Identification and Conformation of Bromadiolone Using HPLC and Molecular Dynamics Simulations

Rodenticides of warfarin group are mainly consisting of bromadiolone(3-(3-(4′-bromobiphenyl-4-yl)-3-hydroxy-1-phenylpropyl)-4-hydroxycoumarin), 3-bromofuran, zinc phosphide etc., having different chemical composition which are frequently used for attempting suicide, perpetrating homicide, accidental inhalation of human being while baiting rats, birds, rabbits in agricultural fields. Bromadiolone, strong and long-acting rodenticide, having anticoagulant properties and also acting as antagonist by disrupting the normal blood clotting mechanisms to vitamin-K, required for blood clotting, and increasing the bleeding tendency in rodents has been taken for finding its reaction mechanisms with different solvent media. The main symptoms of the bromadiolone rodenticides are dizziness, unsteady gait, and abnormal behavior. In the present study, we focused to determine the presence of Bromadiolone in ppm level using HPLC, the reaction mechanism of functional groups (ketone, alcohol, phenol) present in the bromadiolone under the solvent media such as H2O and HCl. The software, Avogadro, has been used to dynamically simulate the Bromadiolone for calculating its optimum energy and to conform the molecular structure under the influence of the water molecule. The reaction mechanism of functional groups in the bromadiolonecombined with the MD simulations may through light to reveal the enzymes activity in damaging the central nervous system which led to fatal.

Download Full-text

A Paramedic Treatment for Modeling Explicitly Solvated Chemical Reaction Mechanisms

10.26434/chemrxiv.6045422.v1 ◽

2018 ◽

Author(s):

Yasemin Basdogan ◽

John Keith

Keyword(s):

Reaction Mechanism ◽

Chemical Reaction ◽

Reaction Mechanisms ◽

Reaction Pathway ◽

Optimization Procedure ◽

Cost Effective ◽

Chemical Reaction Mechanisms ◽

Solvent Molecules ◽

Dynamics Simulations ◽

Mbh Reaction

<div> <div> <div> <p>We report a static quantum chemistry modeling treatment to study how solvent molecules affect chemical reaction mechanisms without dynamics simulations. This modeling scheme uses a global optimization procedure to identify low energy intermediate states with different numbers of explicit solvent molecules and then the growing string method to locate sequential transition states along a reaction pathway. Testing this approach on the acid-catalyzed Morita-Baylis-Hillman (MBH) reaction in methanol, we found a reaction mechanism that is consistent with both recent experiments and computationally intensive dynamics simulations with explicit solvation. In doing so, we explain unphysical pitfalls that obfuscate computational modeling that uses microsolvated reaction intermediates. This new paramedic approach can promisingly capture essential physical chemistry of the complicated and multistep MBH reaction mechanism, and the energy profiles found with this model appear reasonably insensitive to the level of theory used for energy calculations. Thus, it should be a useful and computationally cost-effective approach for modeling solvent mediated reaction mechanisms when dynamics simulations are not possible. </p> </div> </div> </div>

Download Full-text

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

Letters in Drug Design & Discovery ◽

10.2174/1570180815666180604085626 ◽

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.

Download Full-text

Unveiling Carbon Dioxide and Ethanol Diffusion in Carbonated Water-Ethanol Mixtures by Molecular Dynamics Simulations

Molecules ◽

10.3390/molecules26061711 ◽

2021 ◽

Vol 26 (6) ◽

pp. 1711

Author(s):

Mohamed Ahmed Khaireh ◽

Marie Angot ◽

Clara Cilindre ◽

Gérard Liger-Belair ◽

David A. Bonhommeau

Keyword(s):

Carbon Dioxide ◽

Molecular Dynamics ◽

Diffusion Coefficients ◽

Hydrodynamic Radius ◽

Md Simulations ◽

Molecular Models ◽

Experimental Values ◽

Carbon Dioxide Co2 ◽

Dynamics Simulations ◽

Apparent Disagreement

The diffusion of carbon dioxide (CO2) and ethanol (EtOH) is a fundamental transport process behind the formation and growth of CO2 bubbles in sparkling beverages and the release of organoleptic compounds at the liquid free surface. In the present study, CO2 and EtOH diffusion coefficients are computed from molecular dynamics (MD) simulations and compared with experimental values derived from the Stokes-Einstein (SE) relation on the basis of viscometry experiments and hydrodynamic radii deduced from former nuclear magnetic resonance (NMR) measurements. These diffusion coefficients steadily increase with temperature and decrease as the concentration of ethanol rises. The agreement between theory and experiment is suitable for CO2. Theoretical EtOH diffusion coefficients tend to overestimate slightly experimental values, although the agreement can be improved by changing the hydrodynamic radius used to evaluate experimental diffusion coefficients. This apparent disagreement should not rely on limitations of the MD simulations nor on the approximations made to evaluate theoretical diffusion coefficients. Improvement of the molecular models, as well as additional NMR measurements on sparkling beverages at several temperatures and ethanol concentrations, would help solve this issue.

Download Full-text

Mechanism of stacking fault annihilation in 3C-SiC epitaxially grown on Si(001) by molecular dynamics simulations

CrystEngComm ◽

10.1039/d0ce01613f ◽

2021 ◽

Author(s):

Andrey Sarikov ◽

Anna Marzegalli ◽

Luca Barbisan ◽

Massimo Zimbone ◽

Corrado Bongiorno ◽

...

