Molecular simulation of a model of dissolved organic matter

Abstract

A series of atomistic simulations was performed to assess the ability of the Schulten dissolved organic matter (DOM) molecule, a well-established model humic molecule, to reproduce the physical and chemical behavior of natural humic substances. The unhydrated DOM molecule had a bulk density value appropriate to humic matter, but its Hildebrand solubility parameter was lower than the range of current experimental estimates. Under hydrated conditions, the DOM molecule went through conformational adjustments that resulted in disruption of intramolecular hydrogen bonds (H-bonds), although few water molecules penetrated the organic interior. The radius of gyration of the hydrated DOM molecule was similar to those measured for aquatic humic substances. To simulate humic materials under aqueous conditions with varying pH levels, carboxyl groups were deprotonated, and hydrated Na+ or Ca2+ were added to balance the resulting negative charge. Because of intrusion of the cation hydrates, the model metal-humic structures were more porous, had greater solvent-accessible surface areas, and formed more H-bonds with water than the protonated, hydrated DOM molecule. Relative to Na+, Ca2+ was both more strongly bound to carboxylate groups and more fully hydrated. This difference was attributed to the higher charge of the divalent cation. The Ca-DOM hydrate, however, featured fewer H-bonds than the Na-DOM hydrate, perhaps because of the reduced orientational freedom of organic moieties and water molecules imposed by Ca2+. The present work is, to our knowledge, the first rigorous computational exploration regarding the behavior of a model humic molecule under a range of physical conditions typical of soil and water systems.

Cloud Condensation Nuclei properties of model and atmospheric HULIS

“…Activation of bulk SRFA is interim between F3 and F4, consistent with results for estimated molecular weight, and the knowledge that SRFA is dominated by relatively small molecular weight species (Piccolo, 2001;Simpson et al, 2001;Sutton et al, 2005). The same behavior is seen at all supersaturations (see Table 5).…”

Computational and Spectroscopic Investigations of the Molecular Scale Structure and Dynamics of Geologically Important Fluids and Mineral-Fluid Interfaces

“…10. The results quantitatively confirm the predictions based on the earlier smaller-scale simulations (Sutton et al, 2005; that the supramolecular NOM aggregation in aqueous solutions is principally controlled by the strength of the cation-NOM binding, which occurs principally with the NOM carboxylate groups. This aggregation is relatively fast and can be observed in MD simulations on the time scale of just a few nanoseconds.…”

Metal Cation Complexation with Natural Organic Matter in Aqueous Solutions: Molecular Dynamics Simulations and Potentials of Mean Force

“…37 Despite the well recognized uncertainties of the NOM composition and structure, such methods have been successfully used over the last decade to investigate NOM in molecular-scale detail. [38][39][40][41][42][43][44][45][46][47] The TNB (Temple-Northeastern-Birmingham) model of an NOM molecular fragment [38][39][40] used in our work provides a good structural and compositional analog of the Suwannee River NOM commonly used in experimental studies. [43][44][45] Carboxylic groups are the most important interaction sites for metal binding to these molecules, as they are for many other organic and bioorganic molecules.…”

“…Experimental and theoretical studies of the hydration of metal ions [48][49][50][51][52][53] and carboxylic functional groups [54][55][56][57] show that carboxylic groups are sites of strong association of divalent ions with NOM 24,[58][59][60] and that increasing the cation charge density increases the tendency to form a contact ion pair. 44,47 Here we present a computational molecular dynamics (MD) study of the interaction of Na + , Ca 2+ , and Mg 2+ with the carboxylic groups of a TNB NOM fragment and with acetate anion that provides an improved quantitative understanding of the structure and energetics of these interactions. This work is an extension of our previous research on metal-NOM interaction.…”