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Computational Modeling of Polymers
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Computational Modeling 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 (20 April 2022) | Viewed by 48910

Special Issue Editors

Dr. Riccardo Concu

E-Mail Website
Guest Editor
Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal
Interests: QSAR and QSTR models; machine learning; molecular dynamics; coarse-grained; polymers; nanotechnology
Special Issues, Collections and Topics in MDPI journals
Dr. Michael González-Durruthy

E-Mail Website
Guest Editor
Science and Technology Park, University of Porto, 4169-007 Porto, Portugal
Interests: QSAR and QSTR models; machine learning; molecular dynamics; coarse-grained; polymers; nanotechnology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Development of new and innovative polymers is a challenging task. Classical approaches are time and money consuming and should be replaced by computational methodologies that allow a fast and accurate development of innovative materials. Computational modelling has been emerging as alternative approaches and nowadays is indispensable to assist experiments while developing new polymers. In addition, computational methodologies can also help to study and defining mechanical and physical properties of polymers. In this contests, quantum-mechanical calculations, all-atomistic and coarse-grained molecular dynamics simulations and elastic network models, have become a powerful tool for analysing complex physical phenomena, i.e., bond vibrations, diffusion, and rheology of polymeric materials.
The main aim of this special issue is to investigate more recent computational approaches used to develop and study polymers.  This special issue will provide an opportunity for scientists, engineers and practitioners to present their more relevant studies and findings in this area.

Dr. Riccardo Concu
Dr. Michael González-Durruthy
Guest Editors

Manuscript Submission Information

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Keywords

  • Computational Modelling
  • Polymers
  • Quantum-Mechanical Calculations
  • All-Atomistic Molecular Dynamics
  • Coarse-Grained Molecular Dynamics
  • Elastic Network Model

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Published Papers (15 papers)

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Research

29 pages, 2547 KiB  
Article
Theoretical and Experimental Investigation of Shape Memory Polymers Programmed below Glass Transition Temperature
by Kartikey Shahi and Velmurugan Ramachandran
Polymers 2022, 14(13), 2753; https://doi.org/10.3390/polym14132753 - 5 Jul 2022
Cited by 10 | Viewed by 2777
Abstract
An epoxy-based shape memory polymer (SMP) is synthesized and examined for its deterioration in shape fixity due to springback and isothermal viscoelastic recovery at different ambient temperatures. Shape fixity depends not only on material properties but also on programming conditions. A constitutive finite [...] Read more.
An epoxy-based shape memory polymer (SMP) is synthesized and examined for its deterioration in shape fixity due to springback and isothermal viscoelastic recovery at different ambient temperatures. Shape fixity depends not only on material properties but also on programming conditions. A constitutive finite deformation model is incorporated to predict the behavior of the proposed SMP and find maximum shape fixity. A programming approach is followed in which, in contrast to hot programming, the SMPs are neither heated before deformation nor cooled afterward but are deformed at ambient temperature and then stress-relaxed. The proximity of the programming temperature to the glass transition temperature plays a crucial role in determining the shape fixity of SMP. It has been found that the SMP with a glass transition temperature of 42.9 °C can achieve maximum shape fixity of 92.25% when programmed at 23 °C with 100 min stress relaxation time. Thermal contraction and dynamic tests are performed in the Dynamic Mechanical Analyzer (DMA) to determine structural relaxation properties and distinguish the programming temperature in the cold, warm or hot temperature zone. The shape memory tests are carried out using temperature-controlled UTM to determine the shape fixity and shape recovery of SMP. The SMPs are subjected to a full thermomechanical cycle with different stress relaxation times and programming temperatures. Full article
(This article belongs to the Special Issue Computational Modeling of Polymers)
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24 pages, 3208 KiB  
Article
Constitutive Equations for Analyzing Stress Relaxation and Creep of Viscoelastic Materials Based on Standard Linear Solid Model Derived with Finite Loading Rate
by Che-Yu Lin, Yi-Cheng Chen, Chen-Hsin Lin and Ke-Vin Chang
Polymers 2022, 14(10), 2124; https://doi.org/10.3390/polym14102124 - 23 May 2022
Cited by 16 | Viewed by 7429
Abstract
The viscoelastic properties of materials such as polymers can be quantitatively evaluated by measuring and analyzing the viscoelastic behaviors such as stress relaxation and creep. The standard linear solid model is a classical and commonly used mathematical model for analyzing stress relaxation and [...] Read more.
