Adsorption of fumaramide [2]rotaxane and its components on a solid substrate: a coverage-dependent study

The coverage-dependent adsorption on Au(111) of a fumaramide [2]rotaxane and its components, a benzylic amide macrocycle and a fumaramide thread, is studied using high-resolution electron energy loss spectroscopy (HREELS). Up to monolayer coverage, the relative intensity of out-of-plane to in-plane phenyl ring vibrational modes indicates that the macrocycle adopts an orientation with the phenyl rings largely parallel to the surface. The formation of a chemisorption bond is evidenced by the presence of a Au-O stretching vibration. In contrast, the thread shows no evidence of chemisorption or a preferential orientation. The introduction of the thread into the macrocycle partly disrupts the film order so that the resulting chemisorbed rotaxane shows intermediate behavior with a preferential orientation up to 0.5 ML coverage. A decrease in film order and the absence of a preferred molecular orientation is observed for all three molecules at multilayer coverages. The spectral differences are addressed by molecular dynamics simulations in terms of the mobility of the phenyls of the three molecules on Au(111).     

Theoretical Investigations of the Activation of CO_2 on the Transition Metal-doped Cu(100) and Cu(111) Surfaces

Periodic density functional theory calculations have been performed to investigate the chemisorption behavior of CO_2 molecule on a series of surface alloys that are built by dispersing individual middle-late transition metal(TM) atoms(TM = Fe, Co, Ni, Ru, Rh, Pd, Ag, Os, Ir, Pt, Au) on the Cu(100) and Cu(111) surfaces. The most stable configurations of CO_2 chemisorbed on different TM/Cu surfaces are determined, and the results show that among the late transition metals, Co, Ru, and Os are potentially good dopants to enhance the chemisorption and activation of CO_2 on copper surfaces. To obtain a deep understanding of the adsorption property, the bonding characteristics of the adsorption bonds are carefully examined by the crystal orbital Hamilton population technique, which reveals that the TM atom primarily provides d orbitals with z-component, namely d_z~2, d_(xz), and d_(yz) orbitals to interact with the adsorbate.     

A Dual‐Response [2]Rotaxane Based on a 1,2,3‐Triazole Ring as a Novel Recognition Station

Two novel multilevel switchable [2]rotaxanes containing an ammonium and a triazole station have been constructed by a Cu^I‐catalyzed azide–alkyne cycloaddition reaction. The macrocycle of [2]rotaxane containing a C6‐chain bridge between the two hydrogen bonding stations exhibits high selectivity for the ammonium cation in the protonated form. Interestingly, the macrocycle is able to interact with the two recognition stations when the bridge between them is shortened. Upon deprotonation of both [2]rotaxanes, the macrocycle moves towards the triazole recognition site due to the hydrogen‐bond interaction between the triazole nitrogen atoms and the amide groups in the macrocycle. Upon addition of chloride anion, the conformation of [2]rotaxane is changed because of the cooperative recognition of the chloride anion by a favorable hydrogen‐bond donor from both the macrocycle isophthalamide and thread triazole CH proton.     

The reactive chemisorption of alkyl iodides at Cu(110) and Ag(111) surfaces: a combined STM and XPS study

