Molecular dynamics simulation of the initial stages of attachment of two goethite (a-FeOOH) nanoparticles in a sodium perchlorate solution.

Andrew Felmy, E. J. Bylaska, K. M. Rosso, J. R. Rustad, and T. P Straatsma, Pacific Northwest National Laboratory

Research Objectives
Our effort consists of two types of molecular level simulations in key areas of geochemistry/biogeochemistry: (1) in microbial surface-mediated processes, the effects of lipopolysaccharides present on gram-negative bacteria; (2) in mineral surface interactions, providing a molecular-scale understanding of surface complexation reactions at oxide, oxyhydroxide, and silicate minerals through the use of molecular modeling calculations.

Computational Approach
We use a variety of computational chemistry methods (density functional theory [DFT], molecular mechanics/dynamics, Car-Parrinello, kinetic theories), and codes that are a part of NWChem. Besides NWChem, we also use parameterized classical potential models to calculate bulk and surface properties for the interaction of water and hydroxide with Fe/Al surfaces. These models are based upon parameterizations from ab initio calculations, and they have been particularly successful in predicting structures, surface charging, and water chemistry of iron-oxide surfaces.

Accomplishments
A molecular model for the rough lipopolysaccharide (LPS) membrane of Pseudomonas aeruginosa was designed based on experimentally determined structural information. An electrostatic model was based on Hartree-Fock self-consistent-field calculations of the complete LPS molecule to obtain partial atomic charges. Molecular dynamics simulations of the rough LPS membrane of P. aeruginosa were carried out under periodic boundary conditions, such that the membrane consists of a periodic double layer of LPS/phospholipid molecules externally exposed to aqueous environments.

The Parallel Projector Augmented-Wave Code (PAW) method allows us to simulate many new types of materials at a first-principles level, including iron-oxides. During FY01 we modified the PAW program to add load balancing, and we added a mulipole ewald sum (i.e., not just s-component charges) to the program to calculate solids.

We performed free-space PAW and Gaussian DFT NWChem simulations for a series of first-row transition metal monoxides and dioxides, ScO, TiO, VO, CrO, MnO, FeO, TiO₂, VO₂, CrO₂, and FeO₂. These small molecules, which are well characterized experimentally, are an extreme test of the reliability of an ab initio method because they have a large number of low-lying states, many with high spin multiplicity. For the monoxides, the agreement in structural parameters was quite good between the two methods and with experiment. The worst-case difference was for the CrO molecule, with absolute differences in distance, frequency, and binding energy. For the dioxides, the agreement between the two methods was also quite good. The worst-case difference was for the TiO₂ molecule, with absolute differences in distance, angle, frequency, and atomization energy.

Significance
(1) Subsurface microbial processes can control the rates of oxidation/reduction reactions, modify and enhance mineral dissolution and precipitation reactions, and adsorb metals and other ions at the microbial surface, but our theoretical understanding of these processes is very limited. (2) The ubiquitous occurrence, high specific surface area, and strong binding to a large number of cations, anions, metal ions, and organic chelates makes Fe/Al oxides and oxyhydroxides important adsorbing surfaces. Difficulties in characterizing the structure and energetics of these sites obstruct the development of improved thermodynamic models for adsorption.

Publications
James R. Rustad, "Molecular models of surface relaxation, hydroxylation, and surface charging at oxide-water interfaces," Reviews in Mineralogy and Geochemistry 42, 169 (2001).

R. D. Lins and T. P. Straatsma, "Computer simulation of the rough lipopolysaccharide membrane of Pseudomonas aeruginosa," Biophys. J. 81, 1037 (2001).

Eric J. Bylaska, Marat Valiev, Ryoichi Kawai, and John H. Weare, "Parallel implementation of the projector augmented plane wave method for charged systems," Comp. Phys. Comm. (submitted).