Abstract:

Dataset supporting the publication dx.doi.org/10.1021/jp4029694. Molecular Modeling of Green Leaf Volatile Methyl Salicylate on Atmospheric Air/Water Interfaces. Representative GROMACS input files used in the simulations reported in this paper. We investigated the adsorption of a green leaf volatile (GLV) compound, Methyl salicylate (MeSA), on atmospheric air/water interfaces at 298 K using thermodynamic integration (TI), potential of mean force (PMF) calculations, and classical molecular dynamics (MD) simulations. Our molecular models can reproduce experimental results of the 1-octanol/water partition coefficient of MeSA. A deep free energy minimum was found for MeSA at the air/water interface, which is mainly driven by energetic interactions between MeSA and water. At the interface, the oxygenated groups in MeSA tend to point toward the water side of the interface, with the aromatic group of MeSA lying farther away from water. Increases in the concentrations of MeSA lead to reductions in the height of the peaks in the MeSA−MeSA g(r) functions, a slowing down of the dynamics of both MeSA and water at the interface, and a reduction in the interfacial surface tension. Our results indicate that MeSA has a strong thermodynamic preference to remain at the air/water interface, and thus chemical reactions with atmospheric oxidants are more likely to take place at this interface, rather than in the water phase of atmospheric water droplets or in the gas phase.

Suggested Citation:

Hung, Francisco. 2014. Dataset for: Molecular Modeling of Green Leaf Volatile Methyl Salicylate on Atmospheric Air/Water Interfaces. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/N7DZ0699

Publications:

Liyana-Arachchi, T. P., Hansel, A. K., Stevens, C., Ehrenhauser, F. S., Valsaraj, K. T., & Hung, F. R. (2013). Molecular Modeling of the Green Leaf Volatile Methyl Salicylate on Atmospheric Air/Water Interfaces. The Journal of Physical Chemistry A, 117(21), 4436–4443. doi:10.1021/jp4029694

Purpose:

Methyl salicylate (MeSA) is a green leaf volatile (GLV) compound that is emitted in significant amounts by plants, especially when they are under stress conditions. GLVs can then undergo chemical reactions with atmospheric oxidants, yielding compounds that contribute to the formation of secondary organic aerosols (SOAs). Our results indicate that MeSA has a strong thermodynamic preference to remain at the air/water interface, and thus chemical reactions with atmospheric oxidants are more likely to take place at this interface, rather than in the water phase of atmospheric water droplets or in the gas phase.

Data Parameters and Units:

MD: compounds SOL, BEN PMF: compounds SOL, BEN, FRI TI: OCTANOL: compounds CT, SOL, BEN TI: WATER: compounds SOL, BEN .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 [pairs] [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, dhh .mdp-- include file (defined constants) .top-- water and graphite topology file .submit-- batch file

Methods:

All our molecular simulations were conducted using the GROMACS software,(41) and all the simulation snapshots in this study were generated using the VMD software.(42) (41) 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[ACS Full Text ACS Full Text], [CAS] (42) Humphrey, W.; Dalke, A.; Schulten, K.VMD: Visual Molecular Dynamics J. Mol. Graphics 1996, 14, 33– 38.

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