hand-controlled-manipulation-single-molecules-via-scanning-probe

Hand Controlled Manipulation of Single Molecules via a Scanning Probe Microscope with a 3D Virtual Reality Interface

Considering organic molecules as the functional building blocks of future nanoscale technology, the question of how to arrange and assemble such building ...

Forschungszentrum Jülich

Jülich Aachen Research Alliance (JARA)

The effect of molecular flexibility on the surface ordering of complex organic adsorbates is explored, using alpha,omega-dihexylquaterthiophene (DH4T) and mixed DH4T|tetracene phases on Ag(111) as model systems. The structure of DH4T/Ag(111) interfaces is determined by the flexibility of the hexyl chains at either end of the quaterthiophene backbone: Above 273 K, DH4T forms a nematic liquid crystalline phase with a director close to the [112] direction of the silver substrate. At 273 K, a reversible phase transition to a long-range ordered, point-on-line coincident phase is observed. However, this ordered state is still affected substantially by the flexible nature of DH4T, which materializes in a large number of local structural defects. If traces of DH4T are coevaporated with tetracene, inclusions of a 1:1 stoichiometric DH4T|tetracene phase are found in a tetracene/Ag(111) matrix (alpha-phase). In this mixed phase, the two surface enantiomers of pro-chiral DH4T on one hand and tetracene on the other form a complex stripe structure. The mixed phase shows a higher degree of order than present at the pure DH4T/Ag(111) interface, which also lacks chiral organization. The addition of tetracene molecules as structural templates stabilizes certain conformations of DH4T and thus, by balancing its structural flexibility, allows the surface-induced chirality of DH4T to become a decisive factor in determining the structure of the mixed phase.

Molecular flexibility as a factor affecting the surface ordering of organic adsorbates on metal substrates.

Local, noncovalent intermolecular interactions in organic monolayers have been directly imaged using scanning tunneling hydrogen microscopy (STHM). Unprecedented spatial resolution directly reveals the relation between the intermolecular interactions, the molecular chemical structure, and the ordering in the film.

Direct imaging of intermolecular bonds in scanning tunneling microscopy.

Individual Xe atoms as well as single CO and CH(4) molecules adsorbed at the tip apex of a scanning tunneling microscope (STM) function as microscopic force sensors that change the tunneling current in response to the forces acting from the surface. An STM equipped with any of these sensors is able to image the short-range Pauli repulsion and thus resolve the inner structure of large organic adsorbate molecules. Differences in the performance of the three studied sensors suggest that the sensor functionality can be tailored by tuning the interaction between the sensor particle and the STM tip.

Single molecule and single atom sensors for atomic resolution imaging of chemically complex surfaces.

The understanding and control of epitaxial growth of organic thin films is of crucial importance in order to optimize the performance of future electronic devices. In particular, the start of the submonolayer growth plays an important role since it often determines the structure of the first layer and subsequently of the entire molecular film. We have investigated the structure formation of 3,4,9,10-perylene-tetracarboxylic dianhydride and copper-phthalocyanine molecules on Au(111) using pair-potential calculations based on van der Waals and electrostatic intermolecular interactions. The results are compared with the fundamental lateral structures known from experiment and an excellent agreement was found for these weakly interacting systems. Furthermore, the calculations are even suitable for chemisorptive adsorption as demonstrated for copper-phthalocyanine/Cu(111), if the influence of charge transfer between substrate and molecules is known and the corresponding charge redistribution in the molecules can be estimated. The calculations are of general applicability for molecular adsorbate systems which are dominated by electrostatic and van der Waals interaction.

Modeling intermolecular interactions of physisorbed organic molecules using pair potential calculations.

We present evidence for a partly chemisorptive bonding between single monolayers of copper-II-phthalocyanine (CuPc) and 3,4,9,10-perylene-tetracarboxylic-dianhydride (PTCDA) that are stacked on Ag(111). A commensurate registry between the two molecular layers and the substrate, i.e., a common crystallographic lattice for CuPc and PTCDA films as well as for the Ag(111) surface, indicates that the growth of the upper layer is dominated by the structure of the lower. Photoemission spectroscopy clearly reveals a gradual filling of the lowest unoccupied molecular orbital of PTCDA due to CuPc adsorption, which proves the chemisorptive character.

