scholarly journals Spotlight onto surfactant–steam–bitumen interfacial behavior via molecular dynamics simulation

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Mohammadali Ahmadi ◽  
Zhangxin Chen
Keyword(s):  
Molecular Interactions ◽  
Distribution Functions ◽  
Thermal Recovery ◽  
Dynamics Simulation ◽  
Solvent Accessible Surface Area ◽  
Radius Of Gyration ◽  
Interfacial Behavior ◽  
Oil Sand ◽  
Thermal Methods ◽  
Bitumen Recovery

AbstractHeavy oil and bitumen play a vital role in the global energy supply, and to unlock such resources, thermal methods, e.g., steam injection, are applied. To improve the performance of these methods, different additives, such as air, solvents, and chemicals, can be used. As a subset of chemicals, surfactants are one of the potential additives for steam-based bitumen recovery methods. Molecular interactions between surfactant/steam/bitumen have not been addressed in the literature. This paper investigates molecular interactions between anionic surfactants, steam, and bitumen in high-temperature and high-pressure conditions. For this purpose, a real Athabasca oil sand composition is employed to assess the phase behavior of surfactant/steam/bitumen under in-situ steam-based bitumen recovery. Two different asphaltene architectures, archipelago and Island, are used to examine the effect of asphaltene type on bitumen's interfacial behavior. The influence of having sulfur heteroatoms in a resin structure and a benzene ring's effect in an anionic surfactant structure on surfactant–steam–bitumen interactions are investigated systematically. The outputs are supported by different analyses, including radial distribution functions (RDFs), mean squared displacement (MSD), radius of gyration, self-diffusion coefficient, solvent accessible surface area (SASA), interfacial thickness, and interaction energies. According to MD outputs, adding surfactant molecules to the steam phase improved the interaction energy between steam and bitumen. Moreover, surfactants can significantly improve steam emulsification capability by decreasing the interfacial tension (IFT) between bitumen and the steam phase. Asphaltene architecture has a considerable effect on the interfacial behavior in such systems. This study provides a better and more in-depth understanding of surfactant–steam–bitumen systems and spotlights the interactions between bitumen fractions and surfactant molecules under thermal recovery conditions.

Xanthine oxidase inhibitory activity of Euphorbia peplus L. phenolics

2021 ◽  
Vol 24 ◽  
Author(s):  
Emadeldin M. Kamel ◽  
Noha A. Ahmed ◽  
Ashraf A. El-Bassuony ◽  
Omnia E. Hussein ◽  
Barakat Alrashdi ◽  
...  
Keyword(s):  
Xanthine Oxidase ◽  
Active Site ◽  
Inhibitory Activity ◽  
Drug Binding ◽  
Dynamics Simulation ◽  
Solvent Accessible Surface Area ◽  
Radius Of Gyration ◽  
Euphorbia Peplus

Background: Various phenolics show inhibitory activity towards xanthine oxidase (XO), an enzyme that generates reactive oxygen species which cause oxidative damage. Objective: This study investigated the XO inhibitory activity of Euphorbia peplus phenolics. Methods: The dried powdered aerial parts of E. peplus were extracted, fractioned and phenolics were isolated and identified. The XO inhibitory activity of E. peplus extract (EPE) and the isolated phenolics was investigated in vitro and in vivo. Results: Three phenolics were isolated from the ethyl acetate fraction of E. peplus. All isolated compounds and the EPE showed inhibitory activity towards XO in vitro. In hyperuricemic rats, EPE and the isolated phenolics decreased uric acid and XO activity. Molecular docking showed the binding modes of isolated phenolics with XO, depicting significant interactions with the active site amino acid residues. Molecular dynamics simulation trajectories confirmed the interaction of isolated phenolics with XO by forming hydrogen bonds with the active site residues. Also, the root mean square (RMS) deviations of XO and phenolics-XO complexes achieved equilibrium and fluctuated during the 10 ns MD simulations. The radius of gyration and solvent accessible surface area investigations showed that different systems were stabilized at ≈ 2500 ps. The RMS fluctuations profile depicted that the drug binding site exhibited a rigidity behavior during the simulation. Conclusion: In vitro, in vivo and computational investigations showed the XO inhibitory activity of E. peplus phenolics. These phenolics might represent promising candidates for the development of XO inhibitors.