The viscoelastic properties of materials such as polymers can be quantitatively evaluated by measuring and analyzing the viscoelastic behaviors such as stress relaxation and creep. The standard linear solid model is a classical and commonly used mathematical model for analyzing stress relaxation and creep behaviors. Traditionally, the constitutive equations for analyzing stress relaxation and creep behaviors based on the standard linear solid model are derived using the assumption that the loading is a step function, implying that the loading rate used in the loading process of stress relaxation and creep tests is infinite. Using such constitutive equations may cause significant errors in analyses since the loading rate must be finite (no matter how fast it is) in a real stress relaxation or creep experiment. The purpose of this paper is to introduce the constitutive equations for analyzing stress relaxation and creep behaviors based on the standard linear solid model derived with a finite loading rate. The finite element computational simulation results demonstrate that the constitutive equations derived with a finite loading rate can produce accurate results in the evaluation of all viscoelastic parameters regardless of the loading rate in most cases. It is recommended that the constitutive equations derived with a finite loading rate should replace the traditional ones derived with an infinite loading rate to analyze stress relaxation and creep behaviors for quantitatively evaluating the viscoelastic properties of materials. Full article
(This article belongs to the Special Issue Computational Modeling of Polymers)
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12 pages, 3080 KiB  
Article
Analysis of Thermoelastic Interaction in a Polymeric Orthotropic Medium Using the Finite Element Method
by Ibrahim Abbas, Aatef Hobiny, Hashim Alshehri, Sorin Vlase and Marin Marin
Polymers 2022, 14(10), 2112; https://doi.org/10.3390/polym14102112 - 22 May 2022
Cited by 16 | Viewed by 1712
Abstract
In this work, the finite element technique is employed to evaluate the effects of thermal relaxation durations on temperature, displacements, and stresses in a two-dimensional, polymeric, orthotropic, elastic medium. The problem is considered in a homogeneous, polymeric, orthotropic medium in the context of [...] Read more.
In this work, the finite element technique is employed to evaluate the effects of thermal relaxation durations on temperature, displacements, and stresses in a two-dimensional, polymeric, orthotropic, elastic medium. The problem is considered in a homogeneous, polymeric, orthotropic medium in the context of the Green and Lindsay model with two thermal relaxation times. The bounding surface of the half-space was subjected to a heat flux with an exponentially decaying pulse. Finite element techniques were used to solve the governing formulations, with eight-node isoparametric rectangular elements with three degrees of freedom (DOF) per node. The developed method was calculated using numerical results applied to the polymeric, orthotropic medium. The findings were implemented and visually shown. Finally, the results were displayed to demonstrate the differences between classical dynamic coupling (CT), the Lord–Shulman (LS) and the Green and Lindsay (GL) models. Full article
(This article belongs to the Special Issue Computational Modeling of Polymers)
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11 pages, 2755 KiB  
Article
A Trefoil Knot Polymer Chain Translocates through a Funnel-like Channel: A Multi-Particle Collision Dynamics Study
by Xiaohui Wen, Deyin Wang, Jiajun Tang and Zhiyong Yang
Polymers 2022, 14(6), 1164; https://doi.org/10.3390/polym14061164 - 15 Mar 2022
Viewed by 1989
Abstract
With combining multi-particle collision dynamics (MPCD) for the solvent and molecular dynamics (MD) for the polymer chains, we have studied the conformation and untying behaviors of a trefoil knot polymer chain translocated through a confined funnel-like channel. For the trefoil knot chain, we [...] Read more.
