Dissociation of individual molecules with electrons from the tip of a scanning tunneling microscope

The scanning tunneling microscope (STM) can be used to select a particular adsorbed molecule, probe its electronic structure, dissociate the molecule by using electrons from the STM tip, and then examine the dissociation products. These capabilities are demonstrated for decaborane(14) (B(10)H(14)) molecules adsorbed on a silicon(111)-(7 x 7) surface. In addition to basic studies, such selective dissociation processes can be used in a variety of applications to control surface chemistry on the molecular scale.     

Vibrationally resolved fluorescence excited with submolecular precision

Tunneling electrons from a scanning tunneling microscope (STM) were used to excite photon emission from individual porphyrin molecules adsorbed on an ultrathin alumina film grown on a NiAl(110) surface. Vibrational features were observed in the light-emission spectra that depended sensitively on the different molecular conformations and corresponding electronic states obtained by scanning tunneling spectroscopy. The high spatial resolution of the STM enabled the demonstration of variations in light-emission spectra from different parts of the molecule. These experiments realize the feasibility of fluorescence spectroscopy with the STM and enable the integration of optical spectroscopy with a nanoprobe for the investigation of single molecules.     

"Molecule corrals" for studies of monolayer organic films

Scanning tunneling microscopy (STM) studies have demonstrated that monolayer-deep, flat-bottomed, circular etch pits can be grown on highly ordered pyrolytic graphite by high-temperature etching in the presence of oxygen. In this work, these graphite etch pits are used as "molecule corrals" to isolate ensembles of molecules for study by STM. The nucleation of self-assembled molecular films in the corrals took place by nucleation events separate from those leading to self-assembly on the surrounding terrace and allowed the measurement of the nucleation rate constant in the corrals. The dependence of the nucleation rate for self-assembly on pit size shows that nucleation occurs at open terrace sites and that step edges (that is, the corral's perimeter) and confinement inhibit film growth.     

Creating favorable geometries for directing organic photoreactions in alkanethiolate monolayers

The products of photoreactions of conjugated organic molecules may be allowed by selection rules but not observed in solution reactions because of unfavorable reaction geometries. We have used defect sites in self-assembled alkanethiolate monolayers on gold surfaces to direct geometrically unfavorable photochemical reactions between individual organic molecules. High conductivity and stochastic switching of anthracene-terminated phenylethynylthiolates within alkanethiolate monolayers, as well as in situ photochemical transformations, have been observed and distinguished with the scanning tunneling microscope (STM). Ultraviolet light absorbed during imaging increases the apparent heights of excited molecules in STM images, a direct manifestation of probing electronically excited states.     

Scanning tunneling microscopy and atomic force microscopy: application to biology and technology

The scanning tunneling microscope (STM) and the atomic force microscope (AFM) are scanning probe microscopes capable of resolving surface detail down to the atomic level. The potential of these microscopes for revealing subtle details of structure is illustrated by atomic resolution images including graphite, an organic conductor, an insulating layered compound, and individual adsorbed oxygen atoms on a semiconductor. Application of the STM for imaging biological materials directly has been hampered by the poor electron conductivity of most biological samples. The use of thin conductive metal coatings and replicas has made it possible to image some biological samples, as indicated by recently obtained images of a recA-DNA complex, a phospholipid bilayer, and an enzyme crystal. The potential of the AFM, which does not require a conductive sample, is shown with molecular resolution images of a nonconducting organic monolayer and an amino acid crystal that reveals individual methyl groups on the ends of the amino acids. Applications of these new microscopes to technology are demonstrated with images of an optical disk stamper, a diffraction grating, a thin-film magnetic recording head, and a diamond cutting tool. The STM has even been used to improve the quality of diffraction gratings and magnetic recording heads.     

