Self-assembly of L-tryptophan on Cu(111) studied by low-temperature scanning tunneling microscopy

The self-assembly of L-tryptophan on Cu(111) is investigated by an ultrahigh vacuum scanning tunneling microscope (STM) at 4.4 K. A series of novel supramolecular structures have been prepared with different annealing temperatures.     

一氧化碳共吸附法确定叔丁胺分子在Cu(111)表面的吸附位

采用扫描隧道显微镜(STM)和密度泛函理论(DFT)研究了78 K时单个叔丁胺分子在Cu(111)表面的吸附位. 我们提出以共吸附的一氧化碳√3 ×√3 超结构为基底铜原子的标识方法, 确定了低覆盖度的叔丁胺分子在Cu(111)表面的吸附位为顶位. 而采用单个一氧化碳分子标识基底铜原子的位置, 同样得出了叔丁胺分子的吸附位为顶位. 此外, 还采用DFT计算叔丁胺分子在Cu(111)表面的优势吸附构型. 理论计算结果表明顶位吸附构型为能量最稳定的构型, 与实验结果相吻合.     

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.     

Modification of Supramolecular Binding Motifs Induced By Substrate Registry: Formation of Self‐Assembled Macrocycles and Chain‐Like Patterns

The self‐assembly properties of two Zn^II porphyrin isomers on Cu(111) are studied at different coverage by means of scanning tunneling microscopy (STM). Both isomers are substituted in their meso‐positions by two voluminous 3,5‐di(tert‐butyl)phenyl and two rod‐like 4′‐cyanobiphenyl groups, respectively. In the trans‐isomer, the two 4′‐cyanobiphenyl groups are opposite to each other, whereas they are located at right angle in the cis‐isomer. For coverage up to one monolayer, the cis‐substituted porphyrins self‐assemble to form oligomeric macrocycles held together by antiparallel CN???CN dipolar interactions and CN???H‐C(sp²) hydrogen bonding. Cyclic trimers and tetramers occur most frequently but everything from cyclic dimers to hexamers can be observed. Upon annealing of the samples at temperatures >150 °C, dimeric macrocyclic structures are observed, in which the two porphyrins are bridged by Cu atoms, originating from the surface, under formation of two CN???Cu???NC coordination bonds. The trans‐isomer builds up linear chains on Cu(111) at low coverage, whereas for higher coverage the molecules assemble in a periodic, densely packed structure. Both cis‐ and trans‐bis(4′‐cyanobiphenyl)‐substituted Zn^II porphyrins behave very differently on Cu(111) compared to similar porphyrins in literature on less reactive surfaces such as Au(111) and Ag(111). On the latter surfaces, there is no signal visible between molecular orientation and the crystal directions of the substrate, whereas on Cu(111), very strong adsorbate–substrate interactions have a dominating influence on all observed structures. This strong porphyrin–substrate interaction enables a much broader variety of structures, including also less favorable intermolecular bonding motifs and geometries.     

On‐Surface Metalation and 2D Self‐Assembly of Pyrphyrin Molecules Into Metal‐Coordinated Networks on Cu(111)

The metalation of the tetradentate molecule pyrphyrin by copper substrate atoms on a Cu(111) surface is studied. Pyrphyrin, in contrast to porphyrin, consists of four fused pyridine groups instead of pyrrol groups. Using thermal desorption spectroscopy (TDS ) and N 1s X‐ray photoelectron spectroscopy (XPS ), we show that metalation of the monolayer of pyrphyrin with Cu atoms from the Cu(111) surface occurs at 377 K. The formation of an extended two‐dimensional (2D) network is observed with scanning tunneling microscopy (STM ). A honeycomb‐like lattice of metalated pyrphyrin molecules is formed by intermolecular connection via the two cyano groups at the periphery of pyrphyrin as well as Cu adatoms. Dehydrogenation at the periphery of the molecule is observed during annealing at 520 K. The surface‐adsorbed metal‐pyrphyrin has the potential to serve as a molecular catalyst.     

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.     

Low-temperature mobility and structure formation of a prochiral aromatic thiol (2,5-dichlorothiophenol) on Cu(111)

We present a low-temperature scanning tunneling microscopy study of increasing coverages of 2,5-dichlorothiophenol, an asymmetrically halo-substituted aromatic thiol, on Cu(111). At low coverage, deprotonation of the thiol occurs spontaneously upon adsorption at 80 K. Albeit the low deposition temperature, we find the formation of adsorbate islands at low coverage, which coalesce into a well-ordered film of horizontally adsorbed molecules at increasing coverage. This behavior indicates (i) significant mobility of the thiols on Cu(111) even at low temperatures and (ii) attractive adsorbate-adsorbate interactions. At higher coverages intermolecular interactions prevent long-range diffusion of adsorbates and thermal activation of the S-H bond becomes necessary. A close analysis of the molecular films reveals chiral recognition between neighboring molecules, which leads to the formation of enantiopure areas on the surface. Upright orientation of individual molecules starts at the boundaries between such phases and can be induced by scanning tunneling microscopy.     

