Visual Scanning of the Chemical Structure of Single Molecules at Angstrom Resolution

Nanocavity plasmonic fields can create Raman images of molecular vibration for a visual system that can map the chemical structure of single-molecule.

This visual system has 0.1 nanometer (an angstrom) resolution.

They merge the images at several different vibration modes to generate the image with the chemical structure.

Arxiv has the full article.

Scanning Raman picoscopy (SRP) is the first optical microscopy technique that has the ability to visualize the vibrational modes of a molecule and to directly construct the structure of a molecule in real space. The protocol established in this proof-of-principle demonstration can be generalized to identify other molecular systems, and can become a more powerful tool with the aid of imaging recognition and machine learning techniques. The ability of such Ångström-resolved scanning Raman picoscopy techniques to determine the chemical structure of unknown molecules will undoubtedly arouse extensive interest of researchers in the fields of chemistry, physics, materials, biology and so on, and is expected to stimulate active research in the fields, as SRP develops into a mature and universal technology.

Above- Ångström-resolved Raman images of distinct vibrational modes for a single molecule by scanning Raman picoscopy. (a) Schematic of SRP technique. The nanocavity defined by the silver tip and substrate generates a strong and highly confined plasmonic field, which is used for the excitation and emission enhancement of the Raman signals from a single molecule. The STM topograph of a single target molecule adsorbed on Ag(100) is shown at the bottom (−0.02 V, 2 pA, 2.5 nm × 2.5 nm). (b) Typical Raman spectra acquired at representative positions labelled in (a): lobe (red), gap (green) and center (blue). The spectrum on the bare Ag surface is also shown in black, confirming the clean tip condition free of contamination

. Completing full molecular structure by
assembling bridging units and central metal atom. (a, b) SRP mapping images for the Raman peaks at 841 cm−1 (a) and 925 cm−1 (b), respectively. (c) Partially determined molecular structure including the bridging units. (d, e) SRP mapping images for the two low-wavenumber Raman peaks at 211 cm−1 (d) and 362 cm−1 (e), respectively. (f) Fully determined molecular structure of the Mg-porphine molecule. (g) Merged SRP image by overlaying four different image patterns shown on the right for the vibration modes at 211 cm−1, 841 cm−1, 1463 cm−1 and 3072 cm−1. (h) Artistic view of the Mg-porphine molecule showing how four colored “Legos” in (g) are assembled into a complete molecular structure, with pyrrole rings in red, pyrrole C−H bonds in yellow, bridging C−H bonds in green and central Mg atom in blue.

The strong spatial confinement of a nanocavity plasmonic field has made it possible to visualize the inner structure of a single molecule and even to distinguish its vibrational modes in real space. With such ever-improved spatial resolution, it is anticipated that full vibrational imaging of a molecule could be achieved to reveal molecular structural details. Here we demonstrate full Raman images of individual vibrational modes on the Ångström level for a single Mg-porphine molecule, revealing distinct characteristics of each vibrational mode in real space. Furthermore, by exploiting the underlying interference effect and Raman fingerprint database, we propose a new methodology for structural determination, coined as scanning Raman microscopy, to show how such ultrahigh-resolution spectromicroscopic vibrational images can be used to visually assemble the chemical structure of a single molecule through a simple Lego-like building process.

4 thoughts on “Visual Scanning of the Chemical Structure of Single Molecules at Angstrom Resolution”

  1. I think that water molecules are so fundamental to just about everything we are interested in that we need all the data we can get.

  2. A water molecule is too simple to bother with this technique. It’s symmetric with only one type of bond. A simple (non-scanning) Raman reading would do. You can find both the Raman spectrum and molecular structure of water online.

    What they’re measuring here are spectra at several points on the molecule. The image is reconstructed from that data. It’s not taken directly.

    edit: The images that are shown here are just mappings of individual frequencies in the Raman spectrum. They show how these individual frequencies change in intensity over the scanned area. Since each Raman frequency corresponds to a particular vibrational mode of the molecule, their spacial mappings correspond to the parts of the molecule where those vibrations occur.

    A water molecule should appear as a single water-shaped blob with little variation across the active frequencies. But then again, it might surprise us, so on 2nd thought, it may be worth a look after all.

  3. Looks like the limitation would be relatively flat molecules. Things like coiled proteins or cage structures could be difficult. But this still covers the vast majority of small molecules (smaller than a few hundred atoms or so; the molecule shown here has 37).

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