Abstract:

Dataset supporting the publication Ice Growth from Supercooled Aqueous Solutions of Benzene, Naphthalene, and Phenanthrene. Dataset supporting the publication dx.doi.org/10.1021/jp304921c. Representative GROMACS input files supporting this publication. MD simulations of ice growth from supercooled water containing dissolved aromatic molecules, namely, benzene, naphthalene, and phenanthrene.

Suggested Citation:

Hung, Francisco. 2014. Dataset for: Ice Growth from Supercooled Aqueous Solutions of Benzene, Naphthalene, and Phenanthrene. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/N7T43R1X

Publications:

Liyana-Arachchi, T. P., Valsaraj, K. T., & Hung, F. R. (2012). Ice Growth from Supercooled Aqueous Solutions of Benzene, Naphthalene, and Phenanthrene. The Journal of Physical Chemistry A, 116(33), 8539–8546. doi:10.1021/jp304921c

Purpose:

The first objective of our simulations is to explore the fate of those aromatic molecules after the freezing process, namely, how likely it is for these molecules to become trapped inside the crystalline structure of ice or if they are displaced to the QLL or to the interface with air.

Data Parameters and Units:

MD_FREEZING: compounds SOL, BEN PMF_ICE: compounds ICE, SOL, BEN, FRI PMF_WATER: compounds SOL, BEN, FRI .gro-- compounds verses OW, HW1, HW2, OL1, OL2 .itp-- atom types: name, bond_type, mass, charge, ptype, sigma, epsilon .itp-- [atoms] nr, type, resnr, resid, atom, cgnr, charge, mass [bonds] ai, aj, fu, b0, kb [angles] ai, aj, ak, funct, th0, cth [dihedrals] ai, aj, ak, al, funct, phi0, cp, mult .itp--[moleculetype] molname, nrexcl [atoms] id, at type, res nr, residu name, at name, cg, nr, charge [settles] funct, doh, dhhmdp-- include file (defined constants) .top-- water and graphite topology file.submit-- batch file

Methods:

MD simulations were conducted using the GROMACS software. (see 33) (33) Hess, B.; Kutzner, C.; van der Spoel, D.; Lindahl, E. GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. J. Chem. Theory Comput. 2008, 4, 435−447. Details of all these simulations were exactly the same as those described thoroughly in (15) and (16). We first successfully verified that our combination of force fields could reproduce experimental values of the free energies of hydration of these aromatics (see 17). Afterward, we performed PMF calculations for adsorption of gas-phase benzene and phenanthrene on air/ice systems, which indicates that there is a thermodynamic incentive for these molecules to remain at the interface and that the PMF minimum becomes deeper with an increasing number of aromatic rings in the hydrocarbon. (15) Liyana-Arachchi, T. P.; Valsaraj, K. T.; Hung, F. R. A molecular simulation study of the adsorption of naphthalene and ozone on atmospheric air/ice interfaces. J. Phys. Chem. A 2011, 115, 9226−9236. (16) Liyana-Arachchi, T. P.; Valsaraj, K. T.; Hung, F. R. Adsorption of naphthalene and ozone on atmospheric air/ice interfaces coated with surfactants: A molecular simulation study. J. Phys. Chem. A 2012,116, 2519−2528. (17)Vacha, R.; Jungwirth, P.; Chen, J.;Valsaraj, K. T. Adsorption of polycyclic aromatic hydrocarbons at the air-water interface: Molecular dynamics simulations and experimental atmospheric observations. Phys. Chem. Chem. Phys. 2006, 8, 4461−4467.

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