Bulletin of the American Physical Society
2007 APS March Meeting
Volume 52, Number 1
Monday–Friday, March 5–9, 2007; Denver, Colorado
Session P42: Focus Session: Biological and Chemical Self-Assembly at Surfaces |
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Sponsoring Units: DMP Chair: Kalyanaraman Ramki, Washington University in St. Louis Room: Colorado Convention Center 505 |
Wednesday, March 7, 2007 11:15AM - 11:51AM |
P42.00001: Directing the assembly of nanostructured films with living cells Invited Speaker: This talk describes our recent discovery of the ability of living cells to organize extended nanostructures and nano-objects in a manner that creates a unique, highly biocompatible nano//bio interface (\textit{Science} \textbf{313}, 337-340, 2006). We find that, using short chain phospholipids to direct the formation of thin film silica mesophases during evaporation-induced self-assembly, the introduction of cells (so far yeast and bacteria) alters profoundly the inorganic self-assembly pathway. Cells actively organize around themselves an ordered, multilayered lipid-membrane that interfaces coherently with a lipid-templated silica mesophase. This bio/nano interface is unique in that it withstands drying (even evacuation) without cracking or the development of tensile stresses -- yet it maintains accessibility to molecules, proteins/antibodies, plasmids, etc - introduced into the 3D silica host. Additionally cell viability is preserved for weeks to months in the absence of buffer, making these constructs useful as standalone cell-based sensors. The bio/nano interfaces we describe do not form `passively' -- rather they are a consequence of the cell's ability to sense and actively respond to external stimuli. During \textit{EISA}, solvent evaporation concentrates the extracellular environment in osmolytes. In response to this hyperosmotic stress, the cells release water, creating a gradient in pH, which is maintained within the adjoining nanostructured host and serves to localize lipids, proteins, plasmids, lipidized nanocrystals, and a variety of other components at the cellular surface. This active organization of the bio/nano interface can be accomplished during ink-jet printing or selective wetting -- processes allowing patterning of cellular arrays - and even spatially-defined genetic modification. [Preview Abstract] |
Wednesday, March 7, 2007 11:51AM - 12:03PM |
P42.00002: ABSTRACT WITHDRAWN |
Wednesday, March 7, 2007 12:03PM - 12:15PM |
P42.00003: STM studies of the molecular-level organization of chiral tartaric acid domains on Ag(111) Nancy Santagata, Amit Lakhani, Darryl DeWitt, Thomas Pearl The expression of chirality in molecular domains on surfaces has important implications for enantioselective catalysis and chemically tuned thin films. In this talk we will discuss the organizational structure of a chiral molecule, tartaric acid (C4H6O6), weakly bound to an achiral metal surface, Ag(111), as studied with low temperature scanning tunneling microscopy (STM). Molecularly resolved images of both (R, R)- and (S, S)- tartaric acid on Ag(111) will be presented, and the role of intermolecular hydrogen bonding in stereospecific domain and superlattice formation will be addressed. In addition, we will consider chiral domain formation and phase separation from a racemic mixture of both tartaric acid enantiomers. Finally, we will present data that indicates a proposed multilayer structure and discuss the growth mode associated with its formation. [Preview Abstract] |
Wednesday, March 7, 2007 12:15PM - 12:27PM |
P42.00004: Inter- and intramolecular dispersion in a highly ordered organic molecular crystal. Stephen Berkebile, Peter Puschnig, Georg Koller, Falko P. Netzer, Michael G. Ramsey The inter- and intramolecular dispersion in organic molecular crystals have been predicted by theory, but never measured to a satisfying degree. Further, organic pi-conjugated molecules, as they are intrinsically one-dimensional objects with a well-defined number of repeating units, serve as a simple model for understanding what happens to the basic electronic structure in systems of limited size and low dimensions. Here, the band structure of a highly ordered and crystalline para-sexiphenyl (6P) film has been measured using angle-resolved photoemission spectroscopy (ARUPS) in the three directions important to charge transport in organic devices. The ARUPS behavior reveals both strong intermolecular dispersion perpendicular to the molecular axis and intramolecular dispersion along the axis of the molecules. The data will be shown to be in very good agreement with calculations in terms of the extent of the band dispersion, the ARUPS intensity and the k-spread of the peaks associated with quantum size effects. [Preview Abstract] |
Wednesday, March 7, 2007 12:27PM - 12:39PM |
