Chemical identification of individual surface atoms by atomic force microscopy

Scanning probe microscopy is a versatile and powerful method that uses sharp tips to image, measure and manipulate matter at surfaces with atomic resolution. At cryogenic temperatures, scanning probe microscopy can even provide electron tunnelling spectra that serve as fingerprints of the vibrational properties of adsorbed molecules and of the electronic properties of magnetic impurity atoms, thereby allowing chemical identification. But in many instances, and particularly for insulating systems, determining the exact chemical composition of surfaces or nanostructures remains a considerable challenge. In principle, dynamic force microscopy should make it possible to overcome this problem: it can image insulator, semiconductor and metal surfaces with true atomic resolution, by detecting and precisely measuring the short-range forces that arise with the onset of chemical bonding between the tip and surface atoms and that depend sensitively on the chemical identity of the atoms involved. Here we report precise measurements of such short-range chemical forces, and show that their dependence on the force microscope tip used can be overcome through a normalization procedure. This allows us to use the chemical force measurements as the basis for atomic recognition, even at room temperature. We illustrate the performance of this approach by imaging the surface of a particularly challenging alloy system and successfully identifying the three constituent atomic species silicon, tin and lead, even though these exhibit very similar chemical properties and identical surface position preferences that render any discrimination attempt based on topographic measurements impossible.     

Amplification of chirality in two-dimensional enantiomorphous lattices

The concept of chirality dates back to 1848, when Pasteur manually separated left-handed from right-handed sodium ammonium tartrate crystals. Crystallization is still an important means for separating chiral molecules into their two different mirror-image isomers (enantiomers), yet remains poorly understood. For example, there are no firm rules to predict whether a particular pair of chiral partners will follow the behaviour of the vast majority of chiral molecules and crystallize together as racemic crystals, or as separate enantiomers. A somewhat simpler and more tractable version of this phenomenon is crystallization in two dimensions, such as the formation of surface structures by adsorbed molecules. The relatively simple spatial molecular arrangement of these systems makes it easier to study the effects of specific chiral interactions; moreover, chiral assembly and recognition processes can be observed directly and with molecular resolution using scanning tunnelling microscopy. The enantioseparation of chiral molecules in two dimensions is expected to occur more readily because planar confinement excludes some bulk crystal symmetry elements and enhances chiral interactions; however, many surface structures have been found to be racemic. Here we show that the chiral hydrocarbon heptahelicene on a Cu111 surface does not undergo two-dimensional spontaneous resolution into enantiomers, but still shows enantiomorphism on a mesoscopic length scale that is readily amplified. That is, we observe formation of racemic heptahelicene domains with non-superimposable mirror-like lattice structures, with a small excess of one of the heptahelicene enantiomers suppressing the formation of one domain type. Similar to the induction of homochirality in achiral enantiomorphous monolayers by a chiral modifier, a small enantiomeric excess suffices to ensure that the entire molecular monolayer consists of domains having only one of two possible, non-superimposable, mirror-like lattice structures.     

Extended surface chirality from supramolecular assemblies of adsorbed chiral molecules

The increasing demand of the chemical and pharmaceutical industries for enantiomerically pure compounds has spurred the development of a range of so-called 'chiral technologies' (ref. 1), which aim to exert the ultimate control over a chemical reaction by directing its enantioselectivity. Heterogeneous enantioselective catalysis is particularly attractive because it allows the production and ready separation of large quantities of chiral product while using only small quantities of catalyst. Heterogeneous enantioselectivity is usually induced by adsorbing chiral molecules onto catalytically active surfaces. A mimic of one such catalyst is formed by adsorbing (R,R)-tartaric acid molecules on Cu(110) surfaces: this generates a variety of surface phases, of which only one is potentially catalytically active, and leaves the question of how adsorbed chiral molecules give rise to enantioselectivity. Here we show that the active phase consists of extended supramolecular assemblies of adsorbed (R,R)-tartaric acid, which destroy existing symmetry elements of the underlying metal and directly bestow chirality to the modified surface. The adsorbed assemblies create chiral 'channels' exposing bare metal atoms, and it is these chiral spaces that we believe to be responsible for imparting enantioselectivity, by forcing the orientation of reactant molecules docking onto catalytically active metal sites. Our findings demonstrate that it is possible to sustain a single chiral domain across an extended surface--provided that reflection domains of opposite handedness are removed by a rigid and chiral local adsorption geometry, and that inequivalent rotation domains are removed by successful matching of the rotational symmetry of the adsorbed molecule with that of the underlying metal surface.     