With combining multi-particle collision dynamics (MPCD) for the solvent and molecular dynamics (MD) for the polymer chains, we have studied the conformation and untying behaviors of a trefoil knot polymer chain translocated through a confined funnel-like channel. For the trefoil knot chain, we found that the untying knot behavior mostly happens during the translocation process, and the translocation behavior of linear chains is also simulated as a comparison. Some characteristics of the trefoil knot chain during translocation process, such as average gyration radius <Rg> and the average end-to-end distances <S> are discussed, and we statistic the scale relations of the translocation time versus the chain length, and that of the chain rigidity. This study may help to understand translocation behaviors of the knotted linear polymer chain in the capillary flow field. Full article
(This article belongs to the Special Issue Computational Modeling of Polymers)
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13 pages, 1957 KiB  
Article
Problems with Applying the Ozawa–Avrami Crystallization Model to Non-Isothermal Crosslinking Polymerization
by Sergey Vyazovkin and Andrey Galukhin
Polymers 2022, 14(4), 693; https://doi.org/10.3390/polym14040693 - 11 Feb 2022
Cited by 7 | Viewed by 3179
Abstract
Ozawa has modified the Avrami model to treat non-isothermal crystallization kinetics. The resulting Ozawa–Avrami model yields the Avrami index (n) and heating/cooling function (χ(T)). There has been a number of recent applications of the Ozawa–Avrami model to [...] Read more.
Ozawa has modified the Avrami model to treat non-isothermal crystallization kinetics. The resulting Ozawa–Avrami model yields the Avrami index (n) and heating/cooling function (χ(T)). There has been a number of recent applications of the Ozawa–Avrami model to non-isothermal crosslinking polymerization (curing) kinetics that have determined n and have used χ(T) in place of the rate constant (k(T)) in the Arrhenius equation to evaluate the activation energy (E) and the preexponential factor (A). We analyze this approach mathematically as well as by using simulated and experimental data, highlighting the following problems. First, the approach is limited to the processes that obey the Avrami model. In cases of autocatalytic or decelerating kinetics, commonly encountered in crosslinking polymerizations, n reveals a systematic dependence on temperature. Second, χ(T) has a more complex temperature dependence than k(T) and thus cannot produce exact values of E and A via the Arrhenius equation. The respective deviations can reach tens or even hundreds of percent but are diminished dramatically using the heating/cooling function in the form [χ(T)]1/n. Third, without this transformation, the Arrhenius plots may demonstrate breakpoints that leads to questionable interpretations. Overall, the application of the Ozawa–Avrami model to crosslinking polymerizations appears too problematic to be justified, especially considering the existence of well-known alternative kinetic techniques that are flexible, accurate, and computationally simple. Full article
(This article belongs to the Special Issue Computational Modeling of Polymers)
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12 pages, 3268 KiB  
Article
Predicting the Mechanical Response of Polyhydroxyalkanoate Biopolymers Using Molecular Dynamics Simulations
by Karteek K. Bejagam, Nevin S. Gupta, Kwan-Soo Lee, Carl N. Iverson, Babetta L. Marrone and Ghanshyam Pilania
Polymers 2022, 14(2), 345; https://doi.org/10.3390/polym14020345 - 17 Jan 2022
Cited by 9 | Viewed by 3397
Abstract
Polyhydroxyalkanoates (PHAs) have emerged as a promising class of biosynthesizable, biocompatible, and biodegradable polymers to replace petroleum-based plastics for addressing the global plastic pollution problem. Although PHAs offer a wide range of chemical diversity, the structure–property relationships in this class of polymers remain [...] Read more.
