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Mixed quantum-classical molecular dynamics method has been applied to vibrational relaxation of a hydrophilic model NO in supercritical water at various densities along an isotherm above the critical temperature. The relaxation rate was determined based on Fermi’s golden rule at each state point and showed an inverse S-shaped curve as a function of bulk density. The hydration number was also calculated as a function of bulk density based on the calculated radial distribution function, which showed a good correlation with the relaxation rate. Change of the survival probability of the solute vibrational state was analyzed as a function of time together with the trajectory of the solvent water and the interaction with it. We will show that the solvent molecule resides near the solute molecule for a while and the solvent contributes to the relaxation by the random-noiselike Coulombic interaction only when it stays near the solute. After the solvent leaves the solute, it shows no contribution to the relaxation. The relaxation mechanism for this system is significantly different from the collisional one found for a nonpolar solute in nonpolar solvent in Paper I. Then, the relaxation rate is determined, on average, by the hydration number or local density of the solvent. Thus, the density dependence of the relaxation rate for the polar solute in supercritical water is apparently similar to that found for the nonpolar solute in nonpolar solvent, although the molecular process is quite different from each other. [ABSTRACT FROM AUTHOR]

In the hidden variable theory, Bohm proved a connection between the Schrödinger and Hamilton–Jacobi equations and showed the existence of classical paths, for which the generalized Bohr quantization condition is valid. In this paper we prove similar properties, starting from the equivalence between the Schrödinger and wave equations in the case of the conservative bound systems. Our approach is based on the equations and postulates of quantum mechanics without using any additional postulate. Like in the hidden variable theory, the above properties are proven without using the approximation of geometrical optics or the semiclassical approximation. Since the classical paths have only a mathematical significance in our analysis, our approach is consistent with the postulates of quantum mechanics. [ABSTRACT FROM AUTHOR]

Deterministic thermostats are frequently employed in nonequilibrium molecular dynamics simulations in order to remove the heat produced irreversibly over the course of such simulations. The simplest thermostat is the Gaussian thermostat, which satisfies Gauss’s principle of least constraint and fixes the peculiar kinetic energy. There are of course infinitely many ways to thermostat systems, e.g., by fixing ∑i|pi|μ+1. In the present paper we provide, for the first time, convincing arguments as to why the conventional Gaussian isokinetic thermostat (μ=1) is unique in this class. We show that this thermostat minimizes the phase space compression and is the only thermostat for which the conjugate pairing rule holds. Moreover, it is shown that for finite sized systems in the absence of an applied dissipative field, all other thermostats (μ≠1) perform work on the system in the same manner as a dissipative field while simultaneously removing the dissipative heat so generated. All other thermostats (μ≠1) are thus autodissipative. Among all μ thermostats, only the μ=1 Gaussian thermostat permits an equilibrium state. [ABSTRACT FROM AUTHOR]

This paper investigates the conformational and scaling properties of long linear polymer chains. These investigations are done with the aid of Monte Carlo (MC) and molecular dynamics (MD) simulations. Chain lengths that comprise several orders of magnitude to reduce errors of finite size scaling, including the effect of solvent quality, ranging from the athermal limit over the θ-transition to the collapsed state of chains are investigated. Also the effect of polydispersity on linear chains is included which is an important issue in the real fabrication of polymers. A detailed account of the hybrid MD and MC simulation model and the exploited numerical methods is given. Many results of chain properties in the extrapolated limit of infinite chain lengths are documented and universal properties of the chains within their universality class are given. An example of the difference between scaling exponents observed in actual solvents and those observed in the extremes of “good solvents” and “θ-solvents” in simulations is provided by comparing simulation results with experimental data on low density polyethylene. This paper is concluded with an outlook on the extension of this study to branched chain systems of many different branching types. [ABSTRACT FROM AUTHOR]

Hybrid molecular dynamics (MD) simulations, which combine density functional theory (DFT) descriptions of a molecule with a molecular mechanics (MM) modeling of its solvent environment, have opened the way towards accurate computations of solvation effects in the vibrational spectra of molecules. Recently, Wheeler et al. [ChemPhysChem 4, 382 (2002)] have suggested to compute these spectra from DFT/MM-MD trajectories by diagonalizing the covariance matrix of atomic fluctuations. This so-called principal mode analysis (PMA) allegedly can replace the well-established approaches, which are based on Fourier transform methods or on conventional normal mode analyses. By scrutinizing and revising the PMA approach we identify five conditions, which must be guaranteed if PMA is supposed to render exact vibrational frequencies. Besides specific choices of (a) coordinates and (b) coordinate systems, these conditions cover (c) a harmonic intramolecular potential, (d) a complete thermal equilibrium within the molecule, and (e) a molecular Hamiltonian independent of time. However, the PMA conditions [(c)–(d)] and [(c)–(e)] are generally violated in gas phase DFT-MD and liquid phase DFT/MM-MD trajectories, respectively. Based on a series of simple analytical model calculations and on the analysis of MD trajectories calculated for the formaldehyde molecule in the gas phase (DFT) and in liquid water (DFT/MM) we show that in both phases the violation of condition (d) can cause huge errors in PMA frequency computations, whereas the inevitable violations of conditions (c) and (e), the latter being generic to the liquid phase, imply systematic and sizable underestimates of the vibrational frequencies by PMA. We demonstrate that the huge errors, which are caused by an incomplete thermal equilibrium violating (d), can be avoided if one introduces mode-specific temperatures Tj and calculates the frequencies from a “generalized virial” (GV) expression instead from PMA. Concerning ways to additionally remove the remaining errors, which GV still shares with PMA, we refer to Paper II of this work [M. Schmitz and P. Tavan, J. Chem. Phys. 121, 12247 (2004)]. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

In an extensive computer simulation study, the transport coefficients of the Lennard-Jones model fluid were determined with high accuracy from equilibrium molecular-dynamics simulations. In the frame of time-correlation function theory, the generalized Einstein relations were employed to evaluate the transport coefficients. This second of a series of four papers presents the results for the self-diffusion coefficient, and discusses and interprets the behavior of this transport coefficient in the fluid region of the phase diagram. The uncertainty of the self-diffusion data is estimated to be 1% in the gas region and 0.5% at high-density liquid states. With the very accurate data, even fine details in the shape of the self-diffusion isotherms are resolved, and the previously little-investigated behavior of the self-diffusion coefficient at low-density gaseous states is analyzed in detail. Finally, aspects of the mass transport mechanisms on the molecular scale are explored by an analysis of the velocity autocorrelation functions. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

In this paper, investigation of the structure of palladium nanowire has been performed by using genetic algorithm simulation based on the molecular dynamics. Our calculation employs a well-fitted, tight-binding many-body potential for Pd atoms. Some local atomic structures and defects in nanowires have been reported. The melting behavior of palladium nanowire has also been investigated. An interesting result is that the diffusion of the central atoms results in the beginning of the melting. The moving central atoms build up a monostrand atomic chain during the melting process. The single atomic chain is very stable which can exist in a wide temperature region (800–950 K). The formation of the single atomic chain causes some new defects in the nanowire. And the new defects result in the decrease of the thermal stability of the nanowire. Interestingly, the liquid from the nanowire melting has a supercooled feature because the splitting of the second peak of pair correlation function is observed. The curves of the internal energy and the local cluster are used to monitor the phase transition. The melting of the nanowire is not only due to the single atomic diffusion, but also the diffusion of the local clusters. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

