Effect of halo substitution on the geometry of arenethiol films on Cu(111)

Incomplete coverages of p-fluorothiophenol, p-chlorothiophenol, and p-bromothiophenol form ordered islands on a Cu(111) surface even at low temperatures. The complexity of the molecular patterns increases from a simple (3 x 4) superlattice to a honeycomb (8 x 8)R19 degrees structure with increasing substituent electronegativity. We propose a model based on quadrupolar intermolecular interactions to account for this observation.     

Structural evolution of perfluoro-pentacene films on Ag(111): transition from 2D to 3D growth

The structural evolution and thermal stability of perfluoro-pentacene (PF-PEN) thin films on Ag(111) have been studied by means of low-temperature scanning tunnelling microscopy (STM), low-energy electron diffraction (LEED), atomic force microscopy (AFM), X-ray photoelectron spectroscopy (XPS), and thermal desorption spectroscopy (TDS). Well-defined monolayer films can be prepared by utilizing the different adsorption energy of mono- and multilayer films and selectively desorbing multilayers upon careful heating at 380 K, whereas at temperatures above 400 K, a dissociation occurs. In the first monolayer, the molecules adopt a planar adsorption geometry and form a well-ordered commensurate (6 × 3) superstructure where molecules are uniformly oriented with their long axis along the <110> azimuth. This molecular orientation is also maintained in the second layer, where molecules exhibit a staggered packing motif, whereas further deposition leads to the formation of isolated, tall islands. Moreover, on smooth silver surfaces with extended terraces, growth of PF-PEN onto beforehand prepared long-range ordered monolayer films at elevated temperature leads to needle-like islands that are uniformly aligned at substrate steps along <110> azimuth directions.     

Coverage-dependent Orientations of Dy@C82 Molecules on Au(111) Surface

The adsorption and molecular orientation of Dy@C82 isomer I on Au(111) has been investi-gated using ultrahigh-vacuum scanning tunneling microscopy at 80 K. At low coverages, the Dy@C82 molecules tend to grow along the step edges of Au(111), forming small clusters and molecular chains. Adsorption of Dy@C82 on the edges is dominated by the fullerene-substrate interaction and presents various molecular orientations. At higher coverages, the Dy@C82 is found to form ordered islands consisting of small domains of equally oriented molecules. The Dy@C82 molecules in the islands prefer the adsorption configurations with the major C2 axis being approximately parallel to the surface of the substrate. Three preferable orientations of the Dy@C82 molecules are found in a two-dimensional hexagonal close packed overlayer. These observations are attributed to the interplay of the fullerene-substrate interaction and dipole-dipole interaction between the metallofullerenes.     

Water adsorption on Rh(111) at 20 K: from monomer to bulk amorphous ice

The adsorption of water (D(2)O) molecules on Rh(111) at 20 K was investigated using infrared reflection absorption spectroscopy (IRAS). At the initial stage of adsorption, water molecules exist as monomers on Rh(111). With increasing water coverage, monomers aggregate into dimers, larger clusters (n = 3-6), and two-dimensional (2D) islands. Further exposure of water molecules leads to the formation of three-dimensional (3D) water islands and finally to a bulk amorphous ice layer. Upon heating, the monomer and dimer species thermally migrate on the surface and aggregate to form larger clusters and 2D islands. Based on the temperature dependence of OD stretching peaks, we succeeded in distinguishing water molecules inside 2D islands from those at the edge of 2D islands. From the comparison with the previous vibrational spectra of water clusters on other metal surfaces, we conclude that the number of water molecules at the edge of 2D islands is comparable with that of water molecules inside 2D islands on the Rh(111) surface at 20 K. This indicates that the surface migration of water molecules on Rh(111) is hindered as compared with the cases on Pt(111) and Ni(111) and thus the size of 2D islands on Rh(111) is relatively small.     

