Statistical and energetic analysis of hydrogen bonds in short and long peptide nanotapes/nanofibers using molecular dynamics simulations

Exploring How System Dimensions and Periodic Boundary Conditions Influence the Molecular Dynamics Simulation of A6H Peptide Self-Assembly Nanostructures

“…The findings reveal that the HB-interaction persists for around 1.6 ns in the A 6 H-11 system, whereas in the A 6 H-33 system, it endures for about 1.9 ns. Peptide−water interactions oscillate between 0.1 and 0.2 ns, a typical result found in other studies such as de Almeida et al 49 and findings by van der Spoel. 44 Table 3 provides a detailed breakdown of these results, comparing them with those obtained for the center of the A 6 H-33 structure, elucidating the influence of PBCs on this statistical analysis.…”

“…Recent studies have highlighted the importance of HBs in maintaining membrane structures, influencing the arrangement of certain amino acids. , HBs also play a role in permeability properties, as they can form between water molecules and polar groups in the membrane structure, allowing for hydration of these structures. These bonds can be formed and broken enabling changes and adaptation of the membrane structure.…”

Investigating Chlorination and Migration Mechanism of NaCl on C−S−H: DFT and AIMD Study**

“…Improvements can be achieved with DFT‐D3 [30–31] which better accounts for van‐der‐Waals interactions and underlying electron‐electron interactions. Molecular dynamics (MD) [32–34] is a computational method that can simulate different temperatures on the atomic scale. Some researchers had studied the atomic density, orientation, H‐bonds, and diffusion coefficient of chloride ion in C−S−H by MD simulation [35–38] .…”