A global investigation of phase equilibria using the perturbed-chain statistical-associating-fluid-theory approach

The recently developed perturbed-chain statistical-associating-fluid theory (PC-SAFT) is investigated for a wide range of model parameters including the parameter m representing the chain length and the thermodynamic temperature T and pressure p. This approach is based upon the first-order thermodynamic perturbation theory for chain molecules developed by Wertheim [M. S. Wertheim, J. Stat. Phys. 35, 19 (1984); ibid. 42, 459 (1986)] and Chapman et al. [G. Jackson, W. G. Chapman, and K. E. Gubbins, Mol. Phys. 65, 1 (1988); W. G. Chapman, G. Jackson, and K. E. Gubbins, ibid. 65, 1057 (1988)] and includes dispersion interactions via the second-order perturbation theory of Barker and Henderson [J. A. Barker and D. Henderson, J. Chem. Phys. 47, 4714 (1967)]. We systematically study a hierarchy of models which are based on the PC-SAFT approach using analytical model calculations and Monte Carlo simulations. For one-component systems we find that the analytical model in contrast with the simulation results exhibits two phase-separation regions in addition to the common gas-liquid coexistence region: One phase separation occurs at high density and low temperature. The second demixing takes place at low density and high temperature where usually the ideal-gas phase is expected in the phase diagram. These phenomena, which are referred to as "liquid-liquid" and "gas-gas" equilibria, give rise to multiple critical points in one-component systems, as well as to critical end points and equilibria of three fluid phases, which can usually be found in multicomponent mixtures only. Furthermore, it is shown that the liquid-liquid demixing in this model is not a consequence of a "softened" repulsive interaction as assumed in the theoretical derivation of the model. Experimental data for the melt density of polybutadiene with molecular mass Mw=45,000 gmol are correlated here using the PC-SAFT equation. It is shown that the discrepancies in modeling the polymer density at ambient temperature and high pressure can be traced back to the liquid-liquid phase separation predicted by the equation of state at low temperatures. This investigation provides a basis for understanding possible inaccuracies or even unexpected phase behavior which can occur in engineering applications of the PC-SAFT model aiming at predicting properties of macromolecular substances.     

Isotopic replacement in ionic systems: the 4He2+ + 3He-->3He 4He+ + 4He reaction

Full quantum dynamics calculations have been carried out for the ionic reaction (4)He(2) (+)+(3)He and state-to-state reactive probabilities have been obtained using both time-dependent and time-independent approaches. An accurate ab initio potential-energy surface has been employed for the present quantum dynamics and the two sets of results are shown to be in agreement with each other. The results for zero total angular momentum suggest a marked presence of atom exchange (isotopic replacement) reaction with probabilities as high as 60%. The reaction probabilities are only weakly dependent on the initial vibrational state of the reactants, while they are slightly more sensitive to the degree of rotational excitation. A brief discussion of the results for selected higher total angular momentum values is also presented, while the l-shifting approximation [S. K. Gray et al., Phys. Chem. Chem. Phys. 1, 1141 (1999)] has been used to provide estimates of the total reaction rates for the title process. Such rates are found to be large enough to possibly become experimentally accessible.     

A semiclassical reactive flux method for the calculation of condensed phase activated rate constants

A semi classical reactive flux algorithm for calculating thermally activated rate constants is presented which is based on a semi-classical transition state theory due to Chapman, Garrett and Miller [J. Chem. Phys. 63 (1975) 2710]. This reactive flux technique, when combined with the semiclassical TST, enables one to describe dynamical recrossings of the transition state on the same footing as tunneling effects. Most importantly, the method is readily applied to nonlinear multidimensional systems over a wide range of temperatures. It will be shown that the method works very well for a variety of existing models.     

Wave packet dynamics of H2(v1=8-14)+H2(v2=0-2): the role of the potential energy surface on different reactive and dissociative processes

A time-dependent wave packet method has been used to study different competing products of H(2)+H(2) collisions: four center reaction, collision induced dissociation, reactive dissociation, and three-body complex formation. A three-degree-of-freedom reduced dimensionality model has been used for five different geometries of the colliding complex (parallel H, crossed X, collinear L, and two T-shaped geometries T(I) and T(II)), with reactants in selected vibrational states with one diatom vibrationally "hot" and the other one vibrationally "cold." Product probabilities have been calculated using two potential energy surfaces [J. Chem. Phys. 101, 4004 (1994); J. Chem. Phys. 116, 666 (2002)] in order to compare their performance in the dynamics. The regions of the potential energy surfaces responsible of the threshold behavior of the probabilities have been identified. Overall, we have found that the most recent potential energy surface is less anisotropic, provides a smaller propensity for insertion-type processes, and gives lower energy thresholds.     

