A quantitative approach to hydrogen bonding at a metal surface

Discarding metal incorporation in pyrazole macrocycles and the role of the substrate on single-layer assemblies

Pyrazole derivatives are key in crystal engineering and liquid crystal fields and thrive in agriculture, pharmaceutical, or biomedicine industries. Such versatility relies in their supramolecular bond adaptability when forming hydrogen bonds or metal-pyrazole complexes. Interestingly, the precise structure of pyrazole-based macrocycles forming widespread porous structures is still unsolved. We bring insight into such fundamental question by studying the self-assembled structures of a bis-pyrazole derivative sublimed in ultra-high-vacuum conditions (without solvents) onto the three (111) noble metal surfaces. By means of high-resolution scanning tunneling microscopy that is validated by gas phase density functional theory calculations, we find a common hexagonal nanoporous network condensed by triple hydrogen bonds at the molecule-metal interface. Such assembly is disrupted and divergent after annealing: (i) on copper, the molecular integrity is compromised leading to structural chaos, (ii) on silver, an incommensurate new oblique structure requiring molecular deprotonation is found and, (iii) on gold, metal-organic complexes are promoted yielding irregular chain structures. Our findings confirm the critical role of these metals on the different pyrazole nanoporous structure formation, discarding their preference for metal incorporation into the connecting nodes whenever there is no solvent involved.

High-fidelity self-assembly of crystalline and parallel-oriented organic thin films by π-π stacking from a metal surface

Organic semiconductor applications will significantly benefit from atomically precise, cofacial stacking of extended π-conjugated molecular systems for efficient charge transport. Surface-assisted self-assembly of poly(hetero)cyclic molecules via donor-acceptor type π-π stacking is a promising strategy to organize functional, many-layered architectures. We have employed tris(N-phenyltriazole) as a model system to achieve molecular-level structural ordering through more than 20 molecular layers from its own metal-templated monolayer. Effective charge transport through such layers enabled molecular-resolution imaging by scanning tunneling microscopy. The structure and chemical composition of the films, grown on Ag(111) or Au(100), were further analyzed by noncontact atomic force microscopy and X-ray photoelectron spectroscopy, revealing a cofacial stacking geometry of the molecular layers. Scanning tunneling spectroscopy measurements show a decrease of the band gap with increasing film thickness, consistent with π-π stacking and electron delocalization. The present study provides new strategies for the fabrication of normally inaccessible structural motifs, atomic precision in organic films, and the effective conduction of electrons through multiple organic molecular stacks.

Steric blocking as a tool to control molecular film geometry at a metal surface

The application of steric blocking in surface science is exemplified by the control of surface patterns through the selective methylation of pentacenetetrone. Pentacenetetrones interact (with one another) on Cu(111) via intermolecular hydrogen bonding involving the carbonyl oxygen and the adjacent hydrogen atoms. Steric blocking of the intermolecular interaction by the successive insertion of inert methyl groups at terminal locations transforms a dense molecular pattern first into isolated double rows and eventually into single rows in a highly predictable fashion. Density functional theory modeling reveals the underlying energetics.

Do two-dimensional "noble gas atoms" produce molecular honeycombs at a metal surface?

Anthraquinone self-assembles on Cu(111) into a giant honeycomb network with exactly three molecules on each side. Here we propose that the exceptional degree of order achieved in this system can be explained as a consequence of the confinement of substrate electrons in the pores, with the pore size tailored so that the confined electrons can adopt a noble-gas-like two-dimensional quasi-atom configuration with two filled shells. Formation of identical pores in a related adsorption system (at different overall periodicity due to the different molecule size) corroborates this concept. A combination of photoemission spectroscopy with density functional theory computations (including van der Waals interactions) of adsorbate-substrate interactions allows quantum mechanical modeling of the spectra of the resultant quasi-atoms and their energetics.

Achieving chiral resolution in self-assembled supramolecular structures through kinetic pathways

Chiral phase transitions were studied in a self-assembled 2,6-dibromoanthraquinones supramolecular system prepared on Au(111) using scanning tunneling microscopy. As the molecules were deposited at about 150 K, they formed heterochiral chevron structures (a racemate) consisting of two alternating prochiral molecular rows. When the as-deposited sample was warmed to 300 K followed by cooling to 80 K, phase-separated homochiral structures (a conglomerate), as well as the chevron structures, were observed. We propose molecular models for the structures that are in good agreement with ab initio studies and can be explained by hydrogen bonds and halogen bonds. We found that heterochiral chevron structures were more stable than homochiral structures due to two additional [Formula: see text] halogen bonds per molecule. We considered kinetic pathways for the phase transitions that were made possible via a disordered liquid phase entropically stabilized at 300 K. We show how chiral resolution can be achieved by exploiting kinetic paths allowed in supramolecular systems.

Electrons, photons, and force: quantitative single-molecule measurements from physics to biology

Single-molecule measurement techniques have illuminated unprecedented details of chemical behavior, including observations of the motion of a single molecule on a surface, and even the vibration of a single bond within a molecule. Such measurements are critical to our understanding of entities ranging from single atoms to the most complex protein assemblies. We provide an overview of the strikingly diverse classes of measurements that can be used to quantify single-molecule properties, including those of single macromolecules and single molecular assemblies, and discuss the quantitative insights they provide. Examples are drawn from across the single-molecule literature, ranging from ultrahigh vacuum scanning tunneling microscopy studies of adsorbate diffusion on surfaces to fluorescence studies of protein conformational changes in solution.