Nanomatch Morphology Calculator

Properties	Notes
HOMO, LUMO	byproduct
Dipole (property not yet described / available)	byproduct
Morphology	recommended

Workflow

The Nanomatch Morphology Calculator workflow is essentially the first part of the Nanomatch Mobility Calculator workflow (Nanomatch Mobility Calculator), which is terminated after the morphology is generated and analyzed.

Nanomatch Morphology Calculator Workflow
Nanomatch Software	Scientific Role	Illustration
Parametrizer	Geometry optimization
DihedralParametrizer	Computation of intramolecular forcefields
Deposit	Simulation of the physical vapor deposition (PVD) to obtain atomistic morphology

Implemented Scientific Methods

The following scientific methods are implemented in the Nanomatch Morphology Calculator:

Molecular Structure Optimization

obabel, xtb, and Density Functional Theory (DFT) are used to generate initial 3D conformers, pre-optimize and optimize the geometry, and compute partial charges via an electrostatic potential (ESP) fit for single molecules in a vacuum. DFT optimization is performed with def2-TZVP/B3LYP level of theory.

Morphology Generation

The DEPOSIT protocol [1] simulates physical vapor deposition to generate thin-film morphologies with atomistic resolution. This involves Monte Carlo (MC) based basin hopping with simulated annealing (SA) to model intermolecular interactions during deposition. In total, 1000 molecules are deposited into a box with a base size of 100x100 Å.

Output

Displayed Results

The data below will be displayed as the workflow ends (backend name: result.yml):

ZUOUZKKEUPVFJK-UHFFFAOYSA-N:
  HOMO:
    value: -6.304540838835274
  LUMO:
    value: -0.9858224534777202
  dipole:
    results:
      dipole_vector:
      - -1.3524802844422331e-05
      - 3.1223022592016277e-06
      - 1.662349335263646e-05
    value: 2.1656629345848317e-05
  morphology:
    results:
      average_neighbors:
        unit: Angstrom
        value: 17.6
      mass_density:
        std: 0.01
        unit: g/cm3
        value: 1.14
      molecular_volume:
        unit: nm3
        value: 0.23
      number_density:
        std: 9.9e+19
        unit: 1/cm3
        value: 4.36e+21
      rdf_first_peak:
        unit: Angstrom
        value: 4.921630094043887
    value: 'file: structure.cml'

The table below explains each parameter, its meaning, units, and other relevant information (field “value” is occasionally omitted).

Parameter	Description	Units	Value	Additional Information
HOMO	Highest Occupied Molecular Orbital	eV	-6.304540838835274	HOMO
LUMO	Lowest Unoccupied Molecular Orbital	eV	-0.9858224534777202	LUMO
dipole_vector	Components of the dipole moment vector	Debye (D)	(-1.3524802844422331e-05, 3.1223022592016277e-06, 1.662349335263646e-05)	Vector representation of the dipole moment
dipole	Magnitude of the dipole moment	Debye (D)	2.1656629345848317e-05	Magnitude of the dipole moment
average_neighbors	Average distance to neighboring molecules	Å	17.6	Average distance to neighboring molecules
mass_density	Mass per unit volume	g/cm³	1.14	Standard deviation (std): 0.01 (example value)
molecular_volume	Volume occupied by a single molecule	nm³	0.23
number_density	Number of molecules per unit volume	1/cm³	4.36e+21	Standard deviation (std): 9.9e+19 (example value)
rdf_first_peak	Position of the first peak in the radial distribution function	Å	4.921630094043887	Indicates the most probable intermolecular distance

Files

In addition to parsed output, the following files are available upon the workflow completion:

No.	File	Description	Example
1	output_molecule.mol2	Molecule output file in MOL2 format.	output_molecule.mol2
2	summary_RDF.png	Radial distribution function (RDF).
3	structure.cml	Molecular structure in CML format.	structure.cml
4	visualization_2D _and_3D.png	2D and 3D visualizations of the molecules (center of geometries)