scholarly journals Screening of Potent Phytochemical Inhibitors Against SARS-CoV-2 Main Protease: An Integrative Computational Approach

2021 ◽  
Vol 1 ◽  
Author(s):  
Shafi Mahmud ◽  
Md. Robiul Hasan ◽  
Suvro Biswas ◽  
Gobindo Kumar Paul ◽  
Shamima Afrose ◽  
...  
Keyword(s):  
Root Mean Square ◽  
Global Economy ◽  
Transmission Rate ◽  
Accessible Surface Area ◽  
Dynamics Simulation ◽  
Solvent Accessible Surface Area ◽  
Radius Of Gyration ◽  
Mean Square ◽  
Protease Inhibition ◽  
Main Protease

Coronavirus disease 2019 (COVID-19) is a potentially lethal and devastating disease that has quickly become a public health threat worldwide. Due to its high transmission rate, many countries were forced to implement lockdown protocols, wreaking havoc on the global economy and the medical crisis. The main protease (Mpro) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative virus for COVID-19, represent an effective target for the development of a new drug/vaccine because it is well-conserved and plays a vital role in viral replication. Mpro inhibition can stop the replication, transcription as well as recombination of SARS-CoV-2 after the infection and thus can halt the formation of virus particles, making Mpro a viable therapeutic target. Here, we constructed a phytochemical dataset based on a rigorous literature review and explored the probability that various phytochemicals will bind with the main protease using a molecular docking approach. The top three hit compounds, medicagol, faradiol, and flavanthrin, had binding scores of −8.3, −8.6, and −8.8 kcal/mol, respectively, in the docking analysis. These three compounds bind to the active groove, consisting of His41, Cys45, Met165, Met49, Gln189, Thr24, and Thr190, resulting in main protease inhibition. Moreover, the multiple descriptors from the molecular dynamics simulation, including the root-mean-square deviation, root-mean-square fluctuation, solvent-accessible surface area, radius of gyration, and hydrogen bond analysis, confirmed the stable nature of the docked complexes. In addition, absorption, distribution, metabolism, excretion, and toxicity (ADMET) analysis confirmed a lack of toxicity or carcinogenicity for the screened compounds. Our computational analysis may contribute toward the design of an effective drug against the main protease of SARS-CoV-2.

scholarly journals Phytochemicals from Leucas zeylanica Targeting Main Protease of SARS-CoV-2: Chemical Profiles, Molecular Docking, and Molecular Dynamics Simulations

Biology ◽  
2021 ◽  
Vol 10 (8) ◽  
pp. 789
Author(s):  
Mycal Dutta ◽  
Abu Montakim Tareq ◽  
Ahmed Rakib ◽  
Shafi Mahmud ◽  
Saad Ahmed Sami ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Molecular Dynamics Simulation ◽  
Surface Area ◽  
Dynamics Simulation ◽  
Solvent Accessible Surface Area ◽  
Gas Chromatography Mass Spectrometry ◽  
Radius Of Gyration ◽  
Hydrogen Bond Formation ◽  
Main Protease

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a contemporary coronavirus, has impacted global economic activity and has a high transmission rate. As a result of the virus’s severe medical effects, developing effective vaccinations is vital. Plant-derived metabolites have been discovered as potential SARS-CoV-2 inhibitors. The SARS-CoV-2 main protease (Mpro) is a target for therapeutic research because of its highly conserved protein sequence. Gas chromatography–mass spectrometry (GC-MS) and molecular docking were used to screen 34 compounds identified from Leucas zeylanica for potential inhibitory activity against the SARS-CoV-2 Mpro. In addition, prime molecular mechanics–generalized Born surface area (MM-GBSA) was used to screen the compound dataset using a molecular dynamics simulation. From molecular docking analysis, 26 compounds were capable of interaction with the SARS-CoV-2 Mpro, while three compounds, namely 11-oxa-dispiro[4.0.4.1]undecan-1-ol (−5.755 kcal/mol), azetidin-2-one 3,3-dimethyl-4-(1-aminoethyl) (−5.39 kcal/mol), and lorazepam, 2TMS derivative (−5.246 kcal/mol), exhibited the highest docking scores. These three ligands were assessed by MM-GBSA, which revealed that they bind with the necessary Mpro amino acids in the catalytic groove to cause protein inhibition, including Ser144, Cys145, and His41. The molecular dynamics simulation confirmed the complex rigidity and stability of the docked ligand–Mpro complexes based on the analysis of mean radical variations, root-mean-square fluctuations, solvent-accessible surface area, radius of gyration, and hydrogen bond formation. The study of the postmolecular dynamics confirmation also confirmed that lorazepam, 11-oxa-dispiro[4.0.4.1]undecan-1-ol, and azetidin-2-one-3, 3-dimethyl-4-(1-aminoethyl) interact with similar Mpro binding pockets. The results of our computerized drug design approach may assist in the fight against SARS-CoV-2.

