Classical Molecular Dynamics Study Research Articles

Assessment of Classical Force-Fields for Graphene Mechanics

The unique properties of graphene have attracted the interest of researchers from various fields, and the discovery of graphene has sparked a revolution in materials science, specifically in the field of two-dimensional materials. However, graphene synthesis’s costly and complex process significantly impairs researchers’ endeavors to explore its properties and structure experimentally. Molecular dynamics simulation is a well-established and useful tool for investigating graphene’s atomic structure and dynamic behavior at the nanoscale without requiring expensive and complex experiments. The accuracy of the molecular dynamics simulation depends on the potential functions. This work assesses the performance of various potential functions available for graphene in mechanical properties prediction. The following two cases are considered: pristine graphene and pre-cracked graphene. The most popular fifteen potentials have been assessed. Our results suggest that diverse potentials are suitable for various applications. REBO and Tersoff potentials are the best for simulating monolayer pristine graphene, and the MEAM and the AIREBO-m potentials are recommended for those with crack defects because of their respective utilization of the electron density and inclusion of the long-range interaction. We recommend the AIREBO-m potential for a general case of classical molecular dynamics study. This work might help to guide the selection of potentials for graphene simulations and the development of further advanced interatomic potentials.

A Classical Molecular Dynamics Study of the Effect of the Atomic Force Microscope Tip Shape, Size and Deformation on the Tribological Properties of the Graphene/Au(111) Interface

Atomic force microscopes are used, besides their principal function as surface imaging tools, in the surface manipulation and measurement of interfacial properties. In particular, they can be modified to measure lateral friction forces that occur during the sliding of the tip against the underlying substrate. However, the shape, size, and deformation of the tips profoundly affect the measurements in a manner that is difficult to predict. In this work, we investigate the contribution of these effect to the magnitude of the lateral forces during sliding. The surface substrate is chosen to be a few-layer AB-stacked graphene surface, whereas the tip is initially constructed from face-centered cubic gold. In order to separate the effect of deformation from the shape, the rigid tips of three different shapes were considered first, namely, a cone, a pyramid and a hemisphere. The shape was seen to dictate all aspects of the interface during sliding, from temperature dependence to stick–slip behavior. Deformation was investigated next by comparing a rigid hemispherical tip to one of an identical shape and size but with all but the top three layers of atoms being free to move. The deformation, as also verified by an indentation analysis, occurs by means of the lower layers collapsing on the upper ones, thereby increasing the contact area. This collapse mitigates the friction force and decreases it with respect to the rigid tip for the same vertical distance. Finally, the size effect is studied by means of calculating the friction forces for a much larger hemispherical tip whose atoms are free to move. In this case, the deformation is found to be much smaller, but the stick–slip behavior is much more clearly seen.

What Happens to a Pyrrole Hemithioindigo Photoswitch Trapped in a Fluorescent Protein?

Artificial molecular photoswitches that can be reversibly controlled into different configurations by external light stimulation have broad application prospects in various fields, such as materials and chemical biology. Among them, the pyrrole hemithioindigo (PHT) photoswitch has a geometric structure similar to that of the fluorescent protein chromophore. What happens when the chromophore is replaced by PHT, and does it achieve similar functions to the original one? To answer these questions, we carried out ONIOM(QM/MM) and classical molecular dynamics studies on the photoisomerization mechanism and spectroscopic properties of PHT in the fluorescent protein. The results showed that in the protein environment, the fate of excited PHT is governed by the competition between fluorescence emission and hula-twist isomerization. Due to the strong steric hindrance effects caused by the interlacing residues in the protein that restrict the PHT conformation transformation, the cis-to-trans isomerization process of PHT needs to overcome a barrier of at least 4.9 kcal/mol; thus, fluorescence emission is more dominant in competition. It is also found that the intermolecular interaction between LYS67 and the carbonyl oxygen of PHT has a significant effect on the fluorescence emission. These results revealed the photochemical reaction mechanism of a light-driven molecular switch in the fluorescent protein and provided further theoretical support for the field of chemical biology.

