Surface Signatures of Bioactivity: MD Simulations of 45S and 65S Silicate Glasses

ABSTRACTNetwork structures of several kinds of oxide glasses were analyzed by means of neutron or x-ray diffraction method and molecular dynamics (MD) simulations including silicate, borate and tellurite glasses. The basic scheme of the structure highly depends on the bonding nature of network forming oxide, but the size of the alkali ions is another important factor to control the network structure of the glass. Structures of silicate glasses are rather easily reproduced by means of MD simulation, whereas borate or tellurite glass structures are hard to be constructed by MD calculation with only 2-body potentials. It is necessary to use adequate potentials to control the bonding angles of O-M-O or M-O-M. The network structure of tellurite glass seems very complex because of the shape of structural units with low symmetry, the use of a new kind of potential was found indispensable to reproduce the glass structure by MD.In addition to the network structure, the polarization of ions seems to be important to understand the whole vision of oxide glass structures. A new kind of MD was developed which took polarization of ions into account to understand the mixed alkali effects in silicate glasses.

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Ion-exchange mechanisms and interfacial reaction kinetics during aqueous corrosion of sodium silicate glasses

npj Materials Degradation ◽

10.1038/s41529-021-00159-4 ◽

2021 ◽

Vol 5 (1) ◽

Author(s):

Lu Deng ◽

Katsuaki Miyatani ◽

Michinori Suehara ◽

Shin-ichi Amma ◽

Madoka Ono ◽

...

Keyword(s):

Ion Exchange ◽

Reaction Kinetics ◽

Interfacial Reaction ◽

Md Simulations ◽

Interfacial Reactions ◽

Silicate Glasses ◽

Initial Surface ◽

Aqueous Corrosion ◽

Oxygen Tetrahedron ◽

Property Changes

AbstractThe ion-exchange and associated interfacial reaction mechanisms of silicate glasses are critical in elucidating their aqueous corrosion behaviors, surface modification and property changes, hence have potential impact on both science and technology. This work reports findings of the atomic and nanoscale details of the glass–water interfacial reactions revealed by applying reactive force field (ReaxFF) based molecular dynamics (MD) simulations, from which the key mechanisms of the ion exchange, as well as the kinetics of associated interfacial reactions, are elucidated. It was found that the Na+ and H+ ion exchange can happen between two oxygen ions on a single silicon oxygen tetrahedron or adjacent tetrahedra. In addition, the clustered reaction of two non-bridging oxygens mediated by an adjacent water molecule was also identified. The latter reaction might be the main mechanism of water transport after initial surface reactions that consume the non-bridging oxygen species on the surface. Water molecules thus can play two roles: as an intermediate during the proton transfer processes and as a terminator of the clustered reactions. Statistical analyses were performed to obtain reaction kinetics and the results show that silanol formation is a more favored process than the silanol re-formation within the first 3 ns of interfacial reactions. The results obtained thus shed lights on the complex ion-exchange mechanisms during glass hydration and enable more detailed understanding of the corrosion and glass–water interactions of silicate glasses.

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Direct observations of radiation-enhanced transformations in glass

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100075543 ◽

1983 ◽

Vol 41 ◽

pp. 354-355

Author(s):

J. F. DeNatale ◽

D. G. Howitt

Keyword(s):

Glass Matrix ◽

Diffusion Mechanism ◽

Bubble Formation ◽

Silicate Glasses ◽

Phase Decomposition ◽

Direct Observations ◽

Thin Foils ◽

Oxygen Bubble ◽

Electron Energy Loss ◽

Kinetics Of

The electron irradiation of silicate glasses containing metal cations produces various types of phase separation and decomposition which includes oxygen bubble formation at intermediate temperatures figure I. The kinetics of bubble formation are too rapid to be accounted for by oxygen diffusion but the behavior is consistent with a cation diffusion mechanism if the amount of oxygen in the bubble is not significantly different from that in the same volume of silicate glass. The formation of oxygen bubbles is often accompanied by precipitation of crystalline phases and/or amorphous phase decomposition in the regions between the bubbles and the detection of differences in oxygen concentration between the bubble and matrix by electron energy loss spectroscopy cannot be discerned (figure 2) even when the bubble occupies the majority of the foil depth.The oxygen bubbles are stable, even in the thin foils, months after irradiation and if van der Waals behavior of the interior gas is assumed an oxygen pressure of about 4000 atmospheres must be sustained for a 100 bubble if the surface tension with the glass matrix is to balance against it at intermediate temperatures.

