Molecular dynamics simulations studies of nanoparticles in an isotropic liquid crystal matrix: Single particle behavior and pairwise interactions

We report results of molecular dynamics simulation studies of the behavior of spherical nanoparticles (NPs) in a dense isotropic nematogen matrix comprised of soft spherocylinders (SSCs). The SSCs exhibit a tendency for frustrated planar anchoring at the NP surface that results in a long-range (compared to the size of the NPs and SSCs) reduction in local orientational ordering and increased fluctuations in local orientational ordering compared to the pure isotropic phase of the SSCs. The potential of mean force between two nanoparticles exhibits a novel long-range repulsive tail separated from short-range molecular packing peaks by a shallow local minimum in free energy. The long-range repulsion is caused by NP-induced ordering fluctuations while the shallow minimum results from increased local ordering within the confinement region in between two NPs. The influence of the NPs on local orientational order in the nematogen matrix and the nematogen-induced interaction between NPs are found to depend strongly on the size of the NPs.     

Observations concerning the treatment of long-range interactions in molecular dynamics simulations

Molecular dynamics simulations of pure water employing two different empirical water models have been used to study the effects of different methods for truncation of long-range interactions in molecular mechanics calculations. As has been observed previously in integral equation studies, “shifting” these interactions on an atom-by-atom basis was found to produce artificial structuring in the water and affect diffusion rates. In cases where some form of short-range truncation must be used, the ST2 switching function applied on a group-by-group basis was found to be the most realistic procedure. If atom-based shifting must be employed, a cutoff distance greater than or equal to 12.0 Å was found to be required to produce realistic results. © 1993 John Wiley & Sons, Inc.     

Molecular dynamics simulations of peptide-surface interactions

Proteins, which are bioactive molecules, adsorb on implants placed in the body through complex and poorly understood mechanisms and directly influence biocompatibility. Molecular dynamics modeling using empirical force fields provides one of the most direct methods of theoretically analyzing the behavior of complex molecular systems and is well-suited for the simulation of protein adsorption behavior. To accurately simulate protein adsorption behavior, a force field must correctly represent the thermodynamic driving forces that govern peptide residue-surface interactions. However, since existing force fields were developed without specific consideration of protein-surface interactions, they may not accurately represent this type of molecular behavior. To address this concern, we developed a host-guest peptide adsorption model in the form of a G(4)-X-G(4) peptide (G is glycine, X is a variable residue) to enable determination of the contributions to adsorption free energy of different X residues when adsorbed to functionalized Au-alkanethiol self-assembled monolayers (SAMs). We have previously reported experimental results using surface plasmon resonance (SPR) spectroscopy to measure the free energy of peptide adsorption for this peptide model with X = G and K (lysine) on OH and COOH functionalized SAMs. The objectives of the present research were the development and assessment of methods to calculate adsorption free energy using molecular dynamics simulations with the GROMACS force field for these same peptide adsorption systems, with an oligoethylene oxide (OEG) functionalized SAM surface also being considered. By comparing simulation results to the experimental results, the accuracy of the selected force field to represent the behavior of these molecular systems can be evaluated. From our simulations, the G(4)-G-G(4) and G(4)-K-G(4) peptides showed minimal to no adsorption to the OH SAM surfaces and the G(4)-K-G(4) showed strong adsorption to the COOH SAM surface, which is in agreement with our SPR experiments. Contrary to our experimental results, however, the simulations predicted a relatively strong adsorption of G(4)-G-G(4) peptide to the COOH SAM surface. In addition, both peptides were unexpectedly predicted to adsorb to the OEG surface. These findings demonstrate the need for GROMACS force field parameters to be rebalanced for the simulation of peptide adsorption behavior on SAM surfaces. The developed methods provide a direct means of assessing, modifying, and validating force field performance for the simulation of peptide and protein adsorption to surfaces, without which little confidence can be placed in the simulation results that are generated with these types of systems.     

