DOI: 10.5061/dryad.cfxpnvxmn
title: Single-molecule infrared spectroscopy with scanning tunneling microscopy

description: Probing vibrations at the single-molecule level is essential for achieving
 bond-specific chemical control. Here, we introduce a new measurement
 scheme that integrates frequency-tunable infrared excitation with scanning
 tunneling microscopy to characterize vibration-mediated nuclear motions of
 single molecules. We first validated the technique by monitoring the
 infrared-induced rotation of the ethynyl radical, and then applied it to
 pyrrolidine, mapping its conformational dynamics. The resulting broadband
 spectra captured fundamental vibrational modes together with rich overtone
 and combination bands inaccessible by conventional methods, confirmed with
 isotopic substitutions. Density functional theory calculations showed that
 delocalized modes coupled with pyrrolidine ring puckering drive the
 structural transition, revealing altered selection rules compared to
 traditional infrared spectroscopy. This new experimental platform enables
 probing of molecular vibrations and transformations with atomic precision.
description: # Single-molecule infrared spectroscopy with scanning tunneling microscopy
 Dataset DOI:
 [10.5061/dryad.cfxpnvxmn](https://doi.org/10.5061/dryad.cfxpnvxmn) ## Data
 overview This dataset contains raw and processed data supporting the
 manuscript **“Single-molecule infrared spectroscopy with scanning
 tunneling microscopy”**. The study introduces **Infrared Integrated
 Scanning Tunneling Microscopy (IRiSTM)** to characterize
 vibration-mediated nuclear motions of **single molecules**—specifically
 **ethynyl radicals** and **pyrrolidine**—on a Cu(100) surface. Included
 materials: * **Raw STM scans**: Nanonis `.sxm` * **Processed vibrational
 action/switching spectra & occupation metrics**: `.xlsx` * **Origin
 project for photocurrent mapping**: `.opju` * **Two archives**: home-built
 software + point-by-point raw IRiSTM datasets (`.zip`) Files are organized
 primarily by **manuscript figure number** and can be interpreted
 independently using the definitions below. ## Contents * [File
 organization](#file-organization) * [File formats and suggested
 software](#file-formats-and-suggested-software) * [Variable
 definitions](#variable-definitions) * [File list and
 descriptions](#file-list-and-descriptions) * [Figure 1](#figure-1) *
 [Figure 2](#figure-2) * [Figure 3](#figure-3) * [Figure 4](#figure-4) *
 [Figure 5](#figure-5) * [Archives](#archives) ## File organization * **By
 figure number (Fig. 1–5)**: figure-linked raw scans and processed
 numerical data. * **Archives**: software + raw point-by-point datasets
 used to generate IRiSTM spectra and analyses. ## File formats and
 suggested software | Format | What it contains | Suggested software |
 Notes | | ------- |
 ------------------------------------------------------------------------------------ | ----------------------------------------- | ------------------------------------------------------------------------------------------- | | `.sxm` | Raw STM scan data (topography + metadata) | Nanonis; **Gwyddion**; WSxM | Metadata includes scan size (nm), pixel resolution, sample bias (V), tunneling current (pA) | | `.xlsx` | Raw/processed numerical data (spectra, rates, occupation, time traces, photocurrent) | Excel; Google Sheets; home-built software | Data stored as numeric matrices without headers. (see details below) | | `.opju` | Photocurrent mapping plots/analysis (lock-in detection; Fig. 3) | OriginLab Origin | Contains 2D maps and topography used in Fig. 3D–F | | `.zip` | Code + raw point-by-point IRiSTM datasets | Standard archive utility (e.g., 7-Zip) | Included homebuilt software. | Open-source viewers: * Gwyddion: [http://gwyddion.net/](http://gwyddion.net/) * Origin Viewer (free): [https://www.originlab.com/viewer/](https://www.originlab.com/viewer/) ## Variable definitions ### 1) Spectra files (labeled “Rate” or “Spectra”) Processed spectra/occupation files typically contain three numeric columns. | Column | Variable | Units | Meaning | | ------ | ---------------------------------- | ----------------: | ------------------------------------------------------------------------- | | 1 | Wavenumber | cm⁻¹ | Incident infrared laser frequency (independent variable) | | 2 | Normalized switching/rotation rate | events / M pulses | Molecular events per 10⁶ laser pulses, normalized to