Structural properties and phase transitions in a silica clathrate

Melanophlogite, a low-pressure silica polymorph, has been extensively studied at different temperatures and pressures by molecular dynamics simulations. While the high-temperature form is confirmed as cubic, the low-temperature phase is found to be slightly distorted, in agreement with experiments. With increasing pressure, the crystalline character is gradually lost. At 8 GPa, the radial distribution function is consistent with an amorphous state. Like pristine glass, the topology changes, plastic behavior, and permanent densification appear above ～12 GPa, triggered by Si coordination number changes. We predict that a partial crystalline and amorphous sample can be obtained by recovering the sample from a pressure of ～12-16 GPa.     

Atomistic molecular dynamics simulations of shock compressed quartz

Atomistic non-equilibrium molecular dynamics simulations of shock wave compression of quartz have been performed using the so-called BKS semi-empirical potential of van Beest, Kramer, and van Santen [Phys. Rev. B 43, 5068 (1991)] to construct the Hugoniot of quartz. Our scheme mimics the real world experimental set up by using a flyer-plate impactor to initiate the shock wave and is the first shock wave simulation that uses a geometry optimised system of a polar slab in a three-dimensional system employing periodic boundary conditions. Our scheme also includes the relaxation of the surface dipole in the polar quartz slab which is an essential pre-requisite to a stable simulation. The original BKS potential is unsuited to shock wave calculations and so we propose a simple modification. With this modification, we find that our calculated Hugoniot is in good agreement with experimental shock wave data up to 25 GPa, but significantly diverges beyond this point. We conclude that our modified BKS potential is suitable for quartz under representative pressure conditions of the Earth core, but unsuitable for high-pressure shock wave simulations. We also find that the BKS potential incorrectly prefers the β-quartz phase over the α-quartz phase at zero-temperature, and that there is a β → α phase-transition at 6 GPa.     

Densification of silica glass at ambient pressure

We show that densification of silica glass at ambient pressure as observed in irradiation experiments can be attributed to defect generation and subsequent structure relaxation. In our molecular dynamics simulations, defects are created by randomly removing atoms, by displacing atoms from their nominal positions in an otherwise intact glass, and by assigning certain atom excess kinetic energy (simulated ion implantation). The former forms vacancies; displacing atoms and ion implantation produce both vacancies and "interstitials." Appreciable densification is induced by these defects after equilibration of the defective glasses. The structural and vibrational properties of the densified glasses are characterized, displaying resembling features regardless of the means of densification. These results indicate that relaxation of high free-energy defects into metastable amorphous structures enriched in atomic coordination serves as a common mechanism for densification of silica glass at ambient pressure.     

Terbium Crown-Ether Complex as a Stable Photoprobe

Terbium ion-4'carboxybenzo-18crown-6-ether complex (TbCCE) photoprobe is a sensitive and stable luminescent photoprobe used to detect low (9.4 x10⁻⁹ mol L⁻¹) concentrations of nalbuphine (NAL) in serum and pharmaceutical formulations. Here we discuss molecular modeling of the interacting species using DFT and TD-DFT. The results reveal strong binding energy of TbCCE (−153.36 kJ/mol) and explain the results of Stern-Volmer bimolecular quenching analysis due to the presence of NAL in the proximity (at 2.403 Å apart from Tb ion) of the emissive TbCCE. Ab Initio molecular dynamic (AIMD) simulations are used to explain the dynamical changes of TbCCE molecular kinetic energy in its S₁ state induced by collision with NAL. The AIMD simulates collisions between interacting molecules, which are reflected in the observed quenching of the photoprobe. Kinetic energy changes during molecular motions in the S₁ state of TbCCE in presence of NAL indicate energy transfer process leading to quenching starting at 57 fs at NAL-TbCCE distance is ~ 1.6 Å. The excited state AIMD simulations carried out in this work suggest a new avenue for future research on luminescence quenching.     

Short-time Fourier transform analysis of ab initio molecular dynamics simulation: collision reaction between CN and C4H6

Collision reactions between cyano radical (CN) and dimethylacetylene (C4H6) are thought to occur in the atmosphere of Saturn's moon Titan. However, it is difficult to reproduce reactions occurring in unique environments to study their dynamical processes. In this study, collision reactions between CN and C4H6 were investigated using ab initio molecular dynamics (AIMD) simulations. The simulation results were categorized into three kinds: nonreactive collision, incorporation, and substitution. Short-time Fourier transform analysis of velocity autocorrelation functions obtained by the AIMD simulations, which has been recently developed by our research group, was performed to examine the nonequilibrium condition of the vibrational states. Spectrograms, which correspond to the time evolution of power spectra, clarify the relationship between the three reaction channels and the dynamical changes of the vibrational states.     

