Sami Paavilainen

Imaging Bond Formation Between a Gold Atom and Pentacene on an Insulating Surface

A covalent bond between an individual pentacene molecule and a gold atom was formed by means of single-molecule chemistry inside a scanning tunneling microscope junction. The bond formation is reversible, and different structural isomers can be produced. The single-molecule synthesis was done on ultrathin insulating films that electronically isolated the reactants and products from their environment. Direct imaging of the orbital hybridization upon bond formation provides insight into the energetic shifts and occupation of the molecular resonances.

Analysis of Twisting of Cellulose Nanofibrils in Atomistic Molecular Dynamics Simulations

We use atomistic molecular dynamics simulations to study the crystal structure of cellulose nanofibrils, whose sizes are comparable with the crystalline parts in commercial nanocellulose. The simulations show twisting, whose rate of relaxation is strongly temperature dependent. Meanwhile, no significant bending or stretching of nanocellulose is discovered. Considerations of atomic-scale interaction patterns bring about that the twisting arises from hydrogen bonding within and between the chains in a fibril.

Single-Molecule Synthesis and Characterization of Metal−Ligand Complexes by Low-Temperature STM

We present scanning tunneling microscopy (STM)-based single-molecule synthesis of linear metal-ligand complexes starting from individual metal atoms (iron or nickel) and organic molecules (9,10-dicyanoanthracene) deposited on an ultrathin insulating film. We directly visualize the frontier molecular orbitals by STM orbital imaging, from which, in conjunction with detailed density functional theory calculations, the electronic structure of the complexes is inferred. Our studies show how the order of the molecular orbitals and the spin-state of the complex can be engineered through the choice of the metal atom. The high-spin iron complex has a singly occupied delocalized orbital with a large spin-splitting that points to the use of these engineered complexes as modular building blocks in molecular spintronics.

Role of translational and vibrational energy in the dissociative chemisorption of methane on Pd{110}

Abstract Dissociative adsorption of methane has been investigated on Pd {1 1 0} by using molecular beam surface scattering. The initial sticking probability has been determined in the translational energy range of 7–95 kJ/mol and at selected vibrational energies from 300 to 700 K. The measured initial sticking probability is found to increase strongly with both translational and vibrational energy of CH4 molecules. The activation of the dissociative chemisorption of CH4 induced by the vibrational energy is shown to depend on the translational energy and is attributed to the excitation of the bending modes of the incident molecule. We have also performed molecular dynamics simulations to investigate the dissociation mechanism theoretically. The simulations clearly demonstrate that an efficient energy transfer occurs upon adsorption between the translational and vibrational energies of the incident CH4 molecule, which thereby facilitates the deformation of the molecular structure of CH4 resulting in dissociation.

How endoglucanase enzymes act on cellulose nanofibrils: role of amorphous regions revealed by atomistic simulations

AbstractTransformation of cellulose into monosaccharides can be achieved in a chemical process performed by a special group of enzymes known as cellulases. We have used atomistic molecular dynamics simulations to study endoglucanase II (Cel5A) that is one of the proteins in this group. Based on the atomistic simulation results, we discuss how the Cel5A enzyme interacts with cellulose fibrils comprised of both crystalline and amorphous regions. We show that the enzyme’s carbohydrate-binding domain prefers to interact with crystalline regions of cellulose, while the catalytic domain has a high affinity to the amorphous regions of fibrils. In particular, through electrostatic interactions the catalytic domain attracts loose glucose chains to its catalytic cleft. The atomistic details of the enzyme–cellulose interaction are presented and the implications for practical applications are briefly discussed.

Submolecular imaging of chloronitrobenzene isomers on Cu(111).

