Yao Houndonougbo

A Combined Experimental−Computational Investigation of Carbon Dioxide Capture in a Series of Isoreticular Zeolitic Imidazolate Frameworks

A series of five zeolitic imidazolate frameworks (ZIFs) have been synthesized using zinc(II) acetate and five different 4,5-functionalized imidazole units, namely ZIF-25, -71, -93, -96, and -97. These 3-D porous frameworks have the same underlying topology (RHO) with Brunauer-Emmet-Teller surface areas ranging from 564 to 1110 m(2)/g. The only variation in structure arises from the functional groups that are directed into the pores of these materials, which include -CH(3), -OH, -Cl, -CN, -CHO, and -NH(2); therefore these 3-D frameworks are ideal for the study of the effect of functionality on CO(2) uptake. Experimental results show CO(2) uptake at approximately 800 Torr and 298 K ranging from 0.65 mmol g(-1) in ZIF-71 to 2.18 mmol g(-1) in ZIF-96. Molecular modeling calculations reproduce the pronounced dependence of the equilibrium adsorption on functionalization and suggest that polarizability and symmetry of the functionalization on the imidazolate are key factors leading to high CO(2) uptake.

A molecular dynamics algorithm for mixed hard-core/continuous potentials

A new molecular dynamics algorithm is presented for integrating the equations of motion for a system of particles interacting with mixed continuous-impulsive forces. This method, which has been called collision Verlet, is constructed using operator splitting techniques similar to those that have been used successfully to generate a variety of molecular dynamics integrators. In numerical experiments, the collision Verlet method is shown to be superior to previous methods with respect to stability and energy conservation in long simulations.

Prediction of phase equilibria and transport properties in carbon-dioxide expanded solvents by molecular simulation

We review our recent work on the calculations of the phase equilibrium and transport properties in carbon-dioxide (CO2) expanded liquids (CXLs) via Monte Carlo and molecular dynamics (MD) simulations. Gibbs ensemble Monte Carlo simulations were performed to determine the volume expansion, the pressure–composition and pressure–density phase diagrams for CO2 expanded acetonitrile, acetone, methanol, ethanol, acetic acid, toluene and 1-octene. MD simulations were conducted to compute the translational diffusion coefficients, rotational correlation times and shear viscosities in CO2 expanded acetonitrile. Potential parameters for the pure component together with standard mixing rules were used to describe the interactions between the mixture components. A good agreement between simulation results and available experimental data is achieved. The simulation results for the volume expansion, the pressure–composition and pressure–density phase diagrams were in some cases superior to the Peng–Robinson (PR) equation of state correlations, showing the ability of molecular simulation to predict CXL properties for their use as solvent media in engineering processes.

Transport properties of CO2-expanded acetonitrile from molecular dynamics simulations

Carbon-dioxide-expanded liquids, which are mixtures of organic liquids and compressed CO2, are novel media used in chemical processing. The authors present a molecular simulation study of the transport properties of liquid mixtures formed by acetonitrile and carbon dioxide, in which the CO2 mole fraction is adjusted by changing the pressure, at a constant temperature of 298 K. They report values of translational diffusion coefficients, rotational correlation times, and shear viscosities of the liquids as function of CO2 mole fraction. The simulation results are in good agreement with the available experimental data for the pure components and provide interesting insights into the largely unknown properties of the mixtures, which are being recognized as important novel materials in chemical operations. We find that the calculated quantities exhibit smooth variation with composition that may be represented by simple model equations. The translational and rotational diffusion rates increase with CO2 mole fraction for both the acetonitrile and carbon dioxide components. The shear viscosity decreases with increasing amount of CO2, varying smoothly between the values of pure acetonitrile and pure carbon dioxide. Our results show that adjusting the amount of CO2 in the mixture allows the variation of transport rates by a factor of 3-4 and liquid viscosity by a factor of 8. Thus, the physical properties of the mixture may be tailored to the desired range by changes in the operating conditions of temperature and pressure.

Effects of CMAP and electrostatic cutoffs on the dynamics of an integral membrane protein: the phospholamban study.

Abstract In our effort to understand the microscopic structure and dynamics of phospholamban (PLB), a small integral membrane protein, we have performed a series of 5–20 ns molecular dynamics simulations to explore the influence of environment (solution and lipid bilayer) and force field (CMAP correction and Ewald summation) on the protein behavior. Under all simulation conditions, we have observed the same major features: existence of two well-defined helical domains at the N- and C-termini, and large-amplitude rigid-body motions of these domains. The average inter-helix angle of PLB was sensitive to the environment. In the methanol and water solution trajectories, the two helical domains tended to adopt a closed orientation, with the inter-helix angle below 90°, while in the lipid bi-layer the domains tend to be in an open conformation, with the inter-helix angle above 90°. Within each studied environment, simulations employing different force field models provided qualitatively similar description of PLB structure and dynamics. The only significant discrepancy was the presence of π-helical hydrogen bonds in trajectories generated with the standard CHARMM22 force field. Simulations with the CMAP correction, with both cutoff and Ewald electrostatics, exhibited predominantly α-helical and some 310-helical hydrogen bonding interactions, and no π-helical hydrogen bonding, in accord with NMR data. Thus, our results indicate that models including CMAP, with both cutoff and Ewald electrostatics, provide the most realistic description of PLB structure and dynamics. Results obtained from these simulations are in a good agreement with the experimental observables. These include helical secondary structure of PLB, the range explored by the inter-helix angle in methanol, as well as the inter-helix distance and C- terminal helix orientation in the DPPC bi-layer. The observed effect of opening up of the PLB inter-helix angle in the lipid environment relative to solution is also qualitatively reproduced in the simulations, as is the more rigid and compact structure of the C-terminal domain in the membrane relative to solution. The populations of conformations with relatively open inter-domain angles, as well as large fluctuations of this coordinate in DPPC bi-layers allow the N-terminal helix to come into contact with the PLB binding site on the calcium ATPase. Additionally, the presence of a twisting motion around the helical axis enables the helix to orient the correct face to the binding site. Another interesting observation is that the phosphorylation sites Ser16 and Thr17 are essentially always accessible to solvent, and presumably also to phosphorylation.

Constant-temperature molecular-dynamics algorithms for mixed hard-core/continuous potentials

We present a set of second-order, time-reversible algorithms for the isothermal (NVT) molecular-dynamics (MD) simulation of systems with mixed hard-core/continuous potentials. The methods are generated by combining real-time Nose thermostats with our previously developed Collision Verlet algorithm [Mol. Phys. 98, 309 (1999)] for constant energy MD simulation. In all we present five methods, one based on the Nose–Hoover [Phys. Rev. A 31, 1695 (1985)] equations of motion and four based on the Nose–Poincare [J. Comput. Phys. 151, 114 (1999)] real-time formulation of Nose dynamics. The methods are tested using a system of hard spheres with attractive tails and all correctly reproduce a canonical distribution of instantaneous temperature. The Nose–Hoover based method and two of the Nose–Poincare methods are shown to have good energy conservation in long simulations.