A procedure for the Raman spectra calculation of vitreous and molten silicates was presented in this paper. It includes molecular dynamics MD simulation for the generation of equilibrium configurations, Wilson’s GF matrix method for the calculations of eigenfrequencies and corresponding vectors, electro-optical parameters method (EOPM) for the Raman intensity calculations, and the bond polarizability model (BPM) for the determination of polarizability and polarizability derivative. One of the most important characteristics of this procedure is the achievement of the partial Raman spectra of five tetrahedral units, as well as the total spectral envelope. In this paper, the calculation was carried out for the vitreous and molten calcium silicates with different compositions and at various temperatures. It is worthwhile to note that the calculation is based on statistical configurations distribution in the space and so it is not needed to artificially adjust the full width at half maximum (FWHM) of spectra. It was also tested through the good agreement of the calculated spectra with the experimental, including some regularity of spectral properties. According to the calculation, the symmetrical stretching of whole tetrahedral units, to which the stretching of Si-Onb bond gives the main contribution to intensity, is proven to be the dominance in the high-frequency range (800–1200 cm-1) and the symmetrical bending of Si-Ob-Si, to which the stretching of Si-Ob bond exhibits the main contribution, is the dominance in the medium-frequency range (400–700 cm-1). As the first theoretical results, the Raman scattering coefficient of each Qi was found little change along with the variation of composition and temperature. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

In this paper the investigation of the dynamical processes of liquid alkali metals is executed by analyzing the time scales of relaxation processes in liquids. The obtained theoretical dynamic structure factor S(k,ω) for the case of liquid lithium is found to be in excellent agreement with the recently received inelastic x-ray scattering data. The comparison and interrelation with other theories are given here. Finally, an important part of this paper is the confirmation of the scale uniformity of the dynamic processes in liquid alkali metals predicted by some previous molecular dynamic simulation studies. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

In this paper we present a theoretical and computational study of the energetics and temporal dynamics of Coulomb explosion of molecular clusters of deuterium (D2)n/2 (n=480-7.6×104, cluster radius R0=13.1–70 Å) in ultraintense laser fields (laser peak intensity I=1015–1020W cm-2). The energetics of Coulomb explosion was inferred from the dependence of the maximal energy EM and the average energy Eav of the product D+ ions on the laser intensity, the laser pulse shape, the cluster radius, and the laser frequency. Electron dynamics of outer cluster ionization and nuclear dynamics of Coulomb explosion were investigated by molecular dynamics simulations. Several distinct laser pulse shape envelopes, involving a rectangular field, a Gaussian field, and a truncated Gaussian field, were employed to determine the validity range of the cluster vertical ionization (CVI) approximation. The CVI predicts that Eav, EM∝R02 and that the energy distribution is P(E)∝E1/2. For a rectangular laser pulse the CVI conditions are satisfied when complete outer ionization is obtained, with the outer ionization time toi being shorter than both the pulse width and the cluster radius doubling time τ2. By increasing toi, due to the increase of R0 or the decrease of I, we have shown that the deviation of Eav from the corresponding CVI value (EavCVI) is (EavCVI-Eav)/EavCVI≃(toi/2.91τ2)2. The Gaussian pulses trigger outer ionization induced by adiabatic following of the laser field and of the cluster size, providing a pseudo-CVI behavior at sufficiently large laser fields. The energetics manifest the existence of a finite range of CVI size dependence, with the validity range for the applicability of the CVI being R0≤(R0)I, with (R0)I representing an intensity dependent boundary radius. Relating electron dynamics of outer ionization to nuclear dynamics for Coulomb explosion induced by a Gaussian pulse, the boundary radius (R0)I and the corresponding ion average energy (Eav)I were inferred from simulations and described in terms of an electrostatic model. Two independent estimates of (R0)I, which involve the cluster size where the CVI relation breaks down and the cluster size for the attainment of complete outer ionization, are in good agreement with each other, as well as with the electrostatic model for cluster barrier suppression. The relation (Eav)I∝(R0)I2 provides the validity range of the pseudo-CVI domain for the cluster sizes and laser intensities, where the energetics of D+ ions produced by Coulomb explosion of (D)n clusters is optimized. The currently available experimental data [Madison et al., Phys. Plasmas 11, 1 (2004)] for the energetics of Coulomb explosion of (D)n clusters (Eav=5–7 keV at I=2×1018 W cm-2), together with our simulation data, lead to the estimates of R0=51–60 Å, which exceed the experimental estimate of R0=45 Å. The predicted anisotropy of the D+ ion energies in the Coulomb explosion at I=1018 W cm-2 is in accord with experiment. We also explored the laser frequency dependence of the energetics of Coulomb explosion in the range ν=0.1–2.1 fs-1 (λ=3000–140 nm), which can be rationalized in terms of the electrostatic model. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

The dissociation and association dynamics of N[sub 2]O[sub 4]⇋2NO[sub 2] in liquid state are studied by classical molecular dynamics simulations of reactive liquid NO[sub 2]. An OSPP+LJ potential between NO[sub 2] molecules, which is a sum of an orientation-sensitive pairwise potential (OSPP) between N–N atoms proposed in Paper I [J. Chem. Phys. 115, 10852 (2001)] and Lennard-Jones potentials between N–O and O–O atoms, has been used in the simulation. The reaction dynamics is studied as a function of well depth D[sub e] and anisotropy factors of the OSPP potential: A[sub θ] (0≤A[sub θ]≤1) for the rocking angle and A[sub τ] (0≤A[sub τ]≤0.5) for the torsional angle of relative NO[sub 2]–NO[sub 2] orientation. The lifetime τ[sub D] of initially prepared NO[sub 2] dimers is found to increase as D[sub e] increases, A[sub θ] increases, and A[sub τ] decreases. Dissociation and association dynamics are studied in detail around the extreme limit of pure NO[sub 2]-dimer liquid: D[sub e]=0.12×10[sup -18] J, A[sub θ]=0.5, and A[sub τ]=0.1, which has been found to reproduce both the observed liquid phase equilibrium properties and Raman band shapes of the dissociation mode very well. The dissociation dynamics from microscopic reaction trajectories is compared with the potential of the mean force (PMF) as a function of the N–N distance R. The PMF of reactive liquid NO[sub 2] shows a transition state barrier at R=2.3–2.5 Å, and NO[sub 2]-trimer structure is found to be formed at the barrier. Two types of dissociation of the NO[sub 2] dimer—the dissociation by collisional activation of the reactive mode to cross the dissociation limit and the NO[sub 2]-mediated dissociation via bond transfer—are studied. The latter needs less free energy and is found to be much more probable. The dissociation trajectories and PMF in reactive liquid NO[sub 2] are compared with those of a reactive NO[sub 2] pair in inert solvent N[sub 2]O[sub 4]. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

