Abstract:

Dataset supporting the publication dx.doi.org/10.1039/C3CP44090G. Molecular simulations of green leaf volatiles and atmospheric oxidants on air/water interfaces. Representative GROMACS input files used in the simulations reported in this paper. Green leaf volatiles (GLVs) are oxygenated hydrocarbons that are emitted by plants, especially under stress conditions such as mechanical damage and local weather changes. GLVs can react with photochemically-generated oxidants (e.g., OH radicals) in atmospheric water drops, and contribute to the formation of secondary organic aerosols (SOAs). Here we investigated the adsorption of a gas phase GLV, 2-methyl-3-buten-2-ol (MBO) and OH radicals on atmospheric air/water interfaces using classical molecular dynamics (MD) simulations and potential of mean force (PMF) calculations. Our models can reproduce experimental values of the free energy of hydration of MBO and ˙OH, as well as 1-octanol/water partition coefficients of MBO determined experimentally in this study. Both MBO and ˙OH have a strong thermodynamic incentive to remain at the air/water interface, with their density profiles overlapping significantly at the interface. These results suggest that chemical reactions between MBO and ˙OH are more likely to take place at the interface, rather than inside the bulk of water droplets or in the vapor phase. We found a significant number of contacts between MBO and ˙OH in our simulations, which could lead to reactions between these two species.

Suggested Citation:

Hung, Francisco. 2014. Dataset for: Molecular simulations of green leaf volatiles and atmospheric oxidants on air/water interfaces. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/N7JQ0Z06

Publications:

Liyana-Arachchi, T. P., Stevens, C., Hansel, A. K., Ehrenhauser, F. S., Valsaraj, K. T., & Hung, F. R. (2013). Molecular simulations of green leaf volatiles and atmospheric oxidants on air/water interfaces. Physical Chemistry Chemical Physics, 15(10), 3583. doi:10.1039/c3cp44090g

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_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 [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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