Classical Molecular Dynamics Approach Research Articles

Effect of incorporated amide blocks on the glass transition in polyesteramides

Incorporation of amide blocks is a common strategy used to promote the thermal and mechanical performances of polyesteramides. Meanwhile, glass transition temperature (Tg) is often used as one of the key parameters for measuring their physiochemical properties. Using a classical molecular dynamics approach, the Tg values of polyesteramides with a varying amide content are predicted by distinguishing their density variations with temperature. The predicted Tg values are in agreement with the measurements with an overestimation of about 2.6–6.5%. The incorporation of amide blocks favors the formation of interchain hydrogen bonds (HB). Although the relationship between Tg and HB formation has been well established, our simulations reveal that the entanglement of polyesteramide backbones leads to the Tg reduction at a high amide content, which is caused by the interplay between inter- and intra-chain HB numbers. The revealed molecular mechanism of Tg dependence on amide addition is helpful for the molecular design of functional polyesteramides.

Proton-polaron and thermionic identity of BaCeO3 polymorph for intermediate temperature fuel cell technology: A first principles and molecular dynamics approach

This study employs first principles and classical molecular dynamics approach to investigate distinct proton landscape and scattering events among aristotype and hettotype BaCeO3 polymorph. We systematically sampled different migration pathways to examine the thermionic behaviour and lattice disorder against the activation energy profile as a function of operating temperatures. According to DFT outcomes, the asymmetric landscape among hettotype structures entails a feeble vacancy formation energy (Evac = 0.326 eV and 0.485 eV) with noticeable lattice strain (ε = 0.258 % and 0.167 %) and desirable proton transfer pathway relative to aristotype counterpart. The transport characteristics from molecular dynamics on the other hand reveals an accelerated proton transfer at intermediate temperatures (300–550 °C) due to symmetric hydrogen bonding around the proton neighbourhood with a curtailed translational barrier from the low frequency lattice phonons. However, repellent response at elevated temperatures (>550 °C) illustrates the advent of ambipolar characteristics (H+/O2−), structural phase transitions, defect scattering events and the rise of artificial barrier as localized proton traps via proton polaron and defect (VO..) interactions. The study as a result accentuates the demand of structural and dynamical coherence to extend the commercial utility of BaCeO3 polymorph for the fuel cell technology.

Markov State Models for Electrostatic Channeling in Bioelectrocatalysis

Multistep biocatalytic cascades benefit from channeling mechanisms that guide intermediate transport between active sites. Channeling approaches such as electrostatic interactions and steric confinement are best exemplified in natural biocatalytic complexes such as tryptophan synthase and malate dehydrogenase–citrate synthase, but are also amenable to application in de novo cascades designed to accomplish chemical conversion and energy production.We have recently conducted an extensive computational study of the Malate Dehydrogenase–Citrate Synthase (MDH-CS) complex, which displays a positively charged patch on its surface, capably of electrostatically channeling a negatively-charged oxaloacetate intermediate. Our collaborators have demonstrated experimentally that mutation of residues in the positively-charged patch can strongly effect intermediate transport, as measured by lag time, the time required for the second of a two-reaction cascade to approach steady state [1].Using classical molecular dynamics approaches to study the transport of oxaloacetate in the presence of the charged surface, we created a Markov State model that effectively maps the prevalence of the intermediate across the enzyme surface as well as in bulk solution. Building the model involved seeding the possible states of the intermediate using metadynamics to force the intermediate out of low-energy states and to explore the overall energy landscape. Once assembled, this model enables us to study the dominant pathways of intermediate transport, for example contrasting transport along the charged enzyme surface with diffusion into the bulk solution. A “hub score” approach enabled identification of key residues that control intermediate traversal over the charged surface, and we are able to calculate pathway efficiency that is directly relatable to lag time [2].We will discuss a new, fast finite-difference approach to predict lag times for these multidimensional complexes. The steady-state transition matrix of the Markov state model is easily converted to a material balance for each node in the network. Using the model, the lag time of MDH-CS was determined computationally to be comparable to experiment for both the original and mutant complex. Using the model, the the dynamics of each of the four possible reaction pathways between the the two source (MDH) active sites and the two sink (CS) sites could be studied independently. This analysis provides a dynamic model for intermediate transport in an electrostatically channeled system, and can be used as a predictive tool to provide mechanistic insight into path dominance. B. Bulutoglu, K. E. Garcia, F. Wu, S. D. Minteer and S. Banta, ACS Chem. Bio., 11, 2847–2853 (2016). doi:10/f9c5cpY. Xie, S. D. Minteer, S. Banta and S. C. Barton, ACS Nanosci. Au, 2, 414 (2022). doi:10/gqkvtq