One-particle correlation function in evanescent wave dynamic light scattering

In order to interpret measured intensity autocorrelation functions obtained in evanescent wave scattering, their initial decay rates have been analyzed recently [P. Holmqvist, J. K. G. Dhont, and P. R. Lang, Phys. Rev. E 74, 021402 (2006); B. Cichocki, E. Wajnryb, J. Blawzdziewicz, J. K. G. Dhont, and P. R. Lang, J. Chem. Phys. 132, 074704 (2010); J. W. Swan and J. F. Brady, ibid. 135, 014701 (2011)]. A theoretical analysis of the longer time dependence of evanescent wave autocorrelation functions, beyond the initial decay, is still lacking. In this paper we present such an analysis for very dilute suspensions of spherical colloids. We present simulation results, a comparison to cumulant expansions, and experiments. An efficient simulation method is developed which takes advantage of the particular mathematical structure of the time-evolution equation of the probability density function of the position coordinate of the colloidal sphere. The computer simulation results are compared with analytic, first and second order cumulant expansions. The only available analytical result for the full time dependence of evanescent wave autocorrelation functions [K. H. Lan, N. Ostrowsky, and D. Sornette, Phys. Rev. Lett. 57, 17 (1986)], that neglects hydrodynamic interactions between the colloidal spheres and the wall, is shown to be quite inaccurate. Experimental results are presented and compared to the simulations and cumulant expansions.     

The role of the excited electronic states in the C+ + H2O reaction

The electronic excited states of the [COH2]+ system have been studied in order to establish their role in the dynamics of the C+ + H2O-->[COH]+ +H reaction, which is a prototypical ion-molecule reaction. The most relevant minima and saddle points of the lowest excited state have been determined and energy profiles for the lowest excited doublet and quartet electronic states have been computed along the fragmentation and isomerization coordinates. Also, nonadiabatic coupling strengths between the ground and the first excited state have been computed where they can be large. Our analysis suggests that the first excited state could play an important role in the generation of the formyl isomer, which has been detected in crossed beam experiments [D. M. Sonnenfroh et al., J. Chem. Phys. 83, 3985 (1985)], but could not be explained in quasiclassical trajectory computations [Y. Ishikawa et al., Chem. Phys. Lett. 370, 490 (2003); J. R. Flores, J. Chem. Phys. 125, 164309 (2006)].     

Analysis of experimental data for the nucleation rate of water droplets

A formula for the stationary nucleation rate J is proposed and used for analysis of experimental data for the dependence of J on the supersaturation ratio S in isothermal homogeneous nucleation of water droplets in vapors. It is found that the experimental data are described quite successfully by the proposed formula which is based on (i) the Gibbs presentation of the nucleation work in terms of overpressure, (ii) the Girshick-Chiu [J. Chem. Phys. 93, 1273 (1990); 94, 826 (1991)] self-consistency correction to the equilibrium cluster size distribution, and (iii) the Reguera-Rubi [J. Chem. Phys. 115, 7100 (2001)] kinetic accounting of the nucleus translational-rotational motion. The formula, like that of Wolk and Strey [J. Phys. Chem. B 105, 11683 (2001)], could be used as a semiempirical relation describing the J(S) dependence for nucleation in vapors of single-component droplets or crystals of substances with insufficiently well known equations of state.     

