RMC_POT (Reverse Monte Carlo using POTentials), a computer code for modeling the structure of disordered systems containing molecules of arbitrary complexity, using flexible molecular constraints and non-bonding potentials

TL;DR

This paper introduces RMC_POT, a novel Reverse Monte Carlo modeling code that incorporates molecular potentials to better preserve molecular geometry and energetic considerations, improving structural modeling of disordered molecular systems.

Contribution

The new code uses bond, angle, and dihedral potentials instead of fixed constraints, enabling more realistic modeling of complex molecular disordered systems.

Findings

Successfully modeled liquid dimethyl trisulfide structure

Achieved more sensible results than previous RMC methods

Applicable to liquids and amorphous solids with molecules up to 100 atoms

Abstract

An approach has been devised and tested for preserving the molecular geometry and taking into account energetic considerations during Reverse Monte Carlo modeling. Instead of the commonly used fixed neighbour constraints, where molecules are held together by constraining distance ranges available for the specified atom pairs, here molecules are kept together via bond, angle and dihedral potential energies. The scaled total potential energy contributed to the measure of the goodness-of-fit, thus the atoms could be prevented from drifting apart. In some of the simulations (Lennard-Jones and Coulombic) non-bonding potentials were also applied. The algorithm was successfully tested for the X-ray structure factor based structure study of liquid dimethyl trisulfide, for which material now significantly more sensible results have been obtained than during previous attempts via any earlier version of Reverse Monte Carlo modeling. It is envisaged that structural modeling of a large class of materials, primarily liquids and amorphous solids containing molecules of up to about 100 atoms, will make use of the new code in the near future.