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 …

Pyridine derivative platinum complexes: Synthesis, molecular structure, DFT and initial anticancer activity studies

E Kutlu, FM Emen, G Kismali, NK Kınaytürk… - Journal of Molecular …, 2021 - Elsevier
Novel pyridine derivative platinum complexes with the general formula [PtCl 2 L 2](L 1: 2-
fluoropyridine, L 2: 2-amino-3-methyl pyridine) were synthesized and their structural …

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 …

Theory and computation of nuclear shielding

T Kupka - 2020 - books.rsc.org
A review of the literature published from January to December 2019 on theoretical aspects
of nuclear magnetic shielding is presented. It covers both non-relativistic and relativistic …

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 …

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 …

Coordination of redox ions within a membrane-binding peptide: a tale of aromatic rings

R Fu, MT Rooney, R Zhang… - The journal of physical …, 2021 - ACS Publications
The amino-terminal-copper-and-nickel-binding (ATCUN) motif, a tripeptide sequence
ending with a histidine, confers important functions to proteins and peptides. Few high …

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 …