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Polymers
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Molecular Dynamics Simulations of Polymers
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Molecular Dynamics Simulations of Polymers

A special issue of Polymers (ISSN 2073-4360). This special issue belongs to the section "Polymer Physics and Theory".

Deadline for manuscript submissions: closed (30 November 2022) | Viewed by 40099

Special Issue Editor

Dr. Aleksandar Y. Mehandzhiyski

E-Mail Website
Guest Editor
Laboratory of Organic Electronics (LOE), Department of Science and Technology (ITN), Linköping University, Linköping, Sweden
Interests: modelling of polymers; cellulose; composite materials; chemical reactions; interfacial systems

Special Issue Information

Dear Colleagues,

Polymers are macromolecules with a large variety of chemical structures and morphologies which determine their unique and various properties. They are widely used in many different areas, from medicine to the aerospace industry. Understanding polymers’ interactions and morphology on the atomistic scale is of paramount importance to interpret and improve their properties. In recent years, molecular dynamics simulations have become a standard tool alongside experiments to understand the morphology of polymers on the atomistic scale. Often, molecular dynamics brings valuable information to interpret experimental data. Molecular dynamics are sometimes referred to as “computational microscopy” because of the ability to see like through a microscope the interactions between atoms and molecules, their structure, and organization.

This Special Issue aims to collect scientific articles and reviews from various topics related to molecular dynamics simulations of polymers, such as morphology, mechanical properties, phase behavior, and optical and electrical properties, to name a few. Both atomistic and coarse-grained molecular dynamics contributions are welcome. In addition, synthetic as well as natural polymer-related research will be considered. We hope that this Special Issue can further help to promote the use of molecular dynamics simulations in contemporary polymer research.

Dr. Aleksandar Y. Mehandzhiyski
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Polymers is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • molecular dynamics
  • atomistic simulations
  • coarse-grained simulations
  • morphology
  • natural polymers
  • synthetic polymers
  • conducting polymers

Published Papers (20 papers)

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19 pages, 9830 KiB  
Article
Coarse-Grained Molecular Dynamics Simulation of Polycarbonate Deformation: Dependence of Mechanical Performance by the Effect of Spatial Distribution and Topological Constraints
by Tatchaphon Leelaprachakul, Atsushi Kubo and Yoshitaka Umeno
Polymers 2023, 15(1), 43; https://0-doi-org.brum.beds.ac.uk/10.3390/polym15010043 - 22 Dec 2022
Cited by 2 | Viewed by 1867
Abstract
Polycarbonate is an engineering plastic used in a wide range of applications due to its excellent mechanical properties, which are closely related to its molecular structure. We performed coarse-grained molecular dynamics (CGMD) calculations to investigate the effects of topological constraints and spatial distribution [...] Read more.
Polycarbonate is an engineering plastic used in a wide range of applications due to its excellent mechanical properties, which are closely related to its molecular structure. We performed coarse-grained molecular dynamics (CGMD) calculations to investigate the effects of topological constraints and spatial distribution on the mechanical performance of a certain range of molecular weights. The topological constraints and spatial distribution are quantified as the number of entanglements per molecule (Ne) and the radius of gyration (Rg), respectively. We successfully modeled molecular structures with a systematic variation of Ne and Rg by controlling two simulation parameters: the temperature profile and Kuhn segment length, respectively. We investigated the effect of Ne and Rg on stress–strain curves in uniaxial tension with fixed transverse strain. The result shows that the structure with a higher radius of gyration or number of entanglements has a higher maximum stress (σm), which is mainly due to a firmly formed entanglement network. Such a configuration minimizes the critical strain (εc). The constitutive relationships between the mechanical properties (σm and εc) and the initial molecular structure parameters (Ne and Rg) are suggested. Full article
(This article belongs to the Special Issue Molecular Dynamics Simulations of Polymers)
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10 pages, 1223 KiB  
Article
Fractional Coupling of Primary and Johari–Goldstein Relaxations in a Model Polymer
by Carlo Andrea Massa, Francesco Puosi and Dino Leporini
Polymers 2022, 14(24), 5560; https://0-doi-org.brum.beds.ac.uk/10.3390/polym14245560 - 19 Dec 2022
Cited by 1 | Viewed by 898
Abstract
A polymer model exhibiting heterogeneous Johari–Goldstein (JG) secondary relaxation is studied by extensive molecular-dynamics simulations of states with different temperature and pressure. Time–temperature–pressure superposition of the primary (segmental) relaxation is evidenced. The time scales of the primary and the JG relaxations are found [...] Read more.
