1.- Origin of the apparent (2 × 1) topography of the Si(100) − c(4 × 2) surface observed in low-temperature STM images PHYSICAL REVIEW B 83, 201302(R) (2011)

2.- Manipulating Molecular Quantum States with Classical Metal Atom Inputs: Demonstration of a Single Molecule NOR Logic Gate ACS NANO VOL 5 No 2, 1436-1440 (2011)

3.- Demonstration of a NOR logic gate using a single molecule and two surface gold atoms to encode the logical input PHYSICAL REVIEW B 83,155443 (2011)

4.- Measuring Si-C60 chemical forces via single molecule spectroscopy CHEM. COMMUN., 2011, 47, 10575-10577 (2011)

5.- STM and AFM high resolution intramolecular imaging of a single decastarphene molecule CHEMICAL PHYSICS LETTERS, 511, 482 (2011)

6.- Molecules for organic electronics studied one by one PHYSICAL CHEMISTRY CHEMICAL PHYSICS 13, 14421–14426 (2011)

7.- The Effects of Electron_Hole Pair Coupling on the Infrared Laser-Controlled Vibrational Excitation of NO on Au(111) JOURNAL OF PHYSICAL CHEMISTRY A, 115, 10698 (2011)

8.- Controlling on-surface polymerization by hierarchical and substrate-directed growth NATURE CHEMISTRY 4, 215 (2012)

9.- Electronic properties of STM-constructed dangling-bond dimer lines on a Ge(001)-(2×1):H surface PHYSICAL REVIEW B 86, 125307 (2012)

10.- Precise Orientation of a Single C60 Molecule on the Tip of a Scanning Probe Microscope PHYSICAL REVIEW LETTERS 108, 268302 (2012)

11- Identifying passivated dynamic force microscopy tips on H:Si(100) APPLIED PHYSICS LETTERS 100, 233120 (2012)

12.- Role of orbital overlap in atomic manipulation PHYSICAL REVIEW B 85, 235305 (2012)

13.- Polymerization on stepped surfaces: Alignment of polymers and identification of catalytic sites ANGEW. CHEM. INT. Ed. 51, 5096 (2012)

14.- Voltage-dependent conductance of a single graphene nanoribbon NATURE NANOTECHNOLOGY 7, 713 (2012)

15.- Mapping the Excited States of Single Hexa-peri-benzocoronene Oligomers ACSnano VOL. 6,NO. 4,3230–3235,(2012)

16.- Mapping the first electronic resonances of a Cu phthalocyanine STM tunnel junction J. PHYS.: CONDENS. MATTER 24 354011 (2012)

17.- Electronic and magnetic properties of molecule-metal interfaces: Transition-metal phthalocyanines adsorbed on Ag(100) PHYSICAL REVIEW B 85, 155437 (2012)

18.- Spin doping of individual molecules by using single-atom manipulation NANO LETTERS 12, 3609 (2012)

19.-Bottom-up zu molekularen Nanostrukturen (in German) NACHRICHTEN AUS DER CHEMIE, 60, Oktober (2012)

20.-STM manipulation of a subphthalocyanine double-wheel molecule on Au(111) J. PHYS.: CONDENS. MATTER 24 (2012) 404001 (6pp)

21.- Contacting a Conjugated Molecule with a Surface Dangling Bond Dimer on a Hydrogenated Ge(001) Surface Allows Imaging of the Hidden Ground Electronic State ACSnano VOL.7 NO.11 10105–10111 (2013)

22.- Manipulation of a single molecule ground state by means of gold atom Contacts Chemical Physics Letters 587 (2013) 35–39

23.- Switching Mechanisms for Single-Molecule Logic Gates Architecture and Design of Molecule Logic Gates and Atom Circuits, Springer Series Advances in Atom and Single Molecule Machines: ISBN: 978-3-642-33136-7 (2013) pages 55-69.

24.- SPM Imaging of Trinaphthylene Molecular States on a Hydrogen Passivated Ge(001) Surface Architecture and Design of Molecule Logic Gates and Atom Circuits, Springer Series Advances in Atom and Single Molecule Machines: ISBN: 978-3-642-38808-8 (2013), pages 105-114.

25.-Electronic Structure and Properties of Graphen Nanoribbons: Zigzag and Armchair Edges Architecture and Design of Molecule Logic Gates and Atom Circuits, Springer Series Advances in Atom and Single Molecule Machines: ISBN: 978-3-642-38808-8 (2013), pages 81-90.

26.-Structural development and energy dissipation insimulated silicon apices Beilstein J. Nanotechnol.(2013), 4,941–948

27.-Submolecular Resolution Imaging of C60: From Orbital Density to Bond Order Proceedings of the 3rd AtMol International Workshop, Berlin 24-25 September 2012, “Imaging and Manipulating Molecular Orbitals” Advances in Atom and Single Molecule Machines - Series Editor: Christian Joachim, Springer, ISBN: 978-3-642-38808-8 (2013) pages 195-206

28.- Mechanical Conformation Switching of a Single Pentacene Molecule on Si(100)-(2 × 1) J. Phys. Chem. C, 117, 26040−26047 (2013)

20.-Aligning the Band Gap of Graphene Nanoribbons by Monomer Doping ANGEW. CHEM. INT, Ed., 52, 4422 –4425 (2013)

29.- Modular Synthesis of Monomers for On-Surface Polymerization to Graphene Architectures SYNLETT, 24, 0259–0263 (2013)

30.-Moving Nanostructures: Pulse-Induced Positioning of Supramolecular Assemblies ACSnano VOL. 7, NO. 1, 191–197, (2013)

31.- Electron transport through dangling-bond silicon wires on H-passivated Si(100) J. PHYS.: CONDENS. MATTER 25 025503 (2013)

32.-Polymerization of Polyanthrylene on a Titanium Dioxide (011)-(2 _ 1)Surface Angew. Chem. (2013), 125, 1 – 5

33.-Adsorption Site Determination of a Molecular Monolayer via Inelastic Tunneling Nano Lett. (2013), 13, 2346−2350

34.-Tunneling electron induced rotation of a copper phthalocyanine molecule on Cu(111) PHYSICAL REVIEW B 88, 075410 (2013)

35.-Controlling intramolecular hydrogen transfer in a porphycene molecule with single atoms or molecules located nearby Nature Chemistry Vol 6 January (2014)

36.-Substrate-controlled linking of molecular building blocks: Au(111) vs. Cu(111) Surface Science 627 (2014) 70–74

Origin of the apparent (2 × 1) topography of the Si(100) − c(4 × 2) surface observed in low-temperature STM images

PHYSICAL REVIEW B 83, 201302(R) (2011)

Authors
C. Manzano (1), W.-H. Soe (1), H. Kawai (1), M. Saeys (2), and C. Joachim (1,3)
1 IMRE, A∗STAR (Agency for Science, Technology and Research), 3 Research Link, Singapore 17602
2 Department of Chemical and Biomolecular Engineering, National University of Singapore, 4
Engineering Drive 4, Singapore 117576
3 CEMES and MANA Satellite, CNRS, 29 rue J. Marvig, F-31055 Toulouse Cedex, France

Abstract
Low-temperature scanning tunneling microscope (STM) images of the Si(100) surface showing apparent (2 × 1) atom dimer lines have recently been reported. Using experimental and theoretical approaches, it is demonstrated how those (2 × 1)-like images result from a c(4 × 2) surface reconstruction imaged at high bias voltages. In the STM junction, the surface contribution of 3p x surface-state electronic resonances relative to the 3p z states is bias voltage dependent. The apparent (2 × 1) STM images result from an increase in the number of bulk Si electronic channels amplifying Si(100)-c(4 × 2) surface 3p x surface states contribution to the tunneling current with respect to the one of 3p z states.