Direct evaluation of the lifetime matrix by the hyperquantization algorithm: narrow resonances in the F + H2 reaction dynamics and their splitting for nonzero angular momentum

We propose a new method for the direct and efficient evaluation of the Felix Smith's lifetime Q matrix for reactive scattering problems. Simultaneous propagation of the solution to a set of close-coupled equations together with its energy derivative allows one to avoid common problems pertinent to the finite-difference approach. The procedure is implemented on a reactive scattering code which employs the hyperquantization algorithm and the Johnson-Manolopoulos [J. Comput. Phys. 13, 455 (1973); J. Chem. Phys 85, 6425 (1986)] propagation to obtain the complete S matrix and scattering observables. As an application of the developed formalism, we focus on the total angular momentum dependence of narrow under-barrier resonances supported by van der Waals wells of the title reaction. Using our method, we fully characterize these metastable states obtaining their positions and lifetimes from Lorentzian fits to the largest eigenvalue of the lifetime matrix. Remarkable splittings of the resonances observed at J>0 are rationalized in terms of a hyperspherical model. In order to provide an insight on the decay mechanism, the Q-matrix eigenvectors are analyzed and the dominant channels populated during the decomposition of metastable states are determined. Possible relevance of the present results to reactive scattering experiments is discussed.     

Quasiclassical trajectory study of the Cl+CH4 reaction dynamics on a quadratic configuration interaction with single and double excitation interpolated potential energy surface

An ab initio interpolated potential energy surface (PES) for the Cl+CH(4) reactive system has been constructed using the interpolation method of Collins and co-workers [J. Chem. Phys. 102, 5647 (1995); 108, 8302 (1998); 111, 816 (1999); Theor. Chem. Acc. 108, 313 (2002)]. The ab initio calculations have been performed using quadratic configuration interaction with single and double excitation theory to build the PES. A simple scaling all correlation technique has been used to obtain a PES which yields a barrier height and reaction energy in good agreement with high level ab initio calculations and experimental measurements. Using these interpolated PESs, a detailed quasiclassical trajectory study of integral and differential cross sections, product rovibrational populations, and internal energy distributions has been carried out for the Cl+CH(4) and Cl+CD(4) reactions, and the theoretical results have been compared with the available experimental data. It has been shown that the calculated total reaction cross sections versus collision energy for the Cl+CH(4) and Cl+CD(4) reactions is very sensitive to the barrier height. Besides, due to the zero-point energy (ZPE) leakage of the CH(4) molecule to the reaction coordinate in the quasiclassical trajectory (QCT) calculations, the reaction threshold falls below the barrier height of the PES. The ZPE leakage leads to CH(3) and HCl coproducts with internal energy below its corresponding ZPEs. We have shown that a Gaussian binning (GB) analysis of the trajectories yields excitation functions in somehow better agreement with the experimental determinations. The HCl(v'=0) and DCl(v'=0) rotational distributions are as well very sensitive to the ZPE problem. The GB correction narrows and shifts the rotational distributions to lower values of the rotational quantum numbers. However, the present QCT rotational distributions are still hotter than the experimental distributions. In both reactions the angular distributions shift from backward peaked to sideways peaked as collision energy increases, as seen in the experiments and other theoretical calculations.     

Revisiting roaming trajectories in ketene isomerization at higher dimensionality

Roaming dynamics have been observed in a three-dimensional model of the ketene isomerization reaction. The roaming trajectories sample the region between the outer potential barriers closest to the respective ketene isomers and involve turning points along the reaction coordinate in a polar representation. These roaming trajectories avoid the intrinsic reaction coordinate and the intermediates to which it is associated. Thus, one-dimensional transition state theory (TST) is generally insufficient as has been confirmed through an analysis of the reactive flux along the dividing surface (DS). A global representation of the DS, however, leads to accurate TST rate constants. The exact and TST microcanonical rates of isomerization have been obtained for the three-dimensional model and compare well to experiment. The global DS is therefore particularly important for obtaining rates in reactions that exhibit roaming. This work thus confirms the findings of our previous two-dimensional treatment of ketene isomerization (Ulusoy et al. in J. Phys. Chem. A 117:7553–7560, 2013).     

Complex wave patterns in an effective reaction-diffusion model for chemical reactions in microemulsions

An effective medium theory is employed to derive a simple qualitative model of a pattern forming chemical reaction in a microemulsion. This spatially heterogeneous system is composed of water nanodroplets randomly distributed in oil. While some steps of the reaction are performed only inside the droplets, the transport through the extended medium occurs by diffusion of intermediate chemical reactants as well as by collisions of the droplets. We start to model the system with heterogeneous reaction-diffusion equations and then derive an equivalent effective spatially homogeneous reaction-diffusion model by using earlier results on homogenization in heterogeneous reaction-diffusion systems [S.Alonso, M.Ba?r, and R.Kapral, J. Chem. Phys. 134, 214102 (2009)]. We study the linear stability of the spatially homogeneous state in the resulting effective model and obtain a phase diagram of pattern formation, that is qualitatively similar to earlier experimental results for the Belousov-Zhabotinsky reaction in an aerosol OT (AOT)-water-in-oil microemulsion [V.K.Vanag and I.R.Epstein, Phys. Rev. Lett. 87, 228301 (2001)]. Moreover, we reproduce many patterns that have been observed in experiments with the Belousov-Zhabotinsky reaction in an AOT oil-in-water microemulsion by direct numerical simulations.     

