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Mahfud R. Molecular Dynamics Computational Study of Sustainable Green Surfactant for Application in Chemical Enhanced Oil Recovery. ACS OMEGA 2024; 9:27177-27191. [PMID: 38947786 PMCID: PMC11209909 DOI: 10.1021/acsomega.4c01332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Revised: 05/30/2024] [Accepted: 06/05/2024] [Indexed: 07/02/2024]
Abstract
Green surfactant (GS) flooding, an environmentally friendly chemical Enhanced Oil Recovery (cEOR) method, is explored in this molecular dynamics (MD) simulation study. This study evaluates the ability of (S)-2-dodecanamido-aminobutanedioic as a GS for cEOR, assessing its performance with hexane (C6), dodecane (C12), and eicosane (C20) as representative oils. In the case of the bulk system, a comprehensive molecular-level investigation provides structural details such as the radial distribution function, solvent-accessible surface area, GS adsorption dynamics, diffusivity, and emulsion stability of the GS, oil, and water systems. Also the impact of the three distinct oils on interfacial tension was examined in the existence of GS molecules. The findings reveal rapid GS molecule aggregation and adsorption on oil droplets, with various impacts on emulsion stability depending on the oil type. Additionally, GS enhances the aggregation of heavy C20 oil molecules in a water medium. The study demonstrates GS's role as an effective emulsifier, facilitating oil droplet recovery, with electrostatic interactions governing micelle formation and van der Waals interactions influencing oil droplet emulsification. These results align with prior experimental data, affirming GS's promising application potential in cEOR while prioritizing environmental sustainability.
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Affiliation(s)
- Riyad Mahfud
- International college of
engineering and management, Muscat 111, Oman
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2
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Eliasquevici R, Bernardino K. Counter-ion adsorption and electrostatic potential in sodium and choline dodecyl sulfate micelles - a molecular dynamics simulation study. J Mol Model 2024; 30:101. [PMID: 38467947 DOI: 10.1007/s00894-024-05897-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 03/03/2024] [Indexed: 03/13/2024]
Abstract
CONTEXT Choline-based surfactants are interesting both from the practical point of view to obtaining environmental-friendly surfactants as well as from the theoretical side since the interactions between the choline and surfactants can help to understand self-assembly phenomena in deep eutectic solvents. Although no significant change was noticed in the micelle size and shape due to the exchange of the sodium counter-ion by choline in our simulations, the adsorption of the choline cation over the micelle surface is stronger than the adsorption of the sodium, which leads to a reduction of the exposed surface area of the micelle and remarkable effects over the electrostatic potential. The choline neutralizes the surface charge of the surfactant better than sodium; however, this is partially compensated by a stronger water orientation around the SDS micelle. The balance between the contributions from the surfactant, the counter-ion, and water to the electrostatic potential leads to a complex pattern with alternate regions of positive and negative potential at the micelle/water interface which can be important to the incorporation of other charged species at the micelle surface as well as for the interaction between micelles in solution. METHODS To evaluate the effects of the counter-ion substitution, micelles of sodium dodecyl sulfate (SDS) and choline dodecyl sulfate (ChDS) were studied and compared by means of molecular dynamics simulations in aqueous solution. In both cases, the simulations started from pre-assembled micelles with 60 dodecyl sulfate ions and 240-ns simulations were performed at NPT ensemble at T = 323.15 K and P = 1 bar using the Gromacs software with the OPLS-AA force field to describe dodecyl sulfate and choline, Åqvist parameters for sodium, and SPC model for water molecules.
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Affiliation(s)
- Rafaela Eliasquevici
- Laboratório de Química Computacional, Departamento de Química, Universidade Federal de São Carlos, Rod. Washington Luiz S/N, São Carlos, 13565-905, Brazil
| | - Kalil Bernardino
- Laboratório de Química Computacional, Departamento de Química, Universidade Federal de São Carlos, Rod. Washington Luiz S/N, São Carlos, 13565-905, Brazil.
