Bicomponent hydrogen-bonded nanostructures formed by two complementary molecular Landers on Au(111) (original) (raw)
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Acs Nano, 2010
Supramolecular self-assembly on surfaces, guided by hydrogen bonding interactions, has been widely studied, most often involving planar compounds confined directly onto surfaces in a planar twodimensional (2-D) geometry and equipped with structurally rigid chemical functionalities to direct the selfassembly. In contrast, so-called molecular Landers are a class of compounds that exhibit a pronounced threedimensional (3-D) structure once adsorbed on surfaces, arising from a molecular backboard equipped with bulky groups which act as spacer legs. Here we demonstrate the first examples of extended, hydrogen-bonded surface architectures formed from molecular Landers. Using high-resolution scanning tunnelling microscopy (STM) under well controlled ultrahigh vacuum conditions we characterize both one-dimensional (1-D) chains as well as five distinct long-range ordered 2-D supramolecular networks formed on a Au(111) surface from a specially designed Lander molecule equipped with dual diamino-triazine (DAT) functional moieties, enabling complementary NH · · · N hydrogen bonding. Most interestingly, comparison of experimental results to STM image calculations and molecular mechanics structural modeling demonstrates that the observed molecular Lander-DAT structures can be rationalized through characteristic intermolecular hydrogen bonding coupling motifs which would not have been possible in purely planar 2-D surface assembly because they involve pronounced 3-D optimization of the bonding configurations. The described 1-D and 2-D patterns of Lander-DAT molecules may potentially be used as extended molecular molds for the nucleation and growth of complex metallic nanostructures.
Adsorption behavior of Lander molecules on Cu(110) studied by scanning tunneling microscopy
The Journal of Chemical Physics, 2002
The adsorption of a large organic molecule, named Lander, has been studied on a Cu͑110͒ substrate by scanning tunneling microscopy ͑STM͒. At low temperatures three different conformations of the molecule are observed on the flat surface terraces. At room temperature the Lander molecules are highly mobile and anchor preferentially to step edges. There the molecules cause a rearrangement of the Cu step atoms leading to the formation of Cu nanostructures that are adapted to the dimension of the molecule, as revealed directly by STM manipulation experiments. Upon annealing to 500 K the molecules order at higher coverages partially into small domains. In all cases the exact adsorption conformation of the molecules was identified through an interplay with elastic scattering quantum chemistry calculations.
H-bonding supramolecular assemblies of PTCDI molecules on the Au (111) surface
2009
Using a combination of scanning tunneling microscopy (STM) in ultrahigh vacuum (UHV) and a systematic theoretical method based on considering all possible hydrogen bond connections between molecules with subsequent density functional theory (DFT) calculations, we studied supramolecular assemblies of highly symmetrical rectangular PTCDI molecules on the Au(111) surface. We show, using a systematic prediction procedure followed by ab initio density functional calculations, that just over 10 monolayer structures are possible assuming two molecules in the primitive cell, some of which would appear indistinguishable in the STM images. By breaking down these structures into distinct assemblies, we predict six possible phases. Two of these had been observed previously: a canted phase seen on a number of surfaces including Au(111) and a brick wall phase seen so far only on the NaCl(001) surface. Using STM imaging of PTCDI molecules on the Au(111) surface in ultrahigh vacuum, we discovered a completely new "domino" phase, also predicted by our theory, in which molecules attach to each other rather like dominoes, to form squares repeated periodically across the surface. The interaction of the molecules with the gold surface seems to influence the orientation of the phases but not necessarily their stability.