Commensurability and mobility in two-dimensional molecular patterns on graphite

Two-dimensional molecular patterns were obtained by the adsorption of long-chain alkanes, alcohols, fatty acids, and a dialkylbenzene from organic solutions onto the basal plane of graphite. In situ scanning tunneling microscopy (STM) studies revealed that these molecules organize in lamellae with the extended alkyl chains oriented parallel to a lattice axis within the basal plane of graphite. The planes of the carbon skeletons, however, can be oriented either predominantly perpendicular to or predominantly parallel with the substrate surface, causing the lamellar lattice to be either in or near registry with the substrate (alkanes and alcohols) or not in registry (fatty acids and dialkylbenzenes). In the case of the alcohols and the dialkylbenzene the molecular axes are tilted by +30 degrees or -30 degrees with respect to an axis normal to the lamella boundaries, giving rise to molecularly well-defined domain boundaries. Fast STM image recording allowed the spontaneous switch between the two tilt angles to be observed in the alcohol monolayers on a time scale of a few milliseconds.     

Direct observation of native DNA structures with the scanning tunneling microscope

Uncoated double-stranded DNA dissolved in a salt solution was deposited on graphite and imaged in air with the scanning tunneling microscope (STM). The resolution was such that the major and minor grooves could be distinguished. The pitch of the helix varied between 27 and 63 angstroms in the images obtained. Thus the STM can be useful for structural studies of a variety of uncoated and isolated biomolecules.     

Enzymatic modification of transfer RNA

The molecular events leading to the synthesis of mature tRNA are only now becoming amenable to experimental study. In bacterial and mammalian cells tRNA genes are transcribed into precursor tRNA. These molecules, when isolated, contain additional nucleotides at both ends (20) of the mature tRNA and lack most modified nucleosides. Presumably, specific nucleases ("trimming" enzymes) cut the precursor to proper tRNA size. The C-C-A nucleotide sequence of the amino acid acceptor end common to all tRNA's does not seem to be coded by tRNA genes (30), and may be added to the trimmed molecules by the tRNA-CMP-AMP-pyrophosphorylase (71). Modifications at the polynucleotide level of the heterocyclic bases or the sugar residues give rise to the modified nucleosides in tRNA. Although newly available substrates have allowed the detection of more of the enzymes involved in these reactions, there is still no knowledge about the sequence of modification or trimming events leading to the synthesis of active tRNA. Progress in these studies may not be easy because enzyme preparations free of nucleases or other tRNA modifying enzymes are required. The role of the modified nucleosides in the biological functions of tRNA is still unknown. Possibly pseudouridine is required for ribosome mediated protein synthesis; some other modified nucleosides in tRNA are not required for this reaction, but may enhance its rate. What might be the role of the large variety of modified nucleosides in tRNA? One is tempted to speculate that such nucleosides are important in other cellular processes in which tRNA is thought to participate such as virus infection, cell differentiation, and hormone action (2, 3). Mutants in a number of tRNA-modifying enzymes are needed in order to extend our knowledge of their purpose and of tRNA involvement in other biological processes. But unless tRNA-modifying enzymes specific for a particular tRNA species exist, no simple selection procedure can be devised. Possibly some of the regulatory mutants of amino acid biosynthesis may prove to affect tRNA-modifying enzymes (72). Transfer RNA's are macromolecules well suited for the study of nucleic acid-protein interactions. The tRNA molecules are structurally very similar, and they interact with a large number of enzymes or protein factors (2, 3). Each aminoacyl-tRNA synthetase, for instance, very precisely recognizes a set of cognate isoacceptor tRNA's (2, 73). The availability of the tRNA- modifying enzymes adds another dimension to the problem of the nature of specific recognition of tRNA by proteins. There are some tRNA-modifying enzymes, such as the uracil-tRNA methylase, which may recognize all tRNA species, while others, such as the isopentenyl-tRNA transferase, probably recognize only a selected set of tRNA molecules, even with different amino acid accepting capacities. With well-characterized RNA precursor and tRNA molecules we can hope to delineate those features of primary, secondary, and tertiary structure involved in the specific interactions of tRNA with these enzymes.     

