Structural and molecular properties of complexes of biomolecules and metal-organic frameworks: dispersion-corrected DFT treatment.

Investigation of complexes of nanostructured materials and biomolecules has attracted much attention by various researchers as it can contribute to coherent growth and extended application of nanostructures in different technologies. In this research, following a comprehensive approach, we examined the interaction between different amino acids and metal-organic frameworks (MOFs) at atomic scale using computational chemistry. For this purpose, we employed the density functional theory (DFT-D2) calculations 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. We found strong interactions between the amino acids and MOF through their polar groups as well as aromatic rings in the gas phase. However, our findings were significantly different in solvent media, where water molecules prevent the amino acids from approaching the active sites of MOF, causing weak attractions between them. The evaluation of nature of interaction between the amino acids and MOF by the atoms-in-molecules (AIM) theory shows that the electrostatic attractions are the main force contributing to bond formation between the interacting entities. Furthermore, our DFT-PBE model of theory was validated against the comprehensive MP2 quantum level of theory.

Theoretical assessments on the interaction between amino acids and the g-Mg3N2 monolayer: dispersion corrected DFT and DFT-MD simulations.

The interaction of a few amino acids (AAs) with the graphene-like magnesium nitride (g-Mg3N2) monolayer has been investigated with density functional theory (DFT) simulations. The Mg site was found to cause significant attraction with the polar active sites of AAs. Such AAs, are capable of producing electrostatics bonding with -48.012 (kcal mol-1) of interaction energy for tyrosine. The good consistency of the DFT interaction energy with the second-order Møller-Plesset method was found. Furthermore, the DFT-MD simulation of the tyrosine/g-Mg3N2 system demonstrated that this host-guest system is stable at ambient conditions. The electronic structures and quantum molecular descriptors were calculated, and the results revealed that the g-Mg3N2 monolayer is sensitive to the interaction with AAs. Our first-principles outcomes suggest comprehensive visions into the functionalization of g-Mg3N2, and anticipate its applicability as an unprecedented nanovector for AAs. In addition, g-Mg3N2 nanosheets can be utilized as biosensors for biomolecules detection. These are very hopeful for promising biological and pharmaceutical applications of g-Mg3N2.

Understanding structural and molecular properties of complexes of nucleobases and Au13 golden nanocluster by DFT calculations and DFT-MD simulation.

The characterization of the complexes of biomolecules and nanostructures is highly interesting and benefits the rational development and design of nano-materials and nano-devices in nano-biotechnology. In this work, we have used dispersion corrected density functional theory (DFT-D) as well as DFT based molecular dynamics simulations to provide an atomistic understanding of interaction properties of DNA nucleobases and Au13 nanocluster. Various active sites of interacting molecules considering their relative orientation and distance are explored. Our goal is to stimulate the binding characteristics between two entities and evaluate this through the interaction energy, the charge transfer, the electronic structure, and the specific role of the molecular properties of the nucleobase-Au13 system. The primary outcomes of this comprehensive research illuminated that nucleic bases have potent affinity for binding to the Au cluster being chemisorption type and following the trend: Adenine > Cytosine > Guanine > Thymine. The AIM analysis indicated that the binding nature of the interacting species was predominantly partial covalent and high polar. We discuss the bearing of our findings in view of gene-nanocarrier, biosensing applications as well as nanodevices for sequencing of DNA.

Molecular simulation of efficient removal of H2S pollutant by cyclodextrine functionalized CNTs.

DFT-D3 calculations were carried out to investigate interaction of H2S and CH4 between numerous functionalized CNTs (f-CNTs), including hydroxyl, carboxyl, and cyclodextrin groups as potential candidates for selective adsorption and elimination of toxic pollutants. It was found that pristine CNTs as well as nanotube surface of functionalized CNTs cannot stably adsorb the H2S molecule (adsorption energy of -0.17 eV). However, H2S adsorption was significantly enhanced with different magnitudes upon the functionalization of CNT. For f-CNTs, H2S adsorption was accompanied by releasing energies in the range between -0.34 to -0.54 eV where the upper limit of this range belongs to the cyclodextrin-functionalized CNT (CD-CNT) as the consequence of the existence of both dispersion and electrostatic interactions between the adsorbate and substrate. Findings also demonstrated a significantly weaker interaction between CH4 and CD-CNT in comparison to the H2S molecule with adsorption energy of -0.14 eV. Electronic properties of the selected substrates revealed no significant changes in the inherent electronic properties of the CNTs after functionalizing and adsorbing the gas molecules. Moreover, DFTB-MD simulation demonstrated high adsorption capacity as well as CD-CNT ability for H2S molecules against the CH4 one under ambient condition.

Hydrogen purification performance of a nanoporous hexagonal boron nitride membrane: molecular dynamics and first-principle simulations.

Membranes have attracted much attention for the efficient separation of gas mixtures, due to their specific structural and unique properties. In this work, density functional theory (DFT) and molecular dynamic (MD) simulations have been employed to evaluate the performance of nanoporous hexagonal boron nitride (h-BN) monolayers for hydrogen purification. Various porous membranes were designed, and full structural relaxation was carried out by using DFT calculations and then MD simulations to investigate the H2 purification performance of the nanoporous h-BN membranes. It was found that the selectivity for H2 gas over N2 gas was highly sensitive to the type and width of the pores. The h-BN membrane containing pores with short and long sides both of about 3 Å (pore 1B-3N) demonstrated optimal selectivity for H2 molecules, while the permeability of the pore 5B-5N + 4H membrane (short side of about 4.4 Å) was much higher than that of other counterparts. Furthermore, DFT calculations were performed to validate the MD simulation observations as well as to explain the selectivity performance of the most desirable pore membrane. We demonstrated that the 1B-3N pore is a far superior membrane to other counterparts and exhibits an excellent potential for applications in hydrogen purification, clean energy combustion, and the design of novel membranes for gas separation.

Enantioseparation performance of CNTs as chiral selectors for the separation of ibuprofen isomers: a dispersion corrected DFT study.

The enantioseparation of chiral drugs has been of great interest in the modern pharmaceutical industry since the majority of bioorganic compounds are chiral. In this work, we have investigated the ability of pristine and defected (10, 5) chiral carbon nanotubes (CNTs) in enantioseparation of chiral R-/S-ibuprofen isomers. The interactions between the two enantiomers of ibuprofen and the outer surface and inner side wall of the chiral CNTs have been evaluated. We utilized dispersion-corrected density functional theory (DFT) calculations within the framework of the GGA-PBE scheme for the systems under study. The results indicated that the inner side walls of the defected (10, 5) CNTs exhibited the highest energy difference (ΔU0) between the pairs of considered enantiomers with the energy difference of about 1.4 kcal mol-1, indicating that these nanotubes are a promising candidate in enantioseparation processes. The effect of solvation has also been considered in the calculations and it was found that changing the dielectric properties of the medium cannot affect the overall interactions between the drug and CNT. The electronic properties of the considered systems did not change upon the interaction between the incorporated molecules and the type of interaction was found to be dispersion-governed physisorption.