Negative Dielectric Constant of Water at a Metal Interface.

Water polarizability at a metal interface plays an essential role in electrochemistry. We devise a classical molecular dynamics approach with an efficient description of metal polarization and a novel ac field method to measure the local dielectric response of interfacial water. Water adlayers next to the metal surface exhibit higher-than-bulk in-plane and negative out-of-plane dielectric constants, the latter corresponding physically to overscreening of the applied field. If we account for the gap region at the interface, the average out-of-plane dielectric constant is quite low (ε_{⊥}≈2), in agreement with reported measurements on confined thin films.

Effect of Temperatures and Graphene on the Mechanical Properties of the Aluminum Matrix: A Molecular Dynamics Study.

Graphene has become an ideal reinforcement for reinforced metal matrix composites due to its excellent mechanical properties. However, the theory of graphene reinforcement in graphene/aluminum matrix composites is not yet well developed. In this paper, the effect of different temperatures on the mechanical properties of the metal matrix is investigated using a classical molecular dynamics approach, and the effects of the configuration and distribution of graphene in the metal matrix on the mechanical properties of the composites are also described in detail. It is shown that in the case of a monolayer graphene-reinforced aluminum matrix, the simulated stretching process does not break the graphene as the strain increases, but rather, the graphene and the aluminum matrix have a shearing behavior, and thus, the graphene "pulls out" from the aluminum matrix. In the parallel stretching direction, the tensile stress tends to increase with the increase of the graphene area ratio. In the vertical stretching direction, the tensile stress tends to decrease as the percentage of graphene area increases. In the parallel stretching direction, the tensile stress of the system tends to decrease as the angle between graphene and the stretching direction increases. It is important to investigate the effect of a different graphene distribution in the aluminum matrix on the mechanical properties of the composites for the design of high-strength graphene/metal matrix composites.

Structural and Dynamic Disturbances Revealed by Molecular Dynamics Simulations Predict the Impact on Function of CCT5 Chaperonin Mutations Associated with Rare Severe Distal Neuropathies

Mutations in genes encoding molecular chaperones, for instance the genes encoding the subunits of the chaperonin CCT (chaperonin containing TCP-1, also known as TRiC), are associated with rare neurodegenerative disorders. Using a classical molecular dynamics approach, we investigated the occurrence of conformational changes and differences in physicochemical properties of the CCT5 mutations His147Arg and Leu224Val associated with a sensory and a motor distal neuropathy, respectively. The apical domain of both variants was substantially but differently affected by the mutations, although these were in other domains. The distribution of hydrogen bonds and electrostatic potentials on the surface of the mutant subunits differed from the wild-type molecule. Structural and dynamic analyses, together with our previous experimental data, suggest that genetic mutations may cause different changes in the protein-binding capacity of CCT5 variants, presumably within both hetero- and/or homo-oligomeric complexes. Further investigations are necessary to elucidate the molecular pathogenic pathways of the two variants that produce the two distinct phenotypes. The data and clinical observations by us and others indicate that CCT chaperonopathies are more frequent than currently believed and should be investigated in patients with neuropathies.

On the exploration of the melting behavior of metallic compounds and solid solutions via multiple classical molecular dynamics approaches: application to Al-based systems.

