Molecular dynamics simulation of interaction between bio-molecules and metal-organic frameworks for efficient gene delivery at the nanoscale
Subject Areas : Iranian Journal of Organic ChemistryAnahita Bakhshandeh 1 , Fatemeh Ardestani 2 , Hamid Reza Ghorbani 3
1 -
2 -
3 -
Keywords: Amino acids, nanotechnology, DFT, Functionalization, MOFs,
Abstract :
To fabricate functional surfaces structures for protein immobilization without losing biological activity, the interaction between different amino acids and metal-organic frameworks (MOFs) has been evaluated. The density functional theory (DFT-D2) calculations were used to afford a molecular description of the interaction properties of the amino acids and MOF-5 by examining the interaction energy and the electronic structure of the amino acid/MOF complexes. Strong interactions were recorded between the amino acids and MOF through their polar groups as well as aromatic rings in the gas phase. Based on the results, water molecules prevent the amino acids from approaching the active sites of MOF, causing weak attractions between them. The interaction energies were calculated by considering the basis set superposition error correction. The interaction energies obtained at the range of +11 to -13 kcal/mol, for GLY-MOF in the presence of water molecules while in the case of the gas phase the estimated values range from -5 to -57 kcal/mol. Results showed GLY molecules cannot form a stable complex in the water media. The complication of all selected AAs is found exothermic process and energetically favorable and thus can form stable complexes with the MOF-5 at the gas phase. The accuracy of the DFT-PBE model was validated against the comprehensive MP2 quantum level of theory. The evaluation of the nature of the interaction between the amino acids and MOF by the atoms-in-molecules (AIM) theory showed that the electrostatic attractions are the main force contributing to bond formation between the interacting entities.