Ionic hydrogen bonds controlling two-dimensional supramolecular systems at a metal surface

Hydrogen-bond formation between ionic adsorbates on an Ag(111) surface under ultrahigh vacuum was studied by scanning tunneling microscopy/spectroscopy (STM/STS), X-ray photoelectron spectroscopy (XPS), near-edge X-ray absorption fine structure (NEXAFS), and molecular dynamics calculations. The adsorbate, 1,3,5-benzenetricarboxylic acid (trimesic acid, TMA), self-assembles at low temperatures (250-300 K) into the known open honeycomb motif through neutral hydrogen bonds formed between carboxyl groups, whereas annealing at 420 K leads to a densely packed quartet structure consisting of flat-lying molecules with one deprotonated carboxyl group per molecule. The resulting charged carboxylate groups form intermolecular ionic hydrogen bonds with enhanced strength compared to the neutral hydrogen bonds; this represents an alternative supramolecular bonding motif in 2D supramolecular organization.     

Stereochemical effects in supramolecular self-assembly at surfaces: 1-D versus 2-D enantiomorphic ordering for PVBA and PEBA on Ag(111)

We present investigations on noncovalent bonding and supramolecular self-assembly of two related molecular building blocks at a noble metal surface: 4-[trans-2-(pyrid-4-yl-vinyl)]benzoic acid (PVBA) and 4-[(pyrid-4-yl-ethynyl)]benzoic acid (PEBA). These rigid, rodlike molecules comprising the same complementary moieties for hydrogen bond formation are comparable in shape and size. For PVBA, the ethenylene moiety accounts for two-dimensional (2-D) chirality upon confinement to a surface; PEBA is linear and thus 2-D achiral. Molecular films were deposited on a Ag(111) surface by organic molecular beam epitaxy and characterized by scanning tunneling microscopy. At low temperatures (around 150 K), both species form irregular networks of flat lying molecules linked via their endgroups in a diffusion-limited aggregation process. In the absence of kinetic limitations (adsorption or annealing at room temperature), hydrogen-bonded supramolecular assemblies form which are markedly different. With PVBA, enantiomorphic twin chains in two mirror-symmetric species running along a high-symmetry direction of the substrate lattice form by diastereoselective self-assembly of one enantiomer. The chirality signature is strictly correlated between neighboring twin chains. Enantiopure one-dimensional (1-D) supramolecular nanogratings with tunable periodicity evolve at intermediate coverages, reflecting chiral resolution in micrometer domains. In contrast, PEBA assembles in 2-D hydrogen-bonded islands, which are enantiomorphic because of the orientation of the supramolecular arrangements along low-symmetry directions of the substrate. Thus, for PVBA, chiral molecules form 1-D enantiomorphic supramolecular structures because of mesoscopic resolution of a 2-D chiral species, whereas with PEBA, the packing of an achiral species causes 2-D enantiomorphic arrangements. Model simulations of supramolecular ordering provide a deeper understanding of the stability of these systems.     

Dianhydride-amine hydrogen bonded perylene tetracarboxylic dianhydride and tetraaminobenzene rows

We have investigated the coadsorption of perylene tetracarboxylic dianhydride (PTCDA) and tetraaminobenzene (TAB) on the Ag/Si(111)-square root(3) x square root(3) R30 degree surface using scanning tunneling microscopy. At room temperature, PTCDA islands with square and herringbone ordering are formed which, on exposure to TAB, are converted into an intermixed phase in which PTCDA and TAB form alternating rows. From our images, we determine the relative placement of TAB and PTCDA molecules and conclude that the row structure is stabilized by hydrogen bonding between dianhydride and diamine groups. We confirm that this hydrogen bonding junction is stable using ab initio calculations and show that the proposed geometry is consistent with calculated intermolecular dimensions.     

Quasi chiral phase separation in a two-dimensional orientationally disordered system: 6-nitrospiropyran on Au(111)

The adsorption and chiral expression of 6-nitrospiropyran (SP6) molecules on a Au(111) surface are studied by scanning tunneling microscopy (STM) in combination with density functional theory (DFT) calculations. Both the chirality and the adsorption orientation of each adsorbed SP6 molecule are determined. The racemic mixture of SP6 enantiomers forms two-dimensional (2D) domains with same close packed positional orders but different internal orientational structures due to the random distribution of two adsorption orientations in each domain. However, all these orientationally disordered 2D domains undergo spontaneous quasi chiral phase separation; the 2D SP6 domains separate into 1D homochiral chains in which the SP6 molecules adopt two orientations randomly. This novel phenomenon is attributed to the preferential formation of the energetic favorable configurations with both the C-H...O weak hydrogen bonds and the pi-stacking of the two moieties of each SP6 molecule.     