Commensurate registry and chemisorption at a hetero-organic interface.

The basis for a quantum-mechanical description of matter is electron wave functions. For atoms and molecules, their spatial distributions and phases are known as orbitals. Although orbitals are very powerful concepts, experimentally only the electron densities and -energy levels are directly observable. Regardless whether orbitals are observed in real space with scanning probe experiments, or in reciprocal space by photoemission, the phase information of the orbital is lost. Here, we show that the experimental momentum maps of angle-resolved photoemission from molecular orbitals can be transformed to real-space orbitals via an iterative procedure which also retrieves the lost phase information. This is demonstrated with images obtained of a number of orbitals of the molecules pentacene (C22H14) and perylene-3,4,9,10-tetracarboxylic dianhydride (C24H8O6), adsorbed on silver, which are in excellent agreement with ab initio calculations. The procedure requires no a priori knowledge of the orbitals and is shown to be simple and robust.

Imaging the wave functions of adsorbed molecules.

Scanning probe microscopy (SPM) plays an important role in the investigation of molecular adsorption. The possibility to probe the molecule-surface interaction while tuning its strength through SPM tip-induced single-molecule manipulation has particularly promising potential to yield new insights. We recently reported experiments, in which 3,4,9,10-perylene-tetracarboxylic-dianhydride (PTCDA) molecules were lifted with a qPlus-sensor and analyzed these experiments by using force-field simulations. Irrespective of the good agreement between the experiment and those simulations, systematic inconsistencies remained that we attribute to effects omitted from the initial model. Here we develop a more realistic simulation of single-molecule manipulation by non-contact AFM that includes the atomic surface corrugation, the tip elasticity, and the tip oscillation amplitude. In short, we simulate a full tip oscillation cycle at each step of the manipulation process and calculate the frequency shift by solving the equation of motion of the tip. The new model correctly reproduces previously unexplained key features of the experiment, and facilitates a better understanding of the mechanics of single-molecular junctions. Our simulations reveal that the surface corrugation adds a positive frequency shift to the measurement that generates an apparent repulsive force. Furthermore, we demonstrate that the scatter observed in the experimental data points is related to the sliding of the molecule across the surface.

The role of surface corrugation and tip oscillation in single-molecule manipulation with a non-contact atomic force microscope.

In low-energy electron microscopy (LEEM) we commonly encounter images which, beside amplitude contrast, also show signatures of phase contrast. The images are usually interpreted by following the evolution of the contrast during the experiment, and assigning gray levels to morphological changes. Through reconstruction of the exit wave, two aspects of LEEM can be addressed: (1) the resolution can be improved by exploiting the full information limit of the microscope and (2) electron phase shifts which contribute to the image contrast can be extracted. In this article, linear exit wave reconstruction from a through-focal series of LEEM images is demonstrated. As a model system we utilize a heteromolecular monolayer consisting of the organic molecules 3,4,9,10-perylene tetracarboxylic dianhydride and Cu-II-Phthalocyanine, adsorbed on a Ag(111) surface.

Focal-series reconstruction in low-energy electron microscopy.

Although geometric and electronic properties of any physical or chemical system are always mutually coupled by the rules of quantum mechanics, counterintuitive coincidences between the two are sometimes observed. The coadsorption of the organic molecules 3,4,9,10-perylene tetracarboxylic dianhydride and copper-II-phthalocyanine on Ag(111) represents such a case, since geometric and electronic structures appear to be decoupled: one molecule moves away from the substrate while its electronic structure indicates a stronger chemical interaction, and vice versa for the other. Our comprehensive experimental and ab-initio theoretical study reveals that, mediated by the metal surface, both species mutually amplify their charge-donating and -accepting characters, respectively. This resolves the apparent paradox, and demonstrates with exceptional clarity how geometric and electronic bonding parameters are intertwined at metal-organic interfaces.