Molecular dynamics simulations of the oxidation of aluminum nanoparticles

The oxidation of aluminum nanoparticles is studied with classical molecular dynamics and the Streitz-Mintmire (Streitz, F. H.; Mintmire, J. W. Phys. Rev. B 1994, 50, 11996) electrostatic plus (ES+) potential that allows for the variation of electrostatic charge on all atoms in the simulation. The structure and charge distributions of bulk crystalline alpha-Al(2)O(3), a surface slab of alpha-Al(2)O(3) with an exposed (0001) basal plane, and an isolated Al(2)O(3) nanoparticle are studied. Constant NVT simulations of the oxidation of aluminum nanoparticles are also performed with different oxygen exposures. The calculations simulate a thermostated one-time exposure of an aluminum nanoparticle to different numbers of surface oxygen atoms. In the first set of oxidation studies, the overall approximate ratios of Al to O in the nanoparticle are 1:1 and 2:1. The nanoparticles are annealed to 3000 K and are then cooled to 500, 1000, or 1500 K. The atomic kinetic energy is scaled during the simulation to maintain the desired temperature. The structure and charge distributions in the oxidized nanoparticles differ from each other and from those of the bulk Al(2)O(3) phases. In the Al(1)O(1) simulation, an oxide shell forms that stabilizes the shape of the particle, and thus the original structure of the nanoparticle is approximately retained. In the case of Al(1)O(0.5), there is insufficient oxygen to form a complete oxide shell, and the oxidation results in particles of irregular shapes and rough surfaces. The particle surface is rough, and the nanoparticle is deformed.     

Molecular dynamics simulations of the melting of aluminum nanoparticles

Molecular dynamics simulations are performed to determine the melting points of aluminum nanoparticles of 55-1000 atoms with the Streitz-Mintmire [Phys. Rev. B 1994, 50, 11996] variable-charge electrostatic plus potential. The melting of the nanoparticles is characterized by studying the temperature dependence of the potential energy and Lindemann index. Nanoparticles with less than 850 atoms show bistability between the solid and liquid phases over temperature ranges below the point of complete melting. The potential energy of a nanoparticle in the bistable region alternates between values corresponding to the solid and liquid phases. This bistability is characteristic of dynamic coexistence melting. At higher temperatures, only the liquid state is stable. Nanoparticles with more than 850 atoms undergo a sharp solid-liquid-phase transition characteristic of the bulk solid phase. The variation of the melting point with the effective nanoparticle radius is also determined.     

Mapping long-range interactions in alpha-synuclein using spin-label NMR and ensemble molecular dynamics simulations

The intrinsically disordered protein alpha-synuclein plays a key role in the pathogenesis of Parkinson's disease (PD). We show here that the native state of alpha-synuclein consists of a broad distribution of conformers with an ensemble-averaged hydrodynamic radius significantly smaller than that expected for a random coil structure. This partial condensation is driven by interactions between the highly charged C-terminus and a large hydrophobic central region of the protein sequence. We suggest that this structure could inhibit the formation of alpha-synuclein aggregates, which are thought to be the cytotoxic species responsible for neurodegeneration in PD.     

Molecular dynamics simulations of multilayer films of polyelectrolytes and nanoparticles

We performed molecular dynamics simulations of multilayer assemblies of flexible polyelectrolytes and nanoparticles. The film was constructed by sequential adsorption of oppositely charged polymers and nanoparticles in layer-by-layer fashion from dilute solutions. We have studied multilayer films assembled from oppositely charged polyelectrolytes, oppositely charged nanoparticles, and mixed films containing both nanoparticles and polyelectrolytes. For all studied systems, the multilayer assembly proceeds through surface overcharging after completion of each deposition step. There is almost linear growth in the surface coverage and film thickness. The multilayer films assembled from nanoparticles show better layer stratification but at the same time have higher film roughness than those assembled from flexible polyelectrolytes.     

Molecular dynamics simulations of pressure effects on hydrophobic interactions.