The chemisorption of methyl and phenyl iodide has been studied at Cu(110) and Ag(111) surfaces at 290 K with STM and XPS. At both surfaces dissociative adsorption of both molecules leads to chemisorbed iodine, with the STM showing c(2 x 2) and (square root 3 x square root 3)R30 structures at the Cu(110) and Ag(111) surfaces, respectively. At the Cu(110) surface a comparison of coexisting c(2 x 2) I(a) and p(2 x 1) O(a) domains shows the iodine adatoms to be chemisorbed in hollow sites with evidence at low coverage for diffusion in the (110) direction. In the case of methyl iodide no carbon adsorption is observed at either the silver or the copper surfaces, but chemisorbed phenyl groups are imaged at the Cu(110) surface after exposure to phenyl iodide. The STM images show the phenyl groups as bright features approximately 0.7 nm in diameter and 0.11 nm above the iodine adlayer, reaching a maximum surface concentration after approximately 6 Langmuir exposure. However, the phenyl coverage decreases with subsequent exposures to PhI and is negligible by approximately 1000 L exposure, consistent with the formation and desorption of biphenyl. The adsorbed phenyls are located above hollow sites in the substrate, they are stabilized at the top and bottom of step edges and in paired chains (1.1 nm apart) on the terraces with a regular interphenyl spacing within the chains of 1.0 nm in the (110) direction. The interphenyl ring spacing and diffusion of individual phenyls from within the chains shows that the chains do not consist of biphenyl species but may be a precursor to their formation. Although the XPS data shows carbon present at the Ag(111) surface after exposure to PhI, no features attributable to phenyl groups were observed by STM.     

Self-assembly of alkanethiol monolayers on Ag-Au(111) alloy surfaces

The self-assembly of ethanethiol (C(2)) and 1-octanethiol (C(8)) on Ag-Au(111) alloy films was studied by X-ray photoelectron spectroscopy (XPS), cyclic voltammetry (CV), and scanning tunneling microscopy (STM), to illuminate how the monolayer structures and chemisorption-induced substrate defect structures depend on the alloy composition. The thiolate packing density at saturation increased approximately linearly with increasing Ag ratio. The CV data for reductive desorption of thiolates evidenced predominant or major contributions of Ag atoms to the substrate-sulfur interactions for the alloy surfaces. The STM study supported the lack of elemental periodicity on Ag-Au(111) and the consequent absence of periodicity in substrate-sulfur bonding. For C(8)-covered films, we observed systematic changes of substrate defect structures from elevated monatomic islands on Ag(111) to vacancy island structure on Au(111), in good correlation with the reductive desorption characteristics. The former type of defects can be explained best in terms of breakup of atomic terraces under excess thiolate packing density for Ag(111) and Ag-rich Ag-Au(111). As for the vacancy island formation, the present results are not agreeable with the chemical etching model but compatible with the lattice relaxation model.     

A molecular shuttle for driving a multilevel fluorescence switch

A [2]rotaxane-based molecular shuttle comprised a macrocycle mechanically interlocked to a chemical "dumbbell" has been prepared in high yields by a thermodynamically controlled, template-induced clipping procedure. This molecular shuttle has two different recognition sites, namely, -NH2 +- and amide, separated by a phenyl unit. The macrocycle exhibits high selectivity for the -NH2+- recognition sites in the protonated form through noncovalent interactions, which include 1) N+-H...O hydrogen bonds; 2) C-H...O interactions between the CH2NH2+CH2 protons on the thread and the oligo(ethylene glycol) unit in the macrocycle; 3) pi...pi stacking interaction between macrocycle and aromatic unit. Upon deprotonation of the [2]rotaxane the macrocycle glides to the amide recognition site due to the hydrogen bonds between the -CONH- group and the oligo(ethylene glycol) unit in the macrocycle. The deprotonation process requires about 10 equivalents of base (iPr2NEt) in polar acetone, while the amount of base is only 1.2 equivalents in apolar tetrachloroethane. Upon addition of Li+, the conformation of the [2]rotaxane was altered as a result of the collective interactions of 1) hydrogen bonds between pyridine nitrogen and amide hydrogen atoms; 2) coordination between the oligo(ethylene glycol) unit, amide oxygen atom and Li+ cation. Then, when Zn2+ ions are added, the macrocycle returns to the deprotonated -NH- recognition site owing to coordination of the macrocycle and -NH- from the axle with the Zn2+ ion. All the above-mentioned movement processes are reversible through the alternate addition of TFA/iPr2NEt, Li/[12]-crown-4 and Zn2+/ethylenediaminetetraacetate (EDTA), by virtue of hydrogen bonding and metal-ion complexation. Significantly, the three independent movement processes are all accompanied by fluorescent responses: 1) complete repression in the protonated form; 2) low-level expression in the deprotonated form; 3) medium-level expression following addition of Li+; 4) high-level expression on complexation with Zn2+.     

