Molecular Dynamics Insights for Screening the Ability of Polymers to Remove Pesticides from Water

The use of pesticides in agriculture is known to have environmental impacts, namely it leads to underground and spring water contamination. Thus, it turns out that nowadays general-endeavor towards the sustainability of farmer production requires novel strategies to capture pesticides from water and soils. We propose a methodology based on molecular dynamics simulations to identify polymers that are potentially featured to be applied for pesticide remediation in water and soils. We have employed cymoxanil (CYM), glufosinate ammonium (GLF), imidacloprid (IMI) and mancozeb (MAN) as pesticides, and have tested polymers with different characteristics as removing agents. Specifically, we have investigated oligomers of polypropylene (PP), poly(acrylic acid) protonated (PAAH) and deprotonated (PAA), and chitosan protonated (CTH) and deprotonated (CT). It has been found that all oligomers show a certain degree of selectivity concerning the interaction with the tested pesticides.     

Molybdenum Disulphide Precipitation in Jet Reactors: Introduction of Kinetics Model for Computational Fluid Dynamics Calculations

In our previous work, we used the population balance method to develop a molybdenum disulphide kinetics model consisting of a set of differential equations and constants formulated to express the kinetics of complex chemical reactions leading to molybdenum disulphide precipitation. The purpose of the study is to improved the model to describe the occurring phenomena more thoroughly and have introduced computational fluid dynamics (CFD) modelling to conduct calculations for various reactor geometries. CFD simulations supplemented with our nucleation and growth kinetics model can predict the impact of mixing conditions on particle size with good accuracy. This introduces another engineering tool for designing efficient chemical reactors.     

Molecular Modelling and Simulations of Light-Harvesting Decanuclear Ru-Based Dendrimers for Artificial Photosynthesis

The structure of a decanuclear photo- and redox-active dendrimer based on Ru(II) polypyridine subunits, suitable as a light-harvesting multicomponent species for artificial photosynthesis, has been investigated by means of computer modelling. The compound has the general formula [Ru{(μ-dpp)Ru[(μ-dpp)Ru(bpy)₂]₂}₃](PF₆)₂₀ ( Ru10 ; bpy=2,2′-bipyridine; dpp=2,3-bis(2′-pyridyl)pyrazine). The stability of possible isomers of each monomer was investigated by performing classical molecular dynamics (MD) and quantum mechanics (QM) simulations on each monomer and comparing the results. The number of stable isomers is reduced to 36 with a prevalence of MER isomerism in the central core, as previously observed by NMR experiments. The simulations on decanuclear dendrimers suggest that the stability of the dendrimer is not linked to the stability of the individual monomers composing the dendrimer but rather governed by the steric constrains originated by the multimetallic assembly. Finally, the self-aggregation of Ru10 and the distribution of the counterions around the complexes is investigated using Molecular Dynamics both in implicit and explicit acetonitrile solution. In representative examples, with nine and four dendrimers, the calculated pair distribution function for the ruthenium centers suggests a self-aggregation mechanism in which the dendrimers are approaching in small blocks and then aggregate all together. Scanning transmission electron microscopy complements the investigation, supporting the formation of different aggregates at various concentrations.     

Hemodynamics and Wall Shear Stress of Blood Vessels in Aortic Coarctation with Computational Fluid Dynamics Simulation

The purpose of this study was to identify the characteristics of blood flow in aortic coarctation based on stenotic shape structure, stenosis rate, and the distribution of the wall load delivered into the blood vessels and to predict the impact on aneurysm formation and rupture of blood vessels by using a computational fluid dynamics modeling method. It was applied on the blood flow in abdominal aortic blood vessels in which stenosis occurred by using the commercial finite element software ADINA on fluid-solid interactions. The results of modeling, with an increasing stenosis rate and Reynolds number, showed the pressure drop was increased and the velocity was greatly changed. When the stenosis rate was the same, the pressure drop and the velocity change were larger in the stenosis with a symmetric structure than in the stenosis with an asymmetric one. Maximal changes in wall shear stress were observed in the area before stenosis and minimal changes were shown in stenosis areas. The minimal shear stress occurred at different locations depending on the stenosis shape models. With an increasing stenosis rate and Reynolds number, the maximal wall shear stress was increased and the minimal wall shear stress was decreased. Through such studies, it is thought that the characteristics of blood flow in the abdominal aorta where a stenosis is formed will be helpful in understanding the mechanism of growth of atherosclerosis and the occurrence and rupture of the abdominal aortic flow.     