Global and local expression of chirality in serine on the Cu{110} surface

Establishing a molecular-level understanding of enantioselectivity and chiral resolution at the organic-inorganic interfaces is a key challenge in the field of heterogeneous catalysis. As a model system, we investigate the adsorption geometry of serine on Cu{110} using a combination of low-energy electron diffraction (LEED), scanning tunneling microscopy (STM), X-ray photoelectron spectroscopy (XPS), and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy. The chirality of enantiopure chemisorbed layers, where serine is in its deprotonated (anionic) state, is expressed at three levels: (i) the molecules form dimers whose orientation with respect to the substrate depends on the molecular chirality, (ii) dimers of L- and D-enantiomers aggregate into superstructures with chiral (-1 ?2; 4 0) lattices, respectively, which are mirror images of each other, and (iii) small islands have elongated shapes with the dominant direction depending on the chirality of the molecules. Dimer and superlattice formation can be explained in terms of intra- and interdimer bonds involving carboxylate, amino, and β-OH groups. The stability of the layers increases with the size of ordered islands. In racemic mixtures, we observe chiral resolution into small ordered enantiopure islands, which appears to be driven by the formation of homochiral dimer subunits and the directionality of interdimer hydrogen bonds. These islands show the same enantiospecific elongated shapes those as in low-coverage enantiopure layers.     

Hierarchical chiral framework based on a rigid adamantane tripod on Au(111)

We have investigated the tripod-shaped bromo adamantane trithiol (BATT) molecule on Au(111) using scanning tunneling microscopy (STM) at 4.7 K. Adsorption of BATT leads to formation of highly ordered self-assembled monolayers (SAMs) with three-point contacts on Au(111). The structure of these SAMs has been found to have a two-tiered hierarchical chiral organization. The self-assembly of achiral monomers produces chiral trimers, which then act as the building blocks for chiral hexagonal supermolecules. SAMs begin to form from the racemic mixture of assembled molecules in ribbon-shaped islands, followed by the transformation to enantiomeric domains when SAM layers develop two-dimensionally across hcp domains. Such a chiral phase transition at the two-dimensional domain can arise from a subtle balance between molecule-substrate and intermolecular interactions. Two structural factors, the S atom (stabilization) and the methylene groups (chirality) located just above the S atom, induce the chiral ordering of BATT on Au(111).     

Effect of terminal substituents on self‐assembly behavior of porphyrin molecules on Ag(110)

Effect of terminal substituents on self‐assembly behavior of porphyrin molecules has been studied with three derivatives modified with distinctly different substituents, 5,15‐(di‐3,5‐di‐tert‐butylphenyl) porphyrin, 5,15‐(dimesityl) porphyrin, and 5,15‐(di‐4‐ethynylphenyl) porphyrin. Scanning tunneling microscopy and density functional calculations reveal that 5,15‐(di‐3,5‐di‐tert‐butylphenyl) porphyrin, 5,15‐(dimesityl) porphyrin, and 5,15‐(di‐4‐ethynylphenyl) porphyrin spontaneously give different ordered structures on Ag(110) surface both at room temperature and after annealing. It is clear that the tert‐butylphenyl substituent could increase the intermolecular van der Waals interactions to form stable network structure under condition of thermal activation, whereas the mesityl substituent plays an essential role in the formation of rigid chain structure as a result of the CH–π interactions between the mesityl groups of molecule enantiomers. Moreover, the ethynylphenyl substituent could induce metal atoms to coordinate with ethynyl to form organometallic chains. Copyright © 2016 John Wiley & Sons, Ltd.     

Angle-resolved photoemission spectroscopy study of adsorption process and electronic structure of silver on ZnO(1010)

The adsorption process and valence band structure of Ag on ZnO(1010) have been investigated by angle-resolved photoelectron spectroscopy utilizing synchrotron radiation. The coverage-dependent measurements of the Ag 4d band structure reveal that the Ag bands with a dispersing feature are formed even at low coverages and that the basic structure of the bands is essentially the same throughout the submonolayer region. These results indicate that the Ag atoms aggregate to form islands with an atomically ordered structure from the low coverages. Upon annealing the Ag-covered surface at 900 K, the Ag 4d band undergoes only a minor change, suggesting that the ordered structure within the Ag islands is persistent against mild annealing. From the dispersive feature of the Ag 4d states, we propose that the atomic structure has locally rectangular symmetry with a good lattice matching with the ZnO(1010) surface.     

