Potential energy surfaces for oxygen adsorption, dissociation, and diffusion at the Pt(321) surface

We report a first-principles, periodic supercell analysis of oxygen adsorption, diffusion, and dissociation at the kinked Pt(321) surface. Binding energies and binding site preferences of isolated oxygen atoms and molecules have been determined, and we show that both atomic and molecular oxygen prefer binding in bridge sites involving coordinatively unsaturated kink Pt atoms. Binding energies of atomic and molecular oxygen in different sites correlate well with the average metallic Pt coordination number of Pt atoms forming each site, although differences exist between adsorbates in symmetrically similar sites due to the inherent chirality of the surface. Atomic O in the strongest binding bridge sites experiences relatively small energy barriers for diffusion to neighboring sites compared to O on Pt(111). However, due to the structure of the surface, O diffusion is only rapid between different sites around the kink Pt atom, whereas the effective long-range tracer diffusion, as determined from a simple course-grain model, is shown to be anisotropic and slower than on the Pt(111) surface. Four dissociation pathways for O(2) at low coverage are also reported and found to be in agreement with experimental observations of facile dissociation, even at low temperature.     

Enantiospecific adsorption of cysteine at chiral kink sites on Au(110)-(1 x 2)

Enantiospecific adsorption of cysteine molecules onto chiral kink sites on the Au(110)-(1x2) surface was observed by scanning tunneling microscopy. l- and d-cysteine dimers were found to adopt distinctly different adsorption geometries at S kinks, which can be understood from the need to reach specific, optimum molecule-substrate interaction points. Extended, homochiral domains of l/d-cysteine were furthermore observed to grow preferentially from R/S kinks. The results constitute the first direct, microscopic observation of enantiospecific molecular interaction with chiral sites on a metal single-crystal surface.     

The influence of anions and kink structure on the enantioselective electro-oxidation of glucose

The electro-oxidation of glucose in sulfuric acid using well-defined chiral platinum single crystal electrodes has been demonstrated previously to be an enantioselective reaction with the degree of enantioselectivity being dependent on the surface density of kink sites. The chirality of the surface originates from the microstructure of the kink site whereby the sequence of the three fundamental adsorption sites [111], [100] and [110] constituting the kink may be viewed from the electrolyte phase either in a clockwise (R-enantiomer) or anti-clockwise (S-enantiomer) fashion. In the present study, this work is extended to examine the role of both kink structure and specifically adsorbed anions on the mechanism of chiral discrimination. Kinked surfaces based on [111] terraces (Pt[976],Pt[643] and Pt[531]),[100] terraces (Pt[721]) and [110] terraces (Pt[11,7,1] and Pt[841]) have been investigated and both the magnitude and potential dependence of the enantioselective electro-oxidation of glucose characterised. Additionally, the changes engendered by interchanging the character of the two steps whose confluence form the kink whilst maintaining the symmetry of the terrace has also been examined via a comparison of Pt[643] and Pt[431]. Low energy electron diffraction (LEED) was used to confirm that all surfaces when clean and thermally annealed were in their (1 x 1) state. Cyclic voltammetry (CV) confirmed this finding for flame-annealed electrodes after cooling in hydrogen. Three general points emerge from the electro-oxidation studies: (i) The highest degree of enantioselectivity is exhibited by kink sites adjacent to [111] and [110] terraces in sulfuric acid. (ii) The adsorption of specifically adsorbed anions like bisulfate/sulfate influences strongly the chiral discriminatory behaviour of all surfaces. (iii) No electro-oxidation takes place at [110] sites, as evidenced by complete overlap of the [110] step hydrogen underpotential deposition (UPD) charge in glucose and glucose-free solutions. Nonetheless it is deduced that [110] sites must play some part in the initial orienting of the glucose molecule prior to reaction. Ideas based on these findings are developed in order to rationalise in particular the influence of anion adsorption on the initial enantioselective interaction of the glucose molecule with the chiral surface.     