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Peng J, Song X, Li X, Jiang Y, Liu G, Wei Y, Xia Q. Molecular Dynamics Study on the Aggregation Behavior of Triton X Micelles with Different PEO Chain Lengths in Aqueous Solution. Molecules 2023; 28:molecules28083557. [PMID: 37110791 PMCID: PMC10146536 DOI: 10.3390/molecules28083557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 04/02/2023] [Accepted: 04/16/2023] [Indexed: 04/29/2023] Open
Abstract
The aggregation structure of Triton X (TX) amphiphilic molecules in aqueous solution plays an important role in determining the various properties and applications of surfactant solutions. In this paper, the properties of micelles formed by TX-5, TX-114, and TX-100 molecules with different poly(ethylene oxide) (PEO) chain lengths in TX series of nonionic surfactants were studied via molecular dynamics (MD) simulation. The structural characteristics of three micelles were analyzed at the molecular level, including the shape and size of micelles, the solvent accessible surface area, the radial distribution function, the micelle configuration, and the hydration numbers. With the increase of PEO chain length, the micelle size and solvent accessible surface area also increase. The distribution probability of the polar head oxygen atoms on the surface of the TX-100 micelle is higher than that in the TX-5 or TX-114 micelle. In particular, the tail quaternary carbon atoms in the hydrophobic region are mainly located at the micelle exterior. For TX-5, TX-114, and TX-100 micelles, the interactions between micelles and water molecules are also quite different. These structures and comparisons at the molecular level contribute to the further understanding of the aggregation and applications of TX series surfactants.
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Affiliation(s)
- Jin Peng
- School of Chemistry and Chemical Engineering, Linyi University, Linyi 276000, China
| | - Xiaoju Song
- School of Chemistry and Chemical Engineering, Linyi University, Linyi 276000, China
| | - Xin Li
- School of Chemistry and Chemical Engineering, Linyi University, Linyi 276000, China
| | - Yongkang Jiang
- School of Chemistry and Chemical Engineering, Linyi University, Linyi 276000, China
| | - Guokui Liu
- School of Chemistry and Chemical Engineering, Linyi University, Linyi 276000, China
| | - Yaoyao Wei
- School of Chemistry and Chemical Engineering, Linyi University, Linyi 276000, China
| | - Qiying Xia
- School of Chemistry and Chemical Engineering, Linyi University, Linyi 276000, China
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4
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Wei Y, Wang X, Dong L, Liu G, Xia Q, Yuan S. Molecular dynamics study on the effect of surfactant mixture on their packing states in mixed micelles. Colloids Surf A Physicochem Eng Asp 2021. [DOI: 10.1016/j.colsurfa.2021.127714] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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5
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Effect of Triton X-100 surfactant on the interfacial activity of ionic surfactants SDS, CTAB and SDBS at the air/water interface: A study using molecular dynamic simulations. Colloids Surf A Physicochem Eng Asp 2020. [DOI: 10.1016/j.colsurfa.2020.125284] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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6
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Wei Y, Liu G, Wang H, Xia Q, Yuan S. Exploring relationship of the state of N-dodecyl betaine in the solution monomer, at the interface and in the micelle via configurational entropy. Colloids Surf A Physicochem Eng Asp 2020. [DOI: 10.1016/j.colsurfa.2020.124975] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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7
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Jahan I, Nayeem SM. Conformational dynamics of superoxide dismutase (SOD1) in osmolytes: a molecular dynamics simulation study. RSC Adv 2020; 10:27598-27614. [PMID: 35516947 PMCID: PMC9055598 DOI: 10.1039/d0ra02151b] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 06/25/2020] [Indexed: 11/23/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease caused by the misfolding of Cu, Zn superoxide dismutase (SOD1). Several earlier studies have shown that monomeric apo SOD1 undergoes significant local unfolding dynamics and is the predecessor for aggregation. Here, we have employed atomistic molecular dynamics (MD) simulations to study the structure and dynamics of monomeric apo and holo SOD1 in water, aqueous urea and aqueous urea-TMAO (trimethylamine oxide) solutions. Loop IV (zinc-binding loop) and loop VII (electrostatic loop) of holo SOD1 are considered as functionally important loops as they are responsible for the structural stability of holo SOD1. We found larger local unfolding of loop IV and VII of apo SOD1 as compared to holo SOD1 in water. Urea induced more unfolding in holo SOD1 than apo SOD1, whereas the stabilization of both the form of SOD1 was observed in ternary solution (i.e. water/urea/TMAO solution) but the extent of stabilization was higher in holo SOD1 than apo SOD1. The partially unfolded structures of apo SOD1 in water, urea and holo SOD1 in urea were identified by the exposure of the hydrophobic cores, which are highly dynamic and these may be the initial events of aggregation in SOD1. Our simulation studies support the formation of aggregates by means of the local unfolding of monomeric apo SOD1 as compared to holo SOD1 in water.
