Published January 18, 2022 | Version 1.2.0
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Solution-phase Molecular Rotation Calculation for Dipolar Relaxation Times

Creators

  • 1. University of Colorado - Boulder
  • 2. National Renewable Energy Lab

Description

This python package is used to calculate the dipolar relaxation time for a solute molecule in a low-dielectric solvent. The packages takes .xyz files generated by 3D molecular modeling software to approximate the solute molecule as an ellipsoid. This ellipsoid is found by calculating the three inertial axes of the molecule and then uses the distance from the center-of-mass to the furthest atomic coordinate along that inertial axis to determine the length of the three ellipsoid axis. Frictional theory, both due to the shape of the solvent-solute interaction and dielectric friction caused by the solvent, is applied to calculate the time the solute molecule takes to rotate 2π about each of the three axes; given an input energy of kT. Finally, the position of the positive and negative charge density can be input to approximate the dipolar relaxation time by a weighted harmonically averaging of the three ellipsoid axes' rotational times.

Notes

This package was designed for molecules that have geometries close to an ellipsoid. Additionally, one must calculate new solvents' ellipsoid axes' lengths (which can be done with this package) and corresponding temperature-dependent viscosity coefficients to investigate new solvents. Only a handful of solvents are included in the external file labeled "Solvent_info". Rotational times calculated with this package have been compared to literature values collected by various techniques with good agreement.

Files

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Additional details

References

  • Gavezzotti, A. The Calculation of Molecular Volumes and the Use of Volume Analysis in the Investigation of Structured Media and of Solid-State Organic Reactivity. J. Am. Chem. Soc.105, 5220–5225, DOI: 10.1021/ja00354a007 (1983).
  • Klüner, R. P. & Dölle, A. Friction coefficients and correlation times for anisotropic rotational diffusion of molecules in liquids obtained from hydrodynamic models and 13C relaxation data. J. Phys. Chem. A101, 1657–1661, DOI:10.1021/jp963417t (1997).
  • Youngren, G. K. & Acrivos, A. Rotational friction coefficients for ellipsoids and chemical molecules with the slip boundary condition.The J. Chem. Phys.63, 3846–3848, DOI: 10.1063/1.431879 (1975).
  • Hubbard, J. B. Friction on a rotating dipole.The J. Chem. Phys.69, 947–955, DOI: 10.1063/1.436693 (1978).
  • Zwanzig, R. Dielectric friction on a rotating dipole.The J. Chem. Phys.38, 1605–1606, DOI: 10.1063/1.1776930 (1963).
  • Papazyan, A. & Maroncelli, M. Rotational dielectric friction and dipole solvation: Tests of theory based on simulations of simple model solutions.The J. Chem. Phys.102, 2888–2919, DOI: 10.1063/1.468667 (1995).