Fragment-Based Ab Initio Molecular Dynamics Simulation for Combustion

We develop a fragment-based ab initio molecular dynamics (FB-AIMD) method for efficient dynamics simulation of the combustion process. In this method, the intermolecular interactions are treated by a fragment-based many-body expansion in which three- or higher body interactions are neglected, while two-body interactions are computed if the distance between the two fragments is smaller than a cutoff value. The accuracy of the method was verified by comparing FB-AIMD calculated energies and atomic forces of several different systems with those obtained by standard full system quantum calculations. The computational cost of the FB-AIMD method scales linearly with the size of the system, and the calculation is easily parallelizable. The method is applied to methane combustion as a benchmark. Detailed reaction network of methane reaction is analyzed, and important reaction species are tracked in real time. The current result of methane simulation is in excellent agreement with known experimental findings and with prior theoretical studies.     

An Iterative Method for Producing Equilibrated Symmetric Three‐Arm Star Polymer Melts in Molecular Dynamics

Melts of symmetric three‐arm stars are generated using a novel iterative method. In this method, an equilibrated low molecular weight configuration is used to generate progressively higher molecular weights by affine scaling and equilibration. At each stage in the progression, the synthetically lowered entanglement density allows bypassing of the exponentially large relaxation times of branched polymers. The quality of equilibration was assessed by measuring the mean dimensions, distribution of dimensions, and internal length scales of the polymers. The total time required to generate the progression of equilibrated configurations was seen to scale as the Rouse time of the highest molecular weight.

     

Predictors of Cavitation in Glassy Polymers under Tensile Strain: A Coarse‐Grained Molecular Dynamics Investigation

The nucleation of cavities in a homogeneous polymer under tensile strain is studied in a coarse‐grained MD simulation. To establish a causal relation between local microstructure and the onset of cavitation, a detailed analysis of some local properties is presented. In contrast to common assumptions, the nucleation of a cavity is neither correlated to a local loss of density nor to stress at the atomic scale or the chain‐end density in the nondeformed state. Instead, a cavity in glassy polymers nucleates in regions that display a low bulk elastic modulus. Even if the localization of a cavity is not directly predictable from the initial configuration, the elastically weak zones identified in the initial state emerge as favorite spots for cavity formation.

     

Hydrogen Adsorption and Diffusion in p‐tert‐Butylcalix[4]arene: An Experimental and Molecular Simulation Study

Experimental adsorption isotherms were measured and computer simulations were performed to determine the nature of the H₂ gas uptake in the low‐density p‐tert‐butylcalix[4]arene (tBC) phase. ¹H NMR peak intensity measurements for pressures up to 175 bar were used to determine the H₂ adsorption isotherm. Weak surface adsorption (up to ≈2 mass % H₂) and stronger adsorption (not exceeding 0.25 mass % or one H₂ per calixarene bowl) inside the calixarene phase were detected. The latter type of adsorbed H₂ molecule has restricted motion and shows a reversible gas adsorption/desorption cycle. Pulsed field gradient (PFG) NMR pressurization/depressurization measurements were performed to study the diffusion of H₂ in the calixarene phases. Direct adsorption isotherms by exposure of the calixarene phase to pressures of H₂ gas to ≈60 bar are also presented, and show a maximum H₂ adsorption of 0.4 H₂ per calixarene bowl. Adsorption isotherms of H₂ in bulk tBC have been simulated using grand canonical Monte Carlo calculations in a rigid tBC framework, and yield adsorptions of ≈1 H₂ per calixarene bowl at saturation. Classical molecular dynamics simulations with a fully flexible calixarene molecular force field are used to determine the guest distribution and inclusion energy of the H₂ in the solid with different loadings.     

Molecular Dynamics Investigation of the Thermo‐Responsive Polymer Poly(N‐isopropylacrylamide)

Using molecular dynamics simulations with an OPLS force field, the lower critical solution temperature (LCST) of single‐ and multiple‐chain PNIPAM solutions in water is investigated. The sample containing ten polymer chains shows a sudden drop in size and volume at 305 K. Such an effect is absent in the single‐chain system. Large fluctuations of the physical properties of a short single‐chain prevent any clear detection of the LCST for the chosen model system, at least on the time scale of 200 ns. The results provide evidence that a critical number of PNIPAM monomer units must be present in the simulated system before MD simulations are capable to detect conformational changes unambiguously.

     

Coupling Effects of Electrostatic Interactions and Salt Concentration Gradient in Polymer Translocation through a Nanopore: A Coarse-Grained Molecular Dynamics Simulations Study

We study the influence of polymer pore interactions and focus on the role played by the concentration gradient of salt in the translocation of polyelectrolytes (PE) through nanopores explicitly using coarse-grained Langevin dynamics simulations. The mean translocation time is calculated by varying the applied voltage, the pH, and the salt concentration gradient. Changing the pH can alter the electrostatic interaction between the protein pore and the polyelectrolyte chain. The polymer pore interaction is weakened by the increase in the strength of the externally applied electric field that drives translocation. Additionally, the screening effect of the salt can reduce the strong charge-charge repulsion between the PE beads which can make translocation faster. The simulation results show there can be antagonistic or synergistic coupling between the salt concentration-induced screening effect and the drift force originating from the salt concentration gradient thereby affecting the translocation time. Our simulation results are explained qualitatively with free energy calculations.     

