scholarly journals HP-induced supra-molecular organization of guest molecules in FER-type zeolites

2014 ◽  
Vol 70 (a1) ◽  
pp. C1469-C1469
Author(s):  
Rossella Arletti ◽  
Simona Quartieri ◽  
Giovanna Vezzalini ◽  
Ettore Fois ◽  
Gloria Tabacchi
Keyword(s):  
Silicone Oil ◽  
Md Simulations ◽  
Membered Ring ◽  
Molecular Organization ◽  
Water Molecules ◽  
Structural Refinement ◽  
Guest Molecules ◽  
Guest Species ◽  
Dynamics Simulations ◽  
Stiffening Effect

The response to pressure of a synthetic all-silica ferrierite (Si-FER) and of a natural ferrierite from Monastir (Sardinia, Italy) (Mon-FER, Na0.56 K1.19 Mg2.02 Ca0.52 Sr0.14)(Al6.89Si29.04)O72 ·17.86 H2O) is here investigated combining HP synchrotron XRPD experiments and molecular dynamics simulations. The experiments were carried out by using penetrating (methanol:ethanol:water 16:3:1, m.e.w.; ethanol:water 1:3, e.w.) and non-penetrating (silicone oil, s.o.) pressure transmitting media (PTM). In Si-FER compressed in e.w., both water (w.) and ethanol molecules (e.) enter the pore system even at 0.2 GPa. The structural refinement of the data collected at 0.8 GPa reveals 8 w. and 4 e. molecules in the 10- and 6-membered ring channels, in tight agreement with the results of MD simulations. In Si-FER compressed at 0.2 GPa in m.e.w., only water molecules penetrate the 10-membered ring channels (15 per u.c.), organized in chains running along the channel axis. The interactions among the guest species and the framework oxygen atoms are very weak, due to the hydrophobicity of the framework. Upon decompression, the intruded extra-molecules are not completely released, so giving rise to new materials with different extra-framework contents. The results obtained for Si-FER compressed in m.e.w. and s.o. were compared to those obtained for Mon-FER, demonstrating that the zeolite composition and the PTM strongly influence the overall elastic parameters of the investigated samples. Specifically, Mon-FER shows a much higher rigidy than Si-FER in both media, due to the stiffening effect of the numerous extraframework species present in the natural sample. The higher rigidity of Si-FER in m.e.w. with respect to s.o. can be explained by the penetration, in the former case, of the PTM molecules, which contribute to stiffen the framework.

scholarly journals Determination of Reference Chemical Potential Using Molecular Dynamics Simulations

2010 ◽  
Vol 2010 ◽  
pp. 1-5 ◽  
Author(s):  
Krishnadeo Jatkar ◽  
Jae W. Lee ◽  
Sangyong Lee
Keyword(s):  
Molecular Dynamics ◽  
Gas Hydrates ◽  
Chemical Potential ◽  
Md Simulations ◽  
Water Molecules ◽  
Chemical Potential Difference ◽  
Guest Molecules ◽  
Experimental Values ◽  
Dynamics Simulations

A new method implementing molecular dynamics (MD) simulations for calculating the reference properties of simple gas hydrates has been proposed. The guest molecules affect interaction between adjacent water molecules distorting the hydrate lattice, which requires diverse values of reference properties for different gas hydrates. We performed simulations to validate the experimental data for determining , the chemical potential difference between water and theoretical empty cavity at the reference state, for structure II type gas hydrates. Simulations have also been used to observe the variation of the hydrate unit cell volume with temperature. All simulations were performed using TIP4P water molecules at the reference temperature and pressure conditions. The values were close to the experimental values obtained by the Lee-Holder model, considering lattice distortion.

Effect of Different Salt Concentrations on Dimethyl Sulfoxide (DMSO) Nanocluster Structures by Molecular Dynamics Simulations

2020 ◽  
Vol 20 (8) ◽  
pp. 4799-4806
Author(s):  
Peng Xie ◽  
Shubin Jin ◽  
Chenggang Sun ◽  
Yushu Xie
Keyword(s):  
Aqueous Solution ◽  
Dimethyl Sulfoxide ◽  
Water Cluster ◽  
Water Solution ◽  
Md Simulations ◽  
Water Molecules ◽  
Nacl Concentration ◽  
Dynamics Simulations ◽  
Simulation Systems ◽  
Decentralized Model

We performed MD simulations to examine dimethyl sulfoxide (DMSO) nanocluster structures in NaCl aqueous solution with different concentrations (0.45 g/100 mL, 0.9 g/100 mL, 1.8 g/100 mL, 2.7 g/100 mL, and 3.6 g/100 mL). Results showed that interaction between Na+ and DMSO at the first solvation shells was weakened due to acceleration rotational influence of ion driven by NaCl concentration. We investigated the tetrahedral order parameter and average H-B number of water molecules. These results indicated that NaCl influenced the solvation structure of water cluster, but that of DMSO was not affected by NaCl. We also found that Na+ was prior solvated by water solution in these mixture systems, and Cl− only existed in the water cluster in our simulation systems. Consequently, we herein proposed a decentralized model that depicts microphysical structure images of DMSO in NaCl aqueous solution systems.