Structure and Energetics of model amphiphilic molecules at the water liquid-vapor interface. A molecular dynamics study

A molecular dynamics study of adsorption of p-n-pentylphenol at infinite dilution at the water liquid-vapor interface is reported. The calculated free energy of adsorption is -8.8 +/- 0.7 kcal/mol, in good agreement with the experimental value of -7.3 kcal/mol. The transition between the interfacial region and the bulk solution is sharp and well-defined by energetic, conformational, and orientational criteria. At the water surface, the phenol head group is mostly immersed in aqueous solvent. The most frequent orientation of the hydrocarbon tail is parallel to the interface, due to dispersion interactions with the water surface. This arrangement of the phenol ring and the alkyl chain requires that the chain exhibits a kink. As the polar head group is being moved into the solvent, the chain length increases and the tail becomes increasingly aligned toward the surface normal, such that the nonpolar part of the molecule exposed to water is minimized. The same effect was achieved when phenol was replaced by a more polar head group, phenolate. This result underscores the difference between hydrophobic hydration at the surface and in the bulk solvent, when nonpolar molecular fragments adopt compact conformations.     

Stripping voltammetry of carbon monoxide oxidation on stepped platinum single-crystal electrodes in alkaline solution

The electrochemical oxidation of a CO adlayer on Pt[n(111)x(111)] electrodes, with n = 30, 10, and 5, Pt(111), Pt(110) as well as a Pt(553) electrode (with steps of (100) orientation) in alkaline solution (0.1 M NaOH) has been studied using stripping voltammetry. On these electrodes, it is possible to distinguish CO oxidation at four different active oxidation sites on the surface, i.e. sites with (111), (110) and (100) orientation, and kink sites. The least active site for CO oxidation is the (111) terrace site. Steps sites are more active than the (111) terrace sites, the (110) site oxidizing CO at lower potential than the (100) site. The CO oxidation feature with the lowest overpotential (oxidation potential as low as 0.35 V vs. RHE) was ascribed to oxidation of CO at kink sites. The amount of CO oxidized at the active step or kink sites vs. the amount of CO oxidized at the (111) terrace sites depends on the concentration of the active sites and the time given for the terrace-bound CO to reach the active site. By performing CO stripping on the stepped surfaces at different scan rates, the role of CO surface diffusion is probed. The possible role of electronic effects in explaining the unusual activity and dynamics of CO adlayer oxidation in alkaline solution is discussed.     

Mechanistic insights into the proline-directed enantioselective heterogeneous hydrogenation of isophorone

The adsorption rates onto a range of platinum single-crystal surfaces of key species involved in the proline-directed heterogeneous enantioselective hydrogenation of isophorone were investigated by electrochemical means. Specifically, the uptakes of the prochiral reactant (isophorone), the chiral hydrogenation product (3,3,5-trimethylcyclohexanone), and the chiral directing agent ((R)- and (S)-proline) were examined. The effects of R,S chiral kink sites on the adsorption of (R,S)-proline were also studied. The reactant adsorbs approximately 105 times faster than the chiral modifier so that under conditions of competitive adsorption the latter is entirely excluded from the metal surface. Supplementary displacement and reaction rate measurements carried out with practical Pd/carbon catalysts show that under certain reaction conditions isophorone quickly displaces preadsorbed proline from the metal surface. Thus both kinetics and thermodynamics ensure that the chiral modifier can play no role in any surface-mediated process that leads to enantiodifferentiation. These results are fully consistent with the recent proposal1 that the crucial step leading to enantiodifferentiation occurs in the solution phase and not at the metal surface. In addition, it is found that there is no preferred diastereomeric interaction between (R,S)-proline and R,S step kink sites on Pt{643} and Pt{976}, implying that such sites do not play a role in determining the catalytic behavior of supported metal nanoparticles.     

CO和CH3O在Cu2O(111)表面吸附特性及共吸附的理论研究

基于密度泛函理论, 采用广义梯度近似方法结合周期平板模型, 对Cu₂O(111)非极性表面上CO和CH₃O的吸附和共吸附进行了系统的研究. 计算了CO以4种吸附模式和CH₃O以O端在Cu₂O(111)表面上的吸附, 通过对不同吸附位置的吸附能、几何构型参数和Mulliken电荷的计算和比较发现, Cu₂O(111)表面上配位未饱和铜离子(Cu_CUS)为CO的活性吸附位; 配位饱和铜离子(Cu_CSA)为CH₃O的活性吸附位. CO和CH₃O吸附于Cu₂O(111)表面后, 表面弛豫现象明显改善. CO和CH₃O与Cu₂O(111)表面能够形成共吸附体系, CO和CH₃O之间的相互作用力达到75.89 kJ/mol, 为典型的化学作用, 有助于促进CO和CH₃O反应形成表面物种CH₃OCO, 计算结果与实验事实一致.     

