STM studies on porphyrins

Porphyrins are promising components to be used in molecular electronics due to their rich electronic/photonic properties. Preparation of supramolecular architectures of porphyrins on solid surfaces would constitute a basis for further development toward molecular circuitry or other constructs for molecular electronics applications. Assemblies on surfaces can be probed with scanning tunneling microscopy (STM) at submolecular resolutions to reveal the arrangements and conformations of molecules on an individual molecule basis. The electronic characteristics within a single porphyrin molecule can also be probed by means of the same technique. This review summarizes the status quo of STM studies on porphyrins on surfaces with regard to their assemblies, structures, and electronic properties at the single molecule level.     

Controlling Single Molecule Conductance by a Locally Induced Chemical Reaction on Individual Thiophene Units

Among the prerequisites for the progress of single‐molecule‐based electronic devices are a better understanding of the electronic properties at the individual molecular level and the development of methods to tune the charge transport through molecular junctions. Scanning tunneling microscopy (STM) is an ideal tool not only for the characterization, but also for the manipulation of single atoms and molecules on surfaces. The conductance through a single molecule can be measured by contacting the molecule with atomic precision and forming a molecular bridge between the metallic STM tip electrode and the metallic surface electrode. The parameters affecting the conductance are mainly related to their electronic structure and to the coupling to the metallic electrodes. Here, the experimental and theoretical analyses are focused on single tetracenothiophene molecules and demonstrate that an in situ‐induced direct desulfurization reaction of the thiophene moiety strongly improves the molecular anchoring by forming covalent bonds between molecular carbon and copper surface atoms. This bond formation leads to an increase of the conductance by about 50 % compared to the initial state.     

Single-molecule chemistry and physics explored by low-temperature scanning probe microscopy

It is well known that scanning probe techniques such as scanning tunnelling microscopy (STM) and atomic force microscopy (AFM) routinely offer atomic scale information on the geometric and the electronic structure of solids. Recent developments in STM and especially in non-contact AFM have allowed imaging and spectroscopy of individual molecules on surfaces with unprecedented spatial resolution, which makes it possible to study chemistry and physics at the single molecule level. In this feature article, we first review the physical concepts underlying image contrast in STM and AFM. We then focus on the key experimental considerations and use selected examples to demonstrate the capabilities of modern day low-temperature scanning probe microscopy in providing chemical insight at the single molecule level.     

Effects of hydrogen-bond environment on single particle and pair dynamics in liquid water

We have performed molecular dynamics simulations of liquid water at 298 and 258 K to investigate the effects of hydrogen-bond environment on various single-particle and pair dynamical properties of water molecules at ambient and supercooled conditions. The water molecules are modelled by the extended simple point charge (SPC/E) model. We first calculate the distribution of hydrogen-bond environment in liquid water at both temperatures and then investigate how the self-diffusion and orientational relaxation of a single water molecule and also the relative diffusion and relaxation of the hydrogen-bond of a water pair depend on the nature of the hydrogen-bond environment of the tagged molecules. We find that the various dynamical quantities depend significantly on the hydrogen-bond environment, especially at the supercooled temperature. The present study provides a molecular-level insight into the dynamics of liquid water under ambient and supercooled conditions.     

Amino-carboxylic recognition on surfaces: from 2D to 2D + 1 nano-architectures

The control of the electronic properties of the interfaces between small organic molecules and the substrate is key for the development of efficient and reliable organic-based devices. A promising and widely covered route is to interpose a Self-Assembled Monolayer (SAM) to bridge the molecular film and the electrode. The morphology and the electronic level alignment of the triple substrate-SAM-organic layered system can be tuned by properly selecting the SAM composition. We have recently proposed a novel approach to the problem where, under ultra-high vacuum conditions, a molecular film is anchored to the SAM by exploiting the recognition between molecules functionalized, respectively, with -NH(2) and -COOH end-groups. Here we briefly review the role of the amino-carboxylic interaction in the formation of ordered organic 2-dimensional architectures on solid surfaces. We then describe the anchoring process of carboxylic molecules on amine based SAMs we have recently reported on. New results are presented showing how multiple anchoring sites per molecule may be exploited for tailoring the molecular orientation as well as the density of the anchored molecules.     