Simulation of nucleation in almost hard-sphere colloids: the discrepancy between experiment and simulation persists

In this paper we examine the phase behavior of the Weeks-Chandler-Andersen (WCA) potential with βε = 40. Crystal nucleation in this model system was recently studied by Kawasaki and Tanaka [Proc. Natl. Acad. Sci. U.S.A. 107, 14036 (2010)], who argued that the computed nucleation rates agree well with experiment, a finding that contradicted earlier simulation results. Here we report an extensive numerical study of crystallization in the WCA model, using three totally different techniques (Brownian dynamics, umbrella sampling, and forward flux sampling). We find that all simulations yield essentially the same nucleation rates. However, these rates differ significantly from the values reported by Kawasaki and Tanaka and hence we argue that the huge discrepancy in nucleation rates between simulation and experiment persists. When we map the WCA model onto a hard-sphere system, we find good agreement between the present simulation results and those that had been obtained for hard spheres [L. Filion, M. Hermes, R. Ni, and M. Dijkstra, J. Chem. Phys. 133, 244115 (2010); S. Auer and D. Frenkel, Nature 409, 1020 (2001)].     

Water increases rates of epoxidation by Mn(III)porphyrins/imidazole/IO4(-) in CH2Cl2. Analogy with peroxidase and chlorite dismutase

Manganese(III)-meso-tetraphenylporphyrin [Mn(TPP)] and manganese(III)-meso-tetrakis(pentafluorophenyl)porphyrin [Mn(TPFPP)] catalyse the epoxidation of cyclooctene by IO(4)(-) in the presence of excess imidazoles, in both dry CH(2)Cl(2) and CH(2)Cl(2) saturated with H(2)O. The reaction rates of the electron deficient Mn(TPFPP) are a factor 24 less than those of Mn(TPP); however, the former increases 15-30 times in the presence of water, while those of Mn(TPP) do so by a factor of 2-3. The most striking catalytic enhancement caused by the addition of water was observed with 2-methylimidazole and Mn(TPFPP). As deprotonation of imidazoles may play a significant role in the presence of water, we found that manganese(III)-meso-tetrakis(phenyl-4-sulfonato)porphyrin [Mn(TPPS)] decreases the NH proton pK(a) of axially coordinated imidazole from 14.2 to 9.5. We conclude that the imidazole ligand is partially deprotonated in the presence of water. The latter enables the solvation of imidazolium ions that are formed simultaneously. The imidazolate form of the co-catalyst is a much stronger donor than the imidazole itself, providing electron density to Mn(III) and thus promoting oxygen transfer. The failure of N-methylimidazole to increase the reaction rates upon addition of water supports this hypothesis. A functionally related deprotonation has been shown to occur in horseradish peroxidase (J. S. de Ropp, V. Thanabal, G. N. La Mar, J. Am. Chem. Soc. 1985, 107, 8270-8272) and in chlorite dismutase (B. R. Goblirsch, B. R. Streit, J. L. Dubois, C. M. Wilmot, J. Biol. Inorg. Chem. 2010, 15, 879-888). Mn(III)porphyrins in combination with imidazoles and water constitute a functional biomimetic model of peroxidases.     

A global 12-dimensional ab initio potential energy surface and dynamical studies for the SiH4+H-->SiH3+H2 reaction

A global 12-dimensional ab initio interpolated potential energy surface (PES) for the SiH(4)+H-->SiH(3)+H(2) reaction is presented. The ab initio calculations are based on the unrestricted quadratic configuration interaction treatment with all single and double excitations together with the cc-pVTZ basis set, and the modified Shepard interpolation method of Collins and co-workers [K. C. Thompson et al., J. Chem. Phys. 108, 8302 (1998); M. A. Collins, Theor. Chem. Acc. 108, 313 (2002); R. P. A. Bettens and M. A. Collins, J. Chem. Phys. 111, 816 (1999)] is applied. Using this PES, classical trajectory and variational transition state theory calculations have been carried out, and the computed rate constants are in good agreement with the available experimental data.     