An Update on Molecularly Imprinted Polymer Design through a Computational Approach to Produce Molecular Recognition Material with Enhanced Analytical Performance

Molecularly imprinted polymer (MIP) computational design is expected to become a routine technique prior to synthesis to produce polymers with high affinity and selectivity towards target molecules. Furthermore, using these simulations reduces the cost of optimizing polymerization composition. There are several computational methods used in MIP fabrication and each requires a comprehensive study in order to select a process with results that are most similar to properties exhibited by polymers synthesized through laboratory experiments. Until now, no review has linked computational strategies with experimental results, which are needed to determine the method that is most appropriate for use in designing MIP with high molecular recognition. This review will present an update of the computational approaches started from 2016 until now on quantum mechanics, molecular mechanics and molecular dynamics that have been widely used. It will also discuss the linear correlation between computational results and the polymer performance tests through laboratory experiments to examine to what extent these methods can be relied upon to obtain polymers with high molecular recognition. Based on the literature search, density functional theory (DFT) with various hybrid functions and basis sets is most often used as a theoretical method to provide a shorter MIP manufacturing process as well as good analytical performance as recognition material.     

First Principles Neural Network Potentials for Reactive Simulations of Large Molecular and Condensed Systems

Modern simulation techniques have reached a level of maturity which allows a wide range of problems in chemistry and materials science to be addressed. Unfortunately, the application of first principles methods with predictive power is still limited to rather small systems, and despite the rapid evolution of computer hardware no fundamental change in this situation can be expected. Consequently, the development of more efficient but equally reliable atomistic potentials to reach an atomic level understanding of complex systems has received considerable attention in recent years. A promising new development has been the introduction of machine learning (ML) methods to describe the atomic interactions. Once trained with electronic structure data, ML potentials can accelerate computer simulations by several orders of magnitude, while preserving quantum mechanical accuracy. This Review considers the methodology of an important class of ML potentials that employs artificial neural networks.     

从头算分子动力学研究O-与CH_3F反应的产物通道

在B3LYP/6-31+G(d,p)理论水平下采用基于波恩-奥本海默近似的从头算分子动力学方法重新研究了O-与CH3F反应经抽氢生成OH-和生成H2O的两条产物通道.反应轨线从反应初始过渡态开始,采用300K时的热取样确定初始条件,同时为对比不同的初始碰撞平动能条件下产物通道的变化,分别限定过渡矢量上的能量为2.1、36.8及62.8kJ·mol-1进行轨线计算,所有轨线计算的结果表明抽氢生成OH-的过程始终为主要的产物通道.我们的计算不仅进一步证实了以往实验的结论,而且描绘了抽氢生成OH-和生成H2O这两个产物通道在反应出口势能面上的动态反应路径,更为深刻地揭示了该反应的微观机理.     

Quantum Mechanics/Molecular Mechanics Simulations Show Saccharide Distortion is Required for Reaction in Hen Egg-White Lysozyme

Hybrid quantum mechanics/molecular mechanics (QM/MM) calculations on lysozyme show significant distortion of the bound saccharide is required to facilitate the catalytic reaction.     

Molecular Dynamic Study of Mechanism Underlying Nature of Molecular Recognition and the Role of Crosslinker in the Synthesis of Salmeterol-Targeting Molecularly Imprinted Polymer for Analysis of Salmeterol Xinafoate in Biological Fluid

The rational preparation of molecularly imprinted polymers (MIPs) in order to have selective extraction of salmeterol xinafoate (SLX) from serum was studied. SLX is an acting β-adrenergic receptor agonist used in the treatment of asthma and has an athletic performance-enhancing effect. Molecular dynamics were used for the simulation of the SLX-imprinted pre-polymerization system, to determine the stability of the system. The computational simulation showed that SLX as a template, 4-hydroxyethyl methacrylate (HEMA) as a monomer, and trimethylolpropane trimethacrylate (TRIM) as a crosslinker in mol ratio of 1:6:20 had the strongest interaction in terms of the radial distribution functional. To validate the computational result, four polymers were synthesized using the precipitation polymerization method, and MIP with composition and ratio corresponding with the system with the strongest interaction as an MD simulation result showed the best performance, with a recovery of 96.59 ± 2.24% of SLX in spiked serum and 92.25 ± 1.12% when SLX was spiked with another analogue structure. Compared with the standard solid phase extraction sorbent C-18, which had a recovery of 79.11 ± 2.96%, the MIP showed better performance. The harmony between the simulation and experimental results illustrates that the molecular dynamic simulations had a significant role in the study and development of the MIPs for analysis of SLX in biological fluid.     

