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 …

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

LBA Oliveira, G Colherinhas - Journal of Molecular Liquids, 2020 - Elsevier
Here we present calculations of electrical, energetic and magnetic properties of the amino
acids arginine, aspartic acid, glutamic acid, histidine and lysine in water solution. The …

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 …

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

LBA Oliveira, WB Cardoso, G Colherinhas - Journal of Molecular Liquids, 2021 - Elsevier
In the present paper, we investigated the polarization effects on different amino acids (AAs)
structures, ie, Serine, Threonine, Cysteine, Methionine, Asparagine, and Glutamine. Initially …

Fullerene C60 spectroscopy in [BMIM][PF6] ionic liquid: Molecular dynamics study using polarization effects

WB Cardoso, G Colherinhas - Journal of Molecular Structure, 2022 - Elsevier
We employ molecular dynamics (MD) simulations to assess the electrical behavior of the
atomic charges of a fullerene immersed in an ionic liquid (and water). From solute-solvent …

EF4K bola-amphiphilic peptide nanomembrane: structural, energetic and dynamic properties using molecular dynamics

ER de Sousa, DX de Andrade, G Colherinhas - Journal of Molecular …, 2022 - Elsevier
In this work, we developed a theoretical study on peptide membranes formed by the EF 4 K
amino acid sequence. The experimentally proven membrane structure was used as a basis …

Quantifying fluctuations of average solvent environments for embedding calculations

CE González-Espinoza, CA Rumble… - Journal of Chemical …, 2022 - ACS Publications
The viability and effectiveness of replacing an ensemble of embedded solute calculations by
a single calculation using an average description of the solvent environment are evaluated …

Theoretical study on symmetric and asymmetric stacking in the self-assembly of bola-amphiphilic peptides into membranes with mixtures of EF4E and KF4K

ER de Sousa, G Colherinhas - Journal of Molecular Liquids, 2024 - Elsevier
In this work, we conducted a study on peptide membranes formed by the amino acid
sequences EF 4 E and KF 4 K with the aim of obtaining energetic and structural results for …

Employing molecular dynamics simulations and DFT calculations to elucidate the energetic, structural, and spectroscopic attributes of (poly) valines in water solution

RC Prado, K Mendanha, LBA Oliveira… - Chemical Physics …, 2024 - Elsevier
In this study, we explored how the growth of peptide chains containing valines impacts
nuclear magnetic resonance (NMR) and optical absorption spectra. Results stem from …

[HTML][HTML] TD-DFT absorption spectrum of (poly) threonine in water: A study combining molecular dynamics and quantum mechanics calculations

K Mendanha, RC Prado, LBA Oliveira… - Chemical Physics …, 2021 - Elsevier
We develop a study using Molecular Dynamics and DFT to investigate the absorption
spectrum of (Thr) n in-water. Results of MD-simulations characterize the solute-solvent …