Interplay between time-temperature transformation and the liquid-liquid phase transition in water

We study the new water model proposed by Mahoney and Jorgensen [J. Chem. Phys. 112, 8910 (2000)], which is closer to real water than previously proposed classical pairwise additive potentials. We simulate the model in a wide range of deeply supercooled states and find (i) the existence of a nonmonotonic "nose-shaped" temperature of maximum density line and a nonreentrant spinodal, (ii) the presence of a low-temperature phase transition, (iii) the free evolution of bulk water to ice, and (iv) the time-temperature-transformation curves at different densities.     

Anomaly in the stability limit of liquid 3He

We propose that the liquid-gas spinodal line of 3He reaches a minimum at 0.4 K. This feature is supported by our cavitation measurements. We also show that it is consistent with extrapolations of sound-velocity measurements. Speedy [J. Phys. Chem. 86, 3002 (1982)] previously proposed this peculiar behavior for the spinodal of water and related it to a change in sign of the expansion coefficient alpha, i.e., a line of density maxima. 3He exhibits such a line at positive pressure. We consider its extrapolation to negative pressure. Our discussion raises fundamental questions about the sign of alpha in a Fermi liquid along its spinodal.     

First self-assembly study of large π-conjugated corrole dimers on solid substrates

Our study focus on β,β′-doubly linked corrole dimers (CDs) on mica and Au(1 1 1) surface using samples prepared by the synthetic method described by Osuka group appeared on recent publication [S. Hiroto, K. Furukawa, H. Shinokubo, A. Osuka, J. Am. Chem. Soc. 128 (2006) 12380]. Atomic force microscopy (AFM) and scanning tunneling microscopy (STM) were used to investigate the self-assembled structure of corrole dimers adsorbed on mica and Au(1 1 1) surfaces respectively at room temperature in air. The CDs adopt a dissimilar adsorption modality due to the different surface free energy of the different substrates. These types of molecular layers provide a useful platform for the study of surface and interface phenomena outside a vacuum system. It is potentially useful for practical fabrication of molecular devices because of the simplicity of the sample preparation and the stability of the interface in ambient conditions.     

A molecular dynamics study on the role of attractive and repulsive forces in excess heat capacity at constant volume of dense fluids

The curves of experimental heat capacity against density show a minimum around and below the critical temperature (Tc), but at higher temperatures, this minimum is not observed. In this study, the role of attractive and repulsive forces on excess heat capacity of Lennard–Jones (LJ) dense fluids has been investigated using a molecular dynamics simulation technique. LJ potential is divided into attractive and repulsive parts. From the molecular dynamics calculations, potential energy and heat capacities have been obtained for Argon at temperatures of 100–500?K. The repulsive forces play the main role in causing the heat capacities at temperatures greater than critical point. Around and below the critical temperature, the role of repulsion is dominant at high densities, but attraction has the main role at low densities, consequently at middle densities, a minimum is formed.     

Adsorption of molecular gases on porous materials in the SAFT-VR approximation

A simple molecular thermodynamic approach is applied to the study of the adsorption of gases of chain molecules on solid surfaces. We use a model based on the Statistical Associating Fluid Theory for Variable Range (SAFT-VR) potentials [A. Gil-Villegas, A. Galindo, P.J. Whitehead, S.J. Mills, G. Jackson, A.N. Burgess, J. Chem. Phys. 106 (1997) 4168] that we extend by including quasi-two-dimensional approximation to describe the adsorption properties of these types of real gas [A. Martínez, M. Castro, C. McCabe, A. Gil-Villegas, J. Chem. Phys. 126 (2007) 074707]. The model is applied to ethane, ethylene, propane, and carbon dioxide adsorbed on activated carbon and silica gel, which are porous media of significant industrial interest. We show that the adsorption isotherms obtained by means of the present SAFT-VR modeling are in fair agreement with the experimental results provided in the literature.     

Non-perturbative wave-packet calculations of time-resolved four-wave-mixing signals

We extend a method proposed by Seidner et al. [J. Chem. Phys. 103, 3998 (1995)] to extract directional terms from a time-dependent molecular polarization to obtain time-resolved four-wave-mixing (FWM) signals. Instead of employing perturbation theory, the total polarization induced in the molecular sample by the interaction with several femtosecond laser pulses is determined by solving the time-dependent Schr?dinger equation for the nuclear dynamics in coupled electronic states numerically exact. Repeating the calculation for several combinations of relative phases of the involved fields leads to a linear system of equations for the contributions emitted in different directions. Gas-phase I₂ molecules serve as a numerical example. Received: 22 September 1999 / Published online: 30 June 2000     

