Molecular Models

# 1 Overview

The Molecular Model Database of the Boltzmann-Zuse Society for Computational Molecular Engineering, referred to as the MolMod database, contains materials relations (force ﬁelds) for around 150 low-molecular fluids for materials modelling using molecular dynamics (MD) and Monte Carlo (MC) solvers. The MolMod database has been published by Stephan et al. [Stephan, 2019]. These force fields are known to describe vapour-liquid equilibrium data (e.g., saturated densities, vapour pressures, enthalpies of vaporization) with a good accuracy. In most cases, correlations to experimental data for these quantities were used to parameterize these molecular models. Predictions of other properties, such as transport properties, were tested and found to be in good agreement with experimental data in many cases.

The present materials relations, i.e. force fields, can be combined with the following physics equations:
• Classical mechanical equations of motion; this is typically an MD solver.
• Partition function and phase-space density (e.g., Boltzmann distribution); this is typically an MC solver.

The present molecular models are atomistic in cases where each atom of the molecule is represented by at least one interaction site, e.g., for nitrogen, oxygen, halogens, and noble gases. In other cases, a united-atom approach is followed, yielding a mesoscopic materials model where (some or all) interaction sites correspond to groups of atoms; e.g., the 2CLJQ models for refrigerants are of the mesoscopic type. Also ion models are included in the MolMod database.

The force fields in the MolMod database are defined by multi-centre Lennard-Jones 12-6 potentials with superimposed point charges, dipoles, and quadrupoles. They can be easily combined for describing mixtures using combining rules, e.g., the modified Lorentz-Berthelot rule. In some cases, multiple models for the same substance were developed, e.g., for methane (one model as a simple Lennard-Jones fluid and one as Lennard-Jones truncated & shifted). The database also contains a set of ion models that can be used for modelling electrolyte systems.

Note: The present nomenclature is registered as a semantic asset in the Taxonda dashboard of the European Materials Modelling Council (EMMC). It is based on the Review of Materials Modelling (RoMM) [de Baas, 2017].

# Units

The parameters of the presented molecular force fields are given in different forms and units for the various simulation programs. Table 1 summarizes the different units of the properties depending on the respective simulation programs. Note that the dipole moment and the quadrupole moment are given in units of Debye and Buckingham, respectively.

 Name Symbol ms2 ls1 LAMMPS Gromacs Internal Coordinates Length σ Å Å Å nm - Energy ε $\varepsilon/k_\text{B}$ in K $\varepsilon/k_\text{B}$ in K eV kJ/mol - Charge q e q $(k_\text{C}/k_\text{B})^{1/2}$ in C e e - Mass M g/mol u g/mol u - Distance M Å Å Å nm Å Angle $\theta$,$\phi$ ° ° ° ° ° Dipole$^{\mathrm{(a)}}$ μ D μ $(k_\text{C}/k_\text{B})^{1/2}$ in ÅC D - - Quadrupole$^{\mathrm{(b)}}$ Q B Q $(k_\text{C}/k_\text{B})^{1/2}$ in Å$^2$C - - -

Table 1: Overview of the different types of interaction potentials and the units of their parameters depending on the simulation program. The Boltzmann constant ($k_\text{B}$) und the Coulomb's constant ($k_\text{C}$) are each given in their SI units. $^{\mathrm{(a)}}$ is given in Debye ($\mathrm{D}=0.2082\times e \times Å$). $^{\mathrm{(b)}}$ is given in Buckingham ($\mathrm{B}=\mathrm{D}\timesÅ$).

# Naming

The molar masses and the names of the substances are adopted from the "NIST Chemistry WebBook". The corresponding IUPAC-name and further common trivial names of substances available in the MolMod database are also deposited. Such are not displayed on the webfrontend, but the search field in the list of substances atoms and molecules/ions can be used to search trivial- or IUPAC substance names.

# Molecule Pictures

The MolMod database shows and provides visualizations of the molecular models in different formats and settings. The visualizations of molecular models visualize interaction sites of the corresponding molecular model, which have a mass M>0. For the molecular models contained in the MolMod database, the following interaction sites belong to the category of sites that have mass M>0: (1) Lennard-Jones interaction sites and (2) point charges that model a hydrogen atom. The size of the individual Lennard-Jones interaction sites in the visualizations of the molecular models are proportional to the respective force field parameter sigma (radius=4*sigma); the size of the point charges representing a hydrogen atom has been set to a fixed value for all pictures (radius=10). The colour sheme employed for the visualizations of the molecular models was adapted from Refs. [Corey, 1953]. Table 2 shows the RGB color code according to the CPK scheme (named after R. Corey, L. Pauling, and W. Koltun).

The axes drawn in the pictures represent the main axes of the molecular model. Furthermore the names of the interaction sites are also indicated in the visualizations. If, however, an interaction site is covered by other sites due to the selected perspective or relative size of interaction sites, the site name is noted in grey at the corresponding place of the site. However, if a molecular model consists of several sites of the same type (same interaction parameters), these identical site names are not displayed individually, but instead the site name is only displayed once followed by "(i)".

In addition, all pictures of the molecular models shown on the website are provided for download in different variations on the respective pages of the molecular models. Furthermore, the source code files for creating the images in the program "VMD" on a Linux machine are also provided. These source code files can be slightly customized on the website before downloading.

 Site-name rgb-Code Color Ar 0.502 0.502 0.502 Ba 0.000 0.000 0.000 Be 0.761 0.761 0.761 Br 0.651 0.651 0.651 C 0.565 0.565 0.565 Ca 0.239 0.239 0.239 CBrF2 1.000 1.000 1.000 CCl2 0.400 0.400 0.400 CF2 0.396 0.396 0.396 CF2Cl 1.000 1.000 1.000 CF3 0.525 0.525 0.525 CH 0.784 0.784 0.784 CH2 0.824 0.824 0.824 CH2Br 1.000 1.000 1.000 CH2Br2 1.000 1.000 1.000 CH2Cl2 1.000 1.000 1.000 CH2F2 1.000 1.000 1.000 CH2I2 1.000 1.000 1.000 CH3 0.863 0.863 0.863 CH3 0.863 0.863 0.863 CH4 0.902 0.902 0.902 CHCl2 1.000 1.000 1.000 CHF2 1.000 1.000 1.000 Cl 0.122 0.122 0.122 Cs 0.341 0.341 0.341 F 0.565 0.565 0.565 H 1.000 1.000 1.000 I 0.580 0.580 0.580 K 0.561 0.561 0.561 Kr 0.361 0.361 0.361 Li 0.800 0.800 0.800 Mg 0.541 0.541 0.541 N 0.188 0.188 0.188 Na 0.671 0.671 0.671 Ne 0.702 0.702 0.702 NH 0.361 0.361 0.361 NH2 0.400 0.400 0.400 NH3 0.439 0.439 0.439 O 1.000 1.000 1.000 OH 0.784 0.784 0.784 Rb 0.439 0.439 0.439 S 1.000 1.000 1.000 Si 1.000 1.000 1.000 Sr 0.000 0.000 0.000 X 1.000 1.000 1.000 Xe 0.259 0.259 0.259

Table 2: The RGB color code according to the CPK scheme, which is used on the MolMod database.