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.     

Study on the interaction between tetracene and Cu(110) surface

The electronic structure of tetracene on Cu (110) surface has been studied by using ultraviolet photoemission spectroscopy (UPS). The emission features from the organic molecule are located from 1 to 10 eV below the Fermi level, and they shift in binding energy with increasing the coverage of the organic material. For the surface with multilayer of tetracene, six well-resolved features were found at 1.90, 3.40, 4.70, 5.95, 6.95, and 9.15 eV below the Fermi level, respectively. On the surface with a lower coverage of tetracene, angle-resolved UPS measurements suggest that the molecular plane is parallel to the substrate. Density functional theory calculation confirms the flat-lying adsorption mode and shows that the tetracene molecule prefers to be adsorbed on the long bridge site with its long axis in the [110] azimuth.     

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.     

Valence electronic properties of n-channel organic materials based on fluorinated derivatives of perylene diimides

The valence electronic states of three kinds of fluorinated derivatives of perylene diimides, D2MFPP, D3MFPP, and D4MFPP, on Cu(110) and SiO(2)Si surface were studied by photoemission and density functional calculations. When these organic molecules were deposited on the Cu(110) and thermally oxidized SiO(2) surfaces, five well-resolved photoemission features originating from the molecules were observed. On Cu(110) surface, two emission features with pi-like character increased their binding energy with increasing the coverage of organic molecule, indicating a strong interaction between the organic molecules and Cu substrate. The density functional calculations suggest flat-lying adsorption geometry for D3MFPP and D4MFPP on Cu(110) surface.     

DOPA醌在Cu(100)表面吸附的密度泛函理论研究

采用广义梯度密度泛函理论(GGA)的BLYP方法结合周期性平板模型,以原子簇Cu41为模拟表面,对DOPA醌分子在Cu(100)表面不同位置的吸附模型进行了构型优化、能量计算以及Mulliken布居分析,结果表明通过相邻的羰基垂直吸附在表面的桥位是其最佳吸附方式,吸附能为247.2310kJ/mol;其次为顶位、顶位R45和穴位,吸附能分别为227.7162kJ/mol、220.7305kJ/mol和217.8456kJ/mol。Mulliken布居分析结果表明整个吸附体系发生了由Cu原子向DOPA醌分子的电荷转移。     

氢原子在Be(0001)表面吸附的密度泛函理论研究

采用第一性原理的密度泛函理论研究单个氢原子和多个氢原子在Be(0001)表面吸附性质.给出了氢吸附Be(0001)薄膜表面的原子结构、吸附能、饱和度、功函数、偶极修正等特性参数.同时也讨论了相关吸附性质与氢原子覆盖度(0.06-1.33ML)的关系.计算结果表明:氢原子的吸附位置与覆盖度之间有强烈的依赖关系,覆盖度低于0.67ML时,氢原子能量上易于占据fcc或hcp的中空位置;覆盖度为0.78ML时,中空位与桥位为氢原子的最佳吸附位;覆盖度在0.89到1.00ML时,桥位是氢原子吸附能量最有利的位置;以上覆盖度中Be(0001)表面最外层铍原子的结构均没有发生明显变化.当覆盖度为1.11-1.33ML,高覆盖度下Be(0001)表面的最外层铍原子部分发生膨胀,近邻氢原子渗入到铍表面次层,氢原子易于占据在hcp和桥位.吸附结构中的氢原子比氢分子中的原子稳定.当覆盖度大1.33ML时,计算结果没有发现相对于氢分子更稳定的吸氢结构.同时从分析偶极修正和氢原子吸附垂直高度随覆盖度的变化关系判断氢覆盖度为1.33ML时,在Be(0001)表面吸附达到饱和.     

An integrated experimental and theoretical investigation of the vibrational modes and molecular structure of a new Cu(II)–phosphocreatine complex

A new complex of Cu(II) of stoichiometry [Cu(PCr)(H₂O)] was prepared from aqueous solution at pH 6. Its synthesis, characterization, thermogravimetric, vibrational spectroscopy, and electron paramagnetic resonance analyses were described and suggest that phosphocreatine (PCr) in solid state is acting as a tridentate ligand (the nitrogen atom of the guanidine group and the oxygen atoms of the phosphate group and the carboxylate group being the donor atoms). The fourth position is occupied by a water molecule. These results were confirmed through computational calculations (DFT/B3LYP:6-311G theoretical procedure). The tetra coordination of Cu(II) arranged in a quadratic planar geometry was found to be more stable in the DFT calculations. The calculated vibrational spectrum agrees well with the FT-IR experimental spectrum.     

