[show abstract][hide abstract] ABSTRACT: We use cryogenic scanning tunneling microscopy and spectroscopy and density-functional theory calculations to inspect the modulation of electronic states of aromatic molecules. The molecules are self-assembled on a Cu(111) surface forming molecular networks in which the molecules are in different contact configurations, including laterally coupled to different numbers of coordination bonds and vertically adsorbed at different heights above the substrate. We quantitatively analyze the molecular states and find that a delocalized empty molecular state is modulated by these multiple contacts in a cooperative manner: its energy is down shifted by $0:16 eV for each additional lateral contact and by $0:1 eV as the vertical molecule-surface distance is reduced by 0.1 Å in the physisorption regime. We also report that in a molecule-metal-molecule system the bridging metal can mediate the electronic states of the two molecules. The electronic structure of a molecule is subject to the coupling of the molecule with its environment [1,2]. A thorough understanding of this issue is of great importance in the field of molecular electronics considering that the characteristics of molecular devices are determined by the molecular electronic structures and their contacts . For example, a metal-molecule interface may strongly modify the molecular orbitals, and consequently, molecu-lar conductance . As one of the ultimate goals of molecular electronics is to realize single-molecule devices, wherein single molecules are connected to electrodes, one needs to understand how molecule-electrode coupling affects the molecular electronic structures at the level of individual molecules. Scanning tunneling microscopy and spectroscopy (STM-STS) have been used to address this challenging problem owing to their capability of resolving geometric details of molecule-metal contacts and simultaneously measuring the single-molecule elec-tronic properties. These studies revealed in great detail that the molecular frontier orbitals are modulated when the molecules are coupled to metal atoms or a metal substrate [4–14]. So far, most of these studies focused on molecules coupled to one or at most two metal contacts. In future single-molecule devices, however, the molecules will be mostly connected to multiple electrodes, for ex-ample, to source, drain and gate electrodes in a field-effect transistor [15–20]. It is highly desirable to study individual molecules that are coupled to multiple metal contacts. In this Letter, we report on a combined study with low-temperature STM-STS and density-functional theory (DFT) of the electronic structures of extended aromatic molecules that are coupled with multiple metal contacts. The molecules are attached laterally to two or three neigh-boring molecules through metal-ligand coordination bonds and vertically to a metal surface at different distance. These parameters can be separately varied in the experi-ments, so this system provides an arena to inspect the contribution of different contacts individually and collec-tively. We used two-dimensional metal-organic coordina-tion networks self-assembled on a Cu(111) surface as our model system . As shown in Fig. 1(a), molecules of 1,3,5-tris(pyridyl)benzene (TPyB) self-assemble into a honeycomb network structure, wherein the adjacent TPyB molecules are linked via pyridyl-Cu-pyridyl coordi-nation bonds involving the molecules' N atoms [22,23]. In the interior of the network domains each molecule is laterally coupled through three coordination bonds while at the edge of the network domains each molecule is coupled through two coordination bonds. Besides the lateral coupling, vertically the molecules are adsorbed at different sites of the Cu(111) atomic lattice (hollow or top) and at different adsorption heights, which gives rise to different coupling strengths ranging from weak physisorp-tion to strong chemisorption. Hence the molecules are in contact with multiple metal contacts, which mimic multi-terminal single-molecule devices. We used low-temperature (4.9 K) STM to resolve the lateral and vertical contact configuration of the molecules and used STS to reveal the molecular electronic structures. We applied DFT calculations (with van der Waals interactions included) to simulate and interpret the experimental data .
[show abstract][hide abstract] ABSTRACT: Molecular structures that permit intramolecular rotational motion have the potential to function as molecular rotors. We have employed density functional theory and vibrational frequency analysis to study the characteristic structure and vibrational behavior of the molecule (4('),4(")-(bicyclo[2,2,2]octane-1,4-diyldi-4,1-phenylene)-bis-2,2('):6('),2(")-terpyridine. IR active vibrational modes were found that favor intramolecular rotation. To demonstrate the rotor behavior of the isolated single molecule, ab initio molecular dynamics simulations at various temperatures were carried out. This molecular rotor is expected to be thermally triggered via excitation of specific vibrational modes, which implies randomness in its direction of rotation.