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Coloration of Ce-doped Multicomponent Silicate Glasses by Electron Irradiation

Journal of Inorganic Materials ◽

10.15541/jim20140016 ◽

2014 ◽

Vol 29 (10) ◽

pp. 1018

Author(s):

FU Xin-Jie ◽

SONG Li-Xin ◽

LI Jia-Cheng

Keyword(s):

Electron Irradiation ◽

Silicate Glasses

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Efficient Treatment of Fixed and Induced Dipolar Interactions

MRS Proceedings ◽

10.1557/proc-653-z7.22 ◽

2000 ◽

Vol 653 ◽

Author(s):

Celeste Sagui ◽

Thoma Darden

Keyword(s):

Molecular Dynamics ◽

Md Simulations ◽

Lagrangian Formalism ◽

Dipolar Interactions ◽

Time Step ◽

Efficient Treatment ◽

Particle Mesh Ewald ◽

Fixed Charges ◽

Self Consistency ◽

Induced Dipoles

AbstractFixed and induced point dipoles have been implemented in the Ewald and Particle-Mesh Ewald (PME) formalisms. During molecular dynamics (MD) the induced dipoles can be propagated along with the atomic positions either by interation to self-consistency at each time step, or by a Car-Parrinello (CP) technique using an extended Lagrangian formalism. The use of PME for electrostatics of fixed charges and induced dipoles together with a CP treatment of dipole propagation in MD simulations leads to a cost overhead of only 33% above that of MD simulations using standard PME with fixed charges, allowing the study of polarizability in largemacromolecular systems.

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Spotting Differences in Molecular Dynamic Simulations of Influenza A M2 Protein-Ligand Complexes by Varying M2 construct, Lipid Bilayer and Force Field

10.26434/chemrxiv.11365943.v1 ◽

2019 ◽

Author(s):

Dimitrios Kolokouris ◽

Iris Kalenderoglou ◽

Panagiotis Lagarias ◽

Antonios Kolocouris

Keyword(s):

Molecular Dynamic ◽

Lipid Bilayer ◽

Influenza A ◽

Md Simulations ◽

Membrane Curvature ◽

Buffer Size ◽

M2 Protein ◽

Dynamic Simulations ◽

Amphipathic Helices ◽

Drug Protein Binding

<p>We studied by molecular dynamic (MD) simulations systems including the inward<sub>closed</sub> state of influenza A M2 protein in complex with aminoadamantane drugs in membrane bilayers. We varied the M2 construct and performed MD simulations in M2TM or M2TM with amphipathic helices (M2AH). We also varied the lipid bilayer by changing either the lipid, DMPC or POPC, POPE or POPC/cholesterol (chol), or the lipids buffer size, 10x10 Å<sup>2 </sup>or 20x20 Å<sup>2</sup>. We aimed to suggest optimal system conditions for the computational description of this ion channel and related systems. Measures performed include quantities that are available experimentally and include: (a) the position of ligand, waters and chlorine anion inside the M2 pore, (b) the passage of waters from the outward Val27 gate of M2 S31N in complex with an aminoadamantane-aryl head blocker, (c) M2 orientation, (d) the AHs conformation and structure which is affected from interactions with lipids and chol and is important for membrane curvature and virus budding. In several cases we tested OPLS2005, which is routinely applied to describe drug-protein binding, and CHARMM36 which describes reliably protein conformation. We found that for the description of the ligands position inside the M2 pore, a 10x10 Å<sup>2</sup> lipids buffer in DMPC is needed when M2TM is used but 20x20 Å<sup>2</sup> lipids buffer of the softer POPC; when M2AH is used all 10x10 Å<sup>2</sup> lipid buffers with any of the tested lipids can be used. For the passage of waters at least M2AH with a 10x10 Å<sup>2</sup> lipid buffer is needed. The folding conformation of AHs which is defined from hydrogen bonding interactions with the bilayer and the complex with chol is described well with a 10x10 Å<sup>2</sup> lipids buffer and CHARMM36. </p>