P42.00005: Kinetics-driven growth mechanism of self-organized pentacene thin films Abdullah Al-Mahboob, Jerzy T. Sadowski, Yasunori Fujikawa, Kazuo Nakajima, Toshio Sakurai The growth kinetics of self-organized, highly ordered (001)-oriented pentacene (Pn) thin films was studied in situ by low-energy electron microscopy (LEEM) and complementary density functional theory calculations. We propose a model of `molecule incorporation-controlled' growth mechanism, according to which the attachment pathway at the island edge and the attachment energy of crystallization unit, rather than step or surface energies, determine the island shape in the kinetic growth of organic molecular thin film. We have found that experimentally observed growth anisotropy can be reproduced exactly by our model, if molecule attachment at island-edge is realized in the form of herringbone pair, for all low-indexed growth directions of Pn thin film. The observed kinetic anisotropy also results in a preference in Pn domain orientations, which tend to have the $<$01$>^{\ast }$ direction of the surface lattice aligned with the direction of the gradient density of supplied molecular flux. [Preview Abstract] |
Wednesday, March 7, 2007 12:39PM - 12:51PM |
P42.00006: Improved Molecular Dynamics simulations of hexane on graphite near monolayer completion M.W. Roth, M.J. Connolly, Carlos Wexler, Paul A. Gray We present the results of computer simulations of hexane on graphite near monolayer completion utilizing NAMD Scalable Molecular Dynamics in parallel computing environments. We include hydrogens explicitly on the hexane molecules, and the graphite substrate is represented as six all - atom graphene sheets. Results presented for temperatures between T = 100 K and T = 200 K have features which differ from those obtained using the united Atom (UA) model, where hydrogens are suppressed. Various structural and thermodynamic quantities show that the improvement obtained from explicitly including hydrogens come not only from their interaction with the substrate but also by their manipulation of in - plane space. [Preview Abstract] |
Wednesday, March 7, 2007 12:51PM - 1:03PM |
P42.00007: Nucleation and post-growth relaxation of tetracene thin films on silicon oxide. Jun Shi, X. R. Qin We demonstrate that layered morphology of tetracene films on silicon oxide can be achieved at room temperature via vacuum evaporation. Island size distribution analysis shows that tetracene nucleation in a high-flux growth regime is diffusion-mediated with a critical island size $i$ =3, similar to that in pentacene growth. A pronounced post-growth relaxation has been observed on a time scale of minutes. It is suggested that the high flux rate is crucial in the growth kinetics of forming the layered morphology and also important in overcoming the effect of post-growth relaxation which is sensitive to the film coverage and substrates. [Preview Abstract] |
Wednesday, March 7, 2007 1:03PM - 1:15PM |
P42.00008: Designing Self-assembled Nanostructures: Metal -- Organic Molecule Coordination Networks at Surfaces Steven L. Tait, A. Langner, N. Lin, S. Stepanow, C. Rajadurai, M. Ruben, K. Kern Networks of isolated metal atoms and organic ligands can be designed to self-assemble at surfaces in desired patterns, producing regular 2D nanopore lattices, whose dimensions and properties can be controlled by selection of the organic ligand. We constructed such a network by coordination of molecules containing pyridyl groups with the inherent adatom population on a Cu(100) surface at room temperature. We produced the same network on Ag(100) and Ag(111) by depositing Cu atoms with molecules, showing the network rigidity on different substrates. Rectangular networks with higher complexity were formed from two species of organic ligands with metal atom nodes. The nanopore size and aspect ratio can be tuned by independently selecting the two ligand species. Some properties of these designed nanostructures can be `tuned' by rational selection of the organic molecule and metal components. We have especially explored the adsorption of simple molecules on these networks, which may be of interest for future chemical or catalytic applications. The ability to tailor the size and functionality of nanometer-scale arrays produced by self assembly represents a unique opportunity for molecular recognition, heterogeneous catalysis, and other fields. [Preview Abstract] |
Wednesday, March 7, 2007 1:15PM - 1:27PM |