constant photon flux | | 3 | 99% confidence interval (CI) | same as Col. 2 | Statistical uncertainty of rate measurement | **Normalization:** To account for wavelength-dependent photon flux, raw rates are normalized by the factor **λ~ref~** **/ λ** (where λ~ref~ = 6300 nm), so reported spectra correspond to a constant photon flux. ### 2) Occupation files (labeled “Occupation”) | Column | Variable | Units | Meaning | | ------ | ---------------------------- | -------------: | -------------------------------------------------------------------------- | | 1 | Wavenumber | cm⁻¹ | Incident infrared laser frequency | | 2 | High-state occupation ratio | unitless (0–1) | Fraction of time in “High” state: **t~High~** **/ (t~High~** **+ t~Low~)** | | 3 | 99% confidence interval (CI) | unitless | Statistical uncertainty of the occupation ratio | ### 3) Time traces (e.g., `Fig_1C.xlsx`) | Column | Variable | Units | Meaning | | ------ | ------------- | --------------------: | ---------------------------------------------------------- | | 1 | Time | s | Time axis | | 2 | Tip height ΔZ | as exported (pm or Å) | Vertical displacement of STM tip tracking molecular height | ### 4) Photocurrent spectra (e.g., `Fig_3C.xlsx`) | Column | Variable | Units | Meaning | | ------ | ----------------------------- | ----: | --------------------------------- | | 1 | Wavenumber | cm⁻¹ | Incident infrared laser frequency | | 2 | Lock-in detected photocurrent | pA | IR-modulated tunneling current | **Uncertainty key:** baseline lock-in fluctuations are **± 0.0304 pA** (99% CI, N = 50). ### 5) Origin Project File details (Fig_3C_Mapping.opju) This Origin project contains the **source 2D datasets (matrices)** and the **graph windows** used to generate **Figure 3D–F** (photocurrent mapping + reference topography). The project is organized into the following components. ### A. Data Matrices (2D gridded maps) Each matrix represents an image defined on a spatial grid. In all matrices below, **X and Y are lateral coordinates** and **Z is the mapped signal**. **Matrix 1 — Topography (STM reference image)** * **Internal name:** `MBook1` * **Meaning:** Constant-current STM topography used as the spatial reference for the photocurrent maps. * **Axes / units:** * **X, Y:** nm (spatial coordinates) * **Z:** m (topographic height; may be displayed in pm or Å depending on Origin settings) **Matrix 2 — Photocurrent (on resonance)** * **Internal name:** `with1685` * **Meaning:** Lock-in detected photocurrent map acquired **on resonance** (IR tuned to **5934 cm⁻¹**). * **Axes / units:** * **X, Y:** nm (spatial coordinates) * **Z:** A (lock-in detected current amplitude; convertible to pA via *I~pA~* ~=~  *I~A~* × 10^12^) **Matrix 3 — Photocurrent (off resonance)** * **Internal name:** `OffRwave1650` * **Meaning:** Lock-in detected photocurrent map acquired **off resonance** (IR tuned to **6060 cm⁻¹**). * **Axes / units:** * **X, Y:** nm (spatial coordinates) * **Z:** A (lock-in detected current amplitude; convertible to pA via *I~pA~* = *I~A~* × 10^12^) ### B. Graph Windows (visualizations stored in the project) **Graph 1 — Fig. 3D** * **Meaning:** 2D color map visualization of the **on-resonance** photocurrent matrix (`with1685`). * **Axes:** X (nm), Y (nm) * **Color scale:** lock-in detected current (A; optionally displayed as pA) **Graph 2 — Fig. 3E** * **Meaning:** 2D color map visualization of the **off-resonance** photocurrent matrix (`OffRwave1650`). * **Axes:** X (nm), Y (nm) * **Color scale:** lock-in detected current (A; optionally displayed as pA) **Export / reuse notes:** * Users can open `Fig_3C_Mapping.opju` in Origin/Origin Viewer and navigate to **Graph 1/2** to view the stored map visualizations. * Underlying matrices (`MBook1`, `with1685`, `OffRwave1650`) can be exported from Origin as ASCII/CSV for analysis outside Origin. ## File list and descriptions Files are named according to the corresponding Figure number in the main text. ### Figure 1 **Context:** Characterization of photo-induced rotation of single ethynyl (**C₂H**) radicals on Cu(100) among four equivalent adsorption sites. **Raw STM scans** * `Fig_1B_Down.sxm`: STM topographic scan (30 mV, 20 pA) showing ethynyl in “Down” orientation. * `Fig_1B_Left.sxm`: Ethynyl rotated to “Left” orientation. * `Fig_1B_Right.sxm`: Ethynyl rotated to “Right” orientation. * `Fig_1B_Up.sxm`: Ethynyl rotated to “Up” orientation. **Processed / source data** * `Fig_1C.xlsx`: Action (rotation) time trace for Fig. 1C. Discrete ΔZ steps indicate rapid rotation events under resonant C–H excitation. * `Fig_1D_C2D.xlsx`: Processed deuterated ethynyl (**C₂D**) IR spectra for Fig. 1D (rate vs wavenumber). Peaks correspond to C–D stretch and overtones. * `Fig_1D_C2H.xlsx`: Processed ethynyl (**C₂H**) IR spectra for Fig. 1D. Peaks include C–H stretch and overtones. ### Figure 2 **Context:** Conformational switching of pyrrolidine on Cu(100) between **“High” (axial)** and **“Low” (equatorial)** states. * `Fig_2B.sxm`: Raw STM image (20 mV, 20 pA) showing a large-area scan of pyrrolidine molecules. * `Fig_2F_Inset.sxm`: Raw STM data for the inset in Fig. 2F showing single-molecule topography. ### Figure 3 **Context:** Broadband vibrational spectroscopy of pyrrolidine derived from switching rates and direct photocurrent measurements. * `Fig_3A.xlsx`: Processed pyrrolidine IR spectra for Fig. 3A (rate vs wavenumber, 1587–7700 cm⁻¹), revealing fundamental/overtone/combination bands. * `Fig_3B.xlsx`: Processed pyrrolidine occupation for Fig. 3B (High-state occupation vs wavenumber). Dips indicate vibrations that preferentially drive High→Low transitions. * `Fig_3C_Mapping.opju`: Origin project containing photocurrent mapping visualization used for Fig. 3C (includes 2D maps and constant-current topography; corresponds to Fig. 3D–F). See "Variable definitions" section 5 for internal structure details. * `Fig_3C.xlsx`: Pyrrolidine photocurrent spectra for Fig. 3C (lock-in photocurrent vs wavenumber), acquired with active Z-compensation to suppress thermal background. ### Figure 4 **Context:** Isotope-dependent vibrational spectra comparing pyrrolidine, **N-deuterated (Pyrro N–D)**, and **fully C-deuterated (Pyrro D8)** isotopologues. **Pyrro D8** * `Fig_4_D8_IR_Occupation.xlsx`: Occupation data. * `Fig_4_D8_IR_Rate.xlsx`: IR spectra (switching rate vs wavenumber). Note the redshift of C–D stretching modes relative to C–H modes. **Pyrro N–D** * `Fig_4_ND_IR_Occupation.xlsx`: Occupation data. * `Fig_4_ND_IR_Rate.xlsx`: IR spectra (switching rate vs wavenumber). Highlights redshift of N–D stretching modes relative to N–H modes. **Standard pyrrolidine** * `Fig_4_Pyrro_IR_Occupation.xlsx`: Occupation data. * `Fig_4_Pyrro_IR_Rate.xlsx`: IR spectra (switching rate vs wavenumber). ### Figure 5 **Context:** Microscopic chemical identification of mixed isotopologues using resonant IR excitation at fingerprint frequencies. * `Fig_5A.sxm`: Raw STM scan for Fig. 5A (no photoexcitation); morphologically identical molecules. * `Fig_5B.sxm`: Excitation @ 2034 cm⁻¹; selective activation of Pyrro D8 (C–D stretch). * `Fig_5C.sxm`: Excitation @ 2300 cm⁻¹; selective activation of Pyrro N–D (N–D stretch). * `Fig_5D.sxm`: Excitation @ 2890 cm⁻¹; C–H stretch resonance (inactive for switching). * `Fig_5E.sxm`: Excitation @ 3225 cm⁻¹; activation of N–H bond–containing species. * `Fig_5F.sxm`: Excitation @ 5938 cm⁻¹; activation via 2ν(C–H) overtone. ## Archives ### Archive 1: `HomeBuilt_Software.zip` **Description:** Custom software suite used for data acquisition, post-processing, and visualization. **Licensing:** Provided under **CC0** to ensure compatibility with the Dryad repository. **Usage:** * **Visualization:** Contains **HTML-based visualization tools** (Java/web-based) to visualize the data corresponding to all figures in the main text. **How to run:** Open the `.html` files in a modern web browser. * **Data Processing:** Includes **Python-based software** designed to extract switching rates from the raw single-action traces (contained in Archive 2). It calculates the average rates and 99% confidence intervals used to generate the final `.xlsx` spectra. * **Acquisition Support:** Includes a **LabVIEW utility** used during experiments that performs three key functions: 1. Records the time trace of tip height variations. 2. Automatically calculates the occupation ratio and switching rate for the current dataset. 3. Automatically re-centers the tip after each recording to compensate for lateral thermal drift. ### Archive 2: `Raw_data_IRiSTM.zip` **Description:** Original, unprocessed point-by-point raw data for IRiSTM spectra. **Organization:** Three folders: * `Fig 1 C2H_C2D`: Raw time-series data for ethynyl rotation. * `Fig 3 Pyrrolidine_PhotoCurrent`: Raw lock-in amplifier outputs for photocurrent measurements. * `Fig 4 Pyrro_D8_ND_rate_plus_occupation`: Raw switching event logs for isotope comparisons.