Project

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Molecular self-assemblies, their metallic substrates, and quasicrystal surfaces: a computational approach

Applicant Passerone Daniele
Number 132375
Funding scheme Project funding (Div. I-III)
Research institution Eidg. Materialprüfungs- und Forschungsanstalt (EMPA)
Institution of higher education Swiss Federal Laboratories for Materials Science and Technology - EMPA
Main discipline Condensed Matter Physics
Start/End 01.10.2010 - 31.03.2012
Approved amount 106'312.00
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Keywords (7)

Simulation; Self-assembly; Molecular Dynamics; Surface science; nanostructures; metallic alloys; density functional theory

Lay Summary (English)

Lead
Lay summary
The project concerns the continuation of the following two projects:1.Computational study of the surfaces of quasicrystals (116130)2.Atomistic simulation of surface-supported molecular nanostructures (116073)Nanostructures. Molecular devices appear as very promising for future applications in electronics, optics, sensors, and functional surfaces. However, within a technological context, it is clear that the development of future functional organic/inorganic interfaces is critically dependent on establishing a fundamental understanding of the various bonding and lateral interactions that govern the ultimate orientation, conformation and two-dimensional organization of complex molecules at a surface. The most advanced experimental tools like scanning tunneling microscopy and spectroscopy, and x-ray photoelectron diffraction are often successful in investigating such structures. However, a theoretical basis for such beautiful experiments is often limited either by the complexity of the problem or by the lack of appropriate models for physical and chemical situations. The present project shall try to exemplify a strategy that adopts methods at different theory and length scale levels for a selected number of molecule/substrate systems. This strategy is based on the following points:1.Characterization of clean surfaces with classical and ab initio simulation using both density functional theory (DFT) based methods and appropriate force fields. 2.Choice and construction of interaction potentials for classical simulations.3.Modeling molecular adsorption. Identifying the kind of interactions involved with the help of quantum chemistry calculations on restricted systems.4. Developing force fields for the interaction of molecules with the substrate. Quasicrystals. Since their discovery, quasicrystals have been the object of an interesting experimental and theoretical debate. The O. Gröning group at EMPA recently investigated the valence electronic structure of QC, by means of scanning tunneling microscopy and spectroscopy (STM/STS) at low temperatures (5 K). These measures have revealed signatures of a spiky local density of states (LDOS) near the Fermi energy, exhibiting narrow peaks and pseudo-gaps of the order of 50 meV FWHM. Moreover, structural aspects involving surface free energy, friction, diffusion, surface reconstructions, are still largely non-understood at the theoretical level. This project proposes a novel and complete strategy for the computational attack of QC surfaces. It relies on existing methods for the classical simulation of alloys, and requires a continuous interplay with experimental and high level ab initio data.
Direct link to Lay Summary Last update: 21.02.2013

Responsible applicant and co-applicants

Employees

Publications

Publication
Self-Assembly and Two-Dimensional Spontaneous Resolution of Cyano-Functionalized [7]Helicenes on Cu(111)
Stohr M, Boz S, Schar M, Nguyen MT, Pignedoli CA, Passerone D, Schweizer WB, Thilgen C, Jung TA, Diederich F (2011), Self-Assembly and Two-Dimensional Spontaneous Resolution of Cyano-Functionalized [7]Helicenes on Cu(111), in ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 50(42), 9982-9986.
Supramolecular Engineering through Temperature-Induced Chemical Modification of 2H-Tetraphenylporphyrin on Ag(111): Flat Phenyl Conformation and Possible Dehydrogenation Reactions
Di Santo G, Blankenburg S, Castellarin-Cudia C, Fanetti M, Borghetti P, Sangaletti L, Floreano L, Verdini A, Magnano E, Bondino F, Pignedoli CA, Nguyen MT, Gaspari R, Passerone D, Goldoni A (2011), Supramolecular Engineering through Temperature-Induced Chemical Modification of 2H-Tetraphenylporphyrin on Ag(111): Flat Phenyl Conformation and Possible Dehydrogenation Reactions, in CHEMISTRY-A EUROPEAN JOURNAL, 17(51), 14354-14359.
s-orbital continuum model accounting for the tip shape in simulated scanning tunneling microscope images
Gaspari R, Blankenburg S, Pignedoli CA, Ruffieux P, Treier M, Fasel R, Passerone D (2011), s-orbital continuum model accounting for the tip shape in simulated scanning tunneling microscope images, in PHYSICAL REVIEW B, 84(12), 125417-125423.
Free energy calculations offer insights into the influence of receptor flexibility on ligand-receptor binding affinities
Dolenc J, Riniker S, Gaspari R, Daura X, van Gunsteren WF (2011), Free energy calculations offer insights into the influence of receptor flexibility on ligand-receptor binding affinities, in JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 25(8), 709-716.
An ab initio insight into the Cu(111)-mediated Ullmann reaction.
Nguyen Manh-Thuong, Pignedoli Carlo A, Passerone Daniele (2011), An ab initio insight into the Cu(111)-mediated Ullmann reaction., in Physical chemistry chemical physics : PCCP, 13(1), 154-60.
The role of van der Waals interactions in surface-supported supramolecular networks
Nguyen MT, Pignedoli CA, Treier M, Fasel R, Passerone D (2010), The role of van der Waals interactions in surface-supported supramolecular networks, in PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 12(4), 992-999.
Two-Dimensional Polymer Formation on Surfaces: Insight into the Roles of Precursor Mobility and Reactivity
Bieri M, Nguyen MT, Groning O, Cai JM, Treier M, Ait-Mansour K, Ruffieux P, Pignedoli CA, Passerone D, Kastler M, Mullen K, Fasel R (2010), Two-Dimensional Polymer Formation on Surfaces: Insight into the Roles of Precursor Mobility and Reactivity, in JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 132(46), 16669-16676.
Stability and dynamics of small molecules trapped on graphene
Erni R, Rossell MD, Nguyen MT, Blankenburg S, Passerone D (2010), Stability and dynamics of small molecules trapped on graphene, in PHYSICAL REVIEW B, 82(16), 165443-165448.
Atomistic insight into the adsorption site selectivity of stepped Au(111) surfaces
Gaspari R, Pignedoli CA, Fasel R, Treier M, Passerone D (2010), Atomistic insight into the adsorption site selectivity of stepped Au(111) surfaces, in PHYSICAL REVIEW B, 82(4), 041408-041411.
Tailoring Low-Dimensional Organic Semiconductor Nanostructures
Treier M, Nguyen MT, Richardson NV, Pignedoli C, Passerone D, Fasel R (2009), Tailoring Low-Dimensional Organic Semiconductor Nanostructures, in NANO LETTERS, 9(1), 126-131.