A polymer model exhibiting heterogeneous Johari–Goldstein (JG) secondary relaxation is studied by extensive molecular-dynamics simulations of states with different temperature and pressure. Time–temperature–pressure superposition of the primary (segmental) relaxation is evidenced. The time scales of the primary and the JG relaxations are found to be highly correlated according to a power law. The finding agrees with key predictions of the Coupling Model (CM) accounting for the decay in a correlation function due to the relaxation and diffusion of interacting systems. Nonetheless, the exponent of the power law, even if it is found in the range predicted by CM (0<ξ<1), deviates from the expected one. It is suggested that the deviation could depend on the particular relaxation process involved in the correlation function and the heterogeneity of the JG process. Full article
(This article belongs to the Special Issue Molecular Dynamics Simulations of Polymers)
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15 pages, 5086 KiB  
Article
Morphological Effect of Side Chain Length in Sulfonated Poly(arylene ether sulfone)s Polymer Electrolyte Membranes via Molecular Dynamics Simulation
by Xue Li, Hong Zhang, Cheng Lin, Ran Tian, Penglun Zheng and Chenxing Hu
Polymers 2022, 14(24), 5499; https://0-doi-org.brum.beds.ac.uk/10.3390/polym14245499 - 15 Dec 2022
Viewed by 1330
Abstract
With the recognition of the multiple advantages of sulfonated hydrocarbon-based polymers that possess high chemical and mechanical stability with significant low cost, we employed molecular dynamics simulation to explore the morphological effects of side chain length in sulfonated polystyrene grafted poly(arylene ether sulfone)s [...] Read more.
With the recognition of the multiple advantages of sulfonated hydrocarbon-based polymers that possess high chemical and mechanical stability with significant low cost, we employed molecular dynamics simulation to explore the morphological effects of side chain length in sulfonated polystyrene grafted poly(arylene ether sulfone)s (SPAES) proton exchange membranes. The calculated diffusion coefficients of hydronium ions (H3O+) are in range of 0.61–1.15 × 10−7 cm2/s, smaller than that of water molecules, due to the electrical attraction between the oppositely charged sulfonate group and H3O+. The investigation into the radial distribution functions suggests that phase segregation in the SPAES membrane is more probable with longer side chains. As the hydration level of the membranes in this study is relatively low (λ = 3), longer side chains correspond to more water molecules in the amorphous cell, which provides better solvent effects for the distribution of sulfonated side chains. The coordination number of water molecules and hydronium ions around the sulfonate group increases from 1.67 to 2.40 and from 2.45 to 5.66, respectively, with the increase in the side chain length. A significant proportion of the hydronium ions appear to be in bridging configurations coordinated by multiple sulfonate groups. The microscopic conformation of the SPAES membrane is basically unaffected by temperature during the evaluated temperature range. Thus, it can be revealed that the side chain length plays a key role in the configuration of the polymer chain and would contribute to the formation of the microphase separation morphology, which profits proton transport in the hydrophilic domains. Full article
(This article belongs to the Special Issue Molecular Dynamics Simulations of Polymers)
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18 pages, 4752 KiB  
Article
Adhesion of Bis-Salphen-Based Coordination Polymers to Graphene: Insights from Free Energy Perturbation Study
by Sergey Pyrlin, Veniero Lenzi, Alexandre Silva, Marta Ramos and Luís Marques
Polymers 2022, 14(21), 4525; https://0-doi-org.brum.beds.ac.uk/10.3390/polym14214525 - 26 Oct 2022
Viewed by 1166
Abstract
Manipulation of nanoscale objects using molecular self-assembly is a potent tool to achieve large scale nanopatterning with small effort. Coordination polymers of bis-salphen compounds based on zinc have demonstrated their ability to align carbon nanotubes into micro-scale networks with an unusual “rings-and-rods” pattern. [...] Read more.
Manipulation of nanoscale objects using molecular self-assembly is a potent tool to achieve large scale nanopatterning with small effort. Coordination polymers of bis-salphen compounds based on zinc have demonstrated their ability to align carbon nanotubes into micro-scale networks with an unusual “rings-and-rods” pattern. This paper investigates how the compounds interact with pristine and functionalized graphene using density functional theory calculations and molecular dynamic simulations. Using the free energy perturbation method we will show how the addition of phenyl side groups to the core compound and functionalization of graphene affect the stability, mobility and conformation adopted by a dimer of bis-(Zn)salphen compound adsorbed on graphene surface and what it can reveal about the arrangement of chains of bis-(Zn)salphen polymer around carbon nanotubes during the self-assembly of microscale networks. Full article
(This article belongs to the Special Issue Molecular Dynamics Simulations of Polymers)
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21 pages, 3706 KiB  
Article
A Tractable, Transferable, and Empirically Consistent Fibrous Biomaterial Model
by Nicholas Filla, Yiping Zhao and Xianqiao Wang
Polymers 2022, 14(20), 4437; https://0-doi-org.brum.beds.ac.uk/10.3390/polym14204437 - 20 Oct 2022
Cited by 1 | Viewed by 1327
Abstract
Stochastic modeling is a useful approach for modeling fibrous materials that attempts to recreate fibrous materials’ structure using statistical data. However, several issues remain to be resolved in the stochastic modeling of fibrous materials—for example, estimating 3D fiber orientation distributions from 2D data, [...] Read more.
