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Visualizing vibrational normal modes of a single molecule with atomically confined light


The internal vibrations of molecules drive the structural transformations that underpin chemistry and cellular function. While vibrational frequencies are measured by spectroscopy, the normal modes of motion are inferred through theory because their visualization would require microscopy with ångström-scale spatial resolution—nearly three orders of magnitude smaller than the diffraction limit in optics1. Using a metallic tip to focus light and taking advantage of the surface-enhanced Raman effect2 to amplify the signal from individual molecules, tip-enhanced Raman spectromicroscopy (TER-SM)3,4 reaches the requisite sub-molecular spatial resolution5, confirming that light can be confined in picocavities6,7,8,9,10 and anticipating the direct visualization of molecular vibrations11,12,13. Here, by using TER-SM at the precisely controllable junction of a cryogenic ultrahigh-vacuum scanning tunnelling microscope14,15,16, we show that ångström-scale resolution is attained at subatomic separation between the tip atom and a molecule in the quantum tunnelling regime of plasmons6,8,9,17. We record vibrational spectra within a single molecule, obtain images of normal modes and atomically parse the intramolecular charges and currents driven by vibrations. Our analysis provides a paradigm for optics in the atomistic near-field.

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Fig. 1: Confinement of TERS signal.
Fig. 2: Spectral variation and principal component analysis.
Fig. 3: Visualization of vibrational normal modes.
Fig. 4: Close-ups of TER-SM images and their simulations.

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Data availability

The data supporting the findings of this study are available within the paper. Experimental source data for Figs. 14 are provided with the paper.


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This research was supported by the NSF Center for Chemical Innovation dedicated to Chemistry at the Space-Time Limit (CHE-1414466). Theoretical calculations were performed on the UCI Greenplanet cluster system (CHE-0840513). We thank P. El-Khoury for advice on DFT calculations. We have benefited from discussions with L. Jensen, X. Chen and P. Liu.

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Nature thanks Eric Le Ru and the other anonymous reviewer(s) for their contribution to the peer review of this work.

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Authors and Affiliations



J.L. and K.T.C. carried out experimental work and data analysis. J.L. performed theoretical simulations. N.T. produced nanoscopically smooth silver tips and performed preliminary principal component analysis. J.L. and V.A.A. conceived and coordinated the project and authored the paper with input from all co-authors.

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Correspondence to Joonhee Lee or V. Ara Apkarian.

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Extended data figures and tables

Extended Data Fig. 1 Conformational transformation of CoTPP on Cu(100).

a, An imaging sequence starting at −0.5 V is followed by repeated scans at –12 mV. The size of the images is 35 × 35 Å2. The pressing scanning condition at −12 mV leads to planarity of the phenyl groups. b, Optimized geometry of a free CoTPP molecule and flat geometry of an adsorbed CoTPP molecule with artificially flattened phenyl rings. c, Lattice registry of the flat CoTPP and the marker CO molecule, which adsorbs on the copper on-top site.

Extended Data Fig. 2 Disappearance of the Kondo resonance.

The Kondo resonance observed on the saddled CoTPP adsorbed on the Au(111) surface disappears on the flat CoTPP adsorbed on the Cu(100) surface. The gap distances are set at 1 nA, +0.2 V and 1 nA, −0.2 V for Au and Cu, respectively.

Extended Data Fig. 3 Gap dependence of Raman intensity and vibrational frequency.

a, b, Measurements on cobalt (a) and pyrrole (b). Colour-coded vertical grid lines in the leftmost graph indicate vibrational modes analysed in terms of intensity and frequency shift in the middle and right panels, respectively. The extracted powers n from the curve fit (I = azn) are indicated in the corresponding colours.

Extended Data Fig. 4 Maps of omitted normal modes.

The modes presented here are extensively delocalized and do not yield unique assignments.

Extended Data Fig. 5 Dominance of Δαzz in the observed TERS.

Raman images of the 388-cm−1 mode, simulated using out-of-plane (zz) and in-plane (xx) polarizability differences, and the map of the xx component of the polarizability at equilibrium (α0,xx). The Δαzz component reproduces the experiment, whereas the Δαxx fails despite its large magnitude. The charge accumulation at the edges upon polarization is demonstrated in both Δαxx and α0,xx. This trend applies to all of the observed normal modes.

Extended Data Fig. 6 Vibrational Stark effect of the C–H stretch.

Evolution of the C–H stretch upon tuning of the integration window. The image size and resolution are 28 × 28 Å2 and 80 × 80 pixels, respectively. Images are low-pass-filtered for clarity.

Extended Data Fig. 7 Schematic diagram for the resolution of near-field optical microscopy.

a, Local electric field along the z axis, Ez, arising from a charge. Only the z component is considered because in-plane dipoles induced by tangential components are cancelled by their images in the metallic substrate. b, Comparison between the fourth power of the Coulomb field distribution (q = 1) and equivalent Gaussian with the associated FWHM value.

Extended Data Fig. 8 Selection rules of atomistic TERS.

Top right, orientationally averaged Raman spectrum of the free molecule. The intensities of the selected vibrational modes shown in Fig. 3 are indicated by red dots and dashed lines. Bottom right, atomic polarizability differences and their colour-coded amplitudes in atomic units. The colour represents the phase of the out-of-plane atomic dynamic dipole associated with \({\alpha }_{zz}^{i}\). Left, while a nonlocal excitation leads to the cancellation of induced dipoles (top), the atomistic near field samples each radiating vertical dipole that is reinforced by its image (bottom). h0 and σ0 are Rayleigh length and waist, respectively, as defined in ‘Gaussian optics’ in Methods.

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Lee, J., Crampton, K.T., Tallarida, N. et al. Visualizing vibrational normal modes of a single molecule with atomically confined light. Nature 568, 78–82 (2019).

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