Effects of surface hydrophobization on the growth of self-assembled monolayers on silicon

The growth of self-assembled monolayers from octadecyltrichlorosilane (OTS) on modified silicon surfaces has been investigated. The influence of different immersion times in a deactivation reagent on the growth mechanism and the ordering of the films has been studied. Characterization of the films and the submonolayer coverage has been performed with tapping mode atomic force microscopy, ellipsometry, and infrared spectroscopy. We found that a deactivation of active sites led to a higher mobility of adsorbed molecules on the surface resulting in circular islands of highly ordered alkylsiloxane. However, upon prolonged immersion in OTS these ordered islands did not continue to grow and full monolayer coverage could not be obtained. Instead, an exchange reaction with the deactivation reagent leading to a disordered film between the ordered islands was observed. This was confirmed by external reflection infrared spectroscopy.     

Formation of highly ordered and orientated gold islands: effect of immersion time on the molecular adlayer structure of pentafluorobenzenethiols (PFBT) SAMs on Au(111)

Self-assembled monolayers (SAMs) of pentafluorobenzenethiol (PFBT) on Au(111) substrates, prepared with different immersion times (ITs) at room temperature, were studied using scanning tunneling microscopy (STM) and infrared reflection-absorption spectroscopy (IRRAS). In the present study, the focus was on several important points of interest in the field of SAMs. First, the gold islands formed upon adsorption of PFBT molecules on the gold surface were monitored at different ITs in terms of their size, density, and shape. After short ITs (5 to 30 min), small gold islands with rounded shape were formed. These gold islands were arranged in a rather regular fashion and found to be quite mobile under the influence of the STM-tip during the scanning. When the IT was increased to 16 h, the results revealed the formation of highly ordered and orientated gold islands with very unusual shapes with straight edges meeting at 60° or 120° running preferentially along the [11(-)0] substrate directions. The density of the gold islands was found to decrease with increasing IT until they almost disappeared from the SAMs prepared after 190 h of IT. On top of the gold islands, the PFBT molecules were found to adopt the closely packed (10√3 × 2) structure. Second, a number of structural defects such as disordered regions at the domain boundaries and dark row(s) of molecules within the ordered domains of the PFBT SAMs were observed at different ITs. The SAMs prepared after 190 h of IT were found to be free of these defects. Third, at low and moderate ITs, a variation in the PFBT molecular contrast was observed. This contrast variation was found to depend mainly on the tunneling parameters. Finally, our results revealed that the organization process of PFBT SAMs is IT-dependent. Consequently, a series of structural phases, namely, α, β, γ, δ, and ε were found. The α-, β-, γ-, and δ-phases were typically accompanied by the ε-phase that appeared on top of gold islands. With increasing IT, the α→β→ γ→δ→ε phase transitions took place. The resulting ε-phase, which covered the entire gold surface after 190 h of IT, yielded well-ordered self-assembled monolayers with large domains having a (10√3 × 2) superlattice structure.     

Oriented organic islands and one-dimensional chains on a Au(111) surface fabricated by electrodeposition: an STM study

Organic islands and oriented one-dimensional (1D) chains are fabricated on a Au(111) surface by electrodeposition. The cyclic voltammograms (CVs) of Au(111) in solutions containing nitrobenzene and picric acid show an electrochemical reaction in a negative potential region, which results in irreversible reductive deposition. The deposition process is monitored by in situ electrochemical scanning tunneling microscopy (ECSTM). At the double layer potential region, for example, nitrobenzene molecules form a well-defined adlayer in a (square root(3) x square root(3)) structure. With potential shifting negative to the reductive region, nitrobenzene is reduced to hydroxyaminobenzene. Organic islands were formed first and then aggregated into ordered 1D chains. The formation of these organic islands and 1D chains is completely potential-dependent. Intriguingly, the so-prepared islands and 1D chains are well-oriented along the reconstructed lines of the underlying Au(111) substrate and stable under ambient conditions even if the sample was removed from electrolyte solution. The results reported here provide a simple and effective method to fabricate oriented organic nanodots and nanowires on a solid surface by an electrochemical technique.     