Low-Temperature Bitumen Recovery from Oil-Sand Reservoirs Using Ionic Liquids

SPE Journal ◽  
2019 ◽  
Vol 24 (05) ◽  
pp. 2409-2422 ◽  
Author(s):  
Elsayed Abdelfatah ◽  
Paula Berton ◽  
Robin D. Rogers ◽  
Steven L. Bryant
Keyword(s):  
Ionic Liquids ◽  
Ambient Temperature ◽  
Viscosity Reduction ◽  
Primary Amines ◽  
Oil Sand ◽  
High Recovery ◽  
Sand Column ◽  
Thermal Methods ◽  
Solution Mining ◽  
Bitumen Recovery

Summary Steam injection is widely used for bitumen recovery. However, steam is not efficient for shallow or thin reservoirs because of heat loss in the wellbore or to surrounding formations. Numerous alternatives have been proposed, including the addition of solvents and replacement of steam with volatile solvents. Here, we describe a new technology that combines nonvolatile ionic liquids (ILs) and waterflooding for bitumen recovery that can deliver high recovery at ambient temperature. Different ILs were designed for complete dispersal/dissolution of bitumen at ambient temperature. The designed ILs were tested in coreflood experiments with high–grade oil–sand ore from Alberta. Two different scenarios were tested: continuous injection of ILs at different injection rates and injection of a slug of ILs followed by water injection. Different slug volumes were tested at a constant injection rate. After ILs injection, the oil sand was removed from the column, and the remaining bitumen was quantified using a modified Dean–Stark method. Viscosity and solid–content measurements of the recovered samples at breakthrough were conducted. Bitumen recovery by the designed ILs can be thought of as a solution mining process. Tuning the physical and chemical properties of the ILs is the most important aspect of achieving the desired interaction with the oil–sand system. Properties of the designed IL depend on the selected cation and anion, and the strength of their intermolecular interaction. Primary amines mixed with the oleic acid chosen for IL1 form a viscous IL that can recover bitumen, leaving a slight amount of bitumen behind, but a large pressure gradient. Changing the cation to tertiary amines produces significantly less–viscous ILs, which completely recover the bitumen in the oil–sand column. Moreover, the cation can be tailored to significantly minimize the fines (clay) migration and viscosity of the recovered bitumen and to provide compatibility with an aqueous phase. In all cases, these recoveries are significant, compared with the currently used technologies. This work proves that bitumen recovery from oil sand is possible at low temperatures by means of a process analogous to solution mining with the design of the proper ILs, in contrast to viscosity–reduction processes achieved by thermal methods. The properties of these ILs can be tuned for different recovery mechanisms. Thus, this work establishes the basis for developing a new class of in–situ recovery processes with high recovery efficiencies and low environmental impact.

scholarly journals Reappraisal of Trifluperidol against NSP-3 protein: Potential therapeutic for COVID-19

2020 ◽  
Author(s):  
Ajita Pandey
Keyword(s):  
Root Mean Square ◽  
Dynamics Simulation ◽  
Solvent Accessible Surface Area ◽  
Radius Of Gyration ◽  
Scoring Functions ◽  
Mean Square ◽  
Structural Protein ◽  
Approved Drugs ◽  
Fda Approved Drugs