Polyhydroxyalkanoates (PHAs) have emerged as a promising class of biosynthesizable, biocompatible, and biodegradable polymers to replace petroleum-based plastics for addressing the global plastic pollution problem. Although PHAs offer a wide range of chemical diversity, the structure–property relationships in this class of polymers remain poorly established. In particular, the available experimental data on the mechanical properties is scarce. In this contribution, we have used molecular dynamics simulations employing a recently developed forcefield to predict chemical trends in mechanical properties of PHAs. Specifically, we make predictions for Young’s modulus, and yield stress for a wide range of PHAs that exhibit varying lengths of backbone and side chains as well as different side chain functional groups. Deformation simulations were performed at six different strain rates and six different temperatures to elucidate their influence on the mechanical properties. Our results indicate that Young’s modulus and yield stress decrease systematically with increase in the number of carbon atoms in the side chain as well as in the polymer backbone. In addition, we find that the mechanical properties were strongly correlated with the chemical nature of the functional group. The functional groups that enhance the interchain interactions lead to an enhancement in both the Young’s modulus and yield stress. Finally, we applied the developed methodology to study composition-dependence of the mechanical properties for a selected set of binary and ternary copolymers. Overall, our work not only provides insights into rational design rules for tailoring mechanical properties in PHAs, but also opens up avenues for future high throughput atomistic simulation studies geared towards identifying functional PHA polymer candidates for targeted applications. Full article
(This article belongs to the Special Issue Computational Modeling of Polymers)
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22 pages, 4342 KiB  
Article
Changes in the Local Conformational States Caused by Simple Na+ and K+ Ions in Polyelectrolyte Simulations: Comparison of Seven Force Fields with and without NBFIX and ECC Corrections
by Natalia Lukasheva, Dmitry Tolmachev, Hector Martinez-Seara and Mikko Karttunen
Polymers 2022, 14(2), 252; https://doi.org/10.3390/polym14020252 - 8 Jan 2022
Cited by 9 | Viewed by 2231
Abstract
Electrostatic interactions have a determining role in the conformational and dynamic behavior of polyelectrolyte molecules. In this study, anionic polyelectrolyte molecules, poly(glutamic acid) (PGA) and poly(aspartic acid) (PASA), in a water solution with the most commonly used K+ or Na+ counterions, [...] Read more.
Electrostatic interactions have a determining role in the conformational and dynamic behavior of polyelectrolyte molecules. In this study, anionic polyelectrolyte molecules, poly(glutamic acid) (PGA) and poly(aspartic acid) (PASA), in a water solution with the most commonly used K+ or Na+ counterions, were investigated using atomistic molecular dynamics (MD) simulations. We performed a comparison of seven popular force fields, namely AMBER99SB-ILDN, AMBER14SB, AMBER-FB15, CHARMM22*, CHARMM27, CHARMM36m and OPLS-AA/L, both with their native parameters and using two common corrections for overbinding of ions, the non-bonded fix (NBFIX), and electronic continuum corrections (ECC). These corrections were originally introduced to correct for the often-reported problem concerning the overbinding of ions to the charged groups of polyelectrolytes. In this work, a comparison of the simulation results with existing experimental data revealed several differences between the investigated force fields. The data from these simulations and comparisons with previous experimental data were then used to determine the limitations and strengths of these force fields in the context of the structural and dynamic properties of anionic polyamino acids. Physical properties, such as molecular sizes, local structure, and dynamics, were studied using two types of common counterions, namely potassium and sodium. The results show that, in some cases, both the macroion size and dynamics depend strongly on the models (parameters) for the counterions due to strong overbinding of the ions and charged side chain groups. The local structures and dynamics are more sensitive to dihedral angle parameterization, resulting in a preference for defined monomer conformations and the type of correction used. We also provide recommendations based on the results. Full article
(This article belongs to the Special Issue Computational Modeling of Polymers)
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24 pages, 5262 KiB  
Article
Assessing the Compressive and Impact Behavior of Plastic Safety Toe Caps through Computational Modelling
by Pedro Veiga Rodrigues, Bruno Ramoa, Ana Vera Machado, Philip Cardiff and João Miguel Nóbrega
Polymers 2021, 13(24), 4332; https://doi.org/10.3390/polym13244332 - 10 Dec 2021
Cited by 8 | Viewed by 3457
Abstract
Toe caps are one of the most important components in safety footwear, but have a significant contribution to the weight of the shoe. Efforts have been made to replace steel toe caps by polymeric ones, since they are lighter, insulated and insensitive to [...] Read more.