Effect of molecular mass on supramolecular organisation of poly(4,4'-dioctyl-2,2':5',2'-terthiophene)

The effect of the chain length on the type and extent of the 2D supramolecular organization in poly(4,4'-dioctyl-2,2':5',2'-terthiophene) (PDOTT) monomolecular layers deposited on highly oriented pyrolytic graphite (HOPG) is studied by scanning tunneling microscopy (STM) and analyzed in terms of molecular modeling. The strictly monodispersed fractions of increasing molecular mass used in this study were obtained by chromatographic fractionation of the crude product of 4,4'-dioctyl-2,2':5',2'-terthiophene oxidative polymerization. STM investigations of PDOTT layers, deposited on HOPG from poly- and monodispersed fractions, show that polydispersity can be considered as a key factor seriously limiting supramolecular ordering. This is a consequence of significant differences in the type of supramolecular order observed for molecules of different chain length. It has been demonstrated that shorter molecules (consisting of 6 and 9 thiophene units) form well-defined two-dimensional islands, while the interactions between longer molecules (consisting of 12 and 15 thiophene units) become anisotropic. Consequently, for higher molecular mass fractions, the supramolecular organization is one-dimensional and consists of more or less separated rows of ordered macromolecules. In this case an increase of the chain length leads to amplification of the intermolecular interactions proceeding via interdigitation of the alkyl substituents of adjacent molecules. Polydispersed fractions show much less ordered organization because of the incompatibility of the supramolecular structures of molecules of different molecular masses. This finding is of crucial importance for the application of polythiophene derivatives in organic and molecular electronics since ordered supramolecular organization constitutes the condition sine qua non of good electrical transport properties.     

Vertical and lateral order in adsorbed water layers on anatase TiO2(101)

The structure and energetics of thin water overlayers on the (101) surface of TiO(2)-anatase have been studied through first-principles molecular dynamics simulations at T = 160 K. At one monolayer coverage, H(2)O molecules are adsorbed at the 5-fold Ti sites (Ti(5c)), forming an ordered crystal-like 2D layer with no significant water-water interactions. For an adsorbed bilayer, H(2)O molecules at both Ti(5c) and bridging oxygen (O(2c)) sites form a partially ordered structure, where the water oxygens occupy regular sites but the orientation of the molecules is disordered; in addition, stress-relieving defects are usually present. When a third layer is adsorbed, very limited parallel and perpendicular order is observed above the first bilayer. The calculated energetics of multilayer adsorption is in good agreement with recent temperature-programmed desorption data.     

Water adsorption, desorption, and clustering on FeO(111)

The adsorption of water on FeO(111) is investigated using temperature programmed desorption (TPD) and infrared reflection absorption spectroscopy (IRAS). Well-ordered 2 ML thick FeO(111) films are grown epitaxially on a Pt(111) substrate. Water adsorbs molecularly on FeO(111) and desorbs with a well resolved monolayer peak. IRAS measurements as a function of coverage are performed for water deposited at 30 and 135 K. For all coverages (0.2 ML and greater), the adsorbed water exhibits significant hydrogen bonding. Differences in IRAS spectra for water adsorbed at 30 and 135 K are subtle but suggest that water adsorbed at 135 K is well ordered. Monolayer nitrogen TPD spectra from water covered FeO(111) surfaces are used to investigate the clustering of the water as a function of deposition or annealing temperature. Temperature dependent water overlayer structures result from differences in water diffusion rates on bare FeO(111) and on water adsorbed on FeO(111). Features in the nitrogen TPD spectra allow the monolayer wetting and 2-dimensional (2D) ordering of water on FeO(111) to be followed. Voids in a partially disordered first water layer exist for water deposited below 120 K and ordered 2D islands are found when depositing water above 120 K.     

