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 …

Elucidating the structure of merocyanine dyes with the ASEC-FEG method. Phenol blue in solution

LR Franco, I Brandão, TL Fonseca… - The Journal of chemical …, 2016 - pubs.aip.org
The electronic structure of phenol blue (PB) was investigated in several protic and aprotic
solvents, in a wide range of dielectric constants, using atomistic simulations. We employed …

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 …

Isotropic magnetic shielding constants of retinal derivatives in aprotic and protic solvents

G Colherinhas, TL Fonseca, MA Castro… - The Journal of …, 2013 - pubs.aip.org
We investigate the nuclear isotropic shielding constants σ (13 C) and σ (17 O) of isomers of
retinoic acid and retinal in gas-phase and in chloroform, acetonitrile, methanol, and water …

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 …

GIAO⿿ DFT isotropic magnetic shielding constants and spin⿿ spin coupling of tartaric acid in water solution

B Fideles, LBA Oliveira, G Colherinhas - Chemical Physics Letters, 2016 - Elsevier
We investigate the nuclear isotropic shielding constants and spin⿿ spin coupling for oxygen
and carbons atoms of isomers of tartaric acid in gas phase and in water solutions by Monte …

Solvent effects on the spectroscopic properties of cannabinoids derivatives: A theoretical study using PCM

RC Prado, VS Filho, SA Portes… - … Journal of Quantum …, 2024 - Wiley Online Library
Abstract Using the Polarizable Continuum Model (PCM), we investigated the solvent effect
on the spectroscopic properties of three different groups of molecules with potential …

Molecular dynamic simulations, GIAO‐NMR and TD‐DFT spectroscopy analyze for zwitterionic isoleucine (ILE)N, 1 ≤ N ≤ 6, in water solution

K Mendanha, RC Prado, LBA Oliveira… - Journal of …, 2021 - Wiley Online Library
In this article, we investigate the effects of the isoleucine (ILE) N amino acid chain growth,
N= 1.0. 6, the ILE conformational effect as well as the solvent presence on the electrical and …

GIAO-DFT-NMR characterization of fullerene-cucurbituril complex: the effects of the C60@CB[9] host-guest mutual interactions

G Colherinhas, EE Fileti, T Malaspina - Journal of Molecular Modeling, 2018 - Springer
Magnetic shielding constants for an isolated fullerene C 60, cucurbituril CB [9], and the host-
guest complex C 60@ CB [9] were calculated as a function of separation of the monomers …