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

K Mendanha, G Colherinhas - The Journal of Physical Chemistry …, 2024 - ACS Publications
This work presents a study on the effects of periodic boundary conditions (PBC) on the
energetic/structural properties and hydrogen bond dynamics (HB) using molecular dynamics …

A6H polypeptide membranes: Molecular dynamics simulation, GIAO-DFT-NMR and TD-DFT spectroscopy analysis

D Andrade, G Colherinhas - Journal of Molecular Liquids, 2020 - Elsevier
Abstract In this work, Molecular Dynamics simulation (MD), GIAO-DFT-NMR, and TD-DFT
results are obtained to study structural, energetic, dynamics, and spectroscopy properties of …

Updating atomic charge parameters of aliphatic amino acids: a quest to improve the performance of molecular modeling via sequential molecular dynamics and DFT …

G Colherinhas - Physical Chemistry Chemical Physics, 2021 - pubs.rsc.org
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 …

Gold Nanoparticles‐Modified 2D Self‐Assembled Amphiphilic Peptide Nanosheets with High Biocompatibility and Photothermal Therapy Efficiency

Y Xu, P He, G Gu, D Zhu, X Luan… - Macromolecular Rapid …, 2024 - Wiley Online Library
Amphiphilic peptides have garnered significant attention due to their highly designable and
self‐assembling behaviors. Self‐assembled peptides hold excellent potential in various …

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

ED Alves, DX de Andrade, AR de Almeida… - Journal of Molecular …, 2021 - Elsevier
Recently, a series of organic structures formed by peptide self-assembly have been
reported, among which stand out the peptide nanomembranes with promising applications …

Assessing the DOPC-cholesterol interactions and their influence on fullerene C60 partitioning in lipid bilayers

ED Alves, G Colherinhas, SA Mendanha - Journal of Molecular Liquids, 2020 - Elsevier
We propose a computational Molecular Dynamic (MD) study to evaluate the interaction of C
60 fullerene in contact with lipid membranes, as a function of the bilayers cholesterol …

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

G Colherinhas - Journal of Molecular Liquids, 2021 - Elsevier
In this theoretical work we develop simulations of classical molecular dynamics sequentially
combined with quantum calculations to obtain an update of the atomic charges of the …

The influence of polar and non-polar interactions on the self-assembly of peptide nanomembranes and their applications: An atomistic study using classical molecular …

D Andrade, G Colherinhas - Journal of Molecular Liquids, 2020 - Elsevier
In this work, structural and energetic properties of five peptide membranes are investigated
via fully atomistic molecular dynamics simulations. The membranes are made up of peptides …

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

ED Alves, DX de Andrade, AR de Almeida… - Journal of Molecular …, 2022 - Elsevier
In this work, we develop molecular dynamics simulations to investigate the structural and
dynamic behavior of hydrogen bonds in A 6 X-type peptide structures (X= D, K, and R) in the …

Elucidating NH2-I3V3A3G3K3-COOH and NH2-K3G3A3V3I3-COOH polypeptide membranes: A classical molecular dynamics study

D Andrade, LBA Oliveira, G Colherinhas - Journal of Molecular Liquids, 2019 - Elsevier
In this paper, polypeptide membranes composed by surfactant-like peptides were studied by
using molecular dynamics simulations. The studied membranes are composed by 15 amino …