Adsorption and thermal decomposition of 2-octylthieno[3,4-b]thiophene on Au(111)

The adsorption and thermal stability of 2-octylthieno[3,4-b]thiophene (OTTP) on the Au(111) surfaces have been studied using scanning tunneling microscopy (STM), temperature programmed desorption (TPD), and X-ray photoelectron spectroscopy (XPS). UHV-STM studies revealed that the vapor-deposited OTTP on Au(111) generated disordered adlayers with monolayer thickness even at saturation coverage. XPS and TPD studies indicated that OTTP molecules on Au(111) are stable up to 450K and further heating of the sample resulted in thermal decomposition to produce H(2) and H(2)S via C-S bond scission in the thieno-thiophene rings. Dehydrogenation continues to occur above 600K and the molecules were ultimately transformed to carbon clusters at 900K. Highly resolved air-STM images showed that OTTP adlayers on Au(111) prepared from solution are composed of a well-ordered and low-coverage phase where the molecules lie flat on the surface, which can be assigned as a (9×2√33)R5° structure. Finally, based on analysis of STM, TPD, and XPS results, we propose a thermal decomposition mechanism of OTTP on Au(111) as a function of annealing temperature.     

The reactive chemisorption of alkyl iodides at Cu(110) and Ag(111) surfaces: a combined STM and XPS study

The chemisorption of methyl and phenyl iodide has been studied at Cu(110) and Ag(111) surfaces at 290 K with STM and XPS. At both surfaces dissociative adsorption of both molecules leads to chemisorbed iodine, with the STM showing c(2 x 2) and (square root 3 x square root 3)R30 structures at the Cu(110) and Ag(111) surfaces, respectively. At the Cu(110) surface a comparison of coexisting c(2 x 2) I(a) and p(2 x 1) O(a) domains shows the iodine adatoms to be chemisorbed in hollow sites with evidence at low coverage for diffusion in the (110) direction. In the case of methyl iodide no carbon adsorption is observed at either the silver or the copper surfaces, but chemisorbed phenyl groups are imaged at the Cu(110) surface after exposure to phenyl iodide. The STM images show the phenyl groups as bright features approximately 0.7 nm in diameter and 0.11 nm above the iodine adlayer, reaching a maximum surface concentration after approximately 6 Langmuir exposure. However, the phenyl coverage decreases with subsequent exposures to PhI and is negligible by approximately 1000 L exposure, consistent with the formation and desorption of biphenyl. The adsorbed phenyls are located above hollow sites in the substrate, they are stabilized at the top and bottom of step edges and in paired chains (1.1 nm apart) on the terraces with a regular interphenyl spacing within the chains of 1.0 nm in the (110) direction. The interphenyl ring spacing and diffusion of individual phenyls from within the chains shows that the chains do not consist of biphenyl species but may be a precursor to their formation. Although the XPS data shows carbon present at the Ag(111) surface after exposure to PhI, no features attributable to phenyl groups were observed by STM.     

Coverage and nearest-neighbor dependence of adsorbate diffusion

We present data on the coverage and nearest-neighbor dependences of the diffusion of CO on Cu(111) by time-lapsed scanning tunneling microscope (STM) imaging. Most notable is a maximum in diffusivity of CO at a local coverage of one molecule per 20 substrate atoms and a repulsion between CO molecules upon approach closer than three adsites, which in combination with a less pronounced increase in potential energy at the diffusion transition state, leads to rapid diffusion of CO molecules around one another. We propose a new method of evaluating STM-based diffusion data that provides all parameters necessary for the modeling of the dynamics of an adsorbate population.     

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.     

Role of conformation in the electronic properties of chemisorbed pyridine on Cu(110): an STM/STS study

Pyridine was chemisorbed on Cu(110) at 10 K and observed using STM at 5 K as dosed and after annealing to temperatures between 20 and 300 K. At very low coverage, two molecular species with different apparent heights are observed to coexist. The higher species is assigned to a pyridine molecule bonded with its symmetry axis perpendicular to the surface plane, while the lower species is assigned to a pyridine molecule that is tilted down toward the surface plane. At low coverage, the tilted pyridine species predominates on the surface, but as the total surface coverage of pyridine increases, the molecules stand up until the upright geometry becomes favored. Measurements of the STS of the two species show different molecular resonances derived from the lowest unoccupied pyridine pi* orbitals. The tilted pyridine species has a peak in the unoccupied local density of states at 2.6 +/- 0.1 eV, whereas the upright pyridine species has a peak at 2.3 +/- 0.1 eV.     

