Lock and key behaviours of an aromatic carboxylic acid molecule with differing conformations on an Au (111) surface

Tricarboxylic acid derivative with three-fold symmetry in physisorbed monolayers is an important organic molecule for applications in nanotechnology. In this paper, the behaviour of a single tricarboxylic acid derivative, 1,3,5-tris(carboxymethoxy)benzene (TCMB, C₆H₃(OCH₂COOH)₃) on an Au (111) substrate at 50 K is investigated by molecular dynamics simulation. Four possible conformations of the TCMB molecule adsorbed on the Au (111) substrate are found, the difference of which is the orientation of the CH2 chain. They also display different trajectories of movement and dynamical behaviours. As the molecule migrates across the Au (111) surface, the translational motion of TCMB is always accompanied by rotational motion. The lock-and-key (LAK) geometry between the TCMB molecule of different conformations and atomic arrangement of the Au (111) surface was also observed in this study, and the result has been verified by an ab initio calculation.     

Understanding formation of molecular rotor array on Au(111) surface

The motion of single molecules on surfaces plays an important role in nanoscale engineering and bottom-up construction of complex devices at single molecular scale. In this article, we review the recent progress on single molecular rotors self-assembled on Au(111) surfaces. We focus on the motion of single phthalocyanine molecules on the reconstructed Au(111) surface based on the most recent results obtained by scanning tunneling microscopy (STM). An ordered array of single molecular rotors with large scale is self-assembled on Au(111) surface. Combined with first principle calculations, the mechanism of the surface-supported molecular rotor is investigated. Based on these results, phthalocyanine molecules on Au (111) are a promising candidate system for the development of adaptive molecular device structures.     

Self-assembly and growth of manganese phthalocyanine on an Au（111） surface

Self-assembly and growth of manganese phthalocyanine (MnPc) molecules on an Au(111) surface is investigated by means of low-temperature scanning tunneling microscopy. At the initial stage, MnPc molecules preferentially occupy the step edges and elbow sites on the Au(111) surface, then they are separately adsorbed on the face-centered cubic and hexagonal closely packed regions due to a long-range repulsive molecule—molecule interaction. After the formation of a closely packed monolayer, molecular islands with second and third layers are observed.     

Ordered structures of two sulfur containing donor molecules on the Au(111) surface

We report experiments by low energy electron diffraction (LEED) and scanning tunneling microscopy (STM) on ordered structures of two sulfur-containing π-conjugated molecules on the Au(111)-surface, namely tetrabenzothianthrene (TBTA) and tetrathiotetracene (TTT). These molecules are candidates for donors in charge transfer salts. On Au(111) both molecules form long-range ordered structures that are commensurate to the top-most surface layer. For TBTA, the reconstruction of the Au(111) surface is maintained, whereas it is lifted by TTT. Both molecules lie flat on the surface. For TBTA, the structure indicates that the molecule is planarized upon adsorption.     

Adsorption and rotational barrier for a single azobenzene molecule on Au(111) surface

The orientation switching of a single azobenzene molecule on Au(111) surface excited by tunneling electrons and/or photons has been demonstrated in recent experiments. Here we investigate the rotation behavior of this molecular rotor by first-principles density functional theory(DFT) calculation. The anchor phenyl ring prefers adsorption on top of the fcc hollow site, simulated by a benzene molecule on close packed atomic surface. The adsorption energy for an azobenzene molecule on Au(111) surface is calculated to be about 1.76 e V. The rotational energy profile has been mapped with one of the phenyl rings pivots around the fcc hollow site, illustrating a potential barrier about 50 me V. The results are consistent with experimental observations and valuable for exploring a broad spectrum of molecules on this noble metal surface.     