Toe caps are one of the most important components in safety footwear, but have a significant contribution to the weight of the shoe. Efforts have been made to replace steel toe caps by polymeric ones, since they are lighter, insulated and insensitive to magnetic fields. Nevertheless, polymeric solutions require larger volumes, which has a negative impact on the shoe’s aesthetics. Therefore, safety footwear manufacturers are pursuing the development of an easy, low-cost and reliable solution to optimize this component. In this work, a solid mechanics toolbox built in the open-source computational library, OpenFOAM®, was used to simulate two laboratory standard tests (15 kN compression and 200 J impact tests). To model the polymeric material behavior, a neo-Hookean hyper-elasto-plastic material law with J2 plastic criteria was employed. A commercially available plastic toe cap was characterized, and the collected data was used for assessment purposes. Close agreements, between experimental and simulated values, were achieved for both tests, with an approximate error of 5.4% and 6.8% for the displacement value in compression and impact test simulations, respectively. The results clearly demonstrate that the employed open-source finite volume computational models offer reliable results and can support the design of toe caps for the R&D footwear industry. Full article
(This article belongs to the Special Issue Computational Modeling of Polymers)
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11 pages, 748 KiB  
Article
Artificial Neural Network Modeling of Glass Transition Temperatures for Some Homopolymers with Saturated Carbon Chain Backbone
by Elena-Luiza Epure, Sîziana Diana Oniciuc, Nicolae Hurduc and Elena Niculina Drăgoi
Polymers 2021, 13(23), 4151; https://doi.org/10.3390/polym13234151 - 27 Nov 2021
Cited by 3 | Viewed by 1986
Abstract
The glass transition temperature (Tg) is an important decision parameter when synthesizing polymeric compounds or when selecting their applicability domain. In this work, the glass transition temperature of more than 100 homopolymers with saturated backbones was predicted using a neuro-evolutive technique combining Artificial [...] Read more.
The glass transition temperature (Tg) is an important decision parameter when synthesizing polymeric compounds or when selecting their applicability domain. In this work, the glass transition temperature of more than 100 homopolymers with saturated backbones was predicted using a neuro-evolutive technique combining Artificial Neural Networks with a modified Bacterial Foraging Optimization Algorithm. In most cases, the selected polymers have a vinyl-type backbone substituted with various groups. A few samples with an oxygen atom in a linear non-vinyl hydrocarbon main chain were also considered. Eight structural, thermophysical, and entanglement properties estimated by the quantitative structure–property relationship (QSPR) method, along with other molecular descriptors reflecting polymer composition, were considered as input data for Artificial Neural Networks. The Tg’s neural model has a 7.30% average absolute error for the training data and 12.89% for the testing one. From the sensitivity analysis, it was found that cohesive energy, from all independent parameters, has the highest influence on the modeled output. Full article
(This article belongs to the Special Issue Computational Modeling of Polymers)
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12 pages, 671 KiB  
Article
Temperature Dependence of Conformational Relaxation of Poly(ethylene oxide) Melts
by Hye Sol Kim, Taejin Kwon, Chung Bin Park and Bong June Sung
Polymers 2021, 13(22), 4049; https://doi.org/10.3390/polym13224049 - 22 Nov 2021
Cited by 5 | Viewed by 2866
Abstract
The time-temperature superposition (TTS) principle, employed extensively for the analysis of polymer dynamics, is based on the assumption that the different normal modes of polymer chains would experience identical temperature dependence. We aim to test the critical assumption for TTS principle by investigating [...] Read more.
