A-Site Distribution in La1−xSrxMnO3: a Computational Study

2008 ◽  
Vol 1074 ◽  
Author(s):  
Yun Hee Jang ◽  
François Gervais ◽  
Yves Lansac
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Colossal Magnetoresistance ◽  
Computational Study ◽  
Mixed Valence ◽  
Magnetic Tunnel Junction ◽  
Md Simulations ◽  
Site Distribution ◽  
Mixed Valence Manganites ◽  
A Site

ABSTRACTThe possibility of an A-site (La3+/Sr2+) ordering in a colossal magnetoresistance manganite (CMR) La3/4Sr1/4MnO3 was explored using molecular dynamics (MD) simulations with a newly developed force field (FF) and quantum mechanics (QM) calculations on the structures obtained from MD. The calculated degrees of stabilization (enthalpy gain) of various patterns of A-site ordering are not significant enough to overcome the accompanying entropy loss, supporting the random A-site distribution in La3/4Sr1/4MnO3. This approach combining MD and QM as well as the versatile FF developed in this study should be useful to investigate the structures and functions of magnetic tunnel junction devices involving mixed-valence manganites.

scholarly journals The β-cyclodextrin/benzene complex and its hydrogen bonds – a theoretical study using molecular dynamics, quantum mechanics and COSMO-RS

2013 ◽  
Vol 9 ◽  
pp. 118-134 ◽  
Author(s):  
Jutta Erika Helga Köhler ◽  
Nicole Grczelschak-Mick
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Hydrogen Bonds ◽  
Md Simulations ◽  
Benzene Molecule ◽  
Glucose Unit ◽  
Hand Orientation ◽  
Different Temperatures ◽  
Dynamics Simulations ◽  
The Right

Four highly ordered hydrogen-bonded models of β-cyclodextrin (β-CD) and its inclusion complex with benzene were investigated by three different theoretical methods: classical quantum mechanics (QM) on AM1 and on the BP/TZVP-DISP3 level of approximation, and thirdly by classical molecular dynamics simulations (MD) at different temperatures (120 K and 273 to 300 K). The hydrogen bonds at the larger O2/O3 rim of empty β-CDs prefer the right-hand orientation, e.g., O3-H…O2-H in the same glucose unit and bifurcated towards …O4 and O3 of the next glucose unit on the right side. On AM1 level the complex energy was −2.75 kcal mol−1 when the benzene molecule was located parallel inside the β-CD cavity and −2.46 kcal mol−1 when it was positioned vertically. The AM1 HOMO/LUMO gap of the empty β-CD with about 12 eV is lowered to about 10 eV in the complex, in agreement with data from the literature. AM1 IR spectra displayed a splitting of the O–H frequencies of cyclodextrin upon complex formation. At the BP/TZVP-DISP3 level the parallel and vertical positions from the starting structures converged to a structure where benzene assumes a more oblique position (−20.16 kcal mol−1 and −20.22 kcal mol−1, resp.) as was reported in the literature. The character of the COSMO-RS σ-surface of β-CD was much more hydrophobic on its O6 rim than on its O2/O3 side when all hydrogen bonds were arranged in a concerted mode. This static QM picture of the β-CD/benzene complex at 0 K was extended by MD simulations. At 120 K benzene was mobile but always stayed inside the cavity of β-CD. The trajectories at 273, 280, 290 and 300 K certainly no longer displayed the highly ordered hydrogen bonds of β-CD and benzene occupied many different positions inside the cavity, before it left the β-CD finally at its O2/O3 side.

scholarly journals Computational Study of C-X-C Chemokine Receptor (CXCR)3 Binding with Its Natural Agonists Chemokine (C-X-C Motif) Ligand (CXCL)9, 10 and 11 and with Synthetic Antagonists: Insights of Receptor Activation towards Drug Design for Vitiligo

