Mechanical Molecular Dynamics Simulations Research Articles

A damage-tolerant hybrid aluminum composite reinforced with carbon nanotube and zirconia: study of strengthening mechanisms by combined experiments and molecular dynamics simulations

Aluminum composites, reinforced with CNT and ZrO2 particles, were synthesized via powder metallurgy, undergoing mechanical testing and molecular dynamics (MD) simulations. Hybrid reinforcement significantly increased strength and hardness while preserving toughness through extrinsic toughening mechanisms, preventing a substantial drop in energy absorption. MD simulations revealed dislocation nucleation at reinforcement interfaces, enhancing material strength during propagation. Various reinforcements activated specific strengthening mechanisms, quantified by models. The hybrid composite exhibited excellent strength enhancement and maintained toughness up to a specific reinforcement content. Despite a reduction in energy absorption, the remarkable strength improvement suggests synergistic reinforcement effects, suitable for high-performance, lightweight materials.

Three-metal ion mechanism of cross-linked and uncross-linked DNA polymerase β: A theoretical study.

In our recent publication, we have proposed a revised base excision repair pathway in which DNA polymerase β (Polβ) catalyzes Schiff base formation prior to the gap-filling DNA synthesis followed by β-elimination. In addition, the polymerase activity of Polβ employs the "three-metal ion mechanism" instead of the long-standing "two-metal ion mechanism" to catalyze phosphodiester bond formation based on the fact derived from time-resolved x-ray crystallography that a third Mg2+ was captured in the polymerase active site after the chemical reaction was initiated. In this study, we develop the models of the uncross-linked and cross-linked Polβ complexes and investigate the "three-metal ion mechanism" vs the "two-metal ion mechanism" by using the quantum mechanics/molecular mechanics molecular dynamics simulations. Our results suggest that the presence of the third Mg2+ ion stabilizes the reaction-state structures, strengthens correct nucleotide binding, and accelerates phosphodiester bond formation. The improved understanding of Polβ's catalytic mechanism provides valuable insights into DNA replication and damage repair.

Bayesian Mechanistic Inference, Statistical Mechanics, and a New Era for Monte Carlo.

On the one hand, much of computational chemistry is concerned with "bottom-up" calculations which elucidate observable behavior starting from exact or approximated physical laws, a paradigm exemplified by typical quantum mechanical calculations and molecular dynamics simulations. On the other hand, "top down" computations aiming to formulate mathematical models consistent with observed data, e.g., parametrizing force fields, binding or kinetic models, have been of interest for decades but recently have grown in sophistication with the use of Bayesian inference (BI). Standard BI provides an estimation of parameter values, uncertainties, and correlations among parameters. Used for "model selection," BI can also distinguish between model structures such as the presence or absence of individual states and transitions. Fortunately for physical scientists, BI can be formulated within a statistical mechanics framework, and indeed, BI has led to a resurgence of interest in Monte Carlo (MC) algorithms, many of which have been directly adapted from or inspired by physical strategies. Certain MC algorithms─notably procedures using an "infinite temperature" reference state─can be successful in a 5-20 parameter BI context which would be unworkable in molecular spaces of 103 coordinates and more. This Review provides a pedagogical introduction to BI and reviews key aspects of BI through a physical lens, setting the computations in terms of energy landscapes and free energy calculations and describing promising sampling algorithms. Statistical mechanics and basic probability theory also provide a reference for understanding intrinsic limitations of Bayesian inference with regard to model selection and the choice of priors.

An Update in Computational Methods for Environmental Monitoring: Theoretical Evaluation of the Molecular and Electronic Structures of Natural Pigment-Metal Complexes.

Metals are beneficial to life, but the presence of these elements in excessive amounts can harm both organisms and the environment; therefore, detecting the presence of metals is essential. Currently, metal detection methods employ powerful instrumental techniques that require a lot of time and money. Hence, the development of efficient and effective metal indicators is essential. Several synthetic metal detectors have been made, but due to their risk of harm, the use of natural pigments is considered a potential alternative. Experiments are needed for their development, but they are expensive and time-consuming. This review explores various computational methods and approaches that can be used to investigate metal-pigment interactions because choosing the right methods and approaches will affect the reliability of the results. The results show that quantum mechanical methods (ab initio, density functional theory, and semiempirical approaches) and molecular dynamics simulations have been used. Among the available methods, the density functional theory approach with the B3LYP functional and the LANL2DZ ECP and basis set is the most promising combination due to its good accuracy and cost-effectiveness. Various experimental studies were also in good agreement with the results of computational methods. However, deeper analysis still needs to be carried out to find the best combination of functions and basis sets.