Scanning tunneling microscopy and scanning tunneling spectroscopy studies of planar and nonplanar naphthalocyanines on graphite (0001). Part 1: effect of nonplanarity on the adlayer structure and voltage-induced flipping of nonplanar tin-naphthalocyanine

The adsorption of base-free naphthalocyanine (Nc), a planar molecule, and tin-naphthalocyanine (SnNc), a nonplanar molecule, on a freshly cleaved highly oriented pyrolytic graphite (HOPG) surface at low sample temperature (50 K) has been studied using a variable-temperature scanning tunneling microscope in ultra-high vacuum conditions. The planar molecules form large areas of defect-free ordered monolayer with high molecular packing density while the nonplanar molecules show different phases of adsorption with lower molecular packing density. The SnNc adlayers follow the same geometry as the graphite substrate and form pure phases of adsorption with either all molecules in a Sn(2+) up or Sn(2+) down geometry. Moreover, a one-dimensional selectivity is observed in still another phase of Sn(2+) down geometry. Multilayers show a completely different kind of adsorption in each case. Nc molecules show columnar pi-stacking whereas the SnNc molecules exhibit noncolumnar stacking. Distinctly, a voltage-induced flipping of nonplanar tin-naphthalocyanine in the monolayer has been observed which can possibly be applied to single-molecular information storage.     

Atomic force microscopy characterization of room-temperature adlayers of small organic molecules through graphene templating

We report on the use of graphene templating to investigate the room-temperature structure and dynamics of weakly bound adlayers at the interfaces between solids and vapors of small organic molecules. Monolayer graphene sheets are employed to preserve and template molecularly thin adlayers of tetrahydrofuran (THF) and cyclohexane on atomically flat mica substrates, thus permitting a structural characterization of the adlayers under ambient conditions through atomic force microscopy. We found the first two adlayers of both molecules adsorb in a layer-by-layer fashion, and atomically flat two-dimensional islands are observed for both the first and the second adlayers. THF adlayers form initially as rounded islands but, over a period of weeks, evolve into faceted islands, suggesting that the adlayers possess both liquid and solid properties at room temperature. Cyclohexane adlayers form crystal-like faceted islands and are immobile under the graphene template. The heights of the second adlayers of THF and cyclohexane are measured to be 0.44 ± 0.02 and 0.50 ± 0.02 nm, respectively, in good agreement with the layer thicknesses in the monoclinic crystal structure of THF and the Phase I "plastic crystal" structure of cyclohexane. The first adlayers appear slightly thinner for both molecules, indicative of interactions of the molecules with the mica substrate.     

Co-adsorption of water and hydrogen on Ni(111)

We have studied the surface coverage dependence of the co-adsorption of D and D(2)O on the Ni(111) surface under UHV conditions. We use detailed temperature-programmed desorption studies and high resolution electron energy loss spectroscopy to show how pre-covering the surface with various amounts of D affects adsorption and desorption of D(2)O. Our results show that the effects of co-adsorption are strongly dependent on D-coverage. In the deuterium pre-coverage range of 0-0.3 ML, adsorption of deuterium leaves a fraction of the available surface area bare for D(2)O adsorption, which shows no significant changes compared to adsorption on the bare surface. Our data indicate phase segregation of hydrogen and water into islands. At low post-coverages, D(2)O forms a two-phase system on the remaining bare surface that shows zero-order desorption kinetics. This two phase system likely consists of a 2-D solid phase of extended islands of hexamer rings and a 2-D water gas phase. Increasing the water post-dose leads at first to 'freezing' of the 2-D gas and is followed by formation of ordered, multilayered water islands in-between the deuterium islands. For deuterium pre-coverages between 0.3 and 0.5 ML, our data may be interpreted that the water hexamer ring structure, (D(2)O)(6), required for the formation of an ordered multilayer, does not form anymore. Instead, more disordered linear and branched chains of water molecules grow in-between the extended, hydrophobic deuterium islands. These deuterium islands have a D-atom density in agreement with a (2x2)-2D structure. The disordered water structures adsorbed in-between form nucleation sites for growth of 3-D water structures. Loss of regular lateral hydrogen bonding and weakened interaction with the substrate reduces the binding energy of water significantly in this regime and results in lowering of the desorption temperature. At deuterium pre-coverages greater than 0.5 ML, the saturated (2x2)-2D structure mixes with (1x1)-1D patches. The mixed structures are also hydrophobic. On such surfaces, submonolayer doses of water lead to formation of 3-D water structures well before wetting the entire hydrogen-covered surface.     