Quantum molecular dynamic simulations of warm dense carbon monoxide

Using quantum molecular dynamic simulations, we have studied the thermophysical properties of warm dense carbon monoxide under extreme conditions. The principal Hugoniot pressure up to 286 GPa, which is derived from the equation of state, is calculated and compared with available experimental and theoretical data. The chemical decomposition of carbon monoxide has been predicted at 8 GPa by means of pair correlation function and the charge density distribution. Based on Kubo-Greenwood formula, the dc electrical conductivity and the optical reflectivity are determined, and the nonmetal-metal transition for shock compressed carbon monoxide is observed around 40 GPa.     

Hydration shell structure and dynamics of curium(III) in aqueous solution: first principles and empirical studies

Results of ab initio molecular dynamics (AIMD), quantum mechanics/molecular mechanics (QM/MM), and classical molecular dynamics (CMD) simulations of Cm(3+) in liquid water at a temperature of 300 K are reported. The AIMD simulation was based on the Car-Parrinello MD scheme and GGA-PBE formulation of density functional theory. Two QM/MM simulations were performed by treating Cm(3+) and the water molecules in the first shell quantum mechanically using the PBE (QM/MM-PBE) and the hybrid PBE0 density functionals (QM/MM-PBE0). Two CMD simulations were carried out using ab initio derived pair plus three-body potentials (CMD-3B) and empirical Lennard-Jones pair potential (CMD-LJ). The AIMD and QM/MM-PBE simulations predict average first shell hydration numbers of 8, both of which disagree with recent experimental EXAFS and TRLFS value of 9. On the other hand, the average first shell hydration numbers obtained in the QM/MM-PBE0 and CMD simulations was 9, which agrees with experiment. All the simulations predicted an average first shell and second shell Cm-O bond distance of 2.49-2.53 ? and 4.67-4.75 ? respectively, both of which are in fair agreement with corresponding experimental values of 2.45-2.48 and 4.65 ?. The geometric arrangement of the 8-fold and 9-fold coordinated first shell structures corresponded to the square antiprism and tricapped trigonal prisms, respectively. The second shell hydration number for AIMD QM/MM-PBE, QM/MM-PBE0, CMD-3B, and CMD-LJ, were 15.8, 17.2, 17.7, 17.4, and 16.4 respectively, which indicates second hydration shell overcoordination compared to a recent EXAFS experimental value of 13. Save the EXAFS spectra CMD-LJ simulation, all the computed EXAFS spectra agree fairly well with experiment and a clear distinction could not be made between configurations with 8-fold and 9-fold coordinated first shells. The mechanisms responsible for the first shell associative and dissociative ligand exchange in the classical simulations have been analyzed. The first shell mean residence time was predicted to be on the nanosecond time scale. The computed diffusion constants of Cm(3+) and water are in good agreement with experimental data.     

Ab initio molecular dynamics with discrete variable representation basis sets: techniques and application to liquid water

Finite temperature ab initio molecular dynamics (AIMD), in which forces are obtained from "on-the-fly" electronic structure calculations, is a widely used technique for studying structural and dynamical properties of chemically active systems. Recently, we introduced an AIMD scheme based on discrete variable representation (DVR) basis sets, which was shown to have improved convergence properties over the conventional plane wave (PW) basis set [Liu,Y.; et al. Phys. Rev. B 2003, 68, 125110]. In the present work, the numerical algorithms for the DVR based AIMD scheme (DVR/AIMD) are provided in detail, and the latest developments of the approach are presented. The accuracy and stability of the current implementation of the DVR/AIMD scheme are tested by performing a simulation of liquid water at ambient conditions. The structural information obtained from the present work is in good agreement with the result of recent AIMD simulations with a PW basis set (PW/AIMD). Advantages of using the DVR/AIMD scheme over the PW/AIMD method are discussed. In particular, it is shown that a DVR/AIMD simulation of liquid water in the complete basis set limit is possible with a relatively small number of grid points.     

Phase diagram of supercooled water confined to hydrophilic nanopores

We present a phase diagram for water confined to cylindrical silica nanopores in terms of pressure, temperature, and pore radius. The confining cylindrical wall is hydrophilic and disordered, which has a destabilizing effect on ordered water structure. The phase diagram for this class of systems is derived from general arguments, with parameters taken from experimental observations and computer simulations and with assumptions tested by computer simulation. Phase space divides into three regions: a single liquid, a crystal-like solid, and glass. For large pores, radii exceeding 1 nm, water exhibits liquid and crystal-like behaviors, with abrupt crossovers between these regimes. For small pore radii, crystal-like behavior is unstable and water remains amorphous for all non-zero temperatures. At low enough temperatures, these states are glasses. Several experimental results for supercooled water can be understood in terms of the phase diagram we present.     

