Capturing a Molecule’s Infrared Fingerprint with Scanning Tunneling Microscopy

Researchers at the University of California San Diego, led by Assistant Professor Shaowei Li, have developed a method to measure the vibrational spectrum of a single molecule using infrared light integrated with scanning tunneling microscopy. The technique, described in the journal Science, brings infrared spectroscopy into the single molecule regime and offers a new way to study how energy flows through chemical bonds at the nanoscale.

Liang, K., Wang, Z., Quan, W., Shi, Y., Zhou, H., Bi, L., Yin, Z., Romero, N., Young, M., & Li, S. (2026). Single-molecule infrared spectroscopy with scanning tunneling microscopy. Science, 391(6787), 807–811. https://doi.org/10.1126/science.adz6643

Infrared spectroscopy has long been one of the most widely used tools in chemistry. Molecules absorb infrared radiation at frequencies that correspond to specific bond vibrations. These vibrational signatures function as fingerprints, allowing chemists to identify chemical structures and probe interactions. However, traditional infrared spectroscopy measures signals from large ensembles of molecules. Even the most sensitive instruments typically require millions or more molecules to produce a detectable response.

Assistant Professor Shaowei Li from University of California San Diego stated,

“Infrared spectroscopy is one of our most powerful tools, but until now it has always been an ensemble technique. This gives us a way to see, at the most fundamental level, how vibrational energy couples to molecular motion.”

The UC San Diego team addressed this limitation by combining infrared excitation with scanning tunneling microscopy, or STM. STM is known for its ability to image and manipulate individual atoms and molecules by measuring the quantum tunneling current between a sharp metal tip and a conductive surface. By integrating infrared light into the STM setup, the researchers created what they call infrared integrated scanning tunneling microscopy, abbreviated as IRiSTM.

The concept is straightforward but technically demanding. When a molecule adsorbed on a surface is illuminated with infrared light, its chemical bonds can absorb energy and begin to vibrate. These vibrations subtly influence the electronic structure of the molecule and therefore the tunneling current measured by the STM tip. By monitoring changes in the tunneling signal while sweeping the infrared frequency, the team could detect vibrational resonances from a single molecule.

This approach effectively converts vibrational absorption into an electrical signal that can be read at the atomic scale. Instead of measuring bulk infrared absorption through transmitted or reflected light, the technique senses how vibrational excitation alters electron tunneling at one specific location.

Capturing the vibrational spectrum of an individual molecule is more than a technical milestone. It enables researchers to observe how local environments influence molecular behavior. In conventional measurements, variations across a sample are averaged out. Surface defects, neighboring molecules, and nanoscale heterogeneity are masked by ensemble statistics. With IRiSTM, it becomes possible to examine one molecule at a time and compare how identical chemical structures behave under slightly different local conditions.

The team demonstrated the method by probing molecules adsorbed on conductive substrates under controlled conditions. By correlating the infrared frequency with changes in the tunneling current, they reconstructed vibrational spectra that align with known molecular fingerprints. Computational modeling supported the interpretation of the signals and helped clarify how vibrational energy couples to electronic states in the tunneling junction.

One of the long term goals in chemistry is to direct reactions by selectively exciting specific bonds. If energy can be delivered to a targeted vibrational mode, it may be possible to bias reaction pathways at the molecular level. While such control remains a complex challenge, single molecule infrared spectroscopy provides a clearer picture of how vibrational energy is distributed and dissipated.

The integration of optical excitation with scanning probe techniques has been explored before, but combining infrared light with STM at the single molecule level required careful engineering. The setup had to deliver stable infrared illumination without compromising the sensitivity of the tunneling measurement. Thermal drift, tip stability, and background noise all become critical factors when detecting signals from one molecule.

Reports accompanying the publication highlight the broader context of nanoscale spectroscopy. Advances in tip enhanced Raman spectroscopy and other scanning probe optical methods have steadily pushed spatial resolution downward. The UC San Diego approach extends that trajectory into the infrared regime, where many biologically and chemically relevant vibrations occur.

From a research perspective, the implications extend into catalysis, surface chemistry, and molecular electronics. Catalytic reactions often occur at specific sites on surfaces where local atomic arrangements influence reactivity. Being able to record vibrational spectra from individual adsorbed molecules could clarify how active sites differ from their surroundings. Similarly, in molecular electronics, understanding how vibrational modes couple to charge transport is central to device performance.

The technique also reinforces the trend toward hybrid instrumentation. Modern analytical platforms increasingly combine optical, electronic, and computational elements. Rather than relying on a single detection principle, researchers integrate complementary approaches to overcome sensitivity limits.

Although the current work was conducted under controlled laboratory conditions, further refinement could expand its accessibility. Improvements in infrared sources, detector sensitivity, and probe stability may help transition the method from specialized setups to broader adoption in surface science laboratories.

For now, the study demonstrates that infrared spectroscopy need not remain confined to ensemble measurements. By merging light based excitation with atomic scale electrical detection, the researchers have shown that the vibrational signature of a single molecule can be measured directly. In practical terms, this provides chemists with a tool to investigate molecular structure and energy flow at a resolution that was previously out of reach.

As nanoscale characterization continues to evolve, techniques like IRiSTM suggest that traditional analytical boundaries can be reconsidered. Infrared spectroscopy, once defined by bulk measurements, now extends to the scale of a single molecular voice.