Unexpected interplay of bonding height and energy level alignment at heteromolecular hybrid interfaces.

One of the paramount goals in nanotechnology is molecular-scale functional design, which includes arranging molecules into complex structures at will. The first steps towards this goal were made through the invention of the scanning probe microscope (SPM), which put single-atom and single-molecule manipulation into practice for the first time. Extending the controlled manipulation to larger molecules is expected to multiply the potential of engineered nanostructures. Here we report an enhancement of the SPM technique that makes the manipulation of large molecular adsorbates much more effective. By using a commercial motion tracking system, we couple the movements of an operator's hand to the sub-angstrom precise positioning of an SPM tip. Literally moving the tip by hand we write a nanoscale structure in a monolayer of large molecules, thereby showing that our method allows for the successful execution of complex manipulation protocols even when the potential energy surface that governs the interaction behaviour of the manipulated nanoscale object(s) is largely unknown.

Patterning a hydrogen-bonded molecular monolayer with a hand-controlled scanning probe microscope.

Van der Waals (vdW) forces act ubiquitously in condensed matter. Despite being weak on an atomic level, they substantially influence molecular and biological systems due to their long range and system-size scaling. The difficulty to isolate and measure vdW forces on a single-molecule level causes our present understanding to be strongly theory based. Here we show measurements of the attractive potential between differently sized organic molecules and a metal surface using an atomic force microscope. Our choice of molecules and the large molecule-surface separation cause this attraction to be purely of vdW type. The experiment allows testing the asymptotic vdW force law and its validity range. We find a superlinear growth of the vdW attraction with molecular size, originating from the increased deconfinement of electrons in the molecules. Because such non-additive vdW contributions are not accounted for in most first-principles or empirical calculations, we suggest further development in that direction.

Non-additivity of molecule-surface van der Waals potentials from force measurements.

Recently, the family of high-resolution scanning probe imaging techniques using decorated tips has been complemented by a method based on inelastic electron tunneling spectroscopy (IETS). The new technique resolves the inner structure of organic molecules by mapping the vibrational energy of a single carbon monoxide (CO) molecule positioned at the apex of a scanning tunneling microscope (STM) tip. Here, we explain high-resolution IETS imaging by extending a model developed earlier for STM and atomic force microscopy (AFM) imaging with decorated tips. In particular, we show that the tip decorated with CO acts as a nanoscale sensor that changes the energy of its frustrated translation mode in response to changes of the local curvature of the surface potential. In addition, we show that high resolution AFM, STM, and IETS-STM images can deliver information about the charge distribution within molecules deposited on a surface. To demonstrate this, we extend our mechanical model by taking into account electrostatic forces acting on the decorated tip in the surface Hartree potential.

Origin of High-Resolution IETS-STM Images of Organic Molecules with Functionalized Tips.

We introduce a scanning probe technique that enables three-dimensional imaging of local electrostatic potential fields with subnanometer resolution. Registering single electron charging events of a molecular quantum dot attached to the tip of an atomic force microscope operated at 5 K, equipped with a qPlus tuning fork, we image the quadrupole field of a single molecule. To demonstrate quantitative measurements, we investigate the dipole field of a single metal adatom adsorbed on a metal surface. We show that because of its high sensitivity the technique can probe electrostatic potentials at large distances from their sources, which should allow for the imaging of samples with increased surface roughness.

Scanning Quantum Dot Microscopy.

Interfaces between organic molecules and solid surfaces play a prominent role in heterogeneous catalysis, molecular sensors and switches, light-emitting diodes, and photovoltaics. The properties and the ensuing function of such hybrid interfaces often depend exponentially on molecular adsorption heights and binding strengths, calling for well-established benchmarks of these two quantities. Here we present systematic measurements that enable us to quantify the interaction of benzene with the Ag(111) coinage metal substrate with unprecedented accuracy (0.02 Å in the vertical adsorption height and 0.05 eV in the binding strength) by means of normal-incidence x-ray standing waves and temperature-programed desorption techniques. Based on these accurate experimental benchmarks for a prototypical molecule-solid interface, we demonstrate that recently developed first-principles calculations that explicitly account for the nonlocality of electronic exchange and correlation effects are able to determine the structure and stability of benzene on the Ag(111) surface within experimental error bars. Remarkably, such precise experiments and calculations demonstrate that despite different electronic properties of copper, silver, and gold, the binding strength of benzene is equal on the (111) surface of these three coinage metals. Our results suggest the existence of universal binding energy trends for aromatic molecules on surfaces.