Arylthio-substituted coronenes as tailored building blocks for molecular electronics

The electron transport through molecules in molecular devices is typically influenced by the nature of the interfaces with the contacting electrodes and by the interactions between neighbouring molecules. It is a major goal of molecular electronics to adjust the electronic function of a molecular device by tailoring the intrinsic molecular properties and the interfacial and intermolecular interactions. Here, we report on the tunability of the electronic properties of coronene derivatives, namely dodecakis(arylthio)coronenes (DATCs), which are found to exhibit a three-dimensional aromatic system. Scanning tunnelling microscopy (STM), spectroscopy (STS) and simulations based on the density functional theory (DFT) are employed to characterize the structural and electronic properties of these molecules deposited on Au(111) surfaces. It is shown that modifications of the peripheral aryl-groups allow us to specifically affect the self-assembly and the charge transport characteristics of the molecules. Molecular assemblies like supramolecular wires with highly delocalized orbitals and single molecules with molecular "quantum dot" characteristics are obtained in this way.     

STM study of morphology and electron transport features in cytochrome c and nanocluster molecule monolayers.

The morphology and electron tunneling through single cytochrome c and nanocluster Pt(5)(CO)(7)[P(C(6)H(5))](4) molecules organized as monolayer Langmuir-Blodgett (LB) films on graphite substrate have been studied experimentally using scanning tunneling microscopy (STM) and spectroscopy techniques with sub-nanometer spatial resolution in a double barrier tunnel junction configuration STM tip-monomolecular film-conducting substrate at ambient conditions. STM images of the films revealed globular structures with characteristic diameters (approximately 3.5 nm for the protein molecule and approximately 1.2 nm for the nanocluster). The spectroscopic study by recording the tunneling current-bias voltage (I-V) curves revealed tunneling I-V characteristics with features as steps of different width and heights that are dependent on the STM tip position over the molecule in the monolayer, giving evidence for sequential discrete electron-tunneling effects with the combination of the single electron Coulomb-charging energy and the electronic energy level separation (molecular spectrum) in such immobilized metalloprotein and nanocluster structures that can be of interest for the development of bioelectronic and hybrid functional nanosystems.     

Metal–organic interaction probed by First Principles STM simulations

The Review is devoted to recent progress made from the combination of Scanning Tunneling Microscope (STM) experiments and First Principles atomistic simulations in the chemical characterization of metal–organic interfaces. Density Functional Theory (DFT) has now reached the point to mimic in a quantitative way two pillars of the STM probe: the imaging mode convoluting the topographic and electronic properties and the spectroscopy modes comprising of elastic and inelastic detection ways. We present a selection of hybrid interfaces ranging from isolated benzene derivatives to thin honeycomb carbon film – a single graphene layer – deposited onto transition metal surfaces. The direct experimental analysis of these interfaces was error-prone, necessitating the confrontation with First Principles atomistic simulations. The few examples thus illustrate the power of different kinds of STM simulations to complement the STM data, in order to unambiguously identify the chemical structure of organic adsorbates.     

Properties of large organic molecules on metal surfaces

The adsorption of large organic molecules on surfaces has recently been the subject of intensive investigation, both because of the molecules’ intrinsic physical and chemical properties, and for prospective applications in the emerging field of nanotechnology. Certain complex molecules are considered good candidates as basic building blocks for molecular electronics and nanomechanical devices. In general, molecular ordering on a surface is controlled by a delicate balance between intermolecular forces and molecule–substrate interactions. Under certain conditions, these interactions can be controlled to some extent, and sometimes even tuned by the appropriate choice of substrate material and symmetry. Several studies have indicated that, upon molecular adsorption, surfaces do not always behave as static templates, but may rearrange dramatically to accommodate different molecular species. In this context, it has been demonstrated that the scanning tunnelling microscope (STM) is a very powerful tool for exploring the atomic-scale realm of surfaces, and for investigating adsorbate–surface interactions. By means of high-resolution, fast-scanning STM unprecedented new insight was recently achieved into a number of fundamental processes related to the interaction of largish molecules with surfaces such as molecular diffusion, bonding of adsorbates on surfaces, and molecular self-assembly. In addition to the normal imaging mode, the STM tip can also be employed to manipulate single atoms and molecules in a bottom–up fashion, collectively or one at a time. In this way, molecule-induced surface restructuring processes can be revealed directly and nanostructures can be engineered with atomic precision to study surface quantum phenomena of fundamental interest. Here we will present a short review of some recent results, several of which were obtained by our group, in which several features of the complex interaction between large organic molecules and metal surfaces were revealed. The focus is on experiments performed using STM and other complementary surface-sensitive techniques.     