Isolated heterometallic Cr7Ni rings grafted on Au(111) surface

A study of the deposition of heterometallic antiferromagnetically coupled rings onto gold surfaces is reported. Two new {Cr7Ni} rings, [NH2nPr2][Cr7NiF8(3-tpc)16] (1) (where 3-tpc=3-thiophenecarboxylate) and [nBuNH2CH2CH2SH] [Cr7NiF8(O2CtBu)16] (2) have been made and structurally characterized. They have been deposited from the liquid phase on Au(111) and the adsorbed molecules compared by means of scanning tunneling microscopy (STM) and X-ray photoemission spectroscopy (XPS). In both cases a two-dimensional distribution of individually accessible {Cr7Ni} heterometallic rings on the gold surface has been obtained, exploiting the direct grafting of sulfur-functionalized clusters. There is a competition between the chemisorption of the {Cr7Ni} clusters and a thiolic self-assembled monolayer (SAM) formed by free ligands. In 2, the presence of a single sulfur ligand should force the molecule to graft with the ring axis normal to the surface. The cluster stability in the STM images and the S-2p energy positions demonstrate, for both functionalizations, the strength of the grafting with the gold surface.     

Adsorption geometry variation of 1,4-benzenedimethanethiol self-assembled monolayers on Au(111) grown from the vapor phase

1,4-benzenedimethanethiol was chemisorbed from the vapor phase onto Au(111). The chemisorption geometry, molecular orientation, and bonding properties were studied at different degrees of surface coverage by photoelectron spectroscopy, metastable deexcitation spectroscopy, and near-edge x-ray absorption fine structure spectroscopy at the carbon K edge. Two main chemisorption regimes were identified: at low coverage the molecules adopt a flat configuration, then, as the molecular density of the first layer increases, the reduction of the available chemisorption sites induces the newly bonded molecules to assume a vertical alignment, with only one of the sulphur head groups interacting with the substrate. Experimental results were interpreted on the basis of theoretical calculations that we performed on the free molecule concerning the molecular orbitals' density of states and simulated x-ray absorption.     

Synthesis of a [2]rotaxane incorporating a "magic sulfur ring" by the thiol-ene click reaction

The mild and highly efficient thiol-ene click reaction has been used to construct a rotaxane incorporating dibenzo-24-crown-8 (DB24C8) and a dibenzylammonium-derived thread in high yield under the irradiation of UV light. A rotaxane containing a disulfide linkage in the macrocycle was also synthesized by the thiol-ene click reaction. It has been demonstrated that the formation of the [2]rotaxane with the disulfide bond in the macrocycle occurs by a mechanism that is different to the threading-followed-by-stoppering process. The successful construction of a rotaxane directly from its constituent components, the macrocycle containing a disulfide linkage and the dibenzylammonium hexafluorophosphate salt, suggests that the space within the macrocycle incorporating the disulfide linkage is smaller than the phenyl unit and a plausible reaction mechanism has been proposed as follows: A small amount of the initiator forms two radicals upon the absorption of UV irradiation; the radicals act as a "key" to "unlock" the disulfide bond in the macrocycle. The resulting crown ether like moiety in the macrocycle is clipped around the ammonium ion center in the dumb-bell-shaped compound. The [2]rotaxane is generated upon recombination of the disulfide linkage.     