Rastertunnelmikroskopie an chiralen Molekülen: Nanochemie

The imaging and manipulation capabilities of the scanning tunnelling microscope (STM) render possible a novel nanoscale chemistry based on experiments with single molecules. Herein, we address several aspects of a nanoscale stereochemistry using the STM. As an example, we investigate 1‐nitronaphthalene on Au(111). 1‐Nitronaphthalene becomes chiral upon planar adsorption on the metal surface. High‐resolution STM images reflect the asymmetric electronic structure of the molecules and allow for the determination of the absolute configuration of any individual molecule within complex molecular structures. At medium coverage, spontaneous breaking of the chiral symmetry results in the formation of homochiral conglomerates, while at high coverage racemic structures prevail. Finally, the tip of the STM is used to separate “supramolecule‐by‐supramolecule” a racemic mixture of chiral 1‐nitronaphthalene aggregates into the enantiopure compounds.     

Dipole driven bonding schemes of quinonoid zwitterions on surfaces

The permanent dipole of quinonoid zwitterions changes significantly when the molecules adsorb on Ag(111) and Cu(111) surfaces. STM reveals that sub-monolayers of adsorbed molecules can exhibit parallel dipole alignment on Ag(111), in strong contrast with the antiparallel ordering prevailing in the crystalline state and retrieved on Cu(111) surfaces, which minimizes the dipoles electrostatic interaction energy. DFT shows that the rearrangement of electron density upon adsorption is a result of donation from the molecular HOMO to the surface, and back donation to the LUMO with a concomitant charge transfer that effectively reduces the overall charge dipole.     

4-Mercaptopyridine on Au(111): a scanning tunneling microscopy and spectroscopy study

The adsorption of 4-mercaptopyridine (4MPy) molecules on reconstructed Au(111) is investigated by Scanning Tunneling Microscopy (STM) and Spectroscopy (STS) at low temperature and under ultra-high vacuum (UHV) conditions. As made visible by STM, at low coverage (<10%) 4MPy adsorbs preferentially at elbow sites of the Herringbone reconstruction and at step edges of the Au(111). Increasing coverage (but still <30%) results in formation of molecular chains followed, at even higher coverage, by a 3-dimensional growth. Detailed analysis of z-V spectroscopy (ramping the tunneling bias V while keeping the tunneling current constant) provides information on the bias dependent apparent height of a single 4MPy/Au(111) as well as on the local density of states (LDOS) of single and chain 4MPy molecules in comparison to the bare Au(111) surface revealing a significant shift of the lowest unoccupied molecular orbital (LUMO) towards lower energy for molecules within chains. Additionally, the data provide no evidence that for these samples prepared in UHV the adsorption of 4MPy on Au(111) requires mediating Au adatoms. Also, clear indications are given that the adsorption does not induce a strong reduction of the Au DOS close to its Fermi energy. Finally, in context of the apparent STM height of 4MPy molecules, the behavior of the differential barrier height Φ(diff)(V) = (?(z)?(V)I/?(V)I)(2) on bare Au(111) and 4MPy/Au(111) is analyzed and the corresponding experimental values are applied to recover the LDOS of the molecule for unoccupied states according to a previously published numerical recipe [B. Koslowski, H. Pfeifer and P. Ziemann, Phys. Rev. B, 2009, 80, 165419 and M. Ziegler, N. Néel, A. Sperl, J. Kr?ger, and R. Berndt, Phys. Rev. B, 2009, 80, 125402]. In this way, one obtains a spectrum comprising a constant DOS of the Shockley-like surface state of Au(111) and a Lorentzian line attributed to the LUMO of 4MPy.     

Hydrogen and coordination bonding supramolecular structures of trimesic acid on Cu(110)

The adsorption of trimesic acid (TMA) on Cu(110) has been studied in the temperature range between 130 and 550 K and for coverages up to one monolayer. We combine scanning tunneling microscopy (STM), low-energy electron diffraction (LEED), reflection absorption infrared spectroscopy (RAIRS), X-ray photoemission spectroscopy (XPS), and density functional theory (DFT) calculations to produce a detailed adsorption phase diagram for the TMA/Cu(110) system as a function of the molecular coverage and the substrate temperature. We identify a quite complex set of adsorption phases, which are determined by the interplay between the extent of deprotonation, the intermolecular bonding, and the overall energy minimization. For temperatures up to 280 K, TMA molecules are only partly deprotonated and form hydrogen-bonded structures, which locally exhibit organizational chirality. Above this threshold, the molecules deprotonate completely and form supramolecular metal-organic structures with Cu substrate adatoms. These structures exist in the form of single and double coordination chains, with the molecular coverage driving distinct phase transitions.     