Vapor-Condensation Generation and STM Analysis of Fullerene Tubes

Fullerene tubular structures can be generated by vapor condensation of carbon on an atomically flat graphite surface. Scanning tunneling microscope (STM) images revealed the presence of tubes with extremely small diameters (from 10 to 70 angstroms), most of which are terminated by hemispherical caps. Atomic resolution images of such structures showed that the tubes have a helical graphitic nature. The formation of the tubes under the quasi-free conditions suggests that the growth to tubular rather than spherical configurations is preferred for "giant fullerenes."     

Molecular structure of DNA by scanning tunneling microscopy

Uncoated DNA molecules marked with an activated tris(l-aziridinyl) phosphine oxide (TAPO) solution were deposited on gold substrates and imaged in air with the use of a high-resolution scanning tunneling microscope (STM). Constant-current and gap-modulated STM images show clear evidence of the helicity of the DNA structure: pitch periodicity ranges from 25 to 35 angstroms, whereas the average diameter is 20 angstroms. Molecular structure within a single helix turn was also observed.     

Rectification of STM Current to Graphite Covered with Phthalocyanine Molecules

The scanning tunneling microscope (STM) can be used to measure current-voltage characteristics on an atomic scale. The attachment of copper phthalocyanine molecules, in contrast to a variety of other molecules, to graphite changes the electrical characteristics of the STM from relatively symmetric to highly asymmetric or rectifying. Evidence is presented to show that the asymmetry arises because of the electronic energy levels of the copper phthalocyanine. The organic molecules were bonded to the graphite by an acid-base reaction that may have wide applicability.     

Small-diameter silicon nanowire surfaces

Small-diameter (1 to 7 nanometers) silicon nanowires (SiNWs) were prepared, and their surfaces were removed of oxide and terminated with hydrogen by a hydrofluoric acid dip. Scanning tunneling microscopy (STM) of these SiNWs, performed both in air and in ultrahigh vacuum, revealed atomically resolved images that can be interpreted as hydrogen-terminated Si (111)-(1 x 1) and Si (001)-(1 x 1) surfaces corresponding to SiH3 on Si (111) and SiH2 on Si (001), respectively. These hydrogen-terminated SiNW surfaces seem to be more oxidation-resistant than regular silicon wafer surfaces, because atomically resolved STM images of SiNWs were obtained in air after several days' exposure to the ambient environment. Scanning tunneling spectroscopy measurements were performed on the oxide-removed SiNWs and were used to evaluate the electronic energy gaps. The energy gaps were found to increase with decreasing SiNW diameter from 1.1 electron volts for 7 nanometers to 3.5 electron volts for 1.3 nanometers, in agreement with previous theoretical predictions.     

Elementary structural motifs in a random network of cytosine adsorbed on a gold(111) surface

Nonsymmetrical organic molecules adsorbed on solid surfaces may assemble into random networks, thereby providing model systems for organic glasses that can be directly observed by scanning tunneling microscopy (STM). We investigated the structure of a disordered cytosine network on a gold(111) surface created by thermal quenching, to temperatures below 150 K, of the two-dimensional fluid present on the surface at room temperature. Comparison of STM images to density functional theory calculations allowed us to identify three elementary structural motifs (zigzag filaments and five- and six-membered rings) that underlie the whole supramolecular random network. The identification of elementary structural motifs may provide a new framework for understanding medium-range order in amorphous and glassy systems.     

Electrospray ionization for mass spectrometry of large biomolecules

Electrospray ionization has recently emerged as a powerful technique for producing intact ions in vacuo from large and complex species in solution. To an extent greater than has previously been possible with the more familiar "soft" ionization methods, this technique makes the power and elegance of mass spectrometric analysis applicable to the large and fragile polar molecules that play such vital roles in biological systems. The distinguishing features of electrospray spectra for large molecules are coherent sequences of peaks whose component ions are multiply charged, the ions of each peak differing by one charge from those of adjacent neighbors in the sequence. Spectra have been obtained for biopolymers including oligonucleotides and proteins, the latter having molecular weights up to 130,000, with as yet no evidence of an upper limit.     