Molecules ◽  
2020 ◽  
Vol 25 (19) ◽  
pp. 4413
Author(s):  
Giovanny Aguilera-Durán ◽  
Antonio Romo-Mancillas
Keyword(s):  
Molecular Dynamics ◽  
Computational Study ◽  
Md Simulations ◽  
Receptor Activation ◽  
Activation Mechanism ◽  
Coarse Grained ◽  
Dimensional Structure ◽  
Cytotoxic Lymphocytes ◽  
Ligand Interaction ◽  
Α Subunit

Vitiligo is a hypopigmentary skin pathology resulting from the death of melanocytes due to the activity of CD8+ cytotoxic lymphocytes and overexpression of chemokines. These include CXCL9, CXCL10, and CXCL11 and its receptor CXCR3, both in peripheral cells of the immune system and in the skin of patients diagnosed with vitiligo. The three-dimensional structure of CXCR3 and CXCL9 has not been reported experimentally; thus, homology modeling and molecular dynamics could be useful for the study of this chemotaxis-promoter axis. In this work, a homology model of CXCR3 and CXCL9 and the structure of the CXCR3/Gαi/0βγ complex with post-translational modifications of CXCR3 are reported for the study of the interaction of chemokines with CXCR3 through all-atom (AA-MD) and coarse-grained molecular dynamics (CG-MD) simulations. AA-MD and CG-MD simulations showed the first activation step of the CXCR3 receptor with all chemokines and the second activation step in the CXCR3-CXCL10 complex through a decrease in the distance between the chemokine and the transmembrane region of CXCR3 and the separation of the βγ complex from the α subunit in the G-protein. Additionally, a general protein–ligand interaction model was calculated, based on known antagonists binding to CXCR3. These results contribute to understanding the activation mechanism of CXCR3 and the design of new molecules that inhibit chemokine binding or antagonize the receptor, provoking a decrease of chemotaxis caused by the CXCR3/chemokines axis.

scholarly journals Simulating Absorption Spectra of Flavonoids in Aqueous Solution: A Polarizable QM/MM Study

Molecules ◽  
2020 ◽  
Vol 25 (24) ◽  
pp. 5853
Author(s):  
Sulejman Skoko ◽  
Matteo Ambrosetti ◽  
Tommaso Giovannini ◽  
Chiara Cappelli
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Hydrogen Bonding ◽  
Force Field ◽  
Absorption Spectra ◽  
Computational Study ◽  
Md Simulations ◽  
Quantum Mechanical ◽  
Hydrogen Bonding Interactions

We present a detailed computational study of the UV/Vis spectra of four relevant flavonoids in aqueous solution, namely luteolin, kaempferol, quercetin, and myricetin. The absorption spectra are simulated by exploiting a fully polarizable quantum mechanical (QM)/molecular mechanics (MM) model, based on the fluctuating charge (FQ) force field. Such a model is coupled with configurational sampling obtained by performing classical molecular dynamics (MD) simulations. The calculated QM/FQ spectra are compared with the experiments. We show that an accurate reproduction of the UV/Vis spectra of the selected flavonoids can be obtained by appropriately taking into account the role of configurational sampling, polarization, and hydrogen bonding interactions.

scholarly journals Repurposing the Combination Drug of Favipiravir, Hydroxychloroquine and Oseltamivir as a Potential Inhibitor Against SARS-CoV-2: A Computational Study

2021 ◽  
Author(s):  
Pooja Yadav ◽  
PAPIA CHOWDHURY
Keyword(s):  
Molecular Dynamics ◽  
Computational Study ◽  
Md Simulations ◽  
Receptor Protein ◽  
Interaction Energies ◽  
Combination Drug ◽  
Hydrogen Bond Interaction ◽  
Energy Interaction ◽  
Combination Drugs ◽  
The World

