Query: Supramolecular assembly, chirality, and electronic properties of rubrene studied by STM and STS

Candidate papers:

abstract: This thesis presents the first experimental results of a scanning tunneling microscopy (STM) and scanning tunneling spectroscopy (STS) investigation of rubrene at the supramolecular, molecular and submolecular level. Based on its semiconducting and fluorescent properties, this molecule is of particular interest in view of the emerging fields of molecular electronics and optoelectronics which could one day replace the conventional technology relying on semiconductors such as silicon and gallium arsenide. The goal is the substitution of these inorganic materials by cheap and flexible layers of semiconducting organic molecules for a new class of diodes and transistors, as well as the realization of electronic switches based on individual molecules. One fundamental approach is to take advantage of the molecular self assembly behavior which results in the creation of well ordered supramolecular structures. The investigations of the self assembly of rubrene adsorbed on metal surfaces (Au(111) Au(100) Ag(111) and Ag(100) which were carried out within the framework of this thesis, show a surprising diversity of supramolecular structures. Amongst other shapes, the molecules organize themselves into geometries of perfect hexagonal and pentagonal symmetry and create multifaceted patterns on the surface. A fascinating peculiarity consists in the spontaneous construction of nested structures which are built up by a hierarchical self assembly of individual molecules into pentagonal supermolecules which form in a second step perfect supramolecular decagons. The geometric shape of rubrene is characterized by a structural asymmetry leading to the existence of two mirror imaged versions of the molecule which are not superimposable to each other, such as for instance our left and right hand or the helical DNA. The aspect of chirality is crucial for basic processes in living systems and calls for a fundamental understanding of the interaction mechanisms occurring between chiral molecules. The experiments on rubrene reveal that the intermolecular bonding differentiates between the two chiral types of the molecule (chiral recognition) yielding the self organization into homochiral structures. These assemblies exhibit a geometry which is again chiral, demonstrating a propagation of chirality throughout the three stages of the supramolecular hierarchy. The semiconducting behavior of rubrene is furthermore probed by STS measurements detecting the energetic positions of the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) The experimental data uncover that different adsorption conformations exhibit characteristic HOMO energies and reveal adsorption conformations of rubrene which preserve the intrinsic electronic structure of the free molecule. Furthermore, a switching of the molecular conformation and the electronic structure of one rubrene conformer is induced with the STM.
author_names: M C Blum
title: Supramolecular assembly, chirality, and electronic properties of rubrene studied by STM and STS
year: 2006

abstract: The self assembly of functional molecules into uniform nanostructures with innovational properties has attracted extensive research interest. In the present work, the assembly structures and electronic properties of a novel type of truxene derivative, e.g. truxene porphyrin derivatives, were studied, for the first time, on a highly oriented pyrolytic graphite (HOPG) surface. Scanning tunneling microscopy (STM) images revealed that the truxene porphyrin compounds could be parallelly arranged into long ranged lamellar patterns. Density functional theory (DFT) calculations helped explain the assembly mechanisms further. Besides, order distribution of the smaller compound 1T1P in the 1,3,5 tris(10 carboxydecyloxy) benzene (TCDB) host network was achieved, which is a reflection of the dimensional effect in the host guest assembly. Furthermore, together with theoretical analyses, scanning tunneling spectroscopy (STS) measurements were conducted to investigate the electronic properties of truxene porphyrin compounds. Results showed that the metalation of the porphyrin units could have a significant effect on the band gap and the position of the gap center. The study enhances our understanding of the assembly mechanism of truxene derivatives at the molecular level and paves the way towards fabricating truxene based functional nanodevices.
author_names: Haijun Xu

Hongyu Shi

Yuhong Liu

Jian Song

Xinchun Lu

Claude P Gros

Ke Deng

Qingdao Zeng
title: Assembly structures and electronic properties of truxene porphyrin compounds studied by STM/STS.
venue: Dalton transactions
year: 2019