Stochastic modeling is a useful approach for modeling fibrous materials that attempts to recreate fibrous materials’ structure using statistical data. However, several issues remain to be resolved in the stochastic modeling of fibrous materials—for example, estimating 3D fiber orientation distributions from 2D data, achieving the desired fiber tortuosity distributions, and dealing with fiber–fiber penetration. This work proposes innovative methods to (1) create a mapping from 2D fiber orientation data to 3D fiber orientation probability distributions, and vice versa; and (2) provide a means to select parameters de novo for random walks employing the popularized von Mises–Fisher distribution given that the desired tortuosity of the path is known. The proposed methods are incorporated alongside previously developed stochastic modeling techniques to simulate fiber network structures. First, fiber orientation distributions vary significantly depending on how a fibrous material is formed, and projection distortion affects the measurement of fiber orientation distributions when reported as 2D data such as histograms or polar plots. Relationships are developed to estimate 3D fiber orientation distributions from 2D data, accounting for projection distortion and the variety of orientation distributions observed in fibrous materials. We show that without correcting for projection distortion, fiber orientation distribution parameters could have errors of up to 100%. Second, in stochastic modeling, fiber tortuosity is usually treated with random walks, but no relationship is available for choosing random walk inputs to generate a desired fiber tortuosity. Relationships are also developed to relate the input parameters of von Mises–Fisher random walks to the expected tortuosity of the generated path—a necessary link to modeling fiber tortuosity distributions tractably and with empirical consistency. Using the developed relationships, we show that modeling of tortuous fibers from a distribution could be sped up by ~1200-fold and the uncertainty of selecting appropriate parameters could be eliminated. Third, randomly placing fibers in a simulation domain inevitably results in fiber–fiber penetration, and correcting this issue requires changes to the simulated fibrous material structure through non-penetration conditions. No thorough remedy can be offered here, but we statistically quantify the effects of enforcing non-penetration conditions on the fiber shape and orientation changes as well as the overall fibrous material model. This work offers tractable and transferable methods for treating fiber orientation and tortuosity that allow for empirical consistency in the stochastic modeling of fibrous materials. Full article
(This article belongs to the Special Issue Molecular Dynamics Simulations of Polymers)
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13 pages, 2012 KiB  
Article
Characterization of the Interaction of Polymeric Micelles with siRNA: A Combined Experimental and Molecular Dynamics Study
by Franck Marquet, Filip Stojceski, Gianvito Grasso, Viorica Patrulea, Andrea Danani and Gerrit Borchard
Polymers 2022, 14(20), 4409; https://0-doi-org.brum.beds.ac.uk/10.3390/polym14204409 - 19 Oct 2022
Cited by 1 | Viewed by 1519
Abstract
The simulation of large molecular systems remains a daunting challenge, which justifies the exploration of novel methodologies to keep computers as an ideal companion tool for everyday laboratory work. Whole micelles, bigger than 20 nm in size, formed by the self-assembly of hundreds [...] Read more.
The simulation of large molecular systems remains a daunting challenge, which justifies the exploration of novel methodologies to keep computers as an ideal companion tool for everyday laboratory work. Whole micelles, bigger than 20 nm in size, formed by the self-assembly of hundreds of copolymers containing more than 50 repeating units, have until now rarely been simulated, due to a lack of computational power. Therefore, a flexible amphiphilic triblock copolymer (mPEG45-α-PLL10-PLA25) containing a total of 80 repeating units, has been emulated and synthesized to embody compactified nanoconstructs of over 900 assembled copolymers, sized between 80 and 100 nm, for siRNA complexing purposes. In this study, the tailored triblock copolymers containing a controlled number of amino groups, were used as a support model to address the binding behavior of STAT3-siRNA, in the formation of micelleplexes. Since increasingly complex drug delivery systems require an ever more optimized physicochemical characterization, a converging description has been implemented by a combination of experimentation and computational simulations. The computational data were advantageous in allowing for the assumption of an optimal N/P ratio favoring both conformational rigidifications of STAT3-siRNA with low competitive phenomena at the binding sites of the micellar carriers. These calculations were consistent with the experimental data showing that an N/P ratio of 1.5 resulted in a sufficient amount of complexed STAT3-siRNA with an electrical potential at the slipping plane of the nanopharmaceuticals, close to the charge neutralization. Full article
(This article belongs to the Special Issue Molecular Dynamics Simulations of Polymers)
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15 pages, 11617 KiB  
Article
Molecular Dynamics Investigation of Hyaluronan in Biolubrication
by Masahiro Susaki and Mitsuhiro Matsumoto
Polymers 2022, 14(19), 4031; https://0-doi-org.brum.beds.ac.uk/10.3390/polym14194031 - 26 Sep 2022
Cited by 1 | Viewed by 1211
Abstract
Aqueous solution of strongly hydrophilic biopolymers is known to exhibit excellent lubrication properties in biological systems, such as the synovial fluid in human joints. Several mechanisms have been proposed on the biolubrication of joints, such as the boundary lubrication and the fluid exudation [...] Read more.