Systematic identification and repurposing of FDA-approved drugs as antibacterial agents against Streptococcus pyogenes: In silico and in vitro studies

Streptococcus pyogenes (Group A Streptococcus - GAS) is a human pathogen causing wide range of infections and toxin-mediated diseases in human beings of all age groups with fatality of 10–30 %. The limited success of antibiotics and the non-availability of vaccines makes GAS a global burden. The multi-subunit RNA polymerase (RNAP) is a validated bacterial therapeutic target as it is involved in transcription and can arrest growth. Of the five subunits of this enzyme complex, the β-subunit (RpoC) has attracted specific attention as a drug target, particularly in the switch region. Here we attempt to repurpose non-antimicrobial drugs to act as RpoC inhibitors against S. pyogenes. In this study, 1826 FDA approved drugs have been identified through high-throughput virtual screening. Free Energy Perturbation (FEP) based binding free energy calculations have been performed at the final step of the virtual screening funnel to ensure high accuracy in silico results. Three compounds identified have been tested for susceptibility of S. pyogenes MTCC 442 strain and two antibiotic-resistant clinical isolates of S. pyogenes using microdilution assay. Among the three, two drugs Amlodipine Besylate (Amd) and Ranitidine hydrochloride (Rnt) have shown inhibition against all the tested strains and its mechanism of interaction with RpoC has been studied. The docked complexes were analyzed to understand the binding mode of the drugs to the target. Classical Molecular Dynamics studies for RpoC-Rnt complex and the two stable conformations of RpoC-Amd complex was carried out. Root Mean Square Deviation (RMSD), Root Mean Square Fluctuation (RMSF), Radius of Gyration (RoG) and Solvent Accessible Surface Area (SASA) of the complexes were plotted and studied. The thermodynamic parameters of protein-drug were experimentally determined using Isothermal Titration Calorimetry (ITC). Infrared spectroscopic studies and Fluorescence quenching studies provided insights into the secondary structural changes in RpoC on binding to the drugs.

Computational Assessment of a Dual-Action Ru(II)-Based Complex: Photosensitizer in Photodynamic Therapy and Intercalating Agent for Inducing DNA Damage.

A combined quantum-mechanical and classical molecular dynamics study of a recent Ru(II) complex with potential dual anticancer action is reported here. The main basis for the multiple action relies on the merocyanine ligand, whose electronic structure allows the drug to be able to absorb within the therapeutic window and in turn efficiently generate 1O2 for photodynamic therapy application and to intercalate within two nucleobases couples establishing reversible electrostatic interactions with DNA. TDDFT outcomes, which include the absorption spectrum, triplet states energy, and spin-orbit matrix elements, evidence that the photosensitizing activity is ensured by an MLCT state at around 660 nm, involving the merocyanine-based ligand, and by an efficient ISC from such state to triplet states with different characters. On the other hand, the MD exploration of all the possible intercalation sites within the dodecamer B-DNA evidences the ability of the complex to establish several electrostatic interactions with the nucleobases, thus potentially inducing DNA damage, though the simulation of the absorption spectra for models extracted by each MD trajectory shows that the photosensitizing properties of the complex remain unaltered. The computational results support that the anti-tumor effect may be related to multiple mechanisms of action.

On the key role of electrolyte–electrode van der Waals interactions in the simulation of ionic liquids-based supercapacitors

The performance of supercapacitors is governed by the structure and dynamics of ions at the solid/liquid interface. At the molecular scale, these properties result from a subtle combination of electrolyte–electrolyte and electrolyte–electrode interactions. Although the former are well captured by conventional force fields, validated against experiments, the latter are much more difficult to parameterize accurately. In this work, by using constant potential classical molecular dynamics, we investigate the effect of the strength of the electrode–electrolyte van der Waals interactions on the interfacial properties for a system composed of the 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ionic liquid and a graphite electrode. We show that stronger van der Waals interactions lead to a decrease in the exchange of co-ions by counter-ions with the increase of potential difference and, thus, to a lower capacitance of the devices. The ion exchange dynamics is strongly affected, but the charging rate remains constant over the whole range of studied parameters. This study emphasizes the need for a careful parameterization of force fields for electrode materials in future classical molecular dynamics studies.

Concurrent Characterization of Surface Diffusion and Intermixing of Ge on Si: A Classical Molecular Dynamics Study

AbstractThe surface diffusion and intermixing of Ge ad‐atoms over Si (001) 2 × 1 substrates using classical molecular dynamics (CMD) simulations are characterized here. Several interatomic potentials, parametrizations, and parameter mixing rules are contemplated. A novel simulation scheme is devised to characterize the effective frequency of surface diffusion and intermixing events overcoming the inherent difficulties related to their interdependency in heteroepitaxial systems. The effective energy barriers of these events encompass different atomistic mechanisms weighted by their occurrence probabilities. The overall description of surface diffusion and intermixing based on Stillinger–Weber (SW) potential is in agreement with ab initio calculations and experimental observations, though some atomistic details differ. This study is extended to Si(001) substrates with stressed Ge monolayers grown on top. It is found that Ge ad‐atom dynamics is accelerated with respect to the case of the pure Si substrate and that diffusion across dimer rows is mainly mediated by the atomic exchange of the Ge ad‐atom with a Ge atom on the surface.