 Manipulating Molecular Quantum States with Classical Metal Atom Inputs: Demonstration of a Single Molecule NOR Logic Gate

ACS NANO VOL 5 No 2, 1436-1440 (2011)

Authors
We-HyoSoe(†,*), Carlos Manzano(†), Nicolas Renaud(‡), Paula de Mendoza(§), Abir De Sarkar(†), Francisco Ample(†), Mohamed Hliwa(‡), Antonio M. Echavarren(§), Natarajan Chandrasekhar(†), and Christian Joachim(†,‡)
† IMRE, A*STAR (Agency for Science, Technology and Research), 3 Research Link, 117602, Singapore
‡ CEMES, CNRS, 29 rue J.Marvig, 31055 Toulouse Cedex, France
§ Institute of Chemical Research of Catalonia (ICIQ), Avenida Països Catalans 16, 43007 Tarragona, Spain

Abstract
Quantum states of a trinaphthylene molecule were manipulated by putting its naphthyl branches in contact with single Au atoms. One Au atom carries 1-bit of classical information input that is converted in to quantum information through out the molecule.The Au-trinaphthylene electronic interactions give rise to measurable energy shifts of the molecular electronic states demonstrating a NOR logic gate functionality. The NOR truth table of the single molecule logic gate was characterized by means of scanning tunnelling spectroscopy.


 Demonstration of a NOR logic gate using a single molecule and two surface gold atoms to encode the logical input

PHYSICAL REVIEW B 83,155443 (2011)

Authors
W.-H. Soe,1,* C. Manzano,1 A. De Sarkar,1 F. Ample,1 N. Chandrasekhar,1 N. Renaud,2,* P. de Mendoza,3 A. M. Echavarren,3 M. Hliwa, 4,5 and C. Joachim1,4
1 IMRE, ASTAR (Agency for Science, Technology and Research),3 Research Link, 117602 Singapore
2 Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, USA
3 Institut of Chemical Research of Catalonia (ICIQ), Av.Paısos Catalans 16,E-43007 Tarragona, Spain
4 CEMES & MANA Satellite, CNRS, 29 rue J.Marvig,F-31055 Toulouse Cedex, France
5 Faculte des Sciences Ben M’Sik, Universite HassanII Mohammedia, B.P. 7955 Sidi Othman, Casablanca, Morroco
*wh-soe@imre.a-star.edu.sg, n-renaud@northwestern.edu

Abstract
A logic gate has been implemented in a single trinaphthylene molecule. Each logical input controls the position of a surface Au atom that is brought closer or further away from the end of one of the naphthyl branch. Each Au atom carries 1 bit of information and is able to deform non locally and to shift in energy the molecular electronic states of the trinaphthylene. Probed at the end of the third naphthyl branch using scanning tunneling spectroscopy, the variations of the tunneling current intensity as a function of the Au atoms position measures the logical out put of the gate. We demonstrate both theoretically and experimentally that these variations respect the truth table of a NOR logic gate.


Measuring Si-C60 chemical forces via single molecule spectroscopy

CHEM. COMMUN., 2011, 47, 10575-10577 (2011)

Authors
C. Chiutu, A. Stannard, A. M. Sweetman and P. Moriarty
School of Physics and Astronomy, University of Nottingham, Nottingham NG7 2RD, UK.

Abstract
We measure the short-range chemical force between a silicon-terminated tip and individual adsorbed C60 molecules using frequency modulation atomic force microscopy. The interaction with an adsorbed fullerene is sufficiently strong to drive significant atomic rearrangement of tip structures.

STM and AFM high resolution intramolecular imaging of a single decastarphene molecule

CHEMICAL PHYSICS LETTERS, 511, 482 (2011)

Authors
O. Guillermet (a,b), S.Gauthier (a), C.Joachim (a), P. de Mendoza (c), T. Lauterbach (c), A. Echavarren (c)
(a) CNRS, CEMES (Centre d’Elaboration des Matériaux et d’Etudes Structurales), BP 94347, 29 rue Jeanne Marvig, F-31055 Toulouse, France
(b) Université de Toulouse, UPS, 118 route de Narbonne, 31062 Toulouse, France
(c) Institute of Chemical Research of Catalonia (ICIQ), Avenida Països Catalans, 43007 Tarragona, Spain

Abstract
Single decastarphene molecules, adsorbed on Cu(111) and on a bilayer of NaCl/Cu(111) are imaged by a combination of low temperature scanning tunneling microscopy (STM) and dynamic atomic force microscopy in the non-contact mode (nc-AFM). This dual imaging technique provides the intramolecular electron density maps of the frontier molecular orbitals via the STM images and the atomic scale skeleton via its constant-height frequency shift nc-AFM images. Recording both images at the same time opens the way to exactly locate the valence states electronic density map of the imaged molecule on its atomic scale skeleton.


Molecules for organic electronics studied one by one

PHYSICAL CHEMISTRY CHEMICAL PHYSICS 13, 14421–14426 (2011)

Authors
Jörg Meyer (a), Anja Wadewitz (a), Lokamani (a), Cormac Toher (a), Roland Gresser (b), Karl Leo (b), Moritz Riede (b), Francesca Moresco (*,a) and Gianaurelio Cuniberti (a,c)
a Institute for Materials Science and Max Bergmann Center of Biomaterials, Dresden University of Technology, 01062 Dresden, Germany.
* E-mail:francesca.moresco@tu-dresden.de
b Institut für Angewandte Photophysik (IAPP), Technische Universität Dresden, 01062 Dresden, Germany
Engineering Drive 4, Singapore 117576
c Division of IT Convergence Engineering, POSTECH, Pohang 790-784, Republic of Korea

Abstract
The electronic and geometrical structure of single difuoro-bora-1,3,5,7-tetraphenyl-aza-dipyrromethene(aza-BODIPY)molecules adsorbed on the Au(111)surface is investigated by low temperature scanning tunneling microscopy and spectroscopy in conjunction with abinitio density functional theory simulations of the density of states and of the interaction with the substrate. Our DFT calculations indicate that the aza-BODIPY molecule forms a chemical bond with the Au(111)substrate, with distortion of the molecular geometry and significant charge transfer between the molecule and the substrate. Nevertheless, most likely due to the low corrugation of the Au(111)surface,diffusion of the molecule is observed for applied bias inexcess of 1V.

The Effects of Electron_Hole Pair Coupling on the Infrared Laser-Controlled Vibrational Excitation of NO on Au(111)

JOURNAL OF PHYSICAL CHEMISTRY A, 115, 10698 (2011)

Authors
J. C. Tremblay, S. Monturet, P. Saalfrank
Institut für Chemie, Universität Potsdam, Karl-Liebknecht-Straße 24-25, D-14476 Potsdam-Golm, Germany. jean.c.tremblay@gmail.com

Abstract
In this work, we present theoretical simulations of laser-driven vibrational control of NO adsorbed on a gold surface. Our goal is to tailor laser pulses to selectively excite specific modes and vibrational eigenstates, as well as to favor photodesorption of the adsorbed molecule. To this end, various control schemes and algorithms are applied. For adsorbates at metallic surfaces, the creation of electron–hole pairs in the substrate is known to play a dominant role in the transfer of energy from the system to the surroundings. These nonadiabatic couplings are included perturbatively in our reduced density matrix simulations using a generalization of the state-resolved position-dependent anharmonic rate model we recently introduced. An extension of the reduced density matrix is also proposed to provide a sound model for photodesorption in dissipative systems.



