Adsorption processes are utilized in both medicine and industry. It is important to have an understanding of adsorption processes to better predict the outcomes and discern potential difficulties. The primary objective of this research is to further the understanding of the nature and extent of the adsorption process in solution, which is a function of the chemical composition of the adsorbates, adsorbents, and solvent. This was accomplished by employing experimental studies as well as thermodynamic calculations and molecular dynamic simulations. Four activated carbons were used as the model adsorbents in this study. And, barbital, phenobarbital and primidone were used to elucidate the structural features of the adsorbates that were most responsible for the interaction with activated carbons. A Two-Mechanism Langmuir-Like Equation (TMLLE) was proposed to describe the independent presence of two adsorption mechanisms: non-site-specific adsorption and site-specific adsorption. The analyses of data generated by both previous investigators and current studies, suggest that the TMLLE allows an accurate analysis of the adsorption process. Based on the parameters in the TMLLE, the Modified Crisp Model and the van’t Hoff Model were employed to determine the Gibbs free energy changes for both site-specific adsorption and non-site-specific adsorption. Comparing the Gibbs free energy changes calculated by the Modified Crisp Model and the van’t Hoff Model (site-specific adsorption case), it is concluded that 5 water molecules are displaced by a phenobarbital molecule on the surface of activated carbons. And, for non-site-specific adsorption, it is concluded that 12 water molecules are displaced by a phenobarbital molecule on the nonpolar (hydrocarbon) part of the activated carbon surface. The adsorption of phenobarbital from solution by activated carbons has been simulated by employing Molecular Dynamic (MD) Modeling. The predicted differential Gibbs free energy values for site-specific adsorption at pH 2-9 were consistent with the thermodynamic calculations. And, the present MD simulations provide a good basis for the further understanding and quantitatively assessment of the adsorption driven by hydrophobic bonding. The conclusions reached in the current studies are expected to be applicable to a wide range of similar adsorption processes.

A refinement of a minimal model for protein folding originally proposed by Imamura is presented. The representation of the alpha-helix has been improved by adding in explicit modelling of the entire peptide unit. A four-helix bundle consisting of four alpha-helices and three loop regions is generated with the parallel tempering Monte Carlo scheme. Six native states are found for the given sequence, four U-bundle and two Z-bundle states. All six states have energies of E approx -218ε and all appear equally likely to occur in simulation. The highest probability of folding a native state is found to be at a hydrophobic strength of Ch = 0.8 which agrees with the value of Ch = 0.7 used by Imamura in his studies of alpha to beta structural conversions. Two folding stages are observed in the temperature spectrum dependent on the magnitude of the hydrophobic strength parameter. The two stages observed as temperature decreases are 1) the hydrophobic energy causes the random coil to collapse into a compact globule 2) the secondary structure starts forming below a temperature of about T = 0.52ε/kB. The temperature of the first stage, which corresponds to the characteristic collapse temperature Tθ, is highly dependent on the hydrophobic strength. The temperature of the second stage is constant with respect to hydrophobic strength. Attempts to measure the characteristic folding temperature, Tf , from the structural overlap function proved to be difficult due mostly to the presence of six minima and the complications that arose in the parallel tempering Monte Carlo scheme. However, a rough estimate of Tf is obtained at each hydrophobic strength from a native state density analysis. Tf is found to be significantly lower than Tθ.

A refinement of a minimal model for protein folding originally proposed by Imamura is presented. The representation of the alpha-helix has been improved by adding in explicit modelling of the entire peptide unit. A four-helix bundle consisting of four alpha-helices and three loop regions is generated with the parallel tempering Monte Carlo scheme. Six native states are found for the given sequence, four U-bundle and two Z-bundle states. All six states have energies of E approx -218ε and all appear equally likely to occur in simulation. The highest probability of folding a native state is found to be at a hydrophobic strength of Ch = 0.8 which agrees with the value of Ch = 0.7 used by Imamura in his studies of alpha to beta structural conversions. Two folding stages are observed in the temperature spectrum dependent on the magnitude of the hydrophobic strength parameter. The two stages observed as temperature decreases are 1) the hydrophobic energy causes the random coil to collapse into a compact globule 2) the secondary structure starts forming below a temperature of about T = 0.52ε/kB. The temperature of the first stage, which corresponds to the characteristic collapse temperature Tθ, is highly dependent on the hydrophobic strength. The temperature of the second stage is constant with respect to hydrophobic strength. Attempts to measure the characteristic folding temperature, Tf , from the structural overlap function proved to be difficult due mostly to the presence of six minima and the complications that arose in the parallel tempering Monte Carlo scheme. However, a rough estimate of Tf is obtained at each hydrophobic strength from a native state density analysis. Tf is found to be significantly lower than Tθ.