Evaporation of Lennard-Jones fluids

Evaporation and condensation at a liquid/vapor interface are ubiquitous interphase mass and energy transfer phenomena that are still not well understood. We have carried out large scale molecular dynamics simulations of Lennard-Jones (LJ) fluids composed of monomers, dimers, or trimers to investigate these processes with molecular detail. For LJ monomers in contact with a vacuum, the evaporation rate is found to be very high with significant evaporative cooling and an accompanying density gradient in the liquid domain near the liquid/vapor interface. Increasing the chain length to just dimers significantly reduces the evaporation rate. We confirm that mechanical equilibrium plays a key role in determining the evaporation rate and the density and temperature profiles across the liquid/vapor interface. The velocity distributions of evaporated molecules and the evaporation and condensation coefficients are measured and compared to the predictions of an existing model based on kinetic theory of gases. Our results indicate that for both monatomic and polyatomic molecules, the evaporation and condensation coefficients are equal when systems are not far from equilibrium and smaller than one, and decrease with increasing temperature. For the same reduced temperature T/T(c), where T(c) is the critical temperature, these two coefficients are higher for LJ dimers and trimers than for monomers, in contrast to the traditional viewpoint that they are close to unity for monatomic molecules and decrease for polyatomic molecules. Furthermore, data for the two coefficients collapse onto a master curve when plotted against a translational length ratio between the liquid and vapor phase.     

Optimal use of data in parallel tempering simulations for the construction of discrete-state Markov models of biomolecular dynamics

Parallel tempering (PT) molecular dynamics simulations have been extensively investigated as a means of efficient sampling of the configurations of biomolecular systems. Recent work has demonstrated how the short physical trajectories generated in PT simulations of biomolecules can be used to construct the Markov models describing biomolecular dynamics at each simulated temperature. While this approach describes the temperature-dependent kinetics, it does not make optimal use of all available PT data, instead estimating the rates at a given temperature using only data from that temperature. This can be problematic, as some relevant transitions or states may not be sufficiently sampled at the temperature of interest, but might be readily sampled at nearby temperatures. Further, the comparison of temperature-dependent properties can suffer from the false assumption that data collected from different temperatures are uncorrelated. We propose here a strategy in which, by a simple modification of the PT protocol, the harvested trajectories can be reweighted, permitting data from all temperatures to contribute to the estimated kinetic model. The method reduces the statistical uncertainty in the kinetic model relative to the single temperature approach and provides estimates of transition probabilities even for transitions not observed at the temperature of interest. Further, the method allows the kinetics to be estimated at temperatures other than those at which simulations were run. We illustrate this method by applying it to the generation of a Markov model of the conformational dynamics of the solvated terminally blocked alanine peptide.     

Quantum and classical study of surface characterization by three-dimensional helium atom scattering

Exact time-dependent wavepacket calculations of helium atom scattering from model symmetric, chiral, and hexagonal surfaces are presented and compared with their classical counterparts. Analysis of the momentum distribution of the scattered wavepacket provides a convenient method to obtain the resulting energy and angle resolved scattering distributions. The classical distributions are characterized by standard rainbow scattering from corrugated surfaces. It is shown that the classical results are closely related to their quantum counterparts and capture the qualitative features appearing therein. Both the quantum and classical distributions are capable of distinguishing between the structures of the three surfaces.     

A sulfone-based strategy for the preparation of 2,4-disubstituted furan derivatives

2,4-Disubstituted furans are prepared by treating 2,3-dibromo-1-phenylsulfonyl-1-propene (DBP, 2) with 1,3-diketones under basic conditions. The furan-forming step involves a deacetylation, and the selectivity of this process depends upon the steric demand of the R group. The substituent in position 4 is elaborated by reaction of sulfonyl carbanions with alkyl halides, acyl halides, and aldehydes. Oxidative or reductive desulfonylation produces the 2,4-disubstituted furans in 60-92% yield. This strategy has been used to prepare rabdoketone A (12) and the naturally occurring nematotoxic furoic acid 13.     

Magnetic circular dichroism and absorption spectra of methylidyne in a krypton matrix

Electronic absorption and magnetic circular dichroism spectra are reported for the A(2)Δ, B(2)Σ(-), and C(2)Σ(+) ← X(2)Π transitions of methylidyne radicals isolated in a Kr matrix at cryogenic temperatures. The results are interpreted in the framework of a model in which the X(2)Π term is split by combination of spin-orbit and crystal-field interactions with the atoms of the host matrix. Analysis of the zeroth moments of the spectra yields an empirical spin-orbit coupling constant A(Π) = 11 ± 2 cm(-1) and orbital reduction factor κ = 0.26 ± 0.05, corresponding to a crystal-field splitting of V(Π) = 43 ± 10 cm(-1) for the X(2)Π term. For the A(2)Δ excited-state term, analysis of the first MCD moments gives a spin-orbit coupling constant of A(Δ) = 4.4 ± 0.9 cm(-1).     

Crystal structures, EPR and magnetic properties of 2-ClC6H4CNSSN˙ and 2,5-Cl2C6H3CNSSN˙

The β-sheet structure associated with chlorinated aromatics (d(Cl···Cl)≈ 4.0 ?) has been implemented to drive formation of π-stacked structures of dithiadiazolyl radicals. Both title compounds exhibit an increase in paramagnetism above 150 K but solid-state EPR studies indicate that the origin of the paramagnetism in these two systems is different.     

The role of molecular modeling in confined systems: impact and prospects

Molecular modeling at the electronic and atomistic levels plays an important and complementary role to experimental studies of confinement effects. Theory and atomistic simulation can provide fundamental understanding, determine the limits of well known macroscopic laws such as Kelvin's equation, provide predictions for systems that are difficult to study via experiment (e.g. adsorption of highly toxic gases), and can be used to gain detailed molecular level information that may not be accessible in the laboratory (e.g. the local structure and composition of confined phases). We describe the most important and useful methods that are based firmly on quantum mechanics and statistical mechanics, including ab intio and classical density functional theories, and Monte Carlo and molecular dynamics simulation. We discuss their strengths and limitations. We then describe examples of applications of these methods to adsorption and equilibrium properties, including testing the Kelvin equation, determination of pore size distributions and capillary phenomena. Applications to self and transport diffusion, including single-file and anomalous diffusion, and viscous flow in nanoporous materials are described. The use of these methods to understand confinement effects on chemical reactions in heterogeneous media is treated, including effects on reaction equilibria, rates and mechanism. Finally we discuss the current status of molecular modeling in this area, and the outlook and future research needs for the next few years. The treatment is suitable for the general technical reader.     

Crown ethers at the aqueous solution-air interface. Part 2. Electrolyte effects, ethylene oxide hydration and temperature behaviour

Vibrational Sum Frequency Spectroscopy (VSFS) was employed to study adsorbing films of 4-Nitro Benzo-15-Crown-5 (NB15C5) and Benzo-15-Crown-5 (B15C5) at the aqueous solution-air interface. The surface of the solution is strongly influenced by the presence of crown ether species. Changes in the orientation of NB15C5 were monitored as a function of solution concentration, by targeting the ratio of peak intensities of the CN and NO(2) vibrational modes. The water of hydration has also been probed as a function of crown concentration, salt concentration, and temperature. The latter study strongly suggests that the surface can be treated as a charged interface, and that the associated ordered water decreases with increasing ionic strength of the bulk solution.