Scaling laws for lattice distortions: Application to high entropy alloys.

Lattice distortions are intrinsic features of all solid solution alloys associated with varying atomic radii; this phenomenon facilitates the formation of single-phase solid solutions. Using high-entropy alloys (HEAs), as an example, we investigate the influence of variations in inter-atomic separations for stabilizing and controlling their structural, mechanical, and thermodynamic properties. This is done through a combination of statistical mechanics analysis and molecular dynamics simulations on simplified 2D systems, as well as a 3D crystals with harmonic and anharmonic inter-atomic bonds with varying natural inter-atomic separations. We demonstrate that the impact of this inter-atomic length disorder (representing static lattice distortion) and temperature fluctuations (representing dynamic lattice distortion) on fundamental and universal thermodynamic, structural, and elastic characteristics are similar and can be unified through effective temperature; i.e. a scaling law for HEAs that establishes a relationship between these factors. This scaling law reveals that different HEAs (i.e. varying degrees of local lattice distortions) collapse onto a single curve when plotted against the effective temperature. We demonstrate that lattice distortion significantly enhances the stability of solid solution alloys (relative to phase separation or ordering by effectively increasing the temperature of the system; this stabilization effect is particularly pronounced in HEAs).

QM/MM study of the catalytic reaction of aphid myrosinase

Brevicoryne brassicae, an aphid species, exclusively consumes plants from the Brassicaceae family and employs a sophisticated defense mechanism involving a myrosinase enzyme that breaks down glucosinolates obtained from its host plants. In this work, we employed combined quantum mechanical and molecular mechanical (QM/MM) calculations and molecular dynamics (MD) simulations to study the catalytic reaction of aphid myrosinase. A proper QM region to study the myrosinase reaction should contain the whole substrate, models of Gln-19, His-122, Asp-124, Asn-166, Glu-167, Lys-173, Tyr-180, Val-228, Tyr-309, Tyr-346, Ile-347, Glu-374, Glu-423, Trp-424, and a water molecule. The calculations show that Asp-124 and Glu-423 must be charged, His-122 must be protonated on NE2, and Glu-167 must be protonated on OE2. Our model reproduces the anomeric retaining characteristic of myrosinase and indicates that the deglycosylation reaction is the rate-determining step of the reaction. Based on the calculations, we propose a reaction mechanism for aphid myrosinase-mediated hydrolysis of glucosinolates with an overall barrier of 15.2 kcal/mol. According to the results, removing a proton from Arg-312 or altering it to valine or methionine increases glycosylation barriers but decreases the deglycosylation barrier.

Preparation of reed fibers reinforced graft-modified starch-based adhesives based on quantum mechanical simulation and molecular dynamics simulation

Starch is a biomass polymer material with a high yield and comprehensive source. It is used as a raw material for preparing adhesives because of its highly active hydroxyl group. However, poor adhesion and water resistance hinder the application of starch-based adhesives (SBAs). Based on this, the starch was modified through graft copolymerization with itaconic acid as a cross-linking agent, methyl methacrylate and methyl acrylate as copolymers. Additionally, reed fibers were synergistically modified with polydopamine deposition to prepare an environmentally friendly SBA used in plywood production. Fourier transform infrared spectroscopy (FT-IR), nuclear magnetic resonance spectroscopy (1H NMR), X-ray diffraction (XRD), and thermogravimetric analysis (TG) demonstrate that copolymerization of methyl methacrylate and methyl acrylate with starch improves the shear strength, water resistance, and thermal stability of the SBA. Compared to unmodified starch, the modified SBA exhibits a 129 % increase in dry strength and achieves a wet strength of 1.36 MPa. Fukui function, Frontier orbit theory, and molecular dynamics simulation have shown that itaconic acid promotes the copolymerization of starch and acrylate monomers. The modified starch has fewer hydrogen bonds, less order, and a denser macromolecular network structure, which provides a reference for studying the molecular interaction mechanisms of SBAs.

