Data from: Potentials of mean force fail to describe chemical bond-breaking in solution
Data files
Oct 13, 2025 version files 45.90 GB
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README.md
1.87 KB
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repository_upload.zip
45.90 GB
Abstract
Many liquid phase studies assume that the potential energy surfaces of reacting molecules are the same as in the gas phase, neglecting complex solvent dynamics that can completely alter the nature of chemical reactivity. Even studies that include solvent effects typically only consider them in an average, equilibrium way as part of a potential of mean force (PMF). In this work, we use mixed quantum/classical simulations to compare how equilibrium and non-equilibrium solvent motions affect the photodissociation of a simple diatomic molecule, NaK+, in liquid tetrahydrofuran. A PMF analysis shows that as the excited-state molecule dissociates with the solvent at equilibrium, the bonding electron remains associated with K+ at short bond distances but eventually localizes on Na+ at the end of dissociation. When we examine nonequilibrium dynamical photodissociation trajectories, however, we find that they fall into three distinct categories: about a quarter of them have the bonding electron mainly associated with Na+, another quarter stay mainly associated with K+, and about half have the bonding electron shared roughly equally between the two ions. The results show that equilibrium PMFs cannot accurately describe the dynamics of bond-breaking chemical reactions in solution, because there is insufficient time for the solvent to reach equilibrium on the time scale over which bond dissociation occurs.
Dataset DOI: 10.5061/dryad.vhhmgqp63
Description of the data and file structure
Files and variables
File: repository_upload.zip
Description:
This zip file contains this READ.ME and 3 folders, described below
- eqb_PMF (folder)
- Contains the equilibrium umbrella sampling trajectories with bond distance held at 4.00 to 7.75 angstroms, increment by 0.25 angstroms
- Sub-folder name is the corresponding bond distance in angstroms (e.g., the sub-folder named 4.00 contains data for Na--K bond held at 4.00 angstroms)
- Each distance sub-folder contains:
- The xyz files (e.g., dist4.00.xyz is the xyz file for Na--K bond distance held at 4.00 angstroms, located in sub-folder 4.00)
- First electronic excited state wavefunction cube file (es_wavefunction.cube)
- 1st shell THF coordination number (THF_CN.txt): the first column is time (in fs), the second column is Na CN, and the third column is K CN.
- non_eqb (folder)
- Contains 20 sub-folders (1 through 20), corresponding to the 20 non-eqb trajectories
- Within each sub-folder, there are the following files:
- The xyz files (e.g., trajec1.xyz is the xyz file for trajectory 1, located in sub-folder 1)
- First electronic excited state wavefunction cube file (es_wavefunction.cube)
- 1st shell THF coordination number (THF_CN.txt): the first column is time (in fs), the second column is Na CN, and the third column is K CN.
- Other (folder)
- Contains gas_phase_es_wavefunction.cube:
- Excited state wavefunction cube file for NaK+ in the gas phase
- Contains (i) Na0.xyz, (ii) Na1.xyz, (iii) K0.xyz, (iv) K1.xyz:
- The xyz files for (i) single Na atom, (ii) single Na+ ion, (iii) single K atom, and (iv) single K+ ion, respectively, in liquid THF