Cyano‐Functionalized Triarylamines on Coinage Metal Surfaces: Interplay of Intermolecular and Molecule–Substrate Interactions

The self‐assembly of cyano‐functionalized triarylamine derivatives on Cu(111), Ag(111) and Au(111) was studied by means of scanning tunnelling microscopy, low‐energy electron diffraction, X‐ray photoelectron spectroscopy and density functional theory calculations. Different bonding motifs, such as antiparallel dipolar coupling, hydrogen bonding and metal coordination, were observed. Whereas on Ag(111) only one hexagonally close‐packed pattern stabilized by hydrogen bonding is observed, on Au(111) two different partially porous phases are present at submonolayer coverage, stabilized by dipolar coupling, hydrogen bonding and metal coordination. In contrast to the self‐assembly on Ag(111) and Au(111), for which large islands are formed, on Cu(111), only small patches of hexagonally close‐packed networks stabilized by metal coordination and areas of disordered molecules are found. The significant variety in the molecular self‐assembly of the cyano‐functionalized triarylamine derivatives on these coinage metal surfaces is explained by differences in molecular mobility and the subtle interplay between intermolecular and molecule–substrate interactions.     

Self-assembly and conformation of tetrapyridyl-porphyrin molecules on Ag(111)

We present a low-temperature scanning tunneling microscopy (STM) study on the supramolecular ordering of tetrapyridyl-porphyrin (TPyP) molecules on Ag(111). Vapor deposition in a wide substrate temperature range reveals that TPyP molecules easily diffuse and self-assemble into large, highly ordered chiral domains. We identify two mirror-symmetric unit cells, each containing two differently oriented molecules. From an analysis of the respective arrangement it is concluded that lateral intermolecular interactions control the packing of the layer, while its orientation is induced by the coupling to the substrate. This finding is corroborated by molecular mechanics calculations. High-resolution STM images recorded at 15 K allow a direct identification of intramolecular features. This makes it possible to determine the molecular conformation of TPyP on Ag(111). The pyridyl groups are alternately rotated out of the porphyrin plane by an angle of 60 degrees.     

Cyclotrimerization‐Induced Chiral Supramolecular Structures of 4‐Ethynyltriphenylamine on Au(111) Surface

Cyclotrimerization‐induced chiral supramolecular structures of 4‐ethynyltriphenylamine (ETPA) have been synthesized on the Au(111) surface through alkyne‐based reactions. Whereas the ETPA molecules adsorbed on the Au(111) surface remain inert and form a close‐packed self‐assembled structure at room temperature, the combination of scanning tunneling microscopy observations and theoretical calculations unambiguously reveal that the ETPA molecules cyclotrimerize to form new trimer‐like species—1,3,5‐tris[4‐(diphenylamino)phenyl]benzene (TPAPB)—after annealing at 323 K. Further annealing drives these cyclotrimerized TPAPB molecules to form chiral hexagonal supramolecular structures with an extraordinary self‐healing ability.     

Geometric and Electronic Behavior of C60 on PTCDA Hydrogen Bonded Network

Self-assembled supramolecular networks are promising spacer layer for electronic decoupling from the metal substrate.However,the mechanism behind of how the intrinsic electronic structure of spacer layers affects the adsorbate is still unclear.Here a hydrogen bonded network composed of n-type semiconducting molecules 3,4,9,10-perylene-tetracarboxylic-dianhydride(PTCDA)is prepared under ultra-high vacuum to serve as a spacer layer for functional organics C60 on Au(111).The geometric and electronic information of C60 was investigated by scanning tunneling microscopy and scanning tunneling spectroscopy(STM/STS)at 5 K.Effective decoupling from the metal surface yields an energy gap of 3.67 eV for C602nd,merely considering the HOMO-LUMO peak separation.The broadening of resonance peaks in STS measurements however indicates unneglected interlayer interactions in this hetero-organic system.Moreover,we scrutinize the nucleation sites of C60 on PTCDA layer and attribute this to the decreased diffusion capability on a less dense molecular arrangement possessing inhomogeneous spatial distribution of unoccupied molecular orbitals.     

