Molecular mechanics and quantum mechanical modeling of hexane soot structure and interactions with pyrene

J D Kubicki

doi:10.1186/1467-4866-1-41

Abstract

Molecular simulations (energy minimizations and molecular dynamics) of an n-hexane soot model developed by Smith and co-workers (M. S. Akhter, A. R. Chughtai and D. M. Smith, Appl. Spectrosc., 1985, 39, 143; ref. 1) were performed. The MM+ (N. L. Allinger, J. Am. Chem. Soc., 1977, 395, 157; ref. 2) and COMPASS (H. Sun, J. Phys. Chem., 1998, 102, 7338; ref. 3) force fields were tested for their ability to produce realistic soot nanoparticle structure. The interaction of pyrene with the model soot was simulated. Quantum mechanical calculations on smaller soot fragments were carried out. Starting from an initial 2D structure, energy minimizations are not able to produce the observed layering within soot with either force field. Results of molecular dynamics simulations indicate that the COMPASS force field does a reasonably accurate job of reproducing observations of soot structure. Increasing the system size from a 683 to a 2732 atom soot model does not have a significant effect on predicted structures. Neither does the addition of water molecules surrounding the soot model. Pyrene fits within the soot structure without disrupting the interlayer spacing. Polycyclic aromatic hydrocarbons (PAH), such as pyrene, may strongly partition into soot and have slow desorption kinetics because the PAH-soot bonding is similar to soot–soot interactions. Diffusion of PAH into soot micropores may allow the PAH to be irreversibly adsorbed and sequestered so that they partition slowly back into an aqueous phase causing dis-equilibrium between soil organic matter and porewater.

Highlights

The importance of black carbon in the environment has been recognized for some time
The soot model was ®rst subjected to energy minimization from the 2D structure,[1] molecular dynamics (MD) simulations were carried out using the minimum energy structure as the starting con®guration
The initial hexane soot model structure[1] consists of aromatic regions from 2 to 64 fused rings that are terminated with H atoms and carbonyl groups

Summary

Introduction

The importance of black carbon in the environment has been recognized for some time (see ref. 4 and references therein). When soot particles form an aerosol, soot surfaces can act as a heterogeneous catalyst in a number of environmentally important atmospheric reactions.5±7 When deposited in soils and sediments, soot has a signi®cant inuence on the transport and bioavailability of some organic contaminants due to their strong partitioning into soot.[8] In addition, organic contaminants, such as polycyclic aromatic hydrocarbons (PAH), can form simultaneously with soot in the combustion process.[9] trace amounts of soot can play a disproportionate role in the long-term sequestration of otherwise biodegradable compounds.[10] In addition, soot may represent the more hydrophobic end-member in the distributed reactivity model for soil organic matter of Weber and coworkers[11] or the glassy/rubbery model of Pignatello and coworkers.[12] Both of these models suggest a component of soil organic matter that has a high af®nity for hydrophobic organic molecules with a rigid structure that can support voids large enough for molecules to diffuse into Soot has these qualities it certainly is not the only component of soil organic matter that may play a role in the long-term adsorption of organic contaminants

Objectives

Methods

Results

Conclusion