The role of gold adatoms in the electronic and structural properties of supramolecular architectures at Au(111) surfaces

This thesis is focused on the computational characterization of the atomic scale properties of supramolecular structures at surfaces by means of ab-initio density-functional theory (DFT) techniques, and proceed in parallel with the experimental activity of the Low Temperature Scanning Tunneling Microscopy (LT-STM) group at the IOM-CNR TASC Laboratory. In particular, the different roles played by native gold adatoms in the self-assembly of various molecular structures has been deeply analysed

Toward fractioning of isomers through binding-induced acceleration of azobenzene switching

The E/Z isomerization process of a uracil-azobenzene derivative in which the nucleobase is conjugated to a phenyldiazene tail is studied in view of its ability to form triply-H-bonded complexes with a suitably complementary 2,6-diacetylamino-4-pyridine ligand. UV-Vis and 1H-NMR investigations of the photochemical and thermal isomerization kinetics show that the thermal Z→E interconversion is four-fold accelerated upon formation of the H-bonded complex. DFT calculations show that the formation of triple H-bonds triggers a significant elongation of the N=N double bond, caused by an increase of its πg∗ antibonding character. This results in a reduction of the N=N torsional barrier and thus in accelerated thermal Z→E isomerization. Combined with light controlled E→Z isomerization this enables controllable fractional tuning of the two configurational isomers

Binary Conformational Switches in a Porphyrin Chain: Tautomerization and Stereoisomerization

In the last decade, hydrogen (H-)tautomerization, that is, a reaction that involves simple intramolecular proton transfer, has been studied in single phthalocyanine, porphyrin, and porphycene derivatives as a prototypical single molecular conductance switch. Here, by means of low-temperature scanning tunneling microscopy and density functional theory calculations, we report a binary H-tautomerism and stereoisomeric conformational switch in (amino-functionalized) porphyrins assembled in molecular chains on a gold surface. We show that the formation of the chain is crucial for the binary tautomeric switch mechanism as the single molecule switches differently. Our findings suggest that the (amino-)functionalization of molecules can be exploited not only to drive the formation of molecular self-assemblies but also to steer their switching properties

Bifunctional Behavior of a Porphyrin in Hydrogen-Bonded Donor–Acceptor Molecular Chains on a Gold Surface

Peculiar hydrogen-bonded molecular chains are spontaneously created from the self-assembly on a gold surface of a porphyrin functionalized with four aromatic amine moieties. The molecular chains are formed by a sequence of dyads, where the same molecule behaves alternately as a hydrogen-bond acceptor or donor as a whole at all its four aromatic amino groups. This remarkable bifunctional behavior is due to the conformational flexibility of the functionalizing amino groups that switch from a planar, aniline-like conformation in donors to a pyramidal, amine-like one in acceptors. Furthermore, we show that the acceptor porphyrins can trap gold adatoms underneath their center. Combined scanning tunneling microscopy experiments and density functional theory calculations characterize the structural and electronic modifications suffered by such molecules to establish amino 12amino interactions. Notably, scanning tunneling spectroscopy measurements show that the highest occupied molecular orbital 12lowest unoccupied molecular orbital gaps of the acceptors and donors are, respectively, larger and smaller with respect to the isolated molecule according to the reduced extent of conjugation occurring in the acceptors. In summary, experimental and theoretical results reveal a remarkable hydrogen-bonded complex where the amino groups act as both hydrogen-bond donors and acceptors and suggest how hydrogen bonding can modify the geometrical and potentially also the electronic structures of highly conjugated molecules

CCDC 1474613: Experimental Crystal Structure Determination

Related Article: Rosaria Vulcano, Paolo Pengo, Simone Velari, Johan Wouters, Alessandro De Vita, Paolo Tecilla, Davide Bonifazi|2017|J.Am.Chem.Soc.|139|18271|doi:10.1021/jacs.7b09568,An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

CCDC 1435201: Experimental Crystal Structure Determination

Related Article: Rosaria Vulcano, Paolo Pengo, Simone Velari, Johan Wouters, Alessandro De Vita, Paolo Tecilla, Davide Bonifazi|2017|J.Am.Chem.Soc.|139|18271|doi:10.1021/jacs.7b09568,An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

CCDC 1435200: Experimental Crystal Structure Determination

Related Article: Rosaria Vulcano, Paolo Pengo, Simone Velari, Johan Wouters, Alessandro De Vita, Paolo Tecilla, Davide Bonifazi|2017|J.Am.Chem.Soc.|139|18271|doi:10.1021/jacs.7b09568,An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

CCDC 1435199: Experimental Crystal Structure Determination

Related Article: Rosaria Vulcano, Paolo Pengo, Simone Velari, Johan Wouters, Alessandro De Vita, Paolo Tecilla, Davide Bonifazi|2017|J.Am.Chem.Soc.|139|18271|doi:10.1021/jacs.7b09568,An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

Trapping of Charged Gold Adatoms by Dimethyl Sulfoxide on a Gold Surface

10siWe report the formation of dimethyl sulfoxide (DMSO) molecular complexes on Au(111) enabled by native gold adatoms unusually linking the molecules via a bonding of ionic nature, yielding a mutual stabilization between molecules and adatom(s). DMSO is a widely used polar, aprotic solvent whose interaction with metal surfaces is not fully understood. By combining X-ray photoelectron spectroscopy, low temperature scanning tunneling microscopy, and density functional theory (DFT) calculations, we show that DMSO molecules form complexes made by up to four molecules arranged with adjacent oxygen terminations. DFT calculations reveal that most of the observed structures are accurately reproduced if, and only if, the negatively charged oxygen terminations are linked by one or two positively charged Au adatoms. A similar behavior was previously observed only in nonstoichiometric organic salt layers, fabricated using linkage alkali atoms and strongly electronegative molecules. These findings suggest a motif for anchoring organic adlayers of polar molecules on metal substrates and also provide nanoscale insight into the interaction of DMSO with gold.partially_openembargoed_20160616Feng, Zhijing; Velari, Simone; Cossaro, Albano; Castellarin-Cudia, Carla; Verdini, Alberto; Vesselli, Erik; Dri, Carlo; Peressi, Maria; De Vita, Alessandro; Comelli, GiovanniFeng, Zhijing; Velari, Simone; Cossaro, Albano; Castellarin Cudia, Carla; Verdini, Alberto; Vesselli, Erik; Dri, Carlo; Peressi, Maria; DE VITA, Alessandro; Comelli, Giovann