Quantum mechanical calculation of nanomaterial-ligand interaction energies by molecular fractionation with conjugated caps method

Dawei Zhang

doi:10.1038/srep44645

Abstract

Molecular fractionation with conjugate caps (MFCC) method is introduced for the efficient estimation of quantum mechanical (QM) interaction energies between nanomaterial (carbon nanotube, fullerene, and graphene surface) and ligand (charged and neutral). In the calculations, nanomaterials are partitioned into small fragments and conjugated caps that are properly capped, and the interaction energies can be obtained through the summation of QM calculations of the fragments from which the contribution of the conjugated caps is removed. All the calculations were performed by density functional theory (DFT) and dispersion contributions for the attractive interactions were investigated by dispersion corrected DFT method. The predicted interaction energies by MFCC at each computational level are found to give excellent agreement with full system (FS) calculations with the mean energy deviation just a fractional kcal/mol. The accurate determination of nanomaterial-ligand interaction energies by MFCC suggests that it is an effective method for performing QM calculations on nanomaterial-ligand systems.

Highlights

The growing interest to study the electronic structures of large and complex systems such as protein, DNA, RNA, nanomaterials and other polymers in an efficient manner leads to the development of many computational schemes, which can cope with the limitation of computational resources
Fragment molecular orbital (FMO) approach[9,10,11,12,13] was proposed for ab initio calculations of large biomolecules
MFCC approach was employed only to study biomolecules, but later on MFCC based attempt to study nanomaterials was reported by Li et al in 2005 in which BN nanotubes were optimized using both MP2/6-31G* and HF/3-21G levels and the predicted total energy of unit BN and infinite BN nanotubes by MFCC were found to be almost equal to the extrapolated values from conventional MP2 and HF calculations on smaller tubes[30]

Summary

Introduction

The growing interest to study the electronic structures of large and complex systems such as protein, DNA, RNA, nanomaterials and other polymers in an efficient manner leads to the development of many computational schemes, which can cope with the limitation of computational resources. The computational effort in the MFCC approach scales linearly with the molecule size, making it practical to deal with realistic large macromolecular systems. This method has been used for the calculation of interaction energies of protein with water[27], drugs[28], and ligands[29]. Ab-initio calculation of large protein-ligand systems with 3680, 1798 and 1060 atoms which are beyond the reach of traditional computational methods has been made possible by using the MFCC approach[32]. MFCC approach was employed only to study biomolecules, but later on MFCC based attempt to study nanomaterials was reported by Li et al in 2005 in which BN nanotubes were optimized using both MP2/6-31G* and HF/3-21G levels and the predicted total energy of unit BN and infinite BN nanotubes by MFCC were found to be almost equal to the extrapolated values from conventional MP2 and HF calculations on smaller tubes[30]

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Conclusion