Threading-followed-by-shrinking protocol for the synthesis of a [2]rotaxane incorporating a Pd(II)-salophen moiety

This communication describes a new protocol for the construction of [2]rotaxanes: "threading-followed-by-shrinking". This approach involves the threading of a rodlike unit through a crown ether-like macrocycle and then shrinking the size of the macrocycle's cavity through coordination of a transition-metal ion by a salophen moiety in the macrocycle. The self-assembly of the macrocycle and a thread, followed by addition of palladium acetate, afforded the [2]rotaxane, which contains a palladium(II)-salophen moiety, after counterion exchange. This [2]rotaxane was characterized fully by NMR and IR spectroscopic, mass spectrometric, and elemental and X-ray crystallographic analyses.     

Adsorption and thermal decomposition of 2-octylthieno[3,4-b]thiophene on Au(111)

The adsorption and thermal stability of 2-octylthieno[3,4-b]thiophene (OTTP) on the Au(111) surfaces have been studied using scanning tunneling microscopy (STM), temperature programmed desorption (TPD), and X-ray photoelectron spectroscopy (XPS). UHV-STM studies revealed that the vapor-deposited OTTP on Au(111) generated disordered adlayers with monolayer thickness even at saturation coverage. XPS and TPD studies indicated that OTTP molecules on Au(111) are stable up to 450K and further heating of the sample resulted in thermal decomposition to produce H(2) and H(2)S via C-S bond scission in the thieno-thiophene rings. Dehydrogenation continues to occur above 600K and the molecules were ultimately transformed to carbon clusters at 900K. Highly resolved air-STM images showed that OTTP adlayers on Au(111) prepared from solution are composed of a well-ordered and low-coverage phase where the molecules lie flat on the surface, which can be assigned as a (9×2√33)R5° structure. Finally, based on analysis of STM, TPD, and XPS results, we propose a thermal decomposition mechanism of OTTP on Au(111) as a function of annealing temperature.     

Preparation and heck reaction of multidentate carbosilane films derived from focally functionalized and allyl-terminated dendrons on hydrogen-terminated silicon(111) surfaces

Multidentate carbosilane films were prepared by thermally induced hydrosilylation of allyl-terminated carbosilane dendrons of generations 0, 1, and 2 (G0-G2) on hydrogen-terminated silicon(111) surfaces. The dendron molecules contain three (G0), nine (G1), and twenty-seven (G2) allyl groups at the periphery, and a bromophenyl functional group at the focal point. The dendron films were characterized by contact-angle goniometry, ellipsometry, Fourier transform infrared spectroscopy in the attenuated total reflection mode, and X-ray photoelectron spectroscopy (XPS). Upon hydroboration of the remaining allyl groups in the films, the percentage of the introduced boron atoms in the films were measured by XPS. The results indicate the presence of roughly 20%, 27%, and 46% of unreacted allyl groups in the G0, G1, and G2 films, respectively. The mechanistic aspects of the chemisorption of these dendron molecules on H-Si(111) surfaces are discussed. XPS studies indicate that seven G0 molecules cover approximately the same area on the substrate as three G1 molecules and one G2 molecule. After treatment of the G0, G1, and G2 films with 4-fluorostyrene under the Heck reaction conditions, the XPS studies indicate that about 84%, 71%, and 55% of the Br atoms were consumed, yielding the replacement of ca. 58-70% of the reacted Br atoms by the fluorostyryl groups. The remaining bromophenyl groups were inactive toward the Heck reaction, probably due to their disfavorable position/orientation in the films.     

Structures and properties of self-assembled monolayers of bistable [2]rotaxanes on Au (111) surfaces from molecular dynamics simulations validated with experiment

