Grantee Research Project Results

2000 Progress Report: Molecular Modeling of Hydrophobic Organic Contaminants Uptake and Sequestration by Soil Organic Matter

EPA Grant Number: R825540C002
Subproject: this is subproject number 002 , established and managed by the Center Director under grant R825540
(EPA does not fund or establish subprojects; EPA awards and manages the overall grant for this center).
Center: Duke University Center for Environmental Implications of NanoTechnology
Center Director: Wiesner, Mark R.
Title: Molecular Modeling of Hydrophobic Organic Contaminants Uptake and Sequestration by Soil Organic Matter
Investigators: Johnson, James H. , Diallo, Mamadou S.
Institution: Howard University
EPA Project Officer: Hahn, Intaek
Project Period:    
Project Period Covered by this Report: January 1, 1999 through September 30, 2000
RFA: Hazardous Substance Research Centers - HSRC (1989) RFA Text |  Recipients Lists
Research Category: Hazardous Substance Research Centers , Land and Waste Management

Objective:

The primary objective of this research is to develop a molecular level understanding of the uptake of hydrophobic organic compounds (HOCs) by a model soil organic matter (SOM); Chelsea humic acid (HA). More specifically, we seek to:
1. Develop and validate 3-D molecular models of Chelsea HA
2. Calculate the binding energy of phenanthrene, naphthalene, anthracene, chlorobenzene, dichlorobenzene, trichhlorobenze and tetrachlorobenzene with Chelsea humic acid (CHA).
3. Assess the extent to which the Flory Huggens enthalpic interaction parameter can be correlated with phenomenological parameters of HOC such as the Freundlich capacity parameter (Kf) and site energy heterogeneity factor (n) measured by Dr. Weilin Huang (Drexel University) and Dr. Walter Weber (University of Michigan).
4. Analyze the temperature-dependence of phenanthrene sorption onto Chelsea HA collected by Dr. Walt Weber and Dr. Weilin Huang.
5. Estimate the activation energy barriers felt by HOCs (e.g, phenanthrene) as they diffuse through Chelsea HA matrices.

Progress Summary:

Rationale: The interactions of hydrophobic organic compounds (HOCs) with soil organic matter (SOM) determine to a large extent their fate and transport in subsurface systems. These interactions can result in strong binding and slow release of HOCs from contaminated soil and sediments. This apparent sequestration of HOCs has a significant impact on their mobility, reactivity and bioavailability in natural systems and engineered environmental systems. Despite several decades of investigations, the physical chemistry of HOC uptake and sequestration by SOM is not understood. Because of this, the validity of existing phenomenological models of HOC uptake by SOM such as the partitioning model and the Dual Reactive Domain model (DRM) remains to be established. Thus, a molecular level understanding of the uptake and sequestration of HOCs by SOM is critically needed to improve our ability to: (i) predict their environmental fate, (ii) conduct more rigorous assessments of their toxicity and (iii) set more "risk" based cleanup standards for contaminated soils and sediments.

Approach: The starting point of any molecular level investigations of the physicochemical behavior of a given compound is the bond topology, that is, a list of connection between all its atoms. Given the bond topology, a builder from any of the commercially available molecular modeling software can be used to generate a starting 3-D structural model for subsequent estimations of the thermodynamic and physicochemical properties of the compound from atomistic simulations. Because HAs are operationally defined as "solubility" classes of compounds, the development of 2-D and 3-D structural models for these compounds has been a major challenge to environmental and soil chemists. The conventional approach to structure elucidation is the traditional trial-and-error approach by which chemists infer a structural model from a given set of analytical data. Over the last two decades, several investigators have used this conventional approach to generate 2-D and 3-D structural models for humic substances (HS). There are, however, two major impediments to this conventional approach for modeling HS. First, the structure elucidation process is carried out manually. Thus, it is prohibitively time consuming for large and multifunctional geomacromolecules such as HS. Second and more importantly, when several isomers can be built from the same analytical data set, the conventional approach does not provide any means of selecting the "appropriate" isomers. Thus, the ability of structural models generated with the conventional approach to describe the specific chemistry of HS from a given source remains to be established. We have developed a hierarchical approach for modeling HS (Figure 1). This novel approach combines experimental characterization data with computer assisted structure elucidation (CASE) and atomistic simulations to generate a representative sample of 3-D structural models that can be built from a given analytical data set (Figure 1).

