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.     

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.     

Controlling Metalation Reaction of Phthalocyanine with Cobalt at Single-Molecule Level on Au(111) Surface

Metalation reaction of metal-free phthalocyanine molecule with Co atom adsorbed on Au(111) surface has been studied in situ at single atom/molecule scale by low-temperature scanning tunneling microscopy (STM) experiment combined with simulations based on density function theory calculations. Through manipulations using STM tip, we showed a controlled manner to have a single metal-free phthalocyanine molecule react with a Co atom to form Co phthalocyanine molecule. In this reaction process, an intermediate state originating from $\pi$-d interaction between the metal-free phthalocyanine molecule and Co atom has been identified. Moreover, we also revealed that the redox reaction represented as bond breaking and bond forming relative to the Co and pyrrolic N atoms, not pyrrolic H atoms, is a key process for dehydrogenation and metalation reaction. Our DFT calculations provided theoretical supporting for the above conclusions, and further understanding of the related mechanisms.     

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.     

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.     

氢原子吸附的Cu(100)表面原子结构和电子态

用密度泛函理论的总能计算研究了金属铜(100)面的表面原子结构以及在不同覆盖度时氢原子的吸附状态. 研究结果表明, 在Cu(100)c(2×2)/H表面体系中, 氢原子吸附的位置是在空洞位置, 距最外层Cu原子层的距离为0.052 nm, 相应的Cu—H键长为0.189 nm, 并通过计算结构参数优化否定了其它的吸附位置模型. 总能计算得出Cu(100)c(2×2)/H表面的功函数为4.47 eV, 氢原子在这一体系的吸附能为2.37 eV(以孤立氢原子为能量参考点). 通过与衬底原子的杂化, 氢原子形成了具有二维特征的氢能带结构, 在费米能级以下约0.8 eV处出现的表面局域态是Cu(S)-H-Cu(S-1)型杂化的结果. 采用Cu(100)表面p(1×1)、p(2×2)和p(3×3)的三种氢吸附结构分别模拟1, 1/4, 1/9的原子单层覆盖度, 计算结果表明, 随着覆盖度的增加, 被吸附的氢原子之间的距离变短, 使得它们之间的静电排斥和静电能增大, 从而导致表面吸附能和吸附H原子与最外层Cu原子间垂直距离(ZH-Cu)逐渐减小. 在较低的覆盖度下, 氢原子对Cu(100)表面的影响主要表现为单个原子吸附作用的形式. 通过总能计算还排除了Cu(100)表面(根号2×2根号2)R45°-2H缺列再构吸附模型的可能性.     

Surface bonding and dynamical behavior of the CH3SH molecule on Au(111)

The chemisorption of the undissociated CH3SH molecule on the Au(111) surface has been studied at 5 K using scanning tunneling microscopy (STM) and density functional theory (DFT) calculations. The molecule was found to adsorb on atop Au sites on the defect-free surface. CH3SH undergoes hindered rotation about the Au-S bond on the defect-free surface which is seen in STM as a time-averaged 6-fold pattern. The pattern suggests that the potential minima directions occur for the rotating molecule at the six hollow sites surrounding the atop adsorption site. The barrier for rotation, obtained by DFT calculations, is approximately 0.1 kcal.mol(-1). At low coverages, preferential adsorption occurs at defect sites in the surface, namely, the herringbone "elbows" and random atomic step sites. Molecules adsorbed on these sites do not exhibit rotational freedom.     

Monolayer structure of tetracene on Cu (100) surface: parallel geometry

The geometrical arrangement of tetracene on Cu (100) surface at monolayer coverage is studied by using scanning tunneling microscopy measurement and density functional theory (DFT) calculations. Tetracene molecule is found to be oriented with its molecular plane parallel to the substrate surface, and no perpendicular geometry is observed at this coverage. The molecule is aligned either in the [011] or [011] direction due to the fourfold symmetry of the Cu (100) surface. DFT calculations show that the molecule with the "flat-lying" mode has larger adsorption energy than that with the "upright standing" mode, indicating that the former is the more stable structure. With the flat-lying geometry, the carbon atoms prefer to be placed between surface Cu atoms. The molecular center prefers to be located at the bridge site between two nearest surface Cu atoms.     