abstract: The design, synthesis and self assembly of supramolecular nanostructures with attractive physical and chemical characteristics have drawn much attention during recent decades, mainly due to their applications in a vast number of fields, including chemistry, physics and engineering. The development of novel electronic devices, smart surfaces and pre programmed architectures, among others, have been envisaged. The present thesis concerns to the self assembly and the electronic properties of p expanded macrocycles into ordered supramolecular architectures, investigated by means of scanning tunneling microscopy (STM) and spectroscopy (STS) at the solidliquid interface between organic solutions and highly oriented pyrolytic graphite (HOPG) Particularly, self assembled monolayers of macrocycles of four p expanded macrocyclic oligothiophene 8 mers were investigated. One of the macrocycles, cyclo[8](3,4dibutyl 2,5 thienylene ethynylene) 8T8A, contains eight ethynylenes, while two other macrocycles are the photoisomers Z,Z 8T6A and E,E 8T6A, where two of the ethynylenes in opposite positions of the ring are replaced by cisand trans ethylenes, respectively. An additional macrocycle, E 8T7A, corresponds to seven ethynylenes and one trans ethylene groups. STM height images reveal hexagonally ordered 2D networks with small differences in the unit cells. Current voltage (I V) characteristics confirm the expected donor like character of the macrocycles with very similar LUMO positions for all macrocycles, and HOMO positions independent of the amount of ethynylene and ethylene groups. Cyclic STS measurements indicate that Z,Z 8T6A switches to its isomer E,E 8T6A after formation of a most stable cationic species, consistent with voltammetry and chemical oxidation experiments. This result represents the first reported electrochemi
author_names: C E Gonzalez

J A David
title: Self Assembly and Electronic Properties of p expanded Macrocycles
year: 2018

abstract: Porphyrins and phthalocyanines are currently a prevalent topic with great potential due to their abundant photonic/electronic properties. The study of porphyrin or phthalocyanine supramolecular arc.
author_names: Yuxin Qian

Bo Liu

Wu-biao Duan

Qingdao Zeng
title: Assemblies of porphyrin and phthalocyanine derivatives studied by STM
year: 2018