A molecular dynamics study of nitric oxide in water: diffusion and structure

We present molecular dynamics simulations of the diffusion coefficients and structure of water-nitric oxide mixtures at ambient (298 K) and in vivo (310 K) conditions. A two-site rigid-body molecular model with partial charges and a Lennard-Jones potential on both sites is proposed for nitric oxide and used in conjunction with the extended simple point-charge model for liquid water in our simulations. The diffusion coefficients obtained from the simulations are in good agreement with experimental data. The results from intermolecular partial pair functions show that under these thermodynamic conditions, the existence of nitric oxide in liquid water has little impact on the structure of water and the tendency to form H bonds between water molecules. We also find that it is unlikely that H bonds form between the hydrogen atoms in water and either the nitrogen or the oxygen atom on the nitric oxide at the temperatures and densities examined in this study. This study suggests that in low concentrations nitric oxide molecules exist as free molecules in liquid water rather than forming complexes with water molecules.     

A scanning tunneling microscopy study of self-assembled nickel(II) octaethylporphyrin deposited from solutions on HOPG

The adsorption of nickel(II) octaethylporphyrin (NiOEP) from benzene and chloroform solutions on highly ordered pyrolytic graphite (HOPG) was investigated with a scanning tunneling microscope (STM) operated in ambient conditions. STM images show that NiOEP self-assembles on the graphite surface and that the molecules lie flat and form 2D lattices with spacings of 1.58 +/- 0.03 nm by 1.46 +/- 0.06 nm with a lattice angle of 69 degrees +/- 4 degrees averaged over both solvents. We were unable to eliminate the possibility that one unit cell distance is twice the above-reported distance. The corresponding molecular packing density, 4.5 +/- 0.3 x 10(13) molecules/cm(2), was essentially the same for benzene and chloroform solution deposition. These results differ somewhat from the structure revealed by high-resolution STM images of NiOEP on Au (111). The lack of apparent height (image intensity) in the constant current STM image of the alkane region of alkane-substituted metal porphyrins is attributed to a combination of changes in alkane configuration relative to the ring and associated changes in electronic coupling with HOMO and LUMO.     

STM studies of single molecules: molecular orbital aspects

As a fundamental and frequently referred concept in modern chemistry, the molecular orbital plays a vital role in the science of single molecules, which has become an active field in recent years. For the study of single molecules, scanning tunneling microscopy (STM) has been proven to be a powerful scientific technique. Utilizing specific distribution of the molecular orbitals at spatial, energy, and spin scales, STM can explore many properties of single molecule systems, such as geometrical configuration, electronic structure, magnetic polarization, and so on. Various interactions between the substrate and adsorbed molecules are also understood in terms of the molecular orbitals. Molecular engineering methods, such as mode-selective chemistry based on the molecular orbitals, and resonance tunneling between the molecular orbitals of the molecular sample and STM tip, have stimulated new advances of single molecule science.     

STM studies of photochemistry and plasmon chemistry on metal surfaces

We review our recent studies of photochemistry and plasmon chemistry of dimethyl disulfide, (CH₃S)₂, molecules adsorbed on metal surfaces using a scanning tunneling microscope (STM). The STM has been used not only for the observation of surface structures at atomic spatial resolution but also for local spectroscopies. The STM combined with optical excitation by light can be employed to investigate chemical reactions of single molecules induced by photons and localized surface plasmons. This technique allows us to gain insights into reaction mechanisms at a single molecule level. The experimental procedures to examine the chemical reactions using the STM are briefly described. The mechanism for the photodissociation reaction of (CH₃S)₂ molecules adsorbed on metal surfaces is discussed based on both the experimental results obtained with the STM and the electronic structures calculated by density functional theory. The dissociation reaction of the (CH₃S)₂ molecule induced by the optically excited plasmon in the STM junction between a Ag tip and metal substrate is also described. The reaction mechanism and pathway of this plasmon-induced chemical reaction are discussed by comparison with those proposed in plasmon chemistry.     

In situ scanning tunneling microscopy of DNA-modified gold surfaces: bias and mismatch dependence

In situ scanning tunneling microscopy has been performed on DNA-modified gold surfaces under physiological conditions. The STM images of DNA-modified gold surfaces are strongly dependent on the applied potential and percentage of DNA duplexes containing a single base mismatch. At negative surface potentials we observe reproducible features that are attributed to DNA agglomerates where the DNA duplexes are in the upright orientation; at positive potentials, when DNA molecules lie down on the surface, the film is transparent, and only the gold surface is distinguishable. These observations indicate that DNA possesses a non-negligible local density of states which can be probed when the DNA duplex is in the upright orientation. By varying the percentage of DNA duplexes containing a single base mismatch, we have observed a dramatic change in the image contrast as a result of the perturbation induced by the mismatch on the electronic pathway inside the DNA. These results emphasize the central role of the integrity of the pi-stack for DNA charge transport. Duplex DNA is a promising candidate in molecular electronics, but only in arrangements where the orbitals can efficiently overlap with the electronic states of the electrodes and the environment does not constrain the DNA in non-native, poorly stacked conformations.     

