DICE: A Monte Carlo code for molecular simulation including the configurational bias Monte Carlo method

HM Cezar, S Canuto, K Coutinho - Journal of Chemical …, 2020 - ACS Publications
Solute–solvent systems are an important topic of study, as the effects of the solvent on the
solute can drastically change its properties. Theoretical studies of these systems are done …

Theoretical investigation on the linear and nonlinear optical properties of DAPSH crystal

C Valverde, R Medeiros, LR Franco, FAP Osório… - Scientific Reports, 2023 - nature.com
The linear polarizability, first and second hyperpolarizabilities of the asymmetric unit of
DAPSH crystal are studied and compared with available experimental results. The …

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 …

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 …

Understanding Nonlinear Optical Phenomena in N-Pyrimidinyl Stilbazolium Crystals via a Self-Consistent Electrostatic Embedding–DFT Approach

R Medeiros, LR Franco, FAP Osório, C Valverde… - ACS …, 2024 - ACS Publications
Density functional theory (DFT) and time-dependent density functional theory (TD-DFT) have
been used to investigate the nonlinear optical (NLO) properties of phenolic N-pyrimidinyl …

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 …