Classical Molecular Dynamics Simulations Research Articles

Ion-Specific Effects on Ion and Polyelectrolyte Solvation.

Ion-specific effects on aqueous solvation of monovalent counter ions, Na+, K+, Cl-, and Br-, and two model polyeletrolytes (PEs), poly(styrene sulfonate) (PSS) and poly(diallyldimethylammonium) (PDADMA) were here studied with ab initio molecular dynamics (AIMD) and classical molecular dynamics (MD) simulations based on the OPLS-aa force-field which is an empirical fixed point-charge force-field. Ion-specific binding to the PE charge groups was also characterized. Both computational methods predict similar response for the solvation of the PEs but differ notably in description of ion solvation. Notably, AIMD captures the experimentally observed differences in Cl- and Br- anion solvation and binding with the PEs, while the classical MD simulations fail to differentiate the ion species response. Furthermore, the findings show that combining AIMD with the computationally less costly classical MD simulations allows benefiting from both the increased accuracy and statistics reach.

Long-Chain Lipids Facilitate Insertion of Large Nanoparticles into Membranes of Small Unilamellar Vesicles.

Insertion of hydrophobic nanoparticles into phospholipid bilayers is limited to small particles that can incorporate into a hydrophobic membrane core between two lipid leaflets. Incorporation of nanoparticles above this size limit requires the development of challenging surface engineering methodologies. In principle, increasing the long-chain lipid component in the lipid mixture should facilitate incorporation of larger nanoparticles. Here, we explore the effect of incorporating very long phospholipids (C24:1) into small unilamellar vesicles on the membrane insertion efficiency of hydrophobic nanoparticles that are 5-11 nm in diameter. To this end, we improve an existing vesicle preparation protocol and utilized cryogenic electron microscopy imaging to examine the mode of interaction and evaluate the insertion efficiency of membrane-inserted nanoparticles. We also perform classical coarse-grained molecular dynamics simulations to identify changes in lipid membrane structural properties that may increase insertion efficiency. Our results indicate that long-chain lipids increase the insertion efficiency by preferentially accumulating near membrane-inserted nanoparticles to reduce the thermodynamically unfavorable disruption of the membrane.

Enhanced Elastocaloric Effects in γ-Graphyne.

The global emphasis on sustainable technologies has become a paramount concern for nations worldwide. Specifically, numerous sustainable methods are being explored as promising alternatives to the well-established vapor-compression technologies in cooling and heating devices. One such avenue gaining traction within the scientific community is the elastocaloric (eC) effect. This phenomenon holds promise for efficient cooling and heating processes without causing environmental harm. Studies carried out at the nanoscale have demonstrated the efficiency of the eC effect, proving to be comparable to that of state-of-the-art macroscopic systems. In this study, we used classical molecular dynamics simulations to investigate the elastocaloric effect for the recently synthesized γ-graphyne. Our analysis goes beyond obtaining changes in eC temperature and the coefficient of performance (COP) for two species of γ-graphyne nanoribbons (armchair and zigzag). We also explore their dependence on various conditions, including whether they are deposited on a substrate or prestrained. Our findings reveal a substantial enhancement in the elastocaloric effect for γ-graphyne nanoribbons when subjected to prestrain, amplifying it by at least 1 order of magnitude. Under certain conditions, the changes in the eC temperature and the COP of the structures reach expressive values as high as 224 K and 14, respectively. We discuss the implications of these results by examining the shape and behavior of the carbon-carbon bond lengths within the structures.

Reactive molecular dynamics simulations of lithium-ion battery electrolyte degradation

The development of reliable computational methods for novel battery materials has become essential due to the recently intensified research efforts on more sustainable energy storage materials. Here, we use a recently developed framework allowing to consistently incorporate quantum-mechanical activation barriers to classical molecular dynamics simulations to study the reductive solvent decomposition and formation of the solid electrolyte interphase for a graphite/carbonate electrolyte interface. We focus on deriving condensed-phase effective rates based on the elementary gas-phase reduction and decomposition energy barriers. After a short initial transient limited by the elementary barriers, we observe that the effective rate shows a transition to a kinetically slow regime influenced by the changing coordination environment and the ionic fluxes between the bulk electrolyte and the interface. We also discuss the impact of the decomposition on the ionic mobility. Thus, our work shows how elementary first-principles properties can be mechanistically leveraged to provide fundamental insights into electrochemical stability of battery electrolytes.