Dirac t-Boron Nitride Monolayer as an Appealing Binder-Free Anode for Alkali Metal Ion Batteries.

The development of universal anode materials with superlative electrochemical performance poses a great challenge for rechargeable alkali metal (AM) ion battery technologies. In the present work, the viability of the gapless Dirac t-BN (tetragonal boron nitride) monolayer as a lightweight binder-free anode has been systematically evaluated via comprehensive first-principles calculations. Aside from the desirable electronic conductivity, the t-BN monolayer exhibits an excellent ionic conductivity as well due to its moderate affinity for Li, Na, and K atoms with favorable in-plane barriers of 0.36, 0.18, and 0.19 eV, respectively. Meanwhile, the presence of B4N4 octagons allows the AM atoms to penetrate through the t-BN monolayer. Excitingly, the host material delivers an ultrahigh specific capacity up to 1080 mA h g-1 for Li, 5400 mA h g-1 for Na, and 2160 mA h g-1 for K in the wake of low mean open-circuit voltages of 0.033, 0.203, and 0.300 V at the half-cell level. According to the standard hydrogen electrode methodology, the energy densities are forecasted to be as large as 3240, 13500, and 5680 mW h g-1 for Li, Na, and K ion batteries, respectively, with robust thermal stability up to at least 400 K. The safety and cycling durability of the t-BN monolayer are jointly corroborated via the moderate mechanical strengths and ab initio molecular dynamics simulations at the maximum intercalated states, as well as via the small lattice changes and its ultrahigh tolerable ultimate tensile strain. These findings unambiguously promise that the t-BN monolayer can serve as an appealing candidate for anode applications in AM ion batteries.

Modelling bulk and surface characteristics of cubic CeO2, Gd2O3, and gadolinium-doped ceria using a partial charge framework.

The development and characterization of materials for solid oxide fuel cells (SOFC) is an important step towards sustainable energy technologies. This present study models cubic CeO2, Gd2O3, and gadolinium-doped ceria (GDC) using newly constructed interaction potentials based on a partial atom charge framework. The interaction model was validated by comparing the structural properties with experimental reference data, which were found to be in good agreement. Validation of the potential model was conducted considering the surface stability of CeO2 and Gd2O3. Additionally, the accuracy of the novel potential model was assessed by comparing the oxygen diffusion coefficient in GDCn (n = 4-15) and the associated activation energy. The results demonstrate that the novel potential model is capable of describing the oxygen diffusion in GDC. In addition, this study compares the vibrational properties of the bulk with density functional theory (DFT) calculations, using a harmonic frequency analysis that avoids the need for computationally expensive quantum mechanical molecular dynamics (QM MD) simulations. The potential is compatible with a reactive water model, thus providing a framework for the simulation of solid-liquid interfaces.

A hybrid forces Quantum Mechanical Charge Field Molecular Dynamics of Cs+ ion in aqueous ammonia: A solvation lability, “structure breaking” phenomenon and hydrogen bond properties

AbstractThe dynamics and structure of Cs+ solvation in an aqueous ammonia solution have been investigated using the Quantum Mechanical Charge Field Molecular Dynamics (QMCF‐MD) simulation method. The system contained 18.6% ammonia in aqueous solution at 298.15 K. The QM region was set to a radius of 7.0 Å to include the first and second solvation shells. The Hartree‐Fock (HF) level was applied to calculate the ion‐ligand and ligand–ligand interactions in the QM region using the LANL2DZ‐ECP basis set for the ion and DZP‐Dunning for the ligands. The radial distribution revealed only one solvation shell, indicating a labile solvation structure. The various coordination number of ligands suggests an instant exchange between them. The mean residence times of 1.29 and 0.9 ps were less than in the pure water and liquid ammonia system, indicating higher mobility ligands of the aqueous ammonia system. The preferential factor 0.55 supports the hypothesis that the Cs+ ion prefers to be dissolved in water. As the ligands moves further away from the ion, the observed number of hydrogen bonds increases, revealing the “structure‐breaking” property of the Cs+ ion. The minimum angle ligand‐ion‐ligand tends to be higher near the ion, confirming this phenomenon.