First-principles investigation of the adsorption of the 2,5-pyridine di-carboxylic acid onto the Cu(011) surface

First-principles calculations within the density functional theory (DFT) framework have been performed in order to investigate various conformations of the 2,5-pyridine di-carboxylic acid (PDCA) molecule adsorbed onto the Cu(011) surface. By means of DFT calculations the adsorption geometry, the bond formation and the electronic properties of PDCA molecule conformations on the Cu(011) surface have been studied. The most important structural property is the orientation of the COOH H atom which can point either toward the aromatic ring or toward the vacuum. This H atom position determines the possible reactions in which the adsorbed molecule can get involved and also has a significant impact on the value of the Cu-molecule system work function. Thus, we find that simply by changing the H atom orientation (from up to down) the Cu-molecule system work function can be varied with more than 2.5 eV. This is a significant result as a lot of effort is put nowadays in finding efficient ways for the in situ variation of the systems work function. Scanning tunneling microscopy (STM) images, reflexion absorption infrared vibrational spectra (RAIRS) as well as various thermodynamic properties (adsorption entropies, enthalpies) have also been investigated in order to get a better insight into the system studied and to provide support to possible experimental studies (STM or RAIRS experiments).     

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.     

Interaction between benzenedithiolate and gold: classical force field for chemical bonding

We have constructed a group of classical potentials based on ab initio density-functional theory (DFT) calculations to describe the chemical bonding between benzenedithiolate (BDT) molecule and gold atoms, including bond stretching, bond angle bending, and dihedral angle torsion involved at the interface between the molecule and gold clusters. Three DFT functionals, local-density approximation (LDA), PBE0, and X3LYP, have been implemented to calculate single point energies (SPE) for a large number of molecular configurations of BDT-1, 2 Au complexes. The three DFT methods yield similar bonding curves. The variations of atomic charges from Mulliken population analysis within the molecule/metal complex versus different molecular configurations have been investigated in detail. We found that, except for bonded atoms in BDT-1, 2 Au complexes, the Mulliken partial charges of other atoms in BDT are quite stable, which significantly reduces the uncertainty in partial charge selections in classical molecular simulations. Molecular-dynamics (MD) simulations are performed to investigate the structure of BDT self-assembled monolayer (SAM) and the adsorption geometry of S adatoms on Au (111) surface. We found that the bond-stretching potential is the most dominant part in chemical bonding. Whereas the local bonding geometry of BDT molecular configuration may depend on the DFT functional used, the global packing structure of BDT SAM is quite independent of DFT functional, even though the uncertainty of some force-field parameters for chemical bonding can be as large as approximately 100%. This indicates that the intermolecular interactions play a dominant role in determining the BDT SAMs global packing structure.     

Raman spectroscopic and density functional theory studies on a benzothiazole-2-thione derivative

The two tautomers of 7H-[1,3]dioxolo[4′,5′,4,5]benzo[1,2-d]thiazole-6-thione (DBTT) have been investigated by FT-IR and FT-Raman combined with density functional theory (DFT) calculations at the B3LYP level and 6-311+G** basis sets. On the basis of optimized structures, the harmonic force fields, vibrational frequencies and Raman intensities were calculated and scaled. The assignment of the fundamental vibrations for this molecule in its thione form was performed according to the potential energy distribution (PED) analysis. We have also discussed the adsorption behavior of DBTT on gold by means of SERS and DFT calculations at the same level. It revealed that the DBTT exhibited stable conformation of benzothiazole-2-thione (BTT) form both in solid and on gold surfaces; in addition, DBTT molecule is chemisorbed to the gold through both N and the exocyclic S atoms in its thione form and its molecular plane is perpendicular to the surface as BTT. The results show that the substituted groups in the phenyl ring have changed the characters such as the charge density in heterocyclic atoms and so on, but have little influence on the tautomeric preference of the BTT molecule and adsorption orientation on gold.     