Selectivity in vibrationally mediated single-molecule chemistry

The selective excitation of molecular vibrations provides a means to directly influence the speed and outcome of chemical reactions. Such mode-selective chemistry has traditionally used laser pulses to prepare reactants in specific vibrational states to enhance reactivity or modify the distribution of product species. Inelastic tunnelling electrons may also excite molecular vibrations and have been used to that effect on adsorbed molecules, to cleave individual chemical bonds and induce molecular motion or dissociation. Here we demonstrate that inelastic tunnelling electrons can be tuned to induce selectively either the translation or desorption of individual ammonia molecules on a Cu(100) surface. We are able to select a particular reaction pathway by adjusting the electronic tunnelling current and energy during the reaction induction such that we activate either the stretching vibration of ammonia or the inversion of its pyramidal structure. Our results illustrate the ability of the scanning tunnelling microscope to probe single-molecule events in the limit of very low yield and very low power irradiation, which should allow the investigation of reaction pathways not readily amenable to study by more conventional approaches.     

Manipulation of atoms across a surface at room temperature

Since the realization that the tips of scanning probe microscopes can interact with atoms at surfaces, there has been much interest in the possibility of building or modifying nanostructures or molecules directly from single atoms. Individual large molecules can be positioned on surfaces, and atoms can be transferred controllably between the sample and probe tip. The most complex structures are produced at cryogenic temperatures by sliding atoms across a surface to chosen sites. But there are problems in manipulating atoms laterally at higher temperatures--atoms that are sufficiently well bound to a surface to be stable at higher temperatures require a stronger tip interaction to be moved. This situation differs significantly from the idealized weakly interacting tips of scanning tunnelling or atomic force microscopes. Here we demonstrate that precise positioning of atoms on a copper surface is possible at room temperature. The triggering mechanism for the atomic motion unexpectedly depends on the tunnelling current density, rather than the electric field or proximity of tip and surface.     

Selective assembly on a surface of supramolecular aggregates with controlled size and shape.

The realization of molecule-based miniature devices with advanced functions requires the development of new and efficient approaches for combining molecular building blocks into desired functional structures, ideally with these structures supported on suitable substrates 1-4.Supramolecular aggregation occurs spontaneously and can lead to controlled structures if selective and directional non-covalent interactions are exploited. But such selective supramolecular assembly has yielded almost exclusively crystals or dissolved structures 5; the self-assembly of absorbed molecules into larger structures 6-8, in contrast, has not yet been directed by controlling selective intermolecular interactions. Here we report the formation of surface-supported supramolecular structures whose size and aggregation pattern are rationally controlled by tuning the non-covalent interactions between individual absorbed molecules.Using low-temperature scanning tunnelling microscopy, we show that substituted porphyrin molecules adsorbed on a gold surface form monomers, trimers, tetramers or extended wire-like structures. We find that each structure corresponds in a predictable fashion to the geometric and chemical nature of the porphyrin substituents that mediate the interactions between individual adsorbed molecules.Our findings suggest that careful placement of functional groups that are able to participate in directed non-covalent interactions will allow the rational design and construction of a wide range of supramolecular architectures absorbed to surfaces.     

Two-electron dissociation of single molecules by atomic manipulation at room temperature

Using the tip of a scanning tunnelling microscope (STM) to mechanically manipulate individual atoms and molecules on a surface is now a well established procedure. Similarly, selective vibrational excitation of adsorbed molecules with an STM tip to induce motion or dissociation has been widely demonstrated. Such experiments are usually performed on weakly bound atoms that need to be stabilized by operating at cryogenic temperatures. Analogous experiments at room temperature are more difficult, because they require relatively strongly bound species that are not perturbed by random thermal fluctuations. But manipulation can still be achieved through electronic excitation of the atom or molecule by the electron current tunnelling between STM tip and surface at relatively high bias voltages, typically 1-5 V. Here we use this approach to selectively dissociate chlorine atoms from individual oriented chlorobenzene molecules adsorbed on a Si(111)-7 x 7 surface. We map out the final destination of the chlorine daughter atoms, finding that their radial and angular distributions depend on the tunnelling current and hence excitation rate. In our system, one tunnelling electron has nominally sufficient energy to induce dissociation, yet the process requires two electrons. We explain these observations by a two-electron mechanism that couples vibrational excitation and dissociative electron attachment steps.     