Bistable [2]rotaxanes display controllable switching properties in solution, on surfaces, and in devices. These phenomena are based on the electrochemically and electrically driven mechanical shuttling motion of the ring-shaped component, cyclobis(paraquat-p-phenylene) (CBPQT(4+)) (denoted as the ring), between a tetrathiafulvalene (TTF) unit and a 1,5-dioxynaphthalene (DNP) ring system located along a dumbbell component. When the ring is encircling the TTF unit, this co-conformation of the rotaxane is the most stable and thus designated the ground-state co-conformer (GSCC), whereas the other co-conformation with the ring surrounding the DNP ring system is less favored and so designated the metastable-state co-conformer (MSCC). We report here the structure and properties of self-assembled monolayers (SAMs) of a bistable [2]rotaxane on Au (111) surfaces as a function of surface coverage based on atomistic molecular dynamics (MD) studies with a force field optimized from DFT calculations and we report several experiments that validate the predictions. On the basis of both the total energy per rotaxane and the calculated stress that is parallel to the surface, we find that the optimal packing density of the SAM corresponds to a surface coverage of 115 A(2)/molecule (one molecule per 4 x 4 grid of surface Au atoms) for both the GSCC and MSCC, and that the former is more stable than the latter by 14 kcal/mol at the optimum packing density. We find that the SAM retains hexagonal packing, except for the case at twice the optimum packing density (65 A(2)/molecule, the 3 x 3 grid). For the GSCC and MSCC, investigated at the optimum coverage, the tilt of the ring with respect to the normal is theta = 39 degrees and 61 degrees, respectively, while the tilt angle of the entire rotaxane is psi = 41 degrees and 46 degrees , respectively. Although the tilt angle of the ring decreases with decreasing surface coverage, the tilt angle of the rotaxane has a maximum at 144 A(2)/molecule (the 4 x 5 grid/molecule) of 50 degrees and 51 degrees for the GSCC and MSCC, respectively. The hexafluorophosphate counterions (PF(6)(-)) stay localized around the ring during the 2 ns MD simulation. On the basis of the calculated density profile, we find that the thickness of the SAM is 40.5 A at the optimum coverage for the GSCC and 40.0 A for MSCC, and that the thicknesses become less with decreasing surface coverage. The calculated surface tension at the optimal packing density is 45 and 65 dyn/cm for the GSCC and MSCC, respectively. This difference suggests that the water contact angle for the GSCC is larger than for the MSCC, a prediction that is verified by experiments on Langmuir-Blodgett monolayers of amphiphilic [2]rotaxanes.     

Solvent effects on the adsorption and self-organization of Mn12 on Au(111)

A sulfur-containing single molecule magnet, [Mn12O12(O2CC6H4SCH3)16(H2O)4], was assembled from solution on a Au(111) surface affording both submonolayer and monolayer coverages. The adsorbate morphology and the degree of coverage were inspected by scanning tunneling microscopy (STM), while X-ray photoelectron spectroscopy (XPS) allowed the determination of the chemical nature of the adsorbate on a qualitative and quantitative basis. The properties of the adsorbates were found to be strongly dependent on the solvent used to dissolve the magnetic complex. In particular, systems prepared from tetrahydrofuran solutions gave arrays of isolated and partially ordered clusters on the gold substrate, while samples prepared from dichloromethane exhibited a homogeneous monolayer coverage of the whole Au(111) surface. These findings are relevant to the optimization of magnetic addressing of single molecule magnets on surfaces.     

Binding of glycine and L-cysteine on Si(111)-7 x 7

The adsorption of glycine and l-cysteine on Si(111)-7 x 7 was investigated using high-resolution electron energy loss spectroscopy (HREELS) and X-ray photoelectron spectroscopy (XPS). The observation of the characteristic vibrational modes and electronic structures of NH3+ and COO- groups for physisorbed glycine (l-cysteine) demonstrates the formation of zwitterionic species in multilayers. For chemisorbed molecules, the appearance of nu(Si-H), nu(Si-O), and nu(C=Omicron) and the absence of nu(O-H) clearly indicate that glycine and l-cysteine dissociate to produce monodentate carboxylate adducts on Si(111)-7 x 7. XPS results further verified the coexistence of two chemisorption states for each amino acid, corresponding to a Si-NH-CH2-COO-Si [Si-NHCH(CH2SH)COO-Si] species with new sigma-linkages of Si-N and Si-O, and a NH2-CH2-COO-Si [NH2CH(CH2SH)COO-Si] product through the cleavage of the O-H bond, respectively. Glycine/Si(111)-7 x 7 and l-cysteine/Si(111)-7 x 7 can be viewed as model systems for further modification of Si surfaces with biological molecules.     