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Stacking Faults ◽

Md Simulations ◽

Stacking Fault ◽

Dynamics Simulations

In this work, annihilation mechanism of stacking faults (SFs) in epitaxial 3C-SiC layers grown on Si(001) substrates is studied by molecular dynamics (MD) simulations. The evolution of SFs located in...

Download Full-text

Molecular Dynamics Simulations of Crystal Nucleation near Interfaces in Incompatible Polymer Blends

Polymers ◽

10.3390/polym13030347 ◽

2021 ◽

Vol 13 (3) ◽

pp. 347

Author(s):

Wenlin Zhang ◽

Lingyi Zou

Keyword(s):

Molecular Dynamics ◽

Polymer Blends ◽

Md Simulations ◽

Nucleation And Growth ◽

Crystal Nucleation ◽

Crystalline Order ◽

Mobile Species ◽

Deep Supercooling ◽

Crystallizable Polymer ◽

Dynamics Simulations

We apply molecular dynamics (MD) simulations to investigate crystal nucleation in incompatible polymer blends under deep supercooling conditions. Simulations of isothermal nucleation are performed for phase-separated blends with different degrees of incompatibility. In weakly segregated blends, slow and incompatible chains in crystallizable polymer domains can significantly hinder the crystal nucleation and growth. When a crystallizable polymer is blended with a more mobile species in interfacial regions, enhanced molecular mobility leads to the fast growth of crystalline order. However, the incubation time remains the same as that in pure samples. By inducing anisotropic alignment near the interfaces of strongly segregated blends, phase separation also promotes crystalline order to grow near interfaces between different polymer domains.

Download Full-text

H2 Transformations on Graphene Supported Palladium Cluster: DFT-MD Simulations and NEB Calculations

Catalysts ◽

10.3390/catal10111306 ◽

2020 ◽

Vol 10 (11) ◽

pp. 1306

Author(s):

Francesco Ferrante ◽

Antonio Prestianni ◽

Marco Bertini ◽

Dario Duca

Keyword(s):

Atomic Hydrogen ◽

Density Functional ◽

Hydrogen Molecule ◽

Md Simulations ◽

Vacant Site ◽

Functional Theory ◽

H2 Adsorption ◽

Palladium Cluster ◽

Supported Palladium ◽

Dynamics Simulations

Molecular dynamics simulations based on density functional theory were employed to investigate the fate of a hydrogen molecule shot with different kinetic energy toward a hydrogenated palladium cluster anchored on the vacant site of a defective graphene sheet. Hits resulting in H2 adsorption occur until the cluster is fully saturated. The influence of H content over Pd with respect to atomic hydrogen spillover onto graphene was investigated. Calculated energy barriers of ca. 1.6 eV for H-spillover suggest that the investigated Pd/graphene system is a good candidate for hydrogen storage.

Download Full-text

Molecular dynamics simulations and CD spectroscopy reveal hydration-induced unfolding of the intrinsically disordered LEA proteins COR15A and COR15B from Arabidopsis thaliana

Physical Chemistry Chemical Physics ◽

10.1039/c6cp02272c ◽

2016 ◽

Vol 18 (37) ◽

pp. 25806-25816 ◽

Cited By ~ 13

Author(s):

Carlos Navarro-Retamal ◽

Anne Bremer ◽

Jans Alzate-Morales ◽

Julio Caballero ◽

Dirk K. Hincha ◽

...

Keyword(s):

Experimental Data ◽

Molecular Dynamics ◽

Arabidopsis Thaliana ◽

Molecular Dynamics Simulations ◽

Md Simulations ◽

Cd Spectroscopy ◽

Lea Proteins ◽

Intrinsically Disordered ◽

Dynamics Simulations ◽

Crowded Environment

Unfolding of intrinsically unstructured full-length LEA proteins in a differentially crowded environment can be modeled by 30 ns MD simulations in accordance with experimental data.

Download Full-text

Simulated Breathing: Application of Molecular Dynamics Simulations to Pulmonary Lung Surfactant

Symmetry ◽

10.3390/sym13071259 ◽

2021 ◽

Vol 13 (7) ◽

pp. 1259

Author(s):

Maksymilian Dziura ◽

Basel Mansour ◽

Mitchell DiPasquale ◽

P. Charukeshi Chandrasekera ◽

James W. Gauld ◽

...

Keyword(s):

Molecular Dynamics ◽

Pulmonary Surfactant ◽

Lung Surfactant ◽

Protein Composition ◽

Md Simulations ◽

Building Blocks ◽

Future Research ◽

Total Composition ◽

Protein Components ◽

Dynamics Simulations

In this review, we delve into the topic of the pulmonary surfactant (PS) system, which is present in the respiratory system. The total composition of the PS has been presented and explored, from the types of cells involved in its synthesis and secretion, down to the specific building blocks used, such as the various lipid and protein components. The lipid and protein composition varies across species and between individuals, but ultimately produces a PS monolayer with the same role. As such, the composition has been investigated for the ways in which it imposes function and confers peculiar biophysical characteristics to the system as a whole. Moreover, a couple of theories/models that are associated with the functions of PS have been addressed. Finally, molecular dynamic (MD) simulations of pulmonary surfactant have been emphasized to not only showcase various group’s findings, but also to demonstrate the validity and importance that MD simulations can have in future research exploring the PS monolayer system.

Download Full-text