DFT study of oxygen adsorption on modified nanostructured gold pyramids

Periodic DFT calculations are used to predict and investigate the adsorption behavior of molecular oxygen on Au, Au/Pt, and Pt surfaces. To obtain an array of pyramids containing surface atoms with the lowest possible coordination number, a nano-modified surface consisting of a symmetrically "modified" (100) surface was used. The effect of atom substitution (organized alloying) is investigated. The adsorption of molecular oxygen on a pure gold pyramid is exothermic by 0.77 eV for the end-on adsorption mode. In the case of a pure platinum pyramid, the end-on adsorption mode was found to dissociate; however, a side-on geometry was encountered with an energy of adsorption of 2.3 eV. This value is in line with the fact that the adsorption energy of small molecules does not vary much on Pt surfaces with different indices. Additionally, some geometrically related trends of the surface deformation in relation to its composition and after adsorption of molecular oxygen are highlighted.     

DFT study of gas-phase adsorption of benzotriazole on Cu(111), Cu(100), Cu(110), and low coordinated defects thereon

The adsorption of benzotriazole--an outstanding corrosion inhibitor for copper--on Cu(111), Cu(100), Cu(110), and low coordinated defects thereon has been studied and characterized using density functional theory (DFT) calculations. We find that benzotriazole can either chemisorb in an upright geometry or physisorb with the molecular plane being nearly parallel to the surface. While the magnitude of chemisorption energy increases as passing from densely packed Cu(111) to more open surfaces and low coordinated defects, the physisorption energy is instead rather similar on all three low Miller index surfaces. It is pointed out that due to a large dipole moment of benzotriazole the dipole-dipole interactions are rather important. For perpendicular chemisorption modes the lateral repulsion is very long ranged, extending up to the nearest-neighbor distance of about 60 bohrs, whereas for parallel adsorption modes the lateral interactions are far less pronounced and the molecules experience a weak attraction at distances ?25 bohrs. The chemisorption energies were therefore extrapolated to zero coverage by a recently developed scheme and the resulting values are -0.60, -0.73, and -0.92 eV for Cu(111), Cu(100), and Cu(110), respectively, whereas the zero-coverage physisorption energy is about -0.7 eV irrespective of the surface plane. While the more densely packed surfaces are not reactive enough to interact with the molecular π-system, the reactivity of Cu(110) appears to be at the onset of such interaction, resulting in a very stable parallel adsorption structure with an adsorption energy of -1.3 eV that is ascribed as an apparent chemisorption+physisorption mode.     

Electron paramagnetic resonance structure investigation of copper complexation in a hemicarcerand

The double-bridged hemicarcerand [A,B-(CH2OH)2-cavitand]-(CH2NHCH2)2-[A,B-(CH2OH)2-cavitand] 23 (and several other related compounds) was synthesized by the condensation of the two complementary precursors A,B-(CH2NH2)2(CH2OH)2-cavitand and A,B-(CH2Br)2(CH2OAc)2-cavitand followed by hydrolysis of the acetate groups. This hemicarcerand has nitrogen and oxygen donor atoms located on the interior of the spherical cavity and thus allows endohedral coordination of metal ions. The cavity has a volume of approximately 0.12 nm3, a value obtained by calculating a Connolly-type contact surface and the molecular electrostatic potential. The Cu2+ complex of hemicarcerand 23 was studied in detail by EPR and DFT calculations at the UB3LYP/6-31G level to verify the anticipated endohedral nature of the metal complex. It could be shown that the copper ion is coordinated to four oxygen donor atoms and no deviation from axial symmetry at the copper site could be detected. No direct coordination to nitrogen atoms of the hemicarcerand could be observed; however, complexation with DMF solvent molecules was detected by ESEEM and HYSCORE experiments. The closed structure of the hemicarcerand was also confirmed by an evaluation of proton-copper distances. Results from DFT calculations are in accord with the EPR results, and further support suggested coordination of the Cu(II) within the hemicarcerand cavity by four oxygen donor atoms.     

Room temperature water splitting at the surface of magnetite

An array of surface science measurements has revealed novel water adsorption behavior at the Fe(3)O(4)(001) surface. Following room temperature exposure to water, a low coverage of hydrogen atoms is observed, with no associated water hydroxyl group. Mild annealing of the hydrogenated surface leads to desorption of water via abstraction of surface oxygen atoms, leading to a reduction of the surface. These results point to an irreversible splitting of the water molecule. The observed phenomena are discussed in the context of recent DFT calculations (Mulakaluri, N.; Pentcheva, R.; Scheffler, M. J. Phys. Chem. C 2010, 114, 11148), which show that the Jahn-Teller distorted surface isolates adsorbed H in a geometry that could kinetically hinder recombinative desorption. In contrast, the adsorption geometry facilitates interaction between water hydroxyl species, which are concluded to leave the surface following a reactive desorption process, possibly via the creation of O(2).     