Aqueous solution of strongly hydrophilic biopolymers is known to exhibit excellent lubrication properties in biological systems, such as the synovial fluid in human joints. Several mechanisms have been proposed on the biolubrication of joints, such as the boundary lubrication and the fluid exudation lubrication. In these models, mechanical properties of synovial fluid containing biopolymers are essential. To examine the role of such biopolymers in lubrication, a series of molecular dynamics simulations with an all-atom classical force field model were conducted for aqueous solutions of hyaluronan (hyaluronic acid, HA) under constant shear. After equilibrating the system, the Lees-Edwards boundary condition was imposed, with which a steady state of uniform shear flow was realized. Comparison of HA systems with hydrocarbon (pentadecane, PD) solutions of similar mass concentration indicates that the viscosity of HA solutions is slightly larger in general than that of PDs, due to the strong hydration of HA molecules. Effects of added electrolyte (NaCl) were also discussed in terms of hydration. These findings suggest the role of HA in biolubirication as a load-supporting component, with its flexible character and strong hydration structure. Full article
(This article belongs to the Special Issue Molecular Dynamics Simulations of Polymers)
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20 pages, 11175 KiB  
Article
Modeling Solution Drying by Moving a Liquid-Vapor Interface: Method and Applications
by Yanfei Tang, John E. McLaughlan, Gary S. Grest and Shengfeng Cheng
Polymers 2022, 14(19), 3996; https://0-doi-org.brum.beds.ac.uk/10.3390/polym14193996 - 23 Sep 2022
Cited by 3 | Viewed by 1627
Abstract
A method of simulating the drying process of a soft matter solution with an implicit solvent model by moving the liquid-vapor interface is applied to various solution films and droplets. For a solution of a polymer and nanoparticles, we observe “polymer-on-top” stratification, similar [...] Read more.
A method of simulating the drying process of a soft matter solution with an implicit solvent model by moving the liquid-vapor interface is applied to various solution films and droplets. For a solution of a polymer and nanoparticles, we observe “polymer-on-top” stratification, similar to that found previously with an explicit solvent model. Furthermore, “polymer-on-top” is found even when the nanoparticle size is smaller than the radius of gyration of the polymer chains. For a suspension droplet of a bidisperse mixture of nanoparticles, we show that core-shell clusters of nanoparticles can be obtained via the “small-on-outside” stratification mechanism at fast evaporation rates. “Large-on-outside” stratification and uniform particle distribution are also observed when the evaporation rate is reduced. Polymeric particles with various morphologies, including Janus spheres, core-shell particles, and patchy particles, are produced from drying droplets of polymer solutions by combining fast evaporation with a controlled interaction between the polymers and the liquid-vapor interface. Our results validate the applicability of the moving interface method to a wide range of drying systems. The limitations of the method are pointed out and cautions are provided to potential practitioners on cases where the method might fail. Full article
(This article belongs to the Special Issue Molecular Dynamics Simulations of Polymers)
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21 pages, 5384 KiB  
Article
Modeling the Phase Equilibria of Associating Polymers in Porous Media with Respect to Chromatographic Applications
by Xiu Wang, Zuzana Limpouchová, Karel Procházka, Rahul Kumar Raya and Yonggang Min
Polymers 2022, 14(15), 3182; https://0-doi-org.brum.beds.ac.uk/10.3390/polym14153182 - 04 Aug 2022
Cited by 2 | Viewed by 1346
Abstract
Associating copolymers self-assemble during their passage through a liquid chromatography (LC) column, and the elution differs from that of common non-associating polymers. This computational study aims at elucidating the mechanism of their unique and intricate chromatographic behavior. We focused on amphiphilic diblock copolymers [...] Read more.
Associating copolymers self-assemble during their passage through a liquid chromatography (LC) column, and the elution differs from that of common non-associating polymers. This computational study aims at elucidating the mechanism of their unique and intricate chromatographic behavior. We focused on amphiphilic diblock copolymers in selective solvents, performed the Monte Carlo (MC) simulations of their partitioning between a bulk solvent (mobile phase) and a cylindrical pore (stationary phase), and investigated the concentration dependences of the partition coefficient and of other functions describing the phase behavior. The observed abruptly changing concentration dependences of the effective partition coefficient demonstrate the significant impact of the association of copolymers with their partitioning between the two phases. The performed simulations reveal the intricate interplay of the entropy-driven and the enthalpy-driven processes, elucidate at the molecular level how the self-assembly affects the chromatographic behavior, and provide useful hints for the analysis of experimental elution curves of associating polymers. Full article
(This article belongs to the Special Issue Molecular Dynamics Simulations of Polymers)
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17 pages, 8068 KiB  
Article
Conformational Dynamics of Glucagon-like Peptide-2 with Different Electric Field
by Jingjie Su, Tingting Sun, Yan Wang and Yu Shen
Polymers 2022, 14(13), 2722; https://0-doi-org.brum.beds.ac.uk/10.3390/polym14132722 - 03 Jul 2022
Cited by 3 | Viewed by 1358
Abstract
Molecular dynamics (MD) simulation was used to study the influence of electric field on Glucagon-like Peptide-2 (GLP-2). Different electric field strengths (0 V/nm ≤ E ≤ 1 V/nm) were mainly carried out on GLP-2. The structural changes in GLP-2 were analyzed by the [...] Read more.
