High-resolution STM imaging of novel single G4-DNA molecules

The molecular morphology of long G4-DNA wires made by a novel synthetic method was, for the first time, characterized by high-resolution scanning tunneling microscopy (STM). The STM images reveal a periodic structure seen as repeating "bulbs" along the molecules. These bulbs reflect the helix morphology of the wires. The STM measurements were supported by a statistical morphology analysis of the DNA pitch length and apparent height relative to the surface. In the absence of X-ray and NMR data for these wires, the STM measurements provide a unique alternative to characterize the helix morphology.     

Adsorption of Large Organic Molecules on Clean and Hydroxylated Rutile TiO2(110) Surfaces

Behavior of large organic molecules equipped with spacer groups (Violet Landers, VL) on the TiO₂(110)‐(1×1) surfaces is investigated by means of high‐resolution scanning tunneling microscopy (STM). Two distinct adsorption geometries are observed. We demonstrate that the molecule adsorption morphology can be alternated by well‐controlled STM tip‐induced manipulation. It is used to probe the mobility of molecules and reveals locking in one of the analyzed adsorption sites, thus allow to enhance or reduce the mobility along the [001] direction. Field induced hydrogen desorption is used to perform lateral STM manipulation on a hydroxyl‐free surface, which provides insight into the influence of surface hydroxyl groups on the molecule behavior. The ability to image with submolecular resolution both the central board and the spacer groups of the VL molecule is demonstrated.     

四苯基卟啉铜分子的扫描隧道显微镜成像

本文首次以ＬＢ技术将四苯基卟啉铜（ＣｕＴＰＰ）分子沉积到高定向热解石墨上，并用ＳＴＭ研究其表面形貌，得到了原子级分辨的ＣｕＴＰＰ分子的表面形貌图，结果表明，ＣｕＴＰＰ分子具有近似圆状平面结构，分子直径为１．０ｎｍ，与理论结果十分吻合，结合ＳＴＭ原理，讨论了有机大分子ＳＴＭ成像的条件。     

Scanning tunneling microscope imaging of (CH3S)2 on Cu(111)

Scanning tunneling microscope (STM) images of isolated molecules of dimethyl disulfide, (CH(3)S)(2), adsorbed on the Cu(111) surface were successfully obtained at a sample temperature of 4.7 K. A (CH(3)S)(2) molecule appears as an elliptic protrusion in the STM images. From density functional theory calculation, it was suggested that the bright part in the protrusion corresponds to the molecular orbital which is widely spread around H atoms in each CH(3) group in the (CH(3)S)(2) molecule. The STM images revealed that the molecules have a total of six equivalent adsorption orientations on Cu(111), which are given by the combination of three equivalent adsorption sites and two conformational isomers for each adsorption site.     

Formation of one-dimensional C60 rows on TiO2(110)-1 x 2-cross-link structure and their local polymerization

Adsorption and growth of a C(60) monolayer on a TiO(2)(110)-1 x 2-cross-link structure were investigated by scanning tunneling microscopy (STM). Single C(60) molecules were preferentially anchored at the cross-link site due to interaction with undercoordinated Ti cations, and C(60) rows grew along the troughs between the 1 x 2-added rows. The C(60) monolayer structure is characterized by closely packed (r(C(60)-C(60)) = 1.0 nm) C(60) rows that are paired with every second added row (separation of paired rows is 1.1 nm). By applying a high negative bias voltage (-3.5 V) to an STM tip on the C(60) monolayer, C(60) oligomers were formed accompanied with the contraction of C(60)-C(60) distance along the C(60) row and bright contrast in the STM image.     

The initial growth behavior of perylene on Cu(100)

Using scanning tunneling microscopy (STM) together with density functional theory (DFT) the growth behavior of perylene on the Cu(100) substrate has been investigated. As revealed by STM images, perylene molecules prefer to adopt lying configuration with their molecular plane parallel to the substrate, and two symmetrically equivalent ordered domains were observed. DFT calculations show that perylene molecule prefers to adsorb on the top site of substrate Cu atoms with its long molecular axis aligning along the [011] or [01-1] azimuth of the substrate which is the most stable adsorption geometry according to its highest binding energy. Consequently, two adsorption structures of c(8×4) and c(8×6), each containing two perylene molecules per unit cell, are proposed based on our STM images. The growth mechanism for ordered perylene domains on Cu(100) can be attributed to the balance between weak adsorbate-adsorbate interaction and comparable adsorbate-substrate interaction.     