The time-temperature superposition (TTS) principle, employed extensively for the analysis of polymer dynamics, is based on the assumption that the different normal modes of polymer chains would experience identical temperature dependence. We aim to test the critical assumption for TTS principle by investigating poly(ethylene oxide) (PEO) melts, which have been considered excellent solid polyelectrolytes. In this work, we perform all-atom molecular dynamics simulations up to 300 ns at a range of temperatures for PEO melts. We find from our simulations that the conformations of strands of PEO chains in melts show ideal chain statistics when the strand consists of at least 10 monomers. At the temperature range of T= 400 to 300 K, the mean-square displacements (⟨Δr2(t)⟩) of the centers of mass of chains enter the Fickian regime, i.e., ⟨Δr2(t)⟩∼t1. On the other hand, ⟨Δr2(t)⟩ of the monomers of the chains scales as ⟨Δr2(t)⟩∼t1/2 at intermediate time scales as expected for the Rouse model. We investigate various relaxation modes of the polymer chains and their relaxation times (τn), by calculating for each strand of n monomers. Interestingly, different normal modes of the PEO chains experience identical temperature dependence, thus indicating that the TTS principle would hold for the given temperature range. Full article
(This article belongs to the Special Issue Computational Modeling of Polymers)
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13 pages, 3129 KiB  
Article
Nanocomposite of Fullerenes and Natural Rubbers: MARTINI Force Field Molecular Dynamics Simulations
by Jiramate Kitjanon, Wasinee Khuntawee, Saree Phongphanphanee, Thana Sutthibutpong, Nattaporn Chattham, Mikko Karttunen and Jirasak Wong-ekkabut
Polymers 2021, 13(22), 4044; https://doi.org/10.3390/polym13224044 - 22 Nov 2021
Cited by 9 | Viewed by 2770
Abstract
The mechanical properties of natural rubber (NR) composites depend on many factors, including the filler loading, filler size, filler dispersion, and filler-rubber interfacial interactions. Thus, NR composites with nano-sized fillers have attracted a great deal of attention for improving properties such as stiffness, [...] Read more.
The mechanical properties of natural rubber (NR) composites depend on many factors, including the filler loading, filler size, filler dispersion, and filler-rubber interfacial interactions. Thus, NR composites with nano-sized fillers have attracted a great deal of attention for improving properties such as stiffness, chemical resistance, and high wear resistance. Here, a coarse-grained (CG) model based on the MARTINI force field version 2.1 has been developed and deployed for simulations of cis-1,4-polyisoprene (cis-PI). The model shows qualitative and quantitative agreement with the experiments and atomistic simulations. Interestingly, only a 0.5% difference with respect to the experimental result of the glass transition temperature (Tg) of the cis-PI in the melts was observed. In addition, the mechanical and thermodynamical properties of the cis-PI-fullerene(C60) composites were investigated. Coarse-grained molecular dynamics (MD) simulations of cis-PI-C60 composites with varying fullerene concentrations (0–32 parts per hundred of rubber; phr) were performed over 200 microseconds. The structural, mechanical, and thermal properties of the composites were determined. The density, bulk modulus, thermal expansion, heat capacity, and Tg of the NR composites were found to increase with increasing C60 concentration. The presence of C60 resulted in a slight increasing of the end-to-end distance and radius of the gyration of the cis-PI chains. The contribution of C60 and cis-PI interfacial interactions led to an enhancement of the bulk moduli of the composites. This model should be helpful in the investigations and design of effective fillers of NR-C60 composites for improving their properties. Full article
(This article belongs to the Special Issue Computational Modeling of Polymers)
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18 pages, 33417 KiB  
Article
Compressive Properties and Constitutive Model of Semicrystalline Polyethylene
by Kebin Zhang, Wenbin Li, Yu Zheng, Wenjin Yao and Changfang Zhao
Polymers 2021, 13(17), 2895; https://doi.org/10.3390/polym13172895 - 27 Aug 2021
Cited by 6 | Viewed by 3715
Abstract
The mechanical properties of polyethylene (PE) materials are greatly influenced by their molecular structures, environmental temperature, and strain rate. In this study, static and dynamic compression tests were performed on two semicrystalline PE materials—ultrahigh molecular weight polyethylene (UHMWPE) and high-density polyethylene (HDPE). The [...] Read more.
