Bubble point pressure estimates from Gibbs ensemble simulations

Bubble pressure points of ethanol–1,1,1,2,3,3,3-heptafluoropropane (HFC-227ea refrigerant) mixtures from the third Industrial Fluid Properties Simulation Challenge are computed using publicly available molecular simulation software. Several published force fields are compared against the known answers provided in the contest guidelines and the best force fields are used to make predictions for the unknown results.     

A complementary thermodynamic limit for classical Coulomb matter

The canonical equilibrium measure of classical two-component Coulomb matter with regularized interactions is analyzed in a finite volume. It is shown that, in the mean-field regime, the one-particle density is inhomogeneous on a new characteristic length scale _inh. For a system ofN positive andN negative particles, _inh and the characteristic length scale of correlations _corr (=Debye screening length) are related via _inh=(2N)^1/2 _corr. The major conceptual conclusion that is drawn from this is that one needs two nontrivial complementary thermodynamic limits to define the equilibrium thermodynamics of two-component Coulomb systems. One of them is the standard thermodynamic limit (infinite volume), where one takesN, _corr fixed. Its complementary limit is characterized byN, _inh fixed, and is a finite-volume inhomogeneous mean-field limit. The most prominent new feature in the mean-field thermodynamic limit, which is absent in the standard thermodynamic limit, is an anomalous first-order phase transition where the Coulomb system explodes or implodes, respectively. The phase transition is connected with the existence of a metastable plasma phase far below the ionization temperature.     

Surface properties of finite classical Coulomb systems: Debye-Hückel approximation and computer simulations

We report analytical and numerical studies of surface correlations in finite, homogeneously polarizable, classical Coulomb systems placed in an insulating or conducting environment. Their purpose is to understand the phenomenological, shape-dependent laws of electrostatics, from the point of view of statistical mechanics; we focus on the knowledge of the dielectric susceptibility of the system, a quantity proportional to the equilibrium fluctuation of the system's instantaneous polarization per unit volume. This goal has been achieved for a system in a conducting state. The picture is that the shape-dependent part of the susceptibilities results from the action of unbounded observables (the second moments of the instantaneous polarization of the system) on long-range surface correlations and that the relations of electrostatics are verified by means of shape-dependent thermodynamic limits. This picture is supported (i) by exact solutions and asymptotic analysis of the Debye-Hückel approximation of multicomponent plasmas in disks and spheres with insulating and conducting environment and also in ellipses in a vacuum, and (ii) by computer simulations of a one-component plasma in a disk with different environments, notably a conducting environment with permeable and impermeable wall. These observations have revealed for the first time the reason why the susceptibility of a conducting disk in a conductor with impermeable walls diverges linearly with the radius of the disk: this is due to the occurrence of long-range radial correlations in the conductor. These findings are quantitatively interpreted in terms of a novel canonical Debye-Huckel approximation as contrasted to the ordinary grand canonical version. Lastly a fresh look at the problem of the surface correlations of a conductor in a vacuum, which places the observer close to the surface of the conductor but in the vacuum, is presented and applied to the disk, the ellipse, the cylinder, the sphere, and the wedge.     

Computation of density of perfluoroalkyl methacrylates: a molecular modeling approach

Molecular dynamics simulations have been carried out on different perfluoroalkyl methacrylates to predict their densities. Density calculations on selected perfluoroalkyl methacrylates have been performed using molecular dynamics in the NPT ensemble by employing COMPASS force field. The calculated density values compared quite well with the experimental data reported in the literature.     

Quantitative weight of evidence method for combining predictions of quantitative structure-activity relationship models

ABSTRACT

A method for combining statistical-based QSAR predictions of two or more binary classification models is presented. It was assumed that all models were independent. This facilitated the combination of positive and negative predictions using a quantitative weight of evidence (qWoE) procedure based on Bayesian statistics and the additivity of the logarithms of the likelihood ratios. Previous studies combined more than one prediction but used arbitrary strengths for positive and negative predictions. In our approach, the combined models were validated by determining the sensitivity and specificity values, which are performance metrics that are a point of departure for obtaining values that measure the weight of evidence of positive and negative predictions. The developed method was experimentally applied in the prediction of Ames mutagenicity. The method achieved a similar accuracy to that of the experimental Ames test for this endpoint when the overall prediction was determined using a combination of the individual predictions of more than one model. Calculating the qWoE value would reduce the requirement for expert knowledge and decrease the subjectivity of the prediction. This method could be applied to other endpoints such as developmental toxicity and skin sensitisation with binary classification models.     