Molecular conductance: chemical trends of anchoring groups

Combining density functional theory calculations for molecular electronic structure with a Green function method for electron transport, we calculate from first principles the molecular conductance of benzene connected to two Au leads through different anchoring atoms-S, Se, and Te. The relaxed atomic structure of the contact, different lead orientations, and different adsorption sites are fully considered. We find that the molecule-lead coupling, electron transfer, and conductance all depend strongly on the adsorption site, lead orientation, and local contact atomic configuration. For flat contacts the conductance decreases as the atomic number of the anchoring atom increases, regardless of the adsorption site, lead orientation, or bias. For small bias this chemical trend is, however, dependent on the contact atomic configuration: an additional Au atom at the contact with the (111) lead changes the best anchoring atom from S to Se, although for large bias the original chemical trend is recovered.     

利凡诺分子模板聚合物的吸附与识别特性研究

以利凡诺药物为模板分子,α-甲基丙烯酸为功能基单体,乙二醇二甲基丙烯酸酯为交联剂,选用分子模板技术,合成了一种新的具有类似于酶或药物受体结合部位为结构特征的分子模板聚合物.研究了它对利凡诺和其它底物的吸附特性和选择性识别能力.结果表明,与组成相同的非模板聚合物相比,利凡诺分子模板聚合物有较大的吸附性能和高度的选择性及识别能力.静电作用和氢键在吸附和识别过程中发挥着重要作用.     

Role of Surface Molecular Architecture and Energetics of Hydrogen Bonding Sites in Adsorption of Polymers and Surfactants

Hydrogen bonding is generally thought to be an ubiquitous adsorption mechanism, which often foils selective adsorption schemes. Through investigation of hydrogen bonding energy and its dependence on surface molecular architecture, it may be possible to develop new methodologies to control the adsorption of surfactants and polymeric flocculants, depressants, and dispersants used in particulate processing industries. A model system using St?ber silica spheres and polyethylene oxide, a polymer known for its ability to form hydrogen bonds, was examined. The effect of two different surface treatments of the silica particles, calcination and rehydroxylation, upon the adsorption of two polymer molecular weights was studied. The adsorption behavior was then linked to the respective surface structures via characterization of the surfaces using FTIR, NMR, and Raman techniques. In this paper role of hydrogen bonding sites and surface architecture on adsorption is discussed. Copyright 2000 Academic Press.     

Multilayer adsorption of water at a rutile TiO2)(110) surface: towards a realistic modeling by molecular dynamics

We present a model combining ab initio concepts and molecular dynamics simulations for a more realistic treatment of complex adsorption processes. The energy, distance, and orientation of water molecules adsorbed on stoichiometric and reduced rutile TiO(2)(110) surfaces at 140 K are studied via constant temperature molecular dynamics simulations. From ab initio calculations relaxed atomic geometries for the surface and the most probable adsorption sites were derived. The study comprises (i) large two-dimensional surface supercells, providing a realistically low concentration of surface oxygen defects, and (ii) a water coverage sufficiently large to model the onset of the growth of a bulk phase of water on the surface. By our combined approach the influence of both, the metal oxide surface, below, and the bulk water phase, above, on the water molecules forming the interface between the TiO(2) surface and the water bulk layer is taken into account. The good agreement of calculated adsorption energies with experimental temperature programmed desorption spectra demonstrates the validity of our model.     