abstract: In this paper we report the study of the change in electrical properties of zigzag carbon nanotubes (10, 0) under uniaxial compressive and tensile deformation using Density Functional Theory (DFT) calculation. There is an energy gap of 0.972 eV between occupied and unoccupied region in the optimized structure calculation. We found that the band gap of the semi conducting zigzag (10, 0) CNTs decreases as the strain increases for both compressive and tensile deformation. Different profiles of charge density appear for tensile and compressive deformations. The charge density of compressed state is more localized in the z direction of C C bonds. Meanwhile, charge density of elongated state is localized in the diagonal C C bonds direction. At the large tensile strain, the C C bonds break at the z direction C C bonds. ICOHP analysis shows that the bond strength of CNT drastically decreases under tensile deformation. Keyword: band gap, carbon nanotubes, charge density, density functional theory. INTRODUCTION The development of science and technology has evolved into the era of nanotechnology. Among the many nanostructured materials, carbon nanotubes (CNTs) have attracted considerable attention. Compared to other nanoscale materials, single walled carbon nanotubes (SWCNT) possess particularly outstanding physical and electronic properties. Due to the extremely small size of CNTs, the evaluation of its mechanical properties, such as elastic modulus and tensile/compressive strength presents significant challenges to researchers who work in nanomechanics. Electronic states of single walled carbon nanotubes (SWNCT) such as Density of states (DOS) and band gap, could be correlated with their finite mechanical deformation behavior. The study of this effect is important in view of the ability to manipulate individual nanotubes for many applications. Recently, Obitayo and Liu [1] have been developed carbon nanotubes as strain sensor its I V characteristic behavior due to axial change has been explored. In that work, they conclude that for carbon nanotube based strain sensing applications, the small gap semiconducting single walled carbon nanotubes offer the greatest sensitivity. Even though many research have studied the change of electronics properties of nanotubes under uniaxial deformation [1 3] the theoretical approach in investigating the band gap changes has not been revealed up completely. Because of the nanoscale size of CNTs, the experiments to measure the properties of individual CNT are quite difficult. Therefore, the ab initio calculations have been regarded as a powerful tool to study properties of CNTs. In the present report, we calculate the atomic and electronic structure changes of the CNTs under tensile and compressive deformation by using Density Functional Theory (DFT) calculation. We focused on band gap and bond strength changes due to mechanical uniaxial tensile and compressive deformation. COMPUTATIONAL DETAILS We carried out the first principles calculations on the density functional theory (DFT) level, using the "Vienna ab initio simulation package" [4 6] The calculation was performed in QC Cluster at Department of Physics ITB. Generalized gradient approximation (GGA) with the Perdew Burke Ernzerhof (PBE) [7] functional is selected in our calculations. A plane wave basis set was employed within the framework of the projector augmented wave method.[8, 9] K points (1 x 1 x 17 Monkhorst Pack grid) were used in this simulations. One k point in the two perpendicular directions was enough because the distance between the individual tubes was chosen very large (16 A) so that the interaction between them was negligible. We selected zigzag type semiconducting CNTs (10,0) The axial direction (z) of these CNTs was selected as the tensile direction. Before we started the tensile test, the z dimension of the supercells and the initial atomic configuration were completely relaxed. These relaxed z dimensions of the supercells were used as a reference when calculating the applied strains in the following discussion. The electronic properties of zigzag CNT can be obtained by using electronic density of states calculations. The optimized structure data from SCF calculations can be used to reduce calculation time and neglect structural optimization process. Generally, the mesh K point sampling for DOS calculation is higher than that of SCF calculations for calculation's accuracy. To know further the nature of bonding of elongated /compressed CNT, we projected plane waves to local orbital basis functions to extract the crystal orbital Hamilton population COHP) [10] The integration of COHP for all energies up to EF gives integrated COHP (ICOHP) to render a quasiquantitative interpretation [11] of the net bonding characteristics. This ICOHP were calculated by using the program Local Orbital Basis Suite towards Electronic Structure Reconstruction (LOBSTER) [11 13] VOL. 13, NO. 7, APRIL 2018 ISSN 1819 6608 ARPN Journal of Engineering and Applied Sciences (c)2006 2018 Asian Research Publishing Network (ARPN) All rights reserved. www.arpnjournals.com 2391 RESULT AND DISCUSSIONS Change in density of states during deformation From the DFT calculation using VASP software, we got the optimized structure of zigzag CNTs (10, 0) The zigzag edge (10, 0) CNT has two different carboncarbon (C C) bond length, 1.42 A and 1.43 A. The diameter of this optimize structure is 7.89 A. Our optimized CNTs model was then be compressed and elongated in uniaxial direction (z direction) There is an energy gap of 0.972 eV between occupied and unoccupied region, which indicates that the system is semiconducting. This result is in agreement with other first principle calculation studies which have been published [14 16] This result is also supported by experimental and theoretical approach results from other studies. According to the chiral vector information, the pristine zigzag edge (10,0) CNT is semiconducting material [17] This result is also in a good agreement with experimental result by using scanning tunneling microscopy (STM) and scanning tunneling spectroscopy (STS) [17, 18] The electronic structures of CNTs with various structures under axial strain are evaluated by DFT calculations. To analyze the band gap dependency on uniaxial deformation, we observe the DOS of the deform structure of zigzag edge CNT (10, 0) The band gap versus strain curves for a zigzag (10, 0) CNTs during the tensile tests are shown in Figure 1. Negative value means that the final deformed structure is shorter than the optimize bulk structure (compressed) Vice versa, the positive value shows that the final deformed structure is longer than the optimize bulk structure (elongated) Previous work on semiconducting CNTs shows the same result with this work. The band gap for the semiconducting zigzag (10, 0) CNTs displays some variation upon deformation, but most of it decreases as the strain increases [16] This calculation result also shows that there is semiconductor metallic transition of the CNTs. The (10,0) zigzag tube has zero band gap like graphene at the strain of 8.3% which means that it possesses metallic electronic properties at this state and returns to the semiconducting state as the strain increases. Since another work suggests that the small gap semiconducting single walled carbon nanotubes offer the greatest sensitivity for the sensor application, we can conclude that CNT (10, 0) can be a good candidate for CNT based strain sensors. Figure 1. The band gap versus strain for semi conducting zigzag (10,0) CNTs. Deformation electron density VOL. 13, NO. 7, APRIL 2018 ISSN 1819 6608 ARPN Journal of Engineering and Applied Sciences (c)2006 2018 Asian Research Publishing Network (ARPN) All rights reserved. www.arpnjournals.com 2392 Figure 2. (a) Focused area for charge density analyzing; Charge density of the (10,0) zigzag CNT under: (b) 2% (c) 10% compressive and (e) 1% (f) 10% tensile strain. Figure 2 shows change in the charge density of the (10,0) zigzag CNT under compressive and tensile strain. We analyze the two dimensional charge density slice of the semiconducting zigzag (10, 0) CNTs focusing on the red circle area shown in the Figure 2(a) Charge density of the CNT before imposed by uniform stretching or compressed of the initial atomic configuration in the z direction is shown in Figure 2(b) Charge density during the compressive deformation is shown in Figure 2(c) and (d) it can be seen that the charge density becomes more localized in the z direction C C bonds and the angle of the hexagonal carbon formation decreases. The amount of localized charge density also increases as the compressive strain increase. The different profile appears during tensile deformation. The charge density, as shown in Figure 2(e) and (f) decreases as the tensile strain increase. The Charge density is localized in the diagonal C C bonds. At large strain, i.e. 7% for tensile and 5% for compression, the C C bonds break at the z direction C C bonds. This indicates that for more than 7% tensile and 5% compressive strain, CNT starts to break and no longer efficient to be used as a sensor. Because when some C C bonds are broken, the CNT is in plastic region, so when it is strained, it will not return to its original shape. For the strain sensor application, CNT should be able to return to its original shape, it means that the CNT should be in the elastic region. From our charge density analysis, the elastic region of CNT (10, 0) might be below 7% tensile and 5% compressive strain. From this figure also we can conclude that the bond strength of the CNT under compressive deformation is higher compared to that of tensile deformation. It is indicated by the higher value of the electron density in compressive deformation compared to tensile deformation at the same strain. To study further about this bond strength, we perform the ICOHP calculation. Bond strength Integratin
author_names: Irfan Dwi Aditya
title: ELECTRONIC PROPERTIES OF SEMICONDUCTING ZIGZAG 10 0 CARBON NANOTUBES DUE TO UNIAXIAL STRAIN
year: 2018