We report results on the pressure effects on hydrophobic interactions obtained from molecular dynamics simulations of aqueous solutions of methanes in water. A wide range of pressures that is relevant to pressure denaturation of proteins is investigated. The characteristic features of water-mediated interactions between hydrophobic solutes are found to be pressure-dependent. In particular, with increasing pressure we find that (1) the solvent-separated configurations in the solute-solute potential of mean force (PMF) are stabilized with respect to the contact configurations; (2) the desolvation barrier increases monotonically with respect to both contact and solvent-separated configurations; (3) the locations of the minima and the barrier move toward shorter separations; and (4) pressure effects are considerably amplified for larger hydrophobic solutes. Together, these observations lend strong support to the picture of the pressure denaturation process proposed previously by Hummer et al. (Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 1552): with increasing pressure, the transfer of water into protein interior becomes key to the pressure denaturation process, leading to the dissociation of close hydrophobic contacts and subsequent swelling of the hydrophobic protein interior through insertions of water molecules. The pressure dependence of the PMF between larger hydrophobic solutes shows that pressure effects on the interaction between hydrophobic amino acids may be considerably amplified compared to those on the methane-methane PMF.     

Molecular dynamics and thermodynamic simulations of segregation phenomena in binary metal nanoparticles

Journal of Thermal Analysis and Calorimetry - An approach combining atomistic molecular dynamics (MD) and thermodynamic simulations has been applied to predict the distribution of components in...     

A mode coupling theory description of the short- and long-time dynamics of nematogens in the isotropic phase

Optical heterodyne-detected optical Kerr effect (OHD-OKE) experimental data are pre-sented on nematogens 4-(trans-4-n-octylcyclohexyl)isothiocyanatobenzene (8-CHBT), and 4-(4-pentyl-cyclohexyl)-benzonitrile (5-PCH) in the isotropic phase. The 8-CHBT and 5-PCH data and previously published data on 4-pentyl-4-biphenylcarbonitrile (5-CB) are analyzed using a modification of a schematic mode coupling theory (MCT) that has been successful in describing the dynamics of supercooled liquids. At long time, the OHD-OKE data (orientational relaxation) are well described with the standard Landau-de Gennes (LdG) theory. The data decay as a single exponential. The decay time diverges as the isotropic to nematic phase transition is approached from above. Previously there has been no theory that can describe the complex dynamics that occur at times short compared to the LdG exponential decay. Earlier, it has been noted that the short-time nematogen dynamics, which consist of several power laws, have a functional form identical to that observed for the short time behavior of the orientational relaxation of supercooled liquids. The temperature-dependent orientational dynamics of supercooled liquids have recently been successfully described using a schematic mode coupling theory. The schematic MCT theory that fits the supercooled liquid data does not reproduce the nematogen data within experimental error. The similarities of the nematogen data to the supercooled liquid data are the motivation for applying a modification of the successful MCT theory to nematogen dynamics in the isotropic phase. The results presented below show that the new schematic MCT theory does an excellent job of reproducing the nematogen isotropic phase OHD-OKE data on all time scales and at all temperatures.     

Molecular dynamics simulations of the interactions between platinum clusters and carbon platelets

Molecular dynamics simulations have been performed with two reactive force fields to investigate the structure of a Pt100 cluster adsorbed on the three distinct sides of a carbon platelet. A revised Reax force field for the carbon-platinum system is presented. In the simulations, carbon platelet edges both with and without hydrogen termination have been studied. It is found that the initial mismatch between the atomic structure of the platelet egde and the adsorbed face of the Pt100 cluster leads to a desorption of a few platinum atoms from the cluster and the subsequent restructuring of the cluster. Consequently, the average Pt-Pt bond length is enlarged in agreement with experimental results. This change in the bond length is supposed to play an important role in the enhancement of the catalytic activity, which is demonstrated by studying the changes in the bond order of the platinum atoms. We found an overall shift to lower values as well as a loss of the well-defined peak structure in the bond-order distribution.     

Molecular dynamics simulations of side chain liquid crystal polymer molecules in isotropic and liquid-crystalline melts