Status: To illustrate this new approach, we used quantitative and qualitative structural data as input to the CASE program SIGNATURE to generate a sample of 16 3-D structural models of Chelsea humic acid (HA). We then used these models as starting structures to carry out constant pressure and constant temperature (NPT) molecular dynamics simulations followed by energy minimization to estimate the strain energies, bulk densities and Hildebrand solubility parameters of the computer generated structural models. The estimated bulk densities and solubility parameters were compared with literature values to select a sample of 6 Chelsea HA model isomers (Figure 2) as representative structural models that "best match" the input analytical data. We then used this representative sample of structural models as starting 3-D structures to calculate reliable estimates of the thermodynamic properties [i.e, density, molar volume and solubility parameter] needed to assess the predictive capability of the Flory-Huggens model of HOC binding to dissolved Alrdich HA [a model HA with H/C and O/C ratios similar to those for Chelsea HA] without using any adjustable parameter. As shown in Figure 3 and Table 1, the Flory-Huggens model provides an adequate description of the binding of nonpolar organic solutes to dissolved Aldrich HA with prediction errors ranging from a low value 0.91 % to a high value of 13%. We are currently carrying out an assessment the ability of Flory-Huggens model to describe the linear and nonlinear sorption of hydrophobic organic compounds (HOCs) to soil Chelsea HA without using any adjustable parameter.

Technology Transfer: We have developed a very unique and general procedure for modeling natural organic matter (NOM) (Figure 1). We believe this constitutes a major advance in environmental chemistry given the fact accurate and reliable structural models that capture the relevant chemistry for SOM from a given source have not yet been achieved. This lack of reliable 3-D structural models for SOM is the primary reason behind our limited understanding of HOC uptake and sequestration by SOM. We are taking all the necessary steps to introduce our new methodology to the environmental science and engineering community. We have recently presented the preliminary results of this work at the symposium "Computational Methods in Environmental Chemistry" organized by the ACS Division of Environmental Chemistry during the 219 ACS National Meeting in San Francisco (CA). March 26-30, 2000. An extended abstract describing this work (reference 13 of this report) has been published in the ACS Division of Environmental Chemistry Preprints of Extended Abstracts (Vol 40, No 1, pages 343-347). We have submitted a manuscript to Environmental Science and Technology describing our new methodology and its potential impact in environmental process modeling.

Table 1: Comparison of Predicted and Measured Binding Constants of Organic Solutes to Dissolved Aldrich Humic Acid (1)

Compounds	logKbi, measured	logKbi, predicted	Prediction Error (%)
TCE	2.20	2.18	0.91
Toluene	2.27	2.16	4.84
Naphthalene	3.02	3.20	5.96
Phenanthrene	4.00	4.43	10.75
Anthracene	4.21	4.48	6.41
Fluorene	3.95	4.23	7.09
Biphenyl	3.22	3.16	1.86
p,p'-DDT	5.61	5.54	1.25
1,4-DCB	2.92	3.13	7.19
1,2,4-TCB	3.11	3.51	12.80

Journal Articles on this Report : 1 Displayed | Download in RIS Format

Publications Views

Other subproject views:	All 2 publications	1 publications in selected types	All 1 journal articles
Other center views:	All 7 publications	3 publications in selected types	All 2 journal articles

Publications

Type	Citation	Sub Project	Document Sources
Journal Article	Diallo MS, Simpson A, Gassman P, Faulon JL, Johnson JH, Goddard WA III, Hatcher PG. 3-D structural modeling of humic acids through experimental characterization, computer assisted structure elucidation and atomistic simulations. 1. Chelsea soil humic acid. Environmental Science & Technology 2003;37(9):1783-1793.	R825540C002 (2000)	Full-text: ACS Publications Full Text Exit Other: ACS Publications PDF Exit

Supplemental Keywords:

RFA, Scientific Discipline, INTERNATIONAL COOPERATION, Waste, Water, TREATMENT/CONTROL, Chemical Engineering, Contaminated Sediments, Treatment Technologies, Environmental Chemistry, Hazardous Waste, Bioremediation, Ecology and Ecosystems, Hazardous, Environmental Engineering, molecular modeling, sequestration, contaminant transport, in situ remediation, fate and transport , bioavailability, biodegradation, contaminated sediment, kinetic studies, contaminated soil, bioremediation of soils, contaminants in soil, groundwater remediation, in-situ bioremediation, contaminated groundwater, environmentally acceptable endpoints, hazardous organic compounds, bioacummulation, bioaccumulation, alternative endpoints, contaminated soils

Progress and Final Reports:

Original Abstract

Final

Main Center Abstract and Reports:

R825540    Duke University Center for Environmental Implications of NanoTechnology

Subprojects under this Center: (EPA does not fund or establish subprojects; EPA awards and manages the overall grant for this center).
R825540C001 Development and Verification of A Molecular Modeling Approach for Predicting the Sequestration and Bioavailability/Biotoxicity Reduction of Organic Contaminants by Soils and Sediments
R825540C002 Molecular Modeling of Hydrophobic Organic Contaminants Uptake and Sequestration by Soil Organic Matter
R825540C003 The Use of Microfiltration and Ultrafiltration Membranes for the Separation, Recovery, and Reuse of Surfactant/Contaminant Solutions
R825540C004 A Contained Simulation of Field Application of Genetically Engineered Microorganisms (Gems) for the Bioremediation of PCB Contaminated Soils