Controlling on-surface polymerization by hierarchical and substrate-directed growth

NATURE CHEMISTRY 4, 215 (2012)

Authors
 L. Lafferentz (a,c), V. Eberhardt (b), C. Dri (c), C. Africh (c), G. Comelli (c), F. Esch (c),  S. Hecht (b), L. Grill (a)
(a) Department of Physical Chemistry, Fritz-Haber-Institute of the Max-Planck-Society, 14195 Berlin, Germany
(b) Department of Chemistry, Humboldt-Universität zu Berlin, 12489 Berlin, Germany
(c) IOM-CNR Laboratorio TASC, Area Science Park, 34149 Basovizza-Trieste, Italy

Abstract
A key challenge in the field of nanotechnology, in particular in the design of molecular machines, novel materials or molecular electronics, is the bottom-up construction of covalently bound molecular architectures in a well-defined arrangement. To date, only rather simple structures have been obtained because of the limitation of one-step connection processes. Indeed, for the formation of sophisticated structures, step-by-step connection of molecules is required. Here, we present a strategy for the covalent connection of molecules in a hierarchical manner by the selective and sequential activation of specific sites, thereby generating species with a programmed reactivity. This approach leads to improved network quality and enables the fabrication of heterogeneous architectures with high selectivity. Furthermore, substrate-directed growth and a preferred orientation of the molecular nanostructures are achieved on an anisotropic surface. The demonstrated control over reactivity and diffusion during covalent bond formation constitutes a promising route towards the creation of sophisticated multi-component molecular nanostructures.

Electronic properties of STM-constructed dangling-bond dimer lines on a Ge(001)-(2×1):H surface

PHYSICAL REVIEW B 86, 125307 (2012)

Authors
Marek Kolmer (1), Szymon Godlewski (1,*), Hiroyo Kawai(2,†), Bartosz Such (1), Franciszek Krok (1), Mark Saeys (2,3), Christian Joachim (2,4), and Marek Szymonski (1)
(1) Department of Physics of Nanostructures and Nanotechnology, Institute of Physics, Jagiellonian University, Reymonta 4, PL 30-059 Krakow, Poland
(2) Institute of Materials Research and Engineering, 3 Research Link, Singapore 117602, Singapore
(3) Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117576, Singapore
(4) Nanosciences Group & MANA Satellite, CEMES-CNRS, 29 rue Jeanne Marvig, F-31055 Toulouse, France

Abstract
Atomically precise dangling-bond (DB) lines are constructed dimer-by-dimer on a hydrogen-passivated Ge(001)-(2×1):H surface by an efficient scanning tunneling microscope (STM) tip-induced desorption protocol. Due to the smaller surface band gap of the undoped Ge(001) substrate compared to Si(001), states associated with individually created DBs can be characterized spectroscopically by scanning tunneling spectroscopy (STS). Corresponding dI/dV spectra corroborated by first-principle modeling demonstrate that DB dimers introduce states below the Ge(001):H surface conduction band edge. For a DB line parallel to the surface reconstruction rows, the DB-derived states near the conduction band edge shift to lower energies with increasing number of DBs. The coupling between the DB states results in a dispersive band spanning 0.7 eV for an infinite DB line. For a long DB line perpendicular to the surface reconstruction rows, a similar band is not formed since the interdimer coupling is weak. However, for a short DB line (2–3 DBs) perpendicular to the reconstruction rows a significant shift is still observed due to the more flexible dimer buckling.

Precise Orientation of a Single C60 Molecule on the Tip of a Scanning Probe Microscope

PHYSICAL REVIEW LETTERS 108, 268302 (2012)

Authors
C. Chiutu,(1) A. M. Sweetman,(1) A. J. Lakin,(1) A. Stannard,(1) S. Jarvis,(1) L. Kantorovich,(2) J. L. Dunn,(1) and P. Moriarty(1)
(1) School of Physics and Astronomy, University of Nottingham, Nottingham NG7 2RD, United Kingdom
(2) Department of Physics, King’s College London, The Strand, London, WC2R 2LS, United Kingdom

Abstract
We show that the precise orientation of a C60 molecule which terminates the tip of a scanning probe microscope can be determined with atomic precision from submolecular contrast images of the fullerene cage. A comparison of experimental scanning tunneling microscopy data with images simulated using computationally inexpensive Hu¨ckel theory provides a robust method of identifying molecular rotation and tilt at the end of the probe microscope tip. Noncontact atomic force microscopy resolves the atoms of the C60 cage closest to the surface for a range of molecular orientations at tip-sample separations where the molecule-substrate interaction potential is weakly attractive. Measurements of the C60—C60 pair potential acquired using a fullerene-terminated tip are in excellent agreement with theoretical predictions based on a pairwise summation of the van der Waals interactions between C atoms in each cage, i.e., the Girifalco potential

Identifying passivated dynamic force microscopy tips on H:Si(100)

APPLIED PHYSICS LETTERS 100, 233120 (2012)

Authors
Peter Sharp(1), Sam Jarvis(2), Richard Woolley(1), Adam Sweetman(1), Lev Kantorovich(2), Chris Pakes(3), and Philip Moriarty(1)
(1)School of Physics and Astronomy, The University of Nottingham, Nottingham NG7 2RD, United Kingdom
(2)Department of Physics, King’s College London, The Strand, London WC2R 2LS, United Kingdom
(3)Department of Physics, La Trobe University, Victoria 3086, Australia

Abstract
The chemical reactivity of the tip plays a central role in image formation in dynamic force microscopy, but in very many cases the state of the probe is a key experimental unknown. We show here that an H-terminated and thus chemically unreactive tip can be readily identified via characteristic imaging and spectroscopic (F(z)) signatures, including, in particular, contrast inversion, on hydrogen-passivated Si(100). We determine the tip apex termination by comparing site-specific difference force curves with the results of density functional theory, providing a clear protocol for the identification of chemically unreactive tips on silicon surfaces.

Role of orbital overlap in atomic manipulation

PHYSICAL REVIEW B 85, 235305 (2012)

Authors
Sam Jarvis,(1) Adam Sweetman,(1) Joseph Bamidele,(2) Lev Kantorovich,(2) and Philip Moriarty(1)
(1)The School of Physics and Astronomy, The University of Nottingham, Nottingham, NG7 2RD, United Kingdom
(2)Department of Physics, King’s College London, The Strand, London, WC2R 2LS, United Kingdom

Abstract
We conduct ab initio simulations illustrating that the ability to achieve atomic manipulation using a dynamic force microscope depends on the precise orientation of the dangling bond(s) at the tip apex and their charge density with respect to those of surface atoms. Using the Si(100)-c(4 × 2) surface as a prototype, we demonstrate that it is possible to select tip apices capable of performing atomic manipulation tasks which are unachievable using another choice of apex. Specific tip apices can be identified via examination of F(z) curves taken at different lateral positions.