abstract: At present, organic molecules are among the best candidate "building blocks" for the construction of self assembling nanoscale devices based on metal substrates. Control of the formation of specific patterns in the submonolayer regime is usually achieved by appropriate choice and/or functionalization of the adsorbates. The effect of this intervention, though, is limited by the typically short range character of the bonding. We present here a theoretical study on the system rubrene/gold to show that substrate induced molecular charging can instead determine the assembly on larger scales. DFT calculations and electrostatic considerations are used to discuss the charge transfer at the metal/organic interface. This allows rationalization of previous puzzling experimental results and, in particular, of the unusual molecular gap broadening upon adsorption observed in STS spectra. The self assembly process is further studied by means of classical molecular dynamics simulations. The charged adsorbates are modeled as mutually repulsive standing dipoles, with van der Waals interactions intervening at short distances. The striking resemblance between the experimental STM images and the results of our MD simulations shows that this simple model is able to capture the key effects driving the assembly in this system. The competition between long range repulsive interactions and short range attractive forces leads to characteristic and easily recognizable 1D patterns. We suggest that experimental evidence of the presence of similar patterns in other metal/organic systems can provide crucial information on the electronic level alignment at the interface, that is, on the occurrence of charge transfer processes between metal and organic adsorbates.
author_names: Giulia Tomba

Massimiliano Stengel

Wolf-Dieter Schneider

Alfonso Baldereschi

Alessandro De Vita
title: Supramolecular self assembly driven by electrostatic repulsion: The 1D aggregation of rubrene pentagons on Au111.
venue: ACS nano
year: 2010

abstract: Highly ordered assemblies prepared from tetra (4 sulfonatophenyl) phthalocyanine (TSPc) by employing very acidic aqueous solutions were deposited onto Au(111) substrates and studied in UHV using X ray photoelectron spectroscopy (XPS) scanning tunneling microscopy (STM) and orbital mediated tunneling spectroscopy (OMTS) XPS of the TSPc aggregates shows that the ratio of protonated to unprotonated nitrogens does not change with decreasing solution pH. STM images of TSPc deposited from pH <1 solutions reveal ordered branched web like assemblies hundreds of nanometers in length, generally 2 nm tall and having variable widths. High resolution UHV STM images of TSPc aggregates on Au(111) reveal detailed coherent columnar architecture with the phthalocyanine macrocycles orientated parallel to the substrate surface. OMTS was used to identify high energy occupied orbitals, the LUMO of the TSPc aggregates, and the results are contrasted with the same molecular states in unsubstituted metalated phthalocyanines (M.
author_names: Krista R A Nishida