P42.00009: Real-Time Monitoring of Organic Thin Film Morphology by Organic Vapor Phase Deposition Richard R. Lunt, Jay B. Benziger, Stephen R. Forrest We demonstrate the real-time monitoring of the development of crystalline structure in the growth of films by organic vapor-phase deposition (OVPD) using high-pressure reflection high-energy electron diffraction (HP-RHEED). Through control of the probe electron beam energy, sample damage from impinging electrons was avoided and beam attenuation in the 8mTorr OVPD deposition environment was minimized. The growth of copper phthalocyanine (CuPc) on highly oriented pyrolytic graphite was used to demonstrate the ability of such \textit{in-situ} organic-growth monitoring, where it was observed that the first several monolayers formed ordered films independent of the substrate temperature and deposition rate, while the evolution of thicker films was strongly affected by substrate temperature. Higher temperatures resulted in greater in-plane crystalline ordering. We thereby have shown HP-RHEED to be a powerful tool for real-time monitoring of growth morphology, ultimately leading to \textit{in-situ} control of thin film crystalline order. [Preview Abstract] |
Wednesday, March 7, 2007 1:27PM - 1:39PM |
P42.00010: Characterizing the copper-based catalyst for the oxygen-assisted water-gas shift reaction at a sub-nano scale. Aloysius Soon, Mira Todorova, Catherine Stampfl, Bernard Delley To obtain insight into the structure and surface stoichiometry of copper-based catalysts in commercially important chemical reactions such as the oxygen-assisted water-gas shift reaction, we perform density-functional theory calculations to investigate the stability of oxide surfaces. Taking into account the pressure and temperature through the framework of \textit{ab initio} thermodynamics [1,2] our earlier investigation found that for the conditions relevant to technical catalysis, the bulk oxide is energetically most favourable. Using the same technique, we examine the relative stability of low-index copper oxide surfaces [3], and identify two low energy surface structures that are most stable under such conditions which could be catalytically relevant. These oxide surface structures are found to be non-stoichiometric (with surface defects) and exhibit a metallic character. \\ $[1]$ A. Soon, M. Todorova, B. Delley and C. Stampfl, \textit{Phys. Rev. B} \textbf{73}, 165424 (2006) \\ $[2]$ C. Stampfl, \textit{Catal. Today} \textbf{105}, 17 (2005). \\ $[3]$ A. Soon, M. Todorova, B. Delley and C. Stampfl, submitted to \textit{Phys. Rev. B}. [Preview Abstract] |
Wednesday, March 7, 2007 1:39PM - 1:51PM |
P42.00011: First-principles study of the self-organization mechanism of NH$_{3}$ on Si(001) Yong-Sung Kim, Hanchul Kim We have investigated the self-organization of NH$_{3}$ molecules on the Si(001) surface using the first-principles pseudopotential calculations. In order to find out the adsorption pathways and understand the mechanism of self-organization, we have calculated the potential energy surfaces of an incoming NH$_{3}$ molecule with one pre-adsorbed NH$_{3}$ molecule. Based on the results, we propose a kinetic process model of NH$_{3}$ self-organization: (i) the incoming molecules are attracted towards the pre-adsorbed molecules due to the H-bonding interaction. (ii) By forming the H-bond with the pre-adsorbed molecule, an incoming molecule can achieve physisorption states. (iii) Subsequently, the physisorbed NH$_{3}$ molecule is attracted to adjacent ``down'' Si atoms to complete the molecular adsorption process. (iv) Finally, the adsorbed NH$_{3}$ dissociates into NH$_{2}$ and H fragments. The resultant self-organized pattern is in accordance with recent STM experiments. However, it is in stark contrast with the energetically favored pattern that is characterized by H-bond formation between the dissociated fragments. This indicates that the self-organization of NH$_{3}$ on Si(001) is governed by the kinetics rather than the energetics. [Preview Abstract] |
Wednesday, March 7, 2007 1:51PM - 2:03PM |
P42.00012: Structure of tetracene films on hydrogen-passivated Si(001) studied via STM, AFM and NEXAFS Andrew Tersigni, Jun Shi, D. T. Jiang, X. R. Qin Scanning tunneling microscopy (STM), atomic force microscopy (AFM) and near-edge x-ray absorption fine structure (NEXAFS) have been used to study the structure of tetracene films on hydrogen-passivated Si(001). STM imaging of the films with nominal thickness of three monolayers (3 ML) exhibits the characteristic ``herringbone'' molecular packing known from the bulk crystalline tetracene, showing standing molecules on the \textit{ab}-plane. The dimensions and orientation of the herringbone lattice indicate a commensurate structural relationship between the lattice and the crystalline substrate. The corresponding AFM images illustrate that at and above the third layer of the films, the islands are anisotropic, in contrast with the submonolayer fractals, with two preferred growth directions appearing orthogonal to each other. The polarization dependent NEXAFS measurements indicate that the average molecular tilting angle with respect to the surface first increases with the film thickness up to 3 ML, then stabilizes at a value close to the bulk tetracene case afterwards. The combined results indicate a distinct growth morphological change that occurs around a few mononalyers of thickness. [Preview Abstract] |
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