 Polymerization on stepped surfaces: Alignment of polymers and identification of catalytic sites

ANGEW. CHEM. INT. Ed. 51, 5096 (2012)

Authors
Dr. Alex Saywell(1), Jutta Schwarz(2), Prof. Stefan Hecht(2), Dr. Leonhard Grill(1,*)
(1) Department of Physical Chemistry, Fritz Haber Institute of the Max Planck Society, Faradayweg 4–6, 14195 Berlin (Germany) http://www.fhi-berlin.mpg.de/pc/grill/
(29 Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, 12489 Berlin (Germany)
Email: Dr. Leonhard Grill (lgr@fhi-berlin.mpg.de)

Abstract
Surface defects, such as step edges and kinks, are thought to be the ‘active sites’ that induce site-specific chemical reactions on catalytic materials. The catalytic dissociation of a bromine atom from an organic molecule is shown to occur at kink sites on the stepped Au(10,7,7) surface (see scheme; Br=red). The anisotropic surface also facilitates the production of highly aligned polymers, formed by on-surface covalent coupling of monomer units.

 Voltage-dependent conductance of a single graphene nanoribbon

NATURE NANOTECHNOLOGY 7, 713 (2012)

Authors
M. Koch (1), F. Ample (2), C. Joachim (2,3), and L. Grill (1)
(1) Department of Physical Chemistry, Fritz-Haber-Institute of the Max-Planck-Society, 14195 Berlin, Germany
(2) Institute of Materials Research and Engineering (IMRE), 117602 Singapore
(3) Nanosciences Group and MANA Satellite, CEMES-CNRS, 31055 Toulouse, France

Abstract
Graphene nanoribbons could potentially be used to create molecular wires with tailored conductance properties. However, understanding charge transport through a single molecule requires length-dependent conductance measurements and a systematic variation of the electrode potentials relative to the electronic states of the molecule1,2. Here, we show that the conductance properties of a single molecule can be correlated with its electronic states. Using a scanning tunnelling microscope, the electronic structure of a long and narrow graphene nanoribbon, which is adsorbed on a Au(111) surface, is spatially mapped and its conductance then measured by lifting the molecule off the surface with the tip of the microscope. The tunneling decay length is measured over a wide range of bias voltages, from the localized Tamm states over the gap up to the delocalized occupied and unoccupied electronic states of the nanoribbon. We also show how the conductance depends on the precise atomic structure and bending of the molecule in the junction, illustrating the importance of the edge states and a planar geometry.


Mapping the Excited States of Single Hexa-peri-benzocoronene Oligomers

ACSnano VOL. 6,NO. 4,3230–3235,(2012)

Authors
We-Hyo Soe,†,*Hon Seng Wong,†Carlos Manzano,†Maricarmen Grisolia,‡Mohamed Hliwa,‡,§Xinliang Feng,^Klaus Mullen,^and Christian Joachim†,‡
† IMRE, A*STAR (Agency for Science, Technology and Research), 3 Research Link, 117602, Singapore
‡ GNS-CEMES, CNRS, 29 rue J. Marvig, 31055 Toulouse Cedex,France
§ Faculté des Sciences Ben M'Sik, Université Hassan II-Mohammedia, B.P. 7955 Sidi Othman, Casablanca, Morroco,
^ Max Planck Institute for Polymer Research, Ackermannweg 10, D-55128 Mainz, Germany

Abstract
Electronic states of a molecule are usually analyzed via their decomposition in linear superposition of multielectronic Slater determinants built up from monoelectronics molecular orbitals. It is generally believed that a scanning tunneling microscope (STM) is able to map those molecular orbitals. Using a low-temperature ultrahigh vacuum (LT-UHV) STM, the dI/dV conductance maps of large single hexabenzocoronene (HBC) monomer, dimer, trimer, and tetramer molecules were recorded. We demonstrate that the attribution of a tunnel electronic resonance to a peculiar π molecular orbital of the molecule (or σ intermonomer chemical bond) in the STM junction is inappropriate. With an STM weak-measurement-like procedure, adI/dV resonance results from the conductance contribution of many molecular states whose superposition makes it difficult to reconstruct an apparent molecular orbital electron probability density map.

Mapping the first electronic resonances of a Cu phthalocyanine STM tunnel junction

J. PHYS.: CONDENS. MATTER 24 354011 (2012)

Authors
W-H Soe(1), C Manzano(1), H S Wong(1) and C Joachim(1,2)
(1) IMRE, A*STAR (Agency for Science, Technology and Research), 3 Research Link, 117602, Singapore
(2) GNS-CEMES, CNRS, 29 rue J Marvig, 31055 Toulouse Cedex, France

Abstract
Using a low temperature, ultrahigh vacuum scanning tunneling microscope (STM), dI/dV differential conductance maps were recorded at the tunneling resonance energies for a single Cu phthalocyanine molecule adsorbed on an Au(111) surface. We demonstrated that, contrary to the common assumption, such maps are not representative of the molecular orbital spatial expansion, but rather result from their complex superposition captured by the STM tip apex with a superposition weight which generally does not correspond to the native weight used in the standard Slater determinant basis set. Changes in the molecule conformation on the Au(111) surface further obscure the identification between dI/dV conductance maps and the native molecular orbital electronic probability distribution in space.

Electronic and magnetic properties of molecule-metal interfaces: Transition-metal phthalocyanines adsorbed on Ag(100)

PHYSICAL REVIEW B 85, 155437 (2012)

Authors
A. Mugarza, (1,2) R. Robles, (2) C. Krull, (1,2) R. Korytar, (2,3) N. Lorente, (2) and P. Gambardella1, (2,4,5)
(1)Catalan Institute of Nanotecnology (ICN), UAB Campus, E-08193 Bellaterra, Spain
(2)Centre d’Investigacio en Nanociencia i Nanotecnologia, CIN2, (ICN-CSIC), UAB Campus, E-08193 Bellaterra, Spain
(3)Institut fur Nanotechnologie, Karlsruher Institut fur Technologie, Hermann-von-Helmholtzplatz 1,D-76344 Eggenstein-Leopoldshafen, Germany
(4)Institucio Catalana de Recerca i Estudis Avancats (ICREA), E-08193 Barcelona, Spain
(5)Departament de Fisica, UAB Campus, E-08193 Barcelona, Spain

Abstract
We present a systematic investigation of molecule-metal interactions for transition-metal phthalocyanines (TMPc, with TM = Fe, Co, Ni, Cu) adsorbed on Ag(100). Scanning tunneling spectroscopy and density functional theory provide insight into the charge transfer and hybridization mechanisms of TMPc as a function of increasing occupancy of the 3d metal states. We show that all four TMPc receive approximately one electron from the substrate. Charge transfer occurs from the substrate to the molecules, inducing a charge reorganization in FePc and CoPc, while adding one electron to ligand \pi-orbitals in NiPc and CuPc. This has opposite consequences on the molecular magnetic moment: in FePc and CoPc the interaction with the substrate tends to reduce the TM spin, whereas in NiPc and CuPc an additional spin is induced on the aromatic Pc ligand, leaving the TM spin unperturbed. In CuPc, the presence of both TM and ligand spins leads to a triplet ground state arising from intramolecular exchange coupling between d and \pi electrons. In FePc and CoPc the magnetic moment of C and N atoms is antiparallel to that of the TM. The different character and symmetry of the frontier orbitals in the TMPc series leads to varying degrees of hybridization and correlation effects, ranging from the mixed-valence (FePc, CoPc) to the Kondo regime (NiPc, CuPc). Coherent coupling between Kondo and inelastic excitations induces finite-bias Kondo resonances involving vibrational transitions in both NiPc and CuPc and triplet-singlet transitions in CuPc.

