Molecular dynamics simulation of anionic clays containing glutamic acid

Xu, Qian; Zhang, Ni; Yao, Ping; Li, Yuan

doi:10.1016/j.molstruc.2010.05.027

Cited by 7 publications

(4 citation statements)

References 28 publications

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“…Oxygen always acts as an acceptor, and the functional groups, such as NH and OH, act as donors. If the hydrogen‐acceptor distance is less than 2.5 Å and simultaneously the acceptor‐hydrogen‐donor angle O—H—O and O—H—N in our simulation) is more than 90°, the hydrogen bond function can be considered …”

Section: Resultsmentioning

confidence: 99%

Molecular dynamics simulation of nonsteroidal antiinflammatory drugs, naproxen and relafen, in a lipid bilayer membrane

Yousefpour

Iranagh

Nademi

et al. 2013

Int J of Quantum Chemistry

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Naproxen and relafen, as nonsteroidal antiinflammatory drugs, were simulated in neutral and charged forms and their effects on a lipid bilayer membrane were investigated by molecular dynamics simulation using Groningen machine for chemical simulations software (GROMACS). Simulation of 10 systems was performed, which included different dosages of the drug molecules, naproxen and Relafen, in charged and neutral forms, and a mixture of naproxen and Relafen in neutral forms. The effects of the mixture and the individual drugs' dosages on membrane properties, such as electrostatic potential, order parameter, diffusion coefficients, and hydrogen bond formation, were analyzed. Hydration of the drugs in the membrane system was investigated using radial distribution function analysis. Using fully hydrated dimyristoylphosphatidylcholine (DMPC) as a reference system, 128 lipid molecules and water molecules were simulated exclusively, and the same simulation technique was performed on 10 other systems, including drug mixtures and a DMPC membrane. Angular distributions of lipid chains of the membrane were calculated, and the effects of the drug insertion and chain orientation in the membrane were evaluated.

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Section: Resultsmentioning

confidence: 99%

Molecular dynamics simulation of nonsteroidal antiinflammatory drugs, naproxen and relafen, in a lipid bilayer membrane

Yousefpour

Iranagh

Nademi

et al. 2013

Int J of Quantum Chemistry

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“…MD simulations can be used to study the formation of hydrogen bonds, which are determined by defining cutoffs for the acceptor-donor-hydrogen angle (e.g., angles O-H-O and O-H-N higher than 90°) and for the hydrogen-acceptor distances (e.g., less than 2.5 Å) [270,271].…”

Section: Accepted Manuscriptmentioning

confidence: 99%

Shedding light on the puzzle of drug-membrane interactions: Experimental techniques and molecular dynamics simulations

Lopes

Jakobtorweihen

Nunes

et al. 2017

Progress in Lipid Research

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“…Another conclusion to be drawn is that complementary aspects of the adsorption process can be revealed by macroscopic modeling of the adsorption data, spectroscopic studies, chiefly vibrational (ATR, , or SFG) and solid-state NMR, , and molecular modeling. ,− A sound approach to the study of Glu adsorption should combine several of these techniques.…”

Section: Introductionmentioning

confidence: 99%

Glutamic Acid Adsorption and Transformations on Silica

et al. 2011

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We report here on the adsorption and deposition of L-glutamic acid (Glu) on an amorphous silica and its subsequent thermal transformations. When adsorbed from aqueous solutions, Glu only has a low affinity for the silica surface but at high concentrations the adsorbed molecules serve as nuclei for the formation of small glutamic acid crystallites. As long as the Glu loading remains inferior to a saturation limit (about 0.5 molecule nm À2 ), the thermal behavior of adsorbed Glu is significantly different from that of bulk glutamic acid. Two successive condensation steps are observed upon mild thermal activation, and their products have been identified by a combination of techniques including thermogravimetry, in situ IR, solid-state NMR, and ESI-MS. The first step at about 120 °C is a lactam ring closure quantitatively yielding pyroglutamic acid in a first-order reaction. The second step, at 150 °C, probably results in the formation of a highly activated tricyclic imide, PyroGluDKP, and is easily reversible in the presence of water. These reactions have implications for prebiotic peptide formation and for synthetic chemistry.

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Molecular dynamics simulation of anionic clays containing glutamic acid

Cited by 7 publications

References 28 publications

Molecular dynamics simulation of nonsteroidal antiinflammatory drugs, naproxen and relafen, in a lipid bilayer membrane

Molecular dynamics simulation of nonsteroidal antiinflammatory drugs, naproxen and relafen, in a lipid bilayer membrane

Shedding light on the puzzle of drug-membrane interactions: Experimental techniques and molecular dynamics simulations

Glutamic Acid Adsorption and Transformations on Silica

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