Molecular dynamics (MD) simulation was used to study the influence of electric field on Glucagon-like Peptide-2 (GLP-2). Different electric field strengths (0 V/nm ≤ E ≤ 1 V/nm) were mainly carried out on GLP-2. The structural changes in GLP-2 were analyzed by the Root Mean Square Deviation (RMSD), Root Mean Square Fluctuation (RMSF), Radius of Gyration (Rg), Solvent Accessible Surface Area (SASA), Secondary Structure and the number of hydrogen bonds. The stable α—helix structure of GLP-2 was unwound and transformed into an unstable Turn and Coil structure since the stability of the GLP-2 protein structure was reduced under the electric field. Our results show that the degree of unwinding of the GLP-2 structure was not linearly related to the electric field intensity. E = 0.5 V/nm was a special point where the degree of unwinding of the GLP-2 structure reached the maximum at this electric field strength. Under a weak electric field, E < 0.5 V/nm, the secondary structure of GLP-2 becomes loose, and the entropy of the chain increases. When E reaches a certain value (E > 0.5 V/nm), the electric force of the charged residues reaches equilibrium, along the z-direction. Considering the confinement of moving along another direction, the residue is less free. Thus, entropy decreases and enthalpy increases, which enhance the interaction of adjacent residues. It is of benefit to recover hydrogen bonds in the middle region of the protein. These investigations, about the effect of an electric field on the structure of GLP-2, can provide some theoretical basis for the biological function of GLP-2 in vivo. Full article
(This article belongs to the Special Issue Molecular Dynamics Simulations of Polymers)
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12 pages, 7527 KiB  
Article
Effect of Electrostatic Interactions on the Interfacial Energy between Thermoplastic Polymers and Graphene Oxide: A Molecular Dynamics Study
by Mayu Morita, Yutaka Oya, Nobuhiko Kato, Kazuki Mori and Jun Koyanagi
Polymers 2022, 14(13), 2579; https://0-doi-org.brum.beds.ac.uk/10.3390/polym14132579 - 25 Jun 2022
Cited by 8 | Viewed by 2399
Abstract
In this study, the atomistic-scale mechanisms affecting the interfacial stability of a thermoplastic polymer/graphene oxide interface are investigated using molecular dynamics simulations. Different combinations of thermoplastic polymers (polyethersulfone (PES) and polyetherimide (PEI)) and graphene oxides modified with –O–, –OH, and –COOH are prepared. [...] Read more.
In this study, the atomistic-scale mechanisms affecting the interfacial stability of a thermoplastic polymer/graphene oxide interface are investigated using molecular dynamics simulations. Different combinations of thermoplastic polymers (polyethersulfone (PES) and polyetherimide (PEI)) and graphene oxides modified with –O–, –OH, and –COOH are prepared. PES is found to be more strongly stabilized with modified/functionalized graphene oxide in the order of –COOH, –OH, –O–, which is opposite to the stability order of PEI. Our results suggest that these orders of stability are governed by a balance between the following two factors resulting from electrostatic interactions: (1) atoms with a strong charge bias attract each other, thereby stabilizing the interface; (2) the excluded-volume effect of the functional groups on graphene oxide destabilizes the interface by preventing π-π stacking of aromatic rings. Full article
(This article belongs to the Special Issue Molecular Dynamics Simulations of Polymers)
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14 pages, 4629 KiB  
Article
Theoretical Studies of a Silica Functionalized Acrylamide for Calcium Scale Inhibition
by Abdulmujeeb T. Onawole, Ibnelwaleed A. Hussein, Mohammed A. Saad, Nadhem Ismail, Ali Alshami and Mustafa S. Nasser
Polymers 2022, 14(12), 2333; https://0-doi-org.brum.beds.ac.uk/10.3390/polym14122333 - 09 Jun 2022
Cited by 2 | Viewed by 1601
Abstract
The calcium carbonate (CaCO3) scale is one of the most common oilfield scales and oil and gas production bane. CaCO3 scale can lead to a sudden halt in production or, worst-case scenario, accidents; therefore, CaCO3 scale formation prevention is [...] Read more.
The calcium carbonate (CaCO3) scale is one of the most common oilfield scales and oil and gas production bane. CaCO3 scale can lead to a sudden halt in production or, worst-case scenario, accidents; therefore, CaCO3 scale formation prevention is essential for the oil and gas industry. Scale inhibitors are chemicals that can mitigate this problem. We used two popular theoretical techniques in this study: Density Functional Theory (DFT) and Ab Initio Molecular Dynamics (AIMD). The objective was to investigate the inhibitory abilities of mixed oligomers, specifically acrylamide functionalized silica (AM-Silica). DFT studies indicate that Ca2+ does not bind readily to acryl acid and acrylamide; however, it has a good binding affinity with PAM and Silica functionalized PAM. The highest binding affinity occurs in the silica region and not the –CONH functional groups. AIMD calculations corroborate the DFT studies, as observed from the MD trajectory that Ca2+ binds to PAM-Silica by forming bonds with silicon; however, Ca2+ initially forms a bond with silicon in the presence of water molecules. This bonding does not last long, and it subsequently bonds with the oxygen atoms present in the water molecule. PAM-Silica is a suitable calcium scale inhibitor because of its high binding affinity with Ca2+. Theoretical studies (DFT and AIMD) have provided atomic insights on how AM-Silica could be used as an efficient scale inhibitor. Full article
(This article belongs to the Special Issue Molecular Dynamics Simulations of Polymers)
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10 pages, 1876 KiB  
Article
Effects of the Temperature and Salt Concentration on the Structural Characteristics of the Protein (PDB Code 1BBL)
by Dongqing Shao, Qun Zhang, Peng Xu and Zhouting Jiang
Polymers 2022, 14(11), 2134; https://0-doi-org.brum.beds.ac.uk/10.3390/polym14112134 - 24 May 2022
Cited by 5 | Viewed by 1308
Abstract
The effect of the temperature and salt solution on the structural characteristics of the protein 1BBL was investigated by molecular dynamics simulations. The paper presents simulation results regarding the non-bonded energy and the structural stability of the protein immersed in salt solutions with [...] Read more.