Physical Chemistry Chemical Physics, 2010
The self-assembly of flat organic molecules on metal surfaces is controlled, apart from the kinetic factors, by the interplay between the molecule-molecule and molecule-surface interactions. These are typically calculated using standard density functional theory within the generalized gradient approximation, which significantly underestimates nonlocal correlations, i.e. van der Waals (vdW) contributions, and thus affects interactions between molecules and the metal surface in the junction. In this paper we address this question systematically for the Au(111) surface and a number of popular flat organic molecules which form directional hydrogen bonds with each other. This is done using the recently developed first-principles vdW-DF method which takes into account the nonlocal nature of electron correlation [M. Dion et al., Phys. Rev. Lett. 2004, 92, 246401]. We report here a systematic study of such systems involving completely self-consistent vdW-DF calculations with full geometry relaxation. We find that the hydrogen bonding between the molecules is only insignificantly affected by the vdW contribution, both in the gas phase and on the gold surface. However, the adsorption energies of these molecules on the surface increase dramatically as compared with the ordinary density functional (within the generalized gradient approximation, GGA) calculations, in agreement with available experimental data and previous calculations performed within approximate or semiempirical models, and this is entirely due to the vdW contribution which provides the main binding mechanism. We also stress the importance of self-consistency in calculating the binding energy by the vdW-DF method since the results of non-self-consistent calculations in some cases may be off by up to 20%. Our calculations still support the usually made assumption of the molecule-surface interaction changing little laterally suggesting that single molecules and their small clusters should be quite mobile at room temperature on the surface. These findings support a gas-phase modeling for some flat metal surfaces, such as Au(111), and flat molecules, at least as a first approximation.
The Journal of Physical Chemistry B, 2004
The adsorption and ordering of the molecule terephthalic acid (TPA), 1,4-benzene-dicarboxylic acid C 6 H 4 -(COOH) 2 , on the reconstructed Au(111) surface has been studied in situ in ultrahigh vacuum by scanning tunneling microscopy (STM) at room temperature. Two-dimensional (2D) self-assembled supramolecular domains evolve, wherein the well-known one-dimensional (1D) carboxyl H-bond pairing scheme is identified. Since the individual molecules occupy a distinct adsorption site and the supramolecular ordering usually extends over several substrate reconstruction domains, a significant variation in hydrogen bond lengths is encountered, which illustrates the versatility of hydrogen bridges in molecular engineering at surfaces. Ab initio calculations for a 1D H-bonded molecular chain provide insight into the limited geometric response of the molecules in different local environments.
Adsorption structures and energetics of molecules on metal surfaces: Bridging experiment and theory
Progress in Surface Science, 2016
Adsorption geometry and stability of organic molecules on surfaces are key parameters that determine the observable properties and functions of hybrid inorganic/organic systems (HIOSs). Despite many recent advances in precise experimental characterization and improvements in first-principles electronic structure methods, reliable databases of structures and energetics for large adsorbed molecules are largely amiss. In this review, we present such a database for a range of molecules adsorbed on metal single-crystal surfaces. The systems we analyze include noble-gas atoms, conjugated aromatic molecules, carbon nanostructures, and heteroaromatic compounds adsorbed on five different metal surfaces. The overall objective is to establish a diverse benchmark dataset that enables an assessment of current and future electronic structure methods, and motivates further experimental studies that provide ever more reliable data. Specifically, the benchmark structures and energetics from experiment are here compared with the recently developed van der Waals (vdW) inclusive density-functional theory (DFT) method, DFT+vdW surf. In comparison to 23 adsorption heights and 17 adsorption energies from experiment we find a mean average deviation of 0.06Å and 0.16 eV, respectively. This confirms the DFT+vdW surf method as an accurate and efficient approach to treat HIOSs. A detailed discussion identifies remaining challenges to be addressed in future development of electronic structure methods, for which the here presented benchmark database may serve as an important reference. CONTENTS 10 B. Benzene on Pt(111) 11 C. Naphthalene on Ag(111) 11 D. Naphthalene on Cu(111) 11 E. Naphthalene on Pt(111) 12 VIII. Extended and Compacted Carbon Systems on Metal Surfaces 12 A. DIP on Cu(111), Ag(111), and Au(111) 12
Chirality at two-dimensional surfaces: A perspective from small molecule alcohol assembly on Au(111)
The delicate balance between hydrogen bonding and van der Waals interactions determine the stability, structure and chirality of many molecular and supramolecular aggregates weakly adsorbed on solid surfaces. Yet the inherent complexity of these systems makes their experimental study at the molecular level very challenging. In this quest, small alcohols adsorbed on metal surfaces have become a useful model system to gain fundamental insight into the interplay of such molecule-surface and molecule-molecule interactions. Here, through a combination of scanning tunneling microscopy and density functional theory, we compare and