Stability and instability of a hot and dilute nuclear droplet

The diabatic approach to dissipative collective nuclear motion is reformulated in the local-density approximation in order to treat the normal modes of a spherical nuclear droplet analytically. In a first application the adiabatic isoscalar modes are studied and results for the eigenvalues of compressional (bulk) and pure surface modes are presented as function of density and temperature inside the droplet, as well as for different mass numbers and for soft and stiff equations of state. We find that the region of bulk instabilities (spinodal regime) is substantially smaller for nuclear droplets than for infinite nuclear matter. For small densities below 30% of normal nuclear matter density and for temperatures below 5 MeV all relevant bulk modes become unstable with similar growth rates. The surface modes have a larger spinodal region, reaching out to densities and temperatures way beyond the spinodal line for bulk instabilities. Essential experimental features of multifragmentation, like fragmentation temperatures and fragment-mass distributions (in particular the power-law behavior) are consistent with the instability properties of an expanding nuclear droplet, and hence with a dynamical fragmentation process within the spinodal regime of bulk and surface modes (spinodal decomposition). Received: 4 September 2000 / Accepted: 14 November 2000     

Improved endohedral fullerenelike structures of silicon clusters Si31–Si39 by density functional calculations

We extensively search for the endohedral silicon-fullerene structures of Si₃₁–Si₃₉ using the combination of a tight-binding potential with the density functional theory. The resulting structures of our best candidates characterize more compact features comparing to previous isomers [J. Am. Chem. Soc. 126, 13845 (2004); J. Chem. Phys. 124, 164311 (2006)]. Most of our best candidates belong to new families featuring different core/cage combinations or different original carbon fullerene cages with respect to those of previous isomers. Energy calculations reveal that our best candidates are more stable than the previous best ones at the PW91 level, except for n = 34 and 38. The predicted relative stabilities of these isomers remain even at finite temperatures. In addition, the densities of dangling-bond atoms in the surfaces of our Si₃₃ and Si₃₉ isomers are significantly lower than the previous best candidates, as well as lower than those of their neighbors. This finding together with the densities of the active sites in the surfaces of the previous best candidates of Si₃₄ and Si₃₈ is roughly consistent with the observed relative reactivities of the silicon clusters in the size range of n = 31-39.     

Cavity formation and the drying transition in the lennard-jones fluid

By simulation and theory, we study the probability of observing N molecular centers within molecular sized volumes for a Lennard-Jones fluid near liquid-vapor coexistence. For large volumes and small N, the probability distribution differs markedly from Gaussian. The free energy per unit surface area to form empty volumes (i.e., cavities) is a rapidly varying function of the radius for small cavities. It becomes constant for large volumes. The source of these behaviors is the occurrence of drying (i.e., solvent depletion) at the cavity surface. The crossover to drying occurs on microscopic length scales, with significant density depletion found for cavities with radii of the order of two or more Lennard-Jones diameters. Reasonable agreement is found between the simulation results and the theory developed by Lum, Chandler, and Weeks [J. Phys. Chem. B 103, 4570 (1999)].     

Liquid–vapour equilibrium of n -alkanes using interface simulations

Molecular Dynamics simulations were performed to calculate liquid–vapour coexisting properties of n-alkane chains up to 16 carbon atoms using interface simulations. The lattice sum or Ewald method on the dispersion forces of the Lennard–Jones potential was applied to calculate the full interaction. The liquid and vapour coexisting densities were obtained for two flexible force field models, NERD and TraPPE-UA, where the intermolecular interactions are of the Lennard–Jones type. We have recently shown [P. Orea, J. López-Lemus, and J. Alejandre, J. Chem. Phys. 123, 114702 (2005)] that the liquid–vapour densities for simple fluids do not depend on interfacial area and therefore it is possible to use a small number of molecules in a simulation. We show that the same trend is found on the simulation of these hydrocarbon molecules. The phase diagram of ethane/n-decane binary mixtures is also obtained at 410.95 K for the NERD model. The simulation results from this work were compared with those obtained using methods with interfaces using large cut-off distances and with methods without interfaces for the same potential model. In both comparisons, excellent agreement was found. The results of liquid density from the TraPPE-UA model are in good agreement with experimental data while those from the NERD model are underestimated at low temperatures. Our findings are consistent with results published by other authors for small hydrocarbons.     

Thermodynamics of high-pressure ice polymorphs: ices III and V

Thermodynamic properties of high-pressure ice polymorphs, ices III and V, are studied theoretically. The results of TIP4P molecular dynamics simulations in the NPT ensemble are used to calculate the temperature dependence of the specific volume of ices III and V at pressures 0.25 and 0.5 GPa, respectively. New P-V-T equations of state of ices III and V are derived using a method generalizing the one proposed by Fei et al. [J. Chem. Phys. 99 (1993) 5369], and new results concerning the equilibrium phase transitions ice III-water and ice V-water are presented.     