The effect of the temperature and salt solution on the structural characteristics of the protein 1BBL was investigated by molecular dynamics simulations. The paper presents simulation results regarding the non-bonded energy and the structural stability of the protein immersed in salt solutions with different concentrations and temperatures. Our work demonstrates that the electrostatic potential energy and van der Waals energy of the system show the opposite changes with the influence of the external environment. Since the electrostatic potential energy changes more obviously, it is dominated in the non-bonding interactions. The structural parameters, such as the root mean square deviation and the radius of gyration, increased initially and decreased afterward with the increase of the salt concentration. The protein presented the loose structure with a relative low stability when it was immersed in a monovalent solution with a salt concentration of 0.8 mol/L. The salt concentration corresponding to the maximum value of structural parameters in the monovalent salt solution was double that in the divalent salt solution. It was also concluded that the protein presented a compact and stable structure when immersed in salt solutions with a high concentration of 2.3 mol/L. The analysis of the root mean square deviation and root mean square fluctuation of the protein sample also exhibited that the structural stability and chain flexibility are strongly guided by the effect of the temperature. These conclusions help us to understand the structural characteristics of the protein immersed in the salt solutions with different concentrations and temperatures. Full article
(This article belongs to the Special Issue Molecular Dynamics Simulations of Polymers)
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11 pages, 2864 KiB  
Article
Performance Evaluation of Nonacosan-10-ol-Based Polyethylene Packaging Material Using Molecular Dynamics Simulations
by Chandra Mouli R. Madhuranthakam, Sudharsan Pandiyan and Alexander Penlidis
Polymers 2022, 14(9), 1779; https://0-doi-org.brum.beds.ac.uk/10.3390/polym14091779 - 27 Apr 2022
Cited by 3 | Viewed by 1582
Abstract
Packaging material has a significant role in maintaining or altering the shelf life of different products. Polymer materials are extensively used as packaging materials for different perishable and non-perishable products both during transportation and storage. This article aims at developing a new polymer [...] Read more.
Packaging material has a significant role in maintaining or altering the shelf life of different products. Polymer materials are extensively used as packaging materials for different perishable and non-perishable products both during transportation and storage. This article aims at developing a new polymer composite which can be used as packaging material. This new composite addresses the challenge of controlling oxygen diffusion rates during the storage of perishable goods such as vegetables, meat and produce, etc. The proposed new composite primarily consists of nonacosan-10-ol and polyethylene. Molecular dynamics simulations (MDS) are performed by mixing 5.2%, 17.1%, 29.2%, 40.8% and 45.2% (wt/wt) of nonacosan-10-ol to amorphous polyethylene. Mechanical properties such as Young’s modulus/glass transition temperature, and gas transport properties such as diffusion coefficient and diffusion volume are estimated from the MDS and diffusion related simulations consisting of different oxygen concentrations in polyethylene-alone system and polyethylene- nonacosan-10-ol blends. The impact of adding different weight percent of nonacosan-10-ol to polyethylene is quantitatively assessed and optimal composition of the proposed additive is suggested corresponding to minimal oxygen diffusion rate, high elastic modulus and good thermal stability. Full article
(This article belongs to the Special Issue Molecular Dynamics Simulations of Polymers)
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14 pages, 5688 KiB  
Article
A Computational Procedure for Atomistic Modelling of Polyphosphazenes towards Better Capturing Molecular-Level Structuring and Thermo-Mechanical Properties
by Kay Chen and Baris Demir
Polymers 2022, 14(7), 1451; https://0-doi-org.brum.beds.ac.uk/10.3390/polym14071451 - 02 Apr 2022
Cited by 2 | Viewed by 1820
Abstract
Poly(phosphazenes)(PZ) are versatile polymers due to their tunable properties that can be tailored for specific applications. Despite extensive experimental research, not all properties are tested, and the list of PZs studied via molecular simulations is limited. Further, a general procedure to generate and [...] Read more.