Bryan Wiggins

K W Hipps

Ursula Mazur
title: Structural and Electronic Properties of Columnar Supramolecular Assemblies Formed from Ionic Metal Free Phthalocyanine on Au(111)
year: 2011

abstract: A compound two dimensional monolayer mixing Mn atoms and 7,7,8,8 tetracyanoquinoclimethane (TCNQ) molecules was synthesized by supramolecular assembly on a Cu(100) surface under ultrahigh vacuum conditions. The interactions in the Mn(TCNQ)(2) network and in the full system arc analyzed from a molecular orbital perspective and in the light of scanning tunneling microscopy (STM) imaging and simulations. Structural, electronic, and magnetic properties are studied in detail using density functional theory (DFT) calculations. In the absence of Cu and depending on the theoretical method used, the TCNQ species can be formally described as either dianions TCNQ(2 interacting with Mn4+ cations according to ligand held theory (using GGA calculations) or, alternatively, as radical monoanions interacting with Mn2+ cations in a high spin state (using GGA+U calculations) In the complete system including a Cu substrate, whatever theoretical method is used, TCNQs appear as dianions interacting with both Mn2+ cations in a high spin state (d(5) and charged copper surface atoms.
author_names: Xingqiang Shi

Christian Minot

Tzu-Chun Tseng

Steven L Tait

Nian Lin

Rui-Qin Zhang

Klaus Kern

Jorge I Cerda

Michel Andre Van Hove
title: Structural analysis and electronic properties of negatively charged TCNQ: 2D networks of (TCNQ)2Mn assembled on Cu(100)
year: 2010

abstract: On surface metal organic coordination provides a promising way for synthesizing different two dimensional lattice structures that have been predicted to possess exotic electronic properties. Using scanning tunneling microscopy (STM) and spectroscopy (STS) we studied the supramolecular self assembly of 9,10 dicyanoanthracene (DCA) molecules on the Au(111) surface. Close packed islands of DCA molecules and Au DCA metal organic coordination structures coexist on the Au(111) surface. Ordered DCA3 Au2 metal organic networks have a structure combining a honeycomb lattice of Au atoms with a kagome lattice of DCA molecules. Low temperature STS experiments demonstrate the presence of a delocalized electronic state containing contributions from both the gold atom states and the lowest unoccupied molecular orbital of the DCA molecules. These findings are important for the future search of topological phases in metal organic networks combining honeycomb and kagome lattices with strong spin orbit coupling in heavy metal atoms.
author_names: Linghao Yan

Ilona Pohjavirta

Benjamin Alldritt

Peter Liljeroth
title: On Surface Assembly of Au Dicyanoanthracene Coordination Structures on Au(111)
venue: Chemphyschem a European journal of chemical physics and physical chemistry
year: 2019

abstract: Two semiconducting naphthalene bisimides were comparatively studied: NBI (TAA)(2) symmetrically N substituted with triaryl amine and asymmetric NBI TAA Oc with triaryl amine and octyl N substituents. Both compounds show very similar spectroscopic and redox properties but differ in their supramolecular organization. As evidenced by STM, in monolayers on HOPG they form ordered 2D structures, however of different packing patterns. NBI (TAA)(2) does not form ordered 3D structures, yielding amorphous thin films whereas films of NBI TAA Oc are highly crystalline. DFT calculations predict the ionization potential (IP) of 5.22 eV and 5.18 eV for NBI TAA Oc and NBI (TAA)(2) respectively, as well as the electron affinity values (EA) of 3.25 eV and 3.22 eV. These results are consistent with the cyclic voltammetry data which yield similar values of IP (5.20 eV and 5.19 eV) and somehow different values of EA 3.80 eV and 3.83 eV) As judged from these data, both semiconductors should exhibit ambipolar behavior. Indeed, NBI TAA Oc is ambipolar, showing hole and electron mobilities of 4.5 x 10( 5) cm(2)(V s) and of 2.6 x 10( 4) cm(2)(V s) respectively, in the field effect transistor configuration. NBI (TAA)(2) is not ambipolar and yields field effect only in the p channel configuration. This different behavior is rationalized on the basis of structural factors.
author_names: Renata Rybakiewicz

Joanna Zapala

David Djurado

Robert Nowakowski

Petr Toman

Jiri Pfleger

J M Verilhac

Malgorzata Zagorska

Adam Pron
title: Naphthalene bisimides asymmetrically and symmetrically N substituted with triarylamine comparison of spectroscopic, electrochemical, electronic and self assembly properties.
venue: Physical chemistry chemical physics PCCP
year: 2013