DFT study on the selective complexation of B₁₂N₁₂ nanocage with alkali metal ions

<p>Quantum chemistry calculations indicate that BN nanocage is a good candidate for selective complex formation with Li⁺ in the presence of different alkali metal ions.</p> <p>Density functional theory (DFT) calculations were applied at the M05-2X/6-311++G(d,p) level of the theory to investigate the interaction of the B₁₂N₁₂ nanocage (BN) and alkali metal ions (Li⁺, Na⁺, K⁺, Rb⁺ and Cs⁺) in the gas phase and in water. On the basis of the results, BN nanocage is able to form a selective complex with Li⁺. Water, as a solvent, reduces the stability of the metal ion-BN complexes in comparison with the gas phase. Natural bond orbital (NBO) and quantum theory of atoms in molecules (QTAIM) analyses, reveal that the electrostatic interaction between the BN and metal ions can be considered as the driving force for complex formation in which the role of water is of significance. Density of states (DOSs) analysis of the BN nanocage structure in the presence of different metal ions showed a noticeable change in the frontier orbitals, especially in the gas phase, and Fermi level shifting toward the lower values.</p

Sensing Ability of Hybrid Cyclic Nanopeptides Based on Thiourea Cryptands for Different Ions, A Joint DFT-D3/MD Study

Theoretical studies, including quantum chemistry (QM) calculations and 25 ns molecular dynamic (MD) simulations, were performed on two types of hybrid cyclic nanopeptides (HCNPs) that are constructed of tren-capped cryptand (HCNP1) and 1,3,5-triethylbenzene-capped cryptand (HCNP2) for selective complex formation with OAC^–, NO₃^–, HSO₄^–, F^–, Br^–, and Cl^– ions in the gas phase and DMSO. Obtained data by M05-2X, M05-2X-D3, B3LYP, and B3LYP-D3 functionals indicated that HCNPs form a stable complex with F^– in comparison to other ions. DFT-D3 results and quantum theory of atoms in molecules (QTAIM) analysis indicated that dispersion and electrostatic interactions are the most important driving forces in HCNP–ion complex formation, respectively. Moreover, HOMO–LUMO analysis reveals that the reactivity of HCNP2, due to a lower band gap, is more than HCNP1. High sensing ability of the studied HCNPs for different ions was confirmed by Fermi level shifting of HNCPs to higher values during the complex formation. Finally, MD simulation results in DMSO are in good agreement with QM calculations and indicate that F^– forms the most stable complexes with HCNPs because of stronger electrostatic interactions

Antimicrobial peptide interactions with bacterial cell membranes

Antimicrobial peptides (AMPs) are potential alternatives for common antibiotics because of their greater activity and efficiency against a broad range of viruses, bacteria, fungi, and parasites. In this project, two antimicrobial peptides including magainin 2 and protegrin 1 with α-helix and β-sheet secondary structures were selected to investigate their interactions with different lipid bilayers such as 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoserine (POPS), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol (POPG), and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE), POPC/POPG (7:3), POPC/POPS (7:3), POPG/POPE(1:3), and POPG/POPE(3:1). The obtained structures of the AMPs illustrated that protegrin 1 cannot maintain its secondary structure in the solution phase in contrast to magainin 2. The head groups of the lipid units play a key role in the stability of the lipid bilayers. The head parts of the lipid membranes by increasing the internal H-bond contribute to membrane compactness. The POPG and POPS units inside the POPC/POPG and POPC/POPS membranes increase the order of the POPC units. The cationic residues of the AMPs form remarkable electrostatic interactions with the negatively charged membrane surfaces, which play a key role in the stabilization process of the peptide secondary structures. The Arg residues of protegrin 1 and the Gly1, Lys4, Lys10, Lys11, Lys14, and Glu19 of the magainin 2 have the most important roles in the complexation process. The values of Gibbs binding energies (ΔG) indicate that the complexation process between AMPs and different bacterial membranes is favorable from the thermodynamic viewpoint and AMPs could form stable complexes with the lipid bilayers. As a result of ΔG values, protegrin 1 forms a more stable complex with POPG/POPE(3:1), while the α-helix has more affinity to the POPG/POPE(1:3) bacterial membranes. Therefore, it can be considered that β-sheet and α-helix AMPs are more effective against gram-positive and gram-negative bacteria, respectively. The results of this study can provide useful details about the antimicrobial peptide interactions with the bacterial cell, which can be employed for designing new antimicrobial materials with greater efficiency. Communicated by Ramaswamy H. Sarma</p

Quantum Chemistry Aspects of the Solvent Effects on 3,4-Dimethyl-2,5-dihydrothiophen-1,1-dioxide Pyrolysis Reaction

A theoretical density functional theory (DFT) study was employed to investigate solvent effects on a retro-cheletropic ene reaction. The use of a nonpolar solvent in this retro-ene reaction is desirable to improve the reaction rate. Interactions between 14 different solvents and the reaction mixtures (reactant and transition state) were considered using DFT solvation calculations. These results were used to determine the role of solvents on the rate constants. Theoretical calculations at the B3LYP/6-311++G­(d,p) level revealed that in the presence of solvents with low polarity the reaction becomes faster, which is in accordance with experimental data. Transition state–solvent interactions were analyzed by the quantum theory of atoms in molecules (QTAIM) and natural bond orbital (NBO) analysis. Finally, several correlations between electron densities in bond critical points of the C–S bond and interaction energy as well as vibrational frequencies at the transition state have been investigated