Interplay between Hydrogen Bonding and Molecule–Substrate Interactions in the Case of Terephthalic Acid Molecules on Cu(001) Surfaces

Abstract

The adsorption and self-assembling properties of terephthalic acid (TPA) molecules deposited on Cu(001) at room temperature have been systematically studied with both experimental and theoretical tools. The system forms two phases at room temperature: the metastable β-phase and the stable (3 × 3) one. In the case of the β phase, low-energy electron diffraction and scanning tunneling microscopy (STM) results indicate that it has a (9√2 × 2√2) R45° unit cell with exactly the same molecular coverage as the (3 × 3) phase. In addition, the high-resolution X-ray photoelectron-spectroscopy spectra of the O 1s core level indicate that the irreversible β → (3 × 3) transition involves the following two processes: (i) deprotonation of the complete carboxyl groups remaining in the metastable phase and (ii) eventual rearrangement of the molecules into the 3 × 3 configuration. We explored possible molecular configurations for the β phase with different degree of deprotonation (including structures with Cu adatoms) by means of density functional theory calculations. Our theoretical results indicate the formation of strong bonds between the O atoms in carboxylates and the Cu atoms of the surface, which causes a bending of the molecules and a buckling of the first Cu layer. In the (3 × 3) phases, we show that the bending produces observable effects in the molecular STM images. Moreover, the strong interaction between the carboxylates and the Cu atoms at the step edges drives the reorientation of the surface steps along the ⟨100⟩ crystallographic directions.

Hydrogen-bonded clusters of 1, 1′-ferrocenedicarboxylic acid on Au(111) are initially formed in solution

“…In particular, molecules with more than one H-bond donor and/or acceptor can explore a rich configurational space with multiple local minima, potentially forming structures significantly different than those created when only a single synthon is present. [20][21][22][23][24] Here, we describe the deposition of ferrocenedicarboxylic acid (Fc(COOH) 2 ) from solution onto clean Au(111) surfaces. We have previously found that ferrocene with a single COOH group (FcCOOH) forms a variety of complex structures due to the combination of strong COOH-derived hydrogen bonding with C-H• • • O hydrogen bonding; these structures include a cyclic pentamer that assembles aperiodically at high surface coverage to make a two-dimensional quasicrystal.…”

Control of the deprotonation of terephthalic acid assemblies on Ag(111) studied by DFT calculations and low temperature scanning tunneling microscopy

“…Indeed, during our experiments, the intermolecular distances around the defects remain identical to those measured in the pristine lattice. Previous investigations on these molecules demonstrate that these defects are related to the partial deprotonation of the TPA 2,16,18 . Indeed, these latter are not due to the presence of a vacancy in the assembly but to a subtle modification of the contrast between two TPA.…”

“…These molecules are also able to form 2D metal-ligand coordination arrays for example with magnetic atoms such as the high-spin Fe(TPA) 4 assemblies obtained by Gambardella et al on Cu(100) surfaces and conducive to investigations concerning magnetic anisotropy 14 . On the same surface, different studies demonstrate the formation of three different lattices depending on the temperature of the metallic surface during molecule deposition, these networks being also linked to a partial or total deprotonation of TPA 2,15,16 . Recently, White et al use the same molecules on Cu(111) as a model system to study the well-known interplay between intermolecular and adsorbate-substrate interactions 17 .…”

Synthesis and self-association of dibenzothiophene derivatives for simulation of hydrogen bonding interaction in asphaltenes

“…Compounds containing -COOH groups can provide two hydrogen bonds, which are particularly promising and reliable in creating and maintaining surface order. The self-assembly aggregates formed in benzoic acid solutions depends on the number and relative placement of carboxylic acid groups (Lackinge and Heckl 2009;Clair et al 2004;Fuhr et al 2013;Heininger et al 2009;Ye et al 2007). The self-assembly of the derivatives of dibenzothiophene with carboxyl groups affects the physicochemical properties of asphaltenes.…”