Classical molecular dynamics simulations of metallic systems have been extensively applied in recent years for the exploration of the energetic behavior of mesoscale structures and for the generation of thermodynamic and physical properties. The evaluation of the conditions leading to the melting of pure metals and alloys is particularly challenging as it involves at one point the simultaneous presence of both a solid and a liquid phase. Defects such as vacancies, dislocation, grain boundaries and pores typically promote the melting of a solid by locally increasing its free energy which favors the destruction of long-range ordering at the origin of this phase transition. In real materials, many of these defects are microscopic and cannot yet be modelled via conventional atomistic simulations. Still, molecular dynamics-based methodologies are commonly used to estimate the melting temperature of solids. These methods involve the use of mesoscale supercells with various nanoscale defects. Moreover, the deterministic nature of classical MD simulations requires the adequate selection of the initial configuration to be melted. In this context, the main objective of this paper is to quantify the precision of the existing classical molecular dynamics computational methods used to evaluate the melting point of pure compounds as well as the solidus/liquidus lines of Al-based binary metallic systems. We also aim to improve the methodology of different approaches such as the void method, the interface method as well as the grain method to obtain a precise evaluation of the melting behavior of pure metals and alloys. We carefully analyzed the importance of the local chemical ordering on the melting behavior. The ins and outs of different numerical methods in predicting the melting temperature via MD are discussed through several examples related to pure metallic elements, congruently and non-congruently melting compounds as well as binary solid solutions. It is shown that the defect distribution of the initial supercell configuration plays an important role upon the description of the melting mechanism of solids leading to a poor predictive capability of melting temperature if not properly controlled. A new methodology based on defect distribution within the initial configuration is proposed to overcome these limitations.

Classical molecular dynamics study of structural properties of pristine and defective mono-layer 2D h-BNNSs

The structural, stability and vacancy properties of both defect-free and defected 2D h-BNNSs were studied using the classical molecular dynamics (MD) approach. The calculations were performed in the canonical (NVT Evans) and isothermal-isobaric (NPT Hoover) ensembles using the Tersoff potentials with the Verlet leapfrog algorithm to obtain reliable structural properties and energies for defect-free, boron (B) and nitrogen (N) vacancies. B and N defect energies were calculated relative to the bulk defect-free total energies, and the results suggest that N vacancy is the most stable vacancy as compared to the B vacancy. The radial distribution functions (RDF) and structure factors were used to predict the most probable structural form. Mean square displacement (MSD) suggests that the mobility of B and N atoms in the system increases with an increase in the surface area of the nanosheets. Results obtained were compared with the bulk defect-free h-BNNSs.

Water Induced Structural Transformations in Flexible Two-Dimensional Layered Conductive Metal–Organic Frameworks

The flexible and ever-changing layered structure of electrically conductive 2D metal–organic frameworks (MOFs) poses a formidable challenge for establishing any structure–application relationships. Here, we employ a combined quantum mechanics and classical molecular dynamics (MD) approach allowing large-scale/long-time simulations of the dynamics of both dry and hydrated systems to investigate the intrinsic flexibility and dynamical motions of layered 2D MOFs and its effect on their physical and chemical properties. The Co3(HHTP)2 and Cu3(HHTP)2 [HHTP = 2,3,6,7,10,11-hexahydroxytriphenylene] MOFs as two representatives of the layered family of MOFs are studied in great details with a focus on their experimentally observed differential framework stabilities in aqueous solutions. Our MD simulations reproduce structural properties of both MOFs as well as a higher tendency of the Co3(HHTP)2 MOF towards water attack and hydrolysis than its Cu3(HHTP)2 counterpart, in agreement with available experimental reports. The results show the presence of two distinctive metastable metal centers with (pseudo)planar vs (pseudo)tetrahedral configurations where the latter are more positively charged than the former and hence more susceptible to water nucleophilic attacks. The accurate ωB97M-v quantum-mechanical calculations show the higher tendency of the open Co2+ sites for coordination to water molecules than the open Cu2+ sites. Our multifaceted strategy paves the way towards simulation of realistic MOF-based materials and their interface with confined water molecules which is especially relevant to designing more robust water stable materials with desired properties and applications.