Abstract The virus SARS-CoV-2 has created a situation of global emergency all over the world from the last few months. We are witnessing a helpless situation due to COVID-19 as no vaccine or drug is effective against the disease. In the present study, we have tested the repurposing efficacy of some currently used combination drugs against COVID-19. We have tried to understand the mechanism of action of some repurposed drugs:Favipiravir (F), Hydroxychloroquine (H) and Oseltamivir (O). The ADME analysis have suggested strong inhibitory possibility of F, H, O combination towards receptor protein of 3CLpro of SARS-CoV-2 virus. The strong binding affinity, number of hydrogen bond interaction between inhibitor, receptor and lower inhibition constant computed from molecular docking validated the better complexation possibility of F + H + O:3CLprocombination. Various thermodynamical output from Molecular dynamics (MD) simulations like potential energy (Eg), temperature (T), density, pressure, SASA energy, interaction energies, Gibbs free energy (ΔGbind) etc., also favored the complexation between F + H + O and CoV-2 protease. Our in-silico results have recommended the strong candidature of combination drugs Favipiravir, Hydroxychloroquine and Oseltamivir as a potential lead inhibitor for targeting SARS-CoV-2 infections.

Validity of Molecular Dynamics by Quantum Mechanics

2013 ◽  
Author(s):  
Thomas Prevenslik
Keyword(s):  
Molecular Dynamics ◽  
Heat Capacity ◽  
Quantum Mechanics ◽  
Statistical Mechanics ◽  
Quantum Electrodynamics ◽  
Md Simulations ◽  
Tensile Tests ◽  
Electron Pairs ◽  
Linear Motors ◽  
The Continuum

MD is commonly used in computational physics to determine the atomic response of nanostructures. MD stands for molecular dynamics. With theoretical basis in statistical mechanics, MD relates the thermal energy of the atom to its momentum by the equipartition theorem. Momenta of atoms in an ensemble are determined by solving Newton’s equations with inter-atomic forces derived from Lennard-Jones potentials. MD therefore assumes the atom always has heat capacity as otherwise the momenta of the atoms cannot be related to their temperature. In bulk materials, the continuum is simulated in MD by imposing PBC on an ensemble of atoms, the atoms always having heat capacity. PBC stands for periodic boundary conditions. MD simulations of the bulk are valid because atoms in the bulk do indeed have heat capacity. Nanostructures differ from the bulk. Unlike the continuum, the atom confined in discrete submicron geometries is precluded by QM from having the heat capacity necessary to conserve absorbed EM energy by an increase in temperature. QM stands for quantum mechanics and EM for electromagnetic. Quantum corrections of MD solutions that would show the heat capacity of nanostructures vanishes are not performed. What this means is the MD simulations of discrete nanostructures in the literature not only have no physical meaning, but are knowingly invalid by QM. In the alternative, conservation of absorbed EM energy is proposed to proceed by the creation of QED induced non-thermal EM radiation at the TIR frequency of the nanostructure. QED stands for quantum electrodynamics and TIR for total internal reflection. The QED radiation creates excitons (holon and electron pairs) that upon recombination produce EM radiation that charges the nanostructure or is emitted to the surroundings — a consequence only possible by QM as charge is not created in statistical mechanics. Invalid discrete MD simulations are illustrated with nanofluids, nanocars, linear motors, and sputtering. Finally, a valid MD simulation by QM is presented for the stiffening of NWs in tensile tests. NW stands for nanowire.

scholarly journals How membrane lipids influence plasma delivery of reactive oxygen species into cells and subsequent DNA damage: an experimental and computational study

2019 ◽  
Vol 21 (35) ◽  
pp. 19327-19341 ◽  
Author(s):  
Jonas Van der Paal ◽  
Sung-Ha Hong ◽  
Maksudbek Yusupov ◽  
Nishtha Gaur ◽  
Jun-Seok Oh ◽  
...  
Keyword(s):  
Reactive Oxygen Species ◽  
Molecular Dynamics ◽  
Dna Damage ◽  
Lipid Oxidation ◽  
Membrane Lipids ◽  
Computational Study ◽  
Md Simulations ◽  
Phospholipid Vesicle ◽  
Oxygen Species ◽  
Lipid Packing

The combination of phospholipid vesicle experiments and molecular dynamics (MD) simulations illustrate how lipid oxidation, lipid packing and rafts formation may influence the response of healthy and diseased cell membranes to plasma-derived RONS.