High-Performance Dendrite-Free Lithium Metal Anode Based on Metal-Organic Framework Glass.

The performance of lithium metal batteries is severely hampered by uncontrollable dendrite growth and volume change within the anode. This work tackles these obstacles by introducing a novel strategy: applying an isotropic and internal grain-boundary-free layer, specifically, a metal-organic framework (MOF) glass layer with nano-porosity onto the electrochemical plated lithium metal anode. Both ab initio and classical molecular dynamics simulations indicate that the MOF glass layer makes the lithium transport smooth and uniform via its internal monolithic and interfacial advantages. This MOF glass layer with the fast and more uniform lithium diffusion in the monolithic interior and its interface enables dendrite-free lithium plating and stripping through surface confinement effect and interfacial effect. When employed in symmetric batteries, the achieved Li metal anode can operate over 300 hours at 1mA cm-2. The full batteries matched with LiFePO4 exhibit high capacity (148 mAh g-1), excellent rate performance (61 mAh g-1 at 5 C), and outstanding cycling stability (with capacity retention of ∼90% after 1000 cycles). The full batteries matched with high-voltage LiCoO2 also show superior performances. Therefore, the strategy of utilizing a MOF glass layer enables the development of high-performance lithium metal anodes. This article is protected by copyright. All rights reserved.

Stability of C59 Knockout Fragments from Femtoseconds to Infinity

We have studied the stability of C59 anions as a function of time, from their formation on femtosecond timescales to their stabilization on second timescales and beyond, using a combination of theory and experiments. The C59− fragments were produced in collisions between C60 fullerene anions and neutral helium gas at a velocity of 90 km s−1 (corresponding to a collision energy of 166 eV in the center-of-mass frame). The fragments were then stored in a cryogenic ion beam storage ring at the DESIREE facility, where they were followed for up to 1 minute. Classical molecular dynamics simulations were used to determine the reaction cross section and the excitation energy distributions of the products formed in these collisions. We find that about 15% of the C59− ions initially stored in the ring are intact after about 100 ms and that this population then remains intact indefinitely. This means that C60 fullerenes exposed to energetic atoms and ions, such as stellar winds and shock waves, will produce stable, highly reactive products, like C59, that are fed into interstellar chemical reaction networks.

Theoretical and experimental study of molecular interactions between constituents of deep eutectic solvents

In this study, we aimed to elucidate the molecular interactions in deep eutectic solvents (DESs) and acquire additional experimental evidence to increase our understanding of the molecular mechanisms responsible for the preparation of DES. We investigated three N-methylthiourea (NMTU)-based DESs with choline chloride (ChCl), allyltrimethylammonium chloride (ATMAC), and benzyltriethylammonium chloride (BTEAC) as hydrogen bond acceptors (HBA). To accomplish this, we used both experimental techniques including isopiestic, differential scanning calorimetry (DSC), and FTIR measurements as well as molecular dynamics (MD) simulations. The thermal behaviors of the prepared DESs were investigated by DSC method. In order to study the interaction and hydrogen bonding between the DESs constituents, FT-IR analysis and isopiestic measurements were carried out. Constant solvent activity lines of ternary HBA + HBD + solvent mixtures were determined by the isopiestic technique. The large positive deviation of the iso solvent activity lines from the semi-ideal behavior indicates a strong interaction between HBA and HBD, which is much stronger than HBA-HBA and HBD-HBD interactions. Classical MD simulations were performed at 298.15 K to analyze the nanoscopic properties and structure of the DESs. To investigate the interaction between the components and visualize the three-dimensional structure of the DESs, radial distribution functions (RDFs), coordination numbers (CNs), and combined (CDFs), and spatial (SDFs) distribution functions were determined by MD simulations. The obtained theoretical results confirmed the importance of hydrogen bonds in the preparation of DESs and also showed that these systems exhibit different structural arrangements. MD simulations were also used to determine the density of the DESs and the results showed good agreement with the experimental density.