Effect of Temperature on Velocity Profiles of Ions and Water Molecules in Charged Nanotubes

2020 ◽  
Author(s):  
Yu Wang ◽  
Zhenyu Liu
Keyword(s):  
Electroosmotic Flow ◽  
Fluid Transport ◽  
Tube Wall ◽  
High Surface ◽  
Md Simulations ◽  
Velocity Profiles ◽  
Nonequilibrium Molecular Dynamics ◽  
Effect Of Temperature ◽  
Water Molecules ◽  
Dynamics Simulations

Abstract High surface charge density makes it possible for charge inversion to occur in the electrical double layer, in which cases, flow reversal appears for electroosmotic driven flow that is one of the best-known methods of fluid transport based on the electro-kinetic phenomenon. Reverse electroosmotic flow of an aqueous solution of KCl was studied using MD method in this work. Nonequilibrium molecular dynamics simulations were carried out to investigate the effect of temperature on velocity profiles of ions and water molecules confined in charged carbon nanotubes (CNTs) with a diameter of 3.0 nm. The results demonstrate that the temperature dependence of velocity of ions and water molecules is obviously different for various distances to the tube wall. It is found that the temperature has a direct effect on the ion velocity profiles, that is, as the temperature increases, the velocity of either counter-ion or co-ion in the diffuse layer increases significantly though the velocity drops sharply in the vicinity of the tube wall surface. As for water molecules, the MD simulations show plenty of velocity profiles, in which the velocity is slightly positive near the tube wall, but is negative in most of the rest region. The temperature effect on reverse electroosmotic flow is clearly observed, which is reflected in two aspects: the viscosity of the fluid and the velocity profiles of ion and water molecule.

Excess Properties of Water-Methanol Mixtures as Studied by MD Simulations

1991 ◽  
Vol 46 (1-2) ◽  
pp. 95-99 ◽  
Author(s):  
G. Pálinkás ◽  
I. Bakó
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Mole Fraction ◽  
Extreme Values ◽  
Md Simulations ◽  
Excess Properties ◽  
Water Molecules ◽  
Methanol Mixture ◽  
Dynamics Simulations ◽  
Pair Interactions

AbstractMolecular dynamics simulations with pair interactions reproduce experimental excess properties of methanol-water mixtures. Water molecules lose, and methanol molecules gain neighbours in the mixtures as compared to the solvents. The water-methanol mixture with 0.25 mole fraction of methanol, resulting in extreme values for different excess properties, is characterized by the highest number of molecules with maximal number of H-bonded neighbours.

scholarly journals Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Krystel El Hage ◽  
Florent Hédin ◽  
Prashant K Gupta ◽  
Markus Meuwly ◽  
Martin Karplus
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Hydrophobic Effect ◽  
Md Simulations ◽  
Water Molecules ◽  
Human Hemoglobin ◽  
Standard Size ◽  
Wide Range ◽  
Dynamics Simulations

Recent molecular dynamics (MD) simulations of human hemoglobin (Hb) give results in disagreement with experiment. Although it is known that the unliganded (T0) and liganded (R4) tetramers are stable in solution, the published MD simulations of T0 undergo a rapid quaternary transition to an R-like structure. We show that T0 is stable only when the periodic solvent box contains ten times more water molecules than the standard size for such simulations. The results suggest that such a large box is required for the hydrophobic effect, which stabilizes the T0 tetramer, to be manifested. Even in the largest box, T0 is not stable unless His146 is protonated, providing an atomistic validation of the Perutz model. The possibility that extra large boxes are required to obtain meaningful results will have to be considered in evaluating existing and future simulations of a wide range of systems.

scholarly journals HP-induced penetration of guest molecules in high-Si mordenite

2014 ◽  
Vol 70 (a1) ◽  
pp. C1255-C1255
Author(s):  
Simona Quartieri ◽  
Lara Leardini ◽  
Rossella Arletti ◽  
Giovanna Vezzalini
Keyword(s):  
Silicone Oil ◽  
Structural Features ◽  
P Value ◽  
Irreversible Loss ◽  
Guest Molecules ◽  
Rietveld Refinements ◽  
Guest Species ◽  
Full Profile ◽  
Diffraction Patterns