An aspherical ion model (AIM) description of interatomic interactions in alkaline earth oxides MgO, CaO, SrO, and BaO has been obtained. The parameters were determined by matching the forces predicted by the models to those calculated from an ab initio dynamics calculation in finite temperature simulations. The models were shown to be transferable in the sense that they offered equally accurate descriptions of the pure materials over very wide ranges of temperature and pressure and in phases with different coordination number. In the present paper, more wide-ranging transferability considerations are pursued. First, we check transferability between chemically related substances: we transform the model for CaO into a potential for BeO by scaling parameters according to the changes in ion sizes and polarizabilities. Second, we test transferability upon compound formation, by combining the MgO and CaO potentials in order to describe the interatomic interactions in MgO-CaO solid binary mixtures. The results show that the proposed models are able to provide a good description of interatomic interactions in both cases. The calculations demonstrate that the AIM represents the different contributions to the interionic forces faithfully and that the force-matching procedure finds physically meaningful values for the parameters therein. [ABSTRACT FROM AUTHOR]

In this paper (Paper II), the isokinetic dynamics scheme described in Paper I is combined with the plane-wave based Car-Parrinello (CP) ab initio molecular dynamics (MD) method [R. Car and M. Parrinello, Phys. Rev. Lett. 55, 2471 (1985)] to enable the efficient study of chemical reactions and metallic systems. The Car-Parrinello approach employs "on the fly" electronic structure calculations as a means of generating accurate internuclear forces for use in a molecular dynamics simulation. This is accomplished by the introduction of an extended Lagrangian that contains the electronic orbitals as fictitious dynamical variables (often expressed directly in terms of the expansion coefficients of the orbitals in a particular basis set). Thus, rather than quench the expansion coefficients to obtain the ground state energy and nuclear forces at every time step, the orbitals are "propagated" under conditions that allow them to fluctuate rapidly around their global minimum and, hence, generate an accurate approximation to the nuclear forces as the simulation proceeds. Indeed, the CP technique requires the dynamics of the orbitals to be both fast compared to the nuclear degrees of freedom while keeping the fictitious kinetic energy that allows them to be propagated dynamically as small as possible. While these conditions can be easy to achieve in many types of systems, in metals and highly exothermic chemical reactions difficulties arise. (Note, the CP dynamics of metals is incorrect because the nuclear motion does not occur on the ground state electronic surface but it can, nonetheless, provide useful information.) In order to alleviate these difficulties the isokinetic methods of Paper I are applied to derive isokinetic CP equations of motion. The efficacy of the new isokinetic CPMD method is demonstrated on model and realistic systems. The latter include, metallic systems, liquid aluminum, a small silicon sample, the 2 × 1 reconstruction of the silicon 100... [ABSTRACT FROM AUTHOR]

In this paper (Paper I) and a companion paper (Paper II), novel new algorithms and applications of the isokinetic ensemble as generated by Gauss' principle of least constraint, pioneered for use with molecular dynamics 20 years ago, are presented for biophysical, path integral, and Car-Parrinello based ab initio molecular dynamics. In Paper I, a new "extended system" version of the isokinetic equations of motion that overcomes the ergodicity problems inherent in the standard approach, is developed using a new theory of non-Hamiltonian phase space analysis [M. E. Tuckerman et al., Europhys. Lett. 45, 149 (1999); J. Chem. Phys. 115, 1678 (2001)]. Reversible multiple time step integrations schemes for the isokinetic methods, first presented by Zhang [J. Chem. Phys. 106, 6102 (1997)] are reviewed. Next, holonomic constraints are incorporated into the isokinetic methodology for use in fast efficient biomolecular simulation studies. Model and realistic examples are presented in order to evaluate, critically, the performance of the new isokinetic molecular dynamic schemes. Comparisons are made to the, now standard, canonical dynamics method, Nosé-Hoover chain dynamics [G. J. Martyna et al., J. Chem. Phys. 97, 2635 (1992)]. The new isokinetic techniques are found to yield more efficient sampling than the Nosé-Hoover chain method in both path integral molecular dynamics and biophysical molecular dynamics calculations. In Paper II, the use of isokinetic methods in Car-Parrinello based ab initio molecular dynamics calculations is presented. [ABSTRACT FROM AUTHOR]

Time-resolved infrared spectroscopy has the potential to provide unprecedented information about molecular dynamics in liquids. In the case of water, one of the most exciting techniques being developed is transient hole-burning. From experiments on dilute HOD in D[sub 2]O one can obtain the transition frequency time-correlation function for the OH stretch vibration, finding that it decays on a time scale of between 0.5 and 1 ps. In this paper we provide a molecular-level interpretation of this spectral diffusion time-correlation function. First, we verify that for hydrogen-bonded HOD molecules the instantaneous OH frequency is highly correlated with the distance to the (hydrogen-bonded) D[sub 2]O molecule. Second, we show that the instantaneous OH frequency is highly correlated with whether or not the HOD molecule has a hydrogen bond. Finally, we show that the short-time dynamics of the spectral diffusion time-correlation function is due to hydrogen-bond stretching motions, while the longer-time decay observed in the experiments is due to the dynamics of forming and breaking hydrogen bonds. We also present theoretical results that describe recent polarization anisotropy experiments, which measure frequency-dependent rotational dynamics. [ABSTRACT FROM AUTHOR]

The thermal rate constant for a chemical reaction, k(T), can be expressed as the long time limit of the flux-side correlation C[sub fs](t)=tr[e[sup -βĤ/2]&Fcirc;e[sup -βĤ/2]e[sup iĤ/2]e[sup iĤt/h]ĥe[sup -iĤt/h]].. Previous work has focused on semiclassical (SC) approximations [implemented via an initial value representation (IVR)] for the time evolution operators exp(±iĤt/h) in the correlation function, and this paper shows how an SC-IVR can also be used to approximate the Boltzmann operators exp(-βĤ/2). Test calculations show that over a wide temperature range little error is introduced in the rate constant by this SC approximation for the Boltzmann operator. [ABSTRACT FROM AUTHOR]

Vibrational dephasing of the N-N dissociation mode in equilibrium liquid N[SUB2]O[SUB4] ⇋ 2NO[SUB2] in the extreme limit of pure N[SUB2]O[SUB4] is studied by classical molecular dynamics simulations of liquid NO[SUB2]. An OSPP+LJ potential between NO[SUB2] molecules, which is a sum of an orientation-sensitive pairwise potential (OSPP) between N-N atoms proposed in Paper I [J. Chem. Phys. 115, 10852 (2001)] and Lennard-Jones potentials between N-O and O-O atoms, has been used in the simulation. The vibrational correlation function and Raman spectrum of the N-N stretching ν[SUB3] mode of N[SUB2]O[SUB4] are calculated, and are found to be very sensitive to the well depth D[SUBe] and anisotropy factors of OSPP: A[SUBθ2] (0 ⩽A[SUBθ] ⩽ 1) for rocking angle between the N-N bond and ONO direction, and A[SUBτ] (0 ⩽A[SUBτ] ⩽ 1 ) for the torsional angle. As A[SUBτ] increases in equilibrium liquid N[SUB2]O[SUB4]&lahar2;2NO[SUB2], the equilibrium shifts to dissociation, and the isotropic Raman band shifts to low frequency and broadens. The OSPP potential for D[SUBe]=0.12×10[SUP-18] J, A[SUBθ]0=0.5, and A[SUBτ]=0.1 is found to reproduce both the observed liquid phase equilibrium properties and Raman band shapes (peak frequency, bandwidth, and band asymmetry) of the dissociation mode very well. The long persistent positive correlation in the vibrational frequency fluctuation correlation function G[SUBω](t)= 〈Δω(0)Δω(t)〉/〈Δω(0)[SU P2]〉 is mainly ascribed to the slow energy fluctuation in the dissociation mode. It is concluded that the asymmetry of the ν[SUB3] Raman band is due to the scattering by molecular pairs excited in the dissociation mode. [ABSTRACT FROM AUTHOR]