Self-Assembled Monolayers of N-Heterocyclic Olefins on Au(111)

Self-assembled monolayers (SAMs) of N-heterocyclic olefins (NHOs) have been prepared on Au(111) and their thermal stability, adsorption geometry, and molecular order were characterized by X-ray photoelectron spectroscopy, polarized X-ray absorption spectroscopy, scanning tunneling microscopy (STM), and density functional theory (DFT) calculations. The strong σ-bond character of NHO anchoring to Au induced high geometrical flexibility that enabled a flat-lying adsorption geometry via coordination to a gold adatom. The flat-lying adsorption geometry was utilized to further increase the surface interaction of the NHO monolayer by backbone functionalization with methyl groups that induced high thermal stability and a large impact on work-function values, which outperformed that of N-heterocyclic carbenes. STM measurements, supported by DFT modeling, identified that the NHOs were self-assembled in dimers, trimers, and tetramers constructed of two, three, and four complexes of NHO−Au-adatom. This self-assembly pattern was correlated to strong NHO−Au interactions and steric hindrance between adsorbates, demonstrating the crucial influence of the carbon-metal σ-bond on monolayer properties.     

Ab initio study of surface acid-base reactions. The case of molecular and dissociative adsorption of ammonia on the (011) surface of rutile TiO2

The interaction of ammonia molecules with Lewis acid centers (Ti4+ metal ions) of the (011) surface of rutile TiO2 is investigated by density functional theory in order to understand, from first principle, the nature of acid-base reactions on solid surfaces. Unlike the rutile (110) surface that contains alternating rows of 5-fold and 6-fold Ti atoms, all Ti atoms of the (011) surface are 5-fold coordinated. This surface has shown considerable activity for numerous chemical reactions and is thus an ideal prototype. At 1/2 monolayer coverage, with respect to surface Ti atoms, the adsorption energy is found to be equal to 100 kJ mol-1, and drops to 58 kJ mol-1 at one monolayer coverage. Analysis of the electronic density of states (DOS) revealed information regarding the mode of adsorption. In particular, the nitrogen 3a1 and 2a1 orbitals appear to undergo significant changes upon adsorption, in agreement with photoelectron spectroscopy studies. Dissociative adsorption was also investigated on the same surface. Both NH2(Tis) + H(Os) and NH(Tis) + 2H(Os) modes of dissociative adsorption, where s stands for surface, are found to be less stable than the molecular (non dissociated) adsorption.     

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.     

The ordered thin-film growth of organic semiconductor on Ag(110)

Growth of ordered perylene thin films on the Ag(110) surface has been investigated with scanning tunneling microscope. By saturating the surface with a monolayer of perylene molecules, two kinds of ordered structures are simultaneously formed with flat-lying perylene molecules on the Ag(110) surface, in which one is commensurate relative to the Ag substrate with a periodicity of while the other is commensurate with a periodicity of (-2724). There is one molecule within the former unit cell with a surface coverage of 0.1 molecule per Ag atom, while there are two molecules within the latter unit cell, which gives a slightly lower surface coverage of 0.091 molecule per Ag atom. Ab initio calculations have been carried out to identify the adsorption geometry and bonding sites.     

Theoretical study on alkaloid encapsulating via cyclopentano-cucurbit[n]uril (n = 8, 10)/graphene oxide heterojunction

Here, physical chemistry properties of the inclusion complexes of some alkaloids and cyclopentano-cucurbit[8, 10]urils (Cy-CB[8, 10]) were investigated via molecular dynamic (MD) simulations and density functional theory (DFT) calculations. The possibility of the heterojunction formation between cyclopentano-cucurbit[8, 10]urils and graphene oxide was investigated via MD simulation. Based on the results, an effective role of graphene oxide on the encapsulation complex formation, especially in the presence of codeine and morphine was confirmed. DFT (M06-2X) and DFT-D3 (M06-2X-D3) functionals were applied for geometry optimization of the complexes. To have an insight into the atomic level, different analyses, such as natural bond orbital and quantum theory of atoms in molecule analyses were applied and discussed. DFT results confirm that Cy-CB[8] makes a stronger interaction with alkaloids in comparison with Cy-CB[10]. Thermodynamic studies show that the complexation process of codeine inside Cy-CB[n] is more favorable than other complexes. Moreover, energy analysis showed that the van der Walls part plays an important role in alkaloid stabilization inside the Cy-CB[n] cavity.