Can CHARMM36 atomic charges described correctly the interaction between amino acid and water molecules by molecular dynamics simulations

In this work, we observe the behavior of the dipole moment, atomic charges, solute–solvent interactions and NMR spectroscopy of aliphatic amino acids in a water solution via the computational simulations of classical molecular dynamics and DFT quantum calculations. Our results indicate that the convergence of the atomic charge of the solute, from an iterative process, together with the dipole moment of the amino acid, alters the lifetime of hydrogen bonds present in the first solvation shell, resulting in the modification of its structure and dynamics. Using GIAO-DFT-NMR calculations, we assessed the impact of these structural solute–solvent modifications on the magnetic shielding constants of the solute carbon atoms. In this sense, we evaluate the importance of an update in parameters that describe atomic charges present in the CHARMM36 force field.

Updating atomic charge parameters of aliphatic amino acids: a quest to improve the performance of molecular modeling via sequential molecular dynamics and DFT-GIAO-NMR calculations.

Update of CHARMM36's atomic charges for aromatic amino acids in water solution simulations and spectroscopy analysis via sequential molecular dynamics and DFT calculations

With the increasing advancement of knowledge and the widespread use of electronics, the demand for more efficient energy storage devices and materials has increased dramatically. Poly ortho-aminophenol and its composites as the energy storage materials are reviewed in this article. The capacitive properties (specific capacitance, specific energy, specific power, number of charging-discharging cycles, and retention capacitance) of all these composites are fully listed as well as compared with other electrode materials. Electrochemical test diagrams (CV, GCD, and EIS) of some of these materials have been carefully studied. The data show that POAP composites have excellent electrochemical performance compared to pure POAP and other composites. These electrodes have also been tested in the actual devices and have shown excellent performance. Also, the morphological properties and structure of composite (SEM, TEM, BET, Fractal dimension, components) of these electrodes have been reviewed. The synergistic effect between the components has been reported. This polymer has a special electrocatalytic effect that can be used to design innovative electrodes with excellent performance and surface modification. Finally, a summary and insight into future plans are provided. In general, these composites showed excellent electrochemical performance and morphological properties, which shows the high potential of these materials in the application of supercapacitor electrodes.

Comprehensive study on poly ortho-aminophenol composite electrodes and their utilization for supercapacitor applications and green energy storage: A review

Hydroxylic, sulfur-containing and amidic amino acids in water solution: Atomic charges parameters for computational modeling using molecular dynamics simulation and DFT calculations

Atomistic molecular dynamics study on the influence of high temperatures on the structure of peptide nanomembranes candidates for organic supercapacitor electrode

Agnaldo R. de Almeida

Papers

Atomistic molecular dynamics study on the influence of high temperatures on the structure of peptide nanomembranes candidates for organic supercapacitor electrode

Solvent effects on the spectroscopic properties of Damascone derivatives: A sequential Monte Carlo/Quantum Mechanics study

Laminar peptide structure: Energetic and structural evaluation using molecular dynamics

Molecular dynamics study of hydrogen bond in peptide membrane at 150–300 K