Molecular Simulations of Intrinsically Disordered Proteins and Their Binding Mechanisms.

Intrinsically disordered proteins (IDPs) lack well-defined secondary or tertiary structures in solution but are found to be involved in a wide range of critical cellular processes that highlight their functional importance. IDPs usually undergo folding upon binding to their targets. Such binding coupled to folding behavior has widened our perspective on the protein structure-dynamics-function paradigm in molecular biology. However, characterizing the folding upon binding mechanism of IDPs experimentally remains quite challenging. Molecular simulations emerge as a potentially powerful tool that offers information complementary to experiments. Here we present a general computational framework for the molecular simulations of IDP folding upon binding processes that combines all-atom molecular dynamics (MD) and coarse-grained simulations. The classical all-atom molecular dynamics approach using GPU acceleration allows the researcher to explore the properties of the IDP conformational ensemble, whereas coarse-grained structure-based models implemented with parameters carefully calibrated to available experimental measurements can be used to simulate the entire folding upon binding process. We also discuss a set of tools for the analysis of MD trajectories and describe the details of the computational protocol to follow so that it can be adapted by the user to study any IDP in isolation and in complex with partners.

QUAL È LA PIÙ PICCOLA GOCCIA D’ACQUA?

This presentation will bring the reader on a journey across the microscopic world of water clusters. After a brief introduction about molecular spectroscopy, I will show how the semiclassical approximation to quantum molecular dynamics allows for accurate full-dimensional quantum simulations of water cluster vibrational spectra, differently from classical molecular dynamics approaches. I will employ the semiclassical spectroscopy tool to determine the minimal network of surrounding water molecules needed to make the central one display the same vibrational features of liquid water. Remarkably, the minimal surrounding structure eventually responsible for proper solvation is made of just a few water molecules and includes two complete solvation shells.

Relationship between Atomic Structure, Composition, and Dielectric Constant in Zr–SiO2 Glasses

Computational methods, or computer-aided material design (CAMD), used for the analysis and design of materials have a relatively long history. However, the applicability of CAMD has been limited by the scales of computational resources generally available in the past. The surge in computational power seen in recent years is enabling the applicability of CAMD to unprecedented levels. Here, we focus on the CAMD for materials critical for the continued advancement of the complementary metal oxide semiconductor (CMOS) semiconductor technology. In particular, we apply CAMD to the engineering of high-permittivity dielectric materials. We developed a Reax forcefield that includes Si, O, Zr, and H. We used this forcefield in a series of simulations to compute the static dielectric constant of silica glasses for low Zr concentration using a classical molecular dynamics approach. Our results are compared against experimental values. Not only does our work reveal numerical estimations on ZrO2-doped silica dielectrics, it also provides a foundation and demonstration of how CAMD can enable the engineering of materials of critical importance for advanced CMOS technology nodes.

First principle simulation of coated hydroxychloroquine on Ag, Au and Pt nanoparticles

From the first month of the COVID-19 pandemic, the potential antiviral properties of hydroxychloroquine (HCQ) and chloroquine (CQ) against SARS-CoV-2 suggested that these drugs could be the appropriate therapeutic candidates. However, their side effects directed clinical tests towards optimizing safe utilization strategies. The noble metal nanoparticles (NP) are promising materials with antiviral and antibacterial properties that can deliver the drug to the target agent, thereby reducing the side effects. In this work, we applied both the quantum mechanical and classical atomistic molecular dynamics approaches to demonstrate the adsorption properties of HCQ/CQ on Ag, Au, AgAu, and Pt nanoparticles. We found the adsorption energies of HCQ/CQ towards nanoparticles have the following trend: PtNP > AuNP > AuAgNP > AgNP. This shows that PtNP has the highest affinity in comparison to the other types of nanoparticles. The (non)perturbative effects of this drug on the plasmonic absorption spectra of AgNP and AuNP with the time-dependent density functional theory. The effect of size and composition of NPs on the coating with HCQ and CQ were obtained to propose the appropriate candidate for drug delivery. This kind of modeling could help experimental groups to find efficient and safe therapies.