Poly(phosphazenes)(PZ) are versatile polymers due to their tunable properties that can be tailored for specific applications. Despite extensive experimental research, not all properties are tested, and the list of PZs studied via molecular simulations is limited. Further, a general procedure to generate and test PZ systems is lacking. We present an in situ polymerization procedure developed to make, test, and tune the thermo-mechanical properties of four PZs—poly(dichlorophosphazene)(PZ-DC), poly[bis(2,2,2-trifluoroethoxy)]phosphazene (PZ-TFE), poly(2,2,2-trifluoroethoxy-5,6-diazidohexanoxy) phosphazene (PZ-Azido), and poly(2,2,2-trifluoroethoxy-5,6-dinitratohexanoxy)phosphazene (PZ-Nitrato) via molecular dynamics simulations. The predicted thermo-mechanical properties (i.e., density and glass transition temperature) agreed with experimental values when a direct comparison of PZ systems was possible. This demonstrates the reproducibility and reliability of our procedure which will help understand the behaviour of PZs at the molecular scale. Full article
(This article belongs to the Special Issue Molecular Dynamics Simulations of Polymers)
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20 pages, 5110 KiB  
Article
Optimized Anticorrosion of Polypyrrole Coating by Inverted-Electrode Strategy: Experimental and Molecular Dynamics Investigations
by Xiaoqi Zhao, Xiaoyan Liu, Baomin Fan and Xingwen Zheng
Polymers 2022, 14(7), 1356; https://0-doi-org.brum.beds.ac.uk/10.3390/polym14071356 - 27 Mar 2022
Cited by 15 | Viewed by 1932
Abstract
To improve the poor adhesion and the ensuing insufficient anticorrosion efficacy of electropolymerized polypyrrole (PPy) on copper surface, an inverted-electrode strategy was applied after the passivation procedure, for which the compact coating (PPy-I) was deposited on the substrate in a cathodic window. Morphological [...] Read more.
To improve the poor adhesion and the ensuing insufficient anticorrosion efficacy of electropolymerized polypyrrole (PPy) on copper surface, an inverted-electrode strategy was applied after the passivation procedure, for which the compact coating (PPy-I) was deposited on the substrate in a cathodic window. Morphological and physical characterizations revealed that PPy-I exerted satisfactory adhesion strength and suitable thickness and conductivity compared with the analogue prepared via the traditional protocol (PPy-T). Potentiodynamic polarization, electrochemical impedance spectroscopy and frequency modulation were employed to ascertain the propitious protection of PPy-I for copper in artificial seawater (ASW). Due to the dominant electroactivity, the PPy-I-coated sample possessed higher apparent current density and lower charge transfer resistance than its PPy-T-protected counterpart, which maintained the passivation of the substrate. Surface analysis also supported the viability of PPy-I for copper in ASW for a well-protected surface with inferior water wettability. Molecular dynamics simulations evidenced that PPy-I with the higher density retained efficient anticorrosion capacity on copper at elevated temperatures. Therein, the derived time-dependent spatial diffusion trajectories of ions were locally confined with low diffusion coefficients. Highly twisted pore passages and anodic protection behavior arising respectively from the tight coating architecture and electroactivity contributed to the adequate corrosion resistance of PPy-I-coated copper. Full article
(This article belongs to the Special Issue Molecular Dynamics Simulations of Polymers)
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16 pages, 5543 KiB  
Article
The Effect of Cross-Linking Type on EPDM Elastomer Dynamics and Mechanical Properties: A Molecular Dynamics Simulation Study
by Yajian Wang, Huifang Liu, Pengpeng Li and Linbing Wang
Polymers 2022, 14(7), 1308; https://0-doi-org.brum.beds.ac.uk/10.3390/polym14071308 - 24 Mar 2022
Cited by 7 | Viewed by 2424
Abstract
The cross-linking structure of the Ethylene-propylene-diene monomer (EPDM) is made up of a number of cross-linking types, including carbon atoms from the main chain or monomer and ether crosslinks formed during degradation. Through molecular dynamic simulations, the contribution of each type of cross-linked [...] Read more.
The cross-linking structure of the Ethylene-propylene-diene monomer (EPDM) is made up of a number of cross-linking types, including carbon atoms from the main chain or monomer and ether crosslinks formed during degradation. Through molecular dynamic simulations, the contribution of each type of cross-linked structure to the dynamics and mechanical properties of EPDM, the study’s focus, were investigated. Cross-linking between the tertiary carbons of two main chains, cross-linking at the monomer’s unsaturated position, ether cross-linking after oxidation, and other combinations of target cross-linked carbon atoms from different positions, totaling eight types of cross-linked types, were mixed with EPDM free chains in a 1:1 ratio to form eight types of cross-linked EPDMs. These varieties of cross-linked EPDMs were then compared to an uncross-linked EPDM in terms of density, radius of gyration, free volume, mean square displacement, and uniaxial tensile stress-strain curves. It was found that the cross-linking was always proven to have a favorable influence on mechanical characteristics; however, the relaxation inhibition effect varied. The cross-linking between the diene monomer at the C9 position resulted in a more flexible molecular shape and was more than double the free volume of the uncross-linked EPDM, resulting in an improved diffusion ability. The ether cross-linking produced by the oxidation of the side chain cross-linking improved the positive contribution to stiffness and enhanced the inhibitory impact on diffusion properties, whereas the main chain cross-linking had the opposite effect. The research presented in this study leads to a better knowledge of the microscopic aspects underlying EPDM performance. Full article
(This article belongs to the Special Issue Molecular Dynamics Simulations of Polymers)
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11 pages, 12986 KiB  
Article
All-Atom Molecular Dynamics Simulations on a Single Chain of PET and PEV Polymers
by Mattanun Sangkhawasi, Tawun Remsungnen, Alisa S. Vangnai, Rungtiva P. Poo-arporn and Thanyada Rungrotmongkol
Polymers 2022, 14(6), 1161; https://0-doi-org.brum.beds.ac.uk/10.3390/polym14061161 - 14 Mar 2022
Cited by 9 | Viewed by 3780
Abstract
Polyethylene vanillic (PEV), a bio-based material, has mechanical and thermal properties similar to polyethylene terephthalate (PET), the most common polymer used in industries. The present study aimed to investigate and compare their structural dynamics and physical data using a computational approach. The simple [...] Read more.