Single molecule observations of the adsorption sites of methyl isocyanide on Pt(111) by low-temperature scanning tunneling microscopy

Scanning tunneling microscopy (STM) has been used to directly investigate the local structure of methyl isocyanide (CNCH3) adsorbed on Pt(111). At low coverages, CNCH3 is preferentially adsorbed at on-top sites, in agreement with earlier deductions based on vibrational spectroscopy. When dosed at low coverages at 50 K, the molecules tend to adsorb near other CNCH3 molecules with preferred distances of a and a, where a = 2.78 A is the lattice constant of Pt. Annealing the surface to 120 K, however, results in a more uniform separation of the molecules. At higher coverages, the CNCH3 molecules are observed to occupy both on-top and two-fold bridge sites. On the basis of STM image analysis, CNCH3 forms an ordered layer of (2 x 3) periodicity at 0.33 ML. Additional details on the structures of CNCH3 adsorbed at the on-top and two-fold bridge sites are provided by density functional theory (DFT) calculations. At a coverage that saturates the first layer (0.33 ML), the occupation ratio for the on-top and two-fold bridge bonded CNCH3 is 1:1, which is consistent with the results obtained from the combined use of experimental reflection absorption infrared spectroscopy (RAIRS) data and DFT calculations.     

Two-dimensional Molecular Phase Transition of Alkylated-TDPB on Au(111) and Cu(111) Surfaces

The derivatives of aromatic cores bearing alkyl chains with different lengths are of potential interest in on-surface chemistry, and thus have been widely investigated both at liquid-solid interfaces and in vacuum. Here, we report on the structural evaluation of self-assembled 1,3,5-tri(4-dodecylphenyl)benzene(TDPB) molecules with increased molecular coverages on both Au(111) and Cu(111) surfaces. As observed on Au(111), rhombic and herringbone structures emerge successively depending on surface coverage. In the case of Cu(111), the same process of phase conversion is also observed, but with two distinct structures. In comparison, the self-assembled structures on Au(111) surface are packed more densely than that on Cu(111) surface under the same preparation conditions. This may fundamentally result from the higher adsorption energy of TDPB molecules on Cu(111), restricting their adjustment to optimize a thermodynamically favorable molecular packing.     

Conductance of a single molecule C60-SnPc heterojunction

Geometries of molecule-molecule interfaces strongly influence the current passing from one molecule to another. The contact conductance of molecule-molecule junctions which consist of fullerene and tin phthalocyanine molecules is investigated with a low-temperature scanning tunneling microscope. Two types of molecules are deposited onto Cu(111). Fullerene molecules are transferred to tips through controlled contact of STM tips on molecules. The molecule-molecule junctions are formed by approachi...     

Comparing Ullmann Coupling on Noble Metal Surfaces: On‐Surface Polymerization of 1,3,6,8‐Tetrabromopyrene on Cu(111) and Au(111)

The on‐surface polymerization of 1,3,6,8‐tetrabromopyrene (Br₄Py) on Cu(111) and Au(111) surfaces under ultrahigh vacuum conditions was investigated by a combination of scanning tunneling microscopy (STM), X‐ray photoelectron spectroscopy (XPS) and density functional theory (DFT) calculations. Deposition of Br₄Py on Cu(111) held at 300 K resulted in a spontaneous debromination reaction, generating the formation of a branched coordination polymer network stabilized by C?Cu?C bonds. After annealing at 473 K, the C?Cu?C bonds were converted to covalent C?C bonds, leading to the formation of a covalently linked molecular network of short oligomers. In contrast, highly ordered self‐assembled two‐dimensional (2D) patterns stabilized by both Br?Br halogen and Br?H hydrogen bonds were observed upon deposition of Br₄Py on Au(111) held at 300 K. Subsequent annealing of the sample at 473 K led to a dissociation of the C?Br bonds and the formation of disordered metal‐coordinated molecular networks. Further annealing at 573 K resulted in the formation of covalently linked disordered networks. Importantly, we found that the chosen substrate not only plays an important role as catalyst for the Ullmann reaction, but also influences the formation of different types of intermolecular bonds and thus, determines the final polymer network morphology. DFT calculations further support our experimental findings obtained by STM and XPS and add complementary information on the reaction pathway of Br₄Py on the different substrates.