Amino acid ionic liquids as efficient catalysts for CO2 capture: A combined static and dynamic approach

Amino acid ionic liquids (AAILs) have gained significant attention as green solvents that are biocompatible, biodegradable, and useful in various applications, including catalysts, absorbents, and solvents. This study investigates the detailed interactions of three amino acid anions (glycine [Gly]-, histidine [His]-, and arginine [Arg]-) with the cation 1-methoxylbutyl-3-methylimidazolium [MOBMIM]+ and their role in CO2 absorption using quantum mechanical calculations and molecular dynamics (MD) simulations. The Density Functional Theory (DFT) calculations elucidate the reaction mechanisms underlying CO2 absorption and cycloaddition, and facilitate a comparative analysis of the impact of different amino acids on these reactions, and the synergies between them. Notably, arginine displays superior CO2 absorption capacity in comparison to glycine and histidine. Additionally, the cycloaddition reaction with CO2 exhibits a lower energy barrier when arginine is involved. Insights from the MD simulations highlight the higher level of electrostatic interaction between [MOBMIM]+[Arg]- and CO2, relative to the other studied molecules. Moreover, the Lennard Jones interaction emerges as the dominant type of interaction in these systems. The diffusion coefficient for CO2 was highest when interacting with [MOBMIM]+[Gly]-, followed by [MOBMIM]+[Arg]-. Consequently, both MD and DFT investigations converge to suggest that [MOBMIM]+[Arg]- followed by [MOBMIM]+[Gly]- may serve as advantageous choices for CO2 fixation and cycloaddition. The findings from this study underscore the considerable potential of the investigated AAILs as materials conducive to CO2 capture and utilization, thus paving the way for the integration of CO2 capture into valuable chemical products.

Redox-Based Defect Detection in Packed DNA: Insights from Hybrid Quantum Mechanical/Molecular Mechanics Molecular Dynamics Simulations.

The impact of an 8-oxoguanine (8oxoG) defect on the redox properties of DNA within the nucleosome core particle (NCP) was investigated employing hybrid quantum mechanical/molecular mechanics (QM/MM) molecular dynamics simulations of native and 8oxoG-containing NCP systems with an explicit representation of a biologically relevant environment. Two distinct NCP positions with varying solvent accessibility were considered for 8oxoG insertion. In both cases, it is found that the presence of 8oxoG drastically decreases the redox free energy of oxidation by roughly 1 eV, which is very similar to what was recently reported for free native and 8oxoG-containing DNA. In contrast, the effect of 8oxoG on the reorganization free energy is even smaller for packed DNA (decrease of 0.13 and 0.01 eV for defect-free and defect-containing systems, respectively) compared to the one for free DNA (0.25 eV), consistent with the increased rigidity of the NCP as compared to free DNA. Furthermore, the presence of an 8oxoG defect does not yield any significant changes in the packed DNA structure. Such a conclusion favors the idea that in the case of chromatin, defect-induced changes in DNA redox chemistry can also be exploited to detect damaged bases via DNA-mediated hole transfer.

Molecular Mechanism of Labelling Functional Cysteines by Heterocyclic Thiones.

Heterocyclic thiones have recently been identified as reversible covalent warheads, consistent with their mild electrophilic nature. Little is known so far about their mechanism of action in labelling nucleophilic sidechains, especially cysteines. The vast number of tractable cysteines promotes a wide range of target proteins to examine; however, our focus was put on functional cysteines. We chose the main protease of SARS-CoV-2 harboring Cys145 at the active site that is a structurally characterized and clinically validated target of covalent inhibitors. We screened an in-house, cysteine-targeting covalent inhibitor library which resulted in several covalent fragment hits with benzoxazole, benzothiazole and benzimidazole cores. Thione derivatives and Michael acceptors were selected for further investigations with the objective of exploring the mechanism of inhibition of the thiones and using the thoroughly characterized Michael acceptors for benchmarking our studies. Classical and hybrid quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations were carried out that revealed a new mechanism of covalent cysteine labelling by thione derivatives, which was supported by QM and free energy calculations and by a wide range of experimental results. Our study shows that the molecular recognition step plays a crucial role in the overall binding of both sets of molecules.