Chiral recognition capabilities of melamine and cyanuric acid supramolecular structures

Currently, there are numerous papers that discuss local chiral domains in supramolecular structures of achiral molecules established using the STM method, and by using DFT calculations. However, there are no data regarding the obtainment of macroscopically chiral 2D-supramolecular structures from achiral molecules. In this study, melamine and cyanuric acid supramolecular structures were self-assembled on a graphitized carbon black surface, which had a surface structure that was identical to HOPG, and also on the surface of an inert solid support for chromatography. Chirality induction according to the Kondepudi effect was used. For the supramolecular structures, MD calculations showed the possibility of obtaining a chiral structure. To establish macroscopic chirality, we proposed the use of the difference in enantiomer adsorption on the modified adsorbents. For this, two indirect methods were used: static adsorption with a polarimetric control and gas chromatography. Both methods indicated the chiral recognition ability of the adsorbents used.     

Influence of chlorine substitution on the self-assembly of zinc phthalocyanine

The adsorption and ordering of zinc phthalocyanine (ZnPc) and octachloro zinc phthalocyanine (ZnPcCl(8)) on an Ag(111) surface is studied in situ by scanning tunneling microscopy under ultrahigh vacuum. Two-dimensional self-assembled supramolecular domains are observed for these two molecules. We show how substituting chlorine atoms for half of the peripheral hydrogen atoms on ZnPc influences the self-assembly mechanisms. While intermolecular interactions are dominated by van der Waals forces in ZnPc molecular networks, ZnPcCl(8) molecular packing undergoes a sequential phase evolution driven by the creation of C-Cl...H-C hydrogen bonds between adjacent molecules. At the end of this evolution, the final molecular assembly involves all possible hydrogen bonds. Our study also reveals the influence of molecule-substrate interactions through the presence of fault lines generating a stripe structure in the molecular film.     

Two-dimensional polymer formation on surfaces: insight into the roles of precursor mobility and reactivity

We report on a combined scanning tunneling microscopy (STM), X-ray photoelectron spectroscopy (XPS), and density functional theory (DFT) study on the surface-assisted assembly of the hexaiodo-substituted macrocycle cyclohexa-m-phenylene (CHP) toward covalently bonded polyphenylene networks on Cu(111), Au(111), and Ag(111) surfaces. STM and XPS indicate room temperature dehalogenation of CHP on either surface, leading to surface-stabilized CHP radicals (CHPRs) and coadsorbed iodine. Subsequent covalent intermolecular bond formation between CHPRs is thermally activated and is found to proceed at different temperatures on the three coinage metals. The resulting polyphenylene networks differ significantly in morphology on the three substrates: On Cu, the networks are dominated by "open" branched structures, on the Au surface a mixture of branched and small domains of compact network clusters are observed, and highly ordered and dense polyphenylene networks form on the Ag surface. Ab initio DFT calculations allow one to elucidate the diffusion and coupling mechanisms of CHPRs on the Cu(111) and Ag(111) surfaces. On Cu, the energy barrier for diffusion is significantly higher than the one for covalent intermolecular bond formation, whereas on Ag the reverse relation holds. By using a Monte Carlo simulation, we show that different balances between diffusion and intermolecular coupling determine the observed branched and compact polyphenylene networks on the Cu and Ag surface, respectively, demonstrating that the choice of the substrate plays a crucial role in the formation of two-dimensional polymers.     

Luminescence from 3,4,9,10-perylenetetracarboxylic dianhydride on Ag(111) surface excited by tunneling electrons in scanning tunneling microscopy

The electronic excitations induced with tunneling electrons into adlayers of 3,4,9,10-perylenetetracarboxylic dianhydride (PTCDA) on Ag(111) have been investigated by in situ fluorescence spectroscopy in scanning tunneling microscopy (STM). A minute area of the surface is excited by an electron tunneling process in STM. Fluorescence spectra strongly depend on the coverage of PTCDA on Ag(111). The adsorption of the first PTCDA layer quenches the intrinsic surface plasmon originated from the clean Ag(111). When the second layer is formed, fluorescence spectra are dominated by the signals from PTCDA, which are interpreted as the radiative decay from the manifold of first singlet excited state (S(1)) of adsorbed PTCDA. The fluorescence of PTCDA is independent of the bias polarity. In addition, the fluorescence excitation spectrum agrees with that by optical excitation. Both results indicate that S(1) is directly excited by the inelastic impact scattering of electrons tunneling within the PTCDA adlayer.     