药物氟哌酸分子模板聚合物的分子识别特性

采用分子印迹技术合成了对药物氟哌酸有高度选择性的模板聚合物。通过 Ｓｃａｔｃｈａｒｄ分析研究了模板聚合物的选择结合特性。结果表明,以甲基丙烯酸为功能单体的模 板聚合物通过离子作用和氢键作用可以形成两类结合位点。用多点结合模型计算两类不同 结合位点的离解常数分别为Ｋｄ１＝２．９×１０－５ｍｏｌ／Ｌ和Ｋ＝３．２×１０－３ｍｏｌ／Ｌ。结合底物的实 验表明,该聚合物对氟哌酸呈现出高的选择性,有明显的开发应用价值。     

Ni adsorption on Stone-Wales defect sites in single-wall carbon nanotubes

Ni adsorption on Stone-Wales defect sites in (10,0) zigzag and (5,5) armchair single-wall carbon nanotubes was studied using the density functional theory. The stable adsorption sites and their binding energies on different Stone-Wales defect types were analyzed and compared to those on perfect side walls. It was determined that the sites formed via fusions of 7-7 and 6-7 rings are the most exothermic in the cases of (10,0) and (5,5) defective tubes. In addition C-C bonds associated with Stone-Wales defects are more reactive than the case for a perfect hexagon, thus enhancing the stability of the Ni adsorption. Moreover, the Ni adsorption was found to show a noticeable relationship to the orientation of the Stone-Wales defects with respect to the tube axis. The nature of the Ni adsorption on Stone-Wales defects that have the similar orientation is identical, in spite of the different chiralities.     

CO organization at ambient pressure on stepped Pt surfaces: first principles modeling accelerated by neural networks

Step and kink sites at Pt surfaces have crucial importance in catalysis. We employ a high dimensional neural network potential (HDNNP) trained using first-principles calculations to determine the adsorption structure of CO under ambient conditions (T = 300 K and P = 1 atm) on these surfaces. To thoroughly explore the potential energy surface (PES), we use a modified basin hopping method. We utilize the explored PES to identify the adsorbate structures and show that under the considered conditions several low free energy structures exist. Under the considered temperature and pressure conditions, the step edge (or kink) is totally occupied by on-top CO molecules. We show that the step structure and the structure of CO molecules on the step dictate the arrangement of CO molecules on the lower terrace. On surfaces with (111) steps, like Pt(553), CO forms quasi-hexagonal structures on the terrace with the top site preferred, with on average two top site CO for one multiply bonded CO, while in contrast surfaces with (100) steps, like Pt(557), present a majority of multiply bonded CO on their terrace. Short terraced surfaces, like Pt(643), with square (100) steps that are broken by kink sites constrain the CO arrangement parallel to the step edge. Overall, this effort provides detailed analysis on the influence of the step edge structure, kink sites, and terrace width on the organization of CO molecules on non-reconstructed stepped surfaces, yielding initial structures for understanding restructuring events driven by CO at high coverages and ambient pressure.

A neural network potential trained using first-principles calculations enables to understand the adsorption configurations of carbon monoxide on stepped Pt surfaces at ambient pressure.     

Adsorption in Mixtures with Competing Interactions

A binary mixture of oppositely charged particles with additional short-range attraction between like particles and short-range repulsion between different ones in the neighborhood of a substrate preferentially adsorbing the first component is studied by molecular dynamics simulations. The studied thermodynamic states correspond to an approach to the gas–crystal coexistence. Dependence of the near-surface structure, adsorption and selective adsorption on the strength of the wall–particle interactions and the gas density is determined. We find that alternating layers or bilayers of particles of the two components are formed, but the number of the adsorbed layers, their orientation and the ordered patterns formed inside these layers could be quite different for different substrates and gas density. Different structures are associated with different numbers of adsorbed layers, and for strong attraction the thickness of the adsorbed film can be as large as seven particle diameters. In all cases, similar amount of particles of the two components is adsorbed, because of the long-range attraction between different particles.     

Crystal deformation during the growth of kink bands in oriented polyethylene

When oriented polyethylene is sheared at an angle to the orientation axis, kink bands often develop and grow, with a resulting change of the crystalline orientation. Beside the crystalline reorientation, the following changes within the kink bands have been observed with wide-angle x-rays: (a) partial transformation to a monoclinic from the normal orthorhombic unit cell; (b) partial alignment of the orthorhombic b axes; (c) rotation of the orthorhombic c axes of a fraction of the crystals around the kinks by an extra 40 to 60° beyond that of the fibrils; and (d) misalignment of the orthorhombic (hk0) planes by a few degrees. These results are suggested to arise, at least in part, from crystal flattening and from crystal twinning or pseudotwinning on planes intersecting the molecular axes.     