Spin doping of individual molecules by using single-atom manipulation

NANO LETTERS 12, 3609 (2012)

Authors
Roberto Robles, (1) Nicolas Lorente,(1) Hironari Isshiki,(2,3) Jie Liu,(2,3) Keiichi Katoh,(3) Brian K. Breedlove,(3) Masahiro Yamashita,(3) and Tadahiro Komeda(2,4)
(1)Centro de Investigacio´n en Nanociencia y Nanotecnología, CIN2 (CSIC - ICN), Campus de la UAB, E-08193 Bellaterra, Spain
(2)Institute of Multidisciplinary Research for Advanced Materials (IMRAM, Tagen), Tohoku University, 2-1-1, Katahira, Aoba-Ku, Sendai 980-0877, Japan
(3)Department of Chemistry, Graduate School of Science, Tohoku University, Aramaki-Aza-Aoba, Aoba-Ku, Sendai 980-8578, Japan
(4)CREST, Japan Science and Technology Agency (JST), Saitama 332-0012, Japan

Abstract
Being able to control the spin of magnetic molecules at the single-molecule level will make it possible to develop new spin-based nanotechnologies. Gate-field effects and electron and photon excitations have been used to achieve spin switching in molecules. Here, we show that atomic doping of molecules can be used to change the molecular spin. Furthermore, a scanning tunneling microscope was used to place or remove the atomic dopant on the molecule, allowing us to change the molecular spin in a controlled way. Bis(phthalocyaninato)yttrium (YPc2) molecules deposited on an Au (111) surface keep their spin-1/2 magnetic moment due to the small molecule-substrate interaction. However, when Cs atoms were carefully placed onto YPc2 molecules, the spin of the molecule vanished as shown by our conductance measurements and corroborated by the results of density functional theory calculations.

Bottom-up zu molekularen Nanostrukturen (in German)

NACHRICHTEN AUS DER CHEMIE, 60, Oktober (2012)

Authors Marie Gille, Leonhard Grill, Stefan Hecht, Marie Gille, Humboldt Universitat UBER, Leonhard Grill ,Max Planck FHI MPG, Stefan Hecht, Humboldt Universitat UBER, sh@chemie.hu-berlin.de

Abstract
Polymerisationen auf Oberflächen zum Aufbau von Nanostrukturen stehen als Bottom-up-Methoden im Gegensatz zu den bisher für elektronische Bauteile verwendeten Top-down-Methoden, beispielsweise der Lithografie. Das Ziel ist, konjugierte Polymere als leitende und halbleitende Materialien an Stelle der heutigen siliciumbasierten Elektronik einzusetzen.


STM manipulation of a subphthalocyanine double-wheel molecule on Au(111)

J. PHYS.: CONDENS. MATTER 24 (2012) 404001 (6pp)

AuthorsAnja Nickel(1), Joerg Meyer(1), Robin Ohmann(1), Henri-Pierre Jacquot de Rouville(2), Gwenael Rapenne(2,3), Francisco Ample(4), Christian Joachim(2,4), Gianaurelio Cuniberti(1,5) and Francesca Moresco(1)
(1) Institute for Materials Science and Max Bergmann Center of Biomaterials, Technische University at Dresden, D-01062 Dresden, Germany
(2) CNRS, CEMES & MANA Satellite (Centre d’Elaboration des Materiaux et d’Etudes Structurales),BP 94347, 29 rue J Marvig, F-31055 Toulouse, France
(3) Université de Toulouse, UPS, 29 rue J Marvig, F-31055 Toulouse, France
(4) IMRE, A*STAR (Agency for Science, Technology and Research), 3 Research Link, 117602, Singapore
(5) Division of IT Convergence Engineering, POSTECH, Pohang 790-784, Republic of Korea
E-mail: francesca.moresco@nano.tu-dresden.de

Abstract
A new class of double-wheel molecules is manipulated on a Au(111) surface by the tip of a scanning tunneling microscope (STM) at low temperature. The double-wheel molecule consists of two subphthalocyanine wheels connected by a central rotation carbon axis. Each of the subphthalocyanine wheels has a nitrogen tag to monitor its intramolecular rolling during an STM manipulation sequence. The position of the tag can be followed by STM, allowing us to distinguish between the different lateral movements of the molecule on the surface when manipulated by the STM tip.


  Contacting a Conjugated Molecule with a Surface Dangling Bond Dimer on a Hydrogenated Ge(001) Surface Allows Imaging of the Hidden Ground Electronic State

ACSnano VOL. 7 NO. 11 10105–10111 (2013)

Authors

Szymon Godlewski,(1,#,*) Marek Kolmer,(1,#) Hiroyo Kawai,(2,#,*) Bartosz Such,(1) Rafal Zuzak,(1) Mark Saeys,(2,3) Paula de Mendoza (4), Antonio M. Echavarren (4), Christian Joachim,(5) and Marek Szymonski(1)

(1) Centre for Nanometer-Scale Science and Advanced Materials, NANOSAM, Faculty of Physics, Astronomy and Applied Computer Science, Jagiellonian University, Reymonta 4, PL 30-059, Krakow, Poland,
(2) Institute of Materials Research and Engineering, 3 Research Link, Singapore 117602, Singapore,
(3)Department of Chemicaland Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117576, Singapore,
(4) Institute of Chemical Research of Catalonia(ICIQ), Avenida Països Catalans 16, 43007 Tarragona, Spain,
(5) Nanosciences Group & MANA Satellite, CEMES-CNRS, 29 Rue Jeanne Marvig, F-31055 Toulouse, France.
# S. Godlewski, M. Kolmer, and H. Kawai contributed equally to this work.

Abstract
Fabrication of single-molecule logic devices requires controlled manipulation of molecular states with atomic-scale precision. Tuning molecule_substrate coupling is achieved here by the reversible attachment of a prototypical planar conjugated organic molecule to dangling bonds on the surface of a hydrogenated semiconductor. We show that the ground electronic state resonance of a Y-shaped polyaromatic molecule physisorbed on a defect-free area of a fully hydrogenated surface cannot be observed by scanning tunneling microscopy (STM) measurements because it is decoupled from the Ge bulk states by the hydrogen-passivated surface. The state can be accessed by STM only if the molecule is contacted with the substrate by a dangling bond dimer. The reversibility of the attachment processes will be advantageous in the construction of surface atomic-scale circuits composed of single-molecule devices interconnected by the surface dangling bond wires.

  Manipulation of a single molecule ground state by means of gold atom Contacts

Chemical Physics Letters 587 (2013) 35–39

Authors

C. Manzano (a),, W.H. Soe (a), M. Hliwa (c), M. Grisolia (b), H.S. Wong (a), C. Joachim (a),

(a)   IMRE, A⁄STAR (Agency for Science, Technology and Research), 3-Research Link, 117602 Singapore, Singapore
(b)   GNS-CEMES & MANA Satellite, CNRS, 29 rue J. Marvig, 31055 Toulouse Cedex, France
(c)   Faculté des Science Ben M’Sik, Université Hassan II-Mohammedia-Casablanca, Morocco

Abstract
Single gold adatoms were manipulated on a Au(111) surface with the tip of a scanning tunneling microscope to contact selected peripheral p bonds of a single Coronene molecule. Tunnelling  electron spectroscopy and differential conductance mapping of the Au–Coronene complexes show how Coronene’selectronic ground state is shifted down in energy as the function of the number of interacting Au atoms, demonstrating that a Coronene molecule can function like a single molecule counter. The number of interacting atoms can be counted by simply following the linear energy downshift of Coronene’s ground state.


  Switching Mechanisms for Single-Molecule Logic Gates

Architecture and Design of Molecule Logic Gates and Atom Circuits, Springer Series Advances in Atom and Single Molecule Machines: ISBN: 978-3-642-33136-7 (2013) pages 55-69.