Methanol adsorption on the beta-Ga2O3 surface with oxygen vacancies: theoretical and experimental approach

Methanol adsorption on beta-Ga2O3 surface has been studied by Fourier transform infrared spectroscopy (FTIR) and by means of density functional theory (DFT) cluster model calculations. Adsorption sites of tetrahedral and octahedral gallium ions with different numbers of oxygen vacancies have been compared. The electronic properties of the adsorbed molecules have been monitored by computing adsorption energies, optimized geometry parameters, overlap populations, atomic charges, and vibrational frequencies. The gallia-methanol interaction has different behaviors according to the local surface chemical composition. The calculations show that methanol can react in three different ways with the gallia surface giving rise to a nondissociative adsorption, a dissociative adsorption, and an oxidative decomposition. The surface without oxygen vacancies is very reactive and produces the methanol molecule decomposition. The molecule is nondissociatively adsorbed by means of a hydrogen bond between the alcoholic hydrogen atom and a surface oxygen atom and a bond between the alcoholic oxygen atom and a surface gallium atom. Two neighbor oxygen vacancies on tetrahedral gallium sites produce the dissociation of the methanol molecule and the formation of a bridge bond between two surface gallium atoms and the methoxy group.     

Cysteine adsorption on the Au(111) surface and the electron transfer in configuration of a scanning tunneling microscope: A quantum-chemical approach

Adsorption of two forms, molecule and radical, of amino acid L-cysteine (Cys) on the Au₁₂ cluster that simulates the (111) face of single-crystal gold is studied in the framework of the density functional theory. Effects of solvation of adsorbed Cys particles and lateral interaction in a monolayer are analyzed. The simulation predicts a commensurate adsorption energetics of the molecule and radical, with a difference between the “on-top,” “hollow,” and “bridge” positions. An analysis of lateral electrostatic interactions points to the stability of a cluster comprising six Cys particles, which conforms to the size of a fragment observed experimentally. Adsorption calculations are used to build three-dimensional isosurfaces (STM images), where the tungsten needle of the scanning tunneling microscope is simulated by a tungsten atom or by small clusters. The calculated images are sensitive to both the Cys shape and the orientation of adsorbed Cys particles. Calculation results are compared with fresh in situ submolecular-resolution STM data. Simulated images (with commensurate contributions made by sulfur atom and amino group) built for Cys radical adsorbed in the “on-top” position give best conformance to experiment.     

Study of H2O and HOCH2CH2OH Adsorption on the Relaxation Surface of β-Si3N4(0001) by Density Functional Theory

Density functional theory (DFT) B3LYP method is used to theoretically investigate the adsorption conformations of H2O and glycol on the relaxation surface of β-Si3N4(0001) with cluster models. For H2O, the most stable structure is that adsorbed through the H atom lying above a N(3) site of the relaxation surface of β-Si3N4(0001); while for glycol, it is the one adsorbed via the H atom lying above the center of Si(2) and N(3) of the same relaxation surface. The adsorption energy, adsorption bond and transfer electrons of the two adsorbed substances prove that glycol is easy to be adsorbed on the relaxation surface of β-Si3N4(0001).     

Study of H2O and HOCH2CH2OH Adsorption on the Relaxation Surface of β-Si3N4（0001） by Density Functional Theory

Density functional theory （DFT） B3LYP method is used to theoretically investigate the adsorption conformations of H2O and glycol on the relaxation surface of β-Si3N4（0001） with cluster models. For H2O, the most stable structure is that adsorbed through the H atom lying above a N（3） site of the relaxation surface of β-Si3N4（0001）; while for glycol, it is the one adsorbed via the H atom lying above the center of Si（2） and N（3） of the same relaxation surface. The adsorption energy, adsorption bond and transfer electrons of the two adsorbed substances prove that glycol is easy to be adsorbed on the relaxation surface of β-Si3N4（0001）.     

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.     

Raman spectral study of metal-cytosine complexes: a density functional theoretical (DFT) approach

The fluctuation of surface-enhanced Raman scattering (SERS) spectra has been an obstacle to the analysis of the adsorbate on the metal surface. In this paper, we aim at using the density functional theory (DFT) to study the fluctuant Raman spectra of the cytosine molecule which interacts with a coinage metal atom or cation via N1 and N3 sites. The results show that the adsorption site strongly influences the Raman spectral property of cytosine molecule, especially the relative intensity of some bands. In addition, the SERS spectra of cytosine which is adsorbed on the gold, silver, and copper electrodes are measured, and the possible orientation and adsorption site of the cytosine molecule adsorbed on metal electrodes surface are proposed with the help of DFT simulations.     

