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 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 nm
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
Ar0.5020.5020.502
Ba0.0000.0000.000
Be0.7610.7610.761
Br0.6510.6510.651
C0.5650.5650.565
Ca0.2390.2390.239
CBrF21.0001.0001.000
CCl20.4000.4000.400
CF20.3960.3960.396
CF2Cl1.0001.0001.000
CF30.5250.5250.525
CH0.7840.7840.784
CH20.8240.8240.824
CH2Br1.0001.0001.000
CH2Br21.0001.0001.000
CH2Cl21.0001.0001.000
CH2F21.0001.0001.000
CH2I21.0001.0001.000
CH30.8630.8630.863
CH30.8630.8630.863
CH40.9020.9020.902
CHCl21.0001.0001.000
CHF21.0001.0001.000
Cl0.1220.1220.122
Cs0.3410.3410.341
F0.5650.5650.565
H1.0001.0001.000
I0.5800.5800.580
K0.5610.5610.561
Kr0.3610.3610.361
Li0.8000.8000.800
Mg0.5410.5410.541
N0.1880.1880.188
Na0.6710.6710.671
Ne0.7020.7020.702
NH0.3610.3610.361
NH20.4000.4000.400
NH30.4390.4390.439
O1.0001.0001.000
OH0.7840.7840.784
Rb0.4390.4390.439
S1.0001.0001.000
Si1.0001.0001.000
Sr0.0000.0000.000
X1.0001.0001.000
Xe0.2590.2590.259

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