A detailed molecular dynamics simulation study is described for a polysiloxane side chain liquid crystal polymer (SCLCP). The simulations use a coarse-grained model composed of a combination of isotropic and anisotropic interaction sites. On cooling from a fully isotropic polymer melt, we see spontaneous microphase separation into polymer-rich and mesogen-rich regions. Upon application of a small aligning potential during cooling, the structures that form on microphase separation anneal to produce a smectic-A phase in which the polymer backbone is largely confined between the smectic layers. Several independent quenches from the melt are described that vary in the strength of the aligning potential and the degree of cooling. In each quench, defects were found where the backbone chains hop from one backbone-rich region to the next by tunneling through the mesogenic layers. As expected, the number of such defects is found to depend strongly on the rate of cooling. In the vicinity of such a defect, the smectic-A structure of the mesogen-rich layers is disrupted to give nematiclike ordering. Additionally, several extensive annealing runs of approximately 40 ns duration have been carried out at the point of microphase separation. During annealing the polymer backbone is seen to be slowly excluded from the mesogenic layers and lie perpendicular to the smectic-A director. These observations agree with previous assumptions about the structure of a SCLCP and with interpretations of x-ray diffraction and small angle neutron scattering data. The flexible alkyl spacers, which link the backbone to the mesogens, are found to form sublayers around the backbone layer.     

Molecular dynamics simulations of multilayer polyelectrolyte films: effect of electrostatic and short-range interactions

The effect of the strength of electrostatic and short-range interactions on the multilayer assembly of oppositely charged polyelectrolytes at a charged substrate was studied by molecular dynamics simulations. The multilayer buildup was achieved through sequential adsorption of charged polymers in a layer-by-layer fashion from dilute polyelectrolyte solutions. The strong electrostatic attraction between oppositely charged polyelectrolytes at each deposition step is a driving force behind the multilayer growth. Our simulations have shown that a charge reversal after each deposition step is critical for steady multilayer growth and that there is a linear increase in polymer surface coverage after the first few deposition steps. Furthermore, there is substantial intermixing between chains adsorbed during different deposition steps. We show that the polymer surface coverage and multilayer structure are each strongly influenced by the strength of electrostatic and short-range interactions.     

Early chemistry in hot and dense nitromethane: molecular dynamics simulations

We report density functional molecular dynamic simulations to determine the early chemical events of hot (T=3000 K) and dense (rho=1.97 g/cm(3), V/V(0)=0.68) nitromethane (CH(3)NO(2)). The first step in the decomposition process is an intermolecular proton abstraction mechanism that leads to the formation of CH(3)NO(2)H(+) and the aci ion H(2)CNO(2) (-). This event is also confirmed to occur in a fast annealing simulation to a final temperature of 4000 K at rho=2.20 g/cm(3). An intramolecular hydrogen transfer that transforms nitromethane into the aci acid form, CH(2)NO(2)H, accompanies this event. To our knowledge, this is the first confirmation of chemical reactivity with bond selectivity for an energetic material near the Chapman-Jouget state of the fully reacted material. We also report the decomposition mechanism followed up to the formation of H(2)O as the first stable product. We note that similarities in the global features of reactants, intermediates, and products of the reacting fluid seem to indicate a threshold for similar chemistry in the range of high densities and temperatures reported herein.     

Molecular dynamics simulations of the interactions of kinin peptides with an anionic POPG bilayer

We have performed molecular dynamics simulations of peptide hormone bradykinin (BK) and its fragment des-Arg9-BK in the presence of an anionic lipid bilayer, with an aim toward delineating the mechanism of action related to their bioactivity. Starting from the initial aqueous environment, both of the peptides are quickly adsorbed and stabilized on the cell surface. Whereas BK exhibits a stronger interaction with the membrane and prefers to stay on the interface, des-Arg9-BK, with the loss of C-terminal Arg, penetrates further. The heterogeneous lipid-water interface induces β-turn-like structure in the otherwise inherently flexible peptides. In the membrane-bound state, we observed C-terminal β-turn formation in BK, whereas for des-Arg9-BK, with the deletion of Arg9, turn formation occurred in the middle of the peptide. The basic Arg residues anchor the peptide to the bilayer by strong electrostatic interactions with charged lipid headgroups. Simulations with different starting orientations of the peptides with respect to the bilayer surface lead to the same observations, namely, the relative positioning of the peptides on the membrane surface, deeper penetration of the des-Arg9-BK, and the formation of turn structures. The lipid headgroups adjacent to the bound peptides become substantially tilted, causing bilayer thinning near the peptide contact region and increase the degree of disorder in nearby lipids. Again, because of hydrogen bonding with the peptide, the neighboring lipid's polar heads exhibit considerably reduced flexibility. Corroborating findings from earlier experiments, our results provide important information about how the lipid environment promotes peptide orientation/conformation and how the peptide adapts to the environment.     

