Towards the FAIRification of Scanning Tunneling Microscopy Images

In this paper,we describe the data management practices and services developed for making FAIR compliant a scientific archive of Scanning Tunneling Microscopy(STM)images.As a first step,we extracted the instrument metadata of each image of the dataset to create a structured database.We then enriched these metadata with information on the structure and composition of the surface by means of a pipeline that leverages human annotation,machine learning techniques,and instrument metadata filtering.To visually explore both images and metadata,as well as to improve the accessibility and usability of the dataset,we developed"STM explorer"as a web service integrated within the Trieste Advanced Data services(TriDAS)website.On top of these data services and tools,we propose an implementation of the W3C PROV standard to describe provenance metadata of STM images.

Direct Imaging of Molecular Orbitals of Metal Phthalocyanines on Metal Surfaces with an O2-Functionalized Tip of a Scanning Tunneling Microscope

High-resolution scanning tunneling microscope images of iron phthalocyanine and zinc phthalocyanine molecules on Au（111） have been obtained using a functionalized tip of a scanning tunneling microscope （STM）, and show rich intramolecular features that are not observed using clean tips. Ab initio density functional theory calculations and extended Huckel theory calculations revealed that the imaging of detailed electronic states is due specifically to the decoration of the STM tip with O2. The detailed structures are differentiated only when interacting with the highly directional orbitals of the oxygen molecules adsorbed on a truncated, [111]-oriented tungsten tip. Our results indicate a method for increasing the resolution in generic scans and thus, have potential applications in fundamental research based on high-resolution electronic states of molecules on metals, concerning, for example, chemical reactions, and catalysis mechanisms.

Sub-molecular features of single proteins in solution resolved with scanning tunneling microscopy

Scanning tunneling microscopy (STM) can be used to image individual biological molecules, such as proteins, in vacuum or air. This requires sample dehydration and thus may not reflect the native state of the molecule. Extensive efforts have been made to image single proteins in solution using STM; however, the images have revealed only round or oval shapes with no sub-molecular details. Here, we present the sub-molecular features of streptavidin proteins under physiological conditions using a homebuilt low-leakage-current and highstability liquid phase STM. The N-lobe, C-lobe, and C-terminal tail of the epidermal growth factor receptor kinase domains were also resolved in solution. Our results demonstrate that the structure, morphology, and dynamics of a protein molecule can be examined under physiological conditions by the STM. [Figure not available: see fulltext.] © 2016, Tsinghua University Press and Springer-Verlag Berlin Heidelberg.