Mapping the first electronic resonances of a Cu phthalocyanine STM tunnel junction

Using a low temperature, ultrahigh vacuum scanning tunneling microscope (STM), dI/dV differential conductance maps were recorded at the tunneling resonance energies for a single Cu phthalocyanine molecule adsorbed on an Au(111) surface. We demonstrated that, contrary to the common assumption, such maps are not representative of the molecular orbital spatial expansion, but rather result from their complex superposition captured by the STM tip apex with a superposition weight which generally does not correspond to the native weight used in the standard Slater determinant basis set. Changes in the molecule conformation on the Au(111) surface further obscure the identification between dI/dV conductance maps and the native molecular orbital electronic probability distribution in space.     

Interfacial structure of Co porphyrins on Au(111) electrode: Interaction of porphyrin molecules with substrate

Interfacial structures of cobalt(II) porphine (CoP) and [2,3,7,8,12,13,17,18‐octaethyl‐21H,23-H-porphine]cobalt(II) (CoOEP) have been studied on Au(111) electrode using electrochemical scanning tunneling microscopy (EC-STM), in-situ X-ray diffraction, and density functional theory (DFT) calculations. The adsorption of porphyrins affects the reconstruction of Au(111) surface. The adsorption of CoP causes a lifting of the reconstruction to a complete 1 × 1 structure of Au(111). On CoOEP modified Au(111), the unit cell periodicity of the reconstructed substrate structure expands compared with the √3 × 23 structure of bare Au(111). The same expanded substrate structure was observed on Au(111) modified with OEP without the coordinated Co ion; the coordinated metal ion of the adsorbed porphyrin molecule does not affect the substrate structure. This result indicates that the interaction of conjugated π electrons of porphyrin with the substrate is stronger than that of the coordinated Co ion. In-situ X-ray diffraction and DFT calculation support non-covalent interaction of porphyrins with the Au(111) surface.     

通过单分子化学调控单个离子磁性--单分子"手术"开启分子磁性"开关"

报道了如何通过改变单个磁性离子的化学环境来调控其白旋性质．利用扫描隧道显微镜，对吸附于Au（111）表面的单个钴酞菁分子进行化学修饰，通过在针尖上施加一定的电压脉冲，将分子配合体外层的8个氢原子“剪裁”掉，使其与金衬底形成稳定的化学键合．在这个新的人造分子结构中，其中心钴离子的电子态在费米面上出现强烈的共振峰；通过理论的模拟和分析，发现出现这一共振峰的原因是，脱氢和与衬底的化学结合使中心钴离子自旋性质发生改变，从而导致了输运特性中近藤效应（Kondo effect）的出现．     

Au(111)表面单个钴酞菁分子的去氢过程

利用低温超高真空扫描隧道显微镜对单个钴酞菁分子实现了选键化学反应.通过对吸附于Au(111)表面的单个钴酞菁分子外围H原子的"剪裁",并用实验图像和谱学方法,结合第一性原理理论计算研究了逐步去除钴酞菁分子8个外围H原子的过程.理论计算结果再现了实验中所观测到的分子空间构型的变化,并阐明了吸附体系中局域自旋的恢复和变化过程.     

Gold-adatom-mediated bonding in self-assembled short-chain alkanethiolate species on the Au(111) surface

Microscopic evidence for Au-adatom-induced self-assembly of alkanethiolate species on the Au(111) surface is presented. Based on STM measurements and density-functional theory calculations, a new model for the low-coverage self-assembled monolayer of alkanethiolate on the Au(111) surface is developed, which involves the adsorbate complexes incorporating Au adatoms. It is also concluded that the Au(111) herringbone reconstruction is lifted by the alkanethiolate self-assembly because the reconstructed surface layer provides reactive Au adatoms that drive self-assembly.     

Adsorption configurations of carbon monoxide on gold monolayer supported by graphene or monolayer hexagonal boron nitride: a first-principles study

Using density functional theory with a semiempirical van der Waals approach proposed by Grimme, the adsorption behavior of carbon monoxide on a gold monolayer supported by graphene or monolayer hexagonal boron nitride has been investigated. Based on the changes in the Dirac cone of graphene and a Bader charge analysis, we observe that the Au(111) monolayer gains a small charge from graphene and monolayer h-BN. The adsorbed CO molecule adopts similar adsorption configurations on Au(111)/graphene and Au(111)/h-BN with Au-C distance 2.17?2.50 Å and Au-C-O angle of 123.9°–139.6°. Moreover, we found that for low CO coverages, bonding to the gold surface is surprisingly energy-favorable. Yet the CO adsorption binding energy diminishes at high coverage due to the repulsive van der Waals interactions between CO molecules.     

