A theoretical approach on the ability of functionalized gold nanoparticles for detection of Cd2+

We hereby acknowledge Aalto University for providing computational facilities and financial support.Cadmium (Cd) as a toxic element that is widely present in water, soil, and air has important effects on human health, therefore proposing an accurate and selective method for detection of this element is of importance. In this article, by employing full atomistic molecular dynamics (MD) simulations and density functional theory dispersion corrected (DFT-D3) calculations, the effects of 6-mercaptonicotinic acid (MNA) and l-cysteine (CYS) on the stability of gold nanoparticles (AuNPs) and their sensitivity against Cd2+ were investigated. The obtained results indicate that pure AuNPs are not stable in water, while functionalized AuNPs with CYS and MNA groups have considerable stability without aggregation. In other words, the functional groups on the surface of AuNPs elevate their resistance against aggregation by an increase in the repulsive interactions between the gold nanoparticles. Moreover, functionalized AuNPs have considerable ability for selective detection of Cd2+ in the presence of different metal ions. Based on the MD simulation results, MNA-CYS-AuNPs (functionalized AuNPs with both functional groups) have the maximum sensitivity against Cd2+ in comparison with MNA-AuNPs and CYS-AuNPs due to the strong electrostatic interactions. DFT-D3 calculations reveal that the most probable interactions between the metal ions and functional groups are electrostatic, and Cd2+ can aggregate functionalized AuNPs due to strong electrostatic interactions with MNA and CYS groups. Moreover, charge transfer and donor-acceptor analyses show that molecular orbital interactions between the functional groups and Cd2+ can be considered as the driving force for AuNPs aggregation. A good agreement between the theoretical results and experimental data confirms the importance of the molecular modeling methods as a fast scientific protocol for designing new functionalized nanoparticles for application in different fields.Peer reviewe

The effects of amino acid sequence and solvent polarity on the self-assembling of cyclic peptide nanotubes and molecular channel formation inside the lipid bilayer

In this article, the effects of amino acid sequence and solvent polarity on the self-assembling process of cyclic peptides (CPs) were investigated by employing molecular dynamic (MD) simulations and quantum chemistry calculations. As a result, CP dimers are not stable in water, because of hydrogen bond (H-bond) lost between the CP units, while chloroform increases the stability of the CP dimers. MM-PBSA and MM-GBSA calculations confirmed that solvent polarity has an important effect on the stability of the CP dimers. Dynamical behavior of the cyclic peptide nanotubes (CPNTs) in chloroform indicates that CPNTs composed of leucine and phenylalanine are better molecular containers than that of isoleucine. At the next step, the ability of these CPNTs in molecular channel formation inside a fully hydrated DMPC (dimyristoylphosphatidylcholine) bilayer was investigated during 50 ns MD simulations. The obtained results show that only CPNT composed of isoleucine can form a molecular channel inside the DMPC membrane because isoleucine has a greater hydrophobicity than leucine and phenylalanine. This property increases the interactions between the CPNT and lipid residues, which elevates the stability of the CPNT inside the DMPC bilayer. Quantum chemistry calculations and non-covalent interactions analysis indicate that the solvent changes the stability and dynamical behavior of the CPNTs through the change in the H-bond strength. Finally, according to the different analyses, it can be concluded that the amino acid sequence in the CP units has an important role in designing specific nanostructures.Peer reviewe

Application of amino acid ionic liquids for increasing the stability of DNA in long term storage

Publisher Copyright: © 2022 Informa UK Limited, trading as Taylor & Francis Group.The structural stability of DNA is important because of its biological activity. DNAs due to their inherent chemical properties are not stable in an aqueous solution, therefore, a long period of storage of DNA at the ambient condition in bioscience is of importance. Ionic liquids (ILs) as interesting alternatives compared to organic solvents and water due to their considerable properties can be used as new agents to increase the stability of DNA for a long period of storage. In this article, molecular dynamics (MD) simulations and quantum chemistry calculations were applied to investigate the effects of amino acid ionic liquids ([BMIM][Ala], [BMIM][Gly], [BMIM][Val], [BMIM][Pro] and [BMIM][Leu]) on the dynamical behavior and the structural stability of calf thymus DNA. Based on the obtained MD results ILs enter into the solvation shell of the DNA and push away the water molecules from the DNA surface. Structural analysis shows that [BMIM]+ cations can occupy the DNA minor groove without disturbing the double-helical structure of DNA. ILs due to strong electrostatic and van der Waals (vdW) interactions with the DNA structure contribute to the stability of the double-helical structure. Quantum chemistry calculations indicate that the interactions between the [BMIM]+ cation and DNA structure has an electrostatic character. Moreover, this cation forms a more stable complex with the CGCG region of the DNA in comparison with AATT base pairs. Overall, the results of this study can provide new insight into the application of ILs for maintaining DNA stability during long-term storage. Communicated by Ramaswamy H. Sarma.Peer reviewe

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

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

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