The mechanical properties of polyethylene (PE) materials are greatly influenced by their molecular structures, environmental temperature, and strain rate. In this study, static and dynamic compression tests were performed on two semicrystalline PE materials—ultrahigh molecular weight polyethylene (UHMWPE) and high-density polyethylene (HDPE). The stress–strain curves of HDPE and UHMWPE under uniaxial compression at temperatures of −40–120 °C and strain rates of 0.001–5500 s−1 were obtained. The research findings suggest that both the UHMWPE and HDPE showed significant strain rate-strengthening effect and temperature-softening effect. In particular, HDPE exhibited better compression resistance and high-temperature resistance. The relationships between the yield stress and temperature and between the yield stress and strain rate for both materials were fitted, and the Cowper–Symonds constitutive model was built while considering the temperature effect. The parameters of the constitutive model were obtained and input into LS-DYNA software to simulate the dynamic compression process of HDPE. The simulation result was consistent with the test result, validating the accuracy of the constitutive parameters. Full article
(This article belongs to the Special Issue Computational Modeling of Polymers)
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12 pages, 4503 KiB  
Article
Characteristic Structural Knowledge for Morphological Identification and Classification in Meso-Scale Simulations Using Principal Component Analysis
by Natthiti Chiangraeng, Michael Armstrong, Kiattikhun Manokruang, Vannajan Sanghiran Lee, Supat Jiranusornkul and Piyarat Nimmanpipug
Polymers 2021, 13(16), 2581; https://doi.org/10.3390/polym13162581 - 4 Aug 2021
Cited by 2 | Viewed by 2108
Abstract
Meso-scale simulations have been widely used to probe aggregation caused by structural formation in macromolecular systems. However, the limitations of the long-length scale, resulting from its simulation box, cause difficulties in terms of morphological identification and insufficient classification. In this study, structural knowledge [...] Read more.
Meso-scale simulations have been widely used to probe aggregation caused by structural formation in macromolecular systems. However, the limitations of the long-length scale, resulting from its simulation box, cause difficulties in terms of morphological identification and insufficient classification. In this study, structural knowledge derived from meso-scale simulations based on parameters from atomistic simulations were analyzed in dissipative particle dynamic (DPD) simulations of PS-b-PI diblock copolymers. The radial distribution function and its Fourier-space counterpart or structure factor were proposed using principal component analysis (PCA) as key characteristics for morphological identification and classification. Disorder, discrete clusters, hexagonally packed cylinders, connected clusters, defected lamellae, lamellae and connected cylinders were effectively grouped. Full article
(This article belongs to the Special Issue Computational Modeling of Polymers)
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8 pages, 2083 KiB  
Communication
In Silico Characterization of the Interaction between the PBP2a “Decoy” Protein of Resistant Staphylococcus aureus and the Monomeric Units of Eudragit E-100 and Poly(Maleic Acid-alt-Octadecene) Polymers
by Yamil Liscano, Ana Amú, Astrid González, Jose Oñate-Garzón and Constain H. Salamanca
Polymers 2021, 13(14), 2320; https://doi.org/10.3390/polym13142320 - 15 Jul 2021
Cited by 4 | Viewed by 2859
Abstract
Antimicrobial treatment alternatives for methicillin-resistant Staphylococcus aureus (MRSA) are increasingly limited. MRSA strains are resistant to methicillin due to the formation of β-lactamase enzymes, as well as the acquisition of the mecA gene, which encodes the penicillin-binding protein (PBP2a) that reduces the affinity [...] Read more.