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Affiliation(s)
- Ishrat Jahan
- Department of Chemistry, Aligarh Muslim University Aligarh-202002 U.P. India +91-9412527078
| | - Shahid M Nayeem
- Department of Chemistry, Aligarh Muslim University Aligarh-202002 U.P. India +91-9412527078
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Jahan I, Nayeem SM. Effect of Osmolytes on Conformational Behavior of Intrinsically Disordered Protein α-Synuclein. Biophys J 2019; 117:1922-1934. [PMID: 31699336 DOI: 10.1016/j.bpj.2019.09.046] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 09/21/2019] [Accepted: 09/30/2019] [Indexed: 11/20/2022] Open
Abstract
α-Synuclein is an intrinsically disordered protein whose function in a healthy brain is poorly understood. It is genetically and neuropathologically linked to Parkinson's disease (PD). PD is manifested after the accumulation of plaques of α-synuclein aggregates in the brain cells. Aggregates of α-synuclein are very toxic and lead to the disruption of cellular homeostasis and neuronal death. α-Synuclein can also contribute to disease propagation as it may exert noxious effects on neighboring cells. Understanding the mechanism of α-synuclein aggregation will facilitate the problem of dealing with neurodegenerative diseases in general and that of PD in particular. Here, we have used molecular dynamics simulations to investigate the behavior of α-synuclein at various temperatures and in different concentrations of urea and trimethyl amine oxide. The residue region from 61 to 95 of α-synuclein is experimentally known as amyloidogenic. In our study, we have identified some other regions, which also have the propensity to form an aggregate besides this known sequence. Urea being a denaturant interacts more with these regions of α-synuclein through hydrogen bond formation and inhibits the β-sheet formation, whereas trimethyl amine oxide itself does not interact much with the protein and stabilizes the protein by preferentially distributing water molecules on the surface of the protein.
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Affiliation(s)
- Ishrat Jahan
- Department of Chemistry, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Shahid M Nayeem
- Department of Chemistry, Aligarh Muslim University, Aligarh, Uttar Pradesh, India.
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Wei Y, Gao F, Wang H, Liu G, Xia Q, Yuan S. A molecular dynamics study combining with entropy calculation on the packing state of hydrophobic chains in micelle interior. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.03.175] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Arnould A, Cousin F, Salonen A, Saint-Jalmes A, Perez A, Fameau AL. Controlling Foam Stability with the Ratio of Myristic Acid to Choline Hydroxide. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:11076-11085. [PMID: 30149714 DOI: 10.1021/acs.langmuir.8b02261] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The interfacial and foam properties of a model system based on the mixture between myristic acid and choline hydroxide have been investigated as a function of the molar ratio ( R) between these two components and temperature. The aim of this study was to obtain insight on the links between the self-assemblies in bulk and in the foam liquid channels, the surfactant packing at the interface, and the resulting foam properties and stability. A multiscale approach was used combining small angle neutron scattering, specular neutron reflectivity, surface tension measurements, and photography. We highlighted three regimes of foam stability in this system by modifying R: high foam stability for R < 1, intermediate at R ∼ 1, and low for R > 1. The different regimes come from the pH variations in bulk linked to R. The pH plays a crucial role at the molecular scale by setting the ionization state of the myristic acid molecules adsorbed at the gas-liquid interface, which in turn controls both the properties of the monolayer and the stability of the films separating the bubbles. The main requirement to obtain stable foams is to set the pH close to the p Ka in order to have a mixture of protonated and ionized molecules giving rise to intermolecular hydrogen bonds. As a result, a dense monolayer is formed at the interface with a low surface tension. R also modifies the structure of self-assembly in bulk and therefore within the foam, but such a morphological change has only a minor effect on the foam stability. This study confirms that foam stability in surfactant systems having a carboxylic acid as polar headgroup is mainly linked to the ionization state of the molecules at the interface.
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Affiliation(s)
- Audrey Arnould
- Biopolymères Interactions Assemblages INRA , la Géraudière , 44316 Nantes , France
| | - Fabrice Cousin
- Laboratoire Léon-Brillouin , CEA Saclay , 91191 Gif-sur-Yvette CEDEX, France
| | - Anniina Salonen
- Laboratoire de Physique des Solides, UMR 8502, Université of Paris Sud, 91405 Orsay , France
| | - Arnaud Saint-Jalmes
- Institut de Physique de Rennes, UMR CNRS 6251-Université Rennes 1, Rennes 35042 , France
| | - Adrian Perez
- Grupo de Biocoloides, Instituto de Tecnología de Alimentos , Universidad Nacional del Litoral , 1 de Mayo 3250 , Santa Fe 3000 , Argentina
| | - Anne-Laure Fameau
- Biopolymères Interactions Assemblages INRA , la Géraudière , 44316 Nantes , France
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Allen DT, Damestani N, Saaka Y, Lawrence MJ, Lorenz CD. Interaction of testosterone-based compounds with dodecyl sulphate monolayers at the air–water interface. Phys Chem Chem Phys 2018. [DOI: 10.1039/c7cp07611h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The encapsulation of testosterone enanthate into a sodium dodecyl sulphate monolayer.