The Journal of chemical physics 12/2012; 137(23):234302. · 3.09 Impact Factor
[show abstract][hide abstract] ABSTRACT: We propose a possible approach for controlled formation of various 585 (containing pentagonal and octagonal carbon rings) extended line defects (ELDs) by linear adsorption of various kinds of atoms (C, N, B, O) on a graphene substrate, based upon density functional theory and molecular-dynamics (MD) simulations. We find out that the C and N atoms spontaneously transform to 585 ELDs while other elements find specific stable configurations. To confirm the feasibility of forming the ELD from line adsorption, investigation of the critical transformation conditions of the 585 ELD is involved based upon various adsorption models and adsorption densities.
[show abstract][hide abstract] ABSTRACT: The adsorption of N atoms onto a graphene substrate with extended line defects (ELDs) has been investigated by first-principles calculations. In the presence of recently observed extended line defects, the N adatom can be adsorbed onto both top and bridge sites of the graphene lattice. We demonstrate that chemisorption on ELDs in graphene can substantially affect their structural and electronic properties, depending in particular on specific adsorption sites and density. We also find that magnetism can be induced in ELD-graphene by nitrogenation at suitable N densities; a higher density of N adsorption onto the core carbon atoms of the ELD removes this.
Journal of Materials Chemistry 09/2012; 22(39):21167-21172. · 5.97 Impact Factor
[show abstract][hide abstract] ABSTRACT: We revealed a novel extended line defect (ELD) containing tetragonal rings embedded in graphene, formed as a growth fault, with its energetic and dynamic behavior studied via first-principles calculations. In our finding based upon the molecular dynamics simulation, transformation between locally stable ELDs in graphene at high temperatures simultaneously with contrastive electronic properties can be applied to predetermine the formation process and reconstruction of ELDs.
[show abstract][hide abstract] ABSTRACT: Recent studies reveal that reconstruction of close-packed metal surfaces
induced by C60 adsorption is the rule rather than the
exception. Two types of reconstruction are reported for C60
on different surfaces: (1) C60 sinks into a 7-atom hole, such
as on Cu(111); and (2) C60 sits over a 1-atom hole, such as
on Ag(111) and Pt(111). An explanation for the preferred reconstruction
type for different metals has been lacking. Here, we propose a criterion
that predicts which reconstruction type should be expected: Namely, the
formation of a 1- or 7-atom hole is determined only by the substrate
geometric structure, including the surface lattice constant and the
interlayer spacing; remarkably, the reconstruction type appears not to
depend on the substrate electronic structure. Our intuitive geometrical
explanation is validated by comparative first-principles calculations of
the energetics of C60 on Cu(111), Ru(0001), Pt(111), and
Ag(111) surfaces, listed here with increasing surface lattice constant.
This provides a uniform explanation for the different reconstruction
types that are observed experimentally for C60 on different
close-packed metal surfaces. Moreover, our results provide a better
explanation for the decomposition behavior of C60 on
[show abstract][hide abstract] ABSTRACT: We have studied the organometallic intermediate of a surface-supported Ullmann coupling reaction from 4, 4″-dibromo-p-terphenyl to poly(para-phenylene) by scanning tunneling microscopy/spectroscopy and density functional theory calculations. Our study reveals at a single-molecular level that the intermediate consists of biradical terphenyl (ph)(3) units that are connected by single Cu atoms through C-Cu-C bridges. Upon further increasing the temperature, the neighboring biradical (ph)(3) units are coupled by C-C bonds forming poly(para-phenylene) oligomers while the Cu atoms are released.
Journal of the American Chemical Society 08/2011; 133(34):13264-7. · 10.68 Impact Factor
[show abstract][hide abstract] ABSTRACT: Crystal lattice bending in which the lattice compresses and stretches differentially is a very common phenomenon that has frequently been observed in a variety of long nanostructures. The few studies carried out so far on this topic suggest that bending can significantly modify the properties of such nanostructures, and that they therefore deserve closer study. To explore such effects, we use a new strategy, named “cyclic replacement”, to computationally produce bent silicon nanostructures. For these, ab initio density functional theory calculations predict charge separation with electrons and holes localized in different regions (varying with the lattice orientation), and a decreasing band gap is found with increasing curvature. We show that the underlying mechanism can be understood in terms of the different behavior of near-gap wave functions in the stretched and compressed atomic layers. Bent silicon nanostructures may be useful for solar-cell design where type II homojunctions are formed and charge separation could be facilitated by thermalization.