H2O分子在石墨烯扶手型边缘吸附的研究

类似石墨表面,石墨烯可以吸附和脱附各种原子和分子,石墨烯比石墨具有更大表面积,因此,石墨烯的表面性能被广泛关注. 然而较少被关注的是石墨烯边缘C原子的性能. 石墨烯边缘C原子由于存在未配对的电子,因此具有更强的反应活性. 本文采用了SelfConsistentCharge Density Functional Tight Binding(SCCDFTB)方法对H2O分子在石墨烯扶手型边缘的吸附现象进行了研究. 研究发现,石墨烯边缘的峰位C原子具有很好的吸附性,吸附能大约为-0.109~-0.768     

Enantiospecific electrodeposition of a chiral catalyst

Many biomolecules are chiral--they can exist in one of two enantiomeric forms that only differ in that their structures are mirror images of each other. Because only one enantiomer tends to be physiologically active while the other is inactive or even toxic, drug compounds are increasingly produced in an enantiomerically pure form using solution-phase homogeneous catalysts and enzymes. Chiral surfaces offer the possibility of developing heterogeneous enantioselective catalysts that can more readily be separated from the products and reused. In addition, such surfaces might serve as electrochemical sensors for chiral molecules. To date, chiral surfaces have been obtained by adsorbing chiral molecules or slicing single crystals so that they exhibit high-index faces, and some of these surfaces act as enantioselective heterogeneous catalysts. Here we show that chiral surfaces can also be produced through electrodeposition, a relatively simple solution-based process that resembles biomineralization in that organic molecules adsorbed on surfaces have profound effects on the morphology of the inorganic deposits. When electrodepositing a copper oxide film on an achiral gold surface in the presence of tartrate ion in the deposition solution, the chirality of the ion determines the chirality of the deposited film, which in turn determines the film's enantiospecificity during subsequent electrochemical oxidation reactions.     

Imaging and dynamics of light atoms and molecules on graphene

Observing the individual building blocks of matter is one of the primary goals of microscopy. The invention of the scanning tunnelling microscope revolutionized experimental surface science in that atomic-scale features on a solid-state surface could finally be readily imaged. However, scanning tunnelling microscopy has limited applicability due to restrictions in, for example, sample conductivity, cleanliness, and data acquisition rate. An older microscopy technique, that of transmission electron microscopy (TEM), has benefited tremendously in recent years from subtle instrumentation advances, and individual heavy (high-atomic-number) atoms can now be detected by TEM even when embedded within a semiconductor material. But detecting an individual low-atomic-number atom, for example carbon or even hydrogen, is still extremely challenging, if not impossible, via conventional TEM owing to the very low contrast of light elements. Here we demonstrate a means to observe, by conventional TEM, even the smallest atoms and molecules: on a clean single-layer graphene membrane, adsorbates such as atomic hydrogen and carbon can be seen as if they were suspended in free space. We directly image such individual adatoms, along with carbon chains and vacancies, and investigate their dynamics in real time. These techniques open a way to reveal dynamics of more complex chemical reactions or identify the atomic-scale structure of unknown adsorbates. In addition, the study of atomic-scale defects in graphene may provide insights for nanoelectronic applications of this interesting material.     

A metal complex that binds alpha-amino acids with high and predictable stereospecificity.

Molecular recognition is the key step in a wide range of controlled separation and chemical transformation processes, with enzymes performing this task with an unsurpassed degree of selectivity. Enzymes contain only 20 simple amino acids, yet it remains difficult to rationalize or even predict these stereospecific recognition events. Nonetheless, the rational design of receptors able to recognize amino acids stereospecifically is attracting considerable interest because therapeutic drugs, that may be developed from chiral amino acid intermediates, are increasingly required in enantiomerically pure form. Early work has stimulated the development of efficient receptors based on small molecules, but binding of amino acids with high and predictable stereospecificity remains difficult to achieve. Directed molecular evolution, on the other hand, does select for RNA sequences or antibodies that bind amino acids with high specificity, but typically without providing insights into the molecular recognition mechanisms involved. Here we show that a rationally designed metal complex formed from a trivalent cobalt ion and a tetradentate ligand binds natural amino acids, including the simple yet challenging amino acid alanine, with high and predictable regio- and stereospecificity. We expect that our approach will allow the binding as well as separation and stereospecific catalytic formation of its target amino acids.     