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Affiliation(s)
- Daniel T. Allen
- Biological Physics & Soft Matter Group
- Department of Physics
- King's College London
- London WC2R 2LS
- UK
| | - Nikou Damestani
- Biological Physics & Soft Matter Group
- Department of Physics
- King's College London
- London WC2R 2LS
- UK
| | - Yussif Saaka
- Pharmaceutical Biophysics Group
- Institute of Pharmaceutical Science
- King's College London
- London SE1 9NH
- UK
| | - M. Jayne Lawrence
- Division of Pharmacy and Optometry
- School of Health Sciences
- The University of Manchester
- Manchester M13 9PT
- UK
| | - Christian D. Lorenz
- Biological Physics & Soft Matter Group
- Department of Physics
- King's College London
- London WC2R 2LS
- UK
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Saini RK, Shuaib S, Goyal B. Molecular insights into Aβ42protofibril destabilization with a fluorinated compound D744: A molecular dynamics simulation study. J Mol Recognit 2017; 30. [DOI: 10.1002/jmr.2656] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 07/25/2017] [Accepted: 07/26/2017] [Indexed: 12/13/2022]
Affiliation(s)
- Rajneet Kaur Saini
- Department of Chemistry, School of Basic and Applied Sciences; Sri Guru Granth Sahib World University; Fatehgarh Sahib Punjab India
| | - Suniba Shuaib
- Department of Chemistry, School of Basic and Applied Sciences; Sri Guru Granth Sahib World University; Fatehgarh Sahib Punjab India
| | - Bhupesh Goyal
- Department of Chemistry, School of Basic and Applied Sciences; Sri Guru Granth Sahib World University; Fatehgarh Sahib Punjab India
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Shuaib S, Goyal B. Scrutiny of the mechanism of small molecule inhibitor preventing conformational transition of amyloid-β 42 monomer: insights from molecular dynamics simulations. J Biomol Struct Dyn 2017; 36:663-678. [PMID: 28162045 DOI: 10.1080/07391102.2017.1291363] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disorder that is characterized by loss of intellectual functioning of brain and memory loss. According to amyloid cascade hypothesis, aggregation of amyloid-β42 (Aβ42) peptide can generate toxic oligomers and their accumulation in the brain is responsible for the onset of AD. In spite of carrying out a large number of experimental studies on inhibition of Aβ42 aggregation by small molecules, the detailed inhibitory mechanism remains elusive. In the present study, comparable molecular dynamics (MD) simulations were performed to elucidate the inhibitory mechanism of a sulfonamide inhibitor C1 (2,5-dichloro-N-(4-piperidinophenyl)-3-thiophenesulfonamide), reported for its in vitro and in vivo anti-aggregation activity against Aβ42. MD simulations reveal that C1 stabilizes native α-helix conformation of Aβ42 by interacting with key residues in the central helix region (13-26) with hydrogen bonds and π-π interactions. C1 lowers the solvent-accessible surface area of the central hydrophobic core (CHC), KLVFF (16-20), that confirms burial of hydrophobic residues leading to the dominance of helical conformation in the CHC region. The binding free energy analysis with MM-PBSA demonstrates that Ala2, Phe4, Tyr10, Gln15, Lys16, Leu17, Val18, Phe19, Phe20, Glu22, and Met35 contribute maximum to binding free energy (-43.1 kcal/mol) between C1 and Aβ42 monomer. Overall, MD simulations reveal that C1 inhibits Aβ42 aggregation by stabilizing native helical conformation and inhibiting the formation of aggregation-prone β-sheet conformation. The present results will shed light on the underlying inhibitory mechanism of small molecules that show potential in vitro anti-aggregation activity against Aβ42.
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Affiliation(s)
- Suniba Shuaib
- a Department of Chemistry , School of Basic and Applied Sciences, Sri Guru Granth Sahib World University , Fatehgarh Sahib 140406 , Punjab , India
| | - Bhupesh Goyal
- a Department of Chemistry , School of Basic and Applied Sciences, Sri Guru Granth Sahib World University , Fatehgarh Sahib 140406 , Punjab , India
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