Structure and Non-reactive Dynamics of the Dimeric Catalytic Domain of Human Carbonic Anhydrase IX

Despite the availability of high resolution crystal structure of the catalytic domain of human carbonic anhydrase IX (HCA IX-c), its solution structure and functional dynamics are mostly unknown. In this article, we report classical molecular dynamics (MD) simulation studies on the structure and non-reactive dynamics of dimeric HCA IX-c (d-HCA IX-c, with chains A and B) in water and compare them to each chain simulated in water as a monomeric solute (mA/mB). While the average solution structures appear to be largely similar in all systems, d-HCA IX-c shows significant deviations from mA and mB in terms of non-reactive reorganization of the active site needed to initiate the rate determining proton transfer step between a zinc-bound water and one of the sidechain N-atoms of a distal histidine residue (His-64). First, 2−6 water molecules are found to form fluctuating hydrogen bonded networks that would serve as proton paths across the active site. A minimally frustrated core of each monomer in the dimeric protein is found to be associated with a significantly higher likelihood of forming complete proton transfer pathways mediated by 2 water molecules synchronously at the two active sites hosted by the monomeric chains. The relative stability and kinetics of transition between two major sidechain rotamers of His-64 are also found to be affected by dimerization. The sidechain rotation of His-64 is found to involve at least one transition as slow as 105 per second in chain A of d-HCA IX-c thereby rendering it slower than the actual rate determining proton transfer step and suggests important deviation from the widely accepted mechanism of catalysis by HCAs.

Mean force emission theory for classical bremsstrahlung in strongly coupled plasmas

This work presents mean force emission theory, which extends the classical theory of bremsstrahlung emission to strongly coupled plasmas. In the high-frequency limit, the theory reduces to solving for the electron trajectory during a binary collision, but where the electron–ion interactions occur through the potential of mean force. In the low-frequency limit, it uses an autocorrelation formalism that captures effects of multiple collisions and strongly correlated motion. The predictions are benchmarked by comparison with first-principles classical molecular dynamics simulations of a fully ionized hydrogen plasma in which all interactions are repulsive. The comparison shows good agreement up to Coulomb coupling strengths of Γ∼30. The theory improves upon traditional models by including strong coupling effects and systematically including the effect of multiple collisions. Furthermore, mean force emission theory provides evidence that the Drude correction factor commonly used in quantum calculations of optical quantities may not be adequate at strong coupling.

Dust Condensation of SiC, SiO in Asymptotic Giant Branch Stellar Winds-SiC Spectrum

We have chosen the Large Scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) code to calculate the coalescence of silicon carbide (SiC), silicon oxide dust (SiO) in the AGB stellar wind. LAMMPS is a classical molecular dynamics simulation code. At the same time, we consider the effect of temperature on the evolution of molecular dynamics. We also calculated the temperature change of non-spherical SiC, SiO dust coalescence. The condensation temperature range of SiC dust in the AGB stellar wind is [300–500]k and [900–1100]k for SiO. Finally, the infrared spectrum of SiC was calculated using Gaussian 16 software. The 77SiC, 70Si3C3, and 121Si3C3 models have clear characteristic peaks of infrared spectra responding at 5, 8.6, 11.3, 15, 19, and 37 μm.

Thermal transport in fullerene-based molecular junctions: Molecular dynamics simulations.

We investigate phonon thermal transport of fullerene-based single-molecule junctions by employing classical molecular dynamics simulations. 
The thermal conductances of fullerene monomers, dimers, and trimers are computed through three distinct molecular dynamics methods, by following the equilibration dynamics in one method, and using two other nonequilibrium simulation methods. We discuss technical aspects of the simulation techniques, and show that their predictions for the thermal conductance agree. 
Our simulations reveal that the thermal conductance of fullerene monomer and dimer junctions are similar, yet the thermal conductance of trimer junctions is significantly reduced. 
This study could assist in the design of high-performing thermoelectric junctions, where low thermal conductance is desired.

Improving the reliability of machine learned potentials for modeling inhomogeneous liquids.