Structure and speciation in hydrous silica melts. 2. Pressure effects

The effect of pressure on structure and water speciation in hydrated liquid silica is examined over a range of temperatures and compositions. The Feuston-Garofalini (FG) potential is used in isobaric-isothermal Monte Carlo simulations carried out at four pressures (0.25, 1.0, 2.5, and 10 GPa) for seven temperatures (2000 < or = T < or= 9000 K) and five compositions (0.0 < or = x_w < or = 0.4). The FG potential yields a stable melt phase for p > or = 1.0 GPa and/or x_w < or = 0.1 for all temperatures. The volume minimum seen in previous simulations of pure and hydrated liquid silica using the FG potential persists up to 2.5 GPa but is no longer evident at 10 GPa. This is correlated with gradual structural changes of the liquid up to 2.5 GPa and with more significant changes at 10 GPa. Even at high overall concentrations of water (x_w = 0.4), only about 2% of oxygen atoms are present as molecular water species at the lowest temperature. This percentage decreases with increasing pressure and temperature.     

Hybrid Functional and Plane Waves based Ab Initio Molecular Dynamics Study of the Aqueous Fe2+/Fe3+ Redox Reaction**

Kohn-Sham density functional theory and plane wave basis set based ab initio molecular dynamics (AIMD) simulation is a powerful tool for studying complex reactions in solutions, such as electron transfer (ET) reactions involving Fe²⁺/Fe³⁺ ions in water. In most cases, such simulations are performed using density functionals at the level of Generalized Gradient Approximation (GGA). The challenge in modelling ET reactions is the poor quality of GGA functionals in predicting properties of such open-shell systems due to the inevitable self-interaction error (SIE). While hybrid functionals can minimize SIE, standard plane-wave based AIMD at that level of theory is typically 150 times slower than GGA for systems containing ∼100 atoms. Among several approaches reported to speed-up AIMD simulations with hybrid functionals, the noise-stabilized MD (NSMD) procedure, together with the use of localized orbitals to compute the required exchange integrals, is an attractive option. In this work, we demonstrate the application of the NSMD approach for studying the Fe²⁺/Fe³⁺ redox reaction in water. It is shown here that long AIMD trajectories at the level of hybrid density functionals can be obtained using this approach. Redox properties of the aqueous Fe²⁺/Fe³⁺ system computed from these simulations are compared with the available experimental data for validation.     

"Cooperativity blockage" in the mixed alkali effect as revealed by molecular-dynamics simulations of alkali metasilicate glass

The relaxation dynamics of a complex interacting system can be drastically changed when mixing with another component having different dynamics. In this work, we elucidate the effect of the less mobile guest ions on the dynamics of the more mobile host ions in mixed alkali glasses by molecular-dynamics (MD) simulations. One MD simulation was carried out on lithium metasilicate glass with the guest ions created by freezing some randomly chosen lithium ions at their initial locations at 700 K. A remarkable slowing down of the dynamics of the majority mobile Li ions was observed both in the self-part of the density-density correlation function, Fs(k,t), and in the mean-squared displacements. On the other hand, there is no significant change in the structure. The motion of the Li ions in the unadulterated Li metasilicate glass is dynamically heterogeneous. In the present work, the fast and slow ions were divided into two groups. The number of fast ions, which shows faster dynamics (Levy flight) facilitated by cooperative jumps, decreases considerably when small amount of Li ions are frozen. Consequently there is a large overall reduction of the mobility of the Li ions. The result is also in accordance with the experimental finding in mixed alkali silicate glasses that the most dramatic reduction of ionic conductivity occurs in the dilute foreign alkali limit. Similar suppression of the cooperative jumps is observed in the MD simulation data of mixed alkali system, LiKSiO3. Naturally, the effect found here is appropriately described as "cooperativity blockage." Slowing down of the motion of Li ions also was observed when a small number of oxygen atoms chosen at random were frozen. The effect is smaller than the case of freezing some the Li ions, but it is not negligible. The cooperativity blockage is also implemented by confining the Li metasilicate glass inside two parallel walls formed by freezing Li ions in the same metasilicate glass. Molecular-dynamics simulations were performed on the dynamics of the Li ions in the confined glass. Slowing down of the dynamics is largest near the wall and decreases monotonically with distance away from the wall.     

