Nucleation molecular simulations

Hummer, G., Garcia, A. E., and Garde, S. (2001). Helix nucleation kinetics from molecular simulations in explicit solvent. Proteins Struct. Fund. Genet. 42, 77-84. 

Ideally, MD or MC gives a complete description of the equilibrium states of liquids and crystals, and a molecular-level picture of any chemical process occurring within the system, including phase transitions. The limitations are obvious. The calculation is heavy, with some 5,000 molecules at most, and times or time-equivalents of the order of at most milliseconds. Force fields are by necessity restricted to atom-atom empirical ones. One gets at best a blurred and very short glimpse of the simulated process. And yet, appropriately designed molecular simulation is, for example, the only access to molecular aspects of chemical evolution involved in crystal nucleation and growth. 

Molecular simulation methods have been applied to investigate the nucleation mechanism of gas hydrates in the bulk water phase (Baez and Clancy, 1994), and more recently at the water-hydrocarbon interface (Radhakrishnan and Trout, 2002 Moon et al., 2003). The recent simulations performed at the water-hydrocarbon interface provide support for a local structuring nucleation hypothesis, rather than the previously described labile cluster model. 

The method presented in this chapter serves as a link between molecular properties (e.g., cavities and their occupants as measured by diffraction and spectroscopy) and macroscopic properties (e.g., pressure, temperature, and density as measured by pressure guages, thermocouples, etc.) As such Section 5.3 includes a brief overview of molecular simulation [molecular dynamics (MD) and Monte Carlo (MC)] methods which enable calculation of macroscopic properties from microscopic parameters. Chapter 2 indicated some results of such methods for structural properties. In Section 5.3 molecular simulation is shown to predict qualitative trends (and in a few cases quantitative trends) in thermodynamic properties. Quantitative simulation of kinetic phenomena such as nucleation, while tenable in principle, is prevented by the capacity and speed of current computers however, trends may be observed. 

Before a molecular simulation can be performed the cluster" relevant to nucleation must be defined [11,27-29,56,57]. The definition of the cluster is important because there must be some set of criteria that differentiates it from the rest of the... 

We have developed a molecular simulation approach that is based on sophisticated methods from theoretical chemistry to characterize the nucleation process of natural gas hydrates. Recently, Rodger s group at Warwick used molecular simulations and found that LDHIs (specifically tributylammonium-propylsulfonate [TBAPS], poly-vinylpyrollidone [PVP], poly-vinylcaprolactam [PVCap], and poly-dimethylaminoethyl... 

MOLECULAR SIMULATIONS OF WATER FJIEEZING BRINE REJECTION AND HOMOGENEOUS NUCLEATION... 

This contribution shows how molecular simulations can be used to provide better insight into highly relevant natural and technological processes of ice nucleation and freezing. 

R. Radhakrishnan and B. L. Trout, A new approach for studying nucleation phenomena using molecular simulations application to CO2 hydrate clathrates. J. Chem. Phys. 117 (2002), 1786-1796 Nucleation ofcrystalline phases of water in homogeneous and inhomogeneous environments. Phys. Rev. Lett., 90 (2003), 158301-158304 Nucleation of hexagonal ice (Ih) in liquid water. /. Am. Chem. Soc., 125 (2003), 7743-7747. 

Anwar, J., Zahn, D. Uncovering molecular processes in crystal nucleation and growth by using molecular simulation. Angewandte Chemie-Intemational Edition 50, 1996-2013 (2011)... 

Audrey, V.B., Jamshed, A., Ruslan, D., Richard, H. Challenges in molecular simulation of homogeneous ice nucleation. J. Phys. Condens. Matter 20, 494243 (2008)... 

Yi, P., Rutledge, G.C. Molecular simulation of crystal nucleation in n-octane melts. J. Chem. Phys. 131, 134902 (2009)... 

He, X., Shen, Y., Hung, F.R., Santiso, E.E. Molecular simulation of homogeneous nucleation of crystals of an ionic liquid from the melt. J. Chem. Phys. 143, 124506 (2015)... 

Hu WB (2005) Molecular segregation in polymer melt crystallization simulation evidence and unified-scheme interpretation. Macromolecules 38 8712-8718 Hu WB, Cai T (2008) Regime transitions of polymer crystal growth rates molecular simulations and interpretation beyond Lauritzen-Hoffman model. Macromolecules 41 2049-2061 Jeziomy A (1971) Parameters characterizing the kinetics of the non-isothermal crystallization of poly(ethylene terephthalate) determined by DSC. Polymer 12 150-158 Johnson WA, Mehl RT (1939) Reaction kinetics in processes of nucleation and growth. Trans Am Inst Min Pet Eng 135 416-441... 

Stone AJ (1996) The theory of intermolecular forces. Clarendon Press, Oxford Mie G (1903) Zur kinetischen Theorie der einatomigen Korper. Ann Phys 11 657-697 Horsch M, Vrabec J, Hasse H (2008) Modification of the classical nucleation theory based on molecular simulation data for stffface tension, critical nucleus size, and nucleation rate. Phys... 

Influence of additives on nucleation of vanillin experiments and introductory molecular simulations. Cryst. Growth Des 4, 1025-1037. 

Molecular simulations have reproduced regime-transition phenomena (Hu and Cai 2008). However, the growth front of Regime 1 is rather rough, favoring an alternative interpretation based on the intramolecular secondary nucleation model (Hu and Cai 2008). 

If melting is difficult to characterize in molecular terms, nucleation and growth of crystalline particles from the melt is an even more elusive phenomenon. Given the extreme difficulty of obtaining molecular level information, phenomenological, macroscopic nucleation theories have been formulated [13] before and aside from numerical molecular simulation. These theories constitute an almost completely parallel approach to the matter and their description does not belong in this book, although points of contact with molecular level simulations have been explored [14]. 

The most striking news that one learns when studying vapor-liquid phenomena is that not only does the vapor need to nucleate a liquid droplet to condense, but that also the liquid needs to nucleate a gas bubble to evaporate [24]. On the theoretical side, the simulation is made easier because the vapor is relatively simple to handle, on the experimental side, vapor pressure measurements in vapor-liquid equilibrium are fairly easy to perform. The Gibbs ensemble Monte Carlo method (Section 9.8) can be applied to the vapor-liquid equilibrium with considerable success vapor pressure curves, second virial coefficients, and other equilibrium properties can be calculated by molecular simulation, and, remarkably, good results can apparently be obtained by highly accurate ab initio quantum mechanical potentials [25a] or by simple empirical potentials [25b]. 

There is little hope of studying theoretically the complex intermolecular situation sketched in Fig. 13.11 with even modest accuracy, unless evolutionary molecular simulation is employed. Recourse is thus made to the classical arsenal of such simulations, broadly subdivided into Monte Carlo (MC) and Molecular Dynamics (MD). The conceptual foundations of these two methods, and their computational feasibility, are now reviewed again from the perspective of their use for nucleation and growth studies. 

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