Molecular dynamics simulations of solid state recrystallization I: Observation of grain growth in annealed iron nanoparticles

Molecular dynamics simulations of solid state recrystallization and grain growth in iron nanoparticles containing 1436 atoms were carried out. During the period of relaxation of supercooled liquid drops and during thermal annealing of the solids they froze to, changes in disorder were followed by monitoring changes in energy and the migration of grain boundaries. All 27 polycrystalline nanoparticles, which were generated with different grain boundaries, were observed to recystallize into single crystals during annealing. Larger grains consumed the smaller ones. In particular, two sets of solid particles, designated as A and B, each with two grains, were treated to generate 18 members of each set with different thermal histories. This provided small ensembles (of 18 members each) from which rates at which the larger grain engulfed the smaller one, could be determined. The rate was higher, the smaller the degree of misorientation between the grains, a result contrary to the general rule based on published experiments, but the reason was clear. Crystal A, which happened to have a somewhat lower angle of misorientation, also had a higher population of defects, as confirmed by its higher energy. Accordingly, its driving force to recrystallize was greater. Although the mechanism of recrystallization is commonly called nucleation, our results, which probe the system on an atomic scale, were not able to identify nuclei unequivocally. By contrast, our technique can and does reveal nuclei in the freezing of liquids and in transformations from one solid phase to another. An alternative rationale for a nucleation-like process in our results is proposed.     

Molecular dynamics simulations reveal specific interactions of post-translational palmitoyl modifications with rhodopsin in membranes

We present a detailed analysis of the behavior of the highly flexible post-translational lipid modifications of rhodopsin from multiple-microsecond all-atom molecular dynamics simulations. Rhodopsin was studied in a realistic membrane environment that includes cholesterol, as well as saturated and polyunsaturated lipids with phosphocholine and phosphoethanolamine headgroups. The simulation reveals striking differences between the palmitoylations at Cys322 and Cys323 as well as between the palmitoyl chains and the neighboring lipids. Notably the palmitoyl group at Cys322 shows considerably greater contact with helix H1 of rhodopsin, yielding frequent chain upturns with longer reorientational correlation times, and relatively low order parameters. While the palmitoylation at Cys323 makes fewer protein contacts and has increased order compared to Cys322, it nevertheless exhibits greater flexibility with smaller order parameters than the stearoyl chains of the surrounding lipids. The dynamical structure of the palmitoylations-as well as their extensive fluctuations-suggests a complex function for the post-translational modifications in rhodopsin and potentially other G protein-coupled receptors, going beyond their role as membrane anchoring elements. Rather, we propose that the palmitoylation at Cys323 has a potential role as a lipid anchor, whereas the palmitoyl-protein interaction observed for Cys322 suggests a more specific interaction that affects the stability of the dark state of rhodopsin.     

Nucleation of NaCl nanoparticles in supercritical water: molecular dynamics simulations

Formation of NaCl nanoparticles in supercritical water is studied using molecular dynamics simulation method. We have simulated particle nucleation and growth in NaCl-H2O fluids, with salt concentration of 5.1 wt %, in the temperature and density range of 673-1073 K and 0.17-0.34 g/cm(3), respectively. The cluster size distributions, the size of critical nuclei and cluster lifetimes are reported. The size distribution of emerging clusters shows a very strong dependence on the system's density, with larger clusters forming at lower densities. Clusters consisting of approximately 14-24 ions appear critical for the thermodynamic states examined. The local structures of critical clusters are found to be amorphous. The lifetime values for clusters containing more than 20 ions are in the range of 10-50 ps. We have calculated the NaCl nucleation rates, which appear to be on the order of 10(28) cm(-3) s(-1).     

Molecular dynamics simulations of halide glasses

Summary Halide glasses have been extensively studied in recent years because of their potential application as infrared transmitting fibre optic materials. They are believed to be more ionic than glasses based on silica and should therefore be more amenable to molecular dynamics simulation using simple two-body potentials. Here the main features of structural models derived using such techniques are described and compared with available structural data. Possible future applications of this approach are outlined.