Abstract Novel coronavirus disease 2019 (COVID-19) is a highly infectious disease that is caused by the recently discovered severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Because there are no specific vaccines or drugs for SARS-CoV-2, drug repurposing may be a promising approach. SARS-CoV-2 has a positive-sense RNA genome that encodes non-structural proteins (Nsps), which are essential for viral replication in the host cell. Non-structural protein 3 (Nsp3) is a multidomain protein and is the largest protein of the replicase complex. Nsp3 contains an ADP-ribose phosphatase (ADRP) domain, also called the macrodomain, which interferes with the host immune response. In the present study, we used computational regression methods to target the ADRP domain of Nsp3, using FDA-approved drugs. We virtually screened 2,892 FDA-approved drugs, using a combination of molecular docking and scoring functions. Saquinavir and trifluperidol were identified as potential leads and were further investigated using molecular dynamics simulation (MDS) to predict the stability and behavior of the ADRP-drug complexes. Analysis of root mean square deviation, root mean square fluctuation, radius of gyration, solvent accessible surface area and number of hydrogen bonds showed that the ADRP-trifluperidol complex is more stable than the ADRP-saquinavir complex. The screening and the MDS results suggest that trifluperidol is a novel inhibitor of the ADRP domain of Nsp3. Trifluperidol could, therefore, potentially be used to help control the spread of COVID-19, either alone or in combination with antiviral agents. Further in-vitro and in-vivo experiments are necessary to confirm our in silico results.

scholarly journals Molecular Dynamics Simulation of Polyacrylamide Adsorption on Cellulose Nanocrystals

Nanomaterials ◽  
2020 ◽  
Vol 10 (7) ◽  
pp. 1256 ◽  
Author(s):  
Darya Gurina ◽  
Oleg Surov ◽  
Marina Voronova ◽  
Anatoly Zakharov
Keyword(s):  
Molecular Dynamics ◽  
Cellulose Nanocrystals ◽  
Water Environment ◽  
Distribution Functions ◽  
Dynamics Simulation ◽  
Radius Of Gyration ◽  
Radial Distribution Functions ◽  
Dynamical Characteristics ◽  
Polymer Interactions ◽  
Dynamics Simulations

Classical molecular dynamics simulations of polyacrylamide (PAM) adsorption on cellulose nanocrystals (CNC) in a vacuum and a water environment are carried out to interpret the mechanism of the polymer interactions with CNC. The structural behavior of PAM is studied in terms of the radius of gyration, atom–atom radial distribution functions, and number of hydrogen bonds. The structural and dynamical characteristics of the polymer adsorption are investigated. It is established that in water the polymer macromolecules are mainly adsorbed in the form of a coil onto the CNC facets. It is found out that water and PAM sorption on CNC is a competitive process, and water weakens the interaction between the polymer and CNC.

scholarly journals Efficacy of Phytochemicals Derived from Avicennia officinalis for the Management of COVID-19: A Combined In Silico and Biochemical Study

Molecules ◽  
2021 ◽  
Vol 26 (8) ◽  
pp. 2210
Author(s):  
Shafi Mahmud ◽  
Gobindo Kumar Paul ◽  
Mirola Afroze ◽  
Shirmin Islam ◽  
Swagota Briti Ray Gupt ◽  
...  
Keyword(s):  
Root Mean Square ◽  
Antioxidant Activities ◽  
Binding Free Energy ◽  
Healthcare Management ◽  
Dynamics Simulation ◽  
Solvent Accessible Surface Area ◽  
Radius Of Gyration ◽  
Mean Square ◽  
Main Protease ◽  
Avicennia Officinalis