Peptide internal motions on nanosecond time scale derived from direct fitting of (13)C and (15)N NMR spectral density functions

NMR relaxation-derived spectral densities provide information on molecular and internal motions occurring on the picosecond to nanosecond time scales. Using (13)C and (15)N NMR relaxation parameters [T(1), T(2), and NOE] acquired at four Larmor frequencies (for (13)C: 62.5, 125, 150, and 200 MHz), spectral densities J(0), J(omega(C)), J(omega(H)), J(omega(H) + omega(C)), J(omega(H) - omega(C)), J(omega(N)), J(omega(H) + omega(N)), and J(omega(H) - omega(N)) were derived as a function of frequency for (15)NH, (13)C(alpha)H, and (13)C(beta)H(3) groups of an alanine residue in an alpha-helix-forming peptide. This extensive relaxation data set has allowed derivation of highly defined (13)C and (15)N spectral density maps. Using Monte Carlo minimization, these maps were fit to a spectral density function of three Lorentzian terms having six motional parameters: tau(0), tau(1), tau(2), c(0), c(1), and c(2), where tau(0), tau(1) and tau(2) are correlation times for overall tumbling and for slower and faster internal motions, and c(0), c(1), and c(2) are their weighting coefficients. Analysis of the high-frequency portion of these maps was particularly informative, especially when deriving motional parameters of the side-chain methyl group for which the order parameter is very small and overall tumbling motions do not dominate the spectral density function. Overall correlation times, tau(0), are found to be in nanosecond range, consistent with values determined using the Lipari-Szabo model-free approach. Internal motional correlation times range from picoseconds for methyl group rotation to nanoseconds for backbone N-H, C(alpha)-H, and C(alpha)-C(beta) bond motions. General application of this approach will allow greater insight into the internal motions in peptides and proteins.     

Metastable phase equilibria in a Lennard-Jones system

A method of molecular dynamics is used to calculate the pressure, internal energy, and isochoric heat capacity in a system of 2048 Lennard-Jones particles in the range of reduced temperatures from 0.1 to 2.0 and the range of densities from 0.001 to 1.15. Local equations of state for the gas, liquid, and crystalline phases are derived. The spinodals of a superheated (extended) liquid, supersaturated vapor, and superheated (extended) crystal are determined. It is shown that the spinodal of a supercooled liquid is nonexistent. An algorithm to calculate the lines of phase equilibria is constructed. The lines of liquid-gas, liquid-crystal, crystal-gas phase equilibria, and their metastable extensions are determined. It is shown that the metastable extensions of the melting and sublimation lines terminate at the spinodals of the liquid and crystal, respectively. The properties of final critical points in the lines of melting and sublimation are considered.     

可膨胀过热水系统多气核演化过程与临界过热度分析

使用分子动力学方法,研究过热水系统均质沸腾核化过程.采用Langevin 动力学方法控制体积可变系统的温度与压力,更好地模拟了沸腾实际物理过程.得到了液相系统体积连续膨胀、分子间距逐渐增大,最终稳定在汽相的现象学规律.当过热温度较高时,亚稳态液相系统可能在局部形成不同大小的近球形区域：气核,这些气核是不稳定的,处于不断演化之中.通过分析分子所受引力与斥力的共同作用,得到了气核形成与消亡以及多个气核融合的机理.比较了模拟结果与经典沸腾理论的差异,提出了气核生长是比气泡生长更为微观过程的认识.通过研究不同过热 关键词： 过热水系统 分子动力学 气核 临界过热度     

The role of higher-order terms in perturbation approaches to the monomer and bonding contributions in a SAFT-type equation of state for square-well chain fluids

A perturbation theory for square-well chain fluids is developed within the scheme of the (generalised) Wertheim thermodynamic perturbation theory. The theory is based on the Pavlyukhin parametrisations [Y. T. Pavlyukhin, J. Struct. Chem. 53, 476 (2012)] of their simulation data for the first four perturbation terms in the high temperature expansion of the Helmholtz free energy of square-well monomer fluids combined with a second-order perturbation theory for the contact value of the radial distribution function of the square-well monomer fluid that enters into bonding contribution. To obtain the latter perturbation terms, we have performed computer simulations in the hard-sphere reference system. The importance of the perturbation terms beyond the second-order one for the monomer fluid and of the approximations of different orders in the bonding contribution for the chain fluids in the predicted equation of state, excess energy and liquid–vapour coexistence densities is analysed.     