Authors

C. Toher, F. Moresco, and G. Cuniberti,

Institute for Materials Science and Max Bergmann Center of Biomaterials, Dresden University of Technology, 01062 Dresden, Germany

Abstract
Single-molecule logic gates have the potential to fundamentally revolutionize computer architecture. However, performing any type of logic function within a single molecule requires using external inputs to modify one or more of the intrinsic properties of the molecule, such as its geometrical conformation, electronic structure, or spin configuration. In this chapter, we will discuss the variety of different physical mechanisms which have been proposed to induce and control such changes, ranging from applied potential bias and electric fields to chemical interactions to mechanical pressure, focusing in particular on their suitability for use in single-molecule logic circuitry..


  SPM Imaging of Trinaphthylene Molecular States on a Hydrogen Passivated Ge(001) Surface

Architecture and Design of Molecule Logic Gates and Atom Circuits, Springer Series Advances in Atom and Single Molecule Machines: ISBN: 978-3-642-38808-8 (2013), pages 105-114.

Authors

Marek Kolmer (a), Szymon Godlewski (a), Bartosz Such (a), Paula de Mendoza (b), Claudia De Leon (b), Antonio M. Echavarren (b), Hiroyo Kawai (c), Mark Saeys (c,d), Christian Joachim (c,e) and Marek Szymonski (a),

(a)   Centre for Nanometer-Scale Science and Advanced Materials, NANOSAM, Faculty of Physics, Astronomy, and Applied Computer Science, Jagiellonian University, Reymonta 4,30059 Krakow, Poland
(b)   Institute of Chemical Research of Catalonia (ICIQ), Avenida Països Catalans 16, 43007. Tarragona, Spain
(c)   Institute of Materials Research and Engineering, 3 Research Link, Singapore 117602,Singapore
(d)   Department of Chemical and Biomolecular Engineering, National University of Singapore,4 Engineering Drive 4, Singapore 117576, Singapore
(e)   Nanosciences Group & MANA Satellite, CEMES-CNRS, 29 rue Jeanne Marvig, F-31055 Toulouse, France

Abstract
We report on studies concerning individual trinaphthylene molecules (Y molecules) deposited and anchored on the hydrogenated Ge(001):H surface. The characterization of single Y molecules has been performed by means of cryogenic temperature STM imaging using conventional STM tungsten tips and tuning fork-based sensors. In the latter case, a qPlus sensor facilitated simultaneous STM and NC-AFM measurements and thus molecular states were probed by both tunneling current and atomic forces concurrently. We show that the molecules are physisorbed, thus weakly interacting with the substrate. Contrary to the measurements on hydrogenated silicon, for planar aromatic molecules on the hydrogenated germanium, both empty and filled molecular states could be probed by STM.



Electronic Structure and Properties of Graphen Nanoribbons: Zigzag and Armchair Edges

Architecture and Design of Molecule Logic Gates and Atom Circuits, Springer Series Advances in Atom and Single Molecule Machines: ISBN: 978-3-642-38808-8 (2013), pages 81-90.

Authors

Matthias Koch (a), Francisco Ample (b), Christian Joachim (b) and Leonhard Grill (a)
(a)  Department of Physical Chemistry, Fritz-Haber-Institute of the Max-Planck-Society, 14195 Berlin, Germany
University, Reymonta Str. 4, PL 30-059 Krakow, Poland
(b)  Institute of Materials Research and Engineering (IMRE), Singapore, Singapore C. Joachim Nanosciences Group, CEMES-CNRS, Toulouse, France

Structural development and energy dissipation insimulated silicon apices

Beilstein J. Nanotechnol.2013,4,941–948

Authors
Samuel Paul Jarvis(1), Lev Kantorovich (2) and Philip Moriarty (1)
(1) School of Physics and Astronomy, University of Nottingham, Nottingham NG7 2RD, United Kingdom
(2) Department of Physics,King’s College London, The Strand, London WC2R 2LS, United Kingdom

 
Abstract
In this paper we examine the stability of silicon tip apices by using density functional theory (DFT) calculations. We find that some tip structures - modelled as small, simple clusters - show variations in stability during manipulation dependent on their orientation with respect to the sample surface. Moreover, we observe that unstable structures can be revealed by a characteristic hysteretic behaviour present in the F(z) curves that were calculated with DFT, which corresponds to a tip-induced dissipation of hundreds of milli electron volts resulting from reversible structural deformations. Additionally, in order to model the structural evolution of thetip apex within a low temperature NC-AFM experiment, we simulated a repeated tip–surface indentation until the tip structure converged to a stable termination and the characteristic hysteretic behaviour was no longer observed. Our calculations suggest that varying just a single rotational degree of freedom can have as measurable an impact on the tip–surface interaction as a completely different tip structure.

Abstract
Scanning tunneling microscopy is a very suitable instrument for the local probing and spectroscopic characterization of individual molecules, in our case narrow grapheme nanoribbons. The electronic properties of a grapheme nanoribbon can be controlled by its edge structure and width. Bottom-up approaches like on-surface synthesis allow the formation of extended conjugated electronic systems. Moreover, they lead to atomically defined edges which are important as structural defects have been predicted to modify the electronic structure. We have used low temperature scanning tunneling microscopy to investigate the formation, adsorption properties, and electronic structure of single graphene nanoribbons. 10,100-Dibromo-9,90-bianthryl molecules were used as molecular building blocks to form graphene nanoribbons after linking of the monomers and subsequent cyclodehydrogenation. In addition to intact ribbons, the influence of various defects on the electronic states is also investigated.

Submolecular Resolution Imaging of C60: From Orbital Density to Bond Order

Proceedings of the 3rd AtMol International Workshop, Berlin 24-25 September 2012, “Imaging and Manipulating Molecular Orbitals” Advances in Atom and Single Molecule Machines - Series Editor: Christian Joachim, Springer, ISBN: 978-3-642-38808-8 (2013) pages 195-206.

Authors

Philip Moriarty (a)
(a)  School of Physics and Astronomy, University of Nottingham, Nottingham NG7 2RD, UK

Abstract
I review a number of advances and milestones in the acquisition of submolecular resolution scanning probe microscope images of the buckminsterfullerene (C60) molecule. Scanning tunneling microscopy essentially provides an image derived from the local density of states of the electronic structure of a molecule within an energy window defined by the tip-sample bias voltage. These measurements of the local density of states, which are generally interpreted in terms of molecular orbital probability density, have now been complemented by non-contact atomic force microscopy (NC-AFM) images of the internal structure of the molecule. The NC-AFM images yield either atomic resolution (if imaging occurs in the attractive regime of the tip-sample potential), or, in the Pauli exclusion regime, remarkable maps of the charge density of the interatomic bonds. This combination of scanning probe techniques is exceptionally powerful in elucidating the correlations between atomic structure, bond order, and the submolecular distribution and symmetry of electron density.