Azimuthal Dipolar Rotor Arrays on Surfaces

A set of dipolar molecular rotor compounds was designed, synthesized and adsorbed as self-assembled 2D arrays on Ag(111) surfaces. The title molecules are constructed from three building blocks: (a) 4,8,12-trioxatriangulene (TOTA) platforms that are known to physisorb on metal surfaces such as Au(111) and Ag(111), (b) phenyl groups attached to the central carbon atom that function as pivot joints to reduce the barrier to rotation, (c) pyridine and pyridazine units as small dipolar units on top. Theoretical calculations and scanning tunneling microscopy (STM) investigations hint at the fact that the dipoles of neighboring rotors interact through space through pairs of energetically favorable head-to-tail arrangements.     

Dipole driven bonding schemes of quinonoid zwitterions on surfaces

The permanent dipole of quinonoid zwitterions changes significantly when the molecules adsorb on Ag(111) and Cu(111) surfaces. STM reveals that sub-monolayers of adsorbed molecules can exhibit parallel dipole alignment on Ag(111), in strong contrast with the antiparallel ordering prevailing in the crystalline state and retrieved on Cu(111) surfaces, which minimizes the dipoles electrostatic interaction energy. DFT shows that the rearrangement of electron density upon adsorption is a result of donation from the molecular HOMO to the surface, and back donation to the LUMO with a concomitant charge transfer that effectively reduces the overall charge dipole.     

Ab initio molecular dynamics of hydrogen dissociation on metal surfaces using neural networks and novelty sampling

We outline a hybrid multiscale approach for the construction of ab initio potential energy surfaces (PESs) useful for performing six-dimensional (6D) classical or quantum mechanical molecular dynamics (MD) simulations of diatomic molecules reacting at single crystal surfaces. The algorithm implements concepts from the corrugation reduction procedure, which reduces energetic variation in the PES, and uses neural networks for interpolation of smoothed ab initio data. A novelty sampling scheme is implemented and used to identify configurations that are most likely to be predicted inaccurately by the neural network. This hybrid multiscale approach, which couples PES construction at the electronic structure level to MD simulations at the atomistic scale, reduces the number of density functional theory (DFT) calculations needed to specify an accurate PES. Due to the iterative nature of the novelty sampling algorithm, it is possible to obtain a quantitative measure of the convergence of the PES with respect to the number of ab initio calculations used to train the neural network. We demonstrate the algorithm by first applying it to two analytic potentials, which model the H2/Pt(111) and H2/Cu(111) systems. These potentials are of the corrugated London-Eyring-Polanyi-Sato form, which are based on DFT calculations, but are not globally accurate. After demonstrating the convergence of the PES using these simple potentials, we use DFT calculations directly and obtain converged semiclassical trajectories for the H2/Pt(111) system at the PW91/generalized gradient approximation level. We obtain a converged PES for a 6D hydrogen-surface dissociation reaction using novelty sampling coupled directly to DFT. These results, in excellent agreement with experiments and previous theoretical work, are compared to previous simulations in order to explore the sensitivity of the PES (and therefore MD) to the choice of exchange and correlation functional. Despite having a lower energetic corrugation in our PES, we obtain a broader reaction probability curve than previous simulations, which is attributed to increased geometric corrugation in the PES and the effect of nonparallel dissociation pathways.     

Amine‐Directed Hydrogen‐Bonded Two‐Dimensional Supramolecular Structures

Utilizing pure amine hydrogen bonding is a novel approach for constructing two‐dimensional (2D) networks. Further, such systems are capable of undergoing structural modifications due to changes in pH. In this study, we designed a 2D network of triaminobenzene (TAB) molecules that by varying the pH from neutral to acidic, form either ordered or disordered structures on Au(111) surface as revealed in scanning tunneling microscopy images. In near‐neutral solution (pH ≈5.5), protonation of TAB generates charged species capable of forming H‐bonds between amine groups of neighboring molecules resulting in the formation of a 2D supramolecular structure on the electrified surface. At lower pH, due to the protonation of the amine groups, intermolecular hydrogen bonding is no longer possible and no ordered structure is observed on the surface. This opens the possibility to employ pH as a chemical trigger to induce a phase transition in the 2D molecular network of triaminobenzene molecules.     

