Dataset DOI: 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 formats and suggested software
• Variable definitions
• File list and descriptions
  • Figure 1
  • Figure 2
  • Figure 3
  • Figure 4
  • Figure 5
• 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

Open-source viewers:

• Gwyddion: http://gwyddion.net/
• Origin Viewer (free): https://www.originlab.com/viewer/

Variable definitions

1) Spectra files (labeled “Rate” or “Spectra”)

Processed spectra/occupation files typically contain three numeric columns.

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”)

3) Time traces (e.g., Fig_1C.xlsx)

4) Photocurrent spectra (e.g., Fig_3C.xlsx)

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 × 10¹²)

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 × 10¹²)

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.