The recent coronavirus disease 2019 (COVID-19) pandemic is a global threat for healthcare management and the economic system, and effective treatments against the pathogenic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus responsible for this disease have not yet progressed beyond the developmental phases. As drug refinement and vaccine progression require enormously broad investments of time, alternative strategies are urgently needed. In this study, we examined phytochemicals extracted from Avicennia officinalis and evaluated their potential effects against the main protease of SARS-CoV-2. The antioxidant activities of A. officinalis leaf and fruit extracts at 150 µg/mL were 95.97% and 92.48%, respectively. Furthermore, both extracts displayed low cytotoxicity levels against Artemia salina. The gas chromatography–mass spectroscopy analysis confirmed the identifies of 75 phytochemicals from both extracts, and four potent compounds, triacontane, hexacosane, methyl linoleate, and methyl palminoleate, had binding free energy values of −6.75, −6.7, −6.3, and −6.3 Kcal/mol, respectively, in complexes with the SARS-CoV-2 main protease. The active residues Cys145, Met165, Glu166, Gln189, and Arg188 in the main protease formed non-bonded interactions with the screened compounds. The root-mean-square difference (RMSD), root-mean-square fluctuations (RMSF), radius of gyration (Rg), solvent-accessible surface area (SASA), and hydrogen bond data from a molecular dynamics simulation study confirmed the docked complexes′ binding rigidity in the atomistic simulated environment. However, this study′s findings require in vitro and in vivo validation to ensure the possible inhibitory effects and pharmacological efficacy of the identified compounds.

The Role of Geomechanical Observation in Continuous Updating of Thermal-Recovery Simulations With the Ensemble Kalman Filter

SPE Journal ◽  
2013 ◽  
Vol 18 (06) ◽  
pp. 1043-1056 ◽  
Author(s):  
A.. Azad ◽  
R.J.. J. Chalaturnyk
Keyword(s):  
Kalman Filter ◽  
Ensemble Kalman Filter ◽  
History Matching ◽  
Numerical Models ◽  
Thermal Recovery ◽  
Rock Properties ◽  
Observation Data ◽  
Oil Sand ◽  
Thermal Methods ◽  
Cyclic Steam Stimulation

Summary In-situ thermal methods such as steam-assisted gravity drainage (SAGD) and cyclic steam stimulation (CSS) are widely used in oil-sand reservoirs. The physics of such thermal processes is generally well-understood, and it has been shown that rock properties are highly influenced by the geomechanical behavior of the reservoir during these recovery processes. Geomechanics improves the process dynamically, and its response can depict the progress of production within a reservoir. However, the potential of geomechanical monitoring is not usually practiced. With increased implementation of highly instrumented wells and communication technologies providing real-time monitoring data from different sources, combining available data into reservoir geomechanical simulations can improve updating numerical models and the prediction process. This research explores effective uses of geomechanical observation data for history matching and types of geomechanical observation sources adequate for thermal recovery. The ensemble Kalman filter (EnKF), combined with an iterative geomechanical coupled simulator, has been chosen as the data-assimilation algorithm to update the model continuously on the basis of geomechanical observations and production data. The results show that considering geomechanical modeling and observation improves history matching when geomechanical behavior plays a role in the process.

scholarly journals Molecular Dynamics Simulation of Cholera Toxin A-1 Polypeptide

2016 ◽  
Vol 14 (1) ◽  
pp. 188-196 ◽  
Author(s):  
Syed Lal Badshah ◽  
Abdul Naeem Khan ◽  
Yahia Nasser Mabkhot
Keyword(s):  
Molecular Dynamics ◽  
Secondary Structure ◽  
Cholera Toxin ◽  
Root Mean Square ◽  
Host Cells ◽  
Dynamics Simulation ◽  
Solvent Accessible Surface Area ◽  
Radius Of Gyration ◽  
Mean Square ◽  
Toxin A

AbstractA molecular dynamics (MD) simulation study of the enzymatic portion of cholera toxin; cholera toxin A-1 polypeptide (CTA1) was performed at 283, 310 and 323 K. From total energy analysis it was observed that this toxin is stable thermodynamically and these outcomes were likewise confirmed by root mean square deviations (RMSD) investigations. The Cα root mean square fluctuation (RMSF) examinations revealed that there are a number of residues inside CTA1, which can be used as target for designing and synthesizing inhibitory drugs, in order to inactivate cholera toxin inside the human body. The fluctuations in the radius of gyration and hydrogen bonding in CTA1 proved that protein unfolding and refolding were normal routine phenomena in its structure at all temperatures. Solvent accessible surface area study identified the hydrophilic nature of the CTA1, and due to this property it can be a potential biological weapon. The structural identification (STRIDE) algorithm for proteins was successfully used to determine the partially disordered secondary structure of CTA1. On account of this partially disordered secondary structure, it can easily deceive the proteolytic enzymes of the endoplasmic reticulum of host cells.

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