The atomic-scale response of inhomogeneous fluids at interfaces and surrounding solute particles plays a critical role in governing chemical, electrochemical, and biological processes. Classical molecular dynamics simulations have been applied extensively to simulate the response of fluids to inhomogeneities directly, but are limited by the accuracy of the underlying interatomic potentials. Here, we use neural network potentials (NNPs) trained to ab initio simulations to accurately predict the inhomogeneous responses of two distinct fluids: liquid water and molten NaCl. Although NNPs can be readily trained to model complex bulk systems across a range of state points, we show that to appropriately model a fluid's response at an interface, relevant inhomogeneous configurations must be included in the training data. In order to sufficiently sample appropriate configurations of such inhomogeneous fluids, we develop protocols based on molecular dynamics simulations in the presence of external potentials. We demonstrate that NNPs trained on inhomogeneous fluid configurations can more accurately predict several key properties of fluids-including the density response, surface tension and size-dependent cavitation free energies-for liquid water and molten NaCl, compared to both empirical interatomic potentials and NNPs that are not trained on such inhomogeneous configurations. This work therefore provides a first demonstration and framework to extract the response of inhomogeneous fluids from first principles for classical density-functional treatment of fluids free from empirical potentials.

The performance of OPC and OPC3 water models in predictions of 2D structures under nanoconfinement.

Nanoconfined water plays an important role in broad fields of science and engineering. Classical molecular dynamics (MD) simulations have been widely used to investigate water phases under nanoconfinement. The key ingredient of MD is the force field. In this study, we systematically investigated the performance of a recently introduced family of globally optimal water models, OPC and OPC3, and TIP4P/2005 in describing nanoconfined two-dimensional (2D) water ice. Our studies show that the melting points of the monolayer square ice (MSI) of all three water models are higher than the melting points of the corresponding bulk ice Ih. Under the same conditions, the melting points of MSI of OPC and TIP4P/2005 are the same and are ∼90K lower than that of the OPC3 water model. In addition, we show that OPC and TIP4P/2005 water models are able to form a bilayer AA-stacked structure and a trilayer AAA-stacked structure, which are not the cases for the OPC3 model. Considering the available experimental data and first-principles simulations, we consider the OPC water model as a potential water model for 2D water ice MD studies.

Potential energy landscape of a flexible water model: Equation of state, configurational entropy, and Adam-Gibbs relationship.

The potential energy landscape (PEL) formalism is a tool within statistical mechanics that has been used in the past to calculate the equation of states (EOS) of classical rigid model liquids at low temperatures, where computer simulations may be challenging. In this work, we use classical molecular dynamics (MD) simulations and the PEL formalism to calculate the EOS of the flexible q-TIP4P/F water model. This model exhibits a liquid-liquid critical point (LLCP) in the supercooled regime, at (Pc = 150 MPa, Tc = 190 K, and ρc = 1.04 g/cm3) [using the reaction field technique]. The PEL-EOS of q-TIP4P/F water and the corresponding location of the LLCP are in very good agreement with the MD simulations. We show that the PEL of q-TIP4P/F water is Gaussian, which allows us to calculate the configurational entropy of the system, Sconf. The Sconf of q-TIP4P/F water is surprisingly similar to that reported previously for rigid water models, suggesting that intramolecular flexibility does not necessarily add roughness to the PEL. We also show that the Adam-Gibbs relation, which relates the diffusion coefficient D with Sconf, holds for the flexible q-TIP4P/F water model. Overall, our results indicate that the PEL formalism can be used to study molecular systems that include molecular flexibility, the common case in standard force fields. This is not trivial since the introduction of large bending/stretching mode frequencies is problematic in classical statistical mechanics. For example, as shown previously, we find that such high frequencies lead to unphysical (negative) entropy for q-TIP4P/F water when using classical statistical mechanics (yet, the PEL formalism can be applied successfully).