Imaging and vibrational spectroscopy of single pyridine molecules on Ag(110) using a low-temperature scanning tunneling microscope

A scanning tunneling microscope (STM) was used to extract the images of single, isolated pyridine molecules adsorbed on Ag(110) and to record their vibrational spectrum at 13 K. On the STM image, the pyridine molecule appears as an elongated protrusion along the [001] direction on top of a silver atom, indicating that it is bonded through its nitrogen lone pair electrons. STM inelastic electron tunneling spectroscopy of the adsorbed pyridine revealed C-D and C-H stretch modes at 282 and 378 meV, respectively.     

Au(111)表面Verdazyl自由基的构象转换

Pure organic radical molecules on metal surfaces are of great significance in exploration of the electron spin behavior. However, only a few of them are investigated in surface studies due to their poor thermal stability. The adsorption and conformational switching of two verdazyl radical molecules, namely, 1, 5-biisopropyl-3-(benzo[b]benzo[4,5]thieno[2, 3-d]thiophen-2-yl)-6-oxoverdazyl (B2P) and 1, 5-biisopropyl-3-(benzo[b]benzo[4,5]thieno[2, 3-d]thiophen-4-yl)-6-oxoverdazyl (B4P), are studied by scanning tunneling microscopy (STM) and density functional theory (DFT). The adsorbed B2P molecules on Au(111) form dimers, trimers and tetramers without any ordered assembly structure in which two distinct appearances of B2P in STM images are observed and assigned to be its "P" and "T" conformations. The "P" conformation molecules appear in the STM image with a large elliptical protrusion and two small ones of equal size, while the "T" ones appear with a large protrusion and two small ones of different size. Likewise, the B4P molecules on Au(111) form dimers at low coverage, strip structure at medium coverage and assembled structure at high coverage which also consists of above-mentioned two conformations. Both B2P molecules and B4P molecules are held together by weak intermolecular interaction rather than chemical bond. STM tip induced conformational switching of both verdayzl radicals is observed at the bias voltage of +2.0 V. The "T" conformation of B2P can be switched to the "P" while the "P" conformation of B4P can be switched to the "T" one. For both molecules, such a conformational switching is irreversible. The DFT calculations with Perdew-Burke-Ernzerhof version exchange-correlation functional are used to optimize the model structure and simulate the STM images. STM images of several possible molecular conformations with different isopropyl orientation and different tilt angle between verdazyl radical and Au(111) surface are simulated. For conformations with different isopropyl orientation, the STM simulated images are similar, while different tilt angles of verdazyl radical lead to significantly different STM simulated images. Combined STM experiments and DFT simulations reveal that the conformational switching originates from the change of tilting angle between the verdazyl radical and Au(111) surface. The tilt angles in "P" and "T" conformations are 0° and 50°, respectively. In this study, two different adsorption conformations of verdazyl radicals on the Au(111) surface are presented and their exact adsorption structures are identified. This study provides a possible way to study the relationship between the electron spin and configuration conversion of pure organic radical molecules and a reference for designing more conformational switchable radical molecules that can be employed as interesting molecular switches.     

The puzzle of contrast inversion in DNA STM imaging

DNA has been at the center of an imaging effort since the invention of the scanning tunneling microscope (STM). In some of the STM imaging reports the molecules appeared with negative contrast, i.e., "submerged" under the metal background and darker. We demonstrate the phenomenon of contrast inversion in DNA STM imaging by controlled and spontaneous contrast inversions and by the dependence of the DNA apparent height with respect to the surface on the imaging bias voltage. Using these characterizations, we formulate a model explaining the above phenomenon by resonant tunneling through virtual states in the vacuum between the STM tip and the DNA molecule.     

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.     

Star-shaped oligo(p-phenylenevinylene) substituted hexaarylbenzene: purity, stability, and chiral self-assembly

An oligo(p-phenylenevinylene) (OPV)-substituted hexaarylbenzene has been synthesized and fully characterized. Recycling gel permeation chromatography appeared to be a powerful technique to obtain the OPV molecules in a very pure form. X-ray analysis and polarization optical microscopy revealed that the OPV molecule is plastic crystalline at room temperature with an ordered columnar superstructure. In apolar solvents, the molecules self-assemble via a highly cooperative fashion into right-handed chiral superstructures, which are stable even at high temperatures and low concentration. Atomic force microscopy revealed right-handed fibers with a diameter of 6 nm, indicating pi-stacked aggregates; on a silicon oxide substrate, supercoiled chiral structures were observed. STM studies on a liquid-solid interface showed that the star-shaped OPV molecule forms an organized monolayer having a chiral hexagonal lattice.     