We have studied the dynamical properties of doubly and singly occupied structure II N[SUB2] clathrate hydrates by performing a series of classical molecular dynamics calculations. The intermolecular vibrational density of states of the guest molecules show the most explicit changes when going from single to double occupancies. Instead of the narrow peak for single occupancy (at 20 cm[SUP-1]), a broad range of frequencies occurs between 0 and 200 cm[SUP-1] with four modes, which have been assigned to the possible vibrations in the cage. This spectrum provides a unique fingerprint of double occupancy. For the host lattice, the libron band and the optic phonon branch show lower frequencies as compared to single fillings. In contrast, the acoustic phonon branch shifts to lower frequencies for a single filling of the large cases. We find that there is a large vibrational guest-host coupling for both single and double occupancies, although the frequency range is broader in the latter case. There is a significant translational diffusion of the N[SUB2] molecules in the doubly occupied cages. Occasionally both molecules simultaneously migrate from one local energy minimum to another. An orientational order of the N[SUB2] molecules occurs only within the small cages. However, the relative orientation of the two molecules in the doubly occupied cages is preserved in time. [ABSTRACT FROM AUTHOR]

We report experiments on the formation of wave packets consisting of coherently excited ground electronic state rotational levels of I[sub 2], using excitation with an intense nonresonant picosecond laser. As measured in a velocity-map-imaging experiment using Coulomb explosion for the determination of the angular distribution of the molecules, these wave packets display alignment of the internuclear axis along the laser polarization axis, both during the laser interaction and at well-defined time delays following the laser interaction, which correspond to rotational revival times of the molecule. The alignment is studied as a function of the intensity and the pulse duration of the pump laser, the rotational temperature of the molecular beam, the polarization geometry of the pump and probe lasers, and the fragment-ion-charge state used to probe the alignment. We observe experimentally that the alignment at revival times is maximal for intermediate pulse durations of a few picoseconds, where the laser–molecule interaction is neither diabatic nor adiabatic. The alignment increases with intensity, but reaches saturation once the intensity is raised sufficiently high. At this point the degree of alignment is limited by the initial rotational temperature of the molecular beam. Our conclusions are corroborated by model calculations, which are presented in detail in the following paper. © 2002 American Institute of Physics. [ABSTRACT FROM AUTHOR]

As complex as it may seem, a two-dimensional (fifth-order) nonresonant Raman spectrum may provide one of the simplest ways to get at the character of intermolecular dynamics in liquids. Its status as an echo spectroscopy means that it should not only permit us to survey the intermolecular vibrations, it should allow us to ascertain the extent of their coherence. Arriving at a microscopic interpretation of those spectra, however, poses some genuine theoretical challenges. We describe here the first complete molecular dynamics simulation of such a spectrum. By using classical dynamics and focusing on liquid Xe, we find that we are able to produce a spectrum strikingly similar to the experimentally reported (nonmagic-angle) spectra of liquid CS[sub 2]. We observe, in particular, that there is no discernable echo, suggesting that the dynamics is strongly homogeneously broadened. We turn, in a companion paper, to the implications of these results for instantaneousnormal-mode models of liquids. [ABSTRACT FROM AUTHOR]

This paper, the first of a series of papers, examines equilibrium properties of N[sub 2]O[sub 4]⇋NO[sub 2] in liquid state by classical molecular dynamics simulations of liquid NO[sub 2]. An ab initio MO calculation has been carried out to elucidate NO[sub 2]–NO[sub 2] potential, and an orientation-sensitive pairwise potential (OSPP), which can reproduce highly anisotropic character of covalent bonding between N–N, has been formulated. The OSPP potential is parameterized by the well depth D[sub e] and by two anisotropy factors: A[sub θ] (0≤A[sub θ]≤1) the anisotropy factor for the rocking angle between NN bond and ONO direction, and A[sub τ] (0≤A[sub τ]≤1) for torsional angle of the two NO[sub 2] about NN bond. The reactive liquid N[sub 2]O[sub 4] is modeled as liquid NO[sub 2] which interacts with the OSPP potential between N–N atoms and Lennard-Jones potentials between N–O and O–O atoms. Equilibrium properties were found to be very sensitive to the well depth D[sub e] and anisotropy factors of OSPP. The population of more than the NO[sub 2] dimer (3-mer, 4-mer,...) is considerable when anisotropy factors of the NN bond are small. On the other hand, the equilibrium liquid N[sub 2]O[sub 4]⇋2NO[sub 2] is formed, that is, most NO[sub 2] form monomer or dimer and the population of more than 3-mer is very small when A[sub θ]+A[sub τ]>=0.4–0.5. In simulated liquid NO[sub 2]/N[sub 2]O[sub 4], concentration of N[sub 2]O[sub 4] is found to increase as D[sub e] increases, A[sub θ] increases, and A[sub τ] decreases. The equilibrium constant for the dissociation reaction has been derived by computing the potential of mean force as a function of the N–N distance r[sub c] (the reaction coordinate). The OSPP potential for D[sub e]=0.12×10[sup -18] J, A[sub θ]=0.5 and A[sub τ]=0.1 is found to reproduce the observed liquid phase equilibrium properties fairly wel... [ABSTRACT FROM AUTHOR]

Molecular dynamics simulations are used to calculate the surface tension γ and study the structural properties of the liquid–vapor interface of the simple molten salt KI. The focus of the present paper is the effect on the calculated surface tension of different terms in the interionic potential and of the way that long-ranged interactions are treated. Specifically, we analyze the dependence of γ on: (a) boundary conditions employed in the Ewald summations of Coulomb interactions; (b) truncation of dispersion interactions; (c) inclusion of polarization effects. Our results show that (a) the use of vacuum boundary conditions in the direction perpendicular to the interface helps to maintain the mechanical equilibrium of the interface; (b) an Ewald summation of dispersion interactions is necessary to avoid substantial truncation effects; (c) polarization tends to decrease γ by significant amounts, and improves the agreement with experiment. In all cases, a reduction of γ comes with a corresponding increase of the interfacial width. As a structural indicator, the tangential pair distribution functions at the interface are compared with those of the bulk liquid. © 2001 American Institute of Physics. [ABSTRACT FROM AUTHOR]