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.

Atomistic modeling of LiF microstructure ionic conductivity and its influence on nucleation and plating

The formation and degradation of the solid electrolyte interphase (SEI) and its underlying transport properties play an essential role in the overall performance of lithium-ion batteries. This paper presents classical molecular dynamics studies on polycrystalline inorganic lithium fluoride (LiF) layers to model and predict the SEI transport properties. The ionic conductivity is obtained from the lithium-ion diffusivity in polycrystalline structures of LiF using the Nernst-Einstein relation. The predicted molecular dynamics data are used in a continuum scale phase-field model to evaluate the plating kinetics under fast charging conditions. The analysis emphasizes that the SEI ionic conductivity properties impact the plating dynamics, where SEI's low ion conductivity value is prone to large plating and subsequent capacity degradation. The combination of atomic and continuum scale studies shown herein lays a foundation to tune in SEI transport properties to decrease the amount of lithium plating and improve the performance of fast-charging batteries.

Local collective dynamics at equilibrium BCC crystal-melt interfaces.

We present a classical molecular-dynamics study of the collective dynamical properties of the coexisting liquid phase at equilibrium body-centered cubic (BCC) Fe crystal-melt interfaces. For the three interfacial orientations (100), (110), and (111), the collective dynamics are characterized through the calculation of the intermediate scattering functions, dynamical structure factors, and density relaxation times in a sequential local region of interest. An anisotropic speedup of the collective dynamics in all three BCC crystal-melt interfacial orientations is observed. This trend differs significantly from the previously observed slowing down of the local collective dynamics at the liquid-vapor interface [del Rio and González, Acta Mater. 198, 281 (2020)]. Examining the interfacial density relaxation times, we revisit the validity of the recently developed time-dependent Ginzburg-Landau theory for the solidification crystal-melt interface kinetic coefficients, resulting in excellent agreement with both the magnitude and the kinetic anisotropy of the crystal-melt interface kinetic coefficients measured from the non-equilibrium molecular-dynamics simulations.

Adsorption of glyphosate on graphene and functionalized graphenes: A DFT study

A study was carried out under the framework of density functional theory where the adsorption capacity of nine graphene systems with different organic moieties (CO, COOH, OH, O and SH) as glyphosate adsorbents was determined. The systems with the highest adsorption capacities were those with the alcohol, acid, epoxide and thiol substituents, according to energetic parameters such as interaction energy, enthalpy and Gibbs free energy of adsorption. The stability of the interaction is mainly given by hydrogen bonds, which was corroborated by the study of the bond critical points, as well as the index of non-covalent interactions. However, classical molecular dynamics studies suggest the importance of Van der Waals forces in the adsorption phenomenon at 298.15 K. The systems under study show promise for further studies and possible application as glyphosate trapping agents.

Lifetime distribution of clusters in binary mixtures involving hydrogen bonding liquids

Hydrogen bonded liquids are associated liquids and tend to exhibit local inhomogeneity in the form of clusters and segregated sub-nano domains. It is an open question as to whether Hbonded clusters in pure water have common features with the water segregated pockets observed in various aqueous binary mixtures, such as water–alcohol mixtures, for example. In the present study, we demonstrate through classical molecular dynamics studies of the lifetime distributions of the hydrogen bonds in different types of binary mixtures, that these lifetimes exhibit the same universal features in the case of the pure liquids, independently of the species concentrations. The same types of three distinct lifetimes are observed, all of them in the sub picosecond regime. The primary lifetime concerns that of Hbonded dimers, and strongly depends on Hbonding criteria such as the bonding distance. The two others are independent of bonding criteria and appear as universal accross many liquids and mixtures. The secondary lifetime (tau _1 approx 20 fs) concerns Hbonded cluster lifetimes, while the tertiary lifetime (tau _2 approx 50 fs) concerns the topology of these clusters, such as chains or globules, for example. This surprizing separation in three distinct lifetimes suggests the existence of associated three distinct kinetic mechanisms in the very short sub-picosecond time scales, with, in addition, an appealing connection to the concepts of local energy and entropy.