[show abstract][hide abstract] ABSTRACT: In a recent paper, the chemical structure of a molecule was resolved by means of atomic force microscopy (AFM): using a metal tip terminated in a CO molecule, the authors could image the internal bonding arrangement of a pentacene molecule with remarkable spatial resolution (notably better than with other tip terminations), as verified by their first-principles calculations. Here we further explore with first-principles calculations the mechanisms, applicability, and capabilities of this approach for a wider range of situations, by varying the imaged molecule and the tip beyond the experimental cases. In our simulations, a high atomic resolution is found to be dominated by the electronic structure of the last two atoms on the tip apex which are set perpendicularly to the sample molecule. For example, tips terminated in CH(4) or pentacene itself (both having a C-H apex) yield similar images, while tips terminated in O(2) or CO give quite different images. While using a CO-terminated tip successfully resolves the chemical structure of pentacene and of other extended planar networks based on C(6) rings, this tip fails to resolve the structures of benzene (with its single C(6) ring) or nonplanar C(6) networks, such as C(60) or small-diameter carbon nanotubes. Defects (such as N substitution for a C-H group) were also found to significantly influence the image resolution. Our findings indicate that further application of this approach requires, for each sample, careful selection of a suitable "imaging" molecule as tip termination.
[show abstract][hide abstract] ABSTRACT: We have fabricated atom-molecule contacts by attachment of single Cu atoms to terpyridine side groups of bis-terpyridine tetra-phenyl ethylene molecules on a Cu(111) surface. By means of scanning tunneling microscopy, spectroscopy, and density functional calculations, we have found that, due to the localization characteristics of molecular orbitals, the Cu-atom contact modifies the state localized at the terpyridine side group which is in contact with the Cu atom but does not affect the states localized at other parts of the molecule. These results illustrate the contact effects at individual orbitals and offer possibilities to manipulate orbital alignments within molecules.
[show abstract][hide abstract] ABSTRACT: A molecular rotor which includes a central rotator group was investigated by scanning tunneling microscopy at 4.9 K as it was grafted on a Cu(111) surface via its two terminal groups. Topographs with submolecular resolution revealed several distinct molecular conformations which we attribute to different angular orientations of the rotator and which are locally stable states according to density functional theory calculations. Time-resolved tunneling current spectra showed that the rotator undergoes a torsional motion around the molecular long axis as stimulated by tunneling electrons in a one-electron process with an excitation energy threshold of 355 meV. Calculations identified an intrinsic axial vibration mode of the rotator group at 370 meV as adsorbed on the surface, which we propose to be the channel for effectively converting the tunneling electron energy into the mechanical energy of the intramolecular torsion.
[show abstract][hide abstract] ABSTRACT: Molecular states of terpyridine ligands in supramolecular coordination assemblies were investigated by means of scanning tunneling microscopy/spectroscopy conducted at cryogenic temperature. Submolecular-resolved signals manifest that within the molecules, the empty states at the moieties that are directly involved in the coordination are downshifted, whereas the other moieties are unaffected. Theoretical calculations attribute this localized perturbation to the specific characteristics of the ligand’s orbitals; the ligand moieties possess highly localized empty states. Our results demonstrate that it is feasible to electronically modify individual moieties of ligands in supramolecular assemblies by metal coordination.Keywords (keywords): metal−ligand coordination; molecular orbital; scanning tunneling microscopy/spectroscopy; supramolecular assembly; surface
Journal of Physical Chemistry Letters - J PHYS CHEM LETT. 07/2010; 1(15).