Static investigation of the small clusters on the Cu(111) and Au(111) surfaces

The diffusion properties of small clusters Ag_n, Cu_n, and Au_n on the Cu(111) and Au(111) surfaces were studied using the molecular statics (MS) in order to understand the atomistic processes underlying the motion. In this work, the atomic interaction potential is modeled by a semi-empirical Embedded Atom Method (EAM), while the drag method is used to determine the static activation energy for each diffusion path. The presented results indicate that the dimer can diffuse on the (111) surface via the zig-zag and concerted motion mechanisms. The trimer diffuses according to the concerted motion mechanism. For the tetramer diffusion, the mechanism that consumes the least amount of energy is the zig-zag motion, in which only two atoms are needed for the diffusion process at one time. This allows finding a static activation energy smaller compared to the trimer diffusion.     

Coadsorption of gold with chlorine on CeO2 (111) surfaces: A first principles study

To investigate the effects of chlorine on the Au/ceria catalysts,the adsorption of gold or chlorine and their coadsorpiton on the stoichiometric and partially reduced CeO₂（111） surfaces are studied from the first principles.It is found that the adsorption of Au is significantly enhanced by the chlorine preadsorption on the stoichiometric CeO₂（111） surface;while on the partially reduced CeO₂（111） surface,the preadsorbed chlorine inhabits the oxygen vacancy（which is the preferred adsorption site for gold）,leading to a CeOCl phase and the dramatical weakening of the Au adsorption.Therefore,chlorine on the CeO₂（111） surface can affect the Au adsorption thus the activity of the Au/CeO₂ catalyst.     

Influence of film structure on the surface vibrations of Co/Au(111)

The vibrational properties of thin Co layers on a Au(111) surface have been probed by means of inelastic He-atom scattering at primary beam energies between 25 and 67 meV. The observed dependence of the Au(111) Rayleigh mode intensity on Co coverage and annealing temperature as well as the only weak evidence for phonons of the Co film can be explained in terms of the particular growth mode of Co on the Au(111) surface.     

Do methanethiol adsorbates on the Au(111) surface dissociate?

The interaction of methanethiol molecules CH3SH with the Au(111) surface is investigated, and it is found for the first time that the S-H bond remains intact when the methanethiol molecules are adsorbed on the regular Au(111) surface. However, it breaks if defects are present in the Au(111) surface. At low coverage, the fcc region is favored for S atom adsorption, but at saturated coverage the adsorption energies at various sites are almost isoenergetic. The presented calculations show that a methanethiol layer on the regular Au(111) surface does not dimerize.     

STM manipulation of a subphthalocyanine double-wheel molecule on Au(111)

A new class of double-wheel molecules is manipulated on a Au(111) surface by the tip of a scanning tunneling microscope (STM) at low temperature. The double-wheel molecule consists of two subphthalocyanine wheels connected by a central rotation carbon axis. Each of the subphthalocyanine wheels has a nitrogen tag to monitor its intramolecular rolling during an STM manipulation sequence. The position of the tag can be followed by STM, allowing us to distinguish between the different lateral movements of the molecule on the surface when manipulated by the STM tip.     

Kondo effect of an adsorbed cobalt phthalocyanine (CoPc) molecule: the role of quantum interference

It has been shown that by distorting a CoPc molecule adsorbed on a Au(111) surface a Kondo effect is induced with a temperature higher than 200 K. We examine a model in which an atom with strong Coulomb repulsion (Co) is surrounded by four atoms on a square (molecule lobes), with two atoms above and below it representing the apex of the STM tip and an atom on the gold surface (all with a single atomic orbital). The Hamiltonian is solved exactly for the isolated cluster, and, after connecting the leads, the conductance is calculated by standard techniques. Quantum interference prevents the existence of the Kondo effect when the orbitals on the square do not interact (undistorted molecule); the Kondo resonance shows up after switching on that interaction. The weight of the Kondo resonance is controlled by the interplay of couplings to the STM tip and the gold surface and between the molecule lobes.     