限域在扶手椅型SWBNNT内Lys分子手性转变的反应机理

采用量子力学与分子力学组合的ONIOM方法, 研究限域在扶手椅型单壁氮化硼纳米管(SWBNNT)内赖氨酸(Lys)分子手性转变的反应机理. 采用原子中心密度矩阵传播（ADMP)分子动力学方法, 研究Lys分子在SWBNNT(5,5)内手性转变反应通道入口与出口势能面上的动态反应路径, 给出中间体和产物的微观动态反应图像. 结果表明： 随着纳米管管径的减小, 限域其中的Lys分子骨架C原子间的键角明显增大; 手性C上的H与氨基N的距离逐渐变小; 在SWBNNT(5,5)内, 通过2个基元反应Lys分子实现了手性转变; 在SWBNNT(6,6)和SWBNNT(7,7)内, 通过3个和4个基元反应Lys分子实现了手性转变 ; 在SWBNNT(5,5)内, Lys分子手性转变反应决速步骤自由能垒降为最低值190.1 kJ/mol. 在 SWBNNT(7,7)内, 决速步骤能垒与裸反应基本相同.     

Two-step binding mechanism for T-cell receptor recognition of peptide MHC

T cells probe a diverse milieu of peptides presented by molecules of the major histocompatibility complex (MHC) by using the T-cell receptor (TCR) to scan these ligands with high sensitivity and specificity. Here we describe a physical basis for this scanning process by studying the residues involved in both the initial association and the stable binding of TCR to peptide-MHC, using the well-characterized TCR and peptide-MHC pair of 2B4 and MCC-IE(k) (moth cytochrome c, residues 88 103). We show that MHC contacts dictate the initial association, guiding TCR docking in a way that is mainly independent of the peptide. Subsequently, MCC-IE(k) peptide contacts dominate stabilization, imparting specificity and influencing T-cell activation by modulating the duration of binding. This functional subdivision of the peptide-MHC ligand suggests that a two-step process for TCR recognition facilitates the efficient scanning of diverse peptide-MHC complexes on the surface of cells and also makes TCRs inherently crossreactive towards different peptides bound by the same MHC.     

Structural effects on the magnetic hyperthermia properties of iron oxide nanoparticles

Magnetic iron oxide nanoparticles(IONPs) are heavily explored as diagnostic and therapeutic agents due to their low cost, tunable properties, and biocompatibility. In particular, upon excitation with an alternating current(AC) magnetic field, the NPs generate localized heat that can be exploited for therapeutic hyperthermia treatment of diseased cells or pathogenic microbes. In this review, we focus on how structural changes and inter-particle interactions affect the heating efficiency of iron oxide-based magnetic NPs. Moreover, we present an overview of the different approaches to evaluate the heating performance of IONPs and introduce a new theranostic modality based on magnetic imaging guided–hyperthermia.     

Chiral ligand-protected gold nanoclusters: Considering the optical activity from a viewpoint of ligand dissymmetric field

Chirality is a geometric property of a physical, chemical, or biological object, which is not superimposable on its mirror image. Its significant presence has led to a strong demand in the development of chiral drugs, sensors, catalysts, and photofunctional materials. In recent years, chirality of nanoscale organic/inorganic hybrids has received tremendous attention owing to potential applications in chiral nanotechnology. In particular, with the recent progress in the syntheses and characterizations of atomically precise gold nanoclusters protected by achiral thiolates, atomic level origins of their chirality have been unveiled. On the other hand, chirality or optical activity in metal nanoclusters can also be introduced via the surface chiral ligands, which should be universal for the nanosystems. This tutorial review presents some optically-active metal (gold) nanoclusters protected by chiral thiolates or phosphines, and their chiroptical (or circular dichroism; CD) properties are discussed mostly from a viewpoint of the ligand dissymmetric field scheme. The examples are the gold nanoclusters protected by (R)-/(S)-2-phenylpropane-1-thiol, (R)-/(S)-mercaptosuccinic acid, phenylboronate-D/L-fructose complexes, phosphine sulfonate-ephedrinium ion pairs, or glutathione. Some methodologies for versatile asymmetric transformation and chiroptical controls of the nanocluster compounds are also described. In the dissymmetric field model as the origin of optical activity, the chiroptical responses of the gold nanoclusters are strongly associated with coupled oscillator and/or CD stealing mechanisms based on the concept of induced CD (ICD) derived from a perturbation theory, so on this basis, some characteristic features of the observed CD responses of chiral ligand-protected gold nanoclusters are presented in detail. We believe that various kinds of origins of chirality found in ligand-protected gold nanoclusters may provide models for understanding those of many related nanomaterials.     