The fluctuation theorem gives an analytic expression for the probability, in a nonequilibrium system of finite size observed for a finite time, that the dissipative flux will flow in the reverse direction to that required by the second law of thermodynamics. In the present paper a local version of the fluctuation theorem (LFT) is derived heuristically. We find that in the case of planar Poiseuille flow of a Newtonian fluid between thermostated walls, nonequilibrium molecular dynamics simulation results support our proposed LFT. © 2001 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Expanding the set of stable, accurate, and scalable methods for simulating molecular quantum dynamics is important for accelerating the computational exploration of molecular processes. In this paper, we adapt the signed particles Monte Carlo algorithm for solving the transient Wigner equation to scenarios of chemical interest. This approach was used in the past to study electronic processes in semi-conductors, but to the best of our knowledge, it had never been applied to molecular modeling. We present the algorithm and demonstrate its excellent performance on harmonic and double well potentials for electronic and nuclear systems. We explore the stability of the algorithm, discuss the choice of hyper-parameters, and cautiously speculate that it may be used in quantum molecular dynamics simulations. [ABSTRACT FROM AUTHOR]

The function of an enzyme depends on its dynamic structure, and the catalytic mechanism has long been an active focus of research. The principle for interpreting protein selectivity and fidelity stems from optimization of the active site upon protein–substrate complexation, i.e., a lock-and-key configuration, on which most protein–substrate molecule binding recognition, and hence drug discovery, relies. Yet another thought has been to incorporate the protein folding interior tunnels for stereo- and regio-selectivity along the protein–substrate or protein–ligand/inhibitor binding process. Free energy calculations provide valuable information for molecular recognition and protein–ligand binding dynamics and kinetics. In this study, we focused on the kinetics of cytochrome P450 proteins (CYP450s) and the protein interior tunnel structure–dynamics relationship in terms of the substrate binding and leaving mechanism. A case in point is given by the prostaglandin H2 (PGH2) homologous isomerase of prostacyclin synthase. To calculate the reactant and product traversing the tunnels to and from the heme site, the free energy paths and tunnel potentials of mean force are constructed from steered molecular dynamics simulations and adaptive basing force umbrella sampling simulations. We explore the binding tunnels and critical residue lining characteristics for the ligand traverse and the underlying mechanism of CYP450 activity. Our theoretical analysis provides insights into the decisive role of the substrate tunnel binding process of the CYP450 mechanism and may be useful in drug design and protein engineering contexts. [ABSTRACT FROM AUTHOR]

This paper presents a model, which we have designed to get insight into the development of electro-induced instability of a thin toluene emulsion film in contact with the saline aqueous phase. Molecular dynamics (MD) simulations demonstrate the role of charge accumulation in the toluene-film rupture induced by a DC electric field. Two ensembles--NVT and NPT--are used to determine the critical value of the external field at which the film ruptures, the charge distribution and capacitance of the thin film, number densities, and the film structure. The rupture mechanism as seen from this model is the following: in both NVT and NPT ensembles, condenser plates, where the charge density is maximal, are situated at the very border between the bulk aqueous (water) phase and the mixed layer. No ion penetration is observed within the toluene core, thus leaving all the distribution of charges within the mixed zone and the bulk phase that could be attributed to the formation of hydration shells. When the critical electric field is reached within a certain time after the field application, electric discharge occurs indicating the beginning of the rupturing process. The MD simulations indicate that the NPT ensemble predicts a value of the critical field that is closer to the experimental finding. [ABSTRACT FROM AUTHOR]

It has been extensively demonstrated through first principles quantum mechanics calculations that water exhibits strong hydrogen bond cooperativity. Equations of state developed from statistical mechanics typically assume pairwise additivity, meaning they cannot account for these 3-body and higher cooperative effects. In this paper, we extend a second order thermodynamic perturbation theory to correct for hydrogen bond cooperativity in 4 site water. We demonstrate that the theory predicts hydrogen bonding structure consistent spectroscopy, neutron diffraction, and molecular simulation data. Finally, we implement the approach into a general equation of state for water. [ABSTRACT FROM AUTHOR]

Linear response approximations are central to our understanding and simulations of nonequilibrium statistical mechanics. Despite the success of these approaches in predicting nonequilibrium dynamics, open questions remain. Laird and Thompson [J. Chem. Phys. 126, 211104 (2007)] previously formalized, in the context of solvation dynamics, the connection between the static linear-response approximation and the assumption of Gaussian statistics. The Gaussian statistics perspective is useful in understanding why linear response approximations are still accurate for perturbations much larger than thermal energies. In this paper, we use this approach to address three outstanding issues in the context of the "dipole-flip" model, which is known to exhibit nonlinear response. First, we demonstrate how non-Gaussian statistics can be predicted from purely equilibrium molecular dynamics (MD) simulations (i.e., without resort to a full nonequilibrium MD as is the current practice). Second, we show that the Gaussian statistics approximation may also be used to identify the physical origins of nonlinear response residing in a small number of coordinates. Third, we explore an approach for correcting the Gaussian statistics approximation for nonlinear response effects using the same equilibrium simulation. The results are discussed in the context of several other examples of nonlinear responses throughout the literature. [ABSTRACT FROM AUTHOR]

Recent machine learning methods make it possible to model potential energy of atomic configurations with chemical-level accuracy (as calculated from ab initio calculations) and at speeds suitable for molecular dynamics simulation. Best performance is achieved when the known physical constraints are encoded in the machine learning models. For example, the atomic energy is invariant under global translations and rotations; it is also invariant to permutations of same-species atoms. Although simple to state, these symmetries are complicated to encode into machine learning algorithms. In this paper, we present a machine learning approach based on graph theory that naturally incorporates translation, rotation, and permutation symmetries. Specifically, we use a random walk graph kernel to measure the similarity of two adjacency matrices, each of which represents a local atomic environment. This Graph Approximated Energy (GRAPE) approach is flexible and admits many possible extensions. We benchmark a simple version of GRAPE by predicting atomization energies on a standard dataset of organic molecules. [ABSTRACT FROM AUTHOR]

Despite the innumerous papers regarding the study of the ionic liquids as a potential candidate for CO2 capture, many details concerning the structure and dynamics of CO2 in the system are still to be revealed, i.e., the correlation between the local environment structure and the dynamic properties of the substance. This present work relied on the performance of molecular dynamics both for the neat [C2mim][Tf2N] and [C2mim][Tf2N]/CO2 mixtures in an attempt to elucidate the local environment of CO2 and their effects on the dynamic properties of [C2mim][Tf2N]. A slight change in the orientation of the cation and anion could be observed, which was correlated to the cation and anion moving away from each other in order to receive the carbon dioxide. The gas molecules pushed both the cation and the anion away to create sufficient void to its accommodation. The diffusion coefficient of [C2mim]+ is higher than [Tf2N]- regardless the increase of the CO2 concentration. The addition of CO2 in the ionic liquid has shown an increase of 4-5 times for the diffusivity of ions, which was related to the decrease of cation-anion interaction strength. The transport properties' results showed that the addition of CO2 in the ionic liquid generates the fluidization of the system, decreasing the viscosity as a consequence of the local environment structure changing. Likewise, the effect of the type of anion and cation on the system properties was studied considering [Ac]- and [BMpyr]+ ions, showing large effects by the change of anion to [Ac]- which rise from the strong [C2mim]+-[Ac]- interaction, which conditions the solvation of ions by CO2 molecules. [ABSTRACT FROM AUTHOR]