Influence of solvent on the chiral resolution of organic molecules on Au(111): EC-STM study of biphenyl dicarboxylic acid on Au(111) in an aqueous environment

Adsorption-induced chiral resolution of organic molecules is important due to its potential applications in stereo-selective catalysis. We studied the adsorption-induced chiral resolution using a model achiral molecule of 4,4′ biphenyl dicarboxylic acid (BPDA) on Au(111) in 0.1 M perchloric acid (HClO₄) by electrochemical scanning tunneling microscopy (EC-STM). Our experimental data showed that the BPDA molecules formed island structures with distinctive preferred orientations at the length scale of the molecular size. The molecules did not show any orientational ordering above the length scale, indicating that chiral resolution was absent in the aqueous environment. Previously, the molecules were found to have chiral resolution on Au(111) in ultra-high vacuum conditions (UHV). We calculated angle-dependent binding energy between the substrate and a BPDA molecule, the intermolecular interactions between the BPDA molecules, and their interactions with water molecules. The calculations suggest that the absence of chiral resolution in the aqueous environment originated from the decrease in the intermolecular energy of the BPDA molecules due to their hydrogen bonds with the surrounding water molecules. The strength of the hydrogen bonding between BPDA molecules was sufficient to overcome the energy barrier for chiral resolution through rotational motion in UHV, but not in an aqueous environment.     

Surface interactions of Au(I) cyclo-trimer with Au(111) and Al(111) surfaces: A computational study

A plane-wave density functional theory (DFT) study on surface interactions of a cyclo-[Au(μ-Pz)]₃ monolayer (denoted as T), Pz = pyrazolate, with Au(111) and Al(111) surfaces (denoted as M′) has been performed. Structural and electronic properties at the M′–T interfaces are determined from individually optimized structures of M′, T and M′–T. Results show that the gold pyrazolate trimer (T) binds more strongly on the Au(111) surface than on Al(111). Charge redistribution has been observed at both M′–T interfaces, where charge is “pushed” back towards the Au(111) surface from the trimer monolayer in Au(111)–T system, while the opposite happens in the Al(111)–T system where the charge is being pushed toward the trimer monolayer from the Al(111) surface. Considerable changes to the work function of Au(111) and Al(111) surfaces upon the trimer adsorption which arise from monolayer vacuum level shifts and dipole formation at the interfaces are calculated. The interaction between cyclo-[Au(μ-Pz)]₃ with metal surfaces causes band broadening of the gold pyrazolate trimer in M′–T systems. The present study aids better understanding of the role of intermolecular interactions, bond dipoles, energy-level alignment and electronic coupling at the interface of metal electrodes and organometallic semiconductor to help design metal–organic field effect transistors (MOFETs) and other organometallic electronic devices.     

High-temperature morphology of stepped gold surfaces

Molecular dynamics simulations with a classical many-body potential are used to study the high-temperature stability of stepped non-melting metal surfaces. We have studied in particular the Au(111) vicinal surfaces in the (M + 1,M− 1,M) family and the Au(100) vicinals in the (M,1,1) family. Some vicinal orientations close to the non-melting Au(111) surface become unstable close to the bulk melting temperature and facet into a mixture of crystalline (111) regions and localized surface-melted regions. On the contrary, we do not find high-temperature faceting for vicinals close to Au(100), also a non-melting surface. These (100) vicinal surfaces gradually disorder with disappearance of individual steps well below the bulk melting temperature. We have also studied the high-temperature stability of ledges formed by pairs of monatomic steps of opposite sign on the Au(111) surface. It is found that these ledges attract each other, so that several of them merge into one larger ledge, whose edge steps then act as a nucleation site for surface melting.