We compare computer simulations to experimental scanning tunneling microscopy (STM) images of chloronitrobenzene molecules on a Cu(111) surface. The experiments show that adsorption induced isomerization of the molecules takes place on the surface. Furthermore, not only the submolecular features can be seen in the STM images, but different isomers can also be recognized. The Todorov-Pendry approach to tunneling produces simulated STM images which are in good accordance with the experiments. Alongside with STM simulations in a tight-binding basis, ab initio calculations are performed in order to analyze the symmetry of relevant molecular orbitals and to consider the nature of tunneling channels. Our calculations show that while the orbitals delocalized to the phenyl ring create a relatively transparent tunneling channel, they also almost isolate the orbitals of the substitute groups at energies which are relevant in STM experiments. These features of the electronic structure are the key ingredients of the accurate submolecular observations.

Effect of electron-phonon interaction on the formation of one-dimensional electronic states in coupled Cl vacancies

The formation of extended electron states in one-dimensional nanostructures is of key importance for the function of molecular electronic devices. Here, we study the effects of strong electron-phonon interaction on the formation of extended electronic states in intentionally created Cl vacancy pairs and chains in a NaCl bilayer on Cu(111). The interaction between the vacancies was tailored by fabricating vacancy pairs and chains of different orientation and separation with atomic precision using vertical manipulation. Small vacancy separations led to the formation of quantum-well-like vacancy states and localized interface states. By using scanning tunneling spectroscopy, we measured their energy splitting and broadening as a function of the intervacancy separation. Remarkably, the energy splitting between the vacancy states is enlarged by level repulsion resulting from the phonon dressing of the electronic states, as evidenced by theory.

STM simulation of molecules on ultrathin insulating overlayers using tight-binding: Au–pentacene on NaCl bilayer on Cu

Abstract We present fast and efficient tight-binding (TB) methods for simulating scanning tunneling microscopy (STM) imaging of adsorbate molecules on ultrathin insulating films. Due to the electronic decoupling of the molecule from the metal surface caused by the presence of the insulating overlayer, STM can be used to image the frontier molecular orbitals of the adsorbate. These images can be simulated with a very efficient scheme based on hopping integrals which also enables the analysis of phase shifts in the STM current. Au–pentacene complex adsorbed on a NaCl bilayer on Cu substrate provides an intricate model system which has been previously studied both experimentally and theoretically. Our calculations indicate that the complicated shape of the molecular orbitals may cause multivalued constant current surfaces – leading to ambiguity of the STM image. The results obtained using the TB methods are found to be consistent with both DFT calculations and experimental data.

Vibrational assignments and line shapes in inelastic tunneling spectroscopy: H on Cu(100)

We have carried out a computational study of the inelastic electron tunnelling spectrum (IETS) of the two vibrational modes of a single hydrogen atom on a Cu(100) surface in a scanning tunnelling microscopy (STM) junction. This study addresses key issues about vibrational assignment and line shape of observed peaks in IETS within the framework of density functional theory calculations and the Lorente-Persson theory for STM-IETS. We argue that the observation of only a single broad peak in the STM-IETS [L. J. Lauhon and W. Ho Phys. Rev. Lett. 85, 4566 (2000)] is not caused by any symmetry restrictions or any cancellation between inelastic and elastic vibrational contributions for one of the two modes but is due to strongly overlapping superposition of the contributions from the two modes caused by the rather large instrumental broadening and the narrow vibrational energy separation between the modes. In particular, we find that this broadening and the large asymmetry of the vibrational line shapes gives rise to substantial apparent vibrational energy shifts of the two modes and decreases their apparent energy separation.

Coexisting Honeycomb and Kagome Characteristics in the Electronic Band Structure of Molecular Graphene

We uncover the electronic structure of molecular graphene produced by adsorbed CO molecules on a copper (111) surface by means of first-principles calculations. Our results show that the band structure is fundamentally different from that of conventional graphene, and the unique features of the electronic states arise from coexisting honeycomb and Kagome symmetries. Furthermore, the Dirac cone does not appear at the K-point but at the Γ-point in the reciprocal space and is accompanied by a third, almost flat band. Calculations of the surface structure with Kekulé distortion show a gap opening at the Dirac point in agreement with experiments. Simple tight-binding models are used to support the first-principles results and to explain the physical characteristics behind the electronic band structures.