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 …

A combined Monte Carlo/DFT approach to simulate UV‐vis spectra of molecules and aggregates: Merocyanine dyes as a case study

B Tirri, G Mazzone, A Ottochian, J Gomar… - Journal of …, 2021 - Wiley Online Library
The combination of a Monte Carlo (MC) sampling of the configurational space with time
dependent‐density functional theory (TD‐DFT) to estimate vertical excitations energies has …

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

AR de Almeida, DX de Andrade… - Journal of Molecular …, 2022 - Elsevier
In this work, we performed fully atomistic classical molecular dynamics simulations to
characterize the structural and energetic interaction of peptide nanoribbons/nanofibers with …

Stability and Structural Analysis of A6R Polypeptide Nanosheets: A Theoretical Study Using the Classical Molecular Dynamics Simulation

B Proença, LBA Oliveira… - The Journal of Physical …, 2018 - ACS Publications
In this work, we have investigated the interactions of polypeptides composed of the
sequence of six alanines and one arginine (A6R) grouped in three nanosheet structures …

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 …

Dynamic interactions of negatively charged gold nanoparticles (AuNPs) in aqueous environments with different ionic compositions

E Coelho, D Xavier, A Almeida… - Journal of Molecular …, 2024 - Elsevier
This study provides a comprehensive analysis of the interactions between negatively
charged gold nanoparticles (Au) 144 (SRCOO 1−) 60 and both divalent (Mg 2+, Ca 2+) and …

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

AR de Almeida, LBA Oliveira, G Colherinhas - Chemical Physics Letters, 2019 - Elsevier
Abstract The Sequential Monte Carlo/Quantum Mechanics approach was used for
investigate the solvent effect on the solute-solvent structure and spectroscopic properties of …