Deterministic role of structural flexibility on catalytic activity of conductive 2D layered metal-organic frameworks.

A combined quantum mechanics and classical molecular dynamics approach is used to unravel the effects of structural deformations and heterogeneity on catalytic activity of 2D π-stacked layered metal-organic frameworks. Theory predicts that the flexible nature of these materials creates a complex array of catalytically active sites for oxidative dehydrogenation of propane. Using an ensemble approach and oxygen bond formation energy, as an excellent probe, we investigate the catalytic activity down to the single active site level.

Two-dimensional Raman spectroscopy of Lennard-Jones liquids via ring-polymer molecular dynamics.

The simulation of multidimensional vibrational spectroscopy of condensed-phase systems including nuclear quantum effects is challenging since full quantum-mechanical calculations are still intractable for large systems comprising many degrees of freedom. Here, we apply the recently developed double Kubo transform (DKT) methodology in combination with ring-polymer molecular dynamics (RPMD) for evaluating multi-time correlation functions [K. A. Jung et al., J. Chem. Phys. 148, 244105 (2018)], providing a practical method for incorporating nuclear quantum effects in nonlinear spectroscopy of condensed-phase systems. We showcase the DKT approach in the simulation of the fifth-order two-dimensional (2D) Raman spectroscopy of Lennard-Jones liquids as a prototypical example, which involves nontrivial nonlinear spectroscopic observables of systems described by anharmonic potentials. Our results show that the DKT can faithfully reproduce the 2D Raman response of liquid xenon at high temperatures, where the system behaves classically. In contrast, liquid neon at low temperatures exhibits moderate but discernible nuclear quantum effects in the 2D Raman response compared to the responses obtained with classical molecular dynamics approaches. Thus, the DKT formalism in combination with RPMD simulations enables simulations of multidimensional optical spectroscopy of condensed-phase systems that partially account for nuclear quantum effects.

Multicomponent mutual diffusion in the warm, dense matter regime.

We present the formulation, simulations, and results for multicomponent mutual diffusion coefficients in the warm, dense matter regime. While binary mixtures have received considerable attention for mass transport, far fewer studies have addressed ternary and more complex systems. We therefore explicitly examine ternary systems utilizing the Maxwell-Stefan formulation that relates diffusion to gradients in the chemical potential. Onsager coefficients then connect the macroscopic diffusion to microscopic particle motions, evinced in trajectories characterized by positions and velocities, through various autocorrelation functions (ACFs). These trajectories are generated by molecular dynamics (MD) simulations either through the Born-Oppenheimer approximation, which treats the ions classically and the electrons quantum-mechanically by an orbital-free density-functional theory, or through a classical MD approach with Yukawa pair-potentials, whose effective ionizations and electron screening length derive from quantal considerations. We employ the reference-mean form of the ACFs and determine the center-of-mass coefficients through a simple reference-frame-dependent similarity transformation. The Onsager terms in turn determine the mutual diffusion coefficients. We examine a representative sample of ternary mixtures as a function of density and temperature from those with only light elements (D-Li-C, D-Li-Al) to those with highly asymmetric mass components (D-Li-Cu, D-Li-Ag, H-C-Ag). We also follow trends in the diffusion as a function of number concentration and evaluated the efficacy of various approximations such as the Darken approximation.