Li修饰B12N12储氢行为的密度泛函理论研究

采用基于密度泛函理论(DFT)的第一性原理投影缀加波方法, 研究了Li 修饰的B₁₂N₁₂笼子的储氢行为.计算结果表明: Li 原子吸附在B₁₂N₁₂笼子的四元环和六元环相交的B－N桥位上, 相对于其它六个高对称吸附位置更稳定, B₁₂N₁₂笼子周围最多可以吸附3 个Li 原子, 最稳定的构型是三个Li 原子同时吸附在N原子顶位(Top-N site). 每个Li 原子的周围能吸附三个氢分子, 笼子外侧还可以吸附两个氢分子, 内部最多可以吸附5 个氢分子. 考虑到笼内和笼外的吸附, B₁₂N₁₂笼子总的储氢量(氢分子)达到9.1% (w).     

Reaction of 1,2-dibromobenzene with the Si(111)-7x7 surface, a DFT study

Reaction between 1,2-dibromobenzene and the Si(111)-7x7 surface has been studied theoretically on the DFT(B3LYP/6-31G(d)) level. A 12-atom silicon cluster, representing two adatoms and one rest atom of the faulted half of the unit cell, was used to model the silicon surface. The first step of the reaction was a covalent attachment (chemisorption) of an intact 1,2-dibromobenzene molecule to the silicon cluster. Binding energies were calculated to be between 1.04 and 1.14 eV, depending on the orientation of the molecule. A second step of the reaction was the transfer of the Br atom to the silicon cluster. Activation energies for the transfer of the Br atom were calculated to be between 0.4 and 0.6 eV, suggesting that the thermal bromination reaction occurs on a microsecond time scale at room temperature. A third step of the reaction could be the transfer of the second Br atom of the molecule, the desorption of the organic radical, or the change of the adsorption configuration of the radical, depending on the original orientation of the adsorbed intact molecule. A novel, aromatic, two-sigma-bound adsorbed configuration of the C6H4 radical, in which a carbon ring of the radical is perpendicular to the silicon surface, has been introduced to explain previous experimental observations (Surf. Sci. 2004, 561, 11).     

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.     

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.     

O2 induced Cu surface segregation in Au-Cu alloys studied by angle resolved XPS and DFT modelling

Surface segregation effects on polycrystalline Au-Cu alloys (Au(0.80)Cu(0.20), Au(0.85)Cu(0.15) and Au(0.90)Cu(0.10)) were studied at room temperature by angle resolved XPS (ARXPS) and density functional theory (DFT) before and after exposure to O(2). Au surface enrichment was found as predicted from calculations showing that this process is energetically favourable, with a segregation energy for Au in a Cu matrix of -0.37 eV atom(-1). Surface enrichment with Cu was observed after exposure to O(2) due to its dissociative adsorption, in agreement with DFT calculations that predicted an energy gain of -1.80 eV atom(-1) for the transfer of Cu atoms to a surface containing adsorbed oxygen atoms, thus leading to an inversion in surface population.     

First-principles study of the adsorption of formaldehyde on the clean and atomic oxygen covered Cu(1 1 1) surface

The interaction of formaldehyde with the clean and atomic oxygen-covered Cu(1 1 1) surfaces has been studied by means of cluster model density functional calculations in which Cu₂₂(14,8) is used to represent the perfect Cu(1 1 1) surface. The calculations point towards a η¹-H₂CO---O orientation with the oxygen atom almost on top of a copper surface atom. The formaldehyde adsorption energy is of 22–25 kJ/mol and the internal geometry of adsorbed formaldehyde is almost identical to that of the molecule in the gas-phase. The C---O bond is almost parallel to the surface and the conformation with the molecular plane normal to the surface is slightly preferred to the conformation with the molecular plane nearly parallel to the surface. A Cu₂₂---O model where atomic oxygen is adsorbed on a fcc hollow site was used to study the co-adsorption and reaction of formaldehyde with atomic oxygen. Oxygen co-adsorption has a dramatic effect on the formaldehyde adsorption energy which is increased by 50%. The calculated energy barrier for the formation of the dioxymethylene intermediate species through the H₂CO+O→H₂CO₂ reaction is of 36 kJ/mol.