Computational Modeling of Environmental Co-exposure on Oil-Derived Hydrocarbon Overload by Using Substrate-Specific Transport Protein (TodX) with Graphene Nanostructures

2020 ◽  
Vol 20 (25) ◽  
pp. 2308-2325
Author(s):  
Patrícia Viera de Oliveira ◽  
Luiza Goulart ◽  
Cláudia Lange dos Santos ◽  
Jussane Rossato ◽  
Solange Binotto Fagan ◽  
...  
Keyword(s):  
Density Functional ◽  
Oil Spills ◽  
Physical Adsorption ◽  
Health And Safety ◽  
Docking Simulation ◽  
Environmental Modeling ◽  
Transport Protein ◽  
Specific Transport ◽  
Living Organisms ◽  
Graphene Nanostructures

Background: Bioremediation is a biotechnology field that uses living organisms to remove contaminants from soil and water; therefore, they could be used to treat oil spills from the environment. Methods: Herein, we present a new mechanistic approach combining Molecular Docking Simulation and Density Functional Theory to modeling the bioremediation-based nanointeractions of a heterogeneous mixture of oil-derived hydrocarbons by using pristine and oxidized graphene nanostructures and the substrate-specific transport protein (TodX) from Pseudomonas putida. Results: The theoretical evidences pointing that the binding interactions are mainly based on noncovalent bonds characteristic of physical adsorption mechanism mimicking the “Trojan-horse effect”. Conclusion: These results open new horizons to improve bioremediation strategies in over-saturation conditions against oil-spills and expanding the use of nanotechnologies in the context of environmental modeling health and safety.

Corrigendum to: Computational Modeling of Environmental Co-exposure on Oil-Derived Hydrocarbon Overload by Using Substrate-Specific Transport Protein (TodX) with Graphene Nanostructures

2021 ◽  
Vol 21 (9) ◽  
pp. 839-839
Author(s):  
Patrícia Viera de Oliveira ◽  
Luiza Goulart ◽  
Cláudia Lange dos Santos ◽  
Jussane Rossato ◽  
Solange Binotto Fagan ◽  
...  
Keyword(s):  
Computational Modeling ◽  
Transport Protein ◽  
Specific Transport ◽  
Published Paper ◽  
Graphene Nanostructures

Due to an oversight of the publisher, Page no 2310 was missing in the published paper and page no 2311 repeated twice in the article entitled “Computational Modeling of Environmental Co-exposure on Oil-Derived Hydrocarbon Overload by Using Substrate-Specific Transport Protein (TodX) with Graphene Nanostructures, 2020, 20(25), 2308-2325 [1]. The page no 2310 is added in the article and the repetition of page no 2311 is corrected. <p> The original article can be found online at https://doi.org/10.2174/1568026620666200820145412

scholarly journals THE MODELING OF SPILLS RESULTING FROM THE CATASTROPHIC FAILURE OF ABOVE GROUND STORAGE TANKS AND THE DEVELOPMENT OF MITIGATION

2008 ◽  
Vol 2008 (1) ◽  
pp. 949-956
Author(s):  
W. Atherton ◽  
J. W. Ash ◽  
R. M. Alkhaddar
Keyword(s):  
Large Scale ◽  
Structural Integrity ◽  
Oil Spills ◽  
Health And Safety ◽  
The Other ◽  
Catastrophic Failure ◽  
Storage Tanks ◽  
Modes Of Failure ◽  
Mode Of Failure ◽  
Mitigation Technique