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A Hydrogen Bond Between Linear Tetrapyrrole and Conserved Aspartate Causes the Far-Red Shifted Absorption of Phytochrome Photoreceptors

10.26434/chemrxiv.12278780 ◽

2020 ◽

Author(s):

Egle Maximowitsch ◽

Tatiana Domratcheva

Keyword(s):

Hydrogen Bond ◽

Light Adaptation ◽

Positive Charge ◽

Pyrrole Ring ◽

Md Simulations ◽

Spectral Shift ◽

Specific Domain ◽

Study Guides ◽

Rational Engineering ◽

Tuning Mechanism

Photoswitching of phytochrome photoreceptors between red-absorbing (Pr) and far-red absorbing (Pfr) states triggers light adaptation of plants, bacteria and other organisms. Using quantum chemistry, we elucidate the color-tuning mechanism of phytochromes and identify the origin of the Pfr-state red-shifted spectrum. Spectral variations are explained by resonance interactions of the protonated linear tetrapyrrole chromophore. In particular, hydrogen bonding of pyrrole ring D with the strictly conserved aspartate shifts the positive charge towards ring D thereby inducing the red spectral shift. Our MD simulations demonstrate that formation of the ring D–aspartate hydrogen bond depends on interactions between the chromophore binding domain (CBD) and phytochrome specific domain (PHY). Our study guides rational engineering of fluorescent phytochromes with a far-red shifted spectrum.

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Computationally Assisted Design of High Signal-to-Noise Photoinduced Electron Transfer-Based Voltage-Sensitive Dyes

10.26434/chemrxiv.12401753 ◽

2020 ◽

Author(s):

Rishikesh Kulkarni ◽

Anneliese Gest ◽

Chun Kei Lam ◽

Benjamin Raliski ◽

Feroz James ◽

...

Keyword(s):

Electron Transfer ◽

Dft Calculations ◽

Photoinduced Electron Transfer ◽

Density Functional ◽

Embryonic Stem ◽

High Sensitivity ◽

Md Simulations ◽

High Signal ◽

Signal To Noise ◽

Green Fluorescent

<p>High signal-to-noise optical voltage indicators will enable simultaneous interrogation of membrane potential in large ensembles of neurons. However, design principles for voltage sensors with high sensitivity and brightness remain elusive, limiting the applicability of voltage imaging. In this paper, we use molecular dynamics (MD) simulations and density functional theory (DFT) calculations to guide the design of a bright and sensitive green-fluorescent voltage-sensitive fluorophore, or VoltageFluor (VF dye), that uses photoinduced electron transfer (PeT) as a voltage-sensing mechanism. MD simulations predict an 11% increase in sensitivity due to membrane orientation, while DFT calculations predict an increase in fluorescence quantum yield, but a decrease in sensitivity due to a decrease in rate of PeT. We confirm these predictions by synthesizing a new VF dye and demonstrating that it displays the expected improvements by doubling the brightness and retaining similar sensitivity to prior VF dyes. Combining theoretical predictions and experimental validation has resulted in the synthesis of the highest signal-to-noise green VF dye to date. We use this new voltage indicator to monitor the electrophysiological maturation of human embryonic stem cell-derived medium spiny neurons. </p>

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

10.26434/chemrxiv.5938177.v2 ◽

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>

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