Methanol diffusion in H-ZSM-5 catalysts as a function of loading and Si/Al ratio: A classical molecular dynamics study

Methanol diffusion in H-ZSM-5 was studied using classical molecular dynamics at 373 –423 K, using loadings of 3 and 5 molecules per unit cell, in frameworks with Si/Al = 15, 47, 95 191 and a fully siliceous system. While the lower loading exhibits higher diffusivity, self-diffusivities increase at both loadings between Si/Al = 15 and 95, after which they are independent of composition. The trend in diffusivity with Si/Al ratio is explained in terms of methanol-acid site interactions, while the trend with loading is explained in terms of methanol-methanol interactions and the resulting methanol structure in the catalyst pores.

Most Probable Druggable Pockets in Mutant p53-Arg175His Clusters Extracted from Gaussian Accelerated Molecular Dynamics Simulations

p53, a tumor suppressor protein, is essential for preventing cancer development. Enhancing our understanding of the human p53 function and its modifications in carcinogenesis will aid in developing more highly effective strategies for cancer prevention and treatment. In this study, we have modeled five human p53 forms, namely, inactive, distal-active, proximal-active, distal-Arg175His mutant, and proximal-Arg175His mutant forms. These forms have been investigated using Gaussian accelerated molecular dynamics (GaMD) simulations in OPC water model at physiological temperature and pH. Our observations, obtained throughout [Formula: see text] of production run, are in good agreement with the relevant results in the classical molecular dynamics (MD) studies. Therefore, GaMD method is more economic and efficient method than the classical MD method for studying biomolecular systems. The featured dynamics of the five human p53-DBD forms include noticeable conformational changes of L1 and [Formula: see text]-[Formula: see text] loops as well as [Formula: see text]-[Formula: see text] and [Formula: see text]-[Formula: see text] turns. We have identified two clusters that represent two distinct conformational states in each p53-DBD form. The free-energy profiles of these clusters demonstrate the flexibility of the protein to undergo a conformational transition between the two clusters. We have predicted two out of seven possible druggability pockets on the clusters of the Arg175His forms. These two druggability pockets are near the mutation site and are expected to be actual pockets, which will be helpful for the compound clinical progression studies.

Atomistic insight into the formation dynamics of charged point defects: A classical molecular dynamics study ofF+-centers in NaCl

This paper provides an atomistic exploration of the lattice dissipation mechanisms accompanying the formation of charged point defects through a femtosecond resolved study of ${\mathrm{F}}^{+}$-center creation in NaCl. Our findings, following from a classical molecular dynamics based investigation of this model system, point to general range of properties that should be present in similar systems. Immediately after the creation of such a charged defect center, its excess energy is imparted amongst the highest energy optical modes with no clear preference based on their degree of localization. This energy is then dissipated through equilibration amongst a bath of lower energy phonon modes. The temporal behavior primarily follows exponential decay trends at all the temperatures and energies explored, with a small degree of competition between phonon population and depopulation amongst lower energy bath modes. Moreover, the dissipation timescale is found to be approximately the same amongst all phonon energies. A temperature-dependent analysis shows the expected decrease in phonon lifetimes with increasing temperature. This is accompanied by similarly more rapid dissipation of thermal energy around the defect center at lower temperatures when the phonon mean free path is increased. An intuitive phenomenological model based on Langevin dynamics is also provided to interpret the atomistically derived phonon decay characteristics in the temporal domain. More broadly, these results are expected to aid the design and experimental investigation of strongly correlated materials where charged defect centers can play an important role in technological applications.

Aqueous Affinity and Interfacial Dynamics of Anisotropic Buckled Black Phosphorous

