The MOPAC program performs semi-empirical (quantum mechanical) calculations for the evaluation of theoretical descriptors (molecular and electronic properties) of NMs to tackle the size of NMs efficiently, i.e. the large number of atoms in a NM. The effect of solvents can be captured by the COSMO method implemented in MOPAC. To validate the results obtained from MOPAC, the NWChem program package is proposed, applying DFT and wave function based ab initio methods for considerably smaller size of NMs. MD simulations with the GROMACS software for an extensive size of NMs are feasible and faster simulations are guaranteed by making use of GPUs. ESPResSo software performs many-particle simulations of coarse-grained atomistic or bead-spring models for a variety of systems such as polymers, liquid crystals, colloids, polyelectrolytes, and biological systems, such as proteins, DNA, and lipid membranes and therefore a valuable application to investigate bionano interactions of NMs. ESPResSo is free software licensed under the GNU Lesser General Public License. The calculation of interface properties, such as the adsorption free energies at the coarse-grained level are derived using a united atom model, a SmartNanoTox multiscale technique.

SmartNanoTox modelling tools, http://www.smartnanotox.eu/?page_id=143, were developed by H2020 project SmartNanoTox for the prediction of the biological activity of NMs. The tools include NM and biomolecule coarse-graining using Python scripts, evaluation of parameters of interactions such as potentials of mean force for biomolecular segments at the surface of NMs (using freeware Gromacs package), and prediction of protein 3D structure using free iTasser tool. SNT-MT are open source free software licensed under the GNU Lesser General Public License.

For the calculation of the theoretical descriptors, listed in Table 1, with the tools (software) available to provide NanoCommons services to potential users/stakeholders (subject to an application process), essential inputs to utilise the software capabilities are: 1) the chemical information of the NMs research study, 2) datasets (experimental or theoretical), if available, 3) the descriptor name to be evaluated and, 4) the chemical structure (molecular or crystal), if available, i.e., preferably, the cartesian coordinates (xyz atomic structure) of the NMs, as well as, if applicable, the cartesian coordinates of their adsorbates (e.g. proteins or lipids).

 

Table 1: Methodology and software tools for the calculation of theoretical descriptors of NMs

Descriptor name	Method	Simulation package
Band gap	PM6, DFT	MOPAC, NWChem
Ionization potential	PM6, HF, DFT, TDDFT	MOPAC, NWChem
Density of states	PM6, HF, DFT	MOPAC, NWChem
Hydrophobicity	CG	SNT-MT
Dipole moment	PM6 (COSMO), DFT	MOPAC, NWChem
Atomic charge	PM6, DFT	MOPAC, NWChem
Total charge	PM6, DFT	MOPAC, NWChem
Electronegativity	PM6, DFT, LDM	MOPAC, NWChem
Absorption spectra	CIS, TDDFT	MOPAC, NWChem
Binding energies	PM6, DFT, DFTB	MOPAC, GPAW, DFTB+
vdW energy	CG, PM7, DFT	SNT-MT, MOPAC, NWChem, SIESTA
Corona kinetics	CG	ESPResSo
Binding affinities	CG	SNT-MT
Hamaker constants	CG, Lifschitz theory	SNT-MT
Adsorption energies for proteins	CG, DFT, DFTB	SNT-MT, GROMACS, SIESTA, DFTB+
Vibrational frequencies	PM6, MD	MOPAC, GROMACS

 

Abbreviations

• CG: Coarse Grained
• CIS: Configuration Interaction Singles
• COSMO: Conductor-like Screening Model
• DFT: Density Functional Theory
• DFTB: Density Functional Tight-Binding
• DNA: Deoxyribo Nucleic Acid
• ESPResSo: Extensible Simulation Package for Research on Soft Matter
• GROMACS: GROningen MAchine for Chemical Simulations
• HCNP: Hydrophobic Charged Nanoparticles
• HF: Hartree-Fock
• iTasser: Iterative Threading Assembly Refinement

Further information