Substrate-Independent Magnetic Bistability in Monolayers of the Single-Molecule Magnet Dy2ScN@C80 on Metals and Insulators

Magnetic hysteresis is demonstrated for monolayers of the single-molecule magnet (SMM) Dy₂ScN@C₈₀ deposited on Au(111), Ag(100), and MgO|Ag(100) surfaces by vacuum sublimation. The topography and electronic structure of Dy₂ScN@C₈₀ adsorbed on Au(111) were studied by STM. X-ray magnetic CD studies show that the Dy₂ScN@C₈₀ monolayers exhibit similarly broad magnetic hysteresis independent on the substrate used, but the orientation of the Dy₂ScN cluster depends strongly on the surface. DFT calculations show that the extent of the electronic interaction of the fullerene molecules with the surface is increasing dramatically from MgO to Au(111) and Ag(100). However, the charge redistribution at the fullerene-surface interface is fully absorbed by the carbon cage, leaving the state of the endohedral cluster intact. This Faraday cage effect of the fullerene preserves the magnetic bistability of fullerene-SMMs on conducting substrates and facilitates their application in molecular spintronics.     

Adlayer structures of aza- and/or oxo-bridged calix[2]arene[2]triazines on Au(111) investigated by scanning tunneling microscopy (STM)

The adlayers formed by a series of aza- and/or oxo-bridged calix[2]arene[2]triazines on Au(111) surfaces were investigated by scanning tunneling microscopy (STM) and density functional theory (DFT) calculations. 1,3-Alternate configurations of these molecules are preserved on gold surfaces as in their three-dimensional crystals. STM images show that the cavity sizes of these molecules are finely tuned by substituting the bridging nitrogen atom with oxygen atoms, which change the strengths and densities of the intermolecular hydrogen bonds. Hydrogen bond interaction influences the molecular orientation and conformation in the adlayers, and it plays a key role in the formation of these two-dimensional supramolecular architectures. Coadsorption of calix[2]arene[2]triazine with 1,3,5-tris(5-carboxyamyloxy)benzene (TCAB) intervenes with the intermolecular hydrogen bond formations among the calix[2]arene[2]triazine molecules and consequently causes a conformational transition of the calixarene molecules from rhombic to square. These results demonstrate the role of hydrogen bonds in molecular assembly formations.     

Fabrication of surface-supported low-dimensional polyimide networks

Interest in thermal and chemical stability of surface-supported organic networks has stimulated recent attempts to covalently interlink adsorbed molecular species into extended nanostructures. We show, using low-temperature scanning tunneling microscopy, that imidization of anhydrides and amines adsorbed on Au(111) can be thermally initiated under controlled ultrahigh vacuum conditions. Using two types of amine-functionalized polyphenyl molecules together with the organic semiconductor PTCDA, monolayer thick linear polymeric strands and a porous polymeric network with nanoscale dimensions are obtained.     

Coexistence of one- and two-dimensional supramolecular assemblies of terephthalic acid on Pd(111) due to self-limiting deprotonation

The adsorption of terephthalic acid [C(6)H(4)(COOH)(2), TPA] on a Pd(111) surface has been investigated by means of scanning tunneling microscopy (STM), x-ray photoelectron spectroscopy, and near-edge x-ray absorption fine structure spectroscopy under ultrahigh vacuum conditions at room temperature. We find the coexistence of one- (1D) and two-dimensional (2D) molecular ordering. Our analysis indicates that the 1D phase consists of intact TPA chains stabilized by a dimerization of the self-complementary carboxyl groups, whereas in the 2D phase, consisting of deprotonated entities, the molecules form lateral ionic hydrogen bonds. The supramolecular growth dynamics and the resulting structures are explained by a self-limiting deprotonation process mediated by the catalytic activity of the Pd surface. Our models for the molecular ordering are supported by molecular mechanics calculations and a simulation of high resolution STM images.