Preferential permeation of Li+ over Mg2+ through homogenously negatively-charged nanochannels

Positively-charged nanofiltration (NF) membranes have become popular in membrane separation for lithium extraction from salt lake. However, negatively-charged NF membranes hardly achieve a satisfying Li+/Mg2+ selectivity due to the lack of the understanding on the mechanism of the effect of the electrostatic attraction on the Li+/Mg2+ permselective permeation. To this end, classical molecular dynamics simulations were performed to explore the effect of charge density of the negatively-charged nanochannels on the structure and dynamics of the confined Li+ and Mg2+ ions. Surprisingly, an appropriate modification by negative charges could simultaneously achieve a knock-on hopping for efficient Li+ permeation and a remarkable retardation to the Mg2+ self-driven diffusion, which realized a higher preferential permeation to Li+ over Mg2+ through the nanochannels. The underlying mechanism was explored by a series of analysis, including ion occupancy, mean square displacement (MSD), loading/exiting time, and trajectory tracking, etc. It was found that a combination of the elevated ion occupancy and an appropriate attraction by the negatively-charged channel generated an efficient ionic collision between the confined Li+ ions, thus producing a transition from the self-driven diffusion to the knock-on hopping permeation. Due to the higher positive charge, the confined Mg2+ ions hardly allowed a high ion occupancy and strongly interacted with the negatively-charged channel, which significantly retarded the Mg2+ transmembrane permeation. The novel understanding of the mechanism of the Li+/Mg2+ permselective permeation in the negatively-charged nanochannels will guide an effective development of high-performance membranes for Li+/Mg2+ separation.

Simulating the charging mechanism of a realistic nanoporous carbon-based supercapacitor using a fully polarizable model

Nanoporous carbon-based supercapacitors are established energy storage devices, that complement Li-ion batteries in high-power applications. So far, the study of these systems through simulations required drastic simplification of the electrolyte and/or of the electrode. In this work, we use state-of-the-art constant potential classical molecular dynamics simulations, where both the electrode and the electrolyte are polarizable, to study complex carbide-derived carbons with 1-ethyl-3-methylimidazolium bis(trifluoromethane)sulfonyl imide ionic liquid electrolyte. We show that using this set-up allows to obtain integral capacitances (i.e. the main property to characterize supercapacitors) in quantitative agreement with experiments. The simulations, performed in a range of applied potentials of 1V to 4V, then provide microscopic details on the charging mechanism, revealing that it is not symmetrical between the positive and negative electrodes. A pure exchange of ions is observed on the positive electrode, while an ion exchange combined with cation adsorption takes place on the negative one. Our work shows that accounting for the coupling of electrode and electrolyte polarization improves the accuracy of the results, opening the way toward a more quantitative comparison with experiments.

Molecular dynamics simulation of shock waves in Fe and Fe–C: Influence of system characteristics

Pressure-induced phase transformation in iron and its alloys is a classic research topic in solid-state physics, material science, and geophysics. The crystal structure of iron undergoes a phase transformation at a hydrostatic pressure of 13 GPa, changing from a body-centered cubic system to a hexagonal close-packed system. Although extensive research has been carried out on the transformation in iron by using molecular dynamics simulations, there is very limited literature that focuses on the contribution of parent phase orientations, system size, and impurities to the phase evolution. In this work, classic molecular dynamics simulations have been employed to investigate the effects of system size, lattice orientation, and impurity concentration on the pressure-induced phase transformation of iron and iron alloys for the first time. Our results show that the lattice orientation has a strong influence on the phase transition behavior, while the influence of carbon is small. The phase transition is slightly delayed with increasing carbon content, whereas the transition pressure increases from [001] to [011] to [111] orientation. The amount of twinning and stacking faults highly depends on the orientation. It is easiest for solitary waves to travel through [111] lattice orientation. The addition of carbon has a slow-down effect on shock velocities, and this effect increases with carbon content and lattice orientation of the samples from [001] to [011] to [111].

In silico study of therapeutic deep eutectic solvent for tetracaine liquid delivery