Mechanical Conformation Switching of a Single Pentacene Molecule on Si(100)-(2 × 1)

J. Phys. Chem. C, 117, 26040−26047 (2013);

Authors

O. A. Neucheva,(1) F. Ample,(1) and C. Joachim,(1,2)
(1) IMRE (Institute of Materials Research and Engineering), A*STAR (Agency for Science, Technology and Research), 3 Research Link, 117602 Singapore
(2) GNS-CEMES & MANA Satellite, CNRS, 29 rue J. Marvig, 31055 Toulouse Cedex, France

Abstract
The mechanical switching of a single pentacene molecule chemisorbed in a planar configuration along a dimer row of the Si(100)-(2 × 1) surface was performed experimentally using the tip apex of a scanning tunneling microscope. The mechanical switching reaction path was identified theoretically on the ground state potential energy surface of the pentacene/Si(100)-(2 × 1) system. A low-temperature scanning tunneling microscope as well as semiempirical ASED+ molecular mechanical and elastic scattering quantum chemistry (ESQC) calculations were employed to perform the studies. Pushing with the STM tip apex and at zero bias voltage exactly at the center of the chemisorbed pentacene molecule induces a mechanical conformation change of the pentacene from its metastable to its surface stable conformation on the Si(100)-(2 × 1) surface.

Aligning the Band Gap of Graphene Nanoribbons by Monomer Doping

ANGEW. CHEM. INT, Ed., 52, 4422 –4425 (2013)

AuthorsChristopher Bronner,* Stephan Stremlau, Marie Gille, Felix Brauße, Anton Haase, Stefan Hecht,* and Petra Tegeder*, C. Bronner, S. Stremlau, A. Haase, Prof. Dr. P. Tegeder, Fachbereich Physik, Freie University, Berlin, Arnimallee 14, 14195 Berlin (Germany)
E-mail: bronner@zedat.fu-berlin.de   petra.tegeder@physik.fu-berlin.d
Dr. M. Gille, F. Brauße, Prof. Dr. S. Hecht, Department of Chemistry, Humboldt-University zu Berlin Brook-Taylor-Straße 2, 12489 Berlin (Germany)
E-mail:  sh@chemie.hu-berlin.de
Prof. Dr. P. Tegeder, Physikalisch-Chemisches Institut Ruprecht-Karls-University Heidelberg Im Neuenheimer Feld 253, 69120 Heidelberg (Germany)

Abstract
In summary, we have successfully doped graphene nano-ribbons in a well-defined manner by selective nitrogen substitution of the precursor monomers which does not interfere with the on-surface synthesis reaction. Using HREELS in combination with photoelectron spectroscopy, we could show that the band gap is linearly shifted relative to the electronic structure of the environment of the GNR but remains almost unchanged in magnitude, as expected for pyridine-like nitrogen at the edges of armchair GNRs.[13] The positions of the bands and thus the size of the band gap agree well with other experimental data on the pristine GNR. [18] The independence of the size of the band gap on one hand and its alignment relative to the Fermi level on the other hand could prove useful in tailoring the electronic properties of GNR devices. Doping the molecular precursors in a bottom-up fabrication technique furthermore allows a well-defined site selection and dosage of the dopant atoms within defect free GNRs. This should add another powerful item to the toolbox of band gap engineering of graphene nanostructures and, together with width variation and edge shaping, thus contribute to controlling their properties towards technological applications

Modular Synthesis of Monomers for On-Surface Polymerization to Graphene Architectures

SYNLETT, 24, 0259–0263 (2013)

Authors Marie Gille(a), Andreas Viertel(a), Steffen Weidner(b), Stefan Hechta*
(a) Department of Chemistry, Humboldt -Universität zu Berlin, Brook-Tayl or-Str. 2, 12489 Berlin, Germany  Fax +49(30)20936940;  
E-mail: sh@chemie.hu-berlin.de
(b) Bundesanstalt für Materialforschung und -prüfung (BAM), Richard-Willstätter-Str. 11, 12489 Berlin, Germany

Abstract
We developed a modular synthesis of halogenated polycyclic aromatic monomers for on surface polymerization to generate graphene wires, ribbons, and networks.


Moving Nanostructures: Pulse-Induced Positioning of Supramolecular Assemblies

ACSnano VOL. 7, NO. 1, 191–197, (2013)

Authors Anja Nickel,† Robin Ohmann,† Joerg Meyer,† Maricarmen Grisolia,‡ Christian Joachim,‡ Francesca Moresco,†,* and Gianaurelio Cuniberti †,§
†Institute for Materials Science and Max Bergmann Center of Biomaterials, Technische Universität Dresden, D-01062 Dresden, Germany,
‡CNRS, CEMES (Centre d'Elaboration des Matériaux et d'Etudes Structurales) and MANA Satellite, BP 94347, 29 rue J. Marvig, F-31055 Toulouse, France,
§Division of IT Convergence Engineering, POSTECH, Pohang 790-784, Republic of Korea

Abstract
For the development of nanoscale devices, the manipulation of single atoms and molecules by scanning tunneling microscopy is a well-established experimental technique. However, for the construction of larger and higher order structures, it is important to move not only one adsorbate but also several at the same time. Additionally, a major issue in standard manipulation experiments is the strong mechanical interaction of the tip apex and the adsorbate, which can damage the system under investigation. Here, we present a purely electronic excitation method for the controlled movement of a weakly interacting assembly of a few molecules. By applying voltage pulses, this supra molecular nanostructure is moved in a controlled manner without losing its collective integrity. Depending on the polarity and location of the applied voltage, the movement can be driven in predefined directions. Our gentle purely electronic approach for the controlled manipulation of nanostructures opens new ways to construct molecular devices

Electron transport through dangling-bond silicon wires on H-passivated Si(100)

J. PHYS.: CONDENS. MATTER 25 025503 (2013)

Authors Mikaël Kepenekian(1), Frederico D Novaes(1), Roberto Robles(1), Serge Monturet(2), Hiroyo Kawai(3), Christian Joachim(2,3) and Nicolás Lorente(1)
mikael.kepenekian@cin2.es
(1)  Centro de Investigación en Nanociencia y Nanotecnología (CSIC-ICN), Campus de la UAB, E-08193 Bellaterra, Spain
(2)  Centre d'Elaboration des Matériaux et d'Etudes Structurales (CEMES), CNRS, 29 rue J. Marvig, F-31055 Toulouse Cedex, France
(3)  Institute of Materials Research and Engineering, 3 Research Link, Singapore 117602, Singapore

Abstract
We compute the electron transmission through different types of dangling-bond wire on Si(100)–H (2 × 1). Recent progress in the construction of atomic-size interconnects (Weber et al 2012 Science 335 64) shows the possibility to achieve atomic-size circuits via atomic-size wires using silicon surfaces. Hence, electron transport through quasi-1D Si-based structures is a compelling reality. Prior to these achievements, wires formed by controlled desorption of passivating H atoms off the monohydride Si(100) surface have been shown to be subject to 1D correlations and instabilities (Hitosugi et al 1999 Phys. Rev. Lett. 82 4034). The present calculations are based on density functional theory and evaluate the electron transmission though the minimum-energy 1D structures that can be formed when creating dangling-bonds on Si(100)-(2 × 1)-H. The purpose of this study is twofold: (i) to assess the transport properties of these atomic-size wires in the presence of 1D instabilities; (ii) to provide a fingerprint for experimental identification of the instability through the transport characteristics of the wires. To these aims, we evaluate the electron transport through the wires in the absence of instabilities, in the presence of distortions (Jahn–Teller instabilities) and in the presence of magnetic instabilities (ferro- and antiferro-ordering). We find that instabilities substantially reduce the transport capabilities of dangling-bond wires leading to transmissions that vary so differently with electron energy that an unambiguous identification of the wire type should be accessible in transport experiments.