A stable high-index surface of silicon: si(5 5 12)

A stable high-index surface of silicon, Si(5 5 12), is described. This surface forms a 2 x 1 reconstruction with one of the largest unit cells ever observed, 7.7 angstroms by 53.5 angstroms. Scanning tunneling microscopy (STM) reveals that the 68 surface atoms per 2 x 1 unit cell are reconstructed only on a local scale. A complete structural model for the surface is proposed, incorporating a variety of features known to exist on other stable silicon surfaces. Simulated STM images based on this model have been computed by first-principles electronic-structure methods and show excellent agreement with experiment.     

Atomic force microscopy of an organic monolayer

Atomic force microscope images of polymerized monolayers of n-(2-aminoethyl)-10,12-tricosadiynamide revealed parallel rows of molecules with a side-by-side spacing of approximately equal to 0.5 nanometer. Forces used for imaging (10(-8) newton) had no observable effect on the polymer strands. These results demonstrate that atomic force microscope images can be obtained for an organic system.     

Near--Atomic Resolution Imaging of Ferroelectric Liquid Crystal Molecules on Graphite by STM

Near-atomic resolution images of a two-dimensional heteroepitaxial crystal composed of the relatively "functionally rich" chiral liquid crystal mesogen MDW 74 on graphite have been obtained by scanning tunneling microscopy (STM). This work is aimed at developing an improved understanding of the commercially crucial phenomenon of liquid crystal alignment by studying well-characterized surfaces. Herein is reported molecular-level characterization of the surface underlying a ferroelectric liquid crystal in situ, a requisite starting point for understanding the liquid crystal-solid interface at the molecular level. The results are also important in the context of developing a model for the molecular. origins of the contrast observed in STM images of organic monolayers on conductor surfaces. The data and analysis provide strong evidence that neither frontier orbital alone (highest occupied or lowest unoccupied molecular orbital) is sufficient to describe the observed tunneling efficiency.     

Gravitational lens optics

Several instances of multiple imaging of cosmologically distant sources by intervening galaxies and galaxy clusters have been discovered over the past decade. These "gravitational lenses" have distinctive optical properties. Pointlike sources such as quasars generally produce two or four images when lensed, whereas extended sources such as galaxies produce spectacular arcs and rings. The salient features of most of the observations can be reproduced with the use of simple elliptical lens models that approximate the lenses made by ellipsoidal mass distributions such as are common in the universe. In addition to illustrating simple optics in operation on a cosmological scale, multiple images and arcs provide useful probes of the lensing galaxies and clusters. Also, gravitational lenses can make magnified images of cosmologically distant sources and may eventually furnish important cosmographic data such as the Hubble constant.     

Infrared Reflection-Absorption Spectroscopy and STM Studies of Model Silica-Supported Copper Catalysts

The structure of model silica-supported copper catalysts has been investigated with scanning tunneling microscopy (STM) and infrared reflection-absorption spectroscopy (IRAS). The IRAS studies of CO on the model silica-supported copper catalysts indicate that there are several types of copper clusters with surface structures similar to (111), (110), and other high-index planes of single-crystal copper. The STM studies show several types of copper clusters on silica and reveal images of metal clusters on an amorphous oxide support with atomic resolution.     

Identification of the products from the reaction of chlorine with the silicon(111)-(7x7) surface

The various products from the reaction of chlorine (Cl) with the adatom layer of the Si(111)-(7x7) surface have been identified with scanning tunneling microscopy (STM). Initially, a single Cl atom reacts with the adatom dangling bond. At higher surface coverage, additional Cl atoms insert themselves into the Si-Si backbonds between the adatom and rest-atom layers, producing adatoms that have reacted with two or three Cl atoms. These products are characterized by different registries with respect to the underlying rest layer and appear in STM images as adatoms of different sizes, consistent with the breaking of Si-Si backbonds and the formation ofnew Si-Cl bonds.