Self-assembled monolayers of alkaneselenolates on (111) gold and silver

Self-assembled monolayers (SAMs) formed from didodecyl diselenide (C12SeSeC12) and didodecyl selenide (C12SeC12) on (111) Au and Ag substrates were extensively characterized by several complementary techniques. C12SeSeC12 was found to form contamination-free, densely packed, and well-ordered C12Se SAMs on both substrates, whereas the adsorption of C12SeC12 occurred only on Au and resulted in the formation of a SAM-like C12SeC12 film with a low packing density and a conformational disorder. The properties of the C12Se SAMs were compared with those of dodecanethiolate (C12S) SAMs. The packing density, orientational order, and molecular inclination in C12Se/Au and C12S/Au were found to be very similar. In contrast, C12Se/Ag exhibited significantly lower packing density, a lower degree of the conformational and orientational order, and a larger molecular inclination than C12S/Ag. The results suggest a sp3 bonding configuration for the selenium atom on Au and Ag and indicate a larger corrugation of the headgroup-substrate binding energy surface in C12Se/Ag than in C12S/Ag.     

Thiol with an unusual adsorption-desorption behavior: 6-mercaptopurine on Au(111)

A multitechnique study of 6-mercaptopurine (6MP) adsorption on Au(111) is presented. The molecule adsorbs on Au(111), originating short-range ordered domains and irregular nanosized aggregates with a total surface coverage by chemisorbed species smaller than those found for alkanethiol SAMs, as derived from scanning tunneling microscopy (STM) and electrochemical results. X-ray photoelectron spectroscopy (XPS) results show the presence of a thiolate bond, whereas density functional theory (DFT) data indicate strong chemisorption via a S-Au bond and additional binding to the surface via a N-Au bond. From DFT data, the positive charge on the Au topmost surface atoms is markedly smaller than that found for Au atoms in alkanethiolate SAMs. The adsorption of 6MP originates Au atom removal from step edges but no vacancy island formation at (111) terraces. The small coverage of Au islands after 6MP desorption strongly suggests the presence of only a small population of Au adatom-thiolate complexes. We propose that the absence of the Au-S interface reconstruction results from the lack of significant repulsive forces acting at the Au surface atoms.     

A new thermo- and photo-driven [2]rotaxane

A new rotaxane with functional chromophores porphyrin and fluorene as stoppers has been synthesized. It displays dual fluorescent character. The macrocycle ring can shuttle between the fumaramide part and the succinimide part on the dumbbell. Heating and UV light irradiating on the rotaxane lead to the reversible E/Z conversion, driving the ring to shuttle between the two stations. The optical properties of porphyrin and fluorene stoppers of the thread do not change so much while the ring shuttles because the macrocycle does not interact with the two stoppers. However, the active group, propargyloxyl, is introduced onto the two sides of the ring so that the rotaxane has the potential to be functionalized by further decoration.     

Synthesis of triazolium-based mono- and tris-branched [1]rotaxanes using a molecular transporter of dibenzo-24-crown-8

We report a diverted route to [1]rotaxane and tris-branched [1]rotaxane that are devoid of any efficient template and which could not be obtained by classical straightforward strategies. The described chemical route relies on the utilization of a “macrocycle transporter”, which is able first to bind a macrocycle, second to link temporarily a triazolium-containing molecular axle, and third to deliver the macrocycle around the new docked axle through molecular machinery in a [1]rotaxane structure. The extended encircled thread is eventually cleaved by an amine or a triamine to afford the triazolium-containing [1]rotaxanes, releasing at the same time, the macrocycle transporter as a recyclable species.