Site Balance Models in Plasma Processing: A Comparison to Molecular Dynamics Simulations

1995 ◽  
Vol 389 ◽  
Author(s):  
M.E. Barone ◽  
D.B. Graves
Keyword(s):  
Molecular Dynamics ◽  
Steady State ◽  
Molecular Dynamics Simulations ◽  
Phenomenological Models ◽  
Silicon Surface ◽  
Plasma Processing ◽  
Md Simulations ◽  
Balance Model ◽  
Dynamics Simulations ◽  
A Site

ABSTRACTMolecular dynamics (MD) simulations were conducted of Cl+ impact (at 10, 25 and 50 eV) of an initially bare silicon surface, leading to steady state coverage of Cl in a mixed chlorosilyl layer. Our main goal in this study was to compare the MD predictions to models of ion-assisted etching involving the concept of a site balance. For the case of 50 eV Cl+ etching silicon, the coverage vs. exposure results in the simulation could be reasonably well reproduced in a site balance model, but only if the correct parameters in the model were taken from the simulation. The results of the comparison suggest that MD simulations can be helpful in the development of physically sound phenomenological models of ion-assisted etching.

Exploring the hydrated microstructure and molecular mobility in blend polyelectrolyte membranes by quantum mechanics and molecular dynamics simulations

RSC Advances ◽  
2016 ◽  
Vol 6 (42) ◽  
pp. 35517-35526 ◽  
Author(s):  
Ghasem Bahlakeh ◽  
Mohammad Mahdi Hasani-Sadrabadi ◽  
Karl I. Jacob
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Molecular Dynamics Simulations ◽  
Molecular Mobility ◽  
Md Simulations ◽  
Effect Of Water ◽  
Polyelectrolyte Membranes ◽  
Dynamical Behaviors ◽  
Dynamics Simulations ◽  
Water Contents

QMs and MD simulations were employed to investigate the effect of water contents and temperatures on structural and dynamical behaviors of blended PEMs.

scholarly journals Bridging Carotenoid-to-Bacteriochlorophyll Energy Transfer of Purple Bacteria LH2 With Temperature Variations: Insights From Conformational Changes

2021 ◽  
Vol 9 ◽  
Author(s):  
Ruichao Mao ◽  
Xiaocong Wang ◽  
Jun Gao
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Conformational Changes ◽  
Purple Bacteria ◽  
Md Simulations ◽  
Temperature Variations ◽  
Energy Transfers ◽  
N Terminus ◽  
Higher Temperature ◽  
Coupling Strengths

Photosynthesis is a key process for converting light energy into chemical energy and providing food for lives on Earth. Understanding the mechanism for the energy transfers could provide insights into regulating energy transfers in photosynthesis and designing artificial photosynthesis systems. Many efforts have been devoted to exploring the mechanism of temperature variations affecting the excitonic properties of LH2. In this study, we performed all-atom molecular dynamics (MD) simulations and quantum mechanics calculations for LH2 complex from purple bacteria along with its membrane environment under three typical temperatures: 270, 300, and 330 K. The structural analysis from validated MD simulations showed that the higher temperature impaired interactions at N-terminus of both α and β polypeptide helices and led to the dissociation of this hetero polypeptide dimer. Rhodopin-β-D-glucosides (RG1) moved centripetally with α polypeptide helices when temperature increased and enlarged their distances with bacteriochlorophylls molecules that have the absorption peak at 850 nm (B850), which resulted in reducing the coupling strengths between RG1 and B850 molecules. The present study reported a cascading mechanism for temperature regulating the energy transfers in LH2 of purple bacteria.

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