Quantum DFT studies on the drug delivery of favipiravir using pristine and functionalized chitosan nanoparticles.

Considering the spread of the COVID-19 pandemic, finding new drugs along with the development of effective drug delivery methods can help in the treatment of this disease. For this reason, in this research work, the possibility of drug-delivery of Favipiravir (FP), one of the drugs approved in the treatment of COVID-19, by pristine chitosan (Chit) nanoparticles (NP), and functionalized chitosan nanoparticles with N-acylate, N-methyl, O-acetyl, and Oxazoline functional groups was studied using quantum mechanical DFT methods at B3LYP-D3(BJ)/6-311 + g(d,p) theoretical level in water medium. The QTAIM, NBO, DOS, frontier orbital, conceptual-DFT indices, and non-covalent interaction analysis were further implemented to investigate the possible interactions between FP and Chit NPs. The results show that the adsorption of FP on Chit NPs is done through the creation of hydrogen bonds, and the highest absorption energy of - 18.15 kcal/mol between pristine chitosan and FP. In the case of all functionalized Chit NPs, a decrease in the absorption energy is observed, which is more noticeable in the case of N-acylated and O-acetyl functionalize Chit NPs, and indicates the weakening of the van der Waals interactions for these cases. Considering the compatibility of Chit NPs with the human body and their non-toxicity, as well as the fact that factors such as pH, solubility, the ionic strength, and so on can be adjusted to control the release rate using the functionalized Chit NPs, it seems that the results of this work can be a comprehensive guide to design the drug delivery methods of FP drug using Chit NPs, to reduce the symptoms of COVID-19 disease.

Density functional theory evaluation of pristine and BN-doped biphenylene nanosheets to detect HCN.

Hydrogen cyanide (HCN) adsorption on pristine and B-N doped biphenylene nanosheets was investigated by means of density functional theory calculations. According to biphenylene geometry, all distinct possible B-N substitutions were designed. Adsorption energy and electronic structure at the level of M062X/6-31 g (d,p) theory were computed for all possible geometries. Our results reveal that pristine biphenylene nanosheet is not a suitable candidate for HCN detection. Also, for B-N doping, the sensitivity of the nanosheet depends on the B-N doped configuration. One of these derivative structures shows higher sensitivity to HCN adsorption due to the greater change in electronic properties. Moreover, atoms in molecules and natural bond orbital analysis were performed to obtain more in-depth knowledge about the adsorption mechanism. The range of energy for interaction between HCN and the nanosheets belongs to physical adsorption.

DFT, QTAIM, and NBO studies on the trimeric interactions in the protrusion domain of a piscine betanodavirus.

Crystal structure of the protrusion domain (P-domain) of the grouper nervous necrosis virus (GNNV) shows the presence of three-fold trimeric protrusions with two asymmetrical calcium cations along the non-crystallographic three-fold axis. The trimeric interaction natures of the interacting residues and the calcium cations with the neighboring residues within the trimeric interface have been studied by the quantum theory of atoms in molecules (QTAIM) and natural bond orbital (NBO) analyses in the framework of the density-functional theory (DFT) approach. The results revealed that residues Leu259, Val274, Trp280, and Gln322 of subunit A, Arg261, Asp275, Ala277, and Gln322 of subunit B, Leu259, Asp260, Arg261, Ala277, Val278, and Leu324 of subunit C are the main residues involved in the trimeric interactions. Charge-dipole, dipole-dipole, and hydrogen bonding interactions make the significant contributions to these trimeric interactions. Among different interacting residues within trimeric interface, residue pair Arg261 B-Leu259C forms the strongest hydrogen bond inside the interface between subunits B and C. It was also found that calcium cations interact with residues Asp273, Val274, and Asp275 of subunits A, B, and C through charge-charge and charge transfer interactions.

Characterization of cooperative effects in linear alpha-glycylglycine clusters.

The aspects of N-H...O=CNH, N-H...O=CO and C-H...O=CNH interactions are analyzed by applying ab initio and DFT methods as well as Bader theory. We investigated geometry, binding energies, (17)O, (15)N chemical shift tensors, and Atoms in Molecules (AIM) properties of alpha-glycylglycine (alpha-glygly) clusters, via MP2, B3LYP and PW91(XC) methods. Dimer stabilization energies and equilibrium geometries are studied in various levels of theory. MP2 and DFT calculations reveal that for alpha-glygly clusters, stability of N-H...O and C-H...O hydrogen bonds are enhanced significantly as a result of cooperativity effects. Furthermore, a covalent nature is also detected for some hydrogen bondings. The n-dependent trend of (17)O and (15)N chemical shift tensors was reasonably correlated with cooperative effects in hydrogen-bond interactions. Regarding the various N-H...O=CNH, N-H...O=CO and C-H...O=CNH hydrogen bondings, capability of the alpha-glygly clusters for electron localization at the N-H...O and C-H...O bond critical points, depends on the cluster size. This leads to cooperative changes in the hydrogen-bond length and strength as well as (17)O and (15)N chemical shift tensors.