A high-Si mordenite (HS-MOR, SiO2/Al2O3 ~ 200, s.g. Cmcm) was investigated by in-situ synchrotron XRPD under HP using silicone oil (s.o.) as non-penetrating pressure transmitting medium (PTM), and the following penetrating PTM: (16:3:1) methanol: ethanol:water (m.e.w), (3:1) water:ethanol (w:e), ethylene glycol (e.g.) and resorcinol (res). The experiments were performed in DAC at SNBL1 (ESRF, Grenoble). The evolution of the structural features was followed by full profile Rietveld refinements. In the Pamb-1.2 GPa range, the volume contraction of HS-MOR compressed in s.o. (Tab. 1) is the highest found among the HS zeolites studied up to now in the same P range [1-2]. Above this P value, a rapid and irreversible loss of long range order is observed in the diffraction patterns. These findings suggest a gradual P-induced amorphization. The main results of the experiments with penetrating PTM are the following (Tab. 1 and Fig. 1): i) no complete X-ray amorphization and phase transitions achieved up to the highest investigated P; ii) penetration of additional guest species into the channels, even at very low P; iii) lower cell-volume reduction with respect to that found in s.o. in the same P range; iv) partial reversibility of the P-induced effects upon decompression. The lower compressibility of HS-MOR in penetrating PTM with respect to s.o. is due to the entrapping of additional guest molecules, which contributes to sustaining the mordenite framework and stiffening the material.

scholarly journals Chemical substitutions in the selectivity filter of potassium channels do not rule out constricted-like conformations for C-type inactivation

2017 ◽  
Vol 114 (42) ◽  
pp. 11145-11150 ◽  
Author(s):  
Jing Li ◽  
Jared Ostmeyer ◽  
Eliot Boulanger ◽  
Huan Rui ◽  
Eduardo Perozo ◽  
...  
Keyword(s):  
Md Simulations ◽  
Selectivity Filter ◽  
Time Dependent ◽  
Water Molecules ◽  
Computational Results ◽  
Structural Studies ◽  
X Ray ◽  
Chemically Modified ◽  
Dynamics Simulations ◽  
Rule Out

In many K+ channels, prolonged activating stimuli lead to a time-dependent reduction in ion conduction, a phenomenon known as C-type inactivation. X-ray structures of the KcsA channel suggest that this inactivated state corresponds to a “constricted” conformation of the selectivity filter. However, the functional significance of the constricted conformation has become a matter of debate. Functional and structural studies based on chemically modified semisynthetic KcsA channels along the selectivity filter led to the conclusion that the constricted conformation does not correspond to the C-type inactivated state. The main results supporting this view include the observation that C-type inactivation is not suppressed by a substitution of D-alanine at Gly77, even though this modification is believed to lock the selectivity filter into its conductive conformation, whereas it is suppressed following amide-to-ester backbone substitutions at Gly77 and Tyr78, even though these structure-conserving modifications are not believed to prevent the selectivity filter from adopting the constricted conformation. However, several untested assumptions about the structural and functional impact of these chemical modifications underlie these arguments. To make progress, molecular dynamics simulations based on atomic models of the KcsA channel were performed. The computational results support the notion that the constricted conformation of the selectivity filter corresponds to the functional C-type inactivated state of the KcsA. Importantly, MD simulations reveal that the semisynthetic KcsAD-ala77 channel can adopt an asymmetrical constricted-like nonconductive conformation and that the amide-to-ester backbone substitutions at Gly77 and Tyr78 perturb the hydrogen bonding involving the buried water molecules stabilizing the constricted conformation.

Temperature Dependence of the Air/Water Interface Revealed by Polarization Sensitive Sum-Frequency Generation Spectroscopy

2018 ◽  
Author(s):  
Daniel R. Moberg ◽  
Shelby C. Straight ◽  
Francesco Paesani
Keyword(s):  
Temperature Dependence ◽  
Low Frequency ◽  
Potential Energy Function ◽  
Md Simulations ◽  
Sum Frequency Generation ◽  
Water Molecules ◽  
Water Interface ◽  
Sum Frequency ◽  
Air Water Interface ◽  
Frequency Generation

