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

Song

et al. 2017

Sci Rep

Energetic salts/ionic liquids have received increasing attention as fascinating energetic materials, and the use of renewable compounds is a promising approach to developing energetic materials. Until recently, biomolecules have been used as raw materials to develop neutral energetic compounds, whereas research focused on ionic energetic materials obtained from natural bio-renewable frameworks is scarce. This work systematically investigates ionic bio-energetic materials (IBEMs) derived from sustainable natural amino acids. In addition to combustibility, high density, good thermal stability, and one-step preparation, these IBEMs demonstrated apparent hypotoxicity and insensitivity. Moreover, a theoretical examination was performed to explore their appropriate properties. The intriguing results of this study indicates that IBEMs are potential bio-based energetic materials.

Section: Resultsmentioning

confidence: 99%

Insensitive ionic bio-energetic materials derived from amino acids

Song

et al. 2017

Sci Rep

“…In the NPT simulations, pressure was regulated by the isotropic Berendsen method, and temperature was controlled by applying a Langevin thermostat with a relaxation time of 1 ps and collision frequency of 1 ps –1 for the pressure and temperature, respectively. − The SHAKE constraint was applied for all bonds involving hydrogen atoms. , The particle mesh Ewald method with 10 Å direct cutoff was employed to calculate the long-range electrostatic interactions. , All the MD simulations were performed using the Amber 20.0 software package …”

Section: Methods: Computational Detailsmentioning

confidence: 99%

Effects of Ionic Liquids on the Stabilization Process of Gold Nanoparticles

2022

Self Cite

Improving the stability of the gold nanoparticles (AuNPs) is an important challenge in nanoscience, given that the activity and ubiquitous application of the AuNPs in different fields depend largely on their stability in the solution phase. Ionic liquids (ILs) can be used as new alternatives in comparison to water and organic solvents due to their considerable properties to elevate the stability and resistance of the AuNPs against aggregation for a long period of storage. In this study, we employ molecular dynamics simulation and quantum chemistry calculations to investigate the effects of amino acid ILs ( and [BMIM][Ala]) on the stability and aggregation process of the AuNPs from the molecular viewpoint. Our results suggest that ILs can prevent AuNP aggregation. These ILs penetrate the solvation shell of the nanoparticles and by increasing the electrostatic repulsions on the surface of the AuNPs improve their stability against aggregation. Moreover, the [BMIM] + cation is more effective on the stability of the AuNPs in comparison with the corresponding anions. The ring of the cation, due to the stronger interaction with the AuNPs compared to the side chain, contributes predominantly to the stability of the nanostructures. Our quantum chemistry calculations confirm that dispersion interactions between the cation and anions of the ILs and the surface of gold play a key role in the stability of the IL−AuNP complexes. [Leu] − anion has the strongest dispersion interactions with the metal surface and forms the most stable complex with the AuNPs. Overall, the results of this study offer new insights into the properties of amino acid ILs as effective agents to improve the stability of AuNPs for long-term storage.

“…The comparison of the half-life of the SARS-CoV and SARS-CoV-2 viruses in direct contact with the surface of plastic and stainless steel shows that the half-life of the novel coronavirus is longer than the SARS-CoV, in which the SARS-CoV-2 can stay alive on the plastic surface for about 6.8 h. 39 In comparison to the experimental methods by employing computational techniques, it is possible to analyze the dynamical behavior and structural features of the protein on the surface of the substrate from the molecular viewpoint, which can provide useful details to design and develop new sensors. 40,41 Prior investigations revealed that molecular dynamics (MD) methods can give us deep molecular insight regarding the interaction of the protein with the surface of different materials. 42 For instance, Lecot et al studied the ACE2 adsorption process on the surface of SiO 2 (silane monolayer) to design a sensor for SARS-CoV-2 detection.…”

Section: ■ Introductionmentioning

confidence: 99%

On the Sensitivity and Affinity of Gold, Silver, and Platinum Surfaces against the SARS-CoV-2 Virus: A Comparative Computational Study

Khavani

Mehranfar

Mofrad

2023

J. Chem. Inf. Model.

Self Cite

The novel coronavirus disease and its complications have motivated the design of new sensors with the highest sensitivity, and affinity for the detection of the SARS-CoV-2 virus is considered in many research studies. In this research article, we employ full atomistic molecular dynamics (MD) models to study the interactions between the receptor binding domain (RBD) and spike protein of the coronavirus and different metals such as gold (Au), platinum (Pt), and silver (Ag) to analyze their sensitivity against this virus. The comparison between the RBD interactions with ACE2 (angiotensin-converting enzyme 2) and different metals indicates that metals have remarkable effects on the structural features and dynamical properties of the RBD. The binding site of the RBD has more affinity to the surfaces of gold, platinum, and silver than to the other parts of the protein. Moreover, the initial configuration of the RBD relative to the metal surface plays an important role in the stability of metal complexes with the RBD. The binding face of the protein to the metal surface has been changed in the presence of different metals. In other words, the residues of the RBD that participate in RBD interactions with the metals are different irrespective of the initial configurations in which the [Asn, Thr, Tyr], [Ser, Thr, Tyr], and [Asn, Asp, Tyr] residues of the protein have a greater affinity to Ag, Au, and Pt, respectively. The corresponding metals have a considerable affinity to the RBD, which due to strong interactions with the protein can change the secondary structure and structural features. Based on the obtained results during the complexation process between the protein and metals, the helical structure of the protein changes to the bend and antiparallel β-sheets. The calculated binding energies for the RBD complexes with silver, gold, and platinum are −95.03, −138.03, and −133.96 kcal·mol–1, respectively. The adsorption process of the spike protein on the surfaces of different metals represents similar results and indicates that the entire spike protein of the coronavirus forms a more stable complex with the gold surface compared with other metals. Moreover, the RBD of the spike protein has more interactions with the surfaces than with the other parts of the protein. Therefore, it is possible to predict the properties of the coronavirus on the metal surface based on the dynamical behavior of the RBD. Overall, our computational results confirm that the gold surface can be considered as an outstanding substrate for developing new sensors with the highest sensitivity against SARS-CoV-2.