The configurational dependence of binding free energies: A Poisson–Boltzmann study of Neuraminidase inhibitors

The linear finite difference Poisson-Boltzmann (FDPB) equation is applied to the calculation of the electrostatic binding free energies of a group of inhibitors to the Neuraminidase enzyme. An ensemble of enzyme-inhibitor complex conformations was generated using Monte Carlo simulations and the electrostatic binding free energies of subtly different configurations of the enzyme-inhibitor complexes were calculated. It was seen that the binding free energies calculated using FDPB depend strongly on the configuration of the complex taken from the ensemble. This configurational dependence was investigated in detail in the electrostatic hydration free energies of the inhibitors. Differences in hydration energies of up to 7 kcal mol^–1 were obtained for root mean square (RMS) structural deviations of only 0.5 Å. To verify the result, the grid size and parameter dependence of the calculated hydration free energies were systematically investigated. This showed that the absolute hydration free energies calculated using the FDPB equation were very sensitive to the values of key parameters, but that the configurational dependence of the free energies was independent of the parameters chosen. Thus just as molecular mechanics energies are very sensitive to configuration, and single-structure values are not typically used to score binding free energies, single FDPB energies should be treated with the same caution.     

Fractional occupation numbers and spin density functional calculations of degenerate systems

We implemented ab initio self‐consistent field (SCF) fractional occupation numbers (FON) calculation with Dunlap's interpolation scheme for the twisted ethylene, which is a prototype molecule of a σ–π biradical system. The calculational results are compared with those of complete‐active‐space (CAS) SCF and spin‐unrestricted Kohn–Sham (UKS) calculations on potential surfaces, occupation numbers of natural orbitals, and correlation entropies. It was found that the UKS methods gave similar results to CASSCF, while the FON solutions appeared in only the nearly complete degenerate region. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem 93: 317–323, 2003     

Rigid-body dynamics in the isothermal-isobaric ensemble: a test on the accuracy and computational efficiency

We have developed a time-reversible rigid-body (rRB) molecular dynamics algorithm in the isothermal-isobaric (NPT) ensemble. The algorithm is an extension of rigid-body dynamics [Matubayasi and Nakahara, J Chem Phys 1999, 110, 3291] to the NPT ensemble on the basis of non-Hamiltonian statistical mechanics [Martyna, G. J. et al., J Chem Phys 1994, 101, 4177]. A series of MD simulations of water as well as fully hydrated lipid bilayer systems have been undertaken to investigate the accuracy and efficiency of the algorithm. The rRB algorithm was shown to be superior to the state-of-the-art constraint-dynamics algorithm SHAKE/RATTLE/ROLL, with respect to computational efficiency. However, it was revealed that both algorithms produced accurate trajectories of molecules in the NPT as well as NVT ensembles, as long as a reasonably short time step was used. A couple of multiple time-step (MTS) integration schemes were also examined. The advantage of the rRB algorithm for computational efficiency increased when the MD simulation was carried out using MTS on parallel processing computer systems; total computer time for MTS-MD of a lipid bilayer using 64 processors was reduced by about 40% using rRB instead of SHAKE/RATTLE/ROLL.     

苯与丙烯在β分子筛上吸附行为的蒙特卡罗研究

采用巨正则统计系综蒙特卡罗模拟方法研究了β分子筛上苯与丙烯分子的吸附行为. 由分子筛内吸附质粒子云分布可知, 在100 kPa时, 丙烯在分子筛上的吸附量要远远大于苯的吸附量. 由吸附相互作用能分布来看, 苯与分子筛之间相互作用能比丙烯与分子筛之间的相互作用能更负, 这就使苯分子的吸附相对于丙烯分子稳定. 相对而言, 温度变化对丙烯吸附影响远大于对苯吸附的影响, 如100 kPa时, 温度由298 K升高至443 K导致丙烯分子吸附量明显减少, 由每8个晶胞吸附98个丙烯分子减少到80个; 而对苯分子吸附却没有显著的影响. β分子筛上存在着苯和丙烯的竞争吸附, 并且吸附分子之间存在相互作用使两者与分子筛之间的相互作用能分布改变. 在压力范围1×10－3～5.0 kPa, 不同温度下苯与丙烯在分子筛内吸附等温线的模拟结果表明, 在较高温度、较低压力下丙烯的吸附量要小于苯的吸附量.