Spatially resolved observation of crystal-face-dependent catalysis by single turnover counting

Catalytic processes on surfaces have long been studied by probing model reactions on single-crystal metal surfaces under high vacuum conditions. Yet the vast majority of industrial heterogeneous catalysis occurs at ambient or elevated pressures using complex materials with crystal faces, edges and defects differing in their catalytic activity. Clearly, if new or improved catalysts are to be rationally designed, we require quantitative correlations between surface features and catalytic activity--ideally obtained under realistic reaction conditions. Transmission electron microscopy and scanning tunnelling microscopy have allowed in situ characterization of catalyst surfaces with atomic resolution, but are limited by the need for low-pressure conditions and conductive surfaces, respectively. Sum frequency generation spectroscopy can identify vibrations of adsorbed reactants and products in both gaseous and condensed phases, but so far lacks sensitivity down to the single molecule level. Here we adapt real-time monitoring of the chemical transformation of individual organic molecules by fluorescence microscopy to monitor reactions catalysed by crystals of a layered double hydroxide immersed in reagent solution. By using a wide field microscope, we are able to map the spatial distribution of catalytic activity over the entire crystal by counting single turnover events. We find that ester hydrolysis proceeds on the lateral {1010} crystal faces, while transesterification occurs on the entire outer crystal surface. Because the method operates at ambient temperature and pressure and in a condensed phase, it can be applied to the growing number of liquid-phase industrial organic transformations to localize catalytic activity on and in inorganic solids. An exciting opportunity is the use of probe molecules with different size and functionality, which should provide insight into shape-selective or structure-sensitive catalysis and thus help with the rational design of new or more productive heterogeneous catalysts.     

Carbon nanotubes as nanoscale mass conveyors

The development of manipulation tools that are not too 'fat' or too 'sticky' for atomic scale assembly is an important challenge facing nanotechnology. Impressive nanofabrication capabilities have been demonstrated with scanning probe manipulation of atoms and molecules on clean surfaces. However, as fabrication tools, both scanning tunnelling and atomic force microscopes suffer from a loading deficiency: although they can manipulate atoms already present, they cannot efficiently deliver atoms to the work area. Carbon nanotubes, with their hollow cores and large aspect ratios, have been suggested as possible conduits for nanoscale amounts of material. Already much effort has been devoted to the filling of nanotubes and the application of such techniques. Furthermore, carbon nanotubes have been used as probes in scanning probe microscopy. If the atomic placement and manipulation capability already demonstrated by scanning probe microscopy could be combined with a nanotube delivery system, a formidable nanoassembly tool would result. Here we report the achievement of controllable, reversible atomic scale mass transport along carbon nanotubes, using indium metal as the prototype transport species. This transport process has similarities to conventional electromigration, a phenomenon of critical importance to the semiconductor industry.     

Rhizobium--plant signal exchange.

Initial stages in the Rhizobium-legume symbiosis can be thought of as a reciprocal molecular conversation: transmission of a gene inducer from legume host to bacterium, with ensuing bacterial synthesis of a morphogen that is transmitted to the plant, switching the developmental fate of the legume root. These signal molecules have a key role in determining bacterium-host specificity and the purified Nod factor compounds provide useful new tools to probe plant cell function.     

有机手性分子器件的光电特性

目前多种有机手性分子器件虽已研制成功,但其内在的物理机理仍有许多未解之谜,其中手性分子的圆二色性精细结构、手性诱导的自旋选择效应等是有机手性分子研究的核心.为设计基于手性的新型有机功能器件提供理论指导,考虑有机手性分子螺旋势场诱导的自旋-轨道耦合,围绕分子的光电特性及其调控展开了系列研究.根据光致跃迁理论,得到手性分子...     

Formation of chiral morphologies through selective binding of amino acids to calcite surface steps.

Many living organisms contain biominerals and composites with finely tuned properties, reflecting a remarkable level of control over the nucleation, growth and shape of the constituent crystals. Peptides and proteins play an important role in achieving this control. But the general view that organic molecules affect mineralization through stereochemical recognition, where geometrical and chemical constraints dictate their binding to a mineral, seems difficult to reconcile with a mechanistic understanding, where crystallization is controlled by thermodynamic and kinetic factors. Indeed, traditional crystal growth models emphasize the inhibiting effect of so-called 'modifiers' on surface-step growth, rather than stereochemical matching to newly expressed crystal facets. Here we report in situ atomic force microscope observations and molecular modelling studies of calcite growth in the presence of chiral amino acids that reconcile these two seemingly divergent views. We find that enantiomer-specific binding of the amino acids to those surface-step edges that offer the best geometric and chemical fit changes the step-edge free energies, which in turn results in macroscopic crystal shape modifications. Our results emphasize that the mechanism underlying crystal modification through organic molecules is best understood by considering both stereochemical recognition and the effects of binding on the interfacial energies of the growing crystal.