Exact on-event expressions for discrete potential systems

The properties of systems composed of atoms interacting though discrete potentials are dictated by a series of events which occur between pairs of atoms. There are only four basic event types for pairwise discrete potentials and the square-well/shoulder systems studied here exhibit them all. Closed analytical expressions are derived for the on-event kinetic energy distribution functions for an atom, which are distinct from the Maxwell-Boltzmann distribution function. Exact expressions are derived that directly relate the pressure and temperature of equilibrium discrete potential systems to the rates of each type of event. The pressure can be determined from knowledge of only the rate of core and bounce events. The temperature is given by the ratio of the number of bounce events to the number of disassociation/association events. All these expressions are validated with event-driven molecular dynamics simulations and agree with the data within the statistical precision of the simulations.     

On the Use of Accelerated Molecular Dynamics to Enhance Configurational Sampling in Ab Initio Simulations

We have implemented the accelerated molecular dynamics approach (Hamelberg, D.; Mongan, J.; McCammon, J. A. J. Chem. Phys. 2004, 120 (24), 11919) in the framework of ab initio MD (AIMD). Using three simple examples, we demonstrate that accelerated AIMD (A-AIMD) can be used to accelerate solvent relaxation in AIMD simulations and facilitate the detection of reaction coordinates: (i) We show, for one cyclohexane molecule in the gas phase, that the method can be used to accelerate the rate of the chair-to-chair interconversion by a factor of ～1 × 10(5), while allowing for the reconstruction of the correct canonical distribution of low-energy states; (ii) We then show, for a water box of 64 H(2)O molecules, that A-AIMD can also be used in the condensed phase to accelerate the sampling of water conformations, without affecting the structural properties of the solvent; and (iii) The method is then used to compute the potential of mean force (PMF) for the dissociation of Na-Cl in water, accelerating the convergence by a factor of ～3-4 compared to conventional AIMD simulations.(2) These results suggest that A-AIMD is a useful addition to existing methods for enhanced conformational and phase-space sampling in solution. While the method does not make the use of collective variables superfluous, it also does not require the user to define a set of collective variables that can capture all the low-energy minima on the potential energy surface. This property may prove very useful when dealing with highly complex multidimensional systems that require a quantum mechanical treatment.     

Coarse-grained molecular dynamics modeling of strongly associating fluids: thermodynamics, liquid structure, and dynamics of symmetric binary mixture fluids

Symmetric binary mixtures capable of strong association via a highly directional and saturable specific interaction between unlike molecules are investigated by canonical molecular dynamics simulations. The specific interaction of the molecules is defined in a new coarse-grained pair potential that can be applied in continuous molecular dynamics as well as in Monte Carlo simulations. The thermodynamic, structural, and dynamic properties of the associating mixture fluids are investigated as a function of density, temperature, and association strength of the specific interaction. Detailed analysis of the simulation data confirms a two-stage mechanism in the formation of specific bonds with increasing interaction strength, including a fast dimerization process and a subsequent stage of perfecting the bonds. A large heat capacity peak is found during the formation or breaking of the bonds, reflecting the large energy fluctuation introduced by the strong association. The fractions of nonbonded molecules obtained from the simulations as a function of density, temperature, and interaction strength are in excellent agreement with the predictions of Wertheim's thermodynamic perturbation theory. The translational and rotational dynamics of the Tmer mixture are effectively retarded with increasing association strength and are analyzed in terms of autocorrelation functions and a non-Gaussian parameter for the translational dynamics. The lifetimes of molecules in bonded and nonbonded states provide detailed information about the transformation of molecules between the bonded state and the nonbonded state. Finally, simulation sampling problems inherent to strongly interacting systems are easily overcome using the parallel tempering simulation technique. This latter result confirms that with the new continuous coarse-grained simulation potential we have a versatile and flexible interaction potential that can be used with many available molecular dynamics and Monte Carlo algorithms under various ensembles.     

Nano-indentation of a room-temperature ionic liquid film on silica: a computational experiment

We investigate the structure of the [bmim][Tf(2)N]/silica interface by simulating the indentation of a thin (4 nm) [bmim][Tf(2)N] film by a hard nanometric tip. The ionic liquid/silica interface is represented in atomistic detail, while the tip is modelled by a spherical mesoscopic particle interacting via an effective short-range potential. Plots of the normal force (F(z)) on the tip as a function of its distance from the silica surface highlight the effect of weak layering in the ionic liquid structure, as well as the progressive loss of fluidity in approaching the silica surface. The simulation results for F(z) are in near-quantitative agreement with new AFM data measured on the same [bmim][Tf(2)N]/silica interface under comparable thermodynamic conditions.     

