Abstract:
Dataset supporting the publication dx.doi.org/10.1021/jp3002417. Representative GROMACS input files for the molecular dynamics (MD) simulations that were performed to investigate the adsorption of naphthalene and ozone on surfactant-coated air/ice interfaces. The adsorption of gas-phase naphthalene and ozone molecules onto air/ice interfaces coated with different surfactant species (1-octanol, 1-hexadacanol, or 1-octanal) was investigated using classical molecular dynamics (MD) simulations. Naphthalene and ozone exhibit a strong preference to be adsorbed at the surfactant-coated air/ice interfaces, as opposed to either being dissolved into the bulk of the quasi-liquid layer (QLL) or being incorporated into the ice crystals. The QLL becomes thinner when the air/ice interface is coated with surfactant molecules. The adsorption of both naphthalene and ozone onto surfactant-coated air/ice interfaces is enhanced when compared to bare air/ice interface. Both naphthalene and ozone tend to stay dissolved in the surfactant layer and close to the QLL, rather than adsorbing on top of the surfactant molecules and close to the air region of our systems. Surfactants prefer to orient at a tilted angle with respect to the air/ice interface; the angular distribution and the most preferred angle vary depending on the hydrophilic end group, the length of the hydrophobic tail, and the surfactant concentration at the air/ice interface. Naphthalene refers to have a flat orientation on the surfactant coated air/ice interface, except at high concentrations of 1-hexadecanol at the air/ice interface; the angular distribution of naphthalene depends on the specific surfactant and its concentration at the air/ice interface. The dynamics of naphthalene molecules at the surfactant coated air/ice interface slow down as compared to those observed at bare air/ice interfaces. The presence of surfactants does not seem to affect the self-association of naphthalene molecules at the air/ice interface, at least for the specific surfactants and the range of concentrations considered in this study.
Suggested Citation:
Hung, Francisco. 2014. Dataset for: Adsorption of Naphthalene and Ozone on Atmospheric Air/Ice Interfaces Coated with Surfactants: A Molecular Simulation Study. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/N7XW4GRX
Data Parameters and Units:
MD: compounds ICE, SOL, OCT, BEN PMF: compounds ICE, SOL, OCT, BEN, FRI .gro-- compounds verses OI, H1, H2, LI, LI .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 .mdp-- include file (defined constants) .top-- water and graphite topology file .submit-- batch file
Methods:
Classical molecular dynamics (MD) simulations were conducted using the GROMACS software in the NVT ensemble (constant number of molecules, volume, and temperature). (47) 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. In this study, we have used the same models fro water, napthalene, and ozone that we used in our previous studies of adsorption of phenanthrene, naphthalene, and ozone on bare air/ice interfaces. (see 23 and 24) (23) Liyana-Arachchi, T. P.; Valsaraj, K. T.; Hung, F. R. J. Phys. Chem. A 2011, 115, 9226−9236. (24) Chen, J.; Ehrenhauser, F.; Liyana-Arachchi, T. P.; Hung, F. R.; Wornat, M. J.; Valsaraj, K. T. Polycycl. Aromat. Compd. 2011, 31, 201−226.
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