Influence of soft segment structure, hydrogen bonding, and diisocyanate symmetry on morphology and properties of segmented thermoplastic polyurethanes and polyureas.

A comprehensive review of the structure-morphology-property relations in segmented thermoplastic polyurethanes and polyureas (TPU) is provided. Special emphasis is given to the influence of the soft segment structure, polarity, and molecular weight, diisocyanate symmetry and the nature, extent, and strength of hydrogen bonding on the morphology and thermal and mechanical properties of TPUs. Experimental results obtained on composition-dependent TPU morphology and properties by various techniques were also compared by the morphology profiles generated by computational methods such as quantum mechanical calculations and molecular dynamics simulations.

The solvation dynamics of CO2 by quantum mechanical molecular dynamics

The solvation dynamics of CO2 in an aqueous solution were investigated using quantum mechanical molecular mechanical molecular dynamics (QM/MM-MD) simulations. It is demonstrated that the formation of H2CO3 occurs through direct reactions between CO2 and nH2O, with extremely high activation barriers in the gas phase. However, in a solution, the activation energy decreases as the number of H2O molecules increases. Specifically, for the CO2 − H2O system, the activation energy is about 32 kcal/mol, while for the CO2 − 2H2O and CO2 − 3H2O systems, it decreases to 28 kcal/mol and 15 kcal/mol, respectively. These findings suggest that the solvation of CO2 in a solution favors a step-wise mechanism.

Design, Synthesis, Pharmacological Activities, Structure-Activity Relationship, and In Silico Studies of Novel 5-Substituted-2-(morpholinoimino)-thiazolidin-4-ones.

This study is aimed to synthesize morpholine- and thiazolidine-based novel 5-(substituted)benzylidene)-2-(morpholinoimino)-3-phenylthiazolidin-4-ones (3-26) and characterized by molecular spectroscopy. The synthesized compounds were subjected to antioxidant activity with anticholinesterase, tyrosinase, and urease inhibition activities and evaluated the structure-activity relationship (SAR) of enzyme inhibition activities. Compound 11 was found to be the most active antioxidant. In anticholinesterase inhibition, compound 12 (IC50: 17.41 ± 0.22 μM) was the most active against AChE, while compounds 3-26 ( except 3, 8, and 17) showed notable activity against BChE. Compounds 17 (IC50: 3.22 ± 0.70 mM), 15 (IC50: 5.19 ± 0.03 mM), 24 (IC50: 7.21 ± 0.27 mM), 23 (IC50: 8.05 ± 0.11 mM), 14 (IC50: 8.10 ± 0.22 mM), 25 (IC50: 8.40 ± 0.64 mM), 26 (IC50: 8.76 ± 0.90 mM), and 22 (IC50: 9.13 ± 0.55 mM) produced higher tyrosinase inhibition activity. In urease inhibition activity, compounds 20 (IC50: 16.79 ± 0.19 μM), 19 (IC50: 18.25 ± 0.50 μM), 18 (IC50: 20.24 ± 0.77 μM), 26 (IC50: 21.51 ± 0.44 μM), 25 (IC50: 21.70 ± 0.06 μM), and 24 (IC50: 22.49 ± 0.11 μM) demonstrated excellent activities. Besides, the molecular docking study was applied to better understand the inhibitory mechanism between (1-26) compounds and enzymes at the molecular level. According to the results of this study, the synthesized compounds exhibited a better binding affinity toward these enzymes compared to the positive control. Further, molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) binding free energy and molecular dynamics (MD) simulation analyses were performed for AChE with compound 26, which showed high inhibitory activity in silico and in vitro studies. In conclusion, novel morpholine and thiazolidine-based derivative compounds may be pharmacologically effective agents for AChE, BChE, tyrosinase, and urease enzymes.