Numerical study of double-pulse laser ablation of Al

The effect of double laser pulses (DPs) on the ablation process in solids is studied using a hybrid two-temperature model combining a continuum description of the conduction band electrons with a classical molecular dynamics (MD) approach for the ions. The study is concerned with double pulses with delays in the range of 0--50 ps and absorbed laser fluences of 0.5, 1.0, and $1.5\phantom{\rule{0.28em}{0ex}}{\mathrm{J}/\mathrm{m}}^{2}$ [i.e., 1--3 times the ablation threshold for single-pulse ablation (SP)], taking Al as a generic example of simple metals. A detailed analysis, including the assessment of thermodynamic pathways and cavitation rates, leads to a comprehensive picture of the mechanisms active during the different stages of the ablation process initiated by DPs. This study provides an explanation for several phenomena observed in DP ablation experiments. In particular, with respect to SP ablation, crater depths are reduced, which can be explained by the compensation of the rarefaction wave from the first laser pulse with the compression wave from the second pulse, or, at higher fluences and larger delays, by the fact that the target surface is shielded with matter ablated by the first laser pulse. Also, we discuss how smoother surface structures obtained using DPs may be related to features found in the simulations---viz., reduced mechanical strain and peak lattice temperatures. Finally, vaporization appears to be enhanced in DP ablation, which may improve the resolution of emission spectra.

(Invited) Modeling Glassy Electrolytes for All-Solid-State Sodium Ion Batteries

Solid-state sodium ion batteries, a relatively safe and potentially cost-effective technology for electrical grid-scale energy storage, has attracted significant scientific attention in recent times. However, identifying solid electrolytes with high ionic conductivity at room temperature is a requirement in order to commercialize solid state sodium ion batteries. Amorphous sulfide glasses are considered as promising candidates with relatively high ionic conductivity. However, the properties of these electrolytes are highly sensitive to the chemical composition. We present a multiscale approach, which employs atomistic simulations coupled with mesoscale modeling, to analyze and evaluate transport properties of solid glassy electrolytes. As a model system, we studied sodium sulfide – silicon sulfide [xNa2S – (1-x)SiS2] based electrolytes with varying compositions. We determined the ionic conductivities and activation energies for sodium ion hops using ab initio and classical molecular dynamics (MD) approach. These simulations provide fundamental insights into ion conduction mechanisms as well as help to correlate ionic conductivity with glass structure and composition. We further developed a Monte Carlo model to scale up our calculations to a much larger length-scales that are inaccessible by molecular dynamics simulations. Crucial inputs such as Na+ ions distribution and migration energies obtained from classical and ab initio MD served as key inputs to the Monte Carlo model. This model accurately predicts the ionic conductivity of the glasses in agreement with experimental values. Overall, the multiscale model shows excellent promise in identifying optimal glassy electrolytes for sodium ion batteries.

Structure of water clusters on graphene: A classical molecular dynamics approach

The microscopic structure of surface water adsorbed on graphene is elucidated theoretically by classical molecular dynamics simulation. At a low temperature (100 K), the main polygon consisting of hydrogen bonds in single-layered water on graphene is tetragonal, whereas the dominant polygons in double-layered water are tetragonal, pentagonal, and hexagonal. On the other hand, at room temperature, the tetragonal, pentagonal, and hexagonal water clusters are the main structures in both single- and double-layered water.

Ion Solvation and Dynamics at Solid Electrolyte Interphases: A Long Way from Bulk?

Rechargeable lithium-ion battery technology has revolutionized energy storage for small electronic devices. However, a deeper understanding is required of the interfaces present in such devices for this technology to continue to advance. While many insights into the solid electrolyte interphase (SEI) for lithium-ion systems have been collected from decades of study, many questions also remain. In particular, this work is interested in exploring SEI composition and its impact on electrolyte structure and dynamics. By using a previously tested classical molecular dynamics approach, the impact of the crystallinity of the SEI interface as well as its content of organic and inorganic species is assessed. It is found that the presence of an amorphous SEI results in the accumulation of ions at the interface, ordering of solvent molecules, and a slowing down of solvation dynamics. These behaviors are intensified when crystal surfaces from LiF and Li2CO3 are considered. In addition to these general observations, t...