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We present a combined multimethod experimental and theoretical study of the geometric and electronic properties of Co-tetraphenyl-porphyrin ?Co-TPP? molecules adsorbed on a Ag?111? surface. Scanning tunnel- ing microscopy ?STM? topographs reveal that Co-TPP forms highly regular arrays with a square unit cell. Hereby, the Co-TPP molecules do not occupy a unique adsorption site on the Ag?111? atomic lattice. The central Co atom of the Co-TPP is found to reside predominantly above fcc and hcp hollow sites of the substrate, as determined from the photoelectron diffraction patterns. A strong adsorption-induced deformation of Co-TPP involving a saddle-shaped macrocycle is evidenced by high-resolution STM images and quantified by near-edge x-ray absorption fine-structure measurements. By scanning tunneling spectroscopy we resolved discrete molecular electronic states and mapped the pertaining spatial charge-density distribution. Specifically, we discuss the interaction of orbitals originating from the Co-metal center with the porphyrin macrocycle and show that the varying adsorption sites induce a modulation in the Co-TPP lowest unoccupied molecular orbital. These findings are corroborated by density-functional-theory calculations.

The self-assembly of the amino acid L-methionine on Cu(111) was investigated under ultrahigh vacuum (UHV) conditions by scanning tunneling microscopy (STM), helium atom scattering (HAS) and X-ray photoelectron spectroscopy (XPS). The system is strongly influenced by the Substrate reactivity and the deposition temperature. The STM and HAS structural analysis yields that, for temperatures below 273 K, the biomolecules assemble in strings oriented with an angle of - 10 degrees with respect to the < 110 > axes of the substrate. For temperatures above 283 K, a regular and ordered one-dimensional (1D) phase arises following an angle of + 10 degrees with respect to the same directions. High resolution STM data of this ordered 1D arrangement evidence molecular dimerization and dimer alignment into ordered chains which are commensurate with the Cu(111) atomic lattice. XPS measurements reveal that the high temperature ordered phase consists of an exclusively anionic ensemble with a deprotonated carboxylic group and a neutral amino group, while the low temperature phase is heterogeneously composed of both zwitterionic and anionic species, depending on whether the molecules are immobilized in clusters of dimers on the free terraces or at the low-coordinated adsorption sites of the Substrate step-edges. These combined results evidence a structural transformation of the supramolecular assembly which is triggered by a thermally activated process involving the underlying Cu(111) substrate and which carries the intrinsic chiral signature of the adsorbed molecular units.

The engineering of complex architectures from functional molecules on surfaces provides new pathways to control matter at the nanoscale. In this article, we present a combined study addressing the self-assembly of the amino acid l -methionine on Ag(111). Scanning tunneling microscopy data reveal spontaneous ordering in extended molecular chains oriented along high-symmetry substrate directions. At intermediate coverages, regular biomolecular gratings evolve whose periodicity can be tuned at the nanometer scale by varying the methionine surface concentration. Their characteristics and stability were confirmed by helium atomic scattering. X-ray photoemission spectroscopy and high-resolution scanning tunneling microscopy data reveal that the l -methionine chaining is mediated by zwitterionic coupling, accounting for both lateral links and molecular dimerization. This methionine molecular recognition scheme is reminiscent of sheet structures in amino acid crystals and was corroborated by molecular mechanics calculations. Our findings suggest that zwitterionic assembly of amino acids represents a general construction motif to achieve biomolecular nanoarchitectures on surfaces.