A reduced dimensionality quasiclassical and quantum study of the proton transfer reaction H3O(+)+H2O-->H2O+H3O(+)

We report quantum and quasiclassical calculations of proton transfer in the reaction H(3)O(+)+H(2)O in three degrees of freedom, the two OH(+) bond lengths and the OH(+)O angle. The reduced dimensional potential energy surface is obtained from the full dimensional OSS3(p) energy function of H(5)O(2) (+) [L. Ojamae, I. Shavitt, and S. J. Singer, J. Chem. Phys. 109, 5547 (1998)], with an additional long-range correction to reproduce the correct ion-molecule interaction. This surface is used to perform both quasiclassical trajectory and quantum reactive scattering calculations of the zero total angular momentum cumulative reaction probability and cross sections for initial rotational states 0, 1, and 2. Comparison of these quantities are made to assess the importance of quantum effects in this reduced dimensional reaction. Additional quasiclassical cross sections are calculated to obtain the thermal rate constant for the reaction.     

Cavity resonators of metal-coated dielectric nanorods

Metallic nanoparticles bridge the length scale between atoms and crystals, exhibiting mesoscopic properties unique to their size. Thus, they have generated much interest for their potential applications as chemical or biological sensors and particularly as waveguides for light in nanoscale structures. [Y. W. C. Cao, R. C. Jin, and C. A. Mirkin, Science 297, 1536 (2002); H. J. Lezec et al., Science 297, 820 (2002); S. A. Maier, P. G. Kik, and H. A. Atwater, Appl. Phys. Lett. 81, 1714 (2002); J. M. Oliva and S. K. Gray, Chem. Phys. Lett. 379, 325 (2003)]. One important direction of research into the properties of individual metal nanoparticles involves the controlled variation of their geometry, which can yield new and tunable optical properties that simple spherical configurations do not possess. [T. S. Ahmadi, Z. L. Wang, T. C. Green, A. Henglein, and M. A. Ei-Sayed, Science 272, 1924 (1996)]. A prime example of this is the core-shell nanostructure that has a central material surrounded by differing cladding layer.     

Modeling the reactive properties of tandemly activated tRNAs

Tandemly activated tRNAs, bearing amino acid moieties at both the 2'- and 3'-positions of the 3'-terminal adenosine moiety (A(76)), have been shown to participate efficiently in protein synthesis [B. Wang, J. Zhou, M. Lodder, R. D. Anderson, III and S. M. Hecht, J. Biol. Chem., 2006, 281, 13865]. The mechanism by which such activated tRNAs are able to donate both amino acids to the growing polypeptide chain is not well understood. Here we report the chemical behavior and participation in protein synthesis of new bisaminoacyl derivatives of pdCpA and tRNA. Both amino moieties of the aminoacyl groups are shown to be important to enable participation in protein synthesis; paradoxically, they also confer an unanticipated chemical stability toward different nucleophiles. The results obtained suggest a model for participation of bisaminoacylated tRNAs in protein synthesis.     

Low-temperature nucleation in a kinetic Ising model under different stochastic dynamics with local energy barriers

Using both analytical and simulational methods, we study low-temperature nucleation rates in kinetic Ising lattice-gas models that evolve under two different Arrhenius dynamics that interpose between the Ising states a transition state representing a local energy barrier. The two dynamics are the transition-state approximation [T. Ala-Nissila, J. Kjoll, and S. C. Ying, Phys. Rev. B 46, 846 (1992)] and the one-step dynamic [H. C. Kang and W. H. Weinberg, J. Chem. Phys. 90, 2824 (1989)]. Even though they both obey detailed balance and are here applied to a situation that does not conserve the order parameter, we find significant differences between the nucleation rates observed with the two dynamics, and between them and the standard Glauber dynamic [R. J. Glauber, J. Math. Phys. 4, 294 (1963)], which does not contain transition states. Our results show that great care must be exercised when devising kinetic Monte Carlo transition rates for specific physical or chemical systems.