Polyethylene vanillic (PEV), a bio-based material, has mechanical and thermal properties similar to polyethylene terephthalate (PET), the most common polymer used in industries. The present study aimed to investigate and compare their structural dynamics and physical data using a computational approach. The simple model of a single-chain polymer containing 100 repeating units was performed by all-atom molecular dynamics (MD) simulations with refined OPLS–AA force field parameters. As a result, the flexibility of the PEV structure was greater than that of PET. PET and PEV polymers had the predicted glass transition temperature Tg values of approximately 345 K and 353 K, respectively. PEV showed a slightly higher Tg than PET, consistent with current experimental evidence. Full article
(This article belongs to the Special Issue Molecular Dynamics Simulations of Polymers)
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15 pages, 6073 KiB  
Article
Molecular Dynamics Simulation on the Effect of Self-Resistance Electric Heating on Carbon Fiber Surface Chemical Properties and Fiber/PP Interfacial Behavior
by Qingzhu He, Jiaqing Liu, Muhan Zhang, Zhanyu Zhai and Bingyan Jiang
Polymers 2022, 14(5), 1043; https://0-doi-org.brum.beds.ac.uk/10.3390/polym14051043 - 05 Mar 2022
Cited by 5 | Viewed by 2403
Abstract
Carbon fiber-reinforced thermoplastic (CFRT) composites have been dramatically employed in the automotive field on account of their superior performances, such as being light weight and high-strength. Self-resistance electric (SRE) heating provides a solution to the problem of high energy consumption in the conventional [...] Read more.
Carbon fiber-reinforced thermoplastic (CFRT) composites have been dramatically employed in the automotive field on account of their superior performances, such as being light weight and high-strength. Self-resistance electric (SRE) heating provides a solution to the problem of high energy consumption in the conventional process of CFRT composites. The effect of SRE heating on the surface chemical properties of carbon fiber (CF) was investigated by X-ray photoelectron spectroscopy (XPS). XPS analysis suggests that the C-O-C epoxy group, the CF surface, would be degraded after SRE heating with strong current intensity, while there are weak changes in the content of -C-OH, -C-O-C-, -C-NH2 and -COOH groups with current intensity. The interfacial bonding properties and the radial distribution function (RDF) of CF–PP interfaces were carried out by molecular dynamics (MD) simulation. The simulation results show that the adhesion between the PP and the E44 sizing agent is weaker than that between CF and PP. There are no interaction modes between the PP and E44 sizing agent except van der Waals and electrostatic adsorption. The presence of the E44 sizing agent does not change the bonding mechanism at the interface of CF/PP. Full article
(This article belongs to the Special Issue Molecular Dynamics Simulations of Polymers)
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Review

Jump to: Research

18 pages, 2552 KiB  
Review
Current State and Perspectives of Simulation and Modeling of Aliphatic Isocyanates and Polyisocyanates
by Veniero Lenzi, Anna Crema, Sergey Pyrlin and Luís Marques
Polymers 2022, 14(9), 1642; https://0-doi-org.brum.beds.ac.uk/10.3390/polym14091642 - 19 Apr 2022
Cited by 10 | Viewed by 2941
Abstract
Aliphatic isocyanates and polyisocyanates are central molecules in the fabrication of polyurethanes, coatings, and adhesives and, due to their excellent mechanical and stability properties, are continuously investigated in advanced applications; however, despite the growing interest in isocyanate-based systems, atomistic simulations on them have [...] Read more.
Aliphatic isocyanates and polyisocyanates are central molecules in the fabrication of polyurethanes, coatings, and adhesives and, due to their excellent mechanical and stability properties, are continuously investigated in advanced applications; however, despite the growing interest in isocyanate-based systems, atomistic simulations on them have been limited by the lack of accurate parametrizations for these molecular species. In this review, we will first provide an overview of current research on isocyanate systems to highlight their most promising applications, especially in fields far from their typical usage, and to justify the need for further modeling works. Next, we will discuss the state of their modeling, from first-principle studies to atomistic molecular dynamics simulations and coarse-grained approaches, highlighting the recent advances in atomistic modeling. Finally, the most promising lines of research in the modeling of isocyanates are discussed in light of the possibilities opened by novel approaches, such as machine learning. Full article
(This article belongs to the Special Issue Molecular Dynamics Simulations of Polymers)
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