The structure of black phosphorous (BP) is similar to the honeycomb arrangement of graphene, but the layered BP is found to be buckled and highly anisotropic. The buckled surface structure affects interfacial molecule mobility and plays a vital role in various nanomaterial applications. The BP is also known for wettability, droplet formation, stability, and hydrophobicity in the aqueous environment. However, there is a gap concerning the structural and dynamical behavior of water molecules, which is available in abundance for other monoatomic and polyatomic two-dimensional (2D) materials. Motivated by the technological importance, we try to bridge the gap by explaining the surface anisotropy-facilitated behavior of water molecules on bilayer BP using classical and first principles molecular dynamics (MD) simulations. From our classical MD study, we find three distinct layers of water molecules. The water layer closest to the interface is L1, followed by L2 and L3/bulk perpendicular to the BP surface. Water molecules in the L1 layer experience some structural disintegration in hydrogen bond (HB) phenomena compared to the bulk. There is a loss of HB donor-acceptor count per water molecule. The average HB count decreases because of an elevated rate of HB formation and deformation; this would affect the dynamic properties in terms of HB lifetime. Therefore, we observe the reduced lifetime of HB in the layer in close contact with BP, which again complements our finding on the diffusion coefficient of water molecules in distinct layers. Water diffuses relatively faster with diffusion coefficient 3.25 × 10-9 m2 s-1 in L1, followed by L2 and L3. The BP layer shows moderate hydrophobic nature. Our results also indicate the anisotropic behavior as the diffusion along the x-direction is faster than that along the y-direction. The gap in the slope of the x and y components of mean-squared displacement (MSD) complements the pinning effect in an aqueous environment. We observe blue-shifted and red-shifted libration and O-H stretching modes from the calculated power spectra for the L1 water molecules compared to the L2 and L3 molecules from first principles MD simulations. Our analysis may help understand the physical phenomena that occur during the surface wetting of the predroplet formation process observed experimentally.

Classical molecular dynamics study of small samples of amorphous silica : structural and dynamical properties

Ten small size samples of amorphous silica containing 78 atoms have been prepared using classical molecular dynamics and the van Beest-Kramer-van Santen (BKS) empirical potential. Our final goal is to use such samples in a forthcoming publication to compute accurately the thermal properties of silica from first principles calculations. The structural characteristics of these ten samples are in good agreement with experimental data. Dynamical properties, like the mean-square displacement, the vibrational density of states or the dynamic structure factor, have also been investigated and compare relatively well with data from neutron scattering experiments. These small dynamically stable structures can therefore be used subsequently to study more complicated physical properties, like the thermal conductivity or the diffusivity at a reduced computational cost.

A Classical Molecular Dynamics Study on the Effect of Si/Al Ratio and Silanol Nest Defects on Water Diffusion in Zeolite HY

A Classical Molecular Dynamics Study on the Effect of Si/Al Ratio and Silanol Nest Defects on Water Diffusion in Zeolite HY

The atomic structure and dynamics at the CaCO3 vaterite-water interface: A classical molecular dynamics study.

Classical molecular and lattice dynamics were applied to explore the structure and dynamics of water on different surfaces of vaterite, the least abundant calcium carbonate polymorph. Surfaces were generated starting from the three possible structural models for vaterite (monoclinic, hexagonal/trigonal, and triclinic) and pre-screened using their surface energies in an implicit solvent. Surfaces with energies lower than 0.55 J/m2 were then run in explicit water. The majority of these surfaces dissolve in less than 100 ns, highlighting the low stability of this phase in abiotic environments. Three stable surfaces were identified; they exhibited only minor structural changes when in contact with explicit water and did not show any tendency to dissolve during 1 µs molecular dynamics simulations. The computed water density profiles show that all these surfaces have two distinct hydration layers. The water residence time at the various calcium sites was computed to be within 0.7 and 20.5 ns, which suggests that specific Ca ions will be more readily available to bind with organic molecules present in solution. This analysis is a step forward in understanding the structure of this complex mineral and its role in biomineralization, as it provides a solid theoretical background to explore its surface chemistry. In particular, this study provides realistic surface models and predicts the effect of water exchange at the surface active sites on the adsorption of other molecules.

Intermolecular interactions in tetrabutylammonium chloride based deep eutectic solvents: Classical molecular dynamics studies

Deep eutectic solvents (DESs) based on tetrabutylammonium chloride have been studied using atomistic molecular dynamics simulations. Two different hydrogen bond donors (HBDs) glycerol and ethylene glycol were used to explore the effect of HBDs on the structure of DESs. Interaction between the anion and the HBD was found to be the most dominant interaction from the structural analysis using radial and spatial distribution functions. Anions and HBDs interact via hydrogen bonds formed between them. The mean hydrogen bond lifetime for these bonds was found to be relatively shorter in case of ethylene glycol compared to that of glycerol, which agrees with the binding energy of the complexes in the gas phase determined using quantum chemical calculations. Diffusivity of components in DES having ethylene glycol as HBD is higher than that of the DES having glycerol due to the greater extent of hydrogen bonding in the latter. The presence of peaks and anti-peaks in the lower wave vector region in both the DESs signifies the existence of long-range structural ordering. The vapor – liquid interface of both the systems showed enrichment of ions at the interface compared to the bulk region.