Peptides are versatile molecules with applications spanning from biotechnology to nanomedicine. They exhibit a good capability to unbundle carbon nanotubes (CNT) by improving their solubility in water. Furthermore, they are a powerful drug delivery system since they can easily be uptaken by living cells, and their high surface-to-volume ratio facilitates the adsorption of molecules of different natures. Therefore, understanding the interaction mechanism between peptides and CNT is important for designing novel therapeutical agents. In this paper, the mechanisms of the adsorption of antimicrobial peptide Cecropin A-Magainin 2 (CA-MA) on a graphene nanosheet (GNS) and on an ultra-short single-walled CNT are characterized using molecular dynamics simulations. The results show that the peptide coats both GNS and CNT surfaces through preferential contacts with aromatic side chains. The peptide packs compactly on the carbon surfaces where the polar and functionalizable Lys side chains protrude into the bulk solvent. It is shown that the adsorption is strongly correlated to the loss of the peptide helical structure. In the case of the CNT, the outer surface is significantly more accessible for adsorption. Nevertheless when the outer surface is already covered by other peptides, a spontaneous diffusion, via the amidated C-terminus into the interior of the CNT, was observed within 150 ns of simulation time. We found that this spontaneous insertion into the CNT interior can be controlled by the polarity of the entrance rim. For the positively charged CA-MA peptide studied, hydrogenated and fluorinated rims, respectively, hinder and promote the insertion. [ABSTRACT FROM AUTHOR]

The present paper reports the application of a computational framework, based on the quantum master equation, the Fermi's golden Rule, and conventional wavefunction-based methods, to describe electron transport through a spin crossover molecular junction (Fe(bapbpy) (NCS)2, 1, bapbpy = N- (6-(6-(Pyridin-2-ylamino)pyridin-2-yl)pyridin-2-yl)-pyridin-2-amine). This scheme is an alternative to the standard approaches based on the relative position and nature of the frontier orbitals, as it evaluates the junction's Green's function by means of accurate state energies and wavefunctions. In the present work, those elements are calculated for the relevant states of the high- and low-spin species of 1, and they are used to evaluate the output conductance within a given range of bias- and gate-voltages. The contribution of the ground and low-lying excited states to the current is analyzed, and inspected in terms of their 2S + 1 Ms-states. In doing so, it is shown the relevance of treating not only the ground state in its maximum-Ms projection, as usually done in most computationalchemistry packages, but the whole spectrum of low-energy states of the molecule. Such improved representation of the junction has a notable impact on the total conductivity and, more importantly, it restores the equivalence between alpha and beta transport, which means that no spin polarization is observed in the absence of Zeeman splitting. Finally, this work inspects the strong- and weak-points of the suggested theoretical framework to understand electron transport through molecular switchable materials, identifies a pathway for future improvement, and offers a new insight into concepts that play a key role in spintronics. [ABSTRACT FROM AUTHOR]

The solvation of carbon monoxide (CO) in liquid water is important for understanding its toxicological effects and biochemical roles. In this paper, we use ab initio molecular dynamics (AIMD) and CCSD(T)-F12 calculations to assess the accuracy of the Straub and Karplus molecular mechanical (MM) model for CO(aq). The CCSD(T)-F12 CO--H2O potential energy surfaces show that the most stable structure corresponds to water donating a hydrogen bond to the C center. The MMcalculated surface incorrectly predicts that the O atom is a stronger hydrogen bond acceptor than the C atom. The AIMD simulations indicate that CO is solvated like a hydrophobic solute, with very limited hydrogen bonding with water. The MM model tends to overestimate the degree of hydrogen bonding and overestimates the atomic radius of the C atom. The calculated Gibbs energy of hydration using the TIP3P water model is in good agreement with the experiment (9.3 kJ mol-1 expt. vs 10.7 kJ mol-1 calc.). The calculated diffusivity of CO (aq) in TIP3P-model water was 5.1×10-5 cm2/s calc., more than double the experimental value of 2.3 × 10-5 cm2/s. The hydration energy calculated using the TIP4P-FB water model is in poorer agreement with the experiment (ΔG = 6.8 kJ/mol) but the diffusivity is in better agreement (D = 2.5 ± 0.1 × 10-5 cm2/s). [ABSTRACT FROM AUTHOR]

The paper aims at a comparison of techniques based on the kinetic Monte Carlo (kMC) and the conventional Metropolis Monte Carlo (MC) methods as applied to the hard-sphere (HS) fluid and solid. In the case of the kMC, an alternative representation of the chemical potential is explored [E. A. Ustinov and D. D. Do, J. Colloid Interface Sci. 366, 216 (2012)], which does not require any external procedure like the Widom test particle insertion method. A direct evaluation of the chemical potential of the fluid and solid without thermodynamic integration is achieved by molecular simulation in an elongated box with an external potential imposed on the system in order to reduce the particle density in the vicinity of the box ends. The existence of rarefied zones allows one to determine the chemical potential of the crystalline phase and substantially increases its accuracy for the disordered dense phase in the central zone of the simulation box. This method is applicable to both the Metropolis MC and the kMC, but in the latter case, the chemical potential is determined with higher accuracy at the same conditions and the number of MC steps. Thermodynamic functions of the disordered fluid and crystalline face-centered cubic (FCC) phase for the hard-sphere system have been evaluated with the kinetic MC and the standard MC coupled with the Widom procedure over a wide range of density. The melting transition parameters have been determined by the point of intersection of the pressure-chemical potential curves for the disordered HS fluid and FCC crystal using the Gibbs-Duhem equation as a constraint. A detailed thermodynamic analysis of the hardsphere fluid has provided a rigorous verification of the approach, which can be extended to more complex systems. [ABSTRACT FROM AUTHOR]

Diffusion is one of the key subjects of molecular modeling and simulation studies. However, there is an unresolved lack of consistency between Einstein-Smoluchowski (E-S) and Green-Kubo (G-K) methods for diffusion coefficient calculations in systems of complex molecules. In this paper, we analyze this problem for the case of liquid n-triacontane. The non-conventional long-time tails of the velocity autocorrelation function (VACF) are found for this system. Temperature dependence of the VACF tail decay exponent is defined. The proper inclusion of the long-time tail contributions to the diffusion coefficient calculation results in the consistency between G-K and E-S methods. Having considered the major factors influencing the precision of the diffusion rate calculations in comparison with experimental data (system size effects and force field parameters), we point to hydrogen nuclear quantum effects as, presumably, the last obstacle to fully consistent n-alkane description. [ABSTRACT FROM AUTHOR]