Unraveling pyrolysis mechanisms of lignin dimer model compounds: Neural network-based molecular dynamics simulation investigations

Unraveling the pyrolysis mechanisms of lignin is of great importance for effective lignin utilization. However, both conventional quantum mechanical method and molecular dynamics (MD) simulations based on empirical potentials, e.g., the ReaxFF, cannot guarantee simultaneous accuracy and efficiency in exploring lignin pyrolysis mechanisms. Here, we developed a neural network (NN) force field for four types of representative lignin dimers based on 56,164 structures at the level of density functional theory (DFT). Such NN model was demonstrated to possess more accurate predictive power in both energetic and atomistic force properties than ReaxFF and was far more efficient than QM method. The MD simulations with the NN model showed that entire pyrolysis process can be divided into three stages dependent on the reaction temperature: homolytic cleavage of C–C bond and C-O bond, the changes from methoxy group to hydroxy, methyl, and formyl group, ring-opening reactions and the ring structure evolutions, and some novel reactions. The NN-based MD has provided us an atomic-level understanding of lignin pyrolysis and enabled us to build a comprehensive lignin pyrolysis network by means of the reactions disclosed based on the NN-based MD, which provided a useful guide for taking advantage of lignin more effectively.

Origins of Periselectivity and Regioselectivity in Ambimodal Tripericyclic [8+6]/[6+4]/[4+2] Intramolecular Cycloadditions of a Heptafulvenyl-Fulvene.

Quantum mechanical calculations and molecular dynamics simulations have elucidated the reaction mechanism for intramolecular cycloadditions of a heptafulvenyl-fulvene tethered by a trimethylene chain. Prior experiments by Liu and Houk reported the formation of only an endo-[8+6] cycloadduct at 185 °C. Liu et al. later reported an exo-[4+2] Diels-Alder cycloadduct as the major product at 140 °C (Tetrahedron, 1999, 55, 9171). Cycloadditions involve Diels-Alder and an ambimodal intramolecular tripericyclic [8+6]/[6+4]/[4+2] cycloaddition. The mechanistic details explain the experimental reports of temperature dependence on the periselectivity of intramolecular cycloadditions. Additional calculations with multireference-based methods CASSCF and NEVPT2 highlight the artifacts of DFT methods and single-reference wavefunction-based CCSD(T) in the description of complete potential energy surface involving various cycloadditions of the heptafulvenyl-fulvene.

Dynamic deformation behaviors and mechanisms of CoCrFeNi high-entropy alloys

Due to their unique microstructures and chemical compositions, high-entropy alloys (HEAs) exhibit remarkable mechanical properties, such as high strength, excellent ductility and good thermal stability. However, to date, there have been limited studies on the dynamic behaviors of HEAs. Here, we systemically investigated the mechanical behaviors and deformation mechanisms of CoCrFeNi HEAs and their connections under dynamic loading by combining mechanical tests and molecular dynamics simulations. Compressive testing on polycrystalline CoCrFeNi HEA samples at different strain rates showed that both yield and flow stresses increase with strain rate and exhibit a significant strain rate sensitivity due to solid solution strengthening and lattice distortion of the HEA. The strain rate sensitivity of the CoCrFeNi HEA transitions from 0.010 at low strain rates (5.0×10−5–2.5×103 s−1) to 0.333 at high strain rates (2.5×103–6.5×103 s−1). Large-scale molecular dynamics simulations further revealed that this transition is related to the plastic deformation mechanism transition from dislocation nucleation and slip at low strain rates to massive dislocation nucleation and drag at high strain rates. Furthermore, the CoCrFeNi HEA exhibited a remarkable strain-hardening capability at high strain rates, which originated from the formation of primary and secondary nanoscale twins and twin-twin and twin-dislocation interactions. Our current study sheds light on the plastic deformation mechanisms of HEAs under dynamic loading, providing guidance for the design and fabrication of HEAs with excellent dynamic mechanical properties.

Revisiting the structure and dynamics of hydrated Cd2+ in aqueous solutions: Insights from the RI‐SCS‐MP2/MM molecular dynamics simulation

AbstractThe spin component scale MP2/molecular mechanics molecular dynamics simulation investigated the hydration shell formation and hydrated Cd2+ dynamics in the water environment. At the first hydration shell, six water molecules with 2.27 Å for the average distance between water and Cd2+. Dynamical properties were analyzed by computing the water molecule's mean residence time (MRT) in its first and second hydration shells. The MRT of each shell was determined to be 31.8 and 1.92 ps, suggesting the strong influence of Cd2+ in the first hydration shell. The second shell was labile, with an average number of water molecules being 18. Despite the strong interaction between Cd2+ and water molecules in the first shell, the influence of ions in the second hydration shell remained weak.