ABSTRACT The risk of accidents involving the catastrophic failure of storage tanks is estimated to be low, in the region of 5 × l0−6 per tank year. However, recent accidents involving major oil spills at storage facilities located in Belgium (2004) along with USA and England (2005) have shown that tank failures do nevertheless occur. Causalities of such events vary; the consequences however are ordinarily the same, incurring environmental, financial and infrastructure losses. The normal mitigation technique employed to prevent such losses is secondary containment, usually in the form of a bund wall or earthen dyke. Researchers have investigated the reliability of such methods, examining the effects of tank failure, both theoretically and experimentally in terms of loss of containment. A United Kingdom Health and Safety Executive (HSE) review conducted in 1997 concluded that the then available data was limited and focussed attention on the work of Greenspan and Johansson (1981) and the later work of Trobojevic and Slater (1989). This led to the HSE commissioning Liverpool John Moores University (LIMU) in 2003 to undertake a large-scale spill-modelling program with the aim of quantifying the level of overtopping and the magnitudes of the dynamic pressures on the bunds. The study examined the effect of axisymmetric releases on a total of 96 tank and bund arrangements. Such losses have proven to be significant and in some cases the nature of the dynamic pressures has brought in to question the structural integrity of the bunds themselves. Research has since concentrated on modelling alternative modes of failure, such as directional releases, which could be considered to be the more common mode of failure likely to be encountered. The conclusions to this work have generated additional research to investigate possible methods of mitigation that could be incorporated into the design of facilities with the ultimate aim of further reducing losses in the event of tank failure. Two promising methods have been identified, one involving modification to the primary containment (tank) with the other being a change to the design of the profile of the secondary containment (bund wall).

scholarly journals A Multi-Scale Modelling of Aggregation of TiO2 Nanoparticle Suspensions in Water

2021 ◽  
Author(s):  
Giulia Mancardi ◽  
Matteo Alberghini ◽  
Neus Aguilera-Porta ◽  
Monica Calatayud ◽  
Pietro Asinari ◽  
...  
Keyword(s):  
Titanium Dioxide ◽  
Density Functional ◽  
Large Scale ◽  
Molecular Descriptors ◽  
Titanium Dioxide Nanoparticles ◽  
Accurate Determination ◽  
Multi Scale ◽  
Spherical Bead ◽  
Living Organisms ◽  
Dynamics Simulations

Titanium dioxide nanoparticles have risen concerns about their possible toxicity and the European Food Safety Authority recently banned the use of TiO2 nano-additive in food products. Following the intent of relating nanomaterials atomic structure with their toxicity without having to conduct large scale experiments on living organisms, we investigate the aggregation of titanium dioxide nanoparticles using a multi-scale technique: starting from ab initio Density Functional Theory to get an accurate determination of the energetics and electronic structure, we switch to classical Molecular Dynamics simulations to calculate the Potential of Mean Force for the connection of two identical nanoparticles in water; the fitting of the latter by a set of mathematical equations is the key for the upscale. Lastly, we perform Brownian Dynamics simulations where each nanoparticle is a spherical bead. This coarsening strategy allows studying the aggregation of a few thousand nanoparticles. Applying this novel procedure, we find three new molecular descriptors, namely, the aggregation free energy and two numerical parameters used to correct the observed deviation from the aggregation kinetic described by the Smoluchowski theory. Molecular descriptors can be fed into QSAR models to predict the toxicity of a material knowing its physicochemical properties, without having to conduct large scale experiments on living organisms.

scholarly journals Theoretical and Experimental Studies for Inhibition Potentials of Imidazolidine 4-One and Oxazolidine 5-One Derivatives for the Corrosion of Carbon Steel in Sea Water

2020 ◽  
pp. 2776-2796
Author(s):  
Rehab M Kubba ◽  
Nada M. Al-Joborry ◽  
Naeemah J. Al-lami
Keyword(s):  
Carbon Steel ◽  
Density Functional ◽  
Sea Water ◽  
Physical Adsorption ◽  
Population Analysis ◽  
Experimental Studies ◽  
Experimental Methods ◽  
Equilibrium Geometry ◽  
Quantum Mechanical Method ◽  
Derivatives Of