Atomically Local Electric Field Induced Interface Water Reorientation for Alkaline Hydrogen Evolution Reaction

The slow water dissociation process in alkaline electrolyte severely limits the kinetics of HER. The orientation of H₂O is well known to affect the dissociation process, but H₂O orientation is hard to control because of its random distribution. Herein, an atomically asymmetric local electric field was designed by IrRu dizygotic single-atom sites (IrRu DSACs) to tune the H₂O adsorption configuration and orientation, thus optimizing its dissociation process. The electric field intensity of IrRu DSACs is over 4.00×10¹⁰ N/C. The ab initio molecular dynamics simulations combined with in situ Raman spectroscopy analysis on the adsorption behavior of H₂O show that the M−H bond length (M=active site) is shortened at the interface due to the strong local electric field gradient and the optimized water orientation promotes the dissociation process of interfacial water. This work provides a new way to explore the role of single atomic sites in alkaline hydrogen evolution reaction.     

Adsorption of benzene on graphitized thermal carbon black: reduction of the quadrupole moment in the adsorbed phase

The performance of intermolecular potential models on the adsorption of benzene on graphitized thermal carbon black at various temperatures is investigated. Two models contain only dispersive sites, whereas the other two models account explicitly for the dispersive and electrostatic sites. Using numerous data in the literature on benzene adsorption on graphitized thermal carbon black at various temperatures, we have found that the effect of surface mediation on interaction between adsorbed benzene molecules must be accounted for to describe correctly the adsorption isotherm as well as the isosteric heat. Among the two models with partial charges tested, the WSKS model of Wick et al. that has only six dispersive sites and three discrete partial charges is better than the very expensive all-atom model of Jorgensen and Severance. Adsorbed benzene molecules on graphitized thermal carbon black have a complex orientation with respect to distance from the surface and also with respect to loading. At low loadings, they adopt the parallel configuration relative to the graphene surface, whereas at higher loadings (still less than monolayer coverage) some molecules adopt a slant orientation to maximize the fluid-fluid interaction. For loadings in the multilayer region, the orientation of molecules in the first layer is influenced by the presence of molecules in the second layer. The data that are used in this article come from the work of Isirikyan and Kiselev, Pierotti and Smallwood, Pierce and Ewing, Belyakova, Kiselev, and Kovaleva, and Carrott et al.     

A novel approach to characterize the binding orientation of lysozyme on ion-exchange resins

Much work has been done to qualify and quantify chromatographic adsorption and transportation mechanisms in different adsorber materials. An important aspect in all studies is the understanding of the binding mechanism between protein and resin on a molecular level in order to optimize processes on the level of adsorber design. We established a method to determine the binding orientation of lysozyme for different materials under various experimental conditions enabling us to observe changes in the mode of adsorption. We varied the protein load of two different adsorber types, Source 15S, a conventional cation exchange resin and EMD Fractogel SO(3), a tentacle-type cation exchanger. We found similar preferential binding sites for the interaction between lysozyme and the surface of these adsorbers at low surface coverage, however, the tentacle adsorber exhibited multi-point binding whereas the binding on Source was limited to one binding site only. With increasing protein density on the surface, lysozyme rotates from a space-consuming side-on to a space-saving end-on orientation on Fractogel, explaining a higher maximum binding capacity for Fractogel. This re-orientation could not be observed for Source.     

Molecular Dynamics Simulation on Stability of Insulin on Graphene

The adsorption dynamics of a model protein （the human insulin） onto graphene surfaces with different sizes was investigated by molecular dynamics simulations. During the adsorption, it has different effect on the stability of the model protein in the fixed and non-fixed graphene systems. The tertiary structure of the protein was destroyed or partially destroyed, and graphene surfaces shows the selective protection for some α-helices in non-fixed Systems but not in fixed systems by reason of the flexibility of graphene. As indicated by the interaction energy curve and trajectory animation, the conformation and orientation selection of the protein were induced by the properties and the texture of graphene surfaces. The knowledge of protein adsorption on graphene surfaces would be helpful to better understand stability of protein on graphene surfaces and facilitate potential applications of graphene in biotechnology.