[show abstract][hide abstract] ABSTRACT: Ab-initio periodic Hartree-Fock calculations for the structure of the (111) surface of Fe3O4 (magnetite) are presented. The slabs that are derived by an ideal bulk truncation that leaves one or two iron monolayers outside oxygen layers are found to be more stable than others since they preserve most of the coordination of the surface atoms. The stability of the slabs that represent the surface layers depends on the overall composition, specifically on the deviation from stoichiometry, and on the dipole moment perpendicular to the surface. The symmetrical slab with the layer sequence Fe2O4Fe3O4Fe2, terminated on each side by iron bilayers, is the best compromise since symmetry insures the neutrality of the dipole moment. This slab is oxygen deficient. The energetically preferred structure relaxes so that one of the two outermost iron layers moves toward the slab center plane, exchanging sequence with the oxygen layer. The slab with the layer sequence FeO4Fe3O4Fe, which is also symmetric, is terminated by iron single monolayers, would represent an excessive oxidation of the iron atoms. This slab may be reduced by hydrogenation; it is then strongly stabilized and the vertical displacement of the oxygen atoms agrees with the structure determined by LEED[1,2] (the LEED study would not have detected hydrogen).
[show abstract][hide abstract] ABSTRACT: Ab-initio periodic Hartree–Fock calculations for the structure of the (111) surface of Fe3O4 (magnetite) are presented. The slabs that are derived by an ideal bulk truncation that leaves one or two iron monolayers outside oxygen layers are found to be more stable than others since they preserve most of the coordination of the surface atoms. The stability of the slabs that represent the surface layers depends on the overall composition, specifically on the deviation from stoichiometry, and on the dipole moment perpendicular to the surface. The symmetrical slab with the layer sequence Fe2O4Fe3O4Fe2, terminated on each side by iron bilayers, is the best compromise since symmetry insures the neutrality of the dipole moment. This slab is oxygen-deficient. The energetically preferred structure relaxes so that one of the two outermost iron layers moves toward the slab center plane, exchanging sequence with the oxygen layer. The slab with the layer sequence FeO4Fe3O4Fe, which is also symmetric, is terminated by iron single monolayers, would represent an excessive oxidation of the iron atoms. This slab may be reduced by hydrogenation; it is then strongly stabilized and the vertical displacement of the oxygen atoms agrees with the structure determined by LEED (the LEED study would not have detected hydrogen).
[show abstract][hide abstract] ABSTRACT: From periodic Hartree-Fock calculations, the mode of CO chemisorption on MgO(100) is found to vary with the coverage. At low coverage, the best adsoption mode is predicted to be perpendicular to the surface. At higher coverages, the interaction between the adsorbed molecules influences the ordering of the surface. At coverage θ = 12 monolayer, lateral effects dominate and CO is adsorbed parallel to the surface, bridging pairs of nearest-neighbor Mg atoms. At θ = 34, for the c(4 × 2) unit cell, the COs are adsorbed differently: whereas one third of the COs remains perpendicular to the surface, the two other thirds are bent on the surface. In this case, we find two geometrical arrangements that are equally favorable from an energetic standpoint. In a first arrangement, the non-perpendicular COs differ: one of them is tilted off-normal while the other one is parallel to the surface and bridges Mg atoms as at θ = 12. This arrangement therefore distinguishes three kinds of COs. It is very close to results obtained by potential energy calculations. In another model, the two non-perpendicular COs are symmetrically positioned relative to the perpendicular one. This model distinguishes only two kinds of COs in a 2:1 ratio and is very close to results derived from spectroscopies at low temperature.
[show abstract][hide abstract] ABSTRACT: From crystal orbital calculations, benzene is found to chemisorb with nearly equal binding energy on a hollow site and on a bridge site of the Pt(111) face. The chemisorption is stronger and involves larger molecular distortions than on palladium and rhodium surfaces in agreement with experiment. On the hollow site, the benzene molecule undergoes a Kekulé distortion. On the bridge site found experimentally (with or without coadsorbed CO), the benzene molecule undergoes a local C2v distortion with long and short C-C bonds also in qualitative agreement with experiment. The favored azimuthal orientation of pure benzene coincides with that found experimentally only in the presence of CO. According to calculations, CO adsorption is found to weaken the benzene adsorption and reduce its metal-induced distortions but preserved the same orientation.
Surface Review and Letters - SURF REV LETTERS. 01/1995; 2:285-295.