Two derivatives of Iimidazolidin 4-one (IMID4) and Oxazolidin 5-one (OXAZ5), were investigated as corrosion inhibitors of corrosion carbon steel in sea water by employing the theoretical and experimental methods. The results revealed that they inhibit the corrosion process and their %IE followed the order: IMID4 (89.093%) > OXAZ5 (80.179%). The %IE obtained via theoretical and experimental methods were in a good agreement with each other. The thermodynamic parameters obtained by potentiometric polarization measurements have supported a physical adsorption mechanism which followed Langmuir adsorption isotherm. Quantum mechanical method of Density Functional Theory (DFT) of B3LYP with a level of 6-311++G (2d, 2p) were used to calculate the geometrical structure, physical properties and inhibition efficiency parameters, in vacuum and two solvents (DMSO and H2O), all calculated at the equilibrium geometry, and correlated with the experimental %IE. The local reactivity has been studied through Mulliken charges population analysis. The morphology of the surface changes of carbon steel were studied using SEM and AFM techniques.

An Ultimate Investigation on the Adsorption of Amantadine on Pristine and Decorated Fullerenes C59X (X=Si, Ge, B, Al, Ga, N, P, and As): A DFT, NBO, and QTAIM Study

2020 ◽  
pp. 1-17
Author(s):  
Mohsen Doust Mohammadi ◽  
Idris H. Salih ◽  
Hewa Y. Abdullah
Keyword(s):  
Electronic Properties ◽  
Intermolecular Interactions ◽  
Density Functional ◽  
Physical Adsorption ◽  
Single Point ◽  
Basis Set ◽  
Total Density ◽  
Electron Configuration ◽  
Doped Fullerenes ◽  
Donor Acceptor

In this investigation, the feasibility of detecting the amantadine (AMD) molecule onto the outer surface of pristine fullerene (C[Formula: see text]), as well as C[Formula: see text]X ([Formula: see text], Ge, B, Al, Ga, N, P, and As) decorated structures, was carefully evaluated. For achieving this goal, a density functional theory level of study using the HSEH1PBE functional together with a 6-311G(d) basis set has been used. Subsequently, the B3LYP-D3, wB97XD and M062X functionals with a 6-311G(d) basis set were also employed to consider the single point energies. Natural bond orbital (NBO) and the quantum theory of atoms in molecules (QTAIM) were implemented using the B3LYP-D3/6-311G(d) method and the results were compatible with the electronic properties. In this regard, the total density of states (TDOSs), the Wiberg bond index (WBI), natural charge, natural electron configuration, donor–acceptor NBO interactions, and the second-order perturbation energies are performed to explore the nature of the intermolecular interactions. All of the energy calculations and population analyses denote that by adsorbing of the AMD molecule onto the surface of the considered nanostructures, the intermolecular interactions are of the type of strong physical adsorption. Among the doped fullerenes, Ge-doped structure has very high adsorption energy compared to other elements. Generally, it was revealed that the sensitivity of the adsorption will be increased when the AMD molecule interacts with the decorated fullerenes and decrease the HOMO–LUMO band gap; therefore, the change of electronic properties can be used to design suitable nanocarrier.

scholarly journals Thiocarbohydrazones Based on Adamantane and Ferrocene as Efficient Corrosion Inhibitors for Hydrochloric Acid Pickling of C-Steel

Coatings ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 1068
Author(s):  
Abdelwahed R. Sayed ◽  
Hany M. Abd El-Lateef
Keyword(s):  
Density Functional ◽  
Corrosion Inhibitors ◽  
Physical Adsorption ◽  
Protective Layer ◽  
Open Circuit ◽  
Organometallic Complexes ◽  
Important Idea ◽  
Eis Measurements ◽  
Inhibition Performance ◽  
Experimental Findings