Effects of cross-links, pressure and temperature on the thermal properties and glass transition behaviour of polybutadiene

The thermal conductivity κ, heat capacity per unit volume ρc(p) and glass transition behaviour under pressure have been established for medium and high vinyl content polybutadiene PB with molecular weights 2600 and 100,000 and their highly cross-linked (ebonite) states obtained purely by high-pressure high-temperature treatments. Cross-linking eliminates the glass transitions and increases κ by as much as 50% at 295 K and 1 atm, and decreases ρc(p) to a limiting level close to that of the glassy state of PB, which is reached before the ultimate cross-link density is achieved. The pressure and temperature behaviours of κ are strongly changed by cross-links, which increases the effect of temperature but decreases the effect of pressure. We attribute these changes to a cross-linked induced permanent densification and consequential increase of phonon velocity simultaneously as conduction along polymer chains is disrupted. The glass transition temperatures for a time scale of 1 s are described to within 0.5 K by: T(g)(p) = 202.5 (1 + 2.94 p)(0.286) and T(g)(p) = 272.3 (1 + 2.57 p)(0.233) (p in GPa and T in K) up to 1 GPa, for PB2600 and PB100000, respectively, and can be estimated for medium and high vinyl content PBs with molecular weights in between by a constant, pressure independent, shift in temperature.     

Insights into the structure and dynamics of a room-temperature ionic liquid: ab initio molecular dynamics simulation studies of 1-n-butyl-3-methylimidazolium hexafluorophosphate ([bmim][PF6]) and the [bmim][PF6]-CO2 mixture

Ab initio molecular dynamics (AIMD) studies have been carried out on liquid 1-n-butyl-3-methylimidazolium hexafluorophosphate ([bmim][PF6]) and its mixture with CO2 using the Car-Parrinello molecular dynamics (CPMD) method. Results from AIMD and empirical potential molecular dynamics (MD) have been compared and were found to differ in some respects. With a strong resemblance to the crystal, the AIMD simulated neat liquid exhibits many cation-anion hydrogen bonds, a feature that is almost absent in the MD results. The anions were observed to be strongly polarized in the condensed phase. The addition of CO2 increased the probability of this hydrogen bond formation. CO2 molecules in the vicinity of the ions of [bmim][PF6] exhibit larger deviations from linearity in their instantaneous configurations. The polar environment of the liquid induces a dipole moment in CO2, lifting the degeneracy of its bending mode. The calculated splitting in the vibrational mode compares well with infrared spectroscopic data. The solvation of CO2 in [bmim][PF6] is primarily facilitated by the anion, as seen from the radial and spatial distribution functions. CO2 molecules were found to be aligned tangential to the PF6 spheres with their most probable location being the octahedral voids of the anion. The structural data obtained from AIMD simulations can serve as a benchmark to refine interaction potentials for this important room-temperature ionic liquid.     

Nanosecond Rapid Crystallization of Water Induced by Quartz Glass under Dynamic Compression

Optical transmission characteristics of water between quartz glass under shock compression are in situ observed by using the technique of missile-borne light source. Through these transmission properties, the phase transition of liquid water is studied. The experimental results show that liquid water exhibits transparency decline phenomenon when the pressure is lower than 2 GPa under shock compression process, and the transparency variation is related to the existence of quartz glass. So, the transparency decline is attributed to a quartz-induced freezing phenomenon of water.     

Ab initio molecular dynamics simulations of an excited state of X(-)(H(2)O)(3) (X = Cl, I) complex

Upon excitation of Cl(-)(H(2)O)(3) and I(-)(H(2)O)(3) clusters, the electron transfers from the anionic precursor to the solvent, and then the excess electron is stabilized by polar solvent molecules. This process has been investigated using ab initio molecular dynamics (AIMD) simulations of excited states of Cl(-)(H(2)O)(3) and I(-)(H(2)O)(3) clusters. The AIMD simulation results of Cl(-)(H(2)O)(3) and I(-)(H(2)O)(3) are compared, and they are found to be similar. Because the role of the halogen atom in the photoexcitation mechanism is controversial, we also carried out AIMD simulations for the ground-state bare excess electron -- water trimer [e(-)(H(2)O)(3)] at 300 K, the results of which are similar to those for the excited state of X(-)(H(2)O)(3) with zero kinetic energy at the initial excitation. This indicates that the rearrangement of the complex is closely related to that of e(-)(H(2)O)(3), whereas the role of the halide anion is not as important.