DOI: 10.17877/resolv-2025-m7nak2e7
title: Experimental Data for: Internal Vibrational Energy Redistribution Precedes Energy Dissipation into the Solvent upon Photoexcitation of Heme Proteins

description: This project explores the fundamental mechanisms of energy dissipation in photoexcited heme proteins, with a focus on myoglobin and cytochrome c. This is the collected and simulated data used for the paper: "Internal Vibrational Energy Redistribution Precedes Energy Dissipation into the Solvent upon Photoexcitation of Heme Proteins" and is meant to give access to the data for other researchers to enable comparison and further research into this topic. Understanding how proteins manage excess energy is essential for uncovering biological processes such as allosteric communication, radiation protection, and enzyme activity regulation.

Using optical pump–THz probe (OPTP) spectroscopy, this study provides a time-resolved view of how vibrational energy, following photoexcitation at the Soret band, redistributes internally within the protein structure before dissipating into the surrounding aqueous solvent. The measurements reveal distinct time constants (~6–10 ps) that characterize energy flow into water, depending on the protein and solvent (H₂O vs D₂O), highlighting a significant isotope effect.

To interpret the experimental findings, the research integrates a computational thermal diffusion model that simulates energy propagation from the heme center outward. The model successfully reproduces the observed dynamics, supporting a diffusive, rather than ballistic, mode of energy transport through the protein matrix.

Overall, the project delivers key insights into protein–solvent thermal coupling, validates hierarchical vibrational relaxation pathways, and demonstrates the strength of OPTP spectroscopy as a tool for probing ultrafast biomolecular dynamics in a minimally invasive manner.
description: LabVIEW 2023 Q3, LabVIEW 2023 Q3
description: Mathematica, 14
description: The dataset includes both experimental and simulation data:

Experimental data is provided as both the full 3D dimensional data an the parameters extracted from fits, the full spectral data is provided in matrices of both the electric field difference as well as the Fourier transformed spectra units of magnitude (Optical density [OD]) they are in .mat format and additionaly in .tsv files (both .mat/.mx and .tsv contain identical information however only .mat/.mx works with the provided evaluation scripts) for each protein:

One file contains the electric field difference of the collected THz-TDS (Time Domain Spectroscopy) traces (datapulses.tsv).

One file contains the Fourier transform magnitude caluculated form the collected THz field traces (datafouriertransforms.tsv), the data treatment procedure is described in doi:10.13154/294-12492 and doi.org/10.1021/acs.jpcb.3c04874 as well as the PhD thesis of Thorsten Ockelmann 

One file contains the fitting values and function (*_fittingvalues.tsv)

The .tsv files are structured as:

Electric field differences: {Pump-Probe delay [ps], TDS delay [ps], Electric field difference [V], Standard Error}

Fourier transformation magnitudes: {Pump-Probe delay [ps], Frequency [cm⁻¹], Fourier transform magnitude [deltaOD], Standard Error of magnitude error}
 
Fitting values: {Delay, Fourier transformation magnitude,Standard Error of Magnitude Error},{Fitting Function},{Fitting function parameters (with errors)}

Analysis scripts are provided (written in Mathematica) and require the .mat and .mx files. Each protein folder contains the full spectral matrices, the evaluation script in the parent folder compares all datasets.

Simulation data is included as .rtf files containing the simulated temperature of the sample vs time after excitation as reported in the paper and structured in the following way:

Cytochrome c data:
H2O: tmp-cyc-H2O-6000-BC-300K contains temperature [K] (right column) vs time [ps] (left column)
D2O: tmp-cyc-D2O-6000-BC-300K contains temperature [K] (right column) vs time [ps] (left column)
H2O: lntmp-cyc-H2O contains ln(temperature) (right column) vs time [ps] (left column)
D2O: lntmp-cyc-H2O contains ln(temperature) (right column) vs time [ps] (left column)

Myoglobin data:
H2O: tmp-myo-H2O-6000-BC-300K contains temperature [K] (right column) vs time [ps] (left column)
D2O: tmp-myo-D2O-6000-BC-300K contains temperature [K] (right column) vs time [ps] (left column)
H2O: lntmp-myo-H2O contains ln(temperature) (right column) vs time [ps] (left column)
D2O: lntmp-myo-H2O contains ln(temperature) (right column) vs time [ps] (left column)