Estimation of ultrasound induced cavitation bubble temperatures in aqueous solutions

Mean acoustic cavitation bubble temperatures have been measured in a series of aqueous solutions containing C(1)-C(5) aliphatic alcohols, at 355 kHz. The method relies on the distribution of hydrocarbon product yields produced from the recombination of methyl radicals generated on the thermal decomposition of the alcohols. The mean bubble temperature was found to decrease with increasing concentration of alcohol with the effect being more pronounced the higher the molecular weight (the lower the vapour pressure) of the alcohol. It is shown that the decrease in the temperatures measured correlates very well with an increase in the surface excess of the alcohol, similar to that previously reported for the quenching of sonoluminescence in aqueous solutions containing alcohols [J. Phys. Chem. B 101 (1997) 10845; J. Phys. Chem. B 103 (1999) 9231]. The measured temperatures ranged from 4600+/-200 K at zero alcohol concentration to 2300+/-200 K at 0.5 M t-butanol. The validity of the method is discussed and it is concluded that even though a number of assumptions need to be applied the results appear to indicate that the method gives an accurate measure of the mean bubble temperature.     

The structure,dynamics and solvation mechanisms of ions in water from long time molecular dynamics simulations: a case study of CaCl2 (aq) aqueous solutions

Systematic long time (5–20 ns) molecular dynamics (MD) simulations have been carried out to study the structural and dynamical properties of CaCl₂ aqueous solutions over a wide range of concentrations (≤9.26 m) in this study. Our simulations reveal totally different structural characteristics of those yielded from short time (≤1 ns) MD simulations [A.A. Chialvo and J.M. Simonson, J. Chem. Phys. 119, 8052 (2003); T. Megyes, I. Bako, S. Balint, T. Grosz, and T. Radnai, J. Mol. Liq. 129, 63 (2006)]. An apparent discontinuity was found at 4–5 m of CaCl₂ in various properties including ion–water coordination number and self-diffusion coefficient of ions, which were first noticed by Phutela and Pitzer in their thermodynamic modelling [R.C. Phutela and K.S. Pitzer, J. Sol. Chem. 12, 201 (1983)]. In this study, residence time was first taken into consideration in the study of Ca²⁺–Cl^? ion pairing, and it was found that contact ion pair and solvent-sharing ion pair start to form at the CaCl₂(aq) concentrations of about 4.5 and 4 m, respectively, which may be responsible for the apparent discontinuity. In addition, the residence time of water molecules around Ca²⁺ or Cl^? showed that the hydration structures of Ca²⁺ and Cl^? are flexible with short residence time (<1 ns). It needs to be pointed out that it takes much longer simulation time for the CaCl₂–H₂O system to reach equilibrium than what was assumed in previous studies.     

Homogeneous nucleation and growth in iron-platinum vapour investigated by molecular dynamics simulation

Homogeneous nucleation and growth from binary metal vapour is investigated by molecular dynamics simulation. It is focused here mainly on the iron-platinum system with a mole fraction of 0.5. The simulations are started in the highly supersaturated vapour phase. Argon is added as carrier gas removing the heat of condensation from the forming clusters. The embedded atom method is employed for modelling of the force field of iron and platinum. The simulation runs are evaluated with respect to the nucleation rate, monomer temperature, monomer amount, and with respect to the size of the largest cluster in the system including possible pure metal clusters. It turns out that depending on the composition of the complete system pure platinum clusters with sizes up to 10 to 15 atoms are formed in addition to binary clusters. Due to the high temperature of these clusters iron atoms less likely condense at the beginning of the particle formation simulation. This leads to temporary difference in the temperatures of the platinum and the iron subsystems, which eventually approach each other when only binary clusters are present. In summary, the results obtained from the cluster statistics show that pure platinum nucleation and growth can take place to some extent within the binary system.     

Michaelis-Menten mechanism for single-enzyme and multi-enzyme system under stochastic noise and spatial diffusion

The investigation of enzymatic reaction under stochastic effect and spatial effect is an interesting problem. By virtue of Monte Carlo simulation, the stochastic dynamic of enzyme and the related Michaelis-Menten mechanism with stochastic internal noise and spatial diffusion are explored in this article. (i) For the single-enzyme system, two cases, including the fast phosphorylation case [X. S. Xie, et al., J. Phys. Chem. B 109 (2005) 19068] and slow phosphorylation case [X. S. Xie, et al., Nat. Chem. Biol. 2 (2006) 87] are considered. It is found the micro enzymatic velocity rate shows a rough hyperbolic dependence on the substrate concentration, hence obeys the Michaelis-Menten law qualitatively. In addition, our result reveals that diffusion rate can adjust the Michaelis-Menten curve; especially, it is shown that increasing diffusion rate enhances the micro enzyme rate. (ii) For the multi-enzyme system, a typical example, i.e., MAPK signaling pathway is used. We apply the Michaelis-Menten mechanism to the MAPK cascade and give a simple comparison for the signaling ability between the Michaelis-Menten mechanism and the single collision mechanism [J. W. Locasale et al., PLOS Comput. Biol. 4 (2008) e1000099].