the molecular orientation around crack tip also indicates that lower plastic deformation occurs in the plastic zone, which is well correlated with decreased specific nonessential work of fracture betawp in the nanocomposite.

  2. Enhanced Raman sca