Quantitative Prediction of Molecular Adsorption: Structure and Binding of Benzene on Coinage Metals.

Controlled manipulation of single molecules is an important step towards the fabrication of single molecule devices and nanoscale molecular machines. Currently, scanning probe microscopy (SPM) is the only technique that facilitates direct imaging and manipulations of nanometer-sized molecular compounds on surfaces. The technique of hand-controlled manipulation (HCM) introduced recently in Beilstein J. Nanotechnol. 2014, 5, 1926-1932 simplifies the identification of successful manipulation protocols in situations when the interaction pattern of the manipulated molecule with its environment is not fully known. Here we present a further technical development that substantially improves the effectiveness of HCM. By adding Oculus Rift virtual reality goggles to our HCM set-up we provide the experimentalist with 3D visual feedback that displays the currently executed trajectory and the position of the SPM tip during manipulation in real time, while simultaneously plotting the experimentally measured frequency shift (Δf) of the non-contact atomic force microscope (NC-AFM) tuning fork sensor as well as the magnitude of the electric current (I) flowing between the tip and the surface. The advantages of the set-up are demonstrated by applying it to the model problem of the extraction of an individual PTCDA molecule from its hydrogen-bonded monolayer grown on Ag(111) surface.

Article	Year
Molecular flexibility as a factor affecting the surface ordering of organic adsorbates on metal substrates. Langmuir : the ACS journal of surfaces and colloids\| PubMed ID: 17073481	2006
Direct imaging of intermolecular bonds in scanning tunneling microscopy. Journal of the American Chemical Society\| PubMed ID: 20698531	2010
Single molecule and single atom sensors for atomic resolution imaging of chemically complex surfaces. Journal of the American Chemical Society\| PubMed ID: 21962083	2011
Modeling intermolecular interactions of physisorbed organic molecules using pair potential calculations. The Journal of chemical physics\| PubMed ID: 22191896	2011
Commensurate registry and chemisorption at a hetero-organic interface. Physical review letters\| PubMed ID: 22463427	2012
Imaging the wave functions of adsorbed molecules. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 24344291	2014
The role of surface corrugation and tip oscillation in single-molecule manipulation with a non-contact atomic force microscope. Beilstein journal of nanotechnology\| PubMed ID: 24605287	2014
Focal-series reconstruction in low-energy electron microscopy. Microscopy and microanalysis : the official journal of Microscopy Society of America, Microbeam Analysis Society, Microscopical Society of Canada\| PubMed ID: 24717211	2014
Unexpected interplay of bonding height and energy level alignment at heteromolecular hybrid interfaces. Nature communications\| PubMed ID: 24739211	2014
Patterning a hydrogen-bonded molecular monolayer with a hand-controlled scanning probe microscope. Beilstein journal of nanotechnology\| PubMed ID: 25383304	2014
Non-additivity of molecule-surface van der Waals potentials from force measurements. Nature communications\| PubMed ID: 25424490	2014
Origin of High-Resolution IETS-STM Images of Organic Molecules with Functionalized Tips. Physical review letters\| PubMed ID: 25494078	2014
Scanning Quantum Dot Microscopy. Physical review letters\| PubMed ID: 26207484	2015
Quantitative Prediction of Molecular Adsorption: Structure and Binding of Benzene on Coinage Metals. Physical review letters\| PubMed ID: 26230807	2015
Virtual reality visual feedback for hand-controlled scanning probe microscopy manipulation of single molecules. Beilstein journal of nanotechnology\| PubMed ID: 26665087	2015

F. Stefan Tautz

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