W(100) c(2×2)表面的STM图像

用基于第一性原理的密度泛函理论研究了W(100) c(2×2)再构表面的表面弛豫以及扫描隧道显微镜(STM)图像和衬底偏压的关系. 计算所得到的表面原子沿[-110]方向的畸变位移δ为0.027 nm, 畸变能⊿E为80.6 meV·atom-1, 表面原子的弛豫分别为-7.6%(⊿d12/d0)和+0.8%(⊿d23/d0), 功函数Φ为4.55 eV. STM图像模拟表明, 由于表面原子沿[-110]方向的位移, 会导致出现平行于[110]方向的亮暗带状条纹. STM图像中突起所对应的并不是表面或次表面的钨原子, 而是zig-zag型W 原子链中线位置; 而STM暗区对应于原子位置畸变形成的相邻zig-zag型W原子链中间区域. 当衬底负偏压时, STM针尖典型起伏高度大约在0.008-0.013 nm之间; 而当衬底正偏压时, 针尖起伏高度在0.019-0.024 nm之间变化.     

Nucleoside-assisted self-assembly of oligo(p-phenylenevinylene)s at liquid/solid interface: chirality and nanostructures

The formation of DNA nucleoside-assisted π-conjugated nanostructures was studied by means of scanning tunneling microscopy (STM) and force field simulations. Upon adsorption of the achiral oligo(p-phenylenevinylene) (OPV) derivative at the liquid/solid interface, racemic conglomerates with mirror related rosettes are formed. Addition of the DNA nucleosides D- and L-thymidine, which act as "chiral handles", has a major effect on the supramolecular structure and the expression of chirality of the achiral OPV molecules. The influence of these "chiral handles" on the expression of chirality is probed at two levels: monolayer symmetry and monolayer orientation with respect to the substrate. This was further explored by tuning the molar ratio of the building blocks. Molecular modeling simulations give an atomistic insight into the monolayer construction, as well as the energetics governing the assembly. Thymidine is able to direct the chirality and the pattern of OPV molecules on the surface, creating chiral lamellae of π-conjugated dimers.     

Distinguishing Individual DNA Bases in a Network by Non‐Resonant Tip‐Enhanced Raman Scattering

The importance of identifying DNA bases at the single‐molecule level is well recognized for many biological applications. Although such identification can be achieved by electrical measurements using special setups, it is still not possible to identify single bases in real space by optical means owing to the diffraction limit. Herein, we demonstrate the outstanding ability of scanning tunneling microscope (STM)‐controlled non‐resonant tip‐enhanced Raman scattering (TERS) to unambiguously distinguish two individual complementary DNA bases (adenine and thymine) with a spatial resolution down to 0.9 nm. The distinct Raman fingerprints identified for the two molecules allow to differentiate in real space individual DNA bases in coupled base pairs. The demonstrated ability of non‐resonant Raman scattering with super‐high spatial resolution will significantly extend the applicability of TERS, opening up new routes for single‐molecule DNA sequencing.     

Study of adsorption and decomposition of H2O on Ge(100)

The adsorption and decomposition of water on Ge(100) have been investigated using real-time scanning tunneling microscopy (STM) and density-functional theory (DFT) calculations. The STM results revealed two distinct adsorption features of H2O on Ge(100) corresponding to molecular adsorption and H-OH dissociative adsorption. In the molecular adsorption geometry, H2O molecules are bound to the surface via Ge-O dative bonds between the O atom of H2O and the electrophilic down atom of the Ge dimer. In the dissociative adsorption geometry, the H2O molecule dissociates into H and OH, which bind covalently to a Ge-Ge dimer on Ge(100) in an H-Ge-Ge-OH configuration. The DFT calculations showed that the dissociative adsorption geometry is more stable than the molecular adsorption geometry. This finding is consistent with the STM results, which showed that the dissociative product becomes dominant as the H2O coverage is increased. The simulated STM images agreed very well with the experimental images. In the real-time STM experiments, we also observed a structural transformation of the H2O molecule from the molecular adsorption to the dissociative adsorption geometry.     