Polymorphism and phase transformation in the dimethyl sulfoxide solvate of 2,3,5,6‐tetrafluoro‐1,4‐diiodobenzene

A new polymorph (form II) is reported for the 1:1 dimethyl sulfoxide solvate of 2,3,5,6‐tetrafluoro‐1,4‐diiodobenzene (TFDIB·DMSO or C₆F₄I₂·C₂H₆SO). The structure is similar to that of a previously reported polymorph (form I) [Britton (2003). Acta Cryst. E 59 , o1332–o1333], containing layers of TFDIB molecules with DMSO molecules between, accepting I…O halogen bonds from two TFDIB molecules. Re‐examination of form I over the temperature range 300–120 K shows that it undergoes a phase transformation around 220 K, where the DMSO molecules undergo re‐orientation and become ordered. The unit cell expands by ca 0.5 Å along the c axis and contracts by ca 1.0 Å along the a axis, and the space‐group symmetry is reduced from Pnma to P2₁2₁2₁. Refinement of form I against data collected at 220 K captures the (average) structure of the crystal prior to the phase transformation, with the DMSO molecules showing four distinct disorder components, corresponding to an overlay of the 297 and 120 K structures. Assessment of the intermolecular interaction energies using the PIXEL method indicates that the various orientations of the DMSO molecules have very similar total interaction energies with the molecules of the TFDIB framework. The phase transformation is driven by interactions between DMSO molecules, whereby re‐orientation at lower temperature yields significantly closer and more stabilizing interactions between neighbouring DMSO molecules, which lock in an ordered arrangement along the shortened a axis.     

锰的硅化物薄膜在Si(111)-7×7表面的固相反应生长

利用超高真空扫描隧道显微镜(STM)对沉积在Si(111)-7×7重构表面上的锰薄膜在300-650℃之间的固相反应进行了研究.锰原子最初在Si(111)衬底上形成锰的纳米团簇的有序阵列,经过300℃退火后,锰纳米团簇的尺寸增大并且纳米团簇阵列由有序变为无序;当退火温度达到400℃左右时,锰纳米团簇与硅衬底发生反应生成富锰的三维岛状物和由MnSi构成的平板状岛;500℃退火后生成物全部转变为MnSi平板状岛;650℃退火后生成物则由MnSi平板状岛全部转变为富硅的不规则的大三维岛,同时被破坏的衬底表面重新结晶形成7×7结构.     

Nanospace geometry-sensitive molecular assembly

Interaction of a molecule with micropore walls strongly depends on the micropore width. Molecules confined in the micropore tend to form an intermolecular structure inherent to each molecule/pore system in order to lower the whole molecular energy. Supercritical NO is adsorbed in micropores of zolite or activated carbon fiber in the form of a dimer at 303 K. The NO dimerization varies with the micropore width. CCl₄ molecules only in pore of pore width =1.0 nm at 303 K form a plastic crystalline structure which is observed at 246–250 K in the bulk phase. H₂O molecules are associated with each other to form an ordered assembly in carbon micropores at 303 K; the smaller the pore width, the more ordered the assembly structure. The presence of preadsorbed H₂O noticeably enhances adsorption of supercritical CH₄ in carbon micropores at 303 K due to methane nanohydrate formation, which has an optimum pore width of 1 nm.