Strong water-mediated friction asymmetry and surface dynamics of zwitterionic solids at ambient conditions: L-alanine as a case study

Water molecules strongly interact with freshly cleaved (011) surfaces of L-alanine single crystals at low relative humidity (below 10%) promoting diffusion of L-alanine molecules. Species mobility is enhanced above ~40% leading to the formation of two-dimensional islands with long-range order through Ostwald ripening. Scanning force microscopy experiments reveal that both, islands and terraces, are identical in nature (composition and crystallographic structure) but a relevant friction asymmetry appearing upon water-surface interaction evidences that orientation dependent properties exist between them at the molecular level. We interpret this observation as due to water incorporation in the topmost surface crystal structure. Eventually, for high humidity values, surface dissolution and roughening occur.     

Molecular dynamics study on ultrathin liquid water film sheared between platinum solid walls: liquid structure and energy and momentum transfer

Molecular dynamics simulation has been performed on a liquid film that is sheared in between solid surfaces. As a shear is given to the liquid film, a Couette-like flow is generated in the liquid and energy conversion occurs from the macroscopic flow to the thermal energy, which is discharged back to the solid walls. In such a way, momentum and thermal energy fluxes are present simultaneously. And all these thermal and fluid phenomena take place in highly nonequilibrium state where thermal energy is not distributed equally to each degree of freedom of molecular motion in the vicinities of the solid-liquid interface. In the present paper, platinum and water are employed as solid and liquid, respectively. First, the structure and orientation of water molecules in the vicinities of the solid surfaces are analyzed and how these structure and orientation are influenced by the shear is considered. Based on this result, momentum and thermal energy transfer in the vicinities of and at the solid-liquid interfaces are investigated in detail. Results are compared with those of our previous study, in which monatomic and diatomic molecules are employed as liquid.     

Toward room-temperature optical manipulation of small molecules

Room-temperature optical manipulation of small molecules is a challenging issue in the field of material science. To increase optical force for a single molecule trapping, it has been recognized that resonant excitation of molecules should be controlled under the light illumination. Strongly interacting molecules with solid surfaces at electrified interfaces show the exotic behavior of electronic excitation by localized surface plasmon. In this review, we emphases that surface-enhanced Raman scattering can be used to evaluate the resonant excitation of target molecules at interfaces. Under such excitation, the diffusion of small molecules can be controlled by the optical force generated by the intensity gradient of a highly localized electric field.     

Molecular dynamics investigation of the intrinsic structure of water-fluid interfaces via the intrinsic sampling method

Capillary wave fluctuations smooth out the structure of fluid interfaces, making difficult the detailed analysis of the interfacial structure. Most computer simulation investigations performed to date have focused on the computation of average density profiles, ignoring the characterization of the intrinsic structure of the interface. Recent theoretical developments have reversed this situation, making possible the detailed investigation of the interfacial intrinsic structure at an unprecedented level of detail. In this article we investigate via molecular dynamics simulations the intrinsic structure of water-alkane (hexane and dodecane) interfaces. The implementation of the recently introduced, intrinsic sampling method to compute the intrinsic surface of water-fluid interfaces is discussed. We provide quantitative molecular information on the structure, corrugation, and stiffness of the liquid surfaces. The intrinsic structure of water at alkane interfaces is shown to be insensitive to the alkane-chain length, and can be very accurately described by the intrinsic structure of the water free surface.     

Distorted five-fold coordination of Cu2+(aq) from a Car-Parrinello molecular dynamics simulation

The solvation shell structure and dynamics of a single Cu2+ ion in a periodic box with 32 water molecules under ambient conditions has been investigated using Car-Parrinello molecular dynamics simulations in a time-window of 18 ps. Five-fold coordination with four equidistant equatorial water molecules at 2.00 A and one axial water molecule at 2.45 A from the Cu2+ ion is found. A "hole" without water molecules is found on the opposite side of the axial water. The ion-water bonding character for the equatorial water molecules is different from that of the axial water molecules, as shown by a localized orbital analysis of the electronic structure. Moreover, the calculated OD stretching vibrational band for the equatorial water molecules lies ca. 175 cm-1 below the axial-water band, in good agreement with experimental data. The equatorial-water band lies below, and the axial-water band above, the pure liquid D2O band, also in agreement with experimental data.