Self-assembly of PcOC8 and its sandwich lanthanide complex Pr(PcOC8)(2) with oligo(phenylene-ethynylene) molecules

Self-assemblies of octakis(octyloxy) phthalocyanine (PcOC8) and its sandwich lanthanide complex, substituted praseodymium bis(phthalocyanine) (Pr(PcOC8)(2)), with oligo(phenylene-ethynylene) (OPE) have been investigated by scanning tunneling microscopy (STM) on a highly oriented pyrolytic graphite (HOPG) surface. The assemblies were prepared by dissolving the molecules in phenyloctane solution. It was found that both PcOC8 and Pr(PcOC8)(2) can form 4-fold or 6-fold symmetrical adlayers on HOPG. The intramolecular structure of Pr(PcOC8)(2) molecule was revealed by a high-resolution STM image. When OPE molecules are added into phenyloctane solvent, Pr(PcOC8)(2) molecules prefer to form an ordered adlayer at the top of the OPE adlayer, while PcOC8 molecules adsorb on HOPG surface directly and form separated domains with OPE. These results may be helpful to construct surface assemblies and develop molecular electronic devices in the future.     

隧道结电场辅助下叔丁胺分子在Cu(111)表面跳跃(英文)

采用扫描隧道显微镜(STM)于78 K研究了单个叔丁胺分子在Cu(111)表面的横向跃迁现象.研究发现叔丁胺分子的跳跃几率随隧道电流的增加而线性增加,这表明该过程是单电子激发过程;在不同极性的隧道结电场作用下,叔丁基胺分子跳跃行为发生的几率不同,这种现象可以用电场辅助的扩散过程解释.在不同极性电场作用下叔丁胺分子在Cu(111)表面的吸附能和扩散势垒不同,从而表现出不同的跳跃几率.     

Scanning tunneling microscopy studies of pulse deposition of dinuclear organometallic molecules on Au(111)

Ultrahigh-vacuum scanning tunneling microscopy (STM) was used to study trans-[Cl(dppe)2Ru(C Triple Bond C)6Ru(dppe)2Cl] [abbreviated as Ru2, diphenylphosphinoethane (dppe)] on Au(111). This large organometallic molecule was pulse deposited onto the Au(111) surface under ultrahigh-vacuum (UHV) conditions. UHV STM studies on the prepared sample were carried out at room temperature and 77 K in order to probe molecular adsorption and to characterize the surface produced by the pulse deposition process. Isolated Ru2 molecules were successfully imaged by STM at room temperature; however, STM images were degraded by mobile toluene solvent molecules that remain on the surface after the deposition. Cooling the sample to 77 K allows the solvent molecules to be observed directly using STM, and under these conditions, toluene forms organized striped domains with regular domain boundaries and a lattice characterized by 5.3 and 2.7 A intermolecular distances. When methylene chloride is used as the solvent, it forms analogous domains on the surface at 77 K. Mild annealing under vacuum causes most toluene molecules to desorb from the surface; however, this annealing process may lead to thermal degradation of Ru2 molecules. Although pulse deposition is an effective way to deposit molecules on surfaces, the presence of solvent on the surface after pulse deposition is unavoidable without thermal annealing, and this annealing may cause undesired chemical changes in the adsorbates under study. Preparation of samples using pulse deposition must take into account the characteristics of sample molecules, solvent, and surfaces.     

Orbital specific chemistry: controlling the pathway in single-molecule dissociation

A scanning tunneling microscope (STM) was used to control the pathway of the dissociation of single O(2) molecules chemisorbed on Ag(110) at 13 K. Tunneling of electrons from the STM tip into the O(2) caused dissociation of the molecule, giving rise to two adsorbed O atoms separated along the [110] direction. In contrast, the ejection of electrons from the O(2) molecule produced adsorbed O atoms separated along the [001] direction. These results illustrate that control of the dissociation pathway and product formation are associated with a specific molecular orbital located at the Fermi level.     

Internal Architecture and Adsorption Sites of Violet Lander Molecules Assembled on Native and KBr‐Passivated InSb(001) Surfaces

The adsorption of individual Violet Lander molecules self‐assembled on the c(8×2) reconstructed InSb(001) surface in its native form and on the surface passivated with one to three monolayers of KBr is investigated by means of low‐temperature scanning tunneling microscopy (STM). Preferred adsorption sites of the molecules are found on flat terraces as well as at atomic step edges. For molecules immobilized on flat terraces, several different conformations are identified from STM images acquired with submolecular resolution and are explained by the rotation of the 3,5‐di‐tert‐butylphenyl groups around σ bonds, which allows adjustment of the molecular geometry to the anisotropic substrate structure. Formation of ordered molecular chains is found at steps running along substrate reconstruction rows, whereas at the steps oriented perpendicularly no intermolecular ordering is recorded. It is also shown that the molecules deposited at two or more monolayers of the epitaxial KBr spacer do not have any stable adsorption sites recorded with STM. Prospects for the manipulation of single molecules by using the STM tip on highly anisotropic substrates are also explored, and demonstrate the feasibility of controlled lateral displacement in all directions.