Dynamics is essential to the biological functions of many bio-molecules, yet our knowledge of dynamics remains fragmented. Experimental techniques for studying bio-molecules either provide high resolution information on static conformations of the molecule or provide low-resolution, ensemble information that does not shed light on single molecule dynamics. In parallel, bio-molecular dynamics occur at time scale that are not yet attainable through detailed simulation methods. These limitations are especially noticeable when studying transition paths. To address this issue, we report in this paper two methods that derive meaningful trajectories for proteins between two of their conformations. The first method, MinActionPath, uses approximations of the potential energy surface for the molecule to derive an analytical solution of the equations of motion related to the concept of minimum action path. The second method, RelaxPath, follows the same principle of minimum action path but implements a more sophisticated potential, including a mixed elastic potential and a collision term to alleviate steric clashes. Using this new potential, the equations of motion cannot be solved analytically. We have introduced a relaxation method for solving those equations. We describe both the theories behind the two methods and their implementations, focusing on the specific techniques we have used that make those implementations amenable to study large molecular systems. We have illustrated the performance of RelaxPath on simple 2D systems. We have also compared MinActionPath and RelaxPath to other methods for generating transition paths on a well suited test set of large proteins, for which the end points of the trajectories as well as an intermediate conformation between those end points are known. We have shown that RelaxPath outperforms those other methods, including MinActionPath, in its ability to generate trajectories that get close to the known intermediates. We have also shown that the structures along the RelaxPath trajectories remain protein-like. Open source versions of the two programs MinActionPath and RelaxPath are available by request. [ABSTRACT FROM AUTHOR]

Previous work has shown how a symmetrical quasi-classical (SQC) windowing procedure can be used to quantize the initial and final electronic degrees of freedom in the Meyer-Miller (MM) classical vibronic (i.e, nuclear + electronic) Hamiltonian, and that the approach provides a very good description of electronically non-adiabatic processes within a standard classical molecular dynamics framework for a number of benchmark problems. This paper explores application of the SQC/MM approach to the case of very weak non-adiabatic coupling between the electronic states, showing (as anticipated) how the standard SQC/MM approach used to date fails in this limit, and then devises a new SQC windowing scheme to deal with it. Application of this new SQC model to a variety of realistic benchmark systems shows that the new model not only treats the weak coupling case extremely well, but it is also seen to describe the "normal" regime (of electronic transition probabilities ≳ 0.1) even more accurately than the previous "standard" model. [ABSTRACT FROM AUTHOR]

This paper deals with the critical issue of approximating the pre-exponential factor in semiclassical molecular dynamics. The pre-exponential factor is important because it accounts for the quantum contribution to the semiclassical propagator of the classical Feynman path fluctuations. Pre-exponential factor approximations are necessary when chaotic or complex systems are simulated. We introduced pre-exponential factor approximations based either on analytical considerations or numerical regularization. The approximations are tested for power spectrum calculations of more and more chaotic model systems and on several molecules, for which exact quantum mechanical values are available. The results show that the pre-exponential factor approximations introduced are accurate enough to be safely employed for semiclassical simulations of complex systems. [ABSTRACT FROM AUTHOR]

Strong-field ionization and the resulting electronic dynamics are important for a range of processes such as high harmonic generation, photodamage, charge resonance enhanced ionization, and ionization-triggered charge migration. Modeling ionization dynamics in molecular systems from first-principles can be challenging due to the large spatial extent of the wavefunction which stresses the accuracy of basis sets, and the intense fields which require non-perturbative time-dependent electronic structure methods. In this paper, we develop a time-dependent density functional theory approach which uses a Gaussian-type orbital (GTO) basis set to capture strong-field ionization rates and dynamics in atoms and small molecules. This involves propagating the electronic density matrix in time with a time-dependent laser potential and a spatial non-Hermitian complex absorbing potential which is projected onto an atom-centered basis set to remove ionized charge from the simulation. For the density functional theory (DFT) functional we use a tuned range-separated functional LC-PBE*, which has the correct asymptotic 1/r form of the potential and a reduced delocalization error compared to traditional DFT functionals. Ionization rates are computed for hydrogen, molecular nitrogen, and iodoacetylene under various field frequencies, intensities, and polarizations (angle-dependent ionization), and the results are shown to quantitatively agree with time-dependent Schrödinger equation and strong-field approximation calculations. This tuned DFT with GTO method opens the door to predictive all-electron time-dependent density functional theory simulations of ionization and ionization-triggered dynamics in molecular systems using tuned rangeseparated hybrid functionals. [ABSTRACT FROM AUTHOR]

In the present study, variational path integral molecular dynamics and associated hybrid Monte Carlo (HMC) methods have been developed on the basis of a fourth order approximation of a density operator. To reveal various parameter dependence of physical quantities, we analytically solve one dimensional harmonic oscillators by the variational path integral; as a byproduct, we obtain the analytical expression of the discretized density matrix using the fourth order approximation for the oscillators. Then, we apply our methods to realistic systems like a water molecule and a para-hydrogen cluster. In the HMC, we adopt two level description to avoid the time consuming Hessian evaluation. For the systems examined in this paper, the HMC method is found to be about three times more efficient than the molecular dynamics method if appropriate HMC parameters are adopted; the advantage of the HMC method is suggested to be more evident for systems described by many body interaction. [ABSTRACT FROM AUTHOR]

In this paper, we present a new canonical replica exchange molecular dynamics (REMD) simulation method with normal pressure for all replicas (REMD-NV(p)T). This method is suitable for systems for which conventional constant NPT-setups are difficult to implement. In this implementation, each replica has an individual volume, with normal pressure maintained for each replica in the simulation. We derive a novel exchange term and validate this method on the structural properties of SPC/E water and dialanine (Ala2) in the bulk and in the presence of a graphene layer. Compared to conventional constant NPT-REMD and NVT-REMD simulations, we find that the structural properties of our new method are in good agreement with simulations in the NPT-ensemble at all temperatures. The structural properties of the systems considered are affected by high pressures at elevated temperatures in the constant NVT-ensemble, an effect that our method corrects for. Unprojected distributions reveal that essential motions of the peptide are affected by the presence of the barostat in the NPT implementation but that the dynamical eigenmodes of the NV(p)T method are in close quantitative agreement with the NVT-ensemble. [ABSTRACT FROM AUTHOR]

Postcollision multifragmentation which we have recently observed experimentally in C-60-surface impact is the phenomenon of a delayed multiparticle breakup of a highly collisionally vibrationally excited large molecule/cluster (the precursor species) into several polyatomic fragments, after leaving the surface. In this paper, we show that the molecular dynamics simulations of near-grazing C60 collisions with a gold surface at 300 eV impact energy (very similar to the experimental conditions) successfully reproduce the experimentally observed characteristics of the postcollision multifragmentation process. The calculated mass resolved kinetic energy distributions and the time dependent yield curves of the Cn fragments revealed a precursor mediated, velocity correlated, delayed fragmentation event along the outgoing trajectory, far away from the surface. Most of the large fragments (n = 5) are formed within a time window of 2-20 ps after leaving the surface, corresponding to the vertical distances of 3-30 nm from the surface. Analysis of delay times and actual time duration for multifragmentation reveal that a large part can be described as simultaneous postcollision (delayed) multifragmentation events. The delayed nature of the event seems to be due to an early sequence of structural transformations of the precursor. [ABSTRACT FROM AUTHOR]