Vase‐Kite Equilibrium of Resorcin[4]arene Cavitands Investigated Using Molecular Dynamics Simulations with Ball‐and‐Stick Local Elevation Umbrella Sampling

A key feature of resorcin[4]arene cavitands is their ability to switch between a closed/contracted (Vase ) and an open/expanded (Kite ) conformation. The mechanism and dynamics of this interconversion remains, however, elusive. In the present study, the Vase ‐Kite transitions of a quinoxaline‐based and of a dinitrobenzene‐based resorcin[4]arene are investigated using molecular dynamics (MD) simulations in three environments (vacuum, chloroform, and toluene) and at three temperatures (198.15, 248.15, and 298.15 K). The challenge of sampling the Vase ‐Kite transition, which occurs experimentally on the millisecond time scale, is overcome by calculating relative free energies using ball‐and stick local elevation umbrella sampling (B&S‐LEUS) to enhance the statistics on the relevant states and to promote interconversion transitions. Associated unbiased MD simulations also evidence for the first time a complete Vase ‐to‐Kite transition, as well as transitions between degenerate Kite 1 and Kite 2 forms and solvent‐exchange events. The calculated Vase ‐to‐Kite free‐energy changes ΔG are in qualitative agreement with the experimental magnitudes and trends. The level of quantitative agreement is, however, limited by the force‐field accuracy and, in particular, by the approximate treatment of intramolecular interactions at the classical level. The results are in line with a less stable Vase state for the dinitrobenzene compared to the quinoxaline compound, and a negative entropy change ΔS for the Vase ‐to‐Kite transition of the latter compound. Relative free energies calculated for intermediates also suggest that the Vase ‐Kite transition does not follow a concerted mechanism, but an asynchronous one with sequential opening of the flaps. In particular, the conformation involving two adjacent flaps open in a parallel direction (cis‐p) represents a likely intermediate, which has not been observed experimentally to date.     

Ensemble‐Averaged QM/MM Kinetic Isotope Effects for the SN2 Reaction of Cyanide Anions with Chloroethane in DMSO Solution

The existence of solvent fluctuations leads to populations of reactant‐state (RS) and transition‐state (TS) configurations and implies that property calculations must include appropriate averaging over distributions of values for individual configurations. Average kinetic isotope effects 〈KIE〉 for NC^?+EtCl→NCEt+Cl^? in DMSO solution at 30 °C are best obtained as the ratio 〈f_RS〉/〈f_TS〉 of isotopic partition function ratios separately averaged over all RS and TS configurations. In this way the hybrid AM1/OPLS‐AA potential yields 〈KIE〉 values for all six isotopic substitutions (2° α‐²H₂, 2° β‐²H₃, α‐¹¹C/¹⁴C, leaving group ³⁷Cl, and nucleophile ¹³C and ¹⁵N) for this reaction in the correct direction as measured experimentally. These thermally‐averaged calculated KIEs may be compared meaningfully with experiment, and only one of them differs in magnitude from the experimental value by more than one standard deviation from the mean. This success contrasts with previous KIE calculations based upon traditional methods without averaging. The isotopic partition function ratios are best evaluated using all (internal) vibrational and (external) librational frequencies obtained from Hessians determined for subsets of atoms, relaxed to local minima or saddle points, within frozen solvent environments of structures sampled along molecular dynamics trajectories for RS and TS. The current method may perfectly well be implemented with other QM or QM/MM methods, and thus provides a useful tool for investigating KIEs in relation to studies of chemical reaction mechanisms in solution or catalyzed by enzymes.     

CHARMM general force field: A force field for drug‐like molecules compatible with the CHARMM all‐atom additive biological force fields

The widely used CHARMM additive all‐atom force field includes parameters for proteins, nucleic acids, lipids, and carbohydrates. In the present article, an extension of the CHARMM force field to drug‐like molecules is presented. The resulting CHARMM General Force Field (CGenFF) covers a wide range of chemical groups present in biomolecules and drug‐like molecules, including a large number of heterocyclic scaffolds. The parametrization philosophy behind the force field focuses on quality at the expense of transferability, with the implementation concentrating on an extensible force field. Statistics related to the quality of the parametrization with a focus on experimental validation are presented. Additionally, the parametrization procedure, described fully in the present article in the context of the model systems, pyrrolidine, and 3‐phenoxymethylpyrrolidine will allow users to readily extend the force field to chemical groups that are not explicitly covered in the force field as well as add functional groups to and link together molecules already available in the force field. CGenFF thus makes it possible to perform “all‐CHARMM” simulations on drug‐target interactions thereby extending the utility of CHARMM force fields to medicinally relevant systems. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010