Polymerization of Polyanthrylene on a Titanium Dioxide (011)-(2 _ 1)Surface

Angew. Chem. 2013, 125, 1 – 5

Authors Marek Kolmer, Amir A. Ahmad Zebari, Jakub S. Prauzner-Bechcicki,* Witold Piskorz, Filip Zasada, Szymon Godlewski, Bartosz Such, Zbigniew Sojka, and Marek Szymonski M. Kolmer, A. A. Ahmad Zebari, Dr. J. S. Prauzner-Bechcicki, Dr. S. Godlewski, Dr. B. Such, Prof. M. Szymonski
Centre for Nanometer-Scale Science and Advanced Materials, NANOSAM, Faculty of Physics, Astronomy and Applied Computer Science, Jagiellonian University Reymonta 4, 30-059 Krakow (Poland)
E-mail: jakub.prauzner-bechcicki@uj.edu.pl
Dr. W. Piskorz, Dr. F. Zasada, Prof. Z. Sojka Faculty of Chemistry, Jagiellonian University Ingardena 3, 30-060 Krakow (Poland)

Adsorption Site Determination of a Molecular Monolayer via Inelastic Tunneling

Nano Lett. 2013, 13, 2346−2350

Authors Daniel Wegner,(1) Ryan Yamachika,(2) Xiaowei Zhang,(2) Yayu Wang,(2) Michael F. Crommie,(2) and Nicolas Lorente(3)
(1) Physikalisches Institut and Center for Nanotechnology (CeNTech), Westfalische Wilhelms-Universitat Munster, 48149 Münster, Germany
(2) Department of Physics, University of California at Berkeley, and Materials Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720-7300, United States
(3) Centre d’Investigació en Nanociència i Nanotecnologia, CIN2 (CSIC-ICN), Campus de la UAB, 08193 Bellaterra, Spain

Abstract

We have combined scanning tunneling microscopy with inelastic electron tunneling spectroscopy (IETS) and density functional theory (DFT) to study a tetracyanoethylene monolayer on Ag(100). Images show that the molecules arrange in locally ordered patterns with three nonequivalent, but undeterminable, adsorption sites. While scanning tunneling spectroscopy only shows subtle variations of the local electronic structure at the three different positions, we find that vibrational modes are very sensitive to the local atomic environment. IETS detects sizable mode frequency shifts of the molecules located at the three topographically detected sites, which permits us to determine the molecular adsorption sites through identification with DFT calculations.

Tunneling electron induced rotation of a copper phthalocyanine molecule on Cu(111)

PHYSICAL REVIEW B 88, 075410 (2013)

Authors J. Schaffert,(1) M. C. Cottin,(1) A. Sonntag,(1) C. A. Bobisch,(1) R. M¨oller,(1) J.-P. Gauyacq,(2) and N. Lorente(3,4)
(1) Faculty of Physics, Center for Nanointegration Duisburg-Essen (CENIDE), University of Duisburg-Essen,Lotharstr. 1, D-47057 Duisburg, Germany
(2) Institut des Sciences Moleculaires d’Orsay, CNRS-Universite Paris-Sud 11, UMR 8214, Batiment. 351, Universite Paris-Sud, F-91405 Orsay Cedex, France
(3) ICN2–Institut Catala de Nanociencia i Nanotecnologia, Campus UAB, 08193 Bellaterra (Barcelona), Spain
(4) CSIC–Consejo Superior de Investigaciones Cientificas, ICN2 Building, Campus UAB, 08193 Bellaterra (Barcelona), Spain

Abstract

The rates of a hindered molecular rotation induced by tunneling electrons are evaluated using scattering theory within the sudden approximation. Our approach explains the excitation of copper phthalocyanine molecules (CuPc) on Cu(111) as revealed in a recent measurement of telegraph noise in a scanning tunneling microscopy experiment [Schaffert et al., Nat. Mater. 12, 223 (2013)]. A complete explanation of the experimental data is performed by computing the geometry of the adsorbed system, its electronic structure, and the energy transfer between tunneling electrons and the molecule’s rotational degree of freedom. The results unambiguously show that tunneling electrons induce a frustrated rotation of the molecule. In addition, the theory determines the spatial distribution of the frustrated rotation excitation, confirming the striking dominance of two out of four molecular lobes in the observed excitation process. This lobe selectivity is attributed to the different hybridizations with the underlying substrate.

Controlling intramolecular hydrogen transfer in a porphycene molecule with single atoms or molecules located nearby

Nature Chemistry Vol 6 January (2014)

Authors

Takashi Kumagai (a), Felix Hanke (b), Sylwester Gawinkowski (c), John Sharp (b), Konstantinos Kotsis (b), Jacek Waluk (c), Mats Persson (b,d), and Leonhard Grill (a,f)

(a)  Department of Physical Chemistry, Fritz-Haber Institute of the Max-Planck Society, Faradayweg 4–6, 14195 Berlin, Germany
(b)  Surface Science Research Centre and Department of Chemistry, University of Liverpool, Liverpool L69 3BX, UK
(c)  Institute of Physical Chemistry, Polish Academy of Sciences Kasprzaka 44/52, Warsaw 01-224, Poland
(d)  Department of Applied Physics, Chalmers University of Technology, 41296 Go¨teborg, Sweden,
(f)  Department ofPhysical Chemistry, University of Graz, Heinrichstrasse 28, 8010 Graz, Austria
(†)  Present address: Accelrys Ltd, 334 Science Park, CB4 0WN Cambridge, UK

Abstract
Although the local environment of a molecule can play an important role in its chemistry, rarely has it been examined experimentally at the level of individual molecules. Here we report the precise control of intramolecular hydrogen-transfer (tautomerization) reactions in single molecules using scanning tunnelling microscopy. By placing, with atomic precision, a copper adatom close to a porphycene molecule, we found that the tautomerization rates could be tuned up and down in a controlled fashion, surprisingly also at rather large separations. Furthermore, we extended our study to molecular assemblies in which even the arrangement of the pyrrolic hydrogen atoms in the neighbouring molecule influences the tautomerization reaction in a given porphycene, with positive and negative cooperativity effects. Our results highlight the importance of controlling the environment of molecules with atomic precision and demonstrate the potential to regulate processes that occur in a single molecule.

Substrate-controlled linking of molecular building blocks: Au(111) vs. Cu(111)

Surface Science 627 (2014) 70–74

Authors

Matthias Koch (a), Marie Gille (b), Andreas Viertel (b), Stefan Hecht (b), Leonhard Grill (a,c)

(a)  Department of Physical Chemistry, Fritz-Haber-Institute of the Max-Planck-Society, 14195 Berlin, Germany
(b)  Department of Chemistry, Humboldt-Universität zu Berlin, 12489 Berlin, Germany
(c)  Department of Physical Chemistry, University of Graz, Heinrichstrasse 28, 8010 Graz, Austria

Abstract
The coupling of dibromohexabenzocoronene (Br2-HBC) as a precursor molecule is investigated by scanning tunneling microscopy (STM) on two noble metal surfaces: Au(111) and Cu(111). It is found that the on surface polymerization of molecular building blocks equipped with halogen atoms is strongly influenced by the choice of the substrate. While on Au(111) a heating step of up to 520 K is required to activate the molecules and form polymers, on Cu(111) the catalytic reactivity causes activation already below room temperature. Due to the different substrates, the intramolecular bonds in the polymers between the HBC units differ: The HBC molecules are covalently coupled on Au(111) while on Cu(111) a copper adatom mediates the bonding. This effect is proven by the comparison with gas phase calculations and by lateral manipulation with the STMtip. The choice of the substrate thus does not only define the activation temperature but also lead to different bonding strengths between the molecular building blocks.