Recent simulations have improved our knowledge of the molecular-level structure and hydration properties of mixed self-assembled monolayers (SAMs) with equal and unequal alkyl thiols at three different arrangements, namely, random, patchy, and Janus. In our previous work [V. Vasumathi et al., J. Phys. Chem. C 119, 3199-3209 (2015)], we showed that the bending of longer thiols over shorter ones clearly depends on the thiols' arrangements and chemical nature of their terminal groups. In addition, such a thiol bending revealed to have a strong impact on the structural and hydration properties of SAMs coated on gold nanoparticles (AuNPs). In this paper, we extend our previous atomistic simulation study to investigate the bending of longer thiols by increasing the stripe thickness of mixed SAMs of equal and unequal lengths coated on AuNPs. We study also the effect of stripe thickness on the structural morphology and hydration of the coated SAMs. Our results show that the structural and hydration properties of SAMs are affected by the stripe thickness for mixtures of alkyl thiols with unequal chain length but not for equal length. Hence, the stability of the stripe configuration depends on the alkyl's chain length, the length difference between the thiol mixtures, and solvent properties. [ABSTRACT FROM AUTHOR]

The extent to which solvent-mediated effective interactions between nanoparticles can be predicted based on structure and associated thermodynamic estimators for bulk solvents and for solvation of single and pairs of nanoparticles is studied here. As a test of the approach, we analyse the strategy for creating temperature-independent solvent environments using a series of homologous chain fluids as solvents, as suggested by an experimental paper [M. I. Bodnarchuk et al., J. Am. Chem. Soc. 132, 11967 (2010)]. Our conclusions are based on molecular dynamics simulations of Au140(SC10H21)62 nanoparticles in n-alkane solvents, specifically hexane, octane, decane and dodecane, using the TraPPE-UA potential to model the alkanes and alkylthiols. The 140-atom gold core of the nanocrystal is held rigid in a truncated octahedral geometry and the gold-thiolate interaction is modeled using a Morse potential. The experimental observation was that the structural and rheological properties of n-alkane solvents are constant over a temperature range determined by equivalent solvent vapour pressures. We show that this is a consequence of the fact that long chain alkane liquids behave to a good approximation as simple liquids formed by packing of monomeric methyl/methylene units. Over the corresponding temperature range (233-361 K), the solvation environment is approximately constant at the single and pair nanoparticle levels under good solvent conditions. However, quantitative variations of the order of 10%-20% do exist in various quantities, such as molar volume of solute at infinite dilution, entropy of solvation, and onset distance for soft repulsions. In the opposite limit of a poor solvent, represented by vacuum in this study, the effective interactions between nanoparticles are no longer temperature-independent with attractive interactions increasing by up to 50% on decreasing the temperature from 361 K to 290 K, accompanied by an increase in emergent anisotropy due to correlation of mass dipoles on the two nanoparticles. One expects therefore that during self-assembly using solvent evaporation, temperature can be used as a structure-directing factor as long as good solvent conditions are maintained. It also suggests that disordered configurations may emerge as solvent quality decreases due to increasing role of short-range attractions and ligand fluctuation-driven anisotropy. The possibilities of using structural estimators of various thermodynamic quantities to analyse the interplay of ligand fluctuations and solvent quality in self-assembly as well as to design solvation environments are discussed. [ABSTRACT FROM AUTHOR]

In this paper, we investigate the hydrodynamic permeance of water through graphene-based membranes, inspired by recent experimental findings on graphene-oxide membranes. We consider the flow across multiple graphene layers having nanoslits in a staggered alignment, with an inter-layer distance ranging from sub-nanometer to a few nanometers. We compare results for the permeability obtained by means of molecular dynamics simulations to continuum predictions obtained by using the lattice Boltzmann calculations and hydrodynamic modelization. This highlights that, in spite of extreme confinement, the permeability across the graphene-based membrane is quantitatively predicted on the basis of a continuum expression, taking properly into account entrance and slippage effects of the confined water flow. Our predictions refute the breakdown of hydrodynamics at small scales in these membrane systems. They constitute a benchmark to which we compare published experimental data. [ABSTRACT FROM AUTHOR]

In a recent paper by Ngai and Capaccioli ['Unified explanation of the anomalous dynamic properties of highly asymmetric polymer blends,' J. Chem. Phys. 138, 054903 (2013)] the authors claimed that the so-called coupling model (CM) provides a unified explanation of all dynamical anomalies that have been reported for dynamically asymmetric blends over last ten years. Approximately half of the paper is devoted to chain-dynamic properties involving un-entangled polymers. According to the authors, the application of the CM to these results is based on the existence of a crossover at a time tc ≈ 1-2 ns of the magnitudes describing chain-dynamics. Ngai and Capaccioli claimed that the existence of such a crossover is supported by the neutron scattering and MD-simulation results, corresponding to the blend poly(methyl methacrylate)/poly(ethylene oxide), by Niedzwiedz et al. [Phys. Rev. Lett. 98, 168301 (2007)] and Brodeck et al. [Macromolecules 43, 3036 (2010)], respectively. Being one of the authors of these two papers, I will demonstrate here that there is no evidence supporting such a crossover in the data reported in these papers. [ABSTRACT FROM AUTHOR]

Presents methods to approximately evolve path integral centroid variables in real time. Characterization of approximations involved in the centroid molecular dynamics method by mathematical derivations; Methods tested for the equilibrium position correlation functions of three differential one-dimensional nondissipative model systems.

Takaba I et al. i propose an edge expansion parallel cascade selection MD (eePaCS-MD) to investigate the large-amplitude motions of proteins without prior knowledge of the conformational transitions.[30] eePaCS-MD belongs to the class of adaptive enhanced sampling methods that rely on iteratively initiating independent unbiased MD simulations from structures selected from previous runs according to specific rules. Grünewald I et al. i describe a titratable Martini model for constant pH MD simulations,[43] and Michael I et al. i describe a hybrid MC-MD for handling random amino acid mutations and substitutions in protein design - the latter being also handled to treat protonation events.[44] Quantitative determination of free energies in complex systems continues to be important. This issue of JCP highlights both developments in and applications of classical molecular simulation in 67 articles. FORCE FIELD DEVELOPMENT Force field development remains an important subject within the molecular simulation community. [Extracted from the article]

The formulation of quantum statistical mechanics based on the path centroid variable in Feynman path integration is generalized to a phase space perspective, thereby including the momentum as an independent dynamical variable. By virtue of this approach, operator averages and imaginary time correlation functions can be expressed in terms of an averaging over the multidimensional phase space centroid density. The imaginary time centroid-constrained correlation function matrix for the phase space variables is then found to define the effective thermal width of the phase space centroid variable. These developments also make it possible to rigorously analyze the centroid molecular dynamics method for computing quantum dynamical time correlation functions. As a result, the centroid time correlation function as calculated from centroid molecular dynamics is shown to be a well-defined approximation to the exact Kubo transformed position correlation function. This analysis thereby clarifies the underlying role of the equilibrium path centroid variable in the quantum dynamical position correlation function and provides a sound theoretical basis for the centroid molecular dynamics method. [ABSTRACT FROM AUTHOR]

We present nonequilibrium molecular dynamics simulations of pure argon at a temperature of 135 K and density of 1.034 gm/cc using the highly accurate Barker–Fisher–Watts (BFW) model for the intermolecular potential. We consider the BFW potential both with and without the Axilrod–Teller three-body interaction. We find that the three-body potential has a very small effect on the shear viscosity: The predicted value in the presence of three-body forces is 3% less than that obtained without three-body forces. [ABSTRACT FROM AUTHOR]