N′-(adamantan-2-ylidene)hydrazinecarbothiohydrazide and 2-(ferrocenyl-1-ylidene) hydrazinecarbothiohydrazide are used in coordination and organometallic complexes. The important idea of the research in this paper is the principal to prepare thiocarbohydrazones from the reaction of 2-acetylferrocene (Fe-Th) or 2-adamantanone (Ad-Th) with carbonothioic dihydrazide. The materials were elucidated by elemental analysis and spectral data. The as-prepared compounds were applied as effective corrosion inhibitors for HCl pickling of C-steel. Detailed investigations on electrochemical (open circuit potential (OCP) vs. time, potentiodynamic polarization (PDP), and impedance spectroscopy (EIS)) techniques and surface morphology studies are introduced in this work. Results indicated that Fe-Th could deliver greater inhibition performance than Ad-Th, and the highest protection capacity values of 93.6% (Ad-Th) and 97.9% (Fe-Th) were accomplished at 200 ppm. The adsorption of Ad-Th or Fe-Th additives followed the Langmuir isotherm with both the chemical and the physical adsorption with chemisorption predominance. EIS measurements supported a betterment in the capacitive behavior with the corrosion inhibitors. The inhibitors exhibited a mixed-type behavior as observed from the PDP studies. Field emission scanning electron microscopy (FESEM) and Fourier-transform infrared spectroscopy (FTIR) studies emphasize the occurrence of a protective layer of the as-synthesized organic inhibitors on the C-steel interface. Theoretical studies (density functional theory (DFT) calculations and Monte Carlo (MC) simulations) provide appropriate support for the experimental findings. The existing report provides very significant consequences in formulating and designing novel thiocarbohydrazone inhibitors with high protection efficacy.

Resistance to Infection With Intracellular Parasites. Identification of a Candidate Gene

Physiology ◽  
1994 ◽  
Vol 9 (4) ◽  
pp. 178-183
Author(s):  
SM Vidal ◽  
P Gros
Keyword(s):  
Candidate Gene ◽  
Positional Cloning ◽  
Transport Protein ◽  
Natural Resistance ◽  
Specific Transport ◽  
Intracellular Parasites ◽  
Resistance To Infection

In the mouse, natural resistance to infection with unrelated intracellular parasites is controlled by the Bcg locus. With an positional cloning approach, a candidate gene for Bcg has been isolated. This gene encodes for a novel macrophage-specific transport protein, Nramp, which is altered in innately susceptible animals.

scholarly journals In-silico Molecular Docking and ADME/Pharmacokinetic Prediction Studies of Some Novel Carboxamide Derivatives as Anti-tubercular Agents

2020 ◽  
Vol 3 (4) ◽  
pp. 989-1000
Author(s):  
Mustapha Abdullahi ◽  
Shola Elijah Adeniji
Keyword(s):  
Molecular Docking ◽  
Binding Affinity ◽  
In Silico ◽  
Density Functional ◽  
Docking Simulation ◽  
Basis Set ◽  
Hybrid Functional ◽  
Standard Drug

AbstractMolecular docking simulation of thirty-five (35) molecules of N-(2-phenoxy)ethyl imidazo[1,2-a]pyridine-3-carboxamide (IPA) with Mycobacterium tuberculosis target (DNA gyrase) was carried out so as to evaluate their theoretical binding affinities. The chemical structure of the molecules was accurately drawn using ChemDraw Ultra software, then optimized at density functional theory (DFT) using Becke’s three-parameter Lee–Yang–Parr hybrid functional (B3LYP/6-311**) basis set in a vacuum of Spartan 14 software. Subsequently, the docking operation was carried out using PyRx virtual screening software. Molecule 35 (M35) with the highest binding affinity of − 7.2 kcal/mol was selected as the lead molecule for structural modification which led to the development of four (4) newly hypothetical molecules D1, D2, D3 and D4. In addition, the D4 molecule with the highest binding affinity value of − 9.4 kcal/mol formed more H-bond interactions signifying better orientation of the ligand in the binding site compared to M35 and isoniazid standard drug. In-silico ADME and drug-likeness prediction of the molecules showed good pharmacokinetic properties having high gastrointestinal absorption, orally bioavailable, and less toxic. The outcome of the present research strengthens the relevance of these compounds as promising lead candidates for the treatment of multidrug-resistant tuberculosis which could help the medicinal chemists and pharmaceutical professionals in further designing and synthesis of more potent drug candidates. Moreover, the research also encouraged the in vivo and in vitro evaluation study for the proposed designed compounds to validate the computational findings.

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