Antimicrobial treatment alternatives for methicillin-resistant Staphylococcus aureus (MRSA) are increasingly limited. MRSA strains are resistant to methicillin due to the formation of β-lactamase enzymes, as well as the acquisition of the mecA gene, which encodes the penicillin-binding protein (PBP2a) that reduces the affinity for β-lactam drugs. Previous studies have shown that the use of ampicillin-loaded nanoparticles can improve antimicrobial activity on resistant S. aureus strains. However, the biological mechanism of this effect has not yet been properly elucidated. Therefore, this short communication focused on characterizing the in silico interactions of the PBP2a membrane receptor protein from S. aureus against the monomeric units of two polymeric materials previously used in the development of different nanoparticles loaded with ampicillin. Such polymers correspond to Eudragit E-100 chloride (EuCl) and the sodium salt of poly(maleic acid-alt-octadecene) (PAM-18Na). For this, molecular coupling studies were carried out in the active site of the PBP2a protein with the monomeric units of both polymers in neutral and ionized form, as well as with ampicillin antibiotic (model β-lactam drug). The results showed that ampicillin, as well as the monomeric units of EuCl and PAM18Na, described a slight binding free energy to the PBPa2 protein. In addition, it was found that the amino acids of the active site of the PBPa2 protein have interactions of different types and intensities, suggesting, in turn, different forms of protein–substrate coupling. Full article
(This article belongs to the Special Issue Computational Modeling of Polymers)
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20 pages, 2345 KiB  
Article
Predicting the Adsorption of Amoxicillin and Ibuprofen on Chitosan and Graphene Oxide Materials: A Density Functional Theory Study
by Leonardo Anchique, Jackson J. Alcázar, Andrea Ramos-Hernandez, Maximiliano Méndez-López, José R. Mora, Norma Rangel, José Luis Paz and Edgar Márquez
Polymers 2021, 13(10), 1620; https://doi.org/10.3390/polym13101620 - 17 May 2021
Cited by 11 | Viewed by 4248
Abstract
The occurrence, persistence, and accumulation of antibiotics and non-steroidal anti-inflammatory drugs (NSAIDs) represent a new environmental problem due to their harmful effects on human and aquatic life. A suitable absorbent for a particular type of pollutant does not necessarily absorb other types of [...] Read more.
The occurrence, persistence, and accumulation of antibiotics and non-steroidal anti-inflammatory drugs (NSAIDs) represent a new environmental problem due to their harmful effects on human and aquatic life. A suitable absorbent for a particular type of pollutant does not necessarily absorb other types of compounds, so knowing the compatibility between a particular pollutant and a potential absorbent before experimentation seems to be fundamental. In this work, the molecular interactions between some pharmaceuticals (amoxicillin, ibuprofen, and tetracycline derivatives) with two potential absorbers, chitosan and graphene oxide models (pyrene, GO-1, and coronene, GO-2), were studied using the ωB97X-D/6-311G(2d,p) level of theory. The energetic interaction order found was amoxicillin/chitosan > amoxicillin/GO-1 > amoxicillin/GO-2 > ibuprofen/chitosan > ibuprofen/GO-2 > ibuprofen/GO-1, the negative sign for the interaction energy in all complex formations confirms good compatibility, while the size of Eint between 24–34 kcal/mol indicates physisorption processes. Moreover, the free energies of complex formation were negative, confirming the spontaneity of the processes. The larger interaction of amoxicillin Gos, compared to ibuprofen Gos, is consistent with previously reported experimental results, demonstrating the exceptional predictability of these methods. The second-order perturbation theory analysis shows that the amoxicillin complexes are mainly driven by hydrogen bonds, while van der Waals interactions with chitosan and hydrophobic interactions with graphene oxides are modelled for the ibuprofen complexes. Energy decomposition analysis (EDA) shows that electrostatic energy is a major contributor to the stabilization energy in all cases. The results obtained in this work promote the use of graphene oxides and chitosan as potential adsorbents for the removal of these emerging pollutants from water. Full article
(This article belongs to the Special Issue Computational Modeling of Polymers)
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