Awards

Title Year
Poster Prize Quasicrystal Conference Slovenia 2010

Associated projects

Number Title Start Funding scheme
116130 Computational study of the surfaces of quasicrystals 01.02.2008 Project funding (Div. I-III)
136287 Understanding nanofriction and dissipation across phase transitions 01.09.2011 Sinergia
140812 Applied nanoscience: novel catalysts and bottom-up design of graphene-like nanostructures. Computational insight within a surface science laboratory 01.09.2012 Project funding (Div. I-III)
116073 Atomistic simulations of surface-supported molecular nanostructures 01.10.2007 Project funding (Div. I-III)
128754 UP-IPAZIA: “UPgrade and full deployment of the Empa/Eawag computational cluster IPAZIA: towards an interdisciplinary on-site resource for computational sciences” 01.04.2010 R'EQUIP

Abstract

The present application concerns the continuation of the following two projects:1.Computational study of the surfaces of quasicrystals (116130)2.Atomistic simulation of surface-supported molecular nanostructures (116073)For each of these projects, the research is performed by a doctoral student in our group. For project 1, Roberto Gaspari with Michele Parrinello as ETHZ supervisor, and Manh Thuong Nguyen with Matthias Troyer as supervisor.As research advisor of them, I am extremely satisfied of both: although along different paths, both research projects are being crowned by success, and in both cases the scope of the results and of the research is so promising, that I consider worthwhile to ask for an one-year extension of the research period for both projects. Concerning project 1, a considerable amount of time was spent on a problem about metallic surfaces and reconstruction. Although this was away from complex metallic alloys and quasicrystals, the results were so promising that we decided to deepen the problem, slightly delaying the core of the proposal to a later time.Shortened abstract of the original projects.Nanostructures. Molecular devices appear as very promising for future applications in electronics, optics, sensors, and functional surfaces. However, within a technological context, it is clear that the development of future functional organic/inorganic interfaces is critically dependent on establishing a fundamental understanding of the various bonding and lateral interactions that govern the ultimate orientation, conformation and two-dimensional organization of complex molecules at a surface.The most advanced experimental tools like scanning tunneling microscopy and spectroscopy, and x-ray photoelectron diffraction are often successful in investigating such structures.However, a theoretical basis for such beautiful experiments is often limited either by the complexity of the problem or by the lack of appropriate models for physical and chemical situations. The present project shall try to exemplify a strategy that adopts methods at different theory and length scale levels for a selected number of molecule/substrate systems. This strategy is based on the following points:1.Characterization of clean surfaces with classical and ab initio simulation using both density functional theory (DFT) based methods and appropriate force fields. 2.Choice and construction of interaction potentials for classical simulations.3.Modeling molecular adsorption. Identifying the kind of interactions involved with the help of quantum chemistry calculations on restricted systems.4. Developing force fields for the interaction of molecules with the substrate. Quasicrystals. Since their discovery in 1984, quasicrystals (QC) have been the object of an interesting experimental and theoretical debate. The O. Gröning group at EMPA recently investigated the valence electronic structure of QC, by means of scanning tunneling microscopy and spectroscopy (STM/STS) at low temperatures (5 K). These measures have revealed signatures of a spiky local density of states (LDOS) near the Fermi energy, exhibiting narrow peaks and pseudo-gaps of the order of 50 meV FWHM. Moreover, structural aspects involving surface free energy, friction, diffusion, surface reconstructions, are still largely non-understood at the theoretical level. This project proposes a novel and complete strategy for the computational attack of QC surfaces. It relies on existing methods for the classical simulation of alloys, and requires a continuous interplay with experimental and high level ab initio data.
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