Phase characterization molecular simulations

A complete review of spectroscopic methods applied to the analysis of alkyl-modified surfaces with a comprehensive list of spectroscopic indicators of alkyl chain conformational order is provided elsewhere [9] this review will focus on the application of spectroscopic and other relevant experimental techniques for the characterization of shape-selective chromatographic materials. On the whole, it has been observed experimentally that any increase in alkyl stationary-phase conformational order promotes an increase in selectivity for shape-constrained solutes in RPLC separations [9], As a complement to the wealth of spectroscopic and chromatographic data, the use of molecular simulation techniques to visualize and characterize alkyl-modified surfaces may also provide new insights into molecular-level features that control shape selectivity. A review of progress in the field of chromatographic material simulations will also be discussed. 

Both experimental and molecular simulation studies of freezing and melting in porous materials suffer from several difficulties [1]. Difficulties in the experiments include the lack of well-characterized porous materials, difficulty in identifying the nature of the adsorbed phases, and long-lived metastable states. In the simulations, large systems and finite size scaling analysis may be needed to feel confidence in the results, and models of the porous materials may be over-simplified. The somewhat complementary nature of the difficulties in experiment and simulation make it profitable to use both approaches in a combined study. We have therefore adopted such a strategy in our recent work in this area [2-7]. 

Except for the fullerenes, carbon nanotubes, nanohoms, and schwarzites, porous carbons are usually disordered materials, and cannot at present be completely characterized experimentally. Methods such as X-ray and neutron scattering and high-resolution transmission electron microscopy (HRTEM) give partial structural information, but are not yet able to provide a complete description of the atomic structure. Nevertheless, atomistic models of carbons are needed in order to interpret experimental characterization data (adsorption isotherms, heats of adsorption, etc.). They are also a necessary ingredient of any theory or molecular simulation for the prediction of the behavior of adsorbed phases within carbons - including diffusion, adsorption, heat effects, phase transitions, and chemical reactivity. 

Siperstein, F.R. and Gubbins, K.E., (2001). Synthesis and characterization of tern-plated mesoporous materials using molecular simulation. Mol. SimuL, 27, 339-52 Siperstein, F.R. and Gubbins, K.E. (2003). Phase separation and hquid crystal self-assembly in surfactant-inorganic-solvent systems. Langmuir, 19, 2049-57. 

The appropriate thermodynamic and statistical-mechanical formalism for the application of molecular simulation to the study of point defects has been given only recently, by Swope and Andersen [90]. These workers identified the number of lattice sites M as a key thermodynamic variable in the characterization of these systems. A real solid phase is free to adopt a value for M that minimizes the system free energy, because it can in principle create or destroy lattice sites through the migration of molecules to and from the surface of the crystal. The resulting bulk crystal can thus disconnect the molecule number N from the lattice-site number M, and thereby achieve an equilibrium of lattice defects in the form of vacancies and interstitials. 

McCabe, C., Cummings, P. T., and Cui, S. T. 2001. Characterizing the viscosity-temperature dependence of lubricants by molecular simulation. Fluid Phase Equilibr. 183-184 363. 

These characterization studies have been supported by molecular simulations, which have given relevant contributions to the understanding of structure-property relationship of SPS co-crystals and nanoporous phases [51,110,130-134], The main contributions of molecular simulation for SPS cocrystalline and nanoporous phases have been collected in a recent review [135],... 

DFT molecular dynamics simulations were used to investigate the kinetics of the chemical reactions that occur during the induction phase of acid-catalyzed polymerization of 205 [97JA7218]. These calculations support the experimental finding that the induction phase is characterized by the protolysis of 205 followed by a rapid decomposition into two formaldehyde molecules plus a methylenic carbocation (Scheme 135). For the second phase of the polymerization process, a reaction of the protonated 1,3,5-trioxane 208 with formaldehyde yielding 1,3,5,7-tetroxane 209 is discussed (Scheme 136). 

Daidone, I., Amadei, A., and Di Nola, A. (2005). Thermodynamic and kinetic characterization of a beta-hairpin peptide in solution An extended phase space sampling by molecular dynamics simulations in explicit water. Proteins 59, 510-518. 

Ban, K., Saito, Y., and Jinno, K., Characterization of the microscopic surface structure of the octadecylsilica stationary-phase using a molecular-dynamics simulation, Anal. ScL, 20, 1403, 2004. 

At the mesoscopic scale, interactions between molecular components in membranes and catalyst layers control the self-organization into nanophase-segregated media, structural correlations, and adhesion properties of phase domains. Such complex processes can be studied by various theoretical tools and simulation techniques (e.g., by coarse-grained molecular dynamics simulations). Complex morphologies of the emerging media can be related to effective physicochemical properties that characterize transport and reaction at the macroscopic scale, using concepts from the theory of random heterogeneous media and percolation theory. 

When structural and dynamical information about the solvent molecules themselves is not of primary interest, the solute-solvent system may be made simpler by modeling the secondary subsystem as an infinite (usually isotropic) medium characterized by the same dielecttic constant as the bulk solvent, that is, a dielectric continuum. Theoretical interpretation of chemical reaction rates has a long history already. Until recently, however, only the chemical reactions of systems containing a few atoms in the gas phase could be studied using molecular quantum mechanics due to computational expense. Fortunately, very important advances have been made in the power of computer-simulation techniques for chemical reactions in the condensed phase, accompanied by an impressive progress in computer speed (Gonzalez-Lafont et al., 1996). 

In addition to quantitative estimates of material properties, molecular modeling can offer valuable qualitative insights into the dynamical properties of materials, without resorting to direct simulation (e.g., molecular dynamics), where the rigorous treatment of all the dynamics at the atomic scale would be prohibitively time-consuming. To illustrate this point, the second part of this chapter describes recent studies of the relaxation in the crystalline a-phase of PVDF. Molecular modeling provides a way to characterize the mechanism of... 

The attenuation of die dipole of the repeat unit owing to thermal oscillations was modeled by treating the dipole moment as a simple harmonic oscillator tied to the motion of the repeat unit and characterized by the excitation of a single lattice mode, the mode, which describes the in-phase rotation of the repeat unit as a whole about the chain axis. This mode was shown to capture accurately the oscillatory dynamics of the net dipole moment itself, by comparison with short molecular dynamics simulations. The average amplitude is determined from the frequency of this single mode, which comes directly out of the CLD calculation ... 

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