Computer Simulation of Biomolecular Systems Using Molecular Dynamics and Free Energy Perturbation Methods. In: Lipkowitz KB, Boyd DB, editors. Reviews in Computational Chemistry. Hoboken: John Wiley & Sons, Inc.; 1990. pp. 295-320. [DOI: 10.1002/9780470125786.ch8]

Molecular simulation of polycyclic aromatic hydrocarbon sorption to black carbon

Strong sorption of hydrophobic organic contaminants to soot or black carbon (BC) is an important environmental process limiting the bioremediation potential of contaminated soils and sediments. Reliable methods to predict BC sorption coefficients for organic contaminants are therefore required. A computer simulation based on molecular mechanics using force field methods has been applied in this study to calculate BC sorption coefficients of polycyclic aromatic hydrocarbons (PAHs). The free energy difference between PAHs dissolved in water and in water containing a model structure of BC was calculated by thermodynamic integration of Monte Carlo simulated energies of transfer. The free energies were calculated with a hypothetical reference state that has equal free energies in both phases and is therefore cancelled in the calculated free energy difference. The calculated sorption coefficient of phenanthrene (log K(BC) = 5.17 +/- 0.54 L/kg C), fluoranthene (6.33 +/- 0.64 L/kg C) and benzo[a]pyrene (7.38 +/- 0.36 L/kg C) corresponded very well to experimental values available in the literature. Furthermore, an average spacing distance of 3.73 A between PAHs and BC was determined that is only slightly lower than an experimentally determined value of 4.1 A. The method applied in this study enables the calculation of the extent of PAH sorption to a soot surface for which no experimental values are available nor data for related compounds as required in quantitative structure-activity relationships.

The engineering of biomaterials exhibiting recognition and specificity

Although synthetic materials are now widely used in implanted medical devices, they are not engineered for recognition and specificity. This article considers the design of polymer surfaces that might be specifically recognized and trigger normal healing pathways. The technological advances that will contribute to biorecognition biomaterials include surfaces to inhibit non-specific interactions, self-assembly to create ordered surface structures and strategies to place recognition sites on surfaces by random arrays of groups and by templates.