<div> <div> <div> <p>The temperature dependence of the vibrational sum-frequency generation (vSFG) spectra of the the air/water interface is investigated using many-body molecular dynamics (MB-MD) simulations performed with the MB-pol potential energy function. The total vSFG spectra calculated for different polarization combinations are then analyzed in terms of molecular auto-correlation and cross-correlation contributions. To provide molecular-level insights into interfacial hydrogen-bonding topologies, which give rise to specific spectroscopic features, the vSFG spectra are further investigated by separating contributions associated with water molecules donating 0, 1, or 2 hydrogen bonds to neighboring water molecules. This analysis suggests that the low frequency shoulder of the free OH peak which appears at ∼3600 cm−1 is primarily due to intermolecular couplings between both singly and doubly hydrogen-bonded molecules. </p> </div> </div> </div>

Assessing the Antimalarial Potentials of Phytochemicals: Virtual Screening, Molecular Dynamics and In-Vitro Investigations

2019 ◽  
Vol 16 (3) ◽  
pp. 291-300
Author(s):  
Saumya K. Patel ◽  
Mohd Athar ◽  
Prakash C. Jha ◽  
Vijay M. Khedkar ◽  
Yogesh Jasrai ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Structural Integrity ◽  
Md Simulations ◽  
Tylophora Indica ◽  
Multidrug Resistance Protein 1 ◽  
Receptor Complexes ◽  
Resistance Protein ◽  
Dynamics Simulations ◽  
Stable Trajectory

Background: Combined in-silico and in-vitro approaches were adopted to investigate the antiplasmodial activity of Catharanthus roseus and Tylophora indica plant extracts as well as their isolated components (vinblastine, vincristine and tylophorine). </P><P> Methods: We employed molecular docking to prioritize phytochemicals from a library of 26 compounds against Plasmodium falciparum multidrug-resistance protein 1 (PfMDR1). Furthermore, Molecular Dynamics (MD) simulations were performed for a duration of 10 ns to estimate the dynamical structural integrity of ligand-receptor complexes. </P><P> Results: The retrieved bioactive compounds viz. tylophorine, vinblastin and vincristine were found to exhibit significant interacting behaviour; as validated by in-vitro studies on chloroquine sensitive (3D7) as well as chloroquine resistant (RKL9) strain. Moreover, they also displayed stable trajectory (RMSD, RMSF) and molecular properties with consistent interaction profile in molecular dynamics simulations. </P><P> Conclusion: We anticipate that the retrieved phytochemicals can serve as the potential hits and presented findings would be helpful for the designing of malarial therapeutics.

scholarly journals Electrical Breakdown Mechanism of Transformer Oil with Water Impurity: Molecular Dynamics Simulations and First-Principles Calculations

Crystals ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 123
Author(s):  
Bin Cao ◽  
Ji-Wei Dong ◽  
Ming-He Chi
Keyword(s):  
Molecular Dynamics ◽  
Thermal Diffusion ◽  
First Principles ◽  
Electrical Breakdown ◽  
Transformer Oil ◽  
Water Molecules ◽  
Conducting Channel ◽  
Breakdown Mechanism ◽  
Water Impurity ◽  
Dynamics Simulations

Water impurity is the essential factor of reducing the insulation performance of transformer oil, which directly determines the operating safety and life of a transformer. Molecular dynamics simulations and first-principles electronic-structure calculations are employed to study the diffusion behavior of water molecules and the electrical breakdown mechanism of transformer oil containing water impurities. The molecular dynamics of an oil-water micro-system model demonstrates that the increase of aging acid concentration will exponentially expedite thermal diffusion of water molecules. Density of states (DOS) for a local region model of transformer oil containing water molecules indicates that water molecules can introduce unoccupied localized electron-states with energy levels close to the conduction band minimum of transformer oil, which makes water molecules capable of capturing electrons and transforming them into water ions during thermal diffusion. Subsequently, under a high electric field, water ions collide and impact on oil molecules to break the molecular chain of transformer oil, engendering carbonized components that introduce a conduction electronic-band in the band-gap of oil molecules as a manifestation of forming a conductive region in transformer oil. The conduction channel composed of carbonized components will be eventually formed, connecting two electrodes, with the carbonized components developing rapidly under the impact of water ions, based on which a large number of electron carriers will be produced similar to “avalanche” discharge, leading to an electrical breakdown of transformer oil insulation. The water impurity in oil, as the key factor for forming the carbonized conducting channel, initiates the electric breakdown process of transformer oil, which is dominated by thermal diffusion of water molecules. The increase of aging acid concentration will significantly promote the thermal diffusion of water impurities and the formation of an initial conducting channel, accounting for the degradation in dielectric strength of insulating oil containing water impurities after long-term operation of the transformer.

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