Identifying Molecular Species on Surfaces by Scanning Tunneling Microscopy: Methyl Pyruvate on Pd(111)

The structures of low coverages of methyl pyruvate on a Pd(111) surface at 120 K were studied using scanning tunneling microscopy in ultrahigh vacuum. The experimentally observed images were assigned to adsorbate structures using a combination of density functional theory calculations and by simulating the images using the Bardeen method. Two forms of methyl pyruvate were identified. The first, previously found using reflection–absorption infrared spectroscopy, was a flat-lying, keto form of <i>cis</i>-methyl pyruvate. It was characterized by elongated, two-lobed images with the long axes of the images oriented at ∼0 and ∼30° to the close-packed directions. The structure was simulated using clean, CO- and methyl-functionalized gold tips, and the simulated images agreed well with those found experimentally. The simulated structures were not strongly dependent on the tip structure or tip bias. This approach was used to identify the nature of the second species as the enol form of <i>cis</i>-methyl pyruvate with the carbonyl groups located over atop and bridge sites. Again, the orientation of the image with respect to the underlying Pd(111) lattice as well as the calculated image shape agreed well with the experimental images

Formation of Chiral Self-Assembled Structures of Amino Acids on Transition-Metal Surfaces: Alanine on Pd(111)

The structure and self-assembly of alanine on Pd(111) is explored using X-ray photoelectron spectroscopy (XPS), low-energy electron diffraction (LEED), reflection–absorption infrared spectroscopy (RAIRS), and scanning tunneling microscopy (STM), and supplemented by density functional theory (DFT) calculations to explore the stability of the proposed surface structures formed by adsorbing alanine on Pd(111) and to simulate the STM images. Both zwitterionic and anionic species are detected using RAIRS and XPS, while DFT calculations indicate that isolated anionic alanine is significantly more stable than the zwitterion. This observation is rationalized by observing dimeric species when alanine is dosed at ∼270 K and then cooled to trap metastable surface structures. The dimers form due to an interaction between the carboxylate group of anionic alanine with the NH₃⁺ group of the zwitterion. Adsorbing alanine at 290 K results in the formation of dimer rows and tetramers resulting in only short-range order, consistent with the lack of additional diffraction spots in LEED. The stability of various structures is explored using DFT, and the simulated STM images are compared with experiment. This enables the dimer rows to be assigned to the assembly of anionic-zwitterionic dimers and the tetramer to the assembly of two dimers in which three of the alanine molecules undergo a concerted rotation by 30°