The development of a drug delivery liquid formulation of ester – based tetracaine local anaesthetic is synthesised in silico via the formation of a therapeutic deep eutectic solvent in combination with citral, a natural monoterpenoid. The properties of the obtained liquid system, studied at the nanoscopic level, are derived from a combination of quantum chemistry and classical molecular dynamics simulations. The intermolecular forces (hydrogen bonding) were analysed and their relationship with liquid phase properties were established. Water effect on the liquid phase properties were also considered in terms of competing for hydrogen bonding sites in the components of the developed fluid. The systems proposed in this work were studied using CIT (HBA) 1:1 TET (HBD) molar ratio at temperatures ranging from 288 K to 318 K and 1 bar. The hydrogen bond network developed between the oxygen atom in citral molecules and the –NH group in tetracaine molecules under those conditions, confirmed via minimal cluster analysis, is maintained during the addition of water up to 1.3 wt% as the water molecules do not disrupt the intermolecular hydrogen bond but develop new interactions (hydrogen bonds) with citral and tetracaine monomers presented in the fluid. The reported results probed the suitability of the considered system as an alternative drug delivery method as well as the possibility of developing deep eutectic-based formulation of anaesthetics using natural compounds due to the formation of effective and strong intermolecular hydrogen bonds.

Classical molecular dynamics simulation identifies catechingallate as a promising antiviral polyphenol against MPOX palmitoylated surface protein

Cumulative global prevalence of the emergent monkeypox (MPX) infection in the non-endemic countries has been professed as a global public health predicament. Lack of effective MPX-specific treatments sets the baseline for designing the current study. This research work uncovers the effective use of known antiviral polyphenols against MPX viral infection, and recognises their mode of interaction with the target F13 protein, that plays crucial role in formation of enveloped virions. Herein, we have employed state-of-the-art machine learning based AlphaFold2 to predict the three-dimensional structure of F13 followed by molecular docking and all-atoms molecular dynamics (MD) simulations to investigate the differential mode of F13-polyphenol interactions. Our extensive computational approach identifies six potent polyphenols Rutin, Epicatechingallate, Catechingallate, Quercitrin, Isoquecitrin and Hyperoside exhibiting higher binding affinity towards F13, buried inside a positively charged binding groove. Intermolecular contact analysis of the docked and MD simulated complexes divulges three important residues Asp134, Ser137 and Ser321 that are observed to be involved in ligand binding through hydrogen bonds. Our findings suggest that ligand binding induces minor conformational changes in F13 to affect the conformation of the binding site. Concomitantly, essential dynamics of the six-MD simulated complexes reveals Catechin gallate, a known antiviral agent as a promising polyphenol targeting F13 protein, dominated with a dense network of hydrophobic contacts. However, assessment of biological activities of these polyphenols need to be confirmed through in vitro and in vivo assays, which may pave the way for development of new novel antiviral drugs.

Molecular Mechanisms of Sorbed Ion Effects during Boehmite Particle Aggregation.

Classical theories of particle aggregation, such as Derjaguin-Landau-Verwey-Overbeek (DLVO), do not explain recent observations of ion-specific effects or the complex concentration dependence for aggregation. Thus, here, we probe the molecular mechanisms by which selected alkali nitrate ions (Na+, K+, and NO3-) influence aggregation of the mineral boehmite (γ-AlOOH) nanoparticles. Nanoparticle aggregation was analyzed using classical molecular dynamics (CMD) simulations coupled with the metadynamics rare event approach for stoichiometric surface terminations of two boehmite crystal faces. Calculated free energy landscapes reveal how electrolyte ions alter aggregation on different crystal faces relative to pure water. Consistent with experimental observations, we find that adding an electrolyte significantly reduces the energy barrier for particle aggregation (∼3-4×). However, in this work, we show this is due to the ions disrupting interstitial water networks, and that aggregation between stoichiometric (010) basal-basal surfaces is more favorable than between (001) edge-edge surfaces (∼5-6×) due to the higher interfacial water densities on edge surfaces. The interfacial distances in the interlayer between aggregated particles with electrolytes (∼5-10 Å) are larger than those in pure water (a few Ångströms). Together, aggregation/disaggregation in salt solutions is predicted to be more reversible due to these lower energy barriers, but there is uncertainty on the magnitudes of the energies that lead to aggregation at the molecular scale. By analyzing the peak water densities of the first monolayer of interstitial water as a proxy for solvent ordering, we find that the extent of solvent ordering likely determines the structures of aggregated states as well as the energy barriers to move between them. The results suggest a path for developing a molecular-level basis to predict the synergies between ions and crystal faces that facilitate aggregation under given solution conditions. Such fundamental understanding could be applied extensively to the aggregation and precipitation utilization in the biological, pharmaceutical, materials design, environmental remediation, and geological regimes.